bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative analysis of automated MRI brain segmentation in a large longitudinal dataset: Freesurfer vs. FSL
Authors: Quilis-Sancho Javier , Fernandez-Blazquez Miguel A. , Gomez-Ramirez J 
Published: August 2020

AbstractThe study of brain volumetry and morphology of the different brain structures can determine the diagnosis of an existing disease, quantify its prognosis or even help to identify an early detection of dementia. Manual segmentation is an extremely time consuming task and automated methods are thus, gaining importance as clinical tool for diagnosis. In the last few years, AI-based segmentation has delivered, in some cases, superior results than manual segmentation, in both time and accuracy. In this study we aim at performing a comparative analysis of automated brain segmentation. In order to test the performance of automated segmentation methods, the two most commonly used software libraries for brain segmentation Freesurfer and FSL, were put to work in each of the 4028 MRIs available in the study. We find a lack of linear correlation between the segmentation results obtained from Freesurfer and FSL. On the other hand. Freesurfer volume estimates of subcortical brain structures tends to be larger than FSL estimates of same areas. The study builds on an uniquely large, longitudinal dataset of over 4,000 MRIs, all performed with identical equipment to help researchers understand what to expect from fully automated segmentation procedures.
Culture volume influences the dynamics of adaptation under long-term stationary phase
Authors: Gross Jonathan , Avrani Sarit , Katz Sophia , Hershberg Ruth 
Published: August 2020

AbstractEscherichia coliand many other bacterial species, which are incapable of sporulation, can nevertheless survive within resource exhausted media by entering a state termed long-term stationary phase (LTSP). We have previously shown thatE. colipopulations adapt genetically under LTSP in an extremely convergent manner. Here we examine how the dynamics of LTSP genetic adaptation are influenced by varying a single parameter of the experiment - culture volume. We find that culture volume affects survival under LTSP, with viable counts decreasing as volumes increase. Across all volumes, mutations accumulate with time, and the majority of mutations accumulated demonstrate signals of being adaptive. However, positive selection appears to affect mutation accumulation more strongly at higher, compared to lower volumes. Finally, we find that several similar genes are likely involved in adaptation across volumes. However, the specific mutations within these genes that contribute to adaptation can vary in a consistent manner. Combined, our results demonstrate how varying a single parameter of an evolutionary experiment can substantially influence the dynamics of observed adaptation.
FGF signaling induces mesoderm in members of Spiralia
Authors: Andrikou Carmen , Hejnol Andreas 
Published: August 2020

AbstractFGF signaling is involved in mesoderm induction in deuterostomes, but not in flies and nematodes, where it has a role in mesoderm patterning and migration. However, comparable studies in other protostomic taxa are missing in order to decipher whether this mesoderm-inducing function of FGF extends beyond the lineage of deuterostomes. Here, we investigated the role of FGF signaling during mesoderm development in three species of lophophorates, a clade within the protostome group Spiralia. Our gene expression analyses show that the molecular patterning of mesoderm development is overall conserved between brachiopods and phoronids, but the spatial and temporal recruitment of transcription factors differs significantly. Moreover, inhibitor experiments demonstrate that FGF signaling is involved in mesoderm formation, morphogenetic movements of gastrulation and posterior axial elongation. Our findings suggest that the inductive role of FGF in mesoderm possibly predates the origin of deuterostomes.
Use of target-displaying magnetized yeast in screening mRNA display peptide libraries to identify ligands
Authors: Bowen John , Bacon Kaitlyn , Reese Hannah , Rao Balaji M. , Menegatti Stefano 
Published: August 2020

AbstractThis work presents the first use of yeast-displayed protein targets for screening mRNA display libraries of cyclic and linear peptides. The WW domains of Yes-Associated Protein 1 (WW-YAP) and mitochondrial import receptor subunit TOM22 were adopted as protein targets. Yeast cells displaying WW-YAP or TOM22 were magnetized with iron oxide nanoparticles to enable the isolation of target-binding mRNA-peptide fusions. Equilibrium adsorption studies were conducted to estimate the binding affinity (KD) of selected WW-YAP-binding peptides: KD values of 37 μM and 4 μM were obtained for cyclo[M-AFRLC-K] and its linear cognate, and 40 μM and 3 μM for cyclo[M-LDFVNHRSRG-K] and its linear cognate, respectively. TOM22-binding peptide cyclo[M-PELNRAI-K] was conjugated to magnetic beads and incubated with yeast cells expressing TOM22 and luciferase. A luciferase-based assay showed a 4.5-fold higher binding of TOM22+ yeast compared to control cells. This work demonstrates that integrating mRNA and yeast display accelerates the discovery of biospecific peptides.
Open Science Saves Lives: Lessons from the COVID-19 Pandemic
Authors: Besançon Lonni , Peiffer-Smadja Nathan , Segalas Corentin , Jiang Haiting , Masuzzo Paola , Smout Cooper , Billy Eric , Deforet Maxime , Leyrat Clémence 
Published: August 2020

