bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unravelling termite evolution with 47 high-resolution genome assemblies
Authors: Liu Cong , Aumont Cédric , Mikhailova Alina A. , Audisio Tracy , Hellemans Simon , Weng Yi Ming , He Shulin , Clitheroe Crystal , Wang Zongqing , Haifig Ives , Sillam-Dussès David , Buček Aleš , Tokuda Gaku , Šobotník Jan , Harrison Mark C. , McMahon Dino P. , Bourguignon Thomas 
Published: January 2025

AbstractTermites are a lineage of social cockroaches abundant in tropical ecosystems where they are key decomposers of organic matter from wood to soil. Despite their ecological significance, only a handful of reference-quality termite genomes have been sequenced, which is insufficient to unravel the genetic mechanisms that have contributed to their ecological success. Here, we performed sequencing and hybrid assembly of 45 taxonomically and ecologically diverse termites and two cockroaches, resulting in haplotype-merged genome assemblies of 47 species, 22 of which were near-chromosome level. Next, we examined the link between termite dietary evolution and major genomic events. We found that Termitidae, which include ∼80% of described termite species, have larger genomes with more genes and a higher proportion of transposons than other termites. Our analyses identified a gene number expansion early in the evolution of Termitidae, including an expansion of the repertoire of CAZymes, the genes involved in lignocellulose degradation. Notably, this expansion of genomes and gene repertoires coincided with the origin of soil-feeding in Termitidae and remained unchanged in lineages that secondarily reverted to a wood-based diet. Overall, our sequencing effort multiplied the number of available termite genomes by six and provided unprecedented insights into the genome evolution of the most ancient lineage of social insects.
Molecular mechanisms underlying the early steps of floral initiation in seasonal flowering genotypes of cultivated strawberry
Authors: Ziegler Freya MR , Gaston Amèlia , Guy Karine , Devers Marie , Krüger Erika , Brauksiepe Bastienne , Eimert Klaus , Osorio Sonia , Denoyes Béatrice , Usadel Björn 
Published: January 2025

AbstractFloral initiation is required for sexual reproduction in angiosperm plants, and has a significant impact on crop yields. In cultivated strawberry, the molecular basis of floral initiation is poorly understood and most studies have focused on a single genotype grown under controlled conditions. To gain more insight into this process, we conducted a study under natural conditions in two countries using two seasonal flowering cultivars. We focused on the early steps of floral initiation by using samples spanning key developmental stages of the shoot apical meristem. The analysis of differential gene expression in leaf and terminal bud tissues revealed enrichment for genes involved in carbohydrate metabolism and phytohormone pathways in leaves. Other protein classes that were enriched during early floral initiation were associated with cytoskeleton organization, cell cycle regulation, and chromatin structure. We also identified genes associated with the photoperiodic pathway, well-characterized floral integrators such as TFL1 and SOC1, and several linked to phytohormone regulation, such asXTH23,PP2andEIN3.
Identifying transcription factors driving cell differentiation
Authors: Martini Paul , Hartebrodt Anne , Zehn Dietmar , Blumenthal David B. 
Published: January 2025

AbstractCellular differentiation is a fundamental biological process at the core of development and growth in multicellular organisms. Understanding it at the level of transcriptomic regulation opens the possibility for novel biological insights, for steering cell development for therapeutic purposes, and for developing targeted therapies for diseases. While many methods exist that infer developmental trajectories from single-cell RNA sequencing data, only few can effectively determine which biological mechanisms drive differentiation along such trajectories. To close this gap, we developed SwitchTFI (switch transcriptionfactoridentification), a method to identify differentiation-driving regulatory mechanisms and the transcription factors (TFs) that play a key role in them. SwitchTFI infers a cell state transition-specific gene regulatory network (GRN) from a user-provided baseline GRN via decision stump learning and permutation-based significance tests. Key TFs are then extracted by ranking them according to their centralities in the transition GRN. We show that SwitchTFI can identify TFs known to be involved in pancreatic endocrinogenesis and in erythrocyte differentiation and that it outperforms competitor methods with respect to the functional coherence of the predicted driver TFs. SwitchTFI is available as a Python package athttps://github.com/bionetslab/SwitchTFI.
Social and news media in mapping the endangered Mediterranean Monk seal: exceptional data gains but persistent bias
Authors: Castro Andry , Capinha César 
Published: January 2025

