bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting bacterial fitness in Mycobacterium tuberculosis with transcriptional regulatory network-informed interpretable machine learning
Authors: Bustad Ethan , Petry Edson , Gu Oliver , Griebel Braden T. , Rustad Tige R. , Sherman David R. , Yang Jason H. , Ma Shuyi 
Published: September 2024

AbstractMycobacterium tuberculosis(Mtb) is the causative agent of tuberculosis disease, the greatest source of global mortality by a bacterial pathogen. Mtb adapts and responds to diverse stresses such as antibiotics by inducing transcriptional stress-response regulatory programs. Understanding how and when these mycobacterial regulatory programs are activated could enable novel treatment strategies for potentiating the efficacy of new and existing drugs. Here we sought to define and analyze Mtb regulatory programs that modulate bacterial fitness. We assembled a large Mtb RNA expression compendium and applied these to infer a comprehensive Mtb transcriptional regulatory network and compute condition-specific transcription factor activity profiles. We utilized transcriptomic and functional genomics data to train an interpretable machine learning model that can predict Mtb fitness from transcription factor activity profiles. We demonstrated that this transcription factor activity-based model can successfully predict Mtb growth arrest and growth resumption under hypoxia and reaeration using only RNA-seq expression data as a starting point. These integrative network modeling and machine learning analyses thus enable the prediction of mycobacterial fitness under different environmental and genetic contexts. We envision these models can potentially inform the future design of prognostic assays and therapeutic intervention that can cripple Mtb growth and survival to cure tuberculosis disease.
Gut-derived PPAR-γ signaling and risk of bacterial enteric infection: insight from thiazolidinedione users in a US population-based study
Authors: Birabaharan Morgan , Kaelber David C , Nizet Victor , Zarrinpar Amir 
Published: September 2024

AbstractBackground and AimsThe ongoing antimicrobial resistant crisis heralds the need for new therapeutics against enteric infection. In mouse models, colon epithelial peroxisome proliferator-activated receptor-γ (PPAR-γ) signaling limits oxygen and nitrate luminal bioavailability, thereby preventing bacterial pathogen colonization. However, whether this mechanism operates similarly in humans remains uncertain.MethodsTo investigate, we used the cloud-based TriNetX Analytics Platform which aggregates health records from 117 million patients across 66 US healthcare organizations, to assess the risk of bacterial enteric infection among diabetic patients prescribed thiazolidinediones, a class of PPAR-γ agonists, to other anti-diabetes medications.ResultsAmong 85,117 thiazolidinedione users, we observed a 22-49% lower risk of bacterial enteric infections compared to users of other anti-diabetes medications. This reduction in risk was consistent across high-risk individuals, regardless of sex or age. Similar results were replicated in high-risk patients when thiazolidinedione users were directly compared to those on DPP-4 inhibitors.ConclusionThese findings support the potential protective role of PPAR-γ signaling against bacterial enteric infection and call for further clinical investigation.
Diagnostic Performance of Systemic-Immune Inflammation Index for Overall and Complicated Acute Appendicitis: A Systematic Review and a Diagnostic Test Accuracy Meta-Analysis
Authors: Montero Javier Arredondo , Delgado-Miguel Carlos , Riveros Blanca Paola Pérez , Fernández-Atuan Rafael , Rico-Jiménez María 
Published: September 2024