AbstractIn the last decade Open Science principles have been successfully advocated for and are being slowly adopted in different research communities. In response to the COVID-19 pandemic many publishers and researchers have sped up their adoption of Open Science practices, sometimes embracing them fully and sometimes partially or in a sub-optimal manner. In this article, we express concerns about the violation of some of the Open Science principles and its potential impact on the quality of research output. We provide evidence of the misuses of these principles at different stages of the scientific process. We call for a wider adoption of Open Science practices in the hope that this work will encourage a broader endorsement of Open Science principles and serve as a reminder that science should always be a rigorous process, reliable and transparent, especially in the context of a pandemic where research findings are being translated into practice even more rapidly. We provide all data and scripts athttps://osf.io/renxy/.
Immunoreactive peptide maps of SARS-CoV-2 and other human coronaviruses
Authors: Mishra Nischay , Huang Xi , Joshi Shreyas , Guo Cheng , Ng James , Thakkar Riddhi , Wu Yongjian , Dong Xin , Li Qianlin , Pinapati Richard , Sullivan Eric , Caciula Adrian , Tokarz Rafal , Briese Thomas , Lu Jiahai , Lipkin W. Ian 
Published: August 2020

AbstractSerodiagnosis of SARS-CoV-2 infection is impeded by immunological cross-reactivity to the human coronaviruses (HCoV) SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. Here we report the identification of humoral immune responses to SARS-CoV-2 and other HCoV peptides that can be used to detect asymptomatic, mild and, severe SARS-CoV-2 infections, and may enable the discovery of biomarkers for immunity following infection or vaccination.
Homologous recombination defects in Shwachman-Diamond syndrome and Diamond-Blackfan anemia
Authors: Asik Elif , Chatterjee Nimrat , Bertuch Alison A. 
Published: August 2020

ABSTRACTShwachman-Diamond syndrome (SDS) and Diamond-Blackfan anemia (DBA) are ribosomopathies characterized by impaired hematopoiesis and cancer predisposition. The mechanisms underlying cancer predisposition in these disorders are not well understood. We found that LCLs derived from patients with SDS or DBA had a prolonged DNA damage response and hypersensitivity to ionizing radiation, suggesting impaired DNA double strand break (DSB) repair. Consistent with this, depletion of SBDS and RPS19, the most common etiologic factors in SDS and DBA, respectively, resulted in reduced homologous recombination (HR) in HCT116 and U2OS cells. Surprisingly, depletion of EFL1, which functions with SBDS in ribosome biogenesis, did not impair HR and depletion of eIF6, which restores ribosome joining in SBDS-depleted cells, did not rescue the HR defect associated with SBDS depletion. Instead, we found SBDS and RPS19 recruitment to sites of DSBs suggesting that SBDS and RPS19 have more proximate roles in regulating HR, independent of their ribosomal functions. We propose that reduced HR shifts DSB repair toward error-prone NHEJ and this may contribute to oncogenesis in SDS and DBA. Additionally, we found SBDS and RPS19 depleted cells were hypersensitive to PARP inhibition, potentially uncovering a therapeutic target for SDS- and DBA-associated malignancies.
Machine learning reveals time-varying microbial predictors with complex effects on glucose regulation
Authors: Aasmets Oliver , Lüll Kreete , Lang Jennifer M. , Pan Calvin , Kuusisto Johanna , Fischer Krista , Laakso Markku , Lusis Aldons J. , Org Elin 
Published: August 2020

