bluuebunny/crossref_metadata_2025 huggingface dataset:
Respiratory Failure in a Child With Pulmonary Metastatic Osteosarcoma and COVID-19
Authors: Offenbacher Rachel , Fabish Lara , Baker Alissa , Chou Alexander J. , Loeb David M.
Published: August 2020

The novel coronavirus, SARS-CoV-2, causes much more severe disease in adults than in children. Although it is anticipated that immune compromised children and children with cancer may be at higher risk of developing severe or fatal COVID-19, there are no currently published reports of fatal disease in a child with cancer. Because of the discrepancy in disease severity between adult and pediatric patients, we report the case of an adolescent with pulmonary metastatic osteosarcoma who died of COVID-19 early in the course of the pandemic in New York City in the hope that heightening awareness that pulmonary metastatic disease may predispose to a more severe outcome will increase surveillance in this vulnerable population.
Are the Anxiety Levels of Pediatric Hematology-Oncology Patients Different From Healthy Peers During the COVID-19 Outbreak?
Authors: Cakiroglu Suleyman , Yeltekin Ceren , Fisgin Tunc , Oner Ozlem B. , Aksoy Basak A. , Bozkurt Ceyhun
Published: August 2020

The COVID-19 outbreak has caused anxiety among children with hematology-oncology disease and their families, as it has in every segment of society. In this study, we aimed to detect the anxiety levels of children with hematologic or oncologic disease and of their parents after the COVID-19 outbreak. The sample consisted of 15 patients 12 to 18 years of age receiving treatment in the Pediatric Hematology and Oncology Unit in Altinbaş University Medical Faculty Bahçelievler Medikalpark Hospital and 33 parents of the same unit patients between 6 and 18 years of age, and their 35 healthy peers and their parents. The State-Trait Anxiety Inventory was applied to participant children and their parents to evaluate their general anxiety and pandemic-related anxiety levels. Children with a hematology-oncology disease and their families were compared with healthy peers and their families. No significant difference was observed for pandemic-related anxiety levels (P>0.05). Both parent groups exhibited higher anxiety levels with regard to the pandemic than did their children (P<0.05). Children with hematology-oncology disease reported significantly higher trait anxiety levels when compared with healthy peers (P=0.01). The families of children who had not received stem cell transplantation had higher state and trait anxiety scores than the families of children who had received the transplantation (P<0.05). Even though they were in the high-risk group, children with a hematology-oncology disease and their families had pandemic-related anxiety levels comparable with those of healthy peers and their families.
Home Healthcare Clinical Notes Predict Patient Hospitalization and Emergency Department Visits
Authors: Topaz Maxim , Woo Kyungmi , Ryvicker Miriam , Zolnoori Maryam , Cato Kenrick
Published: August 2020

Background

About 30% of home healthcare patients are hospitalized or visit an emergency department (ED) during a home healthcare (HHC) episode. Novel data science methods are increasingly used to improve identification of patients at risk for negative outcomes.

Objectives

The aim of the study was to identify patients at heightened risk hospitalization or ED visits using HHC narrative data (clinical notes).

Methods

This study used a large database of HHC visit notes (n = 727,676) documented for 112,237 HHC episodes (89,459 unique patients) by clinicians of the largest nonprofit HHC agency in the United States. Text mining and machine learning algorithms (Naïve Bayes, decision tree, random forest) were implemented to predict patient hospitalization or ED visits using the content of clinical notes. Risk factors associated with hospitalization or ED visits were identified using a feature selection technique (gain ratio attribute evaluation).

Results

Best performing text mining method (random forest) achieved good predictive performance. Seven risk factors categories were identified, with clinical factors, coordination/communication, and service use being the most frequent categories.

Discussion

This study was the first to explore the potential contribution of HHC clinical notes to identifying patients at risk for hospitalization or an ED visit. Our results suggest that HHC visit notes are highly informative and can contribute significantly to identification of patients at risk. Further studies are needed to explore ways to improve risk prediction by adding more data elements from additional data sources.
Paenibacillus Sepsis and Meningitis in a Premature Infant
Authors: Hunt Brice , Rogers Christopher , Blais Rachel Martin , Adachi Kristina , Sathyavagiswaran Lakshmanan
Published: August 2020

Infections due to bacteria of the genus Paenibacillus are exceedingly rare and therefore predominately described on a case-by-case basis. Here, we present a case of a 25-day-old premature neonate who died from presumed Paenibacillus sepsis and meningitis. Most prior reported cases of Paenibacillus bacteremia were among patients who had prosthetic medical devices, were immunocompromised, or were injection drug users. However, to our knowledge, this is the first reported case of infant death from presumed Paenibacillus thiaminolyticus. This case suggests the potential for severe human infection by an environmental bacterium previously considered to be of little consequence.
Does Episodic Future Thinking Repair Immediacy Bias at Home and in the Laboratory in Patients With Prediabetes?
Authors: Bickel Warren K. , Stein Jeffrey S. , Paluch Rocco A. , Mellis Alexandra M. , Athamneh Liqa N. , Quattrin Teresa , Greenawald Mark H. , Bree Kyle A. , Gatchalian Kirstin M. , Mastrandrea Lucy D. , Epstein Leonard H.
Published: August 2020

Objective

This study aimed to determine if episodic future thinking (EFT) can decrease delay discounting (DD) among adults with prediabetes both in and out of the laboratory. DD measures how much the value of a reinforcer decreases as a function of the delay to receive it.

