bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of antibodies to pan-coronavirus spike peptides in convalescent COVID-19 patients
Authors: Rabets Andrii , Bila Galyna , Grytsko Roman , Samborsky Markian , Rebets Yuriy , Vari Sandor , Pagneux Quentin , Barras Alexandre , Boukherroub Rabah , Szunerits Sabine , Bilyy Rostyslav
Published: August 2020

Coronaviruses are sharing several protein regions notable the spike protein (S) on their enveloped membrane surface, with the S1 subunit recognizing and binding to the cellular receptor, while the S2 subunit mediates viral and cellular membrane fusion. This similarity opens the question whether infection with one coronavirus will confer resistance to other coronaviruses? Investigating patient serum samples after SARS-CoV-2 infection in cross-reactivity studies of immunogenic peptides from Middle East respiratory syndrome coronavirus (MERS-CoV), we were able to detect the production of antibodies also recognizing MERS virus antigens. The cross-reactive peptide comes from the heptad repeat 2 (HR2) domain of the MERS virus spike protein. Indeed, the peptide of the HR2 domain of the MERS spike protein, previously proven to induce antibodies against MERS-CoV is sharing 74% homology with the corresponding sequence of SARS-CoV-19 virus. Sera samples of 47 convalescent SARS-CoV-2 patients, validated by RT-PCR-negative testes 30 days post-infection, and samples of 40 sera of control patients (not infected with SARS-CoV-2 previously) were used to establish eventual cross-bind reactivity with the MERS peptide antigen. Significantly stronger binding (p< 0.0001) was observed for IgG antibodies in convalescent SARS-CoV-2 patients compared to the control group. If used as an antigen, the peptide of the HR2 domain of the MERS spike protein allows discrimination between post-Covid populations from non-infected ones by the presence of antibodies in blood samples. This suggests that polyclonal antibodies established during SARS-CoV-2 infection has the ability to recognize and probably decrease infectiveness of MERS-CoV infections as well as other coronaviruses. The high homology of the spike protein domain suggests in addition that the opposite effect can also be true: coronaviral infections producing cross-reactive antibodies affective against SARS-CoV-19. The collected data prove in addition that despite the core HR2 region being hidden in the native viral conformation, its exposure during cell entry makes it highly immunogenic. Since inhibitory peptides to this region were previously described, this opens new possibilities in fighting coronaviral infections.
Systematic review and patient-level meta-analysis of SARS-CoV-2 viral dynamics to model response to antiviral therapies
Authors: Gastine Silke , Pang Juanita , Boshier Florencia A.T. , Carter Simon J. , Lonsdale Dagan O. , Cortina-Borja Mario , Hung Ivan F.N. , Breuer Judy , Kloprogge Frank , Standing Joseph F.
Published: August 2020

SARS-CoV-2 viral loads change rapidly following symptom onset so to assess antivirals it is important to understand the natural history and patient factors influencing this. We undertook an individual patient-level meta-analysis of SARS-CoV-2 viral dynamics in humans to describe viral dynamics and estimate the effects of antivirals used to-date. This systematic review identified case reports, case series and clinical trial data from publications between 1/1/2020 and 31/5/2020 following PRISMA guidelines. A multivariable Cox proportional hazards regression model (Cox-PH) of time to viral clearance was fitted to respiratory and stool samples. A simplified four parameter nonlinear mixed-effects (NLME) model was fitted to viral load trajectories in all sampling sites and covariate modelling of respiratory viral dynamics was performed to quantify time dependent drug effects. Patient-level data from 645 individuals (age 1 month-100 years) with 6316 viral loads were extracted. Model-based simulations of viral load trajectories in samples from the upper and lower respiratory tract, stool, blood, urine, ocular secretions and breast milk were generated. Cox-PH modelling showed longer time to viral clearance in older patients, males and those with more severe disease. Remdesivir was associated with faster viral clearance (adjusted hazard ratio (AHR) = 9.19,p<0.001), as well as interferon, particularly when combined with ribavirin (AHR = 2.2,p=0.015; AHR = 6.04,p =0.006). Combination therapy should be further investigated. A viral dynamic dataset and NLME model for designing and analysing antiviral trials has been established.
Forecasting PPE Consumption during a Pandemic: The Case of Covid-19
Authors: Lum Kristian , Johndrow James , Cardone April , Fuchs Barry , Cotner Cody E. , Jew Olivia , Parikh Ravi B. , Draugelis Michael , Luong ThaiBinh , Hanish Asaf , Weissman Gary E. , Terwiesch Christian , Volpp Kevin G.
Published: August 2020

Due to the global shortage of PPE caused by increasing number of COVID-19 patients in recent months, many hospitals have had difficulty procuring adequate PPE for the clinicians who care for these patients. Faced with a shortage, hospitals have had to implement new PPE conservation policies. In this paper, we describe a tool to help hospitals better project PPE needs under various conservation policies. Though this tool is built on top of projections of the number of hospitalized COVID-19 patients, it is agnostic as to which model—of which many are available—provides these projections. The tool combines COVID-19 patient census projections with information like staffing ratios and frequency of patient contact to provide projections of the number of items of key types of PPE needed under three built-in conservation scenarios: standard, contingency, and crisis. Users are also able to customize the tool to the specifics of their hospital and design custom conservation policies.
Dynamic causal modeling of the COVID-19 pandemic in northern Italy predicts possible scenarios for the second wave
Authors: Gandolfi Daniela , Pagnoni Giuseppe , Filippini Tommaso , Goffi Alessia , Vinceti Marco , D’Angelo Egidio , Mapelli Jonathan
Published: August 2020