ABSTRACTSocial and news media are increasingly recognised as valuable sources of species distribution data, particularly for rare and endangered species. However, these data sources are prone to biases arising from uneven observation efforts, which pose challenges for their effective use. Despite this, the drivers and extent of such biases remain understudied. Here we investigate the contribution of social and news media to improving the availability of distribution data for a rare and endangered species, the Mediterranean Monk seal (Monachus monachus), in the Madeira and Porto Santo Islands. We also assess the relationship between the distribution data collected and socio-human factors likely to determine spatial and temporal variation in observation effort. We found that media sources provide a remarkable number of observation records for the species (n=302), which compared to the GBIF, iNaturalist andObservation.orgcombined (n=11), represent a 27.5-fold increase. The number of observations exhibited seasonal variation, with annual peaks occurring in the summer months. A generalised linear model assessing the spatial distribution of observation data also revealed a strong positive association with areas of high human concentration. Significant variables included population density, hotel density, and proximity to coastal recreational hotspots such as diving sites and bathing areas/non-open beaches. Our results underscore the potential of social and news media in documenting species distributions, but they also emphasise the importance of accounting for observational biases. Doing so is essential to ensure the reliable and effective application of social and news media sourced data in supporting species conservation efforts and management strategies.
PDP-Miner: an AI/ML tool to detect prophage tail proteins with depolymerase domains across thousands of bacterial genomes
Authors: Gauthier Jeff , Kukavica-Ibrulj Irena , Levesque Roger C. 
Published: January 2025

AbstractMotivationAntibiotic resistance is predicted to become the leading cause of human mortality by 2050. Despite this, no other major antibiotic class has been approved for medical use since 1987. Nevertheless, phage tail proteins offer a promising alternative, given their depolymerase activity toward outer membrane polysaccharides. Several pathogenic bacteria harbor prophages, thus making these prophages’ molecular target already known.ResultsWe therefore developed a wrapper for an existing machine learning-based phage depolymerase prediction tool (Depolymerase-Predictor), called PDP-Miner, which annotates phage tail proteinsab initio, detects depolymerase activity within this candidate protein subset, and then performs post-hoc validation by annotating protein domains thereby allowing the user to investigate for protein domains indicative of depolymerase activity. This tool allowed identification of 10 high confidence phage depolymerase gene candidates across all 1,294Pseudomonasgenomes available on the International Pseudomonas Consortium Database and could likely help detecting other candidates across other genome databases as well.Availability and ImplementationSource code is freely available for download athttp:///www.github.com/jeffgauthier/pdpminer. Implemented in Bash, supported on native Linux or WSL and supports submitting subtasks to a SLURM workload queue. Requires Miniconda3 to install dependencies. This software is free and open source under the GNU General Public License v3.0.Contactjeff.gauthier.1@ulaval.ca;rclevesq@ibis.ulaval.caSupplementary information[add Supp. Mat. URL here when available]
Evaluating the Efficacy of a Hybrid Physical Therapy Technology: A Pilot Study on Wearable Sleeves within a Veteran Patient Population
Authors: Truntzer Jeremy , Gorman Shannon 
Published: January 2025

