bluuebunny/crossref_metadata_2025 huggingface dataset:
Hierarchical Gaussian Processes and Mixtures of Experts to Model COVID-19 Patient Trajectories
Authors: Cui Sunny , Yoo Elizabeth C. , Li Didong , Laudanski Krzysztof , Engelhardt Barbara E.
Published: October 2021

Gaussian processes (GPs) are a versatile nonparametric model for nonlinear regression and have been widely used to study spatiotemporal phenomena. However, standard GPs offer limited interpretability and generalizability for datasets with naturally occurring hierarchies. With large-scale, rapidly-updating electronic health record (EHR) data, we want to study patient trajectories across diverse patient cohorts while preserving patient subgroup structure. In this work, we partition our cohort of over 2000 COVID-19 patients by sex and ethnicity. We develop and apply a hierarchical Gaussian process and a mixture of experts (MOE) hierarchical GP model to fit patient trajectories on clinical markers of disease progression. A case study for albumin, an effective predictor of COVID-19 patient outcomes, highlights the predictive performance of these models. These hierarchical spatiotemporal models of EHR data bring us a step closer toward our goal of building flexible approaches to capture patient data that can be used in real-time systems*.
Monkey Plays Pac-Man with Compositional Strategies and Hierarchical Decision-making
Authors: Yang Qianli , Lin Zhongqiao , Zhang Wenyi , Li Jianshu , Chen Xiyuan , Zhang Jiaqi , Yang Tianming
Published: October 2021

Humans can often handle daunting tasks with ease by developing a set of strategies to reduce decision making into simpler problems. The ability to use heuristic strategies demands an advanced level of intelligence and has not been demonstrated in animals. Here, we trained macaque monkeys to play the classic video game Pac-Man. The monkeys’ decision-making may be described with a strategy-based hierarchical decision-making model with over 90% accuracy. The model reveals that the monkeys adopted the take-the-best heuristic by using one dominating strategy for their decision-making at a time and formed compound strategies by assembling the basis strategies to handle particular game situations. With the model, the computationally complex but fully quantifiable Pac-Man behavior paradigm provides a new approach to understanding animals’ advanced cognition.

One-Sentence Summary

Macaque monkeys play Pac-Man with strategy-based hierarchical decision making, a cognitive capacity hitherto unknown in them.
Self-association configures the NAD+-binding site of plant NLR TIR domains
Authors: Burdett Hayden , Hu Xiahao , Rank Maxwell X. , Maruta Natsumi , Kobe Bostjan
Published: October 2021

TIR domains are signalling domains present in plant nucleotide-binding leucine-rich repeat receptors (NLRs), with key roles in plant innate immunity. They are required for the induction of a hypersensitive response (HR) in effector-triggered immunity, but the mechanism by which this occurs is not yet fully understood. It has been recently shown that the TIR domains from several plant NLRs possess NADase activity. The oligomeric structure of TIR-containing NLRs ROQ1 and RPP1 reveals how the TIR domains arrange into an active conformation, but low resolution around the NAD+ binding sites leaves questions unanswered about the molecular mechanisms linking self-association and NADase activity. In this study, a number of crystal structures of the TIR domain from the grapevine NLR RUN1 reveal how self-association and enzymatic activity may be linked. Structural features previously proposed to play roles involve the “AE interface” (mediated by helices A and E), the “BB-loop” (connecting β-strand B and helix B in the structure), and the “BE interface” (mediated by the BB-loop from one TIR and the “DE surface” of another). We demonstrate that self-association through the AE interface induces conformational changes in the NAD+-binding site, shifting the BB-loop away from the catalytic site and allowing NAD+ to access the active site. We propose that an intact “DE surface” is necessary for production of the signalling product (variant cyclic ADPR), as it constitutes part of the active site. Addition of NAD+ or NADP+ is not sufficient to induce self-association, suggesting that NAD+ binding occurs after TIR self-association. Our study identifies a mechanistic link between TIR self-association and NADase activity.
Dynamic Allostery Highlights the Evolutionary Differences between the CoV-1 and CoV-2 Main Proteases
Authors: Campitelli P. , Lu J. , Ozkan S. B.
Published: October 2021

The SARS-CoV-2 coronavirus has become one of the most immediate and widely-studied systems since its identification and subsequent global outbreak from 2019-2020. In an effort to understand the biophysical changes as a result of mutations, the mechanics of multiple different proteins within the SARS-CoV-2 virus have been studied and compared with SARS-CoV-1. Focusing on the main protease (mPro), we first explored the long range dynamic-relationship, particularly in cross-chain dynamics, using the Dynamic Coupling Index (DCI) to investigate the dynamic coupling between the catalytic site residues and the rest of the protein, both inter and intra chain for the CoV-1 and CoV-2 mPro. We found that there is significant cross-chain coupling between these active sites and distal residues in the CoV-2 mPro but it was missing in CoV-1. The enhanced long distance interactions, particularly between the two chains, suggest subsequently enhanced cooperativity for CoV-2. A further comparative analysis of the dynamic flexibility using the Dynamic Flexibility Index (DFI) between the CoV-1 and CoV-2 mPros shows that the inhibitor binding near active sites induces change in flexibility to a distal region of the protein, opposite in behavior between the two systems; this region becomes more flexible upon inhibitor binding in CoV-1 while it becomes less flexible in the CoV-2 mPro. Upon inspection, we show that, on average, the dynamic flexibility of the sites substituted from CoV-1 to CoV-2 changes significantly less than the average calculated across all residues within the structure, indicating that the differences in behaviors between the two systems is likely the result of allosteric influence, where the new substitutions in COV-2 induce flexibility and dynamical changes elsewhere in the structure.

