bluuebunny/crossref_metadata_2025 huggingface dataset:
Functions of PMS2 and MLH1 important for regulation of divergent repeat-mediated deletions
Authors: Trost Hannah , Lopezcolorado Felicia Wednesday , Merkell Arianna , Stark Jeremy M.
Published: August 2024

Repeat-mediated deletions (RMDs) are a type of deletion rearrangement that utilizes two repetitive elements to bridge a DNA double-strand break (DSB) that leads to loss of the intervening sequence and one of the repeats. Sequence divergence between repeats causes RMD suppression and indeed this divergence must be resolved in the RMD products. The mismatch repair factor, MLH1, was shown to be critical for both RMD suppression and a polarity of sequence divergence resolution in RMDs. Here, we sought to study the interrelationship between these two aspects of RMD regulation (i.e., RMD suppression and polar divergence resolution), by examining several mutants of MLH1 and its binding partner PMS2. To begin with, we show that PMS2 is also critical for both RMD suppression and polar resolution of sequence divergence in RMD products. Then, with six mutants of the MLH1-PMS2 heterodimer, we found several different patterns: three mutants showed defects in both functions, one mutant showed loss of RMD suppression but not polar divergence resolution, whereas another mutant showed the opposite, and finally one mutant showed loss of RMD suppression but had a complex effect on polar divergence resolution. These findings indicate that RMD suppression vs. polar resolution of sequence divergence are distinct functions of MLH1-PMS2.

HIGHLIGHTS

MLH1-PMS2 suppresses divergent repeat-mediated deletions (RMDs).

MLH1-PMS2 promotes polar resolution of sequence divergence.

Several mutants of MLH1-PMS2 affect both aspects of RMDs.

Some MLH1-PMS2 mutants affect only one aspect of RMDs.

Suppression of RMDs vs. polar resolution of divergence appear distinct.
The PVT1, HULC, and HOTTIP expression changes due to treatment in Diffuse Large B-cell lymphoma
Authors: Shahsavari Milad , Arbabian Sedigheh , Hosseini Farzaneh , Razavi Mohamad Reza
Published: August 2024

Diffuse large B-cell lymphoma is the most common histological subtype of non-Hodgkin’s lymphomas. It is an aggressive malignancy that displays great heterogeneity in morphology, genetics, biological behavior and treatment response owing to chromatin remodeling and epigenetics.

Bioinformatic-based approaches were used to understand the possible signaling pathways of the three lncRNAsPVT1,HULC, andHOTTIP. Furthermore, their expression levels were quantitatively evaluated in 100 patients before and after the treatment.

The results revealed that gene expression was significantly upregulated inPVT1,HULC, andHOTTIPby 7.39±8.48-, 5.924±7.536-, and 4.137±5.863 fold, respectively, relative to normal cases. Post-treatment measurement of lncRNA expression indicated thatPVT1andHOTTIPwere significantly downregulated.

Interestingly, the expression levels ofPVT1,HULC, andHOTTIPwere significantly higher in DLBCL patients aged > 60 years than in those aged < 60 years. In addition, there was a significant positive correlation betweenHULCandHOTTIPexpression.

The analysis of overexpressed lncRNA-miRNA interaction indicated different deregulated miRNA targets and the protein targets of upregulated lncRNAs are mainly with histone modification, DNA methylation/demethylation, and protein methyltransferase activity.

Summary blurb

The lncRNAsPVT1,HULC, andHOTTIPexpression is significantly upregulated before treatment and reduce to normal level after treatment. It can be used as diagnostic marker or prognostic means especially in Relapsed/refractory DLBCL.
Exploit Spatially Resolved Transcriptomic Data to Infer Cellular Features from Pathology Imaging Data
Authors: Sui Zhining , Li Ziyi , Sun Wei
Published: August 2024

Digital pathology is a rapidly advancing field where deep learning methods can be employed to extract meaningful imaging features. However, the efficacy of training deep learning models is often hindered by the scarcity of annotated pathology images, particularly images with detailed annotations for small image patches or tiles. To overcome this challenge, we propose an innovative approach that leverages paired spatially resolved transcriptomic data to annotate pathology images. We demonstrate the feasibility of this approach and introduce a novel transfer-learning neural network model, STpath (Spatial Transcriptomics and pathology images), designed to predict cell type proportions or classify tumor microenvironments. Our findings reveal that the features from pre-trained deep learning models are associated with cell type identities in pathology image patches. Evaluating STpath using three distinct breast cancer datasets, we observe its promising performance despite the limited training data. STpath excels in samples with variable cell type proportions and high-resolution pathology images. As the influx of spatially resolved transcriptomic data continues, we anticipate ongoing updates to STpath, evolving it into an invaluable AI tool for assisting pathologists in various diagnostic tasks.
Influential drivers of the cost-effectiveness of respiratory syncytial virus vaccination in European older adults: A multi-country analysis
Authors: Li Xiao , Willem Lander , Johannesen Caroline Klint , Urchueguía-Fornes Arantxa , Lehtonen Toni , Osei-Yeboah Richard , Salo Heini , Orrico-Sánchez Alejandro , Díez-Domingo Javier , Jit Mark ,   PROMISE investigators, Bilcke Joke , Nair Harish , Beutels Philippe
Published: August 2024

Background

We aimed to identify influential drivers of the cost-effectiveness of older adult respiratory syncytial virus (RSV) vaccination in Denmark, Finland, the Netherlands and Valencia-Spain.

