bluuebunny/crossref_metadata_2025_split huggingface dataset:
Case report: Two rare uterine cesarean scar mass cases
Authors: Zhao Xiumin , Huang Danjiang , Yan Dewen , Dai Xingxing , Wang Liping 
Published: March 2023

Rationale:
Gestational trophoblastic neoplasia (GTN) located in the cesarean scar is a rare disease that has imaging appearances similar to those of an exogenous scar incision pregnancy and is often misdiagnosed due to insufficient clinical experience.

Patient concerns:
We report 2 cases of uterine cesarean scar mass. Two patients with different diagnoses had similar clinical complaints as abnormal vaginal bleeding, enlargement of uterus isthmus by physical examination, and mixed echo mass in uterine low segment by ultrasound examination; however, their magnetic resonance imaging images showed very different features.

Diagnoses:
One patient was diagnosed with cesarean scar pregnancy (CSP) and one patient was diagnosed with cesarean scar GTN.

Interventions:
The CSP patient underwent surgery by laparoscopy combined with hysteroscopy after uterine artery embolism and obtained pathological confirmation. The GTN patient received chemotherapy.

Outcomes:
For the CSP patient, her serum β-human chorionic gonadotropin (hCG) concentration returned to normal 2 weeks later, and B-ultrasound showed that the niche was completely repaired 3 months after the operation. The intrauterine lesions of the GTN patient disappeared completely 3 months after serum β-hCG normalization. And her β-hCG was normal at all follow-up visits until now.

Lessons:
Clinicians should consider GTN when identifying masses at scar incision sites. Magnetic resonance imaging images improve the understanding of the imaging features in patients suspected of having CSP/GTN.
Identifying occupational health and safety risks among environmental health officers in Australia and New Zealand through an online survey
Authors: Dine Garry , Reed Sue , Oosthuizen Jacques , Masaka Edmore 
Published: March 2023

To identify the occupational health and safety (OHS) risks among environmental health officers (EHOs) in Australia and New Zealand. The objectives were to profile and compare OHS experiences from different countries and regions to gain a regional perspective on OHS hazards that impact EHOs.
An online hazard exposure survey was conducted among 339 EHOs (Australia: n = 301, 88.8%; New Zealand: n = 38, 11.2%). The Mann–Whitney U test was used to compare 2 ordinal data groups, the Kruskal–Wallis H test was used for more than 2 ordinal groups, and the independent samples t test was used to compare the means of 2 independent groups where the dependent variables were normally distributed. Multiple regression techniques were used to analyze workplace incidents and age groups. A high degree of similarity in the types of workplace exposures and risk perceptions as well as concerns with organizational OHS management commitment were observed among EHOs from the 2 countries. Workplace violence and physical and psychosocial demands were the most commonly reported OHS hazards. Employer type, sex, and age group were significantly related to workplace exposure and OHS experience among EHOs in both countries. This study provides a profile of workplace exposure in the environmental health profession in the 2 countries and offers recommendations for the implementation of preventive action.
Early versus late surgical intervention for cervical spinal cord injury: A protocol for systematic review and meta-analysis
Authors: Yang Chaowei , Yang Xinming 
Published: March 2023

Background:
Acute traumatic cervical spinal cord injury (SCI) is a catastrophic event with substantial physical, emotional, and economic burdens to patients, families, and society. Spinal cord decompression is recommended for the treatment of acute SCI. However, the optimal surgical timing remains controversial. Therefore, we perform a protocol for systematic review and meta-analysis to compare the efficacy of early and late surgical intervention for acute SCI.

Methods:
This systematic review and meta-analysis follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols statement, which have been registered in advance in the International prospective register of systematic reviews (registration number: CRD42023397592). We will search the following databases for randomized controlled trials: the Cochrane Skin Group Trials Register, MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials, Chinese Biomedical Literature Database, Chinese Medical Current Content, and China National Knowledge Infrastructure. The risk of bias of the included studies will be appraised using the Cochrane Collaboration tool for randomized controlled trials. Statistical analysis will be performed using IBM SPSS Statistics (Armonk, NY).

