bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Tocilizumab in Critically Ill Patients With COVID-19: A Quasi-Experimental Study
Authors: Carvalho Victor , Turon Ricardo , Gonçalves Bruno , Ceotto Victor Fraga , Kurtz Pedro , Righy Cássia
Published: July 2020

Objectives

Critically ill patients with COVID-19 may suffer from a cytokine release syndrome (CRS) characterized by remarkably high levels of interleukin 6 (IL-6). We assessed the effects of tocilizumab, an IL-6 receptor antagonist, on intra-hospital mortality and development of positive cultures in patients with COVID-19 admitted to the ICU.

Design

Patients with COVID 19 admitted in the ICU who were treated with tocilizumab plus standard care were enrolled and compared to controls.

Setting

COVID-19 severe disease

Patients

Patients with severe COVID-19 disease admitted in the ICU.

Interventions

Tocilizumab 400 mg IV two doses. Standard and intensive medical care as per institutional clinical protocol.

Measures and Main Results

Main outcome: 1) intra-hospital mortality; Secondary Outcomes: 1) the need for renal replacement therapy, 2) use of antibiotics and positive culture, and 3) inflammatory and oxygenation markers. There was no difference in mortality, need for renal replacement therapy, use of antibiotics or positive cultures between the two groups. The use of corticosteroids was more frequent in the treatment group. Levels of C-reactive protein (CRP) and WBC (white blood cells) counts declined significantly faster in the treatment group. Oxygenation markers rose significantly higher in patients in the tocilizumab group as compared to controls.

Conclusion

Tocilizumab was associated with rapid improvement in oxygenation and a faster decrease of CRP and WBC counts in patients with COVID-19 and should be evaluated as rescue therapy for patients with progressive disease
Size Dependent Particle Removal Efficiency and Pressure Drop of a Dust Cleaning Material For Use as Facemask Filters for Protection during COVID-19
Authors: Dhanraj David , Choudhary Shruti , Raven Pat , Biswas Pratim
Published: July 2020

COVID-19 pandemic has caused a severe demand for facemasks, and this has resulted in the use of those made from alternate media. As SARS-CoV-2 spreads primarily due to airborne droplets, it is critical to verify the filtration efficiency of these alternate media based facemasks. While several media are being tested and used, commercially available dust cleaners have shown reasonable filtration efficiency. This may also be due to the potential electrostatic charge on the surface which enhances capture of the fine particles. In this manuscript, we report the size dependent filtration efficiency studied systematically in a filter holder-based system as 47 mm punches; and test results on a mannequin that was 3D printed wearing a bandana mask that was placed in a chamber.
A Quantitative Lung Computed Tomography Image Feature for Multi-Center Severity Assessment of COVID-19
Authors: Ghosh Biswajoy , Kumar Nikhil , Sadhu Anup K. , Ghosh Nirmalya , Mitra Pabitra , Chatterjee Jyotirmoy
Published: July 2020

The COVID-19 pandemic has affected millions and congested healthcare systems globally. Hence an objective severity assessment is crucial in making therapeutic decisions judiciously. Computed Tomography (CT)-scans can provide demarcating features to identify severity of pneumonia —commonly associated with COVID-19—in the affected lungs. Here, a quantitative severity assessing chest CT image feature is demonstrated for COVID-19 patients. An open-source multi-center Italian database1 was used, among which 60 cases were incorporated in the study (age 27-86, 71% males) from 27 CT imaging centers. Lesions in the form of opacifications, crazy-paving patterns, and consolidations were segmented. The severity determining feature —Lnorm was quantified and established to be statistically distinct for the three —mild, moderate, and severe classes (p-value<0.0001). The thresholds of Lnorm for a 3-class classification were determined based on the optimum sensitivity/specificity combination from Receiver Operating Characteristic (ROC) analyses. The feature Lnorm classified the cases in the three severity categories with 86.88% accuracy. ‘Substantial’ to ‘almost-perfect’ intra-rater and inter-rater agreements were achieved involving expert and non-expert based evaluations (κ-score 0.79-0.97). We trained machine learning based classification models and showed Lnorm alone has a superior diagnostic accuracy over standard image intensity and texture features. Classification accuracy was further increased when Lnorm was used for 2-class classification i.e. to delineate the severe cases from non-severe ones with a high sensitivity (97.7%), and specificity (97.49%). Therefore, key highlights of this severity assessment feature are accuracy, lower dependency on expert availability, and wide utility across different imaging centers.
COVID-19 misinformation: mere harmless delusions or much more? A knowledge and attitude cross-sectional study among the general public residing in Jordan
Authors: Sallam Malik , Dababseh Deema , Yaseen Alaa’ , Al-Haidar Ayat , Taim Duaa , Eid Huda , Ababneh Nidaa A. , Bakri Faris G. , Mahafzah Azmi
Published: July 2020

