bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating single-cell cluster stability using the Jaccard similarity index
Authors: Tang Ming , Kaymaz Yasin , Logeman Brandon , Eichhorn Stephen , Liang ZhengZheng S. , Dulac Catherine , Sackton Timothy B.
Published: May 2020

Motivation

One major goal of single-cell RNA sequencing (scRNAseq) experiments is to identify novel cell types. With increasingly large scRNAseq datasets, unsupervised clustering methods can now produce detailed catalogues of transcriptionally distinct groups of cells in a sample. However, the interpretation of these clusters is challenging for both technical and biological reasons. Popular clustering algorithms are sensitive to parameter choices, and can produce different clustering solutions with even small changes in the number of principal components used, the k nearest neighbor, and the resolution parameters, among others.

Results

Here, we present a set of tools to evaluate cluster stability by subsampling, which can guide parameter choice and aid in biological interpretation. The R package scclusteval and the accompanying Snakemake workflow implement all steps of the pipeline: subsampling the cells, repeating the clustering with Seurat, and estimation of cluster stability using the Jaccard similarity index. The Snakemake workflow takes advantage of high-performance computing clusters and dispatches jobs in parallel to available CPUs to speed up the analysis. The scclusteval package provides functions to facilitate the analysis of the output, including a series of rich visualizations.

Availability

R package scclusteval:https://github.com/crazyhottommy/scclustevalSnakemake workflow:https://github.com/crazyhottommy/pyflow_seuratv3_parameter

Contact

tsackton@g.harvard.edu,tangming2005@gmail.com

Supplementary information

Supplementary data are available atBioinformaticsonline.
The timing and impact of psychiatric, cognitive and motor abnormalities in Huntington’s disease
Authors: McAllister Branduff , Gusella James F. , Landwehrmeyer G. Bernhard , Lee Jong-Min , MacDonald Marcy E. , Orth Michael , Rosser Anne E. , Williams Nigel M. , Holmans Peter , Jones Lesley , Massey Thomas H.
Published: May 2020

Objective

To assess the prevalence, timing and functional impact of psychiatric, cognitive and motor abnormalities in Huntington’s disease (HD) gene carriers, we analysed retrospective clinical data from individuals with manifest HD.

Methods

Clinical features of HD patients were analysed for 6316 individuals in the European REGISTRY study from 161 sites across 17 countries. Data came from clinical history and the patient-completed Clinical Characteristics Questionnaire that assessed eight symptoms: motor, cognitive, apathy, depression, perseverative/obsessive behavior, irritability, violent/aggressive behavior, and psychosis. Multiple logistic regression was used to analyse relationships between symptoms and functional outcomes.

Results

The initial manifestation of HD is increasingly likely to be motor, and less likely to be psychiatric, as age at presentation increases, and is independent of pathogenic CAG repeat length. The Clinical Characteristics Questionnaire captures data on non-motor symptom prevalence that correlate specifically with validated clinical measures. Psychiatric and cognitive symptoms are common in HD gene carriers, with earlier onsets associated with longer CAG repeats. 42.4% of HD patients reported at least one psychiatric or cognitive symptom before motor symptoms, with depression most common. Each non-motor symptom was associated with significantly reduced total functional capacity scores.

Conclusions

Psychiatric and cognitive symptoms are common and functionally debilitating in HD gene carriers. They require recognition and targeting with clinical outcome measures and treatments. However, as it is impossible to distinguish confidently between non-motor symptoms arising from HD and primary psychiatric disorders, particularly in younger pre-manifest patients, non-motor symptoms should not be used to make a clinical diagnosis of HD.
A Deep Feature Learning Approach for Mapping the Brain’s Microarchitecture and Organization
Authors: Balwani Aishwarya H. , Dyer Eva L.
Published: May 2020

Models of neural architecture and organization are critical for the study of disease, aging, and development. Unfortunately, automating the process of building maps of microarchitectural differences both within and across brains still remains a challenge. In this paper, we present a way to build data-driven representations of brain structure using deep learning. With this model we can build meaningful representations of brain structure within an area, learn how different areas are related to one another anatomically, and use this model to discover new regions of interest within a sample that share similar characteristics in terms of their anatomical composition. We start by training a deep convolutional neural network to predict the brain area that it is in, using only small snapshots of its immediate surroundings. By requiring that the network learn to discriminate brain areas from these local views, it learns a rich representation of the underlying anatomical features that allow it to distinguish different brain areas. Once we have the trained network, we open up the black box, extract features from its last hidden layer, and then factorize them. After forming a low-dimensional factorization of the network’s representations, we find that the learned factors and their embeddings can be used to further resolve biologically meaningful subdivisions within brain regions (e.g., laminar divisions and barrels in somatosensory cortex). These findings speak to the potential use of neural networks to learn meaningful features for modeling neural architecture, and discovering new patterns in brain anatomy directly from images.
Metabolic scaling has diversified among species, despite an evolutionary constraint within species
Authors: Beaman Julian E. , Ortiz-Barrientos Daniel , Monro Keyne , Hall Matthew D. , White Craig R.
Published: May 2020