SIGNIFICANCE

Here we have conducted a comparative analysis between the SARS-CoV-1 and SARS-CoV-2 mPro systems to shed mechanistic insight on the biophysical changes associated with the mutations between these two enzymes. Our work shows that the CoV-2 mPro system exhibits enhanced cross-chain communication between catalytic site residues and the rest of the structure. Further, both dynamic coupling and dynamic flexibility analyses indicates that, largely, the dynamic changes as evaluated by DCI and DFI occur at sites other than the mutation sites themselves, indicating that the functional differences between these two proteins are a result of dynamic allostery
Gut Microbiome Signatures Linked to HIV-1 Reservoir Size and Viremia Control
Authors: Borgognone Alessandra , Noguera-Julian Marc , Oriol Bruna , Noël-Romas Laura , Ruiz-Riol Marta , Guillén Yolanda , Parera Mariona , Casadellà Maria , Duran Clara , Puertas Maria C. , Català-Moll Francesc , De Leon Marlon , Knodel Samantha , Birse Kenzie , Manzardo Christian , Miró Jose M. , Clotet Bonaventura , Martinez-Picado Javier , Moltó José , Mothe Beatriz , Burgener Adam , Brander Christian , Paredes Roger ,   the BCN02 Study Group
Published: October 2021

Background

The potential role of the gut microbiome as a predictor of immune-mediated HIV-1 control in the absence of antiretroviral therapy (ART) is still unknown. In the BCN02 clinical trial, which combined the MVA.HIVconsv immunogen with the latency-reversing agent romidepsin in early-ART treated HIV-1 infected individuals, 23% (3/13) of participants showed sustained low-levels of plasma viremia during 32 weeks of a monitored ART pause (MAP). Here, we present a multi-omics analysis to identify compositional and functional gut microbiome patterns associated with HIV-1 control in the BCN02 trial.

Results

Viremic controllers during the MAP (controllers) exhibited higher Bacteroidales/Clostridiales ratio and lower microbial gene richness before vaccination and throughout the study intervention when compared to non-controllers. Longitudinal assessment indicated that the gut microbiome of controllers was enriched in pro-inflammatory bacteria and depleted in butyrate-producing bacteria and methanogenic archaea. Functional profiling also showed that metabolic pathways, including methanogenesis and carbohydrate biosynthesis, were significantly decreased in controllers. Fecal metaproteome analyses confirmed that baseline functional differences were mainly driven by Clostridiales. Participants with high baseline Bacteroidales/Clostridiales ratio had increased pre-existing immune activation-related transcripts. The Bacteroidales/Clostridiales ratio as well as host immune-activation signatures inversely correlated with HIV-1 reservoir size.

Conclusions

This proof-of-concept study suggests the Bacteroidales/Clostridiales ratio as a novel gut microbiome signature associated with HIV-1 reservoir size and immune-mediated viral control after ART interruption.
Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not
Authors: Gu Huiya , Harris Hannah , Olshansky Moshe , Eliaz Yossi , Krishna Akshay , Kalluchi Achyuth , Jacobs Mozes , Cauer Gesine , Pham Melanie , Rao Suhas S.P. , Dudchenko Olga , Omer Arina , Mohajeri Kiana , Kim Sungjae , Nichols Michael H , Davis Eric S. , Udupa Devika , Aiden Aviva Presser , Corces Victor G. , Phanstiel Douglas H. , Noble William Stafford , Seo Jeong-Sun , Talkowski Michael E. , Aiden Erez Lieberman , Rowley M. Jordan
Published: October 2021

Megabase-scale intervals of active, gene-rich and inactive, gene-poor chromatin are known to segregate, forming the A and B compartments. Fine mapping of the contents of these A and B compartments has been hitherto impossible, owing to the extraordinary sequencing depths required to distinguish between the long-range contact patterns of individual loci, and to the computational complexity of the associated calculations. Here, we generate the largest published in situ Hi-C map to date, spanning 33 billion contacts. We also develop a computational method, dubbed PCA of Sparse, SUper Massive Matrices (POSSUMM), that is capable of efficiently calculating eigenvectors for sparse matrices with millions of rows and columns. Applying POSSUMM to our Hi-C dataset makes it possible to assign loci to the A and B compartment at 500 bp resolution. We find that loci frequently alternate between compartments as one moves along the contour of the genome, such that the median compartment interval is only 12.5 kb long. Contrary to the findings in coarse-resolution compartment profiles, we find that individual genes are not uniformly positioned in either the A compartment or the B compartment. Instead, essentially all (95%) active gene promoters localize in the A compartment, but the likelihood of localizing in the A compartment declines along the body of active genes, such that the transcriptional termini of long genes (>60 kb) tend to localize in the B compartment. Similarly, nearly all active enhancers elements (95%) localize in the A compartment, even when the flanking sequences are comprised entirely of inactive chromatin and localize in the B compartment. These results are consistent with a model in which DNA-bound regulatory complexes give rise to phase separation at the scale of individual DNA elements.
Neuropeptidergic regulation of Compulsive Ethanol Seeking in C. elegans
Authors: Salim Chinnu , Kan Ann Ke , Patterson E. Clare , Jee Changhoon
Published: October 2021

