bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational hypothesis: How Intra-hepatic functional heterogeneity may influence the cascading progression of free fatty acid-induced non-alcoholic fatty liver disease (NAFLD)
Authors: Holzhütter Hermann-Georg , Berndt Nikolaus
Published: May 2020

Non-Alcoholic Fatty Liver Disease (NAFLD) is the most common type of chronic liver disease in developed nations, affecting around 25% of the population. Elucidating the factors causing NAFLD in individual patients to progress in different rates and to different degrees of severity, is a matter of active medical research. Here, we aim to provide evidence that the intra-hepatic heterogeneity of rheological, metabolic and tissue-regenerating capacities plays a central role in disease progression. We developed a generic mathematical model that constitutes the liver as ensemble of small liver units differing in their capacities to metabolize potentially cytotoxic free fatty acids (FFAs) and to repair FFA-induced cell damage. Transition from simple steatosis to more severe forms of NAFLD is described as self-amplifying process of cascading liver failure, which to stop depends essentially on the distribution of functional capacities across the liver. Model simulations provided the following insights: (1) A persistently high plasma level of FFAs is sufficient to drive the liver through different stages of NAFLD; (2) Presence of NAFLD amplifies the deleterious impact of additional tissue-damaging hits; and (3) Coexistence of non-steatotic and highly steatotic regions is indicative for the later occurrence of severe NAFLD stages.
Divergent projections of the prelimbic cortex bidirectionally regulate active avoidance
Authors: Diehl Maria M. , Iravedra-García Jorge M. , Morán-Sierra Jonathan , Rojas-Bowe Gabriel , Gonzalez-Díaz Fabiola , Valentín-Valentín Viviana , Quirk Gregory J.
Published: May 2020

The prefrontal cortex (PFC) integrates incoming information to guide our actions. When motivation for food-seeking competes with avoidance, the PFC likely plays a role in selecting the optimal choice. In platform-mediated active avoidance, rats avoid a tone-signaled footshock by stepping onto a nearby platform, delaying access to sucrose pellets. This avoidance requires prelimbic (PL) prefrontal cortex, basolateral amygdala (BLA), and ventral striatum (VS). We previously showed that inhibitory tone responses of PL neurons correlate with avoidability of shock (Diehlet al., 2018). Here, we optogenetically modulated PL terminals in VS and BLA to identify PL outputs regulating avoidance. Photoactivating PL-VS projections reduced avoidance, whereas photoactivating PL-BLA projections increased avoidance. Moreover, photosilencing PL-BLA or BLA-VS projections reduced avoidance, suggesting that VS receives opposing inputs from PL and BLA. Bidirectional modulation of avoidance by PL projections to VS and BLA enables the animal to make appropriate decisions when faced with competing drives.
Database for drug metabolism and comparisons, NICEdrug.ch, aids discovery and design
Authors: MohammadiPeyhani Homa , Chiappino-Pepe Anush , Haddadi Kiandokht , Hafner Jasmin , Hadadi Noushin , Hatzimanikatis Vassily
Published: May 2020

The discovery of a drug requires over a decade of enormous research and financial investments—and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch database, which incorporates 250,000 bio-active molecules, and studied their metabolic targets, fate, and toxicity. NICEdrug.ch includes a unique fingerprint that identifies reactive similarities between drug-drug and drug-metabolite pairs. We use NICEdrug.ch to evaluate inhibition and toxicity by the anticancer drug 5-fluorouracil, and suggest avenues to alleviate its side effects. Clustering based on this fingerprint in statins identified drugs for repurposing. We propose shikimate 3-phosphate for targeting liver-stage malaria with minimal impact on the human host cell. Finally, NICEdrug.ch suggests over 1,300 drugs and food molecules to target COVID-19 and explains their inhibitory mechanisms. The NICEdrug.ch database is accessible online to systematically identify the reactivity of small molecules and druggable enzymes with practical applications in lead discovery and drug repurposing.
Evidence for an apathy phenotype in aged mice
Authors: Jackson Megan G , Lightman Stafford L , Gilmour Gary , Marston Hugh , Robinson Emma S J
Published: May 2020

Apathy is widely reported in patients with neurological disorders or post viral infection but is also seen in otherwise-healthy aged individuals. This study investigated whether aged mice express behavioural and physiological changes indicative of an apathy phenotype. Using measures of motivation to work for reward, we found deficits in the progressive ratio task related to rate of responding. In an effort for reward task, aged mice were less willing to exert effort for high value reward. Aged mice exhibited reduced reward sensitivity and expressed lower measures of anxiety in the novelty supressed feeding test. In a test of cognition (novel object recognition) aged mice showed no impairments but activity was lower in a measure of exploration in a novel environment. Aged mice also showed an attenuated response to restraint stress with lower corticosterone and reduced paraventricular nucleus c-fos activation. Together, these data suggest aged mice show reduced goal-directed behaviour and reduced reward sensitivity and stress reactivity, reflective of emotional blunting and may be a suitable model for pre-clinical apathy research.
MINTyper: An outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads
Authors: Hallgren Malte B. , Overballe-Petersen Søren , Lund Ole , Hasman Henrik , Clausen Philip T. L. C.
Published: May 2020

For detection of clonal outbreaks in clinical settings, we present a complete pipeline that generates a SNP-distance matrix from a set of sequencing reads. Importantly, the program is able to handle a separate mix of both short reads from the Illumina sequencing platforms and long reads from Oxford Nanopore Technologies’ (ONT) platforms as input.