Metabolic rate scales disproportionally with body mass, such that the energetic cost of living is relatively lower in larger organisms. Theory emphasises the importance of fixed physical constraints on metabolic scaling, yet empirical data are lacking with which to assess how evolutionary processes (e.g. mutation, drift, selection) contribute to the observed variation in metabolic scaling across the tree of life. Using a large-scale quantitative genetic study of growth in cockroaches, we show that ontogenetic metabolic scaling is evolutionarily constrained due to an absence of additive genetic variation in juvenile metabolic rate and mass. Using a phylogenetic analysis, we also show that ontogenetic metabolic scaling is more similar among closely related species than among distant relatives, suggesting that the constraints on metabolic scaling are subject to change during lineage diversification. Our results are consistent with growing evidence that there is strong stabilising selection on combinations of mass and metabolic rate within species.
Language impairment with a microduplication in 1q42.3q43
Authors: Benítez-Burraco Antonio , Fernández-Urquiza Maite , Jiménez-Romero Mª Salud
Published: May 2020

Deletions and duplications of the distal region of the long arm of chromosome 1 are associated with brain abnormalities and developmental delay. Because duplications are less frequent than deletions, no detailed account of the cognitive profile of the affected people is available, particularly, regarding their language (dis)abilities. In this paper we report on the cognitive and language features of a girl with one of the smallest interstitial duplications ever described in this region, affecting to 1q42.3q43 (arr[hg19] 1q42.3q43(235,963,632-236,972,276)x3). Standardized tests as well as the analysis of her language use in natural settings suggest that the proband’s speech is severely impaired, exhibiting dysarthric-like features, with speech problems also resulting from a phonological deficit boiling down to a verbal auditory memory deficit. Lexical and grammatical knowledge are also impaired, impacting negatively on both expressive and receptive abilities, seemingly as a consequence of the phonological deficit. Still, her pragmatic abilities seem to be significantly spared, granting her a good command on the principles governing conversational exchanges. In silico analyses (literature mining, network analysis) and in vitro analyses (microarray) point to several genes as potential candidates for the observed deficits in the language domain. These include one gene within the duplicated region (LYST), one predicted functional partner (CMIP), and three genes outside the 1q42.3q43 region, which are all highly expressed in the cerebellum:DDIT4andSLC29A1, found strongly downregulated in the proband compared to their healthy parents, andCNTNAP3, found strongly upregulated.
Chromatin-associated MRN complex protects highly transcribing genes from genomic instability
Authors: Salifou Kader , Burnard Callum , Basavarajaiah Poornima , Helsmoortel Marion , Mac Victor , Depierre David , Grasso Giuseppa , Franckhauser Céline , Beyne Emmanuelle , Contreras Xavier , Dejardin Jérôme , Rouquier Sylvie , Cuvier Olivier , Kiernan Rosemary
Published: May 2020

The MRN-MDC1 complex plays a central role in the DNA damage response (DDR) and repair. Using Proteomics of Isolated Chromatin Fragments (PICh), we identified DDR factors, such as MDC1, among those that become highly associated with a genomic locus upon transcriptional activation. Purification of endogenous MDC1, in the absence of exogenous DNA damage, revealed its interaction with factors involved in gene expression and co-transcriptional RNA processing, in addition to DDR factors. ChIP-seq analysis showed that MDC1 interacting factors, MRE11 and NBS1 subunits of MRN, were co-localized throughout the genome and notably at TSSs and gene bodies of actively transcribing genes. Blockade of transcriptional elongation showed that binding of MRN was dependent on the RNAPII transcriptional complex rather than transcriptionper se. Depletion of MRN increased RNAPII abundance at TSSs and gene bodies of MRE11/NBS1-bound genes. Prolonged exposure of cells to either MRE11- or NBS1-depletion led to single nucleotide polymorphism formation across actively transcribing, MRE11 or NBS1 target genes. These data support a model by which association of the MRN complex with the transcriptional machinery constitutively scans active genes for transcription-induced DNA damage to preserve the integrity of the coding genome.
In silicoanalysis of SNPs in human phosphofructokinase, Muscle (PFKM) gene: An apparent therapeutic target of aerobic glycolysis and cancer
Authors: Rani Yogita , kaur Kamaljit , Sharma Madhvi , Kalia Namarta
Published: May 2020

Phosphofructokinase, muscle (PFKM), a key glycolytic regulatory enzyme is a potential target for cancer therapeutic studies accredited to the employed inefficient phenomenon known as Warburg effect. PFKM is encoded byPFKMgene located at chromosome 12q13.11. Single nucleotide polymorphisms (SNPs) are known to profoundly affect gene expression and protein function. Therefore, the first attempt was made to computationally identify putative functional PFKM variants. These SNPs were further explored to find their probable association with different cancer types. A total of 9694 SNPs were retrieved from dbSNP database. Of which, only 85 validated SNPs with ≥10% minor allele frequency (MAF) were subjected to analysis by softwares including Ensembl Genome browser, FuncPred (SNPinfo), regulomeDB (v 2.0), SIFT and PolyPhen-2. The relative analysis of output obtained classified the selected-SNPs into 11 highly prioritized (HP), 20 moderately prioritized and 54 not/poorly prioritized SNPs. The 11 HP-SNPs were found to have the highest likelihood of being functionally important, evidenced by previous association of rs2269935, rs11168417, rs11609399 and rs2228500 HP-SNPs with cachexia, lung and breast cancer. The study warrants further experiments to confirm the predictive role of prioritized SNPs in cancer etiology and also provides directions to fellow researchers.
Ablation of MYB-dependent leukaemia phenotype in MLL-driven AML correlates with increased expression of MAFB
Authors: Ward C , Cauchy P , Walton DS , Clarke ML , Blakemore D , Grebien F , Garcia P , Frampton J , Volpe G
Published: May 2020