ABSTRACTBackgroundThis study aimed to analyze the systemic-immune inflammation index (SII)’s diagnostic performance in diagnosing acute appendicitis (AA) and discriminating between complicated acute appendicitis (CAA) and non-complicated acute appendicitis (NCAA).MethodsThis review was registered in PROSPERO (CRD42024587430). We included prospective or retrospective original clinical studies evaluating the diagnostic performance of SII in AA. A search was conducted in PubMed, Web of Science, Scopus, and OVID. Search terms and keywords were: (appendicitis OR appendectomy) AND (systemic-immune inflammation index OR SII). Two independent reviewers selected the articles and extracted relevant data. Methodological quality was assessed using the QUADAS2 index. A synthesis of the results, standardization of the metrics, four random-effect meta-analyses, and two Diagnostic Test Accuracy (DTA) meta-analyses were performed.ResultsThirteen studies with data from 9083 participants, including 5255 patients with a confirmed diagnosis of AA and 3828 controls (CG), were included in this review. The random-effect meta-analysis of SII (AA vs. CG) included ten articles (3733 AA and 3510 controls) and resulted in a significant mean difference [95% CI] of 1072.46 [750.55,1394.37] (p<0.001). The random-effect meta-analysis of SII (CAA vs. NCAA) included nine articles (1116 CAA and 2984 NCAA) and resulted in a significant mean difference [95% CI] of 1294.2 [731.54,1856.86] (p<0.001). Subgroup meta-analysis for studies conducted in pediatric-only populations maintained statistical significance. The DTA meta-analysis (AA vs. CG) yielded a pooled sensitivity and specificity [95% CI] of 81.8 [75.2,86.9] % and 79.9 [68.2,88.1] %. The DTA meta-analysis (NCAA vs. CAA) resulted in a pooled sensitivity and specificity [95% CI] of 72.5 [49.6,87.6] % and 82.5 [65.1,92.2] %.ConclusionsSII emerges as a robust tool for diagnosing AA and differentiating between NCAA and CAA. The retrospective nature of most of the included studies and their limited geographical distribution warrant further prospective multicenter studies to validate these findings.FundingNoneRegistrationPROSPERO (CRD42024587430).
Behavioural changes in frontotemporal dementia and their cognitive and neuroanatomical correlates
Authors: Rouse Matthew A. , Husain Masud , Garrard Peter , Patterson Karalyn , Rowe James B. , Lambon Ralph Matthew A. 
Published: September 2024

AbstractBehavioural changes are a central feature of frontotemporal dementia (FTD); they occur in both behavioural-variant (bvFTD) and semantic dementia (SD)/semantic-variant primary progressive aphasia subtypes. In this study, we addressed two current clinical knowledge gaps; (i) are there qualitative or clear distinctions between behavioural profiles in bvFTD and SD, and (ii) what are the precise roles of the prefrontal cortex and anterior temporal lobes in supporting social behaviour? Resolving these conundrums is crucial for improving diagnostic accuracy and for the development of targeted interventions to treat challenging behaviours in FTD. Informant questionnaires to assess behavioural changes included the Cambridge Behavioural Inventory-Revised and two targeted measures of apathy and impulsivity. Participants completed a detailed neuropsychological battery to permit investigation of the relationship between cognitive status (including social-semantic knowledge, general semantic knowledge and executive function) with behaviour change in FTD. To explore changes in regional grey matter volume, a subset of patients had structural MRI. Diagnosis-based group comparisons were supplemented by a transdiagnostic approach which encompassed the spectrum of bvFTD, SD and “mixed” or intermediate cases. Such an approach is sensitive to the systematic graded variation in FTD and allows the neurobiological underpinnings of behaviour change to be explored across an FTD spectrum. We found a wide range of behavioural changes across FTD. Althoughquantitativelymore severe on average in bvFTD, as expected, the item-level analyses found no evidence forqualitativedifferences in behavioural profiles or “behavioural double dissociations” between bvFTD and SD. Comparisons of self and informant ratings revealed strong discrepancies in the perspective of the caregiver versus patient. Logistic regression revealed that neuropsychological measures had better discriminative accuracy for bvFTD versus SD than caregiver-reported behavioural measures. A principal component analysis of all informant questionnaire domains extracted three components, interpreted as reflecting: (1) apathy, (2) challenging behaviours and (3) activities of daily living. More severe apathy in both FTD subtypes was associated with (a) increased levels of impaired executive function and (b) anterior cingulate cortex atrophy. Questionnaire ratings of impaired behaviour did not correlate with either anterior temporal lobe atrophy or degraded social-semantic knowledge. Together, these findings highlight the presence of a wide range of behavioural changes in both bvFTD and SD, which vary by degree rather than quality. We recommend a transdiagnostic approach for future studies of the neuropsychological and neuroanatomical underpinnings of behavioural deficits in FTD.
External validation of prognostic and predictive gene signatures in head and neck cancer patients
Authors: Fossen Erlend I. F. , Moreira-Soares Mauricio , LeBlanc Marissa , Frigessi Arnoldo , Hovig Eivind , Lopez-Perez Laura , Estévez-Priego Estefanía , Hernandez Liss , Cabrera-Umpierrez Maria Fernanda , Fico Giuseppe , Tinhofer Ingeborg , Sachse Vanessa , Scheckenbach Kathrin , Le Tourneau Christophe , Kamal Maud , Thomas Steve , Pring Miranda , Licitra Lisa , De Cecco Loris , Cavalieri Stefano 
Published: September 2024

