bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary diversification reveals distinct somatic versus germline cytoskeletal functions of the Arp2 branched actin nucleator protein
Authors: Stromberg Kaitlin A. , Spain Tristan , Tomlin Sarah A. , Amarillo Kristen Dominique , Schroeder Courtney M. 
Published: February 2023

SummaryBranched actin networks are critical in many cellular processes, including cell motility and division. Arp2, a protein within the 7-membered Arp2/3 complex, is responsible for generating branched actin. Given its essential roles, Arp2 evolves under stringent sequence conservation throughout eukaryotic evolution. We unexpectedly discovered recurrent evolutionary diversification of Arp2 inDrosophila, yielding independently arising paralogsArp2Dinobscuraspecies andArp2D2inmontiumspecies. Both paralogs are unusually testis-enriched in expression relative to Arp2. We investigated whether their sequence divergence from canonical Arp2 led to functional specialization by replacingArp2inD. melanogasterwith eitherArp2DorArp2D2. Despite their divergence, we surprisingly found both complement Arp2’s essential function in the soma, suggesting they have preserved the ability to polymerize branched actin even in a non-native species. However, we found thatArp2D-expressing males are subfertile and display many defects throughout sperm development. We pinpointed two highly diverged structural regions in Arp2D that contribute to these defects: subdomain 2 and the C-terminus. We expected that germline function would be rescued by replacing Arp2D’s long and charged C-terminus with Arp2’s short C-terminus, yet surprisingly, the essential somatic function of Arp2D was lost. Therefore, while Arp2D’s structural divergence is incompatible withD. melanogastersperm development, its unique C-terminus has evolved a critical role in actin polymerization. Our findings suggest canonical Arp2’s function differs between somatic versus germline contexts, and Arp2 paralogs have recurrently evolved and specialized for actin branching in the testis.
Incorporation of TRDV segments into TCR alpha chains
Authors: Volkmar Michael , Fakhr Elham , Zens Stefan , Offringa Rienk , Bury Alice , Gordon Jessica , Huduti Enes , Wölfel Thomas , Wölfel Catherine 
Published: February 2023

AbstractIn human tumor models we tried to identify and clone the TCR of tumor-reactive T cells enriched in mixed lymphocyte tumor-cell cultures (MLTC). In a particular MLTC, we identified a predominant TCR beta chain using the Beta Mark Vbeta Kit, but a corresponding alpha chain could not be amplified via RT-PCR usingTRAV-specific forward primers. Therefore, we applied 5’RACE to obtain the TCR alpha chain sequences. The 5’RACE product revealed an alpha chain that encompassed 89bp of theTRDV15’UTR, followed by theTRDV1coding sequence joined in frame toTRAJ24. The ORF reaching from theTRDV1start codon to theTRACsegment was intact, suggesting a functional TCR. To analyze this MLTC population in greater depth we conducted 10X VDJ sequencing. CellRanger identified the beta chain known from the Beta Mark analysis, but no corresponding alpha chain in the filtered results. The corresponding TRDV-containing TCR alpha chain could, however, be detected in the “all_contig_annotations” files.In a separate project, we performed TCR sequencing of tumor-infiltrating lymphocytes (TILs) in a murine tumor model. Also here, a predominant clonotype contained a TCR alpha chain joiningTrdv2-2in frame toTraj49.Transfection of both TCR cDNAs resulted in cell surface localization of TCR and CD3 as validated by FACS. Tumor recognition of the human, TRDV1-containing TCR could be demonstrated by IFNgamma ELISpot whereas the murine TCR did not recognize a tumor-derived cell line.TRDV-containing alpha chains have been reported in the literature for two HLA I-restricted TCRs against HIV peptides (Ueno et al, Eur J Immunol, 2003). To determine whether such TDRV-containing TCRs are unique events or whether Vdelta segments are commonly incorporated into TCR alpha chains, we queried the NCBI Sequence Read Archive (SRA) for 10X VDJ data and analyzed 21 human and 23 murine datasets. We found that especiallyTRDV1, Trdv1and to some extentTrdv2-2are more commonly incorporated into TCR alpha chains than someTRAVgenes, making theTRDVsegments a relevant contribution to TCR alpha diversity.For apparently solitary beta chains in 10X VDJ datasets, we suggest to scrutinize the “all_contig_annotations” files as these may contain an accompanying, TRDV-containing alpha chain.
EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations
Authors: Biswas Gargi , Mukherjee Debasish , Dutta Nalok , Ghosh Prithwi , Basu Sankar 
Published: February 2023