The COVID-19 pandemic has sparked an intense debate about the factors underlying the dynamics of the outbreak. Mitigating virus spread could benefit from reliable predictive models that inform effective social and healthcare strategies. Crucially, the predictive validity of these models depends upon incorporating behavioral and social responses to infection that underwrite ongoing social and healthcare strategies. Formally, the problem at hand is not unlike the one faced in neuroscience when modelling brain dynamics in terms of the activity of a neural network: the recent COVID-19 pandemic develops in epicenters (e.g. cities or regions) and diffuses through transmission channels (e.g., population fluxes). Indeed, the analytic framework known as “Dynamic Causal Modeling” (DCM) has recently been applied to the COVID-19 pandemic, shedding new light on the mechanisms and latent factors driving its evolution. The DCM approach rests on a time-series generative model that provides — through Bayesian model inversion and inference — estimates of the factors underlying the progression of the pandemic. We have applied DCM to data from northern Italian regions, which were the first areas in Europe to contend with the COVID-19 outbreak. We used official data on the number of daily confirmed cases, recovered cases, deaths and performed tests. The model — parameterized using data from the first months of the pandemic phase — was able to accurately predict its subsequent evolution (including social mobility, as assessed through GPS monitoring, and seroprevalence, as assessed through serologic testing) and revealed the potential factors underlying regional heterogeneity. Importantly, the model predicts that a second wave could arise due to a loss of effective immunity after about 7 months. This second wave was predicted to be substantially worse if outbreaks are not promptly isolated and contained. In short, dynamic causal modelling appears to be a reliable tool to shape and predict the spread of the COVID-19, and to identify the containment and control strategies that could efficiently counteract its second wave, until effective vaccines become available.
Where will they grow from here? Association between height at 24 months and adult attained height in a population with a high prevalence of linear growth restriction
Authors: Schwarz Julia , Yori Pablo Peñataro , Pan William K. , Olortegui Maribel Paredes , Klapheke Robert , Kosek Margaret N.
Published: August 2020

This was a longitudinal observational cohort study to investigate the association of stunting at 24 months of age and attained adult height. A cohort of 104 Peruvian males (n = 47) and females (n = 57) was studied from 24 months to after puberty in a rural community in the Peruvian Amazon located 15 km southeast from the urban center of Iquitos. Anthropometric measures were made at 24 months and after puberty. Height for Age Z (HAZ) Scores were calculated and compared to assess the association of HAZ score at 24 months and adult height. 67.7% of males and 54.1% of females who were stunted at 24 m (HAZ<-2.0) recovered (HAZ>-2.0) after puberty, whereas 6.25% of males and 6.06% of females who were not stunted at 24 m (HAZ>-2.0) became stunted (HAZ<-2.0) after puberty. The first 1000 days are not the only critical window for growth promotion. Global and national initiatives to reduce stunting should not exclusively focus on the first two years of life, but also work to promote the nutritional initiatives to promote optimal nutrition and growth throughout childhood and adolescence.
Poor knowledge of COVID-19 and unfavourable perception of the response to the pandemic by healthcare workers at the Bafoussam Regional Hospital (West Region - Cameroon)
Authors: Fouogue Jovanny Tsuala , Noubom Michel , Kenfack Bruno , Dongmo Norbert Tanke , Tabeu Maxime , Megozeu Linda , Alima Jean Marie , Fogang Yannick Fogoum , Nyam Rim Landry Charles A , Fouelifack Florent Ymele , Fouedjio Jeanne Hortence , Nzogning Manebou Pamela Leonie Fouogue , Bibou Ze Clotaire Damien , Kouam Brice Foubi , Fomete Lauriane Nomene , Tebeu Pierre Marie , Ngowa Kemfang Jean Dupont , Foumane Pascal , Sando Zacharie , Enow Orock George Enownchong
Published: August 2020

Background

The World Health Organization has warned against a dramatic impact of COVID-19 in sub-Saharan Africa unless adequate response strategies are implemented. Whatever the strategy, the role of health care workers is pivotal. We undertook this study to assess knowledge of COVID-19 and perception of the response to the pandemic among the staff of a regional hospital in charge of COVID-19 patients in West Cameroon.

Methods

We used a convenience non probabilistic sampling method to carry out a survey with a self-administered questionnaire from April 14, 2020 to April 29, 2020 at the Bafoussam Regional Hospital (BRH). All the staff was invited to participate. Statistical analyses were done using Microsoft Excel 2010 and Epi-lnfo version 7.1.5.2 software.

