bluuebunny/crossref_metadata_2025_split huggingface dataset:
Keeping and raising zebrafish
Authors: Brand Michael , Granato Michael , Nüsslein-Volhard Christiane 
Published: November 2023

Abstract
Over the past decade, the zebrafish has become an important model organism for biological research. In recent years, more than 1800 zebrafish mutants have been identified, providing a rich resource for the study of embryonic development in vertebrates. An increasing number of laboratories are now starting to use this unique collection of zebrafish mutants for their research. Raising and maintaining zebrafish is more demanding than keeping stocks of invertebrates, but less so than keeping stocks of mammals. This chapter is aimed at giving a background on how to raise mutant and laboratory wild-type stocks and how to maintain them in good breeding conditions. We describe aquarium systems and water conditions as well as procedures to raise and breed zebrafish. While this chapter is aimed primarily at investigators entering the zebrafish field, the recipes and protocols may also provide useful information for experienced zebrafish researchers. The major demands to aquaria systems are posed by the problem of keeping the water in good condition. If the water is not constantly kept clean, the fish will suffer from the toxicity of their own excretions and derivatives thereof. The simplest way to keep the water clean is to keep fish at very low densities and to replace the water at regular intervals. A more elaborate method is to equip the aquaria with biological filters through which the water is circulated and purified. The filters contain material with a large surface area on which bacteria can grow, which degrade toxic ammonium to less toxic nitrates. In larger systems, water from several (often more than 1000) tanks may be recycled through one large common filter (recirculating systems).
Mapping and cloning
Authors: Geisler Robert 
Published: November 2023

Abstract
In order to identify zebrafish genes affected by mutations, both mutations and candidate genes are commonly placed on genome maps (Figure 1). Two types of maps are relevant for this approach: genetic maps, in which the probability of meiotic recombination between markers is used to determine their distance and construct the map; and radiation hybrid maps, in which breakage induced by radiation takes the place of recombination. Mutations can be placed only on genetic maps. This type of map is produced by scoring a large number of polymorphic markers on a panel of F2 fish from a reference cross. Two markers are close to each other if they give a similar pattern of alleles across the panel. Mutations are placed on the map indirectly, by scoring previously mapped markers on a panel of mutant.
RNA editing by cytidine deamination in mammals
Authors: Driscoll Donna M , Innerarity Thomas L 
Published: November 2023

Abstract
The editing of apolipoprotein B (apoB) mRNA was the first example of RNA editing discovered in mammals. The C→U conversion at nucleotide 6666 by a site-specific cytidine deaminase converts a glutamine codon (CAA) to an in-frame stop codon (UAA). apoB is an attractive system for the investigation of RNA editing and processing because the reaction, which can be studied in vitro, involves the modification of a single nucleotide. The past decade has seen tremendous progress in our understanding of the mechanism of apoB mRNA editing. This chapter will focus on the cis-acting sequences that maintain the specificity of editing, the trans-acting factors that mediate this reaction, and the biology of apoB mRNA editing in normal physiology and in transgenic animal models. We hope to provide a historical perspective as well as a discussion of recent developments and controversies in the field.
Bibliographic databases
Authors: Trawick Barton W , McEntyre Johanna R 
Published: November 2023

Abstract
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA. Use of the literature is fundamental to the pursuit of all knowledge. Through searching and reading, we learn what our peers are doing, develop a broader perspective on our field of interest, get: ideas, and confirm our discoveries During the course of twentieth century science, ‘the literature’ has become an expanding knowledge base that represents the collective archive of the work carried out by the international scholarly community. Recent technological advances make an increasing proportion of the literature available electronically (see Figure 1). This chapter offers an introductory guide for molecular biologists to stable bibliographic resources that are available over the Internet.
Internet tools for cell and developmental biologists
Authors: Vize Peter D 
Published: November 2023

