bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allosteric Modulation of Fluorescence Revealed by Hydrogen Bond Dynamics in a Genetically Encoded Maltose Biosensor
Authors: Berksoz Melike , Atilgan Canan 
Published: December 2023

ABSTRACTGenetically encoded fluorescent biosensors (GEFBs) proved to be reliable tracers for many metabolites and cellular processes. In the simplest case, a fluorescent protein (FP) is genetically fused to a sensing protein which undergoes a conformational change upon ligand binding. This drives a rearrangement in the chromophore environment and changes the spectral properties of the FP. Structural determinants of successful biosensors are revealed only in hindsight when the crystal structures of both ligand-bound and ligand-free forms are available. This makes the development of new biosensors for desired analytes a long trial-and-error process. In the current study, we conducted µs-long all atom molecular dynamics (MD) simulations of a maltose biosensor in both theapo(dark) andholo(bright) forms. We performed detailed hydrogen bond occupancy analyses to shed light on the mechanism of ligand induced conformational change in the sensor protein and its allosteric effect on the chromophore environment. We find that two strong indicators for distinguishing bright and dark states of biosensors are due to substantial changes in hydrogen bond dynamics in the system and solvent accessibility of the chromophore.
Identifying Developmental Changes in Functional Brain Connectivity Associated with Cognitive Functioning in Children and Adolescents with ADHD
Authors: Pho B , Stevenson RA , Mohzenszadeh Y , Stojanoski B 
Published: December 2023

AbstractChildren and adolescents diagnosed with Attention Deficit Hyperactivity Disorder (ADHD) often show deficits in various measures of higher-level cognition, such as, memory and executive functioning. Poorer high-level cognitive functioning in children with ADDH has been associated with differences in functional connectivity across the brain, including the frontoparietal network. However, little is known about the developmental changes to cortical functional connectivity profiles associated with higher-order cognitive abilities in this cohort. To characterize changes in the functional brain connectivity profiles related to higher-order cognitive functioning, we analyzed a large dataset(n=479) from the publicly available Healthy Brain Network which included fMRI data collected while children and adolescents between the ages of 6 and 16 watched a short movie-clip. The cohort was divided into two groups, neurotypical youth (n=106), and children and adolescents with ADHD (n=373). We applied machine learning models to functional connectivity profiles generated from the fMRI data to identify patterns of network connectivity that differentially predict cognitive abilities in our cohort of interest. We found, using out-of-sample cross validation, models using functional connectivity profiles in response to movie-watching successfully predicted IQ, visual spatial, verbal comprehension, and fluid reasoning in children ages 6 to 11, but not in adolescents with ADHD. The models identified connections with the default mode, memory retrieval, and dorsal attention networks as driving prediction during early and middle childhood, but connections with the somatomotor, cingulo-opercular, and frontoparietal networks were more important in middle childhood. This work demonstrated that computational models applied to neuroimaging data in response to naturalistic stimuli can identify distinct neural mechanisms associated with cognitive abilities at different developmental stages in children and adolescents with ADHD.
Pangenome comparison ofBacteroides fragilisgenomospecies unveil genetic diversity and ecological insights
Authors: Oles Renee E. , Terrazas Marvic Carrillo , Loomis Luke R. , Hsu Chia-Yun , Tribelhorn Caitlin , Ferre Pedro Belda , Ea Allison , Bryant MacKenzie , Young Jocelyn , Carrow Hannah C. , Sandborn William J. , Dulai Parambir , Sivagnanam Mamata , Pride David , Knight Rob , Chu Hiutung 
Published: December 2023

