bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimising the mirror illusion during mirror therapy: evidence from unimpaired individuals
Authors: Kim J.M. , Challis F.O. , Koo C.Y. , Leung C.L. , Lo L.H. , Yeo S.H. , Punt T.D.
Published: November 2024

Patients recovering from hemiparetic stroke have been shown to benefit from mirror therapy in terms of improving their motor function. The clinical improvement in motor function may differ depending on the mirror therapy protocol used. Previous studies have shown that four parameters are influential: the size of the mirror (large and small), manipulation of objects (with or without), the complexity of action (simple and complex), and movement execution (unilateral and bilateral). We examined the impact of these parameters on the subjective quality (believability) of the mirror illusion in unimpaired participants. Forty healthy participants completed 16 different combinations of the four parameters during mirror visual feedback. Participants rated each trial for its level ofbelievabilityon a 10-point Likert scale. A repeated measures ANOVA was used to examine the data. The large mirror consistently elicited higher ratings than the small mirror. And while bimanual movements generally elicited higher ratings than unimanual movements, ratings for bimanual movements were significantly reduced when participants made complex movements with objects. We attributed these results to the congruency of multisensory information. Conditions that elicit congruency between illusory information and other sensory inputs appear to maximise believability over the illusory hand. The findings of this study reveal the parameters maximising illusion believability in unimpaired participants and have implications for optimal mirror therapy conditions in patients’ groups.
Multiscale networks in Alzheimer’s disease identify brain hypometabolism as central across biological scales
Authors: Lara-Simon Elena , Gispert Juan Domingo , Garcia-Ojalvo Jordi , Villoslada Pablo ,   Alzheimer’s Disease Neuroimaging Initiative
Published: November 2024

Alzheimer’s disease encompasses multiple biological scales, spanning molecular factors, cells, tissues, and behavioral manifestations. The interplay among these scales in shaping the clinical phenotype is not yet fully comprehended. In particular, there is great interest in understanding the heterogeneity of the clinical aspects of AD in order to improve treatment and prevention, by targeting those aspects most susceptible to the disease. Here we employed a systems biology approach to address this issue, utilizing multilayer network analysis and deep phenotyping. This integrative analysis incorporated genomics, cerebrospinal fluid biomarkers, tau and amyloid beta (Aβ) PET imaging, brain MRI data, risk factors, and clinical information (cognitive tests scores, Clinical Dementia Rating and clinical diagnosis) obtained through the ADNI collaboration. Multilayer networks were built based on mutual information between the elements of each layer and between layers. Boolean simulations allowed us to identify paths that transmit dynamic information across layers. The most prominent path that significantly predicted the average cognitive phenotype included the PET radiotracer fluorodeoxyglucose (FDG) in the posterior cingulate. Combinations of different symptomatic variables, mainly related to mental health (depression, mood swings, drowsiness) and vascular features (hypertension, cardiovascular history), were also part of the paths explaining the average phenotype. Our results show that integrating the flow of information across biological scales reveals relevant paths for AD, which can be subsequently explored as potential biomarkers or therapeutic targets.

Author summary

Complex diseases such as Alzheimer’s Disease (AD) involve a diverse array of biological processes. In our investigation, we undertook a systems biology approach to AD using network analysis and deep phenotyping within a prospective cohort of patients, incorporating clinical, imaging, genetics, and omics assessments. The gene, molecular and imaging paths explained variation in central nervous system damage, and in metrics of disease severity. The elucidation of multilayer paths in this context provides insights into the diverse phenotypes of the disease and holds the potential to improve understanding of its pathogenesis.
The Relationship of Antepartum Fetal Heart Rate Patterns to Adverse Pregnancy Outcomes
Authors: Cooke William , Albert Beth , Vatish Manu , Davis Jones Gabriel
Published: November 2024

Introduction

Antepartum fetal heart rate (FHR) patterns are routinely assessed to evaluate fetal wellbeing. Despite their clinical use, the relationship between specific FHR patterns and adverse pregnancy outcomes (APOs) remains unclear. This study aims to investigate the association between antepartum FHR patterns and APOs to improve fetal risk assessment.

Methods

In this retrospective case–control study, we extracted raw antepartum FHR traces from singleton pregnancies between 27+0and 41+6weeks’ gestation recorded at Oxford University Hospitals from January 1991 to February 2024. Adverse outcomes included acidaemia, stillbirth, asphyxia, extended neonatal care unit (NCU) admission, hypoxic–ischaemic encephalopathy (HIE), low Apgar scores and neonatal resuscitation at delivery. After applying inclusion and exclusion criteria, 938 FHR traces with APOs were matched using propensity score matching with 938 traces from normal pregnancy outcomes (NPOs), controlling for gestational age, fetal sex, maternal BMI, maternal age, parity, and trace duration. FHR patterns were extracted using a validated automated algorithm and analysed statistically.

