610 results on '"Allen H"'
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2. Some aspects of national medicine.
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ALLEN HR
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- Humans, Medicine, Public Health
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- 1950
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3. The teaching of medicine: more and more a full time job.
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ALLEN HD Jr
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- Humans, Education, Medical, Medicine
- Published
- 1956
4. Integration of ER protein quality-control mechanisms defines β cell function and ER architecture
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Neha Shrestha, Mauricio Torres, Jason Zhang, You Lu, Leena Haataja, Rachel B. Reinert, Jeffrey Knupp, Yu-Jie Chen, Allen H. Hunter, Gunes Parlakgul, Ana Paula Arruda, Billy Tsai, Peter Arvan, and Ling Qi
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Cell biology ,Metabolism ,Medicine - Abstract
Three principal ER quality-control mechanisms, namely, the unfolded protein response, ER-associated degradation (ERAD), and ER-phagy are each important for the maintenance of ER homeostasis, yet how they are integrated to regulate ER homeostasis and organellar architecture in vivo is largely unclear. Here we report intricate crosstalk among the 3 pathways, centered around the SEL1L-HRD1 protein complex of ERAD, in the regulation of organellar organization in β cells. SEL1L-HRD1 ERAD deficiency in β cells triggers activation of autophagy, at least in part, via IRE1α (an endogenous ERAD substrate). In the absence of functional SEL1L-HRD1 ERAD, proinsulin is retained in the ER as high molecular weight conformers, which are subsequently cleared via ER-phagy. A combined loss of both SEL1L and autophagy in β cells leads to diabetes in mice shortly after weaning, with premature death by approximately 11 weeks of age, associated with marked ER retention of proinsulin and β cell loss. Using focused ion beam scanning electron microscopy powered by deep-learning automated image segmentation and 3D reconstruction, our data demonstrate a profound organellar restructuring with a massive expansion of ER volume and network in β cells lacking both SEL1L and autophagy. These data reveal at an unprecedented detail the intimate crosstalk among the 3 ER quality-control mechanisms in the dynamic regulation of organellar architecture and β cell function.
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- 2023
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5. Comparing multiscale, presence-only habitat suitability models created with structured survey data and community science data for a rare warbler species at the southern range margin.
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Lauren E Whitenack, Sara J Snell Taylor, Aimee Tomcho, and Allen H Hurlbert
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Medicine ,Science - Abstract
Golden-winged Warblers (Vermivora chrysoptera, Parulidae) are declining migrant songbirds that breed in the Great Lakes and Appalachian regions of North America. Within their breeding range, Golden-winged Warblers are found in early successional habitats adjacent to mature hardwood forest, and previous work has found that Golden-winged Warbler habitat preferences are scale-dependent. Golden-winged Warbler Working Group management recommendations were written to apply to large regions of the breeding range, but there may be localized differences in both habitat availability and preferences. Rapid declines at the southernmost extent of their breeding range in Western North Carolina necessitate investigation into landscape characteristics governing distribution in this subregion. Furthermore, with the increase in availability of community science data from platforms such as eBird, it would be valuable to know if community science data produces similar distribution models as systemic sampling data. In this study, we described patterns of Golden-winged Warbler presence in Western North Carolina by examining habitat variables at multiple spatial scales using data from standardized Audubon North Carolina (NC) playback surveys and community science data from eBird. We compared model performance and predictions between Audubon NC and eBird models and found that Golden-winged Warbler presence is associated with sites which, at a local scale (150m), have less mature forest, more young forest, more herb/shrub cover, and more road cover, and at a landscape scale (2500m), have less herb/shrub cover. Golden-winged Warbler presence is also associated with higher elevations and smaller slopes. eBird and Audubon models had similar variable importance values, response curves, and overall performance. Based on variable importance values, elevation, mature forest at the local scale, and road cover at the local scale are the primary variables driving the difference between Golden-winged Warbler breeding sites and random background sites in Western North Carolina. Additionally, our results validate the use of eBird data, since they produce species distribution modeling results that are similar to results obtained from more standardized survey methods.
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- 2023
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6. Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases
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Avinash V. Dharmadhikari, Rajarshi Ghosh, Bo Yuan, Pengfei Liu, Hongzheng Dai, Sami Al Masri, Jennifer Scull, Jennifer E. Posey, Allen H. Jiang, Weimin He, Francesco Vetrini, Alicia A. Braxton, Patricia Ward, Theodore Chiang, Chunjing Qu, Shen Gu, Chad A. Shaw, Janice L. Smith, Seema Lalani, Pawel Stankiewicz, Sau-Wai Cheung, Carlos A. Bacino, Ankita Patel, Amy M. Breman, Xia Wang, Linyan Meng, Rui Xiao, Fan Xia, Donna Muzny, Richard A. Gibbs, Arthur L. Beaudet, Christine M. Eng, James R. Lupski, Yaping Yang, and Weimin Bi
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Exome sequencing ,Microarray ,Structural variation ,Uniparental disomy ,ROH ,Dual molecular diagnoses ,Medicine ,Genetics ,QH426-470 - Abstract
Abstract Background Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains challenging. The purpose of this study is to understand the contribution of CNVs and copy neutral runs of homozygosity (ROH) in molecular diagnosis of patients referred for ES. Methods In a cohort of 11,020 consecutive ES patients, an Illumina SNP array analysis interrogating mostly coding SNPs was performed as a quality control (QC) measurement and for CNV/ROH detection. Among these patients, clinical chromosomal microarray analysis (CMA) was performed at Baylor Genetics (BG) on 3229 patients, either before, concurrently, or after ES. We retrospectively analyzed the findings from CMA and the QC array. Results The QC array can detect ~ 70% of pathogenic/likely pathogenic CNVs (PCNVs) detectable by CMA. Out of the 11,020 ES cases, the QC array identified PCNVs in 327 patients and uniparental disomy (UPD) disorder-related ROH in 10 patients. The overall PCNV/UPD detection rate was 5.9% in the 3229 ES patients who also had CMA at BG; PCNV/UPD detection rate was higher in concurrent ES and CMA than in ES with prior CMA (7.2% vs 4.6%). The PCNVs/UPD contributed to the molecular diagnoses in 17.4% (189/1089) of molecularly diagnosed ES cases with CMA and were estimated to contribute in 10.6% of all molecularly diagnosed ES cases. Dual diagnoses with both PCNVs and SNVs were detected in 38 patients. PCNVs affecting single recessive disorder genes in a compound heterozygous state with SNVs were detected in 4 patients, and homozygous deletions (mostly exonic deletions) were detected in 17 patients. A higher PCNV detection rate was observed for patients with syndromic phenotypes and/or cardiovascular abnormalities. Conclusions Our clinical genomics study demonstrates that detection of PCNV/UPD through the QC array or CMA increases ES diagnostic rate, provides more precise molecular diagnosis for dominant as well as recessive traits, and enables more complete genetic diagnoses in patients with dual or multiple molecular diagnoses. Concurrent ES and CMA using an array with exonic coverage for disease genes enables most effective detection of both CNVs and SNVs and therefore is recommended especially in time-sensitive clinical situations.
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- 2019
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7. A simulation study of the use of temporal occupancy for identifying core and transient species.
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Sara Snell Taylor, Jessica R Coyle, Ethan P White, and Allen H Hurlbert
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Medicine ,Science - Abstract
Transient species, which do not maintain self-sustaining populations in a system where they are observed, are ubiquitous in nature and their presence often impacts the interpretation of ecological patterns and processes. Identifying transient species from temporal occupancy, the proportion of time a species is observed at a given site over a time series, is subject to classification errors as a result of imperfect detection and source-sink dynamics. We use a simulation-based approach to assess how often errors in detection or classification occur in order to validate the use of temporal occupancy as a metric for inferring whether a species is a core or transient member of a community. We found that low detection increases error in the classification of core species, while high habitat heterogeneity and high detection increase error in classification of transient species. These findings confirm that temporal occupancy is a valid metric for inferring whether a species can maintain a self-sustaining population, but imperfect detection, low abundance, and highly heterogeneous landscapes may yield high misclassification rates.
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- 2020
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8. Reconstructing reef fish communities using fish otoliths in coral reef sediments.
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Chien-Hsiang Lin, Brigida De Gracia, Michele E R Pierotti, Allen H Andrews, Katie Griswold, and Aaron O'Dea
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Medicine ,Science - Abstract
Little is known about long-term changes in coral reef fish communities. Here we present a new technique that leverages fish otoliths in reef sediments to reconstruct coral reef fish communities. We found over 5,400 otoliths in 169 modern and mid-Holocene bulk samples from Caribbean Panama and Dominican Republic mid-Holocene and modern reefs, demonstrating otoliths are abundant in reef sediments. With a specially-built reference collection, we were able to assign over 4,400 otoliths to one of 56 taxa (35 families) though mostly at genus and family level. Many otoliths were from juvenile fishes for which identification is challenging. Richness (by rarefaction) of otolith assemblages was slightly higher in modern than mid-Holocene reefs, but further analyses are required to elucidate the underlying causes. We compared the living fish communities, sampled using icthyocide, with the sediment otolith assemblages on four reefs finding the otolith assemblages faithfully capture the general composition of the living fish communities. Radiocarbon dating performed directly on the otoliths suggests that relatively little mixing of sediment layers particularly on actively accreting branching coral reefs. All otolith assemblages were strongly dominated by small, fast-turnover fish taxa and juvenile individuals, and our exploration on taxonomy, functional ecology and taphonomy lead us to the conclusion that intense predation is likely the most important process for otolith accumulation in reef sediments. We conclude that otolith assemblages in modern and fossil reef sediments can provide a powerful tool to explore ecological changes in reef fish communities over time and space.
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- 2019
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9. The proportion of core species in a community varies with spatial scale and environmental heterogeneity
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Molly F. Jenkins, Ethan P. White, and Allen H. Hurlbert
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Occupancy ,Core species ,Spatial scale ,Community size ,Environmental heterogeneity ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Ecological communities are composed of a combination of core species that maintain local viable populations and transient species that occur infrequently due to dispersal from surrounding regions. Preliminary work indicates that while core and transient species are both commonly observed in community surveys of a wide range of taxonomic groups, their relative prevalence varies substantially from one community to another depending upon the spatial scale at which the community was characterized and its environmental context. We used a geographically extensive dataset of 968 bird community time series to quantitatively describe how the proportion of core species in a community varies with spatial scale and environmental heterogeneity. We found that the proportion of core species in an assemblage increased with spatial scale in a positive decelerating fashion with a concomitant decrease in the proportion of transient species. Variation in the shape of this scaling relationship between sites was related to regional environmental heterogeneity, with lower proportions of core species at a given scale associated with high environmental heterogeneity. Understanding this influence of scale and environmental heterogeneity on the proportion of core species may help resolve discrepancies between studies of biotic interactions, resource availability, and mass effects conducted at different scales, because the importance of these and other ecological processes are expected to differ substantially between core and transient species.
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- 2018
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10. Identifying mechanisms of regulation to model carbon flux during heat stress and generate testable hypotheses.
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Allen H Hubbard, Xiaoke Zhang, Sara Jastrebski, Susan J Lamont, Abhyudai Singh, and Carl J Schmidt
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Medicine ,Science - Abstract
Understanding biological response to stimuli requires identifying mechanisms that coordinate changes across pathways. One of the promises of multi-omics studies is achieving this level of insight by simultaneously identifying different levels of regulation. However, computational approaches to integrate multiple types of data are lacking. An effective systems biology approach would be one that uses statistical methods to detect signatures of relevant network motifs and then builds metabolic circuits from these components to model shifting regulatory dynamics. For example, transcriptome and metabolome data complement one another in terms of their ability to describe shifts in physiology. Here, we extend a previously described linear-modeling based method used to identify single nucleotide polymorphisms (SNPs) associated with metabolic changes. We apply this strategy to link changes in sulfur, amino acid and lipid production under heat stress by relating ratios of compounds to potential precursors and regulators. This approach provides integration of multi-omics data to link previously described, discrete units of regulation into functional pathways and identifies novel biology relevant to the heat stress response, in addition to generating hypotheses.
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- 2018
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11. Range expansion and population dynamics of an invasive species: the Eurasian Collared-Dove (Streptopelia decaocto).