Results

Response rate was 76.1% (464/610). Mean age (SD) and average work experience (SD) were 35.0 (8.9) and 8.4 (7.4) years respectively. Sex ratio (M/F) was 101/356. Nursing and midwifery staff (56.8%) and in-patients units (49.94%) were predominant. Knowledge on origin and transmission of SARS-CoV-2 was poor but knowledge of clinical signs and the role of laboratory tests were good. 53.2% of respondents said all therapeutic regimens are only supportive and only a third of them trusted drugs recommended by health authorities. For 36.9% of respondents, herbal remedies can prevent/cure COVID-19. 70% of staffs felt they were not knowledgeable enough to handle COVID-19 cases. 85.6% of respondents thought the BRH had insufficient resources to adequately respond to COVID-19 and 55.6% were dissatisfied with its response to the pandemic (weaknesses: medicines/technologies (74.5%), service delivery (28.1%), human resource (10.9%)). 68% of staff felt insufficiently protected on duty and 76.5% reported that the pandemic significantly reduced non-COVID-19 services. 85.5% said they complied with preventive measures while in the community. For 44% of respondents Cameroonian regulations on COVID-19 corpses should be made more culture-sensitive. 51.2% of respondents were against vaccine trial in their community.

Conclusion

Knowledge of COVID-19 was poor and perception of the response to the pandemic was unfavorable.
Circulating CD8+ MAIT cells correlate with improved outcomes in anti-PD1 treated melanoma patients
Authors: Vorwald Victoria M. , Davis Dana M. , Van Gulick Robert J. , Torphy Robert J. , Borgers Jessica S.W. , Klarquist Jared , Couts Kasey L. , Amato Carol M. , Cogswell Dasha T. , Fujita Mayumi , Davis Timothy , Lozupone Catherine , Medina Theresa M. , Robinson William A. , Gapin Laurent , McCarter Martin D. , Tobin Richard P.
Published: August 2020

While much of the research concerning factors associated with responses to immunotherapies focuses on the contributions of conventional peptide-specific T cells, the role of unconventional T cells, such as mucosalassociated invariant T (MAIT) cells, in human melanoma remains largely unknown. MAIT cells are innate-like T cells expressing a semi-invariant T cell receptor restricted to the non-classical MHC class I molecule MR1 presenting vitamin metabolites derived from bacteria. In this prospective clinical study, we sought to characterize MAIT cells in melanoma patients and determine their association with clinical outcomes. We identified tumor-infiltrating MAIT cells in melanomas across metastatic sites and found that the number of circulating MAIT cells is reduced in melanoma patients. However, circulating MAIT cell frequency is restored by anti-PD1 treatment in responding patients, correlating with treatment responses in which patients with high frequencies of MAIT cells exhibited improved overall survival. These data provide evidence for leveraging MAIT cells and their functions as novel targets for future therapies.
Rethinking Depression in Cities: Evidence and Theory for Lower Rates in Larger Urban Areas
Authors: Stier Andrew J. , Schertz Kathryn E. , Rim Nak Won , Cardenas-Iniguez Carlos , Lahey Benjamin B. , Bettencourt Luís M. A. , Berman Marc G.
Published: August 2020

It is commonly assumed that cities are detrimental to mental health. However, the evidence remains inconsistent and, at most, makes the case for differences between rural and urban environments as a whole. Here, we propose a model of depression driven by an individual’s accumulated experience mediated by social networks. The connection between observed systematic variations in socioeconomic networks and built environments with city size provides a link between urbanization and mental health. Surprisingly, this model predicts lower depression rates in larger cities. We confirm this prediction for US cities using three independent datasets. These results are consistent with other behaviors associated with denser socioeconomic networks and suggest that larger cities provide a buffer against depression. This approach introduces a systematic framework for conceptualizing and modeling mental health in complex physical and social networks, producing testable predictions for environmental and social determinants of mental health also applicable to other psychopathologies.
Phenotyping Neuropsychiatric Symptoms Profiles of Alzheimer’s Disease Using Cluster Analysis on EEG Power
Authors: Liu Friedrich , Fuh Jong-Ling , Peng Chung-Kang , Yang Albert C.
Published: August 2020

There has been an increasing interest in studying electroencephalogram (EEG) as a biomarker of Alzheimer’s disease but the association between EEG signals and patients’ neuropsychiatric symptoms remains unclear. We studied EEG signals of patients with Alzheimer’s disease to explore the associations between patients’ neuropsychiatric symptoms and clusters of patients based on their EEG powers. A total of 69 patients with mild Alzheimer’s disease (the Clinical Dementia Rating = 1) were enrolled and their EEG signals from 19 channels/electrodes were recorded in three sessions for each patient. The EEG power was calculated by Fourier transform for the four frequency bands (beta: 13–40 Hz, alpha: 8–13 Hz, theta: 4–8 Hz, and delta: < 4 Hz). We performed K-means cluster analysis to classify the 69 patients into two distinct groups by the log-transformed EEG powers (4 frequency bands x 19 channels) for the three EEG sessions. In each session, both clusters were compared with each other to assess the differences in their behavioral/psychological symptoms in terms of the Neuropsychiatric Inventory (NPI) score. While EEG band powers were highly consistent across all three sessions before clustering, EEG band powers were different between the two clusters in each session, especially for the delta waves. The delta band powers differed significantly between the two clusters in most channels across the three sessions. Patients’ demographics and cognitive function were not different between both clusters. However, their behavioral/psychological symptoms were different between the two clusters classified based on EEG powers. A higher NPI score was associated with the clustering of higher EEG powers. The results suggest that EEG delta band power correlates to behavioral and psychological symptoms among patients with mild Alzheimer’s disease. The clustering approach of EEG signals may provide a novel and cost-effective method to differentiate the severity of neuropsychiatric symptoms and/or predict the prognosis for Alzheimer’s patients.
A Noninvasive Approach to Optogenetics Using Focused Ultrasound Blood Brain Barrier Disruption for the Delivery of Radioluminescent Particles
Authors: Rich Megan , Zhang Eric , Dickey Ashley , Jones Haley , Cannon Kelli , Bandera Yuriy , Foulger Stephen , Lubin Farah , Bolding Mark
Published: August 2020

