bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of immunosuppressant drug treatment to improve SARS-CoV-2 vaccine efficacy in mice
Authors: Paschall Amy V. , Ozdilek Ahmet , Briner Sydney L. , Brindley Melinda A. , Avci Fikri Y. 
Published: October 2021

AbstractThe COVID-19 pandemic dramatically demonstrated the need for improved vaccination strategies and therapeutic responses to combat infectious diseases. However, the efficacy of vaccines has not yet been demonstrated in combination with commonly used immunosuppressive drug regimens. We sought to determine how common pharmaceutical drugs used in autoimmune disorders can alter immune responses to the SARS-CoV-2 spike protein vaccination.We treated mice with five immunosuppressant drugs (cyclophosphamide, leflunomide, methotrexate, methylprednisolone, and mycophenolate mofetil), each with various mechanisms of action prior to and following immunization with SARS-CoV-2 spike protein. We assessed the functionality of antibody responses to spike protein and compared immune cell populations in mice that received no treatment with those that received continuous or temporarily suspended immune suppressive therapy.All tested immunosuppressants significantly reduced the antibody titers in serum and functional antibody response against SARS-CoV-2 spike protein in immunized mice. Temporarily halting selected immunosuppressants (methylprednisolone and methotrexate, but not cyclophosphamide) improved antibody responses significantly. Through proof-of-principle experiments utilizing a mouse model, we demonstrated that immune suppression in autoimmune disorders through pharmaceutical treatments may impair vaccine response to SARS-CoV-2, and temporary suspension of immunosuppressant treatment may be necessary to mount an effective antibody vaccine response. This work provides feasibility for future clinical assessment of the impact of immunosuppressants on vaccine efficacy in humans.Significance StatementImmunosuppressant regimens are widely used as therapies for a variety of diseases, including autoimmune, inflammatory, and cancer. However, immunosuppressants can impair critical immune responses to vaccination. The impact of standard immunosuppressant use on the critical, developing SARS-CoV-2 vaccination strategies has not been well-described. In this study, we use a mouse model to determine how different immunosuppressant drugs that act through different mechanisms can impair the antibody response to SARS-CoV-2 spike protein, and how modulating these drug regimens may restore antibody levels and function.
Improved detection of evolutionary selection highlights potential bias from different sequencing strategies in complex genomic-regions
Authors: Hayeck Tristan J. , Li Yang , Mosbruger Timothy L. , Bradfield Jonathan P , Gleason Adam G. , Damianos George , Shaw Grace Tzun-Wen , Duke Jamie L. , Conlin Laura K. , Turner Tychele N. , Fernández-Viña Marcelo A. , Sarmady Mahdi , Monos Dimitri S. 
Published: October 2021

AbstractBalancing selection occurs when multiple alleles are kept at elevated frequencies in equilibrium due to opposing evolutionary pressures. A new statistical method was developed to test for selection using efficient Bayesian techniques. Selection signals in three different data sets, generated with variable sequencing technologies, were compared: clinical trios, HLA NGS typed samples, and whole-genome long-read samples. Genome-wide, selection was observed across multiple gene families whose biological functions favor diversification, revealing established targets as well as 45 novel genes under selection. Using high-resolution HLA typing and long-read sequencing data, for the characterization of the MHC, revealed strong selection in expected peptide-binding domains as well as previously understudied intronic and intergenic regions of the MHC. Surprisingly, SIRPA, demonstrated dramatic selection signal, second only to the MHC in most settings. In conclusion, employing novel statistical approaches and improved sequencing technologies is critical to properly analyze complex genomic regions.
Enhanced nociceptive behavior and expansion of associated primary afferents in a rabbit model of cerebral palsy
Authors: Reedich E. J. , Genry L. T. , Singer M. A. , Cavarsan C. F. , Mena Avila E. , Boudreau D. M. , Brennan M. C. , Garrett A. M. , Dowaliby L. , Detloff M. R. , Quinlan K. A. 
Published: October 2021

