bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clusternets: a deep learning approach to probe clustering dark energy
Authors: Chegeni Amirmohammad , Hassani Farbod , Vafaei Sadr Alireza , Khosravi Nima , Kunz Martin 
Published: May 2024

ABSTRACT
Machine learning (ML) algorithms are becoming popular in cosmology for extracting valuable information from cosmological data. In this paper, we evaluate the performance of a convolutional neural network (CNN) trained on matter density snapshots to distinguish clustering dark energy (DE) from the cosmological constant scenario and to detect the speed of sound (cs) associated with clustering DE. We compare the CNN results with those from a Random Forest (RF) algorithm trained on power spectra. Varying the DE equation of state parameter wDE within the range of −0.7 to −0.99 while keeping $c_s^2 = 1$, we find that the CNN approach results in a significant improvement in accuracy over the RF algorithm. The improvement in classification accuracy can be as high as 40 per cent depending on the physical scales involved. We also investigate the ML algorithms’ ability to detect the impact of the speed of sound by choosing $c_s^2$ from the set {1, 10−2, 10−4, 10−7} while maintaining a constant wDE for three different cases: wDE ∈ {−0.7, −0.8, −0.9}. Our results suggest that distinguishing between various values of $c_s^2$ and the case where $c_s^2=1$ is challenging, particularly at small scales and when wDE ≈ −1. However, as we consider larger scales, the accuracy of $c_s^2$ detection improves. Notably, the CNN algorithm consistently outperforms the RF algorithm, leading to an approximate 20 per cent enhancement in $c_s^2$ detection accuracy in some cases.
Discovery of free precession in the magnetar SGR 1806−20 with the ASCA Gas Imaging Spectrometer
Authors: Makishima Kazuo , Uchida Nagomi , Enoto Teruaki 
Published: May 2024

Abstract
Four X-ray datasets of the soft gamma repeater SGR 1806−20, taken with the Gas Imaging Spectrometer (GIS) onboad ASCA, were analyzed. Three of them were acquired over 1993 October 9–20, the last one in 1995 October. Epoch-folding analysis of the 2.8–12 keV signals confirmed the ∼7.6 s pulses in these data, which Kouveliotou et al. (1998, Nature, 393, 235) reported as one of the earliest pulse detections from this object. In the 1995 observation, 3–12 keV pulses were phase modulated with a period of T = 16.4 ± 0.4 ks, and an amplitude of ∼1 s. This makes a fourth example of the behavior observed from magnetars. As in the previous three sources, the pulse-phase modulation of SGR 1806−20 disappeared at ≲2.5 keV, where the soft X-ray component dominates. In the 1993 datasets, this periodic modulation was reconfirmed, and successfully phase-connected coherently across the 11 d interval. As a result, the modulation period was refined to T = 16.435 ± 0.024 ks. The implied high stability of the phenomenon strengthens its interpretation in terms of free precession of the neutron star, which is deformed to an asphericity of ∼10−4, presumably by the stress of toroidal magnetic fields reaching ∼1016 G. Toroidal fields of this level can be common among magnetars.
Polyphenols-based intelligent oral barrier membranes for periodontal bone defect reconstruction
Authors: Chen Enni , Wang Tianyou , Sun Zhiyuan , Gu Zhipeng , Xiao Shimeng , Ding Yi 
Published: May 2024

Abstract
Periodontitis-induced periodontal bone defects significantly impact patients’ daily lives. The guided tissue regeneration and guided bone regeneration techniques, which are based on barrier membranes, have brought hope for the regeneration of periodontal bone defects. However, traditional barrier membranes lack antimicrobial properties and cannot effectively regulate the complex oxidative stress microenvironment in periodontal bone defect areas, leading to unsatisfactory outcomes in promoting periodontal bone regeneration. To address these issues, our study selected the collagen barrier membrane as the substrate material and synthesized a novel barrier membrane (PO/4-BPBA/Mino@COL, PBMC) with an intelligent antimicrobial coating through a simple layer-by-layer assembly method, incorporating reactive oxygen species (ROS)-scavenging components, commercial dual-functional linkers and antimicrobial building blocks. Experimental results indicated that PBMC exhibited good degradability, hydrophilicity and ROS-responsiveness, allowing for the slow and controlled release of antimicrobial drugs. The outstanding antibacterial, antioxidant and biocompatibility properties of PBMC contributed to resistance to periodontal pathogen infection and regulation of the oxidative balance, while enhancing the migration and osteogenic differentiation of human periodontal ligament stem cells. Finally, using a rat periodontal bone defect model, the therapeutic effect of PBMC in promoting periodontal bone regeneration under infection conditions was confirmed. In summary, the novel barrier membranes designed in this study have significant potential for clinical application and provide a reference for the design of future periodontal regenerative functional materials.
Influence of epinephrine reactivity to stress on meat quality in goats
Authors: Shaik Arshad , Batchu Phaneendra , Naldurtiker Aditya , Gurrapu Priyanka , Kouakou Brou , Terrill Thomas H , Kannan Govind 
Published: May 2024