The transcription factor MYB plays a pivotal role in haematopoietic homeostasis and its aberrant expression is involved in the genesis and maintenance of acute myeloid leukaemia (AML). Our previous work has demonstrated that not all AML types display the same dependency onMYBexpression and that MYB dependence is dictated by the nature of the driver mutation. However, whether this difference in MYB dependency is a general trend in AML still remains to be further elucidated. In this study, we investigate the importance ofMYBin human leukaemia by performing siRNA-mediated knock-down in cell line models of AML with different driver lesions. We show that the characteristic reduction in proliferation and the concomitant induction of myeloid differentiation that is observed in MLL-fusion-driven leukaemia uponMYBsuppression is not seen in AML cells with a complex karyotype. By performing transcriptome analysis, we demonstrate that a strong activation ofMAFBexpression driven byMYBablation is restricted to MYB-dependent cells. In line with these observations, stratification of publicly available patient data reveals a reciprocal relationship between the expression ofMYBandMAFB, highlighting a novel connection between those two factors in AML.
A mathematical model for storage and recovery of motor actions in the spinal cord
Authors: Parker David J , Srivastava Vipin
Published: May 2020

Motor outputs are generated by the spinal cord in response to de-scending inputs from the brain. While particular descending commands generate specific outputs, how descending inputs interact with spinal cord circuitry to generate these outputs remains unclear. Here, we suggest that during development particular motor programmes are stored in premotor spinal circuitry, and that these can subsequently be retrieved when the associated descending input is received. We propose that different motor patterns are not stored in the spinal cord as a library of separate programmes, but that the spinal cord orthogonalises and normalises the various inputs, identifies the similarities and differences between them, and stores only the differences: similarities between patterns are recognised and used as a common basis that subsequent input patterns are built upon. By removing redundancy this can greatly increase the storage capacity of a system composed of a finite number of processing units, thus overcoming the problems associated with the storage limits of conventional artificial networks (e.g. ‘catastrophic interference’). Where possible we relate the various stages of the processing to the known circuitry and synaptic properties of spinal cord locomotor networks, and suggest experimental approaches that could test unknown aspects.
LRRK2 regulates AP2M1 phosphorylation cycles to mediate endocytosis and dopaminergic neurodegeneration
Authors: Liu Qinfang , Bautista-Gomez Judith , Higgins Daniel A. , Yu Jianzhong , Xiong Yulan
Published: May 2020

Recent genetic evidence revealed endocytic pathway plays a major role in Parkinson’s disease (PD). However, the molecular mechanism is poorly understood. Here we report that LRRK2, the most genetic cause of PD, binds to and phosphorylates AP2M1, the core component of endocytosis recently implicated in PD risk. Both knockout and overexpression of LRRK2 cause abnormal AP2M1 phosphorylation cycle and in turn endocytic defects. Mechanistically, knockout of LRRK2 decreases AP2M1 phosphorylation required for the initial clathrin coated vesicle (CCV) formation while LRRK2 overexpression inhibits AP2M1 uncoating for entering into a new cycle of CCV formation. Our study also uncovered a novel tissue-specific regulation of AP2M1 phosphorylation by LRRK2. Further, we found LRRK2 phosphorylation on AP2M1 mediates LRRK2-induced neuronal toxicity bothin vitroandin vivo. Importantly, AP2M1 phosphorylation levels are elevated in PD patient fibroblasts. Together, our study provides a direct mechanistic link between LRRK2, AP2 and endocytosis in PD pathogenesis.
HAP40 is a conserved central regulator of Huntingtin and a specific modulator of mutant Huntingtin toxicity
Authors: Xu Shiyu , Li Gang , Ye Xin , Chen Dongsheng , Chen Zhihua , Xu Zhen , Ye Lili , Stimming Erin F. , Marchionini Deanna , Zhang Sheng
Published: May 2020

Perturbation of Huntingtin (HTT)’s physiological function is one postulated pathogenic factor in Huntington’s disease (HD). However, little is known how HTT is regulatedin vivo. In a proteomic study, we isolated a novel ∼40kDa protein as a strong binding partner ofDrosophilaHTT and demonstrated it was the functional ortholog of HAP40, an HTT associated protein shown recently to modulate HTT’s conformation but with unclear physiological and pathologic roles. We showed that in both flies and human cells, HAP40 maintained conserved physical and functional interactions with HTT, loss of HAP40 resulted in similar phenotypes as HTT knockout, including animal viability and autophagy, and more strikingly, HAP40 depletion significantly reduced the levels of endogenous HTT, while HAP40 was mostly degraded via the proteasome in the absence of HTT. Interestingly, polyglutamine expansion in HTT did not affect its affinity for HAP40. However, HAP40 modulated HD pathogenesis inDrosophilamodel by regulating the overall protein levels and the toxicity of full-length mutant HTT. Together, our study uncovers a conserved mechanism governing the stability andin vivofunctions of HTT, and demonstrates that HAP40 is a central and positive regulator of HTT, a potential modulator of HD pathogenesis and a promising candidate for “HTT-lowering” strategy against HD.
An analog to digital converter controls bistable transfer competence development of a widespread bacterial integrative and conjugative element
Authors: Carraro Nicolas , Richard Xavier , Sulser Sandra , Delavat François , Mazza Christian , van der Meer Jan Roelof
Published: May 2020