An improved understanding of the molecular basis of alcohol seeking despite the catastrophic consequences of alcohol abuse is likely to enrich our treatments for Alcohol Use Disorders (AUD) and comorbidities. The compulsive seeking is characterized by an imbalance between the superior drive to substance and disruption in control of substance use. To model the development of compulsive engagement of alcohol seeking, we exploit two distinct behavioral programs of C. elegans in conflict, ethanol preference and avoidance of aversive stimulus, simultaneously. We demonstrate that C. elegans exhibited the recapitulation of the pivotal features of compulsive alcohol seeking in mammals, which are repeated attempts, endurance, and finally aversion-resistant ethanol seeking. We find that the neuropeptide signaling via SEB-3, CRF receptor-like GPCR, facilitates the development of ethanol preference and compels animals to seek ethanol compulsively. Furthermore, our functional genomic approach and behavioral elucidation suggest the interaction between neuropeptidergic signaling, SEB-3 and TKR-1, Neurokinin receptor orthologue, to progress compulsive ethanol seeking behavior.
Neutrophil reverse migration from liver fuels neutrophilic inflammation to tissue injury in Nonalcoholic Steatohepatitis
Authors: Feliz-Norberto Maria , Michael Cassia , de Oliveira Sofia
Published: October 2021

Inflammation is a hallmark in the progression of nonalcoholic-fatty liver disease (NAFLD) to non-alcoholic steatohepatitis (NASH). Patients with NAFLD are characterized by a chronic low-grade systemic metabolic inflammation (i.e., metainflammation), which contributes to exacerbated however dysfunctional immune response. Neutrophils play an important pathological role in NAFLD progression to NASH; however, how NASH and associated chronic systemic inflammation impact overall the neutrophil response to injury is completely unexplored. Here, we investigated how neutrophil response to tissue injury is altered by the presence of NASH. We used a diet-induced NASH zebrafish model combined with tailfin transection in transgenic zebrafish larvae to study neutrophilic inflammation. Live non-invasive confocal microscopy was used to investigate neutrophil recruitment to tailfin injury through time. Photoconvertion of neutrophils at the liver area followed by time-lapse microscopy was performed to evaluate migration of neutrophils from liver to tailfin injury. Metformin and Pentoxifylline were used to pharmacologically reduce NASH and liver inflammation. We found that larvae with NASH display systemic inflammation and increased myelopoiesis. NASH larvae display a dysfunctional and exacerbated neutrophil response to tailfin injury, characterized by increased neutrophil recruitment, and delayed resolution of inflammation. Interestingly, we showed that neutrophils undergo reverse migration from the NASH liver to the wounded tailfin area. Finally, pharmacological treatment of NASH with Pentoxifylline and Metformin significantly reduced systemic chronic inflammation and the exacerbated recruitment of neutrophils to tissue injury. Taken together, our findings suggest that NASH exacerbates neutrophilic inflammation probably via neutrophil priming at the liver, which can further undergo reverse migration and respond to secondary inflammatory triggers such as tissue injury. Reverse migration of primed neutrophils from the liver might be an important mechanism that fuels the exacerbated neutrophil response observed in NASH conditions and associated metainflammation contributing to poor prognosis and increasing death in patients with metabolic syndrome.
Identifying a novel role for the master regulator Tal1 in the Endothelial to Hematopoietic Transition
Authors: Serina Secanechia Yasmin Natalia , Bergiers Isabelle , Rogon Matt , Arnold Christian , Descostes Nicolas , Le Stephanie , Lopez Anguita Natalia , Ganter Kerstin , Kapsali Chrysi , Bouilleau Lea , Gut Aaron , Uzuotaite Auguste , Aliyeva Ayshan , Zaugg Judith , Lancrin Christophe
Published: October 2021

Recent progress in the generation of bona-fide Hematopoietic Stem and Progenitor Cells (HSPCs) in vitro and ex vivo has been built on the knowledge of developmental hematopoiesis, underscoring the importance of understanding in detail this developmental process. Here, we sought to elucidate the function of the hematopoietic regulators Tal1, Lmo2 and Lyl1 in the Endothelial to Hematopoietic Transition (EHT), the process through which HSPCs are generated from endothelial precursors during embryogenesis. We used a mouse embryonic-stem cell (mESC)-based differentiation system to model hematopoietic development, and combined gain-of-function experiments in sorted vascular smooth muscle cells (VSM) with multi-omics to obtain mechanistic insights into the mode of action of Tal1, Lmo2 and Lyl1. We found that these factors promote the silencing of the VSM transcriptional program and the activation of the hematopoietic one. Through this approach and the use of a Tet-on system to control the expression of Tal1 during hematopoietic specification from mESCs, we discovered that its expression in endothelial cells is crucial for the EHT to occur.
Alterations in Connectome Dynamics in Autism Spectrum Disorder: A Harmonized Mega- and Meta-Analysis Study Using the ABIDE Dataset
Authors: Xie Yapei , Xu Zhilei , Xia Mingrui , Liu Jin , Shou Xiaojing , Cui Zaixu , Liao Xuhong , He Yong
Published: October 2021

BACKGROUND

Neuroimaging studies have reported functional connectome aberrancies in autism spectrum disorder (ASD). However, the time-varying patterns of connectome topology in ASD individuals and the connection between these patterns and gene expression profiles remain unknown.

METHODS

To investigate case-control differences in dynamic connectome topology, we conducted mega- and meta-analyses of resting-state functional magnetic resonance imaging data of 939 participants (440 ASD patients and 499 healthy controls, all males) from 18 independent sites, selected from the ABIDE (Autism Brain Imaging Data Exchange) dataset. Functional data was preprocessed and analyzed using harmonized protocols, and brain module dynamics was assessed using a multilayer network model. We further leveraged postmortem brain-wide gene expression data to identify transcriptomic signatures associated with ASD-related alterations in brain dynamics.