Abstract
The magnitude of physiological responses to a stressor can vary among individual goats within a herd; however, whether these differences can differentially affect meat quality is not known. This study was conducted to determine the influence of the magnitude of epinephrine response (ER) to acute stress on muscle metabolome and meat quality in goats. Male Spanish goats (6 mo old) were transported for 180 min. (N = 75 goats; 25 goats/d) to impose stress. Blood samples were obtained after transport for analysis of physiological responses. Goats were slaughtered using humane procedures and samples were collected for muscle metabolomics and meat quality analyses. The data obtained from blood and muscle/meat analysis were then categorized based on epinephrine concentrations into low (LE), medium (ME), and high (HE) ER groups (n = 12/ER group). The physiological and meat quality variables were analyzed as a Completely Randomized Design in SAS, and metabolomics data were analyzed using R software. Plasma glucose concentrations were significantly high in the HE group, low in the LE group, and intermediate in the ME group (P &lt; 0.05). However, leukocyte counts and cortisol, norepinephrine, blood urea nitrogen, and creatine concentrations were not different among the ER groups. Muscle (Longissimus dorsi) glycogen concentrations (15 min postmortem) were significantly higher (P &lt; 0.05) in the ME and LE groups than in the HE group. However, postmortem Longissimus muscle pH and temperature (15 min and 24 h), 24 h calpastatin and desmin levels, and rib chop color (L*, a*, and b*), cooking loss, and Warner-Bratzler shear force values were unaffected by ER. Targeted metabolomics analysis of Longissimus muscle (15 min) revealed that diacyl phosphatidylcholines (C38:0; 40:6) and sphingomyelin (C20:2) were significantly different (P &lt; 0.05) among the ER groups, with the concentrations of these metabolites being consistently high in the LE group. These differential muscle metabolite concentrations suggest that ER can influence biochemical pathways associated with cell membrane integrity and signaling. ER had a significant effect on dopamine concentrations, with the levels increasing with increasing levels of ER. The results indicate that differences in epinephrine reactivity can influence selected physiological responses and muscle metabolites; however, it does not significantly influence meat quality attributes.
The diverse liver viromes of Australian geckos and skinks are dominated by hepaciviruses and picornaviruses and reflect host taxonomy and habitat
Authors:  Mahar Jackie E ,  Wille Michelle ,  Harvey Erin ,  Moritz Craig C ,  Holmes Edward C 
Published: May 2024

Abstract
Lizards have diverse ecologies and evolutionary histories, and represent a promising group to explore how hosts shape virome structure and virus evolution. Yet, little is known about the viromes of these animals. In Australia, squamates (lizards and snakes) comprise the most diverse order of vertebrates, and Australia hosts the highest diversity of lizards globally, with the greatest breadth of habitat use. We used meta-transcriptomic sequencing to determine the virome of nine co-distributed, tropical lizard species from three taxonomic families in Australia and analyzed these data to identify host traits associated with viral abundance and diversity. We show that lizards carry a large diversity of viruses, identifying more than thirty novel, highly divergent vertebrate-associated viruses. These viruses were from nine viral families, including several that contain well known pathogens, such as the Flaviviridae, Picornaviridae, Bornaviridae, Iridoviridae, and Rhabdoviridae. Members of the Flaviviridae were particularly abundant across species sampled here, largely belonging to the genus Hepacivirus: fourteen novel hepaciviruses were identified, broadening the known diversity of this group and better defining its evolution by uncovering new reptilian clades. The evolutionary histories of the viruses studied here frequently aligned with the biogeographic and phylogenetic histories of the hosts, indicating that exogenous viruses may help infer host evolutionary history if sampling is strategic and sampling density high enough. Notably, analysis of alpha and beta diversity revealed that virome composition and richness in the animals sampled here was shaped by host taxonomy and habitat. In sum, we identified a diverse range of reptile viruses that broadly contributes to our understanding of virus-host ecology and evolution.
Expression of HER2 in urothelial carcinoma and its significance
Authors: Chang Yao , Zhao Delong , Wang Zicheng , Zhu Kejia , Guo Andong , Cao Jishuang , Wu Chenrui , Ding Sentai 
Published: May 2024