Since the emergence of the recent coronavirus disease 2019 (COVID-19) and its spread as a pandemic, media was teeming with misinformation that led to psychologic, social and economic consequences among the global public. Probing knowledge and anxiety regarding this novel infectious disease is necessary to identify gaps and sources of misinformation which can help public health efforts to design and implement more focused interventional measures. The aim of this study was to evaluate the knowledge, attitude and effects of misinformation about COVID-19 on anxiety level among the general public residing in Jordan. An online survey was used that targeted people aged 18 and above and residing in Jordan. The questionnaire included items on the following: demographic characteristics of the participants, knowledge about COVID-19, anxiety level and misconceptions regarding the origin of the pandemic. The total number of participants included in final analysis was 3150. The study population was predominantly females (76.0%), with mean age of 31 years. The overall knowledge of COVID-19 was satisfactory. Older age, male gender, lower monthly income and educational levels, smoking and history of chronic disease were associated with perceiving COVID-19 as a very dangerous disease. Variables that were associated with a higher anxiety level during the pandemic included: lower monthly income and educational level, residence outside the capital (Amman) and history of smoking. Misinformation about the origin of the pandemic (being part of a conspiracy, biologic warfare and the 5G networks role) was also associated with higher anxiety and lower knowledge about the disease. Social media platforms, TV and news releases were the most common sources of information about the pandemic. The study showed the potential harmful effects of misinformation on the general public and emphasized the need to meticulously deliver timely and accurate information about the pandemic to lessen the health, social and psychological impact of the disease.
Comparison of seroprevalence of SARS-CoV-2 infections with cumulative and imputed COVID-19 cases: systematic review
Authors: Byambasuren Oyungerel , Dobler Claudia C , Bell Katy , Rojas Diana Patricia , Clark Justin , McLaws Mary-Louise , Glasziou Paul
Published: July 2020

Background

Accurate seroprevalence estimates of SARS-CoV-2 in different populations could clarify the extent to which current testing strategies are identifying all active infection, and hence the true magnitude and spread of the infection. Our primary objective was to identify valid seroprevalence studies of SARS-CoV-2 infection and compare their estimates with the reported, and imputed, COVID-19 case rates within the same population at the same time point.

Methods

We searched PubMed, Embase, the Cochrane COVID-19 trials, and Europe-PMC for published studies and pre-prints that reported anti-SARS-CoV-2 IgG, IgM and/or IgA antibodies for serosurveys of the general community from 1 Jan to 12 Aug 2020.

Results

Of the 2199 studies identified, 170 were assessed for full text and 17 studies representing 15 regions and 118,297 subjects were includable. The seroprevalence proportions in 8 studies ranged between 1%-10%, with 5 studies under 1%, and 4 over 10% - from the notably hard-hit regions of Gangelt, Germany; Northwest Iran; Buenos Aires, Argentina; and Stockholm, Sweden. For seropositive cases who were not previously identified as COVID-19 cases, the majority had prior COVID-like symptoms. The estimated seroprevalences ranged from 0.56-717 times greater than the number of reported cumulative cases – half of the studies reported greater than 10 times more SARS-CoV-2 infections than the cumulative number of cases.

Conclusions

The findings show SARS-CoV-2 seroprevalence is well below “herd immunity” in all countries studied. The estimated number of infections, however, were much greater than the number of reported cases and deaths in almost all locations. The majority of seropositive people reported prior COVID-like symptoms, suggesting that undertesting of symptomatic people may be causing a substantial under-ascertainment of SARS-CoV-2 infections.

Key messages

Systematic assessment of 17-country data show SARS-CoV-2 seroprevalence is mostly less than 10% - levels well below “herd immunity”.

High symptom rates in seropositive cases suggest undertesting of symptomatic people and could explain gaps between seroprevalence rates and reported cases.

The estimated number of infections for majority of the studies ranged from 2-717 times greater than the number of reported cases in that region and up to 13 times greater than the cases imputed from number of reported deaths.
Peramivir, an anti-influenza virus drug, exhibits potential anti-cytokine storm effects
Authors: Zhang Chen-xi , Tu Ye , Kong De-pei , Li Yinghua , Chen Da-gui , Zhang Wan-nian , Su Li , Zhuang Chun-lin , Wang Zhi-bin
Published: July 2020

Coronavirus Disease 2019 (COVID-19) infected by Severe Acute Respiratory Syndrome Coronavirus −2 (SARS-CoV-2) has been declared a public health emergency of international concerns. Cytokine storm syndrome (CSS) is a critical clinical symptom of severe COVID-19 patients, and the macrophage is recognized as the direct host cell of SARS-CoV-2 and potential drivers of CSS. In the present study, peramivir was identified to reduce TNF-α by partly intervention of NF-κB activity in LPS-induced macrophage model. In vivo, peramivir reduced the multi-cytokines in serum and bronchoalveolar lavage fluid (BALF), alleviated the acute lung injury and prolonged the survival time in mice. In human peripheral blood mononuclear cells (hPBMCs), peramivir could also inhibit the release of TNF-α. Collectively, we proposed that peramivir might be a candidate for the treatment of COVID-19 and other infections related CSS.

