bluuebunny/crossref_metadata_2025_split huggingface dataset:
A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a
Authors: Katzmeier Florian , Aufinger Lukas , Dupin Aurore , Quinteiro Jorge , Lenz Matthias , Bauer Ludwig , Klumpe Sven , Sherpa Dawafuti , Dürr Benedikt , Honemann Maximilian , Styazhkin Igor , Simmel Friedrich C. , Heymann Michael 
Published: July 2019

AbstractPoint-of-care testing (POCT) in low-resource settings requires tools that can operate independent of typical laboratory infrastructure. Due to its favorable signal-to-background ratio, a wide variety of biomedical tests utilize fluorescence as a readout. However, fluorescence techniques often require expensive or complex instrumentation and can be difficult to adapt for POCT. To address this issue, we developed a pocket-sized fluorescence detector costing less than $15 that is easy to manufacture and can operate in low-resource settings. It is built from standard electronic components, including an LED and a light dependent resistor, filter foils and 3D printed parts, and reliably detected less than 10 nM fluorescein concentrations (with a lower limit of detection of ≈6.8 nM), which is sufficient to follow typical biochemical reactions used in POCT applications. All assays are conducted on filter paper, which allows for a flat detector architecture to improve signal collection. We validate the device by quantifying in vitro RNA transcription and also demonstrate sequence-specific detection of target RNAs in the nanomolar range using a Cas13a-based fluorescence assay. Cas13a is a RNA-guided, RNA-targeting CRISPR effector with promiscuous RNase activity upon recognition of its RNA target. Cas13a sensing is highly specific and adaptable and in combination with our detector represents a promising approach for nucleic acid POCT. Furthermore, our open-source device architecture could be a valuable educational tool that integrates hardware, software and biochemistry concepts.
A synthetic metabolic network for physicochemical homeostasis
Authors: Pols Tjeerd , Sikkema Hendrik R. , Gaastra Bauke F. , Frallicciardi Jacopo , Śmigiel Wojciech M. , Singh Shubham , Poolman Bert 
Published: July 2019

AbstractOne of the grand challenges in chemistry is the construction of functional out-of-equilibrium networks, which are typical of living cells. Building such a system from molecular components requires control over the formation and degradation of the interacting chemicals and homeostasis of the internal physical-chemical conditions. The provision and consumption of ATP lies at the heart of this challenge. We report thein vitroconstruction in vesicles of a pathway for sustained ATP production that is maintained away from equilibrium by control of energy dissipation. We maintain a constant level of ATP with varying load on the system. The pathway enables us to control the transmembrane fluxes of osmolytes and to demonstrate basic physicochemical homeostasis. Our work demonstrates metabolic energy conservation and cell volume regulatory mechanisms in a cell-like system at a level of complexity minimally needed for life.
Migratory divides coincide with species barriers across replicated avian hybrid zones above the Tibetan Plateau
Authors: Scordato Elizabeth S.C. , Smith Chris C.R. , Semenov Georgy A. , Liu Yu , Wilkins Matthew R. , Liang Wei , Rubtsov Alexander , Sundev Gomboobaatar , Koyama Kazuo , Turbek Sheela P. , Wunder Michael B. , Stricker Craig A. , Safran Rebecca J. 
Published: July 2019

AbstractMigratory divides are proposed to be catalysts for speciation across a diversity of taxa. However, the relative contribution of migratory behavior to reproductive isolation is difficult to test. Comparing reproductive isolation in hybrid zones with and without migratory divides offers a rare opportunity to directly examine the contribution of divergent migratory behavior to reproductive barriers. We show that across replicate sampling transects of two pairs of barn swallow (Hirundo rustica) subspecies, strong reproductive isolation coincided with an apparent migratory divide spanning 20 degrees of latitude. A third subspecies pair exhibited no evidence for a migratory divide and hybridized extensively. Within migratory divides, migratory phenotype was associated with assortative mating, implicating a central contribution of divergent migratory behavior to reproductive barriers. The remarkable geographic coincidence between migratory divides and genetic breaks supports a longstanding hypothesis that the Tibetan Plateau is a substantial barrier contributing to the diversity of Siberian avifauna.
Cognitive control of orofacial and vocal responses in the human frontal cortex
Authors: Loh Kep Kee , Procyk Emmanuel , Neveu Remi , Lamberton Franck , Hopkins William , Petrides Michael , Amiez Céline 
Published: July 2019

