bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data
Authors: Choi Jaeyong , Lee Woochan , Yoon Jung-Ki , Choi Sun Mi , Lee Chang-Hoon , Moon Hyeong-Gon , Cho Sukki , Chung Jin-Haeng , Yang Han-Kwang , Kim Jong-Il 
Published: April 2021

AbstractAlthough single-cell RNA sequencing of xenograft samples has been widely used, no comprehensive bioinformatics pipeline is available for human and mouse mixed single-cell analyses. Considering the numerous homologous genes across the human and mouse genomes, misalignment errors should be evaluated, and a new algorithm is required. We assessed the extents and effects of misalignment errors when using human and mouse combined reference data and developed a new bioinformatics pipeline with expression-based species deconvolution to minimize errors. We also evaluated false-positive signals for a species presumed to originate from ambient RNA of the other species and applied a computational method to remove them. Misaligned reads account for an average of 0.5% of total reads, but such reads were concentrated to few genes that were greatly affected. Human and mouse mixed single-cell data, analyzed using our pipeline, clustered well with unmixed data and showed higher k-nearest-neighbor batch effect test and Local Inverse Simpson’s Index scores than those derived from Cell Ranger. We also applied our pipeline to multispecies multisample single-cell library containing breast cancer xenograft tissue and successfully identified all samples using genomic array and expression. Moreover, diverse cell types in the tumor microenvironment were well captured. We present our bioinformatics pipeline for mixed human and mouse single-cell data, which can also be applied to pooled libraries to obtain cost-effective single-cell data. We also address major consideration points when analyzing multispecies single-cell data for other applications.
Development of a mini-replicon-based reverse-genetics system for rice stripe tenuivirus
Authors: Feng Mingfeng , Li Luyao , Cheng Ruixiang , Yuan Yulong , Dong Yongxin , Chen Minglong , Guo Rong , Yao Min , Xu Yi , Zhou Yijun , Wu Jianxiang , Ding Xin Shun , Zhou Xueping , Tao Xiaorong 
Published: April 2021

ABSTRACTNegative-stranded RNA (NSR) viruses include both animal- and plant-infecting viruses that often cause serious diseases in human and livestock, and in agronomic crops. Rice stripe tenuivirus (RSV), a plant NSR virus with four negative-stranded/ambisense RNA segments, is one of the most destructive rice pathogens in many Asian countries. Due to the lack of a reliable reverse-genetics technology, molecular studies of RSV gene functions and its interaction with host plants are severely hampered. To overcome this obstacle, we developed a mini-replicon-based reverse-genetics system for RSV gene functional analysis inNicotiana benthamiana. We first developed a mini-replicon system expressing RSV genomic RNA3 eGFP reporter (MR3(-)eGFP), a nucleocapsid (NP), and a codon usage optimized RNA-dependent RNA polymerase (RdRpopt), respectively. Using this mini-replicon system we determined that RSV NP and RdRpoptare indispensable for the eGFP expression from MR3(-)eGFP. The expression of eGFP from MR3(-)eGFPcan be significantly enhanced in the presence of NSs and P19-HcPro-γb. In addition, NSvc4, the movement protein of RSV, facilitated eGFP trafficking between cells. We also developed an antigenomic RNA3-based replicon inN. benthamiana.However, we found that the RSVNS3coding sequence acts as acis-element to regulate viral RNA expression. Finally, we made mini-replicons representing all four RSV genomic RNAs. This is the first mini-replicon-based reverse-genetics system for monocot-infecting tenuivirus. We believe that this mini-replicon system described here will allow the studies of RSV replication, transcription, cell-to-cell movement and host machinery underpinning RSV infection in plants.IMPORTANCEPlant-infecting segmented negative-stranded RNA (NSR) viruses are grouped into 3 genera:Orthotospovirus, TenuivirusandEmaravirus. The reverse-genetics systems have been established for members in the generaOrthotospovirusandEmaravirus, respectively. However, there is still no reverse-genetics system available forTenuivirus. Rice stripe virus (RSV) is a monocot-infecting tenuivirus with four negative-stranded/ambisense RNA segments. It is one of the most destructive rice pathogens and causes significant damages to rice industry in Asian countries. Due to the lack of a reliable reverse-genetics system, molecular characterizations of RSV gene functions and the host machinery underpinning RSV infection in plants are extremely difficult. To overcome this obstacle, we developed a mini-replicon-based reverse-genetics system for RSV inNicotiana benthamiana. This is the first mini-replicon-based reverse-genetics system for tenuivirus. We consider that this system will provide researchers a new working platform to elucidate the molecular mechanisms dictating segmented tenuivirus infections in plant.
What is the role of the environment in the emergence of novel antibiotic resistance genes? – A modelling approach
Authors: Bengtsson-Palme Johan , Jonsson Viktor , Heß Stefanie 
Published: April 2021

