553 results on '"Hopkins P"'
Search Results
2. Palbociclib in adults aged 70 years and older with advanced breast cancer: A phase 2 multicenter trial (Alliance A171601)
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Sedrak, Mina S, Lee, Minji K, Ji, Jingran, Satele, Daniel V, Freedman, Rachel A, Poorvu, Philip D, O'Connor, Tracey, Williams, Grant R, Hopkins, Judith O, Muss, Hyman B, Cohen, Harvey Jay, Partridge, Ann H, Carey, Lisa A, Chow, Selina L, Subbiah, Niveditha, Le-Rademacher, Jennifer, and Jatoi, Aminah
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Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Aging ,Women's Health ,Breast Cancer ,Clinical Research ,Clinical Trials and Supportive Activities ,Cancer ,Patient Safety ,6.1 Pharmaceuticals ,Humans ,Pyridines ,Aged ,Female ,Breast Neoplasms ,Piperazines ,Aged ,80 and over ,Prospective Studies ,Antineoplastic Combined Chemotherapy Protocols ,Fulvestrant ,Letrozole ,Age Factors ,Breast cancer ,Older adults ,Palbociclib ,Endocrine therapy ,Oncology and carcinogenesis - Abstract
IntroductionPalbociclib is a widely used treatment for advanced breast cancer in older adults. However, the existing evidence regarding its safety and tolerability in this age group is inconsistent and limited to retrospective subgroup or pooled analyses.Materials and methodsWe conducted a prospective single-arm multicenter phase 2 study to evaluate the safety and tolerability of palbociclib in participants aged 70 years or older with advanced hormone receptor-positive breast cancer. Participants were given palbociclib in combination with their physician's choice of endocrine therapy (letrozole or fulvestrant). The primary endpoint was the incidence of grade 3+ adverse events (AEs) by six months. Secondary endpoints included AE-related dose delays, dose reductions, early discontinuations, and hospitalizations. Additionally, we compared these endpoints by age groups (70-74 and ≥ 75 years).ResultsOf the 90 participants (median age 74 years [70-87]) enrolled, 75.6% (95% confidence interval [CI], 65.4-84.0) had grade 3+ AEs by six months. The most frequent grade 3+ AEs were neutropenia (61%), fatigue (4%), and nausea (3%). Febrile neutropenia was uncommon (1.1%). Due to AEs, 36% had dose delays, 34% had dose reductions, 10% had early discontinuations, and 10% had hospitalizations. Compared to those aged 70-74 years, participants aged ≥75 years had higher rates of early discontinuations (5.9% vs 15.9%, a difference of 9.5% [95% CI 3.5%-22.5%]).DiscussionPalbociclib has an overall favorable safety profile in adults aged ≥70 with advanced breast cancer. However, adults ≥75 years had a trend toward higher rates of AE-related early discontinuations compared to those 70-74 years. Further research is needed to evaluate tolerability and improve the delivery of palbociclib in older adults.Clinicaltrialsgov:NCT03633331.
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- 2024
3. A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Produces Dynamic and Reproducible Changes in the Gut Microbial Ecosystem in Male Rats.
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Thompson, Robert, Bowers, Samuel, Vargas, Fernando, Hopkins, Shelby, Kelley, Tel, Gonzalez, Antonio, Lowry, Christopher, Dorrestein, Pieter, Vitaterna, Martha, Turek, Fred, Knight, Rob, Wright, Kenneth, and Fleshner, Monika
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Parabacteroides ,Ruminiclostridium 5 ,bile acid ,deoxycholic acid ,galactooligosaccharide ,metabolome ,microbiome ,polydextrose ,prebiotic ,Animals ,Prebiotics ,Male ,Gastrointestinal Microbiome ,Rats ,Sprague-Dawley ,Oligosaccharides ,Glucans ,Rats ,Bile Acids and Salts ,Feces ,Bacteria ,RNA ,Ribosomal ,16S ,Diet - Abstract
Despite substantial evidence supporting the efficacy of prebiotics for promoting host health and stress resilience, few experiments present evidence documenting the dynamic changes in microbial ecology and fecal microbially modified metabolites over time. Furthermore, the literature reports a lack of reproducible effects of prebiotics on specific bacteria and bacterial-modified metabolites. The current experiments examined whether consumption of diets enriched in prebiotics (galactooligosaccharides (GOS) and polydextrose (PDX)), compared to a control diet, would consistently impact the gut microbiome and microbially modified bile acids over time and between two research sites. Male Sprague Dawley rats were fed control or prebiotic diets for several weeks, and their gut microbiomes and metabolomes were examined using 16S rRNA gene sequencing and untargeted LC-MS/MS analysis. Dietary prebiotics altered the beta diversity, relative abundance of bacterial genera, and microbially modified bile acids over time. PICRUSt2 analyses identified four inferred functional metabolic pathways modified by the prebiotic diet. Correlational network analyses between inferred metabolic pathways and microbially modified bile acids revealed deoxycholic acid as a potential network hub. All these reported effects were consistent between the two research sites, supporting the conclusion that dietary prebiotics robustly changed the gut microbial ecosystem. Consistent with our previous work demonstrating that GOS/PDX reduces the negative impacts of stressor exposure, we propose that ingesting a diet enriched in prebiotics facilitates the development of a health-promoting gut microbial ecosystem.
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- 2024
4. Nutritional impairment, psychological health and quality of life among older adults with advanced cancer: A secondary analysis of a randomized clinical trial.
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Singhal, Surbhi, Wang, Ying, Qin, Zhaoyang, Peterson, Derick, Dunne, Richard, Culakova, Eva, Hopkins, Judith, Melnyk, Natalia, Onitilo, Adedayo, Targia, Valerie, Mohile, Supriya, and Loh, Kah
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nutritional impairment ,older adults ,psychological health ,quality of life ,Humans ,Quality of Life ,Aged ,Male ,Female ,Neoplasms ,Geriatric Assessment ,Aged ,80 and over ,Nutritional Status ,Mental Health ,Nutrition Assessment ,Malnutrition ,Palliative Care ,Depression - Abstract
BACKGROUND: Nutritional impairment is associated with treatment toxicity and worse overall survival in patients with cancer. We aimed to (1) evaluate the association of nutritional impairment with psychological health and quality of life (QOL) and (2) examine which measures of nutrition had the strongest association with psychological health and QOL among older adults receiving cancer treatment with palliative intent. METHODS: This secondary analysis was performed on baseline data from a nationwide cluster randomized clinical trial (ClinicalTrials.gov identifier: NCT02107443; PI: Mohile). Adults age ≥70 with advanced cancer and ≥1 geriatric assessment (GA) impairment were enrolled from 2014 to 2017. In line with geriatric oncology standards, we defined nutritional impairment as Mini Nutritional Assessment Short Form (MNA-SF) ≤11, body mass index (BMI) 10% involuntary weight loss in the past 6 months. We conducted multivariable linear regressions to evaluate the association of nutritional impairment with each measure of psychological health and QOL: Geriatric Depression Scale (GDS-15, range 0-15), Generalized Anxiety Disorder-7 (GAD-7, range 0-21), NCCN Distress Thermometer (NCCN DT, range 0-10), and Functional Assessment of Cancer Therapy-General (FACT-G, range 0-108). Analyses were adjusted for patient demographics, clinical characteristics, and GA. RESULTS: Among 541 patients, the mean age was 77 (range 70-96) and 60% had nutritional impairment. Mean baseline scores: GDS-15 3.1 (SD 2.7), GAD-7 2.9 (SD 4.0), NCCN DT 2.9 (SD 2.7), and FACT-G 80 (SD 15). In the adjusted model, compared to those with no nutritional impairment, older adults with nutritional impairment had greater depression (β = 0.79, 95% CI 0.36-1.23) and anxiety severity (β = 0.86, 95% CI 0.19-1.53), and worse QOL (β = -6.31, 95% CI -8.62 to -4.00). Of the measures of nutrition, MNA-SF ≤11 demonstrated the strongest associations with depression, anxiety, distress, and QOL. CONCLUSION: Nutritional impairment is associated with impaired psychological health and worse QOL. Clinicians should use the MNA-SF to screen older adults for nutritional impairment and offer tailored supportive interventions.
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- 2024
5. A multidimensional selective landscape drives adaptive divergence between and within closely related Phlox species.
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Goulet-Scott, Benjamin, Farnitano, Matthew, Brown, Andrea, Hale, Charles, Blumstein, Meghan, and Hopkins, Robin
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Selection ,Genetic ,Adaptation ,Physiological ,Species Specificity ,Genetic Speciation ,Genetic Fitness - Abstract
Selection causes local adaptation across populations within species and simultaneously divergence between species. However, it is unclear if either the force of or the response to selection is similar across these scales. We show that natural selection drives divergence between closely related species in a pattern that is distinct from local adaptation within species. We use reciprocal transplant experiments across three species of Phlox wildflowers to characterize widespread adaptive divergence. Using provenance trials, we also find strong local adaptation between populations within a species. Comparing divergence and selection between these two scales of diversity we discover that one suite of traits predicts fitness differences between species and that an independent suite of traits predicts fitness variation within species. Selection drives divergence between species, contributing to speciation, while simultaneously favoring extensive diversity that is maintained across populations within a species. Our work demonstrates how the selection landscape is complex and multidimensional.
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- 2024
6. Computationally restoring the potency of a clinical antibody against Omicron.
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Desautels, Thomas, Arrildt, Kathryn, Zemla, Adam, Lau, Edmond, Zhu, Fangqiang, Ricci, Dante, Cronin, Stephanie, Zost, Seth, Binshtein, Elad, Scheaffer, Suzanne, Dadonaite, Bernadeta, Petersen, Brenden, Engdahl, Taylor, Chen, Elaine, Handal, Laura, Hall, Lynn, Goforth, John, Vashchenko, Denis, Nguyen, Sam, Weilhammer, Dina, Lo, Jacky, Rubinfeld, Bonnee, Saada, Edwin, Weisenberger, Tracy, Lee, Tek-Hyung, Whitener, Bradley, Case, James, Ladd, Alexander, Silva, Mary, Haluska, Rebecca, Grzesiak, Emilia, Earnhart, Christopher, Hopkins, Svetlana, Bates, Thomas, Thackray, Larissa, Segelke, Brent, Lillo, Antonietta, Sundaram, Shivshankar, Bloom, Jesse, Diamond, Michael, Crowe, James, Carnahan, Robert, and Faissol, Daniel
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Animals ,Female ,Humans ,Mice ,Antibodies ,Monoclonal ,Antibodies ,Neutralizing ,Antibodies ,Viral ,COVID-19 ,Mutation ,Neutralization Tests ,SARS-CoV-2 ,Spike Glycoprotein ,Coronavirus ,DNA Mutational Analysis ,Antigenic Drift and Shift ,Drug Design ,Computer Simulation - Abstract
The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1-3 and revealed how quickly viral escape can curtail effective options4,5. When the SARS-CoV-2 Omicron variant emerged in 2021, many antibody drug products lost potency, including Evusheld and its constituent, cilgavimab4-6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign and renew the efficacy of COV2-2130 against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and subsequent variants of concern, and provides protection in vivo against the strains tested: WA1/2020, BA.1.1 and BA.5. Deep mutational scanning of tens of thousands of pseudovirus variants reveals that 2130-1-0114-112 improves broad potency without increasing escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Our computational approach does not require experimental iterations or pre-existing binding data, thus enabling rapid response strategies to address escape variants or lessen escape vulnerabilities.