Methods

A static multi-cohort model was parameterised using country-and age-specific hospitalisations using three approaches: (1) the International Classification of Diseases (ICD)-coded hospitalisations, (2) laboratory RSV-confirmed hospitalisations and (3) time-series modelling (TSM). Plausible hypothetical RSV vaccine characteristics were derived from two protein subunit vaccines for adults aged ³60 years (“60y+”). Costs and quality-adjusted life-years (QALYs) were compared between four strategies: (a) “no intervention” and RSV vaccination in adults (b) 60y+; (c) 65y+; (d) 75y+, from both the healthcare payers’ and societal perspectives. Value of information, probabilistic sensitivity and scenario analyses identified influential drivers.

Results

Besides vaccine price, the hospitalisation estimates were most influential: Using adjusted RSV-ICD-coded hospitalisations at a vaccine price of €150 per dose, no intervention was cost-effective up to willingness-to-pay (WTP) values of €150 000 per QALY gained in Denmark and the Netherlands, and up to €125 000 per QALY gained in Finland. Using the adjusted RSV-confirmed dataset, the findings were consistent in Denmark and comparable in Finland. In Spain-Valencia, the 75y+ strategy became cost-effective at WTP >€55 000. Using TSM-based estimates, the 75y+ strategy was cost-effective at WTP >€45 000, >€101 000, >€41 000 and >€114 000 in Denmark, Finland, the Netherlands and Spain-Valencia, respectively. The (in-hospital) case fatality ratio and the specification of its age dependency were both influential. Duration of protection was found more influential than a variety of plausible waning patterns over the duration of protection.

Conclusion

Data gaps and uncertainties on the RSV-related burden in older adults persist and influence the cost-effectiveness of RSV vaccination. More refined age-and country-specific data on the RSV attributable burden are crucial to aid decision making.
Preliminary reference values for Alzheimer’s disease plasma biomarkers in Congolese individuals with and without Alzheimer’s disease
Authors: Ikanga Jean , Jean Kharine , Medina Priscilla , Patel Saranya Sundaram , Schwinne Megan , Epenge Emmanuel , Gikelekele Guy , Tshengele Nathan , Kavugho Immaculee , Mampunza Samuel , Mananga Lelo , Teunissen Charlotte E. , Stringer Anthony , Rojas Julio C. , Chan Brandon , Lago Argentina Lario , Kramer Joel H. , Boxer Adam L. , Jeromin Andreas , Gross Alden L. , Alonso Alvaro
Published: August 2024

Background

Western countries have provided reference values (RV) for Alzheimer’s disease (AD) plasma biomarkers, but there are not available in Sub-Saharan African populations.

Objective

We provide preliminary RV for AD and other plasma biomarkers including amyloid- β (Aβ42/40), phosphorylated tau-181 and 217 (p-tau181, p-tau217), neurofilament light (Nfl), glial fibrillary acidic protein (GFAP), interleukin 1b and 10 (IL-1b and IL-10) and tumor necrosis factor α (TNFα) in Congolese adults with and without dementia.

Methods

85 adults (40 healthy and 45 dementia) over 50 years old were included. Blood samples were provided for plasma AD biomarkers Aβ42/40 and p-tau181, p-tau217; Nfl and GFAP; IL-1b and IL-10 and TNFα analyzed using SIMOA. Linear and logistic regressions were conducted to evaluate differences in biomarkers by age and gender and neurological status, and for the prediction of dementia status by each individual biomarker. RV were those that optimized sensitivity and specificity based on Youden’s index.

Results

In this sample of 85 adults, 40 (47%) had dementia, 38 (45.0%) were male, overall mean age was 73.2 (SD 7.6) years with 8.3 (5.4) years of education. There were no significant differences in age, gender, and education based on neurological status. Biomarker concentrations did not significantly differ by age except for p-tau181 and GFAP and did not differ by sex. Preliminary cutoffs of various plasma in pg/ml were 0.061 for Aβ42/40, 4.50 for p-tau 181, 0.008 for p-tau 217, 36.5 for Nfl, 176 for GFAP, 1.16 for TNFa, 0.011 for IL-1b, and 0.38 for IL-10. All AUCs ranged between 0.64-0.74. P-tau 217 [0.74 (0.61, 0.86)] followed by GFAP [0.72 (0.61, 0.83), and Nfl [0.71 (0.60, 0.82)] had the highest AUC compared to other plasma biomarkers.

Conclusions

This study provides RV which could be of preliminary utility to facilitate the screening, clinical diagnostic adjudication, classification, and prognosis of AD in Congolese adults.
Global Stroke Burden from Metabolic Risks Across Demographics: Findings from the 2021 Global Burden of Disease Study
Authors: Xue Song , Wu Guoqing
Published: August 2024

Background

Stroke is the second leading cause of death and the primary cause of disability worldwide. Metabolic risks are major contributors to stroke. The global trends in metabolic risk-related stroke from 1990 to 2019, and the differences in mortality and DALYs across various demographic factors, remain unclear.