AbstractSpastic cerebral palsy (CP) is a movement disorder marked by hypertonia and hyperreflexia, and the most prevalent comorbidity is pain. Since spinal nociceptive afferents contribute to both the sensation of painful stimuli as well as reflex circuits involved in movement, we investigated the relationship between prenatal hypoxia-ischemia (HI) injury which can cause CP, and possible changes in spinal nociceptive circuitry. To do this, we examined nociceptive afferents and mechanical and thermal sensitivity of New Zealand White rabbit kits after prenatal HI or a sham surgical procedure. As described previously, a range of motor deficits similar to spastic CP was observed in kits born naturally after HI (40 minutes at ∼70-80% gestation). We found that HI caused an expansion of peptidergic afferents (marked by expression of calcitonin gene-related peptide; CGRP) in both the superficial and deep dorsal horn at postnatal day (P)5. Non-peptidergic nociceptive afferent arborization (labeled by isolectin B4; IB4) was unaltered in HI kits but overlap of the two populations (peptidergic and non-peptidergic nociceptors) was increased by HI. Density of glial fibrillary acidic protein (GFAP) was unchanged within spinal white matter regions important in nociceptive transmission at P5. We found that mechanical and thermal nociception was enhanced in HI kits even in the absence of motor deficits. These findings suggest that prenatal HI injury impacts spinal sensory pathways in addition to the more well-established disruptions to descending motor circuits. In conclusion, changes to spinal nociceptive circuitry could disrupt spinalreflexes and contribute to pain experienced by individuals with CP.Significance StatementPerinatal injuries that cause cerebral palsy (CP) typically involve global insults to the central nervous system and are capable of modulating development of both motor and sensory systems. Most individuals with CP experience pain, yet whether nociception is enhanced in this disorder is unexplored. Here, we demonstrate altered topographic distribution of nociceptive afferents in the spinal cord dorsal horn of neonatal rabbits that experienced hypoxic-ischemic (HI) injury in utero; these anatomical changes were associated with nocifensive behavior indicative of pain-like behaviors. Our findings suggest that CP-causative injuries alter spinal sensory pathways (not only descending motor circuits), contributing to increased pain in CP.
Nanocrown electrodes for reliable and robust intracellular recording of cardiomyocytes and cardiotoxicity screening
Authors: Jahed Zeinab , Yang Yang , Tsai Ching-Ting , Foster Ethan P. , McGuire Allister F. , Yang Huaxiao , Liu Aofei , Forro Csaba , Yan Zen , Jiang Xin , Zhao Ming-Tao , Zhang Wei , Li Xiao , Li Thomas , Pawlosky Annalisa , Wu Joseph C. , Cui Bianxiao 
Published: October 2021

AbstractDrug-induced cardiotoxicity arises primarily when a compound alters the electrophysiological properties of cardiomyocytes. Features of intracellular action potentials (iAPs) are powerful biomarkers that predict proarrhythmic risks. However, the conventional patch clamp techniques for measuring iAPs are either laborious and low throughput or not suitable for measuring electrically connected cardiomyocytes. In the last decade, a number of vertical nanoelectrodes have been demonstrated to achieve parallel and minimally-invasive iAP recordings. Nanoelectrodes show great promise, but the large variability in success rate, signal strength, and the low throughput of device fabrication have hindered them from being broadly adopted for proarrhythmia drug assessment. In this work, we developed vertically-aligned and semi-hollow nanocrown electrodes that are mechanically robust and made through a scalable fabrication process. Nanocrown electrodes achieve >99% success rates in obtaining intracellular access through electroporation, allowing reliable and simultaneous iAP recordings from up to 57 human pluripotent stem-cell-derived cardiomyocytes (hPSC-CMs). The accuracy of nanocrown electrode recordings is validated by simultaneous patch clamp recording from the same cell. Nanocrown electrodes enable prolonged iAP recording for continual monitoring of the same cells upon the sequential addition of four to five incremental drug doses. In this way, the dose-response data is self-referencing, which avoids the cell-to-cell variations inherent to hPSC-CMs. We are hopeful that this technology development is a step towards establishing an iAP screening assay for preclinical evaluation of drug-induced arrhythmogenicity.
Redundant functions of the SLC5A transporters Rumpel Kumpel and Bumpel in ensheathing glial cells
Authors: Yildirim Kerem , Winkler Bente , Pogodalla Nicole , Mackensen Steffi , Baldenius Marie , Garcia Luis , Naffin Elke , Rodrigues Silke , Klämbt Christian 
Published: October 2021

