bluuebunny/crossref_metadata_2025 huggingface dataset:
PUBLIC TRANSIT RIDERSHIP ANALYSIS DURING THE COVID-19 PANDEMIC
Authors: Ahangari Samira , Chavis Celeste , Jeihani Mansoureh
Published: October 2020

This study investigates the effect of the coronavirus (COVID-19) pandemic on public transport ridership in Baltimore and nine other U.S. cities similar to Baltimore, in terms of population and service area, during the first five months of 2020. The analysis is based on ridership numbers, vehicle revenue hours, and vehicles operated in maximum service. A compliance analysis was done between 2020 and 2019, as well as a monthly analysis of 2020 by mode and type of services. In comparison to 2019, the ridership decreases from March, the start of the pandemic, while all ten cities experienced the most decrease in ridership in April.
StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence
Authors: Gemayel Karl , Lomsadze Alexandre , Borodovsky Mark
Published: October 2020

Algorithms of ab initio gene finding were shown to make sufficiently accurate predictions in prokaryotic genomes. Nonetheless, for up to 15-25% of genes per genome the gene start predictions might differ even when made by the supposedly most accurate tools. To address this discrepancy, we have introduced StartLink+, an approach combining ab initio and multiple sequence alignment based methods. StartLink+ makes predictions for a majority of genes per genome (73% on average); in tests on sets of genes with experimentally verified starts the StartLink+ accuracy was shown to be 98-99%. When StartLink+ predictions made for a large set of prokaryotic genomes were compared with the database annotations we observed that on average the gene start annotations deviated from the predictions for ~5% of genes in AT-rich genomes and for 10-15% of genes in GC-rich genomes.
A controlled clinical effectiveness trial of multimodal cognitive rehabilitation on episodic memory functioning in older adults with traumatic brain injury (TBI)
Authors: Cisneros Eduardo , de Guise Elaine , Belleville Sylvie , McKerral Michelle
Published: October 2020

Abstract

Objectives

This study aimed to evaluate the impact of a multimodal cognitive intervention, the Cognitive Enrichment Program (CEP), on episodic memory in traumatic brain injured (TBI) older adults, as compared to an active control group that received usual care in the form of holistic rehabilitation.

Methods

The CEP’s Memory module consisted in memory strategies to promote encoding. Effectiveness was evaluated by psychometric tests (Face-name association, Word list recall, Text memory), while generalization was measured through self-reported questionnaires about daily memory functioning (Self-Evaluation Memory Questionnaire) and psychological well-being (Psychological General Well-Being Index). Measures were obtained before and after intervention, and six months later.

Results

Both groups showed improvement on most measures, but the experimental group showed greater statistically significant improvement. ANCOVA mixed model repeated measures analysis showed a strong group-by-time interaction for theFace-name associationtest, with a large effect size. A significant group-by-time interaction was obtained on three generalization self-report measures, including increased memorization of the content ofConversations, reducedSlips of attention, and increased memory ofPolitical & social Events, with moderate to large effect sizes. Clinically significant improvements were found forPsychological well-beingin the experimental group, where 50% of participants improved to the well-being category and remained stable six months later (9/17; 53%). Also, the number of experimental participants showing severe distress before CEP training (9) was reduced after intervention (5) and remained relatively stable at 6 months.

Conclusions

The CEP is a promising cognitive rehabilitation program that showed high satisfaction in participants and that can not only improve episodic memory in terms of psychometric scores, but also in daily life situations, as well as enhance psychological well-being in older individuals having sustained a TBI.
The Impact of the Affordable Care Act on Colorectal Cancer Incidence and Mortality: the case of Kaiser Permanente of Northern California
Authors: Lee Catherine , Eldridge Elizabeth H. , Reed Mary E. , Lee Jeffrey K. , Kushi Lawrence H. , Spiegelman Donna
Published: October 2020

Background

The Patient Protection and Affordable Care Act (ACA) eliminated cost sharing for preventive services, including colorectal cancer (CRC) screening for individuals aged 50 to 75 with private health insurance. The present study is the first to examine the impact of the no-cost CRC screening due to the ACA on CRC incidence and mortality.

Methods

We modeled trends in CRC incidence and CRC-related mortality in an open cohort of 2,113,283 Kaiser Permanente Northern California (KPNC) members aged 50 years and older between 2003 and 2016 using an interrupted time series design. Individual-level data were analyzed at the month-level. Analyses were adjusted for age, race/ethnicity and sex. As a sensitivity analysis, we considered a controlled approach, with a comparison group of KPNC members covered by health plans with pre-ACA zero cost-sharing for CRC screening.

Results

A total of 178,582,512 person-months were used in the analysis of CRC incidence, of which 48% occurred in the period before the ACA was passed into law (1/1/2003-3/31/2010) and 52% after (4/1/2010-12/31/2016). In primary analyses, the model for CRC incidence indicated a drop in the trend coinciding with the passage of the ACA (change in level incidence rate ratio, IRR: 0.83, 95% CI: 0.77-0.90, p-value < 0.0001), followed by a decrease in trend (change in slope IRR: 0.97/year, 95% CI: 0.93-1.00, p-value = 0.05). Results for CRC-related mortality were similar. Our controlled results indicate that free screening due to the ACA was associated with greater improvements in CRC outcomes among members previously covered by health plans with out-of-pocket costs for screening, compared to health plans with zero cost sharing for screening before the ACA went into effect.

