bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of cost-effective one-step multiplex RT-PCR assay for detecting the SARS-CoV-2 infection using SYBR Green melting curve analysis
Authors: Sarkar Shovon Lal , Alam A. S. M. Rubayet Ul , Das Prosanto Kumar , Pramanik Md. Hasan Ali , Al-Emran Hassan M. , Jahid Iqbal Kabir , Hossain M. Anwar 
Published: May 2021

AbstractTaqMan probe-based expensive commercial real-time (RT) PCR kits are being used in COVID-19 diagnosis. The unprecedented scale of SARS-CoV-2 infections has urgently needed to meet the challenge of testing more persons at a reasonable cost. This study developed a rapid, simple, and cost-effective alternative diagnostic method based on melting curve analysis of SYBR green multiplex assay with a host-specific internal control. A total of 90 randomly selected samples were used for comparing the assay with an available commercial kit to analyse the variation and validity of this in-house developed method. Our customized designed primers specifically detected the virus as similar to commercial kit manufactured by Sansure Biotech Inc. We optimized separately the N, E, S, and RdRp genes by SYBR Green RT-PCR method based on melting curve analysis. Afterwards, a multiplex COVID-19 diagnosis method targeting N and E genes of the virus along with the β-actin gene of the host as an internal control has been established. The total run-time of our proposed method was less than 90 minutes. The cost of each sample processing was less than $2. Overall, this one-step and one-tube method can revolutionize the COVID-19 diagnosis in developing countries.
Higher case fatality rate among obstetric patients with COVID-19 in the second year of pandemic in Brazil: do new genetic variants play a role?
Authors: Takemoto Maíra L S , Nakamura-Pereira Marcos , Menezes Mariane O , Katz Leila , Knobel Roxana , Amorim Melania M R , Andreucci Carla B 
Published: May 2021

AbstractBackgroundIn Brazil, a 20% increase in maternal mortality rate due to COVID-19 is projected for 2020. On January 4, 2021, the P.1 SARS-CoV-2 genetic variant was firstly identified in the country and recent data has indicated an association with higher hospitalization rates and mortality. The impact of P.1 variant in the obstetric population remains unclear.MethodsWe carried out a preliminary analysis of sociodemographic and clinical characteristics of COVID-19 confirmed maternal deaths (between 10-50 years old) comparing cases reported to the Brazilian official severe acute respiratory syndrome (SARS) surveillance system (SS) in 2020 with those from 2021 (until April 12, 2021). This preliminary analysis employed methods described in previous reports from our group.Results803 maternal deaths out of 8,248 COVID-19 maternal SARS cases with a recorded outcome were reported to the SARS-SS since March 2020. Case fatality rate was significantly higher in 2021 (15.6% vs 7.4%). The first three months of 2021 already account for 46.2% of all deaths occurred in the 13-months analysed period. COVID-19 fatal cases from 2021 had a lower proportion of at least one risk factor or comorbidity as compared to 2020 but had a higher frequency of obesity. There were no significant differences in terms of age, type of residence area (urban, rural, or peri-urban), type of funding of the notification unit (public vs. private), COVID-19 diagnostic criteria, pregnancy status (pregnancy or postpartum), cardiovascular disease or diabetes. The proportion of hospitalization, ICU admission, and respiratory support before death was also not significantly different.ConclusionCase fatality rate was increased in the three first months of 2021 when compared to 2020. Once variables related to health care access and demographics are not significantly different and women seem to be healthier in the 2021 sample, such difference may be related to the circulation of more aggressive genetic variants in the country.
Implementation of an interactive mobile application to pilot a rapid assay to detect HIV drug resistance mutations in Kenya
Authors: Vrana Justin D. , Panpradist Nuttada , Higa Nikki , Ko Daisy , Ruth Parker , Kanthula Ruth , Lai James J. , Yang Yaoyu , Sakr Samar R. , Chohan Bhavna , Chung Michael H. , Frenkel Lisa M. , Lutz Barry R. , Klavins Eric , Beck Ingrid A. 
Published: May 2021

