bluuebunny/crossref_metadata_2025 huggingface dataset:
Trends in excess cancer and cardiovascular deaths in Scotland during the COVID-19 pandemic 30 December – 20 April suggest underestimation of COVID-19 related deaths
Authors: Figueroa Jonine D. , Brennan Paul , Theodoratou Evropi , Poon Michael , Purshouse Karin , Din Farhat , Jin Kai , Mesa-Eguiagaray Ines , Dunlop Malcolm , Hall Peter , Cameron David , Wild Sarah , Sudlow Cathie
Published: May 2020

Understanding the trends in causes of death for different diseases during the current COVID-19 pandemic is important to determine whether there are excess deaths beyond what is normally expected. Using the most recent report from National Records Scotland (NRS) on 29 April 2020, we examined the percentage difference in crude numbers of deaths in 2020 compared to the average for 2015-2019 by week of death within calendar year. To determine if trends were similar, suggesting underreporting/underdiagnosed COVID-19 related deaths, we also looked at the trends in % differences for cardiovascular disease deaths. From the first 17 weeks’ of data, we found a peak in excess deaths at week 14 of 2020, about four weeks after the first case in Scotland was detected on 1 March 2020-- but by week 17 these excesses had returned to normal levels, 4 weeks after lockdown in the UK began. Similar observations were seen for cardiovascular disease-related deaths. These observations suggest that the short-term increase in excess cancer and cardiovascular deaths might be associated with undetected/unconfirmed deaths related to COVID-19. Both of these conditions make patients more susceptible to infection and lack of widespread access to testing for COVID-19 are likely to have resulted in under-estimation of COVID-19 mortality. These data further suggest that the cumulative toll of COVID-19 on mortality is likely undercounted. More detailed analysis is needed to determine if these excesses were directly or indirectly related to COVID-19. Disease specific mortality will need constant monitoring for the foreseeable future as changes occur in increasing capacity and access to testing, reporting criteria, changes to health services and different measures are implemented to control the spread of the COVID-19. Multidisciplinary, multi-institutional, national and international collaborations for complementary and population specific data analysis is required to respond and mitigate adverse effects of the COVID-19 pandemic and to inform planning for future pandemics.
Ultra-fast and onsite interrogation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in environmental specimens via surface enhanced Raman scattering (SERS)
Authors: Zhang Dayi , Zhang Xiaoling , Ma Rui , Deng Songqiang , Wang Xinquan , Zhang Xian , Huang Xia , Liu Yi , Li Guanghe , Qu Jiuhui , Zhu Yu , Li Junyi
Published: May 2020

The outbreak of coronavirus infectious disease-2019 (COVID-19) pneumonia challenges the rapid interrogation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human and environmental specimens. In this study, we developed an assay using surface enhanced Raman scattering (SERS) coupled with multivariate analysis to diagnose SARS-CoV-2 in an ultra-fast manner without any pretreatment (e.g., RNA extraction). Using silver-nanorod SERS array functionalized with cellular receptor angiotensin-converting enzyme 2 (ACE2), we obtained strong SERS signals of ACE2 at 1032, 1051, 1089, 1189, 1447 and 1527 cm−1. The recognition and binding of receptor binding domain (RBD) of SARS-CoV-2 spike protein on SERS assay significantly quenched the spectral intensities of most peaks and exhibited a shift from 1189 to 1182 cm−1. On-site tests on 17 water samples with a portable Raman spectrometer proved its accuracy and easy-operation for spot diagnosis of SARS-CoV-2 to evaluate disinfection performance, explore viral survival in environmental media, assess viral decay in wastewater treatment plant and track SARS-CoV-2 in pipe network. Our findings raise a state-of-the-art spectroscopic tool to screen and interrogate viruses with RBD for human cell entry, proving its feasibility and potential as an ultra-fast diagnostic tool for public health.
Evaluating growth pattern and assessing future scenario of COVID-19 epidemic of India
Authors: Patil Nandan L. , Gangavati Lakshmi R.
Published: May 2020

COVID-19 the modern pandemic has spread across the world at a rapid pace. SARS-CoV 2 is highly transmissible and the rate of infection is exponential for heavily infected countries. Asymptotic carriers and longer incubation period have been key towards such a large-scale distribution of disease. Data released by official authorities on COVID-19 cases is significantly affected by various factors such as size of sample, incubation period of disease and time taken to test the sample. These factors mask the useful pattern (signal) of disease spread. Thus, an ingenious method to group data into cycles of five and seven days, for studying pattern of disease spread is undertaken. Occurrence of recurrent peaks as indicated by Adjusted Rate of infection per day indicated the spread of disease has been non-uniform. Currently, India is yet to reach the critical point (peak of epidemic) with adjusted daily cases more than 1000. Increasing testing capacity along with random sampling and sample pooling can help in preventing formation of these peaks in future. The proposed method helps in assessing the current state and for predicting future scenarios epidemics.
A new role for Biofoundries in rapid prototyping, development, and validation of automated clinical diagnostic tests for SARS-CoV-2
Authors: Crone Michael A. , Priestman Miles , Ciechonska Marta , Jensen Kirsten , Sharp David , Randell Paul , Storch Marko , Freemont Paul
Published: May 2020