Abstract
The type of data generated by cell and developmental biologists is often not well suited to presentation in printed media. How can one depict a migrating cell, vesicular cycling, or embryo gastrulation with a small number of still photographs or data tables? Such dynamic processes are better suited to illustration by active means, and the Internet is an effective system for transmitting information in such forms. Dynamic data forms are not the only ones well served by the Internet-three dimensional networks are also more simple to store, visualize, and maintain using database technology. An example of 3D data sets that are well suited to Internet storage and distribution are cross-talking signal transduction pathways, where simple hyperlinks allow users to jump from pathway to pathway in multiple dimensions. This chapter discusses both general principles and specific techniques of using the Internet for the exploration of cell and developmental biology.
Association Between State Paid Family and Medical Leave and Breastfeeding, Depression, and Postpartum Visits
Authors: Perry Madeline F. , Bui Lilian , Yee Lynn M. , Feinglass Joe 
Published: November 2023

OBJECTIVE:
To evaluate the association of state paid family and medical leave policies with the likelihood of breastfeeding, postpartum depression symptoms, and attendance of the postpartum visit.

METHODS:
This was a cross-sectional study that used 2016–2019 data from PRAMS (Pregnancy Risk Assessment Monitoring System) for 43 states and Washington, DC. We describe the association of state paid family and medical leave generosity with rates of breastfeeding, postpartum depression symptoms, and attendance of the postpartum visit. Logistic and Poisson regression models tested the significance of state paid family and medical leave coverage generosity after controlling for individual respondent sociodemographic characteristics, with sensitivity analyses for respondents with deliveries covered by Medicaid insurance.

RESULTS:
Of the 143,131 respondents, representative of an estimated 7,426,725 population, 26.2% lived in eight states and DC with the most generous paid family and medical leave, 20.5% lived in nine states with some paid family and medical leave, and 53.3% lived in 26 states with little or no paid family and medical leave. Overall, 54.8% reported breastfeeding at 6 months or at time of the survey, ranging from 59.5% in the most generous paid family and medical leave states to 51.0% in states with the least paid family and medical leave coverage. Postpartum depression symptoms varied from 11.7% in the most generous states to 13.3% in the least generous states (both P<.001). State differences in postpartum visit attendance rates (90.9% overall) did not differ significantly. After adjusting for respondent characteristics, compared with states with the least paid family and medical leave, breastfeeding was 9% more likely (adjusted incidence rate ratio [aIRR] 1.09, 95% CI, 1.07–1.11) in states with the strongest paid family and medical leave coverage and 32% more likely (aIRR 1.32, 95% CI, 1.25–1.39) in analyses limited to respondents with deliveries covered by Medicaid insurance. A more generous state paid family and medical leave policy was significantly associated with a lower likelihood of postpartum depression symptoms compared with states with the least paid family and medical leave (adjusted odds ratio 0.85, 95% CI, 0.76–0.94) and a modest but significant increase in postpartum visit attendance (aIRR 1.03, 95% CI, 1.01–1.04) among respondents with deliveries covered by Medicaid insurance.

CONCLUSION:
Respondents from states with strong paid family and medical leave had a greater likelihood of breastfeeding and had lower odds of postpartum depression symptoms, with stronger associations among respondents with deliveries covered by Medicaid insurance. Despite major potential health benefits of paid family and medical leave, the United States remains one of the few countries without federally mandated paid parental leave.
New Persistent Opioid Use After Childbirth
Authors: Zipursky Jonathan S. , Everett Karl , Calzavara Andrew , Gomes Tara , Juurlink David N. 
Published: November 2023

OBJECTIVE:
To examine factors associated with new persistent opioid use after childbirth.

METHODS:
We conducted a population-based cohort study of individuals who initiated opioid therapy within 7 days of discharge from hospital after delivery between September 1, 2013, and September 30, 2021. The primary outcome was new persistent opioid use, which was defined as one or more prescriptions for an opioid within 90 days of the first postpartum prescription and one or more subsequent opioid prescriptions in the 91–365 days afterward. We used multivariable logistic regression to assess patient-, pregnancy-, and prescription-related factors associated with new persistent opioid use after delivery.