Results

The APO cohort showed significantly higher basal heart rates (BHR), fewer accelerations, more decelerations, lower short-term variability (STV), and spent a greater proportion of the trace in periods of low variation compared to the NPO cohort (p<0.001). Logistic regression identified prolonged periods of low variation (odds ratio [OR] = 1.92, 95% CI 1.60–2.30,p<0.001), increased decelerations (OR = 1.40, 95% CI 1.22–1.60,p<0.001), reduced accelerations (OR = 0.66, 95% CI 0.55–0.78,p<0.001), elevated BHR (OR = 0.70, 95% CI 0.61–0.80,p<0.001), and decreased STV (OR = 0.72, 95% CI 0.57–0.91,p= 0.006) as significant predictors of APOs.

Conclusions

Specific antepartum FHR patterns are significantly associated with adverse pregnancy outcomes. Detailed analysis of these patterns can enhance fetal risk assessment and inform clinical decision-making. Adoption of standardised interpretation criteria for antepartum FHR monitoring may improve perinatal outcomes.
Clinical Features of Long COVID Patients Coinfected withMycoplasma pneumoniae
Authors: Zhu Xiaodan , Li Yanhua , Wang Jinghua , Gao Weifei
Published: November 2024

Background

Since the SARS-CoV-2 pandemic, many patients have suffered prolonged complications, called “long COVID”.Mycoplasma pneumoniaeis a common respiratory pathogen, Reports of simultaneous long COVID andM. pneumoniaeinfections are rare in the literature.

Methods

We analyzed the clinical data of patients with long COVID-19 who visited the Respiratory Clinic of The Affiliated Hospital of Hangzhou Normal University between January 1 and January 31, 2023, together with their laboratory and radiographic findings, with Pearson’s χ2test.

Results

Fifty-two patients diagnosed with both long COVID andM. pneumoniaeinfection and 77 with long COVID only were compared. The ages, clinical symptoms, and comorbidities of the two groups did not differ significantly (P > 0.05). However, sex and imaging findings differed between the groups.

Conclusions

Our study showed that long COVID–M. pneumoniaecoinfection was more commonly seen in females and patients with typical chest computed tomography images.
Mapping rare protein-coding variants on multi-organ imaging traits
Authors: Fan Yijun , Chen Jie , Fan Zirui , Chirinos Julio , Stein Jason L. , Sullivan Patrick F. , Wang Rujin , Nadig Ajay , Zhang David Y. , Huang Shuai , Jiang Zhiwen , Guan Peter Yi , Qian Xinjie , Li Ting , Li Haoyue , Sun Zehui , Ritchie Marylyn D. , O’Brien Joan , Witschey Walter , Rader Daniel J. , Li Tengfei , Zhu Hongtu , Zhao Bingxin
Published: November 2024

Human organ structure and function are important endophenotypes for clinical outcomes. Genome-wide association studies (GWAS) have identified numerous common variants associated with phenotypes derived from magnetic resonance imaging (MRI) of the brain and body. However, the role of rare protein-coding variations affecting organ size and function is largely unknown. Here we present an exome-wide association study that evaluates 596 multi-organ MRI traits across over 50,000 individuals from the UK Biobank. We identified 107 variant-level associations and 224 gene-based burden associations (67 unique gene-trait pairs) across all MRI modalities, includingPTENwith total brain volume,TTNwith regional peak circumferential strain in the heart left ventricle, andTNFRSF13Bwith spleen volume. The singleton burden model and AlphaMissense annotations contributed 8 unique gene-trait pairs including the association between an approved drug target gene ofKCNA5and brain functional activity. The identified rare coding signals elucidate some shared genetic regulation across organs, prioritize previously identified GWAS loci, and are enriched for drug targets. Overall, we demonstrate how rare variants enhance our understanding of genetic effects on human organ morphology and function and their connections to complex diseases.
Microbiome Dynamics in Tank- and Pond-Reared GIFT Tilapia
Authors: Delamare-Deboutteville Jérôme , Mahmuddin Mahirah , Gan Han Ming , Rodde Charles , Khor Laura , Verner-Jeffreys David , Chadag Vishnumurthy Mohan , Benzie John A.H.
Published: November 2024

Tilapia (Oreochromisspp.) are among the most widely cultivated freshwater finfish species worldwide. The industry increasingly relies on tilapia strains selected for improved growth and other traits, particularly the Genetically Improved Farmed Tilapia (GIFT) strain. Despite the industry’s reliance on tilapia, knowledge of microbiome dynamics in reared tilapia remains limited. Understanding normal successional patterns in the microbiome of farmed tilapia is essential to identify characteristics of what constitutes a healthy microbial community. In this study, we assessed the microbiomes of tank and pond-reared GIFT tilapia by analyzing 568 samples, including water, gut, skin, and gill microbiomes of tilapia, from tank systems housing the source GIFT populations in Malaysia, and compared them to those reared in earthen ponds on another farm in Malaysia. A total of 2,307 amplicon sequence variants (ASVs) were identified, encompassing a broad taxonomic diversity of 39 phyla, 86 classes, 180 orders, 299 families, 501 genera, and 399 species.

Our findings elucidated distinct microbial community structures between rearing environments and across fish tissues, shedding light on intricate host-microbe interactions shaped by environmental conditions and management practices. The gut microbiome of tank-reared tilapia was dominated by Fusobacteriota (71.14%), in contrast to pond-reared fish (22%), while other taxa, such as Bacteroidota, Firmicutes_A, and Cyanobacteria, also varied markedly between environments and sampling periods. Skin and gill samples showed notable variability in the relative abundances of Fusobacteriota and Deinococcota between the two rearing sites. Principal Coordinates Analysis (PCoA) highlighted the distinct clustering of samples by rearing environment, particularly within gut microbiomes. Biomarkers such as Cyanobiaceae (pond water) and Sphingomonadaceae (tank water) underscored the impact of rearing conditions on microbial composition.