Conjugative transfer of the integrative and conjugative element ICEclcinPseudomonasrequires development of a transfer competence state in stationary phase, which arises only in 3-5% of individual cells. The mechanisms controlling this bistable switch between non-active and transfer competent cells have long remained enigmatic. Using a variety of genetic tools and epistasis experiments inP. putida, we uncovered an ‘upstream’ cascade of three consecutive transcription factor-nodes, which controls transfer competence initiation. Initiation activates a feedback loop, which stochastic modeling and experimental data demonstrated acts as a scalable converter of unimodal input to bistable output. The feedback loop further enables prolonged production of a transcription factor that ensures ‘downstream’ transfer competence formation in activated cells. Phylogenetic analyses showed that the ICEclcregulatory factors are widespread amongGamma-andBeta-proteobacteria, highlighting its evolutionary conservation and prime importance to control the behaviour of this wide family of conjugative elements.
Estrogen receptors in human bladder cells regulate innate cytokine responses to differentially modulate uropathogenicE. colicolonization
Authors: Sen Ayantika , Kaul Anil , Kaul Rashmi
Published: May 2020

The bladder epithelial cells elicit robust innate immune responses against urinary tract infections (UTIs) for preventing the bacterial colonization. Physiological fluctuations in circulating estrogen levels in women increase the susceptibility to UTI pathogenesis, often resulting in adverse health outcomes. Dr adhesin bearingEscherichia coli(DrE. coli) cause recurrent UTIs in menopausal women and acute pyelonephritis in pregnant women. DrE. colibind to epithelial cells via host innate immune receptor CD55, under hormonal influence. The role of estrogens or estrogen receptors (ERs) in regulating the innate immune responses in the bladder are poorly understood. In the current study, we investigated the role of ERα, ERβ and GPR30 in modulating the innate immune responses against DrE. coliinduced UTI using human bladder epithelial carcinoma 5637 cells (HBEC). Both ERα and ERβ agonist treatment in bladder cells induced a protection against DrE. coliinvasion via upregulation of TNFα and downregulation of CD55 and IL10, and these effects were reversed by action of ERα and ERβ antagoinsts. In contrast, the agonist-mediated activation of GPR30 led to an increased bacterial colonization due to suppression of innate immune factors in the bladder cells, and these effects were reversed by the antagonist-mediated suppression of GPR30. Further, siRNA-mediated ERα knockdown in the bladder cells reversed the protection against bacterial invasion observed in the ERα positive bladder cells, by modulating the gene expression of TNFα, CD55 and IL10, thus confirming the protective role of ERα. We demonstrate for the first time a protective role of nuclear ERs, ERα and ERβ but not of membrane ER, GPR30 against DrE. coliinvasion in HBEC 5637 cells. These findings have many clinical implications and suggest that ERs may serve as potential drug targets towards developing novel therapeutics for regulating local innate immunity and treating UTIs.

Highlights

Estrogen receptor (ER) subtypes regulate the gene expression of innate immune molecules, CD55, TNFα and IL10 in human bladder epithelial cells impacting the bacterial colonization by DrE. coli.

Activation of nuclear ER subtypes, ERα and ERβ, upregulate the gene expression of proinflammatory cytokine, TNFα, but downregulate the gene expression of anti-inflammatory cytokine, IL10, and DrE. colicolonization receptor, CD55, thus leading to efficient bacterial clearance in human bladder cells.

In contrast, activation of the membrane ER subtype, GPR30, shows opposite effects to ERα and ERβ that were mediated on TNFα, IL10 and CD55 gene expression, thus leading to impaired bacterial clearance of DrE. coliin human bladder cells.

ER subtypes can serve as potential drug candidates for designing new therapies to boost or modulate the local immunity in the human bladder preventing the establishment ofE. coliinfections.
Inhibition of tryptophan 2,3-dioxygenase impairs DNA damage tolerance and repair in glioma cells
Authors: Reed Megan R. , Maddukuri Leena , Ketkar Amit , Byrum Stephanie D. , Zafar Maroof K. , Bostian April C. L. , Tackett Alan J. , Eoff Robert L.
Published: May 2020

Aberrant expression of tryptophan 2,3-dioxygenase (TDO) is a determinant of malignancy and immune response in gliomas in part through kynurenine (KYN)-mediated activation of the aryl hydrocarbon receptor (AhR). In the current study, we investigated the hypothesis that TDO activation in gliomas has a broad impact upon genome maintenance - promoting tolerance of replication stress (RS) and repair of DNA damage. We report that inhibition of TDO activity attenuated recovery from hydroxyurea (HU)-induced RS and increased the genotoxic effects of bis-chloroethylnitrosourea (BCNU), as fork progress was impeded when TDO-deficient glioma cells were treated with BCNU. Activation of the Chk1 arm of the replication stress response (RSR) was reduced when TDO activity was blocked prior to treatment with BCNU, whereas phosphorylation of serine 33 (pS33) on replication protein A (RPA) was enhanced – indicative of increased fork collapse. Restoration of KYN levels protected against some replication-associated effects of BCNU. Inhibition of TDO activity had a strong anti-proliferative effect on glioma-derived cells – enhancing the cytotoxic effects of BCNU. Analysis of results obtained using quantitative proteomics revealed TDO-dependent changes in several signaling pathways – including down-regulation of DNA repair factors and sirtuin signaling. Consistent with these observations, inhibition of TDO diminished SIRT7 recruitment to chromatin, which increased histone H3K18 acetylation – a key mark involved in 53BP1 recruitment to sites of DNA damage. Cells lacking TDO activity exhibited defective recruitment of 53BP1 to gH2AX foci, which corresponded with delayed repair of BCNU-induced DNA breaks. Addition of exogenous KYN increased the rate of break repair. The discovery that TDO activity modulates sensitivity to DNA damage by fueling SIRT7/53BP1 localization to chromatin and repair of BCNU-induced DNA damage highlights the potential for tumor-specific metabolic changes to influence genome stability and may have implications for glioma biology and treatment strategies.
Playing a P300-based BCI VR game leads to changes in cognitive functions of healthy adults
Authors: Bulat Matvey , Karpman Alexandra , Samokhina Alina , Panov Alexander
Published: May 2020