AbstractThe frontal cortical areas critical for human speech production, i.e. the ventrolateral frontal cortex (cytoarchitectonic areas 44 and 45; VLF) and the dorsomedial frontal cortex (DMF) comprising the mid-cingulate cortex (MCC) and the pre-supplementary motor area (preSMA), exist in non-human primates and are implicated in cognitive vocal control functions. The present functional neuroimaging study seeks to define the basic roles of these VLF-DMF network regions in primate vocal production and how they might have been adapted for human speech. We demonstrate that area 44 and the MCC are respectively involved in the cognitive selection of orofacial, non-speech vocal and verbal responses, and the feedback-driven adaptation of these responses – roles that are likely preserved across primates. In contrast, area 45 and preSMA have roles that are specific to human speech: area 45 contributes to active verbal retrieval during learning, while preSMA is involved in processing verbal feedback during orofacial/vocal adaptations.
The lipid transfer protein Saposin B does not directly bind CD1d for lipid antigen loading
Authors: Shamin Maria , Benedyk Tomasz H. , Graham Stephen C. , Deane Janet E. 
Published: July 2019

AbstractLipid antigens are presented on the surface of cells by the CD1 family of glycoproteins, which have structural and functional similarity to MHC class I molecules. The hydrophobic lipid antigens are embedded in membranes and inaccessible to the lumenal lipid-binding domain of CD1 molecules. Therefore, CD1 molecules require lipid transfer proteins for lipid loading and editing. CD1d is loaded with lipids in late endocytic compartments, and lipid transfer proteins of the saposin family have been shown to play a crucial role in this process. However, the mechanism by which saposins facilitate lipid binding to CD1 molecules is not known and is thought to involve transient interactions between protein components to ensure CD1-lipid complexes can be efficiently trafficked to the plasma membrane for antigen presentation. Of the four saposin proteins, the importance of Saposin B (SapB) for loading of CD1d is the most well-characterised. However, a direct interaction between CD1d and SapB has yet to be described. In order to determine how SapB might load lipids onto CD1d, we used purified, recombinant CD1d and SapB and carried out a series of highly sensitive binding assays to monitor direct interactions. Using equilibrium binding analysis, chemical cross-linking and co-crystallisation experiments, under a range of different conditions, we could not demonstrate a direct interaction. This work establishes comprehensively that the role of SapB in lipid loading does not involve direct binding to CD1d. We discuss the implication of this for our understanding of lipid loading of CD1d and propose several factors that may influence this process.
Non-genetic intra-tumor heterogeneity is a major predictor of phenotypic heterogeneity and ongoing evolutionary dynamics in lung tumors
Authors: Sharma Anchal , Merritt Elise , Hu Xiaoju , Cruz Angelique , Jiang Chuan , Sarkodie Halle , Zhou Zhan , Malhotra Jyoti , Riedlinger Gregory M , De Subhajyoti 
Published: July 2019

ABSTRACTImpacts of genetic and non-genetic intra-tumor heterogeneity (ITH) on tumor phenotypes and evolvability remain debated. We analyzed ITH in lung squamous cell carcinoma (LUSC) at the levels of genome, transcriptome, tumor-immune interactions, and histopathological characteristics by multi-region profiling and using single-cell sequencing data. Overall, in LUSC genomic heterogeneity alone was a weak indicator of intra-tumor non-genetic heterogeneity at immune and transcriptomic levels that impacted multiple cancer-related pathways including those related to proliferation and inflammation, which in turn contributed to intra-tumor regional differences in histopathology and subtype classification. Genome, transcriptome, and immune-level heterogeneity influenced different aspects of tumor evolution. Tumor subclones had substantial differences in proliferation score, suggestive of non-neutral clonal dynamics. Scores for proliferation and other cancer-related pathways also showed intra-tumor regional differences, sometimes even within the same subclones. Neo-epitope burden negatively correlated with immune infiltration, indicating potential immune-mediated purifying selection on acquired mutations in these tumors. Taken together, our observations suggest that non-genetic heterogeneity is a major determinant of heterogeneity in histopathological characteristics and impacts evolutionary dynamics in lung cancer.
Causal Inference Engine: A platform for directional gene set enrichment analysis and inference of active transcriptional regulators
Authors: Farahmand Saman , O’Connor Corey , Macoska Jill A. , Zarringhalam Kourosh 
Published: July 2019