AbstractHead and neck squamous cell carcinomas (HNSCC) are aggressive and heterogenous tumors with a high fatality rate. Many gene signatures (GS) have been developed with both prognostic and predictive significance. We aimed to externally validate five published GS in a large European collection of HNSCC patients. Gene expression from 1097 treatment-naïve HNSCC patients’ primary tumors was used to calculate scores for the five GS. Cox proportional hazard models were used to test the association between both 2-year overall survival and 2-year disease-free survival and the signature scores. The predictive role of GS was validated by comparing survival associations in patients receiving specific treatment (i.e., radiotherapy, systemic treatment) versus those who did not. We successfully externally validated all 5 GS, including two prognostic signatures, one signature as prognostic and predictive of sensitivity to systemic treatment, while signatures for cisplatin-sensitivity and radiosensitivity were validated as prognostic only.
Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells
Authors: Wellington Rachel , Cheng Xiaoyi , Campbell Clyde A. , Trapnell Cole , Espin-Palazon Raquel , Hadland Brandon , Doulatov Sergei 
Published: September 2024

ABSTRACTHematopoietic stem cells (HSCs) arise in embryogenesis from a specialized hemogenic endothelium (HE). In this process, HE cells undergo a unique fate change termed endothelial-to-hematopoietic transition, or EHT. While induced pluripotent stem cells (iPSCs) give rise to HE with robust hemogenic potential, the generation of bona fide HSCs from iPSCs remains a challenge. Here, we map single cell dynamics of EHT during embryoid body differentiation from iPSCs and integrate it with human embryo datasets to identify key transcriptional differences betweenin vitroandin vivocell states. We further map ligand-receptor interactions associated with differential expression of developmental programs in the iPSC system. We found that the expression of endothelial genes was incompletely repressed during iPSC EHT. Elevated FGF signaling by FGF23, an endothelial pathway ligand, was associated with differential gene expression betweenin vitroandin vivoEHT. Chemical inhibition of FGF signaling during EHT increased HSPC generation in the zebrafish, while an FGF agonist had the opposite effect. Consistently, chemical inhibition of FGF signaling increased hematopoietic output from iPSCs. In summary, we map the dynamics of EHT from iPSCs at single cell resolution and identify ligand-receptor interactions that can be modulated to improve iPSC differentiation protocols. We show, as proof of principle, that chemical inhibition of FGF signaling during EHT improves hematopoietic output in zebrafish and the iPSC system.
Genes involved in protein folding and chromatin organization buffer genetic variation
Authors: Frickel Jens , Tawfeeq Mohammed T. , Baker Emily , Baco Sara , Rombout Jonas , Voordeckers Karin , Jarosz Daniel F. , Vonesch Sibylle C. , Verstrepen Kevin J. 
Published: September 2024

SUMMARYMutations are not always phenotypically active or show different effects in different individuals. While the mechanisms underlying this variable relationship between mutations and phenotypes are largely elusive, some specific genes may influence the phenotypic effects of cryptic variation. We employ the toolbox ofSaccharomyces cerevisiaeto perform a genome-wide screen aimed at identifying these so-called genetic buffer genes. Measuring the fitness of 1.8 million mutated strains identified a small set of evolutionary conserved buffer genes involved in protein folding and chromatin organization, includingGIM3, SSA2, HOG1andFKH2. Deletion of these genes increases the fitness effect of de novo mutations as well as standing genetic variation, with some mutations becoming adaptive. Moreover, losing a buffer gene results in a decline of standing genetic variation. Together, these results reveal a set of conserved genes that influence the phenotypic outcome of mutations and play a role in complex genetics and incomplete penetrance.
Stable bubble formations in a depth-perturbed Hele-Shaw channel
Authors: Lawless Jack , Keeler Jack , Hazel Andrew L. , Juel Anne 
Published: September 2024