AbstractIt is generally accepted that intervention strategies to curb antibiotic resistance cannot solely focus on human and veterinary medicine but must also consider environmental settings. While the environment clearly has a role in the transmission of resistant bacteria, it is less clear what role it plays in the emergence of novel types of resistance. It has been suggested that the environment constitutes an enormous recruitment ground for resistance genes to pathogens, but the extent to which this actually happens is unknown. In this study, we built a model framework for resistance emergence and used the available quantitative data on the relevant processes to identify the steps which are limiting the appearance of antibiotic resistance determinants in human or animal pathogens. We also assessed the effect of uncertainty in the available data on the model results. We found that in a majority of scenarios, the environment would only play a minor role in the emergence of novel resistance genes. However, the uncertainty around this role is enormous, highlighting an urgent need of more quantitative data to understand the role of the environment in antibiotic resistance development. Specifically, more data is most needed on the fitness costs of antibiotic resistance gene (ARG) carriage, the degree of dispersal of resistant bacteria from the environment to humans, but also the rates of mobilization and horizontal transfer of ARGs. Quantitative data on these processes is instrumental to determine which processes that should be targeted for interventions to curb development and transmission of resistance.
An aging clock using metabolomic CSF
Authors: Hwangbo Nathan , Zhang Xinyu , Raftery Daniel , Gu Haiwei , Hu Shu-Ching , Montine Thomas J. , Quinn Joseph F. , Chung Kathryn A. , Hiller Amie L. , Wang Dongfang , Fei Qiang , Bettcher Lisa , Zabetian Cyrus P. , Peskind Elaine , Li Gail , Promislow Daniel E.L. , Franks Alexander 
Published: April 2021

AbstractQuantifying the physiology of aging is essential for improving our understanding of age-related disease and the heterogeneity of healthy aging. Recent studies have shown that in regression models using “-omic” platforms to predict chronological age, residual variation in predicted age is correlated with health outcomes, and suggest that these “omic clocks” provide measures of biological age. This paper presents predictive models for age using metabolomic profiles of cerebrospinal fluid from healthy human subjects, and finds that metabolite and lipid data are generally able to predict chronological age within 10 years. We use these models to predict the age of a cohort of subjects with Alzheimer’s and Parkinson’s disease and find an increase in prediction error, potentially indicating that the relationship between the metabolome and chronological age differs with these diseases. In our analysis of control subjects, we find the carnitine shuttle, sucrose, biopterin, vitamin E metabolism, tryptophan, and tyrosine to be the most associated with age. We showcase the potential usefulness of age prediction models in a small dataset (n = 85), and discuss techniques for drift correction, missing data imputation, and regularized regression which can be used to help mitigate the statistical challenges that commonly arise in this setting. To our knowledge, this work presents the first multivariate predictive metabolomic and lipidomic models for age using mass spectrometry analysis of cerebrospinal fluid.
Carbon catabolite repression in pectin digestion by phytopathogenDickeya dadantii
Authors: Martis B. Shiny , Droux Michel , Nasser William , Reverchon Sylvie , Meyer Sam 
Published: April 2021

