bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ensembl 2023
Authors: Martin Fergal J , Amode M Ridwan , Aneja Alisha , Austine-Orimoloye Olanrewaju , Azov Andrey G , Barnes If , Becker Arne , Bennett Ruth , Berry Andrew , Bhai Jyothish , Bhurji Simarpreet Kaur , Bignell Alexandra , Boddu Sanjay , Branco Lins Paulo R , Brooks Lucy , Ramaraju Shashank Budhanuru , Charkhchi Mehrnaz , Cockburn Alexander , Da Rin Fiorretto Luca , Davidson Claire , Dodiya Kamalkumar , Donaldson Sarah , El Houdaigui Bilal , El Naboulsi Tamara , Fatima Reham , Giron Carlos Garcia , Genez Thiago , Ghattaoraya Gurpreet S , Martinez Jose Gonzalez , Guijarro Cristi , Hardy Matthew , Hollis Zoe , Hourlier Thibaut , Hunt Toby , Kay Mike , Kaykala Vinay , Le Tuan , Lemos Diana , Marques-Coelho Diego , Marugán José Carlos , Merino Gabriela Alejandra , Mirabueno Louisse Paola , Mushtaq Aleena , Hossain Syed Nakib , Ogeh Denye N , Sakthivel Manoj Pandian , Parker Anne , Perry Malcolm , Piližota Ivana , Prosovetskaia Irina , Pérez-Silva José G , Salam Ahamed Imran Abdul , Saraiva-Agostinho Nuno , Schuilenburg Helen , Sheppard Dan , Sinha Swati , Sipos Botond , Stark William , Steed Emily , Sukumaran Ranjit , Sumathipala Dulika , Suner Marie-Marthe , Surapaneni Likhitha , Sutinen Kyösti , Szpak Michal , Tricomi Francesca Floriana , Urbina-Gómez David , Veidenberg Andres , Walsh Thomas A , Walts Brandon , Wass Elizabeth , Willhoft Natalie , Allen Jamie , Alvarez-Jarreta Jorge , Chakiachvili Marc , Flint Bethany , Giorgetti Stefano , Haggerty Leanne , Ilsley Garth R , Loveland Jane E , Moore Benjamin , Mudge Jonathan M , Tate John , Thybert David , Trevanion Stephen J , Winterbottom Andrea , Frankish Adam , Hunt Sarah E , Ruffier Magali , Cunningham Fiona , Dyer Sarah , Finn Robert D , Howe Kevin L , Harrison Peter W , Yates Andrew D , Flicek Paul 
Published: November 2022

Abstract
Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.
SEdb 2.0: a comprehensive super-enhancer database of human and mouse
Authors: Wang Yuezhu , Song Chao , Zhao Jun , Zhang Yuexin , Zhao Xilong , Feng Chenchen , Zhang Guorui , Zhu Jiang , Wang Fan , Qian Fengcui , Zhou Liwei , Zhang Jian , Bai Xuefeng , Ai Bo , Liu Xinyu , Wang Qiuyu , Li Chunquan 
Published: November 2022

Abstract
Super-enhancers (SEs) are cell-specific DNA cis-regulatory elements that can supervise the transcriptional regulation processes of downstream genes. SEdb 2.0 (http://www.licpathway.net/sedb) aims to provide a comprehensive SE resource and annotate their potential roles in gene transcriptions. Compared with SEdb 1.0, we have made the following improvements: (i) Newly added the mouse SEs and expanded the scale of human SEs. SEdb 2.0 contained 1 167 518 SEs from 1739 human H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) samples and 550 226 SEs from 931 mouse H3K27ac ChIP-seq samples, which was five times that of SEdb 1.0. (ii) Newly added transcription factor binding sites (TFBSs) in SEs identified by TF motifs and TF ChIP-seq data. (iii) Added comprehensive (epi)genetic annotations of SEs, including chromatin accessibility regions, methylation sites, chromatin interaction regions and topologically associating domains (TADs). (iv) Newly embedded and updated search and analysis tools, including ‘Search SE by TF-based’, ‘Differential-Overlapping-SE analysis’ and ‘SE-based TF–Gene analysis’. (v) Newly provided quality control (QC) metrics for ChIP-seq processing. In summary, SEdb 2.0 is a comprehensive update of SEdb 1.0, which curates more SEs and annotation information than SEdb 1.0. SEdb 2.0 provides a friendly platform for researchers to more comprehensively clarify the important role of SEs in the biological process.
Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9
Authors: Mukherjee Supratim , Stamatis Dimitri , Li Cindy Tianqing , Ovchinnikova Galina , Bertsch Jon , Sundaramurthi Jagadish Chandrabose , Kandimalla Mahathi , Nicolopoulos Paul A , Favognano Alessandro , Chen I-Min A , Kyrpides Nikos C , Reddy T B K 
Published: November 2022