Optogenetics, the genetic incorporation of light-sensitive proteins such as Channelrhodopsin-2 (ChR2) into target mammalian neurons, has enabled activation, silencing, and receptor subtype specific neuromodulation with high spatiotemporal resolution. However, the essential components of the ontogenetic system require invasive procedures with very few non-invasive alternatives preventing its use as a translational tool. The implantation of light emitting fibers deep within brain structures is both technically demanding and causes tissue scarring in target brain regions. To overcome these limitations, while maintaining the highly-tuned components of optogenetics we have developed a novel noninvasive alternative. Our approach replaces fibers with light-emitting radioluminescent particles (RLPs) that can be activated non-invasively with X-ray exposure. Here, we report successful noninvasive delivery of RLPs to target brain regions using MRI-guided focused ultrasound (FUS) blood brain barrier opening. In addition, FUS BBBO can be used to deliver viral vectors for light sensitive channel expression. Combined, these components can provide a completely non-invasive optogenetic system.
Path tortuosity changes the transport cost paradigm in terrestrial animals
Authors: Wilson R. P. , Rose K. A. R. , Metcalfe R. S. , Holton M. D. , Redcliffe J. , Gunner R. , Börger L. , Loison A. , Miloš J. , Painter M. S. , Silovský V. , Marks N. , Garel M. , Toigo C. , Marchand P. , Bennett N. C. , McNarry M. A. , Mackintosh K. A. , Brown M. R. , Scantlebury D. M.
Published: August 2020

Animal movement paths are variously tortuous, with high turn rates predicted to be energetically costly, especially at high speeds. Animals travel most efficiently at the speed that gives the lowest cost of transport (COT), a well-defined point for movement in fluid media. However, theoretically, land animals should travel at their maximum speed to minimize COT, which they do not, instead travelling at walking pace. We measured oxygen consumption in humans to demonstrate that the energetic costs of turning increase disproportionately with both speed and angular velocity. This resulted in the minimum COT speed occurring at very low speeds, which reduced with increased path tortuosity. Data on turn rates from six free-ranging terrestrial species underpinned this because all individuals turned faster at the slowest speeds across the full speed range. The optimum movement speed for minimum COT in land animals thus depends on the environment and behavior since both affect track tortuosity.
Re-emergence of BTV serotype 4 in North Macedonia, July 2020
Authors: Flannery John , King Simon , Rajko-Nenow Paulina , Popova Zagorka , Krstevski Kiril , Djadjovski Igor , Batten Carrie
Published: August 2020

Bluetongue virus serotype 4 (BTV-4) was confirmed in sheep in North Macedonia in July 2020. The full genome of this BTV-4 strain (MKD2020/06) was shown to be most closely related (99.74% nt identity) to the Greek GRE2014/08 and the Hungarian HUN1014 strains, indicating the re-emergence of this BTV serotype in the Balkan region since it was last reported in 2017.
The cytoskeleton adaptor protein Sorbs1 controls the development of lymphatic and venous vessels in zebrafish
Authors: Veloso Alexandra , Bleuart Anouk , Orban Tanguy , Bruyr Jonathan , Cabochette Pauline , Germano Raoul F.V. , Bernard Alice , Vanhollebeke Benoit , Martin Maud , Dequiedt Franck
Published: August 2020

Lymphangiogenesis, the formation of lymphatic vessels is tightly linked to the development of the venous vasculature, both at the cellular and molecular levels. Here, we identify a novel role for Sorbs1, the founding member of the SoHo family of cytoskeleton adaptor proteins, in vascular and lymphatic development in zebrafish. We show that Sorbs1 is required for secondary sprouting and emergence of several vascular structures specifically derived from the axial vein. Most notably, formation of the precursor parachordal lymphatic structures is affected insorbs1mutant embryos, severely impacting the establishment of a proper trunk lymphatic network and leading to edema development. We show that Sorbs1 is probably not part of the Vegfc signaling, but instead might interacts with the BMP pathways. Mechanistically, we show that Sorbs1 controls FAK/Src signaling to impact on Rac1 and RhoA GTPases-regulated cytoskeleton processes. Inactivation of Sorbs1 altered cell-extracellular matrix (ECM) contact rearrangement and cytoskeleton dynamics, leading to specific defects in endothelial cell migratory and adhesive properties. Our data thus establish Sorbs1 as an important regulator of lymphangiogenesis distinct from the Vegfc signaling axis, increasing our understanding of context-specific vascular and lymphatic development.
Deep Graph Pose: a semi-supervised deep graphical model for improved animal pose tracking
Authors: Wu Anqi , Buchanan E. Kelly , Whiteway Matthew R , Schartner Michael , Meijer Guido , Noel Jean-Paul , Rodriguez Erica , Everett Claire , Norovich Amy , Schaffer Evan , Mishra Neeli , Salzman C. Daniel , Angelaki Dora , Bendesky Andrés ,   The International Brain Laboratory, Cunningham John , Paninski Liam
Published: August 2020

