bluuebunny/crossref_metadata_2025_split huggingface dataset:
Femicide and Public Health Ethics: Approaching Gender-based Violence and Death in the Health Professions
Authors: Bansal Esha , Patel Krishna , Hassan Yonis , Rice Timothy 
Published: December 2022

Abstract
Femicide is an ongoing public health and human rights crisis of global proportions. Currently, however, there is a relative vacuum of ethics theory and discussion about femicide amongst the health professions. This article draws from three illustrative case examples along the continuum of femicide to explore contemporary ethical concerns relevant to addressing gender-based violence and death through clinical medicine and public health. Using an epistemic justice framework, we analyze the relative invisibility of femicide in public health discourse today, and renew a conversation about ethical issues inherent to health interventions and policy-making around femicide.
Acylation driven by intracellular metabolites in host cells inhibits Cas9 activity used for genome editing
Authors: Zhao Li , You Di , Wang Ting , Zou Zhen-Ping , Yin Bin-Cheng , Zhou Ying , Ye Bang-Ce 
Published: December 2022

Abstract
CRISPR-Cas, the immune system of bacteria and archaea, has been widely harnessed for genome editing, including gene knockouts and knockins, single-base editing, gene activation, and silencing. However, the molecular mechanisms underlying fluctuations in the genome editing efficiency of crispr in various cells under different conditions remain poorly understood. In this work, we found that Cas9 can be ac(et)ylated by acetyl-phosphate or acyl-CoA metabolites both in vitro and in vivo. Several modifications are associated with the DNA or sgRNA binding sites. Notably, ac(et)ylation of Cas9 driven by these metabolites in host cells potently inhibited its binding and cleavage activity with the target DNA, thereby decreasing Crispr genome editing efficiency. This study provides more insights into understanding the effect of the intracellular environment on genome editing application of crispr with varying efficiency in hosts.
DOSE CALCULATION OF PROTON THERAPY BASED ON MONTE CARLO AND EMPIRICAL FORMULA
Authors: Yu Yue , Chen Zhi 
Published: December 2022

AbstractIn this work, we used the Monte Carlo-based TOPAS simulation software to calculate the ambient dose equivalents and annual effective dose due to the secondary neutron field produced in proton therapy, also we introduced a USTC phantom to access the organ equivalent dose. The ambient dose equivalent and annual effective dose were calculated in several positions of interest inside and outside the facility. The simulation results were compared qualitatively to the results of the Empirical Formula, showing that the Empirical Formula calculations overestimated the dose, 28.95 times higher than the MC simulations, on average, which would lead to over shielding. In addition, the highest equivalent dose rate of a single radiation-sensitive organ simulated by TOPAS was 1.50 × 10−9 mSv/a for the eye lens, 2.36 × 10−3 mSv/a for limbs and 1.01 × 10−3 mSv/a for skin, which also meets the limits. Therefore, MC simulation has great advantages in shielding design and safety evaluation. And this work presents a new method to calculate the dose, introducing a more anthropogenic phantom can get more realistic results.
Effects of temperament on reproductive performance of Bos taurus heifers enrolled in the 7-day CO-Synch + controlled internal drug release protocol
Authors: Dias Nicholas W , Timlin Claire L , Santilli Felipe V , Harvey Kelsey M , Cooke Reinaldo F , Clark Sherrie , Currin John F , Mercadante Vitor R G 
Published: December 2022