AbstractIntroductionUsability is an overlooked aspect of implementing lab-based assays, particularly novel assays in low-resource-settings. Esoteric instructions can lead to irreproducible test results and patient harm. To address these issues, we developed a software application based on “Aquarium”, a laboratory-operating system run on a computer tablet that provides step-by-step digital interactive instructions, protocol management, and sample tracking. Aquarium was paired with a near point-of-care HIV drug resistance test, “OLA-Simple”, that detects mutations associated with virologic failure. In this observational study we evaluated the performance of Aquarium in guiding untrained users through the multi-step laboratory protocol with little supervision.MethodsA feasibility study was conducted in a laboratory at Coptic Hope Center in Nairobi, Kenya. To evaluate the training by Aquarium software, twelve volunteers who were unfamiliar with the kit performed the test on blinded samples (2 blood specimens; 5 codons/sample). Steps guided by Aquarium included: CD4+ T-Cell separation, PCR, ligation, detection, and interpretation of test results. Participants filled out a short survey regarding their demographics and experience with the software and kit.Results and discussion12/12 laboratory technicians had no prior experience performing CD4+ separation and 7/12 had no experience performing laboratory-based molecular assays. 12/12 isolated CD4+ T cells from whole blood with yields comparable to isolations performed by trained personnel. The OLA-Simple workflow was completed by all, with correct visual and software interpretation of results for 90% (108/120) and 97% (116/120) of codons, respectively. In the surveys, participants favorably assessed the use of software guidance.ConclusionsAquarium digital instructions enabled first-time users in Kenya to complete the OLA-simple kit workflow with minimal training. Aquarium could increase the accessibility of laboratory assays in low-resource-settings and potentially standardize implementation of clinical laboratory tests.
Looking beyond the obvious: a critical systematic review and meta-analyses of risk factors for fertility problems in a globalized world
Authors: Bayoumi R.R. , Boivin J. , Fatemi H.M. , Hurt L. , Serour G.I. , van der Poel S. , Venetis C. 
Published: May 2021

AbstractBackgroundWell-established risk factors for fertility problems such as smoking have been included in fertility awareness efforts globally. However, these efforts neglect risks that women in low and middle-income countries (LMIC) face.ObjectiveTo address this gap, we identified eight risk factors affecting women in LMIC and the aim of the current review was to estimate the impact of these risks on fertility.MethodsWe conducted systematic reviews and where data was available meta-analyses. We searched Medline, Embase, Cochrane library, regional databases and key organizational websites (1946-June 2016, updated January 2018, latest update taking place in 2021). Two researchers screened and extracted data independently. We included all study designs that assessed exposure to risk in clinical or community-based samples and excluded studies without control groups. The outcome of interest was fertility problems (inability to achieve pregnancy or live birth and neonatal death). We calculated pooled effect estimates from reported effect sizes or raw data. We assessed study quality using the Newcastle-Ottawa Scale. We registered the review with PROSPERO, registration number CRD42016048497.ResultsWe identified 2,418 studies and included 61 (57 in meta-analyses). Results revealed a nine-fold increased risk of inability to become pregnant in genital tuberculosis (OR 8.91, CI 1.89-42.12) and almost threefold in HIV (OR 2.93, CI 1.95-4.42) and bacterial vaginosis (OR 2.81, CI 1.85-4.27). A twofold increased risk of tubal-factor infertility in Female Genital Mutilation/Cutting–Type II/III (OR 2.06, CI 1.03-4.15) and increased post-natal mortality in consanguinity (stillbirth, OR 1.28, CI 1.04-1.57; neonatal death, OR 1.57, CI 1.22-2.02).Strength and limitationsReliability of results was bolstered by a rigorous systematic review methodology that is replicable but limited by methodological shortcomings of the available primary studies and the small number of studies in each meta-analysis.ConclusionsThe risk factors investigated appeared to impact the reproductive process through multiple biological, behavioural, and clinical pathways. Additionally, infection and pelvic inflammatory disease seemed to be common pathways for several risk factors. The complex multifactorial risk profile can be addressed by LMIC using a global health framework to determine which risk factors are significant to their populations and how to tackle them. The subsequent health promotion encompassing these relevant health indicators could translate into more prevention and effective early detection of fertility problems in LMIC. Finally, the findings of multifactorial risk reinforced the need to put fertility as an agenda in global health initiatives.
Hypomethylation of Monoamine Oxidase A promoter/exon 1 region is associated with temper outbursts in Prader-Willi syndrome
Authors: Deest Maximilian , Buchholz Vanessa , Jahn Kirsten , Eberlein Christian , Bleich Stefan , Frieling Helge 
Published: May 2021