Noninvasive behavioral tracking of animals is crucial for many scientific investigations. Recent transfer learning approaches for behavioral tracking have considerably advanced the state of the art. Typically these methods treat each video frame and each object to be tracked independently. In this work, we improve on these methods (particularly in the regime of few training labels) by leveraging the rich spatiotemporal structures pervasive in behavioral video — specifically, the spatial statistics imposed by physical constraints (e.g., paw to elbow distance), and the temporal statistics imposed by smoothness from frame to frame. We propose a probabilistic graphical model built on top of deep neural networks, Deep Graph Pose (DGP), to leverage these useful spatial and temporal constraints, and develop an efficient structured variational approach to perform inference in this model. The resulting semi-supervised model exploits both labeled and unlabeled frames to achieve significantly more accurate and robust tracking while requiring users to label fewer training frames. In turn, these tracking improvements enhance performance on downstream applications, including robust unsupervised segmentation of behavioral “syllables,” and estimation of interpretable “disentangled” low-dimensional representations of the full behavioral video. Open source code is available athttps://github.com/paninski-lab/deepgraphpose.
Aquatic insects are dramatically underrepresented in genomic research
Authors: Hotaling Scott , Kelley Joanna L. , Frandsen Paul B.
Published: August 2020

Aquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. Yet aquatic insect genome biology lags dramatically behind that of terrestrial insects. If genomic effort was spread evenly, one aquatic insect genome would be sequenced for every ∼9 terrestrial insect genomes. Instead, ∼24 terrestrial insect genomes have been sequenced for every aquatic insect genome. This discrepancy is even more dramatic if thequalityof genomic resources is considered; for instance, while no aquatic insect genome has been assembled to the chromosome level, 29 terrestrial insect genomes spanning four orders have. We argue that a lack of aquatic insect genomes is not due to any underlying difficulty (e.g., small body sizes or unusually large genomes) yet it is severely hampering aquatic insect research at both fundamental and applied scales. By expanding the availability of aquatic insect genomes, we will gain key insight into insect diversification and empower future research for a globally important taxonomic group.

Simple Summary

Aquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. Yet aquatic insect genome biology lags dramatically behind that of terrestrial insects. If genomic effort was spread evenly, one aquatic insect genome would be sequenced for every ∼9 terrestrial insect genomes. Instead, ∼24 terrestrial insect genomes have been sequenced for every aquatic insect genome. We argue that the limited availability of aquatic insect genomes is not due to practical limitations—e.g., small body sizes or overly complex genomes—but instead reflects a lack of research interest. We call for targeted efforts to expand the availability of aquatic insect genomic resources to gain key molecular insight into insect diversification and empower future research.
Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens
Authors: Guo Xinyi , Wessels Hans-Hermann , Méndez-Mancilla Alejandro , Haro Daniel , Sanjana Neville E.
Published: August 2020

CRISPR-Cas13 mediates robust transcript knockdown in human cells through direct RNA targeting. Compared to DNA-targeting CRISPR enzymes like Cas9, RNA targeting by Cas13 is transcript- and strand-specific: It can distinguish and specifically knock-down processed transcripts, alternatively spliced isoforms and overlapping genes, all of which frequently serve different functions. Previously, we identified optimal design rules forRfxCas13d guide RNAs (gRNAs), and developed a computational model to predict gRNA efficacy for all human protein-coding genes. However, there is a growing interest to target other types of transcripts, such as noncoding RNAs (ncRNAs) or viral RNAs, and to target transcripts in other commonly-used organisms. Here, we predicted relative Cas13-driven knock-down for gRNAs targeting messenger RNAs and ncRNAs in six model organisms (human, mouse, zebrafish, fly, nematode and flowering plants) and four abundant RNA virus families (SARS-CoV-2, HIV-1, H1N1 influenza and MERS). To allow for more flexible gRNA efficacy prediction, we also developed a web-based application to predict optimal gRNAs for any RNA target entered by the user. Given the lack of Cas13 guide design tools, we anticipate this resource will facilitate CRISPR-Cas13 RNA targeting in common model organisms, emerging viral threats to human health, and novel RNA targets.
Characterization of cells susceptible to SARS-COV-2 and methods for detection of neutralizing antibody by focus forming assay
Authors: Stone E. Taylor , Geerling Elizabeth , Steffen Tara L. , Hassert Mariah , Dickson Alexandria , Spencer Jacqueline F. , Toth Karoly , DiPaolo Richard J. , Brien James D. , Pinto Amelia K.
Published: August 2020

The SARS-CoV-2 outbreak and subsequent COVID-19 pandemic have highlighted the urgent need to determine what cells are susceptible to infection and for assays to detect and quantify SARS-CoV-2. Furthermore, the ongoing efforts for vaccine development have necessitated the development of rapid, high-throughput methods of quantifying infectious SARS-CoV-2, as well as the ability to screen human polyclonal sera samples for neutralizing antibodies against SARS-CoV-2. To this end, our lab has adapted focus forming assays for SARS-CoV-2 using Vero CCL-81 cells, referred to in this text as Vero WHO. Using the focus forming assay as the basis for screening cell susceptibility and to develop a focus reduction neutralization test. We have shown that this assay is a sensitive tool for determining SARS-CoV-2 neutralizing antibody titer in human, non-human primate, and mouse polyclonal sera following SARS-CoV-2 exposure. Additionally, we describe the viral growth kinetics of SARS-CoV-2 in a variety of different immortalized cell lines and demonstrate via human ACE2 and viral spike protein expression that these cell lines can support viral entry and replication.
Computationally Guided Design of BCR-ABL Tyrosine Kinase Inhibitors
Authors: Duan Chenghao , Chu Simon K. S. , Siegel Justin B. , Fell Jason S.
Published: August 2020

