bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct measures of liking and intensity of taste, smell, and chemesthetic stimuli are similar between young people reporting they did or did not have COVID-19
Authors: Leszkowicz Emilia , Bell Katherine , Huang Amy , Nguyen Ha , Reed Danielle R. 
Published: October 2023

AbstractThe recovery period from post-COVID-19 smell and taste dysfunctions varies substantially, lasting from a few days to over a year. We aimed to assess the impact of COVID-19 on post-COVID-19 chemosensory sensitivity in a group of young convalescents of eastern/central European ancestry. We measured subjects’ smell and taste capabilities with a standard testing kit, Monell Flavor Quiz (MFQ), and collected surveys on COVID-19 history. During testing, subjects rated liking and intensity of six odor samples (galaxolide, guaiacol, beta-ionone, trimethylamine, phenylethyl alcohol, 2-ethyl fenchol) and six taste samples (sucralose, sodium chloride, citric acid, phenylthiocarbamide, menthol, capsaicin) on a scale from 1 (dislike extremely, or no intensity) to 9 (like extremely, or extremely intense). There was no statistical difference in intensity ratings or liking of any sample between subjects who reported a history of COVID-19 (n = 34) and those reporting no history (n = 40), independent of presence/absence or severity of smell/taste impairments (P> 0.05). Additionally, neither vaccination status (full vaccination or no vaccination) nor time from the COVID-19 onset (2-27 months) correlated with liking or intensity. These results suggest that most young adults who had COVID-19 recovered their sense of smell and taste.
The Minimal Dataset for Cancer of the 1+Million Genomes Initiative
Authors: Riba Michela , Sala Cinzia , Culhane Aedin , Flobak Åsmund , Patocs Attila , Boye Kjetil , Plevova Karla , Pospíšilová Šárka , Gandolfi Giorgia , Morelli Marco J , Bucci Gabriele , Edsjö Anders , Lassen Ulrik , Al-Shahrour Fátima , Lopez-Bigas Nuria , Hovland Randi , Cuppen Edwin , Valencia Alfonso , Antoine-Poirel Helene , Brandell Richard Rosenquist , Scollen Serena , Marquez Juan Arenas , Belien Jeroen , De Nicolo Arcangela , De Maria Ruggero , Torrents David , Tonon Giovanni 
Published: October 2023

AbstractFor a real impact on healthcare, precision cancer medicine requires accessibility and interoperability of clinical and genomic data across centres and countries. Due to the heterogeneous digitization in Europe and worldwide, the definition of models for standardised data collection and usability becomes mandatory if countries want to work together on this mission. The European Union 1+Million Genomes (1+MG) initiative, supported by the Horizon 2020 Beyond 1 Million Genomes project, aims at outlining data models, guidance, best practices, and technical infrastructures for transnational access to sequenced genomes, including cancer genomes. Within the framework of the cancer-focused Working Group 9, we developed the 1+MG-Minimal Dataset for Cancer (1+MG-MDC)–a data model encompassing 140 items and organized in eight conceptual domains for the collection of cancer-related clinical information and genomics metadata. The 1+MG-MDC, which results from a multidisciplinary effort, leverages pre-existing models and emphasizes the annotation and traceability of multiple aspects relevant to the complex longitudinal path of the cancer disease and its treatment. We strived to make the 1+MG-MDC easy to adopt, yet comprehensive, addressing the needs of both clinicians and researchers. We will periodically revise and update it to ensure it remains fit for purpose. We propose the 1+MG-MDC as a model to create homogeneous databases, which would, in turn, guide discussions on clinical and genomic features with prognostic or therapeutic value and foster real-world data research.
The CLAMP GA-binding transcription factor regulates heat stress-induced transcriptional repression by associating with 3D loop anchors
Authors: Aguilera Joseph , Duan Jingyue , Lee So-min , Ray Mukulika , Larschan Erica 
Published: October 2023

