bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction to Fieldwork and Evolution
Authors: Crawford Michael H 
Published: March 2024

Abstract
Field research is an essential tool of anthropological genetics. What constitutes fieldwork and why is it done? This chapter poses the questions: Who are we? Where did we come from? How did we get here? It summarizes the background and necessary experience for successfully conducting field research. How are multidisciplinary field investigations on human evolution organized? How are the accompanying specialists selected for the fieldwork? Methods of contacting the indigenous communities are discussed and how participants are informed about the risks and benefits of the research. This chapter defines the forces of evolution (mutations, genetic drift, natural selection, and gene flow) and considers the consequences of each force examined.
Background and Preparation for Fieldwork
Authors: Crawford Michael H 
Published: March 2024

Abstract
This chapter discusses the preparation necessary for conducting successful international fieldwork. Travel experience, cultural and linguistic background (in Russian or appropriate languages), and training in biological anthropology and genetics at the University of Washington provided useful preparation. Residence under extreme conditions, such as survival for nine months while living in a tent in a displaced persons camp in the tropical Philippine Islands, while coexisting with mosquitos, snakes and insects, prepared the author for field research in Siberia and Central America. The organization of research teams with experience in writing grant proposals and conducting field research encourages funding from granting agencies, such as the National Science Foundation and the National Institutes of Health. Professional productivity and recognition by scientific organizations facilitates obtaining necessary permissions from participating communities, and governmental organizations.
Black Caribs (Garifuna) of Central America
Authors: Crawford Michael H 
Published: March 2024

Abstract
The Black Caribs (Garifuna) are part of an evolutionary success story. They arose on St. Vincent Island as an amalgam of Native Americans from the Orinoco River Basin of South America and west African slaves. British forcibly transplanted the Garifuna first to Ballicaux Island (small island south of St. Vincent) and then to the Bay Islands close to Honduras. From the Bay Islands the Garifuna relocated to Honduras and because of high fertility and availability of resources, the population expanded rapidly and formed 54 villages spread geographically from Belize to Nicaragua. Initially, blood group data were initially collected for Livingston, Guatemala, and St. Vincent Island. Later studies in Honduras, Belize, Guatemala, and Bay Islands included DNA markers—mitochondrial DNA, nonrecombining Y-chromosome, and autosomal single nucleotide polymorphisms and short tandem repeats. Genetic ancestry, admixture, and population structure were reconstructed for the Garifuna populations.
Genetic Epidemiology
Authors: Crawford Michael H 
Published: March 2024

Abstract
The baboon colony of the Sukhumi Primate Center of Abkhasia displayed a massive increase in the infection from malignant lymphoma. Baboons were initially inoculated with human blood samples from lymphoma patients. The question we posed: Was this lymphoma the result of a virus introduced from a human host? Did the virus spread through the colony through social contact and bites? Unlike the colony of free-ranging baboons, on the outskirts of Sukhumi, they show no signs of the lymphoma. The simian T cell lymphoma virus (STLV-1) appears to be the etiological agent of the Sukhumi lymphoma outbreak. However, based on sequence similarities of baboon and macaque viruses, it appears that interspecies transmission had occurred between the two primate genera and species.
Too simple, too complex, or just right? Advantages, challenges, and guidance for indicators of genetic diversity
Authors: Hoban Sean , da Silva Jessica M , Hughes Alice , Hunter Margaret E , Kalamujić Stroil Belma , Laikre Linda , Mastretta-Yanes Alicia , Millette Katie , Paz-Vinas Ivan , Bustos Lucia Ruiz , Shaw Robyn E , Vernesi Cristiano ,   the Coalition for Conservation Genetics, Funk Chris , Grueber Catherine , Kershaw Francine , MacDonald Anna , Meek Mariah , Mittan Cinnamon , O'Brien David , Ogden Rob , Segelbacher Gernot 
Published: March 2024

