bluuebunny/crossref_metadata_2025 huggingface dataset:
Motiro: an unified non-supervised framework for statistical analysis of probe-based confocal laser endomicroscopy videos of colorectal mucosa
Authors: Sabino Alan U. , Safatle-Ribeiro Adriana V. , Maluf-Filho Fauze , Ramos Alexandre F.
Published: October 2020

Objective

To present Motiro, an unified framework for non-supervised statistical analysis endomicroscopy videos of the colorectal mucosa.

Materials and Methods

We wrote an open-source Python wrapper using ImageJ software with OpenCV, Seaborn and NumPy libraries. It generates a mosaic from the video of the mucosa, evaluates morphometric properties of the crypts, their distribution, and return their statistics. Shannon entropy (and Hellinger distance) are used for quantifying variability (and comparing different mucosa).

Results

The segmentation process applied to normal mucosa of pre(post)- neoadjuvant patient is presented along with the corresponding statistical analysis of morphometric parameters.

Discussion

Our analysis provides estimation of morphometric parameters consistent with available methods, is faster, and, additionally, provides statistical characterization of the mucosa morphometry. Motiro enables the analysis of large amounts of endomicroscopy videos for building a normal rectum features dataset to help on: detection of small variability; classification of post-neoadjuvant recovery; decision about surgical intervention necessity.
Frequent testing regimen based on salivary samples for an effective COVID-19 containment strategy
Authors: Plebani Mario , Aita Ada , Cattelan Anna Maria , Bonfante Francesco , Padoan Andrea , Giaquinto Carlo , Basso Daniela
Published: October 2020

Rapid and accurate diagnostic tests are essential for controlling the ongoing COVID-19 pandemic. Although the current gold standard involves testing of nasopharyngeal swabs specimens by nucleic acid amplification test, such as real-time reverse-transcription polymerase chain reaction (rRT-PCR) to detect the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it presents several limitations that ultimately may translate into a bottleneck in the surveillance regimen. New strategies based on frequent testing using less invasive specimens are urgently needed for containment of the infection. Rapid antigen assay using saliva as a reliable alternative to nasopharyngeal swabs should be proposed as a valuable part of the overall testing strategy.
School closures and SARS-CoV-2. Evidence from Sweden’s partial school closure
Authors: Vlachos Jonas , Hertegård Edvin , Svaleryd Helena
Published: October 2020

To reduce the transmission of SARS-CoV-2 most countries closed schools, despite uncertainty if school closures are an effective containment measure. At the onset of the pandemic, Swedish upper secondary schools moved to online instruction while lower secondary school remained open. This allows for a comparison of parents and teachers differently exposed to open and closed schools, but otherwise facing similar conditions. Leveraging rich Swedish register data, we connect all students and teachers in Sweden to their families and study the impact of moving to online instruction on the incidence of SARS-CoV-2 and COVID-19. We find that among parents, exposure to open rather than closed schools resulted in a small increase in PCR-confirmed infections [OR 1.17; CI95 1.03–1.32]. Among lower secondary teachers the infection rate doubled relative to upper secondary teachers [OR 2.01; CI95 1.52–2.67]. This spilled over to the partners of lower secondary teachers who had a higher infection rate than their upper secondary counterparts [OR 1.29; CI95 1.00–1.67]. When analyzing COVID-19 diagnoses from healthcare visits and the incidence of severe health outcomes, results are similar for teachers but weaker for parents and teachers’ partners. The results for parents indicate that keeping lower secondary schools open had minor consequences for the overall transmission of SARS-CoV-2 in society. The results for teachers suggest that measures to protect teachers could be considered.
Innate lymphoid cell composition associates with COVID-19 disease severity
Authors: García Marina , Kokkinou Efthymia , García Anna Carrasco , Parrot Tiphaine , Palma Medina Laura M. , Maleki Kimia T. , Christ Wanda , Varnaitė Renata , Filipovic Iva , Ljunggren Hans-Gustaf , Björkström Niklas K. , Folkesson Elin , Rooyackers Olav , Eriksson Lars I. , Sönnerborg Anders , Aleman Soo , Strålin Kristoffer , Gredmark-Russ Sara , Klingström Jonas , Mjösberg Jenny ,   the Karolinska KI/K COVID-19 Study Group
Published: October 2020

Objectives

The role of innate lymphoid cells (ILCs) in coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is unknown. Understanding the immune response in COVID-19 could contribute to unravel the pathogenesis and identification of treatment targets. To describe the phenotypic landscape of circulating ILCs in COVID-19 patients and to identify ILC phenotypes correlated to serum biomarkers, clinical markers, and laboratory parameters relevant in COVID-19.

Methods

Blood samples collected from moderately (n=11) and severely ill (n=12) COVID-19 patients as well as healthy control donors (n=16), were analyzed with 18-parameter flow cytometry. Using supervised and unsupervised approaches, we examined the ILC activation status and homing profile. Clinical and laboratory parameters were obtained from all COVID-19 patients and serum biomarkers were analyzed with multiplex immunoassays.

