bluuebunny/crossref_metadata_2025 huggingface dataset:
Forecasting the Spread of COVID-19 under Different Reopening Strategies
Authors: Liu Meng , Thomadsen Raphael , Yao Song
Published: May 2020

We combine COVID-19 case data with mobility data to estimate a modified susceptible-infected-recovered (SIR) model in the United States. In contrast to a standard SIR model, we find that the incidence of COVID-19 spread is concave in the number of infectious individuals, as would be expected if people have inter-related social networks. This concave shape has a significant impact on forecasted COVID-19 cases. In particular, our model forecasts that the number of COVID-19 cases would only have an exponential growth for a brief period at the beginning of the contagion event or right after a reopening, but would quickly settle into a prolonged period of time with stable, slightly declining levels of disease spread. This pattern is consistent with observed levels of COVID-19 cases in the US, but inconsistent with standard SIR modeling. We forecast rates of new cases for COVID-19 under different social distancing norms and find that if social distancing is eliminated there will be a massive increase in the cases of COVID-19.
Multicellular rosettes organize neuropil formation
Authors: Brittin Christopher A. , Santella Anthony , Barnes Kristopher , Moyle Mark W. , Fan Li , Christensen Ryan , Kolotuev Irina , Mohler William A. , Shroff Hari , Colón-Ramos Daniel A. , Bao Zhirong
Published: May 2020

Neuropils are compartments in the nervous system containing dense networks of neurites and synapses which function as information processing centers. Neuropil formation requires structural and functional organization at and across different scales, achieving single-axon precision for circuits that carry out the core functions while simultaneously accommodating variability among individuals [1; 2; 3; 4]. How these organizational features emerge over development is poorly understood. The nerve ring is the primary neuropil inC. elegans, and its structure is thoroughly mapped [5; 6]. We show that prior to axon outgrowth, nerve ring neurons form a ring of multicellular rosettes with surrounding cells to organize the stratified nerve ring structure [7; 8]. Axon bundles which correspond to future nerve ring strata grow from rosette centers, travel along the ring on “bridge” cells that are simultaneously engaged in adjacent rosettes, and assemble into a topographic scaffold of the nerve ring. SAX-3/Robo is required for proper rosette formation and outgrowth from the center. Furthermore, axon contact sites that form early in development are more conserved than the later ones, indicating a temporal component in neuropil structural variability. Our results reveal an unexpected and critical role of collective cell behaviors prior to innervation to pattern a complex neuropil and orchestrate its formation across scales.
Burkholderia thailandensismethylated hydroxy-alkylquinolines: biosynthesis and antimicrobial activity in co-cultures
Authors: Klaus Jennifer R , Majerczyk Charlotte , Moon Stephanie , Epplera Natalie A. , Smith Sierra , Tuma Emily , Groleau Marie-Christine , Asfahl Kyle L. , Smalley Nicole E. , Hayden Hillary S. , Piochon Marianne , Ball Patrick , Dandekar Ajai A. , Gauthier Charles , Déziel Eric , Chandler Josephine R.
Published: May 2020

The bacteriumBurkholderia thailandensisproduces an arsenal of secondary metabolites that have diverse structures and roles in the ecology of this soil-dwelling bacterium. In liquid co-culture experiments,B. thailandensissecretes an antimicrobial that nearly eliminates another soil bacterium,Bacillus subtilis. To identify the antimicrobial, we used a transposon mutagenesis approach. This screen identified antimicrobial-defective mutants with insertions in thehmqA, hmqCandhmqFgenes involved in biosynthesis of a family of 2-alkyl-4(1H)-quinolones called 4-hydroxy-3-methyl-2-alkenylquinolines (HMAQs), which are closely related to thePseudomonas aeruginosa4-hydroxy-2-alkylquinolines (HAQs). Insertions also occurred in the previously uncharacterized gene BTH_II1576. Results confirm that BTH_II1576 is involved in generatingN-oxide derivatives of HMAQs (HMAQ-NO) inB. thailandensisand that HMAQ-NOs are sufficient to eliminateB. subtilisin co-cultures. Moreover, synthetic HMAQ-NO is ∼50-fold more active than HMAQ. Both the methyl group and the length of the carbon side chain account for high activity of HMAQ-NO againstB. subtilis. The results provide new information on the biosynthesis and activities of HMAQs and reveal new insight into how these molecules might be important for the ecology ofB. thailandensis.

IMPORTANCE

The soil bacteriumBurkholderia thailandensisproduces 2-alkyl-4(1H)-quinolones, mostly methylated 4-hydroxy-alkenylquinolines, a family of relatively unstudied metabolites similar to molecules also synthesized byPseudomonas aeruginosa. Several of the methylated 4-hydroxy-alkenylquinolines have antimicrobial activity against other species. We show thatN-oxidated methyl-alkenylquinolines are particularly antimicrobial and sufficient to killBacillus subtilisin co-cultures. We confirmed their biosynthesis requires the previously unstudied protein HmqL. These results provide new information about the biology of 2-alkyl-4(1H)-quinolones, particularly the methylated 4-hydroxy-alkenylquinolines, which are unique toB. thailandensis. This study also has importance for understandingB. thailandensissecondary metabolites and has implications for potential therapeutic development.
Fecal microbiota transplantation efficacy for Clostridium difficile infection: A trans-kingdom battle between donor and recipient gut microbiomes
Authors: Kazemian Negin , Ramezankhani Milad , Sehgal Aarushi , Khalid Faizan Muhammad , Kalkhoran Amir Hossein Zeinali , Narayan Apurva , Wong Gane Ka-Shu , Kao Dina , Pakpour Sepideh
Published: May 2020