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- 2024
7. The impact of low-mode symmetry on inertial fusion energy output in the burning plasma state.
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Ralph, J, Ross, J, Zylstra, A, Kritcher, A, Robey, H, Young, C, Hurricane, O, Pak, A, Callahan, D, Baker, K, Casey, D, Döppner, T, Divol, L, Hohenberger, M, Pape, S, Patel, P, Tommasini, R, Ali, S, Amendt, P, Atherton, L, Bachmann, B, Bailey, D, Benedetti, L, Berzak Hopkins, L, Betti, R, Bhandarkar, S, Biener, J, Bionta, R, Birge, N, Bond, E, Bradley, D, Braun, T, Briggs, T, Bruhn, M, Celliers, P, Chang, B, Chapman, T, Chen, H, Choate, C, Christopherson, A, Clark, D, Crippen, J, Dewald, E, Dittrich, T, Edwards, M, Farmer, W, Field, J, Fittinghoff, D, Frenje, J, Gaffney, J, Gatu Johnson, M, Glenzer, S, Grim, G, Haan, S, Hahn, K, Hall, G, Hammel, B, Harte, J, Hartouni, E, Heebner, J, Hernandez, V, Herrmann, H, Herrmann, M, Hinkel, D, Ho, D, Holder, J, Hsing, W, Huang, H, Humbird, K, Izumi, N, Jarrott, L, Jeet, J, Jones, O, Kerbel, G, Kerr, S, Khan, S, Kilkenny, J, Kim, Y, Geppert-Kleinrath, H, Geppert-Kleinrath, V, Kong, C, Koning, J, Kroll, J, Kruse, M, Kustowski, B, Landen, O, Langer, S, Larson, D, Lemos, N, Lindl, J, Ma, T, MacDonald, M, MacGowan, B, Mackinnon, A, MacLaren, S, MacPhee, A, Marinak, M, Mariscal, D, Marley, E, and Masse, L
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Indirect Drive Inertial Confinement Fusion Experiments on the National Ignition Facility (NIF) have achieved a burning plasma state with neutron yields exceeding 170 kJ, roughly 3 times the prior record and a necessary stage for igniting plasmas. The results are achieved despite multiple sources of degradations that lead to high variability in performance. Results shown here, for the first time, include an empirical correction factor for mode-2 asymmetry in the burning plasma regime in addition to previously determined corrections for radiative mix and mode-1. Analysis shows that including these three corrections alone accounts for the measured fusion performance variability in the two highest performing experimental campaigns on the NIF to within error. Here we quantify the performance sensitivity to mode-2 symmetry in the burning plasma regime and apply the results, in the form of an empirical correction to a 1D performance model. Furthermore, we find the sensitivity to mode-2 determined through a series of integrated 2D radiation hydrodynamic simulations to be consistent with the experimentally determined sensitivity only when including alpha-heating.
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- 2024
8. Interlayer Coupling Controlled Ordering and Phases in Polar Vortex Superlattices.
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Meisenheimer, Peter, Ghosal, Arundhati, Hoglund, Eric, Wang, Zhiyang, Behera, Piush, Gómez-Ortiz, Fernando, Kavle, Pravin, Karapetrova, Evguenia, García-Fernández, Pablo, Raja, Archana, Chen, Long-Qing, Hopkins, Patrick, Junquera, Javier, Ramesh, Ramamoorthy, and Martin, Lane
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3D ordering ,ferroelectrics ,phase change ,polar topologies ,superlattice - Abstract
The recent discovery of polar topological structures has opened the door for exciting physics and emergent properties. There is, however, little methodology to engineer stability and ordering in these systems, properties of interest for engineering emergent functionalities. Notably, when the surface area is extended to arbitrary thicknesses, the topological polar texture becomes unstable. Here we show that this instability of the phase is due to electrical coupling between successive layers. We demonstrate that this electrical coupling is indicative of an effective screening length in the dielectric, similar to the conductor-ferroelectric interface. Controlling the electrostatics of the superlattice interfaces, the system can be tuned between a pure topological vortex state and a mixed classical-topological phase. This coupling also enables engineering coherency among the vortices, not only tuning the bulk phase diagram but also enabling the emergence of a 3D lattice of polar textures.
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- 2024
9. Mental Health Distress and Delayed Contraception Among Older Adolescents and Young Adults
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Harper, Cynthia C, Yarger, Jennifer, Mangurian, Christina, Hopkins, Kristine, Rossetto, Irene, Elmes, Sarah, Hecht, Hannah K, Sanchez, Audrey, Hernandez, Rita, Shokat, Mitra, and Steinberg, Julia R
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Paediatrics ,Health Services and Systems ,Biomedical and Clinical Sciences ,Health Sciences ,Contraception/Reproduction ,Brain Disorders ,Behavioral and Social Science ,Mind and Body ,Prevention ,Mental Health ,Clinical Research ,Clinical Trials and Supportive Activities ,Depression ,Mental health ,Good Health and Well Being ,adolescent and young adult contraception ,anxiety and stress ,delayed contraception ,symptoms of depression ,Medical and Health Sciences ,Public Health ,Biomedical and clinical sciences ,Health sciences - Abstract
Background: Symptoms of mental distress increased sharply during the COVID-19 pandemic, especially among older adolescents and young adults. Mental health distress may make it more challenging for young people to seek other needed health care, including contraception. This study explored the association of symptoms of depression, anxiety, and stress with delays in getting a contraceptive method or prescription. Materials and Methods: Data from a supplementary study (May 15, 2020-March 20, 2023) to a cluster randomized trial in 29 sites in Texas and California were used. The diverse study sample included community college students assigned female at birth of ages 18-29 years (n = 1,665 with 7,023 observations over time). We measured the association of depression (CES-D [Center for Epidemiologic Studies Depression Scale]) or anxiety and stress (DASS-21 [Depression Anxiety Stress Scales]) symptoms with delayed contraceptive care-seeking with mixed-effects multivariable regression with random effects for individual and site. We controlled for age and sociodemographic factors important for access to care. Results: Over one-third of participants (35%) reported they delayed getting the contraceptive method they needed. Multivariable regression results showed increased odds of delayed contraceptive care among participants with symptoms of depression (adjusted odds ratio [aOR] 1.58, 95% confidence interval [CI] 1.27-1.96). Likewise, delays were associated with anxiety and stress symptoms (aOR 1.46, 95% CI 1.17-1.82). Adolescents were more likely to delay seeking contraception than young adults (aOR 1.32, 95% CI 1.07-1.63). Conclusions: Results showed a strong association between mental distress and delayed contraception. Interventions are needed to increase contraceptive access for young people delaying care, along with supportive mental health care services, including for adolescents who face elevated odds of delay. ClinicalTrials.gov Identifier: NCT03519685.
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- 2024
10. Use of telemedicine to obtain contraception among young adults: Inequities by health insurance
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Yarger, Jennifer, Hopkins, Kristine, Elmes, Sarah, Rossetto, Irene, Van Liefde, Danielle, De La Melena, Stephanie, and Harper, Cynthia C
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Reproductive Medicine ,Biomedical and Clinical Sciences ,Public Health ,Health Sciences ,Clinical Research ,Prevention ,Contraception/Reproduction ,Rural Health ,Good Health and Well Being ,Contraception ,Health insurance ,Telehealth ,Telemedicine ,Young adult ,Clinical Sciences ,Paediatrics and Reproductive Medicine ,Public Health and Health Services ,Obstetrics & Reproductive Medicine ,Clinical sciences ,Reproductive medicine ,Health services and systems - Abstract
ObjectivesThe objective of this study was to describe the use of telemedicine for contraception in a sample of young adults and examine differences by health insurance coverage.Study designWe analyzed survey data collected from May 2020 to July 2022 from individuals at risk of pregnancy aged 18 to 29 recruited at 29 community colleges in California and Texas. We used multivariable mixed-effects logistic regression models with random effects for site and individual to compare the use of telemedicine to obtain contraception by insurance status, sociodemographic characteristics, and state.ResultsOur analytic sample included 6465 observations from 1630 individuals. Participants reported using a contraceptive method obtained through telemedicine in just 6% of observations. Uninsured participants were significantly less likely than those privately insured to use contraception obtained through telemedicine (adjusted odds ratio [aOR], 0.54; 95% confidence interval [CI], 0.31-0.97), as were participants who did not know their insurance status (aOR, 0.54; 95% CI, 0.29-0.99). Texas participants were less likely to use contraception obtained via telemedicine than those in California (aOR, 0.42; CI: 0.25-0.69).ConclusionsFew young people in this study obtained contraception through telemedicine, and insurance was crucial for access in both states.ImplicationsAlthough telemedicine holds promise for increasing contraceptive access, we found that few young adults were using it, particularly among the uninsured. Efforts are needed to improve young adults' access to telemedicine for contraception and address insurance disparities.
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- 2024
11. Realizable Learning is All You Need
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Hopkins, Max, Kane, Daniel, Lovett, Shachar, and Mahajan, Gaurav
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Information and Computing Sciences ,Machine Learning ,Clinical Research - Abstract
The equivalence of realizable and agnostic learnability is a fundamentalphenomenon in learning theory. With variants ranging from classical settingslike PAC learning and regression to recent trends such as adversarially robustlearning, it's surprising that we still lack a unified theory; traditionalproofs of the equivalence tend to be disparate, and rely on strongmodel-specific assumptions like uniform convergence and sample compression. In this work, we give the first model-independent framework explaining theequivalence of realizable and agnostic learnability: a three-line blackboxreduction that simplifies, unifies, and extends our understanding across a widevariety of settings. This includes models with no known characterization oflearnability such as learning with arbitrary distributional assumptions andmore general loss functions, as well as a host of other popular settings suchas robust learning, partial learning, fair learning, and the statistical querymodel. More generally, we argue that the equivalence of realizable and agnosticlearning is actually a special case of a broader phenomenon we call propertygeneralization: any desirable property of a learning algorithm (e.g. noisetolerance, privacy, stability) that can be satisfied over finite hypothesisclasses extends (possibly in some variation) to any learnable hypothesis class.
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- 2024
12. Decoupled evolution of the Sex Peptide gene family and Sex Peptide Receptor in Drosophilidae
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Hopkins, Ben R, Angus-Henry, Aidan, Kim, Bernard Y, Carlisle, Jolie A, Thompson, Ammon, and Kopp, Artyom
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Climate Change Impacts and Adaptation ,Biological Sciences ,Ecology ,Evolutionary Biology ,Genetics ,Environmental Sciences ,Biotechnology ,Generic health relevance ,Animals ,Female ,Male ,Biological Evolution ,Drosophila ,Drosophila melanogaster ,Drosophila Proteins ,Peptides ,Receptors ,Peptide ,Reproduction ,Sexual Behavior ,Animal ,coevolution ,gene family evolution ,reproduction ,sexual conflict ,sexual selection - Abstract
Across internally fertilising species, males transfer ejaculate proteins that trigger wide-ranging changes in female behaviour and physiology. Much theory has been developed to explore the drivers of ejaculate protein evolution. The accelerating availability of high-quality genomes now allows us to test how these proteins are evolving at fine taxonomic scales. Here, we use genomes from 264 species to chart the evolutionary history of Sex Peptide (SP), a potent regulator of female post-mating responses in Drosophila melanogaster. We infer that SP first evolved in the Drosophilinae subfamily and has since followed markedly different evolutionary trajectories in different lineages. Outside of the Sophophora-Lordiphosa, SP exists largely as a single-copy gene with independent losses in several lineages. Within the Sophophora-Lordiphosa, the SP gene family has repeatedly and independently expanded. Up to seven copies, collectively displaying extensive sequence variation, are present in some species. Despite these changes, SP expression remains restricted to the male reproductive tract. Alongside, we document considerable interspecific variation in the presence and morphology of seminal microcarriers that, despite the critical role SP plays in microcarrier assembly in D. melanogaster, appears to be independent of changes in the presence/absence or sequence of SP. We end by providing evidence that SP's evolution is decoupled from that of its receptor, Sex Peptide Receptor, in which we detect no evidence of correlated diversifying selection. Collectively, our work describes the divergent evolutionary trajectories that a novel gene has taken following its origin and finds a surprisingly weak coevolutionary signal between a supposedly sexually antagonistic protein and its receptor.