AbstractThe catabolism of pectin from the plant cell walls plays a crucial role in the virulence of the phytopathogenDickeya dadantii. In particular, the timely expression ofpelgenes encoding major pectate lyases is essential to circumvent the plant defense systems and induce a massive pectinolytic activity during the maceration phase. While previous studies identified the role of a positive feedback loop specific to the pectin degradation pathway, here we show that thepelexpression pattern is controlled by a metabolic switch between glucose and pectin. We develop a dynamical and quantitative regulatory model of this process integrating the two main regulators CRP and KdgR related to these two sources of carbon, and reproducing the concentration profiles of the associated metabolites, cAMP and KDG respectively, quantified using a new HPLC method. The model involves only 5 adjustable parameters, and recapitulates the dynamics of these metabolic pathways during bacterial growth together with the regulatory events occurring at the promoters of two majorpelgenes,pelEandpelD. It highlights their activity as an instance of carbon catabolite repression occurring at the transcriptional regulatory level, and directly related to the virulence ofD. dadantii. The model also shows that quantitative differences in the binding properties of common regulators at these two promoters resulted in a qualitative different role ofpelDandpelEin the metabolic switch, and also likely in conditions of infection, explaining their evolutionary conservation as separate genes in this species.
Preparation of “stress-free” concanavalin A-conjugated Dynabeads® magnetic beads for CUT&Tag
Authors: Fujiwara Yasuhiro , Tanno Yuji , Sugishita Hiroki , Kishi Yusuke , Makino Yoshinori , Okada Yuki 
Published: April 2021

ABSTRACTEpigenome research has employed various methods to identify genomic location of proteins of interest, such as transcription factors and histone modifications. A recently established method called CUT&Tag uses a Protein-A Tn5 transposase fusion protein, which cuts the genome and inserts adapter sequences nearby the target protein. Throughout most of the CUT&Tag procedure, cells are held on concanavalin A (con A)-conjugated magnetic beads. Proper holding of cells would be decisive for the accessibility of Tn5 to the chromatin, and efficacy of the procedure of washing cells. However, BioMag®Plus ConA magnetic beads, used in the original CUT&Tag protocol, often exhibit poor suspendability and severe aggregation. Here, we compared the BioMag beads and Dynabeads® magnetic particles of which conjugation of con A was done by our hands, and examined the performance of these magnetic beads in CUT&Tag. Among tested, one of the Dynabeads, MyOne-T1, kept excessive suspendability in a buffer even after overnight incubation. Furthermore, the MyOne-T1 beads notably improved the sensitivity in CUT&Tag assay for H3K4me3. In conclusion, the arrangement and the selection of MyOne-T1 refine the suspendability of beads, which improves the association of chromatin with Tn5, which enhances the sensitivity in CUT&Tag assay.
Rational Selection of PCR Primer/Probe Design Sites for SARS-CoV-2
Authors: Rana Divya RSJB , Pokhrel Nischal , Dulal Santosh 
Published: April 2021

