bluuebunny/crossref_metadata_2025_split huggingface dataset:
LRRK2 coding variants and the risk of Parkinson’s disease
Authors: Lake Julie , Reed Xylena , Langston Rebekah G. , Nalls Mike A. , Gan-Or Ziv , Cookson Mark R. , Singleton Andrew B. , Blauwendraat Cornelis , Leonard Hampton L. 
Published: April 2021

AbstractBackgroundThe leucine-rich repeat kinase 2 (LRRK2) gene harbors both rare highly damaging missense variants (e.g. p.G2019S) and common non-coding variants (e.g. rs76904798) with lower effect sizes that are associated with Parkinson’s disease risk.ObjectivesThis study aimed to investigate in a large meta-analysis whether the LRRK2 GWAS signal represented by rs76904798 is independently associated with Parkinson’s disease risk from LRRK2 coding variation, and whether complex linkage disequilibrium structures with p.G2019S and the 5’ non-coding haplotype account for the association of LRRK2 coding variants.MethodsWe performed a meta-analysis using imputed genotypes from 17,838 cases, 13,404 proxy-cases and 173,639 healthy controls of European ancestry. We excluded carriers of p.G2019S and/or rs76904798 to clarify the role of LRRK2 coding variation in mediating disease risk, and excluded carriers of relatively rare LRRK2 coding variants to assess the independence of rs76904798. We also investigated the co-inheritance of LRRK2 coding variants with p.G2019S, rs76904798 and p.N2081D.ResultsLRRK2 rs76904798 remained significantly associated with Parkinson’s disease after excluding carriers of relatively rare LRRK2 coding variants. LRRK2 p.R1514Q and p.N2081D were frequently co-inherited with rs76904798 and the allele distribution of p.S1647T significantly changed among cases after removing rs76904798 carriers.ConclusionsThese data suggest that the LRRK2 coding variants previously linked to Parkinson’s disease (p.N551K, p.R1398H, p.M1646T and p.N2081D) do not drive the 5’ non-coding GWAS signal. These data, however, do not preclude the independent association of the haplotype p.N551K-p.R1398H and p.M1646T with altered disease risk.
Characterisation of peri-implantation endometrial Treg and identification of an altered phenotype in recurrent pregnancy loss
Authors: Granne Ingrid , Shen Mengni , Rodriguez-Caro Helena , Chadha Gurmeher , O’Donnell Elizabeth , Brosens Jan J. , Quenby Siobhan , Child Tim , Southcombe Jennifer H. 
Published: April 2021

AbstractRecurrent Pregnancy Loss (RPL) affects 2-4% of couples, and with increasing numbers of pregnancy losses the risk of miscarrying a euploid pregnancy is increased, suggesting RPL is a pathology distinct from sporadic miscarriage that is due largely to lethal embryonic aneuploidy. There are a number of conditions associated with RPL including unspecified ‘immune’ pathologies, one of the strongest candidates for dysregulation remains T regulatory cells as depletion in the very early stages of pregnancy in mice leads to pregnancy loss.Human endometrial Treg and conventional CD4T cells were isolated during the peri-implantation period of the menstrual cycle in normal women. We identified an endometrial Treg transcriptomic signature and validated an enhanced regulatory phenotype compared to peripheral blood Treg. Parous women had an altered endometrial Treg transcriptome compared to nulliparity, indicating acquired immunity memory of pregnancy within the Treg population, by comparison endometrial conventional CD4T cells were not altered. We compared primary and secondary RPL to nulliparous or parous controls respectively. Both RPL subgroups displayed differentially expressed Treg gene transcriptomes compared to controls. We found increased cell surface S1PR1 and decreased TIGIT protein expression by Treg in primary RPL, confirming the presence of altered Treg in the peri-implantation RPL endometrium.
The pathogen-encoded signaling receptor Tir exploits host-like intrinsic disorder to assist infection
Authors: Vieira Marta F. M. , Hernandez Guillem , Veloso Tiago , Monteiro Hugo , Arbesú Miguel , Zanzoni Andreas , Cordeiro Tiago N. 
Published: April 2021

