bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting novel mosquito-associated viruses from metatranscriptomic dark matter
Authors: de Andrade Amanda Araújo Serrão , Brustolini Otávio , Grivet Marco , Schrago Carlos G , Vasconcelos Ana Tereza Ribeiro
Published: July 2024

The exponential growth of metatranscriptomic studies dedicated to arboviral surveillance in mosquitoes has yielded an unprecedented volume of unclassified sequences referred to as the virome dark matter. Mosquito-associated viruses are classified based on their host range into Mosquito-specific viruses (MSV) or Arboviruses. While MSV replication is restricted to mosquito cells, Arboviruses infect both mosquito vectors and vertebrate hosts. We developed the MosViR pipeline designed to identify complex genomic discriminatory patterns for predicting novel MSV or Arboviruses from viral contigs as short as 500 bp. The pipeline combines the predicted probability score from multiple predictive models, ensuring a robust classification with Area Under ROC (AUC) values exceeding 0.99 for test datasets. To assess the practical utility of MosViR in actual cases, we conducted a comprehensive analysis of 24 published mosquito metatranscriptomic datasets. By mining this metatranscriptomic dark matter, we identified 605 novel mosquito-associated viruses, with eight putative novel Arboviruses exhibiting high probability scores. Our findings highlight the limitations of current homology-based identification methods and emphasize the potentially transformative impact of the MosViR pipeline in advancing the classification of mosquito-associated viruses. MosViR offers a powerful and highly accurate tool for arboviral surveillance and for elucidating the complexities of the mosquito RNA virome.
Decoding functional proteome information in model organisms using protein language models
Authors: Barrios-Núñez Israel , Martínez-Redondo Gemma I , Medina-Burgos Patricia , Cases Ildefonso , Fernández Rosa , Rojas Ana M
Published: July 2024

Protein language models have been tested and proved to be reliable when used on curated datasets but have not yet been applied to full proteomes. Accordingly, we tested how two different machine learning-based methods performed when decoding functional information from the proteomes of selected model organisms. We found that protein language models are more precise and informative than deep learning methods for all the species tested and across the three gene ontologies studied, and that they better recover functional information from transcriptomic experiments. The results obtained indicate that these language models are likely to be suitable for large-scale annotation and downstream analyses, and we recommend a guide for their use.
Research criteria towards an interdisciplinary Stratospheric Aerosol Intervention assessment
Authors: Tilmes Simone , Rosenlof Karen H , Visioni Daniele , Bednarz Ewa M , Felgenhauer Tyler , Smith Wake , Lennard Chris , Diamond Michael S , Henry Matthew , Harrison Cheryl S , Thompson Chelsea
Published: June 2024

With surface temperatures already reaching unprecedented highs, resulting in significant adverse consequences for societies and ecosystems, there are increasing calls to expand research into climate interventions, including Stratospheric Aerosol Intervention (SAI). However, research and dissemination are currently fragmented and would benefit from a comprehensive international assessment of the current state of knowledge regarding impacts, risks, and recommendations for future SAI research directions. The goals of a scientific assessment would be to describe the current state of SAI research and evaluate proposed scenario-strategy combinations through well-designed evaluation guidelines. The suggested iterative approach would integrate natural and social science considerations to guide future research toward more plausible scenarios and strategy development to reduce uncertainties and minimize the risks of SAI. Here, we outline multidisciplinary research criteria to guide the assessment process and provide an overview of the benefits and risks of proposed SAI applications. We group these criteria into three categories: (1) technical and design requirements, (2) response and impacts, and (3) societal considerations. Including all three categories in a comprehensive assessment of potential SAI applications outlined here promotes enhanced interdisciplinary and international collaborations, intentionally engaging the underrepresented Global South. The assessment structure further promotes the need for recurring reports every few years with globally representative participation and could also be applicable to other Solar Radiation Modification methods or combined approaches. Such assessments are necessary to align research with considerations for decision-makers and the public on the feasibility of SAI in reducing the impacts of climate change and its potential societal and ecological trade-offs.
Effect of a 4-Week Telerehabilitation Program for People With Post-COVID Syndrome on Physical Function and Symptoms: Protocol for a Randomized Controlled Trial
Authors: Reeves Jack M , Spencer Lissa M , Tsai Ling-Ling , Baillie Andrew J , Han Yuna , Leung Regina W M , Bishop Joshua A , Troy Lauren K , Corte Tamera J , Teoh Alan K Y , Peters Matthew , Barton Carly , Jones Lynette , Alison Jennifer A
Published: June 2024