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Spencer N Scheidt and Allen H Hurlbert
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Medicine ,Science - Abstract
Invasive species offer ecologists the opportunity to study the factors governing species distributions and population growth. The Eurasian Collared-Dove (Streptopelia decaocto) serves as a model organism for invasive spread because of the wealth of abundance records and the recent development of the invasion. We tested whether a set of environmental variables were related to the carrying capacities and growth rates of individual populations by modeling the growth trajectories of individual populations of the Collared-Dove using Breeding Bird Survey (BBS) and Christmas Bird Count (CBC) data. Depending on the fit of our growth models, carrying capacity and growth rate parameters were extracted and modeled using historical, geographical, land cover and climatic predictors. Model averaging and individual variable importance weights were used to assess the strength of these predictors. The specific variables with the greatest support in our models differed between data sets, which may be the result of temporal and spatial differences between the BBS and CBC. However, our results indicate that both carrying capacity and population growth rates are related to developed land cover and temperature, while growth rates may also be influenced by dispersal patterns along the invasion front. Model averaged multivariate models explained 35-48% and 41-46% of the variation in carrying capacities and population growth rates, respectively. Our results suggest that widespread species invasions can be evaluated within a predictable population ecology framework. Land cover and climate both have important effects on population growth rates and carrying capacities of Collared-Dove populations. Efforts to model aspects of population growth of this invasive species were more successful than attempts to model static abundance patterns, pointing to a potentially fruitful avenue for the development of improved invasive distribution models.
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- 2014
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12. Clinical, radiological and ultrasonographic findings related to knee pain in osteoarthritis.
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Keith K W Chan, Regina W S Sit, Ricky W K Wu, and Allen H Y Ngai
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Medicine ,Science - Abstract
Pain is the predominant symptom of knee osteoarthritis (OA) and the main reason of disability. Ultrasound is now one of the new imaging modality in Musculoskeletal medicine and its role in assessing the pain severity in the knee osteoarthritis is evaluated in this study.(1) To study the correlation between ultrasonographic (US) findings and pain score and (2) whether ultrasonographic findings show a better association of pain level than conventional X-rays in patients suffering from primary knee osteoarthritis.In this multi-center study, 193 patients with primary knee OA were asked to score their average knee pain using the Western Ontario and McMaster Universities Arthritis (WOMAC) questionnaire;patients would then go for a radiological and an US evaluation of their painful knee. Findings from both imaging modalities will be studied with the associated pain score.Ultrasound showed that knee effusion has positive correlation with pain score upon walking (r = 0.217) and stair climbing (r = 0.194). Presence of suprapatellar synovitis had higher pain score on sitting (Spearman's Rank correlation = 0.355). The medial(r = 0.170) and lateral meniscus protrusion (r = 0.201) were associated with pain score upon stair climbing.Our study found that both imaging modalities shown some significant association with the aspect of pain; neither one is clearly better but rather complementary to each other. A trend is found in both modalities: walking pain is related to pathologies of the either the lateral or medial tibiofemoral joint(TFJ)while stair climbing pain is related to both tibiofemoral joint pathologies and also to the patellofemoral joint (PFJ) pathology. This suggested that biomechanical derangement is an important aspect in OA knee pain.
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- 2014
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13. Spatiotemporal variation in avian migration phenology: citizen science reveals effects of climate change.
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Allen H Hurlbert and Zhongfei Liang
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Medicine ,Science - Abstract
A growing number of studies have documented shifts in avian migratory phenology in response to climate change, and yet there is a large amount of unexplained variation in the magnitude of those responses across species and geographic regions. We use a database of citizen science bird observations to explore spatiotemporal variation in mean arrival dates across an unprecedented geographic extent for 18 common species in North America over the past decade, relating arrival dates to mean minimum spring temperature. Across all species and geographic locations, species shifted arrival dates 0.8 days earlier for every °C of warming of spring temperature, but it was common for some species in some locations to shift as much as 3-6 days earlier per °C. Species that advanced arrival dates the earliest in response to warming were those that migrate more slowly, short distance migrants, and species with broader climatic niches. These three variables explained 63% of the interspecific variation in phenological response. We also identify a latitudinal gradient in the average strength of phenological response, with species shifting arrival earlier at southern latitudes than northern latitudes for the same degree of warming. This observation is consistent with the idea that species must be more phenologically sensitive in less seasonal environments to maintain the same degree of precision in phenological timing.
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- 2012
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14. Inferring ecological processes from taxonomic, phylogenetic and functional trait β-diversity.
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James C Stegen and Allen H Hurlbert
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Medicine ,Science - Abstract
Understanding the influences of dispersal limitation and environmental filtering on the structure of ecological communities is a major challenge in ecology. Insight may be gained by combining phylogenetic, functional and taxonomic data to characterize spatial turnover in community structure (β-diversity). We develop a framework that allows rigorous inference of the strengths of dispersal limitation and environmental filtering by combining these three types of β-diversity. Our framework provides model-generated expectations for patterns of taxonomic, phylogenetic and functional β-diversity across biologically relevant combinations of dispersal limitation and environmental filtering. After developing the framework we compared the model-generated expectations to the commonly used "intuitive" expectation that the variance explained by the environment or by space will, respectively, increase monotonically with the strength of environmental filtering or dispersal limitation. The model-generated expectations strongly departed from these intuitive expectations: the variance explained by the environment or by space was often a unimodal function of the strength of environmental filtering or dispersal limitation, respectively. Therefore, although it is commonly done in the literature, one cannot assume that the strength of an underlying process is a monotonic function of explained variance. To infer the strength of underlying processes, one must instead compare explained variances to model-generated expectations. Our framework provides these expectations. We show that by combining the three types of β-diversity with model-generated expectations our framework is able to provide rigorous inferences of the relative and absolute strengths of dispersal limitation and environmental filtering. Phylogenetic, functional and taxonomic β-diversity can therefore be used simultaneously to infer processes by comparing their empirical patterns to the expectations generated by frameworks similar to the one developed here.
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- 2011
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15. Reaching and stepping respond differently to medication and cueing in Parkinson’s disease
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Allen Hill, Hiram Cantú, Julie N. Côté, and Julie Nantel
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Medicine ,Science - Abstract
Abstract The basal ganglia contribute to internal timekeeping, and dopaminergic medication has been observed to moderate timing deficits associated with Parkinson’s Disease (PD) during single joint movements. However, it is unclear whether similar effects can be observed in multi-joint movements. Twenty-five people with PD and twelve healthy peers performed repetitive reaching and stepping-in-place tasks with and without auditory cues at their self-selected maximal cadence. The PD group was measured ON and OFF medication. Reduced cadence error was found for both groups and tasks when cued, and ON PD exhibited decreased cadence compared to OFF PD. Overall timing variability was no different from controls, but differences were found in estimates of clock and motor variance using the Wing-Kristofferson model of interval timing. A medication and cueing interaction during the reaching task produced increased clock variance in uncued, ON PD. During the stepping task, clock and motor variance of the PD group were unaffected by cues, in contrast to the control group. Serial lag-one correlation was reduced in both groups for cued reaching, but was unaffected by cueing or medication in the PD group when stepping-in-place. These findings suggest that overall timing variability may not capture timing deficits in PD.
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- 2024
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16. A comparative life cycle assessment of toothpaste cream versus toothpaste tablets
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Lance Hongwei Huang, Allen H. Hu, Chien-Hung Kuo, Suphichaya Suppipat, and Lien T.K. Trinh
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Environmental Engineering ,Toothpaste ,business.product_category ,Renewable Energy, Sustainability and the Environment ,business.industry ,Cleaning teeth ,Context (language use) ,Domestic consumption ,Health benefits ,Industrial and Manufacturing Engineering ,Toxicology ,Human health ,Ingredient ,Comparative life cycle assessment ,Environmental Chemistry ,Medicine ,business - Abstract
Toothpaste tablets are claimed as a sustainable oral care solution because of their plastic-free concept and ability to deliver the same health benefits as toothpaste cream without harming the environment. Various studies on the environmental impacts related to toothpaste packaging have been conducted; however, far too little attention has been paid to toothpaste ingredients. Life cycle assessment was employed to evaluate the impacts between cleaning teeth with toothpaste cream and tablets. The functional unit of brushing teeth for 2 min twice a day for 6 months was compared within a cradle-to-grave system boundary. The study was conducted in the context of toothpaste manufacturing and domestic consumption in Thailand. Results show that using toothpaste tablets remarkably contributes to a higher score than applying toothpaste cream, accounting for 188 and 163 millipoints, respectively. About 65% of the total impact is from the use phase, and 20% is from ingredient production. The damage to human health is the biggest concern (10.358 × 10−6 DALY). Sugar alcohols, magnesium stearate, and polyvidone are inactive ingredients in the tablets that cause serious human health problems. Toothpaste manufacturers should reconsider ingredient substitution and redesign an appropriate amount and form of the tablet to mitigate the abovementioned impacts.
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- 2022
17. Cerebrospinal fluid electrolytes and acid-base in diabetic patients
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Te-Hsin Hou, Fu-Chao Liu, Allen H. Li, Huang-Ping Yu, and Chia-Chih Liao
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medicine.medical_specialty ,business.industry ,General Neuroscience ,acid-base ,Neurosciences. Biological psychiatry. Neuropsychiatry ,electrolyte ,medicine.disease ,Gastroenterology ,pCO2 ,cerebrospinal fluid ,Cerebrospinal fluid ,Internal medicine ,Diabetes mellitus ,Orthopedic surgery ,diabetes mellitus ,medicine ,Urologic surgery ,In patient ,business ,Homeostasis ,Whole blood ,Research Article ,RC321-571 - Abstract
Background Diabetes mellitus (DM) has detrimental effects on the function of microvascular beds, resulting in blood–brain barrier (BBB) dysfunction. The objective of the study was to investigate whether DM affects the brain physiology through composition of cerebrospinal fluid (CSF) and compare gas tension and electrolyte levels in CSF between the diabetic and nondiabetic populations. Methods Patients aged between 20 and 70 years scheduled for elective orthopedic or urologic surgery requiring spinal anesthesia were enrolled. They were assigned to either of the two groups (control or type 2 DM). Gas tension and electrolytes in the CSF and whole blood samples were measured in both groups. Results All 49 enrolled patients (24 in the control and 25 in the DM group) completed the study. The concentrations of Na+ and Mg2+ in the blood were significantly lower in the DM group than those in the control. The levels of pCO2 and HCO 3 − {\text{HCO}}_{3}^{-} in the CSF were lower in the DM group than in the control group. In addition, there was a marked increase in the glucose level in both the blood and CSF in the DM group. Conclusion The results show that there were some homeostatic changes in blood and CSF in patients with DM.
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- 2021
18. Tendons exhibit greater resistance to tissue and molecular-level damage with increasing strain rate during cyclic fatigue
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Allen H. Lin, Jeffrey A. Weiss, and Jared L. Zitnay
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Cyclic stress ,Biomedical Engineering ,Strain (injury) ,Peptide binding ,Biochemistry ,Article ,Tendons ,Biomaterials ,Tensile Strength ,Ultimate tensile strength ,medicine ,Animals ,Denaturation (biochemistry) ,Molecular Biology ,Chemistry ,General Medicine ,Strain rate ,Fascicle ,medicine.disease ,Biomechanical Phenomena ,Rats ,Creep ,Biophysics ,Collagen ,Stress, Mechanical ,Biotechnology - Abstract
Musculoskeletal soft connective tissues are commonly injured due to repetitive use, but the evolution of mechanical damage to the tissue structure during repeated loading is poorly understood. We investigated the strain-rate dependence of mechanical denaturation of collagen as a form of structural microdamage accumulation during creep fatigue loading of rat tail tendon fascicles. We cycled tendons at three strain rates to the same maximum stress relative to their rate-dependent tensile strength. Collagen denaturation at distinct points during the fatigue process was measured by fluorescence quantification of collagen hybridizing peptide binding. The amount of collagen denaturation was significantly correlated with fascicle creep strain, independent of the cyclic strain rate, supporting our hypothesis that tissue level creep is caused by collagen triple-helix unfolding. Samples that were loaded faster experienced more creep strain and denaturation as a function of the number of loading cycles relative to failure. Although this increased damage capacity at faster rates may serve as a protective measure during high-rate loading events, it may also predispose these tissues to subsequent injury and indicate a mechanism of overuse injury development. These results build on evidence that molecular-level collagen denaturation is the fundamental mechanism of structural damage to tendons during tensile loading. STATEMENT OF SIGNIFICANCE: This study is the first to investigate the accumulation of denatured collagen in tendons throughout fatigue loading when the maximum stress is scaled with the applied strain rate. The amount of denatured collagen was correlated with creep strain, independent of strain rate, but samples that were cycled faster withstood greater amounts of denaturation before failure. Differential accumulation of collagen damage between fast and slow repetitive loading has relevance toward understanding the prevalence of overuse musculoskeletal injuries following sudden changes in activity level. Since collagen is a ubiquitous biological structural component, the basic patterns and mechanisms of loading-induced collagen damage in connective tissues are relevant for understanding injury and disease in other tissues, including those from the cardiovascular and pulmonary systems.
