bluuebunny/crossref_metadata_2025_split huggingface dataset:
A randomized trial and multisite pooled trial analyses comparing effects of two hormonal implant programs and differing days-on-feed on carcass characteristics and feedlot performance of beef heifers
Authors: Horton Lucas M , Depenbusch Brandon E , Holland Ben P , Word Alyssa B , Streeter Marshall N , Hutcheson John P , Renter David G 
Published: December 2022

Abstract
Research objectives were to evaluate effects of two implant programs for beef heifers fed three different durations (days-on-feed; DOF) on carcass weight and composition (primary outcomes) and feedlot performance (secondary outcomes) at commercial feedlots. Data from a randomized trial in Kansas were analyzed separately and also pooled with data from two previously published trials conducted in Texas. Heifers were randomly allocated to pens within a block, and pens were randomized to treatments in a 2 × 3 factorial randomized complete block design. Implant programs were IH + 200 – an initial Revalor-IH implant [80 mg trenbolone acetate (TBA) and 8 mg estradiol (E2)] and a re-implant after a mean of 98-d (± 10.8 SD) with Revalor-200 (200 mg TBA and 20 mg E2), or XH – Revalor-XH, a single extended-release implant (200 mg TBA and 20 mg E2). Heifers were fed to a baseline endpoint (BASE; pooled mean 166-d ± 11.9 SD), +21, or +42 additional DOF. A total of 10,583 crossbred heifers with mean initial body weight (BW) 315 kg (± 20.1 SD) were enrolled in 144 pens in 24 blocks (treatment replications) across the three trials. General and generalized linear mixed models accounting for clustering of trials, blocks, and pens were used to test for effects of treatments, with significance set at α = 0.05. The only implant program × DOF interaction in pooled analyses was for dry matter intake (DMI; P &lt; 0.01); IH + 200 heifers had lower mean DMI than XH when fed +42 DOF. Gain:feed was higher for IH + 200 compared to XH with dead and removed animals excluded (P &lt; 0.01) or included (P = 0.03). For IH + 200, hot carcass weight (HCW) increased (P &lt; 0.01), USDA Yield Grade (YG) distributions shifted towards lower numerical categories (P &lt; 0.01), and Prime carcasses decreased while Select increased compared to XH (P &lt; 0.01). For each incremental increase in DOF, final BW (P &lt; 0.01) and HCW increased (P &lt; 0.01), while daily gain (P &lt; 0.01) and gain:feed (P &lt; 0.01) decreased. Categories of YG were affected by DOF (P &lt; 0.01); there were fewer YG 1 and 2 and more YG 4 and 5 carcasses for +42 compared to BASE and +21. USDA Quality Grade (QG) distributions differed by DOF (P &lt; 0.01); each incremental increase in DOF resulted in more Prime and fewer Select carcasses. Without meaningful interactions, tested implant programs likely have a consistent effect when heifers are fed to similar DOF, while changes in HCW, QG, and YG may influence marketing decisions when extending DOF.
Association of maternal temperament and offspring disposition on growth performance
Authors: Sims Michael , Cauble Reagan N , Powell Jeremy , Kegley Beth , Foote Andrew P , Salak-Johnson Janeen L , Beck Paul 
Published: December 2022