AbstractIn order to survive when exposed to heat stress (HS), organisms activate stress response genes and repress constitutive gene expression to prevent the accumulation of potentially toxic RNA and protein products. Although many studies have elucidated the mechanisms that drive HS-induced activation of stress response genes across species, little is known about repression mechanisms or how genes are targeted for activation versus repression context-specifically. The mechanisms of heat stress-regulated activation have been well-studied inDrosophila,in which the GA-binding transcription factor GAF is important for activating genes upon heat stress. Here, we show that a functionally distinct GA-binding transcription factor (TF) protein, CLAMP (Chromatin-linked adaptor for MSL complex proteins), is essential for repressing constitutive genes upon heat stress but not activation of the canonical heat stress pathway. HS induces loss of CLAMP-associated 3D chromatin loop anchors associated with different combinations of GA-binding TFs prior to HS if a gene becomes repressed versus activated. Overall, we demonstrate that CLAMP promotes repression of constitutive genes upon HS, and repression and activation are associated with the loss of CLAMP-associated 3D chromatin loops bound by different combinations of GA-binding TFs.
Cell-type-specific characterization of miRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution
Authors: de Sande Ana Hernández , Turunen Tanja , Bouvy-Liivrand Maria , Örd Tiit , Palani Senthil , Tundidor-Centeno Celia , Liljenbäck Heidi , Virta Jenni , Smålander Olli-Pekka , Sinkkonen Lasse , Sauter Thomas , Roivainen Anne , Lönnberg Tapio , Kaikkonen Minna U , Heinäniemi Merja 
Published: October 2023

ABSTRACTMicroRNAs (miRNAs) are a class of regulatory non-coding RNAs that finetune cellular functions by modulating the stability and abundance of their target mRNAs, thereby contributing to regulation of tissue homeostasis. MiRNA genes are transcribed similarly to protein-coding genes and recent studies have enabled their annotation and quantification genome-wide from bulk nascent transcriptomes. Here, we developed an approach to quantify and integrate miRNA gene signatures into single-cell studies. To characterize miRNA gene expression dynamics, we first compared the suitability of droplet and plate-based single-cell RNA-sequencing (scRNA-seq) platforms using the matched datasets provided by the Tabula Muris Senis and Tabula Sapiens consortiums. We found high concordance between the platforms and with cell type-specific bulk expression data. Based on the comprehensive aging profiles, our analysis comparing spleen immune cells between young and old mice revealed a concordant regulation of miRNAs involved in senescence and inflammatory pathways in multiple immune cell types, including up-regulation of mmu-mir-146a, mmu-mir-101a and mmu-mir-30 family genes. To study the aberrant regulation of immune cell homeostasis and tissue inflammation that pre-dispose to aging-related disease development, we collected transcriptome profiles from atherosclerosis development in LDLR-/-ApoB100/100mice. We found an elevated myeloid cell proportion in the adipose tissue and further characterized the cell subtypes based on reproducible transcriptome clusters. We then compared miRNA gene expression in early versus late disease and upon inflammatory challenge to monitor different stages during disease progression. At atherosclerotic stage, pro-inflammatory mmu-mir-511 expression increased in several macrophage subtypes, while immunosuppressive mmu-mir-23b∼mir-24-2∼mir-27b up-regulation was specific to Trem2+ lipid-associated macrophages. The infiltrating monocytes up-regulated mmu-mir-1938 and mmu-mir-22 expression and in classical monocytes maturation further increased mmu-mir-221∼222, mmu-mir-511 and mmu-mir-155 expression. To validate that these changes detected from single cell profiles represent miRNA gene transcriptional regulation, we used nascent transcriptomics data fromex vivomacrophage cultures with pro-inflammatory stimulation, confirming both rapid and long-lasting transcriptional activation of the miRNA loci studied. Collectively, our work enables integrating miRNA gene analysis to current single cell genomics pipelines and facilitates characterization of miRNA regulatory networks during aging and disease development.
Ice thickness control and measurement in the VitroJet for time-efficient single particle structure determination
Authors: Henderikx Rene J.M. , Schotman Maaike J.G. , Shahzad Saba , Fromm Simon A. , Mann Daniel , Hennies Julian , Heidler Thomas V. , Ashtiani Dariush , Hagen Wim J.H. , Jeurissen Roger J.M. , Mattei Simone , Peters Peter J. , Sachse Carsten , Beulen Bart W.A.M.M. 
Published: October 2023

