bluuebunny/crossref_metadata_2025 huggingface dataset:
HPC framework for in-silico trials on 3D virtual human cardiac population to assess drug-induced arrhythmic risk
Authors: Aguado-Sierra Jazmin , Butakoff Constantine , Brigham Renee , Baron Apollo K. , Houzeaux Guillaume , Guerra Jose M. , Carreras Francesc , Filgueiras-Rama David , Iaizzo Paul A. , Iles Tinen L. , Vazquez Mariano
Published: April 2021

Cardiotoxicity continues to be a major health issue worldwide due to the imperative need to access new or repurposed drugs that are safe and effective. Accessibility to affordable drugs is also key to ensure access to drugs to all patients who require them. In this work we propose a workflow for an in-silico clinical trial at the 3D biventricular human population level, to assess cardiac pro-arrhythmic risk after administration of a single or a combination of potentially cardiotoxic drugs.

The proposed workflow aims at reproducing gender-specific ionic channel characteristics that determine different responses of patients to drug-induced arrhythmia. To that end a “normal” virtual population of human 3D hearts at rest and exercise/stress (increased heart rate) was analyzed under the influence of drugs, using computer electrophysiology simulations. The changes in ECG, calcium concentration as well as activation patterns on 3D geometry were evaluated for the signs of arrhythmia. Hydroxychloroquine and Azithromycin were used to demonstrate the workflow. Additionally a series of experiments on a reanimated swine heart utilizing Visible Heart® methodologies were performed to verify the arrhythmic behaviour observed in the in-silico trial.

Our results showed similar results to the recently published clinical trials (21% clinical risk vs 21.8% in-silico trial risk). Evidence of transmurally heterogeneous action potential prolongation after a large dose of hydroxychloroquine was an observed mechanism of arrhythmia, both in the in-vitro and the in-silico model. The proposed workflow for the in-silico clinical drug cardiotoxicity trials allows reproducing the complex behavior of cardiac electrophysiology in a population and verifying drug-induced arrhythmic risk in a matter of a few days as compared to the in-vivo trials. Importantly, our results provided evidence of the normal phenotype variants that produce distinct drug-induced arrhythmogenic outcomes.
Classifying chronic pain using multidimensional pain-agnostic symptom assessments and clustering analysis
Authors: Gilam Gadi , Cramer Eric M. , Webber Kenneth A. , Ziadni Maisa S. , Kao Ming-Chih , Mackey Sean C.
Published: April 2021

Chronic pain conditions present in various forms, yet all feature symptomatic impairments in physical, mental, and social domains. Rather than assessing symptoms as manifestations of illness, we used them to develop a chronic pain classification system. A cohort of real-world treatment-seeking patients completed a multidimensional patient-reported registry as part of a routine initial evaluation in a multidisciplinary academic pain clinic. We applied hierarchical clustering on a training subset of 11448 patients using nine pain-agnostic symptoms. We then validated a three-cluster solution reflecting a graded scale of severity across all symptoms and eight independent pain-specific measures in additional subsets of 3817 and 1273 patients. Negative affect-related factors were key determinants of cluster assignment. The smallest subset included follow-up assessments that were predicted based on baseline cluster assignment. Findings provide a cost-effective classification system that promises to improve clinical care and alleviate suffering by providing putative markers for personalized diagnosis and prognosis.
Endomembrane targeting of human OAS1 p46 augments antiviral activity
Authors: Soveg Frank W. , Schwerk Johannes , Gokhale Nandan S. , Cerosaletti Karen , Smith Julian R. , Pairo-Castineira Erola , Kell Alison M. , Forero Adriana , Zaver Shivam A. , Esser-Nobis Katharina , Roby Justin A. , Hsiang Tien-Ying , Ozarkar Snehal , Clingan Jonathan M. , McAnarney Eileen T. , Stone Amy E. L. , Malhotra Uma , Speake Cate , Perez Joseph , Balu Chiraag , Allenspach Eric J. , Hyde Jennifer L. , Menachery Vineet D. , Sarkar Saumendra N. , Woodward Joshua J. , Stetson Daniel B. , Baillie J. Kenneth , Buckner Jane H. , Gale Michael , Savan Ram
Published: April 2021