Fundamental restoration ecology and community ecology theories can help us better understand the underlying mechanisms of fecal microbiota transplantation (FMT) and to better design future microbial therapeutics for recurrent Clostridium difficile infections (rCDI) and other dysbiosis-related conditions. In a single cohort study, stool samples were collected from donors and rCDI patients one week prior to FMT (pre-FMT) as well as from patients one week following FMT (post-FMT). Using metagenomic sequencing and machine learning methods, our results suggested that the FMT outcome is not only dependent on the ecological structure of the recipients, but also the interactions between the donor and recipient microbiomes, both at the taxonomical and functional levels. Importantly, we observed that the presence of specific bacteria in donors (Clostridiodes spp., Desulfovibrio spp., Odoribacter spp. and Oscillibacter spp.) and the absence of specific fungi (Yarrowia spp.) and bacteria (Wigglesworthia spp.) in recipients prior to FMT could accurately predict FMT success. Our results also suggested a series of interlocked mechanisms for FMT success, including the repair of the disturbed gut microbial ecosystem by transient colonization of nexus species followed by secondary succession of bile acid metabolizers, sporulators, and short chain fatty acid producers. Therefore, a better understanding of such mechanisms can be fundamental key elements to develop adaptive, personalized microbial-based strategies for the restoration of the gut ecosystem.

Importance

There have been a number of studies focusing on understanding the underlying mechanisms in FMT treatment, which can accordingly be used for the optimization of future treatments. However, the current scientific lens has mainly had a uni-kingdom major focus on bacteria, leading to the proposition of the existence of FMT “super-donors”. On the contrary, our preliminary study here suggests that FMT is not necessarily a ‘one stool fits all’ approach and that donor-recipient cross-kingdom microbiota interactions, along with their short-term fluctuations in the gut, bring profound implications in FMT success. The results also conceptualize a series of interlocked mechanisms for FMT success, including first repairing the disturbed gut microbial ecosystem by transient species, followed by secondary succession of indigenous or exogenous bile acid metabolizers, sporulators, and short chain fatty acid producers.
Automatic Detection of COVID-19 and Pneumonia from Chest X-Ray using Transfer Learning
Authors: Pathari Sarath , U Rahul
Published: May 2020

In this study, a dataset of X-ray images from patients with common viral pneumonia, bacterial pneumonia, confirmed Covid-19 disease was utilized for the automatic detection of the Coronavirus disease. The point of the investigation is to assess the exhibition of cutting edge convolutional neural system structures proposed over the ongoing years for clinical picture order. In particular, the system called Transfer Learning was received. With transfer learning, the location of different variations from the norm in little clinical picture datasets is a reachable objective, regularly yielding amazing outcomes. The datasets used in this trial. Firstly, a collection of 24000 X-ray images includes 6000 images for confirmed Covid-19 disease,6000 confirmed common bacterial pneumonia and 6000 images of normal conditions. The information was gathered and expanded from the accessible X-Ray pictures on open clinical stores. The outcomes recommend that Deep Learning with X-Ray imaging may separate noteworthy biomarkers identified with the Covid-19 sickness, while the best precision, affectability, and particularity acquired is 97.83%, 96.81%, and 98.56% individually.
Evaluation of Rural Public Libraries to Address Telemedicine Inequities
Authors: DeGuzman Pamela B. , Siegfried Zack , Leimkuhler Megan E.
Published: May 2020

Introduction

In the United States, access to home-based telemedicine is inequitably distributed due to the limited reach of fixed broadband in rural areas. Public libraries typically offer patrons free access to broadband. Libraries, particularly those in rural regions, need to be evaluated as a site for patients to connect to a health care provider over a video visit. The purpose of this research was to evaluate the technological readiness of public libraries to provide telemedicine support and to determine differences in readiness between rural and urban public libraries.

Methods

We distributed a survey to members of the Virginia Library Association to evaluate technological readiness of Virginia public libraries to support telemedicine use in their facilities. The survey evaluated each library’s availability and speed of fixed broadband internet access, physical equipment, and private space.

Results

Respondents from 39 libraries completed the survey, approximately one-third of which were in rural or small urban areas. All respondents reported fixed broadband, at least four computers, and available staff to assist who technology in their libraries. Eighty-five percent of surveyed libraries reported sufficient broadband speed and a private room available to patrons. There were no significant differences between rural and urban status for any of the library characteristics.

Discussion

Public libraries in Virginia are technologically ready to support patrons connecting to health care providers over telemedicine. Systematic guidelines for library-practice collaborations are needed to support implementation across geographic and socioeconomically diverse areas.
TractLearn: a geodesic learning framework for quantitative analysis of brain bundles
Authors: Attyé Arnaud , Renard Félix , Baciu Monica , Roger Elise , Lamalle Laurent , Dehail Patrick , Cassoudesalle Hélène , Calamante Fernando
Published: May 2020

Deep learning-based convolutional neural networks have recently proved their efficiency in providing fast segmentation of major brain fascicles structures, based on diffusion-weighted imaging. The quantitative analysis of brain fascicles then relies on metrics either coming from the tractography process itself or from each voxel along the bundle.