AbstractThe translocated intimin receptor (Tir) is a central effector of Attaching and Effacing (A/E) pathogens responsible for worldwide foodborne disease cases. Tir acts as a cell-surface receptor in host cells, rewiring intracellular processes to assist infection by targeting multiple host proteins. We sought to understand the basis for Tir binding diversity in signaling. Here, we establish that Tir is a disordered protein with host-like binding motifs. A trait we find prevalent in several other effectors secreted by A/E bacteria. We disclose that Tir has a disordered C-terminal intracellular tail (C-Tir) with non-random structural preferences at phosphorylation sites, including host-like tyrosine-based motifs, with versatile lipid- and SH2 domain binding capability pre-phosphorylation. We show that multi-site tyrosine phosphorylation enables C-Tir to engage SH2 domains in a multivalent manner, consistent with Tir’s scaffold/hub role for host proteins. Last, we uncover Tir’s ability to dimerizes via its partially disordered N-terminal intracellular domain. Collectively, our findings provide an updated picture of Tir’s intracellular side, highlighting its ability to mimic host disordered membrane receptors’ versatility as a molecular strategy for host evasion.SummaryTir is a cell-surface receptor secreted by life-threatening pathogens. Upon delivery into host cells, Tir inserts the host plasma membrane providing a means for these extracellular pathogens to control host intracellular processes. To prevent pathogens from relying on Tir, it is essential to understand its intracellular mechanics. This paper provides a coherent picture of the intracellular side of Tir, highlighting its ability to copycat the interactions of disordered intracellular domains of host immune receptors. This copycatting allows the bacterial pathogens to modulate critical host processes, allowing infection to spread further without triggering the immune system response. This work proposes that other bacterial secreted pathogenic proteins exploit intrinsic disorder to hijack human cells, suggesting a widespread host subversion mechanism.
Nanoparticle Internalization Promotes the Survival of Primary Macrophages
Authors: Jarai Bader M. , Fromen Catherine A. 
Published: April 2021

ABSTRACTMacrophages, a class of tissue resident innate immune cells, are responsible for sequestering foreign objects through the process of phagocytosis, making them a promising target for immune-modulation via particulate engineering. Here, we report that nanoparticle (NP) dosing and cellular internalization via phagocytosis significantly enhances survival ofex vivocultures of primary bone marrow-derived, alveolar, and peritoneal macrophages over particle-free controls. The enhanced survival is attributed to suppression of caspase-dependent apoptosis and is linked to phagocytosis and lysosomal signaling, which was also found to occurin vivo. Uniquely, poly(ethylene glycol)-based NP treatment does not alter macrophage polarization or lead to inflammatory effects. The enhanced survival phenomenon is also applicable to NPs of alternative chemistries, indicating the potential universality of this phenomenon with relevant drug delivery particles. These findings provide a framework for extending the lifespan of primary macrophagesex vivofor drug screening, vaccine studies, and cell therapies and has implications for anyin vivoparticulate immune-engineering applications.
Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection
Authors: Biering Scott B. , Sarnik Sylvia A. , Wang Eleanor , Zengel James R. , Sathyan Varun , Nguyenla Xammy , Van Dis Erik , Catamura Carmelle , Yamashiro Livia H. , Begeman Adam , Stark Jessica C. , Shon D. Judy , Fox Douglas M. , Puschnik Andreas S. , Bertozzi Carolyn R. , Carette Jan E. , Stanley Sarah A. , Harris Eva , Konermann Silvana , Hsu Patrick D. 
Published: April 2021

SUMMARYSARS-CoV-2 can cause a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A systematic understanding of the host factors mediating viral infection or restriction is critical to elucidate SARS-CoV-2 host-pathogen interactions and the progression of COVID-19. To this end, we conducted genome-wide CRISPR knockout and activation screens in human lung epithelial cells with endogenous expression of the SARS-CoV-2 entry factors ACE2 and TMPRSS2. These screens uncovered proviral and antiviral host factors across highly interconnected host pathways, including components implicated in clathrin transport, inflammatory signaling, cell cycle regulation, and transcriptional and epigenetic regulation. We further identified mucins, a family of high-molecular weight glycoproteins, as a prominent viral restriction network. We demonstrate that multiple membrane-anchored mucins are critical inhibitors of SARS-CoV-2 entry and are upregulated in response to viral infection. This functional landscape of SARS-CoV-2 host factors provides a physiologically relevant starting point for new host-directed therapeutics and suggests interactions between SARS-CoV-2 and airway mucins of COVID-19 patients as a host defense mechanism.
Synergistic effect of short- and long-read sequencing on functional meta-omics
Authors: Galata Valentina , Busi Susheel Bhanu , Kunath Benoît Josef , de Nies Laura , Calusinska Magdalena , Halder Rashi , May Patrick , Wilmes Paul , Laczny Cédric Christian 
Published: April 2021