Conclusions

We found that free CRC screening due to the ACA was associated with a decrease in age-, race/ethnicity- and sex-adjusted CRC incidence and CRC-related mortality, after accounting for contemporaneous competing interventions. Furthermore, these findings were robust to the addition of a comparison group with zero cost sharing both pre- and post-ACA.
Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis
Authors: Huang Ni , Perez Paola , Kato Takafumi , Mikami Yu , Okuda Kenichi , Gilmore Rodney C. , Domínguez Conde Cecilia , Gasmi Billel , Stein Sydney , Beach Margaret , Pelayo Eileen , Maldonado Jose , LaFont Bernard , Padilla Ricardo , Murrah Valerie , Maile Robert , Lovell Will , Wallet Shannon , Bowman Natalie M. , Meinig Suzanne L , Wolfgang Matthew C , Choudhury Saibyasachi N. , Novotny Mark , Aevermann Brian D , Scheuermann Richard , Cannon Gabrielle , Anderson Carlton , Marchesan Julie , Bush Mandy , Freire Marcelo , Kimple Adam , Herr Daniel L. , Rabin Joseph , Grazioli Alison , French Benjamin N. , Pranzatelli Thomas , Chiorini John A. , Kleiner David E. , Pittaluga Stefania , Hewitt Stephen , Burbelo Peter D. , Chertow Daniel ,   NIH COVID-19 Autopsy Consortium,   HCA Oral and Craniofacial Biological Network, Frank Karen , Lee Janice , Boucher Richard C. , Teichmann Sarah A. , Warner Blake M. , Byrd Kevin M.
Published: October 2020

Despite signs of infection, the involvement of the oral cavity in COVID-19 is poorly understood. To address this, single-cell RNA sequencing data-sets were integrated from human minor salivary glands and gingiva to identify 11 epithelial, 7 mesenchymal, and 15 immune cell clusters. Analysis of SARS-CoV-2 viral entry factor expression showed enrichment in epithelia including the ducts and acini of the salivary glands and the suprabasal cells of the mucosae. COVID-19 autopsy tissues confirmed in vivo SARS-CoV-2 infection in the salivary glands and mucosa. Saliva from SARS-CoV-2-infected individuals harbored epithelial cells exhibitingACE2expression and SARS-CoV-2 RNA. Matched nasopharyngeal and saliva samples found distinct viral shedding dynamics and viral burden in saliva correlated with COVID-19 symptoms including taste loss. Upon recovery, this cohort exhibited salivary antibodies against SARS-CoV-2 proteins. Collectively, the oral cavity represents a robust site for COVID-19 infection and implicates saliva in viral transmission.
Disruptions to schistosomiasis programmes due to COVID-19: an analysis of potential impact and mitigation strategies
Authors: Kura Klodeta , Ayabina Diepreye , Toor Jaspreet , Hollingsworth T. Deirdre , Anderson Roy M.
Published: October 2020

Background

The 2030 goal for schistosomiasis is elimination as a public health problem (EPHP), with mass drug administration (MDA) of praziquantel to school-aged children (SAC) a central pillar of the strategy. However, due to COVID-19, many mass treatment campaigns for schistosomiasis have been halted with uncertain implications for the programmes.

Method

We use mathematical modelling to explore how postponement of MDA and various mitigation strategies affect achievement of the EPHP goal for Schistosoma mansoni and S. haematobium.

Results

In moderate and some high prevalence settings, the disruption may delay the goal by up to two years. In some high prevalence settings EPHP is not achievable with current strategies, and so the disruption will not impact this. Here, increasing SAC coverage and treating adults can achieve the goal.

The impact of MDA disruption and the appropriate mitigation strategy varies according to the baseline prevalence prior to treatment, the burden of infection in adults and stage of the programme.

Conclusions

Schistosomiasis MDA programmes in medium and high prevalence areas should restart as soon as is feasible, and mitigation strategies may be required in some settings.
Impact of the COVID-19 pandemic on remote mental healthcare and prescribing in psychiatry
Authors: Patel Rashmi , Irving Jessica , Brinn Aimee , Broadbent Matthew , Shetty Hitesh , Pritchard Megan , Downs Johnny , Stewart Robert , Harland Robert , McGuire Philip
Published: October 2020

Objectives

The recent COVID-19 pandemic has disrupted mental healthcare delivery, with many services shifting from in- person to remote patient contact. We investigated the impact of the pandemic on the use of remote consultation and on the prescribing of psychiatric medications.

Design and setting

The Clinical Record Interactive Search tool (CRIS) was used to examine de-identified electronic health records (EHRs) of people receiving mental healthcare from the South London and Maudsley (SLaM) NHS Foundation Trust. Data from the period before and after the onset of the pandemic were analysed using linear regression, and visualised using locally estimated scatterplot smoothing (LOESS).

Participants

All patients receiving care from SLaM between 7th January 2019 and 20th September 2020 (around 37,500 patients per week).