MINTyper performs automated reference identification, alignment, alignment trimming, optional methylation masking and pairwise distance calculations. With this approach, we could rapidly and accurately cluster a set of DNA sequenced isolates, with a known epidemiological relationship to confirm the clustering. Functions were built to allow for both high-accuracy methylation-aware base-called MinION reads (hac_m Q10) and fast generated lower-quality reads (fast Q8) to be used, also in combination with Illumina data. With fast Q8 reads a higher number of base pairs were excluded from the calculated distance matrix, compared to the high-accuracy methylation-aware Q10 base-calling of ONT data. Nonetheless, when using different qualities of ONT data with corresponding input parameters, the clustering of isolates were nearly identical.
Mapping social reward and punishment processing in the human brain: A voxel-based meta-analysis of neuroimaging findings using the Social Incentive Delay task
Authors: Martins D. , Rademacher L. , Gabay A. S. , Taylor R. , Richey J. A. , Smith D. , Goerlich K. S. , Nawijn L. , Cremers H.R. , Wilson R. , Bhattacharyya S. , Paloyelis Y.
Published: May 2020

Social incentives (rewards or punishments) motivate human learning and behaviour, and alterations in the brain circuits involved in the processing social incentives have been linked with several neuropsychiatric disorders. However, questions still remain about the exact neural substrates implicated in social incentive processing. Here, we conducted four Anisotropic Effect Size Signed Differential Mapping voxel-based meta-analyses of fMRI studies investigating the neural correlates of the anticipation and receipt of social rewards and punishments using the Social Incentive Delay task. We map the regions involved in each of these four processes in the human brain, identify decreases in the BOLD signal during the anticipation of both social reward and punishment avoidance that were missed in individual studies due to a lack of power, and characterise the effect size and direction of changes in the BOLD signal for each brain area. Our results provide a better understanding of the brain circuitry involved in social incentive processing and can inform hypotheses about potentially disrupted brain areas linked with dysfunctional social incentive processing during disease.

Highlights

Voxel-based meta-analysis of the neural underpinnings of social incentive processing

We map the brain regions involved in the processing of social incentives in humans

We identify new regions missed in individual studies as a result of lack of power

Our work can inform research on pathological brain processing of social incentives
A computational method for direct imputation of cell type-specific expression profiles and cellular compositions from bulk-tissue RNA-Seq in brain disorders
Authors: Torshizi Abolfazl Doostparast , Duan Jubao , Wang Kai
Published: May 2020

The importance of cell type-specific gene expression in disease-relevant tissues is increasingly recognized in genetic studies of complex diseases. However, the vast majority of gene expression studies are conducted on bulk tissues, necessitating computational approaches to infer biological insights on cell type-specific contribution to diseases. Several computational methods are available for cell type deconvolution (that is, inference of cellular composition) from bulk RNA-Seq data, but cannot impute cell type-specific expression profiles. We hypothesize that with external prior information such as single cell RNA-seq (scRNA-seq) and population-wide expression profiles, it can be a computationally tractable and identifiable to estimate both cellular composition and cell type-specific expression from bulk RNA-Seq data. Here we introduce CellR, which addresses cross-individual gene expression variations by employing genome-wide tissue-wise expression signatures from GTEx to adjust the weights of cell-specific gene markers. It then transforms the deconvolution problem into a linear programming model while taking into account inter/intra cellular correlations, and uses a multi-variate stochastic search algorithm to estimate the expression level of each gene in each cell type. Extensive analyses on several complex diseases such as schizophrenia, Alzheimer’s disease, Huntington’s disease, and type 2 diabetes validated efficiency of CellR, while revealing how specific cell types contribute to different diseases. We conducted numerical simulations on human cerebellum to generate pseudo-bulk RNA-seq data and demonstrated its efficiency in inferring cell-specific expression profiles. Moreover, we inferred cell-specific expression levels from bulk RNA-seq data on schizophrenia and computed differentially expressed genes within certain cell types. Using predicted gene expression profile on excitatory neurons, we were able to reproduce our recently published findings on TCF4 being a master regulator in schizophrenia and showed how this gene and its targets are enriched in excitatory neurons. In summary, CellR compares favorably (both accuracy and stability of inference) against competing approaches on inferring cellular composition from bulk RNA-seq data, but also allows direct imputation of cell type-specific gene expression, opening new doors to re-analyze gene expression data on bulk tissues in complex diseases.
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
Authors: Baßler Kevin , Fujii Wataru , Kapellos Theodore S. , Horne Arik , Reiz Benedikt , Dudkin Erika , Lücken Malte , Reusch Nico , Osei-Sarpong Collins , Warnat-Herresthal Stefanie , Wagner Allon , Bonaguro Lorenzo , Günther Patrick , Pizarro Carmen , Schreiber Tina , Becker Matthias , Händler Kristian , Wohnhaas Christian T. , Baumgartner Florian , Köhler Meike , Theis Heidi , Kraut Michael , Wadsworth Marc H. , Hughes Travis K. , Ferreira Humberto J. G. , Schulte-Schrepping Jonas , Hinkley Emily , Kaltheuner Ines H. , Geyer Matthias , Thiele Christoph , Shalek Alex K. , Feißt Andreas , Thomas Daniel , Dickten Henning , Beyer Marc , Baum Patrick , Yosef Nir , Aschenbrenner Anna C. , Ulas Thomas , Hasenauer Jan , Theis Fabian J. , Skowasch Dirk , Schultze Joachim L.
Published: May 2020

