bluuebunny/crossref_metadata_2025 huggingface dataset:
Early risk assessment for COVID-19 patients from emergency department data using machine learning
Authors: Heldt Frank Stefan , Vizcaychipi Marcela P , Peacock Sophie , Cinelli Mattia , McLachlan Lachlan , Andreotti Fernando , Jovanovic Stojan , Durichen Robert , Lipunova Nadezda , Fletcher Robert A , Hancock Anne , McCarthy Alex , Pointon Richard A , Brown Alexander , Eaton James , Liddi Roberto , Mackillop Lucy , Tarassenko Lionel , Khan Rabia Tahir
Published: May 2020

Background
Since its emergence in late 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic, with more than 4.8 million reported cases and 310 000 deaths worldwide. While epidemiological and clinical characteristics of COVID-19 have been reported, risk factors underlying the transition from mild to severe disease among patients remain poorly understood.

Methods
In this retrospective study, we analysed data of 820 confirmed COVID-19 positive patients admitted to a two-site NHS Trust hospital in London, England, between January 1st and April 23rd, 2020, with a majority of cases occurring in March and April. We extracted anonymised demographic data, physiological clinical variables and laboratory results from electronic healthcare records (EHR) and applied multivariate logistic regression, random forest and extreme gradient boosted trees. To evaluate the potential for early risk assessment, we used data available during patients' initial presentation at the emergency department (ED) to predict deterioration to one of three clinical endpoints in the remainder of the hospital stay: A) admission to intensive care, B) need for mechanical ventilation and C) mortality. Based on the trained models, we extracted the most informative clinical features in determining these patient trajectories.

Results
Considering our inclusion criteria, we have identified 126 of 820 (15%) patients that required intensive care, 62 of 808 (8%) patients needing mechanical ventilation, and 170 of 630 (27%) cases of in-hospital mortality. Our models learned successfully from early clinical data and predicted clinical endpoints with high accuracy, the best model achieving AUC-ROC scores of 0.75 to 0.83 (F1 scores of 0.41 to 0.56). Younger patient age was associated with an increased risk of receiving intensive care and ventilation, but lower risk of mortality. Clinical indicators of a patient's oxygen supply and selected laboratory results were most predictive of COVID-19 patient trajectories.

Conclusion
Among COVID-19 patients machine learning can aid in the early identification of those with a poor prognosis, using EHR data collected during a patient's first presentation at ED. Patient age and measures of oxygenation status during ED stay are primary indicators of poor patient outcomes.
Neural Network Predicts Need for Red Blood Cell Transfusion for Patients with Acute Gastrointestinal Bleeding Admitted to the Intensive Care Unit
Authors: Shung Dennis , Castro Egbert , Huang Jessie , Tay J. Kenneth , Simonov Michael , Laine Loren , Krishnaswamy Smita
Published: May 2020

Structured Summary

Background

Acute gastrointestinal bleeding is the most common gastrointestinal cause for hospitalization. For high risk patients requiring intensive care unit stay, predicting transfusion needs during the first 24 hours using dynamic risk assessment may improve resuscitation.

Aims

Provide dynamic risk prediction for red blood cell transfusion in admitted patients with severe acute gastrointestinal bleeding.

Methods

A patient cohort admitted for acute gastrointestinal bleeding (N = 2,524) was identified from the Medical Information Mart for Intensive Care III (MIMIC-III) critical care database, separated into training (N = 2,032) and validation (N = 492) sets. 74 demographic, clinical, and laboratory test features were consolidated into 4-hour time intervals over the first 24 hours from admission. The outcome measure was the transfusion of red blood cells during each 4-hour time interval. A long short-term memory (LSTM) model, a type of Recurrent Neural Network (RNN), was compared to the Glasgow-Blatchford Score (GBS).

Results

The LSTM model performed better than GBS overall (AUROC 0.81 vs 0.63;P<0.001)and at each 4-hour interval (P<0.01). At high sensitivity and high specificity cutoffs, the LSTM model outperformed GBS (P<0.001). The LSTM model performed better in patients directly admitted from the ED to ICU (0.82 vs 0.63;P<0.001), upper GIB (0.84 vs 0.68;P<0.001), lower GIB (0.77 vs 0.58;P<0.001), and unspecified GIB (0.85 vs 0.64;P<0.001).

Conclusions

A LSTM model can be used to predict the need for transfusion of packed red blood cells over the first 24 hours from admission to help personalize the care of high-risk patients with acute gastrointestinal bleeding.

