bluuebunny/crossref_metadata_2025_split huggingface dataset:
Landscape and Selection of Vaccine Epitopes in SARS-CoV-2
Authors: Smith Christof C. , Entwistle Sarah , Willis Caryn , Vensko Steven , Beck Wolfgang , Garness Jason , Sambade Maria , Routh Eric , Olsen Kelly , Kodysh Julia , O’Donnell Timothy , Haber Carsten , Heiss Kirsten , Stadler Volker , Garrison Erik , Grant Oliver C. , Woods Robert J. , Heise Mark , Vincent Benjamin G. , Rubinsteyn Alex 
Published: June 2020

AbstractThere is an urgent need for a vaccine with efficacy against SARS-CoV-2. We hypothesize that peptide vaccines containing epitope regions optimized for concurrent B cell, CD4+T cell, and CD8+T cell stimulation would drive both humoral and cellular immunity with high specificity, potentially avoiding undesired effects such as antibody-dependent enhancement (ADE). Additionally, such vaccines can be rapidly manufactured in a distributed manner. In this study, we combine computational prediction of T cell epitopes, recently published B cell epitope mapping studies, and epitope accessibility to select candidate peptide vaccines for SARS-CoV-2. We begin with an exploration of the space of possible T cell epitopes in SARS-CoV-2 with interrogation of predicted HLA-I and HLA-II ligands, overlap between predicted ligands, protein source, as well as concurrent human/murine coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, viral source protein abundance, sequence conservation, coverage of high frequency HLA alleles and co-localization of CD4+and CD8+T cell epitopes. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering to select regions with surface accessibility, high sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. From 58 initial candidates, three B cell epitope regions were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we propose a set of SARS-CoV-2 vaccine peptides for use in subsequent murine studies and clinical trials.Abstract Figure
The effects of sustained fitness improvement on the gut microbiome: A longitudinal, repeated measures case-study approach
Authors: Barton Wiley , Cronin Owen , Garcia-Perez Isabel , Whiston Ronan , Holmes Elaine , Woods Trevor , Molloy Catherine B. , Molloy Michael G. , Shanahan Fergus , Cotter Paul D. , O’Sullivan Orla 
Published: June 2020

AbstractObjectiveThe composition and metabolic function of the gut microbiome in the elite athlete differs from that of non-athletes. However, short-term fitness improvement in the sedentary adult does not replicate the microbiome characteristics seen in the athlete. Whether sustained fitness improvement over a prolonged period can lead to pronounced and beneficial alteration in the gut microbiome is unknown. The objective was to explore this possibility.MethodsThis study used a repeated-measures, case-study approach to explore changes in the gut microbiome of two unfit volunteers undertaking progressive exercise training over a 6-month period. Training was to culminate in the completion of a marathon or Olympic-distance triathlon. The volunteers were sampled every two weeks for six months and microbiome, metabolome, diet, body composition, and cardiorespiratory fitness data were recorded.ResultsBoth participants completed their respective goals with improved body composition and fitness parameters over the training period. Increases in α-diversity of the gut microbiota occurred with sustained training and fluctuations occurred in response to training events (e.g., injury, illness and training peaks). Participants’ fat mass and BMI reduced during the study and was significantly associated with increased urinary measurements of N-methyl nicotinate (P value < 0.001) and hippurate (P value < 0.05), and decreased phenylacetylglutamine (P value < 0.05).ConclusionThese results suggest that sustained fitness improvements result in alterations to gut microbiota and physiologically-relevant metabolites. This study provides longitudinal analysis of the response of the gut microbiome to real-world events during progressive fitness training, including intercurrent illness and injury.
Rapid non-invasive detection of Influenza-A-infection by multicapillary column coupled ion mobility spectrometry
Authors: Steppert Claus , Steppert Isabel , Bollinger Thomas , Sterlacci William 
Published: June 2020