Objective

COVID-19 has led to significant morbidity and mortality globally. Post-COVID sequelae can persist beyond the acute and subacute phases of infection, often termed post-COVID syndrome (PCS). There is limited evidence on the appropriate rehabilitation for people with PCS. The aim of this study is to evaluate the effect on exercise capacity, symptoms, cognition, anxiety, depression, health-related quality of life, and fatigue of a 4-week, twice-weekly supervised pulmonary telerehabilitation program compared with usual medical care for people with PCS with persistent respiratory symptoms.

Methods

The study will be a multi-site randomized controlled trial with assessor blinding. Participants with confirmed previous COVID-19 infection and persistent respiratory symptoms who attend a post-COVID respiratory clinic will be randomized 1:1 to either an intervention group of 4 weeks, twice-weekly pulmonary telerehabilitation or a control group of usual medical care. Participants in the control group will be invited to cross-over into the intervention group after the week 4 assessment. Primary outcome: exercise capacity measured by the 1-minute sit-to-stand test. Secondary outcomes: 5 repetition sit-to-stand test; Montreal Cognitive Assessment; COVID-19 Yorkshire Rehabilitation Scale; Chronic Obstructive Pulmonary Disease Assessment Test; 36-Item Short-Form Health Survey; Hospital Anxiety and Depression Scale; Fatigue Severity Scale; and the Kessler Psychological Distress Scale. Outcomes will be collected at baseline, after 4-weeks intervention or control period, after intervention in the cross-over group, and at 12-month follow-up.

Impact

Research into effective rehabilitation programs is crucial given the substantial morbidity associated with PCS and the lack of long-term data for COVID-19 recovery. A short-duration pulmonary telerehabilitation program, if effective compared with usual care, could inform practice guidelines and direct future clinical trials for the benefit of individuals with persistent respiratory symptoms post-COVID.
The State of American Federalism 2023–2024: Judicialization of Gridlocked Politics
Authors: Bromley-Trujillo Rebecca , Dichio Michael A
Published: July 2024

Contemporary American federalism, while characterized by nationalized policy battles in the states, is also increasingly defined by the centralization of power in the federal judiciary. In this introductory piece of the 2023–2024 Annual Review issue, we unpack the judicialization of federalism politics. This process, we argue, has been facilitated by national political gridlock, defined by increasing dysfunction in Congress, and the growth of the administrative presidency. In policy conflicts on subjects ranging from education and the environment to abortion and other individual rights, courts have played an increasingly significant role as the arbiter of the federal–state balance of power. As the articles in this Annual Review illustrate, with a few exceptions, judicialization of federalism has often resulted in the devolution of authority to the states, with significant implications for public policy and democratic institutions.
Effect of corn silage inclusion with different corn processing on finishing steer performance and carcass characteristics
Authors: Miller Jessica L , Meier Nolan R , Wilke Karla H , Erickson Galen E , Loza Pablo L
Published: July 2024