RESULTS:
We identified 118,694 unique deliveries after which opioids were initiated, including 99,399 cesarean (83.7%) and 19,295 vaginal (16.3%) deliveries. Among mothers who initiated an opioid after delivery, 1,282 (10.8/1,000 deliveries) met our definition of new persistent opioid use in the subsequent year. Rates of new persistent opioid use were appreciably higher after vaginal (16.0/1,000) compared with cesarean (9.8/1,000) deliveries. Each additional 30 morphine milligram equivalents in the initial opioid prescription was associated with an increased risk of new persistent use after cesarean (adjusted odds ratio [aOR] 1.06, 95% CI 1.04–1.08) and vaginal (aOR 1.05, 95% CI 1.02–1.08) delivery. A concomitant benzodiazepine prescription after cesarean delivery was associated with a markedly increased risk of persistent opioid use (aOR 2.69, 95% CI 1.60–4.52).

CONCLUSION:
Among people who filled an opioid prescription after delivery, about 1% displayed evidence of persistent opioid use in the subsequent year. Initial prescriptions for large quantities of opioids and a concurrent benzodiazepine prescription may be important modifiable risk factors to prevent new persistent opioid use after delivery.
Pre-Delta, Delta, and Omicron Periods of the Coronavirus Disease 2019 (COVID-19) Pandemic and Health Outcomes During Delivery Hospitalization
Authors: Carlson Jeffrey , Simeone Regina M. , Ellington Sascha , Galang Romeo , DeSisto Carla L. , Fleming-Dutra Katherine , Riley Laura , Meaney-Delman Dana , Tong Van T. 
Published: November 2023

OBJECTIVE:
To examine the relationship between coronavirus disease 2019 (COVID-19) diagnosis at delivery and adverse maternal health and pregnancy outcomes during pre-Delta, Delta, and Omicron variant predominance, with a focus on the time period of Omicron variant predominance.

METHODS:
We conducted a cross-sectional observational study with data from delivery hospitalizations in the Premier Healthcare Database from February 2020 to August 2023. The pre-Delta (February 2020–June 2021), Delta (July 2021–December 2021), and Omicron (January 2022–August 2023) periods of variant predominance were examined. Exposure to COVID-19 was identified by having a diagnostic code for COVID-19 during the delivery hospitalization. Adjusted prevalence ratios (aPRs) were calculated to compare the risks of adverse maternal and pregnancy outcomes for women with and without COVID-19 diagnoses at the time of delivery for each variant period.

RESULTS:
Among 2,990,973 women with delivery hospitalizations, 1.9% (n=56,618) had COVID-19 diagnoses noted at delivery admission discharge, including 26,053 during the Omicron period. Across all variant time periods, the prevalence of many adverse maternal and pregnancy outcomes during the delivery hospitalization was significantly higher for pregnant women with COVID-19 compared with pregnant women without COVID-19. In adjusted models, COVID-19 during the Omicron period was associated with significant increased risks for maternal sepsis (COVID-19: 0.4% vs no COVID-19: 0.1%; aPR 3.32, 95% CI, 2.70–4.08), acute respiratory distress syndrome (0.6% vs 0.1%; aPR 6.19, 95% CI, 5.26–7.29), shock (0.2% vs 0.1%; aPR 2.14, 95% CI, 1.62–2.84), renal failure (0.5% vs 0.2%; aPR 2.08, 95% CI, 1.73–2.49), intensive care unit admission (2.7% vs 1.7%; aPR 1.64, 95% CI, 1.52–1.77), mechanical ventilation (0.3% vs 0.1%; aPR 3.15, 95% CI, 2.52–3.93), in-hospital death (0.03% vs 0.01%; aPR 5.00, 95% CI, 2.30–10.90), stillbirth (0.7% vs 0.6%; aPR 1.17, 95% CI, 1.01–1.36), and preterm delivery (12.3% vs 9.6%; aPR 1.28, 95% CI, 1.24–1.33).