AbstractEmbedding biomolecules in vitreous ice of optimal thickness is critical for structure determination by cryo-electron microscopy. Ice thickness assessment and selection of suitable holes for data collection are currently part of time-consuming preparatory routines performed on expensive electron microscopes. To address this challenge, a routine has been developed to measure ice thickness during sample preparation using an optical camera integrated in the VitroJet. This method allows to estimate the ice thickness with an error below ± 20 nm for ice layers in the range of 0 – 70 nm. Additionally, we implemented pin printing to reproduce and control sample deposition in the VitroJet. The median ice thickness can be reproduced with a standard deviation below ± 11 nm for thicknesses up to 75 nm. Therefore, the ice thickness of buffer-suspended holes on an EM grid can be tuned and measured within the working range relevant for single particle cryo-EM. Single particle structures of apoferritin were determined at two distinct thicknesses of 30 nm and 70 nm. These reconstructions demonstrate the importance of ice thickness for time-efficient cryo-EM structure determination.HighlightsMethods in the VitroJet allow for on-the-fly ice thickness tuning and measurementThe optical camera can estimate ice thickness ranging from 0 – 70 ± 20 nmPin printing enables to reproduce and control median ice thickness up to 75 ± 11 nmStructures of apoferritin require 3.7 x fewer particles in 30 compared to 70 nm ice
Widespread prevalence of a post-translational modification in activation of an essential bacterial DNA damage response
Authors: Kamat Aditya , Tran Ngat T. , Sharda Mohak , Sontakke Neha , Le Tung B. K. , Badrinarayanan Anjana 
Published: October 2023

AbstractDNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The mechanisms by which bacteria detect and respond to such damage remain incompletely understood. Here, we discover a highly conserved but previously uncharacterized transcription factor (Cada2), which orchestrates a methylation-dependent adaptive response inCaulobacter. This response operates independently of the SOS response, governs the expression of genes crucial for direct repair, and is essential for surviving methylation-induced damage. Our molecular investigation of Cada2 reveals a cysteine methylation-dependent post-translational modification and mode of action distinct from itsE. colicounterpart, a trait conserved across all bacteria harboring a Cada2-like homolog instead. Extending across the bacterial kingdom, our findings support the notion of divergence and co-evolution of adaptive response transcription factors and their corresponding sequence-specific DNA motifs. Despite this diversity, the ubiquitous prevalence of adaptive response regulators underscores the significance of a transcriptional switch, mediated by methylation post-translational modification, in driving a specific and essential bacterial DNA damage response.
Absolute Quantification of Viral Proteins from Pseudotyped Vesicular Stomatitis Virus (VSV-GP) using Ultra High-Performance Liquid Chromatography- Multiple Reaction Monitoring (UPLC-MRM)
Authors: Basu Rajeswari , Dambra Richard , Jiang Di , Schätzlein Sophia A. , Njiyang Shu , Ashour Joseph , Chiramel Abhilash I. , Vigil Adam , Papov Vladimir V. 
Published: October 2023