AbstractObjectivesWe explored the expression levels and clinical significance of human epidermal growth factor receptor 2 (HER2) in urothelial carcinoma (UC) tissues.Materials and methodsPatient data were reviewed, and 111 paraffin specimens of UC obtained from the Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, from 2020 to 2021 were collected. Immunohistochemistry was used to detect HER2 protein expression in all UC tumor tissues.χ2and Fisher exact tests were used to analyze the relationship between HER2 protein expression and clinicopathological data (sex, age, histopathological diagnosis, invasiveness, histopathological grade, maximum tumor diameter, muscle invasion, regional lymph node metastasis, and clinical stage).ResultsIn this study, 92 cases (82.88%) showed HER2 protein expression, and there was a statistically significant difference in the distribution of HER2 positivity (immunohistochemistry 2+ and 3+) according to the pathological grades of UC (p= .021). Human epidermal growth factor receptor 2 positivity was not associated with sex, age, histopathological diagnosis, invasiveness, maximum tumor diameter, muscle invasion, regional lymph node metastasis, or clinical stage (allp< .05).ConclusionsHER2 protein is highly expressed in UC, and its expression may be closely related to the high pathological grade of UC.
Pulmonary Epithelial Myoepithelial Carcinoma on 18F-FDG PET/CT
Authors: Huang Shuhui , Dai Hongyuan , Huang Rui 
Published: May 2024

Abstract
Pulmonary epithelial myoepithelial carcinoma is very rare. We reported the imaging finding of pulmonary epithelial myoepithelial carcinoma of bronchus in a 61-year-old man on 18F-FDG PET/CT. An irregular mass with an SUVmax of 6.36 growing along right upper lobe bronchus and multiple pulmonary nodules around the mass were found on 18F-FDG PET/CT. Postoperative pathology demonstrated the diagnosis of epithelial myoepithelial carcinoma.
A chromosome-level genome assembly of the cabbage aphidBrevicoryne brassicae
Authors: Wu Jun , Li Guomeng , Lin Zhimou , Zhang Yangzi , Yu Wenyun , Hu Rong , Zhan Shuai , Chen Yazhou 
Published: May 2024

AbstractThe cabbage aphid,Brevicoryne brassicae, is a major pest on Brassicaceae plants, and causes significant yield losses annually. However, lacking genomic resources hinders the progress in understanding this pest at the level of molecular biology. Here, a high-quality, chromosomal-level genome was assembled forB. brassicaebased on PacBio HIFI long-read sequencing and Hi-C data. The final assembled size was 429.99 Mb with a scaffold N50 of 93.31 Mb. Importantly, 96.2% of the assembled sequences were anchored to eight chromosomes. The genome recovered 98.50% of BUSCO genes and 92.30% of CEGMA genes, supporting the high level of completeness. By combining high-coverage transcriptome data, a total of 22,671 protein-coding genes and 3,594 lncRNA genes were annotated. Preliminary comparative genomic analyses were focused on genes related to host colonisation, such as chemosensory- and detoxification-related genes, as well as those encoding putative protein effectors and cross-kingdom lncRNAYa. In summary, our study presents a contiguous and complete genome forB. brassicaethat will benefit our understanding of the biology of it and other aphids.
More extinction driven by Red Queen in smaller habitats
Authors: Liu Xiao , Zhang Quan-Guo 
Published: May 2024

AbstractPopulations in antagonistic coevolutionary interactions may “run or die”, and their fates are determined by their evolutionary potential. The asymmetry of evolutionary speed between coevolving partners, e.g., resulting from genetic constraints, can be mitigated in larger populations. We hypothesize more frequent extinction driven by antagonistic coevolution when habitat size declines. In bacterium-virus systems, viruses (the consumers) typically suffer an evolutionary disadvantage due to constraints of genetic variation; and this pattern may apply to host-parasite interactions in general. Here in our experiment with the bacteriumPseudomonas fluorescensSBW25 and its lytic phage virus SBW25Φ2, the likelihood of viral extinction was greater in smaller habitats. Among viral populations that did persist, those from small habitats showed lower infectivity and their coevolving bacterial populations had greater densities. Therefore, the impact of habitat size reduction on biodiversity could be exacerbated by coevolutionary processes. Our results also lead to a number of suggestions for biocontrol practices, particularly for evolutionary training of phages.
ctQCimproves biological inferences from single cell and spatial transcriptomics data
Authors: Lakshmanan Vairavan , Kahraman Merve , Macalinao Dominique Camat , Gunn Nicole , Venkatesh Prasanna Nori , Meihuan Chang , Fu Cherylin , Qiang Leow Wei , Tan Iain Beehuat , Prabhakar Shyam 
Published: May 2024