Abstract
Cattle temperament significantly impacts production traits such as reproduction. The objective of this study was to assess the effects of temperament on pregnancy rates to fixed-timed artificial insemination (TAI) in Bos taurus beef heifers. A total of 297 Angus influenced heifers from 3 different locations were evaluated for temperament based on chute score and exit velocity on the first day of the estrus synchronization protocol (d-9) and classified by temperament type based on temperament score (calm ≤ 3 &lt; excitable). Pregnancy status was determined by transrectal ultrasonography approximately 40 d after TAI. Hair from the tail switch was collected at d-9 and at d0 (TAI) for cumulative cortisol evaluation. A subset of 43 heifers from location 3 had blood samples collected at all handling events and evaluated for cortisol concentrations. Overall, 71% of heifers were classified as calm whereas 29% as excitable. Pregnancy rates to TAI were reduced (P = 0.042) in excitable heifers compared to calm heifers (36% vs. 55%, respectively). Mean concentration of cortisol in the hair was reduced over time (P &lt; 0.001) from d-9 (3.5 ± 0.3 pg/mg) to d0 (1.74 ± 0.3 pg/mg) in all heifers, regardless of temperament. In addition, excitable heifers had increased circulating concentrations of cortisol when compared to calm heifers in all handling events (P = 0.015). More interestingly, despite of temperament, concentrations of circulating cortisol were reduced as the protocol events progressed, with greater cortisol concentrations on d-9, intermediate on d-3, and lesser on d0 (P = 0.031). Therefore, the present study demonstrates that heifer temperament has negative effects in pregnancy rates to TAI programs. However, according to blood cortisol concentrations, no chronic stress response was detected due to cattle handling for the TAI protocol. In fact, blood cortisol concentration was reduced between the initiation and completion of the protocol, indicating that heifers were acclimated to handing. These results support the adoption of acclimation protocols and proper cattle handling as a strategy to increase fertility of heifers that are exposed to TAI.
The effects of feeding benzoic acid and/or active dry yeast (Saccharomyces cerevisiae) on fatty acid composition, sensory attributes, and retail shelf-life of beeflongissimus thoracis
Authors: Williams Melissa S , Mandell Ira B , Wood Katharine M , Bohrer Benjamin M 
Published: December 2022

AbstractFifty-nine Angus-cross steers (492 ± SD 36 kg) were arranged in a randomized complete block design and assigned to the following dietary treatments for the final 106 days of the finishing phase: no supplementation (CON), 0.5% benzoic acid (ACD), 3 g/steer/d active dry Saccharomyces cerevisiae (YST), or both [0.5% benzoic acid and 3 g/steer/d S. cerevisiae (AY)]. Steers were slaughtered at a commercial facility where longissimus thoracis (IMPS #107 Beef Rib) samples were retrieved and evaluated for fatty acid composition, sensory attributes, and shelf-life during a simulated retail display period. Data (N = 57) were analyzed using dietary treatment as a fixed effect, blocking weight at the beginning of the study as a random effect, and steer as the experimental unit. Muscle pH and proximate composition (moisture and intramuscular lipid) for longissimus samples were not different (P ≥ 0.39) among dietary treatments. Most fatty acid profile values and calculations were not different among dietary treatments (P ≥ 0.10); however, the n-6:n-3 ratio differed (P = 0.01), with ACD samples having lower n-6:n-3 compared with CON and YST samples while AY samples were intermediate and not different from other dietary treatments. The trained sensory panel did not detect differences among dietary treatments (P ≥ 0.23) for juiciness, beef flavor intensity, or off-flavor intensity; however, they did score AY samples as chewier than ACD samples with CON and YST samples intermediate and not different from other dietary treatments. Yet, tenderness was not different when scored by trained panelists (P = 0.10) or measured instrumentally (P = 0.21). Total color change tended to differ (P = 0.09) during the 12-d simulated retail display period with AY samples experiencing less color change compared with YST samples, while CON and ACD samples were intermediate and not different from other dietary treatments. Lipid oxidation (as measured with TBARS) tended to differ (P = 0.08) following the 12-d simulated retail display period with ACD and AY samples experiencing lower levels of oxidation compared with CON, while YST samples were intermediate and not different from other dietary treatments. Overall, these results suggest there were no negative impacts on meat quality when finishing steers were supplemented with either benzoic acid or S. cerevisiae, and there may even be advantages for fatty acid composition and oxidative stability when steers were supplemented with benzoic acid.
Competency-Based Assessments: Leveraging Artificial Intelligence to Predict Subcompetency Content
Authors: Booth Gregory J. , Ross Benjamin , Cronin William A. , McElrath Angela , Cyr Kyle L. , Hodgson John A. , Sibley Charles , Ismawan J. Martin , Zuehl Alyssa , Slotto James G. , Higgs Maureen , Haldeman Matthew , Geiger Phillip , Jardine Dink 
Published: December 2022

Purpose
Faculty feedback on trainees is critical to guiding trainee progress in a competency-based medical education framework. The authors aimed to develop and evaluate a Natural Language Processing (NLP) algorithm that automatically categorizes narrative feedback into corresponding Accreditation Council for Graduate Medical Education Milestone 2.0 subcompetencies.