Methods

All analyses were based on rates derived from the GBD2021 results (https://vizhub.healthdata.org/gbd-results/). Data were stratified by gender, region, and age. Joinpoint software was used to perform regression analysis of the average annual percent change (AAPC) and its 95% confidence interval to analyze trends from 1990 to 2019. Excel, PowerPoint, and R software were used for plotting and analysis, with p<0.05 considered statistically significant.

Results

From 1990 to 2019, the average annual percent change (AAPC) for age-standardized rates (ASR) of DALYs was -1.70% (−1.81%, -1.58%), and for mortality, the AAPC was -1.57% (−1.68%, -1.46%). As the SDI increased, both the ASR of DALYs and mortality in 2019 showed a significant decline. The AAPC from 1990 to 2019 also exhibited a downward trend with increasing SDI levels. The DALYs and mortality rates of metabolic risk-related stroke predominantly affected individuals aged 75 and above, with a lesser impact on those under 55. For both genders, the 10-55 and 50-74 age groups had the highest DALYs and mortality rates due to metabolic-related intracerebral hemorrhage. For those aged 75-84 and over 85, ischemic stroke was the leading subtype of metabolic-related stroke contributing to DALYs and mortality rates.

Conclusion

This is the first retrospective study on metabolic risk-related stroke on a global scale, summarizing its temporal trends and demographic distribution characteristics. Effective public health strategies are needed to address these disparities and continue reducing the global burden of metabolic risk-related strokes.
Pleiotropy increases parallel selection signatures during adaptation from standing genetic variation
Authors: Lai Wei-Yun , Hsu Sheng-Kai , Futschik Andreas , Schloetterer Christian
Published: August 2024

The phenomenon of parallel evolution, whereby similar genomic and phenotypic changes occur across replicated pairs of population or species, is widely studied. Nevertheless, the determining factors of parallel evolution remain poorly understood. Theoretical studies have proposed that pleiotropy, the influence of a single gene on multiple traits, is an important factor. In order to gain a deeper insight into the role of pleiotropy for parallel evolution from standing genetic variation, we characterized the interplay between parallelism, polymorphism and pleiotropy. The present study examined the parallel gene expression evolution in 10 replicated populations of Drosophila simulans, which were adapted from standing variation to the same new temperature regime. The data demonstrate that parallel evolution of gene expression from standing genetic variation is positively correlated with the strength of pleiotropic effects. The ancestral variation in gene expression is, however, negatively correlated with parallelism. Given that pleiotropy is also negatively correlated with gene expression variation, we conducted a causal analysis to distinguish cause and correlation and evaluate the role of pleiotropy. The causal analysis indicated that both direct (causative) and indirect (correlational) effects of pleiotropy contribute to parallel evolution. The indirect effect is mediated by historic selective constraint in response to pleiotropy. This results in parallel selection responses due to the reduced standing variation of pleiotropic genes. The direct effect of pleiotropy is likely to reflect a genetic correlation among adaptive traits, which in turn gives rise to synergistic effects and higher parallelism.
All of Us diversity and scale improve polygenic prediction contextually with greatest improvements for under-represented populations
Authors: Tsuo Kristin , Shi Zhuozheng , Ge Tian , Mandla Ravi , Hou Kangcheng , Ding Yi , Pasaniuc Bogdan , Wang Ying , Martin Alicia R.
Published: August 2024

Recent studies have demonstrated that polygenic risk scores (PRS) trained on multi-ancestry data can improve prediction accuracy in groups historically underrepresented in genomic studies, but the availability of linked health and genetic data from large-scale diverse cohorts representative of a wide spectrum of human diversity remains limited. To address this need, the All of Us research program (AoU) generated whole-genome sequences of 245,388 individuals who collectively reflect the diversity of the USA. Leveraging this resource and another widely-used population-scale biobank, the UK Biobank (UKB) with a half million participants, we developed PRS trained on multi-ancestry and multi-biobank data with up to ∼750,000 participants for 32 common, complex traits and diseases across a range of genetic architectures. We then compared effects of ancestry, PRS methodology, and genetic architecture on PRS accuracy across a held out subset of ancestrally diverse AoU participants. Due to the more heterogeneous study design of AoU, we found lower heritability on average compared to UKB (0.075 vs 0.165), which limited the maximal achievable PRS accuracy in AoU. Overall, we found that the increased diversity of AoU significantly improved PRS performance in some participants in AoU, especially underrepresented individuals, across multiple phenotypes. Notably, maximizing sample size by combining discovery data across AoU and UKB is not the optimal approach for predicting some phenotypes in African ancestry populations; rather, using data from only AoU for these traits resulted in the greatest accuracy. This was especially true for less polygenic traits with large ancestry-enriched effects, such as neutrophil count (R2: 0.055 vs. 0.035 using AoU vs. cross-biobank meta-analysis, respectively, because of e.g.DARC). Lastly, we calculated individual-level PRS accuracies rather than grouping by continental ancestry, a critical step towards interpretability in precision medicine. Individualized PRS accuracy decays linearly as a function of ancestry divergence, but the slope was smaller using multi-ancestry GWAS compared to using European GWAS. Our results highlight the potential of biobanks with more balanced representations of human diversity to facilitate more accurate PRS for the individuals least represented in genomic studies.
Viral piracy of host RNA phosphatase DUSP11 by avipoxviruses
Authors: Szymanik Kayla H. , Hancks Dustin C. , Sullivan Christopher S.
Published: August 2024

