bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the transcriptional molecular dynamics of shelf life extension and system acquired resistance induction toFusarium pallidoroseumin melon fruits by the use of pulsed-light
Authors: Arge Luis Willian Pacheco , Morais Guilherme Loss , Carvalho Joseane Biso , Zocolo Guilherme Julião , Oster Andréia Hansen , Vasconcelos Ana Tereza Ribeiro de , Diniz Leandro Eugenio Cardamone , Silva Ebenézer de Oliveira , Bordallo Patricia do Nascimento 
Published: March 2024

AbstractMelon is a globally commercialized fruit, and Fusarium rot disease poses a significant threat to post-harvest losses. The conventional use of fungicides raises concerns about chemical residues, prompting exploration into alternative technologies such as Pulsed Light (PL). While PL has been effective in controlling infections in various fruits and vegetables, the precise physiological responses and molecular mechanisms in melon fruits remain incompletely understood. In this study, melon fruits infected with theFusarium pallidoroseumwere treated with different doses of PL (0, 6, 9, and 12 J cm−2), and the impact on both fungal control and fruit shelf life extension was investigated. The 9 J cm−2dose emerged as the most effective in controlling fungal growth without causing damage, inducing beneficial responses. This optimal PL dose upregulated genes in the lignan biosynthesis pathway and the infection upregulated genes involved with systemic acquired resistance, triggered by the pipecolic acid. In this way, the PL treatment and the infection trigger a double mechanism of resistance in melon fruits. A second and third experiment focused on evaluating the extension of melon fruit shelf life and the safe manipulation window post-PL treatment. The results revealed an average shelf life extension of six days and a safe manipulation period of 24 hours. The extension in shelf life was associated with a deviation in information flux from the ethylene biosynthesis to upregulation of the polyamine biosynthesis pathway, which produces nitric oxide, a product that can inhibit ethylene biosynthesis and its action. Furthermore, the observed 24-hour safety period against fungal infection post-PL treatment was characterized as a memory response resistance caused by the upregulation of lignan biosynthesis, which is a potential and efficient alternative to chemical products like fungicides. Overall, this study provides insights into the transcriptional molecular mechanisms through which PL promotes systemic acquired resistance and extends the shelf life of melon fruits.
Visualizing the Spatio-Temporal Dynamics of Clonal Evolution withLinG3Dsoftware
Authors: Hu Anjun , Ojwang’ Awino Maureiq E. , Olumoyin Kayode D. , Rejniak Katarzyna A. 
Published: March 2024

AbstractCancer clonal evolution, especially following anti-cancer treatments, depends on the locations of the mutated cells within the tumor tissue. Cells near the vessels, exposed to higher concentrations of drugs, will undergo a different evolutionary path than cells residing far from the vasculature in the areas of lower drug levels. However, classical representations of cell lineage trees do not account for this spatial component of emerging cancer clones. Here, we propose theLinG3D(Lineage Graphs in 3D) algorithms to trace clonal evolution in space and time. These are an open-source collection of routines (in MATLAB, Python, and R) that enables spatio-temporal visualization of clonal evolution in a two-dimensional tumor slice from computer simulations of the tumor evolution models. These routines draw traces of tumor clones in both time and space, with an option to include a projection of a selected microenvironmental factor, such as the drug or oxygen distribution within the tumor. The utility ofLinG3Dhas been demonstrated through examples of simulated tumors with different number of clones and, additionally, in experimental colony growth assay. This routine package extends the classical lineage trees, that show cellular clone relationships in time, by adding the space component to show the locations of cellular clones within the 2D tumor tissue patch from computer simulations of tumor evolution models.
Exploring the role of temperature and other environmental factors in West Nile virus incidence and prediction in California counties from 2017-2022
Authors: Parker Noah 
Published: March 2024