Abstract
Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritizing species and populations to preserve and recover genetic diversity (e.g., via genetic rescue). Recently, indicators were developed for tracking and reporting genetic diversity status and trends for hundreds of species. The indicators quantify two simple proxies of within-population and among-population genetic diversity and adaptive potential: small effective population size (Ne &lt; 500) and the loss of genetically distinct populations. The indicators must balance scientific credibility, practicality, and simplicity. In the present article, we summarize the advantages of these pragmatic indicators, address critiques by scientists for simplifying assumptions and by policymakers for complexity, and propose potential solutions and next steps. We aim to support practitioners putting indicators into policy, action, legislation, and reporting.
A cell autonomous regulator of neuronal excitability modulates tau in Alzheimer’s disease vulnerable neurons
Authors: Rodriguez-Rodriguez Patricia , Arroyo-Garcia Luis Enrique , Tsagkogianni Christina , Li Lechuan , Wang Wei , Végvári Ákos , Salas-Allende Isabella , Plautz Zakary , Cedazo-Minguez Angel , Sinha Subhash C , Troyanskaya Olga , Flajolet Marc , Yao Vicky , Roussarie Jean-Pierre 
Published: March 2024

Abstract
Neurons from layer II of the entorhinal cortex (ECII) are the first to accumulate tau protein aggregates and degenerate during prodromal Alzheimer’s disease. Gaining insight into the molecular mechanisms underlying this vulnerability will help reveal genes and pathways at play during incipient stages of the disease. Here, we use a data-driven functional genomics approach to model ECII neurons in silico and identify the proto-oncogene DEK as a regulator of tau pathology.
We show that epigenetic changes caused by Dek silencing alter activity-induced transcription, with major effects on neuronal excitability. This is accompanied by the gradual accumulation of tau in the somatodendritic compartment of mouse ECII neurons in vivo, reactivity of surrounding microglia, and microglia-mediated neuron loss. These features are all characteristic of early Alzheimer’s disease.
The existence of a cell-autonomous mechanism linking Alzheimer’s disease pathogenic mechanisms in the precise neuron type where the disease starts provides unique evidence that synaptic homeostasis dysregulation is of central importance in the onset of tau pathology in Alzheimer’s disease.
Hybrid Immunity and SARS-CoV-2 Antibodies: Results of the HEROES–RECOVER Prospective Cohort Study
Authors: Romine James K , Li Huashi , Coughlin Melissa M , Jones Jefferson M , Britton Amadea , Tyner Harmony L , Fuller Sammantha B , Bloodworth Robin , Edwards Laura J , Etolue Jini N , Morrill Tyler C , Newes-Adeyi Gabriella , Olsho Lauren E W , Gaglani Manjusha , Fowlkes Ashley , Hollister James , Bedrick Edward J , Uhrlaub Jennifer L , Beitel Shawn , Sprissler Ryan S , Lyski Zoe , Porter Cynthia J , Rivers Patrick , Lutrick Karen , Caban-Martinez Alberto J , Yoon Sarang K , Phillips Andrew L , Naleway Allison L , Burgess Jefferey L , Ellingson Katherine D 
Published: March 2024

Abstract

Background
There are limited data on whether hybrid immunity differs by count and order of immunity-conferring events (infection with severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] or vaccination against coronavirus disease 2019 [COVID-19]). From a multi-site cohort of frontline workers, we examined the heterogeneity of the effect of hybrid immunity on SARS-CoV-2 antibody levels.

Methods
Exposures included event count and event order, categorized into 7 permutations. Outcome was level of serum antibodies against receptor-binding domain (RBD) of the ancestral SARS-CoV-2 spike protein (total RBD-binding immunoglobulin). Means were examined up to 365 days after each of the first to seventh events.

Results
Analysis included 5793 participants measured from 7 August 2020 to 15 April 2023. Hybrid immunity from infection before 1 or 2 vaccine doses elicited modestly superior antibody responses after the second and third events (compared with infections or vaccine doses alone). This superiority was not repeated after additional events. Among adults infected before vaccination, adjusted geometric mean ratios (95% confidence interval [CI]) of anti-RBD early response (versus vaccinated only) were 1.23 (1.14–1.33), 1.09 (1.03–1.14), 0.87 (.81–.94), and 0.99 (.85–1.15) after the second to fifth events, respectively. Post-vaccination infections elicited superior responses; adjusted geometric mean ratios (95% CI) of anti-RBD early response (versus vaccinated only) were 0.93 (.75–1.17), 1.11 (1.06–1.16), 1.17 (1.11–1.24), and 1.20 (1.07–1.34) after the second to fifth events, respectively.