Results

ILCs were largely depleted from the circulation of COVID-19 patients compared with healthy controls. Remaining circulating ILCs from patients revealed increased frequencies of ILC2 in moderate COVID-19, with a concomitant decrease of ILC precursors (ILCp), as compared with controls. ILC2 and ILCp showed an activated phenotype with increased CD69 expression, whereas expression levels of the chemokine receptors CXCR3 and CCR4 were significantly altered in ILC2 and ILCp, and ILC1, respectively. The activated ILC profile of COVID-19 patients was associated with soluble inflammatory markers, while frequencies of ILC subsets were correlated with laboratory parameters that reflect the disease severity.

Conclusion

This study provides insights into the potential role of ILCs in immune responses against SARS-CoV-2, particularly linked to the severity of COVID-19.
Dynamic dysregulation of IL-6 and genes functional in NETosis, complement and coagulation in severe COVID-19 illness
Authors: Mukhopadhyay Samanwoy , Sinha Subrata , Mohapatra Saroj Kant
Published: October 2020

Comprehensive and unbiased re-analysis of published blood transcriptome data from patients of COVID-19 reveals significant up-regulation of the gene set functional in NETosis, but no evidence of general “cytokine storm”. In severe COVID-19 illness, there is significant up-regulation of complement and coagulation pathway, and negative correlation between NETosis and respiratory function (oxygen saturation). Interestingly, there is an early spike in the level of IL-6 gene expression in severe illness compared to moderate illness. With passing days post-onset, the level of IL-6 expression in severe illness approaches that in moderate illness. The data are consistent with IL-6 acting as a driver of NETosis in the early phase of severe COVID-19 illness, that results in a vicious cycle of NETosis-complement/coagulation-respiratory dysfunction. This has important consequence for timing of rational therapy with anti-IL-6 and NETosis inhibitors in severe COVID-19 illness.
Antivenom accessibility impacts mortality and severity of Brazilian snake envenomation: a geospatial information systems analysis
Authors: Ye Jinny Jing , Scheidt João Felipe Hermann Costa , de Andrade Luciano , Rocha Thiago Augusto Hernandes , Fan Hui Wen , Monteiro Wuelton , Palacios Ricardo , Staton Catherine Ann , Nickenig Vissoci João Ricardo , Gerardo Charles John
Published: October 2020

Background

In 2017, the World Health Organization declared the snakebite envenomation as a neglected tropical disease. Annually, snakebite envenomation causes approximately 400,000 permanent disabilities and 95,000 deaths worldwide. People with the greatest risk of envenomation lack access to adequate health care, including treatment with antivenom. We developed an analysis of accessibility to antivenom in Brazil in order to verify the impacts on mortality.

Methods and Findings

Information about number of accidents, deaths, antivenom, medical assistance, and species, were retrieved from the Brazilian Health Informatics Department (DATASUS) from 2010 to 2015 and analyzed using geostatistics to evaluate the association between snakebite accidents and mortality. An Spatial analysis using Global Moran’s I was performed in order to verify the presence of spatiality as an independent variable to the distribution of the accidents. In addition, we also tested three different analysis of regression using Ordinary Least Square (OLS), Spatial Error, and Geographically Weighed Regression (GWR), together with the information obtained from the DATASUS and sociodemographic indicators, to verify the spatial-temporal distribution of envenomation cases and time to reach the healthcare centers. The regression presenting the lowest Akaike Criterion Information (AIC), highest adjusted R2, and variables with p < 0.05 was selected to represent our model. Lastly, the accessibility index was performed using 2-step floating catchment area based on the amount of hospital beds and inhabitants. This study revealed 141,039 cases of snakebites, 598 deaths, and mortality rate of 3.13 per 1,000,000 inhabitants. Moreover, GWR presented the best fit (AIC = 55477.56; adjusted R2 = 0.55) and showed that illiteracy, income, percentage of urban population, percentage of antivenom, accessibility index for hospital beds with antivenom, proportion of cases with more than 3 hours to reach healthcare are correlated with the mortality rate by snakebite (p < 0.05).

Conclusion

This study identified regions affected by snakebite and how the accessibility to antivenom treatment plays an important role in the mortality in Brazil. Public interventions can located to those most vulnerable regions in order to improve the accident outcome.
Precautionary breaks: planned, limited duration circuit breaks to control the prevalence of COVID-19
Authors: Keeling Matt J. , Guyver-Fletcher Glen , Holmes Alex , Dyson Louise , Tildesley Michael J. , Hill Edward M. , Medley Graham F.
Published: October 2020

The COVID-19 pandemic in the UK has been characterised by periods of exponential growth and decline, as different non-pharmaceutical interventions (NPIs) are brought into play. During the early uncontrolled phase of the outbreak (early March 2020) there was a period of prolonged exponential growth with epidemiological observations such as hospitalisation doubling every 3-4 days (growth rate r ≈ 0.2). The enforcement of strict lockdown measures led to a noticeable decline in all epidemic quantities (r ≈ −0.06) that slowed during the summer as control measures were relaxed (r ≈ −0.02). Since August, infections, hospitalisations and deaths have been rising (precise estimation of the current growth rate is difficult due to extreme regional heterogeneity and temporal lags between the different epidemiological observations) and various NPIs have been applied locally throughout the UK in response.