ABSTRACTInference of active regulatory mechanisms underlying specific molecular and environmental perturbations is essential for understanding cellular response. The success of inference algorithms relies on the quality and coverage of the underlying network of regulator-gene interactions. Several commercial platforms provide large and manually-curated regulatory networks and functionality to perform inference on these networks. Adaptation of such platforms for open-source academic applications has been hindered by the lack of availability of accurate, high-coverage networks of regulatory interactions and integration of efficient causal inference algorithms. In this work, we present CIE, an integrated platform for causal inference of active regulatory mechanisms form differential gene expression data. Using a regularized Gaussian Graphical Model, we construct a transcriptional regulatory network by integrating publicly available ChIP-Seq experiments with gene-expression data from tissue-specific RNA-Seq experiments. Our GGM approach identifies high confidence TF-gene interactions and annotates the interactions with information on mode of regulation (activation vs. repression). Benchmarks against manually-curated databases of TF-gene interactions show that our method can accurately detect mode of regulation. We demonstrate the ability of our platform to identify active transcriptional regulators by using controlledin vitrooverexpression and stem-cell differentiation studies and utilize our method to investigate transcriptional mechanisms of fibroblast phenotypic plasticity.
Deep Learning for Alzheimer’s Disease: Mapping Large-scale Histological Tau Protein for Neuroimaging Biomarker Validation
Authors: Alegro Maryana , Chen Yuheng , Ovando Dulce , Heinser Helmut , Eser Rana , Ushizima Daniela , Tosun Duygu , Grinberg Lea T. 
Published: July 2019

AbstractDeposits of abnormal tau protein inclusions in the brain are a pathological hallmark of Alzheimer’s disease (AD), and are the best predictor of neuronal loss and clinical decline, but have been limited to postmortem assessment. Imaging-based biomarkers to detect tau depositsin vivocould leverage AD diagnosis and monitoring beginning in pre-symptomatic disease stages. Several PET tau tracers are available for research studies, but validation of such tracers against direct detection of tau deposits in brain tissue remains incomplete because of methodological limitations. Confirmation of the biological basis of PET binding requires large-scale voxel-to-voxel correlation has been challenging because of the dimensionality of the whole human brain histology data, deformation caused by tissue processing that precludes registration, and the need to process terabytes of information to cover the whole human brain volume at microscopic resolution. In this study, we created a computational pipeline for segmenting tau inclusions in billion-pixel digital pathology images of whole human brains, aiming at generating quantitative, tridimensional tau density maps that can be used to decipher the distribution of tau inclusions along AD progression and validate PET tau tracers. Our pipeline comprises several pre- and post-processing steps developed to handle the high complexity of these brain digital pathology images. SlideNet, a convolutional neural network designed to process our large datasets to locate and segment tau inclusions, is at the core of the pipeline. Using our novel method, we have successfully processed over 500 slides from two whole human brains, immunostained for two phospho-tau antibodies (AT100 and AT8) spanning several Gigabytes of images. Our artificial neural network estimated strong tau inclusion from image segmentation, which performs with ROC AUC of 0.89 and 0.85 for AT100 and AT8, respectively. Introspection studies further assessed the ability of our trained model to learn tau-related features. Furthermore, our pipeline successfully created 3D tau inclusion density maps that were co-registered to the histology 3D maps.
Cell Fate Clusters in ICM Organoids Arise from Cell Fate Heredity & Division – a Modelling Approach
Authors: Liebisch Tim , Drusko Armin , Mathew Biena , Stelzer Ernst H. K. , Fischer Sabine C. , Matthäus Franziska 
Published: July 2019

