Search

Abstract Although DNA methylation primarily represses TEs, it also represses select genes that are methylated in plant body tissues but demethylated by DNA glycosylases (DNGs) in endosperm or pollen. Either one of two DNGs, MATERNAL DEREPRESSION OF R1 (MDR1) or DNG102, is essential for pollen viability in maize. Using single-pollen mRNA sequencing on pollen-segregating mutations in both genes, we identify 58 candidate DNG target genes that account for 11.1% of the wild-type transcriptome but are silent or barely detectable in other tissues. They are unusual in their tendency to lack introns but even more so in their TE-like methylation (teM) in coding DNA. The majority have predicted functions in cell wall modification, and they likely support the rapid tip growth characteristic of pollen tubes. These results suggest a critical role for DNA methylation and demethylation in regulating maize genes with the potential for extremely high expression in pollen but constitutive silencing elsewhere.

The use of standard protocols in studies supports consistent data collection, improves data quality, and facilitates cross-study analyses. Funded by the National Institutes of Health, the PhenX (consensus measures for Phenotypes and eXposures) Toolkit is a catalog of recommended measurement protocols that address a wide range of research topics and are suitable for inclusion in a variety of study designs. In 2020, a PhenX Working Group of smoking cessation experts followed a well-established consensus process to identify and recommend measurement protocols suitable for inclusion in smoking cessation and smoking harm reduction studies. The broader scientific community was invited to review and provide feedback on the preliminary recommendation of the Working Group. Fourteen selected protocols for measuring smoking cessation, harm reduction, and biomarkers research associated with smoking cessation were released in the PhenX Toolkit ( https://www.phenxtoolkit.org) in February 2021. These protocols complement existing PhenX Toolkit content related to tobacco regulatory research, substance use and addiction research, and other measures of smoking-related health outcomes. Adopting well-established protocols enables consistent data collection and facilitates comparing and combining data across studies, potentially increasing the scientific impact of individual studies.

Abstract Prior to the 19th century, the Mississippi Alluvial Valley (MAV) was a vast bottomland hardwood forest ecosystem with associated wetlands and intrinsic resources. Conversion for human uses in the 20th century transformed the MAV into an agriculturally dominated system. Since the late 1980s, federal and state incentivized conservation programs for landowners have helped restore wetlands on private lands in the MAV. Given the need to evaluate incentivized private lands in relation to waterfowl use, we used a sample of 241 radiomarked female mallards (Anas platyrhynchos) and evaluated their use of private and public lands in the Mississippi portion of the MAV during winters 2010–2015. Our objective was to examine mallard use of public, incentivized private, and non‐incentivized private lands and to evaluate if use changed by time of day and during and after the hunting season. Among all diurnal and nocturnal locations of mallards, 43.3% (n = 3,995) occurred on public lands, 19.5% (n = 1,802) were on incentivized private lands, and 37.2% (n = 3,432) on non‐incentivized private lands. Of mallard locations on incentivized private lands, mallards exhibited greatest use of Wetland Reserve Easements (WRE; 12.4%) and Conservation Reserve Program tracts (CRP; 4.7%). Mallards used public lands more diurnally within hunting seasons and more during hunting seasons than post‐hunting season, which we attributed to the presence of designated sanctuaries that may have provided refuge from hunting and other disturbances. Post‐hunting season, mallards increased their use of incentivized and non‐incentivized private lands, perhaps to exploit seasonal emergent wetland and remnant agricultural foods. Radiomarked mallards used a variety of landcover types across public and private land, reinforcing the importance of habitat complexes for wintering mallards and other dabbling ducks. Conservation program lands, such as CRP and WREs, provide emergent and forested wetlands that complement flooded agricultural lands and natural wetlands in the MAV. When areal availability estimates of incentivized private lands are accessible from government or other partners, we encourage future researchers to investigate selectivity by mallards and other waterfowl of public, incentivized, and non‐incentivized lands.

