bluuebunny/crossref_metadata_2025_split huggingface dataset:
Working memory-related activity in catecholaminergic nuclei in schizophrenia
Authors: Amekran Nada , Mäki-Marttunen Verónica 
Published: August 2023

AbstractSchizophrenia is a complex psychiatric condition in which cortical, subcortical and neuromodulatory alterations have been implicated in its symptom expression. Long standing views of schizophrenia symptoms have posed that alterations in catecholaminergic systems, which explain psychotic symptoms, may be also associated with the cognitive impairments commonly observed in this condition. However, evidence on the involvement of catecholaminergic regions on cognitive functions in schizophrenia remains scarce. Working memory is one cognitive domain where schizophrenia patients present more impairments at higher levels of cognitive load. Here we explored the activation of catecholaminergic regions during a working memory task in schizophrenia. We reanalyzed an openly available functional magnetic resonance imaging dataset where schizophrenia patients and healthy controls were scanned while performing the N-back task. We compared activation of two dopaminergic areas, ventral tegmental area and substantia nigra, and of a noradrenergic nucleus, locus coeruleus, to the presentation of targets, and compared three different levels of cognitive load (0-, 1– and 2-back). We found that across nuclei, higher load was related to lower activation. Furthermore, schizophrenia patients showed reduced activation at the highest load level when compared to healthy controls. These findings point to catecholaminergic systems as mediators of the deficits in effort processing in schizophrenia. Our study lends further support for the importance of including catecholaminergic systems in the mechanisms of cognitive deficits in schizophrenia.
Social contact patterns following the COVID-19 pandemic: a snapshot of post-pandemic behaviour from the CoMix study
Authors: Jarvis Christopher I , Coletti Pietro , Backer Jantien A , Munday James D , Faes Christel , Beutels Philippe , Althaus Christian L. , Low Nicola , Wallinga Jacco , Hens Niel , Edmunds W John 
Published: August 2023

AbstractBackgroundThe COVID-19 pandemic led to unprecedented changes in behaviour. To estimate if these persisted a final new round of the CoMix survey was conducted in four countries at a time when all societal restrictions had been lifted for several months.MethodsWe conducted a survey on a nationally representative sample in the UK, Netherlands (NL), Belgium (BE), and Switzerland (CH). Participants were asked about their contacts and behaviours on the previous day. We calculated contact matrices and compared the contact levels to a pre-pandemic baseline to estimate R0.ResultsData collection occurred from 17 November to 7 December 2022. 7,477 participants were recruited. Some were asked to undertake the survey on behalf of their children. Only 14.4% of all participants reported wearing a facemask on the previous day, varying between 6.7% in NL to 17.8% in CH. Self-reported vaccination rates in adults were similar for each country at around 86%. Trimmed mean recorded contacts were highest in NL with 9.9 (95% confidence interval [CI] 9.0 to 10.8) contacts per person per day and lowest in CH at 6.0 (95% CI 5.4 to 6.6). The number of contacts at home were similar between the countries. Contacts at work were lowest in the UK (1.4 contacts per person per day) and highest in NL at 2.8 contacts per person per day. Other contacts were also lower in the UK at 1.6 per person per day (95% CI 1.4 to 1.9) and highest in NL at 3.4 recorded per person per day (95% CI 4.0 to 4.0). Using the next-generation approach suggests that R0for a close-contact disease would be roughly half pre-pandemic levels in the UK, 80% in NL and intermediate in the other two countries.ConclusionsThe pandemic appears to have resulted in lasting changes in contact patterns that would be expected to have an impact on the epidemiology of many different pathogens. Further post-pandemic surveys are necessary to confirm this finding.
CRISPR-Hybrid: A CRISPR-Mediated Intracellular Directed Evolution Platform for RNA Aptamers
Authors: Su-Tobon Qiwen , Fan Jiayi , Feeney Kevin , Ren Hongyuan , Autissier Patrick , Wang Peiyi , Huang Yingzi , Niu Jia 
Published: August 2023

