bluuebunny/crossref_metadata_2025_split huggingface dataset:
Usefulness of quantitative Loop-Mediated Isothermal Amplification Assay in comparison with real time PCR for the diagnosis of invasive pneumococcal disease
Authors: Peela Sreeram Chandra Murthy , Sistla Sujatha 
Published: December 2022

AbstractBackgroundQuantitative LAMP (qLAMP) assay is one of the recent and emerging diagnostic tests for infectious diseases. Only a few studies exist comparing this assay with quantitative real-time PCR (qPCR) for the diagnosis of invasive pneumococcal disease (IPD). The present study was performed to compare the diagnostic performance of qLAMP assay with qPCR targeting autolysin gene for the diagnosis of invasive pneumococcal disease.Methodology/Principal FindingsNinety six blood samples and 73 CSF samples from patients clinically suspected with community acquired pneumonia and acute meningitis were tested by qPCR and qLAMP assays using previously published primers and protocols. The qPCR was considered as the gold standard test and the diagnostic performance was assessed by calculating sensitivity, specificity, positive and negative predictive values, and kappa coefficient for the level of agreement between the tests. Chi-squared/Fisher exact test was used to compare categorical variables (positive/negative). Thirty two blood samples and 22 CSF samples were positive by qPCR while 24 and 20 samples were positive by qLAMP assay respectively. The sensitivity of qLAMP assay was only 86.4% and 75% when tested on CSF and blood samples respectively. However, the qLAMP assay was in substantial to almost perfect agreement when compared with qPCR. The results were statistically significant in both sample types (P<0.001).ConclusionsThe performance of qLAMP assay can vary based on the specimen type. It has very high specificity and had substantial to almost perfect agreement, and thus may be an alternative to qPCR for the diagnosis of IPD.
Transcriptomic profiling reveals distinct subsets of immune checkpoint inhibitor-induced myositis
Authors: Pinal-Fernandez Iago , Quintana Angela , Milisenda Jose C. , Casal-Dominguez Maria , Muñoz-Braceras Sandra , Derfoul Assia , Torres-Ruiz Jiram , Pak Katherine , Del Orso Stefania , Naz Faiza , Gutierrez-Cruz Gustavo , Milone Margherita , Shelly Shahar , Duque-Jaimez Yaiza , Tobias-Baraja Ester , Matas-Garcia Ana , Garrabou Gloria , Padrosa Joan , Ros Javier , Trallero-Araguás Ernesto , Walitt Brian , Christopher-Stine Lisa , Lloyd Thomas E. , Zhao Chen , Swift Shannon , Rajan Arun , Grau Josep Maria , Selva-O’Callaghan Albert , Liewluck Teerin , Mammen Andrew L. 
Published: December 2022

AbstractObjectivesInflammatory myopathy or myositis is a heterogeneous family of immune-mediated diseases including dermatomyositis (DM), antisynthetase syndrome (AS), immune-mediated necrotizing myopathy (IMNM), and inclusion body myositis (IBM). Immune checkpoint inhibitors (ICI) can also cause myositis (ICI-myositis). This study was designed to define gene expression patterns in muscle biopsies from patients with ICI-myositis.MethodsBulk RNA sequencing was performed on 200 muscle biopsies (35 ICI-myositis, 44 DM, 18 AS, 54 IMNM, 16 IBM, and 33 normal muscle biopsies) and single nuclei RNA sequencing was performed on 22 muscle biopsies (7 ICI-myositis, 4 DM, 3 AS, 6 IMNM, and 2 IBM).ResultsUnsupervised clustering defined three distinct transcriptomic subsets of ICI-myositis: ICI-DM, ICI-MYO1, and ICI-MYO2. ICI-DM included patients with DM and anti-TIF1γ autoantibodies who, like DM patients, overexpressed type 1 interferon-inducible genes. ICI-MYO1 patients had highly inflammatory muscle biopsies and included all patients that developed co-existing myocarditis. ICI-MYO2 was composed of patients with predominant necrotizing pathology and low levels of muscle inflammation. The type 2 interferon pathway was activated both in ICI-DM and ICI-MYO1. Unlike the other types of myositis, all three subsets of ICI-myositis patients overexpressed genes involved in the IL6 pathway.ConclusionsWe identified three distinct types of ICI-myositis based on transcriptomic analyses. The IL6 pathway was overexpressed in all groups, the type I interferon pathway activation was specific for ICI-DM, the type 2 IFN pathway was overexpressed in both ICIDM and ICI-MYO1, and only ICI-MYO1 patients developed myocarditis.
T7 DNA polymerase treatment improves quantitative sequencing of both double-stranded and single-stranded DNA viruses
Authors: Billaud Maud , Theodorou Ilias , Lamy-Besnier Quentin , Shah Shiraz A. , Lecointe François , De Sordi Luisa , De Paepe Marianne , Petit Marie-Agnès 
Published: December 2022