ABSTRACTDuring the mammalian preimplantation phase, cells undergo two subsequent cell fate decisions. During the first cell fate decision, cells become either part of an outer trophectoderm or part of the inner cell mass. Subsequently, the inner cell mass (ICM) segregates into an embryonic and an extraembryonic lineage, giving rise to the epiblast and the primitive endoderm, respectively. Inner cell mass organoids represent an experimental model system for preimplantation development, mimicking the second cell fate decision taking place inin vivomouse embryos. In a previous study, the spatial pattern of the different cell lineage types was investigated. The study revealed that cells of the same fate tend to cluster stronger than expected for purely random cell fate decisions. Three major processes are hypothesised to contribute to the final cell fate arrangements at the mid and late blastocysts or 24 h old and 48 h old ICM organoids, respectively: 1) intra- and intercellular chemical signalling; 2) a cell sorting process; 3) cell proliferation. In order to quantify the influence of cell proliferation on the emergence of the observed cell lineage type clustering behaviour, we developed an agent-based model. Hereby, cells are mechanically interacting with direct neighbours, and exert adhesion and repulsion forces. The model was applied to compare several current assumptions of how inner cell mass neighbourhood structures are generated. We tested how different assumptions regarding cell fate switches affect the observed neighbourhood relationships. The model supports the hypothesis that initial cell fate acquisition is a stochastically driven process, taking place in the early development of inner cell mass organoids. The model further shows that the observed neighbourhood structures can emerge due to cell fate heredity during cell division and allows the inference of a time point for the cell fate decision.STATEMENT OF SIGNIFICANCECell fate decisions in early embryogenesis have been considered random events, causing a random cell fate distribution. Using an agent-based mathematical model, fitted to ICM organoid data, we show that the assumed random distribution of cell fates occurs only for a short time interval, as cell fate heredity and cell division quickly lead to spatial cell fate clustering. Our results show that neighbourhood clustering can emerge without specific neighbourhood interactions affecting the cell fate decision. The approach indicates four consecutive phases of early development: 1) co-expression of cell fate markers, 2) cell fate decision, 3) division and local cell fate clustering, and 4) phase separation, whereby only the phases 1-3 occur in ICM organoids during the first 24h of growth.
Multivariate phenotypic divergence along an urbanization gradient
Authors: Santangelo James S. , Advenard Carole , Rivkin L. Ruth , Thompson Ken A. 
Published: July 2019

AbstractA growing body of evidence suggests that natural populations can evolve to better tolerate the novel environmental conditions associated with urban areas. Invariably, studies of adaptive divergence in urban areas examine only one or a few traits at a time from populations residing only at the most extreme urban and nonurban habitats. Thus, whether urbanization is driving divergence in many traits simultaneously in a manner that varies with the degree of urbanization remains unclear. To address this gap, we generated seed families of white clover (Trifolium repens) collected from 27 populations along an urbanization gradient in Toronto, Canada, and grew them up to measure multiple phenotypic traits in a common garden. Overall, urban populations had later phenology and germination, larger flowers, thinner stolons, reduced cyanogenesis, greater biomass, and were more attractive to pollinators. Pollinator observations revealed near complete turnover between urban and nonurban sites, which may explain some of the observed divergence in floral traits and phenology. Our results suggest that adaptation to urban environments involves multiple organismal traits.
Novel tetraplex qPCR assays for simultaneous detection and identification ofXylella fastidiosasubspecies in plant tissues
Authors: Enora Dupas , Martial Briand , Marie-Agnès Jacques , Sophie Cesbron 
Published: July 2019