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- 2021
19. Sublethal doxorubicin promotes migration and invasion of breast cancer cells: role of Src Family non-receptor tyrosine kinases
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Samia Mohammed, Ronald S Chavez, Allen H Lee, Daniel Canals, Achraf A. Shamseddine, Tyler D. Panzner, Chioma M. Okeoma, Yusuf A. Hannun, Benjamin Newcomb, and Christopher J. Clarke
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0301 basic medicine ,p53 ,Population ,Dasatinib ,Breast Neoplasms ,Ataxia Telangiectasia Mutated Proteins ,Src Family Kinases ,Receptor tyrosine kinase ,03 medical and health sciences ,0302 clinical medicine ,FYN ,Breast cancer ,Cancer stem cell ,Cell Movement ,Cell Line, Tumor ,Fyn ,medicine ,Cell Adhesion ,Humans ,Epithelial–mesenchymal transition ,education ,Protein Kinase Inhibitors ,RC254-282 ,education.field_of_study ,biology ,Dose-Response Relationship, Drug ,Cell growth ,Chemistry ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,030104 developmental biology ,src-Family Kinases ,ATR ,Doxorubicin ,030220 oncology & carcinogenesis ,Cancer cell ,Cancer research ,biology.protein ,Female ,Tumor Suppressor Protein p53 ,Yes ,medicine.drug ,Research Article - Abstract
Background Doxorubicin (Dox) is a widely used chemotherapy, but its effectiveness is limited by dose-dependent side effects. Although lower Dox doses reduce this risk, studies have reported higher recurrence of local disease with no improvement in survival rate in patients receiving low doses of Dox. To effectively mitigate this, a better understanding of the adverse effects of suboptimal Dox doses is needed. Methods Effects of sublethal dose of Dox on phenotypic changes were assessed with light and confocal microscopy. Migratory and invasive behavior were assessed by wound healing and transwell migration assays. MTT and LDH release assays were used to analyze cell growth and cytotoxicity. Flow cytometry was employed to detect cell surface markers of cancer stem cell population. Expression and activity of matrix metalloproteinases were probed with qRT-PCR and zymogen assay. To identify pathways affected by sublethal dose of Dox, exploratory RNAseq was performed and results were verified by qRT-PCR in multiple cell lines (MCF7, ZR75-1 and U-2OS). Regulation of Src Family kinases (SFK) by key players in DNA damage response was assessed by siRNA knockdown along with western blot and qRT-PCR. Dasatinib and siRNA for Fyn and Yes was employed to inhibit SFKs and verify their role in increased migration and invasion in MCF7 cells treated with sublethal doses of Dox. Results The results show that sublethal Dox treatment leads to increased migration and invasion in otherwise non-invasive MCF7 breast cancer cells. Mechanistically, these effects were independent of the epithelial mesenchymal transition, were not due to increased cancer stem cell population, and were not observed with other chemotherapies. Instead, sublethal Dox induces expression of multiple SFK—including Fyn, Yes, and Src—partly in a p53 and ATR-dependent manner. These effects were validated in multiple cell lines. Functionally, inhibiting SFKs with Dasatinib and specific downregulation of Fyn suppressed Dox-induced migration and invasion of MCF7 cells. Conclusions Overall, this study demonstrates that sublethal doses of Dox activate a pro-invasive, pro-migration program in cancer cells. Furthermore, by identifying SFKs as key mediators of these effects, our results define a potential therapeutic strategy to mitigate local invasion through co-treatment with Dasatinib.
- Published
- 2021
20. High-Resolution Exposure Assessment for Volatile Organic Compounds in Two California Residences
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Yilin Tian, William W. Nazaroff, Kasper Kristensen, Yingjun Liu, David M. Lunderberg, Robert J. Weber, Caleb Arata, Pawel K. Misztal, and Allen H. Goldstein
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Air Pollutants ,Volatile Organic Compounds ,Health risk assessment ,Air pollution ,High resolution ,General Chemistry ,010501 environmental sciences ,medicine.disease_cause ,01 natural sciences ,California ,Human exposure ,Air Pollution, Indoor ,Environmental chemistry ,Housing ,medicine ,Humans ,Environmental Chemistry ,Environmental science ,Health risk ,Environmental Monitoring ,0105 earth and related environmental sciences ,Exposure assessment - Abstract
Time spent in residences substantially contributes to human exposure to volatile organic compounds (VOCs). Such exposures have been difficult to study deeply, in part because VOC concentrations and indoor occupancy vary rapidly. Using a fast-response online mass spectrometer, we report time-resolved exposures from multi-season sampling of more than 200 VOCs in two California residences. Chemical-specific source apportionment revealed that time-averaged exposures for most VOCs were mainly attributable to continuous indoor emissions from buildings and their static contents. Also contributing to exposures were occupant-related activities, such as cooking, and outdoor-to-indoor transport. Health risk assessments are possible for a subset of observed VOCs. Acrolein, acetaldehyde, and acrylic acid concentrations were above chronic advisory health guidelines, whereas exposures for other assessable species were typically well below the guideline levels. Studied residences were built in the mid-20th century, indicating that VOC emissions even from older buildings and their contents can substantially contribute to occupant exposures.
- Published
- 2021
21. Physical–Chemical Coupling Model for Characterizing the Reaction of Ozone with Squalene in Realistic Indoor Environments
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Allen H. Goldstein, Pawel K. Misztal, Meixia Zhang, Jianyin Xiong, and Yingjun Liu
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Squalene ,Volatile Organic Compounds ,Ozone ,Air pollution ,General Chemistry ,Models, Theoretical ,010501 environmental sciences ,medicine.disease_cause ,01 natural sciences ,Chemical reaction ,Gas phase ,chemistry.chemical_compound ,chemistry ,Coupling (computer programming) ,Adverse health effect ,Air Pollution, Indoor ,Physical chemical ,Environmental chemistry ,medicine ,Environmental Chemistry ,Environmental science ,0105 earth and related environmental sciences - Abstract
Squalene can react with indoor ozone to generate a series of volatile and semi-volatile organic compounds, some of which may be skin or respiratory irritants, causing adverse health effects. Better understanding of the ozone/squalene reaction and product transport characteristics is thus important. In this study, we developed a physical-chemical coupling model to describe the behavior of ozone/squalene reaction products, that is, 6-methyl-5-hepten-2-one (6-MHO) and 4-oxopentanal (4-OPA) in the gas phase and skin, by considering the chemical reaction and physical transport processes (external convection, internal diffusion, and surface uptake). Experiments without intervention were performed in a single-family house in California utilizing time- and space-resolved measurements. The key parameters in the model were extracted from 5 day data and then used to predict the behaviors in some other days. Predictions from the present model can reproduce the concentration profiles of the three compounds (ozone, 6-MHO, and 4-OPA) well (R2 = 0.82-0.89), indicating high accuracy of the model. Exposure analysis shows that the total amount of 6-MHO and 4-OPA entering the blood capillaries in 4 days can reach 14.6 and 30.1 μg, respectively. The contribution of different sinks to ozone removal in the tested realistic indoor environment was also analyzed.
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- 2021
22. Early overcounting in otoliths: a case study of age and growth for gindai (Pristipomoides zonatus) using bomb 14C dating
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Allen H. Andrews and Taylor R. Scofield
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Aquatic Science ,Biology ,Oceanography ,Biochemistry ,Pristipomoides zonatus ,law.invention ,Fishery ,medicine.anatomical_structure ,Age estimation ,law ,medicine ,Radiocarbon dating ,Molecular Biology ,Otolith - Published
- 2021
23. Collagen denaturation is initiated upon tissue yield in both positional and energy-storing tendons
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Alexandra N. Allan, Jeffrey A. Weiss, S. Michael Yu, Allen H. Lin, Jared L. Zitnay, and Julian L. Kessler
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musculoskeletal diseases ,Mechanical overload ,Linear region ,Yield (engineering) ,0206 medical engineering ,Biomedical Engineering ,Strain (injury) ,02 engineering and technology ,Collagen denaturation ,Biochemistry ,Article ,Physical Phenomena ,Tendons ,Biomaterials ,medicine ,Animals ,Molecular Biology ,Rupture ,Chemistry ,Soft tissue ,General Medicine ,musculoskeletal system ,021001 nanoscience & nanotechnology ,medicine.disease ,020601 biomedical engineering ,Biomechanical Phenomena ,Rats ,Tendon ,medicine.anatomical_structure ,Flexor Digitorum Longus ,Biophysics ,Collagen ,0210 nano-technology ,Biotechnology - Abstract
Tendons are collagenous soft tissues that transmit loads between muscles and bones. Depending on their anatomical function, tendons are classified as positional or energy-storing with differing biomechanical and biochemical properties. We recently demonstrated that during monotonic stretch of positional tendons, permanent denatured collagen begins accumulating upon departing the linear region of the stress-strain curve. However, it is unknown if this observation is true during mechanical overload of other types of tendons. Therefore, the purpose of this study was to investigate the onset of collagen denaturation relative to applied strain, and whether it differs between the two tendon types. Rat tail tendon (RTT) fascicles and rat flexor digitorum longus (FDL) tendons represented positional and energy-storing tendons, respectively. The samples were stretched to incremental levels of strain, then stained with fluorescently labeled collagen hybridizing peptides (CHPs); the CHP fluorescence was measured to quantify denatured collagen. Denatured collagen in both positional and energy-storing tendons begins to increase at the yield strain, upon leaving the linear region of the stress-strain curve as the sample begins to permanently deform. Despite significant differences between the two tendon types, it appears that collagen denaturation is initiated at tissue yield during monotonic stretch, and the fundamental mechanism of failure is the same. At tissue failure, positional tendons had double the percentage of denatured collagen compared to energy-storing tendons, with no difference between 0% control groups. These results have implications in understanding both acute and chronic tendon injuries, which will hopefully lead to improved treatment outcomes.
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- 2020
24. Promoting Collaborative Scholarship During the COVID-19 Pandemic Through an Innovative COVID-19 Data Explorer and Repository at Yale School of Medicine: Development and Usability Study
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Angela Maria Victoria-Castro, Tanima Arora, Michael Simonov, Aditya Biswas, Jameel Alausa, Labeebah Subair, Brett Gerber, Andrew Nguyen, Allen Hsiao, Richard Hintz, Yu Yamamoto, Robert Soufer, Gary Desir, Francis Perry Wilson, and Merceditas Villanueva
- Subjects
Medicine - Abstract
BackgroundThe COVID-19 pandemic sparked a surge of research publications spanning epidemiology, basic science, and clinical science. Thanks to the digital revolution, large data sets are now accessible, which also enables real-time epidemic tracking. However, despite this, academic faculty and their trainees have been struggling to access comprehensive clinical data. To tackle this issue, we have devised a clinical data repository that streamlines research processes and promotes interdisciplinary collaboration. ObjectiveThis study aimed to present an easily accessible up-to-date database that promotes access to local COVID-19 clinical data, thereby increasing efficiency, streamlining, and democratizing the research enterprise. By providing a robust database, a broad range of researchers (faculty and trainees) and clinicians from different areas of medicine are encouraged to explore and collaborate on novel clinically relevant research questions. MethodsA research platform, called the Yale Department of Medicine COVID-19 Explorer and Repository (DOM-CovX), was constructed to house cleaned, highly granular, deidentified, and continually updated data from over 18,000 patients hospitalized with COVID-19 from January 2020 to January 2023, across the Yale New Haven Health System. Data across several key domains were extracted including demographics, past medical history, laboratory values during hospitalization, vital signs, medications, imaging, procedures, and outcomes. Given the time-varying nature of several data domains, summary statistics were constructed to limit the computational size of the database and provide a reasonable data file that the broader research community could use for basic statistical analyses. The initiative also included a front-end user interface, the DOM-CovX Explorer, for simple data visualization of aggregate data. The detailed clinical data sets were made available for researchers after a review board process. ResultsAs of January 2023, the DOM-CovX Explorer has received 38 requests from different groups of scientists at Yale and the repository has expanded research capability to a diverse group of stakeholders including clinical and research-based faculty and trainees within 15 different surgical and nonsurgical specialties. A dedicated DOM-CovX team guides access and use of the database, which has enhanced interdepartmental collaborations, resulting in the publication of 16 peer-reviewed papers, 2 projects available in preprint servers, and 8 presentations in scientific conferences. Currently, the DOM-CovX Explorer continues to expand and improve its interface. The repository includes up to 3997 variables across 7 different clinical domains, with continued growth in response to researchers’ requests and data availability. ConclusionsThe DOM-CovX Data Explorer and Repository is a user-friendly tool for analyzing data and accessing a consistently updated, standardized, and large-scale database. Its innovative approach fosters collaboration, diversity of scholarly pursuits, and expands medical education. In addition, it can be applied to other diseases beyond COVID-19.