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- 2024
13. Whats in This For You? Whats in This For Me?: A Win-Win Perspective of Involving Study Advisory Committee Members in Palliative Care Research.
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Booker-Vaughns, Juanita, Rosini, Dawn, Batra, Romilla, Kizzie-Gillett, Constance, Maguire, Margaret, Navarro, Martha, Reddy Pidatala, Neha, Vaughan, William, Welsh, Sally, Williams, Pluscedia, Young-Brinn, Angela, Van Allen, Kaitlyn, Cuthel, Allison, Liddicoat Yamarik, Rebecca, Flannery, Mara, Goldfeld, Keith, Grudzen, Corita, Dunn, Patrick, Galvin, Robert, Hopkins, Ernest, Isaacs, Eric, and Chan, Garrett
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engagement ,palliative care ,stakeholders ,study advisory committee - Abstract
Study advisory committees (SACs) provide critical value to clinical trials by providing unique perspectives that pull from personal and professional experiences related to the trials healthcare topic. The Emergency Medicine Palliative Care Access (EMPallA) study had the privilege of convening a 16-person SAC from the projects inception to completion. The study team wanted to understand the impact this project had on the SAC members. In this narrative, we use reflective dialogue to share SAC members lived experiences and the impact the EMPallA study has had on members both personally and professionally. We detail the (1) benefits SAC members, specifically patients, and caregivers, have had through working on this project. (2) The importance of recruiting diverse SAC members with different lived experiences and leveraging their feedback in clinical research. (3) Value of community capacity building to ensure the common vision of the clinical trial is promoted.
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- 2024
14. Bokashi fermentation of brewery’s spent grains positively affects larval performance of the black soldier fly Hermetia illucens while reducing gaseous nitrogen losses
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Gebiola, Marco, Rodriguez, Michael V, Garcia, Alexandro, Garnica, Andrea, Tomberlin, Jeffery K, Hopkins, Francesca M, and Mauck, Kerry E
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Environmental Sciences ,Environmental Management ,BSF larvae ,Circular economy ,GHG emissions ,N(2)O ,NH(3) ,Environmental Engineering ,Building ,Chemical engineering ,Environmental management - Abstract
Digestion of waste feedstocks by larvae of the black soldier fly Hermetia illucens (Diptera: Stratiomyidae) (BSF) results in proteins for animal feed and organic fertilizer with a reduced environmental footprint, but it can still have negative environmental effects through greenhouse gas (GHG) and ammonia (NH3) emissions. Both biomass conversion by BSF larvae and associated GHG and NH3 emissions can depend on substrate properties that may be optimized through microbial inoculation pre-treatments, such as bokashi fermentation. Here, we quantified the effects of bokashi fermentation of brewery's spent grains on BSF rearing metrics and associated GHG and NH3 emissions at benchtop scale. We found that bokashi fermentation increased larval biomass by 40% and shortened development time by over two days on average, compared with unfermented spent grains. In line with increased larval growth, CO2 emissions in BSF larvae treatments were 31.0 and 79.0% higher in the bokashi fermented spent grains and Gainesville substrates, respectively, compared to the unfermented spent grains. Adding BSF larvae to the spent grains increased cumulative N2O emissions up to 64.0 mg N2O kg substratedry-1 but there were essentially no N2O emissions when larvae were added to fermented spent grains. Bokashi fermentation also reduced NH3 fluxes from the volatilization of substrate nitrogen in the BSF larvae treatment by 83.7-85.8% during days 7 and 9, possibly by increasing N assimilation by larvae or by reducing the transformation of substrate NH4+ to NH3. Therefore, bokashi fermentation may be applied to improve performance of BSF larvae on a common industrial waste stream and reduce associated emissions.
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- 2023
15. Genomic analysis of advanced breast cancer tumors from talazoparib-treated gBRCA1/2mut carriers in the ABRAZO study.
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Turner, Nicholas, Laird, A, Telli, Melinda, Rugo, Hope, Mailliez, Audrey, Ettl, Johannes, Grischke, Eva-Maria, Mina, Lida, Balmaña, Judith, Fasching, Peter, Hurvitz, Sara, Hopkins, Julia, Albacker, Lee, Chelliserry, Jijumon, Chen, Ying, Conte, Umberto, Wardley, Andrew, and Robson, Mark
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These analyses explore the impact of homologous recombination repair gene mutations, including BRCA1/2 mutations and homologous recombination deficiency (HRD), on the efficacy of the poly(ADP-ribose) polymerase (PARP) inhibitor talazoparib in the open-label, two-cohort, Phase 2 ABRAZO trial in germline BRCA1/2-mutation carriers. In the evaluable intent-to-treat population (N = 60), 58 (97%) patients harbor ≥1 BRCA1/2 mutation(s) in tumor sequencing, with 95% (53/56) concordance between germline and tumor mutations, and 85% (40/47) of evaluable patients have BRCA locus loss of heterozygosity indicating HRD. The most prevalent non-BRCA tumor mutations are TP53 in patients with BRCA1 mutations and PIK3CA in patients with BRCA2 mutations. BRCA1- or BRCA2-mutated tumors show comparable clinical benefit within cohorts. While low patient numbers preclude correlations between HRD and efficacy, germline BRCA1/2 mutation detection from tumor-only sequencing shows high sensitivity and non-BRCA genetic/genomic events do not appear to influence talazoparib sensitivity in the ABRAZO trial.ClinicalTrials.gov identifier: NCT02034916.
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- 2023
16. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells
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Tsuchida, Connor A, Brandes, Nadav, Bueno, Raymund, Trinidad, Marena, Mazumder, Thomas, Yu, Bingfei, Hwang, Byungjin, Chang, Christopher, Liu, Jamin, Sun, Yang, Hopkins, Caitlin R, Parker, Kevin R, Qi, Yanyan, Hofman, Laura, Satpathy, Ansuman T, Stadtmauer, Edward A, Cate, Jamie HD, Eyquem, Justin, Fraietta, Joseph A, June, Carl H, Chang, Howard Y, Ye, Chun Jimmie, and Doudna, Jennifer A
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Biomedical and Clinical Sciences ,Immunology ,Genetics ,Clinical Research ,Gene Therapy ,Biotechnology ,Bioengineering ,5.2 Cellular and gene therapies ,5.1 Pharmaceuticals ,Generic health relevance ,Cancer ,Humans ,Chromosomes ,CRISPR-Cas Systems ,DNA Damage ,Gene Editing ,T-Lymphocytes ,Clinical Trials as Topic ,Chromosome Aberrations ,CAR T cells ,CRISPR screen ,CRISPR-Cas9 ,DNA repair ,T cells ,aneuploidy ,chromosome loss ,clinical trial ,genome editing ,immunoengineering ,genome editing: ,CAR T cells ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
CRISPR-Cas9 genome editing has enabled advanced T cell therapies, but occasional loss of the targeted chromosome remains a safety concern. To investigate whether Cas9-induced chromosome loss is a universal phenomenon and evaluate its clinical significance, we conducted a systematic analysis in primary human T cells. Arrayed and pooled CRISPR screens revealed that chromosome loss was generalizable across the genome and resulted in partial and entire loss of the targeted chromosome, including in preclinical chimeric antigen receptor T cells. T cells with chromosome loss persisted for weeks in culture, implying the potential to interfere with clinical use. A modified cell manufacturing process, employed in our first-in-human clinical trial of Cas9-engineered T cells (NCT03399448), reduced chromosome loss while largely preserving genome editing efficacy. Expression of p53 correlated with protection from chromosome loss observed in this protocol, suggesting both a mechanism and strategy for T cell engineering that mitigates this genotoxicity in the clinic.
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- 2023
17. Towards hyperlocal source identification of pollutants in cities by combining mobile measurements with atmospheric modeling
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Lin, John C, Fasoli, Ben, Mitchell, Logan, Bares, Ryan, Hopkins, Francesca, Thompson, Tammy M, and Alvarez, Ramón A
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Earth Sciences ,Atmospheric Sciences ,Clinical Research ,Sustainable Cities and Communities ,Statistics ,Environmental Engineering ,Meteorology & Atmospheric Sciences ,Atmospheric sciences ,Climate change science ,Environmental engineering - Published
- 2023
18. Evidence for multi-decadal fuel buildup in a large California wildfire from smoke radiocarbon measurements
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Odwuor, A, Yañez, CC, Chen, Y, Hopkins, FM, Moreno, A, Xu, X, Czimczik, CI, and Randerson, JT
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Earth Sciences ,Atmospheric Sciences ,Environmental Sciences ,Life on Land ,biomass burning ,western US forests ,carbon-14 ,aerosol ,ecosystem turnover time ,Meteorology & Atmospheric Sciences - Abstract
In recent decades, there has been a significant increase in annual area burned in California's Sierra Nevada mountains. This rise in fire activity has prompted the need to understand how historical forest management practices affect fuel composition and emissions. Here we examined the total carbon (TC) concentration and radiocarbon abundance (Δ14C) of particulate matter (PM) emitted by the KNP Complex Fire, which occurred during California's 2021 wildfire season and affected several groves of giant sequoia trees in the southern Sierra Nevada. During a 26 h sampling period, we measured concentrations of fine airborne PM (PM2.5), as well as dry air mole fractions of carbon monoxide (CO) and methane (CH4), using a ground-based mobile laboratory. We also collected filter samples of PM2.5 for analysis of TC concentration and Δ14C. High correlation among PM2.5, CO, and CH4 time series confirmed that our PM2.5 measurements captured variability in wildfire emissions. Using a Keeling plot approach, we determined that the mean Δ14C of PM2.5 was 111.6 ± 7.7‰ (n = 12), which was considerably enriched relative to atmospheric carbon dioxide in the northern hemisphere in 2021 (-3.2 ± 1.4‰). Combining these Δ14C data with a steady-state one-box ecosystem model, we estimated that the mean age of fuels combusted in the KNP Complex Fire was 40 years, with a range of 29-57 years. These results provide evidence for emissions originating from woody biomass, larger-diameter fine fuels, and coarse woody debris that have accumulated over multiple decades. This is consistent with independent field observations that indicate high fire intensity contributed to widespread giant sequoia mortality. With the expanded use of prescribed fires planned over the next decade in California to mitigate wildfire impacts, our measurement approach has the potential to provide regionally-integrated estimates of the effectiveness of fuel treatment programs.