RESULTS

Compared to healthy controls, ASD individuals exhibited a higher global mean and lower standard deviation of whole-brain module dynamics, indicating an unstable and less regionally differentiated pattern. More specifically, ASD individuals showed higher module switching, primarily in the medial prefrontal cortex, posterior cingulate gyrus, and angular gyrus, and lower switching in the visual regions. These alterations in brain dynamics were predictive of social impairments in ASD individuals and were linked with expression profiles of genes primarily involved in the regulation of neurotransmitter transport and secretion, as well as with previously identified autism-related genes.

CONCLUSIONS

This study is the first to identify consistent alterations in brain network dynamics in ASD and the transcriptomic signatures related to those alterations, furthering insights into the biological basis behind this disorder.
Color is necessary for specialized face learning in the Northern paper wasp, Polistes fuscatus
Authors: Jernigan Christopher M. , Stafstrom Jay A. , Zaba Natalie C. , Vogt Caleb C. , Sheehan Michael J.
Published: October 2021

Visual individual recognition requires animals to distinguish among conspecifics based on appearance. Though visual individual recognition has been reported in a range of taxa, the features that animals rely on to discriminate between individuals are often not well understood. Northern paper wasp females, Polistes fuscatus, possess individually distinctive color patterns on their faces, which mediate individual recognition. It is currently unclear what facial features P. fuscatus use to distinguish individuals. The anterior optic tubercle, a chromatic processing brain region, is especially sensitive to social experience during development, suggesting that color may be important for recognition in this species. We sought to test the roles of color in wasp facial recognition. Color may be important simply because it creates a pattern. If this is the case, then wasps should perform similarly when discriminating color or grayscale images of the same faces. Alternatively, color itself may be important for recognition, which would predict poorer performance on grayscale image discrimination relative to color images. We found wasps trained on grayscale faces, unlike those trained on color images, did not perform better than chance. Suggesting that color is necessary for the recognition of an image as a face by the wasp visual system.
Sex chromosomes, sex ratios and sex gaps in longevity in plants
Authors: Marais Gabriel AB , Lemaitre J-F.
Published: October 2021

In animals, males and females can display markedly different longevity (also called sex gap in longevity, SGLs). Recent work has revealed that sex chromosomes contribute to establishing these SGLs. X-hemizygosity and toxicity of the Y chromosomes are two mechanisms that have been suggested to reduce male longevity (Z-hemizygosity and W toxicity in females in ZW systems). In plants, SGLs are known to exist but the role of sex chromosomes remains to be established. Here, by using adult sex ratio as a proxy for measuring SGLs, we explored the relationship between sex chromosome and SGLs across 43 plant species. Based on the knowledge recently accumulated in animals, we specifically asked whether: (i) species with XY systems tend to have female-biased sex ratios (reduced male longevity) and species with ZW ones tend to have male-biased sex ratios (reduced female longevity), and (ii) this patterns was stronger in heteromorphic systems compared to homomorphic ones. Our results tend to support these predictions although we lack statistical power because of a small number of ZW systems and the absence of any heteromorphic ZW system in the dataset. We discuss the implications of these findings, which we hope will stimulate further research on sex-differences in lifespan and ageing across plants.
Increased remodeling and impaired adaption to endurance exercise in desminopathy
Authors: Mossakowski Agata A. , Langer Henning T. , Bizieff Alec , Avey Alec M. , Zbinden-Foncea Hermann , Hellerstein Marc , Baar Keith
Published: October 2021

Desminopathy the most common intermediate filament disease in humans. Desmin is an essential part of the filamentous network that aligns myofibrils, anchors nuclei and mitochondria, and connects the z-discs and the sarcolemma. We created a rat model with a mutation in R349P DES, analog to the most frequent R350P DES missense mutation in humans. To examine the effects of a chronic, physiological exercise stimulus on desminopathic muscle, we subjected R349P DES rats and their wildtype (WT) and heterozygous littermates to a treadmill running regime. We saw significantly lower running capacity in DES rats that worsened over the course of the study. We found indicators of increased autophagic and proteasome activity with running in DES compared to WT. Stable isotope labeling and LC-MS analysis displayed distinct adaptations of the proteomes of WT and DES animals at baseline as well as with exercise: While key proteins of glycolysis, mitochondria and thick filaments increased their synthetic activity with running in WT, these proteins were higher at baseline in DES and did not change with running. The results suggest an impairment in adaption to chronic exercise in DES muscle and a subsequent exacerbation in the functional and histopathological phenotype.
A Bidirectional Switch in the Shank3 Phosphorylation State Biases Synapses toward Up or Down Scaling
Authors: Wu Chi-Hong , Tatavarty Vedakumar , Beltran Pierre MJ , Guerrero Andrea , Keshishian Hasmik , Krug Karsten , MacMullan Melanie A , Li Li , Carr Steven A , Cottrell Jeffrey R , Turrigiano Gina G
Published: October 2021