AbstractRecent advances in gene editing and precise regulation of gene expression based on CRISPR technologies have provided powerful tools for the understanding and manipulation of gene functions. Fusing RNA aptamers to the sgRNA of CRISPR can recruit cognate RNA-binding protein (RBP) effectors to target genomic sites, and the expression of sgRNA containing different RNA aptamers permit simultaneous multiplexed and multifunctional gene regulations. Here, we report an intracellular directed evolution platform for RNA aptamers against intracellularly expressed RBPs. We optimized a bacterial CRISPR-hybrid system coupled with FACS, and identified novel high affinity RNA aptamers orthogonal to existing aptamer-RBP pairs. Application of orthogonal aptamer-RBP pairs in multiplexed CRISPR allowed effective simultaneous transcriptional activation and repression of endogenous genes in mammalian cells.
Pangenome evaluation of gene essentiality inStreptococcus pyogenes
Authors: Jespersen Magnus G. , Hayes Andrew J. , Tong Steven Y. C. , Davies Mark R. 
Published: August 2023

AbstractPopulations of bacterial pathogens are made of strains that often have variable gene content, termed the pangenome. Variations in the genetic makeup of a single strain can alter bacterial physiology and fitness in response to different environmental stimuli. To define biologically relevant genes within a genome, genome-wide knockout transposon mutant libraries have been used to identify genes essential for survival or virulence in a particular strain. Such phenotypic studies have been applied in four different genotypes of the major human pathogenStreptococcus pyogenes, yet challenges exist in comparing results across studies conducted in different genetic backgrounds and conditions. To advance genotype-phenotype inferences within a population genomic framework of 250S. pyogenesreference genomes, we systematically re-analysed publicly available transposon sequencing datasets fromS. pyogenesusing a transposon sequencing specific analysis pipeline, Transit. Across 4 genetic backgrounds and 9 phenotypic conditions, 311 genes were highly essential for survival, corresponding to ∼22% of the core genome. Among the 311 genes, functions related to information storage, and processing were overrepresented. Genes associated with cellular processing and signalling were of significantly higher essentiality underin vivoconditions (animal models with differing disease manifestation and site of colonisation) compared toin vitro(varying types of culture media). Finally, essential operons acrossS. pyogenesgenotypes were defined, with an increased number of essential operons detected underin vivoconditions. This study provides an extendible database to which new studies can be added, and a searchable html-based resource to direct future investigations intoS. pyogenespopulation biology.ImportanceStreptococcus pyogenesis a human adapted pathogen occupying restricted ecological niches. Understanding essentiality of genes across different strains and experimental conditions is important to direct research questions and efforts to prevent the large burden of disease caused byS. pyogenes. To this end we systematically reanalysed transposon sequencing studies inS. pyogenesusing transposon sequencing specific methods, integrating them into an extendible meta-analysis framework. This provides a repository of gene essentiality inS. pyogenesfor the community to guide future phenotypic studies.
Escherichia coliMicrocin B17 as a chassis for the development of novel antimicrobial peptides
Authors: Withanage Shamal , Masschelein Joleen , Pinheiro Vitor B. 
Published: August 2023

AbstractAntimicrobial resistance remains an urgent and growing global health problem. Peptides with antimicrobial activity are widespread in nature but are rarely harnessed for application, making them an underexplored and untapped resource. Many harbor post-translational modifications, which are essential for function and have evolved alongside specialized export and immunity machineries – leading to the current paradigm that natural sequences cannot be changed, and curtailing their development as antimicrobial agents. Nonetheless, we found sufficient ambiguity in literature to question if that remained true forE. coliMccB17. We demonstrate that its natural machinery for synthesis, export and immunity, can be co-opted as a platform for novel azole-modified antimicrobial peptide discovery. We show that the sequence space available for exploration is large and densely populated with functional sequences.One-Sentence SummaryE. colican be harnessed as anin vivoplatform for the isolation of novel antimicrobial azole-modified peptides.
Common as well as unique methylation-sensitive DNA regulatory elements in three mammalian SLC9C1 genes
Authors: Gardner Cameron C. , Abele Jason A. , Winkler Thomas J. , Reckers Caroline N. , Anas Sydney A. , James Paul F. 
Published: August 2023

