bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina
Authors: Liang Xulong , Brooks Matthew J , Swaroop Anand 
Published: July 2022

Abstract
The basic motif-leucine zipper (bZIP) transcription factor neural retina leucine zipper (NRL) determines rod photoreceptor cell fate during retinal development, and its loss leads to cone-only retina in mice. NRL works synergistically with homeodomain protein Cone-Rod Homeobox and other regulatory factors to control the transcription of most genes associated with rod morphogenesis and functional maturation, which span over a period of several weeks in the mammalian retina. We predicted that NRL gradually establishes rod cell identity and function by temporal and dynamic regulation of stage-specific transcriptional targets. Therefore, we mapped the genomic occupancy of NRL at four stages of mouse photoreceptor differentiation by CUT&RUN analysis. Dynamics of NRL binding revealed concordance with the corresponding changes in transcriptome of the developing rods. Notably, we identified c-Jun proto-oncogene as one of the targets of NRL, which could bind to specific cis-elements in the c-Jun promoter and modulate its activity in HEK293 cells. Coimmunoprecipitation studies showed the association of NRL with c-Jun, also a bZIP protein, in transfected cells as well as in developing mouse retina. Additionally, shRNA-mediated knockdown of c-Jun in the mouse retina in vivo resulted in altered expression of almost 1000 genes, with reduced expression of phototransduction genes and many direct targets of NRL in rod photoreceptors. We propose that c-Jun-NRL heterodimers prime the NRL-directed transcriptional program in neonatal rod photoreceptors before high NRL expression suppresses c-Jun at later stages. Our study highlights a broader cooperation among cell-type restricted and widely expressed bZIP proteins, such as c-Jun, in specific spatiotemporal contexts during cellular differentiation.
Rocks and Vegetation Cover Improve Body Condition of Desert Lizards during Both Summer and Winter
Authors: Stark Gavin , Ma Liang , Zeng Zhi-Gao , Du Wei-guo , Levy Ofir 
Published: July 2022

AbstractMicrohabitats provide ecological and physiological benefits to animals, sheltering them from predation and extreme temperatures and offering an additional supply of water and food. However, most studies have assumed no energetic costs of searching for microhabitats or moving between them, or considered how the availability of microhabitats may affect the energy reserves of animals and how such effects may differ between seasons. To fill these gaps, we studied how the body condition of lizards is affected by microhabitat availability in the extreme environment of the Judean Desert. In particular, we quantified how vegetation and rock cover in the vicinity of these lizards affect their body condition during summer and winter. First, we used aerial imagery to map the vegetation/rock cover at two study sites. Next, we collected 68 adult lizards and examined how their body condition varies across seasons and availability of vegetation and rock cover. In addition, we examined how vegetation and rock cover may differ in their effective distance (i.e., the distance that best explains body condition of lizards). We found that lizards body condition was better if they were collected closer to a higher availability of vegetation or rocks. However, while close proximity (within 10 m) was the best predictor for the positive effect of rocks, a greater distance (up to 90 m) was the best predictor for the effect of the vegetation cover. Moreover, the positive effect of vegetation was 12-fold higher than the effect of rocks. Interestingly, although the lizards’ body condition during winter was poorer than during summer, the positive effects of rock and vegetation cover remained constant between the seasons. This similarity of benefits across seasons suggests that shaded microhabitats have important additional ecological roles regardless of climate, and that they may provide thermoregulatory benefits in winter too. We also found a synergic effect of vegetation and rock cover on the lizards’ body condition, suggesting that their roles are complementary rather than overlapping. Our research has revealed the importance of shade- and shelter-providing microhabitats in both summer and winter. We suggest that proximity to microhabitat diversity may contribute to better body condition in lizards or, alternatively, facilitates competition and attracts lizards with better body condition. Comprehending the complex interactions between animals and different microhabitats is critical for developing better conservation plans, understanding the risks of climate change, and suggesting mitigation strategies.
Point Prevalence Estimates of Activity-Limiting Long-term Symptoms Among United States Adults ≥1 Month After Reported Severe Acute Respiratory Syndrome Coronavirus 2 Infection, 1 November 2021
Authors: Tenforde Mark W , Devine Owen J , Reese Heather E , Silk Benjamin J , Iuliano A Danielle , Threlkel Ryan , Vu Quan M , Plumb Ian D , Cadwell Betsy L , Rose Charles , Steele Molly K , Briggs-Hagen Melissa , Ayoubkhani Daniel , Pawelek Piotr , Nafilyan Vahé , Saydah Sharon H , Bertolli Jeanne 
Published: July 2022

