bluuebunny/crossref_metadata_2025_split huggingface dataset:
StORF-Reporter: finding genes between genes
Authors: Dimonaco Nicholas J , Clare Amanda , Kenobi Kim , Aubrey Wayne , Creevey Christopher J 
Published: October 2023

Abstract
Large regions of prokaryotic genomes are currently without any annotation, in part due to well-established limitations of annotation tools. For example, it is routine for genes using alternative start codons to be misreported or completely omitted. Therefore, we present StORF-Reporter, a tool that takes an annotated genome and returns regions that may contain missing CDS genes from unannotated regions. StORF-Reporter consists of two parts. The first begins with the extraction of unannotated regions from an annotated genome. Next, Stop-ORFs (StORFs) are identified in these unannotated regions. StORFs are open reading frames that are delimited by stop codons and thus can capture those genes most often missing in genome annotations. We show this methodology recovers genes missing from canonical genome annotations. We inspect the results of the genomes of model organisms, the pangenome of Escherichia coli, and a set of 5109 prokaryotic genomes of 247 genera from the Ensembl Bacteria database. StORF-Reporter extended the core, soft-core and accessory gene collections, identified novel gene families and extended families into additional genera. The high levels of sequence conservation observed between genera suggest that many of these StORFs are likely to be functional genes that should now be considered for inclusion in canonical annotations.
scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species
Authors: Qian Feng-Cui , Zhou Li-Wei , Zhu Yan-Bing , Li Yan-Yu , Yu Zheng-Min , Feng Chen-Chen , Fang Qiao-Li , Zhao Yu , Cai Fu-Hong , Wang Qiu-Yu , Tang Hui-Fang , Li Chun-Quan 
Published: October 2023

Abstract
Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, &gt;400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.
The IUPHAR/BPS Guide to PHARMACOLOGY in 2024
Authors: Harding Simon D , Armstrong Jane F , Faccenda Elena , Southan Christopher , Alexander Stephen P H , Davenport Anthony P , Spedding Michael , Davies Jamie A 
Published: October 2023

Abstract
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; https://www.guidetopharmacology.org) is an open-access, expert-curated, online database that provides succinct overviews and key references for pharmacological targets and their recommended experimental ligands. It includes over 3039 protein targets and 12 163 ligand molecules, including approved drugs, small molecules, peptides and antibodies. Here, we report recent developments to the resource and describe expansion in content over the six database releases made during the last two years. The database update section of this paper focuses on two areas relating to important global health challenges. The first, SARS-CoV-2 COVID-19, remains a major concern and we describe our efforts to expand the database to include a new family of coronavirus proteins. The second area is antimicrobial resistance, for which we have extended our coverage of antibacterials in partnership with AntibioticDB, a collaboration that has continued through support from GARDP. We discuss other areas of curation and also focus on our external links to resources such as PubChem that bring important synergies to the resources.
PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters
Authors: Chow Chi-Nga , Yang Chien-Wen , Wu Nai-Yun , Wang Hung-Teng , Tseng Kuan-Chieh , Chiu Yu-Hsuan , Lee Tzong-Yi , Chang Wen-Chi 
Published: October 2023

Abstract
PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 species. PlantPAN 4.0 can help users characterize the evolutionary differences and similarities among cis-regulatory elements; furthermore, this system can now help in identification of conserved non-coding sequences among homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices for 18305 transcription factors; this expansion helps in exploration of combinational and nucleotide variants of cis-regulatory elements in conserved non-coding sequences. Additionally, the genomic landscapes of regulatory factors were manually updated, and ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) were added. Furthermore, the statistical review and graphical analysis components were improved to offer intelligible information through ChIP-seq data analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces for the identification of promoter regions’ binding preferences by considering experimental condition clusters and peak visualization for all regulatory factors, and the 20 most significantly enriched gene ontology functions for regulatory factors. Thus, PlantPAN 4.0 can effectively reconstruct gene regulatory networks and help compare genomic cis-regulatory elements across plant species and experiments.
ViralZone 2024 provides higher-resolution images and advanced virus-specific resources
Authors: De Castro Edouard , Hulo Chantal , Masson Patrick , Auchincloss Andrea , Bridge Alan , Le Mercier Philippe 
Published: October 2023

Abstract
ViralZone (http://viralzone.expasy.org) is a knowledge repository for viruses that links biological knowledge and databases. It contains data on virion structure, genome, proteome, replication cycle and host-virus interactions. The new update provides better access to the data through contextual popups and higher resolution images in Scalable Vector Graphics (SVG) format. These images are designed to be dynamic and interactive with human viruses to give users better access to the data. In addition, a new coronavirus-specific resource provides regularly updated data on variants and molecular biology of SARS-CoV-2. Other virus-specific resources have been added to the database, particularly for HIV, herpesviruses and poxviruses.
COV2Var, a function annotation database of SARS-CoV-2 genetic variation
Authors: Feng Yuzhou , Yi Jiahao , Yang Lin , Wang Yanfei , Wen Jianguo , Zhao Weiling , Kim Pora , Zhou Xiaobo 
Published: October 2023