Homeostatic synaptic plasticity requires widespread remodeling of synaptic signaling and scaffolding networks, but the role of posttranslational modifications in this process has not been systematically studied. Using deepscale, quantitative analysis of the phosphoproteome in mouse neocortical neurons, we found wide-spread and temporally complex changes during synaptic scaling up and down. We observed 424 bidirectionally modulated phosphosites that were strongly enriched for synapse-associated proteins, including S1539 in the ASD-associated synaptic scaffold protein Shank3. Using a parallel proteomic analysis performed on Shank3 isolated from rat neocortical neurons by immunoaffinity, we identified two sites that were hypo-phosphorylated during scaling up and hyper-phosphorylated during scaling down: one (rat S1615) that corresponded to S1539 in mouse, and a second highly conserved site, rat S1586. The phosphorylation status of these sites modified the synaptic localization of Shank3 during scaling protocols, and dephosphorylation of these sites via PP2A activity was essential for the maintenance of synaptic scaling up. Finally, phosphomimetic mutations at these sites prevented scaling up but not down, while phosphodeficient mutations prevented scaling down but not up. Thus, an activity-dependent switch between hypo- and hyperphosphorylation at S1586/ S1615 of Shank3 enables scaling up or down, respectively. Collectively our data show that activity-dependent phosphoproteome dynamics are important for the functional reconfiguration of synaptic scaffolds, and can bias synapses toward upward or downward homeostatic plasticity.
Fourteen-days Evolution of COVID-19 Symptoms During the Third Wave in Non-vaccinated Subjects and Effects of Hesperidin Therapy: A randomized, double-blinded, placebo-controlled study
Authors: Dupuis Jocelyn , Laurin Pierre , Tardif Jean-Claude , Hausermann Leslie , Rosa Camille , Guertin Marie-Claude , Thibaudeau Karen , Gagnon Lyne , Cesari Frank , Robitaille Martin , Moran John E.
Published: October 2021

COVID-19 symptoms can cause substantial disability, yet no therapy can currently reduce their frequency or duration. We conducted a double-blind placebo-controlled trial of hesperidin 1000 mg once-daily for 14 days in 216 symptomatic non-vaccinated COVID-19 subjects. Thirteen symptoms were recorded after 3, 7, 10 and 14 days. The primary endpoint was the proportion of subjects with any of four cardinal (group A) symptoms: fever, cough, shortness of breath or anosmia. At baseline, symptoms in decreasing frequency were: cough (53.2%), weakness (44.9%), headache (42.6%), pain (35.2%), sore throat (28.7%), runny nose (26.9%), chills (22.7%), shortness of breath (22.2%), anosmia (18.5%), fever (16.2%), diarrhea (6.9%), nausea/vomiting (6.5%) and irritability/confusion (3.2%). Group A symptoms in the placebo vs hesperidin group was 88.8% vs 88.5% (day 1) and reduced to 58.5 vs 49.4 % at day 14 (OR 0.69, 95% CI 0.38–1.27, p = 0.23). At day 14, 15 subjects in the placebo group and 28 in the hesperidin group failed to report their symptoms. In an attrition bias analysis imputing “no symptoms” to missing values, the hesperidin group shows reduction of 14.5 % of group A symptoms from 50.9% to 36.4% (OR: 0.55, 0.32–0.96, p = 0.03). Anosmia, the most frequent persisting symptom (29.3%), was lowered by 7.3% at 25.3 % in the hesperidin group vs 32.6% in the placebo group (p = 0.29). Mean number of symptoms in placebo and hesperidin was 5.10 ± 2.26 vs 5.48 ± 2.35 (day 1) and 1.40 ± 1.65 vs 1.38 ± 1.76 (day 14) (p = 0.92). In conclusion, most non-vaccinated COVID-19 infected subjects remain symptomatic after 14 days with anosmia being the most frequently persisting symptom. Hesperidin 1g daily may help reduce group A symptoms. Earlier treatment of longer duration and/or higher dosage should be tested.
Use of an EHR to inform an administrative data algorithm to categorize inpatient COVID-19 severity
Authors: Garry Elizabeth M. , Weckstein Andrew R. , Quinto Kenneth , Lasky Tamar , Chakravarty Aloka , Leonard Sandy , Vititoe Sarah E. , Easthausen Imaani J. , Rassen Jeremy A. , Gatto Nicolle M.
Published: October 2021

STRUCTURED ABSTRACT

Importance

Algorithms for classification of inpatient COVID-19 severity are necessary for confounding control in studies using real-world data (RWD).

Objective

To explore use of electronic health record (EHR) data to inform an administrative data algorithm for classification of supplemental oxygen or noninvasive ventilation (O2/NIV) and invasive mechanical ventilation (IMV) to assess disease severity in hospitalized COVID-19 patients.

Design

In this retrospective cohort study, we developed an initial procedure-based algorithm to identify O2/NIV, IMV, and NEITHER O2/NIV nor IMV in two inpatient RWD sources. We then expanded the algorithm to explore the impact of adding diagnoses indicative of clinical need for O2/NIV (hypoxia, hypoxemia) or IMV (acute respiratory distress syndrome) and O2-related patient vitals available in the EHR. Observed changes in severity categorization were used to augment the administrative algorithm.

Setting

Optum de-identified COVID-19 EHR data and HealthVerity claims and chargemaster data (March – August 2020).

Participants

Among patients hospitalized with COVID-19 in each RWD source, our motivating example selected dexamethasone (DEX+) initiators and a random selection of patients who were non-initiators of a corticosteroid of interest (CSI-) matched on date of DEX initiation, age, sex, baseline comorbidity score, days since admission, and COVID-19 severity level (NEITHER, O2/NIV, IMV) on treatment index.

Main Outcome and Measures

Inpatient COVID-19 severity was defined using the algorithms developed to classify respiratory support requirements among hospitalized COVID-19 patients (NEITHER, O2/NIV, IMV). Measures were reported as the treatment-specific distributions of patients in each severity level, and as observed changes in severity categorization between the initial procedure-based and expanded algorithms.