Methods

Adults with prediabetes (n = 67) completed a three-session study. At session 1, baseline measures (including DD) were collected. At sessions 2 and 3, participants were prompted to engage in either EFT or control episodic thinking (CET) while completing DD and other measures. In addition, between the completion of sessions 2 and 3, participants engaged in EFT or CET at home and completed DD tasks remotely via smartphones or other Internet-connected devices.

Results

Results showed significant −1.2759 (−20.24%) reductions in DD in the EFT group compared with a + 0.0287 (+0.46%) DD increase in the CET group (p = .0149) in the laboratory; and −0.4095 (−8.85%) reduction in DD in the EFT group compared with a + 0.2619 (+5.64%) increase in the CET group (p = .011) at home. Working memory (measured by Backwards Corsi and Digit Span) was found to moderate the effects of EFT on some measures of DD. EFT did not change measures from the food purchase task or a food ad libitum procedure.

Conclusions

Results show that EFT decreases DD in and out of the laboratory and supports the further exploration of EFT as an intervention for prediabetes and related chronic diseases.

Clinical Trial Registration

NCT03664726.
Vascular underpinning of COVID-19
Authors: Wazny Vanessa , Siau Anthony , Wu Kan Xing , Cheung Christine
Published: August 2020

COVID-19 management guidelines have largely attributed critically ill patients who develop acute respiratory distress syndrome, to a systemic overproduction of pro-inflammatory cytokines. Cardiovascular dysfunction may also represent a primary phenomenon, with increasing data suggesting that severe COVID-19 reflects a confluence of vascular dysfunction, thrombosis and dysregulated inflammation. Here, we first consolidate the information on localized microvascular inflammation and disordered cytokine release, triggering vessel permeability and prothrombotic conditions that play a central role in perpetuating the pathogenic COVID-19 cascade. Secondly, we seek to clarify the gateways which SARS-CoV-2, the causative COVID-19 virus, uses to enter host vascular cells. Post-mortem examinations of patients' tissues have confirmed direct viral endothelial infection within several organs. While there have been advances in single-cell RNA sequencing, endothelial cells across various vascular beds express low or undetectable levels of those touted SARS-CoV-2 entry factors. Emerging studies postulate alternative pathways and the apicobasal distribution of host cell surface factors could influence endothelial SARS-CoV-2 entry and replication. Finally, we provide experimental considerations such as endothelial polarity, cellular heterogeneity in organoids and shear stress dynamics in designing cellular models to facilitate research on viral-induced endothelial dysfunctions. Understanding the vascular underpinning of COVID-19 pathogenesis is crucial to managing outcomes and mortality.
Amaricoccus solimangrovi sp. nov., isolated from mangrove soil
Authors: mo kun-lian , Huang Hui-qin , Wu Qing-juan , Hu Yong-hua
Published: August 2020

Strain HB172011T was isolated from mangrove soil sampled at the Bamenbay mangrove forest, PR China. Cells were easily recognized under the microscope as cocci that were usually arranged in distinctive tetrads. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate belongs to the genus

Amaricoccus

and has 95.6–96.3% 16S rRNA gene sequence similarities to the four

Amaricoccus

type strains. The strain was aerobic or facultatively anaerobic, Gram-stain-negative and non-motile. Cells were found to grow at 10–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.0) and with 0–9.0% (w/v) NaCl (optimum, 2–4%). Major fatty acids were feature 8 (C18:1
ω7c and/or C18:1
ω6c), C16:0, C19:0 cyclo ω8c and summed feature 2 (C16:1 iso I and/or C14:0–3 OH). Genome sequencing revealed a genome size of 4.87 Mbp and a DNA G+C content of 69.9 mol %. Based on these data, strain HB172011T represents a novel species of

Amaricoccus

, for which the name Amaricoccus solimangrovi sp. nov. is proposed. The type strain is HB172011T (=CGMCC 1.16728T=JCM 33334T).
microRNA-dependent control of sensory neuron function regulates posture behaviour inDrosophila
Authors: Klann M. , Issa A.R. , Alonso C.R.
Published: August 2020