Controlling any rise in infection is a compromise between public health and societal costs, with more stringent NPIs reducing cases but damaging the economy and restricting freedoms. Currently, NPI imposition is made in response to the epidemiological state, are of indefinite length and are often imposed at short notice, greatly increasing the negative impact. An alternative approach is to consider planned, limited duration periods of strict NPIs aiming to purposefully reduce prevalence before such emergency NPIs are required. These “precautionary breaks” may offer a means of keeping control of the epidemic, while their fixed duration and the forewarning may limit their society impact. Here, using simple analysis and age-structured models matched to the unfolding UK epidemic, we investigate the action of precautionary breaks. In particular we consider their impact on the prevalence of infection, as well as the total number of predicted hospitalisations and deaths. We find that precautionary breaks provide the biggest gains when the growth rate is low, but offer a much needed brake on increasing infection when the growth rate is higher, potentially allowing other measures (such as contact tracing) to regain control.
Measurement of small droplet aerosol concentrations in public spaces using handheld particle counters
Authors: Somsen G. Aernout , van Rijn Cees , Kooij Stefan , Bem Reinout A. , Bonn Daniel
Published: October 2020

We investigate the role of aerosols in the transmission of SARS-CoV-2 in public spaces. Direct measurement of aerosol concentrations however has proven technically difficult; we propose the use of handheld particle counters as a novel and easily applicable method to measure aerosol concentrations. This allow us to perform measurements in typical public spaces, each differing in volume, number of people and ventilation rate. These data are used to estimate the relation between aerosol persistence time and the risk of infection with SARS-CoV-2.
Real World SOF/VEL/VOX Retreatment Outcomes and Viral Resistance Analysis for HCV Patients with Prior Failure to DAAs
Authors: Smith David A , Bradshaw Daniel , Mbisa Jean , Manso Carmen F , Bibby David , Singer Josh , Thomson Emma , Filipe Ana , Aranday-Cortes Elihu , Ansari M. Azim , Brown Anthony , Hudson Emma , Benselin Jennifer , Healy Brendan , Troke Phil ,   STOP-HCV Consortium,   HCV Research UK, McLauchlan John , Barnes Eleanor , Irving William L
Published: October 2020

Sustained viral response (SVR) rates to first-line Direct Acting Antiviral (DAA) therapy for hepatitis C virus (HCV) infection routinely exceed 95%. However, a small number of patients require retreatment. Sofosbuvir, velpatasvir and voxilaprevir (SOF/VEL/VOX) is a potent DAA combination primarily used for the retreatment of patients failed by first line DAA therapies. Here we evaluate retreatment outcomes and the effects of resistance associated substitutions (RAS) in a real-world cohort, including the largest number of genotype (GT)3 infected patients, to date. 144 patients from the UK were retreated with SOF/VEL/VOX following virologic failure with first-line DAA treatment regimens. Full-length HCV genome, next-generation sequencing was performed prior to retreatment with SOF/VEL/VOX. HCV subtypes were assigned and RAS relevant to each genotype were identified (15% read cut-off). GT1a and GT3a were the two most common subtypes in the cohort, each making up 38% (GT1a n=55, GT3a n=54) of the cohort. 40% (n=58) of patients had liver cirrhosis of whom 7% (n=4) were decompensated, 10% (n=14) had hepatocellular carcinoma (HCC) and 8% (n=12) had received a liver transplant prior to retreatment. The overall re-treatment SVR12 rate was 90% (129/144). On univariate analysis, GT3 infection (50/62; SVR=81%, p=0.009), cirrhosis (47/58; SVR=81%, p=0.01) and prior treatment with SOF/VEL(12/17; SVR=71%, p=0.02) or SOF + DCV (14/19; SVR=74%, p=0.012) were all significantly associated with retreatment failure, but existence of pre retreatment RAS was not when the genotype of the virus is taken into account. The lower SVR rates achieved in patients retreated with SOF/VEL/VOX for patients with GT3 infection, cirrhosis and prior treatment with SOF/VEL or SOF/DCV has important implications for both patients and HCV elimination strategies.
Does autism protect against COVID quarantine effects?
Authors: Guidotti Marco , Gateau Adrien , Malvy Joelle , Bonnet-Brilhault Frédérique
Published: October 2020

Introduction

COVID-19 outbreak has imposed an eight-week confinement in France. During this period, children and their families were exposed to a full-time home life. The aim of this study was to assess the emotional experience and tolerance of children with autism spectrum disorder (ASD) in this particular context.

Method

A clinical survey was proposed to parents and rated by professionals once a week during the quarantine period in France. 95 autistic children followed by the child and adolescent psychiatry department of Tours university hospital were assessed from the 18th of March to the 8th of May. The following clinical points were investigated: child anxiety, family anxiety, behavior problems, impact on sleep, impact on appetite, impact on school work, family tension, confinement intolerance, difficulties to follow a schedule, isolation behavior.

Results

Despite minor changes in family anxiety and school work, no difference was highlighted between clinical scores collected at the beginning and at the end of this period. ASD children with or without intellectual disability had non-significant clinical changes during quarantine. This evolution was also independent of the accommodation type (house or apartment) and the parental status (relationship, separated or isolated).