AbstractInfectious pathogens are a global issue. Global air travelling offers an easy and fast opportunity not only for people but also for infectious diseases to spread around the world within a few days. Also, large public events facilitate increasing infection numbers. Therefore, a rapid on-site screening for infected people is urgently needed.Due to the small size and easy handling, the ion mobility spectrometry coupled with a multicapillary column (MCC-IMS) is a very promising, sensitive method for the on-site identification of infectious pathogens based on scents, representing volatile organic compounds (VOCs).The purpose of this study was to prospectively assess whether identification of Influenza-A-infection based on VOCs by MCC-IMS is possible in breath. Nasal breath was investigated in 24 consecutive persons with and without Influenza-A-infection by MCC-IMS. In 14 Influenza-A-infected patients, infection was proven by PCR of nasopharyngeal swabs. Four healthy staff members and six patients with negative PCR result served as controls. For picking up relevant VOCs in MCC-IMS spectra, software based on cluster analysis followed by multivariate statistical analysis was applied. With only four VOCs canonical discriminant analysis was able to distinguish Influenza-A-infected patients from not infected with 100% sensitivity and 100% specificity.This present proof-of-concept-study yields encouraging results showing a rapid diagnosis of viral infections in nasal breath within 5 minutes by MCC-IMS. The next step is to validate the results with a greater number of patients with Influenza-A-infection as well as other viral diseases, especially COVID-19.Registration number at ClinicalTrials.gov NCT04282135.
Host response-based screening to identify undiagnosed cases of COVID-19 and expand testing capacity
Authors: Cheemarla Nagarjuna R. , Brito Anderson F. , Fauver Joseph R. , Alpert Tara , Vogels Chantal B.F. , Omer Saad B. , Ko Albert I. , Grubaugh Nathan D. , Landry Marie L. , Foxman Ellen F. 
Published: June 2020

AbstractThe COVID-19 pandemic has created unprecedented challenges in diagnostic testing. At the beginning of the epidemic, a confluence of factors resulted in delayed deployment of PCR-based diagnostic tests, resulting in lack of testing of individuals with symptoms of the disease. Although these tests are now more widely available, it is estimated that a three- to ten-fold increase in testing capacity will be required to ensure adequate surveillance as communities reopen1. In response to these challenges, we evaluated potential roles of host response-based screening in the diagnosis of COVID-19. Previous work from our group showed that the nasopharyngeal (NP) level of CXCL10, a protein produced as part of the host response to viral infection, is a sensitive predictor of respiratory virus infection across a wide spectrum of viruses2. Here, we show that NP CXCL10 is elevated during SARS-CoV-2 infection and use a CXCL10-based screening strategy to identify four undiagnosed cases of COVID-19 in Connecticut in early March. In a second set of samples tested at the Yale New Haven Hospital, we show that NP CXCL10 had excellent performance as a rule-out test (NPV 0.99, 95% C.I. 0.985-0.997). Our results demonstrate how biomarker-based screening could be used to leverage existing PCR testing capacity to rapidly enable widespread testing for COVID-19.One Sentence SummaryWe describe a host-response based screening strategy to identify undiagnosed cases of COVID-19 and to expand capacity for PCR-based testing.
Reparations for Black American Descendants of Persons Enslaved in the U.S. and Their Estimated Impact on SARS-CoV-2 Transmission
Authors: Richardson Eugene T. , Malik Momin M. , Darity William A. , Mullen A. Kirsten , Malik Maya , Maybank Aletha , Bassett Mary T. , Farmer Paul E. , Worden Lee , Jones James Holland 
Published: June 2020

AbstractBackgroundIn the United States, Black Americans are suffering from significantly disproportionate incidence and mortality rates of COVID-19. The potential for racial-justice interventions, including reparations payments, to ameliorate these disparities has not been adequately explored.MethodsWe compared the COVID-19 time-varying Rt curves of relatively disparate polities in terms of social equity (South Korea vs. Louisiana). Next, we considered a range of reproductive ratios to back-calculate the transmission rates βi→j for 4 cells of the simplified next-generation matrix (from which R0 is calculated for structured models) for the outbreak in Louisiana. Lastly, we modeled the effect that monetary payments as reparations for Black American descendants of persons enslaved in the U.S. would have had on pre-intervention βi→j.ResultsOnce their respective epidemics begin to propagate, Louisiana displays Rt values with an absolute difference of 1.3 to 2.5 compared to South Korea. It also takes Louisiana more than twice as long to bring Rt below 1. We estimate that increased equity in transmission consistent with the benefits of a successful reparations program (reflected in the ratio βb→b / βw→w) could reduce R0 by 31 to 68%.DiscussionWhile there are compelling moral and historical arguments for racial injustice interventions such as reparations, our study describes potential health benefits in the form of reduced SARS-CoV-2 transmission risk. As we demonstrate, a restitutive program targeted towards Black individuals would not only decrease COVID-19 risk for recipients of the wealth redistribution; the mitigating effects would be distributed across racial groups, benefitting the population at large.FundingETR and LW are supported by NIGMS MIDAS grant R01 GM130900. ETR is also supported by NIAID K08 AI139361. WAD is supported by NIMHD R01 MD011606, NSF SES 1851845, and IES R305A190484. MMM is supported by the Ethics and Governance of Artificial Intelligence Fund.
SWATH-MS based proteomic profiling of Pancreatic Ductal Adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways
Authors: Nweke EE , Naicker P , Aron S , Stoychev S , Devar J , Tabb DL , Jones OJ , Smith MD , Candy GP 
Published: June 2020