Objectives were to determine the effect of corn silage inclusion within dry-rolled corn (DRC) or steam-flaked corn (SFC) finishing diets on cattle growth performance and carcass characteristics. The experiment used British and continental crossbred steers (n = 480; initial body weight [BW] = 389 ± 17 kg) in a 4 × 2 factorial arrangement of treatments with six replications per treatment. Treatments consist of four inclusions of corn silage (0%, 15%, 30%, or 45%; dry matter [DM] basis) within either a DRC or SFC diet. A corn silage by corn processing interaction was observed for dry-matter intake (DMI; P = 0.05). As corn silage inclusion increased in the diet, DMI increased linearly (P < 0.01) for both corn processing methods. DM intake was not different between SFC and DRC-fed cattle at 0% (P = 0.33), 30% (P = 0.90), or 45% (P = 0.31) corn silage inclusion. The interaction was due to the DMI of cattle fed 15% silage, as cattle-fed DRC consumed 0.5 kg/d less (P < 0.01) than cattle on the SFC diet. Quadratic effects were observed for final BW, hot carcass weight (HCW), average daily gain (ADG), feed efficiency (G:F), marbling, and fat depth (P < 0.01), regardless of corn processing. Cattle fed 15% or 30% corn silage gained faster (P < 0.01) than those fed 0% or 45% corn silage. Feed efficiency decreased quadratically (P < 0.01) as silage inclusion increased in the diet with G:F similar for cattle fed 0% and 15% silage and decreased curvilinearly for cattle fed 30% and 45% silage. The incidence of liver abscesses was greater (P = 0.03) in cattle fed 0% corn silage than for steers fed 15%, 30%, or 45% corn silage. Corn processing method, independent of silage, had no effect (P = 0.42) on liver abscess incidence. Feeding SFC increased (P < 0.01) steer final BW and HCW when compared to cattle-fed DRC, regardless of silage inclusion. Corn silage inclusion had similar effects on performance in both DRC diets and SFC diets except for DMI. As corn silage inclusion increased in the diet, feed efficiency decreased linearly (P < 0.01). Cattle-fed SFC gained 7.9% more (P < 0.01) and were 6.7% more efficient (P < 0.01) than cattle-fed DRC. In diets containing either DRC or SFC, corn silage can be included at up to 30% of the diet without negative impacts on ADG or HCW.
Consensus for Operating Room Multimodal Data Management: Identifying Research Priorities for Data-Driven Surgery
Authors: Garcia Vazquez Alain , Verde Juan , Hernandez Lara Ariosto , Mutter Didier , Swanstrom Lee ,   5G-OR Research Committee, 5G-OR Consensus Panel
Published: July 2024

Introduction:

This study aimed to identify research areas that demand attention in multimodal data-driven surgery for improving data management in minimally invasive surgery.

Background:

New surgical procedures, high-tech equipment, and digital tools are increasingly being introduced, potentially benefiting patients and surgical teams. These innovations have resulted in operating rooms evolving into data-rich environments, which, in turn, requires a thorough understanding of the data pipeline for improved and more intelligent real-time data usage. As this new domain is vast, it is necessary to identify where efforts should be focused on developing seamless and practical data usage.

Methods:

A modified electronic Delphi approach was used; 53 investigators were divided into the following groups: a research group (n=9) for problem identification and a narrative literature review, a medical and technical expert group (n=14) for validation, and an invited panel (n=30) for two electronic survey rounds. Round 1 focused on a consensus regarding bottlenecks in surgical data science areas and research gaps, while round 2 prioritized the statements from round 1, and a roadmap was created based on the identified essential and very important research gaps.

Results:

Consensus panelists have identified key research areas, including digitizing operating room (OR) activities, improving data streaming through advanced technologies, uniform protocols for handling multimodal data, and integrating AI for efficiency and safety. The roadmap prioritizes standardizing OR data formats, integrating OR data with patient information, ensuring regulatory compliance, standardizing surgical AI models, and securing data transfers in the next generation of wireless networks.

Conclusions:

This work is an international expert consensus regarding the current issues and key research targets in the promising field of data-driven surgery, highlighting the research needs of many operating room stakeholders with the aim of facilitating the implementation of novel patient care strategies in minimally invasive surgery.
Predictors of Nonhome Discharge After Cervical Disc Replacement
Authors: Subramanian Tejas , Song Junho , Kim Yeo Eun , Maayan Omri , Kamil Robert , Shahi Pratyush , Shinn Daniel , Dalal Sidhant , Araghi Kasra , Asada Tomoyuki , Amen Troy B. , Sheha Evan , Dowdell James , Qureshi Sheeraz , Iyer Sravisht
Published: July 2024

Study Design:

Retrospective review of a national database.

Objective:

The aim of this study was to identify the factors that increase the risk of nonhome discharge after CDR.

Summary of Background Data:

As spine surgeons continue to balance increasing surgical volume, identifying variables associated with patient discharge destination can help expedite postoperative placement and reduce unnecessary length of stay. However, no prior study has identified the variables predictive of nonhome patient discharge after cervical disc replacement (CDR).

