bluuebunny/crossref_metadata_2025_split huggingface dataset:
Health and economic impacts of Lassa vaccination campaigns in West Africa
Authors: Smith David R M , Turner Joanne , Fahr Patrick , Attfield Lauren A , Bessell Paul R , Donnelly Christl A , Gibb Rory , Jones Kate E , Redding David W , Asogun Danny , Ayodeji Oladele Oluwafemi , Azuogu Benedict N , Fischer William A , Jan Kamji , Olayinka Adebola T , Wohl David A , Torkelson Andrew A , Dinkel Katelyn A , Nixon Emily J , Pouwels Koen B , Hollingsworth T Déirdre 
Published: February 2024

AbstractLassa fever is a zoonotic disease identified by the World Health Organization (WHO) as having pandemic potential. This study estimates the health-economic burden of Lassa fever throughout West Africa and projects impacts of a series of vaccination campaigns. We also model the emergence of “Lassa-X” – a hypothetical pandemic Lassa virus variant – and project impacts of achieving 100 Days Mission vaccination targets. Our model predicted 2.7M (95% uncertainty interval: 2.1M-3.4M) Lassa virus infections annually, resulting over ten years in 2.0M (793.8K-3.9M) disability-adjusted life years (DALYs). The most effective vaccination strategy was a population-wide preventive campaign primarily targeting WHO-classified “endemic” districts. Under conservative vaccine efficacy assumptions, this campaign averted $20.1M ($8.2M-$39.0M) in lost DALY value and $128.2M ($67.2M-$231.9M) in societal costs (International dollars 2021). Reactive vaccination in response to local outbreaks averted just one-tenth the health-economic burden of preventive campaigns. In the event of Lassa-X emerging, spreading throughout West Africa and causing approximately 1.2M DALYs within two years, 100 Days Mission vaccination averted 22% of DALYs given a vaccine 70% effective against disease, and 74% of DALYs given a vaccine 70% effective against both infection and disease. These findings suggest how vaccination could alleviate Lassa fever’s burden and assist in pandemic preparedness.
Open Science Practices Among Authors Published in Complementary, Alternative, and Integrative Medicine Journals: An International, Cross-Sectional Survey
Authors: Ng Jeremy Y , Lin Brenda , Kreuder Liliane , Cramer Holger , Moher David 
Published: February 2024

AbstractBackgroundOpen science practices aim to increase transparency in research and increase research availability through open data, open access platforms, and public access. Due to the increasing popularity of complementary, alternative, and integrative medicine (CAIM) research, our study aims to explore current open science practices and perceived barriers among CAIM researchers in their own respective research articles.MethodsWe conducted an international cross-sectional online survey that was sent to authors that published articles in MEDLINE-indexed journals categorized under the broad subject of “Complementary Therapies” or articles indexed under the MeSH term “Complementary Therapies”. Articles were extracted to obtain the names and emails of all corresponding authors. 8,786 researchers were emailed our survey, which included questions regarding participants’ familiarity with open science practices, their open science practices, and perceived barriers to open science in CAIM with respect to participants’ most recently published article. Basic descriptive statistics was generated based on the quantitative data.ResultsThe survey was completed by 292 participants (3.32% response rate). Results indicate that the majority of participants were “very familiar” (n = 83, 31.68%) or “moderately familiar” (n = 83, 31.68%) with the concept of open science practices while creating their study. Open access publishing was the most familiar to participants, with 51.96% (n = 136) of survey respondents publishing with open access. Despite participants being familiar with other open science practices, the actual implementation of these practices was low. Common barriers participants experienced in implementing open science practices include not knowing where to share the study materials, where to share the data, or not knowing how to make a preprint.ConclusionsAlthough participants responded that they were familiar with the concept of open science practices, the actual implementation and uses of these practices were low. Barriers included a lack of overall knowledge about open science, and an overall lack of funding or institutional support. Future efforts should aim to explore how to implement methods to improve open science training for CAIM researchers.
Spatial patterning of the epigenome during vertebrate gastrulation
Authors: Azambuja Ana Paula , Rothstein Megan , Kanno Tatiane Y. , Simoes-Costa Marcos 
Published: February 2024