Many host RNA sensors are positioned in the cytosol to detect viral RNA during infection. However, most positive-strand RNA viruses replicate within a modified organelle co-opted from intracellular membranes of the endomembrane system, which shields viral products from host cell innate immune sensors. Targeting innate RNA sensors to the endomembrane system may enhance their ability to sense viral RNA generated by viruses that use these compartments for replication. Here, we reveal that an isoform of oligoadenylate synthetase 1, OAS1 p46, is prenylated and targeted to the endomembrane system. Membrane localization of OAS1 p46 confers enhanced access to viral replication sites and results in increased antiviral activity against a subset of RNA viruses including flavivirus, picornavirus, and SARS-CoV-2. Finally, our human genetic analysis shows that theOAS1splice-site SNP responsible for production of the OAS1 p46 isoform strongly associates with COVID-19 severity. This study highlights the importance of endomembrane targeting for the antiviral specificity of OAS1 and suggests early control of SARS-CoV-2 replication through OAS1-p46 is an important determinant of COVID-19 severity.
Evaluation of SARS-CoV-2 Entry, Inflammation and New Therapeutics in Human Lung Tissue Cells
Authors: Grau-Expósito Judith , Perea David , Suppi Marina , Massana Núria , Vergara Ander , Soler Maria José , Trinite Benjamin , Blanco Julià , García-Pérez Javier , Alcamí José , Serrano-Mollar Anna , Rosado Joel , Falcó Vicenç , Genescà Meritxell , Buzon Maria J.
Published: April 2021

The development of physiological models that reproduce SARS-CoV-2 infection in primary human cells will be instrumental to identify host-pathogen interactions and potential therapeutics. Here, using cell suspensions directly from primary human lung tissues (HLT), we have developed a rapid platform for the identification of viral targets and the expression of viral entry factors, as well as for the screening of viral entry inhibitors and anti-inflammatory compounds. The direct use of HLT cells, without long-term cell culture andin vitrodifferentiation approaches, preserves main immune and structural cell populations, including the most susceptible cell targets for SARS-CoV-2; alveolar type II (AT-II) cells, while maintaining the expression of proteins involved in viral infection, such as ACE2, TMPRSS2, CD147 and AXL. Further, antiviral testing of 39 drug candidates reveals a highly reproducible method, suitable for different SARS-CoV-2 variants, and provides the identification of new compounds missed by conventional systems, such as VeroE6. Using this method, we also show that interferons do not modulate ACE2 expression, and that stimulation of local inflammatory responses can be modulated by different compounds with antiviral activity. Overall, we present a relevant and rapid method for the study of SARS-CoV-2.

Graphical Abstract

Highlights

Ex vivophysiological systems for the study of SARS-CoV-2-host interactions are scarce. Here, we establish a method using primary human lung tissue (HLT) cells for the rapid analysis of cell tropism and identification of therapeutics.

HLT cells preserve main cell subpopulations, including alveolar type-2 cells, and expression of SARS-CoV-2 entry factors ACE2, CD147, TMPRSS2 and AXL.

HLT cells are readily susceptible to SARS-CoV-2 infection without the need of cell isolation or further cell differentiation.

Antiviral testing in HLT cells allows the rapid identification of new drug candidates against SARS-CoV-2 variants, missed by conventional systems.

Local inflammation is supported in HLT cells and offers the identification of relevant anti-inflammatory compounds for SARS-CoV-2 infection.
Anxiety and Depression in Patients with Pulmonary Hypertension and its Impact on Health-Related Quality of Life
Authors: Saleemi Sarfraz , Alameer Reem , Alsulaim Toka , Alghasab Naif S
Published: April 2021

Background

Pulmonary Hypertension (PH) is a chronic progressive disease which affects quality of life. The prevalence of mood disorders in PH patients in Saudi Arabia is not known.

Objectives

This is a prospective observational study to investigate the prevalence of anxiety and depression in patients with pulmonary hypertension and its effect on health-related quality of life (HRQoL).

Methods

Forty-two PH patients were evaluated for mood disorders by using Hospital Anxiety and Depression Scale (HADS) and health related quality of life was assessed with The Short Form 36 (SF-36) Health Survey questionnaire.

Results

Mean age for the cohort was 42.8 (±13.3) years and 31(73%) were female. Mean pulmonary artery pressure was 46.4 (± 15) mm Hg and 25 (60%) patients had severe PH (mPAP ≥45 mmHg). Thirty-eight (90%) patients were in World Health Organization Functional Class (WHO-FC) II/III and 5 (10%) class IV. HADS anxiety and depression score was positive (11-21) in 4 (10%) and 6 (14%) patients respectively. Presence of anxiety and/or depression affected HRQoL.