Statistical detection of abnormal voxels in the context of disease usually relies on univariate and multivariate statistics models, such as the General Linear Model (GLM). Yet in the case of high-dimensional low sample size data, the GLM often implies high standard deviation range in controls due to anatomical variability, despite the commonly used smoothing process. This can lead to difficulties to detect subtle quantitative alterations from a brain bundle at the voxel scale.

Here we introduce TractLearn, a unified framework for brain fascicles quantitative analyses by using geodesic learning as a data-driven learning task. TractLearn allows a mapping between the image high-dimensional domain and the reduced latent space of brain fascicles using a Riemannian approach.

We illustrate the robustness of this method on a healthy population with test-retest acquisition of multi-shell diffusion MRI data, demonstrating that it is possible to separately study the global effect due to different MRI sessions from the effect of local bundle alterations. We have then tested the efficiency of our algorithm on a sample of 5 age-matched subjects referred with mild traumatic brain injury.

Our contributions are to propose an algorithm based on:

1/ A manifold approach to capture controls variability as standard reference instead of an atlas approach based on a Euclidean mean

2/ The ability to detect global variation of voxels quantitative values, which means that all the voxels interaction in a structure are considered rather than analyzing each voxel independently.

With this regard, TractLearn is a ready-to-use algorithm for precision medicine.

KEY POINT

We provide a statistical test taking into account the interaction between voxels

We propose to use a Riemaniann manifold as reference instead of a Euclidean mean

We demonstrate the usefulness and reliability of the track-weighted contrast
EMSNet: A neural network model with a self-attention mechanism for prehospital prediction of care needs
Authors: Jeong Joo , Kim Yu Jin , Kim Dae Kon , Kim Tackeun , Kim Joonghee
Published: May 2020

Background

An artificial intelligence (AI) system capable of predicting patient needs in the prehospital phase would be instrumental. We sought to develop a neural network (NN) model capable of predicting various care needs at initial contact by emergency medical service (EMS) using multimodal input data.

Methods

We used EMS records of a single emergency department (ED). We implemented two attention-based NN model (I and P) differing only by how they use contextual information. The models predict multiple events, including hospital admission, endotracheal intubation, mechanical ventilation, vasopressor infusion, cardiac catheterization, surgery, intensive care unit (ICU) admission, and cardiac arrest. The input features include both unstructured data (chief complaints, injury summary, past medical history, history of present illness) and structured data (age, sex, pupil status and initial vital signs, level of consciousness, and O2 saturation on pulse oximetry). We applied multi-task learning for training. We evaluated the relative performance of the models compared with a human expert, an emergency physician with 10-year experience as an EMS medical director.

Results

The study population included 42,073 cases. The receiver operating characteristics (ROC) area under the curve (AUC) values of the models I and P ranged from 0.793 to 0.929 and 0.812 to 0.934, respectively. The precision-recall (PR) AUC values ranged from 0.149 to 0.673 and 0.156 to 0.683, respectively. With decision thresholds set to achieve equivalent recall levels, our AI models achieved precision levels not significantly different from those of a human expert except in prediction of mechanical ventilation and ICU admission, where the models achieved superior performance (p=0.030 [model I] and p=0.015 [model P], respectively).

Conclusions

AI models using multimodal input data can predict medical resource requirements at initial contact by EMS with high accuracies.
Covid19db – An online database of trials of medicinal products to prevent or treat COVID-19, with a specific focus on drug repurposing
Authors: Pantziarka Pan , Vandeborne Liese , Meheus Lydie , Bouche Gauthier
Published: May 2020

Background

The global pandemic caused by SARS-CoV-2 virus has prompted an unprecedented international effort to seek medicines for prevention and treatment of infection. Drug repurposing has played a key part in this response. The rapid increase in trial activity has raised questions about efficiency and lack of coordination. Our objective was to develop a user-friendly, open access database to monitor and rapidly identify trials of medicinal products.

Methods

Using the US clinicaltrials.gov (NCT) registry, the EU Clinical Trials Register (EUCTR) and the WHO International Clinical Trials Registry Platform (WHO ICTRP), we identified all COVID-19 trials of medicinal products. Trials that were out of scope and duplicates were excluded. A manual encoding was performed to ascertain key information (e.g. trial aim, type of intervention etc). The database, Covid19db, is published online at:http://www.redo-project.org/covid19db/.

Results

Descriptive statistics of the database from April 4th 2020 through to August 18th show an increase from 186 to 1618 trials, or an average of 10.5 new trials registered per day. Over this period, the proportion of trials including a repurposing arm decreased slightly (from a maximum of 75% to 64% at the end of the covered period) as did the proportion of trials aiming to prevent infection (from a maximum of 16% to 13%). The most popular trial intervention is hydroxychloroquine (212 trials), followed by azithromycin (64 trials), tocilizumab, favipiravir and chloroquine (145 trials). Total planned enrolment is 1064556 participants as of 18thAugust 2020.

