bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence and pandemic spread of small ruminant lentiviruses
Authors: Carrozza Maria-Luisa , Niewiadomska Anna-Maria , Mazzei Maurizio , Abi-Said Mounir R , Hué Stéphane , Hughes Joseph , Gatseva Anna , Gifford Robert J 
Published: January 2023

Abstract
Small ruminant lentiviruses (SRLVs) cause chronic, persistent infections in populations of domestic sheep (Ovis aries) and goats (Capra hircus) worldwide. The vast majority of SRLV infections involve two genotypes (A and B) that spread in association with the emergence of global livestock trade. However, SRLVs have likely been present in Eurasian ruminant populations since at least the early Neolithic period. Here, we use phylogenetic and phylogeographic approaches to reconstruct the origin of pandemic SRLV strains and infer their historical pattern of global spread. We constructed an open computational resource (‘Lentivirus-GLUE’) via which an up-to-date database of published SRLV sequences, multiple sequence alignments (MSAs), and sequence-associated metadata can be maintained. We used data collated in Lentivirus-GLUE to perform a comprehensive phylogenetic investigation of global SRLV diversity. Phylogenies reconstructed from genome-length alignments reveal that the deep divisions in the SRLV phylogeny are consistent with an ancient split into Eastern (A-like) and Western (B-like) lineages as agricultural systems disseminated out of domestication centres during the Neolithic period. These findings are also consistent with historical and phylogeographic evidence linking the early 20th century emergence of SRLV-A to the international export of Central Asian Karakul sheep. Investigating the global diversity of SRLVs can help reveal how anthropogenic factors have impacted the ecology and evolution of livestock diseases. The open resources generated in our study can expedite these studies and can also serve more broadly to facilitate the use of genomic data in SRLV diagnostics and research.
Anti-Müllerian Hormone Level Decline in Patients Undergoing Hysterectomy With and Without Oophorectomy Compared With Natural Menopause
Authors: Santoro Nanette , Flyckt Rebecca , Davis Anne , Finkelstein Joel , Crawford Sybil , Sun Fangbai , Derby Carol , Morrison Anthony , Sluss Patrick , Zhang Heping 
Published: January 2023

OBJECTIVE:
To evaluate the relationship between hysterectomy with and without ovarian conservation and the onset of ovarian failure using anti-müllerian hormone (AMH) levels and imputed final menstrual period (FMP).

METHODS:
A total of 1,428 women with an observed FMP and 232 women who underwent hysterectomy (159 with bilateral salpingo-oophorectomy [BSO], 13 with one ovary conserved, and 60 with both ovaries conserved) and who had serial AMH measurements were included from SWAN (The Study of Women’s Health Across the Nation), a multi-ethnic, multi-site, community-based study. Anti-müllerian hormone levels were sampled annually with at least one presurgery or pre-FMP measurement at least one postsurgery or post-FMP measurement. Surgery-related differences in patterns of AMH levels with respect to surgery date or FMP were estimated using piecewise linear mixed modeling; differences in age at first undetectable AMH level were estimated using survival analyses.

RESULTS:
Patients with conservation of one or both ovaries or natural menopause demonstrated similar patterns of decline in AMH levels when anchored to surgery or FMP. Patients with hysterectomy (all types) had a later counterfactual FMP (52.9±0.2 SEM) compared with the observed FMP in those with natural menopause (52.1±0.1 years, P=.002). Those undergoing BSO had an immediate reduction in AMH level to undetectable after surgery.

CONCLUSION:
Hysterectomy does not lead to a more rapid decline in AMH levels postoperatively compared with natural menopause. Patients undergoing BSO have a rapid loss of AMH, consistent with complete removal of the ovaries. These data suggest that hysterectomy as currently performed does not compromise ovarian reserve.
Pharmacologic Interventions to Minimize Fluid Absorption at the Time of Hysteroscopy
Authors: Désilets Jade , Zakhari Andrew , Chagnon Miguel , Ekmekjian Taline , Nguyen Dong Bach , Smith Jessica Papillon , Mansour Fady W. , Krishnamurthy Srinivasan 
Published: January 2023

OBJECTIVE:
To assess which interventions are effective in reducing fluid absorption at the time of hysteroscopy.