Abstract
The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute (DOE-JGI) continues to maintain its role as one of the flagship genomic metadata repositories of the world. The ever-increasing number of projects and metadata are freely available to the user community world-wide. GOLD’s metadata is consumed by scientists and remains an important source for large-scale comparative genomics analysis initiatives. Encouraged by this active user engagement and growth, GOLD has continued to add new components and capabilities. The new features such as a public Application Programming Interface (API) and Ecosystem landing page as well as the growth of different entities in this current GOLD v.9 edition are described in detail in this manuscript.
ARL13B promotes angiogenesis and glioma growth by activating VEGFA-VEGFR2 signaling
Authors: Chen Limin , Xie Xinsheng , Wang Tiantian , Xu Linlin , Zhai Zhenyu , Wu Haibin , Deng Libin , Lu Quqin , Chen Zhengjun , Yang Xiao , Lu Hua , Chen Ye-Guang , Luo Shiwen 
Published: November 2022

Abstract

Background
Tumor angiogenesis is essential for solid tumor progression, invasion and metastasis. The aim of this study was to identify potential signaling pathways involved in tumor angiogenesis.

Methods
Genetically engineered mouse models were used to investigate the effects of endothelial ARL13B(ADP-ribosylation factor-like GTPase 13B) over-expression and deficiency on retinal and cerebral vasculature. An intracranially transplanted glioma model and a subcutaneously implanted melanoma model were employed to examine the effects of ARL13B on tumor growth and angiogenesis. Immunohistochemistry was used to measure ARL13B in glioma tissues, and scRNA-seq was used to analyze glioma and endothelial ARL13B expression. GST-fusion protein-protein interaction and co-immunoprecipitation assays were used to determine the ARL13B-VEGFR2 interaction. Immunobloting, qPCR, dual-luciferase reporter assay and functional experiments were performed to evaluate the effects of ARL13B on VEGFR2 activation.

Results
Endothelial ARL13B regulated vascular development of both the retina and brain in mice. Also, ARL13B in endothelial cells regulated the growth of intracranially transplanted glioma cells and subcutaneously implanted melanoma cells by controlling tumor angiogenesis. Interestingly, this effect was attributed to ARL13B interaction with VEGFR2, through which ARL13B regulated the membrane and ciliary localization of VEGFR2 and consequently activated its downstream signaling in endothelial cells. Consistent with its oncogenic role, ARL13B was highly expressed in human gliomas, which was well correlated with the poor prognosis of glioma patients. Remarkably, ARL13B, transcriptionally regulated by ZEB1, enhanced the expression of VEGFA by activating Hedgehog signaling in glioma cells.

Conclusions
ARL13B promotes angiogenesis and tumor growth by activating VEGFA-VEGFR2 signaling. Thus, targeting ARL13B might serve as a potential approach for developing an anti-glioma or anti-melanoma therapy.
Models for Zero-Inflated and Overdispersed Correlated Count Data: An Application to Cigarette Use
Authors: Pittman Brian , Buta Eugenia , Garrison Kathleen , Gueorguieva Ralitza 
Published: November 2022