Graphic Abstract
A glycoprotein mutation that emerged during the 2013-2016 Ebola virus epidemic alters proteolysis and accelerates membrane fusion
Authors: Fels J. Maximilian , Bortz Robert H. , Alkutkar Tanwee , Mittler Eva , Jangra Rohit K. , Spence Jennifer S. , Chandran Kartik
Published: July 2020

Genomic surveillance of viral isolates during the 2013-2016 Ebola virus epidemic in Western Africa—the largest and most devastating filovirus outbreak on record—revealed several novel mutations. The responsible strain, named Makona, carries an A to V substitution at position 82 in the glycoprotein (GP), which is associated with enhanced infectivity in vitro. Here, we investigated the mechanistic basis for this enhancement, as well as the interplay between A82V and a T to I substitution at residue 544 of GP, which also modulates infectivity in cell culture. We found that both 82V and 544I destabilize GP with the residue at 544 impacting overall stability, while 82V specifically destabilizes proteolytically cleaved GP. Both residues also promote faster kinetics of lipid mixing of the viral and host membranes in live cells, individually and in tandem, which correlates with faster times to fusion following co-localization with the viral receptor Niemann-Pick C1 (NPC1). Further, GPs bearing 82V are more sensitive to proteolysis by cathepsin L (CatL), a key host factor for viral entry. Intriguingly, CatL processed 82V variant GPs to a novel product of ∼12K size, which we hypothesize corresponds to a form of GP more fully primed for fusion than previously detected. We thus propose a model in which 82V promotes more efficient GP processing by CatL, leading to faster viral fusion kinetics and higher infectivity.

Importance

The 2013-2016 outbreak of Ebola virus disease in West Africa demonstrated the potential for previously localized outbreaks to turn into regional, or even global, health emergencies. With over 28,000 cases and 11,000 confirmed deaths, this outbreak was over 50 times as large as any previously recorded. This outbreak also afforded the largest ever collection of Ebola virus genomic sequence data, allowing new insights into viral transmission and evolution. Viral mutants arising during the outbreak have attracted attention for their potentially altered patterns of infectivity in cell culture, with potential, if unclear, implications for increased viral spread and/or virulence. Here, we report on the properties of one such mutation in the viral glycoprotein, A82V, and its interplay with a previously described polymorphism at position 544. We show that mutations at both residues promote infection and fusion activation in cells, but that A82V additionally leads to increased infectivity under cathepsin-limited conditions, and the generation of a novel glycoprotein cleavage product.
HiG2Vec: Hierarchical Representations of Gene Ontology and Genes in the Poincaré Ball
Authors: Kim Jaesik , Kim Dokyoon , Sohn Kyung-Ah
Published: July 2020

Knowledge manipulation of gene ontology (GO) and gene ontology annotation (GOA) can be done primarily by using vector representation of GO terms and genes for versatile applications such as deep learning. Previous studies have represented GO terms and genes or gene products to measure their semantic similarity using the Word2Vec-based method, which is an embedding method to represent entities as numeric vectors in Euclidean space. However, this method has the limitation that embedding large graph-structured data in the Euclidean space cannot prevent a loss of information of latent hierarchies, thus precluding the semantics of GO and GOA from being captured optimally. In this paper, we propose hierarchical representations of GO and genes (HiG2Vec) that apply Poincaré embedding specialized in the representation of hierarchy through a two-step procedure: GO embedding and gene embedding. Through experiments, we show that our model represents the hierarchical structure better than other approaches and predicts the interaction of genes or gene products similar to or better than previous studies. The results indicate that HiG2Vec is superior to other methods in capturing the GO and gene semantics and in data utilization as well. It can be robustly applied to manipulate various biological knowledge.

Availability

https://github.com/JaesikKim/HiG2Vec

Contact

kasohn@ajou.ac.kr,Dokyoon.Kim@pennmedicine.upenn.edu
The neurokinin-1 receptor is expressed with gastrin-releasing peptide receptor in spinal interneurons and modulates itch
Authors: Sheahan Tayler D. , Warwick Charles A. , Fanien Louis G. , Ross Sarah E.
Published: July 2020

The neurokinin-1 receptor (NK1R, encoded byTacr1) is expressed in spinal dorsal horn neurons and has been suggested to mediate itch. However, previous studies relied heavily on neurotoxic ablation of NK1R spinal neurons, which limited further dissection of their function in spinal itch circuitry. Thus, we leveraged a newly developedTacr1CreERmouse line to characterize the role of NK1R spinal neurons in itch. We show that pharmacological activation of spinal NK1R and chemogenetic activation ofTacr1CreERspinal neurons increases itch behavior, whereas pharmacological inhibition of spinal NK1R suppresses itch behavior. We use fluorescencein situhybridization to characterize the endogenous expression ofTacr1throughout the superficial and deeper dorsal horn, as well as the lateral spinal nucleus.