Methods:

The American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database was queried for patients who underwent primary 1-level or 2-level CDR between 2011 and 2020. Multivariable Poisson regression with robust error variance was employed to identify the predictors for nonhome discharge destination following surgery.

Results:

A total of 7276 patients were included in this study, of which 94 (1.3%) patients were discharged to a nonhome destination. Multivariable regression revealed older age (OR: 1.076, P<0.001), Hispanic ethnicity (OR: 4.222, P=0.001), BMI (OR: 1.062, P=0.001), ASA class ≥3 (OR: 2.562, P=0.002), length of hospital stay (OR: 1.289, P<0.001), and prolonged operation time (OR: 1.007, P<0.001) as predictors of nonhome discharge after CDR. Outpatient surgery setting was found to be protective against nonhome discharge after CDR (OR: 0.243, P<0.001).

Conclusions:

Age, Hispanic ethnicity, BMI, ASA class, prolonged hospital stay, and prolonged operation time are independent predictors of nonhome discharge after CDR. Outpatient surgery setting is protective against nonhome discharge. These findings can be utilized to preoperatively risk stratify expected discharge destination, anticipate patient discharge needs postoperatively, and expedite discharge in these patients to reduce health care costs associated with prolonged length of hospital stay.

Level of Evidence:

IV.
Menopausal knowledge and attitudes of women during the perimenopausal period
Authors: Turan Miral Mukaddes , Bayraktar Tugba
Published: July 2024

Objective

This study aims to determine the relationship between knowledge and attitudes about menopause among women in the perimenopausal period.

Methods

A descriptive and relationship-seeking cross-sectional study was conducted in family health centers in a district of Istanbul between January and March 2023. The study included 300 women in the perimenopausal period. Data were collected through face-to-face interviews using a descriptive information form, a menopause knowledge test, and the Menopause Attitude Scale.

Results

The average age of participants was 45.07 ± 3.50, with 85.3% married, 37.0% having completed primary school, and 55.0% being housewives. The average menopause knowledge score was 12.29 ± 3.75 (out of 20), and the average menopause attitude score was 25.23 ± 6.99 (out of 52). No significant relationship was found between menopause knowledge and attitude scores (r = 0.06, P > 0.05). Women with an income exceeding their expenses had higher menopause knowledge scores (P < 0.05). Unmarried women, those with lower education levels, those with higher incomes, and those living alone had higher menopause attitude scores compared with their counterparts (P < 0.05).

Conclusions

Women's knowledge and attitudes toward menopause are moderate in the perimenopausal period. There is no significant relationship between menopausal knowledge and attitude of women during the perimenopausal period. It was determined that menopause knowledge level differed according to women's income status, and menopause attitude differed according to marital status, educational status, and cohabitation status in this study.
Custom Endoprosthesis-Assisted Pediatric Microsurgical Jaw Reconstruction
Authors: Trotter Collean , O’Brien Devon , Stanton Eloise W. , Roohani Idean , Shakoori Pasha , Urata Mark M. , Hammoudeh Jeffrey A.
Published: July 2024