AbstractIntroductionTraditional musculoskeletal rehabilitation presents a range of challenges that can hinder patient recovery. Cost, access and travel place a significant burden on many health care systems. We completed a pilot study using a wearable biosleeve to determine if such technology might help address many of the current challenges.MethodsPatients were enrolled following knee arthroscopy to receive hybrid physical therapy utilizing a wearable sleeve that tracks joint angles and biometrics in conjunction with a web-based platform that allows provider visibility to patient completion data for assigned protocols.ResultsTen patients, who completed a three-month rehabilitation program, experienced successful outcomes with no adverse events. No difference in adverse outcomes or failure to achieve acceptable motion was found in patients that completed hybrid therapy (in-person and digital) or digital-based therapy alone.ConclusionWhile larger studies are required, this study serves as an important launching point for the potential benefits of integrating wearable technology in musculoskeletal rehabilitation.
General practice workforce retention strategies: an umbrella review
Authors: Jefferson L. , Golder S. , Castro A. , Webster E. , Anderson H. , Dale V. 
Published: January 2025

AbstractObjectiveWe summarise international evidence of interventions to support retention of the general practice workforce, mapping evidence by country, method and workforce group.DesignUmbrella overview of reviews. We mapped evidence according to occupational group, intervention type and outcome to identify trends and gaps.SettingInternational primary care and general practice.ParticipantsGeneral practice workforce, with studies grouped by general practitioners, nurse practitioners and mixed health professional.Main outcome measuresWorkforce retention, including length of employment, stability rates, settlement rates, vacancy rates, unfilled positions, turnover numbers or rates, attrition rates, intentions to stay, leave and return.ResultsOf the 3449 articles identified through database searching and citation tracking, we included 12 reviews. There was a general lack of policy evaluations in some fields and low geographical spread beyond Australia and the US. While stronger evidence exists for interventions such as professional development and fostering supportive environments, mixed findings were reported on financial incentives and limited formal evaluations were found for some intervention types, and professional groups.ConclusionThis overview of research underscores the need for more research evaluating interventions to support the general practice workforce, particularly across wider international settings.
Breaking the Growth Barrier: Stunting Among Afghan Children (6–59 Months) – Insights from the 2023 UNICEF MICS Survey
Authors: Ashor Mokhtar , Haque MD. Sajid Sultan , Baig Shagufta 
Published: January 2025

AbstractStunting has emerged as a significant health problem in South Asia. Afghanistan was hit the hardest with the highest prevalence of stunting in 2018 in the region. With the recent education ban for women and girls, Afghanistan has become prone to even worse satiation. Additionally, with respect to the country’s social and economic profile after the COVID-19 pandemic, the country and its population, specifically women and children, faced challenges in receiving essential living services. The objective of this study was to determine the current prevalence of stunting and the factors that are significantly associated with this disease among children.The study uses the MICS nationally representative dataset in which the survey was conducted from 2022--2023 in Afghanistan by UNICEF. The results revealed a high prevalence rate of stunting among children aged 6--59 months (48%), and several factors (mother and caregiver education, household wealth, children’s age and infectious diseases) were associated with stunted children in the country. The major part of the country in western Afghanistan has more children suffering from stunting than the other parts of the country do.Our findings highlight the importance of mothers’ education in preventing their children from stunting, and our research recommends that the government focus on interventions in the community to increase awareness and make nutritional services available to people in hard-to-reach areas of the country.
Within-country heterogeneity in patterns of social contact relevant for tuberculosis infection transmission, prevention, and care
Authors: LeGrand Kate E. , Edwards Anita , Mohlamonyane Mbali , Dayi Njabulo , Olivier Stephen , Gareta Dickman , Wood Robin , Grant Alison D. , White Richard G. , Middelkoop Keren , Khan Palwasha , McCreesh Nicky 
Published: January 2025

