bluuebunny/crossref_metadata_2025 huggingface dataset:
Flavobacterium supellecticarium sp. nov., isolated from an abandoned construction timber
Authors: Lin Shih-Yao , Chen Wen-Ming , Huang Guan-Hua , Hameed Asif , Chang Chun-Tse , Tsai Chia-Fang , Young Chiu-Chung
Published: May 2020

A bacterial strain CC-CTC003T was isolated from a synthetic wooden board. Cells of strain CC-CTC003T were Gram-stain-negative, rod-shaped, motile by gliding and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in the presence of 1 % NaCl. The phylogenetic analyses based on 16S rRNA genes revealed that strain CC-CTC003T belonged to the genus

Flavobacterium

and was most closely related to

Flavobacterium cerinum

(95.3 % sequence identity),

Flavobacterium maris

(94.9 % sequence identity),

Flavobacterium qiangtangense

(94.8 %) and

Flavobacterium subsaxonicum

(94.7 %) and had less than 94.7 % sequence similarity to other members of the genus. Average nucleotide identity (ANI) values between strain CC-CTC003T and the type strains of other closely related species were 70.1–74.1 %. The digital DNA–DNA hybridization (dDDH) with

F. cerinum

was 19.4 %. Strain CC-CTC003T contained C15 : 0, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1
 ω6c / C16 : 1
 ω7c) and summed feature 9 (C16 : 0 10-methyl / iso-C17 : 1
 ω9c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, two aminolipids and one unidentified glycolipid. The major polyamine was sym-homospermidine and contained MK-6 as major isoprenoid quinone. The DNA G+C content of the genomic DNA was 39.2 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CC-CTC003T should be classified as a novel species, for which the name Flavobacterium supellecticarium sp. nov. is proposed. The type strain is CC-CTC003T (=BCRC 81146T=JCM 32838T).
SARS-CoV-2-reactive interferon-γ-producing CD8+ T cells in patients hospitalized with Coronavirus viral disease-2019
Authors: Gimenez Estela , Albert Eliseo , Torres Ignacio , Remigia Maria Jose , Alcaraz Maria Jesus , Galindo Maria Jose , Blasco Maria Luisa , Solano Carlos , Forner Maria Jose , Redon Josep , Signes-Costa Jaime , Navarro David
Published: May 2020

There is limited information on SARS-CoV-2 T-cell immune responses in patients with Covid-19. Both CD4+ and CD8+ T cells may be instrumental in the resolution of and protection from SARS-CoV-2 infection. Here, we tested 25 hospitalized patients with either microbiologically documented Covid-19 (n=19) or highly suspected of having the disease (n=6) for the presence of SARS-CoV-2-reactive- CD69+-expressing interferon-gamma;-producing-(IFN-gamma;) CD8+ T cells by a flow-cytometry for intracelular cytokine staining assay. Two sets of overlapping peptides encompassing the SARS-CoV-2 Spike glycoprotein N-terminal 1-643 amino acid sequence and the entire sequence of SARS-CoV-2 M protein were used simultaneously as antigenic stimulus. Ten patients (40%) had detectable responses, displaying frequencies ranging from 0.15 to 2.7% (median of 0.57 cells/microlitre; range, 0.43-9.98 cells/microlitre). The detection rate of SARS-CoV-2-reactive IFN-gamma; CD8+ T cells in patients admitted to intensive care was comparable (P=0.28) to that in patients hospitalized in other medical wards. No correlation was found between SARS-CoV-2-reactive IFN-gamma; CD8+ T-cell counts and SARS-CoV-2 S-specific antibody levels. Likewise, no correlation was observed between either SARS-CoV-2-reactive IFN-gamma; CD8+ T cells or S-specific IgG-antibody titers and blood cell count or levels of inflammatory biomarkers. In summary, in this descriptive, preliminary study we showed that SARS-CoV-2-reactive IFN-gamma; CD8+ T cells can be detected in a non-negligible percentage of patients with moderate to severe forms of Covid-19. Further studies are warranted to determine whether quantitation of these T-cell subsets may provide prognostic information on the clinical course of Covid-19.
Impact of Proactive Integrated Care on Chronic Obstructive Pulmonary Disease
Authors: Koff Patricia B. , Min Sung-joon , Diaz Debora L. P. , Freitag Tammie J. , James Shannon S. , Voelkel Norbert F. , Linderman Derek J. , Diaz del Valle Fernando , Albert Richard K. , Bull Todd M. , Beck Arne , Stelzner Thomas J. , Ritzwoller Debra P. , Kveton Christine M. , Carwin Stephanie , Ghosh Moumita , Keith Robert L. , Westfall John M. , Vandivier R. William
Published: May 2020

Background. Up to 50% of COPD patients do not receive recommended care for COPD. To address this important issue, we developed Proactive Integrated Care (Proactive iCare), a healthcare delivery model that couples integrated care with remote monitoring.
Methods. We conducted a prospective, quasi-randomized clinical trial in 511 patients with advanced COPD, or a recent COPD exacerbation, to test whether Proactive iCare impacts patient- centered outcomes and healthcare utilization. Patients were allocated to Proactive iCare (n =352) or Usual Care (n = 159), and were examined for changes in quality of life using the St. Georges Respiratory Questionnaire (SGRQ), symptoms, guideline-based care, and healthcare utilization.
Findings. Proactive iCare improved the total SGRQ by 7-9 units (p<0.0001), symptom SGRQ by 9 units (p<0.0001), activity SGRQ by 6-7 units (p<0.001) and impact SGRQ by 7-11 units (p<0.0001) at 3, 6 and 9 months, compared with Usual Care. Proactive iCare increased the 6-minute walk distance by 40 m (p<0.001), reduced COPD-related urgent office visits by 76 visits per 100 subjects (p<0.0001), identified unreported exacerbations, and decreased smoking (p = 0.01). Proactive iCare also improved cough, sputum, shortness of breath, the BODE index and oxygen titration (p<0.05). Mortality in the Proactive iCare group (1.1%) was not significantly different than mortality in the Usual Care group (3.8%; p = 0.08).
Interpretation. Results suggest that linking integrated care with remote monitoring improves the lives of people with advanced COPD.
High-speed adaptive optics line-scan OCT for cellular-resolution optoretinography
Authors: Pandiyan Vimal Prabhu , Jiang Xiaoyun , Bertelli Aiden Maloney , Kuchenbecker James A. , Sharma Utkarsh , Sabesan Ramkumar
Published: May 2020

