bluuebunny/crossref_metadata_2025_split huggingface dataset:
ITPK1 regulates jasmonate-controlled root development inArabidopsis thaliana
Authors: Pullagurla Naga Jyothi , Shome Supritam , Yadav Ranjana , Laha Debabrata 
Published: June 2023

AbstractJasmonic acid (JA) is a plant hormone that regulates a plethora of physiological processes including immunity and development and is perceived by the F-Box protein, Coronatine-insensitive protein 1(COI1). The discovery of inositol phosphates (InsPs) in the COI1 receptor complex highlights their role in JA perception. InsPs are phosphate-rich signaling molecules that control many aspects of plant physiology. Inositol pyrophosphates (PP-InsPs) are diphosphate containing InsP species of which InsP7and InsP8are the best characterized ones. Different InsP and PP-InsP species are linked with JA-related plant immunity. However, role of PP-InsP species in regulating JA-dependent developmental processes are poorly understood. Recent identification of ITPK1 kinase responsible for the production of 5-InsP7from InsP6in plantaprovides a platform to interrogate possible involvement of ITPK-derived InsP species in JA-related plant development. Herein this study, we report that ITPK1-defective plants exhibit increased root growth inhibition to bioactive JA treatment. Theitpk1plants also show increased lateral root density when treated with JA. Notably, JA treatment does not induce ITPK1 protein level. Gene expression analyses revealed that JA-biosynthetic genes are not differentially expressed in the ITPK1-deficient plants. We further demonstrate that genes encoding different JAZ repressor proteins are severely downregulated in the ITPK1-defective plants. Taken together, our study highlights the role of ITPK1 in regulating JA-dependent root architecture development through controlling expression of different JAZ repressor proteins.
Intraspecies variability in plant and soil chemical properties in a common garden plantation of the energy cropPopulus
Authors: Craig Matthew E , Harman-Ware Anne E , Cope Kevin R , Kalluri Udaya C 
Published: June 2023

AbstractOptimizing crops for synergistic soil carbon (C) sequestration represents a frontier approach toward CO2removal in food and bioenergy production systems. While the central roles of plants in biological C capture and storage belowground in soils is well known, we lack an understanding of how intraspecies variation in bioenergy plants affects soil biogeochemistry. This knowledge gap is exacerbated by spatial heterogeneity in soil and plant systems, and by the difficulty of characterizing belowground plant traits. Here, we sought to obtain first insights on the spatial variation of C and nutrients in soil and plant tissues from a common garden field site of diverse, natural variant,Populus trichocarpagenotypes—grown and characterized previously for aboveground biomass-to-biofuels research. Such field sites represent a potential resource for evaluating genotype-specific effects on soil C, but this usage may be complicated due to dense plantings of intermixed genotypes. Thus, we sampled soils at the scale of individual trees to determine whether it is feasible to detect soil property variation with different plant genotypes in this system. We additionally sampled stem and root tissues to evaluate the potential for inferring important belowground traits based on aboveground-belowground correlations. We found that substantial variation in soil properties could be explained at the scale of individual trees, suggesting that genetically diverse plantations can be used to assess plant-soil correlations. Though we did not observe genotype-specific patterns in soil C, other properties such as soil acid-base chemistry (soil pH and base cations) and bulk density showed genotype-specific correlations. Stem and root nutrient levels were generally not correlated, suggesting that belowground traits should be measured directly. In conclusion, our pilot study suggests that long-term common gardens of genome-wide association study populations represent useful resources for understanding plant genotypic relationships with soil properties inPopulusfield study test plots. These resources could be used to develop verified plant species, geographic region-specific standardized sampling methods, and baseline data. Such context-specific, empirically verified data and models will be necessary for informing applied research strategies in selecting high aboveground productivity genotypes for enhanced soil C storage in managed, commercial scale, woody bioenergy crop plantation systems.
Loss of chromosome Y in regulatory T cells
Authors: Mattisson Jonas , Halvardson Jonatan , Davies Hanna , Bruhn-Olszewska Bożena , Olszewski Paweł , Danielsson Marcus , Bjurling Josefin , Lindberg Amanda , Zaghlool Ammar , Rychlicka-Buniowska Edyta , Dumanski Jan P. , Forsberg Lars A. 
Published: June 2023