Outcome measures

The number of clinical contacts (in-person, remote or non-attended) with mental healthcare professionals per week

Prescribing of antipsychotic and mood stabiliser medications per week

Results

Following the onset of the pandemic, the frequency of in-person contacts was significantly reduced compared to that in the previous year (β coefficient: −5829.6 contacts, 95% CI −6919.5 to −4739.6, p<0.001), while the frequency of remote contacts significantly increased (β coefficient: 3338.5 contacts, 95% CI 3074.4 to 3602.7, p<0.001). Rates of remote consultation were lower in older adults than in working age adults, children and adolescents. Despite this change in the type of patient contact, antipsychotic and mood stabiliser prescribing remained at similar levels.

Conclusions

The COVID-19 pandemic has been associated with a marked increase in remote consultation, particularly among younger patients. However, there was no evidence that this has led to changes in psychiatric prescribing. Nevertheless, further work is needed to ensure that older patients are able to access mental healthcare remotely.
The spatio-temporal landscape of lung pathology in SARS-CoV-2 infection
Authors: Rendeiro André Figueiredo , Ravichandran Hiranmayi , Bram Yaron , Salvatore Steven , Borczuk Alain , Elemento Olivier , Schwartz Robert Edward
Published: October 2020

Recent studies have provided insights into the pathology and immune response to coronavirus disease 2019 (COVID-19)1–8. However thorough interrogation of the interplay between infected cells and the immune system at sites of infection is lacking. We use high parameter imaging mass cytometry9targeting the expression of 36 proteins, to investigate at single cell resolution, the cellular composition and spatial architecture of human acute lung injury including SARS-CoV-2. This spatially resolved, single-cell data unravels the disordered structure of the infected and injured lung alongside the distribution of extensive immune infiltration. Neutrophil and macrophage infiltration are hallmarks of bacterial pneumonia and COVID-19, respectively. We provide evidence that SARS-CoV-2 infects predominantly alveolar epithelial cells and induces a localized hyper-inflammatory cell state associated with lung damage. By leveraging the temporal range of COVID-19 severe fatal disease in relation to the time of symptom onset, we observe increased macrophage extravasation, mesenchymal cells, and fibroblasts abundance concomitant with increased proximity between these cell types as the disease progresses, possibly as an attempt to repair the damaged lung tissue. This spatially resolved single-cell data allowed us to develop a biologically interpretable landscape of lung pathology from a structural, immunological and clinical standpoint. This spatial single-cell landscape enabled the pathophysiological characterization of the human lung from its macroscopic presentation to the single-cell, providing an important basis for the understanding of COVID-19, and lung pathology in general.
Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults
Authors: Ward Helen , Cooke Graham , Atchison Christina , Whitaker Matthew , Elliott Joshua , Moshe Maya , Brown Jonathan C , Flower Barney , Daunt Anna , Ainslie Kylie , Ashby Deborah , Donnelly Christl , Riley Steven , Darzi Ara , Barclay Wendy , Elliott Paul ,   for the REACT study team
Published: October 2020

Background

The prevalence and persistence of antibodies following a peak SARS-CoV-2 infection provides insights into its spread in the community, the likelihood of reinfection and potential for some level of population immunity.

Methods

Prevalence of antibody positivity in England, UK (REACT2) with three cross-sectional surveys between late June and September 2020. 365104 adults used a self-administered lateral flow immunoassay (LFIA) test for IgG. A laboratory comparison of LFIA results to neutralization activity in panel of sera was performed.

Results

There were 17,576 positive tests over the three rounds. Antibody prevalence, adjusted for test characteristics and weighted to the adult population of England, declined from 6.0% [5.8, 6.1], to 4.8% [4.7, 5.0] and 4.4% [4.3, 4.5], a fall of 26.5% [-29.0, −23.8] over the three months of the study. There was a decline between rounds 1 and 3 in all age groups, with the highest prevalence of a positive result and smallest overall decline in positivity in the youngest age group (18-24 years: −14.9% [-21.6, −8.1]), and lowest prevalence and largest decline in the oldest group (75+ years: −39.0% [-50.8, −27.2]); there was no change in antibody positivity between rounds 1 and 3 in healthcare workers (+3.45% [-5.7, +12.7]).

The decline from rounds 1 to 3 was largest in those who did not report a history of COVID-19, (−64.0% [-75.6, −52.3]), compared to −22.3% ([-27.0, −17.7]) in those with SARS-CoV-2 infection confirmed on PCR.

Discussion

These findings provide evidence of variable waning in antibody positivity over time such that, at the start of the second wave of infection in England, only 4.4% of adults had detectable IgG antibodies using an LFIA. Antibody positivity was greater in those who reported a positive PCR and lower in older people and those with asymptomatic infection. These data suggest the possibility of decreasing population immunity and increasing risk of reinfection as detectable antibodies decline in the population.
A quantitative exploration of symptoms in COVID-19 patients: an observational cohort study
Authors: Qu Gaojing , Chen Junwen , Huang Guoxin , Zhang Meiling , Yu Hui , Zhu Haoming , Chen Lei , Wang Dengru , Pei Bin
Published: October 2020

Background

As the spreading of the COVID-19 around the global, we investigated the characteristics and changes of symptoms in COVID-19 patients.