These results establish valuable baseline information on the types of bacteria associated with healthy, genetically defined (GIFT) tilapia strains. This foundational information will help identify specific microbial taxa associated with beneficial or detrimental effects on tilapia health and productivity across varying rearing conditions. Such insights can guide the development of targeted microbiome management strategies to enhance tilapia health and optimize performance.
Identification of a Neuroimmune Circuit that Regulates Allergic Inflammation in the Esophagus
Authors: Kellerman Kendall , Natale Mia , Gerstner Eddie , Rochman Yrina , Rochman Mark , Jankowski Michael P. , Rothenberg Marc E.
Published: November 2024

Eosinophilic esophagitis is a chronic food antigen-driven allergic inflammatory disease associated with symptoms involving the nervous system such as refractory pain. Yet, the role of the nervous system in disease pathogenesis has not received much attention. Herein, we demonstrate that allergen exposure evokes pain-like behavior in association with increased nociceptor signaling and transcriptional responses in dorsal root ganglia. NaV1.8+ sensory nerves were found traveling along the length of the esophagus, organized in distinct bundles adjacent to the basal epithelium, with beta III-tubulin+ sensory nerves distributed more distal to the lumen. Targeted deletion ofIl4rain NaV1.8+ neurons impeded allergen-induced increases in nerve innervation density. Furthermore,Il4ra-/-NaV1.8micehad diminished allergen-induced allergic inflammation in the esophagus including eosinophilia and transcription of pro-inflammatory genes. Translational studies revealed extensive myelinated nerve innervation in the human esophagus, which was increased in patients with eosinophilic esophagitis. Taken together, these data indicate that allergic inflammation is associated with an increase in non-evoked pain, esophageal nerve density, altered sensitivity of sensory neurons, and transcriptional changes in dorsal root ganglia. These finding identify a type 2 neuroimmune circuit that involves the interplay of allergen-induced IL-4 receptor-dependent DRG responses that modify esophageal end-organ inflammatory responses.
Haploinsufficiency of lysosomal enzyme genes in Alzheimer’s disease
Authors: Benitez Bruno A. , Wallace Clare E. , Patel Maulikkumar , Nykanen Niko-Petteri , Yuede Carla M. , Eaton Samantha L. , Pottier Cyril , Cetin Arda , Johnson Matthew , Bevan Mia T. , Gardiner Woodrow D. , Edwards Hannah M. , Doherty Brookelyn M. , Harrigan Ryan T. , Kurian Dominic , Wishart Thomas M. , Smith Colin , Cirrito John R. , Sands Mark S.
Published: November 2024

There is growing evidence suggesting that the lysosome or lysosome dysfunction is associated with Alzheimer’s disease (AD). Pathway analysis of post mortem brain-derived proteomic data from AD patients shows that the lysosomal system is perturbed relative to similarly aged unaffected controls. However, it is unclear if these changes contributed to the pathogenesis or are a response to the disease. Consistent with the hypothesis that lysosome dysfunction contributes to AD pathogenesis, whole genome sequencing data indicate that heterozygous pathogenic mutations and predicted protein-damaging variants in multiple lysosomal enzyme genes are enriched in AD patients compared to matched controls. Heterozygous loss-of-function mutations in the palmitoyl protein thioesterase-1 (PPT1), α-L-iduronidase (IDUA), β-glucuronidase (GUSB), N-acetylglucosaminidase (NAGLU), and galactocerebrosidase (GALC) genes have a gene-dosage effect on Aβ40levels in brain interstitial fluid in C57BL/6 mice and significantly increase Aβ plaque formation in the 5xFAD mouse model of AD, thus providingin vivovalidation of the human genetic data. A more detailed analysis ofPPT1heterozygosity in 18-month-old mice revealed changes in α-, β-, and γ-secretases that favor an amyloidogenic pathway. Proteomic changes in brain tissue from agedPPT1heterozygous sheep are consistent with both the mouse data and the potential activation of AD pathways. Finally, CNS-directed, AAV-mediated gene therapy significantly decreased Aβ plaques, increased life span, and improved behavioral performance in 5xFAD/PPT1+/- mice. Collectively, these data strongly suggest that heterozygosity of multiple lysosomal enzyme genes represent risk factors for AD and may identify precise therapeutic targets for a subset of genetically-defined AD patients.