- Published
- 2024
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25. How the effects of latitude on daylight availability may have influenced the evolution of migration and photoperiodism
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Keith W. Sockman and Allen H. Hurlbert
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photoperiodism ,Ecology ,medicine ,Daylight ,Biology ,Seasonality ,Life history ,medicine.disease ,Annual cycle ,Ecology, Evolution, Behavior and Systematics ,Latitude - Published
- 2020
26. Surface Emissions Modulate Indoor SVOC Concentrations through Volatility-Dependent Partitioning
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Caleb Arata, Pawel K. Misztal, Nathan M. Kreisberg, Sameer Patel, Yingjun Liu, William W. Nazaroff, Peter F. DeCarlo, Erin F. Katz, Allen H. Goldstein, Marina E. Vance, David M. Lunderberg, Yilin Tian, and Kasper Kristensen
- Subjects
Thermal desorption ,Air pollution ,010501 environmental sciences ,medicine.disease_cause ,01 natural sciences ,Air Pollution ,medicine ,Environmental Chemistry ,Mass concentration (chemistry) ,Indoor ,0105 earth and related environmental sciences ,Air Pollutants ,Volatile Organic Compounds ,Volatilisation ,General Chemistry ,Particulates ,Aerosol ,Climate Action ,Air Pollution, Indoor ,Environmental chemistry ,Housing ,Environmental science ,Particle ,Particulate Matter ,Volatilization ,Volatility (chemistry) ,Environmental Sciences - Abstract
Measurements by semivolatile thermal desorption aerosol gas chromatography (SV-TAG) were used to investigate how semivolatile organic compounds (SVOCs) partition among indoor reservoirs in (1) a manufactured test house under controlled conditions (HOMEChem campaign) and (2) a single-family residence when vacant (H2 campaign). Data for phthalate diesters and siloxanes suggest that volatility-dependent partitioning processes modulate airborne SVOC concentrations through interactions with surface-laden condensed-phase reservoirs. Airborne concentrations of SVOCs with vapor pressures in the range of C13 to C23 alkanes were observed to be correlated with indoor air temperature. Observed temperature dependencies were quantitatively similar to theoretical predictions that assumed a surface-air boundary layer with equilibrium partitioning maintained at the air-surface interface. Airborne concentrations of SVOCs with vapor pressures corresponding to C25 to C31 alkanes correlated with airborne particle mass concentration. For SVOCs with higher vapor pressures, which are expected to be predominantly gaseous, correlations with particle mass concentration were weak or nonexistent. During primary particle emission events, enhanced gas-phase emissions from condensed-phase reservoirs partitioned to airborne particles, contributing substantially to organic particulate matter. An emission event related to oven-usage was inferred to deposit siloxanes in condensed-phase reservoirs throughout the house, leading to the possibility of reemission during subsequent periods with high particle loading.
- Published
- 2020
27. INFLUENCES OF UPPER FLORIDAN AQUIFER WATERS ON RADIOCARBON IN THE OTOLITHS OF GRAY SNAPPER (Lutjanus griseus) IN THE GULF OF MEXICO
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Laura Thornton, Robert J. Allman, Allen H. Andrews, Beverly K. Barnett, and Jeffrey P. Chanton
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0106 biological sciences ,010506 paleontology ,Archeology ,Aquifer ,01 natural sciences ,law.invention ,chemistry.chemical_compound ,law ,Lutjanidae ,medicine ,Radiocarbon dating ,0105 earth and related environmental sciences ,Otolith ,geography ,geography.geographical_feature_category ,biology ,010604 marine biology & hydrobiology ,Lutjanus griseus ,biology.organism_classification ,Karst ,Oceanography ,medicine.anatomical_structure ,chemistry ,General Earth and Planetary Sciences ,Carbonate ,Groundwater ,Geology - Abstract
The otoliths (ear stones) of fishes are commonly used to describe the age and growth of marine and freshwater fishes. These non-skeletal structures are fortuitous in their utility by being composed of mostly inorganic carbonate that is inert through the life of the fish. This conserved record functions like an environmental chronometer and bomb-produced radiocarbon (14C)—a 14C signal created by atmospheric testing of thermonuclear devices—can be used as a time-specific marker in validating fish age. However, complications from the hydrogeology of nearshore marine environments can complicate 14C levels, as was the case with gray snapper (Lutjanus griseus) along the Gulf of Mexico coast of Florida. Radiocarbon of these nearshore waters is influenced by freshwater input from the karst topography of the Upper Floridan Aquifer—estuarine waters that are 14C-depleted from surface and groundwater inputs. Some gray snapper likely recruited to this kind of environment where 14C levels were depleted in the earliest otolith growth, although age was validated for individuals that were not exposed to 14C-depleted waters to an age of at least 25 years with support for a 30-year lifespan.
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- 2020
28. Otolith‐Based Age Estimates of Alligator Gar Assessed Using Bomb Radiocarbon Dating to Greater than 60 Years
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Allen H. Andrews, Daniel J. Daugherty, and Nathan G. Smith
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Ecology ,biology ,Management, Monitoring, Policy and Law ,Aquatic Science ,biology.organism_classification ,Archaeology ,Alligator gar ,law.invention ,medicine.anatomical_structure ,law ,medicine ,Radiocarbon dating ,Ecology, Evolution, Behavior and Systematics ,Geology ,Otolith - Published
- 2019
29. Characterizing Airborne Phthalate Concentrations and Dynamics in a Normally Occupied Residence
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Pawel K. Misztal, R. A. Wernis, William W. Nazaroff, David M. Lunderberg, Nathan M. Kreisberg, Allen H. Goldstein, Kasper Kristensen, Yingjun Liu, Yilin Tian, and Caleb Arata
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Vapor pressure ,Phthalic Acids ,Air pollution ,010501 environmental sciences ,medicine.disease_cause ,complex mixtures ,01 natural sciences ,chemistry.chemical_compound ,Plasticizers ,Air Pollution ,Diethylhexyl Phthalate ,MD Multidisciplinary ,medicine ,Humans ,Environmental Chemistry ,Indoor ,0105 earth and related environmental sciences ,Plasticizer ,Phthalate ,General Chemistry ,Particulates ,Phthalic acid ,Key factors ,chemistry ,13. Climate action ,Air Pollution, Indoor ,Environmental chemistry ,Particle ,Environmental science ,Environmental Sciences - Abstract
Phthalate esters, commonly used as plasticizers, can be found indoors in the gas phase, in airborne particulate matter, in dust, and on surfaces. The dynamic behavior of phthalates indoors is not fully understood. In this study, time-resolved measurements of airborne phthalate concentrations and associated gas-particle partitioning data were acquired in a normally occupied residence. The vapor pressure and associated gas-particle partitioning of measured phthalates influenced their airborne dynamic behavior. Concentrations of higher vapor pressure phthalates correlated well with indoor temperature, with little discernable influence from direct occupant activity. Conversely, occupant-related behaviors substantially influenced the concentrations and dynamic behavior of a lower vapor pressure compound, diethyl hexyl phthalate (DEHP), mainly through production of particulate matter during cooking events. The proportion of airborne DEHP in the particle phase was experimentally observed to increase under high particle mass concentrations and lower indoor temperatures in correspondence with theory. Experimental observations indicate that indoor surfaces of the residence are large reservoirs of phthalates. The results also indicate that two key factors influenced by human behavior - temperature and particle mass concentration - cause short-term changes in airborne phthalate concentrations.
- Published
- 2019
30. Reduction of microglial progranulin does not exacerbate pathology or behavioral deficits in neuronal progranulin-insufficient mice
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Madelyn Q. Hoffmann, Anthony J. Filiano, Andrew E. Arrant, Shreya N. Kashyap, Allen H. Young, Erik D. Roberson, Aashka R. Patel, Nicholas R. Boyle, and Vincent C. Onyilo
- Subjects
Male ,0301 basic medicine ,Progranulin ,Pathology ,medicine.medical_specialty ,Cell type ,Biology ,Article ,lcsh:RC321-571 ,Lipofuscin ,03 medical and health sciences ,Progranulins ,0302 clinical medicine ,mental disorders ,medicine ,Animals ,Gliosis ,Social Behavior ,lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry ,Mice, Knockout ,Neurons ,Behavior, Animal ,Microglia ,Brain ,Neuron ,medicine.disease ,Neuronal ceroid lipofuscinosis ,Mice, Inbred C57BL ,030104 developmental biology ,medicine.anatomical_structure ,nervous system ,Neurology ,Frontotemporal Dementia ,Forebrain ,Female ,medicine.symptom ,Haploinsufficiency ,030217 neurology & neurosurgery ,Frontotemporal dementia - Abstract
Loss-of-function mutations in progranulin (GRN), most of which cause progranulin haploinsufficiency, are a major autosomal dominant cause of frontotemporal dementia (FTD). Individuals with loss-of-function mutations on both GRN alleles develop neuronal ceroid lipofuscinosis (NCL), a lysosomal storage disorder. Progranulin is a secreted glycoprotein expressed by a variety of cell types throughout the body, including neurons and microglia in the brain. Understanding the relative importance of neuronal and microglial progranulin insufficiency in FTD pathogenesis may guide development of therapies. In this study, we used mouse models to investigate the role of neuronal and microglial progranulin insufficiency in the development of FTD-like pathology and behavioral deficits. Grn(–/–) mice model aspects of FTD and NCL, developing lipofuscinosis and gliosis throughout the brain, as well as deficits in social behavior. We have previously shown that selective depletion of neuronal progranulin disrupts social behavior, but does not produce lipofuscinosis or gliosis. We hypothesized that reduction of microglial progranulin would induce lipofuscinosis and gliosis, and exacerbate behavioral deficits, in neuronal progranulin-deficient mice. To test this hypothesis, we crossed Grn(fl/fl) mice with mice expressing Cre transgenes targeting neurons (CaMKII-Cre) and myeloid cells/microglia (LysM-Cre). CaMKII-Cre, which is expressed in forebrain excitatory neurons, reduced cortical progranulin protein levels by around 50%. LysM-Cre strongly reduced progranulin immunolabeling in many microglia, but did not reduce total brain progranulin levels, suggesting that, at least under resting conditions, microglia contribute less than neurons to overall brain progranulin levels. Mice with depletion of both neuronal and microglial progranulin failed to develop lipofuscinosis or gliosis, suggesting that progranulin from extracellular sources prevented pathology in cells targeted by the Cre transgenes. Reduction of microglial progranulin also did not exacerbate the social deficits of neuronal progranulin-insufficient mice. These results do not support the hypothesis of synergistic effects between progranulin-deficient neurons and microglia. Nearly complete progranulin deficiency appears to be required to induce lipofuscinosis and gliosis in mice, while partial progranulin insufficiency is sufficient to produce behavioral deficits.