Methods

This was an ambispective observational cohort study, and 133 confirmed COVID-19 patients were included and all symptoms over the course were analyzed qualitatively. The symptoms, their changes over the course in the cohort and in the different clinical types, etc. were illustrated. Differences in different periods and severities were analyzed through Chi square test, association with severity was analyzed through LASSO binomial logistic regression analysis. Inter-correlation and classification of symptoms were completed. Major symptoms were screened and their changes were illustrated.

Results

A total of 43 symptoms with frequencies as 6067 in this cohort. Differences of symptoms in different stages and clinical types were significant. Expectoration, shortness of breath, dyspnea, diarrhea, poor appetite were positively but vomiting, waist discomfort, pharyngeal discomfort, acid reflux were negatively correlated with the combined-severe and critical type; dyspnea was correlated with the critical type. The 17 major symptoms were identified. The average daily frequency of symptoms per case was decreased continuously before the transition into the severe type and increased immediately one day before the transition and then decreased. It was decreased continuously before the transition date of the critical type and increased from the transition into the critical type to the next day and decreased thereafter. Dyspnea (P<0.001), shortness of breath (P<0.01) and chest distress (P<0.05) were correlated with death and their corresponding coefficient was 0.393, 0.258, 0.214, respectively.

Conclusion

The symptoms of COVID-19 patients mainly related to upper respiratory tract infection, cardiopulmonary function, and digestive system. The mild type and the early stage in other types mainly related to upper respiratory tract infection. The cardiopulmonary function and digestive system associated symptoms were found in all other types and stages. Dyspnea was correlated with critical type and dyspnea, shortness of breath, and chest distress were correlated with death. Respiratory dysfunction (or incompleteness) associated symptoms were the characteristic symptoms. The changes of symptoms did not synchronously with the changes of severity before the transition into the severe or critical type.
RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction
Authors: Ramos Thaís A. R. , Galindo Nilbson R. O. , Arias-Carrasco Raúl , da Silva Cecília F. , Maracaja-Coutinho Vinicius , do Rêgo Thaís G.
Published: October 2020

Non-coding RNAs (ncRNAs) are important players in the cellular regulation of organisms from different kingdoms. One of the key steps in ncRNAs research is the ability to distinguish coding/non-coding sequences. We applied 7 machine learning algorithms (Naive Bayes, SVM, KNN, Random Forest, XGBoost, ANN and DL) through 15 model organisms from different evolutionary branches. Then, we created a stand-alone and web server tool (RNAmining) to distinguish coding and noncoding sequences, selecting the algorithm with the best performance (XGBoost). Firstly, we used coding/non-coding sequences downloaded from Ensembl (April 14th, 2020). Then, coding/non-coding sequences were balanced, had their tri-nucleotides counts analysed and we performed a normalization by the sequence length. Thus, in total we built 180 models. All the machine learning algorithms tests were performed using 10-folds cross-validation and we selected the algorithm with the best results (XGBoost) to implement at RNAmining. Best F1-scores ranged from 97.56% to 99.57% depending on the organism. Moreover, we produced a benchmarking with other tools already in literature (CPAT, CPC2, RNAcon and Transdecoder) and our results outperformed them, opening opportunities for the development of RNAmining, which is freely available athttps://rnamining.integrativebioinformatics.me/.
LncRNA Snhg1-driven self-reinforcing regulatory network promotes cardiomyocyte cytokinesis and improves cardiac function
Authors: Li Mengsha , zheng Hao , Chen Yijin , Li Bing , Chen Guojun , Chen Xiaoqiang , Huang Senlin , He Xiang , Wei Guoquan , Xu Tong , Feng Xiaofei , Liao Wangjun , Liao Yulin , Chen Yanmei , Bin Jianping
Published: October 2020

Most of current cardiac regenerative approaches result in very limited cell division. Positive feedback loops are vital for cell division, but their role in CM regeneration remains unclear. We aimed to demonstrate that lncRNA Snhg1 formed a positive feedback loop with c-Myc to induce stable CM cytokinesis. We found that Snhg1 expression was increased in human and mouse fetal and myocardial infarction (MI) hearts, particularly in CMs. Snhg1 overexpression elicited stable CM proliferation and improved post-MI cardiac function. Antagonism of Snhg1 in neonatal mice inhibited CM proliferation and impaired cardiac repair after MI. Proliferative effect was confirmed using cardiac-specific transgenic mice. RNA pull-down assays showed that Snhg1 directly bound to PTEN and activated PI3K-Akt pathway, resulting in c-Myc activation. Chromatin immunoprecipitation experiments showed that Snhg1 expression was upregulated by c-Myc binding to the Snhg1 promoter region, indicating a positive feedback loop between c-Myc and Snhg1. In conclusion, c-Myc/Snhg1/PI3k-Akt positive feedback loop drove sustained activation of cell cycle re-entry and induced stable CM cytokinesis, and thus may be an attractive strategy for promoting heart regenerative response.