BCR-ABLtyrosine kinase inhibitors (TKI) are used to treat the chronic myeloid leukemia (CML). Many TKI have been developed as the primary treatment to the CML.Imatinib, a first generation TKI, directly targetsBCR-ABLwith effective results. As the disease becomes more advanced, patients start to develop resistance toimatinib. Due to this effect it is necessary to generate novel treatments for advanced stage CML. Computational tools can predict new drug candidates to targetBCR-ABL. We have designed two new drug candidates with different levels of modification, based on the predicted structure activity relationships withBCR-ABL. These new drug candidates are predicted to have better binding affinities withBCR-ABLthanimatinib, which can be more potent treatments of the disease.
SARS-CoV-2 infects brain choroid plexus and disrupts the blood-CSF-barrier
Authors: Pellegrini Laura , Albecka Anna , Mallery Donna L. , Kellner Max J. , Paul David , Carter Andrew P. , James Leo C. , Lancaster Madeline A.
Published: August 2020

Coronavirus disease-19 (COVID-19), caused by the SARS-CoV-2 virus, leads primarily to respiratory symptoms that can be fatal, particularly in at risk individuals. However, neurological symptoms have also been observed in patients, including headache, seizures, stroke, and fatigue. The cause of these complications is not yet known, and whether they are due to a direct infection of neural cells, such as neurons and astrocytes, or through indirect effects on supportive brain cells, is unknown. Here, we use brain organoids to examine SARS-CoV-2 neurotropism. We examine expression of the key viral receptor ACE2 in single-cell RNA sequencing (scRNA-seq) revealing that only a subset of choroid plexus cells but not neurons or neural progenitors express this entry factor. We then challenge organoids with both SARS-CoV-2 spike protein pseudovirus and live virus to demonstrate high viral tropism for choroid plexus epithelial cells but not stromal cells, and little to no infection of neurons or glia. We find that infected cells of the choroid plexus are an apolipoprotein and ACE2 expressing subset of epithelial barrier cells. Finally, we show that infection with live SARS-CoV-2 leads to barrier breakdown of the choroid plexus. These findings suggest that neurological complications may result from effects on the choroid plexus, an important barrier that normally prevents entry of immune cells and cytokines into the cerebrospinal fluid (CSF) and brain.
Perspectives on the design and performance of upper-limb wearable stimulation devices for stroke survivors with hemiplegia and spasticity
Authors: Seim Caitlyn E. , Ritter Brandon , Starner Thad E. , Flavin Kara , Lansberg Maarten G. , Okamura Allison M.
Published: August 2020

Background

Vibrotactile stimulation may improve limb function after stroke; however, current studies are limited by the stationary and clinic-based apparatus used to apply this stimulation. A wearable device could provide vibrotactile stimulation in a mobile form factor, enabling further study of this technique.

Objective

The aim of this work is twofold: (1) Design and validate a wearable device for stroke survivors that provides vibrotactile stimulation to the upper limb, and (2) Understand features that influence stroke survivors’ interaction with an upper-limb wearable device.

Methods

A vibrotactile glove was designed to apply stimulation to the stroke-affected hand. This device, the vibrotactile stimulation (VTS) Glove, features small electronics, provides hours of stimulation, and has the appearance of a fingerless fitness glove. We performed two studies. In Study 1, sixteen stroke survivors were given the glove and asked to wear it for three hours daily for eight weeks. Usage time, indicating adherence, was calculated by onboard sensors. The device was evaluated using a log of damages and feedback from participants. Self-reported behaviors during glove use were also collected. In Study 2, eight stroke survivors evaluated new device prototypes in a three-round iterative design study. Interviews were used to collect participant feedback as they donned and doffed the prototypes. Task completion time and correctness were measured. Thematic content analysis was used to define actionable design revisions between each round of evaluation and identify key perspectives on design principles.

Results

The VTS Glove is lightweight, wireless, and durable. Based on Study 1, adherence appears feasible. Each participant recorded over 140 hours wearing the VTS Glove. Participants reported wearing the glove during activities such as church, social events, dining out, and using the computer. However, 69% of participants struggled to extend or insert their fingers to don the device. Our analysis in Study 2 identified six other relevant perspectives from survivors regarding the wearable devices: hand supination is difficult, grip varies without awareness, devices may lead to sweat, separate finger attachments require dexterity, social comfort is perceived as unimportant, and the affected hand is infrequently used. New device designs with revised features (VTS Phalanx, VTS Armband, and VTS Palm) could be donned in an average time of 48 seconds (vs. 5.05 minutes to don the VTS Glove).
Expression partitioning of duplicate genes at single cell resolution inArabidopsisroots
Authors: Coate Jeremy E. , Farmer Andrew D. , Schiefelbein John , Doyle Jeff J.
Published: August 2020