Despite the epidemics of chronic obstructive pulmonary disease (COPD), the cellular and molecular mechanisms of this disease are far from being understood. Here, we characterize and classify the cellular composition within the alveolar space and peripheral blood of COPD patients and control donors using a clinically applicable single-cell RNA-seq technology corroborated by advanced computational approaches for: machine learning-based cell-type classification, identification of differentially expressed genes, prediction of metabolic changes, and modeling of cellular trajectories within a patient cohort. These high-resolution approaches revealed: massive transcriptional plasticity of macrophages in the alveolar space with increased levels of invading and proliferating cells, loss of MHC expression, reduced cellular motility, altered lipid metabolism, and a metabolic shift reminiscent of mitochondrial dysfunction in COPD patients. Collectively, single-cell omics of multi-tissue samples was used to build the first cellular and molecular framework for COPD pathophysiology as a prerequisite to develop molecular biomarkers and causal therapies against this deadly disease.
Mfd regulates RNA polymerase association with hard-to-transcribe regionsin vivo, especially those with structured RNAs
Authors: Ragheb Mark N. , Merrikh Christopher , Browning Kaitlyn , Merrikh Houra
Published: May 2020

RNA polymerase (RNAP) encounters various roadblocks during transcription. These obstacles can impede RNAP movement, influence transcription, ultimately necessitating the activity of RNAP associated factors. One such factor is the bacterial protein Mfd; a highly conserved DNA translocase and evolvability factor that interacts with RNAP. Although Mfd is thought to function primarily in the repair of DNA lesions that stall RNAP, increasing evidence suggests that it may also be important for transcription regulation. However, this is yet to be fully characterized.

To shed light on Mfd’sin vivofunctions, we identified the chromosomal regions where it associates. We analyzed Mfd’s impact on RNAP association and transcription regulation genome-wide. We found that Mfd represses RNAP association at many chromosomal regions. We found that these regions show increased RNAP pausing, suggesting that they are hard-to-transcribe. Interestingly, we noticed that the majority of the regions where Mfd regulates transcription contain highly structured regulatory RNAs. The RNAs identified regulate a myriad of biological processes, ranging from metabolism, to tRNA regulation, to toxin-antitoxin (TA) functions. We found that transcription regulation by Mfd, at least at some TA loci, is critical for cell survival. Lastly, we found that Mfd promotes mutagenesis in at least one toxin gene, suggesting that its function in regulating transcription may promote evolution of certain TA systems, and other regions containing strong RNA secondary structures. We conclude that Mfd is an RNAP co-factor that is important, and at times critical, for transcription regulation at hard-to-transcribe regions, especially those that express structured regulatory RNAs.

Significance

The bacterial DNA translocase Mfd binds to stalled RNAPs and is generally thought to facilitate transcription-coupled DNA repair. Most of our knowledge about Mfd is based on data from biochemical studies. However, little is known about Mfd’s function in living cells, especially in the absence of exogenous DNA damage. Here, we show that Mfd modulates RNAP association and alters transcription at a variety of chromosomal loci, especially those containing highly structured, regulatory RNAs. As such, this work improves our understanding of Mfd’s function in living cells, and assigns it a new function as a transcription regulator.
Multifractality Nature of Microtubule Dynamic Instability Process
Authors: Rezania Vahid , Sudirga Ferry C. , Tuszynski Jack A.
Published: May 2020

The irregularity of growing and shortening patterns observed experimentally in microtubules reflects a dynamical system that fluctuates stochastically between assembly and disassembly phases. The observed time series of microtubule lengths have been extensively analyzed to shed light on structural and dynamical properties of microtubules. Here, for the first time, Multifractal Detrended Fluctuation analysis (MFDFA) has been employed to investigate the multifractal and topological properties of both experimental and simulated microtubule time series. We find that the time dependence of microtubule length possesses true multifractal characteristics and cannot be described by monofractal distributions. Based on the multifractal spectrum profile, a set of multifractal indices have been calculated that can be related to the level of dynamical activities of microtubules. We also show that the resulting multifractal spectra for the simulated data might not be comparable with experimental data.

Statement of Significance

Microtubules are some of the most important subcellular structures involved in a multitude of functions in all eukaryotic cells. In addition to their cylindrical geometry, their polymerization/depolymerization dynamics, termed dynamic instability, is unique among all protein polymers. In this paper we demonstrate that there is a very specific mathematical representation of microtubule growth and shrinkage time series in terms of multifractality. We further show that using this characteristic, one can distinguish real experimental data from synthetic time series generated from computer simulations.
Motion opponency examined throughout visual cortex with multivariate pattern analysis of fMRI data
Authors: Silva Andrew E. , Thompson Benjamin , Liu Zili
Published: May 2020