Significance Statement

Lysosomes play a role in the degradation of aggregation-prone proteins such as amyloid β (Aβ). Homozygous lysosomal enzyme gene defects result in fatal pediatric lysosomal storage diseases and, historically, carriers were considered normal. However, a human genetic analysis identified deleterious heterozygous variants in multiple lysosomal enzyme genes that are enriched in Alzheimer’s disease (AD) patients. Those findings were validatedin vivoby demonstrating that heterozygous loss-of-function (LoF) mutations in five different lysosomal enzyme genes affect Aβ processing and exacerbate Aβ plaque formation. CNS-directed gene therapy ameliorated the effects of a heterozygous LoF mutation in one of those genes in a mouse model of AD. These findings provide insights into the role of lysosomes in AD and have important therapeutic implications.
Sensory History Drives Adaptive Neural Geometry in LP/Pulvinar-Prefrontal Cortex Circuits
Authors: Leow Yi Ning , Barlowe Alexandria , Luo Cindy , Osako Yuma , Jazayeri Mehrdad , Sur Mriganka
Published: November 2024

Prior expectations guide attention and support perceptual filtering for efficient processing during decision-making. Here we show that during a visual discrimination task, mice adaptively use prior stimulus history to guide ongoing choices by estimating differences in evidence between consecutive trials (| Δ Dir |). The thalamic lateral posterior (LP)/pulvinar nucleus provides robust inputs to the Anterior Cingulate Cortex (ACC), which has been implicated in selective attention and predictive processing, but the function of the LP-ACC projection is unknown. We found that optogenetic manipulations of LP-ACC axons disrupted animals’ ability to effectively estimate and use information across stimulus history, leading to | Δ Dir |-dependent ipsilateral biases. Two-photon calcium imaging of LP-ACC axons revealed an engagement-dependent low-dimensional organization of stimuli along a curved manifold. This representation was scaled by | Δ Dir | in a manner that emphasized greater deviations from prior evidence. Thus, our work identifies the LP-ACC pathway as essential for selecting and evaluating stimuli relative to prior evidence to guide decisions.
Differential coping strategies exerted by biofilm and planktonic cells of the beneficial bacteriumB. subtilisin response to the protozoan predatorEntamoeba histolytica
Authors: Kolodkin-Gal Ilana , Murugan Prem Anand , Zanditenas Eva , Ankri Serge
Published: November 2024

The human protozoan parasiteEntamoeba histolyticacauses amebiasis and interacts with both beneficial and harmful members of the microbiome. In previous studies, it was shown thatE. histolyticacan break down pre-established biofilms ofB. subtilisin a time- and dose-dependent manner. Inhibiting parasitic cysteine proteases impairs biofilm degradation. However, it is still unknown whether bacteria can sense this process and respond to the degradation of the biofilms.

Here, our research demonstrates a multi-layered response of probiotic bacteria to the parasite, which differs between planktonic bacteria and pre-established biofilms. Sensing the activity of cysteine proteases fromE. histolytica, the bacteria activate the general stress response and, to a lesser extent, the cell wall stress response, making the surviving biofilm members more resistant to mild stressors. On the other hand, planktonic cells exposed to the predators’ lysate deactivate the expression of genes associated with biofilm formation while inducing their motility to avoid predation. Overall, our results indicate that bacteria have evolved to recognize amoeba predators. Furthermore, the partially digested biofilm cells may have unexpected disadvantages over bacteria that did not encounter a predator. These findings may be useful in developing more efficient probiotic strains that are resilient to amoebiasis.
Large-scale brain network analysis reveals functional-structural dissynchrony in HIV-associated asymptomatic neurocognitive disorders: Functional disturbances precede structural changes
Authors: Zhou Zhongkai , Gong Wenru , Hu Hong , Wang Fuchun , Li Hui , Xu Fan , Li Hongjun , Wang Wei
Published: November 2024

Background

In the era following combined antiretroviral therapy (cART), asymptomatic neurocognitive impairment (ANI) has become the primary stage of HIV-associated neurocognitive disorder (HAND). As a potentially reversible phase, precise identification of ANI is crucial. Multimodal MRI, with its non-invasiveness and high sensitivity, can reveal potential changes in brain network function and structure, providing significant support for exploring biomarkers of HAND and optimizing intervention strategies.This study aims to explore the dynamic changes in the functional network, structural network, and functional-structural coupling in ANI patients using multimodal MRI combined with large-scale brain network analysis.

Methods

A total of 95 participants were included, consisting of a healthy control group (HC, n=48) and an ANI patient group (n=47). Functional and structural connectivity matrices were constructed using resting-state fMRI (rs-fMRI) and diffusion tensor imaging (DTI), and graph theory analysis was used to evaluate global metrics, node characteristics, and functional-structural coupling changes.

Results

Structural Network: No significant changes were observed in the global or local topological properties of the structural network in ANI patients. Functional Network: Significant reorganization was observed in several key regions, including the visual network, executive control network, and default mode network. Functional-Structural Coupling: The functional-structural coupling in the occipital and frontal networks was significantly enhanced. Clinical Relevance: Changes in the functional network and functional-structural coupling were associated with the patients’ immune status, duration of infection, and cognitive performance.