Conclusions

we have developed an open access and regularly updated tool to monitor clinical trials of medicinal products to prevent or treat infection by SARS-CoV-2 globally. Our analysis shows a high number of ‘me-too’ trials, in particular for some repurposed drugs, such as hydroxychloroquine, azithromycin and tocilizumab, substantiating calls for better coordination and better use of trial resources.
Lopinavir-Ritonavir in treatment of COVID-19: A dynamic systematic benefit-risk assessment
Authors: Osborne Vicki , Davies Miranda , Lane Samantha , Evans Alison , Denyer Jacqueline , Dhanda Sandeep , Roy Debabrata , Shakir Saad
Published: May 2020

Background

COVID-19 is an ongoing, global public health crisis for which safe and effective treatments need to be identified. The benefit-risk balance for use of lopinavir-ritonavir in COVID-19 needs to be monitored on an ongoing basis, therefore a systematic benefit-risk assessment was designed and conducted. A key objective of this study was to provide a platform for a dynamic systematic benefit-risk evaluation; although initially this evaluation is likely to contain limited information, it is required due to the urgent unmet public need. Importantly it allows additional data to be incorporated as it becomes available, and re-evaluation of the benefit-risk profile.

Methods

A systematic benefit-risk assessment was conducted using the Benefit-Risk Action team (BRAT) framework. The exposure of interest was lopinavir-ritonavir treatment in COVID-19 compared to standard of care, placebo or other treatments. A literature search was conducted in PubMed and EmBase to identify peer-reviewed papers reporting clinical outcomes. Two clinicians constructed a value tree and ranked key benefits and risks in order of considered clinical importance.

Results

In comparison to standard of care, data for several key benefits and risks were identified for lopinavir-ritonavir. Time to clinical improvement was not significantly different for lopinavir-ritonavir in comparison to standard of care (HR=1.31, 95% CI:0.95, 1.80). There appeared to be fewer serious adverse events with lopinavir-ritonavir (20%) vs standard of care (32%). In particular, there were fewer cases of acute respiratory distress syndrome with lopinavir-ritonavir compared to standard of care (13% vs 27%). Limited data were available for comparison of lopinavir-ritonavir to other treatments.

Conclusions

Based on currently available data, there was no clear benefit for use of lopinavir-ritonavir compared to standard of care in severe COVID-19. Risk data suggested a possible decrease in serious adverse events, including acute respiratory distress syndrome. Overall, the benefit-risk profile for lopinavir-ritonavir in severe COVID-19 cannot be considered positive until further efficacy and effectiveness data become available.
The association between treatment with heparin and survival in patients with Covid-19
Authors: Ayerbe Luis , Risco Carlos , Ayis Salma
Published: May 2020

Objectives

This study investigates the association between the treatment with heparin and mortality in patients admitted with Covid-19.

Methods

Routinely recorded, clinical data, up to the 24th of April 2020, from the 2075 patients with Covid-19, admitted in 17 hospitals in Spain between the 1st of March and the 20th of April 2020 were used. The following variables were extracted for this study: age, gender, temperature, and saturation of oxygen on admission, treatment with heparin, hydroxychloroquine, azithromycin, steroids, tocilizumab, a combination of lopinavir with ritonavir, and oseltamivir, together with data on mortality. Multivariable logistic regression models were used to investigate the associations.

Results

At the time of collecting the data, 301 patients had died, 1447 had been discharged home from the hospitals, 201 were still admitted, and 126 had been transferred to hospitals not included in the study. Median follow up time was 8 (IQR:5-12) days. Heparin had been used in 1734 patients. Heparin was associated with lower mortality when the model was adjusted for age and gender, with OR (95%CI): 0.55 (0.37-0.82) p=0.003. This association remained significant when saturation of oxygen <90%, and temperature >37C were added to de model with OR: 0.54(0.36-0.82) p=0.003, and also when all the other drugs were included as covariates OR: 0.42 (0.26-0.66) p<0.001.

Conclusions

The association between heparin and lower mortality observed in this study can be acknowledged by clinicians in hospitals and in the community. Randomized controlled trials to assess the causal effects of heparin in different therapeutic regimes are required.

-

The administration of heparin was associated with lower mortality in patients admitted with Covid-19.

-

Our findings support that there is a thrombotic component in the development of respiratory distress for these patients.

-

The positive effect of heparin seems consistent and its use, when indicated, could be considered in clinical settings.

-

Randomized controlled trials are necessary to complement observational studies, and assess the causal associations between heparin, in different therapeutic regimes, and clinical outcomes.

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Heparin is easy to administer, its use in ambulatory patients, to prevent admissions, or reduce their duration, could also be considered by clinicians and future researchers.
Factors affecting healthcare workers’ compliance with social and behavioural infection control measures during emerging infectious disease outbreaks: Rapid evidence review
Authors: Brooks Samantha K. , Greenberg Neil , Wessely Simon , Rubin G. James
Published: May 2020

The 2019-2020 outbreak of novel coronavirus has raised concerns about nosocomial transmission; that is, transmission within healthcare settings. Research from previous outbreaks of emerging infectious diseases suggests a major cause of nosocomial transmission is healthcare professionals’ poor compliance with recommended personal protective behaviours. This rapid evidence review explored existing literature on emerging infectious disease outbreaks to identify factors associated with compliance with social and behavioural infection control measures among healthcare staff. 56 papers were reviewed and several positive associations were found: Staff working in emergency or intensive care settings appeared more likely to comply with recommendations than those in other settings, and there was some evidence that contact with confirmed cases could improve compliance. There was some evidence that staff with higher levels of anxiety and higher concern about the risk of infection were more likely to comply with recommended behaviour, and that monitoring from superiors could improve compliance. Several negative associations were also found. Observed non-compliance of colleagues could hinder compliance. Staff identified many barriers to compliance related to personal protective equipment, including availability; perceived difficulty and effectiveness; inconvenience; discomfort; and a negative impact on patient care. There appeared to be many issues regarding the communication and ease of understanding of infection control guidance. Based on the results of this review we recommend provision of training and education tailored for different occupational roles within the healthcare setting; managerial staff ‘leading by example’; ensuring adequate resources for infection control; and timely provision of practical evidence-based infection control guidelines.
The Association Between Biomarkers and Clinical Outcomes in Novel Coronavirus (COVID-19) Pneumonia in a U.S. Cohort
Authors: Ayanian Shant , Reyes Juan , Lynn Lei , Teufel Karolyn
Published: May 2020

Background

The global pandemic caused by COVID-19 remains poorly understood by clinicians. Identifying biologic markers associated with prognosis can help clinicians recognize disease severity.

