bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide association mapping in a sweet cherry germplasm collection (Prunus avium L.) reveals candidate genes for fruit quality traits
Authors: Donkpegan Armel S L , Bernard Anthony , Barreneche Teresa , Quero-García José , Bonnet Hélène , Fouché Mathieu , Le Dantec Loïck , Wenden Bénédicte , Dirlewanger Elisabeth 
Published: September 2023

Abstract
In sweet cherry (Prunus avium L.), large variability exists for various traits related to fruit quality. There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands. With this objective, a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomic fruit quality traits over 2–6 years, and characterized using a genotyping-by-sequencing approach. The SNP coverage collected was used to conduct a genome-wide association study using two multilocus models and three reference genomes. We identified numerous SNP–trait associations for global fruit size (weight, width, and thickness), fruit cracking, fruit firmness, and stone size, and we pinpointed several candidate genes involved in phytohormone, calcium, and cell wall metabolisms. Finally, we conducted a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker–trait associations. This study brings new knowledge of the genetic control of important agronomic traits related to fruit quality, and to the development of marker-assisted selection strategies targeted towards the facilitation of breeding efforts.
Prevalence, Incidence, and Predictors of Kaposi Sarcoma–Associated Herpesvirus Infection Among Young Men Who Have Sex With Men in the Southern United States
Authors: Salyards Maverick , Nijhawan Ank E , Kuo Jacky , Knights Sheena M , Lazarte Susana , Labo Nazzarena , Miley Wendell , Whitby Denise , Hwang Lu-Yu , Kornberg Anna-William , Fujimoto Kayo , Chiao Elizabeth Y 
Published: September 2023

Abstract
Kaposi sarcoma (KS) continues to cause substantial morbidity and mortality in populations at risk in the southern United States. Utilizing biospecimens from the Houston site of the Young Men's Affiliate Project, 351 men who have sex with men had blood tested for KS-associated herpesvirus (KSHV) IgG. Seroprevalence, seroconversion between time points, and demographic and clinical correlates were measured. KSHV prevalence was 36.7% and incidence was 8.9 per 100 person-years. Furthermore, prevalence and incidence were higher among Black individuals, people living with HIV, and those with a history of syphilis. Further research on KSHV risk may improve health disparities in KS diagnosis and outcomes.
Analysis of the Immunostimulatory Effects of Cytokine-Expressing Internal Ribosome Entry Site–Based RNA Adjuvants and Their Applications
Authors: Lee Yu-Sun , Bang Yoo-Jin , Yoo Soyeon , Park Sang-In , Park Hyo-Jung , Kwak Hye Won , Bae Seo-Hyeon , Park Hyeong-Jun , Kim Jae-Yong , Youn Sue-Bean , Roh Gahyun , Lee Seonghyun , Kwon Sung Pil , Bang Eun-Kyoung , Keum Gyochang , Nam Jae-Hwan , Hong So-Hee 
Published: September 2023

Abstract
Developing new adjuvants that can effectively induce humoral and cellular immune responses while broadening the immune response is of great value. In this study, we aimed to develop single-stranded RNA adjuvants expressing (1) granulocyte monocyte colony-stimulating factor or (2) interleukin 18 based on the encephalomyocarditis virus internal ribosome entry site; we also tested their efficacy in combination with ovalbumin or inactivated influenza vaccines. Notably, cytokine-expressing RNA adjuvants increased the expression of antigen-presenting cell activation markers in mice. Specifically, when combined with ovalbumin, RNA adjuvants expressing granulocyte monocyte colony-stimulating factor increased CD4+ T-cell responses, while those expressing interleukin 18 increased CD8+ T-cell responses. Cytokine-expressing RNA adjuvants further increased the frequency of polyclonal T cells with the influenza vaccine and reduced the clinical illness scores and weight loss of mice after viral challenge. Collectively, our results suggest that cytokine-expressing RNA adjuvants can be applied to protein-based or inactivated vaccines to increase their efficacy.
Migration governance in East and Southeast Asia
Authors: Chung Erin , Hollifield James F , Tian Yunchen 
Published: September 2023