Conclusion

The sameness dimension in autism and parents’ adaptation may be involved in this clinical stability during COVID confinement. Moreover, specialized tools and support provided by professionals could have participated to these outcomes and must be regularly promoted in order to help families in this still difficult period.
Epidemiologial Analysis of Patients Presenting to a West London District General Hospital Requiring Admission with Covid-19
Authors: Heald E , Ring N , Vatvani D , Shackleton D
Published: October 2020

Background

Coronavirus has lead to significant morbidity and mortality both within the UK and worldwide. We hypothesise there are local clusters of coronavirus which would therefore be amenable to targeted public health measures.

Methods

This is a retrospective, observational case series conducted in a West London District General Hospital. All patients admitted to hospital with a radiological or microbiological diagnosis of Covid-19 were included (children under 16 years were excluded). Consecutive sampling was used and baseline characteristics including age, sex, postcode and final patient outcome were collected from the electronic health records. Patient origin postcode was plotted to a map of the local area and an online cloud based mapping analysis system was used to generate heat maps and case density maps which were compared to living base layers. The primary outcome was identification of local clusters of cases of coronavirus. Secondary outcome was identification of population characteristics that may provide evidence for more targetted public health intervention in a second wave.

Results

Local clusters of infection were identified within the target population. These appeared to correlate with higher indices of deprivation, poorer overall health and high household occupancy suggesting a role for public health measures to target these areas.

Conclusion

There is a role for targeted public health measures in tackling the spread of coronavirus, paying particular attention to those who live in more deprived areas.
A comparative study of infection and mortality in COVID-19 across countries: A scaling analysis
Authors: Das Ranjan , Hossain Akmal , Mandal Sayak , Pariari Debasmita , Rohj Rohit Kumar , Shukla Swapnil , Varma Rahul Mahavir , Sarma D. D.
Published: October 2020

Analysing infection and mortality data for COVID-19 as a function of days for 54 countries across all continents, we show that there is a simple scaling behaviour connecting these two quantities for any given nation when the data is segmented over few ranges of dates covering the most rapid spread of the pandemic and the recovery, wherever achieved. This scaling is described by two parameters, one representing a shift along the time axis and the other is a normalisation factor, providing a reliable definition of the mortality rate for each country in a given period. The number of segments for any country required in our analyses turns out to be surprisingly few with as many as 16 out of 54 countries being described by a single segment and no country requiring more than three segments. Estimates of the shift and mortality for these 54 countries in different periods show large spreads ranging over 0-16 days and 0.45-19.96%, respectively. Shift and mortality are found to be inversely correlated. Analyses of number of tests carried out for detecting COVID-19 and the number of infections detected due to such tests suggest that an effective way to increase the shift, and therefore, decrease mortality, is to increase number of tests per infection detected. This points to the need of a dynamic management of testing that should accelerate with the rise of the pandemic; it also suggests a basis for adjusting variations in the testing patterns in different geographical locations within a given country.
Quantifying year-round nocturnal bird migration with a fluid dynamics model
Authors: Nussbaumer Raphaël , Bauer Silke , Benoit Lionel , Mariethoz Grégoire , Liechti Felix , Schmid Baptiste
Published: October 2020

The movements of migratory birds constitute huge biomass flows that influence ecosystems and human economy, agriculture and health through the transport of energy, nutrients, seeds, and parasites. To better understand the influence on ecosystems and the corresponding services and disservices, we need to characterize and quantify the migratory movements at various spatial and temporal scales.

Representing the flow of birds in the air as a fluid, we applied a flow model to interpolated maps of bird density and velocity retrieved from the European weather radar network, covering almost a full year. Using this model, we quantified how many birds take-off, fly, and land across Western Europe, (1) to track waves of bird migration between nights, (2) cumulate the number of bird on the ground and (3) quantify the seasonal flow into and out of the study area through several regional transects.

Our results show that up to 188 million (M) birds take-off over a single night. Exemplarily, we tracked a migration wave in spring, in which birds crossed the study area in 4 days with nocturnal flights of approximately 300 km. Over the course of a season, we estimated that 494 million (M) birds entered through the southern transects and, at the same time, 251 M left in the northern transects, creating a surplus of 243 M birds within the study area. Similarly, in autumn, 544 M more birds departed than arrived: 314 M birds entered through the northern transects while 858 M left through the southern transects.

Our study show-cases the potential of combining interdisciplinary data and methods to elucidate the dynamics of avian migration from nightly to seasonal and yearly time-scales and from regional to continental spatial scales.
Multi-modal Single-molecule Imaging with Continuously Controlled Spectral-resolution (CoCoS) Microscopy
Authors: Jeffet Jonathan , Michaeli Yael , Torchinsky Dmitry , Israel-Elgali Ifat , Shomron Noam , Craggs Timothy D. , Ebenstein Yuval
Published: October 2020