Conclusion

The reorganization of the functional network and enhancement of functional-structural coupling during the ANI phase may reflect early manifestations of microscopic pathological changes (such as synaptic and dendritic damage). These changes hold promise as early warning signals in the progression of HAND and provide sensitive biomarkers and important research perspectives for precise diagnosis and early intervention.
Dynamics of genetic circuits inPseudomonas protegens
Authors: Rico Juan , Japón Pablo , Rubio Luis , Goñi-Moreno Ángel
Published: November 2024

The engineering of genetic circuits to perform predefined computations is central to synthetic biology, enabling living cells with new functionalities applicable across various domains. However, these circuits are often specifically tailored to particular cellular hosts, withEscherichia colibeing the most popular. Consequently, their intended functions may not translate well to other organisms, limiting their scope. Understanding circuit dynamics in less familiar organisms is crucial, especially for niche-specific applications requiring cellular chassis different from model organisms generally used in synthetic biology. Here, we develop a combined experimental and theoretical pipeline to evaluate the performance of NOT logic circuits, also called inverters, in the soil bacteriumPseudomonas protegensPf-5—a host renowned for its unique environmental functions and a newcomer to genetic circuitry. Inverters were experimentally tested to characterize input-output functionality, and mathematical modelling was used to infer the dynamic principles of circuit modules. The model quantified the individual impacts of key parameters—such as translation efficiency, repressor performance, and promoter activity—on output levels, enabling predictions about inter-host circuit portability. This parameter calibration revealed unique properties of the chassis, including faster transitions between on and off circuit states compared to the synthetic biology workhorsePseudomonas putida. These characteristics may reflect adaptations to the fluctuating conditions of the plant rhizosphere, where this bacteria thrives. As a result, our work provides DNA parts, circuits and mathematical characterizations to establishP. protegensPf-5 as a viable chassis for environmental synthetic biology.
AcrVIB1 inhibits CRISPR-Cas13b immunity by promoting unproductive crRNA binding accessible to RNase attack
Authors: Wandera Katharina G. , Schmelz Stefan , Migur Angela , Kibe Anuja , Lukat Peer , Achmedov Tatjana , Caliskan Neva , Blankenfeldt Wulf , Beisel Chase L.
Published: November 2024

Anti-CRISPR proteins (Acrs) inhibit CRISPR-Cas immune defenses, with almost all known Acrs acting on the Cas nuclease-CRISPR (cr)RNA ribonucleoprotein (RNP) complex. Here, we show that AcrVIB1, the only known Acr against Cas13b, principally acts upstream of RNP complex formation by promoting unproductive crRNA binding followed by crRNA degradation. AcrVIB1 tightly binds to Cas13b but not to the Cas13b-crRNA complex, resulting in enhanced rather than blocked crRNA binding. However, the more tightly-bound crRNA does not undergo processing and exhibits altered target RNA binding that fails to activate collateral RNA cleavage. The bound crRNA is also accessible to RNases, leading to crRNA turnoverin vivoeven in the presence of Cas13b. Finally, cryo-EM structures revealed that AcrVIB1 binds a helical domain of Cas13b responsible for securing the crRNA, keeping the domain in an untethered state. These findings reveal an Acr that converts an effector nuclease into a crRNA sink to suppress CRISPR-Cas defense.

Highlights

AcrVIB1 binds Cas13b in the absence of a crRNA

The bound AcrVIB1 promotes crRNA binding to Cas13b

The crRNA binds Cas13b unproductively and is accessible to RNases

AcrVIB1 binds the Helical-2 domain of Cas13b, preventing it from securing the crRNA
A single microfluidic device for multi-omics analysis sample preparation
Authors: Ravi Kumar Ranjith Kumar , Haddad Iman , Ndiaye Massamba Mbacke , Marbouty Martial , Vinh Joelle , Verdier Yann
Published: November 2024

Combining different “omics” approaches, such as genomics and proteomics, is necessary to generate a detailed and complete insight into microbiome comprehension. Proper sample collection and processing and accurate analytical methods are crucial in generating reliable data. We previously developed the ChipFilter device for proteomic analysis of microbial samples. We have shown that this device coupled to LC-MS/MS can successfully be used to identify microbial proteins. In the present work, we have developed our workflow to analyze concomitantly proteins and nucleic acids from the same sample. We performed lysis and proteolysis in the device using cultures ofE. coli, B. subtilis, andS. cerevisiae. After peptide recovery for LC-MS/MS analysis, DNA from the same samples was recovered and successfully amplified by PCR for the 3 species. This workflow was further extended to a complex microbial mixture of known compositions. Protein analysis was carried out, enabling the identification of more than 5000 proteins. The recovered DNA was sequenced, performing comparable to DNA extracted with a commercial kit without proteolysis. Our results show that the ChipFilter device is suited to prepare samples for parallel proteomic and genomic analyses, which is particularly relevant in the case of low-abundant samples and drastically reduces sampling bias.
Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages
Authors: Cortés-Martín Adrián , Buttimer Colin , Maier Jessie L. , Tobin Ciara A. , Draper Lorraine A. , Ross R. Paul , Kleiner Manuel , Hill Colin , Shkoporov Andrey N.
Published: November 2024

Background

Bacteriophages (phages) and bacteria within the gut microbiome persist in long-term stable coexistence. These interactions are driven by eco-evolutionary dynamics, where bacteria employ a variety of mechanisms to evade phage infection, while phages rely on counterstrategies to overcome these defences. Among the most abundant phages in the gut are the crAss-like phages that infect members of the Bacteroidales, in particularBacteroides. In this study, we explored some of the mechanisms enabling the co-existence of four phage-Bacteroidales host pairsin vitrousing a multi-omics approach (transcriptomics, proteomics and metabolomics). These included threeBacteroidesspecies paired with three crAss-like phages (Bacteroides intestinalisand ϕcrAss001,Bacteroides xylanisolvensand ϕcrAss002, and an acapsular mutant ofBacteroides thetaiotaomicronwith DAC15), andParabacteroides distasonispaired with the siphovirus ϕPDS1.