Optoretinography – the non-invasive, optical imaging of light-induced functional activity in the retina – stands to provide a critical biomarker for testing the safety and efficacy of new therapies as well as their rapid translation to the clinic. Optical phase change in response to light, as readily accessible in phase-resolved OCT, offers a path towards all-optical imaging of retinal function. However, typical human eye motion adversely affects phase stability and precludes the recording of fast light-induced retinal events. Here we introduce a high-speed line-scan spectral domain OCT with adaptive optics (AO), aimed at volumetric imaging and phase-resolved acquisition of retinal responses to light. By virtue of parallel acquisition of an entire retinal cross-section (B-scan) in a single high-speed camera frame, depth-resolved tomograms at speeds up to 16 kHz were achieved with high sensitivity and phase stability. To optimize spectral and spatial resolution, an anamorphic detection paradigm was introduced enabling improved light collection efficiency and signal roll-off compared to traditional methods. The benefits in speed, resolution and sensitivity were exemplified in imaging nanometer-millisecond scale light-induced optical path length changes in cone photoreceptor outer segments. With 660 nm stimuli, individual cone responses readily segregated into three clusters, corresponding to long, middle and short-wavelength cones. Recording suchoptoretinogramson spatial scales ranging from individual cones, to 100 μm-wide retinal patches offers a robust and sensitive biomarker for cone function in health and disease. Furthermore, incorporating this capability into an easy-to-use and ubiquitous diagnostic platform of OCT enables its widespread application to patient care and drug development.
Arterial blood contrast (ABC) enabled by magnetization transfer (MT): a novel MRI technique for enhancing the measurement of brain activation changes
Authors: Schulz Jenni , Fazal Zahra , Metere Riccardo , Marques José P. , Norris David G.
Published: May 2020

Functional brain imaging in humans is almost exclusively performed using blood oxygenation level dependent (BOLD) contrast. This typically requires a period of tens of milliseconds after excitation of the spin system to achieve maximum contrast, leading to inefficient use of acquisition time, reduced image quality, and inhomogeneous sensitivity throughout the cortex. We utilise magnetisation transfer to suppress the signal differentially from grey matter relative to blood so that the local increase in blood volume associated with brain activation (mainly occurring in the arterioles and capillaries) will increase the measured signal. Arterial blood contrast (ABC) is additive to the residual BOLD effect, but will have its maximum value at the time of excitation. We measured brain activation using combined ABC and residual BOLD contrast at different times post-excitation and compared this to BOLD data acquired under otherwise identical conditions. We conclude that using ABC and measuring shortly after excitation gives comparable sensitivity to standard BOLD but will provide greater efficiency, spatial specificity, improved image quality, and lower inter-subject variability. ABC offers new perspectives for performing functional MRI.
Biomimetic sponges improve muscle structure and function following volumetric muscle loss
Authors: Haas Gabriel , Dunn Andrew , Madsen Josh , Genovese Peter , Lin Andrew , Chauvin Hannah , Au Jeffrey , Paoli Allison , Garg Koyal
Published: May 2020

Skeletal muscle is inept in regenerating after traumatic injuries such as volumetric muscle loss (VML) due to significant loss of basal lamina and the resident satellite cells. Currently, there are no approved therapies for the treatment of muscle tissue following trauma. In this study, biomimetic sponges composed of gelatin, collagen, laminin-111, and FK-506 were used for the treatment of VML in a rodent model. We observed that biomimetic sponge treatment improved muscle structure and function while modulating inflammation and limiting the extent of fibrotic tissue deposition. Specifically, sponge treatment increased the total number of myofibers, type 2B fiber cross-sectional area, myosin: collagen ratio, myofibers with central nuclei, and peak isometric torque compared to untreated VML injured muscles. As an acellular scaffold, biomimetic sponges provide a promising “off-the-shelf” clinical therapy for VML.
HAHmiR.DB: A Server Platform For High Altitude Human miRNA-Gene Coregulatory Networks And Associated Regulatory-Circuits
Authors: Gupta Apoorv , Sugadev Ragumani , Sharma Yogendra Kumar , Kumar Bhuvnesh , Khurana Pankaj
Published: May 2020