Color is a fundamental contrast mechanism in fluorescence microscopy, providing the basis for numerous imaging and spectroscopy techniques. The ever-growing need to acquire high-throughput, dynamic data from multicolor species is driving the development of optical schemes that optimize the achievable spectral, temporal, and spatial resolution needed in order to follow biological, chemical and physical processes. Here we introduce Continuously Controlled Spectral-resolution (CoCoS) microscopy, an imaging scheme that encodes color into spatial read-out in the image plane, with continuous control over the spectral resolution. The concept enables single-frame acquisition of multiple color channels, allowing simultaneous, single-molecule colocalization for barcoding and Förster resonance energy transfer (FRET) experiments. The simple control over the spectral dispersion allows switching between imaging modalities at a click of a button. We demonstrate the utility of CoCoS for multicolor localization microscopy of microRNA barcodes in clinical samples, single-molecule FRET measurements, and single-molecule spectroscopy. CoCoS may be integrated as a simple add-on to existing microscopes and will find use in applications that aim to record dynamic, multicolor localization events such as in multiplex FRET and tracking of multi-component, interacting complexes.
Massive genome decay and insertion sequence expansion drive the evolution of a novel host-restricted bacterial pathogen
Authors: Yebra Gonzalo , Haag Andreas F , Neamah Maan M , Wee Bryan A , Richardson Emily J , Horcajo Pilar , Granneman Sander , Tormo-Más María Ángeles , de la Fuente Ricardo , Fitzgerald J Ross , Penadés José R
Published: October 2020

Background

The emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as those associated with a switch in host or disease tropism are often accompanied by genetic adaptation.Staphylococcus aureusis a multi-host bacterial species comprising strains with distinct tropisms for human and livestock species. A microaerophilic subspecies,Staphylococcus aureussubsp.anaerobius, is responsible for outbreaks of Morel’s disease, a lymphadenitis in small ruminants. However, the evolutionary history ofS. aureussubsp.anaerobiusand its relatedness toS. aureusare unknown.

Results

Evolutionary genomic analyses of clinicalS. aureussubsp.anaerobiusisolates revealed a highly conserved clone that descended from aS. aureusprogenitor about 1000 years ago before differentiating into distinct lineages representing African and European isolates.S. aureussubsp.anaerobiushas undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower thanS. aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, several large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes resulting in a highly fastidious metabolism. Importantly, expansion of ∼87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, representing a novel concept of the IS regulon.

Conclusions

Our findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of theS. aureusgenome through an array of parallel mechanisms.
Generalized paradoxical effects in excitatory/inhibitory networks
Authors: Miller Kenneth D. , Palmigiano Agostina
Published: October 2020

An inhibition-stabilized network (ISN) is a network of excitatory and inhibitory cells at a stable fixed point of firing rates for a given input, for which the excitatory subnetwork would be unstable if inhibitory rates were frozen at their fixed point values. It has been shown that in a low-dimensional model (one unit per neuronal subtype) of an ISN with a single excitatory and single inhibitory cell type, the inhibitory unit shows a “paradoxical” response, lowering (raising) its steady-state firing rate in response to addition to it of excitatory (inhibitory) input. This has been generalized to an ISN with multiple inhibitory cell types: if input is given only to inhibitory cells, the steady-state inhibition received by excitatory cells changes paradoxically, that is, it decreases (increases) if the steady-state excitatory firing rates decrease (increase).

We generalize these analyses of paradoxical effects to low-dimensional networks with multiple cell types of both excitatory and inhibitory neurons. The analysis depends on the connectivity matrix of the network linearized about a given fixed point, and its eigenvectors or “modes”. We show the following: (1) A given cell type shows a paradoxical change in steady-state rate in response to input it receives, if and only if the network with that cell type omitted has an odd number of unstable modes. Excitatory neurons can show paradoxical responses when there are two or more inhibitory subtypes. (2) More generally, if the cell types are divided into two nonoverlapping subsets A and B, then subset B has an odd (even) number of modes that show paradoxical response if and only if subset A has an odd (even) number of unstable modes. (3) The net steady-state inhibition received by any unstable mode of the excitatory subnetwork will change paradoxically,i.e.in the same direction as the change in amplitude of that mode. In particular, this means that a sufficient condition to determine that a network is an ISN is if, in response to an input only to inhibitory cells, the firing rates of and inhibition received by all excitatory cell types all change in the same direction. This in turn will be true if all E cells and all inhibitory cell types that connect to E cells change their firing rates in the same direction.
Structural basis for bivalent binding and inhibition of SARS-CoV-2 infection by human potent neutralizing antibodies
Authors: Yan Renhong , Wang Ruoke , Ju Bin , Yu Jinfang , Zhang Yuanyuan , Liu Nan , Wang Jia , Zhang Qi , Chen Peng , Zhou Bing , Li Yaning , Zhang Shuyuan , Tian Long , Zhong Xinyue , Cheng Lin , Ge Xiangyang , Zhao Juanjuan , Wang Hong-Wei , Wang Xinquan , Zhang Zheng , Zhang Linqi , Zhou Qiang
Published: October 2020