Results

We show that phase variation of individual capsular polysaccharides (CPSs) is the primary mechanism promoting phage co-existence in Bacteroidales, but this is not the only strategy. Alternative resistance mechanisms, while potentially less efficient than CPS phase variation, can be activated to support bacterial survival by regulating gene expression and resulting in metabolic adaptations, particularly in amino acid degradation pathways. These mechanisms, also likely regulated by phase variation, enable bacterial populations to persist in the presence of phages, andvice versa. An acapsular variant ofB. thetaiotaomicrondemonstrated broader transcriptomic, proteomic, and metabolomic changes, supporting the involvement of additional resistance mechanisms beyond CPS variation.

Conclusions

This study advances our understanding of long-term phage-host interaction, offering insights into the long-term persistence of crAss-like phages and extending these observations to other phages, such as ϕPDS1. Knowledge of the complexities of phage-bacteria interactions is essential for designing effective phage therapies and improving human health through targeted microbiome interventions.
Barriers and Facilitators in Implementing Online Educational Interventions for Physicians: Systematic Review of Reviews
Authors: Tolegenova Akbota , Kanderzhanova Akbota , Foster Faye , Colet Paolo , Stolyarova Valentina , Sarria-Santamera Antonio
Published: November 2024

The implementation of online educational interventions for physicians presents both barriers and facilitators that shape the integration of digital learning into medical education frameworks. This systematic review of reviews aims to synthesize evidence on factors influencing the successful implementation of online educational interventions for physicians. We conducted searches across databases including, PubMed/Medline, Cochrane, Web of Science, Embase, PsycInfo, CINAHL spanning the years 2018 to 2023. Inclusion criteria comprised systematic reviews focusing on the implementation of e-learning. Data synthesis followed meta-ethnography principles, with categorization guided by the Consolidated Framework for Implementation Research (CFIR). Twenty-one relevant reviews were analyzed, highlighting factors within the CFIR domains: Innovation, Outer Setting, Inner Setting, Individuals, and Implementation Process. Facilitators included evidence-based practices, adaptability, leadership engagement, and resource availability, while barriers encompassed limited funding, regulatory hurdles, technological constraints, and resistance to change. The results emphasize how crucial it is for healthcare institutions, policymakers, educators, and technology providers to work together in order to effectively incorporate online learning into medical education. In conclusion, the study highlights the importance of tailored implementation strategies and policy recommendations, utilizing evidence-based practices and addressing various factors, to enhance online medical education’s effectiveness and ensure its integration into healthcare systems for improved patient outcomes.
Insulin/insulin-like growth factor signaling pathway promotes higher fat storage inDrosophilafemales
Authors: Biswas Puja , Yu Huaxu , Wat Lianna W. , Miller Colin J. , Huan Tao , Rideout Elizabeth J.
Published: November 2024

InDrosophila, adult females store more fat than males. While the mechanisms that restrict body fat in males are becoming clearer, less is known about how females achieve higher fat storage. Here, we perform a detailed investigation of the mechanisms that promote higher fat storage in females. We show greater intake of dietary sugar supports higher fat storage due to female-biased remodeling of the fat body lipidome. Dietary sugar stimulates a female-specific increase inDrosophilainsulin-like peptide 3 (Dilp3), which acts together with greater peripheral insulin sensitivity to augment insulin/insulin-like growth factor signaling pathway (IIS) activity in adult females. Given that adult-specific IIS inhibition reduced the sex difference in fat storage due to a female-biased decrease in body fat, our data reveal IIS as a key determinant of female fat storage.
Spin alignment of vector mesons induced by local spin density fluctuations
Authors: Xu Kun , Huang Mei
Published: November 2024

We propose a novel mechanism that the spin alignment of vector meson ϕ and K*0 in most central heavy ion collisions is induced by intrinsic quantum chromo dynamics (QCD) without external vortical/magnetic fields. The local spin density fluctuation of quarks due to the axial-vector and tensor interactions between quarks can induce the spin alignments of vector meson. It is found that axial-vector interaction results in ρ00<1/3 for the spin alignment of ϕ meson, while tensor interaction results in ρ00>1/3. We argue that the spin alignment of K*0 due to the spin density fluctuation from flavor-mixing would be a signature or hint of instanton.