AbstractNeuronal processing is energy demanding, and relies on sugar metabolism as an energy source. To provide a constant metabolite supply neurons and glial cells express many glucose and lactate transporters of the solute carrier (SLC) 5A family. Here we dissect the partially redundant functions of three highly related glia specific Drosophila genes encoding SLC5A proteins, Rumpel, Bumpel and Kumpel. While knockdown of rumpel causes several behavioral phenotypes, they are less prominent in rumpel mutants. bumpel and kumpel mutants are viable and fertile, lacking discernible phenotypes. However, in bumpel kumpel double mutants and to an even greater extent in rumpel bumpel kumpel triple mutants oogenesis is disrupted at the onset of the vitollegenic phase. This indicates at least partially redundant functions between these genes. Rescue experiments exploring this effect indicate that oogenesis can be affected by CNS glial cells. Moreover, expression of heterologous mammalian SLC5A transporter proteins, with known transport properties, suggest that Bumpel and/or Kumpel transport glucose or lactate. Overall, our results imply a redundancy in SLC5A nutrient sensing functions in Drosophila glial cells, affecting ovarian development and behavior.
Computational Fingerprints: Modeling Interactions Between Brain Regions as Points in a Function Space
Authors: Poskanzer Craig , Anzellotti Stefano 
Published: October 2021

AbstractIn this paper we propose a novel technique to investigate the nonlinear interactions between brain regions that captures both the strength and the type of the functional relationship. Inspired by the field of functional analysis, we propose that the relationship between activity in two different brain areas can be viewed as a point in function space, identified by coordinates along an infinite set of basis functions. Using Hermite Polynomials as basis functions, we estimate from fMRI data a truncated set of coordinates that serve as a “computational fingerprint,” characterizing the interaction between two brain areas. We provide a proof of the convergence of the estimates in the limit, and we validate the method with simulations in which the ground truth is known, additionally showing that computational fingerprints detect statistical dependence also when correlations (“functional connectivity”) is near zero. We then use computational fingerprints to examine the neural interactions with a seed region of choice: the Fusiform Face Area (FFA). Using k-means clustering across each voxel’s computational fingerprint, we illustrate that the addition of the nonlinear basis functions allows for the discrimination of inter-regional interactions that are otherwise grouped together when only linear dependence is used. Finally, we show that regions in V5 and medial occipital and temporal lobes exhibit significant nonlinear interactions with the FFA.
Cell-ACDC: a user-friendly toolset embedding state-of-the-art neural networks for segmentation, tracking and cell cycle annotations of live-cell imaging data
Authors: Padovani Francesco , Mairhörmann Benedikt , Falter-Braun Pascal , Lengefeld Jette , Schmoller Kurt M. 
Published: October 2021

AbstractLive-cell imaging is a powerful tool to study dynamic cellular processes on the level of single cells with quantitative detail. Microfluidics enables parallel high-throughput imaging, creating a downstream bottleneck at the stage of data analysis. Recent progress on deep learning image analysis dramatically improved cell segmentation and tracking. Nevertheless, manual data validation and correction is typically still required and broadly used tools spanning the complete range of live-cell imaging analysis, from cell segmentation to pedigree analysis and signal quantification, are still needed. Here, we present Cell-ACDC, a user-friendly graphical user-interface (GUI)-based framework written in Python, for segmentation, tracking and cell cycle annotation. We included two state-of-the-art and high-accuracy deep learning models for single-cell segmentation of yeast and mammalian cells implemented in the most used deep learning frameworks TensorFlow and PyTorch. Additionally, we developed and implemented a cell tracking method and embedded it into an intuitive, semi-automated workflow for label-free cell cycle annotation of single cells. The open-source and modularized nature of Cell-ACDC will enable simple and fast integration of new deep learning-based and traditional methods for cell segmentation or downstream image analysis.Source codehttps://github.com/SchmollerLab/Cell_ACDC
Numb reduces Tau levels and prevents neurodegeneration in mouse models of tauopathy in an isoform-specific manner
Authors: Lacomme Marine , Hales Sarah C. , Stevanovic Katarina , Jolicoeur Christine , Bois Therence , Cai Jenny , Desrosiers Melissa , Dalkara Deniz , Cayouette Michel 
Published: October 2021