AbstractWest Nile virus (WNV) is the most common mosquito-borne disease in the United States, resulting in hundreds of reported cases yearly in California alone. The transmission cycle occurs mostly in birds and mosquitoes, making meteorological conditions, such as temperature, especially important to transmission characteristics. Given that future increases in temperature are all but inevitable due to worldwide climate change, determining associations between temperature and WNV incidence in humans, as well as making predictions on future cases, are incredibly important to public health agencies in California. Using surveillance data from the California Department of Public Health (CDPH), meteorological data from the National Oceanic and Atmospheric Administration (NOAA), and vector and host data from VectorSurv, we created GEE autoregressive and zero-inflated regression models to determine the role of temperature and other environmental factors in WNV incidence and predictions. An increase in temperature was found to be associated with an increase in incidence in 11 high-burden Californian counties between 2017-2022 (IRR = 1.06), holding location, time of year, and rainfall constant. A hypothetical increase of two degrees Fahrenheit — predicted for California by 2040 — would have resulted in upwards of 20 excess cases per year during our study period. Using 2017-2021 as a training set, meteorological and host/vector data were able to well-predict 2022 incidence, though the models did overestimate the peak number of cases. The zero-inflated model closely predicted the low number of cases in winter months but performed worse than the GEE model during high-transmission periods. These findings suggests that climate change will, and may be already, altering transmission dynamics and incidence of WNV in California, and provides tools to help predict incidence into the future.Author SummaryWest Nile Virus is a disease that is spread by mosquitoes. Though it commonly infects birds, transmission to humans is possible and can lead to severe health effects. Temperature is known to affect the transmission cycle of West Nile virus, but it is unclear how global warming might change who, or how many people, may get infected with the virus. In this study, the researchers looked at how climate change may affect West Nile virus in California, and how health officials may better be able to predict future cases. The study found that there could be an increase in West Nile virus cases in humans due to increases in temperature in the next 20 years, but that we already have many tools and sources of data to predict cases. These findings reinforce the possible consequences of climate change on human health, and aid in the understanding in the complex relationship between climate and infectious diseases.
Fine-scale oceanographic processes shape marine biodiversity patterns in the Galápagos Islands
Authors: Holman Luke E , Pazmiño Diana A. , Gopalakrishnan Shyam , Forryan Alexander , Hearn Alex R. , Naveira-Garabato Alberto C. , Rius Marc 
Published: March 2024

AbstractUncovering the drivers that shape biodiversity patterns is critical to understand ecological and evolutionary dynamics. Despite evidence that biodiversity composition is influenced by processes at different spatial scales, little is known about the role of fine-scale oceanographic processes on the structure of marine communities. This is particularly important in biodiversity hotspot regions, where small changes in environmental conditions may lead to substantial changes in species composition. We combined ocean modelling and 12S environmental DNA (eDNA) metabarcoding, targeting teleost and elasmobranch species, to explore if oceanographic processes influenced biogeographic patterns around the biodiverse Galápagos Islands. We first detected significant differences in eDNA-measured community structure across the archipelago’s diverse seascape. We found no significant relationship between Lagrangian particle tracking metrics and nektonic biodiversity, and thus developed a novel metric to measure the cumulative seawater flow resistance between pairs of geographic sites. This metric explained a significant proportion of variation in eDNA-measured beta dissimilarity between sites, comparable in influence to important abiotic drivers, such as temperature and geographic distance between sites. Cumulatively, our results indicate that marine communities are particularly sensitive to changes in local current systems, and suggest that fine-scale oceanographic processes may have an underappreciated role in structuring marine communities globally.
PRDM9 drives the location and rapid evolution of recombination hotspots in salmonids
Authors: Raynaud Marie , Sanna Paola , Joseph Julien , Clément Julie , Imai Yukiko , Lareyre Jean-Jacques , Laurent Audrey , Galtier Nicolas , Baudat Frédéric , Duret Laurent , Gagnaire Pierre-Alexandre , de Massy Bernard 
Published: March 2024

