bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Microbiome and Host Inflammatory Gene Expression in Foreskin Tissue
Authors: Maust Brandon S. , Petkov Stefan , Herrera Carolina , Feng Colin , Brown Bryan P. , Lebina Limakatso , Opoka Daniel , Ssemata Andrew , Pillay Natasha , Serwanga Jennifer , Seatlholo Portia , Namubiru Patricia , Odoch Geoffrey , Mugaba Susan , Seiphetlo Thabiso , Gray Clive M. , Kaleebu Pontiano , Webb Emily L. , Martinson Neil , Chiodi Francesca , Fox Julie , Jaspan Heather B. 
Published: August 2022

AbstractAs part of the CHAPS randomized clinical trial, we sequenced a segment of the bacterial 16S rRNA gene from foreskin tissue of 144 adolescents from South Africa and Uganda collected during surgical penile circumcision after receipt of 1 to 2 doses of placebo, emtricitabine with tenofovir disoproxil fumarate, or emtricitabine with tenofovir alafenamide. We found a large proportion ofCorynebacteriumin addition to other anaerobic species.Cutibacterium acneswas more abundant among participants from South Africa than Uganda, though this made no difference in surgical recovery. We did not find a difference in bacterial populations by treatment received nor bacterial taxa that were differentially abundant between participants who received placebo versus active drug. Using RNAseq libraries from foreskin tissue of the same participants, we found negative correlations between the relative abundance of bacterial taxa and the expression of genes downstream of the innate response to bacteria and regulation of the inflammatory response. When participants were divided into clusters based on bacterial community composition, two main clusters emerged which were distinguished by high and low bacterial diversity. Random forest classification showed higher expression ofNFATC3andSELENOSand lower expression ofSTAP1andNLRP6in the higher diversity group compared to the lower. Our results show no difference in the tissue microbiome of the foreskin with short-course PrEP but that bacterial taxa were largely inversely correlated with gene expression, consistent with non-inflammatory colonization.Author SummaryWe investigated the bacterial community of the foreskin of the penis. Previous studies found increased inflammation with certain anaerobic bacteria from swabs taken under the foreskin, but we found that higher relative abundances of the bacteria were correlated with lower expression of inflammatory genes. We did not find different bacteria in participants who received medicine to prevent HIV. Understanding the relationship between bacteria and inflammation in the penis will help us to understand how interventions like penile circumcision reduce the risk of acquiring sexually transmitted infections such as HIV.
Expression and Splicing Mediate Distinct Biological Signals
Authors: Dam Søren Helweg , Olsen Lars Rønn , Vitting-Seerup Kristoffer 
Published: August 2022

AbstractBackgroundThrough alternative splicing, most human genes produce multiple isoforms in a cell-, tissue-, and disease-specific manner. Numerous studies show that alternative splicing is essential for development, diseases and their treatments. Despite these important examples, the extent and biological relevance of splicing are currently unknown.ResultsTo solve this problem, we developed pairedGSEA and used it to profile transcriptional changes in 100 representative RNA-seq datasets. Our systematic analysis demonstrates that changes in splicing, on average, contribute to 48.1% of the biological signal in expression analyses. Gene-set enrichment analysis furthermore indicates that expression and splicing both convey shared and distinct biological signals.ConclusionThese findings establish alternative splicing as a major regulator of the human condition and suggest that most contemporary RNA-seq studies likely miss out on critical biological insights. We anticipate our results will contribute to the transition from a gene-centric to an isoform-centric research paradigm.
The neural signature of magnitude integration between time and numerosity
Authors: Togoli I. , Fornaciai M. , Visibelli E. , Piazza M. , Bueti D. 
Published: August 2022