AbstractPancreatic cancer accounts for 2.8% of new cancer cases worldwide and is projected to become the second leading cause of cancer-related deaths by 2030. Patients of African ancestry appear to be at an increased risk for pancreatic ductal adenocarcinoma (PDAC), with worse severity and outcomes. The purpose of this study was to map the proteomic and genomic landscape of a cohort of PDAC patients of African ancestry.Thirty tissues (15 tumours and 15 normal adjacent tissues) were obtained from consenting South African PDAC patients. Optimisation of the sample preparation method allowed for the simultaneous extraction of high-purity protein and DNA for SWATH-MS and OncoArray SNV analyses.We quantified 3402 proteins with 49 upregulated and 35 downregulated proteins at a minimum 2.1 fold change and FDR adjusted p-value (q-value) ≤ 0.01 when comparing tumour to normal adjacent tissue. Many of the upregulated proteins in the tumour samples are involved in extracellular matrix formation (ECM) and related intracellular pathways. Proteins such as EMIL1, KBTB2, and ZCCHV involved in the regulation of ECM proteins were observed to be dysregulated in pancreatic tumours. Approximately 11% of the dysregulated proteins, including ISLR, BP1, PTK7 and OLFL3, were predicted to be secretory proteins. Additionally, we identified missense mutations in some upregulated proteins, such as MYPN, ESTY2 and SERPINB8. These findings help in further elucidating the biology of PDAC and may aid in identifying future plausible markers for the disease.
Adjusting for Allometric Scaling in ABIDE I Challenges Subcortical Volume Differences in Autism Spectrum Disorder
Authors: Williams Camille Michèle , Peyre Hugo , Toro Roberto , Beggiato Anita , Ramus Franck 
Published: June 2020

AbstractTo properly adjust for total brain volume (TBV), brain allometry – the non-linear scaling relationship between regional volumes and TBV – was considered when examining subcortical volumetric differences between typically developing (TD) and Autistim Spectrum Disorder (ASD) individuals.Autism Brain Imaging Data Exchange I (N = 654) data was analyzed with two methodological approaches: univariate Linear Mixed Effects Models and multivariate Multiple Group Confirmatory Factor Analyses. Analyses were conducted on the entire sample and in subsamples based on age, sex, and Full Scale Intelligence Quotient (FSIQ). A similar ABIDE I study was replicated and the impact of different TBV adjustments on neuroanatomical group differences was investigated.No robust subcortical allometric or volumetric group differences were observed in the entire sample across methods. Exploratory analyses suggested that allometric scaling and volume group differences may exist in certain subgroups defined by age, sex, and/or FSIQ. The type of TBV adjustment influenced some reported volumetric and scaling group differences.This study supports the absence of robust volumetric differences between ASD and TD individuals in the investigated volumes when adjusting for brain allometry, expands the literature by finding no group difference in allometric scaling, and further suggests that differing TBV adjustments contribute to the variability of reported neuroanatomical differences in ASD.
The impact of school reopening on the spread of COVID-19 in England
Authors: Keeling Matt J. , Tildesley Michael J. , Atkins Benjamin D. , Penman Bridget , Southall Emma , Guyver-Fletcher Glen , Holmes Alex , McKimm Hector , Gorsich Erin E. , Hill Edward M. , Dyson Louise 
Published: June 2020

AbstractBy mid-May, cases of COVID-19 in the UK had been declining for over a month; a multi-phase emergence from lockdown was planned, including a scheduled partial reopening of schools on 1st June. Although evidence suggests that children generally display mild symptoms, the size of the school-age population means the total impact of reopening schools is unclear. Here, we present work from mid-May that focused on the imminent opening of schools and consider what these results imply for future policy.We compared eight strategies for reopening primary and secondary schools in England. Modifying a transmission model fitted to UK SARS-CoV-2 data, we assessed how reopening schools affects contact patterns, anticipated secondary infections and the relative change in the reproduction number, R. We determined the associated public health impact and its sensitivity to changes in social-distancing within the wider community.We predicted reopening schools with half-sized classes or focused on younger children was unlikely to push R above one. Older children generally have more social contacts, so reopening secondary schools results in more cases than reopening primary schools, while reopening both could have pushed R above one in some regions. Reductions in community social-distancing were found to outweigh and exacerbate any impacts of reopening. In particular, opening schools when the reproduction number R is already above one generates the largest increase in cases.Our work indicates that while any school reopening will result in increased mixing and infection amongst children and the wider population, reopening schools alone in June was unlikely to push R above one. Ultimately, reopening decisions are a difficult trade-off between epidemiological consequences and the emotional, educational and developmental needs of children. Into the future, there are difficult questions about what controls can be instigated such that schools can remain open if cases increase.
Extended use or re-use of single-use surgical masks and filtering facepiece respirators: A rapid evidence review
Authors: Toomey E , Conway Y , Burton C , Smith S , Smalle M , Chan XH , Adisesh A , Tanveer S , Ross L , Thomson I , Devane D , Greenhalgh T 
Published: June 2020

