bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of sexual differentiation initiation inSchizosaccharomyces pombe
Authors: Kawamukai Makoto 
Published: March 2024

ABSTRACTThe fission yeast Schizosaccharomyces pombe is an excellent model organism to explore cellular events owing to rich tools in genetics, molecular biology, cellular biology, and biochemistry. Schizosaccharomyces pombe proliferates continuously when nutrients are abundant but arrests in G1 phase upon depletion of nutrients such as nitrogen and glucose. When cells of opposite mating types are present, cells conjugate, fuse, undergo meiosis, and finally form 4 spores. This sexual differentiation process in S. pombe has been studied extensively. To execute sexual differentiation, the glucose-sensing cAMP-PKA (cyclic adenosine monophosphate-protein kinase A) pathway, nitrogen-sensing TOR (target of rapamycin) pathway, and SAPK (stress-activating protein kinase) pathway are crucial, and the MAPK (mitogen-activating protein kinase) cascade is essential for pheromone sensing. These signals regulate ste11 at the transcriptional and translational levels, and Ste11 is modified in multiple ways. This review summarizes the initiation of sexual differentiation in S. pombe based on results I have helped to obtain, including the work of many excellent researchers.
Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection
Authors: Liu Erhu , Lyu Hongqiang , Liu Yuan , Fu Laiyi , Cheng Xiaoliang , Yin Xiaoran 
Published: March 2024

AbstractMotivationTopologically associating domains (TADs) are fundamental building blocks of 3D genome. TAD-like domains in single cells are regarded as the underlying genesis of TADs discovered in bulk cells. Understanding the organization of TAD-like domains helps to get deeper insights into their regulatory functions. Unfortunately, it remains a challenge to identify TAD-like domains on single-cell Hi-C data due to its ultra-sparsity.ResultsWe propose scKTLD, an in silico tool for the identification of TAD-like domains on single-cell Hi-C data. It takes Hi-C contact matrix as the adjacency matrix for a graph, embeds the graph structures into a low-dimensional space with the help of sparse matrix factorization followed by spectral propagation, and the TAD-like domains can be identified using a kernel-based changepoint detection in the embedding space. The results tell that our scKTLD is superior to the other methods on the sparse contact matrices, including downsampled bulk Hi-C data as well as simulated and experimental single-cell Hi-C data. Besides, we demonstrated the conservation of TAD-like domain boundaries at single-cell level apart from heterogeneity within and across cell types, and found that the boundaries with higher frequency across single cells are more enriched for architectural proteins and chromatin marks, and they preferentially occur at TAD boundaries in bulk cells, especially at those with higher hierarchical levels.Availability and implementationscKTLD is freely available at https://github.com/lhqxinghun/scKTLD.
Making head and neck cancer clinical data Findable-Accessible-Interoperable-Reusable to support multi-institutional collaboration and federated learning
Authors: Gouthamchand Varsha , Choudhury Ananya , Hoebers Frank J P , Wesseling Frederik W R , Welch Mattea , Kim Sejin , Kazmierska Joanna , Dekker Andre , Haibe-Kains Benjamin , van Soest Johan , Wee Leonard 
Published: March 2024

Abstract

Objectives
Federated learning (FL) is a group of methodologies where statistical modelling can be performed without exchanging identifiable patient data between cooperating institutions. To realize its potential for AI development on clinical data, a number of bottlenecks need to be addressed. One of these is making data Findable-Accessible-Interoperable-Reusable (FAIR). The primary aim of this work is to show that tools making data FAIR allow consortia to collaborate on privacy-aware data exploration, data visualization, and training of models on each other’s original data.

Methods
We propose a “Schema-on-Read” FAIR-ification method that adapts for different (re)analyses without needing to change the underlying original data. The procedure involves (1) decoupling the contents of the data from its schema and database structure, (2) annotation with semantic ontologies as a metadata layer, and (3) readout using semantic queries. Open-source tools are given as Docker containers to help local investigators prepare their data on-premises.