The SARS-CoV-2 pandemic has shown how the rapid rise in demand for patient and community sample testing, required for tracing and containing a highly infectious disease, has quickly overwhelmed testing capability globally. With most diagnostic infrastructure dependent on specialised instruments, their exclusive reagent supplies quickly become bottlenecks in times of peak demand, creating an urgent need for novel approaches to boost testing capacity. We address this challenge by refocusing the full synthetic biology stack available at the London Biofoundry onto the development of alternative patient sample testing pipelines. We present a reagent-agnostic automated SARS-CoV-2 testing platform that can be quickly deployed and scaled, and that accepts a diverse range of reagents. Using an in-house-generated, open-source, MS2-virus-like-particle-SARS-CoV-2 standard, we validate RNA extraction and RT-qPCR workflows as well as two novel detection assays based on CRISPR-Cas and Loop-mediated isothermal Amplification (LAMP) approaches. In collaboration with an NHS diagnostic testing lab, we report the performance of the overall workflow and benchmark SARS-CoV-2 detection in patient samples via RT-qPCR, CRISPR-Cas, and LAMP against clinical test sets. The validated RNA extraction and RT-qPCR platform has been installed in NHS diagnostic labs and now contributes to increased patient sample processing in the UK while we continue to refine and develop novel high-throughput diagnostic methods. Finally, our workflows and protocols can be quickly implemented and adapted by members of the Global Biofoundry Alliance and the wider scientific and medical diagnostics community.
The epidemiologic parameters for COVID-19: A Systematic Review and Meta-Analysis
Authors: Izadi Neda , Taherpour Niloufar , Mokhayeri Yaser , Ghorbani Sahar Sotoodeh , Rahmani Khaled , Nazari Seyed Saeed Hashemi
Published: May 2020

Introduction

The World Health Organization (WHO) declared the outbreak to be a public health emergency and international concern and recognized it as a pandemic. The aim of this study was to estimate the epidemiologic parameters of novel coronavirus (COVID-19) pandemic for clinical and epidemiological help.

Methods

Four electronic databases including Web of Science, Medline (PubMed), Scopus and Google Scholar were searched for literature published from early December 2019 up to 23 March 2020. The “metan” command was used to perform a fixed or random effects analysis. Cumulative meta-analysis was performed using the “metacum” command.

Results

Totally 76 observational studies were included in the analysis. The pooled estimate for R0was 2.99 (95% CI: 2.71-3.27) for COVID-19. The overall R0was 3.23, 1.19, 3.6 and 2.35 for China, Singapore, Iran and Japan, respectively. The overall Serial Interval, doubling time, incubation period were 4.45, 4.14 and 4.24 days for COVID-19. In addition, the overall estimation for growth rate and case fatality rate for COVID-19 were 0.38% and 3.29%, respectively.

Conclusion

Calculating the pooled estimate of the epidemiological parameters of COVID-19 as an emerging disease, could reveal epidemiological features of the disease that consequently pave the way for health policy makers to think more about control strategies.
Optimal Control Strategy Applied to Dynamic Model of Drug Abuse Incident for Reducing Its Adverse Effects
Authors: Islam Md. Azmir Ibne , Biswas Md. Haider Ali
Published: May 2020

The present world is facing a devastating reality as drug abuse prevails in every comer of a society. The progress of a country is obstructed due to the excessive practice of taking drugs by the young generation. Like other countries, Bangladesh is also facing this dreadful situation. The multiple use of drug substances leads an individual to a sorrowful destination and for this reason, the natural behavior of human mind is disrupted. An addicted individual may regain his normal life by proper monitoring and treatment. The objective of this study is to analyze a mathematical model on the dynamics of drug abuse in the perspective of Bangladesh and reduce the harmful consequences with effective control policies using the idea of optimal control theory. The model has been solved analytically introducing a specific optimal goal. Numerical simulations have also been performed to review the behaviors of analytical findings. The analytical results have been verified with the numerical simulations. The analysis of this paper shows that it is possible to control drug addiction if there is less interaction among general people with the addicted individuals. Family based care, proper medical treatment, awareness and educational programs can be the most effective ways to reduce the adverse effects of drug addiction in a shortest possible time.
Predictive mathematical models for the number of individuals infected with COVID-19
Authors: Fokas A.S. , Dikaios N. , Kastis G.A.
Published: May 2020

We model the time-evolution of the number N(t) of individuals reported to be infected in a given country with a specific virus, in terms of a Riccati equation. Although this equation is nonlinear and it contains time-dependent coefficients, it can be solved in closed form, yielding an expression for N(t) that depends on a function α(t). For the particular case that α(t) is constant, this expression reduces to the well-known logistic formula, giving rise to a sigmoidal curve suitable for modelling usual epidemics. However, for the case of the COVID-19 pandemic, the long series of available data shows that the use of this simple formula for predictions underestimates N(t); thus, the logistic formula only provides a lower bound of N(t). After experimenting with more than 50 different forms of α(t), we introduce two novel models that will be referred to as “rational” and “birational”. The parameters specifying these models (as well as those of the logistic model), are determined from the available data using an error-minimizing algorithm. The analysis of the applicability of the above models to the cases of China and South Korea suggest that they yield more accurate predictions, and importantly that they may provide an upper bound of the actual N(t). Results are presented for Italy, Spain, and France.
A mathematical model to investigate the transmission of COVID-19 in the Kingdom of Saudi Arabia
Authors: Alshammari Fehaid Salem
Published: May 2020