Published by the American Physical Society
2024
SN1987A constraints to BSM models with extra neutral bosons near the trapping regime:
U(1)Lμ−Lτ
model as an illustrative example
Authors: Lai Kwang-Chang , Leung Chun Sing Jason , Lin Guey-Lin
Published: November 2024

New physics beyond the Standard Model (BSM) with an extra neutral boson can be constrained from the observation of SN1987A, since productions of this neutral boson in a supernova (SN) could accelerate the SN cooling and potentially lead to a period of the neutrino burst incompatible with the observation. The constraint to the model is formulated by the condition LNB≤3×1052  erg/s according to Raffelt with LNB the luminosity of BSM neutral boson. Computing the above luminosity in the large coupling case, the so-called trapping regime, is nontrivial since the luminosity is a competition between the large production rate and the efficient absorption or decay rate of the neutral boson. We illustrate such a subtlety using U(1)Lμ−Lτ model as an example where the Z′ luminosity, LZ′, from the neutrinosphere is calculated. We calculate Z′ production, absorption, and decay rates through pair-coalescence, semi-Compton, loop-bremsstrahlung from proton-neutron scattering, and their inverse processes in a benchmark SN simulation with muons. We point out that, as the coupling constant

g

Z

′

increases, LZ′ shall be approaching to a constant plateau value for a given mZ′ instead of monotonically decreasing down to zero as obtained in the previous literature. We demonstrate that this plateau phenomenon can be understood by physical arguments and justified by numerical calculations. With a different result on LZ′ from the previous one, we discuss impacts on the constraints to U(1)Lμ−Lτ parameter space by SN1987A. The implication of our result to the similar constraint on a generic BSM model with an extra neutral boson is also discussed.

Published by the American Physical Society
2024
Complex effective actions and gravitational pair creation
Authors: Akhmedov E. T. , Diakonov D. V. , Schubert C.
Published: November 2024

We use different methods to calculate the imaginary part of the gravitational effective action due to a massless scalar field, with a view on perturbative vs nonpertubative and the results of Wondrak [Gravitational pair production and black hole evaporation, ].

Published by the American Physical Society
2024
Modeling of warm dense hydrogen via explicit real-time electron dynamics: Dynamic structure factors
Authors: Svensson Pontus , Aziz Yusuf , Dornheim Tobias , Azadi Sam , Hollebon Patrick , Skelt Amy , Vinko Sam M. , Gregori Gianluca
Published: November 2024

We present two methods for computing the dynamic structure factor for warm dense hydrogen without invoking either the Born-Oppenheimer approximation or the Chihara decomposition, by employing a wave-packet description that resolves the electron dynamics during ion evolution. First, a semiclassical method is discussed, which is corrected based on known quantum constraints, and second, a direct computation of the density response function within the molecular dynamics. The wave-packet models are compared to PIMC and DFT-MD for the static and low-frequency behavior. For the high-frequency behavior the models recover the expected behavior in the limits of small and large momentum transfers and show the characteristic flattening of the plasmon dispersion for intermediate momentum transfers due to interactions, in agreement with commonly used models for x-ray Thomson scattering. By modeling the electrons and ions on an equal footing, both the ion and free electron part of the spectrum can now be treated within a single framework where we simultaneously resolve the ion-acoustic and plasmon mode, with a self-consistent description of collisions and screening.

Published by the American Physical Society
2024
Green hydrogen energy revolution: unleashing India’s competitiveness
Authors: Singh Rohit , Ghosal Debraj
Published: November 2024

Learning outcomes

This case can be used to highlight aspects of strategic management, such as industry analysis as well as country competitiveness. After working through the case and assignment questions, the students will be able to analyse the competitiveness of – the green hydrogen industry in India – while comparing key structural elements with international benchmarks with European Union and China; examine the strategy of India’s Ministry of New and Renewal Energy an anchor entity implementing India’s National Green Hydrogen mission; assess the recent strategy of India’s ministry of new and renewal energy implementing Indian Government’s National Green Hydrogen Mission to contribute to India’s sustainability and climate goals including net zero targets, and motivations for the shift and its fit with the broader external environment; and suggest recommendations that might help Indian Government in achieving its strategic goals of improving India’s competitiveness in green hydrogen energy industry.

Case overview/synopsis

This case, based on actual events, described a situation faced by Raj Kumar Singh, the Cabinet Minister for Power & New & Renewable Energy, Government of India. The “National Green Hydrogen Mission”, launched by the Government of India in January 2023, is seen as a strategic endeavour to position India at the forefront of green hydrogen production globally. The budget allocated for the mission is $2.4bn (INR 19,744 Cr) until FY 2029–2030, and it aspires to stimulate the paradigm shift in India’s energy landscape. The mission seeks to reduce India’s dependence on its energy imports by capitalizing green hydrogen’s potential, lowering the production cost to $1 per kg by 2030, and develop a formidable 5 million metric tons (MMT) annual production capacity with potential expansion to 10 MMT. The success of the mission is dependent of several key factors like decrease in production costs, advancements in electrolyser technology, support system of the government and the strategic collaborations. However, the path towards mission’s success faces challenges such as infrastructure development, storage and distribution. Despite these challenges, the government is determined in its commitment to scale up green hydrogen production, positioning India as a global center for this sustainable energy source. This case provides a rich context for discussions on how policy, technical and economic factors will interact for shaping the future of green hydrogen industry in India.

Complexity academic level

Case applicable for management classes preferably in MBA class.

Supplementary material

Teaching notes are available for educators only. Porter, Michael E. (1990–03 - 01). “The Competitive Advantage of Nations”. Harvard Business Review. No. March–April 1990. ISSN 0017–8012.