All what we see, touch, hear, taste or smell must first be detected by the sensory elements in our nervous system. Sensory neurons, therefore, represent a critical component in all neural circuits and their correct function is essential for the generation of behaviour and adaptation to the environment. Here we report that a gene encoding the evolutionarily conserved microRNA (miRNA)miR-263b, plays a key behavioural role inDrosophilathrough effects on the function of larval sensory neurons. Several independent experiments support this finding. First, miRNA expression analysis by means of amiR-263breporter line, and fluorescent-activated cell sorting coupled to quantitative PCR, both demonstrate expression ofmiR-263binDrosophilalarval sensory neurons. Second, behavioural tests inmiR-263bnull mutants show defects in self-righting: an innate and evolutionarily conserved posture control behaviour that allows the larva to return to its normal position if turned upside-down. Third, competitive inhibition ofmiR-263bin sensory neurons using amiR-263b‘sponge’ leads to self-righting defects. Fourth, systematic analysis of sensory neurons inmiR-263bmutants shows no detectable morphological defects in their stereotypic pattern. Fifth, genetically-encoded calcium sensors expressed in the sensory domain reveal a reduction in neural activity inmiR-263bnull mutants. Sixth,miR-263bnull mutants show a reduced ‘touch-response’ behaviour and a compromised response to sound, both characteristic of larval sensory deficits. Furthermore, bioinformatic miRNA target analysis, gene expression assays, and behavioural phenocopy experiments suggest thatmiR-263bmight exert its effects – at least in part – through repression of the bHLH transcription factoratonal. Altogether, our study suggests a model in which miRNA-dependent control of transcription factor expression affects sensory function and behaviour. Building on the evolutionary conservation ofmiR-263b, we propose that similar processes may modulate sensory function in other animals, including mammals.
The shrubEphedra californicafacilitates arthropod communities along a regional desert climatic gradient
Authors: Braun Jenna , Westphal Michael , Lortie Christopher J.
Published: August 2020

Arthropods underpin arid community dynamics and provide many key ecosystem services. In arid ecosystems, the key habitat components that influence arthropod community structure are relatively understudied.Ephedra californicais a common and widespread shrub with established positive effects on plant and vertebrate animal communities within the drylands of Southern California. The capacity for these positive effects to further support arthropod communities has not been examined. We tested the hypothesis that the physical structure and cover vegetation enhances key measures of arthropod community assembly at nine Californian desert sites that comprise an extensive regional aridity gradient. We contrasted the effects of shrub canopies with ground-covering vegetation on structuring ground-active arthropod communities by surveying ground-active arthropods with pitfall traps and collecting vegetation on the soil surface in the form of residual dry matter (RDM). We collected a total of 5868 individual arthropod specimens for a total of 184 morphospecies. Arthropod abundance and morphospecies richness and RDM biomass and cover were significantly greater beneath the canopy ofE. californicathroughout the region. Total biomass of RDM did not significantly influence arthropod communities, but cover of RDM on the soil surface negatively influenced arthropod abundance. Neither climatic aridity nor downscaled evaporative stress estimates were significant mediators of the arthropodvegetation association patterns. Vegetation thus likely has direct and indirect physical effects on arthropod communities. These canopy versus soil surface vegetation differences will refine sampling of fine-scale patterns of arthropod diversity in drylands. Regional land managers can support arthropod diversity by maintaining populations of foundation shrub species such asE. californica.
Predicting transcriptional responses to cold stress across plant species
Authors: Meng Xiaoxi , Liang Zhikai , Dai Xiuru , Zhang Yang , Mahboub Samira , Ngu Daniel W. , Roston Rebecca L. , Schnable James C.
Published: August 2020

Although genome sequence assemblies are available for a growing number of plant species, gene expression responses to stimuli have been catalogued for only a subset of these species. Many genes show altered transcription patterns in response to abiotic stresses. However, orthologous genes in related species often exhibit different responses to a given stress. Accordingly, data on the regulation of gene expression in one species are not reliable predictors of orthologous gene responses in a related species. Here, we trained a supervised classification algorithm to identify genes that transcriptionally respond to cold stress. A model trained with only features calculated directly from genome assemblies exhibited only modest decreases in performance relative to models trained using genomic, chromatin, and evolution/diversity features. Models trained with data from one species successfully predicted which genes would respond to cold stress in other related species. Cross-species predictions remained accurate when training was performed in cold-sensitive species and predictions were performed in cold-tolerant species and vice versa. Models trained with data on gene expression in multiple species outperformed models trained with data from any single species. These results suggest that classifiers trained on stress data from well-studied species may suffice for predicting gene expression patterns in related, less-studied species with sequenced genomes.
Altered Mediator dynamics during heat shock in budding yeast
Authors: Sarkar Debasish , Zhu Z. Iris , Paul Emily , Landsman David , Morse Randall H.
Published: August 2020