ABSTRACTThe rapidly developing field of oncolytic virus (OV) therapy necessitates development of new and improved analytical approaches for characterization of the virus during production and development. Accurate monitoring and absolute quantification of viral proteins is crucial for OV product characterization and can facilitate the understanding of infection, immunogenicity, and development stages of viral replication. Targeted mass spectrometry methods, like multiple reaction monitoring (MRM), offers a robust way to directly detect and quantify specific targeted proteins represented by surrogate peptides. We have leveraged the power of MRM by combining ultra-high performance liquid chromatography (UPLC) with a Sciex 6500 triple stage quadrupole mass spectrometer to develop an assay that accurately and absolutely quantifies the structural proteins of a pseudotyped vesicular stomatitis virus intended for use as a new biotherapeutic (designated hereafter as VSV-GP) to differentiate it from native VSV. The new UPLC-MRM method provides absolute quantification with the use of heavy labeled reference standard surrogate peptides. When added in known exact amounts to standards and samples, the reference standards normalize and account for any small perturbations during sample preparation and/or instrument performance, resulting in accurate and precise quantification. Because of the multiplexed nature of MRM all targeted proteins are quantified at the same time. The optimized assay has been enhanced to quantify the ratios of the processed GP1 and GP2 proteins while simultaneously measuring any remaining or unprocessed form of the envelope protein GPC (full-length GPC).IMPORTANCEDevelopment of oncolytic viral therapy has gained considerable momentum in the recent years. VSV-GP is a new biotherapeutic emerging in the oncolytic viral therapy platform. Novel analytical assays that can accurately and precisely quantify the viral proteins are a necessity for the successful development of viral vector as a biotherapeutic. We developed a UPLC-MRM based assay to quantify the absolute concentrations of the different structural proteins of VSV-GP. The complete processing of GPC is a pre-requisite for infectivity of the virus. The assay extends the potential for quantifying full-length GPC, which provides an understanding of the processing of GPC (along with the quantification of GP1 and GP2 separately). We used this assay in tracking GPC processing in HEK-293-F production cell lines infected with VSV-GP.
Automatic essay scoring for discussion forum in online learning based on semantic and keyword similarities
Authors: Dhini Bachriah Fatwa , Girsang Abba Suganda , Sufandi Unggul Utan , Kurniawati Heny 
Published: October 2023

PurposeThe authors constructed an automatic essay scoring (AES) model in a discussion forum where the result was compared with scores given by human evaluators. This research proposes essay scoring, which is conducted through two parameters, semantic and keyword similarities, using a SentenceTransformers pre-trained model that can construct the highest vector embedding. Combining these models is used to optimize the model with increasing accuracy.Design/methodology/approachThe development of the model in the study is divided into seven stages: (1) data collection, (2) pre-processing data, (3) selected pre-trained SentenceTransformers model, (4) semantic similarity (sentence pair), (5) keyword similarity, (6) calculate final score and (7) evaluating model.FindingsThe multilingual paraphrase-multilingual-MiniLM-L12-v2 and distilbert-base-multilingual-cased-v1 models got the highest scores from comparisons of 11 pre-trained multilingual models of SentenceTransformers with Indonesian data (Dhini and Girsang, 2023). Both multilingual models were adopted in this study. A combination of two parameters is obtained by comparing the response of the keyword extraction responses with the rubric keywords. Based on the experimental results, proposing a combination can increase the evaluation results by 0.2.Originality/valueThis study uses discussion forum data from the general biology course in online learning at the open university for the 2020.2 and 2021.2 semesters. Forum discussion ratings are still manual. In this survey, the authors created a model that automatically calculates the value of discussion forums, which are essays based on the lecturer's answers moreover rubrics.
The effect of hexagonal boron nitride nanopowders addition on the mechanical behaviors of basalt fabric reinforced composites
Authors: Bakal Gumus Fatma , Yapici Ahmet 
Published: October 2023

Purpose
The purpose of this paper is to investigate the effect of doping element on the structural, thermal properties, mechanical performance and the failure mechanism of hexagonal nano boron nitride (h-BN)-reinforced basalt fabric (BF)/epoxy composites produced by hand lay-up and vacuum bagging technique. h-BN particles doped to composite materials increased the tensile, bending and impact strength of the composite at certain rates while 1 Wt. % h- BN addition shows the highest tensile and flexural strength.

Design/methodology/approach
The epoxy resin was doped with h-BN nanopowder at the certain rates (0, 1, 2 and 4 Wt.%) and the epoxy: hardener ratios used in the study were selected as 80%: 20% by weight. Then, with the aid of a roller by hand lay-up method, a mixture of epoxy + hardeners containing nanoparticles and nanoparticle-free were fed onto BFs, 12 layers of each dimension 30 cm × 30 cm. The surplus epoxy resin was moved away from the composite sheets using the vacuum bagging process and left to cure at room temperature for 24 h. ASTM D3039 for tensile, D7264 for three-point bending and D256 for Izod impact test were performed for the mechanical tests. After the tensile test, the morphologies of the fracture surface were examined with a stereomicroscope and various failure mechanisms are highlighted.