SummaryBackground:Bulk microbiome, as well as virome-enriched shotgun sequencing only reveals the double-stranded DNA (dsDNA) content of a given sample, unless specific treatments are applied. However, genomes of viruses often consist of a circular single-stranded DNA (ssDNA) molecule. Pre- treatment and amplification of DNA using the multiple displacement amplification (MDA) method enables conversion of ssDNA to dsDNA, but this process can lead to over-representation of these circular ssDNA genomes. A more recent alternative permits to bypass the amplification step, as library adapters are ligated to sheared and denatured DNA, after an end-modification step (xGen kit). However, the sonication step might shear ssDNA more efficiently than dsDNA, therefore introducing another bias in virome sequencing. These limitations prompted us to explore an alternative method of DNA preparation for sequencing mixed ssDNA and dsDNA viromes.Results:Using a synthetic mix of viral particles, we made use of the T7 DNA polymerase (T7pol) to convert viral circular ssDNA molecules to dsDNA, while preventing over-replication of such molecules, as is the case with the Phi29 DNA polymerase. Our findings indicate that using T7pol and a mix of degenerated primers to convert ssDNA to dsDNA prior library preparation is a good alternative to the currently used methods. It better represents the original synthetic mixtures compared to MDA or direct application of the xGen kit. Furthermore, when applied to two complex virome samples, the T7pol treatment improved both the richness and abundance in theMicroviridaefraction.Conclusion:We conclude that T7pol pretreatment is preferable to MDA for the shotgun sequencing of viromes, which is easy to implement and inexpensive.
The phased diploid genome assembly ofVitis vinifera cv. Shiraz
Authors: Onetto Cristobal A. , Ward Christopher M. , Borneman Anthony R. 
Published: December 2022

AbstractShiraz (Syrah) is a dark-skinned cultivar of the wine grapeVitis viniferathat forms the basis of some of the world’s most iconic wines. Worldwide, Shiraz is the fourth most planted grapevine cultivar, however it represents the most planted cultivar in Australia. Given the importance of Shiraz to worldwide wine production, a long-read based reference genome assembly for this cultivar was produced and used to investigate the unique genetic diversity and ancestral origins of this iconic variety. Phylogenetic reconstruction using high-quality genome assemblies for wine grape cultivars provided further support of a kinship between Shiraz and Pinot Noir. Harnessing long-read data, transposable element insertions potentially affecting gene function were characterized in Shiraz and assessed relative to other cultivars. This revealed a heterogenous landscape of transposon insertion points across cultivars and uncovered a specific combination of allelic variants at theTPS24terpene synthase locus, which when combined with appropriate environmental triggers, may allow Shiraz to produce high levels of rotundone, the aroma compound responsible for the distinctive peppery characteristics of this cultivar.
A comparison of survey method efficiency for estimating densities of Zebra Mussels (Dreissena polymorpha)
Authors: Ferguson Jake M. , Jiménez Laura , Keyes Aislyn A. , Hilding Austen , McCartney Michael A. , Clair Katie St. , Johnson Douglas H. , Fieberg John 
Published: December 2022