Data Access

All clinical data from MIMIC-III was approved under the oversight of the Institutional Review Boards of Beth Israel Deaconess Medical Center (Boston, MA) and the Massachusetts Institute of Technology (Cambridge, MA). Requirement for individual patient consent was waived because the project did not impact clinical care and all protected health information was deidentified. The data was available on PhysioNet were derived from protected health information that has been de-identified and not subject to HIPAA Privacy Rule restrictions. All use of the data was performed with credentialed access under the oversight of the data use agreement through PhysioNet and the Massachusetts Institute of Technology.
Early antibody response to SARS-CoV-2
Authors: Dittadi Ruggero , Afshar Haleh , Carraro Paolo
Published: May 2020

Background. The role and significance of the immune response to SARS-CoV-2 infection is not yet well known.
Methods. We therefore conducted a study on 46 symptomatic subjects with disease ascertained by laboratory tests to evaluate the presence of IgG and IgM antibodies in these subjects in relation to the time elapsed since the onset of symptoms. The analytical performance of the method used in the study (Maglumi 800, SNIBE, China) and the effect of two different serum and plasma matrices were also assessed.
Results. IgG positivity was demonstrated in 100% of cases 15 days after the onset of the disease. IgM show lower concentrations and do not exceed 77% of cases after 15 days. The analytical performance of the method used was confirmed to be good in terms of imprecision, linearity, commutability in two blood sample matrices.
Conclusion. The serological study through the search for specific IgG for SARS-CoV-2 results in our case series is sensitive and suitable for population research and can also play a role in diagnosis. The diagnostic performance of specific IgMs are lower.
Dreaming during Covid-19 pandemic: Computational assessment of dreams reveals mental suffering and fear of contagion
Authors: Mota Natalia B , Weissheimer Janaina , Ribeiro Marina , De Paiva Mizziara , D'Avila Juliana , Simabucuru Gabriela , Chaves Monica F , Cecchi Lucas , Cirne Jaime , Cecchi Guillermo , Rodrigues Cilene , Copelli Mauro , Ribeiro Sidarta
Published: May 2020

Neuroscience and psychology agree that dreaming helps to cope with negative emotions and learn from experience. The current global threat related to the COVID-19 pandemic led to widespread social isolation. Does dreaming change and/or reflect mental suffering? To address these questions, we applied natural language processing tools to study 239 dream reports from 67 individuals either before the Covid-19 outbreak or during March-April, 2020, when quarantine was imposed in Brazil following the pandemic announcement by the WHO. Pandemic dreams showed a higher proportion of anger and sadness words and higher average semantic similarities to the terms contamination and cleanness. These features were associated with mental suffering related to social isolation, as they explained 39% of the variance in PANSS negative subscale (p=0.0092). These results corroborate the hypothesis that pandemic dreams reflect mental suffering, fear of contagion, and important changes in daily habits.
High-Resolution Metabolic Mapping of the Cerebellum Using a Zoomed Magnetic Resonance Spectroscopic Imaging
Authors: Emir Uzay E. , Sood Jaiyta , Chiew Mark , Thomas Albert , Lane Sean P.
Published: May 2020

Purpose

The human cerebellum plays an important role in functional activity cerebrum which is ranging from motor to cognitive activities since due to its relaying role between spinal cord and cerebrum. The cerebellum poses many challenges to magnetic resonance spectroscopic imaging (MRSI) due to the caudal location, the susceptibility to physiological artifacts and partial volume artifact due to its complex anatomical structure. Thus, in present study, we propose a high-resolution MRSI acquisition scheme for the cerebellum.

Methods

A zoomed or reduced-field of view (rFOV) metabolite-cycled full-intensity magnetic resonance spectroscopic imaging (MRSI) at 3T with a nominal resolution of 62.5 μL was developed. Single-slice rFOV MRSI data were acquired from the cerebellum of 5 healthy subjects with a nominal resolution of 2.5□×□2.5□mm2 in 9□minutes 36. Spectra were quantified with LCModel. A spatially unbiased atlas template of the cerebellum was used for analyzing metabolite distributions in the cerebellum.

Results

The high quality of the achieved spectra enabled to generate a high-resolution metabolic map of total N-acetylaspartate, total creatine, total choline, glutamate+glutamine and myo-inositol with Cramér-Rao lower bounds below 50%. A spatially unbiased atlas template of the cerebellum-based region of interest (ROIs) analysis resulted in spatially dependent metabolite distributions in 9 ROIs. The group-averaging across subjects in the Montreal Neurological Institute-152 template space allowed to generate a very high-resolution metabolite maps in the cerebellum.

Conclusion

These findings indicate that very high-resolution metabolite probing of cerebellum is feasible using rFOV or zoomed MRSI at 3T.
Split-ends is modulating lipid droplet content in adultDrosophilaglial cells and is protective against paraquat toxicity
Authors: Girard Victor , Goubard Valérie , Querenet Matthieu , Seugnet Laurent , Pays Laurent , Nataf Serge , Dufourd Eloïse , Cluet David , Mollereau Bertrand , Davoust Nathalie
Published: May 2020

Glial cells are early sensors of neuronal injury and are able to store lipids in lipid droplets under oxidative stress conditions. Here, we investigated the glial functions of Spen in the context of Parkinson’s disease (PD). Using a data mining approach, we first found that the human ortholog ofspen,SPEN/SHARPbelongs to the set of astrocyte-expressed genes which mRNA levels are significantly different in thesubstantia nigraof PD patients as compared to controls. Interestingly, the retrieved list of differentially expressed genes was enriched in genes involved in lipid metabolism. In aDrosophilamodel of PD, we observed thatspenmutant flies were more sensitive to paraquat intoxication. Moreover, the glia-restricted knockdown ofspenled to the expansion and the accumulation of lipid droplets as well as the inhibition of Notch pathway. Taken together our results show that Spen regulates lipid metabolism and storage in glial cells and by these means contribute to glia-mediated functions in the context of neurodegeneration.
Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane
Authors: Woo Hyeonuk , Park Sang-Jun , Choi Yeol Kyo , Park Taeyong , Tanveer Maham , Cao Yiwei , Kern Nathan R. , Lee Jumin , Yeom Min Sun , Croll Tristan I. , Seok Chaok , Im Wonpil
Published: May 2020

This technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB:6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling suite. Then, using the recently-determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully-glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19), so researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.
Adenosine triphosphate Binding Cassette subfamily C member 1 (ABCC1) overexpression reduces APP processing and increases alpha- versus beta-secretase activity,in vitro
Authors: Jepsen Wayne M. , De Both Matthew , Siniard Ashley L. , Ramsey Keri , Piras Ignazio S. , Naymik Marcus , Henderson Adrienne , Huentelman Matthew J.
Published: May 2020

The organic anion transporter Adenosine triphosphate Binding Cassette subfamily C member 1 (ABCC1), also known asMRP1, has been demonstrated in murine models of Alzheimer’s disease (AD) to export amyloid beta (Abeta) from the endothelial cells of the blood-brain barrier to the periphery, and that pharmaceutical activation of ABCC1 can reduce amyloid plaque deposition in the brain. Here, we show that ABCC1 is not only capable of exporting Abeta from the cytoplasm of human cells, but also that it’s overexpression significantly reduces Abeta production and increases the ratio of alpha- versus beta-secretase mediated cleavage of the Amyloid Precursor Protein (APP), likely via indirect modulation of alpha-, beta-, and gamma-secretase activity.
SugarQuant: a streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics
Authors: Fang Pan , Ji Yanlong , Silbern Ivan , Doebele Carmen , Ninov Momchil , Lenz Christof , Oellerich Thomas , Pan Kuan-Ting , Urlaub Henning
Published: May 2020

Site-specific regulation of protein N-glycosylation is essential in human cells. However, accurate quantification of glycosylation sites and their individual glycan moieties in a cell-wide manner is still technically challenging. Here, we introduce SugarQuant, an integrated mass spectrometry-based pipeline comprising fast protein aggregation capture (PAC)-based sample preparation, optimized multi-notch MS3 LC-MS acquisition (Glyco-SPS-MS3) and a data-processing tool (GlycoBinder) that allows for confident, global identification and quantification of intact glycopeptides in complex biological samples. PAC greatly reduces the overall samplehandling time without compromising sensitivity. Glyco-SPS-MS3 combines high-resolution MS2 and MS3 scans, resulting in enhanced reporter signals of isobaric mass tags, improved detection of N-glycopeptide fragments, and significantly lowered interference in multiplexed quantification. GlycoBinder enables streamlined processing of Glyco-SPS-MS3 data, followed by a two-step database search which increases the identification rates of intact glycopeptides by up to 22% when compared with one-step database search strategies. SugarQuant was applied to identify and quantify more than 5,000 unique glycoforms in Burkitt’s lymphoma cells, and determined complex site-specific glycosylation changes that occurred upon inhibition of fucosylation at high confidence.
Exploring the Sequence Fitness Landscape of a Bridge Between Protein Folds
Authors: Tian Pengfei , Best Robert B.
Published: May 2020

Most foldable protein sequences adopt only a single native fold. Recent protein design studies have, however, created protein sequences which fold into different structures apon changes of environment, or single point mutation, the best characterized example being the switch between the folds of the GA and GB binding domains of streptococcal protein G. To obtain further insight into the design of sequences which can switch folds, we have used a computational model for the fitness landscape of a single fold, built from the observed sequence variation of protein homologues. We have recently shown that such coevolutionary models can be used to design novel foldable sequences. By appropriately combining two of these models to describe the joint fitness landscape of GA and GB, we are able to describe the propensity of a given sequence for each of the two folds. We have successfully tested the combined model against the known series of designed GA/GB hybrids. Using Monte Carlo simulations on this landscape, we are able to identify pathways of mutations connecting the two folds. In the absence of a requirement for domain stability, the most frequent paths go via sequences in which neither domain is stably folded, reminiscent of the propensity for certain intrinsically disordered proteins to fold into different structures according to context. Even if the folded state is required to be stable, we find that there is nonetheless still a wide range of sequences which are close to the transition region and therefore likely fold switches, consistent with recent estimates that fold switching may be more widespread than had been thought.