Method
Ten academic anesthesiologists analyzed 5,935 narrative evaluations on anesthesiology trainees at 4 graduate medical education (GME) programs between July 1, 2019, and June 30, 2021. Each sentence (n = 25,714) was labeled with the Milestone 2.0 subcompetency that best captured its content or was labeled as demographic or not useful. Inter-rater agreement was assessed by Fleiss’ Kappa. The authors trained an NLP model to predict feedback subcompetencies using data from 3 sites and evaluated its performance at a fourth site. Performance metrics included area under the receiver operating characteristic curve (AUC), positive predictive value, sensitivity, F1, and calibration curves. The model was implemented at 1 site in a self-assessment exercise.

Results
Fleiss’ Kappa for subcompetency agreement was moderate (0.44). Model performance was good for professionalism, interpersonal and communication skills, and practice-based learning and improvement (AUC 0.79, 0.79, and 0.75, respectively). Subcompetencies within medical knowledge and patient care ranged from fair to excellent (AUC 0.66–0.84 and 0.63–0.88, respectively). Performance for systems-based practice was poor (AUC 0.59). Performances for demographic and not useful categories were excellent (AUC 0.87 for both). In approximately 1 minute, the model interpreted several hundred evaluations and produced individual trainee reports with organized feedback to guide a self-assessment exercise. The model was built into a web-based application.

Conclusions
The authors developed an NLP model that recognized the feedback language of anesthesiologists across multiple GME programs. The model was operationalized in a self-assessment exercise. It is a powerful tool which rapidly organizes large amounts of narrative feedback.
Molecular genotyping in medullary thyroid cancer
Authors: Newbold Kate 
Published: December 2022

Purpose of review
There has been a significant advance in our understanding of the molecular biology of medullary thyroid cancer (MTC) alongside progress in the development of targeted therapies including multikinase and specific rearranged during transfection inhibitors.

Recent findings
This review will examine the latest data investigating the impact of the genomics of MTC on the prediction of the natural history of an individual's disease and the determination, selection and timing of treatment interventions.

Summary
Recent advances in genotyping in MTC and the development of targeted therapies have impacted on the clinical management of both sporadic and hereditary MTC.
Impact of a Pleural Care Program on the Management of Patients With Malignant Pleural Effusions
Authors: Alwakeel Amr J. , Shieh Benjamin , Gonzalez Anne V. , Beaudoin Stéphane 
Published: December 2022

Background:
Malignant pleural effusions (MPEs) are common and associated with a poor prognosis. Yet, many patients face suboptimal management characterized by repeated, nondefinitive therapeutic procedures and potentially avoidable hospital admissions.

Methods:
We conducted a retrospective comparison of patients who underwent a definitive palliative intervention for MPE (indwelling pleural catheter or pleurodesis) at our center, before and after the implementation of a pleural care program. Targeted interventions included staff education, establishment of formal pleural drainage policies, a pleural clinic with weekday walk-in capacity, and a rapid access pathway for oncology patients. Outcomes assessed were the proportion of emergency room (ER) presentations, hospitalizations, number of nondefinitive pleural procedures, and time-to-definitive palliative procedure.

Results:
A total of 144 patients were included: 69 in the preintervention group and 75 in the postintervention group. Although there was no difference in the proportion of ER presentations before and after interventions (43.5% vs. 38.7%, P=0.56), hospital admissions declined significantly (47.8% vs. 24.0%, P=0.003). The proportion of patients undergoing chest drain insertion decreased significantly (46.4% vs. 13.3%, P<0.001), with a stable low number of nondefinitive procedures per patient (1.6±1.1 vs. 1.3±0.9, P=0.32). A 7-day decrease in median time from presentation-to-definitive palliative procedure (P=0.05) was observed.