ABSTRACTMosaic loss of chromosome Y (LOY) in leukocytes is the most prevalent somatic aneuploidy in aging humans. Men with LOY have increased risks of all-cause mortality and the major causes of death, including many forms of cancer. It has been suggested that the association between LOY and disease risk depends on what type of leukocyte is affected with Y loss, with prostate cancer patients showing higher levels of LOY in CD4+ T lymphocytes. In previous studies, Y loss has however been observed at relatively low levels in this cell type. This motivated us to investigate whether specific subsets of CD4+ T lymphocytes are particularly affected by LOY. Studying publicly available, T lymphocyte enriched, single-cell RNA sequencing datasets from cancer patients, we found that regulatory T cells (Tregs) had significantly more LOY than any other T lymphocytes studied. To validate these findings, we generated a single-cell RNA sequencing dataset comprised of 23 PBMC samples and 32 CD4+ T lymphocytes enriched samples. We observed an increased ratio of Tregs with LOY compared with other CD4+ cells, supported by developmental trajectory analysis of CD4+ T lymphocytes culminating in the Treg subtype. Furthermore, we identify dysregulation of 465 genes in Tregs with Y loss, many involved in the immunosuppressive functions and development of Tregs. Considering that Tregs plays a critical role in the process of immunosuppression; this enrichment for Tregs with LOY might contribute to the increased risk for cancer observed among men with Y loss in leukocytes.
SMaRT-PCR: Sampling with Mask and Reverse Transcriptase PCR, a promising non-invasive diagnostic tool for paediatric pulmonary tuberculosis
Authors: Shaikh Ambreen , Sriraman Kalpana , Vaswani Smriti , Shah Ira , Poojari Vishrutha , Oswal Vikas , Mane Sushant , Rajagara Sakina , Mistry Nerges 
Published: June 2023

AbstractPurposeDiagnostic challenges in pediatric TB, like difficulties obtaining sputum, need for invasive sampling, and suboptimal sensitivity of existing detection tools, advocate for sputum-free, child-friendly, and diagnostically accurate methods. This proof-of-concept study evaluates the diagnostic potential of non-invasivelysampling patient bioaerosols using a mask combined with reverse transcriptase (RT)PCR (SMaRT-PCR) for pediatric TB detection.MethodsIn this case-control study, we recruited 51 children (30 confirmed TB and 21 without TB) aged 2-15. Exhaled bioaerosols were captured on gelatin membrane-layered N-95 masks in a 10-minute process that involved talking, coughing, and breathing. Two mask samples were consecutively collected from children with TB and tested using GeneXpert and in-house RT-PCR for16sandrpoBRNA. The control cohort underwent single mask sampling and testing with RT-PCR. Mask sampling acceptability was assessed using a questionnaire and a Likert-scale.ResultsThe sensitivity and specificity of SMaRT-PCR for detecting16sandrpoBamong 24 treatment naïve patients were 75% and 95%, respectively, comparable to GeneXpert testing in standard samples from the same patients. Mask sampling with GeneXpert had sensitivity of only 13%. Over 90% of children were comfortable with mask sampling, and > 80% were happy or very happy on the Likert scale with the procedure.ConclusionThis is the first study to provide evidence for testing patient bioaerosols as a promising alternative for detecting pediatric TB. SMaRT-PCR has potential in a hub-and-spoke model, where samples collected from remote locations can be centrally tested by RT-PCR at district-level laboratories, enabling equitable access to diagnostic care.
Referral for Cardiac Amyloidosis in Patients who underwent Transcatheter Aortic Valve Replacement: Result of Quality Outcome Project
Authors: Lee Dae Hyun , Eichelberger Gerry , Patel Vandan , Chhaya Ronak , Khadilkar Arjun , Bishops Jennifer , Bezerra Hiram , Oliveira Guilherme , Matar Fadi , Mohanty Bibhu , Fernandez Joel 
Published: June 2023