AbstractXylella fastidiosais an insect-borne bacterium confined to the xylem vessels of plants. This plant pathogen has a broad host range estimated to 560 plant species. Five subspecies of the pathogen with different but overlapping host ranges have been described, but only three subspecies are widely accepted, namely subspeciesfastidiosa,multiplexandpauca. Initially limited to the Americas,Xfhas been detected in Europe since 2013. As management ofX. fastidiosaoutbreaks in Europe depends on the identification of the subspecies, accurate determination of the subspecies in infected plants as early as possible is of major interest. Thus, we developed various tetraplex and triplex qPCR assays forXylella fastidiosadetection and subspecies identificationin plantain a single reaction. We designed primers and probes using SkIf, a bioinformatics tool based onk-mers, to detect specific signatures of the species and subspecies from a dataset of 58 genome sequences representative ofX. fastidiosadiversity. We tested the qPCR assays on 39 target and 30 non-target strains, as well as on 13 different plant species spiked with strains of the different subspecies ofX. fastidiosa, and on samples from various environmental and inoculated host plants. Sensitivity of simplex assays was equal or slightly better than the reference protocol on purified DNA. Tetraplex qPCR assays had the same sensitivity than the reference protocol and allowedX. fastidiosadetection in all spiked matrices up to 103cells.mL−1. Moreover, mix infections of two to three subspecies could be detected in the same sample with tetraplex assays. In environmental plant samples, the tetraplex qPCR assays allowed subspecies identification when the current method based on multilocus sequence typing failed. The qPCR assays described here are robust and modular tools that are efficient for differentiatingX. fastidiosasubspecies directly in plant samples.
SiZer Map to investigate significant features of body-weight profile changes in HIV infected patients in the IeDEA Collaboration
Authors: Harezlak Jaroslaw , Sarwat Samiha , Wools-Kaloustian Kara , Schomaker Michael , Balestre Eric , Law Matthew , Kiertiburanakul Sasisopin , Fox Matthew , Huis in ’t Veld Diana , Musick Beverly Sue , Yiannoutsos Constantin Theodore 
Published: July 2019

AbstractObjectivesWe extend the method of Significant Zero Crossings of Derivatives (SiZer) to address within-subject correlations of repeatedly collected longitudinal biomarker data and the computational aspects of the methodology when analyzing massive biomarker databases. SiZer is a powerful visualization tool for exploring structures in curves by mapping areas where the first derivative is increasing, decreasing or does not change (plateau) thus exploring changes and normalization of biomarkers in the presence of therapy.MethodsWe propose a penalized spline SiZer (PS-SiZer) which can be expressed as a linear mixed model of the longitudinal biomarker process to account for irregularly collected data and within-subject correlations. Through simulations we show how sensitive PS-SiZer is in detecting existing features in longitudinal data versus existing versions of SiZer. In a real-world data analysis PS-SiZer maps are used to map areas where the first derivative of weight change after antiretroviral therapy (ART) start is significantly increasing, decreasing or does not change, thus exploring the durability of weight increase after the start of therapy. We use weight data repeatedly collected from persons living with HIV initiating ART in five regions in the International Epidemiologic Databases to Evaluate AIDS (IeDEA) worldwide collaboration and compare the durability of weight gain between ART regimens containing and not containing the drug stavudine (d4T), which has been associated with shorter durability of weight gain.ResultsThrough simulations we show that the PS-SiZer is more accurate in detecting relevant features in longitudinal data than existing SiZer variants such as the local linear smoother (LL) SiZer and the SiZer with smoothing splines (SS-SiZer). In the illustration we include data from 185,010 persons living with HIV who started ART with a d4T (53.1%) versus non-d4T (46.9%) containing regimen. The largest difference in durability of weight gain identified by the SiZer maps was observed in Southern Africa where weight gain in patients treated with d4T-containing regimens lasted 52.4 weeks compared to 94.4 weeks for those with non-d4T-containing regimens. In the other regions, persons receiving d4T-containing regimens experienced weight gains lasting 51-61 weeks versus 59-77 weeks in those receiving non-d4T-based regimens.DiscussionPS-SiZer, a SiZer variant, can handle irregularly collected longitudinal data and within-subject correlations and is sensitive in detecting even subtle features in biomarker curves.