Rapid ascent to High Altitude (HA) can cause severe damage to body organs and may lead to many fatal disorders. During induction to HA, human body undergoes various physiological, biochemical, hematological and molecular changes to adapt to the extreme environmental conditions. Many literature references hint that gene-expression-regulation and regulatory molecules like microRNAs (miRNAs) and Transcription Factors (TFs) control adaptive responses during HA-stress. These biomolecules are known to interact in a complex combinatorial manner to fine-tune the gene expression and help in controlling the molecular responses during this stress and ultimately help in acclimatization. HAHmiR.DB (High-Altitude Human miRNA Database) is a unique, comprehensive, curated collection of miRNAs that have been experimentally validated to be associated with HA-stress; their level of expression in different altitudes, fold change, experiment duration, biomarker association, disease and drug association, tissue-specific expression level, Gene Ontology (GO) and Kyoto Encyclopaedia of Gene and Genomes (KEGG) pathway associations. As a server platform it also uniquely constructs and analyses interactive miRNA-TF-Gene coregulatory networks and extracts regulatory-circuits/Feed Forward Loops (FFLs) using in-house scripts. These regulatory circuits help to offer mechanistic insights in complex regulatory mechanisms during HA stress. The server can also build these regulatory networks between two and more miRNAs of the database and also identify the regulatory-circuits from this network. Hence HAHmiR.DB is the first-of its-kind database in HA research which a reliable platform to explore, compare, analyse and retrieve miRNAs associated with HA stress, their coregulatory networks and FFL regulatory circuits. HAHmiR.DB is freely accessible athttp://www.hahmirdb.in
Modeling the dynamics of COVID-19 using Q-SEIR model with age-stratified infection probability
Authors: Rayo Joshua Frankie , de Castro Romulo , Sevilleja Jesus Emmanuel , Bongolan Vena Pearl
Published: May 2020

We explore the advantage of age-stratifying the population as an improvement on the quarantine-modified SEIR model. We hypothesize that this would project lower cases of infection for the Philippines because of our country's low median age. We introduce the variable U that is multiplied to the incubation rate sigma; when exposed individuals become infected. U is the dot product of the proxy infection probabilities stratified per age group (F) and the population stratified per age group (P) divided by the total population, similar to calculating mathematical expectation. Proxies were taken from two data sets: Hubei, China with a calculated value of U_CHN=0.4447 and Quezon City, Philippines with U_QC=0.5074. When the majority age group, represented by the median age, is far from the age group with the highest number of infections the number of infected individuals decreases and produces a delayed peaking effect. This new method gives a much lower estimate on peak number of infected cases by 65.2% compared with age-stratification alone; and by 75.2% compared with Q-SEIR alone.
Country-specific optimization of testing rates and unlock measures can help to contain COVID19 infection
Authors: Sarma Uddipan , Ghosh Bhaswar
Published: May 2020

In response to the COVID19 outbreak many countries have implemented lockdown to ensure social distancing. However, long lockdowns globally affected the livelihood of millions of people resulting in subsequent unlocks that started a second wave of infection in multiple countries. Unlocking of the economies critically imposes extra burden on testing and quarantine of the infected people to keep the reproduction number (R0) <1. This, as we demonstrate, requires optimizing a cost-benefit trade-off between testing rate and unlock extent. We delineate a strategy to optimize the trade-off by utilizing a data-trained epidemic model and coupling it with a stochastic agent based model to implement contact tracing. In a country specific manner, we quantitatively demonstrate how combination of unlock and testing can maintain R0 <1.
Chansu Injection Improves the Respiratory Function of Severe COVID-19 Patients
Authors: Hu Fen , Chen Jiao , Chen Hao , Zhu Jin , Wang Chen , Ni Haibin , Cheng Jianming , Cao Peng , Hu Xingxing
Published: May 2020

Chansu and its major active constituent of bufalin have been reported to have broad-spectrum antiviral effects. This study aims to assess the efficacy of Chansu injection in treating patients with severe COVID-19. The patients diagnosed as severe or critical COVID-19 in The First People’s Hospital of Jiangxia District, Wuhan, China from February 5 to March 5, 2020 were randomly allocated in a 1:1 ratio to receive general treatment plus Chansu injection or only general treatment as the control group. The treatment course was 7 days. The changes of PaO2/FiO2 and ROX index indicating respiratory function, the white blood cell (WBC) count, peripheral blood mononuclear lymphocyte (PBML) count, respiratory support step-down time (RSST), and safety indicators for the 7th day were retrospectively analyzed. After 7 days treatment, the oxygenation index was improved in 20 of 21 patients (95.2%) in the treatment group, as compared with 13 of 19 patients (68.4%) in the control group. The PaO2/FiO2 and ROX indices in the treatment group (mean, 226.27±67.35 and 14.01±3.99 respectively) were significantly higher than the control group (mean, 143.23±51.29 and 9.64±5.54 respectively). The RSST was 1 day shorter in the treatment group than the control group. Multivariate regression analysis suggested that Chansu injection contributed the most to the outcome of PaO2/FiO2. No obvious adverse effects were observed. Preliminary data showed that Chansu injection had apparent efficacy in treating patients with severe COVID-19.

Significance Statement

Patients with severe COVID-19 usually have dyspnea and/or hypoxemia one week after the onset of symptoms, and can quickly progress to acute respiratory distress syndrome, septic shock, metabolic acidosis that is difficult to correct, coagulation dysfunction and multiple organs failure. Chansu injection, a widely used drug in clinical cancer and chronic hepatitis B therapy in China, can improve the respiratory function and shorten the respiratory support step-down time with 1 day in patients with severe COVID-19. These preliminary findings raise the possibility that Chansu injection may be helpful in the treatment of patients with severe COVID-19.
Ledidi: Designing genomic edits that induce functional activity
Authors: Schreiber Jacob , Lu Yang Young , Noble William Stafford
Published: May 2020