Results

In the administrative data cohort with 5,524 DEX+ and CSI- patient pairs matched using the initial procedure-based algorithm, 30% were categorized as O2/NIV, 5% as IMV, and 65% as NEITHER. Among patients assigned NEITHER via the initial algorithm, use of an expanded algorithm informed by the EHR-based algorithm shifted 54% DEX+ and 28% CSI- to O2/NIV, and 2% DEX+ and 1% CSI- to IMV. Among patients initially assigned O2/NIV, 7% DEX+ and 3% CSI- shifted to IMV.

Conclusions and Relevance

Application of learnings from an EHR-based exploration to our administrative algorithm minimized treatment-differential misclassification of COVID-19 severity.
Development and validation of a multiplex real-time qPCR assay using GMP-grade reagents for leprosy diagnosis
Authors: de Neves Manta Fernanda Saloum , Jacomasso Thiago , de Cássia Pontello Rampazzo Rita , Maria Moreira Suelen Justo , Zahra Najua , Ribeiro-Alves Marcelo , Krieger Marco Aurélio , Costa Alexandre Dias Tavares , Ozório Moraes Milton
Published: October 2021

Leprosy is a chronic dermato-neurological disease caused by Mycobacterium leprae, an obligate intracellular bacterium. Timely detection is a challenge in leprosy diagnosis, relying on clinical examination and trained health professionals. Furthermore, adequate care and transmission control depend on early and reliable pathogen detection. Here, we describe a qPCR test for routine diagnosis of leprosy-suspected patients. The reaction simultaneously amplifies two specific Mycobacterium leprae targets (16S rRNA and RLEP), and the human 18S rRNA gene as internal control. The limit of detection was estimated to be 2.29 copies of M. leprae genome. Analytical specificity was evaluated using a panel of 20 other skin pathogenic microorganisms and Mycobacteria, showing no cross-reactivity. Intra- and inter-operator Cp variation was evaluated using dilution curves of M. leprae DNA or a synthetic gene, and no significant difference was observed between three operators in two different laboratories. The multiplex assay was evaluated using 97 patient samples with clinical and histopathological leprosy confirmation, displaying high diagnostic sensitivity (91%) and specificity (100%). Validation tests in an independent panel of 50 samples confirmed sensitivity and specificity of 97% and 98%, respectively. Importantly, assay performance remained stable for at least five months. Our results show that the newly developed multiplex qPCR effectively and specifically detects M. leprae DNA in skin samples, contributing to an efficient diagnosis that expedites the appropriate treatment.

Author Summary

Leprosy is a chronic dermato-neurological disease caused by Mycobacterium leprae, an obligate intracellular bacterium. Disease diagnosis is currently performed on skin examinations for clinical signs, bacilli staining in skin smears and invasive skin biopsies. However, the spectrum of clinical manifestations and the low bacterial load can hinder accurate diagnosis, which is critical for providing proper intervention and adequate care as well as for establishing transmission control. Quantitative PCR (qPCR) methods for detecting bacterial DNA are more sensitive and could aid in differentially diagnosing leprosy from other dermatological conditions. In this work, we present a new multiplex qPCR that detects two bacterial genes for the diagnosis and a human gene as an internal reaction control. The new qPCR, developed using GMP-grade reagents, is highly sensitive, specific, reproducible, and stable. The results presented here are the basis of a novel and robust tool with potential to increase the accuracy of leprosy diagnosis in routine or reference laboratories.
T cell stimulation remodels the latently HIV-1 infected cell population by differential activation of proviral chromatin
Authors: Lindqvist Birgitta , Assi Wlaa , Roux Julie , Love Luca , Jütte Bianca B. , Sönnerborg Anders , Tezil Tugsan , Verdin Eric , Svensson J. Peter
Published: October 2021

The reservoir of latently HIV-1 infected cells is heterogeneous. To achieve an HIV-1 cure, the reservoir of activatable proviruses should be eliminated while permanently silenced proviruses may be tolerated. We have developed a method to assess the proviral nuclear microenvironment in single cells. In latently HIV-1 infected cells, a zinc finger protein tethered to the HIV-1 promoter produced a fluorescent signal as a protein of interest came in its proximity, such as the viral transactivator Tat when recruited to the nascent RNA. Tat is essential for viral replication. In these cells we assessed the proviral activation and chromatin composition. By linking Tat recruitment to proviral activity, we dissected the mechanisms of HIV-1 latency reversal and the consequences of HIV-1 production. A pulse of promoter-associated Tat was identified that contrasted to the continuous production of viral proteins. As expected, promoter H3K4me3 led to substantial expression of the provirus following T cell stimulation. However, the activation-induced cell cycle arrest and death led to a surviving cell fraction with proviruses encapsulated in repressive chromatin. Further, this cellular model was used to reveal mechanisms of action of small molecules. In a proof-of-concept study we determined the effect of an enhancer specific CBP/P300-inhibitor on HIV-1 latency reversal. Only proviruses resembling active enhancers, associated with H3K4me1 and H3K27ac, efficiently recruited Tat. Tat-independent HIV-1 latency reversal of unknown significance still occurred. We present a method for single cell assessment of the microenvironment of the latent HIV-1 proviruses, used here to reveal how T cell stimulation modulates the proviral activity and how the subsequent fate of the infected cell depends on the chromatin context.
Highly Reversible Tunable Thermal-repressible Split-T7 RNA polymerases (Thermal-T7RNAPs) for dynamic gene regulation
Authors: Chee Wai Kit David , Yeoh Jing Wui , Dao Viet Linh , Poh Chueh Loo
Published: October 2021