Author Summary

While most proteins self-assemble (or “fold”) to a unique three-dimensional structure, a few have been identified that can fold into two distinct structures. These so-called “metamorphic” proteins that can switch folds have attracted a lot of recent interest, and it has been suggested that they may be much more widespread than currently appreciated. We have developed a computational model that captures the propensity of a given protein sequence to fold into either one of two specific structures (GA and GB), in order to investigate which sequences are able to fold to both GA and GB (“switch sequences”), versus just one of them. Our model predicts that there is a large number of switch sequences that could fold into both structures, but also that the most likely such sequences are those for which the folded structures have low stability, in agreement with available experimental data. This also suggests that intrinsically disordered proteins which can fold into different structures on binding may provide an evolutionary path in sequence space between protein folds.
Spatial organization of transcribed eukaryotic genes
Authors: Leidescher Susanne , Ribisel Johannes , Ullrich Simon , Feodorova Yana , Hildebrand Erica , Bultmann Sebastian , Link Stephanie , Thanisch Katharina , Mulholland Christopher , Dekker Job , Leonhardt Heinrich , Mirny Leonid , Solovei Irina
Published: May 2020

Despite the well-established role of nuclear organization in gene expression regulation, little is known about the reverse: how transcription shapes the spatial organization of the genome. Owing to small sizes of most previously studied genes and the limited resolution of microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here, we make use of several long highly expressed genes and demonstrate that they form transcription loops with polymerases moving along the loops and carrying nascent RNAs. Transcription loops can span across microns resembling lampbrush loops and polytene puffs. Extension and shape of transcription loops suggest their intrinsic stiffness, which we attribute to decoration with multiple voluminous nascent RNPs. Our data contradict the model of transcription factories and indicate that although microscopically resolvable transcription loops are specific for long highly expressed genes, the mechanisms underlying their formation can represent a general aspect of eukaryotic transcription.
Selective inhibition of human translation by a drug-like compound that traps terminated protein nascent chains on the ribosome
Authors: Li Wenfei , Chang Stacey Tsai-Lan , Ward Fred. R , Cate Jamie H. D.
Published: May 2020

Methods to directly inhibit gene expression using small molecules hold promise for the development of new therapeutics targeting proteins that have evaded previous attempts at drug discovery. Among these, small molecules including the drug-like compound PF-06446846 (PF846) selectively inhibit the synthesis of specific proteins, by stalling translation elongation1–4. These molecules also inhibit translation termination4by an unknown mechanism. Using cryo-electron microscopy (cryo-EM) and biochemical approaches, we show that PF846 arrests translation at the stop codon by slowing hydrolysis of the protein nascent chain (NC) from peptidyl-site (P-site) tRNA by eukaryotic release factor 1 (eRF1). After NC hydrolysis from the P-site tRNA, PF846 traps the NC in the ribosome exit tunnel in a compact α-helical conformation that induces 28S rRNA nucleotide rearrangements propagating back to the ribosome peptidyl transferase center (PTC). Mutational analyses and human cell-based experiments elucidate the pivotal amino acids of the NC required for PF846-dependent termination arrest, all of which face the PF846 side of the ribosome exit tunnel. The structural and functional data support a model in which PF846 inhibits translation termination by inducing allosteric conformational rearrangements in the NC and PTC that suppress peptidyl-tRNA hydrolysis promoted by eRF1, and trap the NC in the ribosome exit tunnel. This unprecedented mechanism of action reveals new principles of translation termination and lays the foundation for new therapeutic strategies.
Reverse Pneumatic Artificial Muscles for Application in Low-Cost Artificial Respirators
Authors: Mirvakili Seyed M , Sim Douglas , Langer Robert
Published: May 2020

One of the main challenges associated with mechanical ventilators is their limited availability in pandemics and other emergencies. Therefore, there is a great demand for mechanical ventilators to address this issue. In this work, we propose a low-cost, portable, yet high-performance design for a volume-controlled mechanical ventilator. We are employing pneumatic artificial muscles, such as air cylinders, in the reverse mode of operation to achieve mechanical ventilation. The current design of the device can operate in two modes: controlled mode and assisted mode. Unlike most ICU ventilators, our device does not need a high-pressure air pipeline to operate. With the current design, mechanical ventilation for respiration rate ranging from 10 b/min to 30 b/min with a tidal volume range of 150 mL to 1000 mL and I:E ratio of 1:1 to 1:5 can be performed. We achieved a total cost of less $400 USD to make one device. We estimate the device to cost less than $250 USD when produced in larger volumes.
Travelling spindles create necessary conditions for spike-timing-dependent plasticity in humans
Authors: Dickey Charles W. , Sargsyan Anna , Madsen Joseph R. , Eskandar Emad N. , Cash Sydney S. , Halgren Eric
Published: May 2020

Sleep spindles facilitate memory consolidation in the cortex during mammalian non-rapid eye movement (NREM) sleep. In rodents, phase-locked firing during spindles may facilitate spike-timing-dependent plasticity (STDP) by grouping pre- and post-synaptic cell firing within ∼25ms. Currently, microphysiological evidence in humans for conditions conducive for STDP during spindles is absent. We analyzed local field potentials and supragranular unit spiking during spindles from 10×10 arrays of microelectrodes at 400µm pitch in humans. We found strong tonic and phase-locked increases in firing and co-firing within 25ms during spindles. Co-firing, spindle co-occurrence, and spindle coherence were greatest between sites within ∼2mm, and high co-firing of units on different electrodes was largely restricted to moments of high spindle coherence between those electrodes. Spindles propagated at ∼0.23m/s in distinct patterns, with correlated cell co-firing sequences. These results suggest that spindles may organize spatiotemporal patterns of neuronal co-firing which promote memory consolidation during NREM sleep.
Controlling for background genetic effects using polygenic scores improves the power of genome-wide association studies
Authors: Bennett Declan , O’Shea Donal , Ferguson John , Morris Derek , Seoighe Cathal
Published: May 2020