The development of modern genome editing tools has enabled researchers to make edits with high precision, but has left unsolved the problem of designing these edits. We propose Ledidi, an approach that treats the design of genomic edits as an optimization problem where the goal is to produce the desired output from a predictive model. The discrete nature of biological sequences makes direct optimization challenging, but we overcome this by using the Gumbel-Softmax reparameterization trick. We validate Ledidi by pairing it with the Basenji model, which makes predictions for thousands of functional profiles, and designing edits that affect CTCF binding and induce cell type-specific binding of JUND.
Expanding Covid-19 Testing: Mathematical Guidelines for the Optimal Sample Pool Size Given Positive Test Rate
Authors: Adams Kayleigh
Published: May 2020

Widespread testing is essential to the mitigation of the spread of any virus, and is particularly central to the discussion on transitioning out of national quarantine. Sample pooling is a method that aims to multiply testing capability by using one testing kit for multiple samples, but will only be successful under certain conditions. This paper gives precise guidelines on those conditions for success: for any proposed sample pool size, explicit bounds on the positive infection rate are given that are informed by both discrete and statistical modeling.
Investigational treatments for COVID-19 may increase ventricular arrhythmia risk through drug interactions
Authors: Varshneya Meera , Irurzun-Arana Itziar , Campana Chiara , Dariolli Rafael , Gutierrez Amy , Pullinger Taylor K. , Sobie Eric A.
Published: May 2020

Many drugs that have been proposed for treatment of COVID-19 are reported to cause cardiac adverse events, including ventricular arrhythmias. In order to properly weigh risks against potential benefits, particularly when decisions must be made quickly, mathematical modeling of both drug disposition and drug action can be useful for predicting patient response and making informed decisions. Here we explored the potential effects on cardiac electrophysiology of 4 drugs proposed to treat COVID-19: lopinavir, ritonavir, chloroquine, and azithromycin, as well as combination therapy involving these drugs. Our study combined simulations of pharmacokinetics (PK) with quantitative systems pharmacology (QSP) modeling of ventricular myocytes to predict potential cardiac adverse events caused by these treatments. Simulation results predicted that drug combinations can lead to greater cellular action potential prolongation, analogous to QT prolongation, compared with drugs given in isolation. The combination effect can result from both pharmacokinetic and pharmacodynamic drug interactions. Importantly, simulations of different patient groups predicted that females with pre-existing heart disease are especially susceptible to drug-induced arrhythmias, compared males with disease or healthy individuals of either sex. Overall, the results illustrate how PK and QSP modeling may be combined to more precisely predict cardiac risks of COVID-19 therapies.
Personalizedin-silicodrug response prediction based on the genetic landscape of muscle-invasive bladder cancer
Authors: Krentel Friedemann , Singer Franziska , Lourdes Rosano-Gonzalez María , Gibb Ewan A. , Liu Yang , Davicioni Elai , Keller Nicola , Stekhoven Daniel , Kruithof-de Julio Marianna , Seiler Roland
Published: May 2020

In bladder cancer (BLCA) there are, to date, no reliable diagnostics available to predict the potential benefit of a therapeutic approach. The extraordinarily high molecular heterogeneity of BLCA might explain its wide range of therapy responses to empiric treatments. To better stratify patients for treatment response, we present a highly automated workflow forin-silicodrug response prediction based on a tumor’s individual multi-omic profile. Within the TCGA-BLCA cohort, the algorithm identified a panel of 21 genes and 72 drugs, that suggested personalized treatment for 94,7% of patients - including five genes not yet reported as biomarkers for clinical testing in BLCA. The automated predictions were complemented by manually curated data, thus allowing for accurate sensitivity- or resistance-directed drug response predictions. Manual curation revealed pitfalls of current, and potential of future drug-gene interaction databases. Functional testing in patient derived models and/or clinical trials are next steps to validate ourin-silicodrug predictions.
Late adolescence mortality in mice with brain-specific deletion of the volume-regulated anion channel subunit LRRC8A
Authors: Wilson Corinne S. , Dohare Preeti , Orbeta Shaina , Nalwalk Julia W. , Huang Yunfei , Ferland Russell J. , Sah Rajan , Scimemi Annalisa , Mongin Alexander A.
Published: May 2020

The leucine-rich repeat-containing family 8 member A (LRRC8A) is an essential subunit of the volume-regulated anion channel (VRAC). VRAC is critical for cell volume control, but its broader physiological functions remain under investigation. Recent studies in the field indicate thatLrrc8adisruption in brain astrocytes reduces neuronal excitability, impairs synaptic plasticity and memory, and protects against cerebral ischemia. In the present work, we generated the brain-wide conditional LRRC8A knock-out mice (LRRC8A bKO) usingNestinCre-drivenLrrc8aflox/floxexcision in neurons, astrocytes, and oligodendroglia. LRRC8A bKO animals were born close to the expected Mendelian ratio and developed without overt histological abnormalities, but, surprisingly, all died between 5 and 9 weeks of age with a seizure phenotype, which was confirmed by video and EEG recordings. Brain slice electrophysiology detected changes in the excitability of pyramidal cells and modified GABAergic inputs in the hippocampal CA1 region of LRRC8A bKO. LRRC8A-null hippocampi showed increased immunoreactivity of the astrocytic marker GFAP, indicating reactive astrogliosis. We also found decreased whole-brain protein levels of the GABA transporter GAT-1, the glutamate transporter GLT-1, and the astrocytic enzyme glutamine synthetase. Complementary HPLC assays identified reduction in the tissue levels of the glutamate and GABA precursor glutamine. Together, these findings suggest that VRAC provides vital control of brain excitability in mouse adolescence. VRAC deletion leads to a lethal phenotype involving progressive astrogliosis and dysregulation of astrocytic uptake and supply of amino acid neurotransmitters and their precursors.
Quantitative modeling of the effect of antigen dosage on B-cell affinity distributions in maturating germinal centers
Authors: Molari Marco , Eyer Klaus , Baudry Jean , Cocco Simona , Monasson Rémi
Published: May 2020