Retrograde labeling studies from the parabrachial nucleus show that less than 20% of superficialTacr1CreERdorsal horn neurons are spinal projection neurons, and thus the majority ofTacr1CreERare local interneurons. We then use a combination ofin situhybridization andex vivotwo-photon Ca2+imaging of the spinal cord to establish that NK1R and the gastrin-releasing peptide receptor (GRPR) are coexpressed within a subpopulation of excitatory superficial dorsal horn neurons. These findings are the first to describe a role for NK1R interneurons in itch and extend our understanding of the complexities of spinal itch circuitry.
High-density Neural Recordings from Feline Sacral Dorsal Root Ganglia with Thin-film Array
Authors: Sperry Zachariah J. , Na Kyounghwan , Jun James , Madden Lauren R. , Socha Alec , Yoon Eusik , Seymour John P. , Bruns Tim M.
Published: July 2020

Objective: Dorsal root ganglia (DRG) are promising sites for recording sensory activity. Current technologies for DRG recording are stiff and typically do not have sufficient site density for high-fidelity neural data techniques. Approach: In acute experiments, we demonstrate single-unit neural recordings in sacral DRG of anesthetized felines using a 4.5 μm-thick, high-density flexible polyimide microelectrode array with 60 sites and 30-40 μm site spacing. We delivered arrays into DRG with ultrananocrystalline diamond shuttles designed for high stiffness affording a smaller footprint. We recorded neural activity during sensory activation, including cutaneous brushing and bladder filling, as well as during electrical stimulation of the pudendal nerve and anal sphincter. We used specialized neural signal analysis software to sort densely packed neural signals. Main results: We successfully delivered arrays in five of six experiments and recorded single-unit sensory activity in four experiments. The median neural signal amplitude was 55 μV peak-to-peak and the maximum unique units recorded at one array position was 260, with 157 driven by sensory or electrical stimulation. In one experiment, we used the neural analysis software to track eight sorted single units as the array was retracted ~500 μm. Significance: This study is the first demonstration of ultrathin, flexible, high-density electronics delivered into DRG, with capabilities for recording and tracking sensory information that are a significant improvement over conventional DRG interfaces.
Structural basis of the dynamic human CEACAM1 monomer-dimer equilibrium
Authors: Gandhi Amit K. , Sun Zhen-Yu J. , Kim Walter M. , Huang Yu-Hwa , Kondo Yasuyuki , Bonsor Daniel A. , Sundberg Eric J. , Wagner Gerhard , Kuchroo Vijay K. , Petsko Gregory A. , Blumberg Richard S.
Published: July 2020

Human (h) carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) function depends upon IgV-mediated homodimerization or heterodimerization with host ligands, including hCEACAM5 and hTIM-3, and a variety of microbial pathogens. However, there is little structural information available on how hCEACAM1 transitions between monomeric and dimeric states which in the latter case is critical for initiating hCEACAM1 activities. We therefore mutated residues within the hCEACAM1 IgV GFCC’ face including V39, I91, N97 and E99 and examined hCEACAM1 IgV monomer-homodimer exchange using differential scanning fluorimetry, multi-angle light scattering, X-ray crystallography and/or nuclear magnetic resonance. From these studies, we describe hCEACAM1 homodimeric, monomeric and transition states at atomic resolution and its conformational behavior in solution through NMR assignment of the wildtype (WT) hCEACAM1 IgV dimer and N97A monomer. These studies reveal the flexibility of the GFCC’ face and its important role in governing the formation of hCEACAM1 dimers and potentially heterodimers.
Validation and tuning ofin situtranscriptomics image processing workflows with crowdsourced annotations
Authors: Vo-Phamhi Jenny M. , Yamauchi Kevin A. , Gómez-Sjöberg Rafael
Published: July 2020

Recent advancements inin situmethods, such as multiplexedin situRNA hybridization andin situRNA sequencing, have deepened our understanding of the way biological processes are spatially organized in tissues. Automated image processing and spot-calling algorithms for analyzingin situtranscriptomics images have many parameters which need to be tuned for optimal detection. Having ground truth datasets (images where there is very high confidence on the accuracy of the detected spots) is essential for evaluating these algorithms and tuning their parameters.

We present a first-in-kind open-source toolkit and framework forin situtranscriptomics image analysis that incorporates crowdsourced annotations, alongside expert annotations, as a source of ground truth for the analysis ofin situtranscriptomics images. The kit includes tools for preparing images for crowdsourcing annotation to optimize crowdsourced workers’ ability to annotate these images reliably, performing quality control (QC) on worker annotations, extracting candidate parameters for spot-calling algorithms from sample images, tuning parameters for spot-calling algorithms, and evaluating spot-calling algorithms and worker performance. These tools are wrapped in a modular pipeline with a flexible structure that allows users to take advantage of crowdsourced annotations from any source of their choice. We tested the pipeline using real and syntheticin situtranscriptomics images and annotations from the Amazon Mechanical Turk system obtained via Quanti.us. Using real images fromin situexperiments and simulated images produced by one of the tools in the kit, we studied worker sensitivity to spot characteristics and established rules for annotation QC. We explored and demonstrated the use of ground truth generated in this way for validating spot-calling algorithms and tuning their parameters, and confirmed that consensus crowdsourced annotations are a viable substitute for expert-generated ground truth for these purposes.