Proper recognition of viral pathogens is an essential part of the innate immune response. A common viral replicative intermediate and chemical signal that cells use to identify pathogens is the presence of a triphosphorylated 5’ end (5’ppp) RNA, which activates the cytosolic RNA sensor RIG-I and initiates downstream antiviral signaling. While 5’pppRNA generated by viral RNA-dependent RNA polymerases (RdRps) can be a potent activator of the immune response, endogenous RNA polymerase III (RNAPIII) transcripts can retain the 5’pppRNA generated during transcription and induce a RIG-I-mediated immune response. We have previously shown that host RNA triphosphatase dual-specificity phosphatase 11 (DUSP11) can act on both host and viral RNAs, altering their levels and reducing their ability to induce RIG-I activation. Our previous work explored how artificially altered DUSP11 can impact immune activation, prompting further exploration into natural contexts of altered DUSP11. Here, we have identified viral DUSP11 homologs (vDUSP11s) present in some avipoxviruses. Consistent with the known functions of endogenous DUSP11, we have shown that expression of vDUSP11s: 1) reduces levels of endogenous RNAPIII transcripts, 2) reduces a cell’s sensitivity to 5’pppRNA-mediated immune activation, and 3) restores virus infection defects seen in the absence of DUSP11. Our results identify a virus-relevant context where DUSP11 activity has been co-opted to alter RNA metabolism and influence the outcome of infection.
Psychological Contributors to Pain Before, During, and After Endodontic Procedures: A Scoping Review
Authors: Sadr Atieh , Gholamrezaei Ali , McNeilage Amy G. , Randall Cameron L. , Kapos Flavia P. , Peck Christopher C. , Ashton-James Claire E.
Published: August 2024

Background

Despite an increasingly biopsychosocial approach to pain management in healthcare, the scope of research into the role of psychological factors in endodontic pain is unknown.

Objectives

This study aimed to identify the scope of research into psychological contributors to pain associated with endodontic procedures, as a first step towards addressing psychological contributors to pain in clinical practice.

Method

This scoping review was conducted and reported according to the JBI Manual for Evidence Synthesis and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (extension for scoping reviews). The data search was conducted in MEDLINE, EMBASE, PsycINFO, Web of Science, Scopus, Cochrane Database of Systematic Reviews, and CINAHL databases. For gray literature, we reviewed reference lists, medRxiv pre-prints, ProQuest and EBSCO theses,ClinicalTrials.govand Cochrane trials (via Ovid), and conference materials via Web of Science and Scopus (from inception to July 2023). Each record was screened by two independent reviewers. Data were extracted by one reviewer and cross-verified by a second reviewer.

Results

Forty studies were included in the review. Twelve broad psychological constructs were evaluated in relation to pain for pre-procedural, procedural and post-procedural endodontics: pain expectancies, positive treatment expectancies, depression, anxiety, positive and negative mood (affect), beliefs about pain, desire for control of dental treatments, perceptions of dentists, somatic focus or awareness, pain coping strategies, personality, and psychiatric diagnoses. Pre-procedural pain was most frequently associated with anxiety. Procedural pain was consistently associated with expected pain. Post-procedural pain was associated with expected pain, depression, beliefs about pain, positive treatment expectations, and personality characteristics.

Conclusion

A variety of psychological factors have been investigated in relation to endodontic pain. Whilst associations between endodontic pain and psychological constructs were found, further research is needed to evaluate the strength of these associations, and the scope of evidence for interventions designed to address these psychological contributors to pain in dental practice.

Registration

The search protocol was registered on Open Science Framework in 2021 (DOI number: 10.17605/OSF.IO/FSRJP).
Yellow fever outbreak potential in Djibouti, Somalia and Yemen
Authors: Fraser Keith , Cibrelus Laurence , Horton Jennifer , Kodama Chiori , Staples J. Erin , Gaythorpe Katy A. M.
Published: August 2024

The importation of arbovirus diseases into countries where they are not currently endemic is a global concern, driven by human movement and direct and indirect climate change effects. In the World Health Organization Eastern Mediterranean region, three countries - the Republic of Djibouti, the Federal Republic of Somalia, and the Republic of Yemen - are currently considered to be at potential or moderate risk for yellow fever outbreaks, and an assessment for outbreak potential in the event of importation was sought. Djibouti and Somalia share land borders and significant cross-border movement with countries where yellow fever is endemic, while Yemen is currently experiencing a crisis which has severely impacted healthcare infrastructure, and has already seen suspected outbreaks of other similar arboviruses such as dengue, chikungunya and West Nile.