This study explores how the human brain solves the challenge of flicker noise in motion processing. Despite providing no useful directional motion information, flicker is common in the visual environment and exhibits omnidirectional motion energy which is processed by low-level motion detectors. Models of motion processing propose a mechanism called motion opponency that reduces the processing of flicker noise. Motion opponency involves the pooling of local motion signals to calculate an overall motion direction. A neural correlate of motion opponency has been observed in human area MT+/V5 using fMRI, whereby stimuli with perfectly balanced motion energy constructed from dots moving in counter-phase elicit a weaker BOLD response than non-balanced (in-phase) motion stimuli. Building on this previous work, we used multivariate pattern analysis to examine whether the patterns of brain activation elicited by motion opponent stimuli resemble the activation elicited by flicker noise across the human visual cortex. Robust multivariate signatures of opponency were observed in V5 and in V3A. Our results support the notion that V5 is centrally involved in motion opponency and in the reduction of flicker noise during visual processing. Furthermore, these results demonstrate the utility of powerful multivariate analysis methods in revealing the role of additional visual areas, such as V3A, in opponency and in motion processing more generally.

Highlights

Opponency is demonstrated in multivariate and univariate analysis of V5 data.

Multivariate fMRI also implicates V3A in motion opponency.

Multivariate analyses are useful for examining opponency throughout visual cortex.
Viral-Induced Alternative Splicing of Host Genes Promotes Influenza Replication
Authors: Thompson Matthew G , Dittmar Mark , Mallory Michael J , Bhat Prasanna , Ferretti Max B. , Fontoura Beatriz MA , Cherry Sara , Lynch Kristen W.
Published: May 2020

Viral infection induces the expression of numerous host genes that impact the outcome of infection. Here we show that infection of human lung epithelial cells with Influenza A virus (IAV) also induces a broad program of alternative splicing of host genes. While these splicing-regulated genes are not enriched for canonical regulators of viral infection, we find that many of these genes do impact replication of IAV. Moreover, specific inhibition of the IAV-induced splicing in several cases also attenuates viral infection. We further show that approximately a quarter of the IAV-induced splicing events are regulated by hnRNP K, a host protein that required for efficient splicing of the IAV M transcript in nuclear speckles. Notably, we find that hnRNP K accumulates in nuclear speckles upon IAV infection, which is likely to alter the accessibility of hnRNP K for host transcripts thereby leading to a program of host splicing changes that promote IAV replication.
Further biochemical profiling ofHypholoma fascicularemetabolome reveals its chemogenetic diversity
Authors: Al-Salihi Suhad A.A. , Bull Ian , Al-Salhi Raghad A. , Gates Paul J. , Salih Kifah , Bailey Andy M. , Foster Gary D.
Published: May 2020

There is a desperate need in continuing the search for natural products with novel mechanism to battle the constant increase of microbial drug resistance. Previously mushroom forming fungi were neglected as a source of novel antibiotics, due to the difficulties associated with their culture preparation and genetic tractability. However, modern fungal molecular and synthetic biology tools, renewed the interest in exploring mushroom fungi for novel therapeutics. The aim of this study was to have a comprehensive picture of nine basidiomycetes secondary metabolites (SM), screen their biological and chemical properties to describe the genetic pathways associated with their production.H. fascicularerevealed to be highly active antagonistic species, with antimicrobial activity against three different microorganisms -Bacillus subtilis, Escherichia coliandSaccharomyces cerevisiae-. Extensive genomic comparison and chemical analysis using analytical chromatography, led to the characterisation of more than 15 variant biosynthetic gene clusters and the first identification of a potent antibacterial metabolite-3, 5-dichloromethoxy benzoic acid (3, 5-D)-in this species, for which a biosynthetic gene cluster was predicted. This work demonstrates the great potential of mushroom forming fungi as a reservoir of bioactive natural products which are currently unexplored, and that access to their genomic data and structural diversity natural products via utilizing modern computational analysis and efficient chemical methods, could accelerate the development and applications of such distinct molecules in both pharmaceutical and agrochemical industry.
The Caribbean-Hispanic Alzheimer’s Brain Transcriptome Reveals Ancestry-Specific Disease Mechanisms
Authors: Felsky Daniel , Sariya Sanjeev , Santa-Maria Ismael , French Leon , Schneider Julie A. , Bennett David A. , Mayeux Richard , De Jager Philip L. , Tosto Giuseppe
Published: May 2020

Ethnicity impacts Alzheimer’s disease risk, especially among Caribbean-Hispanics. We report the first RNA-sequencing analysis of brain tissue from 45 Alzheimer’s disease and control Caribbean-Hispanics. Data were compared with two independent samples of non-Hispanic Caucasians (total n=729). By identifying and characterizing those genes with ancestry- and region-specific expression patterns in Alzheimer’s disease, we reveal molecular insights that may help explain epidemiological disparities in this understudied aging population.
Microbial strategies for survival in the glass spongeVazella pourtalesii
Authors: Bayer Kristina , Busch Kathrin , Kenchington Ellen , Beazley Lindsay , Franzenburg Sören , Michels Jan , Hentschel Ute , Slaby Beate M.
Published: May 2020