Experiments involving the coupling of metal and high explosives (HE) are of notable defense-related interest, and we seek to refine the uncertainty quantification associated with models of such experiments. In particular, our focus is on how uncertainty related to the metal constitutive model challenges our ability to infer high explosive model parameters when analyzing focused science experiments. We consider three focused experiments involving an HE accelerating metal: small plate tests with tantalum/LX-14 and tantalum/LX-17 pairings as well as a tantalum/LX-17 cylinder test. For all three models, we perform sensitivity analysis to ascertain the influence of metal strength on the coupled experimental response. Moreover, we calibrate each model in a Bayesian setting and study the quantification of metal strength on the inference of the HE parameters. Based on our results, we offer guidance for future metal/HE experiments. [ABSTRACT FROM AUTHOR]

Loss of quadriceps strength after total knee arthroplasty (TKA) is most pronounced acutely but persists long-term, negatively impacting physical function in daily activities. Neuromuscular electrical stimulation (NMES) early after surgery is an effective adjuvant to standard of care rehabilitation (SOC) for attenuating strength loss following TKA, but the mechanisms whereby NMES maintains strength are unclear. This work aimed to determine the effects of early NMES on quadriceps strength and skeletal muscle fiber size 2 weeks after TKA compared to SOC. Patients scheduled for primary, unilateral TKA were enrolled and randomized into SOC (n = 9) or NMES plus SOC (n = 10) groups. NMES was started within 48 h of TKA, with 45-min sessions twice a day for 2 weeks. Isometric quadriceps strength was assessed preoperatively and 2 weeks following TKA. Vastus lateralis muscle biopsies of the involved leg were performed at the same time points and immunohistochemistry conducted to assess muscle fiber cross-sectional area and distinguish fiber types. Groups did not differ in age, body mass index, sex distribution, or preoperative strength. Both groups got weaker postoperatively, but the NMES group had higher normalized strength. After 2 weeks, the group receiving NMES and SOC had significantly greater MHC IIA and MHC IIA/IIX fiber size compared to SOC alone, with no group differences in MHC I fiber size. These results suggest that NMES mitigates early muscle weakness following TKA, in part, via effects on fast-twitch, type II muscle fiber size. This investigation advances our understanding of how adjuvant, early postoperative NMES aids muscle strength recovery.

Background Online instruction within higher education is a growing trend. Asynchronous online courses vary widely in design elements. Research is needed to evaluate the impact of course design on student outcomes. A large, asynchronous undergraduate medical terminology course was modified to increase authentic language use, student interaction, formative feedback, retrieval practice, and metacognition. The purposes of this study were to describe modified course design elements and evaluate the impact of modifications on student outcomes compared with a standard course implemented concurrently.Methods This prospective, quasi-experimental study included 494 students (modified course, n = 277; standard course, n = 217). Measures included student participation, performance, course satisfaction, self-efficacy (SE), and engagement.Results Participation in assignments was high (88–94%). Students in both courses experienced growth in SE for medical terminology use. Students in the modified course earned significantly higher course grades and reported higher satisfaction levels. No significant differences in SE or exam scores were found between courses. Marginal significance was found for increased behavioral engagement for students in the modified course.Conclusions Modifications based on language learning and learning science principles were feasible to implement within a large, asynchronous online medical terminology course. Modifications resulted in greater student satisfaction and improved course grades. Exam performance was not significantly different between the modified and standard courses. Future research should focus on modifications preparing students for summative assessments.

We hypothesized that pre-consult patient education videos can improve patient understanding about their diagnosis, lead to high satisfaction and low distress. In this pilot study, we developed a patient education video curriculum for patients with newly-diagnosed anal cancer. Comprehension of key content was evaluated by comparing pre- and post-test scores. Patient satisfaction scores were collected. Patient distress scores (0–10) were collected at the beginning of their consult visit prior to seeing the physician. We found that patient education videos prior to consult improved patient understanding, resulted in high patient satisfaction, and low patient distress at the time of consult.

The Gus Schumacher Nutrition Incentive Program (GusNIP) is a federally funded grant program that provides nutrition incentives-subsidies for purchasing fruits and vegetables (FV)-to Supplemental Nutrition Assistance Program (SNAP) participants. GusNIP currently advances nutrition equity by improving FV access for people with low incomes, yet inequities exist within GusNIP. We sought to identify inequities in GusNIP at the community, organization, partner, and individual levels and develop recommendations for farm bill provisions to make the program more equitable. In Spring 2021, a group of nutrition incentive experts (n = 11) from across the country convened to discuss opportunities to enhance equity in GusNIP. The iterative recommendation development process included feedback from key stakeholders (n = 15) and focus group participants with GusNIP lived experience (n = 12). Eleven recommendations to advance equity in GusNIP in the farm bill emerged across six categories: (1) increase total GusNIP funding, (2) increase funding and support to lower-resourced organizations and impacted communities, (3) eliminate the match requirement, (4) support statewide expansion, (5) expand and diversify retailer participation, and (6) expand program marketing. Including these recommendations in the upcoming and future farm bills would equitably expand GusNIP for SNAP participants, program grantees, and communities across the country.