AbstractThe COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss of millions of lives and severe global economic consequences. Every time SARS-CoV-2 replicates, the viruses acquire new mutations in their genomes. Mutations in SARS-CoV-2 genomes led to increased transmissibility, severe disease outcomes, evasion of the immune response, changes in clinical manifestations and reducing the efficacy of vaccines or treatments. To date, the multiple resources provide lists of detected mutations without key functional annotations. There is a lack of research examining the relationship between mutations and various factors such as disease severity, pathogenicity, patient age, patient gender, cross-species transmission, viral immune escape, immune response level, viral transmission capability, viral evolution, host adaptability, viral protein structure, viral protein function, viral protein stability and concurrent mutations. Deep understanding the relationship between mutation sites and these factors is crucial for advancing our knowledge of SARS-CoV-2 and for developing effective responses. To fill this gap, we built COV2Var, a function annotation database of SARS-CoV-2 genetic variation, available at http://biomedbdc.wchscu.cn/COV2Var/. COV2Var aims to identify common mutations in SARS-CoV-2 variants and assess their effects, providing a valuable resource for intensive functional annotations of common mutations among SARS-CoV-2 variants.
TADB 3.0: an updated database of bacterial toxin–antitoxin loci and associated mobile genetic elements
Authors: Guan Jiahao , Chen Yongkui , Goh Ying-Xian , Wang Meng , Tai Cui , Deng Zixin , Song Jiangning , Ou Hong-Yu 
Published: October 2023

Abstract
TADB 3.0 (https://bioinfo-mml.sjtu.edu.cn/TADB3/) is an updated database that provides comprehensive information on bacterial types I to VIII toxin–antitoxin (TA) loci. Compared with the previous version, three major improvements are introduced: First, with the aid of text mining and manual curation, it records the details of 536 TA loci with experimental support, including 102, 403, 8, 14, 1, 1, 3 and 4 TA loci of types I to VIII, respectively; Second, by leveraging the upgraded TA prediction tool TAfinder 2.0 with a stringent strategy, TADB 3.0 collects 211 697 putative types I to VIII TA loci predicted in 34 789 completely sequenced prokaryotic genomes, providing researchers with a large-scale dataset for further follow-up analysis and characterization; Third, based on their genomic locations, relationships of 69 019 TA loci and 60 898 mobile genetic elements (MGEs) are visualized by interactive networks accessible through the user-friendly web page. With the recent updates, TADB 3.0 may provide improved in silico support for comprehending the biological roles of TA pairs in prokaryotes and their functional associations with MGEs.
Risks and benefits of salicylates in food: a narrative review
Authors: Suliburska Joanna , Cholik Rafsan Syabani 
Published: October 2023

Abstract
Salicylates are generally present in plants as part of their defense system against pathogens and environmental stress. Major dietary sources of salicylates were found in spices and herbs, such as curry and paprika (hot powder). Several studies suggest that these natural salicylates offer health benefits in the human body, such as antidiabetic, anticancer, antiviral, and anti-inflammatory properties. However, despite their advantages, salicylates can be harmful to people with allergies, and high doses of salicylates may cause respiratory alkalosis and gastrointestinal bleeding. Additionally, salicylates can interact with certain drugs, such as nonsteroidal anti-inflammatory drugs and warfarin. This narrative review aimed to consolidate recent information on the content of salicylates in food based on the literature, while also highlighting the benefits and risks associated with salicylate consumption in humans. Based on the literature review and analysis of results, it can be concluded that the dietary intake of salicylates in vegetarians can be relatively high, resulting in concentrations of salicylic acid in the blood and urine that are comparable to those observed in patients taking a low dose of aspirin (75 mg). This suggests that a diet rich in salicylates may have potential benefits in preventing and treating some diseases that require low doses of aspirin.
Diet quality indexes for use during pregnancy: a scoping review
Authors: Robb Liska , Joubert Gina , Walsh Corinna May 
Published: October 2023

Abstract

Aims
High diet quality is related to better health outcomes in general. During pregnancy, a high-quality diet is of paramount importance to promote optimal maternal and neonatal outcomes. This is a scoping review of research available on diet quality indexes (DQIs) for use during pregnancy that summarizes the DQIs in terms of development, country of origin, population used, components, scoring and weighting of components, and evaluation. Furthermore, the DQIs are discussed narratively to inform and direct the development of improved and country-specific DQIs for pregnancy.

Methods
The EBSCOhost database was used to identify English-language, peer-reviewed articles published between 2000 and 2023, from which 11 publications were identified that describe the development of pregnancy-specific DQIs. This review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews model.