Since the first confirmed case of SARS-CoV-2 coronavirus (COVID-19) in the 2ndday of March, Saudi Arabia has not report a quite rapid COVD-19 spread compared to America and many European countries. Possible causes include the spread of asymptomatic cases. To characterize the transmission of COVID-19 in Saudi Arabia, this paper applies a susceptible, exposed, symptomatic, asymptomatic, hospitalized, and recovered dynamical model, along with the official COVID-19 reported data by the Ministry of Health in Saudi Arabia. The basic reproduction numberR0is estimated to range from 2.87 to 4.9.
Potential biases arising from epidemic dynamics in observational seroprotection studies
Authors: Kahn Rebecca , Kennedy-Shaffer Lee , Grad Yonatan H. , Robins James M. , Lipsitch Marc
Published: May 2020

The extent and duration of immunity following SARS-CoV-2 infection are critical outstanding questions about the epidemiology of this novel virus, and studies are needed to evaluate the effects of serostatus on reinfection. Understanding the potential sources of bias and methods to alleviate biases in these studies is important for informing their design and analysis. Confounding by individual-level risk factors in observational studies like these is relatively well appreciated. Here, we show how geographic structure and the underlying, natural dynamics of epidemics can also induce noncausal associations. We take the approach of simulating serologic studies in the context of an uncontrolled or a controlled epidemic, under different assumptions about whether prior infection does or does not protect an individual against subsequent infection, and using various designs and analytic approaches to analyze the simulated data. We find that in studies assessing the efficacy of serostatus on future infection, comparing seropositive individuals to seronegative individuals with similar time-dependent patterns of exposure to infection, by stratifying or matching on geographic location and time of enrollment, is essential to prevent bias.
Pharmacological interventions for COVID-19: Protocol for a Rapid Living Systematic Review with network meta-analysis
Authors: Pinto Ana Carolina Pereira Nunes , da Rocha Aline Pereira , Milby Keilla Martins , Rocha-Filho César Ramos , de Assis Reis Felipe Sebastião , Junior Nelson Carvas , Civile Vinicius Tassoni , Santos Rodolfo Rodrigo Pereira , Trevisani Giulia Fernandes Moça , Ferla Laura Jantsch , Ramalho Gabriel Sodré , Puga Maria Eduarda Santos , Trevisani Virgínia Fernandes Moça , Atallah Alvaro Nagib
Published: May 2020

CONTEXT AND OBJECTIVE

Coronavirus disease 2019 (COVID-19) has emerged in China in December 2019 and rapidly spread. Although extraordinary efforts have been made on research regarding pharmacological interventions, none have proven effective. This is the protocol for a rapid living systematic review that aims to compare the effectiveness and safety of different pharmacological interventions for the treatment of COVID-19.

METHODS

rapid living systematic review methodology with Network Meta-Analysis following the recommendations of Cochrane Handbook. We will include randomized controlled trials (RCT) and quasi-RCTs that evaluate single and/or combined pharmacological interventions at any dose for the treatment of COVID-19. We will search PubMed, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), LILACS, Scopus and SciELO to identify potentially eligible studies. No language restrictions will be used in the selection. We will perform the critical appraisal of included studies with the Risk of Bias tool and the certainty of evidence will be evaluated using the Grading of Recommendations Assessment, Development and Evaluation (GRADE).
Predictive Model with Analysis of the Initial Spread of COVID-19 in India
Authors: Ghosh Shinjini
Published: May 2020

The Coronavirus Disease 2019 (COVID-19) has currently ravaged through the world, resulting in over three million confirmed cases and over two hundred thousand deaths, a complete change in daily life as we know it, worldwide lock-downs, travel restrictions, as well as heightened hygiene measures and physical distancing. Being able to analyse and predict the spread of this epidemic-causing disease is hence of utmost importance now, especially as it would help in the reasoning behind important decisions drastically affecting countries and their people, as well as in ensuring efficient resource and utility management. However, the needs of the people and specific conditions of the spread are varying widely from country to country. In this article, we have conducted an in-depth analysis of the spread of COVID-19 in India, patient statistics, as well as proposed a mathematical prediction system that has succeeded in predicting the following day’s number of cases with 83% accuracy, ever since the first COVID-19 case was declared in India.
Low baseline pulmonary levels of cytotoxic lymphocytes as a predisposing risk factor for severe COVID-19
Authors: Duijf Pascal H.G.
Published: May 2020

COVID-19 is caused by the coronavirus SARS-CoV-2 and currently has detrimental human health, community and economic impacts around the world. It is unclear why some SARS-CoV-2-positive individuals remain asymptomatic, while others develop severe symptoms. Baseline pulmonary levels of anti-viral leukocytes, already residing in the lung prior to infection, may orchestrate an effective early immune response and prevent severe symptoms. Using “in silicoflow cytometry”, we deconvoluted the levels of all seven types of anti-viral leukocytes in 1,927 human lung tissues. Baseline levels of CD8+ T cells, resting NK cells and activated NK cells, as well as cytokines that recruit these, are significantly lower in lung tissues with high expression of the SARS-CoV-2 entry receptor ACE2. We observe this in univariate analyses, in multivariate analyses, and in two independent datasets. Relevantly, ACE2 mRNA and protein levels very strongly correlate in human cells and tissues. Above findings also largely apply to the SARS-CoV-2 entry protease TMPRSS2. Both SARS-CoV-2-infected lung cells and COVID-19 lung tissues show upregulation of CD8+ T cell- and NK cell-recruiting cytokines. Moreover, tissue-resident CD8+ T cells and inflammatory NK cells are significantly more abundant in bronchoalveolar lavages from mildly affected COVID-19 patients, compared to severe cases. This suggests that these lymphocytes are important for preventing severe symptoms. Elevated ACE2 expression increases sensitivity to coronavirus infection. Thus, our results suggest that some individuals may be exceedingly susceptible to develop severe COVID-19 due to concomitant high pre-existing ACE2 and TMPRSS expression and low baseline cytotoxic lymphocyte levels in the lung.
Platelet miRNA bio-signature discriminates between dementia with Lewy bodies and Alzheimer disease
Authors: Gámez-Valero Ana , Campdelacreu Jaume , Vilas Dolores , Ispierto Lourdes , Samaniego Daniela , Gascón-Bayarri Jordi , Reñé Ramón , Álvarez Ramiro , Armengol Maria P , Borràs Francesc E. , Beyer Katrin
Published: May 2020

