bluuebunny/crossref_metadata_2025_split huggingface dataset:
Red blood cell distribution as Potential Predictor of Mortality in Diabetic Foot Patients
Authors: Gou Chunmei , Huang Siyi , Huang Li , Wang Tinggang , Huang Guangtao 
Published: September 2024

AbstractBackgroundRed blood cell distribution width (RDW) reflects the heterogeneity of red blood cell volume, which reflects the variable width of red blood cell (RBC). RDW has been proved as predictor of mortality among several diseases. The purpose of this study is to analyze the relationship between RDW and mortality of diabetic foot patients.MethodsWe first collect clinic data from the public database MIMIC-III. Kruskal Wallis rank sum test was used to analyze the association between RDW and DF mortality, and to evaluate the relationship between them. Univariate and multivariate logistic regression analysis was used for determining the risk factors and prognosis of DF patients.ResultsA total of 283 patients were included in this study, with an average age of 64.0 [54.0,70.5] years, including 193 males and 90 females. We divided RDW into three groups (high, moderate and low) according to RDW tertiles and then compared the mortality of the three groups. The high RDW group (RDW > 16.8%) had significant higher mortality (P = 0.031). In multivariate logistic regression analysis, RDW, SOFA score and APS are risk factors for death in diabetic foot. After adjusting for confounding factors in model II, RDW remains a particularly strong predictor of mortality.ConclusionsA total of 283 patients were included in this study, with an average age of 64.0 [54.0,70.5] years, including 1We confirm that RDW is an independent predictor of mortality in DF patients,and the higher the RDW, the higher the mortality of DF patients.
In-Hospital and Long-Term Outcomes in Spontaneous Coronary Artery Dissection (SCAD) with Concurrent Cardiac Arrest: A Systematic Review and Meta-Analysis
Authors: Baqal Omar , Karikalan Suganya A. , Hasabo Elfatih A. , Tareen Haseeb , Futela Pragyat , Qasba Rakhtan K. , Shafqat Areez , Qasba Ruman K. , Hayes Sharonne N. , Tweet Marysia S. , El Masry Hicham Z. , Lee Kwan S. , Shen Win-Kuang , Sorajja Dan 
Published: September 2024

AbstractBackgroundSpontaneous coronary artery dissection (SCAD) is increasingly recognized as an important cause of myocardial infarction (MI). However, our understanding of clinical characteristics that predispose patients to worse outcomes, such as concurrent sudden cardiac arrest (CA), remains limited.ObjectiveWe performed a systematic review and meta-analysis of studies assessing clinical outcomes among SCAD patients with aconcurrent CA.MethodsThis study was performed according to PRISMA guidelines. PubMed, Cochrane, and Scopus were systematically searched using relevant search terms, such as “Spontaneous Coronary Artery Dissection”, “Ventricular Tachycardia”, “Ventricular Fibrillation”, “Sudden Cardiac Death” and “Cardiac Arrest”. The search was conducted from database inception to July 2024. Studies assessing the clinical outcomes of SCAD patients with concurrent CA were included. RevMan 5.4 was used for meta-analysis.ResultsAfter removal of duplicates, 269 studies underwent screening, out of which 10 studies were included (n= 3978 patients, 357 with CA). In-hospital mortality, post-discharge mortality, recurrent MI and recurrent SCAD occurred in 20%, 3%, 12% and 9% of SCAD patients with CA, respectively. When compared to SCAD patients without CA, SCAD patients with CA were at significantly higher risk of in-hospital mortality (RR = 6.75, 95% CI [4.50, 10.14], I2= 0%), post-discharge mortality (RR = 5.86, 95% CI [1.72, 19.91], I2=0%), recurrent MI (RR =3.31, 95% CI [2.03, 5.39], I2=56%), recurrent SCAD (RR = 1.91, 95% CI [1.11, 3.27], I2= 43%), acute heart failure (RR = 4.82, 95% CI [3.22, 7.20], I2=42%), and cardiogenic shock (RR = 6.11, 95% CI [4.07, 9.19], I2=64%). Out of a pooled 24 implanted cardiac defibrillators (ICDs) and 11 wearable cardiac defibrillators (WCDs), there was only one appropriate and one inappropriate ICD discharge recorded over the follow-up period.ConclusionIn this cohort, SCAD with concurrent CA was associated with worse in-hospital and long-term outcomes including in-hospital and post-discharge mortality, acute heart failure, and recurrent MI and SCAD. There was a low long-term rate of administered defibrillator therapies among patients discharged from the hospital with an ICD or WCD. Further research is needed to better delineate optimal management approaches toward this high-risk patient population, including secondary prevention of sudden cardiac death.Graphical abstract
A Comparison of the Sexual Expression, Biomass, Cannabinoid Content, and Seed Production in XXX and XXY Triploid Cannabis
Authors: Paul Nathan , Yanush Ben , Monthony Adrian , Hall Braydon , Babaei Mehdi , Torkamaneh Davoud , Jones AMP 
Published: September 2024