AbstractBackgroundPrader-Willi syndrome (PWS) is a rare neurodevelopmental disorder caused by the absence of paternally expressed and maternally imprinted genes on chromosome 15q 11.2-13. It is associated with a certain behavioural phenotype with repetitive and ritualistic behaviours, skin-picking and temper outbursts. Temper outbursts are characterized by verbal and physical aggression with screaming, destroying property, and/or physical aggression towards others. They drastically effect the quality of life of the individuals as well as the relatives and caregivers. Recent studies show a promising therapeutic effect of serotonin reuptake inhibitors like sertraline on frequency and intensity of outbursts. Monoamine oxidase A (MAOA) (X p11.23) plays a crucial role in the metabolism of monoamines such as serotonin, norepinephrine, and dopamine. Dysregulation in methylation of the CpG island spanning the promoter region and exon 1 of MAOA is implicated in impulsive and aggressive behaviour.MethodsIn the present study, methylation rates of CpG dinucleotides in the MAOA promoter and exon 1 region were determined from DNA derived from whole blood samples of PWS patients (n=32) and controls (n=14) matched for age, sex and BMI via bisulfite sequencing. PWS patients were grouped into those showing temper outbursts, and those who do not.ResultsOverall, PWS patients show a significant lower methylation rate at the promoter/exon 1 region than healthy controls in both sexes. Furthermore, PWS patients, male as well female with temper outbursts show a significant lower methylation rate than those without temper outbursts (p<0.001 and p=0.006)ConclusionThe MAOA promoter/exon 1 region methylation seems to be dysregulated in PWS patients in sense of a hypomethylation, especially in those suffering from temper outbursts. As MAOA is involved in the metabolism of serotonin, we conclude that this dysregulation plays a crucial role in the pathophysiology of temper outbursts in PWS. Furthermore, our findings suggest, that dysregulation of certain genes outside the PWS locus contribute to the behavioural phenotype of PWS.
RT-qPCR-based tests for SARS-CoV-2 detection in pooled saliva samples for massive population screening to monitor epidemics
Authors: Różański Michał , Walczak-Drzewiecka Aurelia , Witaszewska Jolanta , Wójcik Ewelina , Guziński Arkadiusz , Zimoń Bogumił , Matusiak Rafał , Kazimierczak Joanna , Borowiec Maciej , Kania Katarzyna , Paradowska Edyta , Pawełczyk Jakub , Dziadek Jarosław , Dastych Jarosław 
Published: May 2021

AbstractSwab, quantitative, reverse transcription polymerase chain reaction (RT-qPCR) tests remain the gold standard of diagnostics of SARS-CoV-2 infections. However, these tests are costly and time-consuming, and swabbing limits their throughput. We developed a 3-gene, seminested RT-qPCR test with SYBR green-based detection, optimized for testing pooled saliva samples for high-throughput diagnostics of epidemic-affected populations. The proposed two-tier approach depends on decentralized self-collection of saliva samples, pooling, 1st-tier testing with the mentioned highly sensitive screening test and subsequent 2nd-tier testing of individual samples from positive pools with the in vitro diagnostic (IVD) test. The screening test was able to detect 5 copies of the viral genome in 10 µl of isolated RNA with 50% probability and 18.8 copies with 95% probability and reached Ct values that were highly linearly RNA concentration-dependent. In the side-by-side comparison (testing artificial pooled samples), the screening test attained slightly better results than the commercially available IVD-certified RT-qPCR diagnostic test (100% specificity and 89.8% sensitivity vs. 100% and 73.5%, respectively). Testing of 1475 individual clinical samples pooled in 374 pools of 4 revealed 0.8% false positive pools and no false negative pools. In weekly prophylactic testing of 113 people within 6 months, a two-tier testing approach enabled the detection of 18 infected individuals, including several asymptomatic individuals, with a fraction of the costs of individual RT-PCR testing.
Phylogenomics of SAR116 clade reveals two subclades with different evolutionary trajectories and important role in the ocean sulfur cycle
Authors: Roda-Garcia Juan J. , Haro-Moreno Jose M. , Huschet Lukas A. , Rodriguez-Valera Francisco , López-Pérez Mario 
Published: May 2021