Temperature is a physical cue that is easy to apply, allowing cellular behaviors to be controlled in a contactless and dynamic manner via heat-inducible/repressible systems. However, existing heat-repressible systems are limited and rely on thermal sensitive mRNA or transcription factors which function at low temperatures, lack tunability, suffer delays or overly-complex. To provide an alternative mode of thermal regulation, we developed a library of compact, reversible and tunable thermal-repressible split-T7 RNA polymerase systems (Thermal-T7RNAPs) which fuses temperature-sensitive domains of Tlpa protein with split-T7RNAP to enable direct thermal control of the T7RNAP activity between 30 – 42 °C. We generated a large mutant library with varying thermal performances via automated screening framework to extend temperature tunability. Lastly, using the mutants, novel thermal logic circuitry was implemented to regulate cell growth and achieve active thermal control of the cell proportions within co-cultures. Overall, this technology expands avenues for thermal control in biotechnology applications.
Targeting ON-bipolar cells by AAV gene therapy stably reverses LRIT3-congenital stationary night blindness
Authors: Miyadera Keiko , Santana Evelyn , Roszak Karolina , Iffrig Sommer , Visel Meike , Iwabe Simone , Boyd Ryan F , Bartoe Joshua T , Sato Yu , Gray Alexa , Ripolles Garcia Ana , Dufour Valerie L , Byrne Leah C , Flannery John Gerard , Beltran William A , Aguirre Gustavo D.
Published: October 2021

AAV gene therapies aimed at curing inherited retinal diseases to date have typically focused on photoreceptors and retinal pigmented epithelia within the relatively accessible outer retina. However, therapeutic targeting in diseases such as congenital stationary night blindness (CSNB) that involve defects in ON-bipolar cells (ON-BCs) within the mid-retina has been challenged by the relative inaccessibility of the target cell in intact retinas, the limited transduction efficiency of these cells by existing AAV serotypes, poor availability of established ON-BC-specific promoters, and absence of appropriate patient-relevant large animal models. Here, we demonstrate safe and effective ON-BC targeting by AAV gene therapy in a recently characterized naturally-occurring canine model of CSNB, LRIT3-CSNB. To effectively target ON-BCs, new AAV capsid variants with ON-BC tropism and ON-BC specific modified GRM6 promoters were adopted to ensure cell-specific transgene expression. Notably, subretinal injection of one vector, AAVK9#4-shGRM6-cLRIT3-WPRE, significantly recovered rod-derived b-wave in all treated eyes (6/6) of adult dogs injected at 1-3 years of age. The robust therapeutic effect was evident 7 weeks post-injection and was sustained for at least 1 year in all treated eyes. Scotopic vision was significantly improved in treated eyes based on visually-guided obstacle course navigation. Restoration of LRIT3 signals was confirmed by immunohistochemistry. Thus, we report on the first ON-BC functional rescue in a large animal model using a novel AAV capsid variant and modified promoter construct optimized for ON-BC specificity, thereby establishing both proof-of-concept and a novel translational platform for treatment of CSNB in patients with defects in photoreceptor-to-bipolar signaling.
Metabolic Regulation of Mitochondrial Morphologies in Pancreatic Beta Cells: Bioenergetics-Mitochondrial Dynamics Coupling
Authors: Tseng Wen-Wei , Chu Ching-Hsiang , Chang Chen , Lee Yi-Ju , Zhao Shirui , Ho Yi-Ping , Wei An-Chi
Published: October 2021

Cellular bioenergetics and mitochondrial dynamics are crucial for the secretion of insulin by pancreatic beta cells in response to elevated blood glucose concentrations. To obtain better insights into the interactions between energy production and mitochondrial fission/fusion dynamics, we combine live-cell mitochondria imaging with biophysical-based modeling and network analysis to elucidate the principle regulating mitochondrial morphology to match metabolic demand in pancreatic beta cells. A minimalistic differential equation-based model for beta cells was constructed to include glycolysis, oxidative phosphorylation, simple calcium dynamics, and graph-based fission/fusion dynamics controlled by ATP synthase flux and proton leak flux. The model revealed that mitochondrial fission occurs in response to hyperglycemia, starvation, ATP synthase inhibition, uncoupling, and diabetic condition, in which the rate of proton leak exceeds the rate of mitochondrial ATP synthesis. Under these metabolic challenges, the propensities of tip-to-tip fusion events simulated from the microscopic images of the mitochondrial networks were lower than those in the control group and prevented mitochondrial network formation. The modeling and network analysis could serve as the basis for further detailed research on the mechanisms of bioenergetics and mitochondrial dynamics coupling.
Structure of an ant-myrmecophile-microbe community
Authors: Perry Elena K. , Siozios Stefanos , Hurst Gregory D. D. , Parker Joseph
Published: October 2021

