bluuebunny/crossref_metadata_2025_split huggingface dataset:
WITHDRAWN: Neurophysiology of Reciprocal Influence of Cognition and Emotion in Pianistic Performances
Authors: Higuchi Marcia K. K. , Sanchez Tiago A. , Ramos Lucas R. , Fornari N. José E. , Araújo Dráulio B. , Leite João P. 
Published: May 2023

Withdrawal StatementThis manuscript has been withdrawn by bioRxiv as it was submitted and made public without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author
Unraveling the timeline of gene expression: a pseudo-temporal trajectory analysis of single-cell RNA sequencing data
Authors: Cheng Jinming , Smyth Gordon K. , Chen Yunshun 
Published: May 2023

AbstractThere has been a rapid development in single cell RNA sequencing (scRNA-seq) technologies in recent years. Droplet-based single cell platforms such as the 10x Genomics’ Chromium system enable gene expression profiling of tens of thousands of cells per sample. The goal of a typical scRNA-seq analysis is to identify different cell subpopulations and their respective marker genes. Trajectory analysis can also be used to infer the developmental or differentiation trajectories of cells by ordering them along a putative lineage tree based on their gene expression profiles. This analysis positions cells and cell clusters along a pseudotime trajectory that represents a biological process such as cell differentiation, development, or disease progression. Here we demonstrate a time-course analysis to identify genes that are significantly associated with pseudotime. The article demonstrates a comprehensive workflow for performing trajectory inference and time course analysis on a multi-sample single cell RNA-seq experiment of the mouse mammary gland. The workflow uses open-source R software packages and covers all steps of the analysis pipeline, including quality control, doublet prediction, normalization, integration, dimension reduction, cell clustering, trajectory inference, and pseudobulk time course analysis. Sample integration and cell clustering follows theSeuratpipeline while the trajectory inference is conducted using themonocle3package. The pseudo-bulk time course analysis uses the quasi-likelihood framework ofedgeR.
Structural characterization of a pathogenic antibody underlying vaccine-induced immune thrombotic thrombocytopenia (VITT)
Authors: Nguyen Son N. , Le Si-Hung , Ivanov Daniil G. , Ivetic Nikola , Nazy Ishac , Kaltashov Igor A. 
Published: May 2023

AbstractVaccine-induced immune thrombotic thrombocytopenia (VITT) is a rare but extremely dangerous side effect that has been reported for several adenoviral (Ad)-vectored COVID-19 vaccines. VITT pathology had been linked to production of antibodies that recognize platelet factor 4 (PF4), an endogenous chemokine. In this work we characterize anti-PF4 antibodies obtained from a VITT patient’s blood. Intact-mass MS measurements indicate that a significant fraction of this ensemble is comprised of antibodies representing a limited number of clones. MS analysis of large antibody fragments (the light chain, as well as the Fc/2 and Fd fragments of the heavy chain) confirms the monoclonal nature of this component of the anti-PF4 antibodies repertoire, and reveals the presence of a fully mature complex biantennary N-glycan within its Fd segment. Peptide mapping using two complementary proteases and LC-MS/MS analysis were used to determine the amino acid sequence of the entire light chain and over 98% of the heavy chain (excluding a short N-terminal segment). The sequence analysis allows the monoclonal antibody to be assigned to IgG2 subclass and verify that the light chain belongs to the λ-type. Incorporation of enzymatic de-N-glycosylation into the peptide mapping routine allows theN-glycan in the Fab region of the antibody to be localized to the framework 3 region of the VHdomain. This novelN-glycosylation site (absent in the germline sequence) is a result of a single mutation giving rise to an NDT motif in the antibody sequence. Peptide mapping also provides a wealth of information on lower-abundance proteolytic fragments derived from the polyclonal component of the anti-PF4 antibody ensemble, revealing the presence of all four subclasses (IgG1 through IgG4) and both types of the light chain (λ and κ). The structural information reported in this work will be indispensable for understanding the molecular mechanism of VITT pathogenesis.
Vigilance & Cognitive Flexibility: The Effect of Martial Arts Experience on Task Switching
Authors: Johnstone Ashleigh , Marí-Beffa Paloma 
Published: May 2023

AbstractMartial Arts can be considered both a sport and a therapy, combining physical exercise with intense periods of concentration (similar to meditation). Previous research suggests that both exercise and meditation can lead to improvements in executive functions (i.e., cognitive flexibility) in adult participants. Results from our lab have previously suggested that martial artists show improvements in the alerting attentional network – a measure of vigilance. The current research aims to investigate the impact of Martial Arts training on a task-switching protocol to measure both vigilance and cognitive flexibility in typical adults. Here we recruited adult martial artists with at least two years of experience, and control participants with no experience. Participants had to respond to either the shape or the colour of a figure in pure and mixed blocks to provide measures of mixing costs (sustained vigilance) and switching costs (cognitive flexibility). Results demonstrated martial artists did not differ from controls in the pure block, but displayed improved performance in the mixed block, revealing an improvement in mixing costs (vigilance). These benefits in vigilance mirror those previously found in attentional tasks, providing convergent evidence on the impact of Martial Arts training on vigilance.
Intestinal microbiota modulates the anti-tumor effect of oncolytic virus vaccine in colorectal cancer
Authors: Chen Xia , Wang Guang-Jun , Qin Ling , Hu Bing , Li Jun 
Published: May 2023