AbstractThe SLC9C1 gene (which encodes the NHE10 protein) is essential for male fertility in both mice and humans, however the epigenetic mechanisms regulating its testis/sperm-specific gene expression have yet to be studied. Here we identify and characterize DNA regulatory elements of the SLC9C1 gene across three mammalian species: mouse, rat, and human. First,in silicoanalysis of these mammalian SLC9C1 genes identified a CpG island located upstream of the transcription start site in the same relative position in all three genes. Further analysis reveals that this CpG island behaves differently, with respect to gene regulatory activity, in the mouse SLC9C1 gene than it does in the rat and human SLC9C1 gene. The mouse SLC9C1 CpG island displays strong promoter activity by itself and seems to have a stronger gene regulatory effect than either the rat or human SLC9C1 CpG islands. While the function of the upstream SLC9C1 CpG island may be divergent across the three studied species, it appears that the promoters of these three mammalian SLC9C1 genes share similar DNA methylation-sensitive regulatory mechanisms. All three SLC9C1 promoter regions are differentially methylated in lung and testis, being more hypermethylated in lung relative to the testis, and DNA sequence alignments provide strong evidence of primary sequence conservation. Luciferase assays reveal thatin vitromethylation of constructs containing different elements of the three SLC9C1 genes largely exhibit methylation-sensitive promoter activity (reduced promoter activity when methylated) in both HEK 293 and GC-1spg cells. In total, our data suggest that the DNA methylation-sensitive elements of the mouse, rat, and human SLC9C1 promoters are largely conserved, while the upstream SLC9C1 CpG island common to all three species seems to perform a different function in mouse than it does in rat and human. This work provides evidence that while homologous genes can all be regulated by DNA methylation-dependent epigenetic mechanisms, the location of the specific cis-regulatory elements responsible for this regulation can differ across species.
SCP Viz – A universal graphical user interface for single protein analysis in single cell proteomics datasets
Authors: Warshanna Ahmed , Orsburn Benjamin C. 
Published: August 2023

AbstractSingle cell proteomics (SCP) requires the analysis of dozens to thousands of single human cells to draw biological conclusions. However, assessing of the abundance of single proteins in output data presents a considerable challenge, and no simple universal solutions currently exist. To address this, we developed SCP Viz, a statistical package with a graphical user interface that can handle small and large scale SCP output from any instrument or data processing software. In this software, the abundance of individual proteins can be plotted in a variety of ways, using either unadjusted or normalized outputs. These outputs can also be transformed or imputed within the software. SCP Viz offers a variety of plotting options which can help identify significantly altered proteins between groups, both before and after quantitative transformations. Upon the discovery of subpopulations of single cells, users can easily regroup the cells of interest using straightforward text-based filters. When used in this way, SCP Viz allows users to visualize proteomic heterogeneity at the level of individual proteins, cells, or identified subcellular populations. SCP Viz is compatible with output files from MaxQuant, FragPipe, SpectroNaut, and Proteome Discoverer, and should work equally well with other formats. SCP Viz is publicly available athttps://github.com/orsburn/SCPViz. For demonstrations, users can download our test data from GitHub and use an online version that accepts user input for analysis athttps://orsburnlab.shinyapps.io/SCPViz/.Abstract graphic
PTPN2 copper-sensing rapidly relays copper level fluctuations into EGFR/CREB activation and associatedCTR1transcriptional repression
Authors: Ross Matthew O. , Xie Yuan , Owyang Ryan C. , Ye Chang , Zbihley Olivia N.P. , Lyu Ruitu , Wu Tong , Wang Pingluan , Karginova Olga , Olopade Olufunmilayo I. , Zhao Minglei , He Chuan 
Published: August 2023