ABSTRACTMagnitude dimensions such as time and numerosity are fundamental components of our visual experience, allowing us to understand the environment and interact with it. Different magnitudes are however not processed independently from each other, but show a relationship whereby the perception of one dimension depends on the others (“magnitude integration”). In this study, we use electroencephalography (EEG) to address whether such integration may arise from a shared brain processing stage where different dimensions are integrated together, or from independent parallel processes interfering with each other. In the experiment, participants judged either the average numerosity or duration of dynamic dot-array stimuli concurrently modulated in both dimensions. First, the behavioural results show a magnitude integration effect in both tasks, with duration affecting the judgement of numerosity and vice versa. The EEG results further show that both numerosity and duration significantly modulate event-related potentials at several distinct latencies. Crucially, however, we identified a significant interaction between numerosity and duration emerging in a specific latency window (360-460 ms) irrespective of the task performed by participants. In this latency window, the modulation of ERPs provided by the interfering magnitude dimension can be predicted by the strength of the behavioural bias. Our results thus support the idea of different magnitude dimensions converging onto a shared perceptual processing stage mediating their integration. Overall, our results demonstrate a clear electrophysiological signature of magnitude integration between numerosity and time, and provide new evidence for a shared representational system encompassing different magnitude dimensions.
Evolutionary Divergence in the Conformational Landscapes of Tyrosine vs Serine/Threonine Kinases
Authors: Gizzio Joan , Thakur Abhishek , Haldane Allan , Levy Ronald M. 
Published: August 2022

AbstractInactive conformations of protein kinase catalytic domains where the DFG motif has a “DFG-out” orientation and the activation loop is folded present a druggable binding pocket that is targeted by FDA-approved “type-II inhibitors” in the treatment of cancers. Tyrosine Kinases (TKs) typically show strong binding affinity with a wide spectrum of type-II inhibitors while Serine/Threonine Kinases (STKs) usually bind more weakly which we suggest here is due to differences in the folded to extended conformational equilibrium of the activation loop between TKs vs. STKs. To investigate this, we use sequence covariation analysis with a Potts Hamiltonian statistical energy model to guide absolute binding free-energy molecular dynamics simulations of 74 protein-ligand complexes. Using the calculated binding free energies together with experimental values, we estimated free-energy costs for the large-scale (∼17-20Å) conformational change of the activation loop by an indirect approach, circumventing the very challenging problem of simulating the conformational change directly. We also used the Potts statistical potential to thread large sequence ensembles over active and inactive kinase states. The structure-based and sequence-based analyses are consistent; together they suggest TKs evolved to have free-energy penalties for the classical “folded activation loop” DFG-out conformation relative to the active conformation that is, on average, 4-6 kcal/mol smaller than the corresponding values for STKs. Potts statistical energy analysis suggests a molecular basis for this observation, wherein the activation loops of TKs are more weakly “anchored” against the catalytic loop motif in the active conformation, and form more stable substrate-mimicking interactions in the inactive conformation. These results provide insights into the molecular basis for the divergent functional properties of TKs and STKs, and pharmacological implications for the target selectivity of type-II inhibitors.
Senescent cells develop PDK4-dependent hypercatabolism and form an acidic microenvironment to drive cancer resistance
Authors: Dou Xuefeng , Long Qilai , Liu Shuning , Zou Yejun , Fu Da , Chen Xue , Xu Qixia , Wang Changxu , Ren Xiaohui , Zhang Guilong , Fu Qiang , Campisi Judith , Zhao Yuzheng , Sun Yu 
Published: August 2022

AbstractCellular senescence is a state of stable growth arrest, usually accompanied by development of the senescence-associated secretory phenotype (SASP). Although senescent cells remain metabolically active, little is known about their metabolic landscape andin vivopathophysiological implications. Here we show that expression of the pyruvate dehydrogenase (PDH) inhibitory enzyme, pyruvate dehydrogenase kinase 4 (PDK4), is significantly upregulated in human senescent stromal cells. Preferentially expressed upon genotoxicity-induced senescence (GIS), PDK4 is negatively correlated with posttreatment survival of cancer patients. Upon cellular senescence, PDK4 shifts glucose metabolic flux from oxidative phosphorylation to aerobic glycolysis, causing enhanced lactate production and forming an acidic microenvironment. However, distinct from the cancer cell-featured Warburg effect, senescent cells maintain an intensive use of pyruvate through the tricarboxylic acid cycle (TCA), displaying increased respiration and redox activity, indicative of a special form of metabolic reprogramming. Conditioned media from PDK4+stromal cells change global expression and promote malignancy of recipient cancer cellsin vitroand accelerate tumor progressionin vivo. Pharmacologically targeting PDK4 restrains the adverse effects of PDK4 in cell-based assays, while promoting tumor regression and extending posttreatment survival in preclinical trials. Together, our study substantiates the hypercatabolic nature of senescent cells, and reveals a metabolic link between senescence-associated acidic microenvironment and age-related pathologies including but not limited to cancer.
Structural basis of Rho-dependent transcription termination
Authors: Molodtsov Vadim , Wang Chengyuan , Firlar Emre , Kaelber Jason T. , Ebright Richard H. 
Published: August 2022