Few studies have thus far explored the microbiomes of glass sponges (Hexactinellida). The present study seeks to elucidate the composition of the microbiota associated with the glass spongeVazella pourtalesiiand the functional strategies of the main symbionts. We combined microscopic approaches with metagenome-guided microbial genome reconstruction and amplicon community profiling towards this goal. Microscopic imaging revealed that the host and microbial cells appeared within dense biomass patches that are presumably syncytial tissue aggregates. Based on abundances in amplicon libraries and metagenomic data, SAR324 bacteria, Crenarchaeota, Patescibacteria and Nanoarchaeota were identified as abundant members of theV. pourtalesiimicrobiome and their genomic potentials were thus analyzed in detail. A general pattern emerged in that theV. pourtalesiisymbionts had very small genome sizes in the range of 0.5-2.2 Mb and low GC contents, even below those of seawater relatives. Based on functional analyses of metagenome-assembled genomes (MAGs), we propose two major microbial strategies: the “givers”, namely Crenarchaeota and SAR324, heterotrophs and facultative anaerobes, produce and partly secrete all required amino acids and vitamins. The “takers”, Nanoarchaeota and Patescibacteria, are anaerobes with reduced genomes that tap into the microbial community for resources, e.g., lipids and DNA, likely using pili-like structures. We posit that the existence of microbial cells in sponge syncytia together with the low-oxygen conditions in the seawater environment are factors that shape the unique compositional and functional properties of the microbial community associated withV. pourtalesii.

Importance

We investigated the microbial community ofV. pourtalesiithat forms globally unique, monospecific sponge grounds under low-oxygen conditions on the Scotian Shelf, where it plays a key role for its vulnerable ecosystem. The microbial community was found to be concentrated within biomass patches and is dominated by small cells (<1 μm). MAG analyses showed consistently small genome sizes and low GC contents, which is unusual in comparison to known sponge symbionts. These properties as well as the (facultatively) anaerobic metabolism and a high degree of interdependence between the dominant symbionts regarding amino acid and vitamin synthesis are likely adaptations to the unique conditions within the syncytial tissue of their hexactinellid host and the low-oxygen environment.
Oropouche virus glycoprotein topology and cellular requirements for virus assembly
Authors: Barbosa Natalia S. , Concha Juan O. , daSilva Luis L. P. , Crump Colin M. , Graham Stephen C.
Published: May 2020

Oropouche virus (OROV;Genus: Orthobunyavirus) is the etiological agent of Oropouche fever, a debilitating febrile illness common in South America. We used recombinant expression of the OROV M polyprotein, that encodes the surface glycoproteins Gn and Gc plus the non-structural protein NSm, to probe the cellular determinants for OROV assembly and budding. Gn and Gc self-assemble and are secreted independently of NSm. Mature OROV Gn has two predicted transmembrane domains that are crucial for glycoprotein translocation to the Golgi complex and glycoprotein secretion and, unlike related orthobunyaviruses, both transmembrane domains are retained during Gn maturation. Disruption of Golgi function using the drugs brefeldin A and monensin inhibit glycoprotein secretion. Infection studies have previously shown that the cellular Endosomal Sorting Complexes Required for Transport (ESCRT) machinery is recruited to Golgi membranes during OROV assembly and that ESCRT activity is required for virus secretion. A dominant negative form of the ESCRT-associated ATPase VPS4 significantly reduces recombinant OROV glycoprotein secretion and blocks virus release from infected cells, and VPS4 partly co-localizes with OROV glycoproteins and membranes co-stained with Golgi markers. Furthermore, immunoprecipitation and fluorescence microscopy experiments demonstrate that OROV glycoproteins interact with the ESCRT-III component CHMP6, with overexpression of a dominant negative form of CHMP6 significantly reducing OROV glycoprotein secretion. Taken together, our data highlights differences in M polyprotein processing across orthobunyaviruses, that Golgi and ESCRT function are required for glycoprotein secretion, and identifies CHMP6 as an ESCRT-III component that interacts with OROV glycoproteins.

Importance

Oropouche virus causes Oropouche fever, a debilitating illness common in South America that is characterised by high fever, headache, myalgia and vomiting. The tripartite genome of this zoonotic virus is capable of reassortment and there have been multiple epidemics of Oropouche fever in South America over the last 50 years, making Oropouche virus infection a significant threat to public health. However, the molecular characteristics of this arbovirus are poorly understood. We developed a recombinant protein expression system to investigate the cellular determinants of OROV glycoprotein maturation and secretion. We show that the proteolytic processing of the M polypeptide, which encodes the surface glycoproteins (Gn and Gc) plus a non-structural protein (NSm), differs between OROV and its close relative Bunyamwera virus. Furthermore, we demonstrate that OROV M glycoprotein secretion requires the cellular ESCRT membrane-remodelling machinery and identify that the OROV glycoproteins interact with the ESCRT protein CHMP6.
Pushing beyond specifications: Evaluation of linearity and clinical performance of a fully automated SARS-CoV-2 RT-PCR assay for reliable quantification in blood and other materials outside recommendations
Authors: Nörz Dominik , Frontzek André , Eigner Ulrich , Oestereich Lisa , Fischer Nicole , Aepfelbacher Martin , Pfefferle Susanne , Lütgehetmann Marc
Published: May 2020

1

Background

The ongoing SARS-CoV-2 pandemic presents a unique challenge to diagnostic laboratories. There are preliminary studies correlating qRT-PCR results from different materials to clinical outcomes, yet, comparability is limited due to the plethora of different assays used for diagnostics. In this study we evaluate clinical performance and linear range for the SARS-CoV-2 IVD (cobas6800/8800 system, a fully automated sample-to-result platform) in different clinically relevant matrix materials outside official specifications.