AbstractVarious reports of decreased analytical sensitivities of real-time PCR-based detection of Coronavirus Disease 2019 (COVID-19) have been associated with occurrence of mutations in the target area of primer/probe binding. Knowledge about propensities of different genes to undergo mutation can inform researchers to select optimal genes to target for the qPCR design. We analyzed supplementary data from over 45 thousand SARS-CoV-2 genomes provided by Mercatelli et al to calculate the unique and prevalent mutations in different genes of SARS-CoV-2. We found that non-structural proteins in the ORF1ab region were more conserved compared to structural genes. Further factors which need to be relied upon for proper selection of genes for qPCR design are discussed.
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks
Authors: Koehler Leman Julia , Lyskov Sergey , Lewis Steven , Adolf-Bryfogle Jared , Alford Rebecca F. , Barlow Kyle , Ben-Aharon Ziv , Farrell Daniel , Fell Jason , Hansen William A. , Harmalkar Ameya , Jeliazkov Jeliazko , Kuenze Georg , Krys Justyna D. , Ljubetič Ajasja , Loshbaugh Amanda L. , Maguire Jack , Moretti Rocco , Mulligan Vikram Khipple , Nguyen Phuong T. , Ó Conchúir Shane , Roy Burman Shourya S. , Smith Shannon T. , Teets Frank , Tiemann Johanna KS , Watkins Andrew , Woods Hope , Yachnin Brahm J. , Bahl Christopher D. , Bailey-Kellogg Chris , Baker David , Das Rhiju , DiMaio Frank , Khare Sagar D. , Kortemme Tanja , Labonte Jason W. , Lindorff-Larsen Kresten , Meiler Jens , Schief William , Schueler-Furman Ora , Siegel Justin , Stein Amelie , Yarov-Yarovoy Vladimir , Kuhlman Brian , Leaver-Fay Andrew , Gront Dominik , Gray Jeffrey J. , Bonneau Richard 
Published: April 2021

AbstractEach year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.
Cancer-associated fibroblasts actively compress cancer cells and modulate mechanotransduction
Authors: Barbazan Jorge , Pérez-González Carlos , Gómez-González Manuel , Dedenon Mathieu , Richon Sophie , Latorre Ernest , Serra Marco , Mariani Pascale , Descroix Stéphanie , Sens Pierre , Trepat Xavier , Vignjevic Danijela Matic 
Published: April 2021

AbstractDuring tumor progression, cancer-associated fibroblasts (CAFs) accumulate in tumors and produce excessive extracellular matrix (ECM), forming a capsule that enwraps cancer cells. This capsule is a barrier that restricts tumor growth leading to the buildup of intratumoral pressure. Combining genetic and physical manipulationsin vivowith microfabrication and force measurementsin vitro, we found that the CAFs capsule is not a passive barrier but instead actively compresses cancer cells using actomyosin contractility. Cancer cells mechanosense CAF compression, resulting in an altered localization of the transcriptional regulator YAP. Abrogation of CAFs contractilityin vivoleads to the dissipation of compressive forces and impairment of capsule formation. By mapping CAF force patterns in 3D, we show that compression is a CAF-intrinsic property independent of cancer cell growth. Supracellular coordination of CAFs is achieved through fibronectin cables that serve as scaffolds allowing force transmission. Our study unveils that the contractile capsule actively compresses cancer cells, modulates their mechanical signaling, and reorganizes tumor morphology.
Engaging citizens in sustainability research: comparing survey recruitment and responses between Facebook, Twitter and qualtrics
Authors: Bridge Gemma , Armstrong Beth , Reynolds Christian , Wang Changqiong , Schmidt Ximena , Kause Astrid , Ffoulkes Charles , Krawczyk Coleman , Miller Grant , Serjeant Stephen , Oakden Libby 
Published: April 2021