AbstractContextProtein-protein interaction (PPI) is a key component linked to virtually all cellular processes. Be it an enzyme catalysis (‘classic type functions’ of proteins) or a signal transduction (‘non-classic’), proteins generally function involving stable or quasi-stable multi-protein associations. The physical basis for such associations is inherent in the combined effect of shape and electrostatic complementarities (Sc, EC) of the interacting protein partners at their interface, which provides indirect probabilistic estimates of the stability and affinity of the interaction. While Sc is a necessary criterion for inter-protein associations, EC can be favorable as well as disfavored (e.g., in transient interactions). Estimating equilibrium thermodynamic parameters (ΔGbinding, Kd) by experimental means is costly and time consuming, thereby opening windows for computational structural interventions. Attempts to empirically probe ΔGbindingfrom coarse-grain structural descriptors (primarily, surface area based terms) have lately been overtaken by physics-based, knowledge-based and their hybrid approaches (MM/PBSA, FoldX etc.) that directly compute ΔGbindingwithout involving intermediate structural descriptors.MethodsHere we present EnCPdock (www.scinetmol.in/EnCPdock/), a user-friendly web-interface for the direct conjoint comparative analyses of complementarity and binding energetics in proteins. EnCPdock returns an AI-predicted ΔGbindingcomputed by combining complementarity (Sc, EC) and other high-level structural descriptors (input feature vectors), and, renders a prediction accuracy comparable to the state-of-the-art. EnCPdock further locates a PPI complex in terms of its {Sc, EC} values (taken as an ordered pair) in the two-dimensional Complementarity Plot (CP). In addition, it also generates mobile molecular graphics of the interfacial atomic contact network for further analyses. EnCPdock also furnishes individual feature trends along with the relative probability estimates (Prfmax) of the obtained feature-scores with respect to the events of their highest observed frequencies. Together, these functionalities are of real practical use for structural tinkering and intervention as might be relevant in the design of targeted protein-interfaces. Combining all its features and applications, EnCPdock presents a unique online tool that should be beneficial to structural biologists and researchers across related fraternities.
Novel Approach Explains Spatio-Spectral Interactions in Raw Electroencephalogram Deep Learning Classifiers
Authors: Ellis Charles A. , Sattiraju Abhinav , Miller Robyn L. , Calhoun Vince D. 
Published: February 2023

ABSTRACTThe application of deep learning classifiers to resting-state electroencephalography (rs-EEG) data has become increasingly common. However, relative to studies using traditional machine learning methods and extracted features, deep learning methods are less explainable. A growing number of studies have presented explainability approaches for rs-EEG deep learning classifiers. However, to our knowledge, no approaches give insight into spatio-spectral interactions (i.e., how spectral activity in one channel may interact with activity in other channels). In this study, we combine gradient and perturbation-based explainability approaches to give insight into spatio-spectral interactions in rs-EEG deep learning classifiers for the first time. We present the approach within the context of major depressive disorder (MDD) diagnosis identifying differences in frontal δ activity and reduced interactions between frontal electrodes and other electrodes. Our approach provides novel insights and represents a significant step forward for the field of explainable EEG classification.
‘CandidatusTisiphia’ is a widespread Rickettsiaceae symbiont in the mosquitoAnopheles plumbeus(Diptera: Culicidae)
Authors: Davison Helen R. , Crozier Jessica , Pirro Stacy , Werner Doreen , Hurst Gregory D.D. 
Published: February 2023