ABSTRACTAbundance surveys are a common and practical technique to estimate plant or animal densities. Methods used to conduct these surveys often require jointly estimating uncertainty in both counts and detection probability. The estimation of detection probability requires additional measurements that take time, potentially reducing the efficiency of the survey for high-density populations. We conducted quadrat, removal, and distance surveys of zebra mussels (Dreissena polymorpha) in three central Minnesota lakes and used an efficiency measure to help compare survey designs. Survey efficiency depended on both the survey design and the population density. The efficiency of survey designs that required estimates of detection probabilities (relative to designs that did not) decreased with density, leading to a change in the most efficient survey design at high densities. These results demonstrate that the best survey design may be context-specific, requiring some prior knowledge of the underlying population density and the cost/time needed to collect additional information for estimating detection probabilities.
Single-nucleus co-expression networks of dopaminergic neurons support iron accumulation as a plausible explanation to their vulnerability in Parkinson’s disease
Authors: Gómez-Pascual A. , Martirosyan A. , Hebestreit K. , Mameffe C. , Poovathingal S. , Belgard T. G. , Altar C. A. , Kottick A. , Holt M. , Hanson-Smith V. , Cisterna A. , Mighdoll M. , Scannevin R. , Guelfi S. , Botía J. A. 
Published: December 2022

AbstractMotivationgene co-expression networks have been widely applied to identify critical genes and pathways for neurodegenerative diseases such as Parkinson’s and Alzheimer’s disease. Now, with the advent of single-cell RNA-sequencing, we have the opportunity to create cell-type specific gene co-expression networks. However, single-cell RNA-sequencing data is characterized by its sparsity, amongst some other issues raised by this new type of data.ResultsWe present scCoExpNets, a framework for the discovery and analysis of cell-type specific gene coexpression networks (GCNs) from single-cell RNA-seq data. We propose a new strategy to address the problem of sparsity, named iterative pseudo-cell identification. It consists of adding the gene expression of pairs of cells that belong to the same individual and the same cell-type while the number of cells is over 200, thus creating multiple matrices and multiple scGCNs for the same cell-type, all of them seen as alternative and complementary views of the same phenomena. We applied this new tool on a snRNA-seq dataset human post-mortem substantia nigra pars compacta tissue of 13 controls and 14 Parkinson’s disease (PD) cases (18 males and 9 females) with 30-99 years. We show that one of the hypotheses that support the selective vulnerability of dopaminergic neurons in PD, the iron accumulation, is sustained in our dopaminergic neurons network models. Moreover, after successive pseudo-celluling iterations, the gene groups sustaining this hypothesis remain intact. At the same time, this pseudo-celulling strategy also allows us to discover genes whose grouping changes considerably throughout the iterations and provides new insights. Finally, since some of our models were correlated with diagnosis and age at the same time, we also developed our own framework to create covariate-specific GCNs, called CovCoExpNets. We applied this new software to our snRNA-seq dataset and we identified 11 age-specific genes and 5 diagnosis-specific genes which do not overlap.Availability and implementationThe CoExpNets implementations are available as R packages: scCoExpNets for creating single-cell GCNs and CovCoExpNets for creating covariate-specific GCNs. Users can either download the development version via githubhttps://github.com/aliciagp/scCoExpNetsandhttps://github.com/aliciagp/CovCoExpNetsContactalicia.gomez1@um.esSupplementary informationsupplementary data is available online.
Next-generation plasmids for transgenesis in zebrafish and beyond
Authors: Kemmler Cassie L. , Moran Hannah R. , Murray Brooke F. , Scoresby Aaron , Klem John R. , Eckert Rachel L. , Lepovsky Elizabeth , Bertho Sylvain , Nieuwenhuize Susan , Burger Sibylle , D’Agati Gianluca , Betz Charles , Puller Ann-Christin , Felker Anastasia , Ditrychová Karolína , Bötschi Seraina , Affolter Markus , Rohner Nicolas , Lovely C. Ben , Kwan Kristen M. , Burger Alexa , Mosimann Christian 
Published: December 2022