Result:
The results of this systematic review will be published in a peer-reviewed journal.

Conclusion:
This systematic review will provide evidence regarding the optimal timing for spinal cord decompression in patients with acute SCI.
Multidisciplinary nutritional management improves nutritional and hospitalized outcomes of patients with esophageal cancer undergoing chemoradiotherapy: A randomized control trial
Authors: Wang Shu-An , Li Fuchao , Zhu Jiayu , Chen Xiaotian , Ren Wei , Gao Bo 
Published: March 2023

Background:
This study aimed to investigate the effects of multidisciplinary whole-course nutrition management on the nutritional status and complications during the course of treatment in patients with esophageal cancer (EC) undergoing chemoradiotherapy.

Methods:
A total of 36 EC patients undergoing chemoradiotherapy were divided into a control group (n = 18) and an intervention group (n = 18). Participants in the control group were given routine nutritional support, whereas those in the intervention group were provided whole-course nutrition management from the nutrition support team. Nutrition-related indicators, that is, serum albumin level (ALB), hemoglobin (Hb), and C reactive protein were assessed before, during, and after treatment in both groups. The incidence of complications (e.g., lymphocytopenia, radiation esophagitis, and myelosuppression), clinical outcomes, length of hospital stay, and hospital costs were also recorded. Differences between the 2 groups were tested using the Mann–Whitney U and chi-square tests.

Results:
The ALB and Hb levels of the patients in the control group decreased significantly [ALB: −2.6 (−5.6, 0), P = .01; Hb: −12.0 (−27.0, −2.0), P = .04] and C reactive protein increased [8.9 (2.9, 14.9), P = .02] compared to those before treatment, while the indicators of participants in the intervention group did not change (P > .05). The incidence of grade ≥ II lymphocytopenia was higher in the control group than that in the intervention group (33.3% vs 61.1%, P = .03). Moreover, compared with the control group, the average length of hospital stay decreased by 12 days [47 (40, 50) vs 35 (23, 40), P = .001], and in-patient expenses decreased by 20,504 CNY in the intervention group (P = .004).

Conclusion:
Multidisciplinary whole-course nutrition management can maintain the nutritional status of patients with EC undergoing chemoradiotherapy. This may lower the incidence of complications, shorten hospital stays, and reduce in-patient expenses.
The association between statin use and prognosis in esophageal cancer patients: A meta-analysis
Authors: Lv Jing , Chen Peirui , Wu Jianqiang , Wen Zhi , Zhao Changming 
Published: March 2023

Background:
The impact of statin use on the survival of esophageal cancer patients remains unclear now. The aim of this study was to identify the relationship between statin use and the long-term survival of esophageal cancer patients.

Methods:
The PubMed, EMBASE, and Web of Science databases were searched up to August 20, 2022, for relevant studies. The endpoints included overall survival (OS), cancer-specific survival (CSS), recurrence-free survival, and hazard ratios (HRs) with corresponding 95% confidence intervals (CIs) were pooled to assess the association between statin use and the prognosis of esophageal cancer patients. Subgroup analysis based on the pathological type (adenocarcinoma vs squamous cell carcinoma), dose of statin use and tumor stage (tumor-node-metastasis I–III vs IV) was further performed. All statistical analyses were conducted using STATA 12.0 software.

Results:
A total of 7 retrospective studies involving 25,711 participants were included in this meta-analysis. The pooled results indicated that statin use was significantly associated with improved OS (HR = 0.80, 95% CI: 0.74–0.87, P < .001), CSS (HR = 0.77, 95% CI: 0.74–0.89, P < .001), and recurrence-free survival (HR = 0.38, 95% CI: 0.16–0.87, P = .022). Furthermore, subgroup analysis stratified by the pathological type, dose of statin use and tumor stage for OS and CSS showed similar results and indicated the protective role of statin use in the prognosis of esophageal cancer patients.