AbstractCannabis is a multi-billion dollar industry reliant on unpollinated genetically female (XX) plants, as pollination reduces cannabinoid yields and flower quality. The mechanism behind the sexual expression ofC. sativais unclear. This study examines the sexual characteristics of homo- and hetero-gametic triploid cannabis plants (XX(X/Y)) to understand the role of the Y chromosome in cannabis sex determination. Heterogametic triploids were produced by crossing a male diploidC. sativacv. Durban Poison (2n = 2x = 18 + XY) with a tetraploid femaleC. sativacv. Higher Education (2n = 4x = 36 + XXXX) confirmed by flow cytometry and PCR. Measurements include fresh and dry plant weight, dry flower weight, seed counts, seed weights, and cannabinoids quantified using liquid chromatography. Results showed 44.4% of plants were XXY (n= 8), with 75% presenting a monoecious phenotype (n= 6). Of these, 50% produced predominately male flowers (n= 3), while the rest produced predominately female flowers. Plants with predominately female flowers had higher yields and cannabinoids compared to predominantly male plants. XXX genotypes outperformed XXY in several metrics. This study enhances our understanding ofC. sativasex determination and offers insight into breeding and cultivation strategies utilizing triploid cannabis.
Oxytocin receptor controls promiscuity and development in prairie voles
Authors: Sharma Ruchira , Berendzen Kristen M. , Everitt Amanda , Wang Belinda , Williams Gina , Wang Shuyu , Quine Kara , Larios Rose D. , Long Kimberly L. P. , Hoglen Nerissa , Sulaman Bibi Alika , Heath Marie C. , Sherman Michael , Klinkel Robert , Cai Angela , Galo Denis , Caamal Lizandro Chan , Goodwin Nastacia L. , Beery Annaliese , Bales Karen L. , Pollard Katherine S. , Willsey Arthur Jeremy , Manoli Devanand S. 
Published: September 2024

SummaryOxytocin receptor (Oxtr) signaling influences complex social behaviors in diverse species, including social monogamy in prairie voles. How Oxtr regulates specific components of social attachment behaviors and the neural mechanisms mediating them remains unknown. Here, we examine prairie voles lacking Oxtr and demonstrate that pair bonding comprises distinct behavioral modules: the preference for a bonded partner, and the rejection of novel potential mates. Our longitudinal study of social attachment shows that Oxtr sex-specifically influences early interactions between novel partners facilitating the formation of partner preference. Additionally, Oxtr suppresses promiscuity towards novel potential mates following pair bonding, contributing to rejection. Oxtr function regulates coordinated patterns of gene expression in regions implicated in attachment behaviors and regulates the expression of oxytocin in the paraventricular nucleus of the hypothalamus, a principal source of oxytocin. Thus, Oxtr controls genetically separable components of pair bonding behaviors and coordinates development of the neural substrates of attachment.
Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis
Authors: Gustafson Kevin L. , Rodriguez Trevor R. , McAdams Zachary L. , Coghill Lyndon M. , Ericsson Aaron C. , Franklin Craig L. 
Published: September 2024

AbstractTo study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.
Concurrent single-pulse (sp) TMS/fMRI to reveal the causal connectome in healthy and patient populations
Authors: Glick Cameron , Gajawelli Niharika , Sun Yinming , Badami Faizan , Saggar Manish , Etkin Amit 
Published: September 2024