Results
Almost all DQIs (n = 9 of 11) were developed in high-income countries, using dietary intake data from food frequency questionnaires. Several DQIs (n = 5 of 11) used the US Healthy Eating Index as basis and modified it in various ways. Almost all DQIs included both foods and nutrients as components (n = 9 of 11), with vegetables being the most commonly included component alone (n = 8 of 11) or combined with fruit (n = 2 of 11).

Conclusion
Because most DQIs were developed using dietary guidelines, recommendations, and dietary intake data from high-income countries, it is recommended that pregnancy-specific DQIs be developed and validated to reflect the nutrition guidelines for lower-income and culturally diverse countries.
A version of Kalton’s theorem for the space of regular homogeneous polynomials on Banach lattices
Authors: Bu Qingying 
Published: October 2023

Abstract
We give a version of Kalton’s theorem for the space of regular homogeneous polynomials on Banach lattices. As applications, we obtain sufficient conditions for the reflexivity of ${\mathcal P}^r(^nE;F)$, the space of regular n-homogeneous polynomials from a Banach lattice E to a Banach lattice F, and sufficient conditions for the positive Grothendieck property of $\hat{\otimes}_{n,s,|\pi|}E$, the n-fold positive projective symmetric tensor product of a Banach lattice E. Moreover, we also prove that these sufficient conditions are also necessary under the bounded regular approximation property.
Up-regulation of the Trace Amine Receptor, TAAR-1, in the Prefrontal Cortex of Individuals Affected by Schizophrenia
Authors: Imbriglio Tiziana , Alborghetti Marika , Bruno Valeria , Battaglia Giuseppe , Nicoletti Ferdinando , Cannella Milena 
Published: October 2023

Abstract

Background and Hypothesis
Type-1 trace amine-associated receptors (TAAR1) modulate dopaminergic and glutamatergic neurotransmission and are targeted by novel antipsychotic drugs. We hypothesized that schizophrenia (SCZ) causes adaptive changes in TAAR1 expression in the prefrontal cortex.

Study Design
We measured TAAR1 mRNA and protein levels by quantitative PCR and immunoblotting in post-mortem prefrontal cortical samples obtained from 23 individuals affected by SCZ and 23 non-schizophrenic controls (CTRL). Data were correlated with a number of variables in both groups.

Study Results
TAAR1 mRNA levels were largely increased in the SCZ prefrontal cortex, and did not correlate with age, age at onset and duration of SCZ, or duration of antipsychotic treatment. For the analysis of TAAR1 protein levels, CTRL and SCZ were divided into 2 subgroups, distinguished by the extent of neuropathological burden. CTRL with low neuropathological burden (LNB) had lower TAAR1 protein levels than CTRL with high neuropathological burden (HNB), whereas no changes were found between LNB and HNB in the SCZ group. TAAR1 protein levels were lower in CTRL with LNB with respect to all SCZ samples or to SCZ samples with LNB. In the SCZ group, levels showed an inverse correlation with the duration of antipsychotic treatment and were higher in individuals treated with second-generation antipsychotics as compared with those treated with first-generation antipsychotics.

Conclusions
The up-regulation of TAAR1 observed in the SCZ prefrontal cortex supports the development of TAAR1 agonists as new promising drugs in the treatment of SCZ.
The urgency of restructuring the landscape of behavioral medicine: Commentary from early-career diversity institute scholars
Authors: Fowler Lauren A , Quiñones-Cordero Maria M , Sidani Jaime E , Bernhart John A , Mendoza-Vasconez Andrea S , Bannon Sarah M , Unni Elizabeth J 
Published: October 2023

Abstract
Structural and systemic barriers entrenched in academia have sustained for decades, and resulted in a lack of diversity in leadership positions, inequitable workloads for women and underrepresented racial/ethnic groups, and increasing issues with retention of faculty, particularly following the COVID-19 pandemic. Increasing opposition to diversity, equity, and inclusion (DEI) efforts in higher education via legislation, policies, and general anti-DEI sentiment contextualizes the importance of prioritizing DEI. The goal of this commentary is to open discussion among academic institutions regarding changes in DEI culture that will facilitate the growth of diverse early-career faculty (ECF). We use an adapted framework which incorporates DEI into a faculty competency model to (i) guide our discussion of the rationale for restructuring academic systems to promote DEI and (ii) recommend strategies for institutional progress for ECF that can translate across academic institutions. Implementing policies and practices that seek to recruit, retain, and support historically underrepresented ECF are needed, and may involve faculty mentorship programs, establishing equitable funding mechanisms, reforming faculty evaluation practices, and examining and correcting inequities in faculty workloads. The onus is on institutions to recognize and replace the exclusionary practices and biases that have existed within their walls, and continuously promote and monitor their DEI efforts and initiatives to ensure their efficacy. Inclusive academic cultures that demonstrate their value of diversity and commitment to equity promotion at all levels of the organization, including among ECF, are necessary for ensuring excellence in scholarship in academia.
Syndecan-1 levels predict septic shock in critically ill patients with COVID-19
Authors: Aragão Nilcyeli Linhares , Zaranza Marza de Sousa , Meneses Gdayllon Cavalcante , Lázaro Ana Paula Pires , Guimarães Álvaro Rolim , Martins Alice Maria Costa , Aragão Natalia Linhares Ponte , Beliero Andrea Mazza , da Silva Júnior Geraldo Bezerra , Mota Sandra Mara Brasileiro , Albuquerque Polianna Lemos Moura Moreira , Daher Elizabeth De Francesco , De Bruin Veralice Meireles Sales , de Bruin Pedro Felipe Carvalhedo 
Published: October 2023