DATA SOURCE:
Ovid MEDLINE, Ovid EMBASE, PubMed (non-MEDLINE records only), EBM Reviews—Cochrane Central Register of Controlled Trials (CENTRAL), ClinicalTrials.gov, and Web of Science were searched from inception to February 2022 without restriction on language or geographic origin.

METHODS OF STUDY SELECTION:
Following PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, all English-language, full-text articles reporting fluid balance, with an intervention and comparator arm, were included. Title and abstract screening and full-text review were completed independently by two authors. Conflicts were resolved through discussion and consensus. Studies' risk of bias was assessed using the Cochrane Risk of Bias Tool for RCTs and the Newcastle-Ottawa Scale for observational studies.

TABULATION, INTEGRATION, AND RESULTS:
The search identified 906 studies, 28 of which were eligible for inclusion, examining the following interventions: gonadotropin-releasing hormone (GnRH) agonist; ulipristal acetate; vasopressin; danazol; oxytocin; and local, general, and regional anesthesia. A significant reduction in mean fluid absorption was seen in patients preoperatively treated with danazol (−175.7 mL, 95% CI −325.4 to −26.0) and a GnRH agonist (−139.68 mL, 95% CI −203.2, −76.2) compared with patients in a control group. Ulipristal acetate and type of anesthesia showed no difference. Data on type of anesthesia and vasopressin use were not amenable to meta-analysis; however, four studies favored vasopressin over control regarding fluid absorption. Mean operative time was reduced after preoperative treatment with ulipristal acetate (−7.1 min, 95% CI −11.31 to −2.9), danazol (−7.5 min, 95% CI −8.7 to −6.3), and a GnRH agonist (−3.3 min, 95% CI −5.6 to −0.98).

CONCLUSION:
Preoperative treatment with a GnRH agonist and danazol were both found to be effective in reducing fluid absorption and operative time across a range of hysteroscopic procedures. High-quality research aimed at evaluating other interventions, such as combined hormonal contraception, progestin therapy, and vasopressin, are still lacking in the literature.

SYSTEMATIC REVIEW REGISTRATION:
PROSPERO, CRD42021233804.
Association Between Publicly Funded Contraceptive Services and the Abortion Rate in Texas, 2010–2015
Authors: Madison Anita M. , Powers Daniel , Maslowsky Julie , Goyal Vinita 
Published: January 2023

OBJECTIVE:
To evaluate how the availability of contraceptive services was associated with a change in the abortion rate before and after Texas' legislative changes to the family planning budget in 2011 and abortion access in 2013.

METHODS:
In this cross-sectional study, we obtained 2010 and 2015 data on contraceptive provision (number of publicly funded clinics and number of contraceptive clients served per 1,000 reproductive-aged women) from the Guttmacher Institute and county-level abortion data from the Texas Department of State Health Services. We categorized counties as having an abortion rate that increased or declined less than the national rate between 2010 and 2015 (low-decline counties) compared with those having an abortion rate that declined equal to or greater than the national rate between 2010 and 2015 (high-decline counties). We evaluated differences in contraceptive provision between high-decline and low-decline counties and evaluated county characteristics (racial and ethnic composition, unemployment, poverty, uninsured, education, distance to an abortion clinic, deliveries covered by Medicaid, and Catholic hospital marketplace dominance) as potential confounders.

RESULTS:
Of 157 counties that had at least one contraceptive clinic in either 2010 or 2015, 49 were low-decline counties and 108 were high-decline counties. Although the total number of publicly funded family planning clinics increased by 10.8%, there was a 4.7% decrease in the total number of contraceptive clients served statewide. Compared with low-decline counties, high-decline counties had a higher median number of contraceptive clients served per 1,000 women aged 18–44 years (31.9 vs 60.7, P<.05) in 2015. Between 2010 and 2015, the abortion rate decreased 19.7% for each 1.0% increase in contraceptive clients served.