Clinical Perspectives

Most of the current cardiac regenerative approaches result in very limited cell division and little new cardiomyocyte (CM) mass. Positive feedback loops are vital for cell division, but their role in CM regeneration remain unclear. Here, we identified the long noncoding RNA Snhg1 as a driver to induce stable CM division and improve cardiac function after myocardial infarction (MI) by forming a positive feedback loop to sustain PI3K-Akt signaling activation. This finding might provide a novel therapeutic of Snhg1 as a promising regenerative approach to improve the prognosis of patients with heart failure.
Superior performance of human wastewater-associated viral markers compared to bacterial markers in tropical environments
Authors: Sangkaew Watsawan , Kongprajug Akechai , Chyerochana Natcha , Ahmed Warish , Mongkolsuk Skorn , Sirikanchana Kwanrawee
Published: October 2020

Identifying human sewage contamination via microbial source tracking (MST) marker genes has proven useful for effective water quality management worldwide; however, performance evaluations for these genes in tropical areas are limited. Therefore, this research assessed four human-associated MST marker genes in aquatic environments of Central Thailand: human polyomaviruses (JC and BK viruses [HPyVs]), bacteriophage crAssphage (CPQ_056),LachnospiraceaeLachno3, andBacteroidesBacV6-21. HPyV and crAssphage assays were highly sensitive and specific to sewage (n= 19), with no cross-detection in 120 swine, cattle, chicken, duck, goat, sheep, and buffalo composite fecal samples. Lachno3 and BacV6-21 demonstrated high sensitivity but moderate specificity; however, using both markers could improve specificity to >0.80 (max value of 1.00). The most abundant markers in sewage were Lachno3 and BacV6-21 (5.42-8.02 and non-detected-8.05 log10copies/100 mL), crAssphage (5.28-7.38 log10copies/100 mL), and HPyVs (3.66-6.53 log10copies/100 mL), respectively. HPyVs showed higher levels (up to 4.33 log10copies/100 mL) and higher detection rates (92.7%) in two coastal beaches (n= 41) than crAssphage (up to 3.51 log10copies/100 mL and 56.1%). HPyVs were also found at slightly lower levels (up to 5.10 log10copies/100 mL), but at higher detection rates (92.6%), in a freshwater canal (n= 27) than crAssphage (up to 5.21 log10copies/100 mL and 88.9%). Overall, both HPyVs and crAssphage are suggested as human sewage-associated MST markers in aquatic environments of Central Thailand. This study underlines the importance of characterizing and validating MST markers in host groups and environmental waters before including them in a water quality management toolbox.
An Eutherian-Specific microRNA Controls the Translation ofSatb2in a Model of Cortical Differentiation
Authors: Martins Manuella , Galfrè Silvia , Terrigno Marco , Pandolfini Luca , Appolloni Irene , Dunville Keagan , Marranci Andrea , Rizzo Milena , Mercatanti Alberto , Poliseno Laura , Morandin Francesco , Pietrosanto Marco , Helmer-Citterich Manuela , Malatesta Paolo , Vignali Robert , Cremisi Federico
Published: October 2020

Cerebral cortical development is controlled by key transcription factors that specify the neuronal identities in the different cortical layers. These transcription factors are crucial for the identity of the different neurons, but the mechanisms controlling their expression in distinct cells are only partially known. Here we investigate the expression and stability of the mRNAs of Tbr1, Bcl11b, Fezf2, Satb2 and Cux1 in single developing mouse cortical cells. We focus on Satb2 and find that its mRNA expression occurs much earlier than its protein synthesis and in a set of cells broader than expected, suggesting an initially tight control of its translation, which is subsequently de-repressed at late developmental stages. Mechanistically,Satb23’UTR modulates protein translation of GFP reporters during mouse corticogenesis. Byin vitropull-down ofSatb23’UTR-associated miRNAs, we select putative miRNAs responsible for SATB2 inhibition, focusing on those strongly expressed in early progenitor cells and reduced in late cells. miR-541, an Eutherian-specific miRNA, and miR-92a/b are the best candidates and their inactivation triggers robust and premature SATB2 translation in both mouse and human cortical cells. Our findings indicate that RNA interference plays a major role in the timing of cortical cell identity and may be part of the toolkit involved in specifying supra-granular projection neurons.
The distribution of mutational effects on fitness inCaenorhabditis elegansinferred from standing genetic variation
Authors: Gilbert Kimberly J. , Zdraljevic Stefan , Cook Daniel E. , Cutter Asher D. , Andersen Erik C. , Baer Charles F.
Published: October 2020

The distribution of fitness effects for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the distribution of fitness effects (DFE) from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, and non-random mating. Although inference methods aim to control for population size changes, the influence of non-random mating remains incompletely understood, despite being a common feature of many species. We report the distribution of fitness effects estimated from 326 genomes ofCaenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history ofC. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection can conspire to compromise estimates of the DFE from extant polymorphisms. These factors together tend to bias inferences towards weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species likeC. elegans. Improved methods for inferring the distribution of fitness effects are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.
Robust Optical Flow Algorithm for General, Label-free Cell Segmentation
Authors: Robitaille Michael C. , Byers Jeff M. , Christodoulides Joseph A. , Raphael Marc P.
Published: October 2020