Clinician generated segmentation of tumor and healthy tissue regions of interest (ROIs) on medical images is crucial for radiotherapy. However, interobserver segmentation variability has long been considered a significant detriment to the implementation of high-quality and consistent radiotherapy dose delivery. This has prompted the increasing development of automated segmentation approaches. However, extant segmentation datasets typically only provide segmentations generated by a limited number of annotators with varying, and often unspecified, levels of expertise. In this data descriptor, numerous clinician annotators manually generated segmentations for ROIs on computed tomography images across a variety of cancer sites (breast, sarcoma, head and neck, gynecologic, gastrointestinal; one patient per cancer site) for the Contouring Collaborative for Consensus in Radiation Oncology challenge. In total, over 200 annotators (experts and non-experts) contributed using a standardized annotation platform (ProKnow). Subsequently, we converted Digital Imaging and Communications in Medicine data into Neuroimaging Informatics Technology Initiative format with standardized nomenclature for ease of use. In addition, we generated consensus segmentations for experts and non-experts using the Simultaneous Truth and Performance Level Estimation method. These standardized, structured, and easily accessible data are a valuable resource for systematically studying variability in segmentation applications.

Objective: Due to its video based approach, YouTube has become a widely accessed educational resource for patients and trainees. This systematic review characterised and evaluated the peer reviewed literature investigating YouTube as a source of patient or trainee education in vascular surgery. Data sources: A comprehensive literature search was conducted using EMBASE, MEDLINE, and Ovid HealthStar from inception until 19 January 2023. All primary studies and conference abstracts evaluating YouTube as a source of vascular surgery education were included. Review methods: Video educational quality was analysed across several factors, including pathology, video audience, and length. Results: Overall, 24 studies were identified examining 3 221 videos with 123.1 hours of content and 37.1 million views. Studies primarily examined YouTube videos on diabetic foot care (7/24, 29%), peripheral arterial disease (3/24, 13%), carotid artery stenosis (3/24, 13%), varicose veins (3/24, 13%), and abdominal aortic aneurysm (2/24, 8%). Video educational quality was analysed using standardised assessment tools, author generated scoring systems, or global author reported assessment of quality. Six studies assessed videos for trainee education, while 18 studies evaluated videos for patient education. Among the 20 studies which reported on the overall quality of educational content, 10/20 studies deemed it poor, and 10/20 studies considered it fair, with 53% of studies noting poor educational quality for videos intended for patients and 40% of studies noting poor educational quality in videos intended for trainees. Poor quality videos had more views than fair quality videos (mean 27 348, 95% CI 15 154–39 543 views vs. 11 372, 95% CI 3 115–19 629 views, p = .030). Conclusion: The overall educational quality of YouTube videos for vascular surgery patient and trainee education is suboptimal. There is significant heterogeneity in the quality assessment tools used in their evaluation. A standardised approach to online education with a consistent quality assessment tool is required to better support online patient and trainee education in vascular surgery.

Sea turtles are an iconic group of marine megafauna that have been exposed to multiple anthropogenic threats across their different life stages, especially in the past decades. This has resulted in population declines, and consequently many sea turtle populations are now classified as threatened or endangered globally. Although some populations of sea turtles worldwide are showing early signs of recovery, many still face fundamental threats. This is problematic since sea turtles have important ecological roles. To encourage informed conservation planning and direct future research, we surveyed experts to identify the key contemporary threats (climate change, direct take, fisheries, pollution, disease, predation, and coastal and marine development) faced by sea turtles. Using the survey results and current literature, we also outline knowledge gaps in our understanding of the impact of these threats and how targeted future research, often involving emerging technologies, could close those gaps.