AbstractIn many eukaryotes, meiotic recombination occurs preferentially at discrete sites, called recombination hotspots. In various lineages, recombination hotspots are located in regions with promoter-like features and are evolutionarily stable. Conversely, in some mammals, hotspots are driven by PRDM9 that targets recombination away from promoters. Paradoxically, PRDM9 induces the self-destruction of its targets and this triggers an ultra-fast evolution of mammalian hotspots. PRDM9 is ancestral to all animals, suggesting a critical importance for the meiotic program, but has been lost in many lineages with surprisingly little effect on meiosis success. However, it is unclear whether the function of PRDM9 described in mammals is shared by other species. To investigate this, we analyzed the recombination landscape of several salmonids, the genome of which harbors one full-length PRDM9 and several truncated paralogs. We identified recombination initiation sites inOncorhynchus mykissby mapping meiotic DNA double-strand breaks (DSBs). We found that DNA DSBs clustered at hotspots positioned away from promoters, enriched for the H3K4me3 and H3K4me36 marks and the location of which depended on the genotype of full-lengthPrdm9. We observed a high level of polymorphism in the zinc finger domain of full-lengthPrdm9, but not of the truncated paralogs. Moreover, population-scaled recombination maps inO. mykiss,Oncorhynchus kisutchandSalmo salarrevealed a rapid turnover of recombination hotspots caused by PRDM9 target motif erosion. Our results imply that PRDM9 function is conserved across vertebrates and that the peculiar evolutionary runaway caused by PRDM9 has been active for several hundred million years.
Seasonal Patterns of Viromes in Urban Aquatic Environments of Manitoba
Authors: Francis Jhannelle D. , Uyaguari Miguel 
Published: March 2024

ABSTRACTAlthough wastewater and treatment plants harbor many pathogenic organisms’ traditional methods that monitor the microbial quality of wastewater have not changed since the early 1900s and often disregard the presence of other types of significant waterborne pathogens such as viruses. Using advanced technology, our study aims to characterize the taxonomy, functional profiling and seasonal patterns of viral DNA and RNA community structures using metagenomics and quantitative-PCR, for the purpose of establishing the virome distribution in aquatic environment’s receiving wastewater discharge. Environmental water samples were collected at 11 locations in Winnipeg, Manitoba along the Red and Assiniboine Rivers during the Spring, Summer and Fall 2021. Samples were filtered and underwent skimmed milk flocculation for viral concentration.The taxonomic classification of DNA viruses identified from the RefSeq database (available from MG-RAST) and Kraken 2 Viral Genome database were predominately DNA bacteriophages (Myoviridae, Podoviridae and Siphoviridae) which accounted for approximately 90% of each aquatic sample location along the Red and Assiniboine Rivers. Phage related functionalities such as phage tail fiber proteins, phage replication, and phage packaging machinery accounted for 40% of each aquatic samples collected which possibly correspond to the DNA phages that were previously identified. RNA phages such asCystoviridaeandLeviviridaewere identified to a lesser extent accounting for approximately 3 % of each aquatic sample collected, while other viruses such asVirgaviridae, Retroviridae, PicobirnaviridaeandPartiviridaeaccounted for 7%–100% of aquatic samples. The functionalities of RNA viruses were primarily related to metabolic pathways such as potassium homeostasis, respiratory complexes and sialic acid metabolism, essential for RNA viruses to survive in their host.IMPORTANCEMunicipal wastewater effluents discharged into the Red and Assiniboine Rivers of Winnipeg, Manitoba relies on traditional methods that monitor the microbial quality of wastewater focus solely on the detection of fecal bacteria, which are not necessarily good indicators of viruses or other pathogens. There is also a lack of current wastewater system effluent regulations at the federal and provincial level. Furthermore, previous literature has shown that when viral DNA and RNA sequences are blasted against current genomic databases, approximately 50 % of the viral reads are classified as unknown. The significance of our research in characterizing the virome distribution in aquatic environments addresses a knowledge gap in the current effluent guidelines and a need for regulatory practices. In the long run, fecal indicator bacteria combined with the detection of enteric viruses, may complement assessment of water quality in effluents discharged into rivers.
Adaptive admixture atACKR1(the Duffy locus) may have shapedPlasmodium vivaxprevalence in Oman
Authors: Haffener Paige E. , Al-Riyami Arwa Z. , Al-Zadjali Shoaib , Busby George B. J. , Mahdhuri Sulaiman Al , Al-Rawahi Mohammed , Hosni Saif Al , Marhoobi Ali Al , Sheriyani Ammar Al , Leffler Ellen M. 
Published: March 2024