- Published
- 2019
31. Microplate assay for denatured collagen using collagen hybridizing peptides
- Author
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Jared L. Zitnay, Yang Li, Jeffrey A. Weiss, Allen H. Lin, and S. Michael Yu
- Subjects
030203 arthritis & rheumatology ,Mechanical overload ,biology ,Chemistry ,Cartilage ,0206 medical engineering ,02 engineering and technology ,Osteoarthritis ,medicine.disease ,Proteinase K ,020601 biomedical engineering ,Fluorescence ,Staining ,Tendon ,Microplate Reader ,03 medical and health sciences ,0302 clinical medicine ,medicine.anatomical_structure ,medicine ,Biophysics ,biology.protein ,Orthopedics and Sports Medicine - Abstract
The purpose of this study was to develop a microplate assay for quantifying denatured collagen by measuring the fluorescence of carboxyfluorescein bound collagen hybridizing peptides (F-CHP). We have shown that F-CHP binds selectively with denatured collagen, and that mechanical overload of tendon fascicles causes collagen denaturation. Proteinase K was used to homogenize tissue samples after F-CHP staining, allowing fluorescence measurement using a microplate reader. We compared our new assay to our previous image analysis method and the trypsin-hydroxyproline assay, which is the only other available method to directly quantify denatured collagen. Relative quantification of denatured collagen was performed in rat tail tendon fascicles subjected to incremental tensile overload, and normal and ostoeoarthritic guinea pig cartilage. In addition, the absolute amount of denatured collagen was determined in rat tail tendon by correlating F-CHP fluorescence with percent denatured collagen as determined by the trypsin-hydroxyproline assay. Rat tail tendon fascicles stretched to low strains (
- Published
- 2019
32. Analysis of Falls Efficacy Scale and Vulnerable Elders Survey as Predictors of Falls
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Bryan G Kane, Marna Rayl Greenberg, Ryan M. Surmaitis, Robert D. Barraco, Ali Yazdanyar, Allen H Zeng, Jeanne L Jacoby, Alexander Youngdahl, Richard B Chow, and Sofia M. Murillo
- Subjects
Physical Medicine & Rehabilitation ,emergency department ,business.industry ,Trauma center ,Falls efficacy ,Vulnerable elders ,Significant difference ,General Engineering ,elderly falls ,Emergency department ,030204 cardiovascular system & hematology ,fes ,03 medical and health sciences ,0302 clinical medicine ,Falling (accident) ,Scale (social sciences) ,medicine ,Emergency Medicine ,Public Health ,medicine.symptom ,business ,030217 neurology & neurosurgery ,ves ,Demography ,Cohort study - Abstract
Introduction Falls are the leading cause of injury-related death among older adults according to the Centers for Disease Control and Prevention (CDC). The Falls Efficacy Scale (FES) and Vulnerable Elder Survey (VES-13) are validated screening tools used to assess concern of falling, health deterioration and functional decline. We set out to determine if the FES or VES-13 could serve as a predictor of falls among older adults in the Emergency Department (ED) setting. Methods This prospective pilot cohort study was conducted at a Level 1 Trauma Center. ED patients aged ≥65 were eligible for the study if they had a mechanical fall risk defined by CDC criteria. After consent and enrollment, FES and the VES surveys were completed. Participants were followed by phone quarterly, and results of the one-year follow-up self-report of fall history described. Results There were 200 subjects enrolled and after excluding those that were withdrawn, deceased, or lost to follow-up, 184 were available for analysis of their follow-up visit at 12 months. A greater proportion of the participants were women (108 (58.7%) vs 76 (41.3%); P=0.88). The average age of the study participants was 74.2±7.3 years. There was no significant difference in age between men and women (median: 73 vs 73; p=0.47). At the follow-up visit, 33 (17.9%) had a reported fall. The mean age did not significantly differ when comparing those with versus without a fall (75.6 vs 73.9; p=0.24). There was no significant difference in the proportion with a VES-13 ≥ 3 when comparing those with and without a reported fall (45.5% vs 37.8%; p = 0.41). The median FES score did not differ among those with as compared to without a fall (11 vs 10; p=0.12). Conclusions Subjects who had a VES-13 score of ≥3 were statistically no more likely to have fallen than those with a score of
- Published
- 2021
33. Herbal Extract from Codonopsis pilosula (Franch.) Nannf. Enhances Cardiogenic Differentiation and Improves the Function of Infarcted Rat Hearts
- Author
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Chung Dann Kan, Cheng Lin, Jieh Neng Wang, Chou Wen Lin, Lynn Ling-Huei Huang, Allen H. Chang, Ya Li Hsiao, Lain Tze Lee, and Wanchun Liu
- Subjects
0301 basic medicine ,Cardiac function curve ,Cellular differentiation ,Science ,cardiomyocytes ,Traditional Chinese medicine ,030204 cardiovascular system & hematology ,Pharmacology ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Myocardial infarction ,Ecology, Evolution, Behavior and Systematics ,Ejection fraction ,biology ,Codonopsis pilosula ,business.industry ,cardiogenesis ,Paleontology ,medicine.disease ,biology.organism_classification ,030104 developmental biology ,medicine.anatomical_structure ,myocardial infarction ,Space and Planetary Science ,Ventricle ,herbal extracts ,business ,Ligation - Abstract
Background: The roots of Codonopsis pilosula (Franch.) Nannf. have been used in traditional Chinese medicine for treating cardiovascular disease. In the current study, we aimed to discover herbal extracts from C. pilosula that are capable of improving cardiac function of infarcted hearts to develop a potential therapeutic approach. Methods: A mouse embryonic stem (ES) cell-based model with an enhanced green fluorescent protein (eGFP) reporter driven by a cardiomyocyte-specific promoter, the α-myosin heavy chain, was constructed to evaluate the cardiogenic activity of herbal extracts. Then, herbal extracts from C. pilosula with cardiogenic activity based on an increase in eGFP expression during ES cell differentiation were further tested in a rat myocardial infarction model with left anterior descending artery (LAD) ligation. Cardiac function assessments were performed using echocardiography, 1, 3, and 6 weeks post LAD ligation. Results: The herbal extract 417W from C. pilosula was capable of enhancing cardiogenic differentiation in mouse ES cells in vitro. Echocardiography results in the LAD-ligated rat model revealed significant improvements in the infarcted hearts at least 6 weeks after 417W treatment that were determined based on left ventricle fractional shortening (FS), fractional area contraction (FAC), and ejection fraction (EF). Conclusions: The herbal extract 417W can enhance the cardiogenic differentiation of ES cells and improve the cardiac function of infarcted hearts.
- Published
- 2021
34. Inferring Life History Characteristics of the Oceanic Whitetip Shark Carcharhinus longimanus From Vertebral Bomb Radiocarbon
- Author
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Michelle S. Passerotti, Allen H. Andrews, and Lisa J. Natanson
- Subjects
0106 biological sciences ,lcsh:QH1-199.5 ,010504 meteorology & atmospheric sciences ,family Carcharhinidae ,Endangered species ,Ocean Engineering ,lcsh:General. Including nature conservation, geographical distribution ,Aquatic Science ,migration ,Oceanography ,01 natural sciences ,law.invention ,Critically endangered ,vertebrae ,law ,carbon-14 ,medicine ,IUCN Red List ,Radiocarbon dating ,lcsh:Science ,0105 earth and related environmental sciences ,Water Science and Technology ,Otolith ,Global and Planetary Change ,biology ,age validation ,010604 marine biology & hydrobiology ,Pelagic zone ,biology.organism_classification ,Fishery ,Carcharhinus longimanus ,medicine.anatomical_structure ,Threatened species ,lcsh:Q ,diet - Abstract
Oceanic whitetip sharks Carcharhinus longimanus are a cosmopolitan epipelagic species that was once prolific throughout the tropics and subtropics but was recently listed as Critically Endangered by the International Union for the Conservation of Nature and as Threatened under the United States Endangered Species Act. Although historically conspicuous in oceanic fisheries catches, relatively little is known about their habitat use, movement, and life history during migration. Given the paucity of data on migratory patterns and lack of age estimate validation available for this species, we evaluated vertebral growth bands for bomb radiocarbon (14C) patterns to derive additional information on these metrics. Individual growth bands (n = 62) were milled from vertebrae of eight individuals caught in the northwestern Atlantic Ocean. Age estimates based on vertebral growth bands ranged 1–13 years, with capture dates spanning 1978–2004. Plots of vertebral Δ14C relative to regional coral, shark, and fish otolith reference curves suggest age estimates based on presumed annual growth bands were accurate, although specimens were not old enough to capture the most informative portion of the bomb radiocarbon reference period. The magnitude of Δ14C varied among individuals, and individual chronologies demonstrated semi-cyclic patterns of Δ14C depletion and subsequent enrichment, which may be indicative of changes to diet as a function of annual migratory patterns and is supported by recently published telemetry, diet, and stable isotope studies. Although these data are preliminary in nature, they provide some evidence that Δ14C patterns in vertebrae can serve as a multi-purpose tool for life history studies of oceanic sharks.
- Published
- 2020
35. The Case of Asbestos-Exposed Workers: A Psychological Evaluation
- Author
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Mary Byrne, Allen H. Lebovits, and James J. Strain
- Subjects
business.industry ,Environmental health ,Medicine ,business ,medicine.disease_cause ,Asbestos ,Psychological evaluation - Published
- 2020
36. Accumulation of collagen molecular unfolding is the mechanism of cyclic fatigue damage and failure in collagenous tissues
- Author
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Jared L. Zitnay, Jeffrey A. Weiss, Yang Li, Allen H. Lin, Gang Seob Jung, S. Michael Yu, Markus J. Buehler, and Zhao Qin
- Subjects
0303 health sciences ,Cyclic stress ,Multidisciplinary ,Chemistry ,Physiology ,Rate dependent ,Biophysics ,SciAdv r-articles ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Biological repair ,Tendon ,03 medical and health sciences ,Molecular dynamics ,medicine.anatomical_structure ,Fatigue loading ,medicine ,Cyclic loading ,Denaturation (biochemistry) ,0210 nano-technology ,Research Articles ,030304 developmental biology ,Research Article - Abstract
Denatured collagen accumulates during cyclic fatigue loading and explains the micro-damage hypothesis of overuse tissue injury., Overuse injuries to dense collagenous tissues are common, but their etiology is poorly understood. The predominant hypothesis that micro-damage accumulation exceeds the rate of biological repair is missing a mechanistic explanation. Here, we used collagen hybridizing peptides to measure collagen molecular damage during tendon cyclic fatigue loading and computational simulations to identify potential explanations for our findings. Our results revealed that triple-helical collagen denaturation accumulates with increasing cycles of fatigue loading, and damage is correlated with creep strain independent of the cyclic strain rate. Finite-element simulations demonstrated that biphasic fluid flow is a possible fascicle-level mechanism to explain the rate dependence of the number of cycles and time to failure. Molecular dynamics simulations demonstrated that triple-helical unfolding is rate dependent, revealing rate-dependent mechanisms at multiple length scales in the tissue. The accumulation of collagen molecular denaturation during cyclic loading provides a long-sought “micro-damage” mechanism for the development of overuse injuries.