Conclusion:
Statin use is significantly associated with improved long-term survival of esophageal cancer patients and might serve as a promising prognostic indicator in esophageal cancer. However, more prospective high-quality studies are still needed to verify our findings.
Vibration Controlled Transient Elastography to Evaluate Steatosis in Candidate Living Donors for Liver Transplantation
Authors: Palte Eytan , Duong Jimmy K. , Remotti Helen , Burt Joseph , Makkar Jasnit , Samstein Benjamin , Verna Elizabeth C. , Marratta Douglas , Emond Jean C. , Fox Alyson N. 
Published: March 2023

Background.
The ability of vibration controlled transient elastography (VCTE) to reliably exclude significant steatosis in living donor candidates could obviate the need for invasive liver biopsies, expedite the donor approval process, and reduce recipient wait time. We therefore aimed to determine whether VCTE controlled attenuation parameter (CAP) could be used to detect steatosis in potential living donors.

Methods.
Living donor candidates who presented for evaluation between 2016 and 2019 underwent standard donor workup, VCTE, and liver biopsy if indicated. CAP scores were compared with MRI-Fat Fraction and, when available, histologic fat fraction from liver biopsy. Receiver operating characteristic curves were used to identify cutoffs with appropriate sensitivity and specificity for screening. Statistical analysis was conducted using R (version 3.6.0).

Results.
Seventy-nine candidate living donors presented during the study period, of whom 71 were included in the final analysis and of whom 20 underwent liver biopsy. There was a positive correlation between MRI-Fat Fraction and CAP scores with an observed Spearman correlation coefficient of 0.424 (P < 0.01). A CAP score of 271.5 dB/m or less was determined to have 89.8% sensitivity and 75% specificity for detecting <5% steatosis on MRI. The correlation between CAP and steatosis of available histologic samples had a Pearson correlation coefficient of 0.603 (P = 0.005). A CAP cutoff of 276.0 dB/m demonstrated 66.7% sensitivity and 85.7% specificity for detecting <15% histopathologic steatosis and positive and negative predictive values of 71.5% and 82.7%, respectively.

Conclusions.
VCTE can be integrated into living donor evaluation to accurately screen for hepatic steatosis.
Statistical inference with exchangeability and martingales
Authors: Holmes Chris C. , Walker Stephen G. 
Published: March 2023

In this paper, we start by reviewing exchangeability and its relevance to the Bayesian approach. We highlight the predictive nature of Bayesian models and the symmetry assumptions implied by beliefs of an underlying exchangeable sequence of observations. By taking a closer look at the Bayesian bootstrap, the parametric bootstrap of Efron and a version of Bayesian thinking about inference uncovered by Doob based on martingales, we introduce a parametric Bayesian bootstrap. Martingales play a fundamental role. Illustrations are presented as is the relevant theory.This article is part of the theme issue ‘Bayesian inference: challenges, perspectives, and prospects’.
The e-posterior
Authors: Grünwald Peter D. 
Published: March 2023

We develop a representation of a decision maker’s uncertainty based on e-variables. Like the Bayesian posterior, thise-posteriorallows for making predictions against arbitrary loss functions that may not be specified ex ante. Unlike the Bayesian posterior, it provides risk bounds that have frequentist validity irrespective of prior adequacy: if the e-collection (which plays a role analogous to the Bayesian prior) is chosen badly, the bounds get loose rather than wrong, makinge-posterior minimaxdecision rules safer than Bayesian ones. The resulting quasi-conditional paradigm is illustrated by re-interpreting a previous influential partial Bayes-frequentist unification,Kiefer–Berger–Brown–Wolpert conditional frequentist tests, in terms of e-posteriors.This article is part of the theme issue ‘Bayesian inference: challenges, perspectives, and prospects’.
Deep bootstrap for Bayesian inference
Authors: Nie Lizhen , Ročková Veronika 
Published: March 2023