In this paper, we present the results of a study to determine the effect of the P300-based brain-computer interface (BCI) virtual reality game on the cognitive functions of healthy human subjects. This study is a part of on-going research related to evaluation of the the long-term effect of P300 training in Virtual Reality surrounding (VR game) on the cognitive performance of the young healthy population. A comparison of results between 3 groups of participants (15 people each) revealed the progressing difference in cognitive assessment for experimental group played P300 BCI VR game, showing the positive increase in flanker and conjunction visual search task performance associated with selective attention and mental inhibition. We show that the effect is due to the use of P300 BCI paradigm. Our results suggest that P300 BCI games combined with virtual reality can not only be used for rehabilitation in patients with slight mental disorders or elderly, but for increasing some cognitive functions in healthy subjects, giving an additional improvement in learning in case of combination with possible educational tasks or used for attention training

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Accumbens cholinergic interneurons mediate cue-induced nicotine seeking and associated glutamatergic plasticity
Authors: Leyrer-Jackson Jonna M. , Holter Michael , Overby Paula F. , Newbern Jason M. , Scofield Michael D. , Olive M. Foster , Gipson Cassandra D.
Published: May 2020

Nicotine, the primary addictive substance in tobacco, is widely abused. Relapse to cues associated with nicotine results in increased glutamate release within nucleus accumbens core (NAcore), modifying synaptic plasticity of medium spiny neurons (MSNs) which contributes to reinstatement of nicotine seeking. However, the role of cholinergic interneurons (ChIs) within the NAcore in mediating these neurobehavioral processes in unknown. ChIs represent less than 1% of the accumbens neuronal population yet are activated during drug seeking and reward-predicting events. Thus, we hypothesized that ChIs may play a significant role in mediating glutamatergic plasticity that underlies nicotine seeking behavior. Using chemogenetics transgenic rats that express Cre under the control of the choline acetyltransferase (ChAT) promoter, ChIs were bi-directionally manipulated prior to cue-induced reinstatement. Following nicotine self-administration and extinction training, ChIs were activated or inhibited prior to a cue reinstatement session. Following reinstatement, whole-cell electrophysiology from NAcore MSNs was used to assess changes in plasticity, measured via α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) / N-Methyl-D-Aspartate (NMDA) (A/N) ratios. Chemogenetic inhibition of ChIs inhibited cued nicotine seeking and resulted in decreased A/N, whereas activation of ChIs had no effect, demonstrating that ChI inhibition prevents transient synaptic potentiation (t-SP) associated with cue-induced nicotine seeking. To assess potential underlying mechanisms, accumbens α4β2- and α7-containing nicotinic ACh receptors (nAChRs) were pharmacologically inhibited and MSN synaptic morphology was assessed following reinstatement. Inhibition of both nAChR subtypes prevented cue-induced nicotine seeking and t-SP (measured via changes in spine head diameter). Together, these results demonstrate that these neurons mediate cue-induced nicotine reinstatement and underlying synaptic plasticity within the NAcore.
𝓲-SATA: A MATLAB based toolbox to estimate Current Density generated by Transcranial Direct Current Stimulation in an Individual Brain
Authors: Kashyap Rajan , Bhattacharjee Sagarika , Arumugam Ramaswamy , Oishi Kenichi , Desmond John E. , Chen SH Annabel
Published: May 2020

Background

Transcranial Direct Current Stimulation (tDCS) is a technique where a weak current is passed through the electrodes placed on the scalp. The distribution of the electric current induced in the brain due to tDCS is provided by simulation toolbox like Realistic-volumetric-Approach-based-Simulator-for-Transcranial-electric-stimulation (ROAST). However, the procedure to estimate the total current density induced at the target and the intermediary region of the cortex is complex. The Systematic-Approach-for-tDCS-Analysis (SATA) was developed to overcome this problem. However, SATA is limited to standardized headspace only. Here we developindividual-SATA (𝓲-SATA) to extend it to individual head.

Method

T1-weighted images of 15 subjects were taken from two Magnetic Resonance Imaging (MRI) scanners of different strengths. Across the subjects, the montages were simulated in ROAST. 𝓲-SATA converts the ROAST output to Talairach space. The x, y and z coordinates of the anterior commissure (AC), posterior commissure (PC), and Mid-Sagittal (MS) points are necessary for the conversion. AC and PC are detected using the acpcdetect toolbox. We developed a method to determine the MS in the image and cross-verified its location manually using BrainSight®.

Result

Determination of points with 𝓲-SATA is fast and accurate. The 𝓲-SATA provided estimates of the current-density induced across an individual’s cortical lobes and gyri as tested on images from two different scanners.