- Published
- 2020
37. Prioritization and management recommendations of pediatric urology conditions during the COVID-19 pandemic
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Michael Chua, Armando J. Lorenzo, Darius J. Bägli, Allen H Hayashi, Dawn L. MacLellan, Joana Dos Santos, Martin A. Koyle, Stéphane Bolduc, Rodrigo L.P. Romao, Soojin Kim, Daniel T. Keefe, Anne-Sophie Blais, Luis Guerra, Melise A. Keays, Mandy Rickard, Peter Metcalfe, Landan MacDonald, Peter Zhan Tao Wang, Kate H. Moore, Peter M. Anderson, Luis H. Braga, Andrew E. MacNeily, Sumit Dave, Linda Lee, and Natasha Brownrigg
- Subjects
Prioritization ,2019-20 coronavirus outbreak ,medicine.medical_specialty ,Coronavirus disease 2019 (COVID-19) ,business.industry ,Urology ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,MEDLINE ,Paediatric urology ,medicine.disease ,Pediatrics ,Pediatric urology ,Oncology ,Pandemic ,medicine ,Commentary ,Medical emergency ,business - Published
- 2020
38. Safety and tolerability associated with chronic intermittent use of diazepam buccal film in adult, adolescent, and pediatric patients with epilepsy
- Author
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Syndi Seinfeld, Allen H. Heller, Gary Slatko, Buan Carla Valenti, and Michael A. Gelfand
- Subjects
0301 basic medicine ,Adult ,Male ,safety ,Pediatrics ,medicine.medical_specialty ,Adolescent ,Fever ,medicine.drug_class ,Drug Administration Schedule ,03 medical and health sciences ,Epilepsy ,Young Adult ,0302 clinical medicine ,Drug Delivery Systems ,Medicine ,Humans ,Ictal ,Adverse effect ,Child ,benzodiazepines ,Aged ,seizures ,Benzodiazepine ,Diazepam ,business.industry ,Administration, Buccal ,Nausea ,Buccal administration ,Middle Aged ,medicine.disease ,030104 developmental biology ,Treatment Outcome ,Neurology ,Tolerability ,Child, Preschool ,Full‐length Original Research ,rescue ,Observational study ,Anticonvulsants ,Female ,Neurology (clinical) ,business ,030217 neurology & neurosurgery ,medicine.drug - Abstract
Objective Diazepam buccal film (DBF) is in development for treatment of patients experiencing bouts of increased seizure activity. We assessed safety, tolerability, and usability of self‐ or caregiver‐administered DBF in the outpatient setting. Methods Patients aged 2‐65 years needing treatment with a rescue benzodiazepine at least once monthly were eligible for the study. DBF (5‐17.5 mg) was dispensed based on age and body weight. Patients/caregivers administered DBF for up to five seizure episodes per month. Adverse events (AEs) and usability assessments were recorded after the first dose, then every 3 months. Results Onehundred eighteen patients who used ≥1 DBF dose (adults, n = 82; adolescents, n = 19; children, n = 17) were enrolled. Eleven treatment‐related AEs (10 being mild or moderate in severity) occurred in nine (7.6%) patients over a mean of 243 days of follow‐up. No patient discontinued participation because of AEs. Mild local buccal discomfort, buccal swelling, and cheek skin sensitivity were reported by one patient each. Twenty‐two serious AEs were reported; one was treatment‐related. The three deaths reported, all unrelated to DBF, resulted from seizures or seizure with brain malignancy. Self‐administration by adults was attempted on 23.6% (188/795) of use occasions. Administration of DBF occurred under ictal or peri‐ictal conditions on 49.5% (538/1087) of use occasions, and DBF was successfully administered on a first or second attempt on 96.6% (1050/1087) of use occasions. Overall, patients received their dose of DBF on 99.2% (1078/1087) of use occasions. A second DBF dose was required within 24 hours after the first dose on 8.5% (92/1087) of use occasions. Significance In this observational study of chronic intermittent use, DBF was easy to administer, safe, and well tolerated in adult, adolescent, and pediatric patients with epilepsy experiencing seizure emergencies. DBF can be readily self‐administered by adults with epilepsy, as well as successfully administered by a caregiver in seizure emergencies.
- Published
- 2020
39. Indoor Particulate Matter during HOMEChem: Concentrations, Size Distributions, and Exposures
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Erin F. Katz, Yilin Tian, William W. Nazaroff, Peter F. DeCarlo, Sumit Sankhyan, Erin K. Boedicker, Delphine K. Farmer, Marina E. Vance, Joonas Vanhanen, Allen H. Goldstein, and Sameer Patel
- Subjects
Adult ,Air pollution ,010501 environmental sciences ,medicine.disease_cause ,01 natural sciences ,Animal science ,Air Pollution ,medicine ,Environmental Chemistry ,Humans ,Indoor ,Cooking ,Particle Size ,Lung ,0105 earth and related environmental sciences ,Air Pollutants ,Everyday activities ,General Chemistry ,Particulates ,Deposition (aerosol physics) ,Air Pollution, Indoor ,Housing ,Environmental science ,Particulate Matter ,Environmental Sciences ,Environmental Monitoring - Abstract
It is important to improve our understanding of exposure to particulate matter (PM) in residences because of associated health risks. The HOMEChem campaign was conducted to investigate indoor chemistry in a manufactured test house during prescribed everyday activities, such as cooking, cleaning, and opening doors and windows. This paper focuses on measured size distributions of PM (0.001-20 μm), along with estimated exposures and respiratory-tract deposition. Number concentrations were highest for sub-10 nm particles during cooking using a propane-fueled stovetop. During some cooking activities, calculated PM2.5 mass concentrations (assuming a density of 1 g cm-3) exceeded 250 μg m-3, and exposure during the postcooking decay phase exceeded that of the cooking period itself. The modeled PM respiratory deposition for an adult residing in the test house kitchen for 12 h varied from 7 μg on a day with no indoor activities to 68 μg during a simulated day (including breakfast, lunch, and dinner preparation interspersed by cleaning activities) and rose to 149 μg during a simulated Thanksgiving day.
- Published
- 2020
40. Influence of dynamic ozone dry deposition on ozone pollution
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J. W. Munger, L. Neil, A. J. Hogg, Fabien Paulot, Ensheng Weng, G. J. P. Correa, Arlene M. Fiore, Timo Vesala, Larry W. Horowitz, Benjamin Loubet, Allen H. Goldstein, Silvano Fares, Johan Uddling, Ignacio Goded, Ivan Mammarella, Colleen B. Baublitz, Carsten Gruening, Olivia E. Clifton, Patrick Stella, Department of Earth and Environmental Sciences [New York], Columbia University [New York], Lamont-Doherty Earth Observatory (LDEO), National Center for Atmospheric Research [Boulder] (NCAR), NOAA Geophysical Fluid Dynamics Laboratory (GFDL), National Oceanic and Atmospheric Administration (NOAA), Atmospheric and Oceanic Sciences Program [Princeton] (AOS Program), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-Princeton University, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), European Commission - Joint Research Centre [Ispra] (JRC), Department of Environmental Science, Policy, and Management [Berkeley] (ESPM), University of California [Berkeley], University of California-University of California, JRC Institute for Environment and Sustainability (IES), University of Michigan System, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Helsinki, Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS), Harvard University [Cambridge], Hemmera, Ausenco, Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Department of Biological and Environmental Sciences [Gothenburg], University of Gothenburg (GU), Center for Climate Systems Research [New York] (CCSR), NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), National Science Foundation, NOAA's Climate Program Office's Atmospheric Chemistry, Carbon Cycle, and Climate program, National Center for Atmospheric Research, European Union (EU), INAR Physics, Micrometeorology and biogeochemical cycles, Institute for Atmospheric and Earth System Research (INAR), Viikki Plant Science Centre (ViPS), and Ecosystem processes (INAR Forest Sciences)
- Subjects
1171 Geosciences ,FLUXES ,Atmospheric Science ,Ozone ,010504 meteorology & atmospheric sciences ,[SDE.MCG]Environmental Sciences/Global Changes ,AIR-QUALITY ,air pollution ,Air pollution ,Coal combustion products ,nonstomatal deposition ,SOIL-MOISTURE ,Aethalometer ,Atmospheric sciences ,medicine.disease_cause ,01 natural sciences ,chemistry.chemical_compound ,dry deposition ,Earth and Planetary Sciences (miscellaneous) ,medicine ,Mass concentration (chemistry) ,Tropospheric ozone ,earth system modeling ,ATMOSPHERIC CHEMISTRY ,Air quality index ,0105 earth and related environmental sciences ,tropospheric ozone ,Radiative forcing ,DECIDUOUS FOREST ,MODEL ,LAND-COVER ,Geophysics ,chemistry ,13. Climate action ,Space and Planetary Science ,stomatal conductance ,[SDE]Environmental Sciences ,SURFACE OZONE ,Environmental science - Abstract
Identifying the contributions of chemistry and transport to observed ozone pollution using regional-to-global models relies on accurate representation of ozone dry deposition. We use a recently developed configuration of the NOAA GFDL chemistry-climate model - in which the atmosphere and land are coupled through dry deposition-to investigate the influence of ozone dry deposition on ozone pollution over northern midlatitudes. In our model, deposition pathways are tied to dynamic terrestrial processes, such as photosynthesis and water cycling through the canopy and soil. Small increases in winter deposition due to more process-based representation of snow and deposition to surfaces reduce hemispheric-scale ozone throughout the lower troposphere by 5-12 ppb, improving agreement with observations relative to a simulation with the standard configuration for ozone dry deposition. Declining snow cover by the end of the 21st-century tempers the previously identified influence of rising methane on winter ozone. Dynamic dry deposition changes summer surface ozone by -4 to +7 ppb. While previous studies emphasize the importance of uptake by plant stomata, new diagnostic tracking of depositional pathways reveals a widespread impact of nonstomatal deposition on ozone pollution. Daily variability in both stomatal and nonstomatal deposition contribute to daily variability in ozone pollution. Twenty-first century changes in summer deposition result from a balance among changes in individual pathways, reflecting differing responses to both high carbon dioxide (through plant physiology versus biomass accumulation) and water availability. Our findings highlight a need for constraints on the processes driving ozone dry deposition to test representation in regional-to-global models.
- Published
- 2020
41. Pharmacokinetics of clobazam oral soluble film
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Stephen Paul Wargacki, David J. Wyatt, A. Mark Schobel, Allen H. Heller, Buan Carla Valenti, and Cassie Jung
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Adult ,Male ,Clobazam ,Adolescent ,Administration, Oral ,Bioequivalence ,Pharmacology ,Dosage form ,Young Adult ,03 medical and health sciences ,Drug Delivery Systems ,0302 clinical medicine ,Pharmacokinetics ,030225 pediatrics ,Humans ,Medicine ,Single-Blind Method ,Dosing ,Cross-Over Studies ,Dose-Response Relationship, Drug ,business.industry ,Middle Aged ,Crossover study ,Healthy Volunteers ,Therapeutic Equivalency ,Neurology ,Tolerability ,Area Under Curve ,Adjunctive treatment ,Anticonvulsants ,Female ,Neurology (clinical) ,business ,030217 neurology & neurosurgery ,medicine.drug - Abstract
Objective Clobazam oral soluble film (COSF) is a novel dosage form under development for the adjunctive treatment of seizures associated with Lennox-Gastaut syndrome. The present study was undertaken to assess the pharmacokinetics of clobazam administered as single doses of COSF 20 and 10 mg compared with clobazam tablets (CTAB) 20 and 10 mg in healthy adults. A secondary objective was to assess the safety and tolerability of single doses of COSF 20 and 10 mg. Methods A total of 51 adult volunteers were enrolled in a single-dose, open-label, randomized four-sequence, four-period, crossover study with treatments (A) COSF 20 mg, (B) CTAB 20 mg, (C) COSF 10 mg, and (D) CTAB 10 mg. Pharmacokinetic sampling for clobazam and N-desmethylclobazam was carried out until 21 days postdose with a 28-day washout. Subjects were monitored for adverse events (AEs) throughout the study. Visual inspections of the administration site were performed before and after COSF administration to monitor for mucosal irritation. Results COSF at single doses of 10 and 20 mg was bioequivalent to CTAB at equivalent doses for both clobazam and its active metabolite N-desmethylclobazam. The pharmacokinetics of both formulations was dose-proportional at doses of 10 and 20 mg. The number of AEs and the number of subjects experiencing AEs were dose-related across the treatment groups, with somnolence the most common event. None of these events was severe or serious, and most were mild. There was no evidence for local irritation at the administration site following COSF. Significance COSF is a novel clobazam dosage form that is bioequivalent to CTAB. Because of its ease of administration, COSF may be expected to improve adherence, reduce likelihood of dosing error, and provide more accurate dosing than formulations of clobazam that are currently available.