AbstractFluxes in human intra- and extracellular copper levels recently garnered attention for roles in cellular signaling, including affecting levels of the signaling molecule cyclic adenosine monophosphate (cAMP). We herein applied an unbiased temporal evaluation of the whole-genome transcriptional activities modulated by fluctuations in copper levels to identify the copper sensor proteins responsible for driving these activities. We found that fluctuations in physiologically-relevant copper levels rapidly modulate EGFR/MAPK/ERK signal transduction and activation of the transcription factor cAMP response element-binding protein (CREB). Both intracellular and extracellular assays support Cu1+inhibition of the EGFR-phosphatase PTPN2 (and potentially the homologous PTPN1)–via direct ligation to the PTPN2 active site cysteine side chain–as the underlying mechanism of copper-stimulated EGFR signal transduction activation. Depletion of copper represses this signaling pathway. We additionally showi) copper supplementation drives transcriptional repression of the copper importerCTR1andii) CREB activity is inversely correlated withCTR1expression. In summary, our study reveals PTPN2 as a physiological copper sensor and defines a regulatory mechanism linking feedback control of copper-stimulated MAPK/ERK/CREB-signaling andCTR1expression, thereby uncovering a previously unrecognized link between copper levels and cellular signal transduction.
Mutation in SLC45A2 leads to loss of melanin in parrot feathers
Authors: Roy Shatadru Ghosh , Bakhrat Anna , Abdu Moty , Afonso Sandra , Pereira Paulo , Carneiro Miguel , Abdu Uri 
Published: August 2023

AbstractBird plumage coloration is a complex and multi-factorial process that involves both genetic and environmental factors. Diverse pigment groups contribute to plumage variation in different birds. In parrots, the predominant green color results from the combination of two different primary colors-yellow and blue. Psittacofulvin, a pigment uniquely found in parrots, is responsible for the yellow coloration, while blue is suggested to be the result of light scattering by feather nanostructures and melanin granules. So far, genetic control of melanin-mediated blue coloration has been elusive. In this study, we demonstrated that feather from theyellowmutant rose-ringed parakeet displays loss of melanosome granules in spongy layer of feather barb. Using whole genome sequencing, we found that mutation in SLC45A2, an important solute carrier protein in melanin synthetic pathway, is responsible for the sex-linkedyellowphenotype in rose-ringed parakeet. Intriguingly, one of the mutations, P53L found in yellowP. krameriis already reported as P58A/S in the human albinism database, known to be associated with human OCA4. We further showed that mutations inSLC45A2gene affect melanin production also in other members of Psittaculidae family such as alexandrine, and plum-headed parakeets. Additionally, we demonstrate that the mutations associated with the sex-linkedyellowphenotype, localized within the transmembrane domains of the SLC45A2 protein, affect the protein localization pattern. This is the first evidence of plumage color variation involvingSLC45A2in parrots and confirmation of associated mutations in the transmembrane domains of the protein that affect its localization.Article SummaryThe vibrant green tone of parrot plumage emerges from a blend of yellow and blue. While yellow comes from a unique pigment psittacofulvin, the genetics of blue structural color has puzzled scientists. Through novel genetic study, here we identified mutations inSLC45A2gene, causing loss of melanin in feathers that contributes to the blue structural color. This insight opens a new chapter in understanding avian coloration and the complex interplay of feather microstructure and genetics in nature’s palette.
CA-CD: context-aware clickbait detection using new Chinese clickbait dataset with transfer learning method
Authors: Wang Hei-Chia , Maslim Martinus , Liu Hung-Yu 
Published: August 2023

PurposeA clickbait is a deceptive headline designed to boost ad revenue without presenting closely relevant content. There are numerous negative repercussions of clickbait, such as causing viewers to feel tricked and unhappy, causing long-term confusion, and even attracting cyber criminals. Automatic detection algorithms for clickbait have been developed to address this issue. The fact that there is only one semantic representation for the same term and a limited dataset in Chinese is a need for the existing technologies for detecting clickbait. This study aims to solve the limitations of automated clickbait detection in the Chinese dataset.Design/methodology/approachThis study combines both to train the model to capture the probable relationship between clickbait news headlines and news content. In addition, part-of-speech elements are used to generate the most appropriate semantic representation for clickbait detection, improving clickbait detection performance.FindingsThis research successfully compiled a dataset containing up to 20,896 Chinese clickbait news articles. This collection contains news headlines, articles, categories and supplementary metadata. The suggested context-aware clickbait detection (CA-CD) model outperforms existing clickbait detection approaches on many criteria, demonstrating the proposed strategy's efficacy.Originality/valueThe originality of this study resides in the newly compiled Chinese clickbait dataset and contextual semantic representation-based clickbait detection approach employing transfer learning. This method can modify the semantic representation of each word based on context and assist the model in more precisely interpreting the original meaning of news articles.
Enhancing the adoption of building information modeling in the Iranian AEC sector: insights from a Delphi study
Authors: Hatami Nazanin , Rashidi Ali 
Published: August 2023