Surgical treatment of pediatric maxillary and mandibular tumors can cause significant postresection disfigurement, mastication, and speech dysfunction. The need to restore form and function without compromising growth at the recipient and donor sites poses a particular reconstructive dilemma. This study evaluates outcomes of the custom endoprosthesis (CE) compared with noncustom reconstruction (NCR) and introduces an algorithm using CE to optimize available soft tissue reconstructive options. An Institutional Review Board–approved retrospective review of all patients undergoing maxillary or mandibular reconstruction between 2016 and 2022 was completed. The independent variable of interest was CE utilization. Primary outcomes of interest included hardware failure/removal or exposure, major complications, and revision surgeries. Covariates of interest included patient demographics, medical comorbidities, tumor size, and pathologic diagnosis. Statistical analyses including independent t test, χ2 analyses, and univariate/multivariate logistic regression were performed using RStudio version 4.2.1. Fifty-one patients (37 mandible and 14 maxilla) underwent CE or NCR. Of patients, 37% (n = 19) received CE. Of patients who underwent mandibular reconstruction, there were significantly lower rates of hardware exposure (14.3% versus 47.8%, P = 0.018), failure (7.1% versus 43.5%, P = 0.048), major complications (28.6% versus 78.2%, P = 0.008), and revisions (11.1% versus 50.0%, P = 0.002) in the CE cohort compared with the NCR cohort. The rates of hardware failure, exposure, major complications, and revisions did not significantly differ in maxillary reconstructions, however, CE successfully reconstructed significantly larger defects (179.5 versus 74.6 cm3, P = 0.020) than NCRs. Deviating from NCR, the authors propose an algorithm considering anatomical location, extent of resection, and patient age for soft tissue selection. This algorithm yielded improved mandibular reconstructive outcomes and no increase in complications rate in maxillary reconstruction despite larger resection defects. Furthermore, the authors’ initial findings demonstrate that CE is a safe option for pediatric maxillary and mandibular reconstruction that may, in addition, facilitate improved form and function.
Sir Roger James Elliott. 8 December 1928—16 April 2018
Authors: Thorpe Michael F.
Published: July 2024

Roger James Elliott was a theoretical physicist and pioneer in the use of quantum theory in solid state physics, which happened a few years after the invention of quantum mechanics in the late 1920s and which spread into all areas of solid state physics during the years when Roger Elliott was active (roughly the second half of the twentieth century, 1950–2000). He specialized in the magnetic, semiconductor and optical properties of condensed matter, with a particular emphasis on the effects caused by disorder—that is, the absence of periodicity in alloys and amorphous materials. He studied at New College, Oxford, before working as a postdoc at Berkeley. He then returned to England, first to Harwell and then to a faculty position at the University of Reading. During this time he completed his seminal work on the general theory of the optical properties of excitons. He returned to Oxford in 1957, where he was to stay for the remaining 60 years, until his death in 2018. He was the Wykeham professor of physics from 1974 until 1988, and he was awarded the Maxwell Medal in 1968 and the Guthrie Medal in 1990, both from the Institute of Physics. He was knighted in 1987. In his later years he was very active in the Royal Society as Foreign Secretary and also in scientific publishing worldwide after he served as chief executive of Oxford University Press from 1988 until 1993.
Distinct molecular profile of the chick organizer as a stem zone during axial elongation
Authors: Wood Timothy R. , Kucinski Iwo , Voiculescu Octavian
Published: July 2024

The vertebrate organizer plays a crucial role in building the main (antero-posterior) axis of the embryo: it neuralizes the surrounding ectoderm, and is the site of emigration for cells making axial and paraxial mesendoderm during elongation. The chick organizer becomes a stem zone at the onset of elongation; it stops recruiting cells from the neighbouring ectoderm and generates all its derivatives from the small number of resident cells it contains at the end of gastrulation stages. Nothing is known about the molecular identity of this stem zone. Here, we specifically labelled long-term resident cells of the organizer and compared their RNA-seq profile to that of the neighbouring cell populations. Screening by reverse transcription-polymerase chain reaction and
in situ
hybridization identified four genes (
WIF1
,
PTGDS
,
ThPO
and
UCKL1
) that are upregulated only in the organizer region when it becomes a stem zone and remain expressed there during axial elongation. In experiments specifically labelling the resident cells of the mature organizer, we show that only these cells express these genes. These findings molecularly define the organizer as a stem zone and offer a key to understanding how this zone is set up, the molecular control of its cells’ behaviour and the evolution of axial growth zones.
Preparation of Pt and bamboo charcoal co-modified TiO
2
for formaldehyde sensing at room temperature
Authors: Lin Jian-Wei , Wang Yu-Xuan , Xu Hao , Huo Li-Zhu , Yang Xue-Juan , Luo Xi-Ping
Published: July 2024