Conclusions
Evidence of heterogeneity in antibody levels by permutations of infection and vaccination history could inform COVID-19 vaccination policy.
A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome
Authors: Wilson Catherine A , Postlethwait John H 
Published: March 2024

Abstract
Wild zebrafish (Danio rerio) have a ZZ/ZW chromosomal sex-determination system with the major sex locus on the right arm of chromosome-4 (Chr4R) near the largest heterochromatic block in the genome, suggesting that Chr4R transcriptomics might differ from the rest of the genome. To test this hypothesis, we conducted an RNA-seq analysis of adult ZW ovaries and ZZ testes in the Nadia strain and identified 4 regions of Chr4 with different gene expression profiles. Unique in the genome, protein-coding genes in a 41.7 Mb section (Region-2) were expressed in testis but silent in ovary. The AB lab strain, which lacks sex chromosomes, verified this result, showing that testis-biased gene expression in Region-2 depends on gonad biology, not on sex-determining mechanism. RNA-seq analyses in female and male brains and livers validated reduced transcripts from Region-2 in somatic cells, but without sex specificity. Region-2 corresponds to the heterochromatic portion of Chr4R and its content of genes and repetitive elements distinguishes it from the rest of the genome. Region-2 lacks protein-coding genes with human orthologs; has zinc finger genes expressed early in zygotic genome activation; has maternal 5S rRNA genes, maternal spliceosome genes, a concentration of tRNA genes, and a distinct set of repetitive elements. The colocalization of (1) genes silenced in ovaries but not in testes that are (2) expressed in embryos briefly at the onset of zygotic genome activation; (3) maternal-specific genes for translation machinery; (4) maternal-specific spliceosome components; and (5) adjacent genes encoding miR-430, which mediates maternal transcript degradation, suggest that this is a maternal-to-zygotic-transition gene regulatory block.
SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers
Authors: Guo Hongzhe , Zhang Liyuan , Cui Xinran , Cheng Liang , Zhao Tianyi , Wang Yadong 
Published: March 2024

Abstract
Non-coding RNAs (ncRNAs) participate in multiple biological processes associated with cancers as tumor suppressors or oncogenic drivers. Due to their high stability in plasma, urine, and many other fluids, ncRNAs have the potential to serve as key biomarkers for early diagnosis and screening of cancers. During cancer progression, tumor heterogeneity plays a crucial role, and it is particularly important to understand the gene expression patterns of individual cells. With the development of single-cell RNA sequencing (scRNA-seq) technologies, uncovering gene expression in different cell types for human cancers has become feasible by profiling transcriptomes at the cellular level. However, a well-organized and comprehensive online resource that provides access to the expression of genes corresponding to ncRNA biomarkers in different cell types at the single-cell level is not available yet. Therefore, we developed the SCancerRNA database to summarize experimentally supported data on long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular RNA biomarkers, as well as data on their differential expression at the cellular level. Furthermore, we collected biological functions and clinical applications of biomarkers to facilitate the application of ncRNA biomarkers to cancer diagnosis, as well as the monitoring of progression and targeted therapies. SCancerRNA also allows users to explore interaction networks of different types of ncRNAs, and build computational models in the future. SCancerRNA is freely accessible at http://www.scancerrna.com/BioMarker.
On Long Time Behavior for Stochastic Nonlinear Schrödinger Equations with a Multiplicative Noise
Authors: Fan Chenjie , Zhao Zehua 
Published: March 2024

Abstract
In this article, we study mass-critical stochastic nonlinear Schrödinger equations with a multiplicative noise in 3D with a slight time decay ($\langle t \rangle ^{-\epsilon }$ for $\epsilon&gt;0$ arbitrarily small). We prove associated global space-time bounds and the scattering behavior.
The Theological Significance of the History of Science: John Templeton and the Promotion of Science and Religion
Authors: Jordan Peter N 
Published: March 2024