Dementia with Lewy bodies (DLB) is one of the most common causes of degenerative dementia after Alzheimer’s disease (AD) and presents pathological and clinical overlap with both AD and Parkinson’s disease (PD). Consequently, only one in three DLB cases is diagnosed correctly. Platelets, previously related to neurodegeneration, contain microRNAs (miRNAs) whose analysis may provide disease biomarkers. Here, we profiled the whole platelet miRNA transcriptome from DLB patients and healthy controls. Differentially expressed miRNAs were further validated in three consecutive studies from 2017 to 2019 enrolling 162 individuals, including DLB, AD, and PD patients, and healthy controls. Results comprised a 7-miRNA biosignature, showing the highest diagnostic potential for the differentiation between DLB and AD. Additionally, compared to controls, two miRNAs were down-regulated in DLB, four miRNAs were up-regulated in AD, and two miRNAs were down-regulated in PD. Predictive target analysis identified three disease-specific clusters of pathways as a result of platelet-miRNA deregulation. Our cross-sectional study assesses the identification of a novel, highly specific and sensitive platelet-associated miRNA-based bio-signature, which distinguishes DLB from AD.

The paper explained

Problem

Dementia with Lewy bodies (DLB) presents pathological and clinical overlap with both Alzheimer’s (AD) and Parkinson’s disease (PD), which impairs its correct diagnosis. Although numerous papers report peripheral biomarkers for AD, well-established biomarkers for DLB distinguishing it from AD are still missing. Platelet miRNA transcriptome was analyzed in several works, but their putative role as disease biomarkers for neurological disorders has not been assessed. It would be of paramount importance to establish a blood-based bio-signature as a minimally invasive mean for DLB diagnosis, improving differentiation of DLB patients from controls and AD.

Results

Our study revealed that platelet miRNAs might be promising biomarkers for the correct diagnosis of DLB stratifying patients in comparison with overlapping disorders, especially AD, and may help to highlight possible disease-related processes. In this cross-sectional study, which includes 162 individuals (DLB, AD, PD and healthy controls), platelet-associated miRNA content was disease group-specific. Three different miRNA sets together with their predicted targeted pathways were defined.

Impact

This study suggests that platelet miRNA may serve as DLB biomarker allowing the correct diagnosis and stratification in an easily-applied manner in clinical settings, and may help to highlight possible disease-related processes.
Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression ofTMPRSS2andMX1Genes
Authors: Bhattacharyya Chandrika , Das Chitrarpita , Ghosh Arnab , Singh Animesh K. , Mukherjee Souvik , Majumder Partha P. , Basu Analabha , Biswas Nidhan K.
Published: May 2020

COVID-19 pandemic is a major human tragedy. Worldwide, SARS-CoV-2 has already infected over 3 million and has killed about 230,000 people. SARS-CoV-2 originated in China and, within three months, has evolved to an additional 10 subtypes. One particular subtype with a non-silent (Aspartate to Glycine) mutation at 614thposition of the Spike protein (D614G) rapidly outcompeted other pre-existing subtypes, including the ancestral. We assessed that D614G mutation generates an additional serine protease (Elastase) cleavage site near the S1-S2 junction of the Spike protein. We also identified that a single nucleotide deletion (delC) at a known variant site (rs35074065) in a cis-eQTL ofTMPRSS2, is extremely rare in East Asians but is common in Europeans and North Americans. The delC allele facilitates entry of the 614G subtype into host cells, thus accelerating the spread of 614G subtype in Europe and North America where the delC allele is common. The delC allele at the cis-eQTL locus rs35074065 ofTMPRSS2leads to overexpression of bothTMPRSS2and a nearby geneMX1. The cis-eQTL site, rs35074065 overlaps with a transcription factor binding site of an activator (IRF1) and a repressor (IRF2). IRF1 activator can bind to variant delC allele, but IRF2 repressor fails to bind. Thus, in an individual carrying the delC allele, there is only activation, but no repression. On viral entry,IRF1mediated upregulation ofMX1leads to neutrophil infiltration and processing of 614G mutated Spike protein by neutrophil Elastase. The simultaneous processing of 614G spike protein by TMPRSS2 and Elastase serine proteases facilitates the entry of the 614G subtype into host cells. Thus, SARS-CoV-2, particularly the 614G subtype, has spread more easily and with higher frequency to Europe and North America where the delC allele regulating expression ofTMPRSS2andMX1host proteins is common, but not to East Asia where this allele is rare.
Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription
Authors: Pellanda Paola , Dalsass Mattia , Filipuzzi Marco , Loffreda Alessia , Verrecchia Alessandro , Cano Virginia Castillo , Doni Mirko , Morelli Marco J. , Beaulieu Marie-Eve , Soucek Laura , Mazza Davide , Mapelli Marina , Kress Theresia , Amati Bruno , Sabò Arianna
Published: May 2020

Eukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity: how these binding modes are integrated to determine select transcriptional outputs remains unresolved. We designed mutants of the MYC transcription factor bearing substitutions in residues that contact either the DNA backbone or specific bases within the consensus binding motif (E-box), and profiled their DNA-binding and gene-regulatory activities in murine cells. Our data reveal that non-specific DNA binding is required for MYC to engage onto active regulatory elements in the genome, preceding sequence recognition; beyond merely stabilizing MYC onto select target loci, sequence-specific binding contributes to its precise positioning and – most unexpectedly – to transcriptional activationper se. In particular, at any given binding intensity, promoters targeted via the cognate DNA motif were more frequently activated by MYC. Hence, seemingly promiscuous chromatin interaction profiles actually encompass diverse DNA-binding modalities, driving defined, sequence-dependent transcriptional responses.
Global genetic patterns reveal host tropism versus cross-taxon transmission of bat Betacoronaviruses
Authors: Bacus Michael G. , Dayap Stephen Adrian H. , Tampon Nikki Vanesa T. , Udarbe Marielle M. , Puentespina Roberto P. , Villanueva Sharon Yvette Angelina M. , de Cadiz Aleyla E. , Achondo Marion John Michael M. , Murao Lyre Anni E.
Published: May 2020

Emerging infectious diseases due to coronavirus (CoV) infections have received significant global attention in the past decade and have been linked to bats as the original source. The diversity, distribution, and host associations of bat CoVs were investigated to assess their potential for zoonotic transmission. Phylogenetic, network, and principal coordinate analysis confirmed the classification of betacoronaviruses (BetaCoVs) into five groups (2A to 2E) and a potentially novel group, with further division of 2D into five subgroups. The genetic co-clustering of BetaCoVs among closely related bats reflects host taxon-specificity with each bat family as the host for a specific BetaCoV group, potentially a natural barrier against random transmission. The divergent pathway of BetaCoV and host evolution suggests that the viruses were introduced just prior to bat dispersal and speciation. As such, deviant patterns were observed such as for 2D-IV, wherein cross-taxon transmission due to overlap in bat habitats and geographic range among genetically divergent African bat hosts could have played a strong role on their shared CoV lineages. In fact, a few bat taxa especially the subfamily Pteropodinae were shown to host diverse groups of BetaCoVs. Therefore, ecological imbalances that disturb bat distribution may lead to loss of host specificity through cross-taxon transmission and multi-CoV infection. Hence, initiatives that minimize the destruction of wildlife habitats and limit wildlife-livestock-human interfaces are encouraged to help maintain the natural state of bat BetaCoVs in the wild.

Importance

Bat Betacoronaviruses (BetaCoVs) pose a significant threat to global public health and have been implicated in several epidemics such as the recent pandemic by severe acute respiratory syndrome coronavirus 2. Here, we show that bat BetaCoVs are predominantly host-specific, which could be a natural barrier against infection of other host types. However, a strong overlap in bat habitat and geographic range may facilitate viral transmission to unrelated hosts, and a few bat families have already been shown to host multi-CoV variants. We predict that continued disturbances on the ecological balance may eventually lead to loss of host specificity. When combined with enhanced wildlife-livestock-human interfaces, spillover to humans may be further facilitated. We should therefore start to define the ecological mechanisms surrounding zoonotic events. Global surveillance should be expanded and strengthened to assess the complete picture of bat coronavirus diversity and distribution and their potential to cause spillover infections.
Pooling RT-PCR test of SARS-CoV-2 for large cohort of “healthy” and infection-suspected patients: A prospective and consecutive study on 1,000 individuals
Authors: Hirotsu Yosuke , Maejima Makoto , Shibusawa Masahiro , Nagakubo Yuki , Hosaka Kazuhiro , Amemiya Kenji , Sueki Hitomi , Hayakawa Miyoko , Mochizuki Hitoshi , Omata Masao
Published: May 2020

Background

SARS-CoV-2 testing reagents are expected to become in short supply worldwide. However, little is unknown whether the pooling strategy detects SARS-CoV-2 with accuracy.

Method

To validate the feasibility of pooling samples, serial dilution analysis and spike-in experiment were conducted using synthetic DNA and nucleic acids extracted from SARS-CoV-2 positive and negative patients. Furthermore, we studied a total of 1,000 individuals, who were 667 “healthy” (195 healthcare workers and 472 hospitalized patients with other disorders than COVID-19 infection) individuals and 333 infection-suspected patients with cough and fever, were tested.

Results

Serial dilution analysis showed the limit of detection of around 10-100 copies according to National Institute of Infectious Diseases, Japan. Spike-in experiment demonstrated RT-qPCR detect positive signal in pooling samples of SARS-CoV-2 negative and positive patient at the 5-, 10-, 20-fold dilution. By screening with pooling strategy by the end of April, 2020, there are 12 COVID-19 patients in 333 infection suspected patients (3.6%) and zero in 667 “healthy”. We obtained these results with total running 538 times (instead of 1,000 times) by pooling strategy.