Conclusion:
A targeted pleural care program improved MPE palliation through reduction in hospitalizations and chest drain use, and shorter time-to-definitive palliation, despite failing to reduce ER presentations.
Burnout Among US Gastroenterologists and Fellows in Training
Authors: Anderson Joseph C. , Bilal Mohammad , Burke Carol A. , Gaidos Jill K. , Lopez Rocio , Oxentenko Amy S. , Surawicz Christina M. 
Published: December 2022

Background:
Consequences of physician burnout include medical errors, higher rate of staff turnover, and decreased patient satisfaction. We examined the prevalence of burnout and identified the contributing factors in gastroenterologists and fellows in training.

Methods:
We performed 3 separate surveys through the American College of Gastroenterology. (1) A national survey of practicing gastroenterologists in the United States that measured burnout and contributing factors, (2) a survey of gastroenterology fellows in training to determine self-identified burnout, as well as mitigating and exacerbating factors, and (3) a follow-up survey of fellows during the COVID-19 pandemic.

Results:
One thousand and twenty-one persons responded (9.2% response rate) to the first survey, including 756 individuals who completed the Maslach Burnout Inventory survey. Overall, the prevalence of high burnout was 49.3%. Factors associated with high burnout included female sex, younger age, shorter duration in practice, considering the electronic health record non–user-friendly, 2 or more hours of patient-related work at home per day, 8 or more hours of outpatient time per day, 6 or more inpatient consults per day, taking call with procedures 10 or more times per year, and having children at home. With regard to lifestyle factors, taking 20 days or more of vacation time was associated with a lower rate of burnout. The level of burnout for fellows was observed to be high (42.7% in survey 2 and 35.3% in survey 3).

Conclusions:
Burnout is high in gastroenterologists and fellows in training. Specific contributing factors were both systems based and personal and provide insight into changes that can be made to address burnout.
Fury: an experimental dynamo with anisotropic electrical conductivity
Authors: Alboussière T. , Plunian F. , Moulin M. 
Published: December 2022

We report measurements of dynamo action in a new experimental set-up, named Fury, based on the use of an anisotropic electrical conductivity. It consists of a copper rotor rotating inside a copper stator, electrically connected with a thin layer of liquid metal, galinstan. Grooves have been cut in the copper so that, everywhere, electrical conductivity can be considered to be that of copper along two directions while it is zero along the third one. The configuration is efficient and dynamo action can be powered by hand. We have also used a motor with better control, enabling us to drive the rotor at specified velocity or torque functions of time. The structure of the axisymmetric magnetic field produced is found to be close to the numerical modelling using FreeFem++. The experimental dynamo behaves very nearly as expected for a kinematic dynamo, so that the threshold dynamo velocity cannot be exceeded, or only briefly. More mechanical power in the rotor rotation leads to an increase in the magnetic field intensity, the magnetic energy being proportional to the extra mechanical power beyond the threshold. In the transient following a step increase of torque, magnetic and angular velocity oscillations have been observed and explained.
Deep Local Analysis deconstructs protein - protein interfaces and accurately estimates binding affinity changes upon mutation
Authors: Behbahani Yasser Mohseni , Laine Elodie , Carbone Alessandra 
Published: December 2022

AbstractThe spectacular recent advances in protein and protein complex structure prediction hold promise for reconstructing interactomes at large scale and residue resolution. Beyond determining the 3D arrangement of interacting partners, modeling approaches should be able to unravel the impact of sequence variations on the strength of the association. In this work, we report on Deep Local Analysis (DLA), a novel and efficient deep learning framework that relies on a strikingly simple deconstruction of protein interfaces into small locally oriented residue-centered cubes and on 3D convolutions recognizing patterns within cubes. Merely based on the two cubes associated with the wild-type and the mutant residues, DLA accurately estimates the binding affinity change for the associated complexes. It achieves a Pearson correlation coefficient of 0.81 on more than 2 000 mutations, and its generalization capability to unseen complexes is higher than the state-of-the-art methods. We show that taking into account the evolutionary constraints on residues contributes to predictions. We also discuss the influence of conformational variability on performance. Beyond the predictive power on the effects of mutations, DLA is a general framework for transferring the knowledge gained from the available non-redundant set of complex protein structures to various tasks. For instance, given a single partially masked cube, it recovers the identity and physico-chemical class of the central residue. Given an ensemble of cubes representing an interface, it predicts the function of the complex. Source code and models are available athttp://gitlab.lcqb.upmc.fr/DLA/DLA.git.
Monopogen: single nucleotide variant calling from single cell sequencing
Authors: Dou Jinzhuang , Tan Yukun , Kock Kian Hong , Wang Jun , Cheng Xuesen , Tan Le Min , Han Kyung Yeon , Hon Chung Chau , Park Woong Yang , Shin Jay W , Chen Han , Prabhakar Shyam , Navin Nicholas , Chen Rui , Chen Ken 
Published: December 2022