Background: Nutrition is important in autism spectrum disorder (ASD). Because nutritional problems of children with ASD can lead to nutritional deficiencies and this can also directly or indirectly affect symptoms related to autism. We investigated the effect of diet and supplementation treatments on gastrointestinal, behavioral or sleep problems based on the results of literature review. Background: Methods: We generated four questions based on literature. We carried out title and abstract-based search using the Web of Science database. Of 4580 abstracts were identified, 192 papers were reviewed and 55 papers precisely meeting the inclusion criteria. Methods: Results: The studies examining the effects of vitamins, minerals, probiotics, and other supplements on ASD symptoms had different dosages, different treatment durations, small sample sizes and used different scales for evaluation. The results of the studies of the effectiveness of Gluten-Free and Casein-Free (GFCF) and ketogenic diet to reduce gastrointestinal, behavioral and sleeping problems in children and adolescents were contradictory. Results: Conclusions: It is not possible to suggest the GFCF and/or ketogenic diet, vitamins, minerals and probiotics to individual with ASD based on the available evidence. By planning a sufficient and balanced diet, it should be aimed to prevent nutrient deficiency and to ensure growth in accordance with the age in children with ASD. Conclusions

Using data from a participatory ethnography of an urban high school slated for closure, this article examines the impact of comprehensive transformation on the university-school partnership's goal to change from a culture of underachievement and negativity toward a culture of collaboration and excellence. We explore these question/s: How do comprehensive changes in infrastructure, policies, leadership, and instructional practices shape school culture? What role do shifting power relations (generative frictions) and authentic trust play in developing shared ownership of outcomes? We argue generative frictions produced changes in culture that impacted changes in outcomes.

IntroductionThe U. S. Environmental Protection Agency’s Endocrine Disruptor Screening Program (EDSP) Tier 1 assays are used to screen for potential endocrine system–disrupting chemicals. A model integrating data from 16 high-throughput screening assays to predict estrogen receptor (ER) agonism has been proposed as an alternative to some low-throughput Tier 1 assays. Later work demonstrated that as few as four assays could replicate the ER agonism predictions from the full model with 98% sensitivity and 92% specificity. The current study utilized chemical clustering to illustrate the coverage of the EDSP Universe of Chemicals (UoC) tested in the existing ER pathway models and to investigate the utility of chemical clustering to evaluate the screening approach using an existing 4-assay model as a test case. Although the full original assay battery is no longer available, the demonstrated contribution of chemical clustering is broadly applicable to assay sets, chemical inventories, and models, and the data analysis used can also be applied to future evaluation of minimal assay models for consideration in screening.MethodsChemical structures were collected for 6,947 substances via the CompTox Chemicals Dashboard from the over 10,000 UoC and grouped based on structural similarity, generating 826 chemical clusters. Of the 1,812 substances run in the original ER model, 1,730 substances had a single, clearly defined structure. The ER model chemicals with a clearly defined structure that were not present in the EDSP UoC were assigned to chemical clusters using a k-nearest neighbors approach, resulting in 557 EDSP UoC clusters containing at least one ER model chemical.Results and DiscussionPerformance of an existing 4-assay model in comparison with the existing full ER agonist model was analyzed as related to chemical clustering. This was a case study, and a similar analysis can be performed with any subset model in which the same chemicals (or subset of chemicals) are screened. Of the 365 clusters containing >1 ER model chemical, 321 did not have any chemicals predicted to be agonists by the full ER agonist model. The best 4-assay subset ER agonist model disagreed with the full ER agonist model by predicting agonist activity for 122 chemicals from 91 of the 321 clusters. There were 44 clusters with at least two chemicals and at least one agonist based upon the full ER agonist model, which allowed accuracy predictions on a per-cluster basis. The accuracy of the best 4-assay subset ER agonist model ranged from 50% to 100% across these 44 clusters, with 32 clusters having accuracy ≥90%. Overall, the best 4-assay subset ER agonist model resulted in 122 false-positive and only 2 false-negative predictions compared with the full ER agonist model. Most false positives (89) were active in only two of the four assays, whereas all but 11 true positive chemicals were active in at least three assays. False positive chemicals also tended to have lower area under the curve (AUC) values, with 110 out of 122 false positives having an AUC value below 0.214, which is lower than 75% of the positives as predicted by the full ER agonist model. Many false positives demonstrated borderline activity. The median AUC value for the 122 false positives from the best 4-assay subset ER agonist model was 0.138, whereas the threshold for an active prediction is 0.1.ConclusionOur results show that the existing 4-assay model performs well across a range of structurally diverse chemicals. Although this is a descriptive analysis of previous results, several concepts can be applied to any screening model used in the future. First, the clustering of the chemicals provides a means of ensuring that future screening evaluations consider the broad chemical space represented by the EDSP UoC. The clusters can also assist in prioritizing future chemicals for screening in specific clusters based on the activity of known chemicals in those clusters. The clustering approach can be useful in providing a framework to evaluate which portions of the EDSP UoC chemical space are reliably covered by in silico and in vitro approaches and where predictions from either method alone or both methods combined are most reliable. The lessons learned from this case study can be easily applied to future evaluations of model applicability and screening to evaluate future datasets.