AbstractReal-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artefacts from genes and proteins presentin situ. Here, we evaluate short-read-only, long-read-only, and hybrid assembly approaches on four different metagenomic samples of varying complexity and demonstrate how they affect gene and protein inference which is particularly relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic, and metaproteomic data to evaluate the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions and we propose a reference-independent solution based on the synergistic effects of multi-omic data integration for thein situstudy of microbiomes using long-read sequencing data.
A synergistic interaction between HDAC- and PARP inhibitors in childhood tumors with chromothripsis
Authors: Khalid Umar , Simovic Milena , Iskar Murat , Wong John KL , Kumar Rithu , Jugold Manfred , Sill Martin , Bolkestein Michiel , Kolb Thorsten , Hergt Michaela , Devens Frauke , Ecker Jonas , Kool Marcel , Milde Till , Westermann Frank , Lewis Joe , Dietrich Sascha , Pfister Stefan M , Lichter Peter , Zapatka Marc , Ernst Aurélie 
Published: April 2021

ABSTRACTChromothripsis is a form of genomic instability characterized by the occurrence of tens to hundreds of clustered DNA double-strand breaks in a one-off catastrophic event. Rearrangements associated with chromothripsis are detectable in numerous tumor entities and linked with poor prognosis in some of these, such as Sonic Hedgehog medulloblastoma, neuroblastoma and osteosarcoma. Hence, there is a need for therapeutic strategies eliminating tumor cells with chromothripsis. Defects in DNA double-strand break repair, and in particular homologous recombination repair, have been linked with chromothripsis. Targeting DNA repair deficiencies by synthetic lethality approaches, we performed a synergy screen using drug libraries (n = 375 compounds, 15 models) combined with either a PARP inhibitor or cisplatin. This revealed a synergistic interaction between the HDAC inhibitor romidepsin and PARP inhibition. Functional assays, transcriptome analyses, andin vivovalidation in patient-derived xenograft mouse models confirmed the efficacy of the combinatorial treatment.
“Neighbourhood watch” model: embryonic epiblast cells assess positional information in relation to their neighbours
Authors: Lee Hyung Chul , Hastings Cato , Oliveira Nidia M.M. , Pérez-Carrasco Rubén , Page Karen M. , Wolpert Lewis , Stern Claudio D. 
Published: April 2021

AbstractIn many developing and regenerating systems, tissue pattern is established through gradients of informative morphogens, but we know little about how cells interpret these. Using experimental manipulation of early chick embryos including misexpression of an inducer (VG1 or ACTIVIN) and an inhibitor (BMP4), we test two alternative models for their ability to explain how the site of primitive streak formation is positioned relative to the rest of the embryo. In one model, cells read morphogen concentrations cell-autonomously. In the other, cells sense changes in morphogen status relative to their neighbourhood. We find that only the latter model can account for the experimental results, including some counter-intuitive predictions. This mechanism (which we name “neighbourhood watch” model) illuminates the classic “French Flag Problem” and how positional information is interpreted by a sheet of cells in a large developing system.Summary statementIn a large developing system, the chick embryo before gastrulation, cells interpret gradients of positional signals relative to their neighbours to position the primitive streak, establishing bilateral symmetry.
Human Movement Science in The Wild: Can Current Deep-Learning Based Pose Estimation Free Us from The Lab?
Authors: Needham Laurie , Evans Murray , Cosker Darren P. , Wade Logan , McGuigan Polly M. , Bilzon James L. , Colyer Steffi L. 
Published: April 2021