Objective

To describe the association between D-dimer, CRP, IL-6, ferritin, LDH, and clinical outcomes in a cohort of COVID-19 patients treated on the inpatient medical service at a university hospital in Washington, DC.

Design

In this retrospective study, we included all adults admitted to the inpatient medicine service at George Washington University Hospital between March 12, 2020 and May 9, 2020 with laboratory confirmed COVID-19. Clinical and laboratory data were extracted from electronic medical records and compared between survivors not requiring ICU transfer, survivors requiring ICU transfer, survivors requiring intubation, and non-survivors.

Key Results

299 patients were included in our study, of whom 69 required transfer to the ICU, 39 required intubation, and 71 died. Threshold values for IL-6 (≥50 pg/mL), D-dimer (≥3 mcg/mL), ferritin (≥450 ng/mL), CRP (≥100 mg/L), and LDH (1,200 u/L) were found to be statistically significant and independently associated with higher odd of clinical deterioration and death. Hypertension, CVA and heart disease independently had an increased risk of all three outcomes, while CKD had only an increased risk of death. Patient co-morbidities had no effect on the different biomarkers’ significant association with poor patient clinical outcomes, except cancer.

Conclusion

Laboratory markers of inflammation and coagulopathy can help clinicians identify patients who are at high risk for clinical deterioration, independent of clinically significant medical comorbidities.
Did the National lockdown lock COVID-19 down in India, and reduce pressure on health infrastructure?
Authors: Husain Zakir , Das Arup Kumar , Ghosh Saswata
Published: May 2020

Background & objectives: The spread of COVID19 in India has posed a major challenge for policy makers. Policy response in form of imposition of a prolonged national lockdown has imposed substantial costs on the entire population. But the extent to which it has contained the spread of the epidemic needs to be assessed.
Methods: We use an Interrupted Time Series model to assess the success of lockdowns in containing COVID-19. In the second step, we use four variants of the SIR models to develop a counterfactual- what would have happened without the lockdown. These results are compared with actual data. The analysis is undertaken for India, and Maharashtra, Gujarat, Delhi, and Tamil Nadu.
Results: Lockdown has reduced the number of COVID-19 cases by 23.65 to 337.73 lakh in Class I cities and towns, where COVID has mainly spread. It has averted about 0.01 to 0.10 lakh deaths. At the regional level, however, lockdown has averted a health crisis as existing ICU and ventilator facilities for critically ill patients would have been inadequate.
Interpretation & conclusions: Overall, the results for three of the four models reveal that lockdown has a modest impact on spread of COVID-19; the health infrastructure at the national level is not over strained, even at the peak. At the regional level, on the other hand, lockdowns may have been justified. However, given that identification of new cases is limited by levels of daily testing that are low even by Asian standards, analysis based upon official data may have limitations and result in flawed decisions.
Within-host genomics of SARS-CoV-2
Authors: Lythgoe Katrina A. , Hall Matthew , Ferretti Luca , de Cesare Mariateresa , MacIntyre-Cockett George , Trebes Amy , Andersson Monique , Otecko Newton , Wise Emma L. , Moore Nathan , Lynch Jessica , Kidd Stephen , Cortes Nicholas , Mori Matilde , Williams Rebecca , Vernet Gabrielle , Justice Anita , Green Angie , Nicholls Samuel M. , Ansari M. Azim , Abeler-Dörner Lucie , Moore Catrin E. , Peto Timothy E. A. , Eyre David W. , Shaw Robert , Simmonds Peter , Buck David , Todd John A. , Connor Thomas R. , da Silva Filipe Ana , Shepherd James , Thomson Emma C. ,   The COVID-19 Genomics UK (COG-UK) consortium, Bonsall David , Fraser Christophe , Golubchik Tanya
Published: May 2020

Extensive global sampling and whole genome sequencing of the pandemic virus SARS-CoV-2 have enabled researchers to characterise its spread, and to identify mutations that may increase transmission or enable the virus to escape therapies or vaccines. Two important components of viral spread are how frequently variants arise within individuals, and how likely they are to be transmitted. Here, we characterise the within-host diversity of SARS-CoV-2, and the extent to which genetic diversity is transmitted, by quantifying variant frequencies in 1390 clinical samples from the UK, many from individuals in known epidemiological clusters. We show that SARS-CoV-2 infections are characterised by low levels of within-host diversity across the entire viral genome, with evidence of strong evolutionary constraint in Spike, a key target of vaccines and antibody-based therapies. Although within-host variants can be observed in multiple individuals in the same phylogenetic or epidemiological cluster, highly infectious individuals with high viral load carry only a limited repertoire of viral diversity. Most viral variants are either lost, or occasionally fixed, at the point of transmission, consistent with a narrow transmission bottleneck. These results suggest potential vaccine-escape mutations are likely to be rare in infectious individuals. Nonetheless, we identified Spike variants present in multiple individuals that may affect receptor binding or neutralisation by antibodies. Since the fitness advantage of escape mutations in highly-vaccinated populations is likely to be substantial, resulting in rapid spread if and when they do emerge, these findings underline the need for continued vigilance and monitoring.
Evaluation of commercial qPCR kits for detection of SARS-CoV-2 in pooled samples
Authors: Petrovan Vlad , Vrajmasu Virgil , Dimon Paula , Zaulet Mihaela
Published: May 2020