The propagation of polydisperse bubbles inside a rectangular Hele-Shaw channel by the constant volumetric flux flow of an ambient viscous liquid is generally unsteady; pairs of neighboring bubbles will either separate or coalesce because their propagation speeds increase monotonically with their sizes. Thus, any group of bubbles will eventually rearrange itself in order of decreasing size, individual bubbles will separate, and, crucially, there are no stable multiple-bubble states. Remarkably, the introduction of a small axially uniform elevation to the channel's lower boundary (on the order of a percent of the channel's depth) leads to the creation of stable multiple-bubble states and, thus, disrupts the usual reordering by bubble sizes. The constituent bubbles of such states lie in alternation on opposite sides of the elevation. The elevation provides a mechanism for the trailing bubbles to reduce their propagation speeds when approaching their preceding nearest neighbors. The stable multiple-bubble states are always led by the smallest bubble while the trailing bubbles can be arranged in any order and, thus, their number grows factorially as the number of bubbles increases.

Published by the American Physical Society
2024
Theoretical Description of Pump-Probe Experiments in Charge-Density-Wave Materials out to Long Times
Authors: Petrović Marko D. , Weber Manuel , Freericks James K. 
Published: September 2024

We describe coupled nonequilibrium electron-phonon systems semiclassically—Ehrenfest dynamics for the phonons and quantum mechanics for the electrons—using a classical Monte Carlo approach that determines the nonequilibrium response to a large pump field. The semiclassical approach is expected to be accurate, because the phonons are excited to average energies much higher than the phonon frequency, eliminating the need for a quantum description. The numerical efficiency of this method allows us to perform a self-consistent time evolution out to very long times (tens of picoseconds), enabling us to model pump-probe experiments of a charge-density-wave (CDW) material. Our system is a half-filled, one-dimensional (1D) Holstein chain that exhibits CDW ordering due to a Peierls transition. The chain is subjected to a time-dependent electromagnetic pump field that excites it out of equilibrium, and then a second probe pulse is applied after a time delay. By evolving the system to long times, we capture the complete process of lattice excitation and subsequent relaxation to a new equilibrium, due to an exchange of energy between the electrons and the lattice, leading to lattice relaxation at finite temperatures. We employ an indirect (impulsive) driving mechanism of the lattice by the pump pulse due to the direct driving of the electrons. We identify two driving regimes, where the pump can either cause small perturbations or completely invert the initial CDW order. Our work successfully describes the ringing of the amplitude mode in CDW systems that has long been seen in experiment but never successfully explained by microscopic theory. We also describe the fluence-dependent crossover that inverts the CDW order parameter and changes the phonon dynamics. Finally, we illustrate how this method can examine a number of different types of experiments including photoemission, x-ray diffraction, and two-dimensional (2D) spectroscopy.

Published by the American Physical Society
2024
A comprehensive characterization of thiophosgene in the solid state
Authors: Tambornino Frank , Ringelband Sven , Parker Stewart F. , Howard Christopher M. , Fortes Dominic 
Published: September 2024

Thiophosgene is one of the principal C=S building blocks in synthetic chemistry. At room temperature, thiophosgene is a red liquid. While its properties in the liquid and gaseous states are well known, a comprehensive characterization of thiophosgene in its solid state is presented here. Differential scanning calorimetry shows that thiophosgene forms a supercooled melt before rapidly crystallizing. Its melting point is 231.85 K (−41.3 °C). At 80 K, thiophosgene crystallizes in space group P63/m [No. 174, a = b = 5.9645 (2), c = 6.2835 (3) Å, V = 193.59 (2) Å3]. The molecule shows a distinct rotational disorder: all S and Cl positions are of mixed occupancy and the disorder does not resolve at temperatures as low as 10 K, as was shown by neutron powder diffraction. Infrared, Raman and inelastic neutron scattering spectra were collected and assigned with the aid of quantum chemical calculations. A larger ordered structural model allowed for better agreement between the measured and calculated spectra, further indicating that disorder is an inherent feature of solid-state thiophosgene.
Magnetic structure of the noncentrosymmetric magnet Sr2MnSi2O7 through irreducible representation and magnetic space group analyses
Authors: Nambu Y. , Kawamata M. , Pang X. , Murakawa H. , Avdeev M. , Kimura H. , Masuda H. , Hanasaki N. , Onose Y. 
Published: September 2024