Anatase TiO
2
has evolved into one of the most attractive materials for gas sensing owing to its strong oxidation activity and excellent sensing properties. In this study, we prepared Pt and bamboo charcoal co-modified nano-TiO
2
using a one-pot hydrothermal process and applied it to detect formaldehyde. The successful incorporation of the precious metal Pt and bamboo charcoal onto TiO
2
was confirmed by scanning electron microscope, transmission electron microscopy, energy dispersive spectrometer, X-ray diffraction and X-ray photoelectron spectroscopy. Detailed analysis revealed a homogeneous distribution of Pt nanoparticles and bamboo charcoal on the TiO
2
surface, which significantly improved the surface area and facilitated gas adsorption. These modifiers significantly enhanced the response of TiO
2
to formaldehyde, for instance, the response signal increased fourfold, while the response time decreased from 91 to 68 s. The sample with 0.5@Pt and 0.5@C bamboo charcoal performed the best, showcasing the synergistic effect of metal nanoparticles and carbonaceous materials on gas-sensing properties. Our work highlighted the potential of using biomass-derived carbon to enhance the detection of formaldehyde and demonstrated the importance of material characteristics in designing effective gas sensors.
Evaluating the forecasting performance of ensemble sub-epidemic frameworks and other time series models for the 2022–2023 mpox epidemic
Authors: Bleichrodt Amanda , Luo Ruiyan , Kirpich Alexander , Chowell Gerardo
Published: July 2024

During the 2022–2023 unprecedented mpox epidemic, near real-time short-term forecasts of the epidemic’s trajectory were essential in intervention implementation and guiding policy. However, as case levels have significantly decreased, evaluating model performance is vital to advancing the field of epidemic forecasting. Using laboratory-confirmed mpox case data from the Centers for Disease Control and Prevention and Our World in Data teams, we generated retrospective sequential weekly forecasts for Brazil, Canada, France, Germany, Spain, the United Kingdom, the United States and at the global scale using an auto-regressive integrated moving average (ARIMA) model, generalized additive model, simple linear regression, Facebook’s Prophet model, as well as the sub-epidemic wave and
n
-sub-epidemic modelling frameworks. We assessed forecast performance using average mean squared error, mean absolute error, weighted interval scores, 95% prediction interval coverage, skill scores and Winkler scores. Overall, the
n
-sub-epidemic modelling framework outcompeted other models across most locations and forecasting horizons, with the unweighted ensemble model performing best most frequently. The
n
-sub-epidemic and spatial-wave frameworks considerably improved in average forecasting performance relative to the ARIMA model (greater than 10%) for all performance metrics. Findings further support sub-epidemic frameworks for short-term forecasting epidemics of emerging and re-emerging infectious diseases.
The synthesis of
N
,1,4-tri(alkoxy-hydroxybenzyl)-1,4-diazepane-amines: investigations on reaction characteristics and mechanism
Authors: Zenner Anne , Steinmetzer Johannes , Ueberschaar Nico , Freesmeyer Martin , Weigand Wolfgang , Greiser Julia
Published: July 2024

1,4-Diazepane-6-amine (DAZA) can be alkylated with three 2-hydroxybenzyl pendant arms, resulting in hexadentate chelators suitable for coordination of radiometals like
68
Ga. These chelators,
N
,1,4-tri(alkoxy-2-hydroxybenzyl)-DAZA, can be produced via a one-pot synthesis, with the first step being a carbonyl amine condensation of DAZA with two respective 4-alkoxy-2-hydroxybenzaldehydes, followed by reductive amination with sodium borohydride. While the first step of this reaction is predictable, the subsequent reductive amination can result in either mono-, di- or tri(alkoxy-hydroxybenzyl)-DAZA compounds. Seeking to identify dependencies that might allow a specific reaction control towards the formation of either of the three possible products, and particularly towards the favoured trialkylated DAZA compounds, a variety of synthesis trials were performed. Additionally, computational methods were employed to evaluate the underlying reaction mechanism. Synthesis trials verified that the trialkylated DAZA compounds are formed via direct reductive amination of the dialkylated DAZA compounds. Subsequently, a synthetic method was established, leading to an increase in the percentage of the trialkylated DAZA compounds, which allowed the successful isolation of those hexadentate chelators. Additionally, an alternative pathway proceeding via aminal C–N bond insertion of an attacking third carbonyl moiety was evaluated by means of quantum chemical calculations but so far remains entirely hypothetical.
Unique functional diversity during early Cenozoic mammal radiation of North America
Authors: Shupinski Alex B. , Wagner Peter J. , Smith Felisa A. , Lyons S. Kathleen
Published: July 2024