Here we present a mathematical modelling assessment of the risk of introduction and propagation of yellow fever in Djibouti, Somalia and Yemen. This modelling has two components: projecting the risk of importation of infectious individuals into individual administrative regions of the countries of interest, and the use of a dynamic yellow fever model to model yellow fever virus transmission within the same regions.

We present results showing that certain regions of Djibouti, Somalia and Yemen are at higher risk than others for yellow fever outbreaks, with the risk being higher in some areas such as the western coastal regions of Yemen (an area that has experienced recent outbreaks of other arboviruses), regions of Somalia bordering both the Federal Democratic Republic of Ethiopia and the Republic of Kenya, and Djibouti City.
Personalizing dietary interventions by predicting individual vulnerability to glucose excursions
Authors: Brügger Victoria , Kowatsch Tobias , Jovanova Mia
Published: August 2024

Elevated postprandial glucose levels pose a global epidemic and are crucial in cardiometabolic disease management and prevention. A major challenge is inter-individual variability, which limits the effectiveness of population-wide dietary interventions. To develop personalized interventions, it is critical to first predict a person’s vulnerability to postprandial glucose excursions—or elevated post-meal glucose relative to a personal baseline—with minimal burden. We examined the feasibility of personalized models to predict future glucose excursions in the daily lives of 69 Chinese adults with type-2 diabetes (Mage=61.5; 50% women; 2’595 glucose observations). We developed machine learning models, trained on past individual context and meal-based observations, employing low-burden (continuous glucose monitoring) or additional high-burden (manual meal tracking) approaches. Personalized models predicted glucose excursions (F1-score:M=74%; median=78%), with some individuals being more predictable than others. The low burden-models performed better for those with consistent meal patterns and healthier glycemic profiles. Notably, no two individuals shared the same meal and context-based vulnerability predictors. This study is the first to predict individual vulnerability to glucose excursions among a sample of Chinese adults with type-2 diabetes. Findings can help personalize just-in-time-adaptive dietary interventions to unique vulnerability to glucose excursions in daily live, thereby helping improve diabetes management.
3-STEP MODEL- AN EXPLORATIVE NOVEL APPROACH TO CLASSIFY SEPSIS: A LONGITUDINAL OBSERVATIONAL STUDY
Authors: Pilania Jaideep , Panda Prasan Kumar , Das Ananya , Chauhan Udit , Ravikant
Published: August 2024

Introduction

Sepsis remains a critical healthcare challenge worldwide, demanding prompt identification and treatment to improve patient outcomes. Given the absence of a definitive gold standard diagnostic test, there is an imperative need for adjunct diagnostic tools to aid in early sepsis detection and guide effective treatment strategies. This study introduces a novel 3-step model to identify and classify sepsis, integrating current knowledge and clinical guidelines to enhance diagnostic precision.

Methods

This longitudinal observational study was conducted at a tertiary care teaching hospital in northern India. Adult patients admitted with suspected sepsis underwent screening using predefined criteria. The 3-step model consisted of Step 1, assessing dysregulated host response using a National Early Warning Score-2 (NEWS-2) score of ≥6; Step 2, evaluating risk factors for infection; and Step 3, confirming infection presence through clinical, supportive, or confirmatory evidence. Patients were categorized into Asepsis, Possible sepsis, Probable sepsis, or Confirmed sepsis at various intervals during hospitalization.

Results

A total of 230 patients were included. Initial categorization on Day 1 showed 13.0% in Asepsis, 35.2% in Possible sepsis, 51.3% in Probable sepsis, and 0.4% in confirmed sepsis. By Day 7, shifts were observed with 49.7% in Asepsis, 9.5% in Possible sepsis, 25.4% in Probable sepsis, and 15.4% in confirmed sepsis. At discharge or death, categories were 60.4% Asepsis, 5.2% Possible sepsis, 21.7% Probable sepsis, and 12.6% Confirmed sepsis. Transitions between categories were noted throughout hospitalisation, demonstrating the dynamic nature of sepsis progression and response to treatment.

Conclusion

The 3-step model effectively stratifies sepsis status over hospitalization, facilitating early identification and classification of septic patients. This approach holds promise for enhancing diagnostic accuracy, guiding clinical decision-making, and optimizing antibiotic stewardship practices. Further validation across diverse patient cohorts and healthcare settings is essential to confirm its utility and generalizability.
Potential Causal Relationship between Faster Walking Pace and Reduced Migraine Risk: A Mendelian Randomization Study
Authors: Liu Xueen , Zhang Jiale
Published: August 2024

