bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step
Authors: Arumugam Arunkumar , Wong Season 
Published: April 2020

ABSTRACTQuantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection.1–4It has been used by the Centers for Disease Control and Prevention (CDC) and several other companies in their Emergency Use Authorization (EUA) assays. With many PCR-based molecular assays, an extraction step is routinely used as part of the protocol. This step can take up a significant amount of time and labor, especially if the extraction is performed manually. Long assay time, partly caused by slow sample preparation steps, has created a large backlog when testing patient samples suspected of COVID-19. Using flu and RSV clinical specimens, we have collected evidence that the RT-qPCR assay can be performed directly on patient sample material from a nasal swab immersed in virus transport medium (VTM) without an RNA extraction step. We have also used this approach to test for the direct detection of SARS-CoV-2 reference materials spiked in VTM. Our data, while preliminary, suggest that using a few microliters of these untreated samples still can lead to sensitive test results. If RNA extraction steps can be omitted without significantly affecting clinical sensitivity, the turn-around time of COVID-19 tests and the backlog we currently experience can be reduced drastically. Next, we will confirm our findings using patient samples.
PremPRI: Predicting the Effects of Single Mutations on Protein-RNA Interactions
Authors: Zhang Ning , Lu Haoyu , Chen Yuting , Zhu Zefeng , Yang Qing , Wang Shuqin , Li Minghui 
Published: April 2020

ABSTRACTProtein-RNA interactions are crucial for many cellular processes, such as protein synthesis and regulation of gene expression. Missense mutations that alter protein-RNA interaction may contribute to the pathogenesis of many diseases. Here we introduce a new computational method PremPRI, which predicts the effects of single mutations occurring in RNA binding proteins on the protein-RNA interactions by calculating the binding affinity changes quantitatively. The multiple linear regression scoring function of PremPRI is composed of 11 sequence- and structure-based features, and is parameterized on 248 mutations from 50 protein-RNA complexes. Our model shows a good agreement between calculated and experimental values of binding affinity changes with Pearson correlation coefficient of 0.72 and the corresponding root-mean-square error of 0.76 kcal mol−1, outperforming three other available methods. PremPRI can be used for finding functionally important variants, understanding the molecular mechanisms, and designing new protein-RNA interaction inhibitors. PremPRI is freely available athttp://lilab.jysw.suda.edu.cn/research/PremPRI/.
Diminished adherence ofBiomphalaria glabrataembryonic cell line to sporocysts ofSchistosoma mansonifollowing programmed knockout of the allograft inflammatory factor
Authors: Coelho Fernanda Sales , Rodpai Rutchanee , Miller André , Karinshak Shannon E. , Mann Victoria H. , Santos Carvalho Omar dos , Caldeira Roberta Lima , de Moraes Mourão Marina , Brindley Paul J. , Ittiprasert Wannaporn 
Published: April 2020