Abstract
This article explains migration governance in East and Southeast Asia by comparing guestworker programs that have institutionalized labor migration flows between Southeast Asian countries (especially Indonesia, the Philippines, and Vietnam) and the two largest Northeast Asian recipients of labor migration, Japan and South Korea. It demonstrates how these programs have led to heightened competition for skilled labor between countries of destination, while facilitating greater migration flows between countries in Southeast and Northeast Asia. Bilateral economic agreements have engendered highly uneven, underdeveloped frameworks for protecting migrant rights and facilitating migrant integration in countries of destination. The analysis also provides insights into theories of complex interdependence and global migration governance, and shows how migration interdependence (MI) can lead to both cooperation and conflict.
A genome assembly of the Yuma myotis bat, Myotis yumanensis
Authors: Curti Joseph N , Fraser Devaughn , Escalona Merly , Fairbairn Colin W , Sacco Samuel , Sahasrabudhe Ruta , Nguyen Oanh , Seligmann William , Sudmant Peter H , Toffelmier Erin , Vazquez Juan Manuel , Wayne Robert , Shaffer H Bradley , Buchalski Michael R 
Published: September 2023

Abstract
The Yuma myotis bat (Myotis yumanensis) is a small vespertilionid bat and one of 52 species of new world Myotis bats in the subgenus Pizonyx. While M. yumanensis populations currently appear relatively stable, it is one of 12 bat species known or suspected to be susceptible to white-nose syndrome, the fungal disease causing declines in bat populations across North America. Only two of these 12 species have genome resources available, which limits the ability of resource managers to use genomic techniques to track the responses of bat populations to white-nose syndrome generally. Here we present the first de novo genome assembly for Yuma myotis, generated as a part of the California Conservation Genomics Project. The M. yumanensis genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. This high-quality genome is one of the most complete bat assemblies available, with a contig N50 of 28.03 Mb, scaffold N50 of 99.14 Mb, and BUSCO completeness score of 93.7%. The Yuma myotis genome provides a high-quality resource that will aid in comparative genomic and evolutionary studies, as well as inform conservation management related to white-nose syndrome.
AcHZP45 is a repressor of chlorophyll biosynthesis and activator of chlorophyll degradation in kiwifruit
Authors: Wu Ying-ying , Wang Ling-li , Lin Yi-lai , Li Xiang , Liu Xiao-fen , Xu Zi-Hong , Fu Bei-ling , Wang Wen-qiu , Allan Andrew C , Tu Mei-yan , Yin Xue-ren 
Published: September 2023

Abstract
The degradation of chlorophyll during fruit development is essential to reveal a more ‘ripe’ color that signals readiness to wild dispersers of seeds and the human consumer. Here, comparative biochemical analysis of developing fruit of Actinidia deliciosa cv. Xuxiang (‘XX’, green-fleshed) and Actinidia chinensis cv. Jinshi No.1 (‘JS’, yellow-fleshed) indicated that variation in chlorophyll content is the major contributor to differences in flesh color. Four differentially expressed candidate genes were identified: the down-regulated genes AcCRD1 and AcPOR1 involved in chlorophyll biosynthesis, and the up-regulated genes AcSGR1 and AcSGR2 driving chlorophyll degradation. Prochlorophyllide and chlorophyllide, the metabolites produced by AcCRD1 and AcPOR1, progressively reduced in ‘JS’, but not in ‘XX’, indicating that chlorophyll biosynthesis was less active in yellow-fleshed fruit. AcSGR1 and AcSGR2 were verified to be involved in chlorophyll degradation, using both transient expression in tobacco and stable overexpression in kiwifruit. Furthermore, a homeobox-leucine zipper (HD-Zip II), AcHZP45, showed significantly increased expression during ‘JS’ fruit ripening, which led to both repressed expression of AcCRD1 and AcPOR1 and activated expression of AcSGR1 and AcSGR2. Collectively, the present study indicated that different dynamics of chlorophyll biosynthesis and degradation coordinate the changes in chlorophyll content in kiwifruit flesh, which are orchestrated by the key transcription factor AcHZP45.
How numerical treatments of the transition region modify energy flux into the solar corona
Authors: Howson T A , Breu C 
Published: September 2023