Ongoing increases in the size of human genotype and phenotype collections offer the promise of improved understanding of the genetics of complex diseases. In addition to the biological insights that can be gained from the nature of the variants that contribute to the genetic component of complex trait variability, these data bring forward the prospect of predicting complex traits and the risk of complex genetic diseases from genotype data. Here we show that advances in phenotype prediction can be applied to improve the power of genome-wide association studies. We demonstrate a simple and efficient method to model genetic background effects using polygenic scores derived from SNPs that are not on the same chromosome as the target SNP. Using simulated and real data we found that this can result in a substantial increase in the number of variants passing genome-wide significance thresholds. This increase in power to detect trait-associated variants also translates into an increase in the accuracy with which the resulting polygenic score predicts the phenotype from genotype data. Our results suggest that advances in methods for phenotype prediction can be exploited to improve the control of background genetic effects, leading to more accurate GWAS results and further improvements in phenotype prediction.
3D bioprinting of high cell-density heterogeneous tissue models through spheroid fusion within self-healing hydrogels
Authors: Daly Andrew C. , Davidson Matthew D. , Burdick Jason A.
Published: May 2020

Cellular models are needed to study human development and diseasein vitro, including the screening of drugs for toxicity and efficacy. However, current approaches are limited in the engineering of functional tissue models with requisite cell densities and heterogeneity to appropriately model cell and tissue behaviors. Here, we develop a new bioprinting approach to transfer spheroids into self-healing support hydrogels at high resolution, which enables their patterning and fusion into high-cell density microtissues of prescribed spatial organization. As an example application, we bioprint induced pluripotent stem cell-derived cardiac microtissue models with spatially controlled cardiomyocyte and fibroblast cell ratios to replicate the structural and functional features of scarred cardiac tissue that arise following myocardial infarction, including reduced contractility and irregular electrical activity. The bioprintedin vitromodel is combined with functional readouts to probe how various pro-regenerative microRNA treatment regimes influence tissue regeneration and recovery of function as a result of cardiomyocyte proliferation. This method is useful for a range of biomedical applications, including the development of precision models to mimic diseases and for the screening of drugs, particularly where high cell densities and heterogeneity are important.
Electron microscopic observation of infected CCB and whole genome analysis of Koi herpesvirus isolate GY01
Authors: Duan Hongan , Xu Ye , Zhou Yi , Wang Fengzhi , Ding Chao , Cao Jie
Published: May 2020

Background

Cyprinid herpesvirus-3 (CyHV-3), commonly known as Koi herpesvirus (KHV) can induce infectious and acute viremia in common/koi carp (Cyprinus carpio). In an earlier study in this laboratory a KHV isolate GY1506 (KHV GY01 in GeneBank) was isolated from diseased common carp, replicated on CCB cells and identified by PCR targeted on and phylogenetic analysis of thymidine kinase (TK) gene. Electron microscopy examination of GY01 infected CCB cell line and whole genome analysis was studied for further characteristics and epidemiological features of this strain.

Results

Electron microscopy examination of CCB infected with KHV GY01 strain revealed destruct of infected cells including incomplete nuclear membranes, deformed nucleus, marginalized nuclear chromosome, and the virus of different development stages and morphologies in the cytoplasm and nucleus, which resembles the herpesvirus. MEGA X and phyML were used for multiple alignment and phylogenetic analysis of whole genomes of GY01 and other 21 KHV strains available in GeneBank. analysis showed that GY01 was more close to E and KHV-I and was predicted it originated from the same ancestor as the E and KHV-I. Pairwise alignment of strain GY01 and strain E by Geneious software and YASS online version revealed that two strains had high identity(99.1%) at the nucleotide sequence level although variations and disagreement existed. The number and structure arrangement of open reading frames (orfs) or protein-encoding genes of GY01 is very similar to KHV E, and also to KHV-U but different from KHV-I. The characteristics and function of each orf need further study in the future.

Conclusions

Pathogenic changes of infected CCB cells and morphologies of KHV GY01 resembles the herpesvirus. Pairwise, multiple alignment and phylogenetic analysis of whole genomes of GY01 and other 21 KHV strains available in GeneBank demonstrated that the GY01 is closely related to strain KHV E and KHV-I and suggested it originated from the same ancestor as the E and KHV-I.
Viscoelasticity of single macromolecules using Atomic Force Microscopy
Authors: Rajput Shatruhan Singh , Deopa Surya Pratap S , Yadav Jyoti , Ahlawat Vikhyaat , Talele Saurabh , Patil Shivprasad
Published: May 2020

We measured viscoelasticity of single protein molecules using two types of Atomic Force Microscopes (AFM) which employ different detection schemes to measure the cantilever response. We used a commonly available deflection detection scheme in commercial AFMs which measures cantilever bending and a fibre-interferometer based home-built AFM which measures cantilever displacement. For both methods, the dissipation coefficient of a single macromolecule is immeasurably low. The upper bound on the dissipation coefficient is 5 × 10−7kg/s whereas the entropic stiffness of single unfolded domains of protein measured using both methods is in the range of 10 mN/m. We show that in a conventional deflection detection measurement, the phase of bending signal can be a primary source of artefacts in the dissipation estimates. It is recognized that the measurement of cantilever displacement, which does not have phase lag due to hydrodynamics of the cantilever, is better suited for ensuring artefact-free measurement of viscoelasticty compared to the measurement of the cantilever bending. We confirmed that the dissipation coefficient in single macromolecules is below the detection limit of AFM by measuring dissipation in water layers confined between the tip and the substrate using similar experimental parameters. Further, we experimentally determined the limits in which the simple point-mass approximation of the cantilever works in off-resonance operation.

