bluuebunny/crossref_metadata_2025_split huggingface dataset:
A gene-level test for directional selection on gene expression
Authors: Colbran Laura L , Ramos-Almodovar Fabian C , Mathieson Iain 
Published: April 2023

Abstract
Most variants identified in human genome-wide association studies and scans for selection are noncoding. Interpretation of their effects and the way in which they contribute to phenotypic variation and adaptation in human populations is therefore limited by our understanding of gene regulation and the difficulty of confidently linking noncoding variants to genes. To overcome this, we developed a gene-wise test for population-specific selection based on combinations of regulatory variants. Specifically, we use the QX statistic to test for polygenic selection on cis-regulatory variants based on whether the variance across populations in the predicted expression of a particular gene is higher than expected under neutrality. We then applied this approach to human data, testing for selection on 17,388 protein-coding genes in 26 populations from the Thousand Genomes Project. We identified 45 genes with significant evidence (FDR&lt;0.1) for selection, including FADS1, KHK, SULT1A2, ITGAM, and several genes in the HLA region. We further confirm that these signals correspond to plausible population-level differences in predicted expression. While the small number of significant genes (0.2%) is consistent with most cis-regulatory variation evolving under genetic drift or stabilizing selection, it remains possible that there are effects not captured in this study. Our gene-level QX score is independent of standard genomic tests for selection, and may therefore be useful in combination with traditional selection scans to specifically identify selection on regulatory variation. Overall, our results demonstrate the utility of combining population-level genomic data with functional data to understand the evolution of gene expression.
Genetic and genomic analyses of Drosophila melanogaster models of chromatin modification disorders
Authors: MacPherson Rebecca A , Shankar Vijay , Anholt Robert R H , Mackay Trudy F C 
Published: April 2023

Abstract
Switch/sucrose nonfermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 associated factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce the expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration), and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR &lt; 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, an SSRIDD-associated BAF component. k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in the behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in the discovery of drugs that ameliorate deleterious phenotypic effects.
European Patent Enforcement and the UPC: Status Quo and Perspectives ‒ Conference in Luxembourg, 24 and 25 November 2022
Authors: Kapischke Justus 
Published: April 2023

Abstract
The Unified Patent Court (the UPC) will soon open its doors to litigants and harmonise what used to be diverse domestic concepts of patent law. Its jurisprudence will undoubtedly be influenced by the various national practices. To shed light on what the future may look like, practitioners and academics met in Luxembourg to discuss the status quo and perspectives of European patent enforcement. The conference featured panels on important topics in patent enforcement followed by in-depth discussions between the panellists and the audience.
QTL detection and candidate gene analysis of grape white rot resistance by interspecific grape (Vitis vinifera L. × Vitis davidii Foex.) crossing
Authors: Li Peng , Tan Xibei , Liu Ruitao , Rahman Faiz Ur , Jiang Jianfu , Sun Lei , Fan Xiucai , Liu Jihong , Liu Chonghuai , Zhang Ying 
Published: April 2023

Abstract
Grape white rot, a devastating disease of grapevines caused by Coniella diplodiella (Speg.) Sacc., leads to significant yield losses in grape. Breeding grape cultivars resistant to white rot is essential to reduce the regular use of chemical treatments. In recent years, Chinese grape species have gained more attention for grape breeding due to their high tolerance to various biotic and abiotic factors along with changing climatic conditions. In this study, we employed whole-genome resequencing (WGR) to genotype the parents of ‘Manicure Finger’ (Vitis vinifera, female) and ‘0940’ (Vitis davidii, male), along with 101 F1 mapping population individuals, thereby constructing a linkage genetic map. The linkage map contained 9337 single-nucleotide polymorphism (SNP) markers with an average marker distance of 0.3 cM. After 3 years of phenotypic evaluation of the progeny for white rot resistance, we confirmed one stable quantitative trait locus (QTL) for white rot resistance on chromosome 3, explaining up to 17.9% of the phenotypic variation. For this locus, we used RNA-seq to detect candidate gene expression and identified PR1 as a candidate gene involved in white rot resistance. Finally, we demonstrated that recombinant PR1 protein could inhibit the growth of C. diplodiella and that overexpression of PR1 in susceptible V. vinifera increased grape resistance to the pathogen.
On Composition of Torsors
Authors: Florence Mathieu , Izquierdo Diego , Lucchini Arteche Giancarlo 
Published: April 2023