ABSTRACT
The large temperature gradients in the solar transition region present a significant challenge to large-scale numerical modelling of the Sun’s atmosphere. In response, a variety of techniques have been developed which modify the thermodynamics of the system. This sacrifices accuracy in the transition region in favour of accurately tracking the coronal response to heating events. Invariably, the modification leads to an artificial broadening of the transition region. Meanwhile, many contemporary models of the solar atmosphere rely on tracking energy flux from the lower atmosphere, through the transition region and into the corona. In this paper, we quantify how the thermodynamic modifications affect the rate of energy injection into the corona. We consider a series of one-dimensional models of atmospheric loops with different numerical resolutions and treatments of the thermodynamics. Then, using Alfvén waves as a proxy, we consider how energy injection rates are modified in each case. We find that the thermodynamic treatment and the numerical resolution significantly modify Alfvén traveltimes, the eigenfrequencies and eigenmodes of the system, and the rate at which energy is injected into the corona. Alarmingly, we find that the modification of the energy flux is frequency dependent, meaning that it may be difficult to compare the effects of different velocity drivers on coronal heating if they are imposed below an under-resolved transition region, even if the sophisticated thermodynamic adaptations are implemented.
Spatially resolved spectroscopic investigation of the born-again planetary nebula A 78
Authors: Montoro-Molina B , Guerrero M A , Toalá J A 
Published: September 2023

ABSTRACT
We present the analysis of spatially resolved spectroscopic observations of the born-again planetary nebula (PN) A 78 that are used to investigate the chemistry and physical properties of its three main morphological components, namely the inner knots, its eye-like structure, and the low surface-brightness outer nebula. The H-poor chemical abundances of the inner knots confirm the born-again nature of A 78, with an N/O abundances ratio consistent with the predictions of very late thermal pulses (VLTP). On the other hand, the high Ne/O is not expected in VLTP events, which prompts a possible different evolutionary path may be involving a binary system. The low N/O ratio and He/H abundances of the outer shell are indicative of a low-mass progenitor, whereas the chemical abundances of the eye-like structure, which results from the interaction between the H-poor born-again material and the outer nebula, evidence their mixture. Unlike previous works, the extinction is found to be inhomogeneous, being much higher towards the H-poor inner knots, where the presence of large amounts of C-rich dust has been previously reported. Dust-rich material seems to diffuse into outer nebular regions, resulting in zones of enhanced extinction.
A re-assessment of SpArcFiRe’s performance on toy spiral galaxies
Authors: Portman Matthew E , Mesforoush Sahel , Hayes Wayne B 
Published: September 2023

ABSTRACT
Recently, a study (H&T in this work) compared the pitch angle measurements of several methods on toy spiral galaxies. They claimed that their method outperformed the other methods. In particular, they claimed that our method, SpArcFiRe, either failed completely or produced erroneous results on many of their toy galaxies. In this paper, we assess the validity of that claim with respect to: (1) their toy models as realistic approximations of galaxies, and (2) the handling of SpArcFiRe’s parameters to correctly trace the arms of the toy galaxies. We demonstrate that the structure displayed in their toy galaxies deviates significantly from those of real galaxies. Given that SpArcFiRe was designed for and tested against hundreds of thousands of images of real galaxies, SpArcFiRe could not have been expected to work well with default parameters on H&T’s unrealistic toy galaxies. We then review the parameters that affected SpArcFiRe’s ability to measure pitch angles in the toy galaxies, and show that with minor parameter adjustments, SpArcFiRe easily measures the pitch angles of the toy galaxies with mean error less than 1° and maximum error less than 4°, completely eliminating the failures and outliers discussed by H&T.
Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods
Authors: du Plessis Sarah J , Blaxter Mark , Koepfli Klaus-Peter , Chadwick Elizabeth A , Hailer Frank 
Published: September 2023