AbstractBackgroundImmunotherapy such as oncolytic virus has become a powerful cancer treatment but only a part of cancer patients can benefit from it, especially to advanced-stage cancer patients are required new therapeutic strategies to facilitate extended survival. Intestinal microbiota may contribute to colorectal cancer (CRC) carcinogenesis and response to immunotherapy. However, whether and how the modulating effect of intestinal microbiota on oncolytic virus vaccine (OVV) in CRC remains to be investigated.MethodsWe generated a MC38-gp33 CRC mouse model and treated with OVV-gp33 in early- and advanced-stages. Probiotics, fecal microbiota transplantation (FMT) and antibiotics (ABX) were treated to regulate the microbial composition of CRC mice of advanced stage. The tumor growth rate and survival time of mice were recorded. 16S rDNA sequencing analyzed the microbial composition and flow cytometry detected the T cells subsets activity.ResultsOVV-gp33 treatment led to inhibited tumor growth and prolonged survival in the early stage of CRC but did not have a significant effect on the advanced stage of CRC. Moreover, 16S rDNA sequence analysis and flow cytometry showed significant differences in intestinal microbiota composition, microbial metabolites and T-cell subsets in early- and advanced-stage CRC. Probiotic and FMT treatment significantly enhanced the antitumor effect of OVV in advanced stage of CRC with an increased abundance of activated CD8+T cells and a decreased ratio of Treg cells, while depletion of the microbiota by ABX eliminated the antitumor activity of OVV with decreased CD8+T-cell activation and upregulated Treg cells.ConclusionsThese results indicate that intestinal microbiota and microbial metabolites play an important role in the OVV antitumor effect in CRC, furthermore, altering the intestinal microbiota composition can modulate the antitumor and immunomodulatory effect of OVV in CRC.
Environmental radiation exposure at Chornobyl has not systematically affected the genomes or mutagen tolerance phenotypes of local worms
Authors: Tintori Sophia C. , Çağlar Derin , Ortiz Patrick , Chyzhevskyi Ihor , Mousseau Timothy A. , Rockman Matthew V. 
Published: May 2023

ABSTRACTThe 1986 disaster at the Chornobyl Nuclear Power Plant transformed the surrounding region into the most radioactive landscape known on the planet. Questions remain regarding whether this sudden environmental shift selected for species, or even individuals within a species, that are naturally more resistant to radiation exposure.We collected, cultured, and cryopreserved 298 wild nematodes isolates from areas varying in radioactivity within the Chornobyl Exclusion Zone. We sequenced and assembled genomesde novofor 20Oschieus tipulaestrains, analyzed their genomes for evidence of recent mutation acquisition in the field and saw no evidence of an association between mutation and radiation level at the sites of collection. Multigenerational exposure of each of these strains to several mutagens in the lab revealed that strains vary heritably in tolerance to each mutagen, but mutagen tolerance cannot be predicted based on the radiation levels at collection sites.
Advancing scaffold biomimicry: engineering mechanics in microfiber scaffolds with independently controlled architecture using melt electrowriting
Authors: Devlin Brenna L. , Pickering Edmund , Allenby Mark C. , Paxton Naomi C. , Woodruff Maria A. 
Published: May 2023

AbstractMelt electrowriting (MEW) is an additive manufacturing technique characterized by its ability to fabricate micronscale fibers from molten polymers into highly controlled 3D microfiber scaffolds. This emerging technique is gaining traction in tissue engineering and biofabrication research, however limitations in the ability to develop advanced coding to program MEW printers to fabricate scaffolds with complex fiber architectures has inhibited the development of structures with tunable and biomimetic mechanical properties. This study reports a series of non-straight scaffold architectures with combinations of independently controlled X & Y fiber spacing, corrections for MEWjet lag, and characterizations of their influences on scaffold mechanics. Polycaprolactone scaffolds with an elastic modulus ranging from 0.3 to 7.3 MPa were fabricated utilizing scaffolds manufactured from 5 layers of 55 μm fibers. The inclusion of scaffold design corrections in the gcode to compensate for decreasing deposition accuracy with increasing layer height enabled us to correct for discontinuous stress-strain mechanics and improved scaffold fabrication reproducibility. This study provides a comparison between a series of highly reproducible MEW scaffold architectures with non-straight fibers compared to the common crosshatch design to inform the development of more biomimetic scaffolds applicable to a variety of clinical applications. It further illustrates the significant effect toolpath correction has on reducing poor stress-strain mechanics, therefore improving the control, reproducibility, and biomimetic capacity of the MEW technique.
DNA-guided transcription factor cooperativity shapes face and limb mesenchyme
Authors: Kim Seungsoo , Morgunova Ekaterina , Naqvi Sahin , Bader Maram , Koska Mervenaz , Popov Alexander , Luong Christy , Pogson Angela , Claes Peter , Taipale Jussi , Wysocka Joanna 
Published: May 2023