AbstractMycobacterium tuberculosis(Mtb) transmission is driven by variable social, environmental, and biological factors, including the number and duration of indoor contacts. Social contact data can provide information on potential transmission patterns, but is underutilised outside the field of mathematical modelling. We explore three contexts where contact data can provide valuable insights: 1) household contact tracing; 2) infection prevention and control measures (IPC) in congregate settings; and 3) contamination in cluster randomised trials (CRTs).A social contact survey was conducted in three communities with comparable population sizes in South Africa: an urban township and peri-urban and rural clinic catchment areas. Participants reported congregate settings visited over 24-hours, visit durations, and estimated numbers of people present. To correspond with the three contexts, we estimated the proportion of contact hours occurring 1) within the home; 2) in congregate settings outside the home; and 3) outside the participants’ communities.Participants reported a mean of 27.0 (rural), 55.2 (peri-urban), and 73.0 (urban) contact hours. The proportion within the home was similar among rural and peri-urban participants (76.8% and 71.7%), compared to urban (48.6%). Congregate settings visited varied; urban participants spent the most contact hours in retail/office settings (19.9%), peri-urban participants in community-service buildings (20.4%), and rural participants in other peoples’ homes (25.5%). Urban participants reported the highest proportion of contact outside the community (67.0%) compared to rural (38.8%) and peri-urban (21.5%) participants.The heterogeneity in contact patterns has implications for TB interventions. Household contact tracing may be most effective in the rural community where household contact was highest. The diverse range of congregate settings visited suggests that prioritising IPC measures in these locations may enhance their overall efficacy. Considering contact patterns when designing clusters may reduce contamination risk in CRTs. Tailored interventions, informed by local contexts, are essential to reduce TB burden.
Influence of neural network bursts on functional development
Authors: Ramstad Ola Huse , Sandvig Axel , Nichele Stefano , Sandvig Ioanna 
Published: January 2025

1AbstractNetwork bursts or synchronized burst events are a typical activity seen in most in vitro neural networks. Network bursts arise early in development and as networks mature, activity becomes dominated by bursts propagating across the entirety of the network. The reason for this developmental plateau in vitro is unknown, but to bypass it would confer a significant advantage in the use of in vitro networks for computation. As most neurons in a network participate in network bursts, burst onset supersedes any ongoing activity thereby placing a limit on short term computations equal to the recovery period between bursts. By assessing 521 multielectrode array recordings from day 4-39 in vitro we find that network bursts influence the connectivity, but this change is only weakly associated with the origin of the network bursts. The impacts of bursts on functional integration and segregation in neural networks are discussed along with approaches to mitigate the development and propagation of network bursts in vitro. Additionally, we hypothesize that burst initiation zones or pacemakers are viable targets for stimulation for computation in the context of control and reservoir computing.
Weak evidence for heritable changes in response to selection by aphids inArabidopsisaccessions
Authors: Schmid Marc W. , Kropivšek Klara , Wuest Samuel E. , Schmid Bernhard , Grossniklaus Ueli 
Published: January 2025

AbstractIn plants, transgenerational inheritance of certain epialleles has been observed but experimental evidence for selection of epigenetic variation independent of genetic variation is scarce. We extended an experiment simulating selection in response to herbivory inArabidopsis thalianato assess a potential contribution of epigenetic variation to the selected phenotypes within three accessions. To minimize maternal effects, we grew offspring from replicate populations and their ancestors for two generations in a common environment and assessed the phenotypes in the second generation. We found weak evidence for the selection of epigenetic variation: bolting time differed significantly in one accession. Significant differences between populations and maternal lines suggested random residual or novel genetic and/or epigenetic variation. Our results are in conflict with those of a recent study reporting that environment-induced heritable variation is common inArabidopsis. Reanalyzing the data from that study showed that the reported findings resulted from a mix-up of accessions and thus reflected genetic rather than epigenetic variation between accessions. To avoid future misinterpretations of studies investigating epigenetic inheritance, we provide guidelines to design experiments that differentiate between epigenetic and genetic variation and distinguish standing variation fromde novovariation acquired during an experiment.
Nose-to-Brain Healing: Hypoxia-Preconditioned Mesenchymal Stem Cells Prompt Recovery in Hypoxic-Ischemic Encephalopathy Rats
Authors: Serrenho Inês , Carvalho Alexandre M. , Caramelo Inês , Araújo Beatriz , Cardoso Carla M.P. , Manadas Bruno , Baltazar Graça 
Published: January 2025