Data Availability

The iPython notebooks, input images, and In Situ Transcriptomics Annotation (INSTA) pipeline software are available fromhttps://github.com/czbiohub/instapipeline. The SpotImage software is available fromhttps://github.com/czbiohub/spotimage. The files and iPython notebooks used to generate the figures for this paper are available fromhttps://github.com/czbiohub/instapaper.
Accurate detection of circulating tumor DNA using nanopore consensus sequencing
Authors: Marcozzi Alessio , Jager Myrthe , Elferink Martin , Straver Roy , van Ginkel Joost H. , Peltenburg Boris , Chen Li-Ting , Renkens Ivo , van Kuik Joyce , Terhaard Chris , de Bree Remco , Devriese Lot A. , Willems Stefan M. , Kloosterman Wigard P. , de Ridder Jeroen
Published: July 2020

Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the tumor. To detect lowly abundant ctDNA molecules based on somatic variants, extremely sensitive sequencing methods are required. Here, we describe a new technique, CyclomicsSeq, which is based on Oxford Nanopore sequencing of concatenated copies of a single DNA molecule. Consensus calling of the DNA copies increased the base-calling accuracy ∼60x, enabling accurate detection ofTP53mutations at frequencies down to 0.02%. We demonstrate that aTP53-specific CyclomicsSeq assay can be successfully used to monitor tumor burden during treatment for head-and-neck cancer patients. CyclomicsSeq can be applied to any genomic locus and offers an accurate diagnostic liquid biopsy approach that can be implemented in point-of-care clinical workflows.
Diminishing effects of mechanical loading over time during rat Achilles tendon healing
Authors: Khayyeri Hanifeh , Hammerman Malin , Turunen Mikael J , Blomgran Parmis , Notermans Thomas , Guizar-Sicairos Manuel , Eliasson Pernilla , Aspenberg Per , Isaksson Hanna
Published: July 2020

Mechanical loading affects tendon healing and recovery. However, our understanding about how physical loading affects recovery of viscoelastic functions, collagen production and tissue organisation is limited. The objective of this study was to investigate how different magnitudes of loading affects biomechanical and collagen properties of healing Achilles tendons over time.

Achilles tendon from female Sprague Dawley rats were cut transversely and divided into two groups; normal loading (control) and reduced loading by Botox (unloading). The rats were sacrificed at 1, 2- and 4-weeks post-injury and mechanical testing (creep test and load to failure), small angle x-ray scattering (SAXS) and histological analysis were performed.

The effect of unloading was primarily seen at the early time points, with inferior mechanical and collagen properties (SAXS), and reduced histological maturation of the tissue in unloaded compared to loaded tendons. However, by 4 weeks no differences remained. SAXS and histology revealed heterogeneous tissue maturation with more mature tissue at the peripheral region compared to the center of the callus. Thus, mechanical loading advances Achilles tendon biomechanical and collagen properties earlier compared to unloaded tendons, and the spatial variation in tissue maturation and collagen organization across the callus suggests important regional (mechano-) biological activities that require more investigation.
Distinct patterns of activity in individual cortical neurons and local networks in primary somatosensory cortex of mice evoked by mechanical limb stimulation
Authors: Bandet Mischa V. , Dong Bin , Winship Ian R.
Published: July 2020

To distinguish between somatic stimuli, the primary somatosensory cortex should process dissimilar stimuli with distinct patterns of neuronal activation. Two-photon calcium imaging permits simultaneous optical recording of sensory evoked activity in hundreds of cortical neurons during varied sensory stimulation. Hence, it allows a visualization of patterns of activity in individual neurons and local cortical networks in response to distinct stimulation. Here, flavoprotein autofluorescence imaging was used to map the somatosensory cortex of anaesthetized C57BL/6 mice, andin vivotwo-photon Ca2+imaging was used to define patterns of neuronal activation during mechanical stimulation of the contralateral forelimb or hindlimb at various frequencies (3, 10, 100, 200, and 300 Hz). The data revealed that neurons within the limb associated somatosensory cortex exhibit stimulus-specific patterns of activity. Subsets of neurons were found to have sensory-evoked activity that is either primarily responsive to single stimulus frequencies or broadly responsive to multiple frequencies of limb movement. High frequency stimuli were shown to elicit more activation across the population, with a greater percentage of the population responding and greater percentage of cells with high amplitude responses. Stimulus-evoked cell-cell correlations within these neuronal networks varied as a function of frequency of stimulation, such that each stimulus elicited a distinct pattern that was more consistent across multiple trials of the same stimulus compared to trials at different frequencies of stimulation. The variation in cortical response to these artificial stimuli can thus be represented by the population pattern of supra-threshold Ca2+transients, the magnitude and temporal properties of the evoked activity, and the structure of the stimulus-evoked correlation between responsive neurons.
Visualization of giant virus particles using BONCAT labeling and STED microscopy
Authors: Berjón-Otero Mónica , Duponchel Sarah , Hackl Thomas , Fischer Matthias
Published: July 2020

Giant DNA viruses of the phylumNucleocytoviricotaare being increasingly recognized as important regulators of natural protist populations. However, our knowledge of their infection cycles is still very limited due to a lack of cultured virus-host systems and molecular tools to study them. Here, we apply bioorthogonal noncanonical amino acid tagging (BONCAT) to pulse label the marine heterotrophic flagellateCafeteria burkhardaeduring infection with the lytic giant virus CroV. In absence of CroV, we report efficient incorporation of the L-methionine analog L-azidohomoalanine (AHA) into newly synthesized proteins of the methionine prototrophicC. burkhardae. During CroV infection, AHA was predominantly found in viral proteins, and single CroV virions were imaged with stimulated emission depletion (STED) super-resolution microscopy. CroV particles incorporated AHA with 95-100% efficiency while retaining their infectivity, which makes BONCAT/STED a powerful tool to study viral replication cycles in this ecologically relevant marine bacterivore.