CONCLUSION:
Texas counties with higher abortion-rate declines had more publicly funded contraceptive clinics and served more contraceptive clients than counties with lower declines, which may indicate the importance of greater access to publicly funded contraceptive services.
Predictors of Self-Management Behaviors After Discharge Among Unplanned Dialysis Patients
Authors: KAO Yu-Yin , LEE Chien-Te , WANG Ruey-Hsia 
Published: January 2023

ABSTRACT

Background
Patients with unplanned dialysis must perform self-management behaviors to maintain their health in the community after discharge. Understanding the factors that predict the postdischarge self-management behaviors of patients with unplanned dialysis can assist nurses to implement appropriate discharge plans for this population.

Purpose
This study was designed to predict the effects of uncertainty in illness, self-care knowledge, and social-support-related needs during hospitalization on the self-management behaviors of patients with unplanned dialysis during their first 3 months after discharge from the hospital.

Methods
One hundred sixty-nine patients with unplanned dialysis from the nephrology department of a medical center in Taiwan were enrolled in this prospective study using convenience sampling. At hospital admission, demographic, uncertainty in illness, self-care knowledge, and social support information was collected using a structured questionnaire. Information on self-management behavior was collected at 3 months postdischarge when the patients visited outpatient clinics.

Results
Hierarchical multiple regression analyses showed that self-care knowledge, uncertainty in illness, and social support were important predictors of self-management behaviors at 3 months postdischarge, explaining 65.6% of the total variance in self-management behaviors. Social support increased the variance in self-management behaviors by 27.9%.

Conclusions/Implications for Practice
Comprehensive discharge planning to improve the postdischarge self-management behaviors of patients with unplanned dialysis should involve interventions to improve self-care knowledge, reduce uncertainty in illness, and increase social support. Building social support should be given priority attention.
Who decides? Consent for healthcare decisions of minors in the United States
Authors: Stettner Nichole M. , Lavelle Ella N. , Cafferty Patrick 
Published: January 2023

Purpose of review
The purpose of this review is to examine when parents and legal guardians have the authority to make medical decisions on behalf of the minors in their care, when the decisions of healthcare professionals may supersede those of parents and guardians, and under what conditions minors can make healthcare decisions for themselves.

Recent findings
The coronavirus disease 2019 (COVID-19) pandemic has reignited discussion of who should make healthcare decisions for minors. Though serious adverse reactions to COVID-19 vaccines are rare, hesitancy toward pediatric COVID-19 vaccination is prevalent among parents in the United States. This has contributed to large numbers of minors who are not up-to-date or not fully vaccinated against severe acute respiratory syndrome coronavirus 2 infection. Surveys reveal a majority of minors in the United States are willing to receive a COVID-19 vaccine. A number of scholars have recommended allowing adolescents the ability to consent to COVID-19 vaccination without parental approval.

Summary
Allowing adolescents with a minimum age of 15 to consent to vaccination without parental or guardian approval will more quickly enable adolescents to receive new vaccines as they become available, such as the COVID-19 bivalent vaccine.
Association Between Fear of Cancer Recurrence, Fatigue, and Healthy Lifestyle Behaviors Among Breast Cancer Survivors in South Korea
Authors: Jun Hye Suk , Lee Kyungmi 
Published: January 2023

Background
Improving healthy lifestyle behaviors in breast cancer survivors can promote their physical and mental health, thereby reducing the risk of cancer recurrence. Therefore, it is crucial to identify and control the factors affecting healthy lifestyle behaviors among breast cancer survivors.

Objective
This study aimed to examine the effects of physiological, psychological, and situational factors and symptoms on healthy lifestyle behaviors in breast cancer survivors.

Methods
Data were collected from August to September 2021, and a questionnaire was administered through an online breast cancer patient community’s bulletin board. Finally, 162 questionnaires were included in the analysis.

Results
The model was statistically significant, explaining 33.2% of the variance. A decrease in healthy lifestyle behaviors in breast cancer survivors was influenced by an age of 40 years or younger, 5 years or more since a breast cancer diagnosis, low income, fear of cancer recurrence, and fatigue.

Conclusions
Intervention strategies, such as easily accessible online content that accounts for age and survival period after cancer diagnosis, should be used to promote healthy lifestyle behaviors among breast cancer survivors. Healthcare providers should be given appropriate guidelines on managing patients’ fear of cancer recurrence and reducing fatigue to ensure timely access to clinical interventions. Adequate financial support from local communities and governments is needed to promote healthy lifestyle behaviors.