AbstractDistinguishing how genetics impact cellular processes can improve our understanding of variable risk for diseases. Although single-cell omics have provided molecular characterization of cell types and states on diverse tissue samples, their genetic ancestry and effects on cellular molecular traits are largely understudied. Here, we developed Monopogen, a computational tool enabling researchers to detect single nucleotide variants (SNVs) from a variety of single cell transcriptomic and epigenomic sequencing data. It leverages linkage disequilibrium from external reference panels to identify germline SNVs from sparse sequencing data and uses Monovar to identify novel SNVs at cluster (or cell type) levels. Monopogen can identify 100K~3M germline SNVs from various single cell sequencing platforms (scRNA-seq, snRNA-seq, snATAC-seq etc), with genotyping accuracy higher than 95%, when compared against matched whole genome sequencing data. We applied Monopogen on human retina, normal breast and Asian immune diversity atlases, showing that that derived genotypes enable accurate global and local ancestry inference and identification of admixed samples from ancestrally diverse donors. In addition, we applied Monopogen on ~4M cells from 65 human heart left ventricle single cell samples and identified novel variants associated with cardiomyocyte metabolic levels and epigenomic programs. In summary, Monopogen provides a novel computational framework that brings together population genetics and single cell omics to uncover genetic determinants of cellular quantitative traits.
Co-occurrence and cooperation between comammox and anammox bacteria in a full-scale attached growth municipal wastewater treatment process
Authors: Vilardi Katherine , Cotto Irmarie , Bachmann Megan , Parsons Mike , Klaus Stephanie , Wilson Christopher , Bott Charles , Pieper Kelsey , Pinto Ameet 
Published: December 2022

ABSTRACTCooperation between comammox and anammox bacteria for nitrogen removal has been recently reported in laboratory-scale systems including synthetic community construct; however, there are no reports of full-scale municipal wastewater treatment systems with such cooperation. Here, we report intrinsic and extant kinetics as well as genome-resolved community characterization of a full-scale integrated fixed film activated sludge (IFAS) system where comammox and anammox bacteria co-occur and appear to drive nitrogen loss. Intrinsic batch kinetic assays indicated that majority of the aerobic ammonia oxidation was driven by comammox bacteria (1.75 ± 0.08 mg-N/g TS-h) in the attached growth phase with minimal contribution by ammonia oxidizing bacteria. Interestingly, a portion of total inorganic nitrogen (∼8%) was consistently lost during these aerobic assays. Aerobic nitrite oxidation assays eliminated the possibility of denitrification as a cause of nitrogen loss, while anaerobic ammonia oxidation assays resulted in rates consistent with anammox stoichiometry. Full-scale experiments at different dissolved oxygen (DO = 2-6 mg/L) set points indicated persistent nitrogen loss that was partly sensitive to DO concentrations. Genome-resolved metagenomics confirmed high abundance (relative abundance 6.53 ± 0.34%) of twoBrocadia-like anammox populations while comammox bacteria within theCa. Nitrospira nitrosa cluster were lower in abundance (0.37% ± 0.03%) andNitrosomonas-like ammonia oxidizers even lower (0.12% ± 0.02%). Collectively, our study reports for the first time the co-occurrence and co-operation of comammox and anammox bacteria in a full-scale municipal wastewater treatment system.SynopsisComammox and anammox cooperation resulted in dissolved oxygen concentration dependent nitrogen loss in municipal wastewater treatment system.