AbstractIntroductionTransthyretin cardiac amyloidosis (ATTR) is important comorbidity present in 10-15% of severe aortic stenosis (AS). The purpose of this study was to raise awareness of ATTR in patients who underwent transcatheter aortic valve replacement (TAVR) for severe AS among healthcare providers and patients.MethodsWe reviewed 197 consecutive TAVR cases performed from 2019-2020. Based on the presence of predefined high-risk features for ATTR based on prior literature, we subsequently contacted the patients to discuss our clinical suspicion of ATTR and offered a referral to a cardiac amyloid specialist.ResultsWe have identified 125 patients (69.4%) who had high-risk features of ATTR. Of the 105 patients who we were able to contact, 44 patients agreed to referral, 46 patients were not able to be contacted after several attempts, and 15 patients declined referral. Of the 44 patients who agreed to referral, 20 patients completed the evaluation for cardiac amyloidosis, all of which were negative for transthyretin and light chain cardiac amyloidosis.ConclusionIn conclusion, our attempt to detect ATTR in prior TAVR patients was unsuccessful after 2-3 years post-TAVR. We believe that early detection of cardiac amyloidosis close to the timing of TAVR is important and the most effective means.
Mapping the landscape of transcription factor promoter activity during vegetative development in Marchantia
Authors: Romani Facundo , Sauret-Güeto Susanna , Rebmann Marius , Annese Davide , Bonter Ignacy , Tomaselli Marta , Dierschke Tom , Delmans Mihails , Frangedakis Eftychios , Silvestri Linda , Rever Jenna , Bowman John L. , Romani Ignacio , Haseloff Jim 
Published: June 2023

ABSTRACTTranscription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterising the transcriptional activity of TF genes in space and time is a critical step towards understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot-apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 TF genes,Marchantia polymorphais an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally testedin plantareporter fusions for all the TF promoters in the collection and systematically analysed expression patterns in Marchantia gemmae. This allowed us to build a map of precise expression domains and identify a unique set of TFs expressed in the stem-cell zone, providing new insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that the promoter elements characterised here will be useful for cell-type specific expression, synthetic biology applications, and functional genomics.
Evolutionary innovations in germline biology of placental mammals revealed by transcriptomics of first wave spermatogenesis in opossum
Authors: Marshall Kira L , Stadtmauer Daniel J , Maziarz Jamie , Wagner Günter P , Lesch Bluma J 
Published: June 2023

AbstractMammalian spermatogenesis is a deeply conserved developmental program that is essential for fitness. Paradoxically, spermatogenic development also allows rapid divergence in gene expression and is thought to be a source of evolutionary novelty and gene birth. How mammalian spermatogenic cells protect a conserved developmental program while enabling exceptionally rapid divergence in gene expression and function is unknown. Here, we comprehensively profile the spermatogenic gene expression program in grey short-tailed opossum (Monodelphis domestica, a model marsupial) and compare it to equivalent data from the mouse (Mus musculus, a model placental mammal) to discover contrasting forces underlying the unique evolutionary dynamics of gene expression during mammalian spermatogenesis. For the first time, we describe the timing of the ‘first wave’ of opossum spermatogenesis, and we combine bulk transcriptomic data from first-wave juvenile testes with single-cell transcriptomic data from adult testes to define conserved and divergent gene expression programs across the placental-marsupial split. We substantiate and extend our findings using genome-wide chromatin and multi-species transcriptome data and identify three classes of genes with different evolutionary trajectories: a deeply conserved central gene regulatory program governing spermatogenic progression; a separate class of spermatogenic genes exhibiting dynamic expression across placental mammals; and a third set of genes with evidence for directional selection in the placental mammal ancestor and constraint on expression levels within the placental mammalian lineage, representing placental innovations in germline gene expression and including biologically critical modules such as the DNA recombination and repair machinery.
Viral clearance as a surrogate of clinical efficacy for COVID-19 therapies in outpatients: A systematic review and meta-analysis
Authors: Elias Karen M , Khan Shanchita R , Stadler Eva , Schlub Timothy E , Cromer Deborah , Polizzotto Mark N , Kent Stephen J , Turner Tari , Davenport Miles P , Khoury David S 
Published: June 2023