Cell segmentation is crucial to the field of cell biology, as the accurate extraction of cell morphology, migration, and ultimately behavior from time-lapse live cell imagery are of paramount importance to elucidate and understand basic cellular processes. Here, we introduce a novel segmentation approach centered around optical flow and show that it achieves robust segmentation by validating it on multiple cell types, phenotypes, optical modalities, and in-vitro environments without the need of labels. By leveraging cell movement in time-lapse imagery as a means to distinguish cells from their background and augmenting the output with machine vision operations, our algorithm reduces the number of adjustable parameters needed for optimization to two. The code is packaged within a MATLAB executable file, offering an accessible means for general cell segmentation typically unavailable in most cell biology laboratories.
Interpreting the dynamic pathogenesis of Parkinson’s disease by longitudinal blood transcriptome analysis
Authors: Xue Gang , Wang Gang , Shi Qianqian , Wang Hui , Lv Bo-Min , Gao Min , Niu Xiaohui , Zhang Hong-Yu
Published: October 2020

Achieving an improved understanding of the temporal sequence of factors involved in Parkinson’s disease (PD) pathogenesis may accelerate drug discovery. In this study, we performed a longitudinal transcriptome analysis to identify associated genes underlying the pathogenesis of PD at three temporal phases. We firstly found that multiple initiator genes, which are related to processes of olfactory transduction and stem cell pluripotency, indicate PD risk to those subjects at the prodromal phase. And many facilitator genes involved in calcium signaling and stem cell pluripotency contribute to PD onset. We next identified 325 aggravator genes whose expression could lead to disease progression through damage to dopaminergic synapses and ferroptosis via an integrative analysis with DNA methylation. Last, we made a systematic comparison of gene expression patterns across PD development and accordingly provided candidate drugs at different phases in an attempt to prevent the neurodegeneration process.
Deficiency of the splicing factor RBM10 limits EGFR inhibitor response inEGFRmutant lung cancer
Authors: Nanjo Shigeki , Wu Wei , Karachaliou Niki , Blakely Collin M. , Suzuki Junji , Ali Siraj , Kerr D. Lucas , Olivas Victor , Shue Jonathan , Rotow Julia , Mayekar Manasi , Haderk Franziska , Chatterjee Nilanjana , Urisman Anatoly , Kirichok Yuriy , Tan Daniel S. W. , Rosell Rafael , Okimoto Ross A , Bivona Trever G.
Published: October 2020

Molecularly targeted cancer therapy has improved outcomes for cancer patients with targetable oncoproteins, such as mutantepidermal growth factor receptor(EGFR) in lung cancer. Yet, long-term patient survival remains limited because treatment responses are typically incomplete. One potential explanation for the lack of complete and durable responses is that oncogene-driven cancers with activating mutations in theEGFRoften harbor additional co-occurring genetic alterations. This hypothesis remains untested for most genetic alterations that co-occur with mutantEGFR. Here, we report the functional impact of inactivating genetic alteration of the mRNA splicing factorRBM10that co-occur with mutantEGFR. RBM10 deficiency decreased EGFR inhibitor efficacy in patient-derivedEGFRmutant tumor models. RBM10 modulated mRNA alternative splicing of the mitochondrial apoptotic regulator Bcl-x to regulate tumor cell apoptosis during treatment. Genetic inactivation ofRBM10diminished EGFR inhibitor-mediated apoptosis by decreasing the ratio of Bcl-xS-(pro-apoptotic)-to-Bcl-xL(anti-apoptotic) Bcl-x isoforms. RBM10 deficiency was a biomarker of poor response to EGFR inhibitor treatment in clinical samples. Co-inhibition of Bcl-xL and mutant EGFR overcame resistance induced by RBM10 deficiency. This study sheds light on the role of co-occurring genetic alterations, and on the impact of splicing factor deficiency in the modulation of sensitivity to targeted kinase inhibitor cancer therapy.
The Incidence and Severity of COVID-19 in Adult Professional Soccer Players
Authors: Bezuglov Eduard , Lazarev Artemii , Achkasov Evgeniy , Khaitin Vladimir , Romanova Larisa , Butovskiy Mikhail , Khokhlov Vladimir , Tsyplenko Maxim , Linskiy Alexander , Chetverikov Petr , Sugaipov Magomedtagir , Petrov Arseniy , Talibov Oleg
Published: October 2020

Introduction

At present, there are no data regarding the incidence and clinical course of COVID-19 among professional soccer players, and the studies examining putative complications of COVID-19 infections are probabilistic. Thus, examining the incidence of COVID-19 and various aspects of its clinical course in a group of adult professional soccer players would be of great practical interest.

Methods

The incidence, clinical course, and severity of COVID-19 infection, as well as the duration of treatment and return to play were studied by the questioning of the team physicians and medical records assessment in the group of adult professional soccer players representing the clubs of the Russian Premier-League (RPL) during the period of championship resumption from 01.04.2020 until 20.09.2020.

Results

COVID-19 infection was detected in 103 soccer players in the course of COVID-19 screening. This number comprises 14.5% of all soccer players which were on the rosters of RPL soccer teams and which were subject to regular COVID-19 testing.