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- 2023
19. Paleobiology Database User Guide Version 1.0
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Uhen, Mark D., Allen, Bethany, Behboudi, Noushin, Clapham, Matthew E., Dunne, Emma, Hendy, Austin, Holroyd, Patricia A., Hopkins, Melanie, Mannion, Philip, Novack-Gottshall, Phil, Pimiento, Catalina, and Wagner, Peter
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- 2023
20. Gill function in an early arthropod and the widespread adoption of the countercurrent exchange mechanism.
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Hopkins, Melanie, Shu, Degan, Hou, Jin-Bo, and Hughes, Nigel
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Gill ,computational fluid dynamics ,efficient mechanisms ,metazoans ,respiration - Abstract
Rising but fluctuating oxygen levels in the Early Palaeozoic provide an environmental context for the radiation of early metazoans, but little is known about how mechanistically early animals satisfied their oxygen requirements. Here we propose that the countercurrent gaseous exchange, a highly efficient respiratory mechanism, was effective in the gills of the Late Ordovician trilobite Triarthrus eatoni. In order to test this, we use computational fluid dynamics to simulate water flow around its gills and show that water velocity decreased distinctly in front of and between the swollen ends, which first encountered the oxygen-charged water, and slowed continuously at the mid-central region, forming a buffer zone with a slight increase of the water volume. In T. eatoni respiratory surface area was maximized by extending filament height and gill shaft length. In comparison with the oxygen capacity of modern fish and crustaceans, a relatively low weight specific area in T. eatoni may indicate its low oxygen uptake, possibly related to a less active life mode. Exceptionally preserved respiratory structures in the Cambrian deuterostome Haikouella are also consistent with a model of countercurrent gaseous exchange, exemplifying the wide adoption of this strategy among early animals.
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- 2023
21. Putative malignant hyperthermia mutation CaV1.1-R174W is insufficient to trigger a fulminant response to halothane or confer heat stress intolerance.
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Feng, Wei, Lopez, Jose, Antrobus, Shane, Zheng, Jing, Uryash, Arkady, Dong, Yao, Beqollari, Donald, Bannister, Roger, Hopkins, Philip, Beam, Kurt, Allen, Paul, and Pessah, Isaac
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TRPC3/6 ,heat stress intolerance ,knock-in mouse ,malignant hyperthermia susceptibility ,muscle diseases ,ryanodine receptor ,voltage-activated Ca(2+) channels ,Animals ,Mice ,Calcium ,Halothane ,Heat-Shock Response ,Malignant Hyperthermia ,Muscle ,Skeletal ,Mutation ,Ryanodine Receptor Calcium Release Channel ,Large-Conductance Calcium-Activated Potassium Channel alpha Subunits - Abstract
Malignant hyperthermia susceptibility (MHS) is an autosomal dominant pharmacogenetic disorder that manifests as a hypermetabolic state when carriers are exposed to halogenated volatile anesthetics or depolarizing muscle relaxants. In animals, heat stress intolerance is also observed. MHS is linked to over 40 variants in RYR1 that are classified as pathogenic for diagnostic purposes. More recently, a few rare variants linked to the MHS phenotype have been reported in CACNA1S, which encodes the voltage-activated Ca2+ channel CaV1.1 that conformationally couples to RyR1 in skeletal muscle. Here, we describe a knock-in mouse line that expresses one of these putative variants, CaV1.1-R174W. Heterozygous (HET) and homozygous (HOM) CaV1.1-R174W mice survive to adulthood without overt phenotype but fail to trigger with fulminant malignant hyperthermia when exposed to halothane or moderate heat stress. All three genotypes (WT, HET, and HOM) express similar levels of CaV1.1 by quantitative PCR, Western blot, [3H]PN200-110 receptor binding and immobilization-resistant charge movement densities in flexor digitorum brevis fibers. Although HOM fibers have negligible CaV1.1 current amplitudes, HET fibers have similar amplitudes to WT, suggesting a preferential accumulation of the CaV1.1-WT protein at triad junctions in HET animals. Never-the-less both HET and HOM have slightly elevated resting free Ca2+ and Na+ measured with double barreled microelectrode in vastus lateralis that is disproportional to upregulation of transient receptor potential canonical (TRPC) 3 and TRPC6 in skeletal muscle. CaV1.1-R174W and upregulation of TRPC3/6 alone are insufficient to trigger fulminant malignant hyperthermia response to halothane and/or heat stress in HET and HOM mice.
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- 2023
22. Early‐life behavioral features are associated with chronic emesis in rhesus macaques (Macaca mulatta)
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Nakatani, Jamie Y, Pomerantz, Ori, Stockinger, Diane, Christe, Kari, Hopkins, Lincoln, Roberts, Jeffrey A, Reader, Rachel J, and Ardeshir, Amir
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Zoology ,Biological Sciences ,Prevention ,Behavioral and Social Science ,Basic Behavioral and Social Science ,Animals ,Humans ,Case-Control Studies ,Macaca mulatta ,Quality of Life ,Temperament ,Vomiting ,chronic emesis ,early life biobehavioral temperament ,rhesus macaque ,Anthropology ,Behavioral Science & Comparative Psychology - Abstract
Chronic emesis (CE) is a poorly understood condition in human and nonhuman primates that negatively impacts the quality of life. Early identification of risk factors for the development of CE is likely to improve the ability to manage CE cases successfully and is, therefore, desirable. Using a case-control study, we reviewed the necropsy records of the California National Primate Research Center and identified 24 animals with recorded CE, defined as five or more incidents of emesis in 1 month. A group of 89 healthy rhesus macaques (Macaca mulatta), comparable in age and percent time housed indoors, was similarly identified. Next, we investigated the association between the occurrence of CE during later stages of life after infancy and the behavioral temperament scores attained in infancy, age, sex, birth location, rearing condition, history of self-injurious behavior (SIB), and the number of lifetime sedation events. Our analysis revealed that CE was associated with degrees of temperament constructs obtained in infancy (data was available for n = 113), such as Confidence (odds ratio (OR) = 0.45, 95% CI: 0.18, 1.08, p = 0.07), Gentleness (OR = 0.47, 95% CI: 0.23, 0.96, p = 0.03), Nervousness (OR = 2.04, 95% CI: 0.98, 4.23, p = 0.05), and Vigilance (OR = 0.36, 95% CI: 015, 0.87, p = 0.02), suggesting that CE is linked to behavioral phenomenon measured in early life, long before it becomes a medical concern. Our data suggest that CE was positively correlated with a history of SIB (OR 4.26, 95% CI: 0.98, 18.47, p = 0.04). Accurate prediction of CE can then assist behavioral and colony management professionals in making informed decisions regarding the care of animals at risk of developing CE. Moreover, the novel information we reported here could have valuable implications in human medicine, where gastrointestinal distress is a common complaint affecting a person's quality of life.
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- 2023
23. Interrelationships among workload, illness severity, and function on return to work following acute respiratory distress syndrome.
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Su, Han, Thompson, Hilaire, Pike, Kenneth, Kamdar, Biren, Bridges, Elizabeth, Hosey, Megan, Hough, Catherine, Needham, Dale, and Hopkins, Ramona
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ARDS ,Employment ,Impairment ,Intensive care unit ,Job characteristics ,Humans ,Return to Work ,Workload ,Patient Acuity ,Respiratory Distress Syndrome - Abstract
BACKGROUND: Inability to return to work (RTW) is common after acute respiratory distress syndrome (ARDS). OBJECTIVES: The aim of this study is to examine interrelationships among pre-ARDS workload, illness severity, and post-ARDS cognitive, psychological, interpersonal, and physical function with RTW at 6 and 12 months after ARDS. METHODS: We conducted a secondary analysis using the US multicentre ARDS Network Long-Term Outcomes Study. The US Occupational Information Network was used to determine pre-ARDS workload. The Mini-Mental State Examination and SF-36 were used to measure four domains of post-ARDS function. Analyses used structural equation modeling and mediation analyses. RESULTS: Among 329 previously employed ARDS survivors, 6- and 12-month RTW rates were 52% and 56%, respectively. Illness severity (standardised coefficients range: -0.51 to -0.54, p
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- 2023
24. Infant rhesus macaques immunized against SARS-CoV-2 are protected against heterologous virus challenge one year later
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Milligan, Emma C, Olstad, Katherine, Williams, Caitlin A, Mallory, Michael, Cano, Patricio, Cross, Kaitlyn A, Munt, Jennifer E, Garrido, Carolina, Lindesmith, Lisa, Watanabe, Jennifer, Usachenko, Jodie L, Hopkins, Lincoln, Immareddy, Ramya, Lakshmanappa, Yashavanth Shaan, Elizaldi, Sonny R, Roh, Jamin W, Sammak, Rebecca L, Pollard, Rachel E, Yee, JoAnn L, Herbek, Savannah, Scobey, Trevor, Miehlke, Dieter, Fouda, Genevieve, Ferrari, Guido, Gao, Hongmei, Shen, Xiaoying, Kozlowski, Pamela A, Montefiori, David, Hudgens, Michael G, Edwards, Darin K, Carfi, Andrea, Corbett, Kizzmekia S, Graham, Barney S, Fox, Christopher B, Tomai, Mark, Iyer, Smita S, Baric, Ralph, Reader, Rachel, Dittmer, Dirk P, Van Rompay, Koen KA, Permar, Sallie R, and De Paris, Kristina
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Immunization ,Emerging Infectious Diseases ,Infectious Diseases ,Prevention ,Biodefense ,Vaccine Related ,Pneumonia ,Pneumonia & Influenza ,Lung ,Biotechnology ,Development of treatments and therapeutic interventions ,5.1 Pharmaceuticals ,Prevention of disease and conditions ,and promotion of well-being ,3.4 Vaccines ,Infection ,Good Health and Well Being ,Animals ,Humans ,Infant ,SARS-CoV-2 ,COVID-19 Vaccines ,Macaca mulatta ,COVID-19 ,Viral Vaccines ,BNT162 Vaccine ,Antibodies ,Viral ,Antibodies ,Neutralizing ,Biological Sciences ,Medical and Health Sciences - Abstract
The U.S. Food and Drug Administration only gave emergency use authorization of the BNT162b2 and mRNA-1273 SARS-CoV-2 vaccines for infants 6 months and older in June 2022. Yet questions regarding the durability of vaccine efficacy, especially against emerging variants, in this age group remain. We demonstrated previously that a two-dose regimen of stabilized prefusion Washington SARS-CoV-2 S-2P spike (S) protein encoded by mRNA encapsulated in lipid nanoparticles (mRNA-LNP) or purified S-2P mixed with 3M-052, a synthetic Toll-like receptor (TLR) 7/8 agonist, in a squalene emulsion (Protein+3M-052-SE) was safe and immunogenic in infant rhesus macaques. Here, we demonstrate that broadly neutralizing and spike-binding antibodies against variants of concern (VOCs), as well as T cell responses, persisted for 12 months. At 1 year, corresponding to human toddler age, we challenged vaccinated rhesus macaques and age-matched nonvaccinated controls intranasally and intratracheally with a high dose of heterologous SARS-CoV-2 B.1.617.2 (Delta). Seven of eight control rhesus macaques exhibited severe interstitial pneumonia and high virus replication in the upper and lower respiratory tract. In contrast, vaccinated rhesus macaques had faster viral clearance with mild to no pneumonia. Neutralizing and binding antibody responses to the B.1.617.2 variant at the day of challenge correlated with lung pathology and reduced virus replication. Overall, the Protein+3M-052-SE vaccine provided superior protection to the mRNA-LNP vaccine, emphasizing opportunities for optimization of current vaccine platforms. The observed efficacy of both vaccines 1 year after vaccination supports the implementation of an early-life SARS-CoV-2 vaccine.
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- 2023
25. Quantitative Imaging Metrics for the Assessment of Pulmonary Pathophysiology: An Official American Thoracic Society and Fleischner Society Joint Workshop Report.