SummaryTranscription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Althoughin vitrostudies suggest it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how ‘Coordinator’, a long DNA motif comprised of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, while HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in shared regulation of genes involved in cell-type and positional identities, and ultimately shapes facial morphology and evolution.
Investigating individual variability in microstructural-functional coupling in the human cortex
Authors: Patel Raihaan , Dai Alyssa , Valk Sofie L. , Desrosiers-Grégoire Gabriel , Devenyi Gabriel A. , Chakravarty M. Mallar 
Published: May 2023

AbstractUnderstanding the relationship between the structural and functional architecture of the human brain remains a key question in neuroscience. In this regard variation in cortical myelin may provide key insights into the functional organization. Previous findings have demonstrated that regions sharing myeloarchitectonic features are also likely to be structurally and functionally connected. However, this association is not uniform for all regions. For example, the strength of the association, or ‘coupling’, between microstructure and function is regionally heterogeneous, with strong coupling in primary cortices but weaker coupling in higher order transmodal cortices. However, the bases of these observations have been typically made at the group level, leaving much to be understood regarding the individual-level behavioural relevance of microstructural-functional coupling variability. To examine this critical question, we apply a multivariate framework to a combination of high-resolution structural, diffusion, and functional magnetic resonance imaging (MRI) data in a sample of healthy young adults. We identify four distinct patterns of coupling variation that vary across individuals. Remarkably, we find that while microstructural-functional coupling is consistently strong in primary cortices, significant variation in transmodal cortices exists. Importantly, we identified coupling variability maps and their association with behaviour that demonstrate the existence of latent dimensions of variability related to inter-individual performance on cognitive tasks. These findings suggest that the existence of behaviourally relevant coupling variation is a key principle for brain organization.
Inhibition of proprotein convertase subtilisin-like kexin type 9 (PCSK9) potentiates anti-angiogenic therapy in colorectal cancer liver metastases
Authors: Rada Miran , Reynolds Andrew R. , Lazaris Anthoula , Seidah Nabil , Metrakos Peter 
Published: May 2023

AbstractColorectal cancer liver metastatic (CRCLM) tumours present as two main histopathological growth patterns (HGPs) including desmoplastic HGP (DHGP) and replacement HGP (RHGP). The DHGP tumours obtain their blood supply by sprouting angiogenesis, whereas the RHGP tumours utilize an alternative vascularisation known as vessel co-option. In vessel co-option, the cancer cells hijack the mature sinusoidal vessels to obtain blood supply. Vessel co-option has been reported as an acquired mechanism of resistance to anti-angiogenic treatment in CRCLM. Herein, we showed that inhibiting proprotein convertase subtilisin-like kexin type 9 (PCSK9) via clinically approved PCSK9-neutralizing antibody (Evolocumab) can boost the response of vessel co-opting tumours to anti-angiogenic therapy. Mechanistically, we found that PCSK9 inhibition downregulates runt related transcription factor-1 (RUNX1) expression levels in CRCLM cancer cells in vivo, which its expression positively correlates with the development of vessel co-option. Collectively, these results suggest that inhibiting PCSK9 is a promising way to improve the efficacy of anti-angiogenic therapy against vessel co-opting tumours in CRCLM.
ULDNA: Integrating Unsupervised Multi-Source Language Models with LSTM-Attention Network for Protein-DNA Binding Site Prediction
Authors: Zhu Yi-Heng , Yu Dong-Jun 
Published: May 2023

AbstractAccurate identification of protein-DNA interactions is critical to understand the molecular mechanisms of proteins and design new drugs. We proposed a novel deeplearning method, ULDNA, to predict DNA-binding sites from protein sequences through a LSTM-attention architecture embedded with three unsupervised language models pretrained in multiple large-scale sequence databases. The method was systematically tested on 1287 proteins with DNA-binding site annotation from Protein Data Bank. Experimental results showed that ULDNA achieved a significant increase of the DNA-binding site prediction accuracy compared to the state-of-the-art approaches. Detailed data analyses showed that the major advantage of ULDNA lies in the utilization of three pre-trained transformer language models which can extract the complementary DNA-binding patterns buried in evolution diversity-based feature embeddings in residue-level. Meanwhile, the designed LSTM-attention network could further enhance the correlation between evolution diversity and protein-DNA interaction. These results demonstrated a new avenue for high-accuracy deep-learning DNA-binding site prediction that is applicable to large-scale protein-DNA binding annotation from sequence alone.
Investigating the relationship between supply chain finance and supply chain collaborative factors
Authors: Zaman Syed Imran , Khan Sharfuddin Ahmed , Kusi-Sarpong Simonov 
Published: June 2023