ABSTRACTThe SAR116 clade within the class Alphaproteobacteria represents one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. The small number of cultured representatives of SAR116 (only two to date) is a major bottleneck that has prevented an in-depth study at the genomic level to understand the relationship between genome diversity and its role in the marine environment. In this study, we use all publicly available genomes to provide a genomic overview of the phylogeny, metabolism and biogeography within the SAR116 clade. This increased genomic diversity revealed has led to the discovery of two subclades of SAR116 that, despite having similar genome size (ca. 2.4 Mb) and coexist in the same environment, display different properties in their genomic make up. One represents a novel subclade for which no pure cultures have been isolated and is composed mainly of single-amplified genomes (SAGs). Genomes within this subclade showed convergent evolutionary trajectories with more streamlining features, such as low GC content (ca. 30%), short intergenic spacers (<22 bp) and strong purifying selection (low dN/dS). Besides, they were more abundant in metagenomic databases recruiting also at the deep chlorophyll maximum. Less abundant and restricted to the upper photic layers of the global ocean, the other subclade of SAR116, enriched in MAGs, accommodated the only two pure cultures. Genomic analysis suggested that both clades have a significant role in the sulfur cycle with differences in the way in which both clades can metabolize the dimethylsulfoniopropionate (DMSP).IMPORTANCESAR116 clade of Alphaproteobacteria is an ubiquitous group of heterotrophic bacteria inhabiting the surface of the ocean, but the information about their ecology and population genomic diversity is scarce due to the difficulty of getting pure culture isolates. The combination of single-cell genomics and metagenomics has become an alternative approach to study this kind of microbes. Our results expand the understanding of the genomic diversity, distribution, and lifestyles within this clade and provide evidence of different evolutionary trajectories in the genome make-up of the two subclades that could serve to understand how evolutionary pressure can drive different adaptations to the same environment. Therefore, the SAR116 clade represents an ideal model organism for the study of the evolutionary streamlining of genomes in microbes that have relatively close relatedness to each other.
Combinatorial Immunotherapies Overcome MYC-Driven Immune Evasion
Authors: Lee Joyce V. , Housley Filomena , Yau Christina , Van de Mark Daniel , Nakagawa Rachel , Hemmati Golzar , Hernandez Grace A. , Winkler Juliane , Zhang Yibing , Samson Susan , Baas Carole , Esserman Laura J. , Van ‘T Veer Laura J. , Rugo Hope S. , Matloubian Mehrdad , Goga Andrei 
Published: May 2021

AbstractFor many human cancers, including triple negative breast cancer (TNBC), a modest number of patients benefit from immune checkpoint inhibitors, and few experience cancer remission1. Expression of programed death-ligand 1 (PD-L1), tumor immune infiltration, or tumor mutation burden have been widely investigated for predicting cancer immunotherapy response1-5. Whether specific oncogenes diminish response to immunotherapy6-10and whether these effects are reversible remains poorly understood. We predicted thatMYC, an oncogene that is frequently overexpressed11,12and is associated with worse prognosis12, may predict immunotherapy response in patients with TNBC. Here, we report that MYC-elevated TNBCs are resistant to immune checkpoint inhibitors. Using mouse models of TNBC and patient data we report that MYC signaling is associated with low tumor cell PD-L1, low overall immune cell infiltration, and low tumor cell MHC-I expression. Restoring interferon signaling in the tumor reduces MYC expression and increases MHC-I expression. By combining a TLR9 agonist and an agonistic antibody against OX40 with anti-PD-L1, most mice experience complete tumor regression and are protected from new TNBC tumor outgrowth. Our findings demonstrate that MYC-dependent immune evasion is reversible and druggable, and if strategically targeted, may improve outcomes for patients treated with immune checkpoint inhibitors.
ARS2-directed alternative splicing mediates CD28 driven T cell glycolysis and effector function
Authors: Holling G. Aaron , Sharda Anand P. , Honikel Mackenzie M. , James Caitlin M. , Lightman Shivana M. , Qiao Guanxi , Singel Kelly L. , Emmons Tiffany R. , Giridharan Thejaswini , Hou Shengqi , Intlekofer Andrew M. , Higashi Richard M. , Fan Teresa W. M. , Lane Andrew N. , Eng Kevin H. , Segal Brahm H. , Repasky Elizabeth A. , Lee Kelvin P. , Olejniczak Scott H. 
Published: May 2021