AbstractBackgroundAlthough most adults infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) fully recover, a proportion have ongoing symptoms, or post-COVID conditions (PCC), after infection. The objective of this analysis was to estimate the number of United States (US) adults with activity-limiting PCC on 1 November 2021.MethodsWe modeled the prevalence of PCC using reported infections occurring from 1 February 2020 to 30 September 2021, and population-based, household survey data on new activity-limiting symptoms ≥1 month following SARS-CoV-2 infection. From these data sources, we estimated the number and proportion of US adults with activity-limiting PCC on 1 November 2021 as 95% uncertainty intervals, stratified by sex and age. Sensitivity analyses adjusted for underascertainment of infections and uncertainty about symptom duration.ResultsOn 1 November 2021, at least 3.0–5.0 million US adults, or 1.2%–1.9% of the US adult population, were estimated to have activity-limiting PCC of ≥1 month’s duration. Population prevalence was higher in females (1.4%–2.2%) than males. The estimated prevalence after adjusting for underascertainment of infections was 1.7%–3.8%.ConclusionsMillions of US adults were estimated to have activity-limiting PCC. These estimates can support future efforts to address the impact of PCC on the US population.
Comparing the variability of ingredient, strength, and dose form information from electronic prescriptions with RxNorm drug product descriptions
Authors: Lester Corey A , Flynn Allen J , Marshall Vincent D , Rochowiak Scott , Rowell Brigid , Bagian James P 
Published: July 2022

Abstract

Objective
To determine the variability of ingredient, strength, and dose form information from drug product descriptions in real-world electronic prescription (e-prescription) data.

Materials and Methods
A sample of 10 399 324 e-prescriptions from 2019 to 2021 were obtained. Drug product descriptions were analyzed with a named entity extraction model and National Drug Codes (NDCs) were used to get RxNorm Concept Unique Identifiers (RxCUI) via RxNorm. The number of drug product description variants for each RxCUI was determined. Variants identified were compared to RxNorm to determine the extent of matching terminology used.

Results
A total of 353 002 unique pairs of drug product descriptions and NDCs were analyzed. The median (1st–3rd quartile) number of variants extracted for each standardized expression in RxNorm, was 3 (2–7) for ingredients, 4 (2–8) for strength, and 41 (11–122) for dosage forms. Of the pairs, 42.35% of ingredients (n = 328 032), 51.23% of strengths (n = 321 706), and 10.60% of dose forms (n = 326 653) used matching terminology, while 16.31%, 24.85%, and 13.05% contained nonmatching terminology, respectively.

Discussion
A wide variety of drug product descriptions makes it difficult to determine whether 2 drug product descriptions describe the same drug product (eg, using abbreviations to describe an active ingredient or using different units to represent a concentration). This results in patient safety risks that lead to incorrect drug products being ordered, dispensed, and used by patients. Implementation and use of standardized terminology may reduce these risks.

Conclusion
Drug product descriptions on real-world e-prescriptions exhibit large variation resulting in unnecessary ambiguity and potential patient safety risks.
Assessing perceived effectiveness of career development efforts led by the women in American Medical Informatics Association Initiative
Authors: Wei Duo (Helen) , Kukhareva Polina V , Tao Donghua , Sordo Margarita , Pandita Deepti , Dua Prerna , Banerjee Imon , Abraham Joanna 
Published: July 2022

Abstract

Objective
We sought to ascertain perceived factors affecting women’s career development efforts in the American Medical Informatics Association (AMIA) and to provide recommendations for improvements.

Materials and Methods
Data were collected using a 27-item survey administered via the AMIA newsletter and other social channels. Survey questions comprised 3 demographics, 15 Likert-scale, and 9 open-ended items. Likert-scale responses were summarized across respondent ages, career stages, and career domains, and open-ended responses were thematically analyzed.