CONCLUSION:
Despite the possibility of some level of immunity due to previous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, vaccination, or testing differences, risks of adverse outcomes associated with COVID-19 diagnosis at delivery remained elevated during the Omicron variant time period.
Atrial fibrillation: mechanism and clinical management
Authors: Hu Zhicheng , Ding Ligang , Yao Yan 
Published: November 2023

Abstract
Atrial fibrillation (AF), the most common sustained arrhythmia, is associated with a range of symptoms, including palpitations, cognitive impairment, systemic embolism, and increased mortality. It places a significant burden on healthcare systems worldwide. Despite decades of research, the precise mechanisms underlying AF remain elusive. Current understanding suggests that factors like stretch-induced fibrosis, epicardial adipose tissue (EAT), chronic inflammation, autonomic nervous system (ANS) imbalances, and genetic mutations all play significant roles in its development. In recent years, the advent of wearable devices has revolutionized AF diagnosis, enabling timely detection and monitoring. However, balancing early diagnosis with efficient resource utilization presents new challenges for healthcare providers. AF management primarily focuses on stroke prevention and symptom alleviation. Patients at high risk of thromboembolism require anticoagulation therapy, and emerging pipeline drugs, particularly factor XI inhibitors, hold promise for achieving effective anticoagulation with reduced bleeding risks. The scope of indications for catheter ablation in AF has expanded significantly. Pulsed field ablation, as a novel energy source, shows potential for improving success rates while ensuring safety. This review integrates existing knowledge and ongoing research on AF pathophysiology and clinical management, with emphasis on diagnostic devices, next-generation anticoagulants, drugs targeting underlying mechanisms, and interventional therapies. It offers a comprehensive mosaic of AF, providing insights into its complexities.
An atlas of immune cell transcriptomes in human immunodeficiency virus-infected immunological non-responders identified marker genes that control viral replication
Authors: Chen Yahong , Li Xin , Liu Shuran , Ao Wen , Lin Jing , Li Zhenting , Wu Shouli , Ye Hanhui , Han Xiao , Li Dongliang 
Published: November 2023

Abstract

Background:
Previous studies have examined the bulk transcriptome of peripheral blood immune cells in acquired immunodeficiency syndrome patients experiencing immunological non-responsiveness. This study aimed to investigate the characteristics of specific immune cell subtypes in acquired immunodeficiency syndrome patients who exhibit immunological non-responsiveness.

Methods:
A single-cell transcriptome sequencing of peripheral blood mononuclear cells obtained from both immunological responders (IRs) (CD4+ T-cell count >500) and immunological non-responders (INRs) (CD4+ T-cell count <300) was conducted. The transcriptomic profiles were used to identify distinct cell subpopulations, marker genes, and differentially expressed genes aiming to uncover potential genetic factors associated with immunological non-responsiveness.

Results:
Among the cellular subpopulations analyzed, the ratios of monocytes, CD16+ monocytes, and exhausted B cells demonstrated the most substantial differences between INRs and IRs, with fold changes of 39.79, 11.08, and 2.71, respectively. In contrast, the CD4+ T cell ratio was significantly decreased (0.39-fold change) in INRs compared with that in IRs. Similarly, the ratios of natural killer cells and terminal effector CD8+ T cells were also lower (0.37-fold and 0.27-fold, respectively) in the INRs group. In addition to several well-characterized immune cell-specific markers, we identified a set of 181 marker genes that were enriched in biological pathways associated with human immunodeficiency virus (HIV) replication. Notably, ISG15, IFITM3, PLSCR1, HLA-DQB1, CCL3L1, and DDX5, which have been demonstrated to influence HIV replication through their interaction with viral proteins, emerged as significant monocyte marker genes. Furthermore, the differentially expressed genes in natural killer cells were also enriched in biological pathways associated with HIV replication.