ABSTRACTHuman movement researchers are often restricted to laboratory environments and data capture techniques that are time and/or resource intensive. Markerless pose estimation algorithms show great potential to facilitate large scale movement studies ‘in the wild’, i.e., outside of the constraints imposed by marker-based motion capture. However, the accuracy of such algorithms has not yet been fully evaluated. We computed 3D joint centre locations using several deep-learning based pose estimation methods (OpenPose, AlphaPose, DeepLabCut) and compared to marker-based motion capture. Participants performed walking, running and jumping activities while marker-based motion capture data and multi-camera high speed images (200 Hz) were captured. The pose estimation algorithms were applied to 2D image data and 3D joint centre locations were reconstructed. Pose estimation derived joint centres demonstrated systematic differences at the hip and knee (~30 − 50 mm), most likely due to mislabeling of ground truth data in the training datasets. Where systematic differences were lower, e.g., the ankle, differences of 1 − 15 mm were observed depending on the activity. Markerless motion capture represents a highly promising emerging technology that could free movement scientists from laboratory environments. We provide recommendations relating to domain specific datasets and benchmarks, which will be vital to realising this goal.
Hybrid Derivative of Cathelicidin and Human Beta Defensin-2 Against Gram-Positive Bacteria: A Novel Approach for the Treatment of Bacterial Keratitis
Authors: Ting Darren Shu Jeng , Leng Goh Eunice Tze , Mayandi Venkatesh , Busoy Joanna M. F. , Aung Thet Tun , Periayah Mercy Halleluyah , Nubile Mario , Mastropasqua Leonardo , Said Dalia G. , Htoon Hla M. , Barathi Veluchamy Amutha , Beuerman Roger W. , Lakshminarayanan Rajamani , Mohammed Imran , Dua Harminder S. 
Published: April 2021

ABSTRACTBacterial keratitis (BK) is a major cause of corneal blindness globally. This study aimed to develop a novel class of antimicrobial therapy, based on human-derived hybrid host defense peptides (HyHDPs), for treating BK. HyHDPs were rationally designed through combination of functional amino acids in parent HDPs, including LL-37 and human beta-defensin (HBD)-1 to −3. Minimal inhibitory concentrations (MICs) and time-kill kinetics assay were performed to determine the concentration- and time-dependent antimicrobial activity and cytotoxicity was evaluated against human corneal epithelial cells and erythrocytes. In vivo safety and efficacy of the most promising peptide was examined in the corneal wound healing andStaphylococcus aureus(ATCC SA29213) keratitis murine models, respectively. A second-generation HyHDP (CaD23), based on rational hybridization of the middle residues of LL-37 and C-terminal of HBD-2, was developed and was shown to demonstrate good efficacy against methicillin-sensitive and methicillin-resistantS. aureus[MIC=12.5-25.0μg/ml (5.2-10.4μM)] andS. epidermidis[MIC=12.5μg/ml (5.2μM)], and moderate efficacy againstP. aeruginosa[MIC=25-50μg/ml (10.4-20.8μM)]. CaD23 (at 25μg/ml or 2x MIC) killed all the bacteria within 30 mins, which was 8 times faster than amikacin (25μg/ml or 20x MIC). After 10 consecutive passages, CaD23 did not develop any antimicrobial resistance (AMR) whereas amikacin, a commonly used treatment for BK, developed significant AMR (i.e. a 32-fold increase in MIC). Pre-clinical murine studies showed that CaD23 (0.5mg/ml) achieved a median reduction ofS. aureusbioburden by 94% (or 1.2 log10CFU/ml) while not impeding corneal epithelial wound healing. In conclusion, rational hybridization of human-derived HDPs has led to generation of a potentially efficacious and safe topical antimicrobial agent for treating Gram-positive BK, with no/minimal risk of developing AMR.
Effective Ultrasonic Stimulation in Human Peripheral Nervous System
Authors: Riis Thomas , Kubanek Jan 
Published: April 2021

AbstractObjectiveLow-intensity ultrasound can stimulate excitable cells in a noninvasive and targeted manner, but which parameters are effective has remained elusive. This question has been difficult to answer because differences in transducers and parameters—frequency in particular—lead to profound differences in the stimulated tissue volumes. The objective of this study is to control for these differences and evaluate which ultrasound parameters are effective in stimulating excitable cells.MethodsHere, we stimulated the human peripheral nervous system using a single transducer operating in a range of frequencies, and matched the stimulated volumes with an acoustic aperture.ResultsWe found that low frequencies (300 kHz) are substantially more effective in generating tactile and nociceptive responses in humans compared to high frequencies (900 kHz). The strong effect of ultrasound frequency was observed for all pressures tested, for continuous and pulsed stimuli, and for tactile and nociceptive responses.ConclusionThis prominent effect may be explained by a mechanical force associated with ultrasound. The effect is not due to heating, which would be weaker at the low frequency.SignificanceThis controlled study reveals that ultrasonic stimulation of excitable cells is stronger at lower frequencies, which guides the choice of transducer hardware for effective ultrasonic stimulation of the peripheral nervous system in humans.
A novel 5D brain parcellation approach based on spatio-temporal encoding of resting fMRI data from deep residual learning
Authors: Kazemivash Behnam , Calhoun Vince D. 
Published: April 2021