Abstract
Animal behavior is complex and varies in definition, depending upon specific traits under observation. Temperament is one component of behavior, that in cattle, is described as the level of fearfulness to a novel or threatening environment. Temperament is a heritable trait which is important since aggressiveness and docility contribute to reproductive success, growth, and carcass quality. We observed maternal temperament at calving and the subsequent influence, if any, on offspring disposition at weaning and their effects collectively on growth performance and carcass traits. Maternal behaviors at calving were observed at four locations within the University of Arkansas system. Cows were assigned a maternal disposition score (MDS) at calving; a scale from 1 to 5 in which aggression decreases. At weaning, calves were assigned a chute score (CS); a scale from 1 to 6 in which aggression increases. Both scoring systems have been previously established. Blood was collected during the 56-d backgrounding period postweaning for blood glucose analysis. Data were analyzed using GLIMMIX procedures of SAS (α = 0.05). The relationship between the two scoring systems was determined with a Pearson correlation (P = 0.22). Animal was the experimental unit and blocked by location for all dependent variables. Location, sex, diet, and MDS were included in the class as covariables for all growth performance and carcass data related to CS. Cows that were more aggressive birthed heavier calves (P &lt; 0.01) compared to indifferent cows. Calves born to cows with either very aggressive or very attentive (MDS of 2 or 3, respectively) scores were heavier upon feedlot entry (P = 0.03) compared to those from indifferent or apathetic cows (MDS of 4 or 5, respectively). Calves defined as nervous and restless (CS of 3 and 2, respectively) were heavier at weaning compared to docile calves (P &lt; 0.01). Restless calves were heavier compared to nervous calves upon arrival and exiting the feedlot (P ≤ 0.01). Calves that were docile at weaning had greater marbling compared to calves that were restless (P ≤ 0.01). Calves that were restless at weaning had greater lean muscle area compared to calves that were nervous (P = 0.05). No definitive relationship was determined between dam and calf temperament. However, the results suggest temperament does impact growth performance and carcass traits but whether the influence comes from the dam or calf temperament, specifically, remains unanswered.
Genome Sequence Resource of Fusarium graminearum TaB10 and Fusarium avenaceum KA13, Causal Agents of Stored Apple Rot
Authors: Petreš Mladen , Hrustić Jovana , Vučinić Nataša , Ma Li-Jun , Ayhan Dilay Hazal , Grahovac Mila 
Published: December 2022

The filamentous fungus Fusarium graminearum is a well-known cereal pathogen and F. avenaceum is a pathogen with a wide host range. Recently, both species were reported as causal agents of apple rot, raising concerns about postharvest yield losses and mycotoxin contamination. Here, we report genome assemblies of F. avenaceum KA13 and F. graminearum TaB10, both isolated from fruits with symptoms of apple rot. The final F. avenaceum KA13 genome sequence assembly of 41.7 Mb consists of 34 scaffolds, with an N50 value of 2.2 Mb and 15,886 predicted genes. The total size of the final F. graminearum TaB10 assembly is 36.76 Mb, consisting of 54 scaffolds with an N50 value of 1.7 Mb, and it consists of 14,132 predicted genes. These new genomes provide valuable resources to better understand plant-microbe interaction in stored apple rot disease. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Complete Genome Sequence of Xanthomonas citri subsp. citri CQ13, an Alternative Model Strain to Study Citrus Bacterial Canker in China
Authors: Wu Yonglin , Lv Weiwei , Chen Hongyu , Ge Yifei , Liu Chaoying , Ding Xiaojun , Zou Xiuping , Hu Junhua , Li Jingyu , Wang Jihua , Zhang Yunzeng , Zhou Xiaofeng 
Published: December 2022

Xanthomonas citri subsp. citri is a quarantine organism causing citrus bacterial canker in many countries. Sharing research materials worldwide became difficult due to local administrative regulations, which hindered the continuity of studies on this disease. Here, we report a complete genome sequence of X. citri subsp. citri strain CQ13 achieved using a combination of Illumina and Nanopore platforms. The CQ13 genome comprises a circular chromosome (5,142,501 bp; G + C content 64.83%) and two circular plasmids, pXAC33 and pXAC64 (34,102 bp and 64,942 bp; G + C content 61.96 and 61.41%, respectively). Annotation revealed 4,243 protein-coding sequences, six rRNA genes, 53 tRNA genes, 40 ncRNA genes, and 168 pseudogenes. Notably, the analyses of average nucleotide identity, host range, pathogenicity, and type III effector repertoire suggest that CQ13 is particularly closely related to the current model strain 306. Therefore, strain CQ13 could serve as an alternative model strain, and its genome sequence could provide a valuable resource for citrus canker research in China. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Out-of-State Students at State Medical Schools and Increasing Medical Education Debt
Authors: Kraus Molly B. , Hasan Shaina H. , Buckner-Petty Skye A. , Files Julia A. , Hayes Sharonne N. , Habermann Elizabeth B. , LeMond Lisa M. 
Published: December 2022

Purpose
Medical school tuition has increased at alarming rates ahead of inflation over the past 20 years. The authors investigated whether state-funded medical schools have had an increased number of out-of-state matriculants, which may create a diaspora of displaced in-state medical students matriculating to out-of-state programs and incurring substantial debt.