Methods

Assay performance was assessed in human plasma, BAL/BL and transport medium following chemical inactivation. For analytical evaluation, respective matrix materials were spiked with SARS-CoV-2 RNA in ten-fold dilution series. The efficacy of chemical inactivation by guanidine hydrochloride solution was confirmed in cell culture infectivity experiments. For correlation, a total of 235 predetermined clinical samples including respiratory swabs, plasma and BAL/BL were subjected to the SARS-CoV-2 IVD test and results were compared.

Results

The SARS-CoV-2 IVD showed excellent linearity over five to seven log steps depending on matrix material. Chemical inactivation resulted in a reduction in plaque forming units of at least 3.5 log steps, while having no significant impact on assay performance. Inter-run consistency from three different testing sites demonstrated excellent comparability of RT-PCR results (maximum deviation was 1.53 CT). Clinical evaluation for respiratory swabs showed very good agreement with the comparator assay (Positive agreement 95.7%, negative agreement 98.9%).

Conclusion

The SARS-CoV-2 IVD test for the cobas6800/8800 systems offers excellent linear range and inter-run consistency for quantification of SARS-CoV-2 RNA in different matrices outside official specifications.

Highlights

Effective reduction of SARS-CoV-2 infectivity by chemical inactivation without affecting assay performance.

SARS-CoV-2 IVD for the cobas 6800/8800 is linear over up to seven log steps in different materials including human plasma.

Minimal variance of CT values between testing sites indicates high comparability of quantification results.
Investigating spatiotemporal patterns of the COVID-19 in São Paulo State, Brazil
Authors: Alcântara Enner , Mantovani José , Rotta Luiz , Park Edward , Rodrigues Thanan , Carvalho Fernando Campos , Filho Carlos Roberto Souza
Published: May 2020

As of May 16th, 2020, the number of confirmed cases and deaths in Brazil due to COVID-19 hit 233,142 and 15,633, respectively, making the country one of the most affected by the pandemic. The State of Sao Paulo (SSP) hosts the largest number of confirmed cases in Brazil, with over 60,000 cases to date. Here we investigate the spatial distribution and spreading patterns of COVID-19 in the SSP by mapping the spatial autocorrelation and the clustering patterns of the virus in relation to the population density and the number of hospital beds. Moran’s I and LISA clustering analysis indicated that Sao Paulo City is a significant hotspot for both the confirmed cases and deaths, whereas other cities across the State could be considered colder spots. Bivariate Moran’s I also showed that the population density is a key indicator for the number of deaths, whereas the number of hospital beds is less related, implying that the fatality depends substantially on the actual patient’s condition. Social isolation measures throughout the SSP have been gradually increasing since early March, an action that helped to slow down the emergence of the new confirmed cases, highlighting the importance of the safe-distancing measures in mitigating the local transmission within and between cities in the SSP.
Intensive COVID-19 testing associated with reduced mortality - an ecological analysis of 108 countries
Authors: Kenyon Chris
Published: May 2020

Background

Intensive screening and testing for COVID-19 could facilitate early detection and isolation of infected persons and thereby control the size of the epidemic. It could also facilitate earlier and more targeted therapy. These factors could plausibly reduce attributable mortality which was the hypothesis tested in this study.

Methods

Linear regression was used to assess the country-level association between COVID-19 attributable mortality per 100 000 inhabitants (mortality/capita) and COVID-19 tests/capita (number of tests/100 000 inhabitants) controlling for the cumulative number of COVID-19 infections/100 000 inhabitants (cases/capita), the age of the epidemic (number of days between first case reported and 8 April), national health expenditure per capita and WHO world region.

Results

The COVID-19 mortality rate varied between 0.3 and 3110 deaths/100 000 inhabitants (median 30, IQR 8–105). The intensity of testing per 100 000 also varied considerably (median 21,970, IQR 2,735–89,095) as did the number of COVID-19 cases per 100 000 (median 1,600, IQR 340–4,760 cases/100 000). In the multivariate model, the COVID-19 mortality rate was negatively associated with tests/capita (Coef. –0.036, 95% CI –0.047- –0.025) and positively associated with cases/capita (Coef. 0.093, 95% CI 0.819- 1.034).

Conclusions

The results are compatible with the hypothesis that intensive testing and isolation could play a role in reducing COVID-10 mortality rates.
Computerized physical and cognitive training improves the functional architecture of the brain in adults with Down Syndrome: a network science EEG study
Authors: Anagnostopoulou Alexandra , Styliadis Charis , Kartsidis Panagiotis , Romanopoulou Evangelia , Zilidou Vasiliki , Karali Chrysi , Karagianni Maria , Klados Manousos , Paraskevopoulos Evangelos , Bamidis Panagiotis D.
Published: May 2020

Understanding the neuroplastic capacity of people with Down Syndrome (PwDS) can potentially reveal the causal relationship between aberrant brain organization and phenotypic characteristics. We used resting-state EEG recordings to identify how a neuroplasticity-triggering training protocol relates to changes in the functional connectivity of the brain’s intrinsic cortical networks. Brain activity of 12 PwDS before and after a ten-week protocol of combined physical and cognitive training was statistically compared to quantify changes in directed functional connectivity in conjunction with psychosomatometric assessments. PwDS showed increased connectivity within the left hemisphere and from left to right hemisphere, as well as increased physical and cognitive performance. Our findings reveal a strong adaptive neuroplastic reorganization as a result of the training that leads to a less-random network with a more pronounced hierarchical organization. Our results go beyond previous findings by indicating a transition to a healthier, more efficient, and flexible network architecture, with improved integration and segregation abilities in the brain of PwDS. Resting-state electrophysiological brain activity is used here for the first time to display meaningful relationships to underlying DS processes and outcomes of importance in a translational inquiry. This trial is registered with ClinicalTrials.gov IdentifierNCT04390321.