Significance Statement

Single Macromolecules, including unfolded proteins bear rubber-like entropic elasticity and internal friction characterized by finite dissipation coefficient. Direct measurement of this viscoelastic response is important since it plays a significant role, both in polymer physics as well as protein folding dynamics. The viscoelastic response of single polymer chain is difficult and prone to artefacts owing to the complications of hydrodynamics of macroscopic probe itself in the liquid environment. Using a special atomic force microscope, which allows quantitative estimate of viscoelasticity in liquid environments, we measured viscoelastic response of single molecule of Titin. We report here that the dissipation coefficient is below the detection limit of our experiments - with upper bound which is less than reported values in the literature.
Bioinformatic analysis based genome-wide identification, characterization, diversification and regulatory transcription components of RNA silencing machinery genes in wheat (Triticum aestivumL.)
Authors: Akond Zobaer , Rahman Hafizur , Ahsan Md. Asif , Mosharaf Md. Parvez , Alam Munirul , Mollah Md. Nurul Haque
Published: May 2020

Dicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) gene families are known as RNA silencing machinery genes or RNAi genes. They have important activities at post-transcriptional and chromatin modification levels. They regulate gene expression relating to different stresses, growth, and development in eukaryotes. A complete cycle of gene silencing is occurred by the collaboration of these three families. However, these gene families are not yet rigorously studied in the economically important wheat genome. Our bioinformatic analysis based genome-wide identification, characterization, diversification and regulatory components of these gene families identified 7 TaDCL, 39 TaAGO and 16 TaRDR genes from wheat genome against RNAi genes ofArabidopsis thaliana. Phylogenetic analysis of wheat genome withArabidopsisand rice RNAi genes showed that TaDCL, TaAGO and TaRDR proteins are clustered into four, eight and four subgroups respectively. Domain, motif and exon-intron structure analyses showed that the TaDCL, TaAGO and TaRDR proteins conserve identical characteristics within groups while retain diverse differences between groups. GO annotations implied that a number of biological and molecular pathways are linked to RNAi mechanism in wheat. Gene networking between transcription factors and RNAi proteins indicates that ERF is the leading family linked to maximum RNAi genes followed by MIKC-MADS, C2H2, BBR-BPC, MYB, and Dof.Cis-regulatory elements associated to RNAi genes are predicted to act as regulatory components against various environmental conditions. Expressed sequence tag analysis showed that larger numbers of RNAi genes are expressed in different tissues and organs predicted to play roles for healthy plants and grains. Expression analysis of 7 TaDCL genes using qRT-PCR showed that only TaDCL3a and TaDCL3b had root specific significant expression (p-value<0.05) with no expression in leaf validated EST results. Besides, TaDCL3b and TaDCL4 significantly prompted in drought condition indicating their potential role in drought stress tolerance. Overall results would however help researchers for in-depth biological investigation of these RNAi genes in wheat crop improvement.
Laminin N-terminus α31 protein distribution in adult human tissues
Authors: Troughton Lee D. , Reuten Raphael , Sugden Conor J. , Hamill Kevin J.
Published: May 2020

Laminin N terminus α31 (LaNt α31) is a netrin-like protein derived from alternative splicing of the laminin α3 gene. Although LaNt α31 has been demonstrated to influence corneal and skin epithelial cell function, its expression has not been investigated beyond these tissues. In this study, we used immunohistochemistry to characterise the distribution of this protein in a wide-array of human tissue sections in comparison to laminin α3. These data revealed widespread LaNt α31 expression. In epithelial tissue, LaNt α31 was present in the basal layer of the epidermis, throughout the epithelium of the digestive tract, and much of the epithelium of the reproductive system. LaNt α31 was also found throughout the vasculature of most tissues, with enrichment in reticular-like fibres in the extracellular matrix surrounding large vessels. A similar matrix pattern was observed around the terminal ducts in the breast and around the alveolar epithelium in the lung, where basement membrane staining was also evident. Specific enrichment of LaNt α31 was identified in sub-populations of cells of the kidney, liver, pancreas, and spleen, with variations in intensity between different cell types in the collecting ducts and glomeruli of the kidney being of particular note. Intriguingly, LaNt α31 immunoreactivity was also evident in neurons of the central nervous system, in the cerebellum, cerebral cortex, and spinal cord. Together these findings suggest that LaNt α31 may be functionally relevant in a wider range of tissue contexts than previously thought, and provides a valuable basis for investigation into this interesting protein.
Multiple stressors in multiple species: effects of different RDX soil concentrations and differential water-resourcing on RDX fate, plant health, and plant survival
Authors: Lance Richard F. , Butler Afrachanna D. , Jung Carina M. , Lindsay Denise L.
Published: May 2020