The Mediator complex is central to transcription by RNA polymerase II (Pol II) in eukaryotes. In yeast, Mediator is recruited by activators via its tail module and then facilitates assembly of the pre-initiation complex (PIC), including Pol II, setting the stage for productive transcription. Mediator occupies proximal promoter regions only transiently prior to Pol II escape; interruption of the transcription cycle by inactivation or depletion of Kin28 inhibits Pol II escape and stabilizes Mediator occupancy at promoters. However, whether Mediator occupancy and dynamics differ for gene cohorts induced by stress or alternative growth conditions has not been examined on a genome-wide scale. Here we investigate Mediator occupancy following heat shock or CdCl2induction, with or without depletion of Kin28. We find that Pol II occupancy exhibits similar dependence on Mediator under normal and heat shock conditions; however, Mediator occupancy does not increase upon Kin28 depletion at most genes active during heat shock, indicating altered dynamics. Furthermore, Mediator occupancy persists at genes repressed by heat shock or CdCl2induction and exhibits peaks upstream of the proximal promoter whether or not Kin28 is depleted, suggesting that Mediator is recruited by activators but is unable to engage PIC components at these repressed targets. Finally, we show a reduced dependence on PIC components for Mediator occupancy at promoters after heat shock, further supporting an altered dynamics or stronger engagement with activators under these conditions.
Use of High Pressure NMR Spectroscopy to Rapidly Identify Proteins with Internal Ligand-Binding Voids
Authors: Gagné Donald , Azad Roksana , Aramini James M. , Xu Xingjian , Isiorho Eta A. , Edupuganti Uthama R. , Williams Justin , Marcelino Leandro Pimentel , Akasaka Kazuyuki , Gardner Kevin H.
Published: August 2020

Small molecule binding within internal cavities provides a way to control protein function and structure, as exhibited in numerous natural and artificial settings. Unfortunately, most ways to identify suitable cavities require high-resolution structuresa prioriand may miss potential cryptic sites. Here we address this limitation via high-pressure solution NMR spectroscopy, taking advantage of the distinctive nonlinear pressure-induced chemical shift changes observed in proteins containing internal cavities and voids. We developed a method to rapidly characterize such nonlinearity among backbone1H and15N amide signals without needing to have sequence-specific chemical shift assignments, taking advantage of routinely available15N-labeled samples, instrumentation, and 2D1H/15N HSQC experiments. From such data, we find a strong correlation in the site-to-site variability in such nonlinearity with the total void volume within proteins, providing insights useful for prioritizing domains for ligand binding and indicating mode-of-action among such protein/ligand systems. We suggest that this approach provides a rapid and useful way to rapidly assess otherwise hidden dynamic architectures of protein that reflect fundamental properties associated with ligand binding and control.

Significance Statement

Many proteins can be regulated by internally binding small molecule ligands, but it is often not cleara prioriwhich proteins are controllable in such a way. Here we describe a rapid method to address this challenge, using solution NMR spectroscopy to monitor the response of proteins to the application of high pressure. While the locations of NMR signals from most proteins respond to high pressure with linear chemical shift changes, proteins containing internal cavities that can bind small molecule ligands respond with easily identified non-linear changes. We demonstrate this approach on several proteins and protein/ligand complexes, suggesting that it has general utility.
Non-targeted Screening of Commercial CBD Products in the United States Reveals Common Contamination and Adulteration
Authors: Orsburn Ben
Published: August 2020

The production of hemp and products derived from these plants that contain zero to trace amounts of the psychoactive cannabinoid tetrahydrocannabidiol (THC) is a rapidly growing new market in the United States. The most common products today contain relatively high concentrations of the compound cannabidiol (CBD). Recent studies have investigated commercial CBD products using targeted assays and have found varying degrees of misrepresentation and contamination of these products. To expand on previous studies, we demonstrate the application of non-targeted screening by high resolution accurate mass spectrometry to more comprehensively identify potential adulterants and contaminants. We find evidence to support previous conclusions that CBD products are commonly misrepresented in terms of cannabinoid concentrations present. Specifically, we observe a wide variation in relative THC concentrations across the product tested, with some products containing 10-fold more relative signal than others. In addition, we find that several products appear to be purposely adulterated with over the counter drugs such as caffeine and melatonin. We also observe multiple small molecule contaminants that are typically linked to improper production or packaging methods in food or pharmaceutical production. Finally, we present high resolution accurate mass spectrometry data and tandem MS/MS fragments supporting the presence of trace amounts of fluorofentanyl in a single mail order CBD product. We conclude that the CBD industry would benefit from more robust testing regulations and that the cannabis testing industry, in general, would benefit from the use of non-targeted screening technologies.
Temporal uncertainty enhances suppression of neural responses to predictable visual stimuli
Authors: Nara Sanjeev , Lizarazu Mikel , Richter Craig G , Dima Diana C , Cichy Radoslaw M , Bourguignon Mathieu , Molinaro Nicola
Published: August 2020