AbstractThe incidence of type 2 diabetes (T2D) has been increasing globally and a growing body of evidence links type 2 diabetes with altered microbiota composition. Type 2 diabetes is preceded by a long pre-diabetic state characterized by changes in various metabolic parameters. We tested whether the gut microbiome could have predictive potential for T2D development during the healthy and pre-diabetic disease stages. We used prospective data of 608 well-phenotyped Finnish men collected from the population-based Metabolic Syndrome In Men (METSIM) study to build machine learning models for predicting continuous glucose and insulin measures in a shorter (1.5 year) and longer (4.5 year) period. Our results show that the inclusion of gut microbiome improves prediction accuracy for modelling T2D associated parameters such as glycosylated hemoglobin and insulin measures. We identified novel microbial biomarkers and described their effects on the predictions using interpretable machine learning techniques, which revealed complex linear and non-linear associations. Additionally, the modelling strategy carried out allowed us to compare the stability of model performances and biomarker selection, also revealing differences in short-term and long-term predictions. The identified microbiome biomarkers provide a predictive measure for various metabolic traits related to T2D, thus providing an additional parameter for personal risk assessment. Our work also highlights the need for robust modelling strategies and the value of interpretable machine learning.ImportanceRecent studies have shown a clear link between gut microbiota and type 2 diabetes. However, current results are based on cross-sectional studies that aim to determine the microbial dysbiosis when the disease is already prevalent. In order to consider microbiome as a factor in disease risk assessment, prospective studies are needed. Our study is the first study that assesses the gut microbiome as a predictive measure for several type 2 diabetes associated parameters in a longitudinal study setting. Our results revealed a number of novel microbial biomarkers that can improve the prediction accuracy for continuous insulin measures and glycosylated hemoglobin levels. These results make the prospect of using microbiome in personalized medicine promising.
Longitudinal metatranscriptomic analysis of a meat spoilage microbiome detects abundant continued fermentation and environmental stress responses during shelf life and beyond
Authors: Hultman Jenni , Johansson Per , Björkroth Johanna 
Published: August 2020

AbstractMicrobial food spoilage is a complex phenomenon associated with the succession of the specific spoilage organisms (SSO) over the course of time. We performed a longitudinal metatranscriptomic study on a modified atmosphere packaged (MAP) beef product to increase understanding of the longitudinal behavior of a spoilage microbiome during shelf life and onward. Based on the annotation of the mRNA reads, we recognized three stages related to the active microbiome that were descriptive for the sensory quality of the beef: acceptable product (AP), early spoilage (ES) and late spoilage (LS). Both the 16S RNA taxonomic assignments from the total RNA and functional annotations of the active genes showed that these stages were significantly different from each other. However, the functional gene annotations showed more pronounced difference than the taxonomy assignments. Psychrotrophic lactic acid bacteria (LAB) formed the core of the SSO according to the transcribed reads.Leuconostocspecies were the most abundant active LAB throughout the study period, whereas the activity of Streptococcaceae (mainlyLactococcus) increased after the product was spoiled. In the beginning of the experiment, the community managed environmental stress by cold-shock responses which were followed by the expression of the genes involved in managing oxidative stress. Glycolysis, pentose phosphate pathway and pyruvate metabolism were active throughout the study at a relatively stable level. However, the proportional activity of the enzymes in these pathways changed over time. For example, acetate kinase activity was characteristic for the AP stage whereas formate C-acetyltransferase transcription was associated with spoilage.ImportanceIt is generally known which organisms are the typical SSO in foods, whereas the actively transcribed genes and pathways during microbial succession are poorly understood. This knowledge is important since better approaches to food quality evaluation and shelf life determination are needed. Thus, we conducted this study to find longitudinal markers that are connected to quality deterioration. These kind of RNA markers could be used to develop novel type of rapid quality analysis tools in the future. New tools are needed since even though SSO can be detected and their concentrations determined using the current microbiological methods, results from these analyses cannot predict how close timewise a spoilage community is from production of clear sensory defects. Main reason for this is that the species composition of a spoilage community does not change dramatically during late shelf life, whereas the ongoing metabolic activities lead to the development of notable sensory deterioration.
Estimating Prevalence and time Course of Sars-Cov-2 Based on new Hospital Admissions and PCR Tests: Relevance to Vaccination Program Tactical Planning
Authors: Gonzalez Jose E. 
Published: August 2020

ABSTRACTData posted in the COVID 19 tracking website for RT-PCR (PCR) results and hospital admissions are used to estimate the time course of the SARS-CoV-2 pandemic in the United States (1) and individual states. Hospital admissions mitigate positive sampling bias in PCR tests since these were limited in numbers initially. Additionally, their intent was as a diagnostic rather than a surveying tool.By September 17, the United States’ cumulative recovered population is estimated at 45% or 149 million. The remaining susceptible population is 55%, or 50%, excepting the currently infected 5% population. The estimated mortality rate of the cumulative of the total affected population is 0.13% death.States have followed diverse epidemic time courses. New Jersey and New York show SARS-CoV-2 prevalence of 95% and 82%, respectively. Likewise, each state exhibits relatively low current positive PCR results at 1.2 % and 0.8%. Also, these states show about twice the mortality rate of the nation. By comparison, Florida, California, and Texas showed recovered populations percent around 50%, and higher current PCR positive test results ranging from 5% to 9%.This novel approach provides an improved source of information on the pandemic’s full-time course in terms of precision and accuracy in contrast to serological testing, which only views a narrow time slice of its history due to the transient nature of the antibody response and its graduated expression dependency on the severity of the disease. The deficiency of serological testing to estimate the recovered population is made even more acute due to the large proportion of asymptomatic and sub-clinical cases in the COVID-19 pandemic (2,3). T-cell testing, reputedly capable of long-term detection of previously infected individuals, will provide a complete view of the recovered population when it becomes available for large scale use.This New Hospital Admission based method informs a more effective and efficient deployment of a vaccination program since it provides not only a reliable estimate of the susceptible population by state, but it can also provide visibility down to the county level based on COVID-19 hospitalization record independent of PCR testing.
“Come together”: a thematic analysis of experiences with belonging
Authors: Ogundipe Esther , Sælør Knut Tore , Dybdahl Kenneth , Davidson Larry , Biong Stian 
Published: August 2020