ABSTRACTBacteroides fragilisis a Gram-negative commensal bacterium commonly found in the human colon that differentiates into two genomospecies termed division I and II. We leverage a comprehensive collection of 694B. fragiliswhole genome sequences and report differential gene abundance to further support the recent proposal that divisions I and II represent separate species. In division I strains, we identify an increased abundance of genes related to complex carbohydrate degradation, colonization, and host niche occupancy, confirming the role of division I strains as gut commensals. In contrast, division II strains display an increased prevalence of plant cell wall degradation genes and exhibit a distinct geographic distribution, primarily originating from Asian countries, suggesting dietary influences. Notably, division II strains have an increased abundance of genes linked to virulence, survival in toxic conditions, and antimicrobial resistance, consistent with a higher incidence of these strains in bloodstream infections. This study provides new evidence supporting a recent proposal for classifying divisions I and IIB. fragilisstrains as distinct species, and our comparative genomic analysis reveals their niche-specific roles.
Transposase-Assisted Tagmentation: An Economical and Scalable Strategy for Single-Worm Whole-Genome Sequencing
Authors: Wang Zi , Ke Jinyi , Guo Zhengyang , Wang Yang , Lei Kexin , Wang Shimin , Chen Guanghan , shen Zijie , Li Wei , Ou Guangshuo 
Published: December 2023

AbstractAlphaMissense identifies 23 million human missense variants as likely pathogenic, but only 0.1% have been clinically classified. To experimentally validate these predictions, chemical mutagenesis presents a rapid, cost-effective method to produce billions of mutations in model organisms. However, the prohibitive costs and limitations in the throughput of whole-genome sequencing (WGS) technologies, crucial for variant identification, constrain its widespread application. Here, we introduce a Tn5 transposase-assisted tagmentation technique for conducting WGS inC. elegans,E. coli,S. cervisiae, andC. reinhardtii. This method, demands merely 20 minutes of hands-on time for a single worm or single-cell clones and incurs a cost below 10 US dollars. It effectively pinpoints causal mutations in mutants defective in cilia or neurotransmitter secretion and in mutants synthetically sterile with a variant analogous to the oncogenic BRAF(V600E) mutation. Integrated with chemical mutagenesis, our approach can generate and identify missense variants economically and efficiently, facilitating experimental investigations of missense variants in diverse species.
Genomic and Phenotypic Consequences of Bi-Directional Introgression Between Chinese and European Pig Breeds
Authors: Qiu Yibin , Liu Langqing , Huang Min , Ruan Donglin , Ding Rongrong , Zhang Zebin , Zheng Enqin , Wang Shiyuan , Deng Shaoxiong , Cheng Xinyan , Shi Jiaxin , Yang Yingshan , Zhou Fuchen , Huang Sixiu , Yang Huaqiang , Li Zicong , Cai Gengyuan , Yang Jie , Wu Zhenfang 
Published: December 2023

AbstractHistorically, Chinese indigenous pigs were introduced to Europe centuries ago with the aim of enhancing economically important traits in European breeds. In recent decades, there has been a reciprocal introduction of European commercial breeds to China for indigenous pig breeding. Our study investigated the genomes of 418 pigs, revealing a genomics landscape of bi-directional introgression patterns between Chinese and European pig populations. We noted a common occurrence of incomplete linkage disequilibrium between structural variations (SVs) and adjacent single-nucleotide polymorphisms (SNPs) in our population, suggesting that conventional SNP-based analyses might not adequately capture the effect of SVs. Therefore, we examine both the roles of population-level SNPs and SVs in bi-directional introgression patterns, and highlight a show case centered around theBMP2gene. We identified introgressed haplotypes and SVs originating from Southern Chinese indigenous pigs, dispersing widely across various European pig breeds. Concurrently, we noted that the introgressed European haplotypes and SVs have attained high frequencies in Northern Chinese indigenous breeds, likely contributing to improvements in body size. In summary, these findings underscore the significant role of introgression in shaping the genetic composition and phenotypic traits in modern pig breeds.
The dCMP deaminase DCTD and the E3 ligase TOPORS are central mediators of decitabine cytotoxicity
Authors: Carnie Christopher J. , Götz Maximilian J. , Palma-Chaundler Chloe S. , Weickert Pedro , Wanders Amy R. , Serrano-Benitez Almudena , Li Hao-Yi , Gupta Vipul , Blum Christian J. , Sczaniecka-Clift Matylda , Zagnoli-Vieira Guido , D’Alessandro Giuseppina , Richards Sean L. , Gueorguieva Nadia , Beli Petra , Stingele Julian , Jackson Stephen P. 
Published: December 2023