Objectives: Prior observational studies have suggested a potential association between the usual walking pace and migraine. In the present study, we utilized Mendelian randomization (MR) to investigate the presence of causality and elucidate the specific causal relationship between these two variables. Methods: We performed a genome-wide association study on a population of 499,562 individuals of European ancestry, which revealed 34 genetic variants that exhibited a strong association with the usual walking pace. Additionally, we obtained summary statistics for genome-wide association studies on migraine from several sources. To assess the causal estimates, we employed the random effects inverse variance weighted method (IVW) and several other Mendelian randomizations (MR) methods, including MR-Egger, weighted median, Simple mode, Weighted mode, and MR-PRESSO, to confirm the robustness of our results. Results: Our analysis demonstrated a strong causal association between genetically predicted usual walking pace and a decreased risk of migraine, as determined by inverse variance weighted analysis (odds ratio = 0.33; 95% CI = 0.17 to 0.63; P < 0.001). This association was consistently observed across our investigation's various Mendelian randomization (MR) methods. Conclusions: This study supports a potential causal association between increased walking speed and a decreased risk of migraine.
Self-attention based deep learning model for predicting the coronavirus sequences from high-throughput sequencing data
Authors: Wang ZhenNan , Liu Chaomei
Published: August 2024

Transformer models have achieved excellent results in various tasks, primarily due to the self-attention mechanism. We explore using self-attention for detecting coronavirus sequences in high-throughput sequencing data, offering a novel approach for accurately identifying emerging and highly variable coronavirus strains. Coronavirus and human genome data were obtained from the Genomic Data Commons (GDC) and the National Genomics Data Center (NGDC) databases. After preprocessing, a simulated high-throughput sequencing dataset of coronavirus-infected samples was constructed. This dataset was divided into training, validation, and test datasets. The self-attention-based model was trained on the training datasets, tested on the validation and test datasets, and SARS-CoV-2 genome data were collected as an independent test datasets. The results showed that the self-attention-based model outperformed traditional bioinformatics methods in terms of performance on both the test and the independent test datasets, with a significant improvement in computation speed. The self-attention-based model can sensitively and rapidly detect coronavirus sequences from high-throughput sequencing data while exhibiting excellent generalization ability. It can accurately detect emerging and highly variable coronavirus strains, providing a new approach for identifying such viruses.
Secure discovery of genetic relatives across large-scale and distributed genomic data sets
Authors: Hong Matthew M. , Froelicher David , Magner Ricky , Popic Victoria , Berger Bonnie , Cho Hyunghoon
Published: August 2024

Finding relatives within a study cohort is a necessary step in many genomic studies. However, when the cohort is distributed across multiple entities subject to data-sharing restrictions, performing this step often becomes infeasible. Developing a privacy-preserving solution for this task is challenging owing to the burden of estimating kinship between all the pairs of individuals across data sets. We introduce SF-Relate, a practical and secure federated algorithm for identifying genetic relatives across data silos. SF-Relate vastly reduces the number of individual pairs to compare while maintaining accurate detection through a novel locality-sensitive hashing (LSH) approach. We assign individuals who are likely to be related together into buckets and then test relationships only between individuals in matching buckets across parties. To this end, we construct an effective hash function that captures identity-by-descent (IBD) segments in genetic sequences, which, along with a new bucketing strategy, enable accurate and practical private relative detection. To guarantee privacy, we introduce an efficient algorithm based on multiparty homomorphic encryption (MHE) to allow data holders to cooperatively compute the relatedness coefficients between individuals and to further classify their degrees of relatedness, all without sharing any private data. We demonstrate the accuracy and practical runtimes of SF-Relate on the UK Biobank andAll of Usdata sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.
Bloch equations in terahertz magnetic-resonance ellipsometry
Authors: Rindert Viktor , Richter Steffen , Kühne Philipp , Ruder Alexander , Darakchieva Vanya , Schubert Mathias
Published: August 2024

A generalized approach derived from Bloch's equation of motion of nuclear magnetic moments is presented to model the frequency, magnetic field, spin density, and temperature dependencies in the electromagnetic permeability tensor for materials with magnetic resonances. The resulting tensor model predicts characteristic polarization signatures which can be observed, for example, in Mueller matrix element spectra measured. When augmented with thermodynamic considerations and suitable Hamiltonian description of the magnetic eigenvalue spectrum, important parameters such as density, spectral amplitude distribution, relaxation time constants, and geometrical orientation parameters of the magnetic moments can be obtained from comparing the generalized model approach to experimental data. We demonstrate our approach by comparing model calculations with full Mueller matrix element spectra measured at an oblique angle of incidence in the terahertz spectral range, across electron spin resonance quintuplet transitions observed in wurtzite-structure GaN doped with iron. Our model correctly predicts the complexity of the polarization signatures observed in the 15 independent elements of the normalized Mueller matrix for both positive and negative magnetic fields and will become useful for future analysis of frequency and magnetic field-dependent magnetic resonance measurements.

Published by the American Physical Society
2024
95 GeV excess in the Georgi-Machacek model: Single or twin peak resonance
Authors: Ahriche Amine
Published: August 2024

In this work, we investigate the possibility to address the excess observed around 95 GeV in the γγ, ττ, and bb¯ channels as a scalar resonance(s) within the Georgi-Machacek model. In our analysis, we find that the excess can be easily accommodated in the channels (γγ and bb¯) simultaneously, where the 95 GeV candidate is a single peak resonance (SPR) due to a light CP-even scalar. We found that the excess in the ττ channel can be addressed simultaneously with γγ and bb¯ only if the 95 GeV candidate is a twin peak resonance (TPR), i.e., another CP-odd scalar in addition to the CP-even scalar. We demonstrate that the nature of the 95 GeV scalar resonance candidate (SPR or TPR) can be probed via the properties of its di-τ decay.