Author Summary

The effects of cognitive and physical training on the neuroplasticity attributes of people with and without cognitive impairment have been well documented via neurophysiological evaluations and network science indices. However, there is still insufficient evidence for people with Down Syndrome (PwDS). We investigated the effects of a combinational training protocol on the brain network organization of 12 adult PwDS using EEG and network indices coupled with tests assessing their cognitive and physical capacity. We report evidence of adaptational neuroplastic effects, pointing to a transitional state towards a healthier organization with an increased ability to integrate and segregate information. Our findings underline the ability of the DS brain to respond to the cognitive demands of external stimuli, reflecting the possibility of developing independent-living skills.
Glaucoma home-monitoring using a tablet-based visual field test (Eyecatcher): An assessment of accuracy and adherence over six months
Authors: Jones Pete R. , Campbell Peter , Callaghan Tamsin , Jones Lee , Asfaw Daniel S. , Edgar David F. , Crabb David P.
Published: May 2020

Purpose

To assess accuracy and adherence of visual field (VF) home-monitoring in a pilot sample of glaucoma patients.

Design

Prospective longitudinal observation.

Methods

Twenty adults (median 71 years) with an established diagnosis of glaucoma were issued a tablet-perimeter (Eyecatcher), and were asked to perform one VF home-assessment per eye, per month, for 6 months (12 tests total). Before and after home-monitoring, two VF assessments were performed in-clinic using Standard Automated Perimetry (SAP; 4 tests total, per eye).

Results

All 20 participants could perform monthly home-monitoring, though one participant stopped after 4 months (Adherence: 98%). There was good concordance between VFs measured at home and in the clinic (r = 0.94, P < 0.001). In 21 of 236 tests (9%) Mean Deviation deviated by more than ±3dB from the median. Many of these anomalous tests could be identified by applying machine learning techniques to recordings from the tablets’ front-facing camera (Area Under the ROC Curve = 0.78). Adding home-monitoring data to 2 SAP tests made 6 months apart reduced measurement error (between-test measurement variability) in 97% of eyes, with mean absolute error more than halving in 90% of eyes. Median test duration was 4.5mins (Quartiles: 3.9−5.2mins). Substantial variations in ambient illumination had no observable effect on VF measurements (r = 0.07, P = 0.320).

Conclusions

Home-monitoring of VFs is viable for some patients, and may provide clinically useful data.
Sporadic Oncocytic Tumors with Features Intermediate between Oncocytoma and Chromophobe Renal Cell Carcinoma: Comprehensive Clinico-Pathological and Genomic Profiling
Authors: Liu Yajuan J , Ussakli Cigdem , Antic Tatjana , Liu Yuhua , Wu Yu , True Lawrence , Tretiakova Maria S
Published: May 2020

Background

Morphology, clinical behavior, and genomic profiles of renal oncocytoma (RO) and its malignant counterpart chromophobe renal cell carcinoma (ChRCC) are distinctly different. However, there is a substantial group of sporadic oncocytic tumors with peculiar hybrid phenotypes as well as a perplexing degree of morphologic and immunohistochemical overlap between classic RO and ChRCC with eosinophilic cytoplasm. The aim of this study is to provide detailed characterization of these hybrid tumors.

Design

Thirty eight sporadic oncocytic neoplasms with ambiguous morphology from two institutions were reviewed by 4 pathologists. CKIT positivity was used as a selection criterion. We correlated CK7 and S100A1 immunostaining and detailed morphologic features with cytogenetic profiles. DNA from the FFPE tissues was extracted and analyzed using Cytogenomic Microarray Analysis (CMA) to evaluate copy number alterations and ploidy.

Results

CMA categorized cases into 3 groups: RO (N=21), RO variant (N=7) and ChRCC (N=10). Cytogenetic RO had either no CNA (48%) or loss of chromosome 1p, X or Y (52%). RO-variant had additional chromosomal losses [-9q, –14 (n=2), –13] and chromosomal gains [+1q (n=2), +4, +7 (n=2), +13, +19, +20, and +22]. ChRCC were either hypodiploid with numerous monosomies (40%) or hypotetraploid with multiple relative losses (60%). RO, RO-variant and ChRCC groups differed significantly in tumor architecture (p<0.01), stroma (p=0.013), presence of nuclear wrinkling, perinuclear halos and well-defined cell borders in >5% cells (p<0.01), focal cell clearing (p=0.048) and CK7 expression (p<0.02). Pathologic prediction of cytogenetic subtype using only two categories (benign RO or malignant ChRCC) would overcall or undercall up to 40% of tumors that were ChRCC based on cytogenetics. This finding provides the rationale for an intermediate diagnostic category of so-called hybrid tumors (HOCT). HOCT was a heterogeneous group enriched for cytogenetic RO-variant. Other HOCTs have a profile of either RO or ChRCC.