Neutralizing monoclonal antibodies (nAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent promising candidates for clinical intervention against coronavirus virus diseases 2019 (COVID-19). We isolated a large number of nAbs from SARS-CoV-2 infected individuals capable of disrupting proper interaction between the receptor binding domain (RBD) of the viral spike (S) protein and the receptor angiotensin converting enzyme 2 (ACE2). In order to understand the mechanism of these nAbs on neutralizing SARS-CoV-2 virus infections, we have performed cryo-EM analysis and here report cryo-EM structures of the ten most potent nAbs in their native full-length IgG or Fab forms bound to the trimeric S protein of SARS-CoV-2. The bivalent binding of the full-length IgG is found to associate with more RBD in the “up” conformation than the monovalent binding of Fab, perhaps contributing to the enhanced neutralizing activity of IgG and triggering more shedding of the S1 subunit from the S protein. Comparison of large number of nAbs identified common and unique structural features associated with their potent neutralizing activities. This work provides structural basis for further understanding the mechanism of nAbs, especially through revealing the bivalent binding and their correlation with more potent neutralization and the shedding of S1 subunit.
Utilization of cobalamin is ubiquitous in early-branching fungal phyla
Authors: Orłowska Małgorzata , Steczkiewicz Kamil , Muszewska Anna
Published: October 2020

Cobalamin is a cofactor present in essential metabolic pathways in animals and one of the water-soluble vitamins. It is a complex compound synthesized solely by prokaryotes. Cobalamin dependence is scattered across the tree of life. In particular, fungi and plants were deemed devoid of cobalamin. We demonstrate that cobalamin is utilized by all fungal lineages, except for Dikarya. This observation is supported by the genomic presence of both B12 dependent enzymes and cobalamin modifying enzymes. Moreover, the genes identified are actively transcribed in many taxa. Most fungal cobalamin dependent enzymes and cobalamin metabolism proteins are highly similar to their animal homologs. Phylogenetic analyses support a scenario of vertical inheritance of the cobalamin trait with several losses. Cobalamin usage was probably lost in Mucorinae and at the base of Dikarya which groups most of the model organisms which hindered B12-dependent metabolism discovery in fungi. Our results indicate that cobalamin dependence was a widely distributed trait at least in Opisthokonta, across diverse microbial eukaryotes and likely in the LECA.
fastISM: Performant in-silico saturation mutagenesis for convolutional neural networks
Authors: Nair Surag , Shrikumar Avanti , Kundaje Anshul
Published: October 2020

Deep learning models such as convolutional neural networks are able to accurately map biological sequences to associated functional readouts and properties by learning predictive de novo representations. In-silico saturation mutagenesis (ISM) is a popular feature attribution technique for inferring contributions of all characters in an input sequence to the model’s predicted output. The main drawback of ISM is its runtime, as it involves multiple forward propagations of all possible mutations of each character in the input sequence through the trained model to predict the effects on the output. We present fastISM, an algorithm that speeds up ISM by a factor of over 10x for commonly used convolutional neural network architectures. fastISM is based on the observations that the majority of computation in ISM is spent in convolutional layers, and a single mutation only disrupts a limited region of intermediate layers, rendering most computation redundant. fastISM reduces the gap between backpropagation-based feature attribution methods and ISM. It far surpasses the runtime of backpropagation-based methods on multi-output architectures, making it feasible to run ISM on a large number of sequences. An easy-to-use Keras/TensorFlow 2 implementation of fastISM is available at https://github.com/kundajelab/fastISM, and a hands-on tutorial at https://colab.research.google.com/github/kundajelab/fastISM/blob/master/notebooks/colab/DeepSEA.ipynb.
Occurrence and characterization of cyst nematode species (Globoderaspp.) associated with potato crops in Colombia
Authors: Vallejo Daniela , Rojas Diego A. , Martinez John A. , Marchant Sergio , Holguin Claudia M. , Pérez Olga Y.
Published: October 2020

Potato cyst nematodes (PCN) from the genusGloboderaspp. cause major losses in potato (Solanum tuberosum) industry worldwide. Despite their importance, at present little is known about the status of this plant pathogen in cultivated potatoes in Colombia. In this study, a total of 589 samples collected from 75 geographic localities from nine potato producing departments of Colombia were assayed for the presence of potato cyst nematodes. Fifty-seven percent of samples tested positive for PCN. All populations but one were identified asGlobodera pallida, with conspicuous morphometric variation found among populations. Based on phylogenetic analysis of the internal transcribed spacer region (ITS1-5.8S-ITS2) of the rRNA gene and D2-D3 expansion segments of the 28S rRNA gene,G. pallidafrom Colombia formed a monophyletic group closely related to Peruvian populations, with the lowest average number of nucleotide substitutions per site (Dxy= 0.002) and net nucleotide substitutions per site (Da= 0.001), when compared toG. pallidapopulations from South, North America and Europe. A single sample formed a well-supported subclade along withG. rostochiensisandG. tabacumfrom Japan, USA and Argentina. To our knowledge this is the first comprehensive survey ofGloboderapopulations from Colombia that includes morphological and genetic data. Our findings on species diversity and phylogenetic relationships ofGloboderapopulations from Colombia may help elucidate the status and distribution ofGloboderaspecies, and lead to the development of accurate management strategies for the potato cyst nematodes.
CaBagE: a Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing
Authors: Wallace Amelia , Sasani Thomas A. , Swanier Jordan , Gates Brooke L. , Greenland Jeff , Pedersen Brent S. , Varley K-T , Quinlan Aaron R.
Published: October 2020