Published by the American Physical Society
2024
Dynamical origin of neutrino masses and dark matter from a new confining sector
Authors: Berbig Maximilian , Herrero-Garcia Juan , Landini Giacomo
Published: August 2024

A dynamical mechanism, based on a confining non-Abelian dark symmetry, which generates Majorana masses for hyperchargeless fermions, is proposed. We apply it to the inverse seesaw scenario, which allows us to generate light neutrino masses from the interplay of TeV-scale pseudo-Dirac mass terms and a small explicit breaking of lepton number. A single generation of vectorlike dark quarks, transforming under a SU(3)D gauge symmetry, is coupled to a real singlet scalar, which serves as a portal between the dark quark condensate and three generations of heavy sterile neutrinos. Such a dark sector and the Standard Model (SM) are kept in thermal equilibrium with each other via sizable Yukawa couplings to the heavy neutrinos. In this framework, the lightest dark baryon, which has spin 3/2 and is stabilized at the renormalizable level by an accidental dark baryon number symmetry, can account for the observed relic density via thermal freeze-out from annihilations into the lightest dark mesons. These mesons, in turn, decay to heavy neutrinos, which produce SM final states upon decay. This model may be probed by next generation neutrino telescopes via neutrino lines produced from dark matter annihilations.

Published by the American Physical Society
2024
Thermodynamic Stability at the Two-Particle Level
Authors: Kowalski A. , Reitner M. , Del Re L. , Chatzieleftheriou M. , Amaricci A. , Toschi A. , de’ Medici L. , Sangiovanni G. , Schäfer T.
Published: August 2024

We show how the stability conditions for a system of interacting fermions that conventionally involve variations of thermodynamic potentials can be rewritten in terms of one- and two-particle correlators. We illustrate the applicability of this alternative formulation in a multiorbital model of strongly correlated electrons at finite temperatures, inspecting the lowest eigenvalues of the generalized local charge susceptibility in proximity of the phase-separation region. Additionally to the conventional unstable branches, we address unstable solutions possessing a positive, rather than negative, compressibility. Our stability conditions require no derivative of free-energy functions with conceptual and practical advantages for actual calculations and offer a clear-cut criterion for analyzing the thermodynamics of correlated complex systems.

Published by the American Physical Society
2024
What does it take to revolutionize Chinese diets: evidence from a choice experiment on urban Chinese consumers
Authors: Chen Kevin Z. , Yu Luyun , Lin Wen , Ortega David L.
Published: August 2024

Purpose

The purpose is to understand the factors affecting Chinese diet selections and propose strategies for revolutionizing Chinese diets toward healthy ones.

Design/methodology/approach

This study implemented an online discrete choice experiment to identify the factors affecting diet selections among urban Chinese consumers. Four different diet patterns were used to label each of the product alternatives in the experiment, which varied in taste and cost. Specifically, implying the healthiness and sustainability of a diet, the diet alternatives included the average diet, the Chinese Food Guide Pagoda diet, the EAT-Lancet diet and the Flexitarian diet. Using consumer data from six provincial capital cities, we used random parameter logit models to estimate their preferences.

Findings

Diet type and diet cost were found to be more important in urban Chinese consumers' diet selections than the ability to customize taste. The average diet, although not healthy and sustainable, was preferred most by respondents, signaling the challenges of shifting the consumer diet in China. Increasing the cost of the average diet can significantly promote sustainable healthy diet choices among urban Chinese residents. In other words, improving the affordability of sustainable healthy diets would have the potential to fuel the diet revolution in China.

Originality/value

Instead of choices of a single food item, this paper focused on the individual selection of a diet, where different food products can act as substitutes or as complements for one another. We also proposed a way to assess individual preferences and valuations for several different diets.
Does task-technology fit suppress employee innovation in digital transformation? The role of positive emotions and creative self-expectations
Authors: Sun Zhao-Yu , Zhong Xue , Meng Liang , Zhao Yu-Yan
Published: August 2024

Purpose

This study aims to provide a nuanced understanding of the relationship between task-technology fit and employee innovative behavior, as well as the role of creative self-expectations.

Design/methodology/approach

Hierarchical regression analysis was used to test the proposed multilevel model on a sample of 407 employees working in Chinese companies.

Findings

Task-technology fit stimulates employee innovative behavior through the regulation of creative self-expectations and positive emotions. When creative self-expectations is low, the promoting effect of task-technology fit on innovative behavior is enhanced. However, when creative self-expectations is too high, this effect is reversed due to employees’ preference for challenging and complex work.

Practical implications

In the process of enterprise digital transformation, managers should not only focus on the alignment between employees' skills and individual task expectations, but also pay attention to employees' emotions and individual trait differences, to enhance the likelihood of innovative behavior occurrence and achieve successful enterprise digital transformation.