AbstractSymbiotic bacteria alter host biology in numerous ways, including the ability to reproduce or vector disease. Deployment of symbiont control of vector borne disease has focused onWolbachiainteractions withAedesand is hampered inAnophelesby a lack of compatible symbioses. Previous screening found the symbiont ‘Ca. Tisiphia’ inAnopheles plumbeus, an aggressive biter and potential secondary vector of malaria parasites and West Nile virus. We screenAn. plumbeussamples collected over a ten-year period across Germany and use climate databases to assess environmental influence on incidence. We find a 95% infection rate that does not fluctuate with broad environmental factors. Microscopy suggests the infection is maternally inherited based on strong localisation throughout the ovaries. Finally, we assemble a high-quality draft genome of ‘Ca. Tisiphia’ to explore its phylogeny and potential metabolism. This strain is closely related to those found inCulicoidesmidges and shows similar patterns of metabolic potential.An. plumbeusprovides a viable avenue of symbiosis research in anopheline mosquitoes, which to date have one other proven infection of a heritable symbiont. Additionally, it provides future opportunity to study the impacts of ‘Ca. Tisiphia’ on natural and transinfected hosts, especially in relation to reproductive fitness and vector efficiency.
Ready-to-use nanopore platform for ethanolamine quantification using an aptamer-based strand displacement assay
Authors: Quint Isabel , Simantzik Jonathan , Kaiser Lars , Laufer Stefan , Csuk Rene’ , Smith David , Kohl Matthias , Deigner Hans-Peter 
Published: February 2023

AbstractIn recent decades, nanopores have become a promising diagnostic tool. Protein and solid-state nanopores are increasingly used for both RNA/DNA sequencing and small molecule detection. The latter is of great importance because small molecules are difficult or expensive to detect using available methods such as HPLC or LC-MS. Moreover, DNA aptamers are an excellent detection element for sensitive and specific detection of small molecules. Here, we describe a method for the quantification of ethanolamine using Oxford Nanopore’s ready-to-use sequencing platform. To this end, we have developed a strand displacement assay using a binding ethanolamine aptamer and magnetic beads. The displaced aptamer can be detected using the MinION® nanopores and analysed/quantified using our in-house developed analysis software.
Engineered ketocarotenoid biosynthesis in the polyextremophilic red microalgaCyanidioschyzon merolae10D
Authors: Seger Mark , Mammadova Fakhriyya , Villegas-Valencia Melany , Bastos de Freitas Bárbara , Chang Clarissa , Isachsen Iona , Hemstreet Haley , Abualsaud Fatimah , Boring Malia , Lammers Peter J. , Lauersen Kyle J. 
Published: February 2023

AbstractThe polyextremophilic Cyanidiales are eukaryotic red microalgae with promising biotechnological properties arising from their low pH and elevated temperature requirements which can minimize culture contamination at scale.Cyanidioschyzon merolae10D is a cell wall deficient species with a fully sequenced genome that is amenable to nuclear transgene integration by targeted homologous recombination.C. merolaemaintains a minimal carotenoid profile and here, we sought to determine its capacity for ketocarotenoid accumulation mediated by heterologous expression of a green algal β-carotene ketolase (BKT) and hydroxylase (CHYB). To achieve this, a synthetic transgene expression cassette system was built to integrate and expressChlamydomonas reinhardtii(Cr) sourced enzymes by fusing nativeC. merolaetranscription, translation and chloroplast targeting signals to codon-optimized coding sequences. Chloramphenicol resistance was used to select for the integration of synthetic linear DNAs into a neutral site within the host genome.CrBKT expression caused accumulation of canthaxanthin and adonirubin as major carotenoids while co-expression ofCrBKT withCrCHYB generated astaxanthin as the major carotenoid inC. merolae. Unlike green algae and plants, ketocarotenoid accumulation inC. merolaedid not reduce total carotenoid contents, but chlorophyll a reduction was observed. Light intensity affected global ratios of all pigments but not individual pigment compositions and phycocyanin contents were not markedly different between parental strain and transformants. Continuous illumination was found to encourage biomass accumulation and all strains could be cultivated in simulated summer conditions from two different extreme desert environments. Our findings present the first example of carotenoid metabolic engineering in a red eukaryotic microalga and open the possibility for use ofC. merolae10D for simultaneous production of phycocyanin and ketocarotenoid pigments.Abstract Figure
Binary classification of multi-magnification histopathological breast cancer images using late fusion and transfer learning
Authors: Nakach Fatima-Zahrae , Zerouaoui Hasnae , Idri Ali 
Published: February 2023