Introduction: Computational models using data from high-throughput screening assays have promise for prioritizing and screening chemicals for testing under the U.S. Environmental Protection Agency’s Endocrine Disruptor Screening Program (EDSP). The purpose of this work was to demonstrate a data processing method for the determination of optimal minimal assay batteries from a larger comprehensive model, to provide a uniform method of evaluating the performance of future minimal assay batteries compared with the androgen receptor (AR) pathway model, and to incorporate chemical cluster analysis into this evaluation. Although several of the assays in the AR pathway model are no longer available through the original vendor, this approach could be used for future evaluations of minimal assay models for prioritization and screening.Methods: We compared two previously published models and found that an expanded 14-assay model had higher sensitivity for antagonists, whereas the original 11-assay model had slightly higher sensitivity for agonists. We then investigated subsets of assays in the original AR pathway model to optimize overall testing strategies that minimize cost while maintaining sensitivity across a broad chemical space.Results and Discussion: Evaluation of the critical assays across subset models derived from the 14-assay model identified three critical assays for predicting antagonism and two critical assays for predicting agonism. A minimum of nine assays is required for predicting agonism and antagonism with high sensitivity (95%). However, testing workflows guided by chemical structure–based clusters can reduce the average number of assays needed per chemical by basing the assays selected for testing on the likelihood of a chemical being an AR agonist, according to its structure. Our results show that a multi-stage testing workflow can provide 95% sensitivity while requiring only 48% of the resources required for running all assays from the original full models. The resources can be reduced further by incorporating in silico activity predictions.Conclusion: This work illustrates a data-driven approach that incorporates chemical clustering and simultaneous consideration of antagonism and agonism mechanisms to more efficiently screen chemicals. This case study provides a proof of concept for prioritization and screening strategies that can be utilized in future analyses to minimize the overall number of assays needed for predicting AR activity, which will maximize the number of chemicals that can be tested and allow data-driven prioritization of chemicals for further screening under the EDSP.

The University of Rochester and East High School in Rochester, New York, entered into a partnership in 2015, hoping to transform the school to prevent shut down by the state. Both partners were wary because of the district's failed attempts at reform and the history of similar partnerships elsewhere. A new state-level reform option allowed the partners to form an educational partnership organization (EPO) so that they could become equal partners with some autonomy from the district. The partners decided that to succeed, they would need to involve the community. They learned from listening sessions that the community wanted the school to remain open but also wanted everything about it to change. So, instead of taking an incremental approach, they chose to transform the school's structures, culture, leadership model, and curriculum and instruction. Valerie L. Marsh, Shaun C. Nelms, Sarah Peyre, and Joanne Larson describe how the university and the school worked together to transform East on all these fronts.

The nutritional management of children with chronic kidney disease (CKD) is of prime importance in meeting the challenge of maintaining normal growth and development in this population. The objective of this review is to integrate the Pediatric Renal Nutrition Taskforce clinical practice recommendations for children with CKD stages 2-5 and on dialysis, as they relate to the infant from full term birth up to 1 year of age, for healthcare professionals, including dietitians, physicians, and nurses. It addresses nutritional assessment, energy and protein requirements, delivery of the nutritional prescription, and necessary dietary modifications in the case of abnormal serum levels of calcium, phosphate, and potassium. We focus on the particular nutritional needs of infants with CKD for whom dietary recommendations for energy and protein, based on body weight, are higher compared with children over 1 year of age in order to support both linear and brain growth, which are normally maximal in the first 6 months of life. Attention to nutrition during infancy is important given that growth is predominantly nutrition dependent in the infantile phase and the growth of infants is acutely impaired by disruption to their nutritional intake, particularly during the first 6 months. Inadequate nutritional intake can result in the failure to achieve full adult height potential and an increased risk for abnormal neurodevelopment. We strongly suggest that physicians work closely with pediatric renal dietitians to ensure that the infant with CKD receives the best possible nutritional management to optimize their growth and development., Author(s): Vanessa Shaw [sup.1] , Caroline Anderson [sup.2] , An Desloovere [sup.3] , Larry A. Greenbaum [sup.4] , Dieter Haffner [sup.5] , Christina L. Nelms [sup.6] , Fabio Paglialonga [sup.7] [...]