AbstractCD8 T cell activation prompts extensive transcriptome remodeling underlying effector differentiation and function. Regulation of transcriptome composition by the mitogen-inducible nuclear cap-binding complex (CBC) adaptor protein ARS2 has critical cell type-specific consequences, including thymic T cell survival. Here we show that ARS2 was upregulated by CD28 during activation of peripheral T cells, was essential for anti-tumor immunity, and facilitated T cell activation-induced alternative splicing. The novel splicing function of ARS2 was mediated at least in part by recruitment of splicing factors to nascent transcripts including the M2 isoform of pyruvate kinase (Pkm2), a key determinant of CD8 T cell effector properties. Notably, ARS2-directedPkm2splicing occurred days after stimulation of PI3K-indepdendent CD28 signaling and increased glycolysis beyond levels determined by PI3K signaling during T cell priming. Thus, ARS2-directedPkm2splicing represents a mechanism by which CD28 drives glycolytic metabolism, allowing for optimal effector cytokine production and T cell anti-tumor immunity.
Transcriptomes of peripheral blood mononuclear cells from juvenile dermatomyositis patients show elevated inflammation even when clinically inactive
Authors: Roberson Elisha D.O. , Mesa Rosana A. , Morgan Gabrielle A. , Cao Li , Marin Wilfredo , Pachman Lauren M. 
Published: May 2021

AbstractIn juvenile dermatomyositis (JDM), the most common pediatric inflammatory myopathy, weakness is accompanied by a characteristic rash that often becomes chronic, and is associated with vascular damage. We hoped to understand the molecular underpinnings of JDM, particularly in untreated disease, which would facilitate the identification of novel mechanisms and clinical targets that might disrupt disease progression. We studied the RNA-Seq data from untreated JDM peripheral blood mononuclear cells (PBMCs; n=11), PBMCs from a subset of the same patients when clinically inactive (n=8/11), and separate samples of untreated JDM skin and muscle (n=4 each). All JDM samples were compared to non-inflammatory control tissues. The untreated JDM PBMCs showed a strong signature for type1 interferon response, along with IL-1, IL-10, and NF-κB. Surprisingly, PBMCs from clinically inactive JDM individuals had persistent immune activation that was enriched for IL-1 signaling. JDM skin and muscle both showed evidence for type 1 interferon activation and genes related to antigen presentation, and decreased expression of genes related for cellular respiration. Additionally we found that PBMC gene expression correlates with disease activity scores (DAS; skin, muscle, and total domains) and with nailfold capillary end row loop number (an indicator of microvascular damage). This includedotoferlin, which was significantly increased in untreated JDM PBMCs and correlated with all 3 DAS domains. Overall, these data demonstrate that PBMC transcriptomes are informative of molecular disruptions in JDM and provide transcriptional evidence of chronic inflammation despite clinical quiescence.
Modelling the depth-dependent VASO and BOLD responses in human primary visual cortex
Authors: Akbari Atena , Bollmann Saskia , Ali Tonima S , Barth Markus 
Published: May 2021

AbstractFunctional magnetic resonance imaging (fMRI) using a blood-oxygenation-level-dependent (BOLD) contrast is a common method for studying human brain function non-invasively. Gradient-echo (GRE) BOLD is highly sensitive to the blood oxygenation change in blood vessels; however, the spatial signal specificity can be degraded due to signal leakage from activated lower layers to superficial layers in depth-dependent (also called laminar or layer-specific) fMRI. Alternatively, physiological variables such as cerebral blood volume using the VAscular-Space-Occupancy (VASO) contrast have shown higher spatial specificity compared to BOLD. To better understand the physiological mechanisms such as blood volume and oxygenation changes and to interpret the measured depth-dependent responses, models are needed which reflect vascular properties at this scale. For this purpose, we extended and modified the “cortical vascular model” previously developed to predict layer-specific BOLD signal changes in human primary visual cortex to also predict a layer-specific VASO response. To evaluate the model, we compared the predictions with experimental results of simultaneous VASO and BOLD measurements in a group of healthy participants. Fitting the model to our experimental data provided an estimate of CBV change in different vascular compartments upon neural activity. We found that stimulus-evoked CBV change mainly occurs in small arterioles, capillaries and intracortical arteries, and that the contribution from venules and ICVs is small. Our results confirm that VASO is less susceptible to large vessel effects compared to BOLD, as blood volume changes in intracortical arteries did not substantially affect the resulting depth-dependent VASO profiles, whereas depth-dependent BOLD profiles showed a bias towards signal contributions from intracortical veins.