Method
Publicly available data from the Association of American Medical Colleges (AAMC) were accessed from 2004 through 2019 for applicants and matriculants at U.S. state-funded schools. Schools listed as public that reported tuition charges in the AAMC Tuition and Student Fees reports were included in this study. The numbers and trends of medical school applications and trends in tuition costs and average indebtedness were summarized for in-state and out-of-state matriculants. Values were analyzed by group as median and interquartile range (IQR). Group differences were assessed via t tests. P values less than .05 were considered statistically significant.

Results
From 2004 through 2019, the annual number of out-of-state matriculants in state-funded schools increased 7% (16%–23% [7,195–11,144]). Among 74 schools with data in 2004, the median percentage of out-of-state applications increased from 60% (IQR, 31%–74%) to 80% (IQR, 57%–85%; P < .001), and the median percentage of out-of-state matriculants increased from 13% (IQR, 5%–23%) to 17% (IQR, 11%–33%; P < .001). In 2004, the mean (standard error) debt upon completion of medical school (inflation adjusted to 2018 dollars) was $144,100 ($10,950); by 2016, the mean debt had increased to $251,600 ($32,040), a 75% increase over 12 years.

Conclusions
Since 2004, substantial increases have occurred in out-of-state matriculants at state-funded medical schools. This may displace residents from attending their in-state schools, causing them to attend out-of-state or private medical schools, where tuition is typically much higher.
Equal Pay for Equal Work in the Dean Suite: Addressing Occupational Gender Segregation and Compensation Inequities Among Medical School Leadership
Authors: Gottlieb Amy S. , Dandar Valerie M. , Lautenberger Diana M. , Best Cynthia , Jagsi Reshma 
Published: December 2022

In 2022, the Association of American Medical Colleges published data from its annual Dean’s Office Staff Compensation and Dean’s Compensation Surveys in a new report addressing salary equity among medical school leadership. These data, disaggregated by gender and race/ethnicity, represent earnings of the senior most leaders in the dean suite and have historically been shared only with medical school Deans and principal business officers. The report shows that the highest-ranking decanal positions in U.S. medical schools are filled along the lines of traditional gender stereotypes (with men in clinical affairs and research affairs deanships and women in admissions, diversity affairs, faculty affairs, and student affairs deanships) and that the roles held mostly by men carry grander titles (e.g., senior associate dean vs assistant dean) and significantly higher salaries than those typically held by women. Additionally, within the same decanal positions, women earn lower median compensation than men.
In this commentary, the authors describe limited advancement and lower compensation as foregone conclusions for women in medicine and science due to a professional model that places a premium on activities traditionally pursued by men. They define and characterize the impact of this occupational gender segregation in the dean suite and offer a roadmap for an alternative value system that recognizes complementary leadership activities across the mission areas of academic medicine and ensures that the contributions of women in the profession are appropriately recognized, valued, and rewarded.
Predictors of Complications after Breast Reconstruction Surgery: A Systematic Review and Meta-analysis
Authors: Mrad Mohamed Amir , Al Qurashi Abdullah A. , Shah Mardan Qutaiba N.M. , Alqarni Mohammed D. , Alhenaki Ghazlan A. , Alghamdi Muath S. , Fathi Abdulaziz B. , Alobaidi Hussain A. , Alnamlah Abdulrahman A. , Aljehani Saif K. , Daghistani Ghadeer , Alsharif Thamer Hamad 
Published: December 2022

Background:
Breast reconstruction (BR) is a unique surgical procedure that provides patients undergoing mastectomy with significant psychosocial and aesthetic benefits and has also become a crucial part of the treatment pathway for women with breast cancer. Due to methodological inadequacies and the absence of substantial risk factor analysis, no conclusion can be drawn about the correlation between risk variables and post-surgical complications in BR surgery. We aim to identify the potential risk factors associated with postoperative complications.

Methods:
We queried MEDLINE and Cochrane CENTRAL from their inception to March 2022, for published randomized controlled trials and observational studies that assessed complications post-reconstruction procedure in breast cancer patients following mastectomy or evaluated at least one of the following outcomes of major or reoperative complications. The results from the studies were presented as odds ratios with 95% confidence intervals and were pooled using a random-effects model.

Results:
Our pooled analysis demonstrated a significant correlation with BR postoperative complications and risk factors such as diabetes, hypertension, and obesity. Diabetes and the development of seroma were found to have a significant relationship. Risk variables such as age, radiotherapy, COPD, and smoking had no significant connection with 0-to-30-day readmission and 30-to-90-day readmission.