ABSTRACT

Background
The clinical picture of coronavirus disease 2019 (COVID-19)-associated sepsis is similar to that of sepsis of other aetiologies. The present study aims to analyse the role of syndecan-1 (SDC-1) as a potential predictor of septic shock in critically ill patients with COVID-19.

Methods
This is a prospective study of 86 critically ill patients due to COVID-19 infection. Patients were followed until day 28 of hospitalization. Vascular biomarkers, such as vascular cell adhesion protein-1, SDC-1, angiopoietin-1 and angiopoietin-2, were quantified upon admission and associated with the need for vasopressors in the first 7 d of hospitalization.

Results
A total of 86 patients with COVID-19 (mean age 60±16 y; 51 men [59%]) were evaluated. Thirty-six (42%) patients died during hospitalization and 50 (58%) survived. The group receiving vasopressors had higher levels of D-dimer (2.46 ng/ml [interquartile range {IQR} 0.6–6.1] vs 1.01 ng/ml [IQR 0.62–2.6], p=0.019) and lactate dehydrogenase (929±382 U/l vs 766±312 U/l, p=0.048). The frequency of deaths during hospitalization was higher in the group that received vasoactive amines in the first 24 h in the intensive care unit (70% vs 30%, p=0.002). SDC-1 levels were independently associated with the need for vasoactive amines, and admission values &gt;269 ng/ml (95% CI 0.524 to 0.758, p=0.024) were able to predict the need for vasopressors during the 7 d following admission.

Conclusions
Syndecan-1 levels predict septic shock in critically ill patients with COVID-19.
Bioelectrical Synchronisation of Spruce Trees during a Solar Eclipse
Authors: Chiolerio Alessandro , Gagliano Monica , Pilia Silvio , Pilia Paolo , Vitiello Giuseppe , Dehshibi Mohammad Mahdi , Adamatzky Andrew 
Published: October 2023

AbstractRegular light-dark cycles greatly affect organisms, and events like eclipses induce distinctive physiological and behavioural shifts. While well-documented in animals, plant behaviour during eclipses remains largely unexplored. Here we monitored multiple spruce trees to assess their individual and collective bioelectrical responses to a solar eclipse. Trees anticipated the eclipse, synchronising their individual bioelectrical behaviour hours in advance. Older trees displayed greater anticipatory behaviour with early time-asymmetry and entropy increases, characteristic of memory dynamics in open dissipative systems such as trees. These results reveal a complex relationship between individual and collective tree behaviour, shaped by individual age and physiology as well as collective history and memory. This highlights the adaptive significance of synchrony and collective memory in plants, offering new insights on coordinated behaviours in nature.One Sentence SummaryTrees anticipate and respond collectively to a solar eclipse.
The Hill-type equation reveals the regulatory principle of target protein expression led by p53 pulsing
Authors: Shi Xiaomin 
Published: October 2023

AbstractThe central dogma indicates the basic direction of gene expression pathways. For activated gene expression, the quantitative relationship between various links from the binding of transcription factors (TFs) to DNA to protein synthesis remains unclear and debated. There is consensus that at a steady state, protein levels are largely determined by the mRNA level. How can we find this steady state? Taking p53 as an example, based on the previously discovered Hill-type equation that characterizes mRNA expression under p53 pulsing, I proved that the same equation can be used to describe the average steady state of target protein expression. Therefore, at steady state, the average fold changes in mRNA and protein expression under TFs pulsing were the same. This consensus has been successfully demonstrated. For the p53 target geneBAX, the observed fold changes in mRNA and protein expression were 1.40 and 1.28, respectively; the fold changes in mRNA and protein expression calculated using the Hill-type equation were both 1.35. Therefore, using this equation, we can not only fine-tune gene expression, but also predict the proteome from the transcriptome. Furthermore, by introducing two quantitative indicators, we can determine the degree of accumulation and stability of protein expression.