Conclusion

Researchers can use 𝓲-SATA for customizing tDCS-montages. With 𝓲-SATA it is also easier to compute the inter-individual variation in current-density across the target and intermediary regions of the brain. The software is publicly available.
Do M-cells contribute significantly in T-wave morphology during normal and arrhythmogenesis conditions like short QT Syndrome?
Authors: Priya Ponnuraj Kirthi , Jayaraman Srinivasan
Published: May 2020

Aims

This paper proposes to explain the mechanism of M-cells, particularly its role in the T-wave generation and its contribution to arrhythmogenesis in short QT syndrome 2 (SQTS2).

Methods

A 2D transmural anisotropic ventricular model made up of three principal cell types were developed. Different setups in which: a) entire column of mid-myocardial (mid) cells, b) single island of cells c) two island of cells within the mid-layer d) single island of cells in endocardial (endo)-mid layer were considered as M-cells. These setups are stimulated to explain i) contribution of M-cells in T-wave morphology ii) arrhythmia generation phenomena under SQTS2 heterozygous gene mutation by creating pseudo ECGs from the tissue.

Results

Findings infer that setups with an entire layer of M-cells and a higher percentage of epicardial (epi) cells exhibit positive T-waves. Increasing the size of the island in M-cell island setups results in an increased positive T-peak. Placing the M-cell island in the bottom of the mid-layer produced low amplitude T-waves. Further, in two M-cell islands setup, a higher T-wave amplitude was observed when the islands are placed closer than far apart. Moving the M-cell island slightly into the endo layer increases the amplitude of the T-wave. Lastly, on including SQTS2 conditions and pacing with premature beats, an arrhythmia occurs only in those setups containing a layer of M-cells compared to M-cells island setup.

Conclusion

These simulation findings paved the way for a better understanding of the M-cells functionality in T-wave morphology as well as promoting arrhythmogenesis under SQTS2 condition.
Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies
Authors: Barnes Christopher O. , West Anthony P. , Huey-Tubman Kathryn E. , Hoffmann Magnus A.G. , Sharaf Naima G. , Hoffman Pauline R. , Koranda Nicholas , Gristick Harry B. , Gaebler Christian , Muecksch Frauke , Cetrulo Lorenzi Julio C. , Finkin Shlomo , Hagglof Thomas , Hurley Arlene , Millard Katrina G. , Weisblum Yiska , Schmidt Fabian , Hatziioannou Theodora , Bieniasz Paul D. , Caskey Marina , Robbiani Davide F. , Nussenzweig Michel C. , Bjorkman Pamela J.
Published: May 2020

Neutralizing antibody responses to coronaviruses focus on the trimeric spike, with most against the receptor-binding domain (RBD). Here we characterized polyclonal IgGs and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their degree of focus on RBD epitopes, recognition of SARS-CoV, MERS-CoV, and mild coronaviruses, and how avidity effects contributed to increased binding/neutralization of IgGs over Fabs. Electron microscopy reconstructions of polyclonal plasma Fab-spike complexes showed recognition of both S1Aand RBD epitopes. A 3.4Å cryo-EM structure of a neutralizing monoclonal Fab-S complex revealed an epitope that blocks ACE2 receptor-binding on “up” RBDs. Modeling suggested that IgGs targeting these sites have different potentials for inter-spike crosslinking on viruses and would not be greatly affected by identified SARS-CoV-2 spike mutations. These studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived fromVH3-53/VH3-66and similarity to a SARS-CoVVH3-30antibody, providing criteria for evaluating vaccine-elicited antibodies.
Intercellular viral spread and intracellular transposition ofDrosophilagypsy
Authors: Keegan Richard M. , Chang Yung-Heng , Metzger Michael J. , Dubnau Josh
Published: May 2020

It has become increasingly clear that retrotransposons (RTEs) are more widely expressed in somatic tissues than previously appreciated. RTE expression has been implicated in a myriad of biological processes ranging from normal development and aging, to age related diseases such as cancer and neurodegeneration. Long Terminal Repeat (LTR)-retrotransposons are evolutionary ancestors to, and share many features with, exogenous retroviruses. In fact, many organisms contain endogenous retroviruses (ERVs) that derive from an exogenous retrovirus that have integrated into the germ line. These ERVs are inherited in Mendelian fashion like RTEs, and some retain the ability to transmit between cells like viruses, while others develop the ability to act as RTEs. The process of evolutionary transition between LTR-RTE and retroviruses is thought to involve multiple steps by which the element loses or gains the ability to transmit copies between cells versus the ability to replicate intracellularly. But, typically, these two modes of transmission are incompatible because they require assembly in different sub-cellular compartments. Like murine IAP/IAP-E elements, the gypsy family of retroelements in arthropods appear to sit along this evolutionary transition. The fact that gypsy elements have been found to actively mobilize in neurons and glial cells during normal aging and in models of neurodegeneration raises the question of whether their replication in somatic cells occurs via intracellular retrotransposition, intercellular viral spread, or some combination of the two. These modes of replication in somatic tissues would have quite different biological implications. Here, we demonstrate that Drosophila gypsy is capable of both cell-associated and cell-free viral transmission between cultured S2 cells of somatic origin. Further, we demonstrate that the ability of gypsy to move between cells is dependent upon a functional copy of its viral envelope protein. This argues that the gypsy element has transitioned from an RTE into a functional endogenous retrovirus with the acquisition of its envelope gene. On the other hand, we also find that intracellular retrotransposition of the same genomic copy of gypsy can occur in the absence of the Env protein. Thus, gypsy exhibits both intracellular retrotransposition and intercellular viral transmission as modes of replicating its genome.
Lung cancer models reveal SARS-CoV-2-induced EMT contributes to COVID-19 pathophysiology
Authors: Stewart C. Allison , Gay Carl M. , Ramkumar Kavya , Cargill Kasey R. , Cardnell Robert J. , Nilsson Monique B. , Heeke Simon , Park Elizabeth M. , Kundu Samrat T. , Diao Lixia , Wang Qi , Shen Li , Xi Yuanxin , Zhang Bingnan , Della Corte Carminia Maria , Fan Youhong , Kundu Kiran , Gao Boning , Avila Kimberley , Pickering Curtis R. , Johnson Faye M. , Zhang Jianjun , Kadara Humam , Minna John D. , Gibbons Don L. , Wang Jing , Heymach John V. , Byers Lauren Averett
Published: May 2020