Results
We created a federated privacy-preserving visualization dashboard for case mix exploration of 5 distributed datasets with no common schema at the point of origin. We demonstrated robust and flexible prognostication model development and validation, linking together different data sources—clinical risk factors and radiomics.

Conclusions
Our procedure leads to successful (re)use of data in FL-based consortia without the need to impose a common schema at every point of origin of data.

Advances in knowledge
This work supports the adoption of FL within the healthcare AI community by sharing means to make data more FAIR.
Nav1.8 in small dorsal root ganglion neurons contributes to vincristine-induced mechanical allodynia
Authors: Nascimento de Lima Ana Paula , Zhang Huiran , Chen Lubin , Effraim Philip R , Gomis-Perez Carolina , Cheng Xiaoyang , Huang Jianying , Waxman Stephen G , Dib-Hajj Sulayman D 
Published: March 2024

Abstract
Vincristine-induced peripheral neuropathy is a common side effect of vincristine treatment, which is accompanied by pain and can be dose-limiting. The molecular mechanisms that underlie vincristine-induced pain are not well understood. We have established an animal model to investigate pathophysiological mechanisms of vincristine-induced pain. Our previous studies have shown that the tetrodotoxin-sensitive voltage-gated sodium channel Nav1.6 in medium-diameter dorsal root ganglion (DRG) neurons contributes to the maintenance of vincristine-induced allodynia.
In this study, we investigated the effects of vincristine administration on excitability in small-diameter DRG neurons and whether the tetrodotoxin-resistant (TTX-R) Nav1.8 channels contribute to mechanical allodynia. Current-clamp recordings demonstrated that small DRG neurons become hyper-excitable following vincristine treatment, with both reduced current threshold and increased firing frequency. Using voltage-clamp recordings in small DRG neurons, we now show an increase in TTX-R current density and a −7.3 mV hyperpolarizing shift in the half-maximal potential (V1/2) of activation of Nav1.8 channels in vincristine-treated animals, which likely contributes to the hyperexcitability that we observed in these neurons.
Notably, vincristine treatment did not enhance excitability of small DRG neurons from Nav1.8 knockout mice, and the development of mechanical allodynia was delayed but not abrogated in these mice. Together, our data suggest that sodium channel Nav1.8 in small DRG neurons contributes to the development of vincristine-induced mechanical allodynia.
The effect of front-of-package nutrition labelling on product composition
Authors: Bauner Christoph , Rahman Rajib 
Published: March 2024

Abstract
We analyse the effect of front-of-package nutrition labelling using the example of France, where Nutri-Score was adopted in 2017. Our focus is on changes in available products, i.e. on producer choices rather than consumer choices. Employing a difference-in-differences approach, we find that products introduced or altered after the change receive better Nutri-Score ratings than those introduced before the adoption, indicating a shift to items that are healthier overall. In addition, there is some evidence of bunching at the cutoffs for better Nutri-Score grades, which suggests that the improvements are at least in part a strategic reaction to the Nutri-Score introduction.
Endemic does not mean constant as SARS-CoV-2 continues to evolve
Authors: Otto Sarah P , MacPherson Ailene , Colijn Caroline 
Published: March 2024

Abstract
COVID-19 has become endemic, with dynamics that reflect the waning of immunity and re-exposure, by contrast to the epidemic phase driven by exposure in immunologically naïve populations. Endemic does not, however, mean constant. Further evolution of SARS-CoV-2, as well as changes in behavior and public health policy, continue to play a major role in the endemic load of disease and mortality. In this article, we analyze evolutionary models to explore the impact that a newly arising variant can have on the short-term and longer-term endemic load, characterizing how these impacts depend on the transmission and immunological properties of the variants. We describe how evolutionary changes in the virus will increase the endemic load most for a persistently immune-escape variant, by an intermediate amount for a more transmissible variant, and least for a transiently immune-escape variant. Balancing the tendency for evolution to favor variants that increase the endemic load, we explore the impact of vaccination strategies and non-pharmaceutical interventions that can counter these increases in the impact of disease. We end with some open questions about the future of COVID-19 as an endemic disease.
Lack of Immune Resilience Negatively Affects Physical Resilience: Results From the InCHIANTI Follow-Up Study
Authors: Pellegrino Raffaello , Paganelli Roberto , Di Iorio Angelo , Bandinelli Stefania , Mussi Chiara , Sparvieri Eleonora , Volpato Stefano , Tanaka Toshiko , Ferrucci Luigi 
Published: March 2024