ABSTRACTAccumulation of the microtubule-associated protein Tau is linked to neuronal cell death in tauopathies, but how exactly intraneuronal Tau levels are regulated in health and disease remains unclear. Here we identify the trafficking adaptor protein Numb as an essential regulator of Tau homeostasis. Conditional inactivation of Numb in retinal ganglion cells (RGCs) increases monomeric and oligomeric Tau levels, leading to axonal blebbing followed by neuronal cell loss in aged mice. Moreover, in a mouse model of tauopathy, inactivation of Numb in RGCs and spinal motoneurons accelerates neurodegeneration, and leads to precocious hindlimb paralysis. Conversely, overexpression of the long isoform of Numb (Numb-72), but not other isoforms, decreases intracellular Tau levels by promoting the extracellular release of monomeric Tau, and AAV-mediated delivery of Numb-72 in RGCs in vivo prevents neurodegeneration in two different mouse models of tauopathy. Taken together, these results uncover Numb as a modulator of intracellular Tau levels and identify Numb-72 as a novel therapeutic factor for tauopathies.
Enhanced Production of Mesencephalic Dopaminergic Neurons from Lineage-Restricted Human Undifferentiated Stem Cells
Authors: Maimaitili Muyesier , Chen Muwan , Febbraro Fabia , Mermet-Joret Noëmie , Lauritsen Johanne , Ucuncu Ekin , Klæstrup Ida Hyllen , Qvist Per , Nabavi Sadegh , Romero-Ramos Marina , Denham Mark 
Published: October 2021

AbstractThe differentiation of human pluripotent stem cells (hPSCs) into mesencephalic dopaminergic (mesDA) neurons requires a precise combination of extrinsic factors that recapitulates the in vivo environment and timing. Current methods are capable of generating authentic mesDA neurons after long-term culture in vitro; however, when mesDA progenitors are transplanted in vivo, the resulting mesDA neurons are only minor components of the graft. This low yield hampers the broad use of these cells in the clinic. In this study, we genetically modified pluripotent stem cells to generate a novel type of stem cells called lineage-restricted undifferentiated stem cells (LR-USCs), which robustly generate mesDA neurons. LR-USCs are prevented from differentiating into a broad range of nondopaminergic cell types by knocking out genes that are critical for the specification of cells of alternate lineages. Specifically, we target transcription factors involved in the production of spinal cord and posterior hindbrain cell types. When LR-USCs are differentiated under caudalizing condition, which normally give rise to hindbrain cell types, a large proportion adopt a midbrain identity and develop into authentic mesDA neurons. We show that the mesDA neurons are electrophysiologically active, and due to their higher purity, are capable of restoring motor behavior eight weeks after transplantation into 6-hydroxydopamine (6-OHDA)-lesioned rats. This novel strategy improves the reliability and scalability of mesDA neuron generation for clinical use.
Survival Genie, a web platform for survival analysis across pediatric and adult cancers
Authors: Dwivedi Bhakti , Mumme Hope , Satpathy Sarthak , Bhasin Swati S. , Bhasin Manoj 
Published: October 2021

ABSTRACTThe genomics data-driven identification of gene signatures and pathways has been routinely explored for predicting cancer survival and making decisions related to targeted treatments. A large number of packages and tools have been developed to correlate gene expression/mutations to the clinical outcome but lack the ability to perform such analysis based on pathways, gene sets, and gene ratios. Furthermore, in this single-cell omics era, the cluster markers from cancer single-cell transcriptomics studies remain an underutilized prognostic option. Additionally, no bioinformatics online tool evaluates the associations between the enrichment of canonical cell types and survival across cancers. Here we have developed Survival Genie, a web tool to perform survival analysis on single-cell RNA-seq (scRNA-Seq) data and a variety of other molecular inputs such as gene sets, genes ratio, tumor infiltrating immune cells proportion, gene expression profile scores, and tumor mutation burden. For a comprehensive analysis, Survival Genie contains 53 datasets of 27 distinct malignancies from 11 different cancer programs related to adult and pediatric cancers. Users can upload scRNA-Seq data or gene sets and select a gene expression partitioning method (i.e., mean, median, quartile, cutp) to determine the effect of expression levels on survival outcomes. The tool provides comprehensive results including box plots of low and high-risk groups, Kaplan-Meier plots with univariate Cox proportional hazards model, and correlation of immune cell enrichment and molecular profile.The analytical options and comprehensive collection of cancer datasets make Survival Genie a unique resource to correlate gene sets, pathways, cellular enrichment, and single-cell signatures to clinical outcomes to assist in developing next-generation prognostic and therapeutic biomarkers. Survival Genie is open-source and available online at https://bbisr.shinyapps.winship.emory.edu/SurvivalGenie/.
Tracking chromatin state changes using μMap photo-proximity labeling
Authors: Seath Ciaran P. , Burton Antony J. , MacMillan David W. C. , Muir Tom W. 
Published: October 2021