Response to simultaneous stressors is an important facet of plant ecology and land management. In a greenhouse trial, we studied how eight plant species responded to single and combined effects of three RDX soil concentrations and two levels of water-resourcing. In an outdoor trial, we studied the effects of high RDX soil concentration and two levels of water-resourcing in three plant species. Multiple endpoints related to RDX fate, plant health, and plant survival were evaluated in both trials. Starting RDX concentration was the most frequent factor influencing all endpoints. Water-resourcing also had significant impacts, but in fewer cases. For most endpoints, significant interaction effects between RDX concentration and water-resourcing were observed for some species and treatments. Main and interaction effects were typically variable (significant in one treatment, but not in another; associated with increasing endpoint values for one treatment and/or with decreasing endpoint values in another). This complexity has implications for understanding how RDX and water-availability combine to impact plants, as well as for applications like phytoremediation. Two plant species native to the southeastern United States,Ruellia caroliniensis and Salvia coccinea, exhibited treatment responses that suggest they may be useful for phytoremediation, even within complex and changing environments.
Too attractive to self: How pollinators can interfere with the evolution of selfing
Authors: Spigler RB , Smith-Ramesh LM , Kalisz S
Published: May 2020

Pollinators are widely invoked to explain the evolution of selfing despite genetic conditions favoring outcrossing. But their role in maintaining outcrossing despite genetic conditions favoring selfing remains unexplored. We use consumer-resource models to explicitly consider the how the plant-pollinator mutualism can constrain the evolution of selfing. We model outcrossing as a function of attractiveness and account for the cost of attractiveness as a saturating, linear, or exponential function alongside the costs of selfing: inbreeding depression and pollen discounting. We show specific, clear combinations of ecological and genetic conditions where pure selfing can invade a resident population of partial selfers. Complete selfing can evolve in the face of pollen discounting so long as there is a cost to pollinator attraction and reward. However, we also predict conditions under which mixed mating is maintained even when inbreeding depression is low. Our model highlights how under some scenarios mixed mating represents the worst of both worlds, leaving plants to pay the costs of both inbreeding depression and attraction and even leading to extinction. By linking pollinator attraction to the selfing rate, our models provide a likely common mechanism to explain pollen discounting and an alternative evolutionary pathway to the selfing syndrome.
SSRIs modulate asymmetric learning from reward and punishment
Authors: Michely Jochen , Eldar Eran , Erdman Alon , Martin Ingrid M. , Dolan Raymond J.
Published: May 2020

Human instrumental learning is driven by a history of outcome success and failure. We demonstrate that week-long treatment with a serotonergic antidepressant modulates a valence-dependent asymmetry in learning from reinforcement. In particular, we show that prolonged boosting of central serotonin reduces reward learning, and enhances punishment learning. This treatment induced learning asymmetry can result in lowered positive and enhanced negative expectations. A consequential effect is more rewarding, and less disappointing, experiences and this may, in part, explain the slow temporal evolution of serotonin’s well-established antidepressant effects.
ABHD17 enzymes regulate dynamic plasma membrane palmitoylation and N-Ras-dependent cancer growth
Authors: Remsberg Jarrett R. , Suciu Radu M. , Zambetti Noemi A. , Hanigan Thomas W. , Firestone Ari J. , Inguva Anagha , Long Amy , Ngo Nhi , Lum Kenneth M. , Henry Cassandra L. , Richardson Stewart K. , Predovic Marina , Huang Ben , Howell Amy R. , Niphakis Micah J. , Shannon Kevin , Cravatt Benjamin F.
Published: May 2020

A subset of Ras proteins, including N-Ras, depend on a palmitoylation/depalmitoylation cycle to regulate their subcellular trafficking and oncogenicity. General lipase inhibitors such as Palmostatin M block N-Ras depalmitoylation, but lack specificity and target several enzymes displaying depalmitoylase activity. Here, we describe ABD957, a potent and selective covalent inhibitor of the ABHD17 family of depalmitoylases, and show that this compound impairs N-Ras depalmitoylation in human acute myeloid leukemia (AML) cells. ABD957 produced partial effects on N-Ras palmitoylation compared to Palmostatin M, but was much more selective across the proteome, reflecting a plasma membrane-delineated action on dynamically palmitoylated proteins. Finally, ABD957 impaired N-Ras signaling and the growth ofNRAS-mutant AML cells in a manner that synergizes with MEK inhibition. Our findings uncover a surprisingly restricted role for ABHD17 enzymes in modulating the N-Ras palmitoylation cycle and suggest that ABHD17 inhibitors may have value as targeted therapies forNRAS-mutant cancers.
Trimeric SARS-CoV-2 Spike interacts with dimeric ACE2 with limited intra-Spike avidity
Authors: Lui Irene , Zhou Xin X. , Lim Shion A. , Elledge Susanna K. , Solomon Paige , Rettko Nicholas J. , Zha Beth Shoshana , Kirkemo Lisa L. , Gramespacher Josef A. , Liu Jia , Muecksch Frauke , Lorenzi Julio Cesar Cetrulo , Schmidt Fabian , Weisblum Yiska , Robbiani Davide F. , Nussenzweig Michel C. , Hatziioannou Theodora , Bieniasz Paul D. , Rosenburg Oren S. , Leung Kevin K. , Wells James A.
Published: May 2020