Predictive processing has been proposed as a fundamental cognitive mechanism to account for how the brain interacts with the external environment via its sensory systems. In vision, contextual information triggers predictions about the content (“what”) of environmental stimuli to update an internal generative model of the surrounding world. However, visual information dynamically changes across time, and temporal predictability (“when”) may influence the impact of internal predictions on visual processing. In this magnetoencephalography (MEG) study, we investigated how processing feature specific information (“what”) is affected by temporal predictability (“when”). In line with previous findings, we observed suppression of evoked neural responses in the visual cortex for predictable stimuli. Interestingly, we found that temporal uncertainty increased expectation suppression. This suggests that in temporally uncertain scenarios the neurocognitive system invests less resources in integrating bottom-up information. Multivariate pattern analysis showed that predictable visual features could be decoded from neural responses. Temporal uncertainty did not affect decoding accuracy for early visual responses, with the feature specificity of early visual neural activity preserved across conditions. However, decoding accuracy was less sustained over time for temporally jittered than for isochronous predictable visual stimuli. These findings converge to suggest that the cognitive system processes visual features of temporally predictable stimuli in higher detail, while processing temporally uncertain stimuli may rely more heavily on abstract internal expectations.
Neural signatures of attentional engagement during narratives and its consequences for event memory
Authors: Song Hayoung , Finn Emily S. , Rosenberg Monica D.
Published: August 2020

As we comprehend narratives, our attentional engagement fluctuates over time. Despite theoretical conceptions of narrative engagement as emotion-laden attention, little empirical work has characterized the cognitive and neural processes that comprise subjective engagement in naturalistic contexts or its consequences for memory. Here, we relate fluctuations in narrative engagement to patterns of brain coactivation, and test whether neural signatures of engagement predict later recall. In behavioral studies, participants continuously rated how engaged they were as they watched a television episode or listened to a story. Self-reported engagement was synchronized across individuals and driven by the emotional content of the narratives. During fMRI, we observed highly synchronized activity in the default mode network when people were, on average, more engaged in the same narratives. Models based on time-varying whole-brain functional connectivity predicted evolving states of engagement across participants and even across different datasets. The same functional connections also predicted post-scan event recall, suggesting that engagement during encoding impacts subsequent memory. Finally, group-average engagement was related to fluctuations of an independent functional connectivity index of sustained attention. Together, our findings characterize the neural signatures of engagement dynamics and elucidate relationships between narrative engagement, sustained attention, and event memory.
Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis andBrassica rapacultivars
Authors: Calderwood Alexander , Hepworth Jo , Woodhouse Shannon , Bilham Lorelei , Jones D. Marc , Tudor Eleri , Ali Mubarak , Dean Caroline , Wells Rachel , Irwin Judith A. , Morris Richard J.
Published: August 2020

The timing of the floral transition affects reproduction and yield, however its regulation in crops remains poorly understood. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model speciesArabidopsis thalianaand the closely related cropBrassica rapa. A direct comparison of gene expression over time between species shows little similarity, which could lead to the inference that different gene regulatory networks are at play. However, these differences can be largely resolved by synchronisation, through curve registration, of gene expression profiles. We find that different registration functions are required for different genes, indicating that there is no common ‘developmental time’ to which Arabidopsis andB. rapacan be mapped through gene expression. Instead, the expression patterns of different genes progress at different rates. We find that co-regulated genes show similar changes in synchronisation between species, suggesting that similar gene regulatory sub-network structures may be active with different wiring between them. A detailed comparison of the regulation of the floral transition between Arabidopsis andB. rapa, and between twoB. rapaaccessions reveals different modes of regulation of the key floral integratorSOC1, and that the floral transition in theB. rapaaccessions is triggered by different pathways, even when grown under the same environmental conditions. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cyclingB. rapaunder long days and highlights the importance of registration methods for the comparison of developmental gene expression data.
Co-administration of macropinocytosis inhibitory nanoparticles (MiNP) for enhanced nanoparticle circulation time and target tissue accumulation following subcutaneous injection
Authors: Stack Trevor , Liu Yu-gang , Frey Molly , Bobbala Sharan , Vincent Michael , Scott Evan
Published: August 2020

A signficant barrier to the application of nanoparticles for precision medicine is the mononuclear phagocyte system (MPS), a diverse population of phagocytic cells primarily located within the liver, spleen and lymph nodes. The majority of nanoparticles are indiscriminantly cleared by the MPS via macropinocytosis before reaching their intended targets, resulting in side effects and decreased efficacy. This work demonstrates that the biodistribution and desired tissue accumulation of targeted nanoparticles can be significantly enhanced by co-injection with polymeric micelles containing the actin depolymerizing agentlatrunculin A. These macropinocytosis inhibitory nanoparticles (MiNP) were found to selectively inhibit non-specific uptake of a second “effector” nanoparticlein vitrowithout impeding receptor-mediated endocytosis. In tumor bearing mice, co-injection with MiNP in a single multi-nanoparticle formulation significantly increased the accumulation of folate-receptor targeted nanoparticles within tumors. Furthermore, subcutaneous co-administration with MiNP allowed effector nanoparticles to achieve serum levels that rivaled a standard intravenous injection. This effect was only observed if the effector nanoparticles were injected within 24 h following MiNP administration, indicating a temporary avoidance of MPS cells. Co-injection with MiNP therefore allows reversible evasion of the MPS for targeted nanoparticles and presents a previously unexplored method of modulating and improving nanoparticle biodstribution following subcutaneous administration.