Abstract
Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here, we provide a matched comparison of whole genome sequencing versus microsatellite and control region (CR) genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated “stronghold” populations of otter in Britain, derived from regional populations that survived the population crash of the 1950s–1980s. Using whole genome resequencing data from 45 samples from across the British stronghold populations, we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly, we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using CR fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesize that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well-studied species may harbor genetic surprises, if studied using modern high-throughput sequencing methods.
Ovarian stimulation with excessive FSH doses causes cumulus cell and oocyte dysfunction in small ovarian reserve heifers
Authors: Karl Kaitlin R , Schall Peter Z , Clark Zaramasina L , Ruebel Meghan L , Cibelli Jose , Tempelman Robert J , Latham Keith E , Ireland James J 
Published: September 2023

Abstract
Excessive FSH doses during ovarian stimulation in the small ovarian reserve heifer (SORH) cause premature cumulus expansion and follicular hyperstimulation dysgenesis (FHD) in nearly all ovulatory-size follicles with predicted disruptions in cell-signaling pathways in cumulus cells and oocytes (before ovulatory hCG stimulation). These observations support the hypothesis that excessive FSH dysregulates cumulus cell function and oocyte maturation. To test this hypothesis, we determined whether excessive FSH-induced differentially expressed genes (DEGs) in cumulus cells identified in our previously published transcriptome analysis were altered independent of extreme phenotypic differences observed amongst ovulatory-size follicles, and assessed predicted roles of these DEGs in cumulus and oocyte biology. We also determined if excessive FSH alters cumulus cell morphology, and oocyte nuclear maturation before (premature) or after an ovulatory hCG stimulus or during IVM. Excessive FSH doses increased expression of 17 cumulus DEGs with known roles in cumulus cell and oocyte functions (responsiveness to gonadotrophins, survival, expansion, and oocyte maturation). Excessive FSH also induced premature cumulus expansion and oocyte maturation but inhibited cumulus expansion and oocyte maturation post-hCG and diminished the ability of oocytes with prematurely expanded cumulus cells to undergo IVF or nuclear maturation during IVM. Ovarian stimulation with excessive FSH is concluded to disrupt cumulus cell and oocyte functions by inducing premature cumulus expansion and dysregulating oocyte maturation without an ovulatory hCG stimulus yielding poor-quality cumulus–oocyte complexes that may be incorrectly judged morphologically as suitable for IVF during ART.
Tensin 1 regulated by hepatic leukemia factor represses the progression of prostate cancer
Authors: Zhou Hao , Wang Fang 
Published: September 2023

Abstract
Hepatic leukemia factor (HLF), a transcription factor, is dysregulated in many cancers. This study investigates the function of HLF in prostate cancer (PCa) and its relation to tensin 1 (TNS1). Clinical tissues were collected from 24 PCa patients. Duke University 145 (DU145) and PC3 cells overexpressing HLF were established. HLF signaling was downregulated in PCa tissues compared to adjacent tissues and in DU145 and PC3 cells compared to prostate epithelial cells RWPE-1 or prostate stromal cells (WPMY-1). PCa cell lines with overexpression of HLF had reduced proliferative, migratory, and invasive activity, increased apoptosis, and cell mitosis mostly in the G0/G1 phase. HLF induced the TNS1 transcription to activate the p53 pathway. Depletion of TNS1 reversed the anti-tumor effects of HLF on PCa cells and tumor growth and metastasis in vivo. In summary, our findings suggest that HLF suppressed PCa progression by upregulating TNS1 expression and inducing the p53 pathway activation, which might provide insights into novel strategies for combating PCa.
Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation
Authors: Wegrzyn Katarzyna , Oliwa Monika , Nowacka Marzena , Zabrocka Elżbieta , Bury Katarzyna , Purzycki Piotr , Czaplewska Paulina , Pipka Justyna , Giraldo Rafael , Konieczny Igor 
Published: September 2023