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Hsia, Connie, Bates, Jason, Driehuys, Bastiaan, Fain, Sean, Goldin, Jonathan, Hoffman, Eric, Hogg, James, Levin, David, Lynch, David, Ochs, Matthias, Parraga, Grace, Prisk, G, Smith, Benjamin, Tawhai, Merryn, Vidal Melo, Marcos, Woods, Jason, and Hopkins, Susan
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computed tomography ,lung mechanics ,magnetic resonance imaging ,positron emission tomography ,ventilation-perfusion-diffusion ,Humans ,Benchmarking ,Lung ,Lung Diseases ,Pulmonary Emphysema ,Respiration ,Magnetic Resonance Imaging - Abstract
Multiple thoracic imaging modalities have been developed to link structure to function in the diagnosis and monitoring of lung disease. Volumetric computed tomography (CT) renders three-dimensional maps of lung structures and may be combined with positron emission tomography (PET) to obtain dynamic physiological data. Magnetic resonance imaging (MRI) using ultrashort-echo time (UTE) sequences has improved signal detection from lung parenchyma; contrast agents are used to deduce airway function, ventilation-perfusion-diffusion, and mechanics. Proton MRI can measure regional ventilation-perfusion ratio. Quantitative imaging (QI)-derived endpoints have been developed to identify structure-function phenotypes, including air-blood-tissue volume partition, bronchovascular remodeling, emphysema, fibrosis, and textural patterns indicating architectural alteration. Coregistered landmarks on paired images obtained at different lung volumes are used to infer airway caliber, air trapping, gas and blood transport, compliance, and deformation. This document summarizes fundamental good practice stereological principles in QI study design and analysis; evaluates technical capabilities and limitations of common imaging modalities; and assesses major QI endpoints regarding underlying assumptions and limitations, ability to detect and stratify heterogeneous, overlapping pathophysiology, and monitor disease progression and therapeutic response, correlated with and complementary to, functional indices. The goal is to promote unbiased quantification and interpretation of in vivo imaging data, compare metrics obtained using different QI modalities to ensure accurate and reproducible metric derivation, and avoid misrepresentation of inferred physiological processes. The role of imaging-based computational modeling in advancing these goals is emphasized. Fundamental principles outlined herein are critical for all forms of QI irrespective of acquisition modality or disease entity.
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- 2023
26. Perceived Access to Contraception via Telemedicine Among Young Adults: Inequities by Food and Housing Insecurity.
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Yarger, Jennifer, Hopkins, Kristine, Elmes, Sarah, Rossetto, Irene, De La Melena, Stephanie, McCulloch, Charles E, White, Kari, and Harper, Cynthia C
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Humans ,Contraception ,Telemedicine ,Housing ,Food Supply ,Adolescent ,Infant ,Newborn ,Health Services Accessibility ,Female ,Young Adult ,Pandemics ,COVID-19 ,Housing Instability ,access to care ,contraception ,food insecurity ,housing insecurity ,telemedicine ,Health Services ,Clinical Research ,Clinical Trials and Supportive Activities ,Contraception/Reproduction ,Prevention ,Rural Health ,Zero Hunger ,Good Health and Well Being ,Clinical Sciences ,General & Internal Medicine - Abstract
BackgroundTelemedicine expanded rapidly during the COVID-19 pandemic, including for contraceptive services. Data are needed to understand whether young people can access telemedicine for contraception, especially in underserved populations.ObjectiveTo compare young people's perceived access to telemedicine visits for contraception during the COVID-19 pandemic by food and housing insecurity.DesignSupplementary study to a cluster randomized controlled trial in 25 community colleges in California and Texas. Online surveys were administered May 2020 to April 2021. Mixed-effects logistic regression models with random effects for site were used to examine differences in access to contraception through telemedicine by food and housing insecurity status, controlling for key sociodemographic characteristics, including race/ethnicity, non-English primary language, health insurance status, and state of residence, and contraceptive method used.Participants1,414 individuals assigned female at birth aged 18-28.Main measuresSurvey measures were used to capture how difficult it would be for a participant to have a telemedicine visit (phone or video) for contraception.Key resultsTwenty-nine percent of participants were food insecure, and 15% were housing insecure. Nearly a quarter (24%) stated that it would be difficult to have a phone or video visit for contraception. After accounting for sociodemographic factors and type of method used, food insecure (adjusted odds ratio [aOR], 2.17; 95% confidence interval [CI], 1.62-2.91) and housing insecure (aOR, 1.62; 95% CI, 1.13-2.33) participants were significantly more likely to report that it would be difficult to use telemedicine for contraception during the pandemic.ConclusionsUnderserved patients are those who could benefit most from the expansion of telemedicine services, yet our findings show that young people experiencing basic needs insecurity perceive the greatest difficulty accessing these services for essential reproductive care.Trial registrationClinicalTrials.gov Identifier: NCT03519685.
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- 2023
27. Caenorhabditis elegans models for striated muscle disorders caused by missense variants of human LMNA
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Gregory, Ellen F, Kalra, Shilpi, Brock, Trisha, Bonne, Gisèle, Luxton, GW Gant, Hopkins, Christopher, and Starr, Daniel A
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Biological Sciences ,Genetics ,Heart Disease ,Cardiovascular ,Aetiology ,2.1 Biological and endogenous factors ,Animals ,Humans ,Caenorhabditis elegans ,Lamin Type A ,Laminopathies ,Muscle ,Skeletal ,Muscle ,Striated ,Muscular Diseases ,Mutation ,Missense ,Developmental Biology - Abstract
Striated muscle laminopathies caused by missense mutations in the nuclear lamin gene LMNA are characterized by cardiac dysfunction and often skeletal muscle defects. Attempts to predict which LMNA variants are pathogenic and to understand their physiological effects lag behind variant discovery. We created Caenorhabditis elegans models for striated muscle laminopathies by introducing pathogenic human LMNA variants and variants of unknown significance at conserved residues within the lmn-1 gene. Severe missense variants reduced fertility and/or motility in C. elegans. Nuclear morphology defects were evident in the hypodermal nuclei of many lamin variant strains, indicating a loss of nuclear envelope integrity. Phenotypic severity varied within the two classes of missense mutations involved in striated muscle disease, but overall, variants associated with both skeletal and cardiac muscle defects in humans lead to more severe phenotypes in our model than variants predicted to disrupt cardiac function alone. We also identified a separation of function allele, lmn-1(R204W), that exhibited normal viability and swimming behavior but had a severe nuclear migration defect. Thus, we established C. elegans avatars for striated muscle laminopathies and identified LMNA variants that offer insight into lamin mechanisms during normal development.
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- 2023
28. Homomesy via toggleability statistics
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Defant, Colin, Hopkins, Sam, Poznanović, Svetlana, and Propp, James
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Homomesy ,rowmotion ,toggling ,piecewise-linear & birational lift ,\(q\)-analogue - Abstract
The rowmotion operator acting on the set of order ideals of a finite poset has been the focus of a significant amount of recent research. One of the major goals has been to exhibit homomesies: statistics that have the same average along every orbit of the action. We systematize a technique for proving that various statistics of interest are homomesic by writing these statistics as linear combinations of "toggleability statistics" (originally introduced by Striker) plus a constant. We show that this technique recaptures most of the known homomesies for the posets on which rowmotion has been most studied. We also show that the technique continues to work in modified contexts. For instance, this technique also yields homomesies for the piecewise-linear and birational extensions of rowmotion; furthermore, we introduce a \(q\)-analogue of rowmotion and show that the technique yields homomesies for "\(q\)-rowmotion" as well.Mathematics Subject Classifications: 06A07, 05E18, 05A30, 52B05Keywords: Homomesy, rowmotion, toggling, piecewise-linear & birational lift, \(q\)-analogue
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- 2023
29. Paleobiology Database User Guide Version 1.0
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Uhen, Mark D., Allen, Bethany, Behboudi, Noushin, Clapham, Matthew E., Dunne, Emma, Hendy, Austin, Holroyd, Patricia A., Hopkins, Melanie, Mannion, Philip, Novack-Gottshall, Phil, Pimiento, Catalina, and Wagner, Peter
- Abstract
The Paleobiology Database is an online, non-governmental, non-profit public resource for paleontological data. It is organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. This volume is designed to be a comprehensive guide for Paleobiology Database users, both General and Contributory. It covers most database uses from data retrieval and mapping to data contribution of all types. It contains numerous examples to illustrate database use as well as definitions of terms and additional links to numerous other sources. We hope that this user guide will help all users access the great volume of data in the Paleobiology Database and lead others to start and continue to add data to the system.
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- 2023
30. A single-cell atlas of the sexually dimorphic Drosophila foreleg and its sensory organs during development
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Hopkins, Ben R, Barmina, Olga, and Kopp, Artyom
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Biological Sciences ,Biomedical and Clinical Sciences ,Neurosciences ,Genetics ,Dental/Oral and Craniofacial Disease ,1.1 Normal biological development and functioning ,Underpinning research ,Neurological ,Animals ,Male ,Drosophila ,Drosophila melanogaster ,Drosophila Proteins ,Sensory Receptor Cells ,Transcription Factors ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Developmental Biology ,Agricultural ,veterinary and food sciences ,Biological sciences ,Biomedical and clinical sciences - Abstract
To respond to the world around them, animals rely on the input of a network of sensory organs distributed throughout the body. Distinct classes of sensory organs are specialized for the detection of specific stimuli such as strain, pressure, or taste. The features that underlie this specialization relate both to the neurons that innervate sensory organs and the accessory cells they comprise. To understand the genetic basis of this diversity of cell types, both within and between sensory organs, we performed single-cell RNA sequencing on the first tarsal segment of the male Drosophila melanogaster foreleg during pupal development. This tissue displays a wide variety of functionally and structurally distinct sensory organs, including campaniform sensilla, mechanosensory bristles, and chemosensory taste bristles, as well as the sex comb, a recently evolved male-specific structure. In this study, we characterize the cellular landscape in which the sensory organs reside, identify a novel cell type that contributes to the construction of the neural lamella, and resolve the transcriptomic differences among support cells within and between sensory organs. We identify the genes that distinguish between mechanosensory and chemosensory neurons, resolve a combinatorial transcription factor code that defines 4 distinct classes of gustatory neurons and several types of mechanosensory neurons, and match the expression of sensory receptor genes to specific neuron classes. Collectively, our work identifies core genetic features of a variety of sensory organs and provides a rich, annotated resource for studying their development and function.