Results
We received survey responses from 109 AMIA women members. Our findings demonstrate that AMIA had made strides in promoting career development, and the most effective AMIA efforts included social events (83%), panel discussions (80%), and scientific sessions (79%). However, despite these efforts, women members perceived that gender-specific challenges persisted within AMIA, and recognized the need for increased networking opportunities (96%), raising awareness of gender-specific challenges (95%), and encouraging gender proportional representation in leadership (92%).

Discussion
International and national biomedical informatics professional communities have put forth efforts to address gender-specific issues in career development. Yet, our study identified that some of these, including the deep-rooted gender power hierarchy and bias, are still perceived as profound in AMIA.

Conclusion
Even though existing career development efforts for women are highly effective, important perceived gender-specific career development issues require further attention and investigation to improve existing AMIA activities.
Using Twitter data to understand public perceptions of approved versus off-label use for COVID-19-related medications
Authors: Hua Yining , Jiang Hang , Lin Shixu , Yang Jie , Plasek Joseph M , Bates David W , Zhou Li 
Published: July 2022

Abstract

Objective
Understanding public discourse on emergency use of unproven therapeutics is essential to monitor safe use and combat misinformation. We developed a natural language processing-based pipeline to understand public perceptions of and stances on coronavirus disease 2019 (COVID-19)-related drugs on Twitter across time.

Methods
This retrospective study included 609 189 US-based tweets between January 29, 2020 and November 30, 2021 on 4 drugs that gained wide public attention during the COVID-19 pandemic: (1) Hydroxychloroquine and Ivermectin, drug therapies with anecdotal evidence; and (2) Molnupiravir and Remdesivir, FDA-approved treatment options for eligible patients. Time-trend analysis was used to understand the popularity and related events. Content and demographic analyses were conducted to explore potential rationales of people’s stances on each drug.

Results
Time-trend analysis revealed that Hydroxychloroquine and Ivermectin received much more discussion than Molnupiravir and Remdesivir, particularly during COVID-19 surges. Hydroxychloroquine and Ivermectin were highly politicized, related to conspiracy theories, hearsay, celebrity effects, etc. The distribution of stance between the 2 major US political parties was significantly different (P &lt; .001); Republicans were much more likely to support Hydroxychloroquine (+55%) and Ivermectin (+30%) than Democrats. People with healthcare backgrounds tended to oppose Hydroxychloroquine (+7%) more than the general population; in contrast, the general population was more likely to support Ivermectin (+14%).

Conclusion
Our study found that social media users with have different perceptions and stances on off-label versus FDA-authorized drug use across different stages of COVID-19, indicating that health systems, regulatory agencies, and policymakers should design tailored strategies to monitor and reduce misinformation for promoting safe drug use. Our analysis pipeline and stance detection models are made public at https://github.com/ningkko/COVID-drug.
Increasing vitamin D levels to improve fertilization rates in cattle
Authors: Peixoto de Souza Vanessa , Jensen Jared , Whitler William , Estill Charles T , Bishop Cecily V 
Published: July 2022