Conclusion

Pooling samples is feasible for saving test reagents and detecting SARS-CoV-2 in clinical setting to prevent the spread of the virus and nosocomial transmission.
Deciphering the temporal heterogeneity of cancer-associated fibroblast subpopulations in breast cancer
Authors: Venning Freja Albjerg , Zornhagen Kamilla Westarp , Wullkopf Lena , Hajkarim Morteza Chalabi , Won Kyoung Jae , Madsen Chris Denis , Erler Janine Tera
Published: May 2020

Cancer-associated fibroblasts (CAFs) comprise a heterogeneous population of stromal cells within the tumour microenvironment. CAFs exhibit both tumour-promoting and tumour-suppressing functions, making them exciting targets for improving cancer treatments. A careful identification and characterisation of the CAF heterogeneity is thus necessary before implementing CAF-targeted strategies in cancer. With that in mind, we developed a flow cytometry strategy based on exclusion of non-CAF cells and successfully employed it to explore the temporal heterogeneity of CAFs in two models of triple-negative breast cancer (4T1 and 4T07). Analysing 128 murine tumours we identified 5-6 main CAF subpopulations and numerous minor ones based on the analysis of alpha smooth muscle actin, fibroblast activation protein alpha, platelet derived growth factor receptor alpha and beta, CD26/DPP4 and podoplanin. All markers showed temporal changes, and CD26+ CAFs emerged as a large novel subpopulation. These results form the foundation needed for the future elucidation of tumour-promoting CAF subpopulations.
Limited time window for retinal gene therapy in a preclinical model of ciliopathy
Authors: Datta Poppy , Ruffcorn Avri , Seo Seongjin
Published: May 2020

Retinal degeneration is a common clinical feature of ciliopathies, a group of genetic diseases linked to ciliary dysfunction, and gene therapy is an attractive treatment option to prevent vision loss. Although the efficacy of retinal gene therapy is well established by multiple proof-of-concept preclinical studies, its long-term effect, particularly when treatments are given at advanced disease stages, is controversial. Incomplete treatment and intrinsic variability of gene delivery methods may contribute to the variable outcomes. Here, we used a genetic rescue approach to “optimally” treat retinal degeneration at various disease stages and examined the long-term efficacy of gene therapy in a mouse model of ciliopathy. We used a Bardet-Biedl syndrome type 17 (BBS17) mouse model, in which the gene-trap that suppresses Bbs17 (also known as Lztfl1) expression can be removed by tamoxifen administration, restoring normal gene expression systemically. Our data indicate that therapeutic effects of retinal gene therapy decrease gradually as treatments are given at later stages. These results suggest the presence of limited time window for successful gene therapy in certain retinal degenerations. Our study also implies that the long-term efficacy of retinal gene therapy may depend on not only the timing of treatment but also other factors such as the function of mutated genes and residual activities of mutant alleles.
The relationship between fasting-induced torpor, sleep and wakefulness in the laboratory mouse
Authors: Huang Yi G. , Flaherty Sarah J. , Pothecary Carina A. , Foster Russell G. , Peirson Stuart N. , Vyazovskiy Vladyslav V.
Published: May 2020

Torpor is a regulated reversible state of metabolic suppression used by many mammalian species to conserve energy. Although torpor has been studied extensively in terms of general physiology, metabolism and neuroendocrinology, the effects of hypometabolism and associated hypothermia on brain activity and states of vigilance have received little attention. Here we performed continuous monitoring of electroencephalogram (EEG), electromyogram (EMG) and peripheral body temperature in adult, male C57BL/6 mice over consecutive days of scheduled restricted feeding. All animals showed prominent bouts of hypothermia that became progressively deeper and longer as fasting progressed. EEG and EMG were markedly affected by hypothermia, although the typical electrophysiological signatures of NREM sleep, REM sleep and wakefulness allowed us to perform vigilance-state classification in all cases. Invariably, hypothermia bouts were initiated from a state indistinguishable from NREM sleep, with EEG power decreasing gradually in parallel with decreasing body temperature. Furthermore, during deep hypothermia REM sleep was largely abolished, but we observed brief and intense bursts of muscle activity, which resembled the regular motor discharges seen during early ontogeny associated with immature sleep patterns. We conclude that torpor and sleep are electrophysiologically on a continuum, and that, in order for torpor to occur, mice need to first transition through euthermic sleep.
Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia
Authors: Takao Sumiko , Forbes Lauren , Uni Masahiro , Cheng Shuyuan , Pineda Jose Mario Bello , Tarumoto Yusuke , Cifani Paolo , Minuesa Gerard , Chen Celine , Kharas Michael G. , Bradley Robert K. , Vakoc Christopher R. , Koche Richard P. , Kentsis Alex
Published: May 2020

Dysregulated gene expression contributes to most prevalent features in human cancers. Here, we show that most subtypes of acute myeloid leukemia (AML) depend on the aberrant assembly of MYB transcriptional co-activator complex. By rapid and selective peptidomimetic interference with the binding of CBP/P300 to MYB, but not CREB or MLL1, we find that the leukemic functions of MYB are mediated by CBP/P300 co-activation of a distinct set of transcription factor complexes. These MYB complexes assemble aberrantly with LYL1, E2A, C/EBP family members, LMO2 and SATB1. They are organized convergently in genetically diverse subtypes of AML, and are at least in part associated with inappropriate transcription factor co-expression. Peptidomimetic remodeling of oncogenic MYB complexes is accompanied by specific proteolysis and dynamic redistribution of CBP/P300 with alternative transcription factors such as RUNX1 to induce myeloid differentiation and apoptosis. Thus, aberrant assembly and sequestration of MYB:CBP/P300 complexes provide a unifying mechanism of oncogenic gene expression in AML. This work establishes a compelling strategy for their pharmacologic reprogramming and therapeutic targeting for diverse leukemias and possibly other human cancers caused by dysregulated gene control.
Transient coupling between subplate and subgranular layers to L1 neurons before and during the critical period
Authors: Meng Xiangying , Xu Yanqing , Kao Joseph P. Y. , Kanold Patrick O.
Published: May 2020