Originality/value

This study enriches the research on task-technology fit and provides recommendations for organizations to achieve digital transformation.
Democratising futures, reinvigorating democracy? Participatory futures as a tool for citizen voice and influence in local decision-making
Authors: Trowbridge Hayley
Published: August 2024

Purpose

In recent years, democracies across Europe have been challenged in ways this paper has not witnessed on such a scale for generations. It is therefore unsurprising that innovations within democracy are emerging, particularly in terms of participatory and deliberative practices. Focusing specifically on local democracy and decision-making, this paper aims to examine ways of democratising future studies as a means of enhancing citizen participation in democracy.

Design/methodology/approach

The paper draws upon the growing body of work under the umbrella term of “participatory futures” as a way of contextualising and critiquing the “real-world” application and empirical testing of methods within this field by local municipalities.

Findings

It identifies the importance of supporting the development of futures literacy in citizens, public administration officials and political and strategic leaders. The paper demonstrates how broadening the application of existing foresight techniques through their confluence with participatory action research (PAR) principles can create spaces that reignite people’s social imagination. This in turn enables citizens and those working in local municipalities to engage in dialogue about the future.

Originality/value

The paper examines the results of a PAR study, in which innovative participatory future methods were tested as tools for enhancing citizen involvement in local decision-making. Through this, it outlines how foresight practices can be democratised, supporting local democracy to thrive, and identifies future research and practice directions within the field.
Doctors only blame the patients: a systems analysis of polycystic ovarian syndrome (PCOS)
Authors: Mathur Devasheesh
Published: August 2024

Purpose

This study is conducted to understand an emerging public health problem in the garb of polycystic ovarian syndrome (PCOS) that affects about 6–21% of women in reproductive age from a systems perspective.

Design/methodology/approach

The research is conducted in two phases. In phase 1, 15 women suffering from PCOS were interviewed to generate a knowledge map using an interpretive phenomenological research approach. The emerging themes were divided into four categories, namely individual, familial, societal, organizational, medical and systemic. In phase 2, five workshops were conducted with six invited actors to generate a causal loop diagram (CLD) of PCOS. The Standards for Reporting Qualitative Research (SRQR) are used in this study.

Findings

A CLD from an individual's perspective with implications on organizational, societal and system levels.

Research limitations/implications

Awareness of “lifestyle diseases” is increasing, and this research shall help future studies put PCOS in the larger psychosocial context. The geographical location of respondents can be a limitation, as the causal linkages could only be true for the research site.

Practical implications

The CLD provides a comprehensive understanding of complex emerging phenomenon of PCOS.

Social implications

The paper draws attention to factors such as frequently changing doctors, withdrawal from work, medication fatigue, inclination to adopt due to infertility, etc.

Originality/value

This is the first such paper laying out the causal relationships between factors at the individual levels and connecting them to societal, organizational and system levels. This mapping can be useful for policymakers and industry leaders to empathize with PCOS sufferers so that their working conditions can be managed better.
A “quiet quitting” scale: development and validation
Authors: Talukder Md Farid , Prieto Leonel
Published: August 2024

Purpose

Many principles and paradigms that influenced the labour system before the COVID-19 pandemic have changed, and the academic and corporate communities are struggling to make sense of the paradigm shifts the authors have entered. One of the organisational phenomena highlighted after the COVID-19 pandemic is “Quiet quitting”, that is, the tendency for workers to do the bare minimum tasks necessary for their occupations to avoid getting dismissed. This phenomenon may substantially impact both organisations and workers. As a result, academic interest in “Quiet quitting” has recently proliferated. Upon using leader-member exchange, organisational support and social exchange theories, this paper aims to propose and validate a scale measuring the new construct, “Quiet Quitting”.

Design/methodology/approach

A sample of 1,430 valid questionnaires from individuals working in different industries, organisations and regions in the USA were examined using normality and Kaiser–Meyer–Olkin tests, as well as factor, reliability and nomological validity analyses.

Findings

Exploratory and confirmatory factor analyses and reliability and nomological validity evaluations validate the proposed “Quiet Quitting” scale.

Originality/value

To the best of the authors’ knowledge, the proposed and validated “Quiet Quitting” scale is original. Since this scale may help to examine crucial management-worker dynamics in organisations, it may be subsequently developed and used by researchers in future studies.
Unpacking the unintended consequences of socially responsible human resource management: a role stress perspective
Authors: Nguyen Canh Minh , Pham Bao Thai , Chau Duyen Thi Le
Published: August 2024

Purpose

This paper aims to explore the unintended effect of socially responsible human resource management (SRHRM) on employee task performance via three components of role stress: role conflict, role ambiguity and role overload.

Design/methodology/approach

Data was collected from 360 employees who were working in companies in the south of Vietnam and the study hypotheses were tested using structural equation modelling (SEM).

Findings

The results indicate that SRHRM increases role conflict, role ambiguity and role overload, which negatively affect employee task performance.

Practical implications

The key practical implication of our study is that SRHRM may decrease employee task performance via role conflict, role ambiguity and role overload. Managers should be aware of these findings and devise a plan to reduce the role stress that results from implementing SRHRM.

Originality/value

This study provides empirical evidence of the destructive consequences of SRHRM and contributes to a more complete perspective of how SRHRM affects employee performance.