AbstractBackgroundLarval development in an intermediate host gastropod snail of the genusBiomphalariais an obligatory component of the life cycle ofSchistosoma mansoni. Understanding of the mechanism(s) of host defense may hasten the development of tools that block transmission of schistosomiasis. The allograft inflammatory factor 1, AIF, which is evolutionarily conserved and expressed in phagocytes, is a marker of macrophage activation in both mammals and invertebrates. AIF enhances cell proliferation and migration. The embryonic cell line, termed Bge, fromBiomphalaria glabratais a versatile resource for investigation of the snail-schistosome relationship since Bge exhibits a hemocyte-like phenotype. Hemocytes perform central roles in innate and cellular immunity in gastropods and in some cases can kill the parasite. However, the Bge cells do not kill the parasitein vitro.MethodsBge cells were transfected by electroporation with plasmid pCas-BgAIFx4, encoding the Cas9 nuclease and a guide RNA specific for exon 4 of theB. glabrataAIF (BgAIF) gene. Transcript levels for Cas9 and forBgAIF were monitored by quantitative reverse-transcription-PCR and, in parallel, adhesion of gene-edited Bge cells during co-culture with of schistosome sporocysts was assessed.ResultsGene knockout manipulation induced gene-disrupting indels, frequently 1-2 bp insertions and/or 8-30 bp deletions, at the programmed target site; a range from 9 to 17% of the copies of theBgAIF gene in the Bge population of cells were mutated. Transcript levels forBgAIF were reduced by up to 73% (49.5±20.2% S.D,P≤ 0.05, n =12). Adherence byBgAIF gene-edited (ΔBgAIF) Bge to sporocysts diminished in comparison to wild type cells, although cell morphology did not change. Specifically, as scored by a semi-quantitative cell adherence index (CAI), fewer ΔBgAIF than control wild type cells adhered to sporocysts; control CAI, 2.66±0.10, ΔBgAIF, 2.30±0.22 (P≤ 0.01).ConclusionThe findings supported the hypothesis thatBgAIF plays a role in the adherence ofB. glabratahemocytes to sporocysts during schistosome infectionin vitro. This demonstration of the activity of programmed gene editing will enable functional genomics approaches using CRISPR/Cas9 to investigate additional components of the snail-schistosome host-parasite relationship.
The Harsh Microenvironment in Early Breast Cancer Selects for a Warburg Phenotype
Authors: Damaghi Mehdi , West Jeffrey , Robertson-Tessi Mark , Xu Liping , Ferrall-Fairbanks Meghan C. , Stewart Paul A. , Persi Erez , Fridley Brooke L. , Altrock Philipp M. , Gatenby Robert A. , Sims Peter A. , Anderson Alexander R. A. , Gillies Robert J. 
Published: April 2020

AbstractThe harsh microenvironment of ductal carcinomain situ(DCIS) exerts strong evolutionary selection pressures on cancer cells. We hypothesize that the poor metabolic conditions near the ductal center foment the emergence of a Warburg Effect (WE) phenotype, wherein cells rapidly ferment glucose to lactic acid, even in normoxia. To test this hypothesis, we subjected pre-malignant breast cancer cells to different microenvironmental selection pressures using combinations of hypoxia, acidosis, low glucose, and starvation for many months, and isolated single clones for metabolic and transcriptomic profiling. The two harshest conditions selected for constitutively expressed WE phenotypes. RNA-seq analysis of WE clones identified the transcription factors NFкB and KLF4 as potential inducers of the WE phenotype. NFкB was highly phosphorylated in the glycolytic clones. In stained DCIS samples, KLF4 expression was enriched in the area with the harshest microenvironmental conditions. We simulatedin vivoDCIS phenotypic evolution using a mathematical model calibrated from thein vitroresults. The WE phenotype emerged in the poor metabolic conditions near the necrotic core. We propose that harsh microenvironments within DCIS select for a Warburg phenotype through constitutive transcriptional reprogramming, thus conferring a survival advantage and facilitating further growth and invasion.
A dCas9/CRISPR-based targeting system identifies a central role for Ctf19 in kinetochore-derived suppression of meiotic recombination
Authors: Kuhl Lisa-Marie , Makrantoni Vasso , Recknagel Sarah , Vaze Animish N. , Marston Adele L. , Vader Gerben 
Published: April 2020

AbstractIn meiosis, crossover formation between homologous chromosomes is essential for faithful segregation. However, improperly controlled or placed meiotic recombination can have catastrophic consequences on genome stability. Specifically, within centromeres and surrounding regions (i.e.pericentromeres), crossovers are associated with chromosome missegregation and developmental aneuploidy. In organisms ranging from yeast to humans, crossovers are repressed within (peri)centromeric regions. We previously identified a key role for the multi-subunit, kinetochore-associated Ctf19 complex (Ctf19c; the budding yeast equivalent of the human CCAN) in regulating pericentromeric crossover formation. Here, we develop a dCas9/CRISPR-based system that allows ectopic targeting of Ctf19c-subunits to a non-centromeric locus during meiosis. Using this approach, we query sufficiency in meiotic crossover suppression, and identify Ctf19 (the budding yeast homologue of vertebrate CENP-P) as a central mediator of kinetochore-associated crossover control. We show that the effect of Ctf19 is encoded in its NH2-terminal tail, and depends on residues known to be important for the recruitment of the Scc2-Scc4 cohesin regulator to kinetochores. We thus reveal a crucial determinant that links kinetochores to meiotic recombinational control. This work provides insight into localized control of meiotic recombination. Furthermore, our approach establishes a dCas9/CRISPR-based experimental platform that can be utilized to investigate and locally manipulate meiotic crossover control. This platform can easily be adapted in order to investigate other aspects of localized chromosome biology.
How to avoid the tragedy of alternative food networks (AFNs)? The impact of social capital and transparency on AFN performance
Authors: De Bernardi Paola , Bertello Alberto , Venuti Francesco , Foscolo Enrico 
Published: April 2020