Affinity maturation is a complex dynamical process allowing the immune system to generate antibodies capable of recognizing antigens. We introduce a model for the evolution of the distribution of affinities across the antibody population in germinal centers. The model is amenable to detailed mathematical analysis, and gives insight on the mechanisms through which antigen availability controls the rate of maturation and the expansion of the antibody population. It is also capable, upon maximum-likelihood inference of the parameters, to reproduce accurately the distributions of affinities of IgG-secreting cells we measure in mice immunized against Tetanus Toxoid under largely varying conditions (antigen dosage, delay between injections). Both model and experiments show that the average population affinity depends non-monotonically on the antigen dosage. We show that combining quantitative modelling and statistical inference is a concrete way to investigate biological processes underlying affinity maturation (such as selection permissiveness), hardly accessible through measurements.
A transfer-learning approach for first-year developmental infant brain segmentation using deep neural networks
Authors: Wang Yun , Haghpanah Fateme Sadat , Aw Natalie , Laine Andrew , Posner Jonathan
Published: May 2020

The months between birth and age 2 are increasingly recognized as a period critical for neuro-development, with potentially life-long implications for cognitive functioning. However, little is known about the growth trajectories of brain structure and function across this time period. This is in large part because of insufficient approaches to analyze infant MRI scans at different months, especially brain segmentation. Addressing technical gaps in infant brain segmentation would significantly improve our capacity to efficiently measure and identify relevant infant brain structures and connectivity, and their role in long-term development. In this paper, we propose a transfer-learning approach based on convolutional neural network (CNN)-based image segmentation architecture, QuickNAT, to segment brain structures for newborns and 6-month infants separately. We pre-trained QuickNAT on auxiliary labels from a large-scale dataset, fine-tuned on manual labels, and then cross-validated the model’s performance on two separate datasets. Compared to other commonly used methods, our transfer-learning approach showed superior segmentation performance on both newborns and 6-month infants. Moreover, we demonstrated improved hippocampus segmentation performance via our approach in preterm infants.
Study of pre-synaptic internalisation in human schizophrenia brains
Authors: Tzioras Makis , Stevenson Anna J. , Boche Delphine , Spires-Jones Tara L.
Published: May 2020

Aims

Efficient synaptic communication is crucial to maintain healthy behavioural and cognitive processes. Individuals affected by schizophrenia present behavioural symptoms and alterations in decision-making, suggesting altered synaptic integrity as the support of the illness. It is currently unknown how this synaptic change is mediated in schizophrenia, but microglia have been proposed to act as the culprit, actively removing synapses pathologically. Here, we aimed to explore the interaction between microglia and synaptic uptake in human post-mortem tissue.

Methods

We assessed microglial activation and synaptic internalisation by microglia in a post-mortem human tissue of 10 control and 10 schizophrenia cases. Immunohistochemistry was performed to identify microglia (Iba1 and CD68) and the presynaptic terminals (synapsin I).

Results

We found no difference in microglial expression, nor a difference in pre-synaptic protein level phagocyted by microglia between the two groups.

Conclusions

Our findings are consistent with the brain imaging studies in schizophrenia implying that microglia play a role mainly during the early phases of the disease, by example in active synapse remodelling, which is not detected in the chronic stage of the illness.
A benchmark of online COVID-19 symptom checkers
Authors: Munsch Nicolas , Martin Alistair , Gruarin Stefanie , Nateqi Jama , Abdarahmane Isselmou , Weingartner-Ortner Rafael , Knapp Bernhard
Published: May 2020

Background

A large number of online COVID-19 symptom checkers and chatbots have been developed but anecdotal evidence suggests that their conclusions are highly variable. To our knowledge, no study has evaluated the accuracy of COVID-19 symptom checkers in a statistically rigorous manner.

Methods

In this paper, we evaluate 10 different COVID-19 symptom checkers screening 50 COVID-19 case reports alongside 410 non-COVID-19 control cases.

Results

We find that the number of correctly assessed cases varies considerably between different symptom checkers, with Symptoma (F1=0.92, MCC=0.85) showing the overall best performance followed by Infermedica (F1=0.80, MCC=0.61).
Analysis of Crowdsourced Metformin Tablets from Individuals Reveals Widespread Contamination with N-Nitrosodimethylamine (NDMA) and N,N-Dimethylformamide (DMF) in the United States
Authors: Wu Qian , Kvitko Evgenia , Hudspeth Amber , Williams Shannon , Costantino Ryan C. , Kucera Kaury , Light David
Published: May 2020

Reports of metformin drug products contaminated with unacceptable levels of the probable human carcinogen N-Nitrosodimethylamine (NDMA) prompted a national sampling of post-market metformin drug products in early 2020. To broadly sample the United States market and minimize supply chain bias, metformin medication samples were crowdsourced directly from individuals across many states. 155 samples were received, and liquid chromatography-high resolution mass spectrometry tests for a panel of nitrosamines and N,N-Dimethylformamide (DMF) revealed significant levels of NDMA and DMF that relate to formulation. 49% of all medication samples contained detectable levels of NDMA and, when scaled to maximum daily tablet dose, 16% of all medication samples contained NDMA levels exceeding the United States Food and Drug Administration acceptable daily intake (ADI) limit. The highest NDMA detection from the tested samples was 748 ng per 500 mg tablet, which, when scaled to a common 2000 mg per day dosage regimen, is 31 times the ADI limit. The presence of N,N-Dimethylformamide (DMF) across 74% of the sampled metformin products is concerning given its same carcinogenicity categorization as NDMA and proposed role in formation of NDMA. Results underscore the need for continued surveillance of product quality, recalls of tainted medications, and investigation of metformin manufacturing practices.
The p150 Isoform of ADAR1 Blocks Sustained RLR signaling and Apoptosis during Influenza Virus Infection
Authors: Vogel Olivia A. , Han Julianna , Liang Chieh-Yu , Manicassamy Santhakumar , Perez Jasmine T. , Manicassamy Balaji
Published: May 2020