Conclusion:
This meta-analysis shows that risk factors like age, smoking history, high blood pressure, and body mass index (BMI) have a big effect on complications after BR, and patients with risk factors have a high rate of developing infection.
Matrix Metalloproteinases 2 and 9 and Their Tissue Inhibitors in the Diagnostics of Medullary Thyroid Carcinoma
Authors: Vázquez-Lorente Héctor , Dunđerović Duško M. , Tatić Svetislav B. , Radojević-Škodrić Sanja , Gomes Cláudio M. , Paunović Ivan R. , Dragutinović Vesna 
Published: December 2022

Medullary Thyroid Carcinoma (MTC) is a tumor of the neuroendocrine system. In recent years, the need to assess the MTC diagnostic-related parameters has emerged with the aim to elucidate the mechanisms involved in this pathology. The objective of this study was to evaluate the role of Matrix Metalloproteinases (MMPs) 2 and 9, their tissue inhibitors of matrix metalloproteinases (TIMPs), S100 protein, and amyloid in the diagnostic of MTC. Thirty-two samples with MTC (72% women) were included in this cross-sectional study and divided by groups: T category 1 (T1)≤20 mm and T category 2 (T2) 20 to 40 mm of tumor size. MMPs 2 and 9, TIMPs 2 and 1, S100 protein, and calcitonin in tissues were obtained by immunohistochemical techniques. The presence of amyloid in tissue sections was detected on Thioflavin T–stained slides under fluorescent microscope. Percentage of positive cells (P) observed for MMP-2 was higher in those samples presenting T2 MTC with respect to those with T1 MTC (P<0.05). Moreover, P-MMP-2 showed a direct correlation with higher T category of MTC (Rho=0.439, P < 0.001), whereas P-MPP-9 was directly correlated with S100 protein and the intensity of calcitonin in tissues (Rho=0.419, P=0.017; Rho=0.422, P=0.016, respectively. Therefore, MMPs were directly correlated with some traditional biomarkers of MTC. In this regard, P-MMP-2 was more expressed in type 2 MTC. Combining the analysis of traditional and other useful biomarkers of MTC as MMPs 2 and 9 could be a useful strategy in the diagnostic of MTC.
Characterization, and in vitro antibacterial activity of sulfated polysaccharides from freshwater algae Cladophora crispata
Authors: jasem mohanad , Merai Abd- Alwahab , Nizam Adnan Ali 
Published: December 2022

Barada River is characterized by an abundant growth of freshwater algae. In light of the increased interest in algae to find new sources of bioactive compounds, this research, aimed to extract sulfated Polysaccharides (SPs) from freshwater green algae Cladophoracrispata using ultrasonic-assisted extraction methods after cultivates it by the outdoor method. Also we determined and selected its compounds,and we investigation effect SPs as antibacterial agent After extraction, Sephadex gel G-100 was used for the Purification of SPs, where the purifcation gave two fractions, namley F1 and F2. The chemical characterization of crud SPs and its fractions were investigated. The highest carbohydrate and protein contents were found in crude SPs with the ratios of 74.12%, and 4.02%, respectively, while the highest sulfate content 12.17% was found in fraction 2, and the higest uronic content 18.46% was found in fraction 1. Fourier transforms infrared Spectroscopy (FT-IR) used for confirmed the crud and fractions consist of sugar, uronic acids, protein unite, and sulfate groups. Both F1, and F2 consist of rhamnose, galactose, xylose, and ribose based on separation on the High performance liquid chromatography (HPLC). Each fraction has inhibitory effect on bacteria negative and positive gram. F2 have the lowest minimization inhabit concentration (MIC) value against Enterobacteraerogenes and Staphylococcusaureus; where MIC were 28 and 10 mg/ml respectively. Polysaccharides had the most important interest because they have antibacterial properties, making them inter in pharmacy and food applications.
Estimating the epidemic reproduction number from temporally aggregated incidence data: a statistical modelling approach and software tool
Authors: Nash Rebecca K , Cori Anne , Nouvellet Pierre 
Published: December 2022