AbstractNeuroimaging and cognitive neuroscience studies have identified neural circuits linked to anxiety, mood, and trauma-related symptoms and focused on their interaction with the medial prefrontal default mode circuitry. Despite these advances, developing new neuromodulatory treatments based on neurocircuitry remains challenging. It remains unclear which nodes within and controlling these circuits are affected and how their impairment is connected to psychiatric symptoms. Concurrent single-pulse (sp) TMS/fMRI offers a promising approach to probing and mapping the integrity of these circuits. In this study, we present concurrent sp-TMS/fMRI data along with structural MRI scans from 152 participants, including both healthy and depressed individuals. The sp-TMS was administered to 11 different cortical sites, providing a dataset that allows researchers to investigate how brain circuits are modulated by spTMS.
The unique contributions of Rab11 and Rab35 to the completion of cell division
Authors: Gibieža Paulius , Ratkevičiūtė Emilija , Dabkevičiūtė Girstautė , Petrikaitė Vilma 
Published: September 2024

AbstractRab11 and Rab35 were shown to be responsible for wide-scale intracellular membrane trafficking during the last phases of the cell cycle. Even though data suggests that Rab11 and Rab35 are abscission-related, each gives a different phenotype to dividing cells. Moreover, nobody has ever looked at both and systematically compared the two during the regulation of cancer cell division. Hence, the molecular interplay and compensatory mechanisms between Rab11 and Rab35 remain to be established. Our data shows that depletion of Rab11 or Rab35 inhibits cytokinetic abscission and is associated with aberrant levels of F-actin at the intercellular bridge. In contrast, overexpression of functionally similar Rab protein cannot rescue downregulation-associated cytokinetic defects in cancer cells. We also demonstrate that even though Rab11 and Rab35 function in the same molecular pathway, the input that each individual Rab11 and Rab35 carries out during a distinct mitotic M-phase stage differs. Thus, this research study is dedicated to getting a more in-depth understanding of molecular machinery behind Rab11- and Rab35-mediated cell progression from late anaphase to cytokinesis.
Influenza A viruses induce tunnelling nanotube-like structures through the onset of apoptosis
Authors: Weir Daniel , Bentley-Abbot Calum , McCowan Jack , Loney Colin , Roberts Edward , Hutchinson Edward 
Published: September 2024

AbstractAs well as spreading through virions, influenza A viruses (IAVs) can evade antiviral drugs and neutralising antibodies by spreading directly from cell to cell. In cell culture this can occur by the induction of intercellular membrane connections known as tunnelling nanotube-like structures (TLSs), which are capable of trafficking the viral genome between cells. Here, we showed that TLSs are present at the site of IAV infectionsin vivo, and then usedin vitromodels to ask how IAVs induce their formation. We found that TLS induction cannot be induced by cytokine signalling from infected to uninfected cells, but requires IAV replication within cells. IAV replication can form filamentous virions with structural similarities to TLSs, but we found that TLS induction is independent of virion morphology. We therefore looked at the intracellular responses to infection. Using a pan-caspase inhibitor, we found that TLS induction by IAVs requires the onset of apoptosis. Our results, which suggest that IAVs control their ability to spread directly from cell to cell by driving infected cells into apoptosis, identifies a new way in which a virus can manipulate its host to evade antiviral immune responses.Author SummaryInfluenza A viruses (IAVs) spread efficiently through the respiratory tract in the form of extracellular virus particles, but can be restricted by neutralising antibodies and antiviral drugs. IAVs can avoid this restriction by transporting viral genomes directly from one cell to the next. They can do this by inducing the formation of long, thin intercellular connections known as tunnelling nanotube-like structures, which are capable of trafficking viral genomes. In this study, we demonstrate for the first time that tunnelling-nanotube like structures form within IAV infected lungs. We then asked how IAVs induce these structures. We found that cell death pathways triggered by IAV replication induce the formation of tunnelling nanotube-like structures, thereby establishing routes of infection spread to other cells. In this way, the virus exploits the cell death response of its host to ensure that its infection can continue to spread even within the restrictive environment of the respiratory tract.
DNA methylation and demethylation driven regulation of sepsis
Authors: Saini Akhilesh , Kumar Jitendra , Tyagi Purnima , Gautam Vipul , Khanna Rajeev , Kumar Vijay 
Published: September 2024