AbstractThe nucleoside decitabine (5-aza-dC) is used to treat several hematological cancers. Upon triphosphorylation and incorporation into DNA, 5-aza-dC induces covalent DNMT1 DNA-protein crosslinks (DPCs) and DNA hypomethylation. However, 5-aza-dC treatment success varies, and relapse is common. Using genome-scale CRISPR/Cas9 screens, we map factors determining 5-aza-dC susceptibility. Unexpectedly, we find that loss of the dCMP deaminase DCTD causes 5-aza-dC resistance, suggesting that 5-aza-dUMP generation underlies most 5-aza-dC cytotoxicity in wild-type cells. Combining results from a subsequent genetic screen in DCTD-deficient cells with identification of the proximal proteome of DNMT1-DPCs, we uncover the ubiquitin/SUMO1 E3 ligase, TOPORS, as a new DPC repair factor. TOPORS is recruited to DNMT1-DPCs in a SUMO-dependent manner and promotes their degradation. Our study suggests that 5-aza-dC-induced DPCs cause cytotoxicity when DPC repair is compromised, while cytotoxicity in wild-type cells arises from perturbed nucleotide metabolism and lays the foundations for the development of predictive biomarkers for decitabine treatment.
Adipose gene expression profiles and their associations with adaptations in Northern Finncattle, Mirandesa cattle, Yakutian cattle and Holstein cattle
Authors: Ruvinskiy Daniil , Amaral Andreia , Weldenegodguad Melak , Honkatukia Mervi , Lindeberg Heli , Peippo Jaana , Soppela Päivi , Stammler Florian , Uimari Pekka , Ginja Catarina , Kantanen Juha , Pokharel Kisun 
Published: December 2023

AbstractBackgroundThe drastic change in global climate has led to in-depth studies of the genetic resources of native cattle adapted to challenging environments. Native cattle breed data may harbor unique variants that will enable the generation of new tools to improve the adaptation potential of commercial cattle breeds. Adipose tissues are key factors in the regulation of metabolism and energy balance and are crucial for the molecular switches needed to adapt to rapid environmental and nutritional changes. The transcriptome landscape of four adipose tissues was used in this study to investigate the effect of the environment on the gene expression profiles of three local breeds, Yakutian cattle (Sakha Republic), Northern Finncattle (Finland), Mirandesa cattle (Portugal) and commercial Holstein cattle.ResultsA total of 26 animals (12 cows, 14 bulls) yielded 81 samples of perirenal adipose tissue (n=26), metacarpal adipose tissue (n=26), tailhead adipose tissue (n=26) and prescapular adipose tissue (n=3). More than 17,000 genes were expressed in our dataset. Principal component analysis of the normalized expression profiles revealed a differential expression profile of the metacarpal adipose tissue. We found that the genes upregulated in the metacarpal adipose tissue of Yakutian cattle, such asNR4A3,TEKT3, andFGGY, were associated with energy metabolism and response to cold temperatures. In Mirandesa cattle, the upregulated genes in perirenal adipose tissue were related to immune response and inflammation (AVPR2, CCN1, andIL6), while in Northern Finncattle, the upregulated genes appeared to be involved in various physiological processes, including energy metabolism (IGFBP2). According to the sex-based comparisons, the most interesting result was the upregulation of theTPRG1 genein three tissues of Yakutian cattle females, suggesting that adaptation is related to feed efficiency.ConclusionsThe highest number of differentially expressed genes was found between Yakutian cattle and Holstein, several of which were associated with immunity in Yakutian cattle, indicating potential differences in disease resistance and immunity between the two breeds. This study highlights the vast difference in gene expression profiles in adipose tissues between breeds from different climatic environments, most likely highlighting selective pressure and the potential significance of the uniquely important regulatory functions of metacarpal adipose tissue.
Kind minds: using the ‘compassionate kitbag’ in a compassion focused therapy group for adults with intellectual disabilities
Authors: Busfield Andy , Peters Charlotte , McKenzie Karen 
Published: December 2023

Purpose
This paper aims to describe and evaluate the impact of a compassion-focused therapy (CFT) group for adults with intellectual disabilities (ID).