Abstract
There is consistent evidence that immune response declines with aging, with wide interindividual variability and a still unclear relationship with the development of frailty. To address this question, we assessed the role of immune resilience (capacity to restore immune functions), operationalized as the neutrophil-to-lymphocytes ratio (NL-ratio) and monocytes-to-lymphocytes ratio (ML-ratio), in the pathway that from robust status shifts to pre-frailty and frailty, and finally to death. The InCHIANTI study enrolled representative samples from the registry lists of 2 towns in Tuscany, Italy. Baseline data were collected in 1998, with follow-up visits every 3 years. The 1 453 participants enrolled were assessed and followed for lifestyle, clinical condition, physical performance, clinical, and physiological measures. For the purpose of this analysis, we used only 1 022 subjects aged 65 or older at baseline. Participants in the 3 highest deciles of distribution for NL-ratio (&gt;2.44) were more likely to experience a transition from robust to pre-frail, and to overt frailty status. Moreover, NL-ratio (tenth decile &gt; 3.53) and ML-ratio (tenth decile &gt; 2.02) were both predictors of mortality. These results were independent of chronological age, sex, comorbidities, and chronic low-grade inflammation assessed by high sensitivity C-reactive protein measurement. The 2 leucocytes-derived ratios, NL-ratio and ML-ratio, represent markers of immune resilience and predict changes in physical resilience and mortality. These biomarkers are inexpensive because they are based on data routinely collected in clinical practice and can be used to assess the risk of frailty progression and mortality.
Clinical Trials Registration Number: NCT01331512
Azimuthal pore pressure response to teleseismic waves: effects of damage and stress anisotropy
Authors: Panteleev Ivan , Lyakhovsky Vladimir , Shalev Eyal 
Published: March 2024

SUMMARY
Pore pressure oscillations induced by stress variations, including propagating seismic waves from remote earthquakes, have been widely observed in various groundwater systems. The monitored pressure change in wells shows significant water-level oscillations to volumetric strain as well as to S and Love waves. Recent observations demonstrated azimuthal dependence of the pore pressure oscillations with respect to stress indicators and fault zone orientation. Within the fault zone, damage-induced anisotropy is the result of the alignment and orientation of cracks and other internal flaws within the rock. In this work, we provide a complete quantitative description of the pore pressure changes induced by passing seismic waves associated with different orientations and values of principal stress and damage tensor components. The model quantifies the azimuthal dependence of the pore pressure response by a non-dimensional ratio defined as the amplitude of the pressure oscillations induced by a shear strain normalized to the volumetric strain. Three angles and two values are needed to calculate the azimuthal dependence of the pore pressure response: the angle between the directions of the maximum horizontal stress and the seismic event; fault zone orientation; microcrack orientation within the fault zone; and damage and stress values. The model predicts that maximum pore pressure response occurs when microcracks and maximum horizontal stress are in the same orientation, high damage and high stress anisotropy. By adjusting these quantities, we recalculate results of recent seismological studies in the Arbuckle disposal well, Osage County, Oklahoma. The presented model successfully predicts the observed azimuthal dependence in wave-induced fluid pressure response and relates the anisotropic response to tectonic indicators such as the orientations of the maximum horizontal stress, fault zone, and microfractures.
Unravelling the excitation mechanism of very long-period (VLP) tremors in the Gulf of Guinea: evidence for vibrations of thin surface crustal plates
Authors: Xia Yingjie , Feng Xuping , Chen Xiaofei 
Published: March 2024