Conclusions

Genomic profile allows classification of oncocytic tumors with ambiguous morphology into RO, RO-variant and ChRCC. Several architectural and cytologic features combined with CK7 expression are significantly associated with cytogenetic RO, RO-variant or ChRCC tumors. Doubled hypodiploidy by whole genome endoduplication is a common phenomenon in eosinophilic ChRCC.

Parts of this study were presented in an abstract form at the 104th annual meeting of the United Stated and Canadian Academy of Pathology, Boston, March 21–27, 2015
QMRA of SARS-CoV-2 for workers in wastewater treatment plants
Authors: Zaneti Rafael Newton , Girardi Viviane , Spilki Fernando Rosado , Mena Kristina , Westphalen Ana Paula Campos , Colares Evandro Ricardo da Costa , Pozzebon Allan Guedes , Etchepare Ramiro Gonçalves
Published: May 2020

Faecal-oral transmission of SARS-CoV-2 is a hot topic and additional research is needed to elucidate the risks of the novel coronavirus in sanitation systems. This is the first article that investigates the potential health risks of SARS-CoV-2 in sewage to wastewater treatment plants (WWTPs) workers. A quantitative microbial risk assessment (QMRA) is applied for three COVID-19 scenarios (moderate, aggressive and extreme) to study the effect of different stages of the pandemic, in terms of percentage of infected population, on the probability of infection. Results reveal that estimates of viral loads in sewage at the entrance of WWTPs ranged from 1.03×102 to 1.31×104 GC.mL−1 (0.1 to 13.06 PFU.mL−1, respectively) and that estimated risks for the aggressive and extreme scenarios (6.5×10−3 and 3.1×10−2, respectively) were likely to be above a WHO benchmark of tolerable risk used for virus infection of 10−3 and higher than the risk of infection of E. coli, used herein as common pathogen indicator for a relative comparison, thus reinforcing the concern of sewage systems as a transmission pathway of SARS-CoV-2. These findings are helpful as an early-warning tool and in prioritizing upcoming risk management strategies in the sanitation sector during COVID-19 pandemic.
Efficacy and safety of interferon beta-1a in treatment of severe COVID-19: A randomized clinical trial
Authors: Davoudi-Monfared Effat , Rahmani Hamid , Khalili Hossein , Hajiabdolbaghi Mahboubeh , Salehi Mohamadreza , Abbasian Ladan , Kazemzadeh Hossein , Yekaninejad Mir Saeed
Published: May 2020

Objectives: To the best of our knowledge, there is no published study regarding use of IFN beta-1a in the treatment of severe COVID-19. In this randomized clinical trial efficacy and safety of IFN β-1a has been evaluated in patients with severe COVID-19.
Methods: Forty-two patients in the interferon group received IFN beta-1a in addition to the standard of care. Each 44 micrograms/ml (12 million IU/ml) of interferon beta-1a was subcutaneously injected three times weekly for two consecutive weeks. The control group received only the standard of care. Primary outcome of study was time to reach clinical response. Secondary outcomes duration of hospital stay, length of ICU stay, 28-day mortality, effect of early or late administration of IFN on mortality, adverse effects and complications during the hospitalization.
Results: As primary outcome, time to the clinical response was not significantly different between the IFN and the control groups (9.7 +/- 5.8 vs. 8.3 +/- 4.9 days respectively, P=0.95). On day 14, 66.7% vs. 43.6% of patients in the IFN group and the control group were discharged, respectively (OR= 2.5; 95% CI: 1.05- 6.37). The 28-day overall mortality was significantly lower in the IFN then the control group (19% vs. 43.6% respectively, p= 0.015). Early administration significantly reduced mortality (OR=13.5; 95% CI: 1.5-118).
Conclusion: Although did not change time to reach the clinical response, adding to the standard of care significantly increased discharge rate on day 14 and decreased 28-day mortality.
Clinical Trial Registration ID #IRCT20100228003449N28.
Information theoretics for the machine learning detection of functionally conserved and coordinated protein motions
Authors: Babbitt Gregory A.
Published: May 2020

Traditional information theoretic analysis of functionally conserved binding interactions described by multiple sequence alignments are unable to provide direct insights into the underlying strength, spatial distribution, and coordination of the biophysical motions that govern protein binding interactions during signaling and regulatory function. However, molecular dynamic (MD) simulations of proteins in bound vs. unbound conformational states can allow for the combined application of machine learning classification and information theory towards many problems posed by comparative protein dynamics. After both bound and unbound protein dynamic states are adequately sampled in MD software, they can be employed as a comparative training set for a binary classifier capable of discerning the complex dynamical consequences of protein binding interactions with DNA or other proteins. The statistical validation of the learner on MD simulations of homologs can be used to assess its ability to recognize functional protein motions that are conserved over evolutionary time scales. Regions of proteins with functionally conserved dynamics are identifiable by their ability to induce significant correlations in local learning performance across homologous MD simulations. Through case studies of Rbp subunit 4/7 interaction in RNA Pol II and DNA-protein interactions of TATA binding protein, we demonstrate this method of detecting functionally conserved protein dynamics. We also demonstrate how the concepts of relative entropy (i.e. information gain) and mutual information applied to the binary classification states of MD simulations can be used to compare the impacts of molecular variation on conserved dynamics and to identify coordinated motions involved in dynamic interactions across sites.