- Published
- 2018
42. Nature Communications
- Author
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Dasa Gu, Meinrat O. Andreae, Joseph Ching, John E. Shilling, Shantanu H. Jathar, Alla Zelenyuk, Rita Yuri Ynoue, Stephen R. Springston, Marianne Glasius, Chun Zhao, Joel Brito, Manish Shrivastava, Lindsay D. Yee, Eliane G. Alves, Zhe Feng, Suzane S. de Sá, Richard C. Easter, Jerome D. Fast, Helber Barros Gomes, Alex Guenther, Allen H. Goldstein, Adan S. S. Medeiros, Sijia Lou, Henrique M. J. Barbosa, Scot T. Martin, V. Faye McNeill, Rahul A. Zaveri, Ying Liu, Saewung Kim, Paulo Artaxo, Joel A. Thornton, Gabriel Isaacman-VanWertz, Rodrigo Augusto Ferreira de Souza, Jiwen Fan, Larry K. Berg, Jose D. Fuentes, Biogeochemistry Division, Max-Planck-Institut, Universidade de São Paulo (USP), Pacific Northwest National Laboratory (PNNL), Centre for Energy and Environment (CERI EE), Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Lille Douai), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut Mines-Télécom [Paris] (IMT), ATOS Origin, Department of Chemistry, Department of Environmental Science, Policy, and Management, University of California, Technische Universität Dresden = Dresden University of Technology (TU Dresden), Federal University of Sao Paulo (Unifesp), Atmospheric Sciences and Global Change Division, and Civil and Environmental Engineering
- Subjects
0301 basic medicine ,Isoprene ,Aircraft ,Air pollution ,Manaus ,General Physics and Astronomy ,02 engineering and technology ,EPOXIDE FORMATION ,medicine.disease_cause ,Atmospheric sciences ,7. Clean energy ,REACTIVE UPTAKE ,Organic Carbon ,Energy Balance ,CHEMISTRY ,PARTICULATE MATTER ,11. Sustainability ,lcsh:Science ,EMISSIONS ,ComputingMilieux_MISCELLANEOUS ,Carbon Footprint ,Secondary Organic Aerosol ,media_common ,Total organic carbon ,Multidisciplinary ,Amazon rainforest ,NOX ,ISOPRENE EPOXYDIOLS ,021001 nanoscience & nanotechnology ,Energy budget ,Pollution ,LOW-VOLATILITY SOA ,Gas ,Atmospheric chemistry ,[SDE]Environmental Sciences ,Nitrogen Oxides ,0210 nano-technology ,Simulation ,Rainforest ,Chemical transport model ,media_common.quotation_subject ,Science ,Amazonas ,Peroxy Radical ,General Biochemistry, Genetics and Molecular Biology ,Article ,Nitrogen Oxide ,03 medical and health sciences ,Ozone ,Pristine Environment ,MD Multidisciplinary ,Oxidation ,medicine ,Aerosol ,Urban Pollution ,Hydroxyl Radical ,Brasil ,General Chemistry ,ANTHROPOGENIC INFLUENCE ,15. Life on land ,Anthropogenic Source ,030104 developmental biology ,13. Climate action ,Atmospheric Chemistry ,Environmental science ,lcsh:Q ,Biogenic Emission ,Urban Area ,Airborne Survey ,AEROSSOL - Abstract
One of the least understood aspects in atmospheric chemistry is how urban emissions influence the formation of natural organic aerosols, which affect Earth’s energy budget. The Amazon rainforest, during its wet season, is one of the few remaining places on Earth where atmospheric chemistry transitions between preindustrial and urban-influenced conditions. Here, we integrate insights from several laboratory measurements and simulate the formation of secondary organic aerosols (SOA) in the Amazon using a high-resolution chemical transport model. Simulations show that emissions of nitrogen-oxides from Manaus, a city of ~2 million people, greatly enhance production of biogenic SOA by 60–200% on average with peak enhancements of 400%, through the increased oxidation of gas-phase organic carbon emitted by the forests. Simulated enhancements agree with aircraft measurements, and are much larger than those reported over other locations. The implication is that increasing anthropogenic emissions in the future might substantially enhance biogenic SOA in pristine locations like the Amazon., It remains unclear how urban emissions influence the formation of secondary organic aerosols (SOA), including in the Amazon forest. Here, the authors simulate the formation of SOAs in the Amazon using a high-resolution regional chemical transport model. They find that urban emissions of NOx from Manaus enhance the production of biogenic SOA by 60–200%.
- Published
- 2019
43. Life history of abyssal and hadal fishes from otolith growth zones and oxygen isotopic compositions
- Author
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Jeffrey C. Drazen, Gary R. Huss, Brian N. Popp, Mackenzie E. Gerringer, Allen H. Andrews, Thomas D. Linley, Kazuhide Nagashima, Alan J. Jamieson, Natalya D. Gallo, and Malcolm R. Clark
- Subjects
0106 biological sciences ,biology ,010604 marine biology & hydrobiology ,Hadal zone ,Aquatic Science ,Oceanography ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Deep sea ,Notoliparis kermadecensis ,Coryphaenoides ,Abyssal zone ,medicine.anatomical_structure ,Careproctus ,Snailfish ,medicine ,Otolith - Abstract
Hadal trenches are isolated habitats that cover the greatest ocean depths (6,500–11,000 m) and are believed to host high levels of endemism across multiple taxa. A group of apparent hadal endemics is within the snailfishes (Liparidae), found in at least five geographically separated trenches. Little is known about their biology, let alone the reasons for their success at hadal depths around the world. This study investigated the life history of hadal liparids using sagittal otoliths of two species from the Kermadec (Notoliparis kermadecensis) and Mariana (Pseudoliparis swirei) trenches in comparison to successful abyssal macrourids found at the abyssal-hadal transition zone. Otoliths for each species revealed alternating opaque and translucent growth zones that could be quantified in medial sections. Assuming these annuli represent annual growth, ages were estimated for the two hadal liparid species to be from five to 16 years old. These estimates were compared to the shallower-living snailfish Careproctus melanurus, which were older than described in previous studies, expanding the potential maximum age for the liparid family to near 25 years. Age estimates for abyssal macrourids ranged from eight to 29 years for Coryphaenoides armatus and six to 16 years for C. yaquinae. In addition, 18O/16O ratios (δ18O) were measured across the otolith using secondary ion mass spectrometry (SIMS) to investigate the thermal history of the three liparids, and two macrourids. Changes in δ18O values were observed across the otoliths of C. melanurus, C. armatus, and both hadal liparids, the latter of which may represent a change of >5 °C in habitat temperature through ontogeny. The results would indicate there is a pelagic larval stage for the hadal liparids that rises to a depth above 1000 m, followed by a return to the hadal environment as these liparids grow. This result was unexpected for the hadal liparids given their isolated environment and large eggs, and the biological implications and plausibility of interpretations of these data are discussed. This study presents a first look at the life history of some of the deepest-living fishes through otolith analyses.
- Published
- 2018
44. Blue marlin (Makaira nigricans) longevity estimates confirmed with bomb radiocarbon dating
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L Humphreys Robert, Jeffery D. Sampaga, and Allen H. Andrews
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0106 biological sciences ,010504 meteorology & atmospheric sciences ,media_common.quotation_subject ,Aquatic Science ,Biology ,Fish measurement ,01 natural sciences ,law.invention ,law ,medicine ,Radiocarbon dating ,cvg ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,media_common ,Otolith ,Tropical pacific ,Ecology ,Blue marlin ,010604 marine biology & hydrobiology ,cvg.computer_videogame ,Longevity ,Fishery ,medicine.anatomical_structure ,%22">Fish ,Accelerator mass spectrometry - Abstract
The longevity of blue marlin (Makaira nigricans) remains unresolved. The use of fin spines and sagittal otoliths for age reading has led to unconfirmed longevity estimates near 20–30 years. Age validation has been elusive because large individuals are uncommonly caught, and a technique that can be applied to structures that provide estimates of age was absent. The use of otolith chemical signatures has been limited by sagittal otoliths that are very small — whole otolith mass of adult blue marlin rarely exceeds 10 mg for the largest fish. Recent advances in the detection limits of radiocarbon (14C) with accelerator mass spectrometry — coupled with recently acquired knowledge of marine bomb 14C signals spanning the tropical Pacific Ocean — have led to an opportunity to age blue marlin from small amounts of otolith material. In this study, otoliths from a recently collected 1245 lb (565 kg) female blue marlin at a measured 146-inch (371 cm) lower jaw fork length were analyzed for 14C. Estimated longevity was either 12–21 or 32–44 years on the basis of bomb 14C dating. Using multiple lines of evidence, it was determined that the young age scenario was most likely, with evidence for an age close to 20 years using a series of deductions in the bomb 14C dating method.
- Published
- 2018
45. The impact of vascular surgery wound complications on quality of life
- Author
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Edward A. McGillicuddy, Allen H. Hamdan, Mark C. Wyers, C. Keith Ozaki, Neal R. Barshes, Louis L. Nguyen, Samir K. Shah, and Michael Belkin
- Subjects
Male ,medicine.medical_specialty ,Prosthesis-Related Infections ,Time Factors ,medicine.medical_treatment ,Endovascular aneurysm repair ,Blood Vessel Prosthesis Implantation ,Peripheral Arterial Disease ,03 medical and health sciences ,0302 clinical medicine ,Risk Factors ,Blood vessel prosthesis ,medicine ,Humans ,Surgical Wound Infection ,Prospective Studies ,Prospective cohort study ,Aged ,Wound Healing ,business.industry ,030503 health policy & services ,Endovascular Procedures ,Critical limb ischemia ,Perioperative ,medicine.disease ,United States ,Abdominal aortic aneurysm ,Blood Vessel Prosthesis ,Surgery ,Treatment Outcome ,Lower Extremity ,Elective Surgical Procedures ,030220 oncology & carcinogenesis ,Quality of Life ,Female ,medicine.symptom ,0305 other medical science ,Cardiology and Cardiovascular Medicine ,Claudication ,business ,Aortic Aneurysm, Abdominal ,Abdominal surgery - Abstract
Objective In addition to traditional surgical outcomes, perioperative quality of life is being scrutinized as a patient-centric metric. As part of a prospective study in a contemporary surgical cohort, subjective health states were examined in context of postoperative wound complications (WCs). We hypothesized that WCs negatively affect quality of life. Methods The EuroQol (EQ)-5D subjective health state data, comprising five domains with 1 (good) to 3 (poor) ordinal scoring, plus visual analog score, were collected at the day of surgery and at 2 and 4 weeks of follow-up in a study evaluating silver-eluting dressings in 500 patients at three centers. A preference-weighted index was calculated. Groups were defined by no complication (NC) or presence of one or more postoperative WCs. Results Patients (72% male) were a mean age of 67.6 years. Primary indications included critical limb ischemia (41.4%), claudication (31.6%), and abdominal aortic aneurysm (11.2%; open groin access for endovascular aneurysm repair). At least one WC occurred in 148 patients (29.6%). Baseline demographics were similar except mean age (NC group, 67.9 years; WC group, 65.7 years; P = .042) and body mass index (NC group, 27.0 kg/m 2 ; WC group, 28.2 kg/m 2 ). WCs were associated with use of conduit for reconstruction ( P = .002), below-knee incisions ( P = .002), and incision length ( P P = .001) but not at 4 weeks (mean change, +0.044; P = .065) postoperatively. Subgroup analysis showed quality-of-life change after WC was most significant in the claudication group ( P = .008). The EQ-5D visual analog scale score was lowest in groups with rest pain (57.0) and tissue loss (55.1) and highest in the abdominal aortic aneurysm cohort (71.8). Conclusions EQ-5D identified a significantly decreased quality-of-life score 2 weeks after WCs in a cohort undergoing elective infrainguinal arterial surgery. This effect was not present 4 weeks postoperatively.
- Published
- 2016
46. Diazepam buccal film for the treatment of acute seizures
- Author
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Michael A. Rogawski and Allen H. Heller
- Subjects
Status epilepticus ,Dosage form ,03 medical and health sciences ,Behavioral Neuroscience ,Epilepsy ,0302 clinical medicine ,Seizures ,medicine ,Humans ,030212 general & internal medicine ,Dosing ,Diazepam ,business.industry ,Administration, Buccal ,Buccal administration ,Cheek ,medicine.disease ,medicine.anatomical_structure ,Neurology ,Anesthesia ,Acute Disease ,Midazolam ,Anticonvulsants ,Neurology (clinical) ,medicine.symptom ,business ,030217 neurology & neurosurgery ,medicine.drug - Abstract
Benzodiazepines, including diazepam and midazolam, are the mainstay of treatment for seizure emergencies, including acute repetitive seizures. Nonparenteral dosage forms are used when parenteral (intravenous or intramuscular) dosing is not feasible. Currently available nonparenteral dosage forms have limitations in terms of usability, patient and caregiver acceptance, speed of action, and portability. Diazepam buccal film (DBF) is a compact, easily administered diazepam formulation. When placed onto the buccal mucosa inside the cheek, DBF adheres firmly and then rapidly dissolves, delivering diazepam transbucally and via the gastric route. In fasted healthy male volunteers, plasma levels were achieved rapidly after DBF placement in a linear dose-proportional fashion. Bioavailability in adult patients with epilepsy was not significantly different when DBF was applied interictally or periictally (within 5 min of a seizure). Diazepam buccal film was successfully placed and generally used without difficulty, even without patient cooperation immediately after a seizure. In a crossover comparative study with diazepam rectal gel (Diastat®) in adult patients with epilepsy, DBF performed equivalently to the rectal gel, but peak exposures were less variable. Diazepam buccal film is a convenient alternative for out-of-hospital treatment of seizure exacerbations. Proceedings of the 7th London-Innsbruck Colloquium on Status Epilepticus and Acute Seizures.