PurposeAlternative food networks (AFNs) have recently emerged in the food landscape as new ways of food production, distribution and consumption which are alternatives to the traditional food system. Drawing on the tragedy of the commons, this paper aims to test the role played by social capital and transparency in reducing customer's lethargy and thus enhancing AFN performance in terms of frequency and quantity of purchases made by customers.Design/methodology/approachAn ordered probit model was used to analyse data from a strong database of 2,115 Italian AFN customers. Given the novelty of the topic, the quantitative survey was anticipated by a preliminary qualitative study based on in-depth interviews, focus groups and participant observation.FindingsCustomers play an active role in AFN communities, co-creating value together with the other actors of the network. The two independent variables tested in this model, social capital and transparency, positively and significantly affect customers' quantity and frequency of purchases within AFNs, reducing the occurrence of the tragedy of commons.Originality/valueTo the authors' knowledge, this study represents one of the first attempts to measure, through a quantitative method, the effect of performance drivers (i.e. social capital and transparency) on AFN performance. Theoretical, managerial and policy implications will be thoroughly presented and discussed along the paper.
Utilizing short version big five traits on crowdsouring
Authors: Igawa Kousaku , Higa Kunihiko , Takamiya Tsutomu 
Published: April 2020

PurposeThe purpose of this paper is to examine the efficacy of the Japanese ten-item personality inventory (TIPI-J), a short version of the big five (BF) questionnaire, on crowdsourcing. The BF traits are indicators of personality and are said to be an effective predictor of study performance in various occupations. BF can be used in crowdsourcing to predict crowd workers’ performance; however, it will be difficult to use in practice for two reasons like the time-and-effort issue and the bias issue. In this study, an empirical analysis is conducted on crowdsourcing to examine if TIPI-J can solve those issues.Design/methodology/approachTo investigate the issues, two tasks are posted on a crowdsourcing provider. Both TIPI-J and full version BF are conducted before and after selecting crowd workers. Structural validity and convergence validity are tested with correlation analysis between before (TIPI-J) and after (full version BF) data to examine the bias issue. Additionally, those correlations are compared with previous study and significances are examined.FindingsThe correlations in “conscientiousness” is 0.45-0.50, respectively, compared with a previous study, those two correlations did not show significance. This indicates that no clear bias exists.Originality/valueThis is the first research to investigate the efficacy of TIPI-J on crowdsourcing and showed that TIPI-J can be a useful tool for predicting crowd workers’ performance and thus it can help to select appropriate crowd workers.
Coexisting attractors, chaos control and synchronization in a self-exciting homopolar dynamo system
Authors: Chen Xingrong , Xiao Li , Kingni Sifeu Takougang , Moroz Irene , Wei Zhouchao , Jahanshahi Hadi 
Published: April 2020

PurposeThe purpose of this paper is to investigate coexisting attractors, chaos control and synchronization in a self-exciting homopolar dynamo system in this paper.Design/methodology/approachTwo single controllers are designed and added to the proposed 3D autonomous chaotic system, and its stability at zero equilibrium point is guaranteed by applying an appropriate control signal based on the Lyapunov stability theory.FindingsNumerical simulations reveal that the proposed 3D dynamo system exhibits periodic oscillations, double-scroll chaotic attractors and coexisting attractors. Finally, a single controller is designed for the global asymptotic synchronization of a unidirectionally coupled identical 3D autonomous chaotic system.Originality/valueThe derived results of this paper are new and complement some earlier works. The innovation concludes two points in this paper; coexisting attractors are foundthe and an appropriate control signal based on the Lyapunov stability theory is established. The ideas of this paper can be applied to investigate some other homopolar dynamo systems.
The mechanism behind informational fairness and project performance relationship: evidence from Pakistani construction organizations
Authors: Khattak Sumreen Masood , Iqbal Muhammad Zahid , Ikramullah Malik , Raziq Muhammad Mustafa 
Published: April 2020