BackgroundThe time-varying reproduction number (Rt) is an important measure of epidemic transmissibility; it can directly inform policy decisions and the optimisation of control measures. EpiEstim is a widely used software tool that uses case incidence and the serial interval (SI, time between symptoms in a case and their infector) to estimate Rtin real-time. The incidence and the SI distribution must be provided at the same temporal resolution, which limits the applicability of EpiEstim and other similar methods, e.g. for pathogens with a mean SI shorter than the frequency of incidence reporting.MethodsWe use an expectation-maximisation algorithm to reconstruct daily incidence from temporally aggregated data, from which Rtcan then be estimated using EpiEstim. We assess the validity of our method using an extensive simulation study and apply it to COVID-19 and influenza data. The method is implemented in the opensource R package EpiEstim.FindingsFor all datasets, the influence of intra-weekly variability in reported data was mitigated by using aggregated weekly data. Rtestimated on weekly sliding windows using incidence reconstructed from weekly data was strongly correlated with estimates from the original daily data. The simulation study revealed that Rtwas well estimated in all scenarios and regardless of the temporal aggregation of the data. In the presence of weekend effects, Rtestimates from reconstructed data were more successful at recovering the true value of Rtthan those obtained from reported daily data.InterpretationRtcan be successfully recovered from aggregated data, and estimation accuracy can even be improved by smoothing out administrative noise in the reported data.FundingMRC doctoral training partnership, MRC centre for global infectious disease analysis, the NIHR HPRU in Modelling and Health Economics, and the Academy of Medical Sciences Springboard, funded by the AMS, Wellcome Trust, BEIS, the British Heart Foundation and Diabetes UK.
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes
Authors: Zhu Wensi , Shenoy Aditi , Kundrotas Petras , Elofsson Arne 
Published: December 2022

AbstractMotivationDespite near-experimental accuracy on single-chain predictions, there is still scope for improvement among multimeric predictions. Methods like AlphaFold-Multimer and FoldDock can accurately model dimers. However, how well these methods fare on larger complexes is still unclear. Further, evaluation methods of the quality of multimeric complexes are not well established.ResultsWe analysed the performance of AlphaFold-Multimer on a homology-reduced dataset of homo- and heteromeric protein complexes. We highlight the differences between the pairwise and multi-interface evaluation of chains within a multimer. We describe why certain complexes perform well on one metric (e.g., TM-score) but poorly on another (e.g., DockQ). We propose a new score, Predicted DockQ version 2 (pDockQ2), to estimate the quality of each interface in a multimer. Finally, we modelled protein complexes (from CORUM) and identified two highly confident structures that do not have sequence homology to any existing structures.AvailabilityAll scripts, models, and data used to perform the analysis in this study are freely available athttps://gitlab.com/ElofssonLab/afm-benchmark.Contactarne@bioinfo.seSupplementary informationSupplementary data are available atBioinformaticsonline.
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
Authors: Cavlak Meryem Banu , Singh Gagandeep , Alser Mohammed , Firtina Can , Lindegger Joël , Sadrosadati Mohammad , Ghiasi Nika Mansouri , Alkan Can , Mutlu Onur 
Published: December 2022

Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art basecallers employ complex deep learning models to achieve high basecalling accuracy. This makes basecalling computationally-inefficient and memory-hungry; bottlenecking the entire genome analysis pipeline. However, for many applications, the majority of reads do no match the reference genome of interest (i.e., target reference) and thus are discarded in later steps in the genomics pipeline, wasting the basecalling computation.To overcome this issue, we propose TargetCall, the first fast and widely-applicable pre-basecalling filter to eliminate the wasted computation in basecalling. TargetCall’s key idea is to discard reads that will not match the target reference (i.e., off-target reads) prior to basecalling. TargetCall consists of two main components: (1) LightCall, a lightweight neural network basecaller that produces noisy reads; and (2) Similarity Check, which labels each of these noisy reads as on-target or off-target by matching them to the target reference. TargetCall filters out all off-target reads before basecalling; and the highly-accurate but slow basecalling is performed only on the raw signals whose noisy reads are labeled as on-target.Our thorough experimental evaluations using both real and simulated data show that TargetCall 1) improves the end-to-end basecalling performance of the state-of-the-art basecaller by 3.31 × while maintaining high (98.88%) sensitivity in keeping on-target reads, 2) maintains high accuracy in downstream analysis, 3) precisely filters out up to 94.71% of off-target reads, and 4) achieves better performance, sensitivity, and generality compared to prior works. We freely open-source TargetCall to aid future research in pre-basecalling filtering athttps://github.com/CMU-SAFARI/TargetCall.