Significance

Giant DNA viruses are the dominant class of protist-infecting viruses, yet the vast majority of described giant virus-protist systems remain uncultured. One of the better studied cultured systems is composed of the stramenopileCafeteria burkhardae(previouslyC. roenbergensis), the giant Cafeteria roenbergensis virus (CroV) and the virophage mavirus.C. burkhardaeis a widespread marine phagotrophic protist that plays an important role in regulating bacterial populations. In addition to being grazed upon by larger zooplankton,C. burkhardaepopulations are controlled by the lytic giant virus CroV. In turn, CroV is parasitized by the virophage mavirus that increases host population survival in the presence of CroV and forms a mutualistic symbiosis with its host. Despite being of fundamental ecological and evolutionary interest, this tripartite host-virus-virophage system suffers from a lack of molecular tools. Here, we show that CroV particles can be fluorescently labeled and imaged by super-resolution microscopy. To achieve this we established robust procedures for analyzing protist and viral populations and implemented the use of bioorthogonal noncanonical amino acid tagging (BONCAT) in a marine unicellular flagellate.
SMPD3suppresses IDH mutant tumor growth via dual autocrine-paracrine roles
Authors: Balakrishnan Anjali , Saleh Fermisk , Adnani Lata , Chinchalongporn Vorapin , El-Sehemy Ahmed , Olender Thomas , Chen Myra J , Ahmad Shiekh Tanveer , Prokopchuk Oleksandr , Vasan Lakshmy , Touahri Yacine , Islam Rehnuma , Sujanthan Sajeevan , Zinyk Dawn , Comanita Lacrimioara C , Kan Boris , Fleming Taylor , Michael Iacovos P , Morshead Cindi M , Leong Hon S , Okawa Satoshi , Brand Marjorie , Wallace Valerie A , Chan Jennifer A , Schuurmans Carol
Published: July 2020

Isocitrate dehydrogenase (IDH) mutant gliomas, including oligodendroglioma (IDH-O) and astrocytoma (IDH-A), have signature slow-growth rates that are poorly understood. Here, we reveal thatSMPD3,a ceramide-producing sphingomyelinase implicated as a tumor suppressor gene and involved in extracellular vesicle biogenesis, suppresses IDH-mutant tumor growth via autocrine and paracrine actions. In patients with IDH-mutant gliomas, higherSMPD3expression levels correlate with longer survival, consistent with ceramide acting as an anti-oncometabolite.SMPD3knock-down in patient-derived IDH-O cells enhances proliferation cell-autonomously in 2D-culture and 3D-human cerebral organoids, and accelerates tumor growth in mouse orthotopic xenografts. Supporting paracrine actions, IDH-O-derived extracellular vesicles, enriched in ribosomal proteins, induce astrocytic deathin vitro. Furthermore, non-neoplastic glia in IDH-O tumors proliferate abnormally yet undergo apoptosis, concomitant with the acquisition of a translation-enriched transcriptional signature by tumor-associated oligodendrocytes.SMPD3thus suppresses IDH-mutant glioma growth cell-autonomously and phenotypically alters normal glia via extracellular vesicle biogenesis and paracrine actions.
Predictive pre-activation of orthographic and lexical-semantic representations facilitates visual word recognition
Authors: Eisenhauer Susanne , Gagl Benjamin , Fiebach Christian J.
Published: July 2020

To a crucial extent, the efficiency of reading results from the fact that visual word recognition is faster in predictive contexts. Predictive coding models suggest that this facilitation results from pre-activation of predictable stimulus features across multiple representational levels before stimulus onset. Still, it is not sufficiently understood which aspects of the rich set of linguistic representations that are activated during reading – visual, orthographic, phonological, and/or lexical-semantic – contribute to context-dependent facilitation. To investigate in detail which linguistic representations are pre-activated in a predictive context and how they affect subsequent stimulus processing, we combined a well-controlled repetition priming paradigm, including words and pseudowords (i.e., pronounceable nonwords), with behavioral and magnetoencephalography measurements. For statistical analysis, we used linear mixed modeling, which we found had a higher statistical power compared to conventional multivariate pattern decoding analysis. Behavioral data from 49 participants indicate that word predictability (i.e., context present vs. absent) facilitated orthographic and lexical-semantic, but not visual or phonological processes. Magnetoencephalography data from 38 participants show sustained activation of orthographic and lexical-semantic representations in the interval before processing the predicted stimulus, suggesting selective pre-activation at multiple levels of linguistic representation as proposed by predictive coding. However, we found more robust lexical-semantic representations when processing predictable in contrast to unpredictable letter strings, and pre-activation effects mainly resembled brain responses elicited when processing the expected letter string. This finding suggests that pre-activation did not result in ‘explaining away’ predictable stimulus features, but rather in a ‘sharpening’ of brain responses involved in word processing.
Molecular and cellular pathology of monogenic Alzheimer’s disease at single cell resolution
Authors: Marinaro Federica , Haneklaus Moritz , Zhang Zhechun , Strano Alessio , Evans Lewis , Handfield Louis-François , Ryan Natalie S. , Fox Nick C. , Hemberg Martin , Ramanathan Sharad , Livesey Frederick J.
Published: July 2020

Cell and molecular biology analyses of sporadic Alzheimer’s disease brain are confounded by clinical variability, ageing and genetic heterogeneity. Therefore, we used single-nucleus RNA sequencing to characterize cell composition and gene expression in the cerebral cortex in early-onset, monogenic Alzheimer’s disease. Constructing a cellular atlas of frontal cortex from 8 monogenic AD individuals and 8 matched controls, provided insights into which neurons degenerate in AD and responses of different cell types to AD at the cellular and systems level. Such responses are a combination of positively adaptive and deleterious changes, including large-scale changes in synaptic transmission and marked metabolic reprogramming in neurons. The nature and scale of the transcriptional changes in AD emphasizes the global impact of the disease across all brain cell types.