AbstractQuality control (QC) is the first critical step in single cell and spatial data analysis pipelines. QC is particularly important when analysing data from primary human samples, since genuine biological signals can be obscured by debris, perforated cells, cell doublets and ambient RNA released into the “soup” by cell lysis. Consequently, several QC methods for single cell data, employ fixed or data-driven quality thresholds. While these approaches efficiently remove empty droplets, they often retain low-quality cells. Here, we propose cell type-specific QC (ctQC), a stringent, data-driven QC approach that adapts to cell type differences and discards soup and debris. Evaluating single cell RNA-seq data from colorectal tumors, human spleen, and peripheral blood mononuclear cells, we demonstrate thatctQCoutperforms existing methods by improving cell type separation in downstream clustering, suppressing cell stress signatures, revealing patient-specific cell states, eliminating artefactual clusters and reducing ambient RNA artifacts. When applied to sequencing-based spatial RNA profiling data (Slide-seq),ctQCimproved spatial coherence of cell clusters and consistency with anatomical structures. These results demonstrate that strict, data-driven, cell-type-specific QC is applicable to diverse sample types and substantially improves the quality and reliability of biological inferences from single cell and spatial RNA profiles.
Targeting a shared neoepitope derived from non-canonical translation of c-MYConcogene in cancer cells
Authors: Baulu E. , Bolon A. , Etchegaray E. , Raimundo F. , Merienne A. , Martin J. , Grandsire J. , Richard T. , Tonon L. , Dubois C. , Estornes Y. , Boulos R. , Tabone O. , Bonaventura P. , Page A. , Gardet C. , Alcazer V. , Hughes S. , Gillet B. , Gervois N. , Labarrière N. , Wang Q. , Valladeau-Guilemond J. , Chuvin N. , Marcel V. , Diaz J- J. , Depil S. 
Published: May 2024

AbstractCancer cells rely on alternative modes of translation for protein synthesis, promoting internal ribosome entry site (IRES)-dependent translation of mRNA encoding pro-oncogenic factors. Furthermore, ribosomes translate mRNA with lower fidelity in tumor cells. We proposed that these translational modifications in cancer produce shared tumor-specific epitopes derived from IRES-containing oncogenes. To identify such neoepitopes, we developed anin silico-based method that we applied toc-MYC. We showed that the non-canonical translation ofc-MYCmRNA in cancer cells, involving a (+1) ribosomal frameshift, generates a shared neoepitope which induces high-avidity T cells able to kill tumor cellsin vitroandin vivowhile sparing normal cells. Our data provide preclinical rationale for developing immunotherapies targeting thisc-MYC-derived neoepitope and validate a new type of shared translation-associated neoantigens.
Fast and exact gap-affine partial order alignment with POASTA
Authors: van Dijk Lucas R. , Manson Abigail L. , Earl Ashlee M. , Garimella Kiran V , Abeel Thomas 
Published: May 2024

AbstractMotivationPartial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pangenomics, among many others. Current algorithms to compute the optimal, gap-affine partial order alignment do not scale well to larger graphs and sequences. While heuristic approaches exist, they do not guarantee optimal alignment and sacrifice alignment accuracy.ResultsWe present POASTA, a new optimal algorithm for partial order alignment that exploits long stretches of matching sequence between the graph and a query. We benchmarked POASTA against the state-of-the-art on several diverse bacterial gene datasets and demonstrated an average speed-up of 4.1x and up to 9.8x, using less memory. POASTA’s memory scaling characteristics enabled the construction of much larger POA graphs than previously possible, as demonstrated by megabase-length alignments of 342Mycobacterium tuberculosissequences.Availability and implementationPOASTA is available on Github athttps://github.com/broadinstitute/poasta.
Stromal mediated DNA damage promotes high grade serous ovarian cancer initiation
Authors: Garcia Geyon L. , Orellana Taylor , Gorecki Grace , Frisbie Leonard G. , Baruwal Roja , Goldfield Ester , Beddows Ian , MacFawn Ian P. , Britt Ananya K. , Hale Macy M. , Shen Hui , Buckanovich Ronald , Finkel Toren , Drapkin Ronny , Soong T. Rinda , Bruno Tullia C. , Atiya Huda I. , Coffman Lan 
Published: May 2024