PurposeArchitecture, engineering and construction (AEC) is an important industry worldwide and one of the largest economic sectors in several developing countries, particularly in Iran. The Iranian AEC sector suffers from low productivity and needs to adopt building information modeling (BIM) to reduce inefficiencies. Therefore, this paper was conducted to identify the BIM barriers and propose practical solutions to overcome them in Iran.Design/methodology/approachA comprehensive literature review, two rounds of the Delphi technique and semi-structured interviews with 12 Iranian experts in the AEC sector were conducted. The data were analyzed using the mean score, standard deviation and nonparametric tests.FindingsThe present study identified 26 BIM barriers in the Iranian AEC community and provided practical strategies for improving BIM adoption. The identified barriers were categorized into six main groups including source barriers, financial barriers, unawareness barriers, organizational barriers, regulatory barriers and market-demand barriers. The main three BIM barriers in Iran were the lack of government intervention, change-resistant and the gap between industry and academia. Kruskal–Wallis tests revealed that there are no statistically significant differences in perceptions of BIM barriers between respondents. The Mann–Whitney test indicated that there is no statistically significant difference in perceptions between engineers and architects except for one.Originality/valueThere are few studies on BIM adoption across developing countries, particularly in Iran. Moreover, the results can also be used in other developing nations with similar conditions.
Consumer avoidance toward message stream advertising on mobile social media: a stimulus-organism-response perspective
Authors: Li Xiaodong , Liu Zibing , Chen Yuan , Ren Ai 
Published: August 2023

PurposeMessage stream advertising (MSA) has become an increasingly popular option for advertising on mobile social media. However, MSA is often avoided by consumers, and this avoidance deserves more research attention. The purpose of this study is therefore to identify the underlying mechanism and key variables that affect consumer avoidance of MSA in the context of mobile social media.Design/methodology/approachA face-to-face survey was administered to current mobile users of WeChat (N = 438). Structural equation modeling was conducted to test the relationships in the research model.FindingsResults revealed that mobile consumers employ mechanical avoidance methods (i.e. zipping, muting and zapping) against MSA. The findings also demonstrated that advertising intrusiveness (stimulus) is directly linked to negative emotions, perceived entertainment and sense of control (organism), which, in turn, relate to MSA avoidance (response).Originality/valueThe study contributes to the MSA avoidance literature by using the stimulus-organism-response model to deepen the understanding of consumers' MSA avoidance on mobile social media, and it suggests important managerial implications for advertising practitioners and platform operators.
Futuristic portfolio optimization problem: wavelet based long short-term memory
Authors: Abolmakarem Shaghayegh , Abdi Farshid , Khalili-Damghani Kaveh , Didehkhani Hosein 
Published: August 2023

Purpose
This paper aims to propose an improved version of portfolio optimization model through the prediction of the future behavior of stock returns using a combined wavelet-based long short-term memory (LSTM).

Design/methodology/approach
First, data are gathered and divided into two parts, namely, “past data” and “real data.” In the second stage, the wavelet transform is proposed to decompose the stock closing price time series into a set of coefficients. The derived coefficients are taken as an input to the LSTM model to predict the stock closing price time series and the “future data” is created. In the third stage, the mean-variance portfolio optimization problem (MVPOP) has iteratively been run using the “past,” “future” and “real” data sets. The epsilon-constraint method is adapted to generate the Pareto front for all three runes of MVPOP.

Findings
The real daily stock closing price time series of six stocks from the FTSE 100 between January 1, 2000, and December 30, 2020, is used to check the applicability and efficacy of the proposed approach. The comparisons of “future,” “past” and “real” Pareto fronts showed that the “future” Pareto front is closer to the “real” Pareto front. This demonstrates the efficacy and applicability of proposed approach.

Originality/value
Most of the classic Markowitz-based portfolio optimization models used past information to estimate the associated parameters of the stocks. This study revealed that the prediction of the future behavior of stock returns using a combined wavelet-based LSTM improved the performance of the portfolio.