Signaling through retinoic acid inducible gene I (RIG-I) like receptors (RLRs) is tightly regulated, with activation occurring upon sensing of viral nucleic acids, and suppression mediated by negative regulators. Under homeostatic conditions aberrant activation of melanoma differentiation-associated protein-5 (MDA5) is prevented through editing of endogenous dsRNA by RNA editing enzyme Adenosine Deaminase Acting on RNA (ADAR1). In addition, ADAR1 is postulated to play proviral and antiviral roles during viral infections that are dependent or independent of RNA editing activity. Here, we investigated the importance of ADAR1 isoforms in modulating influenza A virus (IAV) replication and revealed the opposing roles for ADAR1 isoforms, with the nuclear p110 isoform restricting versus the cytoplasmic p150 isoform promoting IAV replication. Importantly, we demonstrate that p150 is critical for preventing sustained RIG-I signaling, as p150 deficient cells showed increased IFN-β expression and apoptosis during IAV infection, independent of RNA editing activity. Taken together, the p150 isoform of ADAR1 is important for preventing sustained RIG-I induced IFN-β expression and apoptosis during viral infection.
Osteoarthritis: articular chondrocyte inflammatory signaling leads to enhanced gene expression and function of mechanotransduction channel Piezo1 as a pathogenic feed-forward mechanism
Authors: Lee Whasil , Nims Robert J. , Savadipour Alireza , Leddy Holly , Liu Fang , McNulty Amy , Chen Yong , Guilak Farshid , Liedtke Wolfgang B.
Published: May 2020

Osteoarthritis (OA) is a painful and debilitating condition of synovial joints without any disease-modifying therapies (1, 2). We previously identified mechanosensitive PIEZO channels, PIEZO1 and PIEZO2, both expressed in articular cartilage, to function in chondrocyte mechanotransduction in response to injury (3, 4). We therefore asked whether interleukin-1-mediated inflammatory signaling, as occurs in OA, influences Piezo gene expression and channel function, thus indicative of maladaptive reprogramming that can be rationally targeted. Primary porcine chondrocyte culture and human osteoarthritic cartilage tissue were studied.

We found that interleukin-1α (IL-1α) upregulated Piezo1 in porcine chondrocytes. Piezo1 expression was significantly increased in human osteoarthritic cartilage. Increased Piezo1 expression in chondrocytes resulted in a feed-forward pathomechanism whereby increased function of Piezo1 induced excess intracellular Ca2+, at baseline and in response to mechanical deformation. Elevated resting state Ca2+in turn rarefied the F-actin cytoskeleton and amplified mechanically-induced deformation-microtrauma. As intracellular substrates of this novel OA-related inflammatory pathomechanism, in porcine articular chondrocytes exposed to IL-1α we discovered that enhanced Piezo1 expression depended on p38 MAP-kinase and transcription factors HNF4 and ATF2/CREBP1. CREBP1 directly bound to the proximalPIEZO1gene promoter.

In ensemble, these signaling and genetic re-programming events represent a novel and detrimental Ca2+-driven feed-forward mechanism that can be rationally targeted to stem the progression of OA.

Significance Statement

Osteoarthritis affecting weight-bearing joints is a global health problem, causing loss of mobility and enormous healthcare costs. Disease-modifying approaches are lacking. Here, we report a new cellular mechanism of inflammatory signaling in chondrocytes, the cellular substrate of cartilage. We show how osteoarthritis-relevant levels of interleukin-1α reprogram articular chondrocytes so that they become more susceptible to mechanical trauma, which chondrocytes sense via Piezo1/2 mechanosensitive ion channels. We uncover that IL-1α enhances gene expression of Piezo1 in primary articular chondrocytes underlying Piezo1 gain-of-function. We elucidate the new signaling pathway, from membrane to nucleus, including transcription factors that enhance Piezo1-expression. We also define detrimental effects of gain-of-function of Piezo1, for mechanotransduction and at-rest, that suggest this new reprogramming mechanism to contribute to osteoarthritis pathogenesis.
Distinct domain requirements for EAP45 in HIV budding, late endosomal recruitment, and cytokinesis
Authors: Meng Bo , Vallejo Ramirez Pedro P. , Scherer Katharina M. , Bruggeman Ezra , Kenyon Julia C. , Kaminski Clemens F. , Lever Andrew M.
Published: May 2020

The scission of lipid membranes is a common biological process, often mediated by ESCRT complexes in concert with VPS4 assembling around the separation point. The functions of the ESCRT-I and ESCRT-III complexes are well established in certain of these cellular processes; however, the role of ESCRT-II remains contentious. Here, we devised a SNAP-tag fluorescent labelling strategy to understand the domain requirements of EAP45, the main component of ESCRT-II, in HIV egress, late endosome recruitment, and cytokinesis. We used TIRF microscopy to measure the spatial co-occurrence of the HIV structural polyprotein Gag with full length EAP45 in both fixed and live cells. Gag colocalises with the full length EAP45 comparably to ALIX, but this is lost on deletion of the EAP45 N terminus. Our findings reveal the H0 domain of the EAP45 protein is essential for linking to ESCRT-I during HIV budding and in anchoring at the late endosomal membrane, however in cytokinesis it is the Glue domain that is critical.
Risks and etiology of bacterial vaginosis revealed by species dominance network analysis
Authors: Ma Zhanshan (Sam) , Ellison Aaron M
Published: May 2020