Abstract
This article examines the rationale behind philanthropist John Templeton’s investment in the field of science and religion. His support stems in part from the conviction that historical developments in science are finally leading us to the right understanding of God’s relationship to the created order. The older, mechanical picture of nature that science purportedly gave us implies that God is distant from nature, whereas more recent discoveries are revealing nature’s complexity, elusiveness, intangibility, unpredictability, and creativity and imply God’s intimate presence to, and involvement in, nature. This newer theological picture is consistent with a theological tradition to which Templeton had been exposed since childhood. Believing that science is finally uncovering theological truths about God and God’s relationship to the world, Templeton sought to shape science and (especially) religion so that comparable breakthroughs might continue to flow in the future.
The Integration of Physical Therapists and Occupational Therapists into Burn Wound Care Increases Therapist Productivity, Job Satisfaction, and Multidisciplinary Collaboration
Authors: Schwartzman Amy , Mueller Scott W , Ridgeway Kyle J , Balstad Blaire , Wiktor Arek J 
Published: March 2024

Abstract
When attempting to deliver specialized rehabilitation therapy interventions, physical therapists (PTs) and occupational therapists (OTs) must account for dynamic and logistical patient factors such as daily wound care, pain, difficulty progressing range of motion with dressings donned, and ongoing surgical interventions. Additionally, they must attain institution-specific productivity standards. Given burn patients often require considerable multidisciplinary interventions, efficiently planning and delivering rehabilitation therapy interventions within productivity expectations may prove difficult. The purpose of this study was to assess the feasibility of integrating rehabilitation therapists, PTs and OTs, into daily burn wound care by investigating therapist productivity and multidisciplinary perceptions of this practice change. The quality improvement project involved 6 rehabilitation therapists (3 PTs and 3 OTs) practicing exclusively in the burn unit within an American Burn Association (ABA)-verified burn center at an urban, tertiary care academic medical center. One rehabilitation therapist was responsible for providing interventions within the burn wound care team 5 days a week. General duties included wound assessment, functional wound dressings, and skilled therapeutic interventions such as manual therapy, therapeutic exercise, and compression interventions. The primary outcome was changes in group productivity and individual therapist productivity, as measured by total billed Current Procedural Terminology (CPT) codes per hour worked, which were tracked 22 weeks preimplementation and 28 weeks postimplementation. Program feasibility and general perceptions were assessed by a qualitative questionnaire. For both the entire group of therapists and each individual rehabilitation therapist, billed CPT codes per hour increased postimplementation, 1.81 vs 1.54 (P = .005) and a matched increase of 0.27/h (P = .003). Of the 23 survey respondents, 96% had a favorable impression of the program and reported it eased staffing demands. All respondents reported improved unit workflow and multidisciplinary communication. The majority of multidisciplinary burn team members actively supported the pilot program and commented on improvements in patient care. Full-time rehabilitation therapy participation in wound care increases therapist productivity and job satisfaction. Future efforts, however, should focus on measuring specific patient outcomes and costs as a result of therapist integration into daily wound care practice.
Leptin receptor (+) stromal cells respond to periodontitis and attenuate alveolar bone repair via CCRL2-mediated Wnt inhibition
Authors: Chen Yongliang , Weng Yuteng , Huang Jie , Li Qin , Sun Bin , Wang Haicheng , Wang Zuolin 
Published: March 2024