A substantial fraction of the human genome is difficult to interrogate with short-read DNA sequencing technologies due to paralogy, complex haplotype structures, or tandem repeats. Long-read sequencing technologies, such as Oxford Nanopore’s MinION, enable direct measurement of complex loci without introducing many of the biases inherent to short-read methods, though they suffer from relatively lower throughput. This limitation has motivated recent efforts to develop amplification-free strategies to target and enrich loci of interest for subsequent sequencing with long reads. Here, we present CaBagE, a novel method for target enrichment that is efficient and useful for sequencing large, structurally complex targets. The CaBagE method leverages the stable binding of Cas9 to its DNA target to protect desired fragments from digestion with exonuclease. Enriched DNA fragments are then sequenced with Oxford Nanopore’s MinION long-read sequencing technology. Enrichment with CaBagE resulted in up to 416X coverage of target loci when tested on five genomic targets ranging from 4-20kb in length using healthy donor DNA. Four cancer gene targets were enriched in a single reaction and multiplexed on a single MinION flow cell. We further demonstrate the utility of CaBagE in two ALS patients withC9orf72short tandem repeat expansions to produce genotype estimates commensurate with genotypes derived from repeat-primed PCR for each individual. With CaBagE there is a physical enrichment of on-target DNA in a given sample prior to sequencing. This feature allows adaptability across sequencing platforms and potential use as an enrichment strategy for applications beyond sequencing. CaBagE is a rapid enrichment method that can illuminate regions of the ‘hidden genome’ underlying human disease.
Sero-prevalence of anti-SARS-CoV-2 Antibodies in Addis Ababa, Ethiopia
Authors: Alemu Berhanu Nega , Addissie Adamu , Mamo Gemechis , Deyessa Negussie , Abebe Tamrat , Abagero Abdulnasir , Ayele Wondimu , Abebe Workeabeba , Haile Tewodros , Argaw Rahel , Amogne Wondwossen , Belachew Ayele , Desalegn Zelalem , Teka Brhanu , Kantelhardt Eva , Wossen Mesfin , Abdella Saro , Tollera Getachew , Tadesse Lia
Published: October 2020

Background

Anti-SARS-CoV-2 antibody tests are being increasingly used for sero-epidemiological purposes to provide better understanding of the extent of the infection in the community, and monitoring the progression of the COVID-19 epidemic. We conducted sero-prevalence study to estimate prior infection with with SARS-CoV-2 in Addis Ababa.

Methods

A cross-sectional study was done from April 23 to 28, 2020 among 301 randomly selected residents of Addis Ababa; with no known history of contact with confirmed COVID-19 person. Interviews on socio demographic and behavioural risk factor followed by serological tests were performed for SARS-CoV-2 IgM, and IgG antibodies, using COVID-19 IgG/IgM Rapid Test Cassette. The test has sensitivity of 87·9% and specificity of 100% for lgM; and a sensitivity of 97·2% and specificity of 100% for IgG. RT-PCR test was also done on combined nasopharyngeal and oropharengeal swabs as an important public health consideration.

Findings

The unadjusted antibody-based crude SARS-CoV-2 prevalence was 7·6% and the adjusted true SARS-CoV-2 prevalence was estimated at 8·8% (95% CI 5·5%-11·6%) for the study population. Higher sero-prevalence were observed for males (9.0%), age below 50 years (8.2%), students and unemployed (15.6%), those with primary education (12.1%), smokers (7.8%), alcohol consumers (8.6%), chatt-chewers (13.6%) and shish smokers (18.8%). Seroprevalence was not significantly associated neither with socio-demographic not behavioral characteristics. According to the findings, possibly more individuals had been infected in Addis Ababa than what was being detected and reported by RT-PCR test suggestive of community transmission. The use of serological test for epidemiological estimation of the extent of SARS-CoV-2 epidemic gives a more precise estimate of magnitude which would be used for further monitoring and surveillance of the magnitude of the SARS CoV-2 infection.
Numerical evaluation reveals the effect of branching morphology on vessel transport properties during angiogenesis
Authors: Mirzapour-shafiyi Fatemeh , Kametani Yukinori , Hikita Takao , Hasegawa Yosuke , Nakayama Masanori
Published: October 2020

Blood flow governs transport of oxygen and nutrients into tissues. Hypoxic tissues secrete VEGFs to promote angiogenesis during development and in tissue homeostasis. In contrast, tumors enhance pathologic angiogenesis during growth and metastasis, suggesting suppression of tumor angiogenesis could limit tumor growth. In line with these observations, various factors have been identified to control vessel formation in the last decades. However, their impact on the vascular transport properties of oxygen remain elusive. Here, we take a computational approach to examine the effects of vascular branching on blood flow in the growing vasculature. First of all, we reconstruct the 3D vascular model from the 2D confocal images of the growing vasculature at P6 mouse retina, then simulate blood flow in the vasculature, which is applied for the gene targeting mouse models causing hypo- or hyper-branching vascular formation. Interestingly, hyper-branching morphology attenuates effective blood flow at the angiogenic front and promotes tissue hypoxia. In contrast, vascular hypo-branching enhances blood supply at the angiogenic front of the growing vasculature. Oxygen supply by newly formed blood vessels improves local hypoxia and decreases VEGF expression at the angiogenic front during angiogenesis. Consistent with the simulation results indicating improved blood flow in the hypo-branching vasculature, VEGF expression around the angiogenic front is reduced in those mouse retinas. Conversely, VEGF expression was enhanced in the hyper-branching vasculature in the mouse retina. Our results indicate the importance of detailed flow analysis in evaluating the vascular transport properties of branching morphology of the blood vessels.