SummaryEmbryonic patterning relies on the ability of cells to interpret the spatial information they receive from the environment. In vertebrates, this process begins with the localized activation of signaling systems that mediate axial specification. How embryonic cells record these spatial coordinates within their regulatory states has remained unclear. Here, we report that positional information is encoded within the chromatin landscape of embryonic cells. By utilizing spatially resolved genomic analysis in the avian gastrula, we found that the epigenome is organized in gradients of accessibility along the embryonic axes. Positional gradients of chromatin activation are established at thelociof developmental genes at the onset of gastrulation and can be used to predict the location of cells in amniote embryos. Our results show that axial specification involves the spatial patterning of the epigenome and support the existence of a Cartesian system of chromatin activation in the developing embryo.
The emergence and evolution of gene expression in genome regions replete with regulatory motifs
Authors: Fuqua Timothy , Sun Yiqiao , Wagner Andreas 
Published: February 2024

ABSTRACTGene regulation is essential for life and controlled by regulatory DNA. Mutations can modify the activity of regulatory DNA, and also create new regulatory DNA, a process called regulatory emergence. Non-regulatory and regulatory DNA contain motifs to which transcription factors may bind. In prokaryotes, gene expression requires a stretch of DNA called a promoter, which contains two motifs called -10 and -35 boxes. However, these motifs may occur in both promoters and non-promoter DNA in multiple copies. They have been implicated in some studies to improve promoter activity, and in others to repress it. Here, we ask whether the presence of such motifs in different genetic sequences influences promoter evolution and emergence. To understand whether and how promoter motifs influence promoter emergence and evolution, we start from 50 “promoter islands”, DNA sequences enriched with -10 and -35 boxes. We mutagenize these starting “parent” sequences, and measure gene expression driven by 240’000 of the resulting mutants. We find that the probability that mutations create an active promoter varies more than 200-fold, and is not correlated with the number of promoter motifs. For parent sequences without promoter activity, mutations created over 1’500 new -10 and -35 boxes at unique positions in the library, but only ∼0.3% of these resulted in de-novo promoter activity. Only ∼13% of all -10 and -35 boxes contribute to de-novo promoter activity. For parent sequences with promoter activity, mutations create new -10 and -35 boxes in 11 specific positions that partially overlap with preexisting ones to modulate expression. We also find that -10 and -35 boxes do not repress promoter activity. Overall, our work demonstrates how promoter motifs influence promoter emergence and evolution. It has implications for predicting and understanding regulatory evolution, de-novo genes, and phenotypic evolution.
TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics
Authors: Chen Chin-Wen , Lin Pei-Yi , Lai Ying-Mi , Lin Miao-Hsia , Lin Shu-Yu , Hsu Chuan-Chih 
Published: February 2024

AbstractProtein post-translational modifications (PTMs) are crucial in plant cellular processes, particularly in protein folding and signal transduction. N-glycosylation and phosphorylation are notably significant PTMs, playing essential roles in regulating plant responses to environmental stimuli. However, current sequential enrichment methods for simultaneous analysis of phosphoproteome and N-glycoproteome are labor-intensive and time-consuming, limiting their throughput. Addressing this challenge, this study introduces a novel tandem S-Trap-IMAC-HILIC (S-Trap: suspension trapping; IMAC: immobilized metal ion affinity chromatography; HILIC: hydrophilic interaction chromatography) strategy, termed TIMAHAC, for simultaneous analysis of plant phosphoproteomics and N-glycoproteomics. This approach integrates IMAC and HILIC into a tandem tip format, streamlining the enrichment process of phosphopeptides and N-glycopeptides. The key innovation lies in the use of a unified buffer system and an optimized enrichment sequence to enhance efficiency and reproducibility. The applicability of TIMAHAC was demonstrated by analyzing the Arabidopsis phosphoproteome and N-glycoproteome in response to abscisic acid (ABA) treatment. Up to 1,954 N-glycopeptides and 11,255 phosphopeptides were identified from Arabidopsis, indicating its scalability for plant tissues. Notably, distinct perturbation patterns were observed in the phosphoproteome and N-glycoproteome, suggesting their unique contributions to ABA response. Our results reveal that TIMAHAC offers a comprehensive approach to studying complex regulatory mechanisms and PTM interplay in plant biology, paving the way for in-depth investigations into plant signaling networks.
Concatenation of segmented viral genomes for reassortment analysis
Authors: Ivanova A. , Volchkov P. , Deviatkin A. 
Published: February 2024