PurposeHistopathology biopsy imaging is currently the gold standard for the diagnosis of breast cancer in clinical practice. Pathologists examine the images at various magnifications to identify the type of tumor because if only one magnification is taken into account, the decision may not be accurate. This study explores the performance of transfer learning and late fusion to construct multi-scale ensembles that fuse different magnification-specific deep learning models for the binary classification of breast tumor slides.Design/methodology/approachThree pretrained deep learning techniques (DenseNet 201, MobileNet v2 and Inception v3) were used to classify breast tumor images over the four magnification factors of the Breast Cancer Histopathological Image Classification dataset (40×, 100×, 200× and 400×). To fuse the predictions of the models trained on different magnification factors, different aggregators were used, including weighted voting and seven meta-classifiers trained on slide predictions using class labels and the probabilities assigned to each class. The best cluster of the outperforming models was chosen using the Scott–Knott statistical test, and the top models were ranked using the Borda count voting system.FindingsThis study recommends the use of transfer learning and late fusion for histopathological breast cancer image classification by constructing multi-magnification ensembles because they perform better than models trained on each magnification separately.Originality/valueThe best multi-scale ensembles outperformed state-of-the-art integrated models and achieved an accuracy mean value of 98.82 per cent, precision of 98.46 per cent, recall of 100 per cent and F1-score of 99.20 per cent.
The personas and motivation of religious tourists and their impact on intentions to visit religious sites in Saudi Arabia
Authors: Kayal Ghadeer 
Published: February 2023

PurposeThe purpose of this paper is to provide comprehensive, theoretical and practical knowledge that will assist decision-makers in making informed decisions when promoting several religious sites in the Kingdom of Saudi Arabia (KSA). Specifically, this study examines the popularity of several religious sites, the personas of prospective visitors and their intentions to visit.Design/methodology/approachThe study uses several methodological approaches to fulfil its main objective, namely, Google Trends analysis, K-means cluster analysis and linear regression analysis.FindingsThe results reveal that several religious sites in the KSA are popular and have potential for further consideration by various stakeholders. In addition, four personas were identified which can aid decision-makers and marketing practitioners in designing suitable plans for prospective visitors based on the participants’ motivation and demographics. Furthermore, a significant association was observed among three motivational variables (self-esteem, relationship and physiological needs) and the participants’ intentions to visit.Originality/valueThis study makes an original contribution to the literature, as it examines several religious sites in Saudi Arabia in addition to the sites that are part of the practices of Hajj and Umrah. Furthermore, this study provides comprehensive knowledge in this area to assist both future researchers and practitioners.
Information systems security resilience as a dynamic capability
Authors: Goel Lakshmi , Russell Dawn , Williamson Steven , Zhang Justin Zuopeng 
Published: February 2023