Conclusion

Prevalence of anxiety and depression in PH patients in Saudi Arabia is low (10% and 14% respectively) compared to published studies. The low prevalence may be explained by cultural and social differences and strong family support.
Pathogenic Neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq
Authors: Koster R. , Brandão R.D. , Tserpelis D. , van Roozendaal C.E.P. , van Oosterhoud C.N. , Claes K.B.M. , Paulussen A.D.C. , Sinnema M. , Vreeburg M. , van der Schoot V. , Stumpel C.T.R.M. , Broen M.P.G. , Spruijt L. , Jongmans M.C.J. , Oberstein S.A.J. Lesnik , Plomp A.S. , Misra-Isrie M. , Duijkers F.A. , Louwers M.J. , Szklarczyk R. , Derks K.W.J. , Brunner H.G. , van den Wijngaard A. , van Geel M. , Blok M.J.
Published: April 2021

Purpose

Neurofibromatosis type 1 (NF1) is caused by loss-of-function variants in the NF1 gene. Approximately 10% of these variants affect RNA splicing and are either missed by conventional DNA diagnostics or are misinterpreted by in silico splicing predictions. A targeted RNAseq-based approach was designed to detect pathogenic RNA splicing and associated pathogenic DNA variants.

Methods

RNA was extracted from lymphocytes, followed by targeted NF1 RNAseq. An in-house developed tool (QURNAS) was used to calculate the enrichment score (ERS) for each splicing event.

Results

This method was thoroughly tested using two different patient cohorts with known pathogenic splice-variants. In both cohorts all 56 normal reference transcript exon splice junctions, 24 previously described and 45 novel non-reference splicing events were detected. Additionally, all expected pathogenic splice-variants were detected. Eleven patients with NF1 symptoms were subsequently tested, three of which have a known NF1 DNA variant with a putative effect on RNA splicing. This effect could be confirmed for all 3. The other eight patients were previously without any molecular confirmation of their NF1-diagnosis. A deep-intronic pathogenic splice variant could now be identified for two of them (25%).

Conclusion

Targeted NF1 RNAseq can be successfully used to detect pathogenic RNA splicing variants, complementary to DNA based diagnostics.
Little genomic support for cyclophilin A-matrix metalloproteinase-9 pathway as a therapeutic target for cognitive impairment in APOE4 carriers
Authors: Anderson Emma L , Williams Dylan M , Walker Venexia , Davies Neil M
Published: April 2021

Therapeutic targets for halting the progression of Alzheimers disease pathology are lacking. Recent evidence suggests that APOE4, but not APOE3, activates the cyclophilin A matrix metalloproteinase-9 (CypA MMP9) pathway in the cerebrospinal fluid, leading to an accelerated breakdown of the blood brain barrier (BBB) and thereby causing neuronal and synaptic dysfunction. Furthermore, blockade of the CypA MMP9 pathway in APOE4 knock-in mice restores BBB integrity and subsequently normalizes neuronal and synaptic function. Thus, CypA has been suggested as a potential target for treating APOE4 mediated neurovascular injury and the resulting neuronal dysfunction and degeneration. The odds of drug targets passing through clinical trials are greatly increased if they are supported by genomic evidence. We found little evidence that CypA or MMP9 affected the risk of Alzheimers disease or cognitive impairment using two-sample Mendelian randomization and polygenic risk score analysis in humans. This casts doubt on whether they are likely to represent effective drug targets for cognitive impairment in APOE4 carriers.
Comparative analysis unveils novel changes in serum metabolites and metabolomic networks of retinopathy of prematurity infants
Authors: Yang Yuhang , Yang Qian , Zhang Yinsheng , Lian Chaohui , He Honghui , Zeng Jian , Zhang Guoming
Published: April 2021

Background

Advances in mass spectrometry are providing new insights into the role of metabolomics in the aetiology of many diseases. Studies in retinopathy of prematurity (ROP), for instance, overlooked the role of metabolic alterations in disease development. Here, we employed comprehensive metabolic profiling and gold-standard metabolic analysis to explore major metabolites and metabolic pathways significantly affected in early stages of pathogenesis toward ROP.

Methods

This is a multicentre, retrospective case-control study. We collected serums from 57 ROP cases and 57 strictly baseline matched non-ROP controls. Non-targeted ultrahigh performance liquid chromatography-tandem mass spectroscopy (UPLC-MS/MS) from Metabolon, Inc. was used to detect the metabolites in serum samples. Machine learning was used to unravel most affected metabolites and pathways in ROP development.

Results

Compared to non-ROP controls, we found a significant metabolic perturbation in the ROP serums, featured with an increase in lipid, nucleotide, carbohydrate metabolites and a lower level of peptides. Machine leaning helped to distinguish a cluster of metabolic pathways (glycometabolism, redox homeostasis, lipid metabolism and arginine pathway) that were strongly related to the development of ROP. In addition, we found that the severity of ROP was related to the level of creatinine and ribitol.