Purpose
The purpose of this paper is to explore, describe and interpret two research questions: How do persons with co-occurring mental health and substance abuse problems, living in supportive housing, experience belonging? How do residential support staff experience promoting a sense of belonging for persons with co-occurring mental health and substance abuse problems, living in a supportive housing?

Design/methodology/approach
Individual semi-structured interviews were conducted with five persons with co-occurring mental health and substance abuse problems living in supportive housing in a Norwegian district. In addition, one semi-structured focus group was conducted with nine residential support staff. All interviews were transcribed verbatim and analyzed using thematic analysis.

Findings
Analysis resulted in three main themes: “I do not go to sleep in my pajamas”, “Do I have a choice?” and “Be kind to each other”.

Research limitations/implications
More research on how inclusive practices that are commonly described in guidelines actually affect the experience of residents and residential support staff is needed.

Practical implications
Practices that incorporate a communal and contextual understanding when assigning supportive housing are warranted.

Originality/value
By paying attention to the components of social recovery, this paper provides a nuanced understanding of how persons with co-occurring mental health and substance abuse problems, living in supportive housing, experience belonging. In addition, residential support staffs’ experiences with promoting a sense of belonging for this group are explored.
New novel food regulation and collaboration for innovation
Authors: Grimsby Sveinung 
Published: August 2020

PurposeThe purpose of this paper was to study the novel food (NF) industry in Europe and how regulations have affected companies' collaboration and openness towards other actors during new product development. The research question, therefore, was “How do the European NF regulations affect radical innovation in the food industry?”.Design/methodology/approachA multiphase mixed-methods design was used to combine three sets of data as follows: the NF applications and copies of these from 1997 to 2018; the applications in the first 18 months of the revised NF regulation period after 2018 and interviews with six NF applicant companies and seven experts on NF.FindingsInteractions with research and development (R&D) suppliers appear to be common during development of NF products for companies of all sizes. Ownership of knowledge and a conscious intellectual property rights strategy are important for companies' openness during radical innovation and collaboration. The decentralised NF regulations from 1997 to 2017, with reduced possibilities for data protection, prevented innovation. However, both old and new NF regulations facilitate easy routes for second-to-market approach. Companies of all sizes apply for NF-approved products under the new NF regulations, which ensure data protection.Practical implicationsFuture NF pioneers, food R&D suppliers and food-industry policymakers will benefit from open innovation and NF insights by gaining an understanding of NF regulations and insight into how a policy with open governance affects collaboration and co-creation.Originality/valueThe NF regulations and their effect on radical food innovation have not previously been studied according to innovation management theory. Understanding various forms of selective partnership and collaboration among actors in the food industry is valuable for future growth.
News media influence on public trust in bike-sharing operators in Singapore
Authors: Wong Leonard , Tan Lyon , Wong Rachel , Yeo Su Lin 
Published: August 2020

PurposeThe overnight introduction of tens of thousands of dockless bike-share bicycles in Singapore with its indiscriminate parking drew the attention of the media, which generated extensive news reports on the activities carried out by bike-sharing operators. Given the meteoric rise and fall of the industry, this study examines the influence of agenda-setting of news reporting on the public’s perception of the industry and the impact on the firms’ corporate reputation.Design/methodology/approachUtilizing the Reputation Quotient Index, the study content analyzed 147 textual data of online reports which were crawled over two years between 2017 and 2018 from six mainstream news organizations.FindingsOur findings showed that the news reports carried more negative frames in the headlines and body content. It also found that only five out of six dimensions of the Index were emphasized with varying degrees of importance, indicating that the corporate reputation as determined by the media reports did not collectively represent the operators’ past actions and results with valued outcomes.Practical implicationsPractical implications discussed included the need to integrate corporate strategies into public relations programs and the importance of engaging the media to demonstrate congruence between business objectives and positive social impact on society.Originality/valueAlthough the study limited its data collection only to online media reports, it is one of the few research to provide empirical evidence concerning the media’s influence on the public’s perceptions and reputation of the nascent bike-sharing industry.