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- 2023
31. Monitoring for a new I3 resistance gene-breaking race of F. oxysporum f. sp. lycopersici (Fusarium wilt) in California processing tomatoes following recent widespread adoption of resistant (F3) cultivars: Challenges with race 3 and 4 differentiation methods
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Swett, Cassandra L, Del Castillo Múnera, Johanna, Hellman, Elizabeth, Helpio, Erin, Gastelum, Megan, Lopez Raymundo, Elver, Johnson, Heather, Oguchi, Rino, Hopkins, Aimee, Beaulieu, Justine, and Rodriguez, Fernando
- Subjects
Agricultural ,Veterinary and Food Sciences ,Crop and Pasture Production ,diagnostics ,phenotyping ,race emergence ,Fusarium wilt ,tomato ,overcoming resistance ,Plant Biology ,Crop and pasture production ,Plant biology - Abstract
Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (Fol), causes losses in tomato production worldwide, with major impacts on Californian tomato processing. Single-gene resistance is the primary management tool, but its efficacy has been compromised following the emergence of two successive resistance-breaking races, which, in California, emerged within 12 years of resistance deployment. Fol race 3-resistant (F3) processing tomato cultivars (containing the I3 resistance gene) were deployed in the state starting in approximately 2009. The emergence of a new resistance-breaking race (which would be called race 4) is imminent, and early detection will be critical to delay the spread while new resistance is sought. The detection of Fol race 4 is challenged by the lack of validated, rapid, and accurate diagnostic tools. In evaluating in planta phenotyping methods, this study found that rapid seedling phenotyping is not reliable and generates false positives for nonpathogens. Longer (10 weeks) mature plant assays are the most reliable, but may not be sufficiently timely. As an additional challenge, based on field and greenhouse studies, Fol race 3 can cause symptoms in resistant F3 cultivars at frequencies greater (30%) than expected for off-types (
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- 2023
32. Diverse psychotropic substances detected in drug and drug administration equipment samples submitted to drug checking services in Toronto, Ontario, Canada, October 2019–April 2020
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Scarfone, Kristy M, Maghsoudi, Nazlee, McDonald, Karen, Stefan, Cristiana, Beriault, Daniel R, Wong, Ernest, Evert, Mark, Hopkins, Shaun, Leslie, Peter, Watson, Tara Marie, and Werb, Dan
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Substance Misuse ,Drug Abuse (NIDA only) ,Good Health and Well Being ,Analgesics ,Opioid ,Drug Overdose ,Fentanyl ,Humans ,Illicit Drugs ,Laboratories ,Clinical ,Ontario ,Pharmaceutical Preparations ,Pilot Projects ,Drug overdose ,Etizolam ,Flualprazolam ,Synthetic cannabinoid ,Toronto’s Drug Checking Service Working Group ,Public Health and Health Services ,Substance Abuse - Abstract
BackgroundThe overdose crisis has generated innovative harm reduction and drug market monitoring strategies. In Toronto, Ontario, Canada, a multi-site drug checking service (DCS) pilot project was launched in October 2019. The project provides people who use drugs with information on the chemical composition of their substances, thereby increasing their capacity to make more informed decisions about their drug use and avoid overdose. DCS also provides real-time market monitoring to identify trends in the unregulated drug supply.MethodsSample data were obtained through analyses of drug and used drug administration equipment samples submitted anonymously and free of charge to DCS in downtown Toronto from October 10, 2019, to April 9, 2020, representing the first six months of DCS implementation. Analyses were conducted in clinical laboratories using liquid chromatography- and/or gas chromatography-mass spectrometry (LC-MS, GC-MS) techniques.ResultsOverall, 555 samples were submitted, with 49% (271) of samples that were found to contain high-potency opioids, of which 87% (235) also contained stimulants. Benzodiazepine-type drugs were found in 21% (116) of all samples, and synthetic cannabinoids in 1% (7) of all samples. Negative effects (including overdose, adverse health events, and extreme sedation) were reported for 11% (59) of samples submitted for analysis.ConclusionsToronto's DCS identified a range of high-potency opioids with stimulants, benzodiazepine-type drugs, and a synthetic cannabinoid, AMB-FUBINACA. This information can inform a range of evidence-informed overdose prevention efforts.
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- 2022
33. Reductions in California's Urban Fossil Fuel CO2 Emissions During the COVID‐19 Pandemic
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Yañez, CC, Hopkins, FM, Xu, X, Tavares, JF, Welch, A, and Czimczik, CI
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Earth Sciences ,Physical Geography and Environmental Geoscience ,Climate Change Science ,Geology ,urban ,climate change ,fossil fuel carbon dioxide ,radiocarbon ,community science ,pandemic ,Climate change science ,Physical geography and environmental geoscience - Abstract
Fossil fuel carbon dioxide (CO2) emissions (ffCO2) constitute the majority of greenhouse gas emissions and are the main determinant of global climate change. The COVID-19 pandemic caused wide-scale disruption to human activity and provided an opportunity to evaluate our capability to detect ffCO2 emission reductions. Quantifying changes in ffCO2 levels is especially challenging in cities, where climate mitigation policies are being implemented but local emissions lead to spatially and temporally complex atmospheric mixing ratios. Here, we assess ffCO2 emission patterns associated with pandemic-induced changes to human activity using direct observations of on-road CO2 mole fractions in the Los Angeles (LA) urban area and analyses of the radiocarbon (14C) content of annual grasses collected by community scientists throughout California, USA. With COVID-19 mobility restrictions in place in 2020, we observed a significant reduction in ffCO2 levels across California, especially in urban centers. In LA, on-road CO2 enhancements were 60 ± 16% lower than the corresponding period of 2019 and rebounded to pre-pandemic levels by 2021. Plant 14C analysis indicated ffCO2 reductions of 5 ± 10 ppm in 2020 relative to pre-pandemic observations in LA. However, ffCO2 emission trajectories varied substantially by region and sector as COVID-related restrictions were relaxed. Further development of these techniques could aid efforts to monitor decarbonization in cities, especially in developing countries without established CO2 monitoring infrastructure.
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- 2022
34. A round‐robin approach provides a detailed assessment of biomolecular small‐angle scattering data reproducibility and yields consensus curves for benchmarking
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Trewhella, Jill, Vachette, Patrice, Bierma, Jan, Blanchet, Clement, Brookes, Emre, Chakravarthy, Srinivas, Chatzimagas, Leonie, Cleveland, Thomas E, Cowieson, Nathan, Crossett, Ben, Duff, Anthony P, Franke, Daniel, Gabel, Frank, Gillilan, Richard E, Graewert, Melissa, Grishaev, Alexander, Guss, J Mitchell, Hammel, Michal, Hopkins, Jesse, Huang, Qingqui, Hub, Jochen S, Hura, Greg L, Irving, Thomas C, Jeffries, Cy Michael, Jeong, Cheol, Kirby, Nigel, Krueger, Susan, Martel, Anne, Matsui, Tsutomu, Li, Na, Pérez, Javier, Porcar, Lionel, Prangé, Thierry, Rajkovic, Ivan, Rocco, Mattia, Rosenberg, Daniel J, Ryan, Timothy M, Seifert, Soenke, Sekiguchi, Hiroshi, Svergun, Dmitri, Teixeira, Susana, Thureau, Aurelien, Weiss, Thomas M, Whitten, Andrew E, Wood, Kathleen, and Zuo, Xiaobing
- Subjects
Biochemistry and Cell Biology ,Physical Sciences ,Biological Sciences ,Bioengineering ,Scattering ,Small Angle ,X-Ray Diffraction ,Benchmarking ,Consensus ,Reproducibility of Results ,Proteins ,Solvents ,X-ray scattering ,benchmarking standards ,biomolecular small-angle scattering ,neutron scattering ,scattering-profile calculation ,standards ,Chemical Sciences ,Biophysics ,Biological sciences ,Chemical sciences ,Physical sciences - Abstract
Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0-1 Å-1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q-range to 2.2 Å-1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.
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- 2022
35. A solution to the challenges of interdisciplinary aggregation and use of specimen-level trait data
- Author
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Balk, Meghan A, Deck, John, Emery, Kitty F, Walls, Ramona L, Reuter, Dana, LaFrance, Raphael, Arroyo-Cabrales, Joaquín, Barrett, Paul, Blois, Jessica, Boileau, Arianne, Brenskelle, Laura, Cannarozzi, Nicole R, Cruz, J Alberto, Dávalos, Liliana M, de la Sancha, Noé U, Gyawali, Prasiddhi, Hantak, Maggie M, Hopkins, Samantha, Kohli, Brooks, King, Jessica N, Koo, Michelle S, Lawing, A Michelle, Machado, Helena, McCrane, Samantha M, McLean, Bryan, Morgan, Michèle E, Birch, Suzanne Pilaar, Reed, Denne, Reitz, Elizabeth J, Sewnath, Neeka, Upham, Nathan S, Villaseñor, Amelia, Yohe, Laurel, Davis, Edward B, and Guralnick, Robert P
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Generic health relevance ,Animals ,Biological database ,Evolutionary history ,Ornithology ,Paleobiology ,Phylogenetics ,Systematics - Abstract
Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources assemble species-level trait data, but the data and metadata underlying those trait measurements are often not reported. Here, we introduce FuTRES (Functional Trait Resource for Environmental Studies; pronounced few-tress), an online datastore and community resource for individual-level trait reporting that utilizes a semantic framework. FuTRES already stores millions of trait measurements for paleobiological, zooarchaeological, and modern specimens, with a current focus on mammals. We compare dynamically derived extant mammal species' body size measurements in FuTRES with summary values from other compilations, highlighting potential issues with simply reporting a single mean estimate. We then show that individual-level data improve estimates of body mass-including uncertainty-for zooarchaeological specimens. FuTRES facilitates trait data integration and discoverability, accelerating new research agendas, especially scaling from intra- to interspecific trait variability.
- Published
- 2022
36. DNA Methylation Analysis of Imprinted Genes in the Cortex and Hippocampus of Cross-Fostered Mice Selectively Bred for Increased Voluntary Wheel-Running.
- Author
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Latchney, Sarah, Cadney, Marcell, Hopkins, Austin, and Garland, Theodore
- Subjects
Bisulfite sequencing ,Brain ,Cross-fostering ,Exercise ,Maternal effects ,Parent-of-origin genes ,Animals ,DNA Methylation ,Genomic Imprinting ,Hippocampus ,Mice ,ras-GRF1 - Abstract
We have previously shown that high runner (HR) mice (from a line genetically selected for increased wheel-running behavior) have distinct, genetically based, neurobiological phenotypes as compared with non-selected control (C) mice. However, developmental programming effects during early life, including maternal care and parent-of-origin-dependent expression of imprinted genes, can also contribute to variation in physical activity. Here, we used cross-fostering to address two questions. First, do HR mice have altered DNA methylation profiles of imprinted genes in the brain compared to C mice? Second, does maternal upbringing further modify the DNA methylation status of these imprinted genes? To address these questions, we cross-fostered all offspring at birth to create four experimental groups: C pups to other C dams, HR pups to other HR dams, C pups to HR dams, and HR pups to C dams. Bisulfite sequencing of 16 imprinted genes in the cortex and hippocampus revealed that the HR line had altered DNA methylation patterns of the paternally imprinted genes, Rasgrf1 and Zdbf2, as compared with the C line. Both fostering between the HR and C lines and sex modified the DNA methylation profiles for the paternally expressed genes Mest, Peg3, Igf2, Snrpn, and Impact. Ig-DMR, a gene with multiple paternal and maternal imprinted clusters, was also affected by maternal upbringing and sex. Our results suggest that differential methylation patterns of imprinted genes in the brain could contribute to evolutionary increases in wheel-running behavior and are also dependent on maternal upbringing and sex.