PurposeThe study aims to compare survey recruitment rates between Facebook, Twitter and Qualtrics and to assess the impact of recruitment method on estimates of energy content, food safety, carbon footprint and animal welfare across 29 foods.Design/methodology/approachTwo versions of an online survey were developed on the citizen science platform, Zooniverse. The surveys explored citizen estimations of energy density (kcal) or carbon footprint (Co2) and food safety or animal welfare of 29 commonly eaten foods. Survey recruitment was conducted via paid promotions on Twitter and Facebook and via paid respondent invites on Qualtrics. The study included approximately 500 participants (Facebook, N˜11 (ratings 358), Twitter, N˜85 (ratings 2,184), Qualtrics, N = 398 (ratings 11,910)). Kruskal–Wallis and Chi-square analyses compared citizen estimations with validated values and assessed the impact of the variables on estimations.FindingsCitizens were unable to accurately estimate carbon footprint and energy content, with most citizens overestimating values. Citizen estimates were most accurate for meat products. Qualtrics was the most successful recruitment method for the online survey. Citizen estimates between platforms were significantly different, suggesting that Facebook and Twitter may not be suitable recruitment methods for citizen online surveys.Practical implicationsQualtrics was the favourable platform for survey recruitment. However, estimates across all recruitment platforms were poor. As paid recruitment methods such as Qualtrics are costly, the authors recommend continued examination of the social media environment to develop appropriate, affordable and timely online recruitment strategies for citizen science.Originality/valueThe findings indicate that citizens are unable to accurately estimate the carbon footprint and energy content of foods suggesting a focus on consumer education is needed to enable consumers to move towards more sustainable and healthy diets. Essential if we are to meet the 2030 Sustainable Development Goals of zero hunger, good health and wellbeing and responsible consumption and production. The study highlights the utility of Zooniverse for assessing citizen estimates of carbon footprint, energy content, animal welfare and safety of foods.
Does organisational politics affect leaders’ ability to engage Ghanaian Bankers?
Authors: Dartey-Baah Kwasi , Agbozo Rexford Kojo 
Published: April 2021

PurposeThe purpose of this paper is to investigate the influence of transformational and transactional leadership styles on employees’ work engagement and the moderating effects of perceived organisational politics (POPS) in indigenous Ghanaian Banks.Design/methodology/approachThe study uses a cross-sectional survey design and a quantitative approach to gather data from 430 respondents through the use of structured questionnaire. The covariance-based structural equation modelling was used to analyse the data with the aid of statistical package for social sciences and AMOS.FindingsThe analyses revealed that transformational leaders had a positive influence on employee engagement while transactional leadership did not have a significant influence on employee engagement. POPS also had no influence on employee engagement. Furthermore, POPS failed to moderate the relationship between leadership styles and employee engagement.Practical implicationsThe findings of this study provide important practical implications for managers and policymakers in the banking sector of Ghana in engendering good leadership and political environments that will promote the engagement of employees.Originality/valueThe variables used in this study and the context, present interesting and fresh insights into the interplay between leadership styles, POPS and employee engagement, thereby contributing to the discourse on the leadership and human resource management literature. Furthermore, this study fills a gap in literature and challenges prior conceptions that negative political climates within the public and private banks is chiefly responsible for the recent troubles some banks have faced in Ghana’s banking sector.
Evaluating disaster-related tweet credibility using content-based and user-based features
Authors: Assery Nasser , Xiaohong Yuan (Dorothy) , Xiuli Qu , Kaushik Roy , Almalki Sultan 
Published: April 2021

Purpose
This study aims to propose an unsupervised learning model to evaluate the credibility of disaster-related Twitter data and present a performance comparison with commonly used supervised machine learning models.

Design/methodology/approach
First historical tweets on two recent hurricane events are collected via Twitter API. Then a credibility scoring system is implemented in which the tweet features are analyzed to give a credibility score and credibility label to the tweet. After that, supervised machine learning classification is implemented using various classification algorithms and their performances are compared.

Findings
The proposed unsupervised learning model could enhance the emergency response by providing a fast way to determine the credibility of disaster-related tweets. Additionally, the comparison of the supervised classification models reveals that the Random Forest classifier performs significantly better than the SVM and Logistic Regression classifiers in classifying the credibility of disaster-related tweets.

Originality/value
In this paper, an unsupervised 10-point scoring model is proposed to evaluate the tweets’ credibility based on the user-based and content-based features. This technique could be used to evaluate the credibility of disaster-related tweets on future hurricanes and would have the potential to enhance emergency response during critical events. The comparative study of different supervised learning methods has revealed effective supervised learning methods for evaluating the credibility of Tweeter data.