Superorganismal ant colonies play host to a menagerie of symbiotic arthropods, termed myrmecophiles, which exhibit varying degrees of social integration into colony life. Such systems permit examination of how animal community interactions influence microbial assemblages. Here, we present an ecologically and phylogenetically comprehensive characterization of an ant-myrmecophile-microbe community in Southern California. Using 16S rRNA profiling, we find that microbiotas of the velvety tree ant (Liometopum occidentale) and its cohort of myrmecophiles are distinguished by species-specific characteristics but nevertheless bear signatures of their behavioral interactions. We found that the host ant microbiome was diverse at all taxonomic levels; that of a myrmecophilous cricket was moderately diverse, while microbiotas of three myrmecophilous rove beetles (Staphylinidae), which have convergently evolved symbiosis withLiometopum, were dominated by intracellular endosymbionts. Yet, despite these compositional differences, similarities between ant and myrmecophile microbiotas correlated with the nature and intimacy of their behavioral relationships. Physical interactions such as grooming and trophallaxis likely facilitate cross-species extracellular microbial sharing. Further, phylogenetic comparisons of microbiotas from myrmecophile rove beetles and outgroups revealed a lack of co-cladogenesis of beetles and intracellular endosymbionts, and limited evidence for convergence among the myrmecophiles’ intracellular microbiotas. Comparative genomic analyses of the dominantRickettsiaendosymbiont of the most highly socially integrated myrmecophile imply possible functions unrelated to nutrient-provisioning in the host beetle’s specialized lifestyle. Our findings indicate that myrmecophile microbiotas evolve largely independently of the constraints of deep evolutionary history, and that the transition to life inside colonies, including social interactions with hosts, plays a significant role in structuring bacterial assemblages of these symbiotic insects.
Emergence of rare carbapenemases (FRI, GES-5, IMI, SFC, and SFH-1) in Enterobacterales isolated from surface waters in Japan
Authors: Gomi Ryota , Matsumura Yasufumi , Tanaka Michio , Ihara Masaru , Sugie Yoshinori , Matsuda Tomonari , Yamamoto Masaki
Published: October 2021

Objectives

Carbapenemase-producing Enterobacterales (CPE) pose serious threats to public health. Compared with clinical CPE, the genetic characteristics of environmental CPE are not well understood. This study aimed to characterize the genetic determinants of carbapenem resistance in CPE isolated from environmental waters in Japan.

Methods

Eighty-five water samples were collected from rivers and a lake in Japan. CPE were identified using selective media, and genome sequencing was performed for the obtained isolates (n = 21).

Results

Various rare/novel carbapenemases were identified: GES-5 in Raoultella planticola (n = 1), FRI-8 and FRI-11 in Enterobacter spp. (n = 8), IMI-22 and IMI-23 in Serratia ureilytica (n = 3), and SFC-1, SFC-2 and SFH-1 in Serratia fonticola (n = 9). Genomes of 11 isolates could be closed, allowing the elucidation of the genetic contexts of the carbapenemase genes. The blaGES-5 gene was located within a class 1 integron, In2071 (cassette array, blaGES-5-aacA3-aadA16), on a 33 kb IncP6 plasmid. The blaFRI-8 genes were carried on IncFII(Yp) plasmids ranging in size from 191 kb to 244 kb, and the blaFRI-11 genes were carried on 70 kb and 74 kb IncFII(pECLA)/IncR plasmids. The blaIMI-22 and blaIMI-23 genes were colocated on a 107 kb plasmid. The blaSFC and blaSFH-1 genes were found on putative genomic islands inserted at tRNA-Phe genes in chromosomes.

Conclusions

This study revealed the presence of rare/novel carbapenemases among CPE in aquatic environments, suggesting that the environment may act as a potential reservoir of these minor carbapenemases.
Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts
Authors: Hirata Yoshito , Oda Arisa H. , Motono Chie , Shiro Masanori , Ohta Kunihiro
Published: October 2021

The sparseness of chromosomal contact information and the presence of homologous chromosomes with very similar nucleotide sequences make Hi-C analysis difficult. We propose a new algorithm using allele-specific single-nucleotide variations (SNVs) to reconstruct the three-dimensional (3D) chromosomal architectures from the Hi-C dataset of single diploid cells. Our algorithm has a function to discriminate SNVs specifically found between homologous chromosomes to our “recurrence plot”-based algorithm to estimate the 3D chromosome structure, which does not require imputation for ambiguous segment information. The new algorithm can efficiently reconstruct 3D chromosomal structures in single human diploid cells by employing only Hi-C segment pairs containing allele-specific SNVs. The datasets of the remaining pairs of segments without allele-specific SNVs are used to validate the estimated chromosome structure. This approach was used to reconstruct the 3D structures of human chromosomes in single diploid cells at a 1-Mb resolution. Introducing a subsequent mathematical measure further improved the resolution to 40-kb or 100-kb. The reconstruction data reveals that human chromosomes form chromosomal territories and take fractal structures where the mean dimension is a non-integer value. We also validate our approach by estimating 3D protein/polymer structures.
Machine learning-based modulation of Ca2+-binding affinity in EF-hand proteins and comparative structural insights into site-specific cooperative binding
Authors: Mazumder Mohit , Kumar Sanjeev , Kumar Devbrat , bhattacharya Alok , Gourinath S.
Published: October 2021

Ca2+-binding proteins are present in almost all living organisms and different types display different levels of binding affinities for the cation. Here, we applied two new scoring schemes enabling the user to manipulate the binding affinities of such proteins. We specifically designed a unique EF-hand loop capable of binding calcium with high affinity by altering five residues of the loop based on the scoring scheme. We worked on the N-terminal domain of Entamoeba histolytica calcium-binding protein1 (NtEhCaBP1), and used site-directed mutagenesis to incorporate the designed loop sequence into the second EF hand motif of this protein. The binding isotherms calculated using ITC calorimetry showed a ∼500-fold greater association constant (Ka) for the mutant. The crystal structure of the mutant was also determined, and displayed more compact Ca2+-coordination spheres in both of its EF loops than did the structure of the wildtype protein, consistent with the greater calcium-binding affinities of the mutant. The NtEhCaBP1 mutant was also shown to form a hexamer rather than just a trimer, and this hexamer formation was attributed to the position of the last helix of the mutant having been changed as a result of the strong calcium coordination. Further dynamic correlation analysis revealed that the mutation in the second EF loop changed the entire residue network of the monomer, resulting in a stronger coordination of Ca2+ even in other EF hand loop.