AbstractRho and NusG mediate factor-dependent transcription termination in Escherichia coli. Here, we report preparation of complexes functional in factor-dependent termination from RNA polymerase (RNAP), Rho, NusG, and synthetic nucleic-acid scaffolds, and we report cryo-EM structures of complexes. The structures show that functional factor-dependent pre-termination complexes contain a closed-ring Rho hexamer, have RNA threaded through the central channel of Rho, have 60 nt of RNA interacting sequence-specifically with the exterior of Rho and 6 nt of RNA interacting sequence-specifically with the central channel of Rho, have Rho oriented relative to RNAP such that ATP-hydrolysis-dependent translocation by Rho exerts mechanical force on RNAP, and have NusG bridging Rho and RNAP. The results explain five decades of research on Rho and provide a foundation for understanding Rho function.One sentence summaryCryo-EM reveals the structure of the functional Rho pre-termination complex
Describing small-angle scattering profiles by a limited set of intensities
Authors: Grant Thomas D. 
Published: August 2022

Small-angle scattering (SAS) probes the size and shape of particles at low resolution through the analysis of the scattering of X-rays or neutrons passing through a solution of particles. One approach to extracting structural information from SAS data is the indirect Fourier transform (IFT). The IFT approach parameterizes the real-space pair distribution function [P(r)] of a particle using a set of basis functions, which simultaneously determines the scattering profile [I(q)] using corresponding reciprocal-space basis functions. This article presents an extension of an IFT algorithm proposed by Moore [J. Appl. Cryst. (1980), 13, 168–175] which used a trigonometric series to describe the basis functions, where the real-space and reciprocal-space basis functions are Fourier mates. An equation is presented relating the Moore coefficients to the intensities of the SAS profile at specific positions, as well as a series of new equations that describe the size and shape parameters of a particle from this distinct set of intensity values. An analytical real-space regularizer is derived to smooth the P(r) curve and ameliorate systematic deviations caused by series termination. Regularization is commonly used in IFT methods though not described in Moore's original approach, which is particularly susceptible to such effects. The algorithm is provided as a script, denss.fit_data.py, as part of the DENSS software package for SAS, which includes both command line and interactive graphical interfaces. Results of the program using experimental data show that it is as accurate as, and often more accurate than, existing tools.
Purchase intention of organic foods: are lifestyles of health and sustainability the reason for my purchase decision?
Authors: Kaur Jaspreet , Lavuri Rambabu , Thaichon Park , Martin Brett 
Published: August 2022

PurposeThe purpose of this study is to examine the impact of scarcity and the Lifestyles of Health and Sustainability (LOHAS) consumption tendency on the purchase intention of organic foods. The study used the protection motivation theory and the stimulus-organism-response theory to understand the impact of comparatively new variables like “perceived scarcity” and “perceived consumer effectiveness” (PCE) on the consumer's organic food purchase intentions.Design/methodology/approachThe study is using structural equation modeling with 402 organic food consumers. The participants are regular consumers who bought organic food from specialized shops and supermarkets in the previous few months. The data has been collected at organic food specialized shops and supermarkets that sell organic foods.FindingsThe results showed that LOHAS consumption tendency (LCT), scarcity and PCE positively affect attitude. Similarly, LCT and PCE direct affect trust. Scarcity and PCE directly positive impact on purchase intention of organic food products. Interestingly, LCT had no direct impact on the purchase intention of the product. Trust and attitude were found to be significant mediators impacting purchase intention.Originality/valueThe study contributes to the past theoretical literature on LOHAS consumption by analyzing new constructs like scarcity and PCE in the context of organic food consumption. These findings will be crucial for marketers planning to launch organic products in new markets.
Factors influencing tourists’ nightlife experience in Belgrade
Authors: Seočanac Marijana , Dimitrovski Darko 
Published: August 2022