AbstractMost reassortment identification methods are based on searching for phylogenetic discrepancies between phylogenetic trees for different segments. Other methods use pairwise genetic distances or compare the position of individual genome components in a tree relative to a reference component of the viral genome. However, such approaches are labour-intensive and hardly scalable.Recent advances in the availability of viral sequencing technologies have led to the sequencing of large numbers of pathogen genomes, making manual processing of this large data difficult. At the same time, recombination analysis methods can process almost any number of sequences simultaneously. Such approaches are not suitable for the simultaneous analysis of multiple segments and are therefore not used to search for reassortment events. However, in the case of sequential concatenation of all segments, the methods of recombination analysis can be used to detect traces of reassortment events.The code is available athttps://github.com/melibrun/Concatenation-of-segmented-viral-genomes-for-reassortment-analysis. The service is implemented as a web applicationhttps://melibrun.shinyapps.io/viralsegmentconcatenator1/. It concatenates segmented viral genomes for reassortment analysis. The tool accepts files in GenBank format as input and generates a set of sequences in fasta format that are sequentially concatenated sequences of viral segments named in accordance with the “strain” field of the GenBank record annotation.In order to use recombination search algorithms in the study of reassortment events, we have developed a method (Virus Segment Concatenator, VSC) to automatically concatenate the sequences of all segments of a virus into a single sequence.The applicability of VSC for automated searches for reassortment events was demonstrated using CCHFV, an H5N5 subtype of influenza virus.
Transcriptomic analysis of the human habenula in schizophrenia
Authors: Yalcinbas Ege A. , Ajanaku Bukola , Nelson Erik D. , Garcia-Flores Renee , Eagles Nicholas J. , Montgomery Kelsey D. , Stolz Joshua M. , Wu Joshua , Divecha Heena R. , Chandra Atharv , Bharadwaj Rahul A. , Bach Svitlana , Rajpurohit Anandita , Tao Ran , Pertea Geo , Shin Joo-Heon , Kleinman Joel E. , Hyde Thomas M. , Weinberger Daniel R. , Huuki-Myers Louise A. , Collado-Torres Leonardo , Maynard Kristen R. 
Published: February 2024

AbstractPathophysiology of many neuropsychiatric disorders, including schizophrenia (SCZD), is linked to habenula (Hb) function. While pharmacotherapies and deep brain stimulation targeting the Hb are emerging as promising therapeutic treatments, little is known about the cell type-specific transcriptomic organization of the human Hb or how it is altered in SCZD. Here we define the molecular neuroanatomy of the human Hb and identify transcriptomic changes in individuals with SCZD compared to neurotypical controls. Utilizing Hb-enriched postmortem human brain tissue, we performed single nucleus RNA-sequencing (snRNA-seq; n=7 neurotypical donors) and identified 17 molecularly defined Hb cell types across 16,437 nuclei, including 3 medial and 7 lateral Hb populations, several of which were conserved between rodents and humans. Single molecule fluorescentin situhybridization (smFISH; n=3 neurotypical donors) validated snRNA-seq Hb cell types and mapped their spatial locations. Bulk RNA-sequencing and cell type deconvolution in Hb-enriched tissue from 35 individuals with SCZD and 33 neurotypical controls yielded 45 SCZD-associated differentially expressed genes (DEGs, FDR < 0.05), with 32 (71%) unique to Hb-enriched tissue. eQTL analysis identified 717 independent SNP-gene pairs (FDR < 0.05), where either the SNP is a SCZD risk variant (16 pairs) or the gene is a SCZD DEG (7 pairs). eQTL and SCZD risk colocalization analysis identified 16 colocalized genes. These results identify topographically organized cell types with distinct molecular signatures in the human Hb and demonstrate unique genetic changes associated with SCZD, thereby providing novel molecular insights into the role of Hb in neuropsychiatric disorders.One Sentence SummaryTranscriptomic analysis of the human habenula and identification of molecular changes associated with schizophrenia risk and illness state.
Isolation and characterization of the newStreptomycesphages Kamino, Geonosis, Abafar and Scarif infecting a broad range of host species
Authors: Rackow Bente , Rolland Clara , Mohnen Isabelle , Wittmann Johannes , Müsken Mathias , Overmann Jörg , Frunzke Julia 
Published: February 2024