- Published
- 2019
47. Impact of Air Pollution Controls on Radiation Fog Frequency in the Central Valley of California
- Author
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Maria Cristina Facchini, Dennis D. Baldocchi, E. Gray, Brian C. McDonald, Stefania Gilardoni, and Allen H. Goldstein
- Subjects
biosphere ,Atmospheric Science ,Air pollution ,Climate change ,cloud condensation nuclei (CCN) ,NOx ,Atmospheric sciences ,medicine.disease_cause ,Radiation fog ,fog ,Geophysics ,Space and Planetary Science ,atmosphere ,Earth and Planetary Sciences (miscellaneous) ,medicine ,Environmental science ,land and ocean interactions - Abstract
In California's Central Valley, tule fog frequency increased 85% from 1930 to 1970, then declined 76% in the last 36 winters. Throughout these changes, fog frequency exhibited a consistent north-south trend, with maxima in southern latitudes. We analyzed seven decades of meteorological data and five decades of air pollution data to determine the most likely drivers changing fog, including temperature, dew point depression, precipitation, wind speed, and NOx (oxides of nitrogen) concentration. Climate variables, most critically dew point depression, strongly influence the short-term (annual) variability in fog frequency; however, the frequency of optimal conditions for fog formation show no observable trend from 1980 to 2016. NOx concentration, which has a decreasing north-south concentration gradient, declined continuously over this period, consistent with the long-term temporal and spatial trends in fog. As development in the Central Valley increased direct particle and other pollutant emissions from 1930 to 1970, fog frequency increased. Following the Clean Air Act, particle emissions quickly declined, and NOx emissions declined steadily, reducing the cloud condensation nuclei (CCN) available for fog formation. As a precursor of ammonium nitrate aerosols, which are efficient CCN, we used NOx measurements and emission trends as a proxy for the CCN trend. We conclude that while the short-term fog variability is dominantly driven by climate fluctuations, the longer-term temporal and spatial changes in fog have been driven by changes in air pollution. For conditions close to the dew point, a decrease in fog of 5 days/year per 10 parts per billion NOx decrease occurred across the Central Valley. ©2019. American Geophysical Union. All Rights Reserved.
- Published
- 2019
48. Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases
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Pengfei Liu, Allen H. Jiang, James R. Lupski, Carlos A. Bacino, Jennifer Scull, Seema R. Lalani, Xia Wang, Amy M. Breman, Rajarshi Ghosh, Weimin He, Yaping Yang, Arthur L. Beaudet, Avinash V. Dharmadhikari, Fan Xia, Bo Yuan, Donna M. Muzny, Sami Al Masri, Weimin Bi, Chunjing Qu, Janice L. Smith, Hongzheng Dai, Rui Xiao, Jennifer E. Posey, Shen Gu, Ankita Patel, Sau Wai Cheung, Francesco Vetrini, Linyan Meng, Alicia Braxton, Pawel Stankiewicz, Richard A. Gibbs, Chad A. Shaw, Theodore Chiang, Christine M. Eng, and Patricia A. Ward
- Subjects
Exome sequencing ,Male ,0301 basic medicine ,lcsh:QH426-470 ,DNA Copy Number Variations ,lcsh:Medicine ,Single-nucleotide polymorphism ,Microarray ,Runs of Homozygosity ,Compound heterozygosity ,Structural variation ,03 medical and health sciences ,0302 clinical medicine ,Limit of Detection ,Genetics ,Humans ,Medicine ,Genetic Testing ,Copy-number variation ,Exonic CNV in AR disorders ,Molecular Biology ,Exome ,Genetics (clinical) ,Chromosome Aberrations ,business.industry ,Research ,lcsh:R ,ROH ,Homozygote ,Uniparental disomy ,Microarray Analysis ,medicine.disease ,3. Good health ,lcsh:Genetics ,030104 developmental biology ,030220 oncology & carcinogenesis ,Molecular Medicine ,Female ,Dual molecular diagnoses ,business - Abstract
Background Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains challenging. The purpose of this study is to understand the contribution of CNVs and copy neutral runs of homozygosity (ROH) in molecular diagnosis of patients referred for ES. Methods In a cohort of 11,020 consecutive ES patients, an Illumina SNP array analysis interrogating mostly coding SNPs was performed as a quality control (QC) measurement and for CNV/ROH detection. Among these patients, clinical chromosomal microarray analysis (CMA) was performed at Baylor Genetics (BG) on 3229 patients, either before, concurrently, or after ES. We retrospectively analyzed the findings from CMA and the QC array. Results The QC array can detect ~ 70% of pathogenic/likely pathogenic CNVs (PCNVs) detectable by CMA. Out of the 11,020 ES cases, the QC array identified PCNVs in 327 patients and uniparental disomy (UPD) disorder-related ROH in 10 patients. The overall PCNV/UPD detection rate was 5.9% in the 3229 ES patients who also had CMA at BG; PCNV/UPD detection rate was higher in concurrent ES and CMA than in ES with prior CMA (7.2% vs 4.6%). The PCNVs/UPD contributed to the molecular diagnoses in 17.4% (189/1089) of molecularly diagnosed ES cases with CMA and were estimated to contribute in 10.6% of all molecularly diagnosed ES cases. Dual diagnoses with both PCNVs and SNVs were detected in 38 patients. PCNVs affecting single recessive disorder genes in a compound heterozygous state with SNVs were detected in 4 patients, and homozygous deletions (mostly exonic deletions) were detected in 17 patients. A higher PCNV detection rate was observed for patients with syndromic phenotypes and/or cardiovascular abnormalities. Conclusions Our clinical genomics study demonstrates that detection of PCNV/UPD through the QC array or CMA increases ES diagnostic rate, provides more precise molecular diagnosis for dominant as well as recessive traits, and enables more complete genetic diagnoses in patients with dual or multiple molecular diagnoses. Concurrent ES and CMA using an array with exonic coverage for disease genes enables most effective detection of both CNVs and SNVs and therefore is recommended especially in time-sensitive clinical situations. Electronic supplementary material The online version of this article (10.1186/s13073-019-0639-5) contains supplementary material, which is available to authorized users.
- Published
- 2019
49. A Specific CNOT1 Mutation Results in a Novel Syndrome of Pancreatic Agenesis and Holoprosencephaly through Impaired Pancreatic and Neurological Development
- Author
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Almuth Caliebe, De Franco E, Wong Cc, Inês Barroso, Catherine Tudor, Stefan H. Geyer, Robert Hilbrands, Lukas F. Reissig, Harry Heimberg, Sarah E. Flanagan, Andrew Green, Andrew T. Hattersley, Richard Caswell, Christopher J. Lelliott, Wolfgang Weninger, Rachel A. Watson, Fabrice Prin, Paul Martin Holterhus, Reiner Siebert, Asma Deeb, Barbara Maurer-Gesek, Lango Allen H, Sian Ellard, Lelliott, Christopher [0000-0001-8087-4530], Lango Allen, Hana [0000-0002-7803-8688], Barroso, Ines [0000-0001-5800-4520], Apollo - University of Cambridge Repository, Pathology/molecular and cellular medicine, Diabetes Clinic, Diabetes Pathology & Therapy, and Beta Cell Neogenesis
- Subjects
0301 basic medicine ,Male ,Developmental Disabilities ,Sequence Homology ,medicine.disease_cause ,Infant, Newborn, Diseases ,Mice ,0302 clinical medicine ,Holoprosencephaly ,Missense mutation ,Genetics(clinical) ,genetics ,pancreas ,Genetics (clinical) ,health care economics and organizations ,Mice, Knockout ,Mutation ,neurological ,diabetes ,Pancreatic agenesis ,Syndrome ,Phenotype ,3. Good health ,Pedigree ,medicine.anatomical_structure ,Agenesis ,Mutation (genetic algorithm) ,Female ,Pancreas ,education ,030209 endocrinology & metabolism ,agenesis ,neonatal ,03 medical and health sciences ,Report ,medicine ,Animals ,Humans ,Amino Acid Sequence ,development ,business.industry ,Infant, Newborn ,Infant ,Pancreatic Diseases ,medicine.disease ,Embryo, Mammalian ,Embryonic stem cell ,030104 developmental biology ,Forebrain ,Cancer research ,Nervous System Diseases ,business ,Transcription Factors - Abstract
We report a recurrent CNOT1 de novo missense mutation, GenBank: NM_016284.4; c.1603C>T (p.Arg535Cys), resulting in a syndrome of pancreatic agenesis and abnormal forebrain development in three individuals and a similar phenotype in mice. CNOT1 is a transcriptional repressor that has been suggested as being critical for maintaining embryonic stem cells in a pluripotent state. These findings suggest that CNOT1 plays a critical role in pancreatic and neurological development and describe a novel genetic syndrome of pancreatic agenesis and holoprosencephaly.
- Published
- 2019
50. Reconstructing reef fish communities using fish otoliths in coral reef sediments
- Author
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Aaron O'Dea, Brigida De Gracia, Allen H. Andrews, Michele E. R. Pierotti, Katie Griswold, and Chien-Hsiang Lin
- Subjects
0106 biological sciences ,Geologic Sediments ,Taphonomy ,Coral reef fish ,Marine and Aquatic Sciences ,Social Sciences ,Predation ,01 natural sciences ,Otolith ,law.invention ,law ,Medicine and Health Sciences ,Radiocarbon dating ,Data Management ,Sedimentary Geology ,Marine Fossils ,Multidisciplinary ,geography.geographical_feature_category ,Ecology ,Coral Reefs ,Fossils ,Fishes ,Geology ,Coral reef ,Radioactive Carbon Dating ,Trophic Interactions ,Geography ,medicine.anatomical_structure ,Archaeology ,Community Ecology ,Inner Ear ,Medicine ,Anatomy ,Research Article ,Computer and Information Sciences ,Panama ,Science ,Marine Biology ,Research and Analysis Methods ,010603 evolutionary biology ,Otolithic Membrane ,medicine ,Animals ,Reef ,Chemical Characterization ,Petrology ,Isotope Analysis ,Taxonomy ,Functional ecology ,010604 marine biology & hydrobiology ,Dominican Republic ,Ecology and Environmental Sciences ,Biology and Life Sciences ,Paleontology ,Fishery ,Ears ,Archaeological Dating ,Earth Sciences ,Reefs ,Sediment ,Species richness ,Head - Abstract
Little is known about long-term changes in coral reef fish communities. Here we present a new technique that leverages fish otoliths in reef sediments to reconstruct coral reef fish communities. We found over 5,400 otoliths in 169 modern and mid-Holocene bulk samples from Caribbean Panama and Dominican Republic mid-Holocene and modern reefs, demonstrating otoliths are abundant in reef sediments. With a specially-built reference collection, we were able to assign over 4,400 otoliths to one of 56 taxa (35 families) though mostly at genus and family level. Many otoliths were from juvenile fishes for which identification is challenging. Richness (by rarefaction) of otolith assemblages was slightly higher in modern than mid-Holocene reefs, but further analyses are required to elucidate the underlying causes. We compared the living fish communities, sampled using icthyocide, with the sediment otolith assemblages on four reefs finding the otolith assemblages faithfully capture the general composition of the living fish communities. Radiocarbon dating performed directly on the otoliths suggests that relatively little mixing of sediment layers particularly on actively accreting branching coral reefs. All otolith assemblages were strongly dominated by small, fast-turnover fish taxa and juvenile individuals, and our exploration on taxonomy, functional ecology and taphonomy lead us to the conclusion that intense predation is likely the most important process for otolith accumulation in reef sediments. We conclude that otolith assemblages in modern and fossil reef sediments can provide a powerful tool to explore ecological changes in reef fish communities over time and space.
- Published
- 2019
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