For a Bayesian, the task to define the likelihood can be as perplexing as the task to define the prior. We focus on situations when the parameter of interest has been emancipated from the likelihood and is linked to data directly through a loss function. We survey existing work on both Bayesian parametric inference with Gibbs posteriors and Bayesian non-parametric inference. We then highlight recent bootstrap computational approaches to approximating loss-driven posteriors. In particular, we focus on implicit bootstrap distributions defined through an underlying push-forward mapping. We investigate independent, identically distributed (iid) samplers from approximate posteriors that pass random bootstrap weights through a trained generative network. After training the deep-learning mapping, the simulation cost of such iid samplers is negligible. We compare the performance of these deep bootstrap samplers with exact bootstrap as well as MCMC on several examples (including support vector machines or quantile regression). We also provide theoretical insights into bootstrap posteriors by drawing upon connections to model mis-specification.This article is part of the theme issue ‘Bayesian inference: challenges, perspectives, and prospects’.
Feasibility Study of Ferumoxtyol for Contrast-enhanced MRI of Retroplacental Clear Space Disruption in Placenta Accreta Spectrum (PAS)
Authors: Badachhape Andrew A. , Burnett Brian , Bhandari Prajwal , Devkota Laxman , Bhavane Rohan , Ghaghada Ketan B. , Yallampalli Chandrasekhar , Fox Karin A. , Annapragada Ananth V. 
Published: March 2023

AbstractIntroductionPlacenta accreta spectrum (PAS) occurs when the placenta is pathologically adherent to the myometrium. An intact retroplacental clear space (RPCS) is a marker of normal placentation, but visualization with conventional imaging techniques is a challenge. In this study, we investigate use of an FDA-approved iron oxide nanoparticle, ferumoxytol, for contrast-enhanced magnetic resonance imaging of the RPCS in mouse models of normal pregnancy and PAS. We then demonstrate the translational potential of this technique in human patients presenting with severe PAS (FIGO Grade 3C), moderate PAS (FIGO Grade 1), and no PAS.MethodsA T1-weighted gradient recalled echo (GRE) sequence was used to determine the optimal dose of ferumoxytol in pregnant mice. Pregnant Gab3-/-mice, which demonstrate placental invasion, were then imaged at day 16 of gestation alongside wild-type (WT) pregnant mice which do not demonstrate invasion. Signal-to-noise ratio (SNR) was computed for placenta and RPCS for all fetoplacental units (FPUs) with ferumoxytol-enhanced magnetic resonance imaging (Fe-MRI) and used for the determination of contrast-to-noise ratio (CNR). Fe-MRI was also performed in 3 pregnant subjects using standard T1 and T2 weighted sequences and a 3D magnetic resonance angiography (MRA) sequence. RPCS volume and relative signal were calculated in all three subjects.ResultsFerumoxytol administered at 5 mg/kg produced strong T1 shortening in blood and led to strong placental enhancement in Fe-MRI images. Gab3-/-mice demonstrated loss of hypointense region characteristic of the RPCS relative to WT mice in T1w Fe-MRI. CNR between RPCS and placenta was lower in FPUs of Gab3-/-mice compared to WT mice, indicating higher degrees of vascularization and interruptions throughout the space. In human patients, Fe-MRI at a dose of 5 mg/kg enabled high uteroplacental vasculature signal and quantification of the volume and signal profile in severe and moderate invasion of the placenta relative to a non-PAS case.DiscussionFerumoxytol, an FDA-approved iron oxide nanoparticle formulation, enabled visualization of abnormal vascularization and loss of uteroplacental interface in a murine model of PAS. The potential of this non-invasive visualization technique was then further demonstrated in human subjects. Diagnosis of placental invasion using Fe-MRI may provide a sensitive method for clinical detection of PAS.
The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation inC. elegans
Authors: Emerson Felicity J. , Chiu Caitlin , Lin Laura Y. , Riedel Christian G. , Zhu Ming , Lee Siu Sylvia 
Published: March 2023