Due to the current pandemic, global shortage of reagents has drawn interest in developing alternatives to increase the number coronavirus tests. One such alternative is sample pooling. Here we compared commercial kits that are used in COVID-19 diagnostics, in terms of sensitivity and feasibility for use in pooling. We showed that pooling of up to 60 samples did not affect the efficiency of the kits. Also, the RNA dependent RNA polymerase (RdRp) is a more suitable target in pooled samples than the Envelope (E) protein. This approach could provide an easy method of screening large number of samples and help adjust different government regulations.
Proteomic identification ofCoxiella burnetiieffector proteins targeted to the host cell mitochondria during infection
Authors: Fielden Laura F. , Scott Nichollas E. , Palmer Catherine S. , Khoo Chen Ai , Newton Hayley J , Stojanovski Diana
Published: May 2020

Modulation of the host cell is integral to the survival and replication of microbial pathogens. Several intracellular bacterial pathogens deliver a cohort of bacterial proteins, termed ‘effector proteins’ into the host cell during infection by sophisticated protein translocation systems which manipulate cellular processes and functions. Despite the importance of these proteins during infection the functional contribution of individual effectors is poorly characterised, particularly in intracellular bacterial pathogens with large effector protein repertoires. Technical caveats have limited the capacity to study these proteins during a native infection, with many effector proteins having only been demonstrated to be translocated during over-expression of tagged versions. Here we present development of a novel strategy to examine effector proteins in the context of infection. We coupled a broad, unbiased proteomics-based screen with organelle purification to study the host-pathogen interactions occurring between the host cell mitochondrion and the Gram-negative, Q fever pathogenCoxiella burnetii.We identify 4 novel mitochondrially-targetedC. burnetiieffector proteins, renamed MitochondrialCoxiellaeffector protein (Mce) B to E. Examination of the subcellular localisation of ectopically expressed proteins in epithelial cells confirmed the mitochondrial localisation, demonstrating the robustness of our approach. Subsequent biochemical analysis and affinity enrichment proteomics of one of these effector proteins, MceC, revealed the protein is imported into mitochondria and can interact with components of the mitochondrial quality control machinery. Our study adapts high-sensitivity proteomics to the study of intracellular host-pathogen interactions occurring during infection, providing a robust strategy to examine the sub-cellular localisation of effector proteins during native infection. This approach could be applied to a range of pathogens and host cell compartments to provide a rich map of effector dynamics throughout infection.
The Incubot: A 3D Printer-Based Microscope for Long-Term Live Cell Imaging within a Tissue Culture Incubator
Authors: Merces George O. T. , Kennedy Conor , Lenoci Blanca , Reynaud Emmanuel G. , Burke Niamh , Pickering Mark
Published: May 2020

Commercial live cell imaging systems represent a large financial burden to research groups, while current open source incubator microscopy systems lack adaptability and are sometimes inadequate for complex imaging experimentation. We present here a low-cost microscope designed for inclusion within a conventional tissue culture incubator. The build is constructed using an entry level 3D printer as the basis for the motion control system, with Raspberry Pi imaging and software integration, allowing for reflected, oblique, and fluorescence imaging of live cell monolayers. The open source nature of the design is aimed to facilitate adaptation by both the community at large and by individual researchers/groups. The development of an adaptable and easy-to-use graphic user interface (GUI) allows for the scientist to be at the core of experimental design. Simple modifications of the base GUI code, or generation of an entirely purpose-built script, will allow microscopists to place their experimental design as the priority, as opposed to designing experiments to fit their current equipment. The build can be constructed for a cost of roughly C1000 and thus serves as a low-cost and adaptable addition to the open source microscopy community.

Abstract Figure
Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states
Authors: Bhattacharjee Bornali , Pandit Bhaswati
Published: May 2020

The first Indian cases of COVID-19 caused by SARS-Cov-2 were reported in February 29, 2020 with a history of travel from Wuhan, China and so far above 4500 deaths have been attributed to this pandemic. The objectives of this study were to characterize Indian SARS-CoV-2 genome-wide nucleotide variations, trace ancestries using phylogenetic networks and correlate state-wise distribution of viral haplotypes with differences in mortality rates. A total of 305 whole genome sequences from 19 Indian states were downloaded from GISAID. Sequences were aligned using the ancestral Wuhan-Hu genome sequence (NC_045512.2). A total of 633 variants resulting in 388 amino acid substitutions were identified. Allele frequency spectrum, and nucleotide diversity (π) values revealed the presence of higher proportions of low frequency variants and negative Tajima’s D values across ORFs indicated the presence of population expansion. Network analysis highlighted the presence of two major clusters of viral haplotypes, namely, clade G with the S:D614G, RdRp: P323L variants and a variant of clade L [Lv] having the RdRp:A97V variant. Clade G genomes were found to be evolving more rapidly into multiple sub-clusters including clade GH and GR and were also found in higher proportions in three states with highest mortality rates namely, Gujarat, Madhya Pradesh and West Bengal.
Reciprocal repulsions instruct the precise assembly of parallel hippocampal networks
Authors: Pederick Daniel T. , Lui Jan H. , Gingrich Ellen C. , Xu Chuanyun , Wagner Mark J. , Liu Yuanyuan , He Zhigang , Quake Stephen R. , Luo Liqun
Published: May 2020