Findings
In this study, a series of basalt/epoxy composites with h-BN nanopowders have been prepared to identify the effect of filler ratio on mechanical properties. It has been known from the results of mechanical experiments that the addition of h-BN improves the mechanical performance of materials at a certain rate. The tensile and flexural strengths of h-BN doped composites, increase for concentrations of 1 Wt.% h-BN, but decrease with the increasing content of it. The basalt/epoxy resin composite with higher mechanical properties could be a potential material in the automotive and aerospace industries.

Originality/value
The aim of this study is to contribute to literature within the context of this new combination of composites and their mechanical properties, failure mechanisms. It presents detailed characterization of each composite by using X-ray differaction (XRD), differential scanning calorimetry (DSC), fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy.
Role of bigdata analytics in improving drivers of omni-channel retailing for improving logistics experience
Authors: Mishra Ruchi , Gangwar Hemlata , Sahoo Saumyaranjan 
Published: October 2023

PurposeThe objective of this research is to evaluate and rank the factors influencing omnichannel (OC) logistics, while also investigating the significant impact of big data analytics in improving these drivers of OC logistics.Design/methodology/approachUsing exploratory sequential mixed method design, an in-person interview survey was conducted to identify and stratifies the enablers of OC retailing. These interviews were supplemented with a case study in an apparel firm to prioritise the enablers of OC logistics. Further, a survey was conducted to understand the role of big data analytics in improving drivers of OC logistics as well as the role of Individual capability and organisational capability in big data usage for omnichannel retailing.FindingsFindings represent that information management is the most important driver followed by inventory management and network design for improving OC logistics. Further, significant relationship between big data analytics and drivers of omnichannel logistics has been reported.Practical implicationsThis study identifies and classifies the drivers of OC retailing relating to their level of criticality in OC logistics which will assists practitioners to prioritise their tasks for the successful development of OC logistics. The study will also help practitioners to use BDA for developing the drivers of OC.Originality/valueThe study substantiates and adds to the BDA literature by emphasising the positive role of BDA in development of OC driver and highlighting the significant role of drivers of BDA in its usage.
Use of AHP and grey fixed weight clustering to assess the maturity level of strategic communication management in Brazilian startups
Authors: Timóteo Thiago Rodrigues , Cazeri Gustavo Tietz , Moraes Gustavo Hermínio Salati Marcondes de , Sigahi Tiago F.A.C. , Zanon Lucas Gabriel , Rampasso Izabela Simon , Anholon Rosley 
Published: October 2023

PurposeThe aim of this research was to evaluate the maturity level of strategic communication management implemented by Brazilian startups.Design/methodology/approachThis study employed the analytic hierarchy process (AHP), survey and Grey Fixed Weight Clustering modeling techniques. Three experts with extensive academic and practical experience in the subject participated in the AHP process, providing their opinions on the relative importance of eight variables associated with the topic under investigation, thus enabling their prioritization. Concurrently, data were collected through a survey from 23 respondents who have extensive knowledge about the realities of Brazilian startups. The weights derived from the AHP and the survey data were utilized in the Grey Fixed Weight Clustering modeling.FindingsBased on the opinions of the 23 respondents, the level of implementation of practices related to strategic management, brand management, external image management and internal communication management is superficial. In addition, according to the majority of experts, Brazilian startups exhibited a medium level of maturity to address the key challenges related to communication management. Furthermore, this study reveals that the variables “financial resources allocation,” “stakeholder relationship” and “brand management” were deemed the most significant for the model.Originality/valueThe contributions presented herein can be beneficial for both researchers and startup managers seeking to enhance communication strategies in their organizations. This research also contributes by highlighting how grey systems theory can be extremely useful for conducting decision-making analyses in the context of startups, which is characterized by uncertainty and imprecise information.