Implications for Practice
To improve breast cancer survivors’ healthy lifestyle behaviors, an understanding of the influencing factors and a multidimensional approach are required. Nurses play a role in developing and implementing interventions to improve healthy lifestyle behaviors.
Predictive Value of Ablative Margin Assessment After Microwave Ablation for Local Tumor Progression in Medium and Large Hepatocellular Carcinoma: Computed Tomography–Computed Tomography Image Fusion Method Versus Side-by-Side Method
Authors: Zhou Hongyu , Yang Guanghao , Jing Xiang , Zhou Yan , Ding Jianmin , Wang Yandong , Wang Fengmei , Zhao Lei 
Published: January 2023

Objective
This study aimed to explore the feasibility and predictive value for local tumor progression (LTP) of the computed tomography (CT)–CT image fusion method versus side-by-side method to assess ablative margin (AM) in hepatocellular carcinoma ≥3 cm in diameter.

Materials and Methods
We selected patients with hepatocellular carcinoma ≥3 cm in diameter who underwent microwave ablation and had complete tumor ablation. We used the CT-CT image fusion method and side-by-side method to assess AM separately and divided the lesions into 3 groups: group I, minimum ablative margin (min-AM) <0 mm (the ablation zone did not fully cover the tumor); group II, 0 mm ≤ min-AM <5 mm; and group III, min-AM ≥5 mm.

Results
A total of 71 patients involving 71 lesions were included. The κ coefficient for the agreement between the CT-CT image fusion method and the side-by-side method in assessing min-AM was 0.14 (P = 0.028). Cumulative LTP rate was significantly different between groups by min-AM from the CT-CT image fusion method (P < 0.05) but not by min-AM from the side-by-side method (P = 0.807). Seventeen of the 20 LTP lesions were located at min-AM on fused CT images, with consistency rate of 85%.

Conclusions
Compared with the side-by-side method, the CT-CT image fusion method is more accurate in assessing the AM of eccentrically ablated lesions and shows better predictive value for LTP. The min-AM based on CT-CT image fusion assessment is an important influencing factor for LTP.
ouR Space Commentary: Wellness Perspective From SABI’s Early Career Committee
Authors: Chaurasia Aditi , Yu Lei , Kim Nancy , Wentland Andrew , Pirasteh Ali 
Published: January 2023

Abstract
Radiologists and members-in-training are experiencing higher (and escalating) rates of burnout, resulting in a profound impact on the health of physicians, patients, and the community. Lately, the radiology community has demonstrated a growing awareness of this phenomenon, which has led to emphasis on practicing and promoting wellness. With a myriad of factors contributing to burnout in radiology, a multifaceted approach is pivotal for counteracting burnout and fostering overall well-being, including efforts driven at both organizational and individual levels. This article discusses perspectives from the members of the Early Career Committee at the Society for Advanced Body Imaging (SABI); it explores their beliefs and practical strategies for maintaining personal well-being.
Divergent ecological responses to typhoon disturbance revealed via landscape-scale acoustic monitoring
Authors: Ross Samuel R.P-J. , Friedman Nicholas R. , Dudley Kenneth L. , Yoshida Takuma , Yoshimura Masashi , Economo Evan P. , Armitage David W. , Donohue Ian 
Published: January 2023