AbstractDuring dysregulated inflammation and sepsis, there is a sudden surge of cytokines, such as TNF alpha, IL6, and IL10, which disrupts the body homeostasis. This sudden and rapid increase in cytokine gene expression cannot be explained by the conventional central dogma mechanism. DNA methylation is one of the most significant epigenetic modifications. DNA methylation is mostly associated with the suppression of gene activity, and DNA demethylation is associated with the activation of gene activity. There are numerous transcription factors, such as CREB1, c-FOS, AP-1, IRF1, and EGR1, that play pivotal roles in regulating inflammation. Thus, it was hypothesized that changes in the DNA methylation patterns of cytokine promoter regions or in the promoter regions of these specific transcription factors might be the potential reasons for the increase in cytokine levels during sepsis. During endotoxin stimulation, DNA methyltransferases were suppressed, and DNA methylation levels were altered at the global level. Bisulfite sequencing revealed no change in the DNA methylation patterns of the TNF-alpha, IL6 and IL10 cytokine promoters. The CREB1 and c-FOS transcription factor promoters were demethylated after LPS stimulation and in clinical sepsis samples. Overall, this study highlights the importance of the role of DNA methylation in sepsis.
A mix-and-match reverse genetics system for evaluating genetic determinants of orthobunyavirus neurological disease
Authors: Miettinen Heini M. , Abbott Matthew J. , Evans Alyssa B. 
Published: September 2024

ABSTRACTThe encephalitic orthobunyaviruses have tri-segmented, negative sense RNA genomes and can cause severe neurological disease in humans, including La Crosse virus (LACV), which is the leading cause of pediatric arboviral encephalitis in the United States. However, little is known about the genetic factors that drive neuropathogenesis. Reverse genetics (RG) systems are valuable tools for studying viral genetics and pathogenesis. Plasmid-based cDNA RG systems are available for LACV, however the plasmid backbones are medium-copy number and have a propensity for recombination. We therefore generated a plasmid-based cDNA RG system for LACV utilizing a more stable and high-copy number plasmid backbone. Additionally, we created the first full RG systems for two closely related orthobunyaviruses, Jamestown Canyon virus (JCV), and Inkoo virus (INKV), which have differing reported disease incidences in humans and differing neuropathogenic phenotypes in mice compared to LACV. We compared wild type (wt) viruses with RG-derived viruses in human neuronal cells and in mice, and found that RG-derived viruses maintained the replication and neuropathogenic phenotypes of their wt counterpart. Additionally, we demonstrated that reverse genetics plasmids from different parental viruses can be readily mix-and-matched to generate reassortant viruses. This system provides a valuable genetic tool utilizing viruses with differing neuropathogenic phenotypes to investigate the genetic determinants of orthobunyavirus neuropathogenesis.
A haplotype-resolved chromosome-level genome assembly ofUrochloa decumbenscv. Basilisk resolves its allopolyploid ancestry and composition
Authors: Ryan Camilla , Fraser Fiona , Irish Naomi , Barker Tom , Knitlhoffer Vanda , Durrant Alex , Reynolds Gillian , Kaithakottil Gemy , Swarbreck David , De Vega Jose J. 
Published: September 2024

AbstractHaplotyped-resolved phased assemblies aim to capture the full allelic diversity in heterozygous and polyploid species to enable accurate genetic analyses. However, building non-collapsed references still presents a challenge. Here, we used long-range interaction Hi-C reads (high-throughput chromatin conformation capture) and HiFi PacBio reads to assemble the genome of the apomictic cultivar Basilisks fromUrochloa decumbens(2n = 4x = 36), an outcrossed tetraploid Paniceae grass widely cropped to feed livestock in the tropics. We identified and removed Hi-C reads between homologous unitigs to facilitate their scaffolding and employed methods for the manual curation of rearrangements and misassemblies. Our final phased assembly included the four haplotypes in 36 chromosomes. We found that 18 chromosomes originated from diploidU. brizanthaand the other 18 from eitherU. ruziziensisor diploidU. decumbens.We also identified a chromosomal translocation between chromosomes 5 and 32, as well as evidence of pairing exclusively within subgenomes, except for a homoeologous exchange in chromosome 21. Our results demonstrate that haplotype-aware assemblies accurately capture the allelic diversity in heterozygous species, making them the preferred option over collapsed-haplotype assemblies.
High-Sensitivity Analysis of Native Bacterial Biofilms Using Dynamic Nuclear Polarization-Enhanced Solid-State NMR
Authors: Byeon Chang-Hyeock , Kinney Ted , Saricayir Hakan , Hansen Kasper Holst , Scott Faith , Srinivasa Sadhana , Wells Meghan K. , Mentink-Vigier Frederic , Kim Wook , Akbey Ümit 
Published: September 2024