PurposeIt is important to understand the factors that are significant in supply chain (SC) collaboration decision making and whether supply chain collaborative factors that are considered in the literature are still valid. To date, SC collaboration has not been extensively studied in the literature with supply chain finance (SCF) factors to evaluate SCF performance. Therefore, in this paper, the authors investigate the interrelationships between SCF and supply chain collaborative (SCC) factors for achieving SCF performance. The authors identified the most important factors from the literature on SCF and SCC and with inputs from experts in the textile industry in Pakistan.Design/methodology/approachThe authors employed the Gray-Decision Making Trial and Evaluation Laboratory approach to help examine the cause-and-effect relationship between the factors and identify the influence of each factor on the others.FindingsThe findings showed that the most prominent factors of the study are “level of digitalization”, “information sharing”, and “collaborative communication”, and “most effect factors of this study are incentive alignment” and “information quality”. Furthermore, the “Level of digitalization” was identified as the factor with the central role and most significant correlation with other factors.Research limitations/implicationsThe major implication of the study is that textile industries should effectively develop their supply chain decisions after analyzing their internal and external factors, which will help in developing strategies that will facilitate better management of SCF relationships. The limitations of the study are that only 15 SCF and supply chain collaborative factors were considered, and time and scope are also limited. This study is only applied in the textile industry, so generalization may be limited.Originality/valueTo date, this study is the only one that has taken into consideration SCC with SCF factors to evaluate supply chain performance. This paper therefore makes this initial attempt and original contribution to this discussion, which can be helpful for those working to enhance supply chain performance, such as practitioners and policymakers.
Coming to work with an illness: the role of high-involvement work systems and individual competence on presenteeism
Authors: Islam Md Shamirul , Amin Muslim , Feranita Feranita , Winterton Jonathan 
Published: May 2023

PurposeThis paper aims to examine the effect of high-involvement work systems (HIWSs) on completing work and avoiding distraction as two dimensions of presenteeism. It also investigates competence as a mediator of the effect of HIWS on presenteeism.Design/methodology/approachData were collected from 343 Bangladeshi bank employees using an online survey. The partial least squares-structural equation modelling (PLS-SEM) was employed to assess the abovementioned linkages.FindingsThe findings demonstrate HIWS directly avoid distraction but do not significantly impact the completing work dimension of presenteeism. The findings also indicate that competence mediates the effect of HIWS on completing work but not on avoiding distraction.Originality/valueDrawing on the job demands-resources (JD-R) model, this study empirically demonstrates the contrasting role of HIWS in completing work and avoiding distraction related to presenteeism. It also provides a novel perspective on the unexplored mediating mechanism of competence on the relationship between HIWS and presenteeism and offers new directions for HIWS and presenteeism research.
Asymmetric impact of income and price on kerosene consumption in Cameroon: new evidence from NARDL
Authors: Noumga Jeunesse , Sapnken Flavian Emmanuel , Kinfack Jeutsa Aubin , Tamba Jean Gaston 
Published: May 2023

Purpose
This research paper aims to examine the asymmetric impact of income and price on household consumption of kerosene in Cameroon.

Design/methodology/approach
The methodological approach consists of testing for stationarity using the augmented Dickey–Fuller and Andrews and Zivot tests, determining cointegration using nonlinear autoregressive distributed lag (NARDL) test approach and finally examining asymmetry using the Wald test.

Findings
Results of the stationarity tests reveal that variables are all integrated of order less than two I(2). The NARDL approach indicates that the (positive and negative) income shock and the positive price boom negatively influence consumption in the long- and short-run. The same is true for the negative price shock, but the latter remains insignificant. Furthermore, the Wald test carried out in the study confirms that the cumulative effects of the positive and negative income and price shocks are asymmetric.

Originality/value
The increase in the price of kerosene due to the lifting of subsidies has led to a decrease in household consumption and an unfortunate increase in the loss of tree cover in Cameroon. According to the results, this phenomenon will persist even if the price is reduced. Actions aimed at reducing its production at the expense of liquefied petroleum gas, electricity and renewable energy should be encouraged to limit the loss of vegetation cover. Thus, this study could contribute to solving the problem of deforestation and desertification in Cameroon.