Parallel information processing is a salient feature of complex nervous systems. For example, the medial and lateral hippocampal networks (MHN and LHN) preferentially process spatial- and object-related information, respectively. However, the mechanisms underlying parallel network assembly during development remain largely unknown. Here, we show that complementary expression of cell-surface molecules Teneurin-3 (Ten3) and Latrophilin-2 (Lphn2) in the MHN and LHN, respectively, guides the precise assembly of both the MHN and LHN. Viral-genetic perturbationsin vivodemonstrate that Ten3+ axons are repelled by target-derived Lphn2, revealing that Lphn2/Ten3-mediated repulsion and Ten3/Ten3-mediated attraction cooperate to control precise target selection of MHN axons. In the LHN, Lphn2+ axons are confined to Lphn2+ targets via repulsion from Ten3+ targets. Our findings demonstrate that assembly of parallel hippocampal networks follows a ‘Ten3→Ten3, Lphn2→Lphn2’ rule instructed by reciprocal repulsions.
CRISPR Knockdown ofKcnq3Attenuates the M-current in NPY/AgRP Neurons
Authors: Stincic Todd L. , Bosch Martha A. , Hunker Avery C. , Juarez Barbara , Connors Ashley M. , Zweifel Larry S. , Rønnekleiv Oline K. , Kelly Martin J.
Published: May 2020

Arcuate nucleus Neuropeptide Y/Agouti-related peptide (NPY/AgRP) neurons drive ingestive behavior in response to the internal and external environment of an organism. NPY/AgRP neurons are adjacent to the median eminence, a circumventricular organ, and circulating metabolic factors and hormones communicate the energy state of the animal via these neurons by altering the excitability of NPY/AgRP neurons, which produces an appropriate change in behavior to maintain homeostasis. One example of this plasticity is seen in the M-current, a subthreshold, non-inactivating K+current that acts to modulate excitability. Fasting decreases while estradiol increases the M-current through regulation of subunit mRNA expression ofKcnq 2, 3, & 5. KCNQ2/3 heteromers are thought to mediate the majority of the M-current. Here we used a recently developed single adeno-associated viral (AAV) vector containing a recombinase-dependent Staphylococcus aureus Cas9 (SaCas9) and a single guide RNA againstKcnq3to selectively deleteKcnq3in NPY/AgRP neurons to produce a loss of function in the M-current. We found that this virus was effective at knocking downKcnq3but notKcnq2expression. With the reduced KCNQ3 channel expression NPY/AgRP neurons were more depolarized, exhibited a higher input resistance, and the rheobase current needed to induce firing was significantly reduced, indicative of increased excitability. Although the resulting decrease in the M-current did not overtly alter ingestive behavior, it did significantly reduce the locomotor activity as measured in open field testing. Therefore, the SaCas9-sgKcnq3 is efficient to knock downKcnq3expression thereby reducing the M-current and increasing the excitability of NPY/AgRP neurons.
Older age is associated with sustained detection of SARS-CoV-2 in nasopharyngeal swab samples
Authors: Hattori Takeshi , Amishima Masaru , Morinaga Daisuke , Kamada Keisuke , Nakakubo Sho , Yamashita Yu , Shichinohe Yasuo , Fujisawa Shinichi , Nishida Mutsumi , Nasuhara Yasuyuki , Teshima Takanori , Konno Satoshi
Published: May 2020

PCR testing of nasopharyngeal swab samples is used for the diagnosis of coronavirus disease 2019 (COVID-19) and for determining timing of discharge. The viral load usually declines at convalescent phase, but sometimes remained positive for a long time even after relief of symptoms. In this study, we identified older age is associated with sustained detection of SARS-CoV-2 in nasopharyngeal swab samples.
Combining imaging- and gene-based hypoxia biomarkers in cervical cancer improves prediction of chemoradiotherapy failure independent of intratumor heterogeneity
Authors: Fjeldbo Christina S , Hompland Tord , Hillestad Tiril , Aarnes Eva-Katrine , Günther Clara-Cecilie , Kristensen Gunnar B , Malinen Eirik , Lyng Heidi
Published: May 2020