- Published
- 2022
37. Wildfire, Smoke Exposure, Human Health, and Environmental Justice Need to be Integrated into Forest Restoration and Management
- Author
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D’Evelyn, Savannah M, Jung, Jihoon, Alvarado, Ernesto, Baumgartner, Jill, Caligiuri, Pete, Hagmann, R Keala, Henderson, Sarah B, Hessburg, Paul F, Hopkins, Sean, Kasner, Edward J, Krawchuk, Meg A, Krenz, Jennifer E, Lydersen, Jamie M, Marlier, Miriam E, Masuda, Yuta J, Metlen, Kerry, Mittelstaedt, Gillian, Prichard, Susan J, Schollaert, Claire L, Smith, Edward B, Stevens, Jens T, Tessum, Christopher W, Reeb-Whitaker, Carolyn, Wilkins, Joseph L, Wolff, Nicholas H, Wood, Leah M, Haugo, Ryan D, and Spector, June T
- Subjects
Epidemiology ,Public Health ,Health Sciences ,Lung ,Climate-Related Exposures and Conditions ,Respiratory ,Air Pollution ,Child ,Environmental Exposure ,Environmental Justice ,Forests ,Humans ,Smoke ,United States ,Wildfires ,Wildland fire ,Public health ,Air quality ,Exposure ,Ecological restoration ,Prescribed burning ,Environmental justice ,Interdisciplinary ,Collaborative partnerships - Abstract
Purpose of reviewIncreasing wildfire size and severity across the western United States has created an environmental and social crisis that must be approached from a transdisciplinary perspective. Climate change and more than a century of fire exclusion and wildfire suppression have led to contemporary wildfires with more severe environmental impacts and human smoke exposure. Wildfires increase smoke exposure for broad swaths of the US population, though outdoor workers and socially disadvantaged groups with limited adaptive capacity can be disproportionally exposed. Exposure to wildfire smoke is associated with a range of health impacts in children and adults, including exacerbation of existing respiratory diseases such as asthma and chronic obstructive pulmonary disease, worse birth outcomes, and cardiovascular events. Seasonally dry forests in Washington, Oregon, and California can benefit from ecological restoration as a way to adapt forests to climate change and reduce smoke impacts on affected communities.Recent findingsEach wildfire season, large smoke events, and their adverse impacts on human health receive considerable attention from both the public and policymakers. The severity of recent wildfire seasons has state and federal governments outlining budgets and prioritizing policies to combat the worsening crisis. This surging attention provides an opportunity to outline the actions needed now to advance research and practice on conservation, economic, environmental justice, and public health interests, as well as the trade-offs that must be considered. Scientists, planners, foresters and fire managers, fire safety, air quality, and public health practitioners must collaboratively work together. This article is the result of a series of transdisciplinary conversations to find common ground and subsequently provide a holistic view of how forest and fire management intersect with human health through the impacts of smoke and articulate the need for an integrated approach to both planning and practice.
- Published
- 2022
38. Health-related quality of life outcomes after neoadjuvant chemoradiotherapy for rectal cancer in NRG Oncology/NSABP R-04.
- Author
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Ganz, Patricia A, Hays, Ron D, Spritzer, Karen L, Rogatko, André, Ko, Clifford Y, Colangelo, Linda H, Arora, Amit, Hopkins, Judith O, Evans, Terry L, and Yothers, Greg
- Subjects
Humans ,Rectal Neoplasms ,Neoadjuvant Therapy ,Quality of Life ,Adult ,Aged ,Aged ,80 and over ,Middle Aged ,Female ,Male ,Young Adult ,Chemoradiotherapy ,Surveys and Questionnaires ,clinical trial ,health-related quality of life ,long-term survivors ,neoadjuvant chemoradiotherapy ,neurotoxicity ,rectal cancer ,Prevention ,Cancer ,Clinical Research ,Digestive Diseases ,Aging ,Good Health and Well Being ,Oncology and Carcinogenesis ,Public Health and Health Services ,Oncology & Carcinogenesis - Abstract
BackgroundThere has been limited evaluation of health-related quality of life (HRQOL) in rectal cancer patients receiving neoadjuvant chemoradiotherapy. HRQOL outcomes in the National Surgical Adjuvant Breast and Bowel Project R-04 trial are examined in this article.MethodsBetween 2004 and 2010, R-04 patients were invited to enroll in the HRQOL substudy, with questionnaires administered before randomization, after completion of chemoradiotherapy, and 1-year after surgery. HRQOL measures included: Functional Assessment of Cancer Therapy for colorectal cancer (FACT-C); Short Form-36v.2 Vitality scale; a treatment-specific symptom scale; and the FACT neurotoxicity scale. A 5-year postsurgery assessment was added to the protocol in 2012. Mixed-effects models examined neoadjuvant therapy treatment effects in the 1-year sample and models that explored associations of host factors and treatment impact on 5-year HRQOL.ResultsA total of 1373 patients completed baseline HRQOL and at least one additional assessment. The average age was 58 years (range, 23-85 years), male (68%), and 59% Stage II. There were no statistically significant differences in HRQOL outcomes by treatment arm, but HRQOL worsened from baseline to postneoadjuvant chemoradiotherapy, with statistically significant effect sizes changes ranging from 0.6 (Vitality) to 0.9 (FACT-C Trial Outcome Index). Neurotoxicity was greater in the oxaliplatin-treated groups. Obese/overweight patients had statistically significantly worse FACT-C Trial Outcome Index scores than did underweight/normal weight groups. At 5 years, younger patients and those with normal baseline weight had statistically significantly better physical function scores and older patients had better mental health outcomes.ConclusionsHRQOL did not differ across the four R-04 treatment arms; however, host factors explained significant variation in posttreatment HRQOL.Clinicaltrialsgov: NCT00058474 (https://ClinicalTrials.gov/ct2/show/NCT00058474).Lay summaryThis article reports on the health-related quality of life (HRQOL) outcomes of patients treated with four different chemotherapy regimens combined with radiation in rectal cancer patients before definitive surgical treatment. There were no significant differences in HRQOL by treatment regimen, but all patients experienced decreased vitality (energy) and physical functioning. By 1 year after treatment, most patients had returned to pretreatment vitality and physical functioning, with the exception of increased neurotoxicity. In a subsample of patients assessed at 5 years after surgery, physical function was better in those who at pretreatment were younger, normal weight, and had better performance status. Mental function was better in those who at pretreatment were older and had better performance status.
- Published
- 2022
39. Artificial Intelligence Approach for Estimating Dairy Methane Emissions
- Author
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Jeong, Seongeun, Fischer, Marc L, Breunig, Hanna, Marklein, Alison R, Hopkins, Francesca M, and Biraud, Sebastien C
- Subjects
Environmental Sciences ,Engineering ,Environmental Management ,Machine Learning and Artificial Intelligence ,Climate Action ,Air Pollutants ,Artificial Intelligence ,Farms ,Greenhouse Gases ,Humans ,Manure ,Methane ,artificial intelligence ,methan ,greenhouse ga ,emission ,dair ,aerial image ,dairy ,greenhouse gas ,methane ,EGD-Integrated Emissions Management - Abstract
California's dairy sector accounts for ∼50% of anthropogenic CH4 emissions in the state's greenhouse gas (GHG) emission inventory. Although California dairy facilities' location and herd size vary over time, atmospheric inverse modeling studies rely on decade-old facility-scale geospatial information. For the first time, we apply artificial intelligence (AI) to aerial imagery to estimate dairy CH4 emissions from California's San Joaquin Valley (SJV), a region with ∼90% of the state's dairy population. Using an AI method, we process 316,882 images to estimate the facility-scale herd size across the SJV. The AI approach predicts herd size that strongly (>95%) correlates with that made by human visual inspection, providing a low-cost alternative to the labor-intensive inventory development process. We estimate SJV's dairy enteric and manure CH4 emissions for 2018 to be 496-763 Gg/yr (mean = 624; 95% confidence) using the predicted herd size. We also apply our AI approach to estimate CH4 emission reduction from anaerobic digester deployment. We identify 162 large (90th percentile) farms and estimate a CH4 reduction potential of 83 Gg CH4/yr for these large facilities from anaerobic digester adoption. The results indicate that our AI approach can be applied to characterize the manure system (e.g., use of an anaerobic lagoon) and estimate GHG emissions for other sectors.
- Published
- 2022
40. An Interdisciplinary Flipped Classroom Module on Postpartum Depression Using Telemedicine and Online Teaching.
- Author
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Monasch, Erika M, Wadell, Paula M, Baumann, Sara, Hopkins, Melissa, and Hou, Melody Y
- Subjects
Humans ,Depression ,Postpartum ,Problem-Based Learning ,Telemedicine ,Curriculum ,Teaching ,Female ,Interdisciplinary Studies ,Curriculum and Pedagogy ,Psychiatry - Published
- 2022
41. Determinants of Response to Talazoparib in Patients with HER2-Negative, Germline BRCA1/2-Mutated Breast CancerTalazoparib in Germline BRCA1/2-Mutated Breast Cancer
- Author
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Blum, Joanne L, Laird, A Douglas, Litton, Jennifer K, Rugo, Hope S, Ettl, Johannes, Hurvitz, Sara A, Martin, Miguel, Roché, Henri H, Lee, Kyung-Hun, Goodwin, Annabel, Chen, Ying, Lanzalone, Silvana, Chelliserry, Jijumon, Czibere, Akos, Hopkins, Julia F, Albacker, Lee A, and Mina, Lida A
- Subjects
Clinical Research ,Breast Cancer ,Human Genome ,Genetics ,Cancer ,Good Health and Well Being ,BRCA1 Protein ,BRCA2 Protein ,Breast Neoplasms ,Female ,Germ Cells ,Germ-Line Mutation ,Humans ,Phthalazines ,Poly(ADP-ribose) Polymerase Inhibitors ,Oncology and Carcinogenesis ,Oncology & Carcinogenesis - Abstract
PurposePARP inhibitors (PARPi) have demonstrated efficacy in tumors with germline breast cancer susceptibility genes (gBRCA) 1 and 2 mutations, but further factors influencing response to PARPi are poorly understood.Experimental designBreast cancer tumor tissue from patients with gBRCA1/2 mutations from the phase III EMBRACA trial of the PARPi talazoparib versus chemotherapy was sequenced using FoundationOne CDx.ResultsIn the evaluable intent-to-treat population, 96.1% (296/308) had ≥1 tumor BRCA (tBRCA) mutation and there was strong concordance (95.3%) between tBRCA and gBRCA mutational status. Genetic/genomic characteristics including BRCA loss of heterozygosity (LOH; identified in 82.6% of evaluable patients), DNA damage response (DDR) gene mutational burden, and tumor homologous recombination deficiency [assessed by genomic LOH (gLOH)] demonstrated no association with talazoparib efficacy.ConclusionsOverall, BRCA LOH status, DDR gene mutational burden, and gLOH were not associated with talazoparib efficacy; however, these conclusions are qualified by population heterogeneity and low patient numbers in some subgroups. Further investigation in larger patient populations is warranted.
- Published
- 2022
42. A Fiber‐Based 3D Lithium Host for Lean Electrolyte Lithium Metal Batteries
- Author
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Yu, Sicen, Wu, Zhaohui, Holoubek, John, Liu, Haodong, Hopkins, Emma, Xiao, Yuxuan, Xing, Xing, Lee, Myeong Hwan, and Liu, Ping
- Subjects
Affordable and Clean Energy ,3D host ,high porosity ,lithium metal anode ,RbNO3 ,vapor-grown carbon fiber - Abstract
3D hosts are promising to extend the cycle life of lithium metal anodes but have rarely been implemented with lean electrolytes thus impacting the practical cell energy density. To overcome this challenge, a 3D host that is lightweight and easy to fabricate with optimum pore size that enables full utilization of its pore volume, essential for lean electrolyte operations, is reported. The host is fabricated by casting a VGCF (vapor-grown carbon fiber)-based slurry loaded with a sparingly soluble rubidium nitrate salt as an additive. The network of fibers generates uniform pores of ≈3 µm in diameter with a porosity of 80%, while the nitrate additive enhances lithiophilicity. This 3D host delivers an average coulombic efficiency of 99.36% at 1 mA cm-2 and 1 mAh cm-2 for over 860 cycles in half-cell tests. Full cells containing an anode with 1.35-fold excess lithium paired with LiNi0.8 Mn0.1 Co0.1 O2 (NMC811) cathodes exhibit capacity retention of 80% over 176 cycles at C/2 under a lean electrolyte condition of 3 g Ah-1 . This work provides a facile and scalable method to advance 3D lithium hosts closer to practical lithium-metal batteries.