AbstractNeonatal HIE poses a significant risk factor for neurodevelopment impairment. Therapeutic hypothermia, the current standard of care for this condition, has several constraints and reduced effectivity, especially in more severe cases. Thus, it is necessary to explore novel therapeutics, like MSCs. Although previous studies report that administration of MSCs (from different sources) prompted the recovery of HIE-lesioned animals, high doses are currently used. First, this study compared the efficacy of IN versus IV administration of 50,000 UC-MSCs in a rat model of neonatal HI brain injury. For this cell dose, only IN-UC-MSC therapy reduced infarct volume, an effect accompanied by improvements of motor skills and recognition memory. Also, IN-UC-MSC administration restored myelination in the corpus callosum and mitigated glial reactivity more effectively than IV administration. In a second part of the study, to potentiate the effect of UC-MSCs administration, postnatal rats that underwent HI injury received 25,000 hypoxia-preconditioned UC-MSCs or its secretome two days later, via IN route. The administration of a low-dose of hypoxia-preconditioned UC-MSCs was sufficient to induce neurological recovery and modulation of glial response. Moreover, the administration of the secretome of these cells was enough to induce the same extent of recovery. These findings support the higher potential of IN-UC-MSC administration, compared to IV administration, while enhancing our understanding of hypoxia-preconditioning and the role of the MSC’s secretome in driving a positive therapeutic response, contributing to the development of more effective and feasible treatments for neonatal HIE.
Green Synthesis of Silver Nanoparticles Using SudaneseCandida parapsilosis: A Sustainable Approach to Combat Antimicrobial Resistance
Authors: Ibrahim Nesreen A. A. , Saeed Humodi A , Saeed Samar M. , Mohamed Osama , Ibrahim Sabah A. E. , Mohamed Sofia B. 
Published: January 2025

AbstractBackgroundAntimicrobial resistance (AMR) is a major global health threat, particularly in Sudan, where the overuse and misuse of antibiotics have led to the emergence and spread of multidrug-resistant (MDR) pathogens. Traditional methods to address AMR often fail to provide sustainable solutions. Nanotechnology offers promising alternatives, with silver nanoparticles (AgNPs) demonstrating broad-spectrum antimicrobial properties. This study aims to develop an eco-friendly synthesis of AgNPs usingCandida parapsilosisisolated from Sudanese soil, leveraging untapped fungal biodiversity to combat AMR.ResultsTheCandida parapsilosis-mediated synthesis of AgNPs was successfully characterized using UV-Vis spectroscopy, X-ray diffraction (XRD), and high-resolution transmission electron microscopy (HRTEM), confirming the formation of well-defined nanoparticles. The biosynthesized AgNPs exhibited potent antimicrobial activity against Gram-positive and Gram-negative MDR pathogens. Medium concentrations of AgNPs demonstrated optimal activity, with inhibition zones up to 29 mm forPseudomonas aeruginosa(ATCC27853). MIC and MBC assays revealed AgNPs’ bactericidal efficacy, particularly againstEscherichia coliandKlebsiella pneumoniaeat 0.3125 mg/mL. Synergistic effects with antibiotics, such as ceftazidime and colistin, significantly enhanced antimicrobial activity, with fold increases up to 9.46. AgNPs disrupted bacterial membranes, as evidenced by increased permeability and leakage of nucleic acids.ConclusionsThis study presents a novel and sustainable approach to combating AMR by utilizing Sudanese fungal strains for the green synthesis of AgNPs. The findings highlight the potential of AgNPs as an effective antibacterial agent, particularly in combination with conventional antibiotics, to combat multidrug-resistant pathogens. This research not only offers a cost-effective and environmentally friendly solution to AMR but also underscores the significant potential of integrating microbiology and nanotechnology to address global health challenges. The results could pave the way for future applications in both public health and environmental sustainability.