AbstractBacterial biofilms cause persistent infections that are difficult to treat and contribute greatly to antimicrobial resistance. However, high-resolution structural information on native bacterial biofilms remain very limited. This limitation is primarily due to methodological constraints associated with analyzing complex native samples. Although solid-state NMR (ssNMR) is a promising method in this regard, its conventional applications typically suffer from sensitivity limitations, particularly for unlabeled native samples. Through the use of Dynamic Nuclear Polarization (DNP), we applied sensitivity enhanced ssNMR to characterize nativePseudomonas fluorescenscolony biofilms. The increased ssNMR sensitivity by DNP enabled ultrafast structural characterization of the biofilm samples without isotope-labelling, and chemical or physical modification. We collected 1D13C and15N, and 2D1H-13C,1H-15N and13C-13C ssNMR spectra within seconds/minutes or hours, respectively which enabled us to identify biofilm components as polysaccharides, proteins, and eDNA effectively. This study represents the first application of ultrasensitive DNP ssNMR to characterize a native bacterial biofilm and expands the technical scope of ssNMR towards obtaining insights into the composition and structure of a wide array ofin vitroandex vivobiofilm applications. Such versatility should greatly boost efforts to develop structure-guided approaches for combating infections caused by biofilm-forming microbes.
Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterised sequences in public protein databases
Authors: Brown K. , Firth A. E. 
Published: September 2024

AbstractPublic databases of protein sequences, such as the National Center for Biotechnology Information (NCBI) Protein repository and UniProt, contain millions of proteins identified in samples from specific species but named as uncharacterised, hypothetical or unclassified due to a lack of information about their function. It has been demonstrated previously that many such sequences show high similarity to genes from RNA viruses, either due to viral infection of the original sample, contamination or endogenous viral elements (EVEs) integrated into the genome of the sample species. Many proteins from RNA virus discovery research are also deposited into these repositories but, for various reasons, can only be labelled as uncharacterised and classified taxonomically at a superkingdom or realm level. Sequences from protein repositories not labelled specifically as being derived from the RNA viral RNA dependent RNA polymerase (RdRp) protein are often used as negative controls when looking to identify viral RdRp sequences, so the presence of unlabelled viruses amongst these datasets is problematic.In this study, we screened uncharacterised proteins from two large public protein repositories - NCBI Protein and UniProt - to identify sequences likely to be derived from RNA viral RdRp. 3,560 such sequences were identified, many derived from EVEs. Many previously unknown EVEs were identified and led to characterisation of additional, related sequences. For example, a group of orbivirus-like viruses infecting nematodes was uncovered which appears to have both ancient endogenous and circulating exogenous members. Many recent integrations of mito-like viruses into plant genomes were identified, indicative of current or recent RNA viral activity. In several taxonomic groups, the first example of an EVE, and in some cases the first example of any RNA virus, was uncovered. The large number of EVEs uncovered by this relatively small-scale search suggests that only a fraction of the true diversity of EVEs is currently known.We also explore uncharacterised proteins further by providing provisional taxonomic annotations for RdRps which are currently only listed as members of the Riboviria realm. A number of sequences are identified which are indistinguishable from known, pathogenic viruses but are labelled as bacteria, seemingly as a result of mislabelling or contamination. Sequences which are not RNA viral but show some similarity to RdRp are also analysed, as a potential source of false positives in virus discovery research. Finally, recommendations are made for generating useful negative controls.