PurposeThis study examines the relationship between employees' perceptions of informational fairness and project performance. Furthermore, it examines if this relationship is sequentially mediated by (1) knowledge sharing and role clarity and (2) communication openness and role clarity.Design/methodology/approachData are collected from 302 full-time employees of seven project-based construction organizations in Pakistan. Data are analyzed through variance-based structural equation modeling technique and the Preacher and Hayes' bootstrapping procedure.FindingsResults indicate that project employees' perceptions of informational fairness positively predict project performance. Moreover, this relationship is sequentially mediated by (1) communication openness and role clarity and (2) knowledge sharing and role clarity.Originality/valueThis study provides further insights on the informational fairness and project performance relationship by examining their underlying mechanisms. It draws on the much ignored context of Pakistan, and offers some implications for managers and researchers with regard to how behavioral factors may further enhance project performance.
Why do borrowers default on online loans? An inquiry of their psychology mechanism
Authors: Wang Xiaolun , Xu Yunjie Calvin , Lu Tian , Zhang Chenghong 
Published: April 2020

PurposeIn the online microloan market, the ability to evaluate the credit risk of borrowers is key to business success. Based on the general strain theory, this study proposes a contextualized two-stage model with stress factors, negative affects and constraint factors to explain the psychological mechanism of borrowers' default behaviors.Design/methodology/approachAn online survey is conducted to test the hypotheses. We collect and analyze 713 valid responses through a structural equation model.Findings(1) Economic and social strains experienced by borrowers can cause four types of negative affects: life dissatisfaction, perceived unfairness, inferiority feeling and loneliness; (2) Both strains and negative affects have a considerable effect on borrowers' default intention; (3) Moral norm plays a negative moderating role in the relationship between strains, negative affects and default behavior, whereas perceived deterrence shows a strong main effect.Originality/value(1) This study introduces the GST from sociology and criminology, and contextualizes it in the microloan context to explain default behavior; (2) This study provides a comprehensive and staged psychological mechanism to explain deviant behavior; (3) This study bears critical implications for the current practice in credit assessment and default prevention.
Natural convection of Casson fluid in a square enclosure
Authors: Aghighi Mohammad Saeid , Metivier Christel , Masoumi Hamed 
Published: April 2020

PurposeThe purpose of this paper is to analyze the natural convection of a yield stress fluid in a square enclosure with differentially heated side walls. In particular, the Casson model is considered which is a commonly used model.Design/methodology/approachThe coupled conservation equations of mass, momentum and energy related to the two-dimensional steady-state natural convection within square enclosures are solved numerically by using the Galerkin's weighted residual finite element method with quadrilateral, eight nodes elements.FindingsResults highlight a small degree of the shear-thinning in the Casson fluids. It is shown that the yield stress has a stabilizing effect since the convection can stop for yield stress fluids while this is not the case for Newtonian fluids. The heat transfer rate, velocity and Yc obtained with the Casson model have the smallest values compared to other viscoplastic models. Results highlight a weak dependence of Yc with the Rayleigh number: Yc∼Ra0.07. A supercritical bifurcation at the transition between the convective and the conductive regimes is found.Originality/valueThe originality of the present study concerns the comprehensive and detailed solutions of the natural convection of Casson fluids in square enclosures with differentially heated side walls. It is shown that there exists a major difference between the cases of Casson and Bingham models, and hence using the Bingham model for analyzing the viscoplastic behavior of the fluids which follow the Casson model (such as blood) may not be accurate. Finally, a correlation is proposed for the mean Nusselt number Nu¯.
A meta‐analysis of tract‐based spatial statistics studies examining white matter integrity in cocaine use disorder
Authors: Suchting Robert , Beard Charlotte L. , Schmitz Joy M. , Soder Heather E. , Yoon Jin H. , Hasan Khader M. , Narayana Ponnada A. , Lane Scott D. 
Published: April 2020