AbstractLet $K$ be a field, let $X$ be a connected smooth $K$-scheme, and let $G,H$ be two smooth connected $K$-group schemes. Given $Y \to X$ a $G$-torsor and $Z \to Y$ an $H$-torsor, we study whether one can find an extension $E$ of $G$ by $H$ so that the composite $Z \to X$ is an $E$-torsor. We give both positive and negative results, depending on the nature of the groups $G$ and $H$.
Leader Turnover, Regime Type, and Growth Volatility
Authors: Doces John A , Lupton Danielle L 
Published: April 2023

AbstractHow do leaders influence national-level economic outcomes? We address this question by considering how leadership turnover influences volatility in economic growth. In doing so, we theorize that leaders from mixed regimes will reduce economic volatility due to domestic political incentives to create stable economic outcomes. Furthermore, we decompose the influence of leaders in non-democratic regimes and argue that leaders in party-based authoritarian regimes will also reduce economic volatility. To test our hypotheses, we focus on the effect of leadership turnover due to natural leader death to control for issues of endogeneity. We find that leaders in mixed regimes reduce volatility more than leaders in autocratic and democratic regimes and that leaders in party-based authoritarian regimes reduce volatility more than those in military or monarchy-based regimes. We conclude by explaining the implications of our findings for the study of leaders in international politics and their impact on economic growth and development.
Exogenous fibrolytic enzymes promoted energy and nitrogen utilization and decreased CH4 emission per unit dry matter intake of tan sheep grazed a typical steppe by enhancing nutrient digestibility on China loess plateau
Authors: Shi Hairen , Guo Pei , Zhou Jieyan , Wang Zhen , He Meiyue , Shi Liyuan , Huang Xiaojuan , Guo Penghui , Guo Zhaoxia , Zhang Yuwen , Hou Fujiang 
Published: April 2023

Abstract
Exogenous fibrolytic enzyme (EFE) products in ruminant nutrition may be an important alternative to meet the increased demands for animal products in the future with reduced environmental impacts. This study aimed to evaluate the dose–response of EFE supplementation on the nutrient digestibility, nitrogen and energy utilization, and methane (CH4) emissions of Tan sheep grazed in summer and winter. A total of 20 Tan wether sheep with an initial body weight of 23.17 ± 0.24 kg were used in a randomized complete block design and categorized into two groups. Animals fed orally with 1 g of EFE (10,000 U/g) mixed with 30 mL of water using a drencher constituted the EFE group. For experimental accuracy, the control (CON) group was orally administered with 30 mL of normal saline daily before grazing. The following results were obtained: EFE in the diet increased dry matter intake (DMI) (P &lt; 0.05), average daily gain (ADG) (P &lt; 0.05), and digestibility (P &lt; 0.05) compared with CON in summer and winter. DMI increased but ADG and digestibility decreased in winter compared with those in summer. Sheep fed with the EFE diet increased the concentrations of rumen ammonia nitrogen (P &lt; 0.05) and total volatile fatty acids (P &gt; 0.05), but reduced pH (P &gt; 0.05), compared with CON in summer and winter. EFE increased nitrogen (N) intake, digestible N, retained N, and retained N/digestible N (P &lt; 0.05) but reduced fecal N/N intake, urinary N/N intake, and excretion N/N intake in summer and winter (P &lt; 0.05), compared with CON. Retained N/N intake was reduced and excretion N/N intake increased in winter relative to those in summer. In winter, gross energy (GE), manure E/GE, CH4 emissions, CH4/DMI, and CH4/GE increased but digestion energy and metabolic energy decreased compared with those in summer. Sheep fed with the EFE diet had a greater GE intake than those fed with the CON diet (P &lt; 0.05) but had lesser CH4/DMI and CH4E/GE (P &lt; 0.05) than those fed with the CON diet in both summer and winter. In conclusion, EFE supplementation increased DMI, apparent digestibility, and N deposition rate. These effects were beneficial for animal production. The CH4 emission per unit DMI of grazing Tan sheep was lesser and conducive for augmenting the environmental benefits.
Apoha for Beginners
Authors: Taber John 
Published: April 2023