Design/methodology/approach
People with ID are commonly subjected to stigmatising experiences that can contribute to feelings of shame. CFT targets shame and self-criticism by helping people to cultivate self-compassion. There is evidence to suggest that CFT can be meaningfully adapted for people with ID. Qualitative and quantitative data were collected using a mixed-methods design, aiming to gain a rich evaluation of the CFT group. Eight adults with ID were referred by their local community psychology team. An 11-week group protocol was based on materials from previous research. The protocol included the development of a “compassion box”, aiming to make CFT concepts more concrete and tangible. Questionnaires measuring psychological distress, self-compassion and negative social comparisons were completed pre- and post-group. Feedback from participants and carers were collated and facilitators’ observations were recorded.

Findings
Questionnaire findings were mixed, and some participants found the measures difficult to understand. Participants’ qualitative feedback and facilitators’ observations suggested that the group created feelings of safety and connectedness whilst facilitating engagement and action with shame and self-criticism. Several participants highlighted the usefulness of the ‘”compassion box”, although some barriers were noted.

Originality/value
This paper provides a rich description of how group CFT can be adapted to meet the needs of adults with ID and is the first study of its kind, to the best of the authors’ knowledge, to evaluate the incorporation of the “compassion box”.
Family incivility and organisational citizenship behaviour: roles of negative rumination, workplace friendship and optimism
Authors: Kuriakose Vijay , Bishwas Sumant Kumar 
Published: December 2023

PurposeThis study aims to understand the relationship between family incivility and employees' organisational citizenship behaviour. It also explores the mediating role of negative rumination and the moderating roles of workplace friendship and optimism.Design/methodology/approachTo test the hypothesised relationships, 381 responses were collected from employees at two-time points. The hypothesised relationships were tested using process macros.FindingsThe results indicated that family incivility is negatively related to organisational citizenship behaviour and increases negative rumination. The study also established the mediating role of negative rumination in the relationship between family incivility and organisational citizenship behaviour. The study also supported the buffering role of workplace friendship and optimism in the relationship between family incivility and negative rumination.Research limitations/implicationsThe study findings extend the understanding of how a non-work stressor can influence employee behaviour in the organisation. The study findings provide valuable directions to mitigate family incivility's adverse effects and extend the existing body of knowledge.Originality/valueThe study is unique as it links family events to work outcomes. Only a few scholarly attempts were undertaken to understand the effect of family incivility on employees' work behaviours. By explaining the mechanism and conditions, the study has a unique value to the scholarship.
Designing innovation in urban hotels through guest experience data on interior design
Authors: Gavilan Diana , A. Al-shboul Omar Adeeb 
Published: December 2023

PurposeThis paper aims to identify potential avenues for innovation in urban hotel management by analyzing self-reported data from visitors regarding their experience with interior design.Design/methodology/approachA qualitative exploratory computer-assisted content analysis was conducted to identify the impact of interior design on the guest experience. Leximancer 4.0 software analyzed 2,562 reviews from urban hotels collected through a reservation website.FindingsThe findings reveal that data reported by guests on interior design play a crucial role in shaping guest experiences, both positively and negatively. The esthetic appeal of interior design is shown to impact resting and comfort, affecting overall performance significantly. The study also highlights how different star categories of hotels and variations in visitors' purposes for their stay lead to distinct guest experiences and different opportunities to innovate.Research limitations/implicationsThe study’s results provide evidence for researchers and practitioners of the potential of the guest-reported interior design experience as a valuable source for fostering innovation. In addition, in the hotel industry, innovation may eventually be attained through interior design renovation.Practical implicationsSelf-reported data from guests on interior design is an effective tool for innovation. Making interior design a priority throughout the establishment and ongoing management of a hotel is crucial. By integrating interior design, not only can potential negative experiences be avoided, but greater guest satisfaction can also be achieved during their stay, promoting memorable experiences that align with the hotel category and customer expectations.Social implicationsThis research emphasizes the importance of interior design as a catalyst for innovation and improved social experiences in the hospitality industry. Innovation in interior design can improve hotel performance in several dimensions, including attracting more visitors to the hotel and the area, increasing tourism revenue for local businesses and contributing to the broader societal goal of reducing environmental impact and promoting sustainability.Originality/valueThis article adopts a guest-centered methodology to provide valuable insights for hotel managers to leverage interior design as a tool for innovation in the hospitality industry after showing that interior design enhances guests' experiences, comfort and hotel differentiation.
Estimating public and private sectors' union wage effects in Ghana: is there a disparity?
Authors: Owusu-Afriyie John , Baffour Priscilla Twumasi , Baah-Boateng William 
Published: December 2023