Cortical layer 1 (L1) contains a diverse population of interneurons which can modulate processing in superficial cortical layers but the intracortical sources of synaptic input to these neurons and how these inputs change over development is unknown. We here investigated the changing intracortical connectivity to L1 in primary auditory cortex (A1) in slices of mouse A1 across development using laser-scanning photostimulation. Before P10 L1 cells receive most excitatory input from within L1, L2/3, L4 and L5/6 as well as the subplate. Excitatory inputs from all layers increase and peak during P10-P16, the peak of the critical period. Inhibitory inputs followed a similar pattern. Functional circuit diversity in L1 emerges after P16. In adult, L1 neurons receive ascending inputs from superficial L2/3 and subgranular L5/6, but only few inputs from L4. A subtype of L1 neurons, NDNF+ neurons, follow a similar pattern, suggesting that transient hyperconnectivity is a universal feature of developing cortical circuits. Our results demonstrate that deep excitatory and superficial inhibitory circuits are tightly linked in early development and might provide a functional scaffold for the layers in between. These results suggest that early thalamic driven spontaneous and sensory activity in subplate can be relayed to L1 from the earliest ages on, that the critical period is characterized by high transient columnar hyperconnectivity, and that in particular circuits originating in L5/6 and subplate might play a key role.
Cyrius: accurateCYP2D6genotyping using whole genome sequencing data
Authors: Chen Xiao , Shen Fei , Gonzaludo Nina , Malhotra Alka , Rogert Cande , Taft Ryan J , Bentley David R , Eberle Michael A
Published: May 2020

Responsible for the metabolism of 25% of clinically used drugs,CYP2D6is a critical component of personalized medicine initiatives. GenotypingCYP2D6is challenging due to sequence similarity with its pseudogene paralogCYP2D7and a high number and variety of common structural variants (SVs). Here we describe a novel bioinformatics method, Cyrius, that accurately genotypesCYP2D6using whole-genome sequencing (WGS) data. We show that Cyrius has superior performance (96.5% concordance with truth genotypes) compared to existing methods (84-86.8%). After implementing the improvements identified from the comparison against the truth data, Cyrius’s accuracy has since been improved to 99.3%. Using Cyrius, we built a haplotype frequency database from 2504 ethnically diverse samples and estimate that SV-containing star alleles are more frequent than previously reported. Cyrius will be an important tool to incorporate pharmacogenomics in WGS-based precision medicine initiatives.
Application of aptamers improves CRISPR-based live imaging of plant telomeres
Authors: Khosravi Solmaz , Schindele Patrick , Gladilin Evgeny , Dunemann Frank , Rutten Twan , Puchta Holger , Houben Andreas
Published: May 2020

Development of live imaging techniques for providing information how chromatin is organized in living cells is pivotal to decipher the regulation of biological processes. Here, we demonstrate the improvement of a live imaging technique based on CRISPR/Cas9. In this approach, the sgRNA scaffold is fused to RNA aptamers including MS2 and PP7. When the dead Cas9 (dCas9) is co-expressed with chimeric sgRNA, the aptamer-binding proteins fused to fluorescent protein (MCP-FP and PCP-FP) are recruited to the targeted sequence. Compared to previous work with dCas9:GFP, we show that the quality of telomere labelling was improved in transiently transformedNicotiana benthamianausing aptamer-based CRISPR-imaging constructs. Labelling is influenced by the copy number of aptamers and less by the promoter types. The same constructs were not applicable for labelling of repeats in stably transformed plants and roots. The constant interaction of the RNP complex with its target DNA might interfere with cellular processes.

Highlight

Aptamer-based CRISPR imaging: an opportunity for improving live-cell imaging in plants
Multiple sclerosis iPSC-derived oligodendroglia conserve their intrinsic properties to functionally interact with axons and glia in vivo
Authors: Mozafari Sabah , Starost Laura , Manot-Saillet Blandine , Garcia-Diaz Beatriz , Xu Yu Kang T. , Roussel Delphine , Levy Marion J. F. , Ottoboni Linda , Kim Kee-Pyo , Schöler Hans R. , Kennedy Timothy E. , Antel Jack P. , Martino Gianvito , Angulo Maria Cecilia , Kuhlmann Tanja , Baron-Van Evercooren Anne
Published: May 2020

The remyelination failure in multiple sclerosis (MS) is associated with a migration/differentiation block of oligodendroglia. The reason for this block is highly debated. It could result from disease-related extrinsic regulators of the oligodendroglial biology or reflect MS oligodendrocyte intrinsic properties. To avoid confounding immune-mediated extrinsic effect, we used an immune-deficient, dysmyelinating mouse model, to compare side-by-side induced pluripotent stem-cell-derived O4+ oligodendroglia from MS and healthy donors following their engraftment in the developing CNS. We show that the MS-progeny survives, proliferates and differentiates into oligodendrocytes to the same extent as controls. Quantitative multi-parametric imaging indicates that MS and control oligodendrocytes generate equal amounts of myelin, withbona-fidenodes of Ranvier and promote equal restoration of their host slow conduction. Moreover, the MS-derived progeny expressed oligodendrocyte- and astrocyte-specific connexins and established functional connections with donor and host glial cells. Thus, MS pluripotent stem cell-derived progeny fully integrates into functional axo-glial and glial-glial components, reinforcing the view that the MS oligodendrocyte differentiation block is not due to intrinsic oligodendroglial deficits. These biological findings as well as the fully integrated human-murine chimeric model should facilitate the development of pharmacological or cell-based therapies to promote CNS remyelination.