Abstract
Recently, interest in supplementing vitamin D (Vit D) to improve aspects of health, mainly in human fertility, has emerged. Still, supplementation of Vit D above the minimum required levels has yet to be explored in cattle despite evidence for Vit D receptors in reproductive tissues. The objective of this study was to establish if a dose–response relationship exists between Vit D exposure and success of in vitro production (IVP) of embryos and, if acute supplementation of Vit D improves pregnancy rates during timed artificial insemination (TAI) of dairy cows. Cumulus-oocyte complexes (COCs) were obtained from ovaries acquired from a local abattoir and cultured in five different IVP treatments from three separate collections (Control, 50, 100, 150, and 200 ng/mL of 1,25(OH)2D3; n = 20–30 COCs/group). In Experiment 2, dairy breed cows (n = 100) were synchronized for TAI with the PresynchOvsynch protocol. Cows received 150,000 IU of Vit D (n = 48) or castor oil as control (n = 53) along with gonadotropin-releasing hormone (GnRH) 24 h before TAI. Serum samples were collected before and 24 h after treatment. A small cohort of cows (n = 4) received the same treatments in two separate cycles and follicular fluid (FF) was collected after 24 h for calcidiol (25OHD) analyses. Increased concentrations of Vit D resulted in decreased rates of maturation of COC (150 and 200 ng/mL vs. control and 50 ng/mL; P = 0.01). Supplementation with 50 ng/mL resulted in greater numbers of early blastocyst and blastocyst stage embryos (P &lt; 0.009). Pregnancy at first breeding did not differ (P = 0.13) between groups, but serum 25OHD increased in treated females after 24 h (P = 0.002). The FF 25OHD levels were reflective of serum levels, however, the observed increase in the treatment cycle (P = 0.04) was parallel to an overall increase in serum 25OHD during the entire second cycle, likely due to increased environmental sunlight exposure (March, control vs. May, treatment). A similar increase in the serum 25OHD in the lactating commercial herd maintained in covered housing was not observed, although experiments were conducted during a similar timeframe. This herd had levels of 25OHD near the low end of sufficiency according to National Research Council (NRC) guidelines. We conclude mild Vitamin D supplementation with concentrations at the higher end of NRC guidelines can improve maturation rates of recovered COCs. However, longer term supplementation may be needed to appreciate any benefits on fertility.
Exploring methods to summarize gut microbiota composition for microbiability estimation and phenotypic prediction in swine
Authors: He Yuqing , Tiezzi Francesco , Jiang Jicai , Howard Jeremy , Huang Yijian , Gray Kent , Choi Jung-Woo , Maltecca Christian 
Published: July 2022

Abstract
The microbial composition resemblance among individuals in a group can be summarized in a square covariance matrix and fitted in linear models. We investigated eight approaches to create the matrix that quantified the resemblance between animals based on the gut microbiota composition. We aimed to compare the performance of different methods in estimating trait microbiability and predicting growth and body composition traits in three pig breeds. This study included 651 purebred boars from either breed: Duroc (n = 205), Landrace (n = 226), and Large White (n = 220). Growth and body composition traits, including body weight (BW), ultrasound backfat thickness (BF), ultrasound loin depth (LD), and ultrasound intramuscular fat (IMF) content, were measured on live animals at the market weight (156 ± 2.5 d of age). Rectal swabs were taken from each animal at 158 ± 4 d of age and subjected to 16S rRNA gene sequencing. Eight methods were used to create the microbial similarity matrices, including 4 kernel functions (Linear Kernel, LK; Polynomial Kernel, PK; Gaussian Kernel, GK; Arc-cosine Kernel with one hidden layer, AK1), 2 dissimilarity methods (Bray-Curtis, BC; Jaccard, JA), and 2 ordination methods (Metric Multidimensional Scaling, MDS; Detrended Correspondence analysis, DCA). Based on the matrix used, microbiability estimates ranged from 0.07 to 0.21 and 0.12 to 0.53 for Duroc, 0.03 to 0.21 and 0.05 to 0.44 for Landrace, and 0.02 to 0.24 and 0.05 to 0.52 for Large White pigs averaged over traits in the model with sire, pen, and microbiome, and model with the only microbiome, respectively. The GK, JA, BC, and AK1 obtained greater microbiability estimates than the remaining methods across traits and breeds. Predictions were made within each breed group using four-fold cross-validation based on the relatedness of sires in each breed group. The prediction accuracy ranged from 0.03 to 0.18 for BW, 0.08 to 0.31 for BF, 0.21 to 0.48 for LD, and 0.04 to 0.16 for IMF when averaged across breeds. The BC, MDS, LK, and JA achieved better accuracy than other methods in most predictions. Overall, the PK and DCA exhibited the worst performance compared to other microbiability estimation and prediction methods. The current study shows how alternative approaches summarized the resemblance of gut microbiota composition among animals and contributed this information to variance component estimation and phenotypic prediction in swine.
Circadian clocks and their integration with metabolic and reproductive systems: our current understanding and its application to the management of dairy cows
Authors: Casey Theresa M , Plaut Karen 
Published: July 2022