Gene duplication is a key evolutionary phenomenon, prevalent in all organisms but particularly so in plants, where whole genome duplication (WGD; polyploidy) is a major force in genome evolution. Much effort has been expended in attempting to understand the evolution of duplicate genes, addressing such questions as why some paralogue pairs rapidly return to single copy status whereas, in other pairs, paralogues are retained and may (or may not) diverge in expression pattern or function. The effect of a gene—its site of expression and thus the initial locus of its function—occurs at the level of a cell comprising a single cell type at a given state of the cell’s development. Thus, it is critical to understand the expression of duplicated gene pairs at a cellular level of resolution. UsingArabidopsis thalianaroot single cell transcriptomic data we identify 36 cell clusters, each representing a cell type at a particular developmental state, and analyze expression patterns of over 11,000 duplicate gene pairs produced by three cycles of polyploidy as well as by various types of single gene duplication mechanisms. We categorize paralogue pairs by their patterns of expression, identifying pairs showing strongly biased paralogue/homoeologue expression in different cell clusters. Notably, the precision of cell-level expression data permits the identification of pairs showing alternate bias, with each paralogue comprising 90% or greater of the pair’s expression in different cell clusters, consistent with subfunctionalization at the cell type or cell state level, and, in some cases, at the level of individual cells. We identify a set of over 7,000 genes whose expression in all 36 cell clusters suggests that the single copy ancestor of each was also expressed in all root cells. With this cell-level expression information we hypothesize that there have been major shifts in expression for the majority of duplicated genes, to different degrees depending, as expected, on gene function and duplication type, but also on the particular cell type and state.
A mating-induced reproductive gene promotesAnophelestolerance toPlasmodium falciparuminfection
Authors: Marcenac Perrine , Shaw W. Robert , Kakani Evdoxia G. , Mitchell Sara N. , South Adam , Werling Kristine , Marrogi Eryney , Abernathy Daniel G. , Yerbanga Rakiswendé Serge , Dabiré Roch K. , Diabaté Abdoulaye , Lefèvre Thierry , Catteruccia Flaminia
Published: August 2020

Anophelesmosquitoes have transmittedPlasmodiumparasites for millions of years, yet it remains unclear whether they suffer fitness costs to infection. Here we report that the fecundity of virgin and mated females of two important vectors—Anopheles gambiaeandAnopheles stephensi—is not affected by infection withPlasmodium falciparum, demonstrating that these human malaria parasites do not inflict reproductive costs to their natural mosquito hosts. Additionally, parasite development is not impacted by mating status. However, in field studies using differentP. falciparumisolates inAnopheles coluzzii, we find thatMating-Induced Stimulator of Oogenesis(MISO), a female reproductive gene strongly induced after mating by the sexual transfer of the steroid hormone 20-hydroxyecdysone (20E), protects females from incurring fecundity costs to infection.MISO-silenced females produce fewer eggs as they become increasingly infected withP. falciparum, while parasite development is not impacted by this gene silencing. Interestingly, previous work had shown that sexual transfer of 20E has specifically evolved inCelliaspecies of theAnophelesgenus, driving the co-adaptation of MISO. Our data therefore suggest that evolution of male-female sexual interactions may have promotedAnophelestolerance toP. falciparuminfection in theCelliasubgenus, which comprises the most important malaria vectors.

Author summary

Plasmodium falciparum, the deadliest form of human malaria, is transmitted when femaleAnophelesmosquitoes bite people and take a blood meal in order to develop eggs. To date, it is still poorly understood whetherAnophelesmosquitoes that get infected withP. falciparumsuffer fitness costs. Here, we find that the number of eggs produced byAnopheles gambiaeandAnopheles stephensifemales is not affected byP. falciparuminfection, and that the mating status of the mosquitoes does not impact the parasite. However, in field experiments infecting a related species,Anopheles coluzzii, withP. falciparumusing blood from donors in Burkina Faso, we find that interfering with the expression of a gene normally triggered by the sexual transfer of the steroid hormone 20-hydroxyecdysone induces increasing costs to egg development as females become more infected withP. falciparum, with no impacts on the parasite. The results of our study suggest that pathways triggered by mating may helpAnophelesprevent reproductive costs associated withP. falciparuminfection, providing new insights into evolutionary strategies adopted by anophelines in the face of a longstanding association withPlasmodiumparasites.
Isolation of high yield and quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts
Authors: Stegmayr John , Alsafadi Hani N. , Langwiński Wojciech , Niroomand Anna , Lindstedt Sandra , Leigh Nicholas D. , Wagner Darcy E.
Published: August 2020

Precision-cut lung slices (PCLS) have gained increasing interest as a model to study lung biology and disease, as well as for screening novel therapeutics. In particular, PCLS derived from human tissue can better recapitulate some aspects of lung biology and disease as compared to PCLS derived from animals (e.g.clinical heterogeneity), but access to human tissue is limited. A number of different experimental readouts have been established for use with PCLS, but obtaining high yield and quality RNA for downstream gene expression analysis has remained challenging. This is particularly problematic for utilizing the power of next-generation sequencing techniques, such as RNA-sequencing (RNA-seq), for non-biased and high through-put analysis of PCLS human cohorts. In the current study, we present a novel approach for isolating high quality RNA from a small amount of tissue, including diseased human tissue, such as idiopathic pulmonary fibrosis (IPF). We show that the RNA isolated using this method is of sufficient quality for both RT-qPCR and RNA-seq analysis. Furthermore, the RNA-seq data from human PCLS was comparable to data generated from native tissue and could be used in several established computational pipelines, including deconvolution of bulk RNA-seq data using publicly available single-cell RNA-seq data sets. Deconvolution using Bisque revealed a diversity of cell populations in human PCLS derived from distal lung tissue, including several immune cell populations, which correlated with cell populations known to be present and aberrant in human disease, such as IPF.
Ferrets not infected by SARS-CoV-2 in a high-exposure domestic setting
Authors: Sawatzki Kaitlin , Hill Nichola , Puryear Wendy , Foss Alexa , Stone Jonathon , Runstadler Jonathan
Published: August 2020