BV (bacterial vaginosis) influences 20-40% of women but its etiology is still poorly understood. An open question about the BV is which of the hundreds of bacteria found in the human vaginal microbiome (HVM) are the causal pathogens of BV? Existing attempts to identify them have failed for at least two reasons: (i) a focus on species per se that ignores species interactions; (ii) a lack of systems-level understanding of the HVM. Here, we recast the question of microbial causality of BV by asking if there are any reliable 'signatures' of community composition (or poly-microbial 'cults') associated with it? We apply a new framework (species dominance network analysis by Ma & Ellison (2019: Ecological Monographs) to detect critical structures in HVM networks associated with BV risks and etiology. We reanalyzed the metagenomic datasets of a mixed-cohort of 25 BV patients and healthy women. In these datasets, we detected 15 trio-motifs that occurred exclusively in BV patients. We failed to find any of these 15 trio-motifs in three additional cohorts of 1535 healthy women. Most member-species of the 15 trio motifs are BV-associated anaerobic bacteria (BVAB), Ravel's community-state type indicators, or the most dominant species; virtually all species interactions in these trios are high-salience skeletons, suggesting that those trios are strongly connected 'cults'. The presence of trio motifs unique to BV may act as indicators for its personalized diagnosis and could help elucidate a more mechanistic interpretation of its risks and etiology.
SARS-CoV-2 IgG Antibody Responses in New York City
Authors: Reifer Josh , Hayum Nosson , Heszkel Benzion , Klagsbald Ikey , Streva Vincent A.
Published: May 2020

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a strain of coronavirus that causes coronavirus disease 2019 (Covid-19) and has been declared a global pandemic by the World Health Organization. Total cases of SARS-CoV-2 worldwide exceed 4.8 million, with over 320,000 deaths recorded. Little is known about the body’s immune response to SARS-CoV-2 infection. In this paper, we describe SARS-CoV-2 IgG antibody responses in 28,523 patients from the New York City metropolitan area and report a SARS-CoV-2 IgG positivity rate of 44%, indicating the widespread nature of the pandemic in the city and state of New York. Additionally, for a subset of patients, we report on the correlation between SARS-CoV-2 patient symptom severity and level of SARS-CoV-2 IgG antibody found in the patient sample.
Evaluation of ELISA tests for the qualitative determination of IgG, IgM and IgA to SARS-CoV-2
Authors: Francesca Colavita , Alessandra Brogi , Daniele Lapa , Licia Bordi , Giulia Matusali , Silvia Meschi , Patrizia Marsella , Giulia Tesi , Tommaso Bandini , Antonino Di Caro , Rosaria Capobianchi Maria , Concetta Castilletti
Published: May 2020

Serological assays for anti-SARS-CoV-2 antibodies are now of critical importance to support diagnosis, guide epidemiological intervention, and understand immune response to natural infection and vaccine administration. We developed and validated new anti-SARS-CoV-2 IgG, IgM and IgA ELISA tests (ENZY-WELL SARS-CoV-2 ELISA, DIESSE Diagnostica Senese S.p.a.) based on whole-virus antigens. We used a total of 553 serum samples including samples from COVID-19 suspected and confirmed cases, healthy donors, and patients positive for other infections or autoimmune conditions. Overall, the assays showed good concordance with the indirect immunofluorescence reference test in terms of sensitivity and specificity. Especially for IgG and IgA, we observed high sensitivity (92.5 and 93.6%, respectively); specificity was high (>96%) for all antibody types ELISAs. In addition, sensitivity was linked to the days from symptoms onset (DSO) due to the seroconversion window, and for ENZY-WELL SARS-CoV-2 IgG and IgA ELISAs resulted 100% in those samples collected after 10 and 12 DSO, respectively. The results showed that ENZY-WELL SARS-CoV-2 ELISAs may represent a valid option for both diagnostic and epidemiological purposes, covering all different antibody types developed in SARS-CoV-2 immune response.
The spectrum of COVID-19-associated dermatologic manifestations: an international registry of 716 patients from 31 countries
Authors: Freeman Esther E. , McMahon Devon E. , Lipoff Jules B. , Rosenbach Misha , Kovarik Carrie , Desai Seemal R. , Harp Joanna , Takeshita Junko , French Lars E. , Lim Henry W. , Thiers Bruce H. , Hruza George J. , Fox Lindy P.
Published: May 2020

Key Points

Question

What are the cutaneous manifestations associated with COVID-19 and do they provide insight into the pathophysiology or prognosis?

Findings

In this international registry-based case series of 716 patients representing 31 countries, the most common dermatologic morphologies encountered in the 171 COVID-19 confirmed case included morbilliform, pernio-like, urticarial, macular erythema, vesicular, papulosquamous, and retiform purpura. Retiform purpura was seen exclusively in critically ill, hospitalized patients.

Meaning

COVID-19 is associated with a spectrum of skin findings in affected patients. These cutaneous manifestations may vary depending on the severity of COVID-19.
Impact of gastrointestinal comorbidities in patients with right & left atrial isomerism
Authors: Fotaki Anastasia , L Doughty Victoria , Banya Winston , Giuliani Stefano , Bradley Sarah , S Carvalho Julene
Published: May 2020

Objective

Heterotaxy syndrome (HS), being right atrial isomerism (RAI) or left atrial isomerism (LAI) often presents with congenital heart disease (CHD). Intestinal abnormalities including malrotation are common. We aim to assess the impact of gut abnormalities on outcome in HS.