SummaryBackgroundSurrogates of antiviral efficacy are needed for COVID-19. We investigated the relationship between the virological effect of treatment and clinical efficacy as measured by progression to severe disease in unvaccinated outpatients treated for mild to moderate COVID-19.MethodsWe searched PubMed, Scopus and medRxiv from inception to 27thSeptember 2022, for randomised controlled trials (RCTs) which tested potential treatments for COVID-19 in non-hospitalized patients. We included studies that reported both clinical and virological outcomes. Clinical outcomes were the rate of disease progression (generally hospitalization or death within 28 days of commencing treatment) and virological outcomes were viral load (viral RNA copies in upper respiratory tract swabs) within the first 7 days of treatment. Studies were excluded if they did not report on the outcome of a primary randomised controlled trial, or if results were reported in a more complete form in another publication. Risk of Bias assessment was performed using the RoB 2.0 tool. We used generalised linear models with random effects to assess the association between outcomes and account for study heterogeneity.FindingsWe identified 1372 unique studies of which 14 (with a total of 9257 participants) met inclusion criteria. Larger virological treatment effects at both day 3 and day 5 were associated with decreased odds of progression to hospitalisation or death in unvaccinated ambulatory subjects. The odds ratio (OR) for each extra two-fold reduction in viral load in treated compared to control subjects was 0.54 on both days 3 and 5 post treatment (day 3 95% CI 0.38 to 0.74, day 5 95%CI 0.41 to 0.72). There was no relationship between the odds of hospitalisation or death and virological treatment effect at day 7 (OR 0.91, 95%CI 0.74 to 1.13).InterpretationThis review provides evidence that treatment-induced acceleration of viral clearance within the first 5 days after treatment is a surrogate of clinical efficacy to prevent hospitalisation with COVID-19. Limitations included the aggregation of studies with differing designs, and evidence of risk of bias in some virological outcomes. These findings support the use of viral clearance as an early phase clinical trial endpoint of therapeutic efficacy.FundingThe authors were supported by the Australian Government Department of Health, Medical Research Future Fund, National Health and Medical Research Council and the University of New South Wales.
Machine learning to increase the efficiency of a literature surveillance system: a performance evaluation
Authors: Lokker Cynthia , Abdelkader Wael , Bagheri Elham , Parrish Rick , Cotoi Chris , Navarro Tamara , Germini Federico , Linkins Lori-Ann , Haynes R. Brian , Chu Lingyang , Afzal Muhammad , Iorio Alfonso 
Published: June 2023