AbstractMalaria in humans is largely caused by two divergent species ofPlasmodiumparasites,P. vivaxandP. falciparum, both of which have driven the spread of protective alleles in human populations. Notably, an erythrocyte-specific Duffy null allele (FyES) confers resistance toP. vivaxmalaria and has been identified as a target of strong, recent positive selection in multiple African admixed populations. Here, we evaluate evidence for selection via adaptive admixture in Oman, where compared to neighboring countries,P. vivaxhas recently been less common. Genetic ancestry inference using whole genome sequence data from 100 Omanis suggests 9.8% (95% CI: 7.3-12.2%) of their genetic ancestry is shared with east Africa. At the Duffy locus, we find a high frequency of FyESand an increase to 76% African ancestry. Comparing with blood group serology for the same individuals, we identify an additional Duffy-null allele that is rare but present across multiple Arabian Peninsula (AP) populations. Finally, we estimate the selection coefficient at FyESas 0.031 (95% CI: 0.029-0.034) with likely introduction at least 59 generations ago, older than estimates in other African admixed populations. Although we also observe higher frequency of someP. falciparum-protective alleles in Oman than in other AP populations, African ancestry is not enriched indicating a lack of evidence for adaptive admixture driven byP. falciparumselective pressure. Together, our analyses suggest that Oman’s long history with east African populations resulted in early introduction and selection for Duffy null alleles and may have influenced the prevalence ofP. vivaxin the region.
Long distance avian migrants fail to bring 2.3.4.4b HPAI H5N1 into Australia for a second year in a row
Authors: Wille Michelle , Atkinson Robyn , Barr Ian G. , Burgoyne Charlotte , Bond Alexander L. , Boyle David , Christie Maureen , Dewar Meagan , Douglas Tegan , Fitzwater Teagan , Hassell Chris , Jessop Roz , Klaassen Hiske , Lavers Jennifer L. , Leung Katherine K.-S. , Ringma Jeremy , Sutherland Duncan R. , Klaassen Marcel 
Published: March 2024

AbstractThere is an ongoing and profound burden of lineage 2.3.4.4b high pathogenicity avian influenza (HPAI) H5N1 on wildlife and poultry, globally. Herein we report the continued absence of HPAI and antibodies against lineage 2.3.4.4b HPAI from October – December 2023, in migratory birds shortly after their arrival in Australia. Given the ever-changing phenotype of this virus, worldwide studies on the occurrence, or here absence of the virus, are of critical importance to understand the virus’ dispersal and incursion risk and development of response strategies.
Field size as a predictor of “excellence.” The selection of subject fields in Germany’s Excellence Initiative
Authors: Heinze Thomas , Habicht Isabel M. , Eberhardt Paul , Tunger Dirk 
Published: March 2024

AbstractWe investigate the selection of subject fields in Germany’s “excellence initiative,” a two-phase funding scheme administered by the German Research Foundation (DFG) from 2005 to 2017 to increase international competitiveness of scientific research at German universities. While most empirical studies have examined the “excellence initiative’s” effects at the university level (“elite universities”), we focus on subject fields within universities. Based on both descriptive and logistic regression analyses, we find that the “excellence initiative” reveals a stable social order of public universities based on organizational size, that field selection is biased toward those fields with many professors and considerable grant funding, and that funding success in the second phase largely follows decisions from the first phase. We discuss these results and suggest avenues for future research.
Dissecting depression symptoms: multi-omics clustering uncovers immune-related subgroups and cell-type specific dysregulation
Authors: Hagenberg Jonas ,   BeCOME study group,   OPTIMA study group, Brückl Tanja M. , Erhart Mira , Kopf-Beck Johannes , Ködel Maik , Rehawi Ghalia , Röh-Karamihalev Simone , Sauer Susann , Yusupov Natan , Rex-Haffner Monika , Spoormaker Victor I. , Sämann Philipp , Binder Elisabeth , Knauer-Arloth Janine 
Published: March 2024