AbstractIntroductionCount outcomes in tobacco research are often analyzed with the Poisson distribution. However, they often exhibit features such as overdispersion (variance larger than expected) and zero inflation (extra zeros) that violate model assumptions. Furthermore, longitudinal studies have repeated measures that generate correlated counts. Failure to account for overdispersion, zero inflation, and correlation can yield incorrect statistical inferences. Thus, it is important to familiarize researchers with proper models for such data.Aims and MethodsPoisson and Negative Binomial models with correlated random effects with and without zero inflation are presented. The illustrative data comes from a study comparing a mindfulness training app (Craving to Quit [C2Q], n = 60) with a control app (experience sampling-only app, n = 66) on smoking frequency at 1, 3, and 6 months. Predictors include app, time, the app-by-time interaction, and baseline smoking. Each model is evaluated in terms of accounting for zero inflation, overdispersion, and correlation in the data. Emphasis is placed on evaluating model fit, subject-specific interpretation of effects, and choosing an appropriate model.ResultsThe hurdle Poisson model provided the best fit to the data. Smoking abstinence rates were 33%, 32%, and 28% at 1, 3, and 6 months, respectively, with variance larger than expected by a factor &gt;7 at each follow-up. Individuals on C2Q were less likely to achieve abstinence across time but likely to smoke fewer cigarettes if smoking.ConclusionsThe models presented are specifically suited for analyzing correlated count outcomes and account for zero inflation and overdispersion. We provide guidance to researchers on the use of these models to better inform nicotine and tobacco research.ImplicationsIn tobacco research, count outcomes are often measured repeatedly on the same subject and thus correlated. Such outcomes often have many zeros and exhibit large variances relative to the mean. Analyzing such data require models specifically suited for correlated counts. The presented models and guidelines could improve the rigor of the analysis of correlated count data and thus increase the impact of studies in nicotine and tobacco research using such outcomes.
Slaves and War
Authors: Ducrey Pierre 
Published: November 2022

Abstract
Abstract and Keywords
War, piracy, and banditry resulted in people’s enslavement and were sources of supply for the slave workforce. Many slaves in Graeco-Roman society were the product of conflict, though uncertainties often remain about precise numbers. War was primarily the business of citizens and free men. However, it was normal for armies to include slaves as attendants. In the Greek world, in particular, slaves frequently served as rowers in the fleet; they could also sometimes be involved as combatants in land warfare, especially when conscripted in crisis situations—although it is frequently impossible to calculate numbers of slave combatants. Some slaves took more active initiatives, volunteering to fight or provide logistical support for the state in which they resided, fleeing from servitude, or assisting the enemy. Occasionally, slaves initiated and fought wars of rebellion, especially in late Republican Rome. The roles and impact of slaves in war were often significant, if incalculable.
Cluster formation in neutron-rich Be and B isotopes
Authors: Motoki Hideaki , Suzuki Yoshiki , Kawai Tsuyoshi , Kimura Masaaki 
Published: November 2022

Abstract
Evaluating the formation of clusters in finite and infinite nuclear systems is a fundamental problem in nuclear physics, and the variation in clustering in the isotope chain up to the neutron drip-line is one such intriguing phenomenon. Recently, experiments performed using the (p, pα) reactions have revealed a negative correlation between α-cluster formation and neutron number in Sn isotopes, showing a trend opposite to that theoretically predicted for Be and B isotopes. Although the observed charge radii of the Be and B isotopes suggest the formation of clusters as the neutron drip-line is approached, these radii themselves are not a physical quantity that can directly probe the cluster structure. Here, we directly investigate the cluster formation in Be and B isotopes to elucidate the possibility of clustering as the neutron drip-line is approached. It has been shown that the sum of the S-factors (i.e., S(α), S(6He), and S(8He)) increases as the neutron drip-line approaches, in agreement with those of previous studies. The results indicate that the excess neutrons contribute to the formation of 6He and 8He clusters as well as α clusters. Thus, S(α) is not sufficient to estimate the enhancement of clustering in Be and B isotopes.
Childhood deprivation and Health related quality of life and associated factors among Pediatric cancer patients at National Hospital, Tanzania
Authors: Chubi Mwanaheri , Kibusi Stephen , Chirande Lulu , Juma Shakiru 
Published: November 2022