AbstractTransgenesis is an essential technique for any genetic model. Tol2-based transgenesis paired with Gateway-compatible vector collections has transformed zebrafish transgenesis with an accessible, modular system. Here, we established several next-generation transgenesis tools for zebrafish and other species to expand and enhance transgenic applications. To facilitate gene-regulatory element testing, we generated Gateway middle entry vectors harboring the small mousebeta-globinminimal promoter coupled to several fluorophores, CreERT2, and Gal4. To extend the color spectrum for transgenic applications, we established middle entry vectors encoding the bright, blue-fluorescent protein mCerulean and mApple as an alternative red fluorophore. We present a series of p2A peptide-based 3’ vectors with different fluorophores and subcellular localizations to co-label cells expressing proteins of interest. Lastly, we established Tol2 destination vectors carrying the zebrafishexorhpromoter driving different fluorophores as a pineal gland-specific transgenesis marker active prior to hatching and through adulthood. exorh-based reporters and transgenesis markers also drive specific pineal gland expression in the eye-less cavefish (Astyanax). Together, our vectors provide versatile reagents for transgenesis applications in zebrafish, cavefish, and other models.
Cell-type-specific co-expression inference from single cell RNA-sequencing data
Authors: Su Chang , Xu Zichun , Shan Xinning , Cai Biao , Zhao Hongyu , Zhang Jingfei 
Published: December 2022

AbstractThe inference of gene co-expressions from microarray and RNA-sequencing data has led to rich insights on biological processes and disease mechanisms. However, the bulk samples analyzed in most studies are a mixture of different cell types. As a result, the inferred co-expressions are confounded by varying cell type compositions across samples and only offer an aggregated view of gene regulations that may be distinct across different cell types. The advancement of single cell RNA-sequencing (scRNA-seq) technology has enabled the direct inference of co-expressions in specific cell types, facilitating our understanding of cell-type-specific biological functions. However, the high sequencing depth variations and measurement errors in scRNA-seq data present significant challenges in inferring cell-type-specific gene co-expressions, and these issues have not been adequately addressed in the existing methods. We propose a statistical approach, CS-CORE, for estimating and testing cell-type-specific co-expressions, built on a general expression-measurement model that explicitly accounts for sequencing depth variations and measurement errors in the observed single cell data. Systematic evaluations show that most existing methods suffer from inflated false positives and biased co-expression estimates and clustering analysis, whereas CS-CORE has appropriate false positive control, unbiased co-expression estimates, good statistical power and satisfactory performance in downstream co-expression analysis. When applied to analyze scRNA-seq data from postmortem brain samples from Alzheimer’s disease patients and controls and blood samples from COVID-19 patients and controls, CS-CORE identified cell-type-specific co-expressions and differential co-expressions that were more reproducible and/or more enriched for relevant biological pathways than those inferred from other methods.
What are the criteria for morphological cell death inDunaliella salina?
Authors: Barmshuri Mahnaz , Kholdebarin Bahman , Sadeghi Saber , Faghih Zahra 
Published: December 2022

AbstractBy finding morphological criteria for death in photosynthetic algal cells, one finds that the death of different populations of algae cells is manifested by various morphological changes. Present study, was undertaken to determine morphological criteria to be used in identifying cell death in unicellular green algae in their natural habitats. By applying the principles of formazan crystal formation due to MTT reduction in the presence of cells oxidoreductase enzymes, and the staining of saccharide complexes produced in photosynthesis by iodine reagent, morphological criteria were determined for cell death inDunaliella salinacollected from Maharloo lake and three different types of deaths were identified. Further studies have shown that these criteria can also be applied for fresh water algae and other taxon. Different ways of cell death in unicellular aquatic organisms can be used as monitoring tools for early warning of environmental hazards. We invite scientists, editors and reviewers to embark on establishing a much needed cell death classification committee for identifying different types of cell death and investigate mechanisms involved in unicellular aquatic algal cells.Significance StatementStaining with MTT and iodine reagents, are the best tools for distinguishing damages done to photosynthetic system in aquatic unicellular green algae following which cell death classification will be determined.
Striated muscle-specific base editing enables correction of mutations causing dilated cardiomyopathy
Authors: Grosch Markus , Schraft Laura , Chan Adrian , Küchenhoff Leonie , Rapti Kleopatra , Ferreira Anne-Maud , Kornienko Julia , Li Shengdi , Radke Michael H , Krämer Chiara , Clauder-Münster Sandra , Perlas Emerald , Gotthardt Michael , Dieterich Christoph , van den Hoogenhof Maarten MG , Grimm Dirk , Steinmetz Lars M 
Published: December 2022