AbstractSET-26, HCF-1, and HDA-1 are highly conserved chromatin factors with key roles in development and aging. Here we present mechanistic insights into how these factors regulate gene expression and modulate longevity inC. elegans. We show that SET-26 and HCF-1 cooperate to regulate a common set of genes, and both antagonize the histone deacetylase HDA-1 to limit longevity. We propose a model in which SET-26 recruits HCF-1 to chromatin in somatic cells, where they stabilize each other at the promoters of a subset of genes, particularly mitochondrial function genes, and regulate their expression. HDA-1 opposes SET-26 and HCF-1 on the regulation of a subset of their common target genes and in longevity. Our findings suggest that SET-26, HCF-1, and HDA-1 comprise a mechanism to fine-tune gene expression and longevity and likely have important implications for the mechanistic understanding of how these factors function in diverse organisms, particularly in aging biology.
Flexible parsing, interpretation, and editing of technical sequences with splitcode
Authors: Sullivan Delaney K. , Pachter Lior 
Published: March 2023

AbstractNext-generation sequencing libraries are constructed with numerous synthetic constructs such as sequencing adapters, barcodes, and unique molecular identifiers. Such sequences can be essential for interpreting results of sequencing assays, and when they contain information pertinent to an experiment, they must be processed and analyzed. We present a tool called splitcode, that enables flexible and efficient parsing, interpreting, and editing of sequencing reads. This versatile tool facilitates simple, reproducible preprocessing of reads from libraries constructed for a large array of single-cell and bulk sequencing assays.Availability and ImplementationThe splitcode program is free, open source, and available for download athttp://github.com/pachterlab/splitcode.
VMAP: Vaginal Microbiome Atlas During Pregnancy
Authors: Parraga-Leo Antonio , Oskotsky Tomiko T. , Oskotsky Boris , Wibrand Camilla , Roldan Alennie , Tang Alice , Ha Connie W.Y. , Wong Ronald J. , Minot Samuel S. , Andreoletti Gaia , Kosti Idit , Theis Kevin R. , Ng Sherrianne , Lee Yun S. , Diaz-Gimeno Patricia , Bennett Phillip R. , MacIntyre David A. , Lynch Susan V. , Romero Roberto , Tarca Adi L. , Stevenson David K. , Aghaeepour Nima , Golob Jonathan , Sirota Marina 
Published: March 2023

AbstractThe vaginal microbiome has been shown to be associated with pregnancy outcomes including preterm birth (PTB) risk. Here we present VMAP: Vaginal Microbiome Atlas during Pregnancy (http://vmapapp.org), an application to visualize features of 3,909 vaginal microbiome samples of 1,416 pregnant individuals from 11 studies, aggregated from raw public and newly generated sequences via an open-source tool, MaLiAmPi. Our visualization tool (http://vmapapp.org) includes microbial features such as various measures of diversity, VALENCIA community state types (CST), and composition (via phylotypes and taxonomy). This work serves as a resource for the research community to further analyze and visualize vaginal microbiome data in order to better understand both healthy term pregnancies and those associated with adverse outcomes.
An extended wave of global mRNA deadenylation sets up a switch in translation regulation across the mammalian oocyte-to-embryo transition
Authors: Lee Katherine , Cho Kyucheol , Morey Robert , Cook-Andersen Heidi 
Published: March 2023

AbstractThe oocyte-to-embryo transition (OET) occurs in the absence of new transcription and relies on post-transcriptional gene regulation, including translational control by mRNA poly(A) tail regulation, where cytoplasmic polyadenylation activates translation and deadenylation leads to translational repression and decay. However, how the transcriptome-wide landscape of mRNA poly(A) tails shapes translation across the OET in mammals remains unknown. Here, we performed long-read RNA sequencing to uncover poly(A) tail lengths and mRNA abundance transcriptome-wide in mice across five stages of development from oocyte to embryo. Integrating these data with recently published ribosome profiling data, we demonstrate that poly(A) tail length is coupled to translational efficiency across the entire OET. We uncover an extended wave of global deadenylation during fertilization, which sets up a switch in translation control between the oocyte and embryo. In the oocyte, short-tailed maternal mRNAs that resist deadenylation in the oocyte are translationally activated, whereas large groups of mRNAs deadenylated without decay in the oocyte are later readenylated to drive translation activation in the early embryo. Our findings provide an important resource and insight into the mechanisms by which cytoplasmic polyadenylation and deadenylation dynamically shape poly(A) tail length in a stage-specific manner to orchestrate development from oocyte to embryo in mammals.