SUMMARY
The Gulf of Guinea exhibits a continuous emission of narrow-band and long-period signals (16, 26 and 27 s) on teleseismic records, yet the underlying excitation mechanism remains unclear. This study establishes a connection between these tremors and the vibration of thin, decoupled crustal plates at unexplored volcanoes in the gulf. We first formulate the damped plate oscillation equation, by incorporating the vibration of the thin surface crustal plate and magma flow in the subsurface sill. The findings reveal that a fundamental-mode vibration with a period of several dozen seconds can be induced by a crustal plate that is less than 1.0 km thick but extends over tens of kilometres in both length and width, given a subsurface sill depth exceeding 10.0 cm. The thin plate hypothesis also allows for excitation of a few overtone modes, but such waves in higher frequencies diminish over long distances, leaving only the monotonous fundamental-mode vibration at teleseismic stations. The long duration of Guinea tremors at each recurrence is attributed to the presence of low viscosity basaltic magma, which influences the damping factor. Direct wave loads at the shallow gulf serve as the primary vibration source, accounting for seasonal variations and recurring patterns. Sporadic energy bursts may also occur due to large storms. Radiation patterns of Guinea tremors are linked to the geometric structure of the thin plate. Our theoretical estimates of tremor spectra closely align with observed data, confirming the model’s accuracy in capturing reported Guinea tremor characteristics. This study provides valuable insights into the origins of very long-period tremors at continental volcanoes.
A co-designed evaluation study to identify Breastfeeding Knowledge of General Practitioners’ and Practice Nurses’
Authors: McGuinness Denise , Ni Mhurchu Siobhan , Frazer Kate , Bhardwaj Nancy , Cornally Paula , Cantwell Marie , Cullen Marina , McNamara Edel , McDonald Rita , Carroll Lisa , Cullen Walter , Kincaid Regina , Vickers Niamh 
Published: March 2024

Abstract
The World Health Organization and American Academy of Paediatrics recommend exclusive breastfeeding until 6 months of age, with continued breastfeeding along with complementary solid foods for up to 2 years and beyond. Despite the well-established importance of breastfeeding, Irish rates remain the lowest in Europe. Healthcare professionals’ breastfeeding knowledge and skills have a positive impact on increasing breastfeeding rates. There is limited evidence of the knowledge, attitudes or practices of general practitioners (GPs) and general practice nurses (GPNs), which is essential to breastfeeding in Ireland. The aim of this study was to evaluate the breastfeeding knowledge, attitudes and practices of GPs and GPNs in one community healthcare organisation (CHO) in Ireland. A co-designed evaluation study was used following low-risk ethical exemption (LS-LR-22-161). A modified version of a validated breastfeeding questionnaire was developed. A Project Steering Committee was established that included patient, and public involvement stakeholders. The anonymised survey was distributed via online Qualtrics platform (November 2022–February 2023). STROBE Guidelines were utilised. The overall response rate was 25.9% (n = 121) and valid responses were reported in the article. The total population size was n = 468 (GPs n = 290 and GPNs n = 178). Our pilot study identified that 42.7% (n = 47/110) of respondents never attended a breastfeeding education programme, and 53.9% (n = 55/102) identified that their knowledge could be improved. The majority of respondents, 92.9% (n = 92/99) wish to complete further education in breastfeeding. The results of this pilot study in one CHO in Ireland indicate a gap in knowledge and a need for specific breastfeeding and lactation theoretical and skills training for GPs and GPNs working in primary care to support, promote and protect breastfeeding.
AIF translocation into nucleus caused by Aifm1 R450Q mutation: generation and characterization of a mouse model for AUNX1
Authors: Shi Tao , Chen Ziyi , Li Jin , Wang Hongyang , Wang Qiuju 
Published: March 2024