AbstractIn a subset of patients with mental disorders, such as depression, low-grade inflammation and altered immune marker concentrations are observed. However, these immune alterations are often assessed by only one data type and small marker panels. Here, we used a transdiagnostic approach and combined data from two cohorts to define subgroups of depression symptoms across the diagnostic spectrum through a large-scale multi-omics clustering approach in 237 individuals. The method incorporated age, body mass index (BMI), 43 plasma immune markers and RNA-seq data from peripheral mononuclear blood cells (PBMCs). Our initial clustering revealed four clusters, including two immune-related depression symptom clusters characterized by elevated BMI, higher depression severity and elevated levels of immune markers such as interleukin-1 receptor antagonist (IL-1RA), C-reactive protein (CRP) and C-C motif chemokine 2 (CCL2 or MCP-1). In contrast, the RNA-seq data mostly differentiated a cluster with low depression severity, enriched in brain related gene sets. This cluster was also distinguished by electrocardiography data, while structural imaging data revealed differences in ventricle volumes across the clusters. Incorporating predicted cell type proportions into the clustering resulted in three clusters, with one showing elevated immune marker concentrations. The cell type proportion and genes related to cell types were most pronounced in an intermediate depression symptoms cluster, suggesting that RNA-seq and immune markers measure different aspects of immune dysregulation. Lastly, we found a dysregulation of theSERPINF1/VEGF-A pathway that was specific to dendritic cells by integrating immune marker and RNA-seq data. This shows the advantages of combining different data modalities and highlights possible markers for further stratification research of depression symptoms.
Sickle Cell Disease and Uterine Fibroids: Evaluation of the Prevalence of Fibroids across Sickle Cell Genotypes
Authors: Martin Jonathan G. , Medema Alexis M. , Rikard Blaire K. , van den Hoek Gabrielle , Chisholm Miriam 
Published: March 2024

ABSTRACTIntroductionUterine fibroids are known to affect >80% of premenopausal American women of African descent, and sickle cell disease is known to disproportionately affect people of varying geographical ancestries, particularly those of sub-Saharan African descent. However, previous studies have suggested the two pathologies less frequently co-occur. This study aims to evaluate the prevalence of uterine fibroids in patients with sickle cell disease across a large metropolitan area in the United States.MethodsAfrican American women with sickle cell disease (including HbSS, HbSC, and sickle cell trait genotypes) underwent pelvic imaging (CT/MRI/ultrasound) between February 2011 and August 2018 at two large hospital systems within a single academic institution. Based on retrospective review, the prevalence of uterine fibroids among this cohort was analyzed and compared to published data of fibroid prevalence amongst African American patients without sickle cell disease.ResultsPrior data estimates that the prevalence of uterine fibroids in African American women is about 32 to 40% for those aged 32 to 35 years and up to >80% in premenopausal African American women overall. When compared to the expected prevalence in this cohort, with a median age of 31 years, women with HbSS or HbSC sickle cell disease had a significantly decreased prevalence of uterine fibroids (9.6 to 10.3%), while those with sickle cell trait reflected a prevalence (44.4%) like that of the general population.ConclusionThere was a significantly lower prevalence of uterine fibroids in premenopausal American women of African heritage with sickle cell disease in the study cohort when compared to premenopausal American women of African heritage in the general population. This suggests a higher threshold to ascribe dysfunctional uterine bleeding in premenopausal African-American women with sickle cell disease to uterine fibroids, and a lower threshold to pursue an alternative diagnosis.