AbstractClimate change is increasing the frequency, intensity, and duration of extreme weather events across the globe. Understanding the capacity for ecological communities to withstand and recover from such events is critical. Typhoons are extreme weather events that are expected to broadly homogenise ecological dynamics through structural damage to vegetation and longer-term effects of salinization. Given their unpredictable nature, monitoring ecological responses to typhoons is challenging, particularly for mobile animals such as birds. Here, we report spatially variable ecological responses to typhoons across terrestrial landscapes. Using a high temporal resolution passive acoustic monitoring network across 24 sites on the subtropical island of Okinawa, Japan, we found that typhoons elicit divergent ecological responses among Okinawa’s diverse terrestrial habitats, as indicated by increased spatial variability of biological sound production (biophony) and individual species detections. This suggests that soniferous communities are capable of a diversity of different responses to typhoons. That is, spatial insurance effects among local ecological communities provide resilience to typhoons at the landscape scale. Even though site-level typhoon impacts on soundscapes and bird detections were not particularly strong, monitoring at scale with high temporal resolution across a broad spatial extent nevertheless enabled detection of spatial heterogeneity in typhoon responses. Further, species-level responses mirrored those of acoustic indices, underscoring the utility of such indices for revealing insight into fundamental questions concerning disturbance and stability. Our findings demonstrate the significant potential of landscape-scale acoustic sensor networks to capture the understudied ecological impacts of unpredictable extreme weather events.
MaGplotR: a software for the analysis and visualization of multiple MaGeCK screen datasets through aggregation
Authors: Matía Alejandro , Lorenzo Maria M. , Peng Duo 
Published: January 2023

ABSTRACTMotivationMaGplotR analyzes multiple CRISPR screen datasets, identifies common hits, couples the hits to enrichment analysis and cluster plots, and produces publication-level plots. Output plots give information on the quality control of the screen data (e.g., sgRNA distribution) and show the best hits by aggregation from multiple screen experiments. To maximize comparability, rank is used to identify common hits. MaGplotR can also be used to analyze experiments where a control condition is used for multiple treatment conditions. MaGplotR is easy to use, with even just one argument.Availability and implementationMaGplotR is open-source code under MIT license. It is available athttps://github.com/alematia/MaGplotR.Contactalejandro.matia@inia.csic.es
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat
Authors: Zhao Wei , Johnston Kevin G. , Ren Honglei , Xu Xiangmin , Nie Qing 
Published: January 2023

AbstractNeural communication networks form the fundamental basis for brain function. These communication networks are enabled by emitted ligands such as neurotransmitters, which activate receptor complexes to facilitate communication. Thus, neural communication is fundamentally dependent on the transcriptome. Here we develop NeuronChat, a method and package for the inference, visualization and analysis of neural-specific communication networks among pre-defined cell groups using single-cell expression data. We incorporate a manually curated molecular interaction database of neural signaling for both human and mouse, and benchmark NeuronChat on several published datasets to validate its ability in predicting neural connectivity. Then, we apply NeuronChat to three different neural tissue datasets to illustrate its functionalities in identifying interneural communication networks, revealing conserved or context-specific interactions across different biological contexts, and predicting communication pattern changes in diseased brains with autism spectrum disorder. Finally, we demonstrate NeuronChat can utilize spatial transcriptomics data to infer and visualize neural-specific cell-cell communication.
KOMPUTE: Imputing summary statistics of missing phenotypes in high-throughput model organism data
Authors: Warkentin Coby , O’Connell Michael J. , Lee Donghyung 
Published: January 2023

AbstractMotivationThe International Mouse Phenotyping Consortium (IMPC) is striving to build a comprehensive functional catalog of mammalian protein-coding genes by systematically producing and phenotyping gene-knockout mice for almost every protein-coding gene in the mouse genome and by testing associations between gene loss-of-function and phenotype. To date, the IMPC has identified over 90,000 gene-phenotype associations, but many phenotypes have not yet been measured for each gene, resulting in largely incomplete data; about 75.6% of association summary statistics are still missing in the latest IMPC summary statistics dataset (IMPC release version 16).ResultsTo overcome these challenges, we propose KOMPUTE, a novel method for imputing missing summary statistics in the IMPC dataset. Using conditional distribution properties of multivariate normal, KOMPUTE estimates association Z-scores of unmeasured phenotypes for a particular gene as a conditional expectation given the Z-scores of measured phenotypes. We evaluate the efficacy of the proposed method for recovering missing Z-scores using simulated and real-world data sets and compare it to a singular value decomposition (SVD) matrix completion method. Our results show that KOMPUTE outperforms the comparison method across different scenarios.Availability and implementationAn R package for KOMPUTE is publicly available athttps://github.com/statsleelab/kompute, along with usage examples and results for different phenotype domains athttps://statsleelab.github.io/komputeExamples.Contactleed13@miamioh.eduSupplementary informationSupplementary data are available atBioinformaticsonline.