Purpose
This study aims to understand the impact that the experience environment has on the nightlife experience, as well as to identify the factors from the nightlifescape that most influence the tourists’ experience in Belgrade. Additionally, this study seeks to discover whether these factors changed after the outbreak of the COVID-19 pandemic.

Design/methodology/approach
To achieve the study’s objectives, 679 tourist reviews were collected from one of the most popular travel platforms, TripAdvisor, and analyzed using RapidMiner, the popular software for data/text mining.

Findings
The perception of the physical aspects of the experience environment, the presence of other tourists and the feeling of acceptance are identified as the key factors that influence tourists’ nightlife experience. This study also found that certain factors from the social and sensory environment, such as staff, the presence of other people, the atmosphere and music, had a positive impact on the tourist experience and their intention to recommend the nightlife experience in Belgrade. Moreover, it was discovered that the COVID-19 pandemic did not provoke changes in the main factors influencing tourists’ nightlife experience.

Originality/value
The perception of tourists about Belgrade during the night contributes to the growing body of tourism literature on destination image. Focusing solely on the perception of tourists about Belgrade during the night, this study adds a temporal determinant to the destination image, which can be considered as a valuable add on to the current knowledge in the field.
Stay positive: studying the change patterns in academics' job and life satisfaction during the Covid-19 pandemic through growth curve modeling
Authors: Ghasemy Majid , Frömbling Lena 
Published: August 2022

PurposeDuring the Covid-19 outbreak, universities around the globe were closed or went online due to lockdowns implemented to curb the pandemic's spread. This study aims to examine the changes in Malaysian academics' job and life satisfaction during a testing four-month period, from the beginning of the first Covid-19 lockdown until two months after it ended. It also assesses the impact of affective states and age group on these two constructs.Design/methodology/approachIn this longitudinal study, the authors collected data from 220 academics in Malaysia at three time points in 2020, namely the beginning of the lockdown (April), the end of the lockdown (June) and two months after the lockdown (August). The authors applied multivariate latent growth curve (LGC) modeling to study changes in job satisfaction and life satisfaction. In addition, we added age group, as a time-invariant covariate, as well as positive and negative affect, as two time-varying covariates, to our LGC model. The authors estimated the LGC model using the EQS 6.4 statistical package.FindingsThe results show that both job and life satisfaction were stable over time, although their means were below the average. Positive affect was a significant predictor of both types of satisfaction, and age group was a significant predictor of job satisfaction.Practical implicationsThe main implication the authors draw from this study is connected to job and life satisfaction's mean values being below average. In line with the affective events theory (AET), the authors recommend paying particular attention to work environment features, such as providing sufficient infrastructure for employees working from home and keeping social relations intact. Especially young academics should receive sufficient support.Originality/valueThe study is one of a limited number that examined longitudinal effects during the Covid-19 pandemic in the domains of human resource management and organizational behavior. Hence, this study expands our knowledge of employees' affect and attitudes during an unprecedented global health crisis, particularly in the under-researched area of the Malaysian higher education sector.
Adoption of big data analytics practices for sustainability development in the e-commercesupply chain: a mixed-method study
Authors: Gangwar Hemlata , Mishra Ruchi , Kamble Sachin 
Published: August 2022