Subject code

CSS 11: Strategy.
A cross-comparative analysis of child poverty across sub-Saharan Africa: the case of Francophone and Anglophone African states
Authors: Fonta Cynthia Lum , Gordon David , Toumpakari Zoi
Published: November 2024

Purpose

The institutional structures established by French and British colonists continue to shape the socio-economic landscape of sub-Saharan Africa, potentially contributing to the unequal distribution of child poverty. This study, therefore, has significant relevance as it aims to estimate child poverty disparities within the context of colonial origins in Francophone and Anglophone African countries.

Design/methodology/approach

This study utilised data from the Demographic and Health Surveys (DHS) conducted between 2000 and 2019 involving 22 sub-Saharan African states. A rights-based framework was applied based on the SDG-updated Gordon et al. (2003) methodology to measure child poverty. We then compared child poverty disparities between colonial origins using one-way ANOVA tests and risk ratios to quantify the magnitude of these differences.

Findings

Critically high estimates of sanitation and housing poverty (above 70% prevalence) were observed in the two colonial settings. Children in Francophone states were 1.4 times (RR = 1.4; 95% CI: 1.1–1.8) more likely to experience higher risks of low medical access, almost twice as likely to experience low vaccine uptake (risk ratios-RR = 1.8; 95% CI: 1.2–2.8) or no formal education (RR = 1.7; 95% CI: 1.1–2.5). All other dimensions were equal between colonial origins.

Research limitations/implications

Due to its cross-comparative approach, this study is restricted in making conclusive inferences regarding the causal relationship between colonialism and health/education poverty. Also, given the limited number of countries, particularly Anglophone countries, our sample may not fully represent all French and British ex-colonies. As a follow-up to this study, we intend to repeat this analysis using the harmonised Multiple Indicator Cluster (MIC) surveys, providing a larger number of countries.

Originality/value

Despite similar household poverty levels in both colonial settings, Francophone states had lower access to health and education services than Anglophone states. These findings indicate deeper systemic issues that may be rooted in the historical governance styles of centralisation. More effective decentralisation of healthcare and education services in Francophone countries and improved government commitment to addressing household poverty throughout sub-Saharan Africa are imperative.
Exploring outsourcing dynamics: a comprehensive bibliometric analysis of emerging markets
Authors: Le Minh-Hieu , Le Thu-Thao , Tran Phung Phi
Published: November 2024

Purpose

This research aims to enhance understanding of outsourcing dynamics from emerging markets by employing a bibliometric analysis of relevant scholarly articles. The study explores publication patterns, citation networks, author collaborations and contributions by different countries, offering insights for researchers and practitioners investigating outsourcing in these markets.

Design/methodology/approach

A comprehensive bibliometric analysis was conducted using 197 articles from the SCOPUS database, spanning January 1999 to June 2023. Established bibliometric techniques were utilized to analyze publication patterns, citation networks, author collaborations and country contributions, identifying key research themes and influential authors and institutions.

Findings

The study identified eight distinct research clusters, highlighting interdisciplinary collaborations, influential authors like Thomas Frisanco and Erdener Kaynak, and significant contributions from the United States and the UK. Notable organizational collaborations include the Hong Kong Polytechnic University and the University of Miami. These findings provide valuable insights into outsourcing practices and research trends in emerging markets.

Research limitations/implications

The study acknowledges limitations such as sampling bias, language bias and publication bias, which may affect the generalizability of the findings. Future research should strive for more diverse and representative samples, including non-English publications and studies with non-significant results, to provide a more comprehensive understanding of outsourcing dynamics.

Practical implications

The findings offer practical insights for organizations considering outsourcing from emerging markets, guiding strategic decision-making and policy development. Understanding publication patterns and research themes can help organizations navigate location selection, vendor management, risk mitigation and performance evaluation in these markets.

Social implications

Outsourcing can significantly impact employment, income generation, skill development and overall economic development in emerging markets. Policymakers can use these insights to foster business growth, infrastructure development and investment incentives, contributing to economic growth and employment opportunities.

Originality/value

This study provides a comprehensive bibliometric analysis of outsourcing from emerging markets, filling a gap in the existing literature. The insights gained can guide future research, inform strategic decision-making and enhance the understanding of outsourcing dynamics in these rapidly evolving markets.
Does financial inclusion and financial openness matter for capital market development? Evidence from a panel ARDL-PMG approach
Authors: Otinga Noah Keya , Obi Pat , Waweru Freshia
Published: November 2024

Purpose

This study aims to examine the effect of financial inclusion (FI) and financial openness (FO) on the development of capital markets in Africa.

Design/methodology/approach

The study uses data from 34 countries over 18 years (2004–2021) and adopts the panel autoregressive distributed lag and pooled mean group approach, with economic growth, trade openness, government expenditure and institutional quality as control variables.

Findings

The analysis reveals that both FI and FO contribute to the long-term development of capital markets across all income levels within the sampled countries. The interaction between FI and FO enhances capital market development (CMD) over the long run. This finding indicates that FO particularly enhances the development of capital markets in economies with comparatively lower levels of FI.

Practical implications

The findings of this research underscore the importance for policymakers and professionals to adopt guidelines and regulations that promote FI and openness. Such measures can bolster the development of strong financial systems by improving access to the formal financial sector, and by contributing to the growth of capital markets.

Originality/value

The study is robust to the use of a multidimensional financial and CMD index. It is one of the pioneering studies that explore the relationship between FI and FO, and how this interaction influences CMD.