AbstractIntroductionPediatrics cancer is one of the most important life-threatening, non-communicable diseases worldwide. However, pediatric cancer patients suffer from physical disabilities associated with cancer treatment. However, there is unclear information about level of health-related quality of life and associated factors. Aimed of this study was to assess level of Health-Related Quality of Life among pediatric cancer patients.MethodsA hospital-based Analytical cross-sectional study design with a quantitative approach was employed among 91 conveniently sampled pediatric cancer patients with their parents/caregivers. Self-administered questionnaires were used to collect data. Data were analyzed using SPSS computer software program version 25. One-way ANOVA and linear regression were used to quantify and establish an association between Childhood Deprivation, Health-Related Quality of Life, and associated factors among Pediatric Cancer Patients at 95% CI, and a 5% level of significance.ResultsResults, the response rate was 92.3% (n = 84). The most prominent kind of pediatric cancer was Acute Lymphoblastic Leukemia 30 (35.7%) and Hodgkin lymphoma 11(13%). The mean age of pediatric cancer patients was 10.26±3.90 years while 59 (70.2%) were male. In linear regression, Childhood Deprivation (β=-1.640; P-value< 0.05) on PedsQL™ 4.0 and (β= -2.175; P-value< 0.01) on PedsQL™ 3.0. Findings imply that decreases the level of Childhood Deprivation, the chance of improving Quality of life increases.ConclusionThe magnitude of acute lymphoblastic leukemia is higher among pediatric cancer patients. There was a significant link between pediatric cancers and childhood deprivation and thus, compromised quality of life. Innovative pediatric cancer care policies, guidelines, and or strategies may need to be advocated to address the problem accordingly.
The potential of resilience indicators to signal the risk of disease outbreaks, a systematic review and guide
Authors: Delecroix Clara , van Nes Egbert H. , van de Leemput Ingrid A. , Rotbarth Ronny , Scheffer Marten , Bosch Quirine ten 
Published: November 2022

AbstractTo reduce the consequences of infectious disease outbreaks, the timely implementation of public health measures is crucial. Currently used early-warning systems are highly context-dependent and require a long phase of model building. A proposed solution to anticipate the onset or termination of an outbreak is the use of so-called resilience indicators. These indicators are based on the generic theory of critical slowing down and require only incidence time series. Here we assess the potential for this approach to contribute to outbreak anticipation. We systematically reviewed studies that used resilience indicators to predict outbreaks or terminations of epidemics. We identified 37 studies meeting the inclusion criteria: 21 using simulated data and 16 real-world data. 36 out of 37 studies detected significant signs of critical slowing down before a critical transition (i.e., the onset or end of an outbreak), with a sensitivity (i.e., the proportion of true positive outbreak warnings) ranging from 0.67 to 1 and a lead time ranging from 10 days to 68 months. Challenges include low resolution and limited length of time series, a too rapid increase in cases, and strong seasonal patterns which may hamper the sensitivity of resilience indicators. Alternative types of data, such as Google searches or social media data, have the potential to improve predictions in some cases. Resilience indicators may be useful when the risk of disease outbreaks is changing gradually. This may happen, for instance, when pathogens become increasingly adapted to an environment or evolve gradually to escape immunity. High-resolution monitoring is needed to reach sufficient sensitivity. If those conditions are met, resilience indicators could help improve the current practice of prediction, facilitating timely outbreak response. We provide a step-by-step guide on the use of resilience indicators in infectious disease epidemiology, and guidance on the relevant situations to use this approach.
Long-term humoral response following simultaneous Delta and Omicron BA.1 co-infection
Authors: Saade Carla , Pozzetto Bruno , Novoa Melyssa Yaugel , Lina Bruno , Paul Stéphane , Bal Antonin , Trouillet-Assant Sophie 
Published: November 2022

AbstractTo provide insight into the long-term immune response following bivalent vaccines, we sampled vaccinated patients simultaneously co-infected with Delta and BA.1. We reported that simultaneous exposure to the Delta and BA.1 S protein does not confer an additional immune advantage compared to exposure to the Omicron BA.1 S protein alone.
Autism Classification using Visual and Behavioral Data
Authors: Hriti Nafisa Sadaf , Shaer Karishma , Momin Farhan M Nafis , Mahmud Hasan , Hasan Md. Kamrul 
Published: November 2022