- Published
- 2022
43. New directions for surrogate models and differentiable programming for High Energy Physics detector simulation
- Author
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Adelmann, Andreas, Hopkins, Walter, Kourlitis, Evangelos, Kagan, Michael, Kasieczka, Gregor, Krause, Claudius, Shih, David, Mikuni, Vinicius, Nachman, Benjamin, Pedro, Kevin, and Winklehner, Daniel
- Subjects
hep-ph ,cs.LG ,hep-ex ,physics.comp-ph ,physics.ins-det - Abstract
The computational cost for high energy physics detector simulation in futureexperimental facilities is going to exceed the current available resources. Toovercome this challenge, new ideas on surrogate models using machine learningmethods are being explored to replace computationally expensive components.Additionally, differentiable programming has been proposed as a complementaryapproach, providing controllable and scalable simulation routines. In thisdocument, new and ongoing efforts for surrogate models and differentialprogramming applied to detector simulation are discussed in the context of the2021 Particle Physics Community Planning Exercise (`Snowmass').
- Published
- 2022
44. Assessment of Negative Symptoms in Clinical Trials of Acute Schizophrenia: Test of a Novel Enrichment Strategy.
- Author
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Hopkins, Seth, Tomioka, Sasagu, Ogirala, Ajay, Loebel, Antony, Koblan, Kenneth, and Marder, Stephen
- Subjects
antipsychotic agents ,lurasidone ,trace amine-associated receptor 1 (TAAR1) ,ulotaront - Abstract
Drug trials for negative symptoms in schizophrenia select patients based on the severity and stability of negative symptoms, using criteria that are not suitable for trials of acute exacerbation of schizophrenia. Here we present a method to prognostically enrich subjects having a predefined factor structure in PANSS and apply it to the measurement of negative symptoms specifically in trials of acute schizophrenia. A vector of 1335 elements based on between- and within-item variances, covariances, and differences of PANSS items was created to calculate an index of heterogeneity and to enrich for a predetermined symptom construct in PANSS. Using prerandomization PANSS scores across N = 4876 subjects in 13 trials of acute schizophrenia, we demonstrate an ability to select for a subpopulation having the greatest amount of variance explained across the 7-items of the Marder PANSS negative symptom (MPNS) construct. Network analyses on subjects enriched for MPNS construct confirm that negative symptoms were most influential in overall psychopathology, distinct from subjects without the MPNS construct. As expected for D2 antagonists, drug-placebo differences on negative symptoms with lurasidone were not specific to the subpopulation having the MPNS construct. In contrast, the novel TAAR1 agonist ulotaront demonstrated specific improvements in negative symptoms which were greatest in the MPNS subpopulation. These results demonstrate the utility of a novel prognostic enrichment strategy that can address heterogeneity in clinical trials, where patients can be selected on the basis of a greater likelihood of having the measured symptom construct (negative symptoms) related to the disorder (schizophrenia). ClinicalTrials.gov Identifiers: NCT0296938, NCT00088634, NCT00549718, NCT00615433, NCT00790192.
- Published
- 2022
45. Using Conjoint Experiments to Analyze Election Outcomes: The Essential Role of the Average Marginal Component Effect
- Author
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Bansak, Kirk, Hainmueller, Jens, Hopkins, Daniel J, and Yamamoto, Teppei
- Subjects
Clinical Research ,survey experiments ,elections ,conjoint ,Average Marginal Component Effect ,voter preferences ,causal inference ,AMCE ,Political Science ,Political Science & Public Administration ,Political science - Abstract
Abstract: Political scientists have increasingly deployed conjoint survey experiments to understand multidimensional choices in various settings. In this paper, we show that the average marginal component effect (AMCE) constitutes an aggregation of individual-level preferences that is meaningful both theoretically and empirically. First, extending previous results to allow for arbitrary randomization distributions, we show how the AMCE represents a summary of voters’ multidimensional preferences that combines directionality and intensity according to a probabilistic generalization of the Borda rule. We demonstrate why incorporating both the directionality and intensity of multi-attribute preferences is essential for analyzing real-world elections, in whichceteris paribuscomparisons almost never occur. Second, and in further empirical support of this point, we show how this aggregation translates directly into a primary quantity of interest to election scholars: the effect of a change in an attribute on a candidate’s or party’s expected vote share. These properties hold irrespective of the heterogeneity, strength, or interactivity of voters’ preferences and regardless of how votes are aggregated into seats. Finally, we propose, formalize, and evaluate the feasibility of using conjoint data to estimate alternative quantities of interest to electoral studies, including the effect of an attribute on the probability of winning.
- Published
- 2022
46. An Inexpensive, Wearable Patella Reduction Trainer
- Author
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Hopkins, Mark, Dalley, Matthew, Zinkewich, Felipe, Chujutalli, Ricardo, Bengiamin, Deena I., and Young, Timothy P.
- Subjects
Simulation ,Education ,Technical Skills - Published
- 2022
47. Isotopic Signatures of Methane Emissions From Dairy Farms in California’s San Joaquin Valley
- Author
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Carranza, Valerie, Biggs, Brenna, Meyer, Deanne, Townsend‐Small, Amy, Thiruvenkatachari, Ranga Rajan, Venkatram, Akula, Fischer, Marc L, and Hopkins, Francesca M
- Subjects
Earth Sciences ,Atmospheric Sciences ,Climate Action ,methane ,greenhouse gas emissions ,carbon isotopes ,dairy ,source apportionment ,Geophysics - Abstract
In this study, we present seasonal atmospheric measurements of δ13CCH4 from dairy farms in the San Joaquin Valley of California. We used δ13CCH4 to characterize emissions from enteric fermentation by measuring downwind of cattle housing (e.g., freestall barns, corrals) and from manure management areas (e.g., anaerobic manure lagoons) with a mobile platform equipped with cavity ring-down spectrometers. Across seasons, the δ13CCH4 from enteric fermentation source areas ranged from −69.7 ± 0.6 per mil (‰) to −51.6 ± 0.1‰ while the δ13CCH4 from manure lagoons ranged from −49.5 ± 0.1‰ to −40.5 ± 0.2‰. Measurements of δ13CCH4 of enteric CH4 suggest a greater than 10‰ difference between cattle production groups in accordance with diet. Isotopic signatures of CH4 were used to characterize enteric and manure CH4 from downwind plume sampling of dairies. Our findings show that δ13CCH4 measurements could improve the attribution of CH4 emissions from dairy sources at scales ranging from individual facilities to regions and help constrain the relative contributions from these different sources of emissions to the CH4 budget.
- Published
- 2022
48. Key risk factors for substance use among female sex workers in Soweto and Klerksdorp, South Africa: A cross-sectional study
- Author
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Yeo, Ellis Jaewon, Hlongwane, Khuthadzo, Otwombe, Kennedy, Hopkins, Kathryn L, Variava, Ebrahim, Martinson, Neil, Strathdee, Steffanie A, Coetzee, Jenny, and Milovanovic, Minja
- Subjects
Biomedical and Clinical Sciences ,Public Health ,Health Sciences ,Human Society ,Social Work ,Clinical Research ,Prevention ,Behavioral and Social Science ,Mental Health ,Substance Misuse ,Clinical Trials and Supportive Activities ,Alcoholism ,Alcohol Use and Health ,HIV/AIDS ,Aetiology ,2.3 Psychological ,social and economic factors ,Mental health ,Good Health and Well Being ,Adolescent ,Adult ,Cross-Sectional Studies ,Female ,HIV Seropositivity ,HIV-1 ,Humans ,Physical Abuse ,Prevalence ,Sex Offenses ,Sex Workers ,South Africa ,Substance-Related Disorders ,General Science & Technology - Abstract
IntroductionSex workers in South Africa experience high levels of trauma and mental health issues, but little is known about their drug and alcohol use. This study assessed the prevalence of substance use and its key risk factors amongst female sex workers (FSWs) at two sites in South Africa.MethodsTwo cross-sectional studies were conducted, in Soweto and Klerksdorp, South Africa. Using respondent-driven sampling (RDS) 508 FSWs in Soweto and 156 in Klerksdorp were enrolled. A study-specific survey was used to collect social and demographic information, substance use, mental ill-health, and HIV status. Raw and RDS-adjusted data were analyzed using Chi-squared tests of association. Weighted and unweighted Poisson regression models were used to assess key risk factors for alcohol and drug use at both univariate and multivariate levels.ResultsOf the 664 FSWs, 56.2% were binge drinkers and 29.4% reported using drugs within the last year. Living in a home with regular food (RR: 1.2597, 95% CI: 1.1009-1.4413) and being HIV positive (RR: 1.1678, 95% CI: 1.0227-1.3334) were associated with a higher risk of binge drinking. Having symptoms suggestive of post-traumatic stress disorder (RR: 1.1803, 95% CI: 1.0025-1.3895) and past year physical/sexual abuse from either intimate (RR: 1.3648, 95% CI: 1.1522-1.6167) or non-intimate partners (RR: 1.3910, 95% CI: 1.1793-1.6407) were associated with a higher risk of drug use.DiscussionIn conclusion, our findings demonstrate a high prevalence of alcohol and drug use among FSWs in Soweto and Klerksdorp with site-specific contextual dynamics driving substance use. Site differences highlight the importance of tailoring site-specific substance use harm mitigation for this key population.
- Published
- 2022
49. Observation of solid-state bidirectional thermal conductivity switching in antiferroelectric lead zirconate (PbZrO3)
- Author
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Aryana, Kiumars, Tomko, John A, Gao, Ran, Hoglund, Eric R, Mimura, Takanori, Makarem, Sara, Salanova, Alejandro, Hoque, Md Shafkat Bin, Pfeifer, Thomas W, Olson, David H, Braun, Jeffrey L, Nag, Joyeeta, Read, John C, Howe, James M, Opila, Elizabeth J, Martin, Lane W, Ihlefeld, Jon F, and Hopkins, Patrick E
- Subjects
Physical Sciences ,Engineering ,Classical Physics ,Affordable and Clean Energy - Abstract
Materials with tunable thermal properties enable on-demand control of temperature and heat flow, which is an integral component in the development of solid-state refrigeration, energy scavenging, and thermal circuits. Although gap-based and liquid-based thermal switches that work on the basis of mechanical movements have been an effective approach to control the flow of heat in the devices, their complex mechanisms impose considerable costs in latency, expense, and power consumption. As a consequence, materials that have multiple solid-state phases with distinct thermal properties are appealing for thermal management due to their simplicity, fast switching, and compactness. Thus, an ideal thermal switch should operate near or above room temperature, have a simple trigger mechanism, and offer a quick and large on/off switching ratio. In this study, we experimentally demonstrate that manipulating phonon scattering rates can switch the thermal conductivity of antiferroelectric PbZrO3 bidirectionally by -10% and +25% upon applying electrical and thermal excitation, respectively. Our approach takes advantage of two separate phase transformations in PbZrO3 that alter the phonon scattering rate in different manners. In this study, we demonstrate that PbZrO3 can serve as a fast (
- Published
- 2022
50. Blastic plasmacytoid dendritic cell neoplasm presenting as violaceous forehead plaque
- Author
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Morrison, Georgia Mae, Hopkins, Amy, Knapp, Calvin, Kulkarni, Raj, and Scopetta, John P
- Subjects
blastic ,cutaneous lymphoma ,dendritic cell ,dermatology ,neoplasm ,plasmacytoid - Abstract
A 72-year-old man with a history of squamous cell carcinoma presented to the Portland VA with forehead discoloration. He was initially diagnosed with actinic damage and prescribed topical treatment. However, he returned to clinic months later with a large, violaceous forehead plaque. Upon biopsy, he was diagnosed with blastic plasmacytoid dendritic cell neoplasm (BPDCN), a rare hematological malignancy. This case report illustrates the importance of keeping BPDCN in the differential diagnosis for ecchymotic plaques that fail to respond to first line therapy.
- Published
- 2022
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