Abstract
The circadian system is an inbuilt timekeeping mechanism that tracks the 24-h day through the generation of circadian rhythms. Circadian rhythms enable animals to forecast and anticipate regular changes in their environment, and orchestrate biochemical, physiological and behavioral events so that the right process occurs at the right time. The 24 h rhythms generated by circadian clocks are integrated into homeostatic feedback loops and repair pathways. Metabolic and reproductive systems are highly integrated with the circadian timing system and demonstrate reciprocal regulation. Circadian clocks set the timing of circadian rhythms by gathering temporal information from external and internal signals to include light and nutrients. Exogenous and endogenous factors that function as inputs to the circadian clocks can disrupt their timing when applied at unusual and inappropriate times, and are referred to as chronodisruptors. Changes in the natural light-dark cycle perturb the circadian system. Other chronodisrupters include inappropriately timed food intake and physical activity and biological stress. Knowledge of the biology underlying circadian clock timing is critical to understanding how to maximize health and production efficiency of cattle. Here we review circadian clocks and their function in the regulation of metabolic and reproductive systems as well as the consequence of circadian disruption on mammary development and lactation with a particular focus on recent research findings from studies of dairy cows.
Bone Marrow Stem Cell-Exo-Derived TSG-6 Attenuates 1-Methyl-4-Phenylpyridinium+-Induced Neurotoxicity via the STAT3/miR-7/NEDD4/LRRK2 Axis
Authors: Huang Dezhi , Zhang Mingming , Tan Zhigang 
Published: July 2022

Abstract
Bone marrow mesenchymal stem cell-derived exosome (BMSCs-Exo)-derived TNF-stimulated gene-6 (TSG-6) has anti-inflammatory and antioxidative stress-related properties that may be beneficial in the treatment of Parkinson disease (PD) patients. To elucidate the mechanisms involved, we analyzed the effects of BMSCs-Exo-derived TSG-6 on in vitro models of PD induced with 1-methyl-4-phenylpyridinium (MPP+). TSG-6 was abundant in BMSCs-Exo and it attenuated MPP+-induced neurotoxicity. Moreover, BMSCs-Exo reversed the MPP+-induced toxicity accelerated by neural precursor cells expressed developmentally downregulated 4 (NEDD4) knockdown or miR-7 mimics. Further analysis indicated that NEDD4 combined with leucine-rich repeat kinase 2 (LRRK2) to accelerate ubiquitin degradation of LRRK2. Signal transducer and activator of transcription 3 (STAT3) bound to the miR-7 promoter and miR-7 targeted NEDD4. These data indicate that BMSCs-Exo-derived TSG-6 attenuated neurotoxicity via the STAT3-miR-7-NEDD4 axis. Our results define the specific mechanisms for BMSCs-Exo-derived TSG-6 regulation of MPP+-induced neurotoxicity that are relevant to understanding PD pathogenesis and developing therapies for PD patients.
Diabetes-Related Worries and Coping Among Youth and Young Adults With Type 1 Diabetes
Authors: Taraban Lindsay , Wasserman Rachel , Cao Viena T , Eshtehardi Sahar S , Anderson Barbara J , Thompson Debbe , Marrero David G , Hilliard Marisa E 
Published: July 2022

Abstract

Objective
Although mood and anxiety symptoms are common in youth with type 1 diabetes (T1D), little research has described their worries across developmental stages or the strategies they use to cope with these worries. This secondary data analysis aimed to describe and characterize common T1D-related worries and coping strategies from middle childhood through young adulthood.

Methods
Twenty-three youth (9 children, 7 adolescents, and 7 young adults) completed semistructured qualitative interviews about health-related quality of life. We coded interview transcripts using thematic analysis to generate common themes of diabetes-related worries and coping strategies.

Results
Participants’ worries fell into four major themes: Managing Blood Glucose, Self-Efficacy for Diabetes Management, Interpersonal Relationships, and Lifestyle Impact, and eight youth denied having diabetes-related worries. Coping strategies fell into the three major themes: Attempts to Change Source of Worry, Attempts to Change Reactions to Worry, and Attempts to Orient Away from the Worry.

Conclusions
Youths’ worries about various aspects of living with and feeling able to self-manage diabetes are important to consider across pediatric development as they can impact youths’ participation in daily activities and future plans. By adolescence, youth report longer-term worries about the health and lifestyle implications of diabetes. Youths’ reported coping strategies are generally consistent with existing coping frameworks, though our data suggest some possible refinements. Social support emerged as an important coping strategy for all age groups. Thus, interventions supporting youth in building and strengthening their social networks may be particularly beneficial in helping youth cope with their diabetes-related worries across development.