AbstractBackgroundThe COVID-19 pandemic has led to unprecedented demand for personal protective equipment. Shortages of surgical masks and filtering facepiece respirators has led to the extended use or re-use of single-use respirators and surgical masks by frontline healthcare workers. The evidence base underpinning such practices has been questioned.ObjectivesTo summarise guidance and synthesise systematic review evidence on extended use, re-use or reprocessing of single-use surgical masks or filtering facepiece respirators.MethodsA targeted search of the World Health Organization, European Centre for Disease Prevention and Control, the US Centers for Disease Control and Prevention, and Public Health England websites was conducted to identify guidance. Four databases (Medline, Pubmed, Epistemonikos, Cochrane Database of Systematic Reviews) and three preprint repositories (Litcovid, MedRxiv and Open Science Framework) were searched for relevant systematic reviews. Record screening and data extraction was conducted by two reviewers. Quality of included systematic reviews was appraised using the AMSTAR-2 checklist. Findings were integrated and narratively synthesised to highlight the extent to which key claims in guidance documents were supported by research evidence.ResultsSix guidance documents were identified. All note that extended use or re-use of single-use surgical masks and respirators (with or without reprocessing) should be considered only in situations of critical shortage. Extended use was generally favoured over re-use because of reduced risk of contact transmission. Four high-quality systematic reviews were included: three focused on reprocessing (decontamination) of N95 respirators and one focused on reprocessing of surgical masks. There was limited evidence on the impact of extended use on masks and respirators. Vaporised hydrogen peroxide and ultraviolet germicidal irradiation were highlighted as the most promising reprocessing methods, but evidence on the relative efficacy and safety of different methods was limited. We found no well-established methods for reprocessing respirators at scale.ConclusionsThere is limited evidence on the impact of extended use and re-use of surgical masks and respirators. Where extended use or re-use is being practiced, healthcare organisations should ensure that policies and systems are in place to ensure these practices are carried out safely and in line with available guidance.
Value co-creation features: an empirical case study of B2B collaboration and interactions in New Zealand
Authors: Rashid Yasir , Tanveer Anisha , Shaukat Zeeshan , Sadiq Imran 
Published: June 2020

Purpose
This paper aims to highlight four features of value co-creation among actors in a business-to-business environment. Service-dominant (S-D) logic of marketing is used as a theoretical lens to view at the process of value co-creation.

Design/methodology/approach
Using an interpretive methodological approach, the authors collected empirical material from a single case based in New Zealand. The case was based on the collaboration, interaction and relationship between vendor and client during an information and communication technology (ICT) systems integration project. The unit of analysis was “points of value creation.” Empirical material came from observation, in-depth interviews and documents such as meeting notes and email logs. Interpretation highlighted four features of the value co-creation process: motivators, outcomes, disadvantages and management. Moreover, personal and network aspects of value co-creation process emerged.

Findings
The findings of this study capture benefits, as well as conflicts and frustrations, in a value co-creation process. Furthermore, it provides future research motivations for researchers currently working to develop S-D logic of marketing.

Originality/value
It is suggested that there is relatively little direction on how value co-creation process should be undertaken in different contexts such as retail, education, health care and ICT. There is a need to understand the dynamics and specification of value co-creation process, as the literature is scarce in this field.
Assessment of artificial neural network for thermohydrodynamic lubrication analysis
Authors: Wang Nenzi , Tsai Chih-Ming 
Published: June 2020

Purpose
In this study, artificial neural networks (ANNs) are constructed and validated by using the bearing data generated numerically from a thermohydrodynamic (THD) lubrication model. In many tribological simulations, a surrogate model (meta-model) for obtaining a fast solution with sufficient accuracy is highly desired.

Design/methodology/approach
The THD model is represented by two coupled partial differential equations, a simplified generalized Reynolds equation, considering the viscosity variation across the film thickness direction and a transient energy equation for the 3-D film temperature distribution. The ANNs tested are having a single- or dual-hidden-layer with two inputs and one output. The root-mean-square error and maximum/minimum absolute errors of validation points, when comparing with the THD solutions, were used to evaluate the prediction accuracy of the ANNs.

Findings
It is demonstrated that a properly constructed ANN surrogate model can predict the THD lubrication performance almost instantly with accuracy adequately retained.

Originality/value
This study extends the use of ANNs to the applications other than the analyses dealing with experimental data. A similar procedure can be used to build a surrogate model for computationally intensive tribological models to have fast results. One of such applications is conducting extensive optimum design of tribological components or systems.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-03-2020-0109/