AbstractObjectiveBrain parcellation is an essential aspect of computational neuroimaging research and deals with segmenting the brain into (possibly overlapping) sub-regions employed to study brain anatomy or function. In the context of functional parcellation, brain organization which is often measured via temporal metrics such as coherence, is highly dynamic. This dynamic aspect is ignored in most research, which typically applies anatomically based, fixed regions for each individual, and can produce misleading results.MethodsIn this work, we propose a novel spatio-temporal-network (5D) brain parcellation scheme utilizing a deep residual network to predict the probability of each voxel belonging to a brain network at each point in time.ResultsWe trained 53 4D brain networks and evaluate the ability of these networks to capture spatial and temporal dynamics as well as to show sensitivity to individual or group-level variation (in our case with age).ConclusionThe proposed system generates informative spatio-temporal networks that vary not only across individuals but also over time and space.SignificanceThe dynamic 5D nature of the developed approach provides a powerful framework that expands on existing work and has potential to identify novel and typically ignored findings when studying the healthy and disordered brain.
Homeostatic regulation of axonal Kv1.1 channels accounts for both synaptic and intrinsic modifications in CA3 circuit
Authors: Zbili Mickaël , Rama Sylvain , Benitez Maria-José , Fronzaroli-Molinieres Laure , Bialowas Andrzej , Boumedine-Guignon Norah , Garrido Juan José , Debanne Dominique 
Published: April 2021

AbstractHomeostatic plasticity of intrinsic excitability goes hand-in-hand with homeostatic plasticity of synaptic transmission. However, the mechanisms linking the two forms of homeostatic regulation have not been identified so far. Using electrophysiological, imaging and immunohistochemical techniques, we show here that blockade of excitatory synaptic receptors for 2-3 days induces an up-regulation of synaptic strength at CA3-CA3 connexions and intrinsic excitability of CA3 pyramidal neurons. Activity-deprived connexions were found to express a high release probability, an insensitivity to dendrotoxin, and a lack of depolarization-induced presynaptic facilitation, indicating a loss of presynaptic Kv1.1 function. The down-regulation of Kv1.1 channels in activity-deprived neurons was confirmed by their broader action potentials measured in the axon that were insensitive to dendrotoxin. We conclude that regulation of axonal Kv1.1 channel constitutes a unique mechanism linking intrinsic excitability and synaptic strength that accounts for the functional synergy existing between homeostatic regulation of intrinsic excitability and synaptic transmission.
In situelectro-sequencing in three-dimensional tissues
Authors: Li Qiang , Lin Zuwan , Liu Ren , Tang Xin , Huang Jiahao , He Yichun , Zhou Haowen , Sheng Hao , Shi Hailing , Wang Xiao , Liu Jia 
Published: April 2021

AbstractPairwise mapping of single-cell gene expression and electrophysiology in intact three-dimensional (3D) tissues is crucial for studying electrogenic organs (e.g., brain and heart)1–5. Here, we introducein situelectro-sequencing (electro-seq), combining soft bioelectronics within situRNA sequencing to stably map millisecond-timescale cellular electrophysiology and simultaneously profile a large number of genes at single-cell level across 3D tissues. We appliedin situelectro-seq to 3D human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) patches, precisely registering the CM gene expression with electrophysiology at single-cell level, enabling multimodalin situanalysis. Such multimodal data integration substantially improved the dissection of cell types and the reconstruction of developmental trajectory from spatially heterogeneous tissues. Using machine learning (ML)-based cross-modal analysis,in situelectro-seq identified the gene-to-electrophysiology relationship over the time course of cardiac maturation. Further leveraging such a relationship to train a coupled autoencoder, we demonstrated the prediction of single-cell gene expression profile evolution using long-term electrical measurement from the same cardiac patch or 3D millimeter-scale cardiac organoids. As exemplified by cardiac tissue maturation,in situelectro-seq will be broadly applicable to create spatiotemporal multimodal maps and predictive models in electrogenic organs, allowing discovery of cell types and gene programs responsible for electrophysiological function and dysfunction.