ABSTRACTBackgroundGiven suboptimal performance of Boolean searching to identify methodologically sound and clinically relevant studies in large bibliographic databases such as MEDLINE, exploring the performance of machine learning (ML) tools is warranted.ObjectiveUsing a large internationally recognized dataset of articles tagged for methodological rigor, we trained and tested binary classification models to predict the probability of clinical research articles being of high methodologic quality to support a literature surveillance program.Materials and MethodsUsing an automated machine learning approach, over 12,000 models were trained on a dataset of 97,805 articles indexed in PubMed from 2012-2018 which were manually appraised for rigor by highly trained research associates with expertise in research methods and critical appraisal. As the dataset is unbalanced, with more articles that do not meet criteria for rigor, we used the unbalanced dataset and over- and under-sampled datasets. Models that maintained sensitivity for high rigor at 99% and maximized specificity were selected and tested in a retrospective set of 30,424 articles from 2020 and validated prospectively in a blinded study of 5253 articles.ResultsThe final selected algorithm, combining a model trained in each dataset, maintained high sensitivity and achieved 57% specificity in the retrospective validation test and 53% in the prospective study. The number of articles needed to read to find one that met appraisal criteria was 3.68 (95% CI 3.52 to 3.85) in the prospective study, compared with 4.63 (95% CI 4.50 to 4.77) when relying only on Boolean searching.ConclusionsML models improved by approximately 25% the efficiency of detecting high quality clinical research publications for literature surveillance and subsequent dissemination to clinicians and other evidence users.
Decreasing alpha flow releases task-specific processing paths
Authors: Hanna Jevri , Kim Cora , Rampp Stefan , Buchfelder Michael , Müller-Voggel Nadia 
Published: June 2023

AbstractDirecting and maintaining attention toward relevant information and away from non-relevant information is a critical competence of higher-order nervous systems. Here, we used directed connectivity to investigate how the human brain prioritizes appropriate processing paths when participants are performing a behavioral task requiring attention in the visual or the auditory modality. We show that the efficient transfer of information relevant for the task is mediated by a region- and task-specific decrease of alpha band connectivity from parietal and, in case a motor response is required, motor cortex to the relevant sensory cortices. Further, alpha-band connectivity modulations reliably predict alpha power modulations in the task-related sensory cortices, particularly where the task-irrelevant cortex is inhibited via local alpha power increases. We suggest that the task- and region-specific modulation of alpha-band connectivity in the present study is a basic neuronal mechanism orchestrating the allocation of task-relevant neuronal resources related to and possibly underlying the previously reported sensory alpha power modulations in association with the allocation of competing attentional resources.
Dysregulated Platelet Function in Patients with Post-Acute Sequelae of COVID-19
Authors: Aggarwal Anu , Singh Tamanna K. , Pham Michael , Godwin Matthew , Chen Rui , McIntyre Thomas M. , Scalise Alliefair , Chung Mina K. , Jennings Courtney , Ali Mariya , Park Hiijun , Englund Kristin , Khorana Alok A. , Svensson Lars G. , Kapadia Samir , McCrae Keith R. , Cameron Scott J. 
Published: June 2023

AbstractBackgroundPost-acute sequelae of COVID-19 (PASC), also referred as Long-COVID, sometimes follows COVID-19, a disease caused by SARS-CoV-2. While SARS-CoV-2 is well-known to promote a prothrombotic state, less is known about the thrombosis risk in PASC.AimOur objective was to evaluate the platelet function and thrombotic potential in patients following recovery from SARS-CoV-2 with clear symptoms of PASC.MethodsPASC patients and matched healthy controls were enrolled in the study on average 15 months after documented SARS-CoV-2 infection. Platelet activation was evaluated by Light Transmission Aggregometry (LTA) and flow cytometry in response to platelet surface receptor agonists. Thrombosis in platelet-deplete plasma was evaluated by Factor Xa activity. A microfluidics system assessed thrombosis in whole blood under shear stress conditions.ResultsA mild increase in platelet aggregation in PASC patients through the thromboxane receptor was observed and platelet activation through the glycoprotein VI (GPVI) receptor was decreased in PASC patients compared to age- and sex-matched healthy controls. Thrombosis under shear conditions as well as Factor Xa activity were reduced in PASC patients. Plasma from PASC patients was an extremely potent activator of washed, healthy platelets – a phenomenon not observed when stimulating healthy platelets after incubation with plasma from healthy individuals.ConclusionsPASC patients show dysregulated responses in platelets and coagulation in plasma, likely caused by a circulating molecule that promotes thrombosis. A hitherto undescribed protective response appears to exists in PASC patients to counterbalance ongoing thrombosis that is common to SARS-CoV-2 infection.