Conclusion

In the current study, our results suggested a strong link between metabolic profiling and retinal neovascularization during ROP pathogenesis. These findings provided an insight into identifying novel metabolic biomarkers for ROP diagnosis and prevention.
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

Background

The 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.

Objectives

This 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.

Methods

We 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.

Results

LRRK2 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.

Conclusions

These 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

Recurrent 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

The 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.

Tir 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

Macrophages, 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

SARS-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

Real-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

Chromothripsis 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

In 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 statement

In 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

Human 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

Bacterial 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

Objective

Low-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.

Methods

Here, 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.

Results

We 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.

Conclusion

This 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.

Significance

This 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

Objective

Brain 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.

Methods

In 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.

Results

We 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).

Conclusion

The proposed system generates informative spatio-temporal networks that vary not only across individuals but also over time and space.

Significance

The 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

Homeostatic 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

Pairwise 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.
Sex without crossing over in the yeastSaccharomycodes ludwigii
Authors: Papaioannou Ioannis A. , Dutreux Fabien , Peltier France A. , Maekawa Hiromi , Delhomme Nicolas , Bardhan Amit , Friedrich Anne , Schacherer Joseph , Knop Michael
Published: April 2021

Meiotic recombination is a ubiquitous function of sexual reproduction throughout eukaryotes. Here we report that recombination is extremely suppressed during meiosis in the yeast speciesSaccharomycodes ludwigii. DNA double-strand break formation, processing and repair are required for normal meiosis but do not lead to crossing over. Although the species has retained an intact meiotic gene repertoire, genetic and population analyses suggest the exceptionally rare occurrence of meiotic crossovers. We propose thatSd. ludwigiihas followed a unique evolutionary trajectory that possibly derives fitness benefits from the combination of frequent fertilization within the meiotic tetrad with the absence of meiotic recombination.
DreamDIA-XMBD: deep representation features improve the analysis of data-independent acquisition proteomics
Authors: Gao Mingxuan , Yang Wenxian , Li Chenxin , Chang Yuqing , Liu Yachen , Wang Shun , He Qingzu , Zhong Chuan-Qi , Shuai Jianwei , Yu Rongshan , Han Jiahuai
Published: April 2021

We developed DreamDIA-XMBD, a software suite for data-independent acquisition (DIA) data analysis. DreamDIA-XMBD adopts a data-driven strategy to capture comprehensive information from elution patterns of target peptides in DIA data and achieves considerable improvements on both identification and quantification performance compared with other state-of-the-art methods such as OpenSWATH, Skyline and DIA-NN. More specifically, in contrast to existing methods which use only 6 to 10 selected transitions from spectral library, DreamDIA-XMBD extracts additional features from dozens of theoretical elution profiles originated from different ions of each precursor using a deep representation network. To achieve higher coverage of target peptides without sacrificing specificity, the extracted features are further processed by non-linear discriminative models under the framework of positive-unlabeled learning with decoy peptides as affirmative negative controls. DreamDIA-XMBD is written in Python, and is publicly available athttps://github.com/xmuyulab/Dream-DIA-XMBDfor high coverage and precision DIA data analysis.
Distorted tonotopy severely degrades neural representations of natural speech in noise following acoustic trauma
Authors: Parida Satyabrata , Heinz Michael G.
Published: April 2021

Listeners with sensorineural hearing loss (SNHL) struggle to understand speech, especially in noise, despite audibility compensation. These real-world suprathreshold deficits are hypothesized to arise from degraded frequency tuning and reduced temporal-coding precision; however, peripheral neurophysiological studies testing these hypotheses have been largely limited to in-quiet artificial vowels. Here, we measured single auditory-nerve-fiber responses to a natural speech sentence in noise from anesthetized chinchillas with normal hearing (NH) or noise-induced hearing loss (NIHL). Our results demonstrate that temporal precision was not degraded, and broader tuning was not the major factor affecting peripheral coding of natural speech in noise. Rather, the loss of cochlear tonotopy, a hallmark of normal hearing, had the most significant effects (both on vowels and consonants). Because distorted tonotopy varies in degree across etiologies (e.g., noise exposure, age), these results have important implications for understanding and treating individual differences in speech perception for people suffering from SNHL.
TAOK2 is an ER-localized Kinase that Catalyzes the Dynamic Tethering of ER to Microtubules
Authors: Nourbakhsh Kimya , Ferreccio Amy A. , Bernard Matthew J. , Yadav Smita
Published: April 2021