PurposeWhile the idea of the resilience of information systems security exists, there is a lack of research that conceptualizes, defines and specifies a way to measure it as a dynamic capability. Drawing on relevant cybersecurity and dynamic capabilities literature, this study aims to define Information Systems Security Resilience (ISSR) as a “dynamic capability of a firm to respond to, and recover from, a security attack” and test it as a new construct.Design/methodology/approachThe authors employ a methodology including multiple phases to develop and test this construct of ISSR. The authors first interview senior managers from various organizations to establish the face validity of the construct; then develop and analyze a pilot survey for internal validity and reliability; and finally, design and deploy a field survey to test and externally validate the construct.FindingsThe authors conceptualize and define the construct of ISSR as a dynamic capability, develop a scale for its measurement and test it in a pilot and field survey. The construct is valid, and the measurement tool works. It demonstrates that resilience is something that is done, rather than had. As a capability, organizations need to track and measure ISSR, which is what this tool provides the ability to do.Originality/valueThis research contributes to the information systems and cybersecurity literature and offers valuable insights for organizations to manage their security effectively.
Assessing educational methods for tomorrow's supply chain leaders with the integration of skill development priorities: a fuzzy decision-making approach
Authors: Vazquez Reyes Bengie Omar , Teixeira Tatiane , Colmenero João Carlos , Picinin Claudia Tania 
Published: February 2023

PurposeEffective educational methods are critical for successfully training future supply chain talent. The paper proposes a fuzzy multi-criteria decision-making model to evaluate and select the best educational method for tomorrow's supply chain leaders integrating skill development priorities in an uncertain environment.Design/methodology/approachThe Grounded theory scheme is used to identify SC leaders' skillsets criteria and educational method alternatives. Fuzzy step-wise weight assessment ratio analysis sets the priority and determines the weight of 17 criteria. Eight decision-makers evaluate 13 alternatives using fuzzy linguistic terms. Fuzzy technique for order preference by similarity to ideal solution ranks and shows the most effective educational method. Sensitivity analysis presents the applicability of this study.FindingsIts implementation in a university-industry collaboration case in Brazil, Mentored learning from industry experts is the best educational method. The skill development priorities are data analytics ability, end-to-end supply chain vision and problem-solving. Technical skills are the most important criteria that influence the selection of the optimal option and educational methods related to learning from others rank in the top teaching pool, including multidisciplinary cross-cultural training.Originality/valueThis paper is among the first to evaluate educational methods with skill development priorities integration for supply chain students using fuzzy SWARA–fuzzy TOPSIS. It provides actionable insights: a decision-making procedure for educational method selection, a broad skills profile for supply chain professional success and educational methods that professors can bring to in classroom/virtual environment.
Opportunities for the United States hotel industry to recover from COVID-19: a multi-period DEA analysis of key efficiency determinants
Authors: Schalk-Nador Szilvia Vanessza , Rašovská Ida 
Published: February 2023

PurposeThis study examines empirically the development of efficiency levels in the hotel industry and its key drivers, by juxtaposing pre- and post-COVID-19 results in the four most important cities in the United States in terms of international arrivals.Design/methodology/approachA two-step approach was employed by first utilising the data envelopment analysis method to characterise the efficiency of United States hotels. A multiple linear regression analysis was performed to compare hotel performance in the two years prior to the COVID-19 outbreak with the first two years after the outbreak.FindingsThe results indicated the positive effect of size and the economy hotel category on efficiency, while increasing property age, urban location and a lack of brand affiliation showed a negative effect. During the pandemic, size and the economy category remained significant and positive, whereas urban location continued to represent a negative effect.Practical implicationsThis study assists decision makers regarding prospective investments, supports existing and future portfolio analyses, contributes to observations on competition, and offers a wider perspective of the industry.Originality/valueFirst, this study investigated the evolution of factors that influenced efficiency before and after the outbreak of the COVID-19 pandemic. Second, the results offer insights into the impact of the pandemic on hotels' efficiency levels. Third, the study proposes directions for the restoration of hotel efficiency to pre-COVID-19 levels.