AbstractDilated cardiomyopathy (DCM) is the second most common cause for heart failure with no cure except a high-risk heart transplantation. Approximately 30% of DCM patients harbor heritable mutations which are amenable to CRISPR-based gene therapy1. However, challenges related to delivery of the editing complex and off-target concerns hamper the broad applicability of CRISPR agents in the heart2. We employed a combination of the viral gene transfer vector AAVMYO with superior targeting specificity of heart muscle tissue3and CRISPR base editors to repair patient mutations in the cardiac splice factorRbm20, which cause aggressive and arrhythmogenic DCM4. Using optimized conditions, we could improve splice defects in human iPSC-derived cardiomyocytes (iPSC-CMs) and repair >70% of cardiomyocytes in twoRbm20knock-in mouse models that we generated to serve as anin vivoplatform of our editing strategy. Treatment of juvenile mice restored the localization defect of RBM20 in 75% of cells and splicing of RBM20 targets including TTN. Three months after injection, cardiac dilation and ejection fraction reached wildtype levels. Single-nuclei RNA sequencing (snRNA-seq) uncovered restoration of the transcriptional profile across all major cardiac cell types and whole-genome sequencing (WGS) revealed no evidence for aberrant off-target editing. Our study highlights the potential of base editors combined with AAVMYO to achieve gene repair for treatment of hereditary cardiac diseases.
Vaporous essential oils and isolates restore pyrethroid-treated netting efficacy toAedes aegypti(Diptera: Culicidae)
Authors: Rault Leslie C. , O’Neal Scott T. , Johnson Ellis J. , Anderson Troy D. 
Published: December 2022

AbstractDecreasing opportunities for mosquitoes to bite is critical in the reduction of mosquito-borne pathogen transmission, such asPlasmodium spp. or dengue, yellow fever, and West Nile viruses. Field-evolved resistance to a large selection of synthetic insecticides is crippling efforts to reduce mosquito populations and new strategies are necessary to sustain the efficacy of commercially available tools.Aedes aegypti(L.), among other species, have evolved pyrethroid resistance in the field and the pyrethroid-resistant Puerto Rico (PR) strain is a valuable tool for understanding resistance mechanisms. A previous study showed that pyrethroid efficacy can be enhanced by pre-exposing the PR strain to essential oil vapors before topical application of deltamethrin. Insecticide-treated nets (ITNs) and long-lasting insecticidal nets (LLINs) are current products commercialized for mosquito bite protection, but nets using pyrethroids are losing efficacy in the field due to field-evolved pyrethroid resistance. This study tested essential oils previously identified to affect pyrethroid efficacy, as well as their main isolates, to assess if they can restore the efficacy of pyrethroid-treated LLIN against the PR strain. We show that although amyris (Amyris balsamifera) expectedly decreases net efficacy, increased mortality can be obtained after exposure to tagetes (Tagetes bipinnata) and cajeput (Melaleuca cajuputi)oils, but also after exposure to their isolates, such as dihydro tagetone and ocimene, from 1 h after exposure to the net. This study provides a selection of promising synergists used as vaporous emanations to restore pyrethroid efficacy and counteract field-evolved resistance in mosquitoes.
Genetic diversity landscapes in outcrossing and selfingCaenorhabditisnematodes
Authors: Teterina Anastasia A. , Willis John H. , Lukac Matt , Jovelin Richard , Cutter Asher D. , Phillips Patrick C. 
Published: December 2022

AbstractCaenorhabditisnematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducingCaenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematodeC. remanei. We demonstrate that the genomic distribution of recombination inC. remanei, like the model nematodeC. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being 10-fold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. Convolutional neural networks demonstrate the potential for classifying distinct evolutionary scenarios in simulated populations. Distinguishing these forces confidently with the empirical data, however, will benefit from larger population genomic samples from multiple populations and consideration of an even more extensive training set of simulations.