One Sentence Summary

Alzheimer’s disease brain atlas provides insights into disease mechanisms
A tropane-based ibogaine analog rescues folding-deficient SERT and DAT
Authors: Bhat Shreyas , Guthrie Daryl A. , Kasture Ameya , El-Kasaby Ali , Cao Jianjing , Bonifazi Alessandro , Ku Therese , Giancola JoLynn B. , Hummel Thomas , Freissmuth Michael , Newman Amy Hauck
Published: July 2020

Missense mutations that give rise to protein misfolding are rare, but collectively, defective protein folding diseases are consequential. Folding deficiencies are amenable to pharmacological correction (pharmacochaperoning), but the underlying mechanisms remain enigmatic. Ibogaine and its active metabolite noribogaine correct folding defects in the dopamine transporter (DAT), but they rescue only a very limited number of folding-deficient DAT mutants, which give rise to infantile Parkinsonism and dystonia. Herein, a series of analogs was generated by reconfiguring the complex ibogaine ring system and exploring the structural requirements for binding to wild type transporters, and for rescuing two equivalent synthetic folding-deficient mutants, SERT-PG601,602AA and DAT-PG584,585AA. The most active tropane-based analog (9b) was also an effective pharmacochaperonein vivo, in Drosophila harboring DAT-PG584,585AA and rescued six out of 13 disease-associated human DAT mutantsin vitro.Hence, a novel lead pharmacochaperone has been identified that demonstrates medication development potential for patients harboring DAT mutants.
Adult newborn granule cells confer emotional-state-dependent plasticity in memory retrieval
Authors: Lei Bo , Kang Bilin , Lin Wantong , Chen Haichao , Hao Yuejun , Ma Jian , Shi Songhai , Zhong Yi
Published: July 2020

Achieving optimal behavior requires animals to flexibly retrieve prior knowledge. Here we show that adult newborn granule cells (anbGCs) mediate emotional-state-dependent plasticity of memory retrieval. We find that acute social reward (aSR) enhances memory retrieval by increasing the reactivation of engram cells, while acute social stress (aSS) weakens retrieval and reduces the reactivation. Such bidirectional regulation relies on the activation of distinct populations of anbGCs by aSR and aSS, triggering opposing modifications of dDG activity, which is sufficient to regulate and predict the performance of memory retrieval. Concordantly, in emotional disorder models, aSR-dependent memory plasticity is impaired, while the effect of aSS remains intact. Together, our data revealed that anbGCs mediate plasticity of memory retrieval, allowing animals to flexibly retrieve memory according to the current emotional state, and suggested the essential roles of anbGCs in translating emotional information to the regulation of memory expression.
The representation of bodies in high level visual, prefrontal and inferior parietal cortex varies with explicit vs. implicit expression perception
Authors: Marrazzo Giuseppe , Vaessen Maarten J. , de Gelder Beatrice
Published: July 2020

Recent studies provide an increasingly understanding of how visual objects categories like faces or bodies are represented in the brain but also raised the question whether a category based or more network inspired models are more powerful. Two important and so far sidestepped issues in this debate concern, first, how major category attributes like the emotional expression directly influence category representation and second, whether category and attribute representation are sensitive to task demands. This study investigated the impact of a crucial category attribute like emotional expression on category activity and whether this varies with the participants’ task. Using (fMRI) we measured BOLD responses while participants viewed whole body expressions and performed either an explicit (emotion) or an implicit (shape) recognition task. Our results based on multivariate methods show that the type of task is the strongest determinant of brain activity and can be decoded in EBA, VLPFC and IPL. Brain activity was higher for the explicit task condition in VLPFC and was not emotion specific. This pattern suggests that during explicit recognition of the body expression, body category representation may be strengthened, and emotion and action related activity suppressed. Taken together these results stress the importance of the task and of the role of category attributes for understanding the functional organization of high level visual cortex.
Intermediate adhesion maximizes fluidity and migration velocity of multicellular clusters
Authors: Roy U. , Mugler A.
Published: July 2020

Collections of cells exhibit coherent migration during morphogenesis, cancer metastasis, and wound healing. In many cases, bigger clusters split, smaller sub-clusters collide and reassemble, and gaps continually emerge. The connections between cell-level adhesion and cluster-level dynamics, as well as the resulting consequences for cluster properties such as migration velocity, remain poorly understood. Here we investigate collective migration of one- and two-dimensional cell clusters that collectively track chemical gradients using a mechanism based on contact inhibition of locomotion. We develop both a minimal description based on the lattice gas model of statistical physics, and a more realistic framework based on the cellular Potts model which captures cell shape changes and cluster rearrangement. In both cases, we find that cells have an optimal adhesion strength that maximizes cluster migration speed. The optimum negotiates a tradeoff between maintaining cell-cell contact and maintaining cluster fluidity, and we identify maximal variability in the cluster aspect ratio as a revealing signature. Our results suggest a collective benefit for intermediate cell-cell adhesion.