AbstractInteractions between biomolecules, particularly proteins, underlie all cellular processes, and ultimately control cell fate. Perturbation of native interactions through mutation, changes in expression levels, or external stimuli leads to altered cellular physiology and can result in either disease or therapeutic effects.1,2 Mapping these interactions and determining how they respond to stimulus is the genesis of many drug development efforts, leading to new therapeutic targets and improvements in human health.1 However, in the complex environment of the nucleus it is challenging to determine protein-protein interactions due to low abundance, transient or multi-valent binding, and a lack of technologies that are able to interrogate these interactions without disrupting the protein binding surface under study.3 Chromatin remodelers, modifying enzymes, interactors, and transcription factors can all be redirected by subtle changes to the microenvironment, causing global changes in protein expression levels and subsequent physiology. Here, we describe the Chroma-μMap method for the traceless incorporation of Ir-photosensitizers into the nuclear microenvironment using engineered split inteins. These Ir-catalysts can activate diazirine warheads to form reactive carbenes within a ~10 nm radius, cross-linking with proteins within the immediate microenvironment for analysis via quantitative chemoproteomics.4 We demonstrate this concept on nine different nuclear proteins with varied function and in each case, elucidating their microenvironments. Additionally, we show that this short-range proximity labeling method can reveal the critical changes in interactomes in the presence of cancer-associated mutations, as well as treatment with small-molecule inhibitors. Chroma-μMap improves our fundamental understanding of nuclear protein-protein interactions, as well as the effects that small molecule therapeutics have on the local chromatin environment, and in doing so is expected to have a significant impact on the field of epigenetic drug discovery in both academia and industry.
SSAM-lite: a light-weight web app for rapid analysis of spatially resolved transcriptomics data
Authors: Tiesmeyer Sebastian , Sahay Shashwat , Müller-Bötticher Niklas , Eils Roland , Mackowiak Sebastian D. , Ishaque Naveed 
Published: October 2021

1AbstractThe combination of a cell’s transcriptional profile and location defines its function in a spatial context. Spatially resolved transcriptomics (SRT) has emerged as the assay of choice for characterizing cells in situ. SRT methods can resolve gene expression up to single-molecule resolution. A particular computational problem with single-molecule SRT methods is the correct aggregation of mRNA molecules into cells. Traditionally, aggregating mRNA molecules into cell-based features begins with the identification of cells via segmentation of the nucleus or the cell membrane. However, recently a number of cell-segmentation-free approaches have emerged. While these methods have been demonstrated to be more performant than segmentation-based approaches, they are still not easily accessible since they require specialized knowledge of programming languages and access to large computational resources. Here we present SSAM-lite, a tool that provides an easy-to-use graphical interface to perform rapid and segmentation-free cell-typing of SRT data in a web browser. SSAM-lite runs locally and does not require computational experts or specialized hardware. Analysis of a tissue slice of the mouse somatosensory cortex took less than a minute on a laptop with modest hardware. Parameters can interactively be optimized on small portions of the data before the entire tissue image is analyzed. A server version of SSAM-lite can be run completely offline using local infrastructure. Overall, SSAM-lite is portable, lightweight, and easy to use, thus enabling a broad audience to investigate and analyze single-molecule SRT data.Availability and ImplementationSSAM-lite is an open-source browser-based web application with source code freely available on Github via https://github.com/HiDiHlabs/ssam-lite. Stable releases can be accessed via https://ssam-lite.bihealth.org and https://ssam-lite.netlify.app, and developmental releases can be accessed via https://dev--ssam-lite.netlify.app. The source code for a locally deployable server version, SSAM-lite-server, is available on GitHub via https://github.com/HiDiHlabs/ssam-lite-server. Both versions require a modern browser with JavaScript and WebGL support. Detailed user guides and documentation can be found at https://ssam-lite.readthedocs.io.