The asymptomatic course was observed in 43.7% of cases (n=45). These players were isolated and their clinical condition was monitored closely. Clinical symptoms were observed in 56.3% of cases (n=58), the most common symptoms being fatigue, headache, fever, and anosmia.

Conclusions

COVID-19 infection was commonly diagnosed among adult professional soccer players continuously residing in Russia. However, the majority of infections had a mild course and did not impair return to regular exercise.
Automated segmentation and description of the internal morphology of human permanent teeth by means of micro-CT
Authors: Haberthür David , Hlushchuk Ruslan , Wolf Thomas Gerhard
Published: October 2020

Micro-CT is a powerful tool to analyze and visualize the internal morphology of human permanent teeth. It is increasingly used for investigation of epidemiological questions to provide the dentist with the necessary information required for successful endodontic treatment. The aim of the present paper was to propose an image processing method to automate parts of the work needed to fully describe the internal morphology of human permanent teeth.

One hundred and four human teeth were scanned on a high-resolution micro-CT using an automatic specimen changer. Python code in a Jupyter notebook was used to verify and process the scans, prepare the datasets for description of the internal morphology and to measure the apical region of he tooth.

The presented method offers an easy, non-destructive, rapid and efficient approach to scan, check and preview micro-computer tomographic datasets of a large number of teeth. It is a helpful tool for the detailed description and characterization of the internal morphology of human permanent teeth using automated segmentation by means of micro-CT with full reproducibility and high standardization.
Crystal structure of Al2.95Cr0.59, a phase closely related to the η-phase in the binary Al–Cr system
Authors: Geng Xu , Wen Bin , Fan Changzeng
Published: October 2020

The monoclinic η-phase in the binary Al–Cr system was initially named by Bradley & Lu [Bradley & Lu (1937). J. Inst. Met. 60, 319–337] as having the composition Al11Cr2 (Al:Cr ratio = 5.5:1). Its crystal structure was later refined [Cao & Kuo (2008). J. Alloys Compd.
458, 30, 319–337] to have a slightly lower Al content (Al:Cr ratio = 5.16:1). In the present work, a monoclinic phase with composition Al2.95Cr0.59 (Al:Cr ratio = 5.04:1) was obtained by high-pressure sintering (HPS) of a stoichiometric Al11Cr2 mixture. Structure analysis of this phase, hereafter named η′, revealed a close relationship to the previously reported η-Al11Cr2 structure, but with different mixed-occupied sites. Five fully occupied sites exhibit refined site occupation factors of 0.899 (5), 0.984 (4), 0.977 (5), 0.946 (4) and 0.945 (4) for the corresponding Al atoms. Moreover, there are no split Al sites in the η′-structure as reported for the η-structure. The refined chemical composition of the η′-phase revealed that it comprises two Al atoms fewer and two Cr atoms more than the previously reported η-Al11Cr2 phase.
Eco-innovation and the circular economy in the automotive industry
Authors: Maldonado-Guzmán Gonzalo , Garza-Reyes Jose Arturo , Pinzón-Castro Yesenia
Published: October 2020

Purpose

Circular economy is emerging as a new sustainability paradigm. Similarly, eco-innovation is being recognized as one of the most important mechanisms that allow the transition from a linear to a circular economy in production processes, as there is a strong relationship between eco-innovation (eco-innovation of products, processes and management) and circular economy activities. However, the relationship between eco-innovation and circular economy is an issue that has been isolated and little analyzed in the academic literature. Therefore, this research fills this gap by exploring the interdependence between eco-innovation and circular economy.

Design/methodology/approach

The research is conducted through an extensive literature review from where a research framework consisting of two measurement scales, 18 items and three hypotheses were developed. A self-administered questionnaire was distributed and 460 responses were obtained from companies in the automotive and auto parts industry in Mexico. The data obtained were analyzed through confirmatory factor analysis, descriptive statistics and structural equation modeling.

Findings

The results suggest that eco-innovation of products, process and management has a significant positive impact on the circular economy of companies in the automotive and auto parts industry.

Practical implications

The findings of this research can inform managers in the automotive sector and policymakers when formulating and deploying environmentally sustainable strategies.

Originality/value

This paper fills a research gap by expanding the limited body of knowledge that relates eco-innovation and circular economy and providing some evidence of their relationship. The research also allows the unique characteristics of eco-innovation and the circular economy to be understood within a particular context, growing in this manner the body of knowledge on this field.
Open innovation in family firms: empirical evidence about internal and external knowledge flows
Authors: Del Vecchio Pasquale , Secundo Giustina , Rubino Michele , Garzoni Antonello , Vrontis Demetris
Published: October 2020

Purpose

The purpose of this paper is to shed light on how family firms execute open innovation strategies by managing internal and external knowledge flows (KF) to provide a deeper understanding of family firms’ ability to innovate through traditions and create value across generations.

Design/methodology/approach

Empirical evidence was collected using an online survey of a sample of 208 Apulian entrepreneurs, who were members of the association of young entrepreneurs of Confindustria in the Apulia region (southern Italy).