PurposeThe study aims to identify the potential drivers of big data analytics (BDA) practices in the supply chain and develop a sustainability evaluation model to evaluate drivers of big data for sustainability development.Design/methodology/approachThe mixed-method approach was applied to assess sustainability dimensions and calculate the score using two phases. In Phase I, the BDA drivers in the e-commerce industry were finalised using the partial least square based structural equation modelling (PLS-SEM) method. In Phase II, a case study in the Indian fashion e-commerce industry was carried out to evaluate sustainability dimensions with respect to drivers of BDA and the sustainability score was calculated using the fuzzy analytical hierarchical process (AHP) method.FindingsThe index for economic sustainability (0.220), social sustainability (0.142) and environmental sustainability (0.182) were derived. The higher index value of economic sustainability compared to social sustainability and environmental sustainability signified those drivers of big data bring social and environmental uncertainty along with economic sustainability.Research limitations/implicationsThe study will help practitioners promote BDA use for developing environmental/social/economic sustainability in supply chains. Policymakers must ensure whether the integration of BDA practices brings down cost and brings strategic value for ensuring big data success. The study will help managers decide a constant trade-off between the requirement for social, environmental and economic performance.Originality/valueThe study corroborates and adds to the BDA literature by emphasising the positive role of BDA in sustainability development in the supply chain area and highlighting the significant role of different drivers of BDA in sustainability development.
Education for sustainable development and sustainability consciousness: evidence from Malaysian universities
Authors: Saleem Atif , Aslam Sarfraz , Sang Guoyuan , Dare Philip Saagyum , Zhang Tianxue 
Published: August 2022

PurposeThis study aims to understand the practices and perceptions of education for sustainable development (ESD) in the university classrooms of Malaysia, exploring how holistic, pluralistic and action-oriented approaches to ESD were linked to their knowingness, attitudes and behavior regarding sustainability.Design/methodology/approachThe perceptions of 2,678 students and 1,013 teachers from a range of undergraduate and postgraduate courses at four Malaysian universities were surveyed. Their views of ESD and sustainability consciousness (SC) were recorded on five-point Likert-type scales, and the resulting data was investigated using descriptive and analytical statistics.FindingsHolistic, pluralistic and action-oriented approaches to ESD teaching and learning were widespread in Malaysian universities, with significant associations found between ESD approaches and SC. While all three approaches enhanced each aspect of SC, the results indicated the need to develop action-oriented approaches more fully.Originality/valueThis research underlines the importance of sustainability education in the context of higher education. It provides empirical evidence for developing action-oriented approaches to ESD and confirms the utility of holistic content and pluralistic pedagogy to the teaching and learning of sustainability.
Teachers’ competencies in education for sustainable development in the context of Vietnam
Authors: Thao Nguyen Phuong , Kieu Thi Kinh , Schruefer Gabriele , Nguyen Ngoc-Anh , Nguyen Yen Thi Hoang , Vien Thong Nguyen , Hai Yen Ngo Thi , Ha Tran Thai , Phuong Doan Thi Thanh , Duy Hai Tuong , Dieu Cuc Nguyen , Van Hanh Nguyen 
Published: August 2022

Purpose
This study aims to investigate specific professional competencies of teachers to implement education for sustainable development (ESD) in the contexts of Vietnam.

Design/methodology/approach
The authors carried out a Delphi study with eight ESD experts in Vietnam to collect their expertise viewpoints regarding teachers’ ESD professional competencies.

Findings
In total, 13 competencies related to three dimensions (content knowledge/cognitive, pedagogical and pedagogical content knowledge, motivation and volition) were highlighted by ESD experts.

Research limitations/implications
The proposed teachers’ competencies were based on the ideas of a small group of experts, and the results need to be tested, refined and confirmed by further work. Besides, in this study, we have not defined the levels of achievement for each competency as well as developed assessment tools.

Practical implications
The specific professional competencies for teachers can be considered as a foundation for developing educational offers focusing on promoting the specific teachers’ professional competencies in basic ESD training.

Originality/value
Studies on educators’ professional competencies for ESD mostly were conducted in western countries. However, competencies do not exist independently; instead, they should be considered in specific contexts of teaching, school, culture and society. This research is among one of the first studies that contextualizes teachers’ competencies in a non-western context.