Author Summary

Blood vessels are important for the transport of various substances, such as oxygen, nutrients, and cells, to the entire body. Control of blood vessel formation is thought to be important in health and disease. In the last decades, various factors which regulate blood vessel branching morphology have been identified. Gene modification of some of these identified factors results in hyper-branching of the vasculature while others cause hypo-branching of the vessel. Given the importance of the transport property of the blood vessel, it is important to examine the effect of these identified factors on the transport property of the affected vascular morphology. In line with these facts, we reconstruct 3D vessel structures from 2D confocal microscopy images. We then simulate blood flow in the structures numerically. Interestingly, our results suggest vessel network complexity negatively affects the blood perfusion efficiency and tissue oxygenation during angiogenesis. Thus, our results highlight the importance of flow analysis considering the detailed 3D branching pattern of the vascular network to quantitatively evaluate its transport properties.
Analysis of selection methods to develop novel phage therapy cocktails against antimicrobial resistant clinical isolates of bacteria
Authors: Haines Melissa EK , Hodges Francesca E , Nale Janet Y , Mahony Jennifer , van Sinderen Douwe , Kaczorowska Joanna , Alrashid Bandar , Akter Mahmuda , Brown Nathan , Sauvageau Dominic , Sicheritz-Ponten Thomas , Thanki Anisha M , Millard Andrew D , Galyov Edouard E , Clokie Martha RJ
Published: October 2020

Antimicrobial resistance (AMR) is a major problem globally. The main bacterial organisms associated with urinary tract infection (UTI) associated sepsis are E. coli and Klebsiella along with Enterobacter species. These all have AMR strains known as ESBL (Extended Spectrum Beta-Lactamase), which are featured on the WHO priority pathogens list as ‘critical’ for research. Bacteriophages (phages) as viruses that can infect and kill bacteria, could provide an effective tool to tackle these AMR strains.

There is currently no ‘gold standard’ for developing a phage cocktail. Here we describe a novel approach to develop an effective phage cocktail against a set of ESBL-producing E. coli and Klebsiella largely isolated from patients in UK hospitals. By comparing different measures of phage efficacy, we show which are the most robust, and suggest an efficient screening cascade that could be used to develop phage cocktails to target other AMR bacterial species.

A target panel of 38 ESBL-producing clinical strains isolated from urine samples was collated and used to test phage efficacy. After an initial screening of 68 phages, six were identified and tested against these 38 strains to determine their clinical coverage and killing efficiency. To achieve this, we assessed four different methods to assess phage virulence across these bacterial isolates. These were the Direct Spot Test (DST), the Efficiency of Plating (EOP) assay, the planktonic killing assay and the biofilm assay.

The final ESBL cocktail of six phages could effectively kill 23/38 strains (61%) for Klebsiella 13/19 (68%) and for E. coli 10/19 (53%) based on the planktonic killing assay data. The ESBL E. coli collection had six isolates from the prevalent UTI-associated ST131 sequence type, five of which were targeted effectively by the final cocktail. Of the four methods used to assess phage virulence, the data suggests that planktonic killing assays are as effective as the much more time-consuming EOPs and data for the two assays correlates well. This suggests that planktonic killing is a good proxy to determine which phages should be used in a cocktail. This assay when combined with the virulence index also allows ‘phage synergy’ to inform cocktail design.
Selective Attention Modulates Neural Envelope Tracking of Informationally Masked Speech in Healthy Older Adults
Authors: Kurthen Ira , Galbier Jolanda , Jagoda Laura , Neuschwander Pia , Giroud Nathalie , Meyer Martin
Published: October 2020

Speech understanding in noisy situations is compromised in old age. This study investigated the energetic and informational masking components of multi-talker babble noise and their influence on neural tracking of the speech envelope in a sample of healthy older adults. Twenty-three older adults (age range 65 - 80 years) listened to an audiobook embedded in noise while their electroencephalogram (EEG) was recorded. Energetic masking was manipulated by varying the signal-to-noise ratio (SNR) between target speech and background talkers and informational masking was manipulated by varying the number of background talkers. Neural envelope tracking was measured by calculating temporal response functions (TRFs) between speech envelope and EEG. Number of background talkers, but not SNR modulated the amplitude of an earlier (around 50 ms time lag) and a later (around 300 ms time lag) peak in the TRFs. Selective attention, but not working memory or peripheral hearing additionally modulated the amplitude of the later TRF peak. Finally, amplitude of the later TRF peak was positively related to accuracy in the comprehension task. The results suggest that stronger envelope tracking is beneficial for speech-in-noise understanding and that selective attention is an important ability supporting speech-in-noise understanding in multi-talker scenes.