1AbstractCurrently Autism Spectrum Disorder (ASD) is diagnosed via the combination of multiple medical tools and screening tests that require extensive amounts of time and money. Autism diagnosis can be formulated as a typical machine learning classification problem between ASD patients and a control group consisting of neurotypical individuals. In order for this to yield accurate results, large datasets with different modalities are required. However, the unavailability of such robust datasets stands as a threat to this automated diagnosis. To resolve this, we propose a method of Autism Classification using Visual and Behavioral Data. The proposed technique relates datasets of two modalities (visual and behavioral) collected from similar participants by generating common attributes among the records and distributing these records into sub classes. Then records within these subclasses are combined to form an integrated dataset. Finally, decision level fusion is performed on the multimodal data. The main contribution of our work can be outlined as follows: an accuracy of 97.57% in autism classification has been obtained from the integrated data, which is higher than detection from only visual data, we have shown that combining data within sub classes based on common attributes is more accurate than combining them arbitrarily, and finally, we have introduced a novel, integrated multimodal dataset in the ASD domain.
Synthesis and Biological Evaluation of New Isoxazolyl Steroids as Anti-Prostate Cancer Agents
Authors: Rudovich Anton S. , Peřina Miroslav , Krech Anastasiya V. , Novozhilova Maria Y. , Tumilovich Anastasia M , Shkel Tatyana V. , Grabovec Irina P. , Kvasnica Miroslav , Mada Lukáš , Zavialova Maria G. , Mekhtiev Arif R. , Jorda Radek , Zhabinskii Vladimir N. , Khripach Vladimir A. 
Published: November 2022

AbstractSteroids with a nitrogen-containing heterocycle in the side chain are known as effective inhibitors of androgen signaling and/or testosterone biosynthesis, thus showing beneficial effects for the treatment of prostate cancer. In this work, a series of 3β-hydroxy-5-ene steroids containing an isoxazole fragment in the side chain was synthesized. The key steps included the preparation of Weinreb amide, its conversion to acetylenic ketones, and the 1,2- or 1,4-addition of hydroxylamine, depending on the solvent used. The biological activity of the obtained compounds was studied in a number of tests, including their effects on 17α-hydroxylase and 17,20-lyase activity of human CYP17A1 and the ability of selected compounds to affect the downstream androgen receptor signaling. Three derivatives diminished the transcriptional activity of androgen receptor and displayed reasonable antiproliferative activity. The candidate compound24j, (17R)-17-((3-(2-hydroxy-propan-2-yl)isoxazol-5-yl)methyl)-androst-5-en-3β-ol, suppressed the androgen receptor signaling and decreased its protein level in two prostate cancer cell lines, LNCaP and LAPC-4. Interaction of compounds with CYP17A1 and androgen receptor was confirmed and described by molecular docking.
Internal Validation of the ForenSeq Kintelligence Kit for Application to Forensic Genetic Genealogy
Authors: Peck Michelle A. , Koeppel Alexander F. , Gorden Erin M. , Bouchet Jessica L. , Heaton Mary C. , Russell David A. , Reedy Carmen R. , Neal Christina M. , Turner Stephen D. 
Published: November 2022

AbstractForensic Genetic Genealogy (FGG) requires high density single nucleotide polymorphism (SNP) profiles to infer distant relationships. The ForenSeq Kintelligence kit is a recently developed method targeting approximately 10,000 SNPs that were selected to be compatible with genetic genealogy databases, while avoiding medically relevant SNPs. The targeted PCR method is ideal for low input and degraded samples, which are particularly challenging for microarray analysis. We made modifications to library preparation and sample pooling to further enhance the performance of low input samples. To align this FGG method with forensic laboratory standards, we performed an internal validation study in accordance with the Scientific Working Group on DNA Analysis Methods Validation Guidelines for DNA Analysis Methods. The sensitivity and precision and accuracy studies produced accurate and reliable profiles down to 0.05 ng of DNA. The mixture and contamination studies demonstrated that the method could detect the presence of a minor contributor down to 0.02 ng, while system wide contamination was negligible. Nonprobative bone, fired shell casing, and adhesive tape samples performed well with inputs ranging from 0.05 to 1.0 ng of DNA. A bone with a high degradation index and tested at 0.1 ng DNA input resulted in a call rate of 92.9% and a heterozygosity rate of 0.387. We demonstrated the importance of both call rate and heterozygosity rate to assess profile performance. Validating FGG methods is critical to ensuring the reliability and utility of SNP profiles that will be uploaded to genetic genealogy databases for the purpose of generating investigative leads.