Described in this paper is a control method for a permanent magnet synchronous motor (PMSM) based on a decoupled speed and flux control technique where the speed and the flux of the PMSM are controlled separately. The actual torque and the feedback flux of the PMSM are directly calculated from the stator currents, while the speed and the angular position are read from the motor. Therefore, no flux/torque or speed/position estimators are required. A separate flux controller is used to generate the d-axis current error. The speed controller is used to generate the reference torque, while the q-axis current error is generated by the constant torque relation. The performance of the overall control system is examined using the Matlab/Simulink environment. The experimental work is tested using dSPACE DS1104. The performance of the motor is presented with reference speed step change. The simulation and the hardware results prove the effectiveness of the proposed method in controlling the speed and flux of a three-phase PMSM.

Abstract Clinician generated segmentation of tumor and healthy tissue regions of interest (ROIs) on medical images is crucial for radiotherapy. However, interobserver segmentation variability has long been considered a significant detriment to the implementation of high-quality and consistent radiotherapy dose delivery. This has prompted the increasing development of automated segmentation approaches. However, extant segmentation datasets typically only provide segmentations generated by a limited number of annotators with varying, and often unspecified, levels of expertise. In this data descriptor, numerous clinician annotators manually generated segmentations for ROIs on computed tomography images across a variety of cancer sites (breast, sarcoma, head and neck, gynecologic, gastrointestinal; one patient per cancer site) for the Contouring Collaborative for Consensus in Radiation Oncology challenge. In total, over 200 annotators (experts and non-experts) contributed using a standardized annotation platform (ProKnow). Subsequently, we converted Digital Imaging and Communications in Medicine data into Neuroimaging Informatics Technology Initiative format with standardized nomenclature for ease of use. In addition, we generated consensus segmentations for experts and non-experts using the Simultaneous Truth and Performance Level Estimation method. These standardized, structured, and easily accessible data are a valuable resource for systematically studying variability in segmentation applications.

Unbalanced issues and power quality problems can be handled using shunt active power filters (APFs). Under weak grid conditions and unbalanced grid impedance, the unbalanced three-phase load leads to unbalanced grid currents and point-of-common-coupling voltages. As a result, there will be a significant fluctuation in the real and reactive power of the grid. Several shunt APF control methods were used to solve unbalanced problems. Both voltages and currents measurements are required in the control method. Proposed in this article is a new voltage sensorless control method of shunt APF by using current measurements only. The reference current of the controller was determined from the positive-sequence component of the measured load currents. The APF was controlled by a PR controller. The proposed approach can eliminate fluctuation in the real and reactive power and balance point-of-common-coupling voltages and grid currents. Simulation and hardware experiments were used to verify the proposed method’s performance.

In this paper, a vector controlled PMSM drive based on a proportional–resonance controller (PR) under open circuit fault (OCF) is proposed. The PR controller is used to generate the stator voltages. While the field-oriented control (FOC) approach has been implemented using the pulse width modulation (PWM) technology. The simulation is built using MATLAB/ Simulink. Hardware experiments were performed, and the results captured using dSPACE DS1104. The behaviour of the PMSM is studied under three operations: healthy, faulty, and post-fault operation. Moreover, the speed control of the PMSM under the three operations has been presented. The simulation and the experimental results show a fast dynamic response with some ripple in the response of speed and torque during the healthy and post-fault operations. On the other hand, during the OCF, the ripple in the torque and speed response increases. However, the proposed method proves its efficacy by keeping the motor speed nearly at the input reference speed as well as guaranteeing the continued operation of the PMSM with good steady-state and dynamic performance.