Ferrets (Mustela putorius furo) are mustelids of special relevance to laboratory studies of respiratory viruses and have been shown to be susceptible to SARS-CoV-2 infection and onward transmission. Here, we report the results of a natural experiment where 29 ferrets in one home had prolonged, direct contact and constant environmental exposure to two humans with symptomatic COVID-19. We observed no evidence of SARS-CoV-2 transmission from humans to ferrets based on RT-PCR and ELISA. To better understand this discrepancy in experimental and natural infection in ferrets, we compared SARS-CoV-2 sequences from natural and experimental mustelid infections and identified two surface glycoprotein (Spike) mutations associated with mustelids. While we found evidence that ACE2 provides a weak host barrier, one mutation only seen in ferrets is located in the novel S1/S2 cleavage site and is computationally predicted to decrease furin activity. These data support that host factors interacting with the novel S1/S2 cleavage site may be a barrier in ferret SARS-CoV-2 susceptibility and that domestic ferrets are at low risk of natural infection from currently circulating SARS-CoV-2. This may be overcome in laboratory settings using concentrated viral inoculum, but the effects of ferret host-adaptations require additional investigation.
Restricted differentiative capacity of Wt1-expressing peritoneal mesothelium in postnatal and adult mice
Authors: Wilm Thomas P , Tanton Helen , Mutter Fiona , Foisor Veronica , Middlehurst Ben , Ward Kelly , Benameur Tarek , Hastie Nicholas , Wilm Bettina
Published: August 2020

Previously, genetic lineage tracing based on the mesothelial marker Wt1, appeared to show that peritoneal mesothelial cells have a range of differentiative capacities and are the direct progenitors of vascular smooth muscle in the intestine. However, it was not clear whether this was a temporally limited process or continued throughout postnatal life. Here, using a conditional Wt1-based genetic lineage tracing approach, we demonstrate that the postnatal and adult peritoneum covering intestine, mesentery and body wall only maintained itself and failed to contribute to other visceral tissues. Pulse-chase experiments of up to 6 months revealed that Wt1-expressing cells remained confined to the peritoneum and failed to differentiate into cellular components of blood vessels or other tissues underlying the peritoneum. Ablation of Wt1 in adult mice did not result in changes to the intestinal wall architecture. In the heart, we observed that Wt1-expressing cells maintained the epicardium and contributed to coronary vessels in newborn and adult mice. Our results demonstrate that Wt1-expressing cells in the peritoneum have limited differentiation capacities, and that contribution of Wt1-expressing cells to cardiac vasculature is based on organ-specific mechanisms.
Towards Reproducible Brain-Wide Association Studies
Authors: Marek Scott , Tervo-Clemmens Brenden , Calabro Finnegan J. , Montez David F. , Kay Benjamin P. , Hatoum Alexander S. , Donohue Meghan Rose , Foran William , Miller Ryland L. , Feczko Eric , Miranda-Dominguez Oscar , Graham Alice M. , Earl Eric A. , Perrone Anders J. , Cordova Michaela , Doyle Olivia , Moore Lucille A. , Conan Greg , Uriarte Johnny , Snider Kathy , Tam Angela , Chen Jianzhong , Newbold Dillan J. , Zheng Annie , Seider Nicole A. , Van Andrew N. , Laumann Timothy O. , Thompson Wesley K. , Greene Deanna J. , Petersen Steven E. , Nichols Thomas E. , Yeo B.T. Thomas , Barch Deanna M. , Garavan Hugh , Luna Beatriz , Fair Damien A. , Dosenbach Nico U.F.
Published: August 2020

Magnetic resonance imaging (MRI) continues to drive many important neuroscientific advances. However, progress in uncovering reproducible associations between individual differences in brain structure/function and behavioral phenotypes (e.g., cognition, mental health) may have been undermined by typical neuroimaging sample sizes (median N=25)1,2. Leveraging the Adolescent Brain Cognitive Development (ABCD) Study3(N=11,878), we estimated the effect sizes and reproducibility of these brain-wide associations studies (BWAS) as a function of sample size. The very largest, replicable brain-wide associations for univariate and multivariate methods were r=0.14 and r=0.34, respectively. In smaller samples, typical for brain-wide association studies (BWAS), irreproducible, inflated effect sizes were ubiquitous, no matter the method (univariate, multivariate). Until sample sizes started to approach consortium-levels, BWAS were underpowered and statistical errors assured. Multiple factors contribute to replication failures4–6; here, we show that the pairing of small brain-behavioral phenotype effect sizes with sampling variability is a key element in wide-spread BWAS replication failure. Brain-behavioral phenotype associations stabilize and become more reproducible with sample sizes of N⪆2,000. While investigator-initiated brain-behavior research continues to generate hypotheses and propel innovation, large consortia are needed to usher in a new era of reproducible human brain-wide association studies.