AbstractStreptomyces, a multifaceted genus of soil-dwelling bacteria within the phylum Actinobacteria, features intricate phage-host interactions shaped by its complex life cycle and the synthesis of a diverse array of specialized metabolites. Here, we describe the isolation and characterization of four novelStreptomycesphages infecting a variety of different host species. While phage Kamino, isolated onStreptomyces kasugaensis, is predicted to be temperate and encodes a serine integrase in its genome, phages Geonosis (isolated onS. griseus) and phages Abafar and Scarif, isolated onS. albidoflavus, are virulent phages. Phages Kamino and Geonosis were shown to amplify well in liquid culture leading to a pronounced culture collapse already at low titres. Determination of the host range by testing >40 differentStreptomycesspecies identified phages Kamino, Abafar and Scarif as broad host range phages, with Kamino showing productive infections on 15 different species. Isolated phages were further tested regarding their sensitivity to antiphage molecules. Here, the strongest effects were observed for the DNA-intercalating molecule daunorubicin. Overall, the phages described in this study expand the publicly available portfolio of phages infectingStreptomycesand will be instrumental for advancing the mechanistic understanding of the intricate antiviral strategies employed by these multicellular bacteria.
Thermal plasticity in protective wing pigmentation is modulated by genotype and food availability in an insect model of seasonal polyphenism
Authors: van Bergen E , Atencio G , Saastamoinen M , Beldade P 
Published: February 2024

ABSTRACTDevelopmental plasticity refers to the phenomenon whereby an organism’s phenotype depends on the environmental conditions experienced during development. This plasticity can match phenotype to ecological conditions and help organisms to cope with environmental heterogeneity, including differences between alternating seasons. Experimental studies of developmental plasticity often focus on the impact of individual environmental cues and do not take explicit account of genetic variation. In contrast, natural environments are complex, comprising multiple variables with combined effects that are poorly understood and may vary among genotypes. We investigated the effects of multifactorial environments on the development of the seasonally plastic eyespots ofBicyclus anynanabutterflies. Eyespot size is known to depend on developmental temperature and to be involved in alternative seasonal strategies for predator avoidance. In nature, both temperature and food availability undergo seasonal fluctuations. However, our understanding of whether thermal plasticity in eyespot size varies in relation to food availability and across genotypes remains limited. To address this, we investigated the combined effects of temperature (T; two levels: 20°C and 27°C) and food availability (N; two levels: control and limited) during development. We examined their impact on wing and eyespot size in adult males and females from multiple genotypes (G; 28 families). We found evidence of thermal and nutritional plasticity, and of temperature-by-nutrition interactions (significant TxN) on the size of eyespots in both sexes. Food limitation resulted in relatively smaller eyespots and tempered the effects of temperature. Additionally, we found differences among families for thermal plasticity (significant GxT effects), but not for nutritional plasticity (non-significant GxN effects) nor for the combined effects of temperature and food limitation (non-significant GxTxN effects). Our results reveal the context dependence of thermal plasticity, with the slope of thermal reaction norms varying across genotypes and across nutritional environments. We discuss these results in light of the ecological significance of pigmentation and the value of considering thermal plasticity in studies of the biological impact of climate change.
Population genomics resolves cryptic species of the ecologically flexible genusLaspinema(cyanobacteria)1
Authors: Dvořák Petr , Skoupý Svatopluk , Jarošová Hana , Páleníčková Kateřina , Stanojković Aleksandar 
Published: February 2024