Magnetic structures of the noncentrosymmetric magnet Sr2MnSi2O7 were examined through neutron diffraction for powder and single-crystalline samples, as well as magnetometry measurements. All allowed magnetic structures for space group P
421
m with the magnetic wavevector q
m = (0, 0, ½) were refined via irreducible representation and magnetic space group analyses. The compound was refined to have in-plane magnetic moments within the magnetic space group Cmc21.1′
c
(No. 36.177) under zero field, which can be altered to P212121.1′
c
(No. 19.28) above μ0
H = 0.067 (5) T to align induced weak-ferromagnetic components within one layer on the ab plane. All refined parameters are provided following the recent framework based upon the magnetic space group, which better conveys when exchanging crystallographic information for commensurate magnetic structures.
Money value, risk perception and behavior: evidence from the Brazilian market
Authors: Lopes Luis Felipe Dias , Santos Anavaléria Vieira , da Silva Deoclécio Junior Cardoso , Sonza Igor Bernardi , Knebel Baggio Daniel , de Moura Gilnei Luiz , Silva Wesley Vieira da , da Veiga Claudimar Pereira 
Published: September 2024

PurposeThis research sheds light on the distinct decision-making behaviors and perceptions related to the value attributed to money, uncovering nuances in the interrelationship between money valuation and its ensuing influence on risk perceptions and related behaviors, mainly focusing on financial education.Design/methodology/approachExecuted in the Brazilian market, this study employs a quantitative approach, encompassing 663 participants and deploying comprehensive statistical methodologies – principally, structural equation modeling based on variances – to scrutinize the amassed primary data.FindingsThe insights from the study reveal a significant impact of both negative money value (NMV) and positive money value (PMV) on participants' financial decisions, profoundly shaping perceptions, acceptances and responses to risk. Consequently, this study underscores the pivotal role the perceived value of money plays in sculpting financial behaviors and formulating risk management strategies. Distinctly, this research emphasizes intrinsic monetary values, extending unprecedented insights by delineating aversive behaviors toward losses and risks and probing the repercussions of both negative and positive monetary values.Originality/valueIt acts as an avant-garde exploration, unveiling new perspectives on upcoming consumers' anticipated financial decision-making approaches and pinpointing areas warranting deeper exploration and comprehension within the fluid consumer market landscape.
Ingesting digital archives into long-term storage system through free open-source software in South Africa
Authors: Shekgola Mahlatse Moses , Ngoepe Mpho 
Published: September 2024

Purpose
In South Africa, public institutions face challenges in transitioning their digital records to trusted digital repositories due to a deficiency in skills, infrastructure and systems. Free and open-source software (FOSS) presents a viable solution for facilitating the transfer of digital archives for permanent preservation. Despite the existence of FOSS policy in South Africa, the public sector has yet to fully use it to engage in the development and implementation of products for records management and archive preservation using open-source software. This study aims to explore the ingestion of digital archives into an approved long-term storage system through FOSS in South Africa with the view of developing a framework.

Design/methodology/approach
The study adopted a qualitative research approach to collect data through interviews with purposively selected participants (records managers, archivists and IT officials) from national government departments that have implemented records management systems for digital curation of archives, as well as the National Archives and Records Services of South Africa (NARSSA), which regulates archives and records management, and the State Information Technology Agency, which regulates information technology in government.

Findings
The findings of the study suggest that the systematic transfer of digital materials from public entities to NARSSA, as required by statute, has not taken place.

Research limitations/implications
The study specifically targeted national government departments that have implemented digital archives and records management systems. Consequently, perspectives from departments that have not implemented these solutions were excluded.

Originality/value
A framework is proposed for the transfer of digital archives, using interoperable FOSS, from government agencies responsible for records management to NARSSA for archival preservation. This framework, it is hoped, will facilitate infrastructure and skills development in the management of records and preservation of archives through open platforms.