Abstract
Mutations in AIFM1, encoding for apoptosis-inducing factor (AIF), cause AUNX1, an X-linked neurologic disorder with late-onset auditory neuropathy (AN) and peripheral neuropathy. Despite significant research on AIF, there are limited animal models with the disrupted AIFM1 representing the corresponding phenotype of human AUNX1, characterized by late-onset hearing loss and impaired auditory pathways. Here, we generated an Aifm1 p.R450Q knock-in mouse model (KI) based on the human AIFM1 p.R451Q mutation. Hemizygote KI male mice exhibited progressive hearing loss from P30 onward, with greater severity at P60 and stabilization until P210. Additionally, muscle atrophy was observed at P210. These phenotypic changes were accompanied by a gradual reduction in the number of spiral ganglion neuron cells (SGNs) at P30 and ribbons at P60, which coincided with the translocation of AIF into the nucleus starting from P21 and P30, respectively. The SGNs of KI mice at P210 displayed loss of cytomembrane integrity, abnormal nuclear morphology, and dendritic and axonal demyelination. Furthermore, the inner hair cells and myelin sheath displayed abnormal mitochondrial morphology, while fibroblasts from KI mice showed impaired mitochondrial function. In conclusion, we successfully generated a mouse model recapitulating AUNX1. Our findings indicate that disruption of Aifm1 induced the nuclear translocation of AIF, resulting in the impairment in the auditory pathway.
Causal modulation of lipid metabolism may shape the inflammatory microenvironment and potentially augment immunotherapy: a comprehensive genetic landscape revealed by Mendelian randomization analysis
Authors: Li Wenjie , Wang Wei 
Published: March 2024

Abstract
Previous observational and experimental studies have suggested a relationship between statin treatments and the augmentation of immunotherapy effects; however, the causal role of statin usage in promoting antitumor immunity remains largely unexplored. Utilizing large-scale genome-wide association studies, we conducted a Mendelian Randomization (MR) analysis to examine the association between genetically proxied inhibition of the gene for 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), a specific target of statins, and 524 immunotherapy-related profiles, encompassing immune cells, inflammatory cytokines, immune checkpoints, and gut microbiota. Our findings indicated a suggestive association between statin therapy and proinflammatory as well as antitumor effects; notably, inhibition of HMGCR demonstrated a robust link with increased susceptibility of various immune cell types, including basophil cells, white blood cells, eosinophil cells, neutrophil cells, activated CD8+ T cells, dendritic cells, and natural killer cells; furthermore, a causal relationship was observed between statin use and a decrease in terminal CD8+ T cells, granulocytes, monocytes, and myeloid-derived suppressor cells; genetically proxied statin usage was also significantly associated with elevated levels of proinflammatory cytokines and immunotherapy-related gut microbiota; importantly, the potential inhibition of HMGCR in influencing the response to immunotherapy was confirmed in the real-world cohorts. This study provides novel insights into the regulatory role of HMGCR inhibition in antitumor immunity, suggesting that strategies targeting HMGCR or lipid regulation may hold therapeutic potential for enhancing the efficacy of immunotherapy.
Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring
Authors: Lynes Mackenzie M , Jay Zackary J , Kohtz Anthony J , Hatzenpichler Roland 
Published: March 2024

Abstract
Over the past decade, environmental metagenomics and polymerase chain reaction-based marker gene surveys have revealed that several lineages beyond just a few well-established groups within the Euryarchaeota superphylum harbor the genetic potential for methanogenesis. One of these groups are the Archaeoglobi, a class of thermophilic Euryarchaeota that have long been considered to live non-methanogenic lifestyles. Here, we enriched Candidatus Methanoglobus hypatiae, a methanogen affiliated with the family Archaeoglobaceae, from a hot spring in Yellowstone National Park. The enrichment is sediment-free, grows at 64–70°C and a pH of 7.8, and produces methane from mono-, di-, and tri-methylamine. Ca. M. hypatiae is represented by a 1.62 Mb metagenome-assembled genome with an estimated completeness of 100% and accounts for up to 67% of cells in the culture according to fluorescence in situ hybridization. Via genome-resolved metatranscriptomics and stable isotope tracing, we demonstrate that Ca. M. hypatiae expresses methylotrophic methanogenesis and energy-conserving pathways for reducing monomethylamine to methane. The detection of Archaeoglobi populations related to Ca. M. hypatiae in 36 geochemically diverse geothermal sites within Yellowstone National Park, as revealed through the examination of previously published gene amplicon datasets, implies a previously underestimated contribution to anaerobic carbon cycling in extreme ecosystems.