Abstract
The impaired bone healing in tooth extraction sockets due to periodontitis presents a major obstacle to restoring oral health. The mechanisms regulating the osteogenic capacity of jawbone-derived stromal cells in the periodontitis microenvironment remain elusive. Leptin receptor (LepR) expressing stromal cells, which largely overlap with Cxcl12-abundant reticular (CAR) cells in bone tissue, rapidly proliferate and differentiate into bone-forming cells during extraction socket healing to support alveolar bone repair. In this study, we identify that CCRL2 is significantly expressed and inhibits osteogenesis in LepR+/CAR cells of alveolar bones with periodontitis. The Ccrl2-KO mice exhibit significant improvements in bone healing in extraction sockets with periodontitis. Specifically, the binding of CCRL2 to SFRP1 on the surface of LepR+/CAR cells can amplify the suppressive effect of SFRP1 on Wnt signaling under inflammation, thus hindering the osteogenic differentiation of LepR+/CAR cells and resulting in poor bone healing in extraction sockets with periodontitis. Together, we clarify that the CCRL2 receptor of LepR+/CAR cells can respond to periodontitis and crosstalk with Wnt signaling to deteriorate extraction socket healing.
The chromatin remodeling factor Arid1a cooperates with Jun/Fos to promote osteoclastogenesis by epigenetically upregulating Siglec15 expression
Authors: Zhang Yongxing , Sun Hangxiang , Huang Fei , Chen Yang , Ding Xiying , Zhou Chenhe , Wu Yan , Zhang Qing , Ma Xiao , Wang Jun , Yue Rui , Shen Li , Sun Xuxu , Ye Zhaoming 
Published: March 2024

Abstract
Osteoporosis is characterized by an imbalance between osteoclast-mediated bone resorption and osteoblast-related bone formation, particularly increased osteoclastogenesis. However, the mechanisms by which epigenetic factors regulate osteoclast precursor differentiation during osteoclastogenesis remain poorly understood. Here, we show that the specific knockout of the chromatin remodeling factor Arid1a in bone marrow–derived macrophages (BMDMs) results in increased bone mass. The loss of Arid1a in BMDM inhibits cell–cell fusion and maturation of osteoclast precursors, thereby suppressing osteoclast differentiation. Mechanistically, Arid1a increases the chromatin access in the gene promoter region of sialic acid–binding Ig-like lectin 15 (Siglec15) by transcription factor Jun/Fos, which results in the upregulation of Siglec15 and promotion of osteoclast differentiation. However, the loss of Arid1a reprograms the chromatin structure to restrict Siglec15 expression in osteoclast precursors, thereby inhibiting BMDM differentiation into mature osteoclasts. Deleting Arid1a after ovariectomy (a model for postmenopausal bone loss) alleviated bone loss and maintained bone mass. In summary, epigenetic reprogramming mediated by Arid1a loss suppresses osteoclast differentiation and may serve as a promising therapeutic strategy for treating bone loss diseases.
The systematics of the amphidromous shrimp Macrobrachium tenellum (Smith, 1871) (Decapoda: Caridea: Palaemonidae) from the Mexican Pacific slope
Authors: Meza-Sánchez Iris Gabriela , Maeda-Martínez Alejandro M , Obregón-Barboza Hortencia , García-Velazco Humberto , Rodríguez-Almaraz Gabino A , Ruiz-Campos Gorgonio , Murugan Gopal 
Published: March 2024

Abstract
We had previously revised the systematics of four species of MacrobrachiumSpence Bate, 1868 from the Pacific coast of Mexico, including the Baja California Peninsula (BCP): M. americanumSpence Bate, 1868, M. digueti (Bouvier, 1895), M. hobbsi Nates & Villalobos in Villalobos Hiriart & Nates Rodríguez, 1990, and M. occidentale Holthuis, 1950. Genetic analyses of the mitochondrial markers 16S ribosomal RNA (16S) and cytochrome oxidase I (COI) of individuals of these morphological species from BCP have shown that, even facing the Gulf of California (Sea of Cortés) as an apparent marine ecological barrier, they are conspecific to their respective genetic lineages (species) found from the Pacific slope of mainland Mexico. We discuss the systematics of the fifth species of Macrobrachium from the Mexican Pacific slope, M. tenellum (Smith, 1871) to test the hypothesis that individuals of the putative M. tenellum from BCP belong to the same species from the Pacific slope of mainland Mexico. We revised the morphological characters of taxonomic importance using material obtained in the field and voucher material deposited in Mexican scientific collections, and performed molecular genetic analyses with newly generated fragments of the mitochondrial markers 16S and COI. We conclude, as in our previous studies on Macrobrachium species of the region, that the examined specimens of the putative M. tenellum from BCP belong to the same species found on the Pacific slope of mainland Mexico, and that oceanic dispersal is responsible for the distribution of the species of Macrobrachium in the peninsula rather than by vicariant events.