Abstract
This study proposes, as an entryway into the complex debate about ‘exclusion’ (apoha) in Indian philosophy, that the main idea underlying Dignāga’s theory of apoha is that the relation between a word and its meaning—all the individuals that it can refer to—is established more by noticing what it is not used for than what it is used for. The Mīmāṃsā philosopher Kumārila raises a number of objections based on his construal of an apoha as a ‘non-existence’ (abhāva), but he also zeroes in on the problem of how, if apohas are known only by language and inference, they could ever be known at all. In this connection, he criticises Dignāga’s idea that the meaning of a word is learned by noticing that it is not used for things other than its usual referent. It seems, then, that much of what Dharmakīrti is doing in his discussion of apoha is to provide, in response to Kumārila, an account of how perceptual experiences of distinct particulars that have the same effects naturally give rise to an ascertainment of their exclusion from other entities, which can then be assigned as the meaning of an expression.
Photoluminescence in mammal fur: 111 years of research
Authors: Reinhold Linda M , Rymer Tasmin L , Helgen Kristofer M , Wilson David T 
Published: April 2023

Abstract
Photoluminescence in the pelage of mammals, a topic that has gained considerable recent research interest, was first documented in the 1700s and reported sporadically in the literature over the last century. The first detailed species accounts were of rabbits and humans, published 111 years ago in 1911. Recent studies have largely overlooked this earlier research into photoluminescent mammalian taxa and their luminophores. Here we provide a comprehensive update on existing research on photoluminescence in mammal fur, with the intention of drawing attention to earlier pioneering research in this field. We provide an overview on appropriate terminology, explain the physics of photoluminescence, and explore pigmentation and the ubiquitous photoluminescence of animal tissues, before touching on the emerging debate regarding visual function. We then provide a chronological account of research into mammalian fur photoluminescence, from the earliest discoveries and identification of luminophores to the most recent studies. While all mammal fur is likely to have a general low-level photoluminescence due to the presence of the protein keratin, fur glows luminously under ultraviolet light if it contains significant concentrations of tryptophan metabolites or porphyrins. Finally, we briefly discuss issues associated with preserved museum specimens in studies of photoluminescence. The study of mammal fur photoluminescence has a substantial history, which provides a broad foundation on which future studies can be grounded.
Analysis of particle therapy registries based on a unified treatment policy for esophageal cancer
Authors: Tokumaru Sunao , Ishikawa Hitoshi , Soejima Toshinori , Kimoto Takuya , Takakusagi Yosuke , Tamamura Hiroyasu , Wada Hitoshi , Taguchi Hiroshi , Uchinami Yusuke , Hiroshima Yuichi , Hojo Hidehiro , Kamei Takashi , Muto Manabu , Igeta Masataka 
Published: April 2023

Abstract
This study aimed to evaluate the efficacy and safety of particle therapy (proton beam therapy and carbon-ion radiotherapy) for esophageal cancer by analyzing prospective nationwide registry data from particle therapy facilities throughout Japan. Patients diagnosed with esophageal cancer who received particle therapy between May 2016 and June 2018 were recruited from the registries of 12 particle therapy centers in Japan. Eventually, we enrolled 174 patients who met the inclusion criteria. Of the 174 patients, 137 (78.7%) were male, with a median age of 69 years (range: 41–88 years). Clinical stages included I (n = 55; 31.6%), II (n = 31; 17.8%), III (n = 82; 47.1%), IV (n = 3; 1.7%) and unknown (n = 3; 1.7%) (Union for International Cancer Control, seventh edition), and the median follow-up period was 908 days (range: 76–1669 days) for all patients. The 3-year overall survival (OS) rate, the 3-year progression-free survival (PFS) rate and the 3-year local control (LC) rates were 60.5, 53.2 and 72.7%, respectively. For each clinical stage, the 3-year OS rates were I, 84.8%; II, 60.3% and III, 42.9%; the 3-year PFS rates were I, 71.9%; II, 58.3% and III, 37.0% and the 3-year LC were I, 78.4%; II, 79.8% and III, 65.2%, respectively. Notably, four patients (2.3%) with ≥Grade 3 cardiopulmonary toxicities were observed (Common Terminology Criteria for Adverse Events, version 5.0). Our study showed that particle therapy for esophageal cancer has lower rates of adverse cardiopulmonary events than X-ray radiotherapy.
A qualitative analysis of female patient perspectives on physician communication regarding sexual dysfunction associated with pelvic radiotherapy
Authors: Morgan Orly , Schnur Julie , Caban-Martinez Alberto J , Duenas-Lopez Mariana , Huang Marilyn , Portelance Lorraine , Elkhadem Adam , Marshall Deborah C 
Published: April 2023