Purpose: Emerging biomarkers from medical imaging or molecular characterization of tumor biopsies open up for combining the two and exploiting their synergy in treatment planning. We compared pretreatment classification of locally advanced cervical cancer patients by two previously validated imaging- and gene-based hypoxia biomarkers, appraised the influence of intratumor heterogeneity, and investigated the benefit of combining them in prediction of chemoradiotherapy failure.
Experimental Design: Hypoxic fraction, determined from dynamic contrast enhanced (DCE)-MR images, and an expression signature of 6 hypoxia-responsive genes were used as imaging- and gene-based biomarker, respectively, in 118 patients. Intratumor heterogeneity was assessed by variance analysis. The biomarkers were combined using a dimension reduction procedure.
Results: The two biomarkers classified 75% of the patients with the same hypoxia status. Inconsistent classification in some cases was not related to imaging-defined intratumor heterogeneity in hypoxia, and hypoxia status of the slice covering the biopsy region was representative of the whole tumor. Hypoxia assessed by gene expression was independent on tumor cell fraction in the biopsies and showed minor heterogeneity across multiple samples in 9 tumors. Inconsistent classification was therefore rather caused by a difference in the hypoxia phenotype reflected by the biomarkers, providing a rational for combining them into a composite score. This score showed improved prediction of treatment failure (HR:7.3) compared to imaging (HR:3.8) and genes (HR:3.0) and significant prognostic impact in multivariate analysis with clinical variables.
Conclusion: Combining our imaging- and gene-based biomarkers enables more precise and informative assessment of hypoxia-related chemoradiotherapy resistance in cervical cancer.
Crystallization and X-ray analysis of Borrelia burgdorferi β-barrel assembly machinery A
Authors: Dong Shishang , Chu Hongguan , Wen Kangning , Yu Qianqian , Li Hui , Wang Changhui , Qin Xiaochun
Published: May 2020

Mitochondria, chloroplasts and several species of bacteria have outer membrane proteins (OMPs) that perform many essential biological functions. The β-barrel assembly machinery (BAM) complex is one of the OMPs of Borrelia burgdorferi, the pathogenic spirochete that causes Lyme disease, and its BamA component (BbBamA) includes a C-terminal β-barrel domain and five N-terminal periplasmic polypeptide-transport-associated (POTRA) domains, which together perform a central transport function. In the current work, the production, crystallization and X-ray analysis of the three N-terminal POTRA domains of BbBamA (BbBamA-POTRA P1–P3; residues 30–273) were carried out. The crystals of BbBamA-POTRA P1–P3 belonged to space group P21, with unit-cell parameters a = 45.353, b = 111.538, c = 64.376 Å, β = 99.913°. The Matthews coefficient was calculated to be 2.92 Å3 Da−1, assuming the presence of two molecules per asymmetric unit, and the corresponding solvent content was 57.9%. Owing to the absence of an ideal homology model, numerous attempts to solve the BbBamA-POTRA P1–P3 structure using molecular replacement (MR) failed. In order to solve the structure, further trials using selenomethionine derivatization are currently being carried out.
Structure of heme d
1-free cd
1 nitrite reductase NirS
Authors: Klünemann Thomas , Blankenfeldt Wulf
Published: May 2020

A key step in anaerobic nitrate respiration is the reduction of nitrite to nitric oxide, which is catalysed by the cd
1 nitrite reductase NirS in, for example, the Gram-negative opportunistic pathogen Pseudomonas aeruginosa. Each subunit of this homodimeric enzyme consists of a cytochrome c domain and an eight-bladed β-propeller that binds the uncommon isobacteriochlorin heme d
1 as an essential part of its active site. Although NirS has been well studied mechanistically and structurally, the focus of previous studies has been on the active heme d
1-bound form. The heme d
1-free form of NirS reported here, which represents a premature state of the reductase, adopts an open conformation with the cytochrome c domains moved away from each other with respect to the active enzyme. Further, the movement of a loop around Trp498 seems to be related to a widening of the propeller, allowing easier access to the heme d
1-binding side. Finally, a possible link between the open conformation of NirS and flagella formation in P. aeruginosa is discussed.
Crystal structure of dimethyl 5-(4-ethylphenyl)-4-[(4-ethylphenyl)ethynyl]-6,11-diphenyl-1,3,6,11-tetrahydro-2H-6,11-epoxycyclopenta[a]anthracene-2,2-dicarboxylate
Authors: Meng Xiang-Zhen , Cheng Dong
Published: May 2020

In the central fused ring system of the title compound, C51H42O5, all of the five-membered rings are in an envelope conformation. The dihedral angle between the two benzene rings in the fused ring system is 74.66 (7)°. In the crystal, molecules are linked by C—H...π interactions, forming a layer parallel to the ab plane. Each molecule acts as a double donor as well as a double acceptor of the C—H...π interactions. Hirshfeld surface analysis and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H...H (61.4%) and C...H/H...C (25.3%) contacts.
1-Ethyl 2-methyl 3,4-bis(acetyloxy)pyrrolidine-1,2-dicarboxylate: crystal structure, Hirshfeld surface analysis and computational chemistry
Authors: Dallasta Pedroso Sofia , Caracelli Ignez , Zukerman-Schpector Julio , Soto-Monsalve Monica , De Almeida Santos Regina H. , Correia Carlos Roque D. , Llanes Garcia Ariel L. , Kwong Huey Chong , Tiekink Edward R. T.
Published: May 2020

The title compound, C13H19NO8, is based on a tetra-substituted pyrrolidine ring, which has a twisted conformation about the central C—C bond; the Cm—Ca—Ca—Cme torsion angle is 38.26 (15)° [m = methylcarboxylate, a = acetyloxy and me = methylene]. While the N-bound ethylcarboxylate group occupies an equatorial position, the remaining substituents occupy axial positions. In the crystal, supramolecular double-layers are formed by weak methyl- and methylene-C—H...O(carbonyl) interactions involving all four carbonyl-O atoms. The two-dimensional arrays stack along the c axis without directional interactions between them. The Hirshfeld surface is dominated by H...H (55.7%) and H...C/C...H (37.0%) contacts; H...H contacts are noted in the inter-double-layer region. The interaction energy calculations point to the importance of the dispersion energy term in the stabilization of the crystal.