Methods

We reviewed cardiology records of HS patients regarding presence of CHD, time for cardiac intervention, presence of gastrointestinal (GI) abnormalities and type/time of surgery. A questionnaire about GI status was sent to patients <18 years old. Kaplan-Meier curves were derived for survival data.

Results

Data were available for 195 patients (49 RAI, 146 LAI) of 247 identified. Questionnaires were sent to 77 families, 47 replied. CHD was present in all RAI and 63.7% of LAI cases. Thirty-eight patients had abdominal surgery (19.5%), similar rate in RAI and LAI (20.4% vs 19.1%, p=0.92). Ladd procedure was performed in 17 (44.7%), non-Ladd in 12 (31.5%) and both procedures in nine patients (23.7%). Ten-year freedom from Ladd procedure for all was 86% (RAI=87%; LAI=85%, p=0.82). Freedom from any GI surgery at one year was 86% (RAI=86%; LAI=86%, p=0.98) and at ten years was 80% (RAI=77%; LAI=81%, p=0.65). Ten-year freedom from cardiac surgery was 34% (RAI=7%; LAI=42%, p<0.0001).

Conclusions

In our cohort, one in five patients required abdominal surgery, mostly in their first year, similar in RAI and LAI. Between one and ten years of follow up the impact of GI abnormalities on outcome was minimal. Medium term survival was related to CHD.

ARTICLE SUMMARY

STRENGTHS AND LIMITATIONS OF THIS STUDY

This study is the largest cohort study investigating the impact of gastrointestinal abnormalities in cardiology patients with heterotaxy syndrome.

It is the first clinical study to show that HS patients suffer from a wider spectrum of abdominal abnormalities, other than typical malrotation, varying in severity from asymptomatic malrotation to complete non-rotation, namely atresia at multiple intestinal levels. This is relevant in prenatal family counseling but also raises questions regarding the indication of elective Ladd procedure in all heterotaxy syndrome patients, as a different procedure might be indicated.

Patient morbidity was investigated from both the cardiology and gastrointestinal point 12 of view.

Its main limitations in design is that is not a prospective study. Cardiology records have been reviewed with regards to GI symptomatology, screening investigations and procedures.

It involved both reviewing the medical records and directly contacting the family for the subcohort that was below 18 years old and lived in the UK, in an attempt to minimise any data errors. Our records were consistent with the information provided by parents/guardians in all cases but one.
Electric Field Induced Wetting of a Hydrophobic Gate in a Model Nanopore Based on the 5-HT3Receptor Channel
Authors: Klesse Gianni , Tucker Stephen J. , Sansom Mark S.P.
Published: May 2020

In this study we examined the influence of a transmembrane voltage on the hydrophobic gating of nanopores using molecular dynamics simulations. We observed electric field induced wetting of a hydrophobic gate in a biologically inspired model nanopore based on the 5-HT3receptor in its closed state, with a field of at least ∼100 mV nm−1was required to hydrate the pore. We also found an unequal distribution of charged residues can generate an electric field intrinsic to the nanopore which, depending on its orientation, can alter the effect of the external field, thus making the wetting response asymmetric. This wetting response could be described by a simple model based on water surface tension, the volumetric energy contribution of the electric field, and the influence of charged amino acids lining the pore. Finally, the electric field response was used to determine time constants characterising the phase transitions of water confined within the nanopore, revealing liquid-vapour oscillations on a time scale of ~5 ns. This time scale was largely independent of the water model employed and was similar for different sized pores representative of the open and closed states of the pore. Furthermore, our finding that the threshold voltage required for hydrating a hydrophobic gate depends on the orientation of the electric field provides an attractive perspective for the design of rectifying artificial nanopores.

ToC/Abstract Graphic
Characterization ofmWakeexpression in the murine brain
Authors: Bell Benjamin J. , Wang Annette A. , Kim Dong Won , Blackshaw Seth , Wu Mark N.
Published: May 2020

Structure-function analyses of the mammalian brain have historically relied on anatomically-based approaches. In these investigations, physical, chemical, or electrolytic lesions of anatomical structures are applied, and the resulting behavioral or physiological responses assayed. An alternative approach is to focus on the expression pattern of a molecule whose function has been characterized and then use genetic intersectional methods to optogenetically or chemogenetically manipulate distinct circuits. We previously identified WIDE AWAKE (WAKE) inDrosophila, a clock output molecule that mediates the temporal regulation of sleep onset and sleep maintenance. More recently, we have studied the mouse homolog, mWAKE/ANKFN1, and found that its role in the circadian regulation of arousal is conserved. Here, we perform a systematic analysis of the expression pattern ofmWakemRNA, protein, and cells throughout the adult mouse brain. We find that mWAKE labels neurons in a restricted, but distributed manner, in multiple regions of the hypothalamus (including the suprachiasmatic nucleus), the limbic system, sensory processing nuclei, and additional specific brainstem, subcortical, and cortical areas. Interestingly, mWAKE is also observed in non-neuronal ependymal cells. In addition, to describe the molecular identities and clustering ofmWake+cells, we provide detailed analyses of single cell RNA sequencing data from the hypothalamus, a region with particularly significant mWAKE expression. These findings lay the groundwork for future studies into the potential role ofmWake+cells in the rhythmic control of diverse behaviors and physiological processes.