Abstract

Background
Sexual dysfunction is a known side effect of pelvic radiotherapy, resulting from a complex intersection of physiologic and psychosocial factors. Maintaining sexual function is relevant to long-term quality of life and is an important aspect of survivorship. Many female patients report being insufficiently informed before treatment about the potential sexual side effects of radiation therapy.

Aim
To elucidate how radiation oncologists communicate sexual function side effects with their female patients and how discussing sexual side effects of cancer treatment can positively affect patient-physician rapport.

Methods
Semistructured interviews in English and Spanish were conducted with 20 female participants who received pelvic radiation as part of their cancer treatment. Patients responded to advertisements or were referred by physicians. All interviews were conducted virtually between June and October 2021. Thematic analysis was conducted with NVivo. Patients also completed an online demographics survey in REDCap.

Outcomes
We found 4 primary themes addressing patient perspectives on patient-physician communication of sexual dysfunction and how it affected the cancer care experience.

Results
Theme 1: This may be expected, but I didn’t expect it! The participants who were not properly informed about sexual side effects felt blindsided and embarrassed about their symptoms. Theme 2: I do not feel like a woman anymore . . . The psychological impact included lower self-esteem and no longer feeling sexy nor like a woman. Theme 3: Fine, I’ll deal with this myself! Patients turned to the internet rather than their doctors for answers once they began experiencing symptoms, and they found information, normalization, and community online. Theme 4: Ask me about my sex life and find out if sex is a priority for me. Participants emphasized that their radiation oncologist should take a sexual history early to monitor sexual dysfunction and to identify individual patient priorities surrounding sex posttreatment.

Clinical Implications
This evidence provides a guide to patient-physician communication that may help to mitigate the impacts of radiotherapy on female sexual function as well as the negative impact that the absence of communication about sexual dysfunction may have on patient-physician trust.

Strengths and Limitations
While this project did have a small sample size, there is considerable diversity in race, education level, and age, with interviews conducted in Spanish and English.

Conclusion
Overall these findings provide physicians with important information about the unmet information needs of patients and their preferences for how to help them feel more prepared and less distressed when sexual dysfunction occurs.
The once-invisible legacy of Elizabeth L. Kerr, a naturalist in the early 20th century, and her contributions to Colombian ornithology
Authors: Soto-Patiño Juliana , Certuche-Cubillos Katherine , Díaz-Cárdenas Jessica , Garzón-Lozano Daniela , Guzmán-Moreno Estefanía , Niño-Rodríguez Nelsy , Pérez-Amaya Natalia , Ocampo-Peñuela Natalia 
Published: April 2023

Abstract
Mrs. Elizabeth L. Kerr was a bird and mammal collector who traveled to Colombia in the early 20th century when women had very limited access to education or scientific expeditions. Despite her notable contributions to Colombian ornithology, including collecting the holotype of a new species to science (Chocó Tinamou—Crypturellus kerriae), her name is not mentioned in historical accounts of ornithology in Colombia. Here, we describe what we know about Kerr’s life as a collector and her legacy in the study of Colombian birds. We highlight the fact that Kerr has become a role model for female naturalists and provide a short account of an all-female ornithological expedition to resurvey one of Kerr’s collecting sites. By bringing Kerr’s legacy to the public eye, we hope to raise awareness of implicit bias and barriers faced by women in science.
N6-methyladenosine RNA methylation modulates liquid‒liquid phase separation in plants
Authors: Kang Hunseung , Xu Tao 
Published: April 2023