The endoplasmic reticulum (ER) depends on extensive association with the microtubule cytoskeleton for its structure, function and mitotic inheritance. The identity of molecular tethers that mediate ER-microtubule coupling, and mechanisms through which dynamic tethering is regulated are poorly understood. Here, we identify, Thousand And One amino acid Kinase 2 (TAOK2) as a pleiotropic protein kinase that mediates tethering of ER to microtubules. We show that TAOK2 is a unique multipass membrane spanning serine/threonine kinase localized in distinct ER domains via four transmembrane and amphipathic helices. Usingin vitroand cellular assays, we find that TAOK2 directly binds microtubules with high affinity. We define the minimal TAOK2 determinants that induce ER-microtubule tethering, and delineate the mechanism for its autoregulation. While ER membrane dynamics are increased in TAOK2 knockout cells, the movement of ER along growing microtubule plus-ends is disrupted. We show that ER-microtubule tethering is tightly regulated by catalytic activity of TAOK2 in both interphase and mitotic cells, perturbation of which leads to profound defects in ER morphology and cell division. Our study identifies TAOK2 as an ER-microtubule tether, and reveals a kinase-regulated mechanism for control of ER dynamics critical for cell growth and division.
EEG Spectral Feature Modulations Associated with Fatigue in Robot-Mediated Upper Limb Gross Motor and Fine Motor Interactions
Authors: Dissanayake Udeshika Chaturangee , Steuber Volker , Amirabdollahian Farshid
Published: April 2021

This paper investigates the EEG spectral feature modulations associated with fatigue induced by robot-mediated upper limb gross motor and fine motor interactions. Twenty healthy participants were randomly assigned to either perform a gross motor interaction with HapticMASTER or a fine motor interaction with SCRIPT passive orthosis for 20 minutes or until volitional fatigue. EEG relative and ratio band power measures were estimated from the data recorded before and after the interactions. Paired-samplest-tests found a significant increase in relative alpha band power on FC3, C3, P3 electrodes, and (θ+α)/βandα/βon C3 electrode following the gross motor interaction. Conversely, relative delta band power on C3 significantly decreased. A significant increase in relative alpha band power on FP1, C3 electrodes and relative theta band power on C4 electrode were found following the fine motor interaction whereas relative delta band power on FP1 electrode significantly decreased. Most participants reported an increase in their physical fatigue level following the gross movements and an increase in their mental fatigue level following the fine movements. Findings affirm that changes to localised brain activity patterns are an indication of fatigue developed from the robot-mediated interactions. It can be concluded that regional differences in the prominent EEG spectral features are most likely due to the differences in the nature of the task (fine/gross motor and distal/proximal upper limb) that may have differently altered an individual’s physical and mental fatigue level. The findings could potentially be utilised to monitor and moderate fatigue during robot-mediated post-stroke therapies.
Optoception: perception of optogenetic brain stimulation
Authors: Luis-Islas Jorge , Luna Monica , Floran Benjamin , Gutierrez Ranier
Published: April 2021

How do animals experience brain manipulations? Optogenetics has allowed us to manipulate selectively and interrogate neural circuits underlying brain function in health and disease. However, it is currently unknown whether mice could perceive arbitrary optogenetic stimulation in addition to their evoked physiological functions. To address this issue, mice were trained to report an optogenetic stimulation as a cue to obtain rewards and avoid punishments. It was found that mice could perceive optogenetic manipulations regardless of the brain area modulated, their rewarding effects, or the stimulation of glutamatergic, GABAergic, and dopaminergic cell types. We named this phenomenon optoception. Using optoception, mice could learn to execute two different sets of instructions based on the laser frequency. Importantly, optoception can occur either activating or silencing a single cell type. Our findings revealed that mice’s brains are capable of “monitoring” their self-activity, albeit indirectly, perhaps via interoception or as a discriminative stimulus, opening a new way to introduce information to the brain and control brain-computer interfaces.
Undersampling and the inference of coevolution in proteins
Authors: Kleeorin Yaakov , Russ William P. , Rivoire Olivier , Ranganathan Rama
Published: April 2021

Protein structure, function, and evolution depend on local and collective epistatic interactions between amino acids. A powerful approach to defining these interactions is to construct models of couplings between amino acids that reproduce the empirical statistics (frequencies and correlations) observed in sequences comprising a protein family. The top couplings are then interpreted. Here, we show that as currently implemented, this inference is always biased, a problem that fundamentally arises from the distinct scales at which epistasis occurs in proteins in the context of limited sampling. We show that these issues explain the ability of current approaches to predict tertiary contacts between amino acids and the inability to obviously expose larger networks of functionally-relevant, collectively evolving residues called sectors. This work provides a necessary foundation for more deeply understanding and improving evolution-based models of proteins.