COVID-19 is an infectious disease caused by SARS-CoV-2, which enters host cells via the cell surface proteins ACE2 and TMPRSS2. Using a variety of normal and malignant models and tissues from the aerodigestive and respiratory tracts, we investigated the expression and regulation ofACE2andTMPRSS2. We find thatACE2expression is restricted to a select population of highly epithelial cells. Notably, infection with SARS-CoV-2 in cancer cell lines, bronchial organoids, and patient nasal epithelium, induces metabolic and transcriptional changes consistent with epithelial to mesenchymal transition (EMT), including upregulation ofZEB1andAXL, resulting in an increased EMT score. Additionally, a transcriptional loss of genes associated with tight junction function occurs with SARS-CoV-2 infection. The SARS-CoV-2 receptor, ACE2, is repressed by EMT via TGFbeta, ZEB1 overexpression and onset of EGFR TKI inhibitor resistance. This suggests a novel model of SARS-CoV-2 pathogenesis in which infected cells shift toward an increasingly mesenchymal state, associated with a loss of tight junction components with acute respiratory distress syndrome-protective effects. AXL-inhibition and ZEB1-reduction, as with bemcentinib, offers a potential strategy to reverse this effect. These observations highlight the utility of aerodigestive and, especially, lung cancer model systems in exploring the pathogenesis of SARS-CoV-2 and other respiratory viruses, and offer important insights into the potential mechanisms underlying the morbidity and mortality of COVID-19 in healthy patients and cancer patients alike.
Restarting after COVID-19: A Data-driven Evaluation of Opening Scenarios
Authors: Aravindakshan Ashwin , Boehnke Jörn , Gholami Ehsan , Nayak Ashutosh
Published: May 2020

To contain the COVID-19 pandemic, several governments introduced strict Non-Pharmaceutical Interventions (NPI) that restricted movement, public gatherings, national and international travel, and shut down large parts of the economy. Yet, the impact of the enforcement and subsequent loosening of these policies on the spread of COVID-19 is not well understood. Accordingly, we measure the impact of NPI on mitigating disease spread by exploiting the spatio-temporal variations in policy measures across the 16 states of Germany. This quasi-experiment identifies each policy’s effect on reducing disease spread. We adapt the SEIR (Susceptible-Exposed-Infected-Recovered) model for disease propagation to include data on daily confirmed cases, intra- and inter-state movement, and social distancing. By combining the model with measures of policy contributions on mobility reduction, we forecast scenarios for relaxing various types of NPIs. Our model finds that, in Germany, policies that mandated contact restrictions (e.g., movement in public space limited to two persons or people co-living), initial business closures (e.g., restaurant closures), stay-at-home orders (e.g., prohibition of non-essential trips), non-essential services (e.g., florists, museums) and retail outlet closures led to the sharpest drops in movement within and across states. Contact restrictions were the most effective at lowering infection rates, while border closures had only minimal effects at mitigating the spread of the disease, even though cross-border travel might have played a role in seeding the disease in the population. We believe that a deeper understanding of the policy effects on mitigating the spread of COVID-19 allows a more accurate forecast of the disease spread when NPIs are (partially) loosened, and thus also better informs policymakers towards making appropriate decisions.
The effectiveness of eight nonpharmaceutical interventions against COVID-19 in 41 countries
Authors: Brauner Jan M. , Mindermann Sören , Sharma Mrinank , Stephenson Anna B. , Gavenčiak Tomáš , Johnston David , Leech Gavin , Salvatier John , Altman George , Norman Alexander John , Monrad Joshua Teperowski , Besiroglu Tamay , Ge Hong , Mikulik Vladimir , Hartwick Meghan A. , Teh Yee Whye , Chindelevitch Leonid , Gal Yarin , Kulveit Jan
Published: May 2020

Background

Governments are attempting to control the COVID-19 pandemic with nonpharmaceutical interventions (NPIs). However, it is still largely unknown how effective different NPIs are at reducing transmission. Data-driven studies can estimate the effectiveness of NPIs while minimizing assumptions, but existing analyses lack sufficient data and validation to robustly distinguish the effects of individual NPIs.

Methods

We collect chronological data on NPIs in 41 countries between January and May 2020, using independent double entry by researchers to ensure high data quality. We estimate NPI effectiveness with a Bayesian hierarchical model, by linking NPI implementation dates to national case and death counts. To our knowledge, this is the largest and most thoroughly validated data-driven study of NPI effectiveness to date.