Abstract
For DNA replication initiation in Bacteria, replication initiation proteins bind to double-stranded DNA (dsDNA) and interact with single-stranded DNA (ssDNA) at the replication origin. The structural–functional relationship of the nucleoprotein complex involving initiator proteins is still elusive and different models are proposed. In this work, based on crosslinking combined with mass spectrometry (MS), the analysis of mutant proteins and crystal structures, we defined amino acid residues essential for the interaction between plasmid Rep proteins, TrfA and RepE, and ssDNA. This interaction and Rep binding to dsDNA could not be provided in trans, and both are important for dsDNA melting at DNA unwinding element (DUE). We solved two crystal structures of RepE: one in a complex with ssDNA DUE, and another with both ssDNA DUE and dsDNA containing RepE-specific binding sites (iterons). The amino acid residues involved in interaction with ssDNA are located in the WH1 domain in stand β1, helices α1 and α2 and in the WH2 domain in loops preceding strands β1’ and β2’ and in these strands. It is on the opposite side compared to RepE dsDNA-recognition interface. Our data provide evidence for a loop-back mechanism through which the plasmid replication initiator molecule accommodates together dsDNA and ssDNA.
A multi-scale expression and regulation knowledge base forEscherichia coli
Authors: Lamoureux Cameron R , Decker Katherine T , Sastry Anand V , Rychel Kevin , Gao Ye , McConn John Luke , Zielinski Daniel C , Palsson Bernhard O 
Published: September 2023

AbstractTranscriptomic data is accumulating rapidly; thus, scalable methods for extracting knowledge from this data are critical. Here, we assembled a top-down expression and regulation knowledge base for Escherichia coli. The expression component is a 1035-sample, high-quality RNA-seq compendium consisting of data generated in our lab using a single experimental protocol. The compendium contains diverse growth conditions, including: 9 media; 39 supplements, including antibiotics; 42 heterologous proteins; and 76 gene knockouts. Using this resource, we elucidated global expression patterns. We used machine learning to extract 201 modules that account for 86% of known regulatory interactions, creating the regulatory component. With these modules, we identified two novel regulons and quantified systems-level regulatory responses. We also integrated 1675 curated, publicly-available transcriptomes into the resource. We demonstrated workflows for analyzing new data against this knowledge base via deconstruction of regulation during aerobic transition. This resource illuminates the E. coli transcriptome at scale and provides a blueprint for top-down transcriptomic analysis of non-model organisms.
TTD: Therapeutic Target Database describing target druggability information
Authors: Zhou Ying , Zhang Yintao , Zhao Donghai , Yu Xinyuan , Shen Xinyi , Zhou Yuan , Wang Shanshan , Qiu Yunqing , Chen Yuzong , Zhu Feng 
Published: September 2023

Abstract
Target discovery is one of the essential steps in modern drug development, and the identification of promising targets is fundamental for developing first-in-class drug. A variety of methods have emerged for target assessment based on druggability analysis, which refers to the likelihood of a target being effectively modulated by drug-like agents. In the therapeutic target database (TTD), nine categories of established druggability characteristics were thus collected for 426 successful, 1014 clinical trial, 212 preclinical/patented, and 1479 literature-reported targets via systematic review. These characteristic categories were classified into three distinct perspectives: molecular interaction/regulation, human system profile and cell-based expression variation. With the rapid progression of technology and concerted effort in drug discovery, TTD and other databases were highly expected to facilitate the explorations of druggability characteristics for the discovery and validation of innovative drug target. TTD is now freely accessible at: https://idrblab.org/ttd/.