AbstractThe fundamental steps in high-grade serous ovarian cancer (HGSOC) initiation are unclear, thus providing critical barriers to the development of prevention or early detection strategies for this deadly disease. Increasing evidence demonstrates most HGSOC starts in the fallopian tube epithelium (FTE). Current models propose HGSOC initiates when FTE cells acquire increasing numbers of mutations allowing cells to evolve into serous tubal intraepithelial carcinoma (STIC) precursors and then to full blown cancer. Here we report that epigenetically altered mesenchymal stem cells (termed high risk MSC-hrMSCs) can be detected prior to the formation of ovarian cancer precursor lesions. These hrMSCs drive DNA damage in the form of DNA double strand breaks in FTE cells while also promoting the survival of FTE cells in the face of DNA damage. Indicating the hrMSC may actually drive cancer initiation, we find hrMSCs induce full malignant transformation of otherwise healthy, primary FTE resulting in metastatic cancerin vivo. Further supporting a role for hrMSCs in cancer initiation in humans, we demonstrate that hrMSCs are highly enriched in BRCA1/2 mutation carriers and increase with age. Combined these findings indicate that hrMSCs may incite ovarian cancer initiation. These findings have important implications for ovarian cancer detection and prevention.
Enzymes enabling the biosynthesis of various C20polyunsaturated fatty acids in a sea urchinHemicentrotus pulcherrimus
Authors: Peng Yingying , Haga Yutaka , Kabeya Naoki 
Published: May 2024

AbstractSea urchins, integral to marine ecosystems and valued as a delicacy in Asia and Europe, contain physiologically important long-chain (>C20) polyunsaturated fatty acids (PUFA) in their gonads, including arachidonic acid (ARA, 20:4n-6), eicosapentaenoic acid (EPA, 20:5n-3), and unusual non-methylene interrupted fatty acids (NMI-FA) such as 20:2Δ5,11. Although these fatty acids may partially be derived from their diet, such as macroalgae, the present study onHemicentrotus pulcherrimushas uncovered multiple genes encoding enzymes involved in LC-PUFA biosynthesis. Specifically, three fatty acid desaturases (FadsA, FadsC1 and FadsC2) and thirteen elongation of very-long chain fatty acids proteins (Elovl-like, Elovl1/7-like, Elovl2/5-like, Elovl4-like, Elovl8-like, Elovl6-like A to H) were identified in their genome and transcriptomes. Functional analysis showed that FadsA and FadsC2 function as a Δ5 desaturase and a Δ8 desaturase, respectively, enabling the conversion of 18:2n-6 and 18:3n-3 into ARA and EPA, respectively, along with Elovl, particularly Elovl6-like C. Elovl6-like C demonstrates elongase activity towards both C18PUFA and monounsaturated fatty acids (MUFA). Consequently, FadsA and Elovl6-like C enable to synthesise several NMI-FA, including 20:2Δ5,11and 20:3Δ5,11,14, from C18precursors. This indicates thatH. pulcherrimuscan endogenously synthesise a wide variety of C20PUFA and NMI-FA, highlighting active biosynthesis pathways within sea urchins.
PCBS: an R package for fast and accurate analysis of bisulfite sequencing data
Authors: Lande Kathryn , Williams April E. 
Published: May 2024

AbstractMotivationWhole-genome bisulfite sequencing is a powerful tool for analyzing chromatin methylation genome-wide, but analysis of whole-genome bisulfite data is hampered by slow, inaccurate, and inflexible pipelines.ResultsWe developed PCBS, a computationally efficient R package for Whole Genome Bisulfite Sequencing analysis that demonstrates remarkable accuracy and flexibility compared to current tools. PCBS identifies differentially methylated loci and differentially methylated regions and offers novel functionality that allows for more targeted methylation analyses. PCBS uses minimal computational resources; a complete pipeline in mouse can run on a local RStudio instance in a matter of minutes.Availability and ImplementationPCBS is an R package available under a GNU GPLv3 license at:https://github.com/katlande/PCBSand from CRAN:https://CRAN.R-project.org/package=PCBS. Instructions for use are available at:https://katlande.github.io/PCBS/.Supplementary Information“Supplementary data are available on BioRXiv.”