SIGNIFICANCE

Cells have been observed to migrate faster and more efficiently in clusters than as individuals. We conjecture that adhesion among cells and with the extracellular environment plays an important role in achieving higher-speed for the entire cluster. We carry out our analyses analytically and computationally, by employing a simplistic one-dimensional model and a realistic two-dimensional model which capture the essential features of multicellular migration. Our study demonstrates that an optimal cell-cell adhesion, which corresponds to maximal cellular rearrangement and loose packing, leads to a higher migration velocity for a multicellular cluster, acting as a crucial factor in effective movement of a collection of cells in a coordinated and directed fashion.
Spectral Signatures of L-DOPA-Induced Dyskinesia Depend on L-DOPA Dose and are Suppressed by Ketamine
Authors: Ye Tony , Bartlett Mitchell J. , Sherman Scott J. , Falk Torsten , Cowen Stephen L.
Published: July 2020

L-DOPA-induced dyskinesias (LID) are debilitating motor symptoms of dopamine-replacement therapy for Parkinson’s disease (PD) that emerge after years of L-DOPA treatment. While there is an abundance of research into the cellular and synaptic origins of LID, less is known about how LID impacts systems-level circuits and neural synchrony, how synchrony is affected by the dose and duration of L-DOPA exposure, or how potential novel treatments for LID, such as sub-anesthetic ketamine, alter this activity. Sub-anesthetic ketamine treatments have recently been shown to reduce LID, and ketamine is known to affect neural synchrony. To investigate these questions, we measured movement and local-field potential (LFP) activity from the motor cortex (M1) and the striatum of preclinical rodent models of PD and LID. In the first experiment, we investigated the effect of the LID priming procedures and L-DOPA dose on neural signatures of LID. Two common priming procedures were compared: a high-dose procedure that exposed unilateral 6-hydroxydopamine-lesioned rats to 12 mg/kg L-DOPA for 7 days, and a low-dose procedure that exposed rats to 7 mg/kg L-DOPA for 21 days. Consistent with reports from other groups, 12 mg/kg L-DOPA triggered LID and 80-Hz oscillations; however, these 80-Hz oscillations were not observed after 7 mg/kg administration despite clear evidence of LID, indicating that 80-Hz oscillations are not an exclusive signature of LID. We also found that weeks-long low-dose priming resulted in the emergence of non-oscillatory broadband gamma activity (> 30 Hz) in the striatum and theta-to-high-gamma cross-frequency coupling (CFC) in M1. In a second set of experiments, we investigated how ketamine exposure affects spectral signatures of low-dose L-DOPA priming. During each neural recording session, ketamine was delivered through 5 injections (20 mg/kg,i.p.) administered every 2 hours. We found that ketamine exposure suppressed striatal broadband gamma associated with LID but enhanced M1 broadband activity. We also found that M1 theta-to-high-gamma CFC associated with the LID on-state was suppressed by ketamine. These results suggest that ketamine’s therapeutic effects are region specific. Our findings also have clinical implications, as we are the first to report novel oscillatory signatures of the common low-dose LID priming procedure that more closely models dopamine replacement therapy in individuals with PD. We also identify neural correlates of the anti-dyskinetic activity of sub-anesthetic ketamine treatment.
Characterization of gene repression by designed transcription activator-like effector dimer proteins
Authors: Becker NA , Peters JP , Schwab TL , Phillips WJ , Wallace JP , Clark KJ , Maher LJ
Published: July 2020

Gene regulation by control of transcription initiation is a fundamental property of living cells. Much of our understanding of gene repression originated from studies of theE. coli lacoperon switch, where DNA looping plays an essential role. To validate and generalize principles fromlacfor practical applications, we previously described artificial DNA looping driven by designed Transcription Activator-Like Effector Dimer (TALED) proteins. Because TALE monomers bind the idealized symmetricallacoperator sequence in two orientations, our prior studies detected repression due to multiple DNA loops. We now quantitatively characterize gene repression in livingE. coliby a collection of individual TALED loops with systematic loop length variation. Fitting of a thermodynamic model allows unequivocal demonstration of looping and comparison of the engineered TALED repression system with the natural lac repressor system.

Statement of Significance

We are designing and testing in living bacteria artificial DNA looping proteins engineered based on principles learned from studies of theE. colilac repressor. The engineered proteins are based on artificial dimers of Transcription Activator-Like Effector (TALE) proteins that have programmable DNA binding specificities. The current work is the first to create unique DNA repression loops using this approach. Systematic study of repression as a function of loop size, with data fitting to a thermodynamic model, now allows this system to be compared in detail with lac repressor loops, and relevant biophysical parameters to be estimated. This approach has implications for the artificial regulation of gene expression.