Abstract Figure

TOC Text: Polymeric macropinocytosis inhibiting nanoparticles reduce non-specific uptake of an “effector” nanoparticle by cells of the mononuclear phagocyte system. This macropinocytosis specific inhibition allows for greater accumulation and uptake of targeted nanoparticles in tissues of interest thereby increasing their efficacy and reducing side effects.
Epitopes targeted by T cells in convalescent COVID-19 patients
Authors: Quadeer Ahmed A. , Ahmed Syed Faraz , McKay Matthew R.
Published: August 2020

Knowledge of the epitopes of SARS-CoV-2 that are targeted by T cells in convalescent patients is important for understanding T cell immunity against COVID-19. This information can aid the design, development and assessment of COVID-19 vaccines, and inform novel diagnostic technologies. Here we provide a unified description and meta-analysis of emerging data of SARS-CoV-2 T cell epitopes compiled from 15 independent studies of cohorts of convalescent COVID-19 patients. Our analysis demonstrates the broad diversity of T cell epitopes that have been collectively recorded for SARS-CoV-2, while also identifying a selected set of immunoprevalent epitopes that induced consistent T cell responses in multiple cohorts and in a large fraction of tested patients. The landscape of SARS-CoV-2 T cell epitopes that we describe can help guide future immunological studies, including those related to vaccines and diagnostics. A web-based platform has been developed to help complement these efforts.
3D Deconvolution Processing for STEM Cryo-Tomography
Authors: Waugh Barnali , Wolf Sharon G. , Fass Deborah , Branlund Eric , Kam Zvi , Sedat John , Elbaum Michael
Published: August 2020

The complex environment of biological cells and tissues has motivated development of three dimensional imaging in both light and electron microscopies. To this end, one of the primary tools in fluorescence microscopy is that of computational deconvolution. Wide-field fluorescence images are often corrupted by haze due to out-of-focus light, i.e., to cross-talk between different object planes as represented in the 3D image. Using prior understanding of the image formation mechanism, it is possible to suppress the cross-talk and reassign the unfocused light to its proper sourcepost facto. Electron tomography based on tilted projections also exhibits a cross-talk between distant planes due to the discrete angular sampling and limited tilt range. By use of a suitably synthesized 3D point spread function, we show here that deconvolution leads to similar improvements in volume data reconstructed from cryo-scanning transmission electron tomography (CSTET), namely a dramatic in-plane noise reduction and improved representation of features in the axial dimension. Contrast enhancement is demonstrated first with colloidal gold particles, and then in representative cryo-tomograms of intact cells. Deconvolution of CSTET data collected from the periphery of an intact nucleus revealed partially condensed, extended structures in interphase chromatin.

Significance statement

Electron tomography is used to reveal the structure of cells in three dimensions. The combination with cryogenic fixation provides a snapshot in time of the living state. However, cryo-tomography normally requires very thin specimens due to image formation by conventional phase contrast transmission electron microscopy (TEM). The thickness constraint can be relaxed considerably by scanning TEM (STEM), yet three-dimensional (3D) reconstruction is still subject to artifacts inherent in the collection of data by tilted projections. We show here that deconvolution algorithms developed for fluorescence microscopy can suppress these artifacts, resulting in significant contrast enhancement. The method is demonstrated by cellular tomography of complex membrane structures, and by segmentation of chromatin into distinct, contiguous domains of heterochromatin and euchromatin at high and low density, respectively.
Mechanistic Studies of the Stabilization of Insulin Helical Structure by Coomassie Brilliant Blue
Authors: Dolui Sandip , Pariary Ranit , Saha Achintya , Ratha Bhisma N , Harikishore Amaravadhi , Saha Susmita , Swarnakar Snehasikta , Bhunia Anirban , Maiti Nakul C
Published: August 2020

Human insulin (HI) is an essential protein hormone and its biological activity mostly depends on folded and active conformation in the monomeric state. The present investigation established that Coomassie Brilliant Blue G-250 (CBBG), a small multicyclic hydroxyl compound can reversibly bind to the hormonal protein dimer and maintained most of α-helical folds crucial for biological function of the enzyme. The solution-state 1D NMR and isothermal calorimetric analysis showed a sub-micromolar binding affinity of the molecule to HI. 2D NOESY NMR established that the HI dimer undergoes residue level local conformational change upon binding to CBBG. The chemical shift perturbation and the NOE parameters of active protons of amino acid residues throughout the polypeptides further suggested that CBBG upon binding the protein stabilize α-helixes of both the A and B subunits of the hormonal protein. The changes in Gibb’s free energy (∆G) of the binding was of ~−11.1 kcal/mol and suggested a thermodynamically favourable process. The changes in enthalpy (∆H) and entropy term (T∆S) were −57.2 kcal/mol and −46.1 kcal/mol, respectively. The negative changes in entropy and the NOE transfer effectiveness of several residues in the presence of CBBG molecules indicated that the binding was an enthalpy driven favourable equilibrium process. The NMR-based atomic resolution data and molecular docking studies confirmed that the CBBG binds to HI at the dimeric stage and prevents the availability of the crucial residue segments that partake directly in further oligomerization and subsequent fibrillation. Extended computational analysis based on chemical shift perturbation of protons of active residues further established receptor-ligand based pharmacophore model comprised of 5 hydrophobic and a hydrogen bond acceptor features that can anchor the residues at the A and B chains of HI and inhibit the partial unfolding and hydrophobic collapse to nucleate the fibrillation. Taken together, the results demonstrated that CBBG and their close analogues might be useful to develop a formulation that will maintain the active and functional form of the hormonal protein for a significantly longer time.