Conclusions:
We generated an atlas of immune cell transcriptomes in HIV-infected IRs and INRs. Host genes associated with HIV replication were identified as markers of, and were found to be differentially expressed in, different types of immune cells.
Implications of the Increasing Convergence of Video Gaming and Gambling: A Narrative Review
Authors: Mills Devin J. , Anthony Wen Li , Lee Uibin , Nower Lia 
Published: November 2023

ABSTRACT
Two of the most popular recreational activities, video gaming and gambling, have converged in a number of different ways including through (1) social casino gaming, (2) loot boxes, (3) skin betting, (4) esports betting, and (5) play-to-earn video gaming. These convergences have brought about concerns, surrounding the increased risk of problems related to excessive use. The present paper reviews the current literature across these 5 areas of convergence, summarizing the implications for policy and future research. The findings from our review generally underscore the modest to strong increase in risk for harms due to these convergences that has important policy implications for regulation. However, much of the research continues to draw from convenience sampling and cross-sectional study designs. Therefore, though concerns regarding continued convergence persist, there is a strong need for further research in this area that utilizes more rigorous methods and employs a broader assessment of both video gaming and gambling engagement.
Deux des activités récréatives les plus populaires, les jeux vidéo et les jeux d’argent, ont convergé de différentes manières, notamment par le biais : (1) des jeux de casino sociaux, (2) des coffres de butin, (3) des paris Skin, (4) des paris sportifs en ligne, et (5) des jeux vidéo où l’on gagne de l’argent. Ces convergences ont suscité des inquiétudes quant au risque accru de problèmes liés à une utilisation excessive. Le présent document passe en revue la littérature actuelle dans ces cinq domaines de convergence, en résumant les implications pour la politique et la recherche future. Les résultats de notre examen soulignent généralement l’augmentation modeste à forte du risque de dommages due à ces convergences, qui a d’importantes implications politiques pour la réglementation. Toutefois, une grande partie de la recherche continue de s’appuyer sur des échantillonnages de commodité et des études transversales. Par conséquent, bien que les inquiétudes concernant la poursuite de la convergence persistent, il est absolument nécessaire de poursuivre les recherches dans ce domaine en utilisant des méthodes plus rigoureuses et en procédant à une évaluation plus large des jeux vidéo et de l’engagement dans les jeux d’argent.
Dose–response analysis of protracted absorbed organ dose and site-specific cancer incidence in Sweden after the Chernobyl nuclear power plant accident
Authors: Tondel Martin , Nordquist Tobias , Isaksson Mats , Rääf Christopher , Wålinder Robert 
Published: November 2023

Background:
Adult males in Sweden exhibit an increased risk of cancer associated with an increased absorbed dose to the colon from the Chernobyl accident.

Methods:
A closed cohort, with information on hunter status, included all individuals living in northern Sweden in 1986. Complete annual information on exposure to 137Cs at the dwelling coordinate was available for a total of 2,104,101 individuals. A nested case-control method with four controls matched for year of cancer diagnosis and year of birth, was used. Individual absorbed organ doses were calculated between 1986 and 2020 including external and internal exposure. Hazard ratios (HR) per mGy with 95% confidence intervals (95% CI) were calculated using conditional logistic regression adjusted for rural/nonrural habitat, education level and pre-Chernobyl cancer incidence 1980 to 1985. A total of 161,325 cancer cases in males and 144,439 in females were included.

Results:
The adjusted HR per mGy for all cancer sites combined was 1.027 (95% CI = 1.022, 1.031) in males and 1.011 (95% CI = 1.006, 1.017) in females. In a post hoc analysis accounting for both remaining confounding from hunter lifestyle and the pre-Chernobyl cancer incidence by county, the adjusted HR per mGy for all cancer sites combined was 1.014 (95% CI = 1.009, 1.019) in males and 1.000 (95% CI = 0.994, 1.006) in females. The post hoc analysis suggested an increased risk of cancer in the colon, pancreas, and stomach, respectively, in males, and lymphoma in females.

Conclusions:
Increased cancer risk estimates were found for some specific cancer sites but remaining uncontrolled confounding due to hunter lifestyle could not be ruled out.