A serious public health crisis is currently unfolding due to the SARS-CoV-2 pandemic. SARS-CoV-2 viral entry depends on an interaction between the receptor binding domain of the trimeric viral Spike protein (Spike-RBD) and the dimeric human angiotensin converting enzyme 2 (ACE2) receptor. While it is clear that strategies to block the Spike/ACE2 interaction are promising as anti-SARS-CoV-2 therapeutics, our current understanding is insufficient for the rational design of maximally effective therapeutic molecules. Here, we investigated the mechanism of Spike/ACE2 interaction by characterizing the binding affinity and kinetics of different multimeric forms of recombinant ACE2 and Spike-RBD domain. We also engineered ACE2 into a split Nanoluciferase-based reporter system to probe the conformational landscape of Spike-RBDs in the context of the Spike trimer. Interestingly, a dimeric form of ACE2, but not monomeric ACE2, binds with high affinity to Spike and blocks viral entry in pseudotyped virus and live SARS-CoV-2 virus neutralization assays. We show that dimeric ACE2 interacts with an RBD on Spike with limited intra-Spike avidity, which nonetheless contributes to the affinity of this interaction. Additionally, we demonstrate that a proportion of Spike can simultaneously interact with multiple ACE2 dimers, indicating that more than one RBD domain in a Spike trimer can adopt an ACE2-accessible “up” conformation. Our findings have significant implications on the design strategies of therapeutic molecules that block the Spike/ACE2 interaction. The constructs we describe are freely available to the research community as molecular tools to further our understanding of SARS-CoV-2 biology.
Chemogenetic manipulation of microglia inhibits neuroinflammation and neuropathic pain in mice
Authors: Yi Min-Hee , Liu Yong U. , Liu Kevin , Chen Tingjun , Bosco Dale B. , Zheng Jiaying , Xie Manling , Zhou Lijun , Qu Wenchun , Wu Long-Jun
Published: May 2020

Microglia play an important role in the central sensitization and chronic pain. However, a direct connection between microglial function and the development of neuropathic painin vivoremains incompletely understood. To address this issue, we applied chemogenetic approach by using CX3CR1creER/+:R26LSL-hM4Di/+transgenic mice to enable expression of inhibitory Designer Receptors Exclusively Activated by Designer Drugs (Gi DREADD) exclusively in microglia. We found that microglial Gi DREADD activation inhibited spinal nerve transection (SNT)-induced microglial reactivity as well as chronic pain initiation and maintenance. Gi DREADD activation downregulated the transcription factor interferon regulatory factor 8 (IRF8) and its downstream target pro-inflammatory cytokine interleukin 1 beta (IL-1β). Usingin vivospinal cord recording, we found that activation of microglial Gi DREADD attenuated synaptic transmission following SNT. Our results demonstrate that microglial Gi DREADD reduces neuroinflammation, synaptic function and neuropathic pain after peripheral nerve injury. Thus, chemogenetic approaches provide a potential opportunity for interrogating microglial function and neuropathic pain treatment.
Sweet taste of heavy water
Authors: Abu Natalie Ben , Mason Philip E. , Klein Hadar , Dubovski Nitzan , Shoshan-Galeczki Yaron Ben , Malach Einav , Pražienková Veronika , Maletínská Lenka , Tempra Carmelo , Chamorro Victor Cruces , Cvačka Josef , Behrens Maik , Niv Masha Y. , Jungwirth Pavel
Published: May 2020

Hydrogen to deuterium isotopic substitution has only a minor effect on physical and chemical properties of water and, as such, is not supposed to influence its neutral taste. Here we conclusively demonstrate that humans are, nevertheless, able to distinguish D2O from H2O by taste. Indeed, highly purified heavy water has a distinctly sweeter taste than same-purity normal water and adds to perceived sweetness of sweeteners. In contrast, mice do not prefer D2O over H2O, indicating that they are not likely to perceive heavy water as sweet. HEK 293T cells transfected with the TAS1R2/TAS1R3 heterodimer and chimeric G-proteins are activated by D2O but not by H2O. Lactisole, which is a known sweetness inhibitor acting via the TAS1R3 monomer of the TAS1R2/TAS1R3, suppresses the sweetness of D2O in human sensory tests, as well as the calcium release elicited by D2O in sweet taste receptor-expressing cells. The present multifaceted experimental study, complemented by homology modelling and molecular dynamics simulations, resolves a long-standing controversy about the taste of heavy water, shows that its sweet taste is mediated by the human TAS1R2/TAS1R3 taste receptor, and opens way to future studies of the detailed mechanism of action.

One sentence summary

Heavy water elicits sweet taste for humans via the TAS1R2/TAS1R3 taste receptor.