Findings

The study derives a model that explains the most relevant factors behind the innovation processes developed by young entrepreneurs in family firms: network membership benefits; KF; track record of innovation; and the entrepreneurial attitude of employees.

Research limitations/implications

By integrating insights from different research streams, namely, innovation management, open innovation and family firms, the study provides a novel contribution to the open innovation process in family firms.

Practical implications

The study offers interpretative lenses for entrepreneurs and managers to understand the most suitable knowledge transfer process for encouraging open innovation in family firms, taking into consideration young entrepreneurs’ traditions and interpersonal skills, the KF in local ecosystems and network benefits as the main variables supporting the innovation process.

Originality/value

This study creates a link between open innovation and family firm research by providing an empirically grounded model illustrating how the innovation process is realized in family firms.
Introducing public procurement tenders as part of corporate communications: a typological analysis based on CSR reporting indicators
Authors: Knebel Sebastian , Seele Peter
Published: October 2020

Purpose

Corporations have to increasingly include corporate social responsibility (CSR) communication by responding to public procurement tenders because of the recently revised Government Procurement Agreement (GPA) concluded by the World Trade Organization (WTO). The authors argue that procurement tenders are to be seen as part of corporate communications, particularly when aligned with CSR reporting and performance indicators as proposed by the Global Reporting Initiative (GRI). The recently published ISO 20400 on sustainable procurement lacks a clear usage indication of sustainability indicators (SIs). This paper aims to close this gap.

Design/methodology/approach

The paper performs a typological analysis of sustainability indicators in a sample of 665 currently used SIs. Furthermore, the paper conceptualizes a SIs selector for Sustainable Public Procurement (SPP) which is based on the typological analysis and acknowledges recent developments in the evolution of SIs.

Findings

The SIs typology results in three indicator types. The typology leads to the conceptualization of SI’s selector for sustainable public procurement. It enables professionals to build indicators for SPP considering the context of sustainability with impact valuations and allows scholars to advance research on measurement and decision-making.

Originality/value

To the authors’ best knowledge, this is the first introduction of procurement tender processes as part of corporate communications. Furthermore, the derived typology contributes an overview of existing SIs used in CSR communication. The paper contributes a self-responsible and pragmatic approach to CSR theory as private business self-regulation and a definition of SIs for corporate communications.
Model validation of factors limiting the use of prefabricated construction systems in Turkey
Authors: Gumusburun Ayalp Gulden , Ay Ilhami
Published: October 2020

Purpose

Prefabricated construction technology enables relatively faster and easier construction of building structures at a lower project cost, providing improved quality control with minimal material waste. Despite the advantages of prefabricated construction systems, they are not extensively used in Turkey because of specific yet largely undefined challenges. Therefore, the purpose of this study aims to determine the factors currently affecting the extensive use of prefabricated construction systems in Turkey.

Design/methodology/approach

The reasons for such systems not being used extensively in Turkey were examined using responses to a questionnaire distributed amongst architects working at design firms, prefabricated-building manufacturers and contractors. The obtained survey data were statistically analysed using the SPSS 22 and LISREL 8.7 software to rank the severity of the identified challenges and determine the most critical factors.

Findings

Eight critical factors groups affecting the use of prefabricated construction systems and their associated factors were identified according the responses provided by the participants. Potential solutions and recommendations were proposed based on these factor groups that are expected facilitate the implementation of prefabricated construction systems in Turkey.

Originality/value

Little previous research has provided insight into the specific factors limiting the use of prefabricated construction systems. This study accordingly approaches the subject considering all phases of prefabricated construction systems and presents a structural model of the factors obtained by a confirmatory factor analysis for application to expand the use of prefabricated construction systems.
An evolutionary game analysis of user-pay public–private partnership projects
Authors: Song Danrong , Song Jinbo , Yuan Hehui , Fan Yu
Published: October 2020

Purpose

With the growing demand for infrastructure and public services in recent years, PPP-UP have attracted a great deal of attention. However, while the user focuses on the payment for use and the private sector is concerned with its return on investment, the public sector pays more attention to the efficient utilization of public funds. In order to analyze the willingness of each stakeholder to join PPP-UP, an evolutionary game model involving the three parties is constructed.

Design/methodology/approach

An evolutionary game model is established that considers the users and the public and private sectors in user-pay public-private-partnership projects (PPP-UP). Eight scenarios of equilibriums and the game's evolutionary stable strategies are analyzed, and the corresponding stability conditions are then obtained. A situation where all three players are willing to cooperate in theory is also examined. The key influencing parameters that affect cooperation behaviors are further discussed.

Findings

First, the results illustrate that by properly adjusting the influencing factors, the cooperation status among the three parties can be changed along with certain evolutionary trends. Second, it is hard to modify unsatisfactory evolutionary stability by small changes in both the price compensation of and the construction and operation compensation. Third, it is necessary to involve the users in the decision-making process in PPP-UP and take their demands regarding benefits and payments into account.

Originality/value

In this paper, we focus on PPP-UP to research interactions among the public and private sectors and the users. Based on the analysis of the evolutionary game, to facilitate the successful implementation and development of a project, several conditions are needed to ensure tripartite cooperation. Several recommendations are then proposed for decision-makers in PPP-UP.