AbstractCyanobacterial taxonomy is entering the genomic era, but only a few taxonomic studies have employed population genomics, which provides a framework and a multitude of tools to understand species boundaries. Phylogenomic and population genomic analyses previously suggested that several cryptic lineages emerged within the genusLaspinema. Here, we apply population genomics to define boundaries between these lineages and propose new cryptic species,Laspinema olomoucenseandLaspinema palackyanum. Moreover, we sampled soil and puddles across Central Europe and sequenced the 16S rRNA and 16S-23S ITS of the isolatedLaspinemastrains. Together with database mining of 16S rRNA sequences, we found that the genusLaspinemahas a cosmopolitan distribution and inhabits a wide variety of habitats, including freshwater, saline water, mangroves, soil crusts, soils, puddles, and the human body.
Overexpressing NRT2.7 induces nitrate export from the vacuole and increases growth of Arabidopsis
Authors: Armengaud Patrick , De Angeli Alexis , Berquin Patrick , Bréhaut Virginie , Durand Mickaël , Daniel-Vedele Françoise , Krapp Anne , Filleur Sophie 
Published: February 2024

AbstractNitrogen nutrition is essential for crop yield but applying fertilizers has detrimental effects on the environment. Compartmenting nitrate into vacuoles is one of the options to develop Nitrogen-efficient crop adapted to less fertilizers. Only few proteins involved in nitrate transport on the tonoplast have been identified. CLCa is the major transporter involved in nitrate storage in Arabidopsis but it can also facilitate nitrate remobilization from the vacuole in guard cells. Several other nitrate transporters amongst NRT2.7 have been localized in this membrane. The transport mechanism of NRT2.7 has not yet been defined as this protein is present mainly in seed cells that are not easily amenable for electrophysiology analysis. Here, we investigated NRT2.7 function through its ectopic overexpression in aclcaknock-out mutant. Although the growth diminution ofclcaon nitrogen sufficient medium was complemented, nitrate homeostasis was not restored by NRT2.7 activity. Moreover, NRT2.7 ectopic overexpression in wild-type background (WT) increased growth under limiting nitrogen supply, suggesting that NRT2.7 stimulates nitrate efflux from vacuoles. This hypothesis was demonstrated by electrophysiological nitrate flux measurements on isolated vacuoles. This discovery of NRT2.7 function and more largely the coupling of vacuolar nitrate fluxes with growth under low nitrate supply, will enable new strategies for engineering better NUE for a more sustainable agriculture.HighlightThe overexpression of the nitrate transporter NRT2.7 stimulates growth by increasing the export of nitrate from the vacuole, the main cell compartment for nitrate storage.
A novelPSMB8isoform associated with multiple sclerosis lesions induces P-body formation
Authors: Shaw Benjamin C. , Williams Jessica L. 
Published: February 2024

AbstractMultiple sclerosis (MS) is an inflammatory and demyelinating disease of the central nervous system (CNS). Current therapies primarily target the inflammatory component of the disease and are highly effective in early stages of MS while limited therapies have an effect in the more chronic progressive stages of MS where resident glia have a larger role. MS lesions tend to be inflammatory even after the initial peripheral immune cell invasion has subsided and this inflammation is known to cause alternative splicing events. We used qPCR of normal-appearing white matter and white matter lesions from postmortem MS tissue,in vitrostudies, and immunostaining in MS tissue to investigate the alternative splicing of one gene known to be important during recovery in an animal model of MS,PSMB8. We found a novel, intron-retained isoform which has not been annotated, upregulated specifically in MS patient white matter lesions. We found that this novel isoform activates the nonsense-mediated decay pathway in primary human astrocytes, the most populous glial cell in the CNS, and is then degraded. Overexpression of this isoform in astrocytes leads to an increased number of processing bodiesin vitro, the primary site of mRNA decay. Finally, we demonstrated that MS white matter lesions have a higher burden of processing bodies compared to normal-appearing white matter, predominantly in GFAP-positive astrocytes. The increase in alternative splicing of thePSMB8gene, the stress that this alternative splicing causes, and the observation that processing bodies are increased in white matter lesions suggests that the lesion microenvironment may lead to increased alternative splicing of many genes. This alternative splicing may blunt the protective or reparative responses of resident glia in and around white matter lesions in MS patients.