PurposeThis study seeks to estimate union wage effect in the public and private sectors of Ghana, respectively. It also seeks to ascertain whether the union wage effect in the two sectors varies.Design/methodology/approachThe authors use data from the Ghana Living Standards Survey 6 (GLSS 6, 2012/2013) and Ghana Labour Force Survey (GLFS, 2015). In terms of estimation technique, the authors employ the Blinder–Oaxaca decomposition technique to estimate union wage effect in public and private sectors, respectively.FindingsThe findings indicate that union wage effect in the public sector is positive and higher relative to that of the private sector.Practical implicationsThe findings imply that strict enforcement of Section 82 of Labour Act 2003 (Act 651) will curb the political influence of public sector unions over their employer (Government).Originality/valueThis research paper has not been presented to any journal for publication and it is the authors' original work.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-01-2023-0045
Predicting food waste reduction behavior among students in higher education institutions
Authors: Valentin Alvin Patrick , Dela Vega Aivanne Miguel , Kho Marc Ivenson , Licayan Sean Russel , Nierras Elijah Liam , Pabalate Jose Carlos 
Published: December 2023

Purpose
This study aims to determine and analyze the predictors of food waste reduction intention and behavior among higher education institutions (HEIs) using an extended version of the theory of planned behavior (TPB).

Design/methodology/approach
This study empirically tested an extended TPB model through regression analyses using data obtained through an online survey.

Findings
Attitude toward food waste reduction, subjective norms, perceived behavioral control and food waste knowledge predicted intention to reduce food waste. Furthermore, the intention to reduce food waste predicted food waste reduction behavior.

Research limitations/implications
The results imply that extending the TPB by adding food waste knowledge significantly predicted food waste reduction intention and behavior.

Practical implications
The study identified factors that predict food waste reduction behavior and suggested ways to influence Filipino students in HEIs to reduce food waste.

Originality/value
The findings support the inclusion of food waste knowledge to the TPB in predicting food waste reduction intention and behavior among students in HEIs.
Experimental study on seismic behavior of RC beams confined by corroded stirrups
Authors: Shu Jingxiao , Lu Yao , Liang Yan 
Published: December 2023

PurposeTo understand the seismic behavior of reinforced concrete (RC) beams confined by corroded stirrups, low-reversed cyclic loading tests were carried out on seven RC beam specimens with different stirrup corrosion levels and stirrup ratios to investigate their mechanical characteristics.Design/methodology/approachThe failure mode, hysteresis behavior, skeleton curves, ductility, stiffness degradation and energy dissipation behavior of RC specimens are compared and discussed. The experimental results showed that the restraint of concrete provided by corroded stirrups is reduced, which leads to a decline in seismic performance.FindingsFor the specimens with the same ratios of stirrup, as the corrosion level increased, the load-carrying capacity, stiffness, plastic deformation capacity and energy-dissipation capacity dropped significantly. Compared with the uncorroded specimen, the failure modes of specimens with high corrosion level changed from ductile bending failure to brittle failure. For the specimens with the same levels of corrosion, the higher the stirrup ratio was, the stronger the restraint effect of the stirrups on the concrete, and the seismic behavior of the specimens was obviously improved.Originality/valueIn this paper, a total of seven full-size RC beam specimens at joints with different stirrup corrosion levels and stirrup ratios were designed and constructed to explore the influences of corrosion levels and stirrup ratios of stirrups on the seismic performances. The failure modes, strain of reinforcement, hysteretic curves, skeleton curves, stiffness degradation and ductility factor of RC specimens are compared and discussed.