Results

We model each NPI’s effect as a multiplicative (percentage) reduction in the reproduction number R. We estimate the mean reduction in R across the countries in our data for eight NPIs: mandating mask-wearing in (some) public spaces (2%; 95% CI: −14%–16%), limiting gatherings to 1000 people or less (2%; −20%–22%), to 100 people or less (21%; 1%–39%), to 10 people or less (36%; 16%–53%), closing some high-risk businesses (31%; 13%–46%), closing most nonessential businesses (40%; 22%–55%), closing schools and universities (39%; 21%–55%), and issuing stay-at-home orders (18%; 4%–31%). These results are supported by extensive empirical validation, including 15 sensitivity analyses.

Conclusions

Our results suggest that, by implementing effective NPIs, many countries can reduce R below 1 without issuing a stay-at-home order. We find a surprisingly large role for school and university closures in reducing COVID-19 transmission, a contribution to the ongoing debate about the relevance of asymptomatic carriers in disease spread. Banning gatherings and closing high-risk businesses can be highly effective in reducing transmission, but closing most businesses only has limited additional benefit.
The binding mechanism ofStreptococcus suisaccessory virulence factor and adhesin SadP to globotetraosylceramide
Authors: Johansson Miralda Madar , Bélurier Eva , Papageorgiou Anastassios C. , Sundin Anders P. , Rahkila Jani , Kallonen Teemu , Nilsson Ulf J. , Maatsola Santeri , Nyholm Thomas K.M. , Käpylä Jarmo , Corander Jukka , Leino Reko , Finne Jukka , Teneberg Susann , Haataja Sauli
Published: May 2020

Streptococcus suisis part of the pig commensal microbiome and a major pathogen causing pneumonia and meningitis in pigs and occasionally also zoonotic meningitis. According to genomic analysis,S. suisis divided into asymptomatic carriage, respiratory and systemic strains with distinct genomic signatures. The virulence factorS. suisadhesin P (SadP) recognizes the galabiose Galα1–4Gal-oligosaccharide. Based on its oligosaccharide fine specificity, SadP can be divided into subtypes PNand PO. We show here that subtype PNis distributed in the systemic strains that cause meningitis, whereas type POis found in asymptomatic carriage and respiratory strains. Both types of SadP are shown to predominantly bind to pig lung globotriaosylceramide (Gb3). However, SadP adhesin from systemic subtype PNstrain also binds to globotetraosylceramide (Gb4). Mutagenesis studies of the galabiose-binding domain of type PNSadP adhesin showed that the amino acid asparagine-285, which is replaced by an aspartate residue in type Po SadP, was required for binding to Gb4 and, strikingly, it was also required for interaction with the glycomimetic inhibitor phenylurea-galabiose. Molecular dynamics simulations provided further insight into the role of Asn-285 for Gb4 and phenylurea-galabiose binding, suggesting additional hydrogen bonding to terminal GalNAc of Gb4 and urea-group. Thus, the Asn-285-mediated molecular mechanism of type PNSadP binding to Gb4 could be used as a candidate to selectively targetS. suisin invasive systemic disease without interfering with commensal strains, which may open up new venues for developing intervention strategies against this pathogen.
Polymer-assisted intratumoral delivery of ethanol: Preclinical investigation of safety and efficacy in a murine breast cancer model
Authors: Nief Corrine A. , Morhard Robert , Chelales Erika , Alvarez Daniel Adrianzen , Bourla Ioanna , Lam Christopher T. , Sag Alan A. , Crouch Brian T. , Mueller Jenna L. , Katz David , Dewhirst Mark W. , Everitt Jeffrey I. , Ramanujam Nirmala
Published: May 2020

Focal tumor ablation with ethanol could provide benefits in low-resource settings because of its low overall cost, minimal imaging technology requirements, and acceptable clinical outcomes. Unfortunately, ethanol ablation is not commonly utilized because of a lack of predictability of the ablation zone, caused by inefficient retention of ethanol at the injection site. To create a predictable zone of ablation, we have developed a polymer-assisted ablation method using ethyl cellulose (EC) mixed with ethanol. EC is ethanol-soluble and water-insoluble, allowing for EC-ethanol to be injected as a liquid and precipitate into a solid, occluding the leakage of ethanol upon contact with tissue. The aims of this study were to compare the 1) safety, 2) release kinetics, 3) spatial distribution, 4) necrotic volume, and 5) overall survival of EC-ethanol to conventional ethanol ablation in a murine breast tumor model. Non-target tissue damage was monitored through localized adverse events recording, ethanol release kinetics with Raman spectroscopy, injectate distribution within vivoimaging, target-tissue necrosis with NADH-diaphorase staining, and overall survival by proxy of tumor growth. EC-ethanol exhibited decreased localized adverse events, a slowing of the release rate of ethanol, more compact injection zones, 5-fold increase in target-tissue necrosis, and longer overall survival rates compared to the same volume of pure ethanol. A single 150 µL dose of 6% EC-ethanol achieved a similar survival probability rates to six daily 50 µL doses of pure ethanol used to simulate a slow-release of ethanol over 6 days. Taken together, these results demonstrate that EC-ethanol is safer and more effective than ethanol alone for ablating tumors.

Graphical Abstract

The inclusion of ethylcellulose limits extra-tumoral leakage of ethanol and increases the target-tissue ablation.