Abstract
Membraneless biomolecular condensates form distinct subcellular compartments that enable a cell to orchestrate numerous biochemical reactions in a spatiotemporal-specific and dynamic manner. Liquid‒liquid phase separation (LLPS) facilitates the formation of membraneless biomolecular condensates, which are crucial for many cellular processes in plants, including embryogenesis, the floral transition, photosynthesis, pathogen defense, and stress responses. The main component required for LLPS is a protein harboring key characteristic features, such as intrinsically disordered regions, low-complexity sequence domains, and prion-like domains. RNA is an additional component involved in LLPS. Increasing evidence indicates that modifications in proteins and RNAs play pivotal roles in LLPS. In particular, recent studies have indicated that N6-methyladenosine (m6A) modification of messenger RNA is crucial for LLPS in plants and animals. In this review, we provide an overview of recent developments in the role of mRNA methylation in LLPS in plant cells. Moreover, we highlight the major challenges in understanding the pivotal roles of RNA modifications and elucidating how m6A marks are interpreted by RNA-binding proteins crucial for LLPS.
Age-Related Differences in Job Search Behavior: Do Older Jobseekers Need a Larger Social Network?
Authors: Guillemyn Inés , Horemans Jeroen 
Published: April 2023

Abstract
Increasing the employment rate of individuals aged 55+ is a key challenge in many OECD countries. While labor market discrimination and policy measures have been put forward as possible explanations, the role of job search remains largely unexplored. Yet, it determines to a large extent the match between supply and demand on the labor market. In this paper, we examine age-related differences in job search behavior. As skills have often become outdated for older workers, but job mobility may enhance their employment, we analyze search behavior for the unemployed as well as the employed adopting multiple parameters: job search intensity, use of the public employment agency, and social networking. The results indicate that jobseekers of different age employ different search methods, and that this relationship should be analyzed within the employment context of the jobseeker.
A 15-Year Review of 260 Children With Auditory Neuropathy Spectrum Disorder: I. Demographic and Diagnostic Characteristics
Authors: Morlet Thierry , Parkes William , Pritchett Cedric , Venskytis Emily , DeVore Brooke , O’Reilly Robert C. 
Published: April 2023

Objectives:
The aim of the study was to review the demographic and clinical characteristics of all pediatric patients diagnosed with auditory neuropathy spectrum disorder (ANSD) by a pediatric health care system from 2005 to 2020 and examine whether or not our diagnostic capabilities in an ANSD population have evolved as our institutional experience has grown and knowledge in the field has expanded.

Design:
This was a retrospective study reviewing the demographic data, medical history, imaging studies, audiological and speech-language data, type of audiological intervention and mode of communication in 260 pediatric patients diagnosed with ANSD over a 15-year period.

Results:
The study revealed that male and female children were equally affected with all levels of hearing detection being represented and that about 40% of affected children were premature and most were admitted to the neonatal intensive care unit. More than a third of our patients presented with a complex medical history and/or neural involvement while about 30% were full-term newborns with normal pregnancy, no prenatal complications or infections, normal birth weight, no neonatal intensive care unit need, no hyperbilirubinemia, no respiratory distress requiring ventilation, and no known syndrome. Review of audiological findings confirms that otoacoustic emissions are not always present in ANSD cases, and that the presence of an abnormal wave V on the auditory brainstem response tracings (only present at high intensities and with an absent intensity/latency function) is not a rare finding and should not immediately be dismissed as not being a case of ANSD.

Conclusions:
This review of ANSD diagnosis over a 15-year period clearly reveals the drastic improvements made in the identification of ANSD, with a drastic decrease in the age at diagnosis and a reduction in the percentage of misdiagnosed patients. The study also stresses the need for continued improvement in different areas such as genetic studies and physiological measures to help clinicians distinguish between pre- and postsynaptic ANSD.