AbstractTract‐based spatial statistics (TBSS) of diffusion tensor imaging (DTI) studies have consistently shown diminished white matter (WM) integrity for individuals with cocaine use disorder (CUD). The present study used seed‐based d mapping (SDM) to determine the extent to which a systematic difference in the WM integrity of cocaine users may exist (as compared with that of healthy controls). Articles from 2006 (when TBSS was first developed) to present were reviewed, with eight selected for inclusion. Meta‐analysis found lower fractional anisotropy (FA) in the genu of the corpus callosum for cocaine users, with a small‐to‐moderate peak effect size (Hedge's g = −0.331). Sensitivity analyses mostly supported the robustness of the obtained difference. Differences detected at exploratory thresholds for significance suggested insult to WM integrity extending beyond the corpus callosum. The present results compliment a previous region‐of‐interest (ROI)‐based meta‐analysis of DTI studies in individuals with CUD. These findings have significant implications for the potential role of neuroprotective agents in the treatment of CUD and merit additional iteration as more studies accrue in the literature.
Achieving therapeutic gains for regional youth with emergent mental health issues through parental family system–based groups: Findings from a qualitative study
Authors: Hurley John , Lawler Madeleine , Bray Angeline , Oeding‐Erdel Nagina 
Published: April 2020

AbstractObjectiveThis paper reports findings from a study that sought to better understand the experiences of parents and their children with emergent mental health challenges following the parent's participation in a nurse‐led therapeutic group.DesignThis was an explorative qualitative study using semi‐structured interviews which were then thematically analysed.SettingFindings from this single‐site study are drawn from regional Australia.ParticipantsTwenty parents and seven of their children aged between 13 and 24.InterventionsFamily systems based therapeutic group intervention delivered to the parents of young people attending headspace.Main outcome measureIn line with qualitative research approaches, the participants lived experience was the outcome measure.ResultThree key themes were found in the data: (a) improved parent‐child relationships, (b) understanding and being understood and (c) multi‐generational perspectives.ConclusionRegional and remote regions are challenged with comparatively fewer and less diverse services for youth mental health than in urban centres. Findings from this exploratory study highlight that young people can experience therapeutic gains where their parents are the recipients of the intervention. Recommendations from these findings include pursuing further research on the therapeutic gains of parental family system‐based groups.
Development of a 1‐year risk‐prediction nomogram for good functional response with anti‐VEGF agents in naive diabetic macular oedema
Authors: Gabrielle Pierre‐Henry , Massin Pascale , Arnould Louis , Couturier Aude , Bouché‐Pillon Jacques , Maupin Edouard , Aho‐Glele Serge , Bron Alain M. , Kodjikian Laurent , Creuzot‐Garcher Catherine 
Published: April 2020

AbstractPurposeTo develop a risk‐prediction nomogram based on baseline variables for good functional response during the 1st year of treatment with anti‐VEGF agents in naive diabetic macular oedema (DME).MethodsThis retrospective study included patients presenting naive‐DME treated with anti‐VEGF therapy at Dijon University Hospital (France) between 1 February 2012 and 31 March 2015 (derivation cohort). We studied baseline variables that had significant associations with a good functional response to anti‐VEGF agents during the 1st year of treatment. We used a program to generate a nomogram based on a binary logistic regression predictive model. Then, this nomogram was tested on data from a separate cohort of naive‐DME patients from a multicenter study involving 20 French ophthalmologic centres between January 2014 and June 2015 (validation cohort).ResultsAge, baseline BCVA and ellipsoid zone integrity on spectral‐domain optical coherence tomography (SD‐OCT) are functional prognostic factors and were used to build a nomogram. The nomogram showed excellent discrimination for good functional responders (area under the curve (AUC) = 0.906, 95% confidence interval (95% CI) = [0.849–0.964], p = 0.004). The discriminative power of this nomogram was tested on the validation cohort data, demonstrating good discrimination of good functional responders (AUC = 0.942, 95% CI = [0.898–0.986], p < 0.001).ConclusionThis nomogram provides a useful estimation of a good functional response in naive‐DME patients treated with anti‐VEGF agents.