One Sentence Summary

Multiple Sclerosis oligodendroglia, regardless of major immune manipulators, are intrinsically capable of myelination and making functional axo-glia and glia-glia connections after engraftment in the murine CNS, reinforcing the view that the MS oligodendrocyte differentiation block is not due to major intrinsic oligodendroglial deficits but most likely to environmental conditions.
Phase-amplitude coupling profiles differ in frontal and auditory cortices
Authors: García-Rosales Francisco , López-Jury Luciana , González-Palomares Eugenia , Cabral-Calderin Yuranny , Kössl Manfred , Hechavarria Julio C.
Published: May 2020

Neural oscillations are at the core of important computations in the mammalian brain. Interactions between oscillatory activities in different frequency bands, such as delta (1-4 Hz), theta (4-8 Hz), or gamma (>30 Hz), are a powerful mechanism for binding fundamentally distinct spatiotemporal scales of neural processing. Phase-amplitude coupling (PAC) is one such plausible and well-described interaction, but much is yet to be uncovered regarding how PAC dynamics contribute to sensory representations. In particular, although PAC appears to have a major role in audition, the characteristics of coupling profiles in sensory and integration (i.e. frontal) cortical areas remain obscure. Here, we address this question by studying PAC dynamics in the frontal-auditory field (FAF; an auditory area in the bat frontal cortex) and the auditory cortex (AC) of the batCarollia perspicillata. By means of simultaneous electrophysiological recordings in frontal and auditory cortices examining local-field potentials (LFPs), we show that the amplitude of gamma-band activity couples with the phase of low-frequency LFPs in both structures. Our results demonstrate that the coupling in FAF occurs most prominently in delta/high-gamma frequencies (1-4/75-100 Hz), whereas in the AC the coupling is strongest in the theta/low-gamma (2-8/25-55 Hz) range. We argue that distinct PAC profiles may represent different mechanisms for neuronal processing in frontal and auditory cortices, and might complement oscillatory interactions for sensory processing in the frontal-auditory cortex network.
Transcriptional memory-like imprints and enhanced functional activity in γδ T cells following resolution of malaria infection
Authors: Kumarasingha Rasika , Ioannidis Lisa J. , Abeysekera Waruni , Studniberg Stephanie , Wijesurendra Dinidu , Mazhari Ramin , Poole Daniel P. , Mueller Ivo , Schofield Louis , Hansen Diana S. , Eriksson Emily M.
Published: May 2020

γδ T cells play an essential role in the immune response to malaria infection. However, long-lasting effects of malaria infection on the γδ T cell population still remain inadequately understood. This study investigated transcriptional changes and memory-like functional capacity of malaria pre-exposed γδ T cells using aPlasmodium chabaudiinfection model. We show that multiple genes associated with effector function (chemokines, cytokines and cytotoxicity) and antigen-presentation were upregulated inP. chabaudi-exposed γδ T cells compared to γδ T cells from naïve mice. This transcriptional profile was positively correlated with profiles observed in conventional memory CD8+T cells and was accompanied by enhanced reactivation upon secondary encounter withPlasmodium-infected red blood cellsin vitro. Collectively our data demonstrate thatPlasmodiumexposure result in “memory-like imprints” in the γδ T cell population and also promotes γδ T cells that can support antigen-presentation during subsequent infections.
A histone-like motif in yellow fever virus contributes to viral replication
Authors: Mourão Diego , Chen Shoudeng , Schaefer Uwe , Bozzacco Leonia , Carneiro Leticia A. , Gerber Alan , Adura Carolina , Dill Brian D. , Molina Henrik , Carroll Thomas , Paul Matthew , Bhanu Natarajan V. , Garcia Benjamin A. , Joberty Gerard , Rioja Inmaculada , Prinjha Rab K. , Roeder Robert G. , Rice Charles M. , MacDonald Margaret R. , Patel Dinshaw , Tarakhovsky Alexander
Published: May 2020

The mimicry of host proteins by viruses contributes to their ability to suppress antiviral immunity and hijack host biosynthetic machinery1. Host adaptation to evade this exploitation depends on host protein functional redundancy2. Non-redundant, essential host proteins have limited potential to adapt without severe consequences3. Histones, which are essential for genome architecture and control of gene expression, are among the most evolutionary conserved proteins4. Here we show that the capsid protein of the flavivirus yellow fever virus (YFV), mimics histone H4 and interferes with chromatin gene regulation by BRD4, a bromodomain and extraterminal domain (BET) protein. Two acetyl-lysine residues of YFV capsid are embedded in a histone-like motif that interacts with the BRD4 bromodomain, affecting gene expression and influencing YFV replication. These findings reveal histone mimicry as a strategy employed by an RNA virus that replicates in the cytosol5and define convergent and distinct molecular determinants for motif recognition of the viral mimic versus histone H4.