TOC
Scanning ion conductance microscopy reveals differences in the ionic environments of gram positive and negative bacteria
Authors: Cremin Kelsey , Jones Bryn , Teahan James , Meloni Gabriel N. , Perry David , Zerfass Christian , Asally Munehiro , Soyer Orkun S. , Unwin Patrick R.
Published: August 2020

This paper reports on the use of scanning ion conductance microscopy (SICM) to locally map the ionic properties and charge environment of two live bacterial strains: the gramnegativeEscherichia coliand the gram-positiveBacillus subtilis. SICM results find heterogeneities across the bacterial surface, and significant differences among the grampositive and -negative bacteria. The bioelectrical environment of theB. subtiliswas found to be considerably more negatively charged compared toE. coli. SICM measurements, fitted to a simplified finite element method (FEM) model, revealed surface charge values of −80 to −140 mC m−2for the gram-negativeE. coli. The gram-positiveB. subtilisshow a much higher conductivity around the cell wall, and surface charge values between −350 and −450 mC m−2were found using the same simplified model. SICM was also able to detect regions of high negative charge nearB. subtilis, not detected in the topographical SICM response and attributed to extracellular polymeric substance. To further explore how theB. subtiliscell wall structure can influence the SICM current response, a more comprehensive FEM model, accounting for the physical properties of the gram-positive cell wall, was developed. The new model provides a more realistic description of the cell wall and allowed investigation of the relation between its key properties and SICM currents, building foundations to further investigate and improve understanding of the gram-positive cellular microenvironment.

Abstract Figure
DNA methylation in cockroaches is essential in early embryo development and reduces gene expression noise
Authors: Ventos-Alfonso Alba , Ylla Guillem , Montañes Jose-Carlos , Belles Xavier
Published: August 2020

The influence of DNA methylation on gene behavior, and its consequent phenotypic effects appear to be very important, but the details are not well understood. Insects offer a diversity of DNA methylation modes, making them an excellent lineage for comparative analyses. However, functional studies have tended to focus on quite specialized holometabolan species, such as wasps, bees, beetles, and flies. Here we have studied DNA methylation in a hemimetabolan insect, the cockroachBlattella germanica, a model of early-branching insects. In this cockroach, one of the main genes responsible for DNA methylation,DNA methyltransferase 1(DNMT1), is expressed in early embryogenesis. In our experiments,DNMT1interference by RNAi reduces DNA methylation and impairs blastoderm formation. Using Reduced Representation Bisulfite Sequencing (RRBS) and transcriptomic analyses, we observed that hypermethylated genes are associated with metabolism and are highly expressed, whereas hypomethylated genes are related to signaling and have low expression levels. Moreover, the expression change in hypermethylated genes is greter than that in hypomethylated genes, whereas hypermethylated genes have less expression variability than hypomethylated genes. The latter observation has also been reported for humans and inArabidopsisplants. A reduction in expression noise may therefore be one of the few universal effects of DNA methylation.
Predicting Chemical Shifts with Graph Neural Networks
Authors: Yang Ziyue , Chakraborty Maghesree , White Andrew D
Published: August 2020

Abstract

Inferring molecular structure from NMR measurements requires an accurate forward model that can predict chemical shifts from 3D structure. Current forward models are limited to specific molecules like proteins and state of the art models are not differentiable. Thus they cannot be used with gradient methods like biased molecular dynamics. Here we use graph neural networks (GNNs) for NMR chemical shift prediction. Our GNN can model chemical shifts accurately and capture important phenomena like hydrogen bonding induced downfield shift between multiple proteins, secondary structure effects, and predict shifts of organic molecules. Previous empirical NMR models of protein NMR have relied on careful feature engineering with domain expertise. These GNNs are trained from data alone with no feature engineering yet are as accurate and can work on arbitrary molecular structures. The models are also efficient, able to compute one million chemical shifts in about 5 seconds. This work enables a new category of NMR models that have multiple interacting types of macromolecules.
Imaging meningeal inflammation in CNS autoimmunity identifies a therapeutic role for BTK inhibition
Authors: Bhargava Pavan , Kim Sol , Reyes Arthur Anthony , Grenningloh Roland , Boschert Ursula , Absinta Martina , Pardo-Villamizar Carlos , Van Zijl Peter , Zhang Jiangyang , Calabresi Peter A
Published: August 2020

Leptomeningeal inflammation in multiple sclerosis is associated with worse clinical outcomes and greater cortical pathology. Despite progress in identification of this process in multiple sclerosis patients using post-contrast FLAIR imaging, early trials attempting to target meningeal inflammation have been unsuccessful. There is a lack of appropriate model systems to screen potential therapeutic agents targeting meningeal inflammation. We utilized ultra-high field (11.7 Tesla) MRI to perform post-contrast FLAIR imaging in SJL/J mice with experimental autoimmune encephalomyelitis induced using immunization with proteolipid protein peptide (PLP139-151) and complete Freund’s adjuvant. Imaging was performed in both a cross-sectional and longitudinal fashion at time-points ranging from 2 to 14 weeks post-immunization. Following imaging, we euthanized animals and collected tissue for pathological evaluation, which identified dense cellular infiltrates corresponding to areas of contrast-enhancement involving the leptomeninges. These areas of meningeal inflammation contained B cells (B220+), T cells (CD3+) and myeloid cells (Mac2+). We also noted features consistent with tertiary lymphoid tissue within these areas – presence of peripheral node addressin (PNAd) positive structures, CXCL13 producing cells and FDC-M1+ follicular dendritic cells. In the cortex adjacent to areas of meningeal inflammation we identified astrocytosis, microgliosis, demyelination and evidence of axonal stress/damage. Since areas of meningeal contrast enhancement persisted over several weeks in longitudinal experiments, we utilized this model to test the effects of a therapeutic intervention on established meningeal inflammation. We randomized mice with evidence of meningeal contrast enhancement on MRI scans performed at 6 weeks post-immunization, to treatment with either vehicle or evobrutinib (a Bruton’s tyrosine kinase inhibitor) for a period of 4 weeks. These mice underwent serial imaging and we examined the effect of treatment on the areas of meningeal contrast enhancement and noted a significant reduction in the evobrutinib group compared to vehicle (30% reduction versus 5% increase;P= 0.003). We utilized ultra-high field MRI imaging to identify areas of meningeal inflammation and to track them over time in SJL/J mice with experimental autoimmune encephalomyelitis and then utilized this model to identify Bruton’s tyrosine kinase inhibition as a novel therapeutic approach to target meningeal inflammation. The results of this study provide support for future studies in multiple sclerosis patients with imaging evidence of meningeal inflammation.
eQTpLot: a user-friendly R package for the visualization and colocalization of eQTL and GWAS signals
Authors: Drivas Theodore G. , Lucas Anastasia , Ritchie Marylyn D.
Published: August 2020

Genomic studies increasingly integrate expression quantitative trait loci (eQTL) information into their analysis pipelines, but few tools exist for the visualization of colocalization between eQTL and GWAS results. Those tools that do exist are limited in their analysis options, and do not integrate eQTL and GWAS information into a single figure panel, making the visualization of colocalization difficult.

To address this issue, we developed the intuitive and user-friendly R package eQTpLot. eQTpLot takes as input standard GWAS and eQTL summary statistics, and optional pairwise LD information, to generate a series of plots visualizing colocalization, correlation, and enrichment between eQTL and GWAS signals for a given gene-trait pair. With eQTpLot, investigators can easily generate a series of customizable plots clearly illustrating, for a given gene-trait pair: 1) colocalization between GWAS and eQTL signals, 2) correlation between GWAS and eQTL p-values, 3) enrichment of eQTLs among trait-significant variants, 4) the LD landscape of the locus in question, and 5) the relationship between the direction of effect of eQTL signals and the direction of effect of colocalizing GWAS peaks. These clear and comprehensive plots provide a unique view of eQTL-GWAS colocalization, allowing for a more complete understanding of the interaction between gene expression and trait associations.

In summary, eQTpLot provides a unique, user-friendly, and intuitive means of visualizing eQTL and GWAS signal colocalization, incorporating novel features not found in other eQTL visualization software. We believe eQTpLot will prove a useful tool for investigators seeking a convenient and customizable visualization of eQTL and GWAS data colocalization.

Availability and Implementation

the eQTpLot R package and tutorial are available athttps://github.com/RitchieLab/eQTpLot
Cortical Magnification in Human Visual Cortex Parallels Task Performance around the Visual Field
Authors: Benson Noah C. , Kupers Eline R. , Barbot Antoine , Carrasco Marisa , Winawer Jonathan
Published: August 2020

Human vision has striking radial asymmetries, with performance on many tasks varying sharply with stimulus polar angle. Performance is generally better on the horizontal than vertical meridian, and on the lower than upper vertical meridian, and these asymmetries decrease gradually with deviation from the vertical meridian. Here we report cortical magnification at a fine angular resolution around the visual field. This precision enables comparisons between cortical magnification and behavior, between cortical magnification and retinal cell densities, and between cortical magnification in twin pairs. We show that cortical magnification in human primary visual cortex, measured in 163 subjects, varies substantially around the visual field, with a pattern similar to behavior. These radial asymmetries in cortex are larger than those found in the retina, and they are correlated between monozygotic twin pairs. These findings indicate a tight link between cortical topography and behavior, and suggest that visual field asymmetries are partly heritable.