Mammals influence nearly all aspects of energy flow and habitat structure in modern terrestrial ecosystems. However, anthropogenic effects have probably altered mammalian community structure, raising the question of how past perturbations have done so. We used functional diversity (FD) to describe how the structure of North American mammal palaeocommunities changed over the past 66 Ma, an interval spanning the radiation following the K/Pg and several subsequent environmental disruptions including the Palaeocene–Eocene Thermal Maximum (PETM), the expansion of grassland, and the onset of Pleistocene glaciation. For 264 fossil communities, we examined three aspects of ecological function: functional evenness, functional richness and functional divergence. We found that shifts in FD were associated with major ecological and environmental transitions. All three measures of FD increased immediately following the extinction of the non-avian dinosaurs, suggesting that high degrees of ecological disturbance can lead to synchronous responses both locally and continentally. Otherwise, the components of FD were decoupled and responded differently to environmental changes over the last ~56 Myr.
Cerebral ischaemic stroke results in altered mucosal IgA responses and host-commensal microbiota interactions
Authors: Hurry Madeleine , Wong Raymond , Díaz-Marugan Laura , De Leon Bianca , Benakis Corinne , Waisman Ari , Allan Stuart M. , Lawrence Catherine B. , Brough David , Hepworth Matthew R.
Published: June 2024

Stroke is a devastating neurological event with a high risk of mortality, but also results in long-term sequalae in survivors that extend beyond the central nervous system. Notably, these include gastrointestinal dysfunction and alterations in the commensal microbiota in both patients and mouse models, which have been suggested to contribute to secondary infection and poor outcome following stroke. Strikingly changes in commensal microbial community composition occur rapidly in both humans and animal models following stroke and correlate with disease severity. Despite these observations the underpinning mechanisms that drive alterations in the microbiota post-stroke remain poorly understood. The gastrointestinal tract is home to a complex network of tissue-resident immune cells that act constitutively to maintain microbial community and prevent bacterial-driven inflammation. Here we demonstrate that mice subjected to ischaemic stroke exhibit alterations in the intestinal immune system, most notably in antibody secreting B cells and the production of Immunoglobulin A (IgA) – a major effector response against commensal microbes. Mice lacking secretory IgA binding to commensal bacteria exhibit a partial reversion of stroke-induced changes in microbiota composition. Notably we also report increases in B cell and IgA-producing plasma cell frequencies in the brain and meninges following stroke. Together these findings demonstrate stroke is associated with perturbations in antibody producing immune responses both in mucosal tissues and the CNS following stroke, which in part explain stroke-induced changes in the intestinal microbiota. A mechanistic understanding of the immunological basis of stroke-associated pathologies in the periphery may open new avenues to manage the secondary complications and long-term prognosis of patients suffering from neurological disease.
MicroWorldOmics: A “One step for All” desktop application for comprehensive analysis in microbiome and virome and exploring “Dark Matter” from MicroWorld
Authors: Li Runze , Dong Wei , Wang Mingjie , Hu Xiaoqing , Wan Jiao , Yang Zhuang
Published: June 2024

A large amount of high-throughput sequencing data generated in ecology, medicine, and pharmacy has increasingly raised the complexity of data analysis and interpretation. However, the microbiome and virome field still lacks a convenient and programming-free desktop application for the comprehensive analysis in microbiome and virome data, particularly in virome analysis and ‘Dark Matter’ exploration. Therefore, a plugin development mode desktop service, MicroWorldOmics, is proposed with a convenient and one-stop pipeline for life sciences and biomedical fields. Plugin development allows users to analyze data in parallel and interactively, while these tasks usually require advanced bioinformatician to achieve. MicroWorldOmics is a software widely used in microbiome and virome, containing 90 sub-applications, including four main functions: epidemiological analysis, metagenomic/amplicons and virome comprehensive analysis, and exploring ‘Dark matter’. More than 80 Python modules and 600 R packages are invoked in all aspects of bioinformatics analysis, statistical analysis, deep learning, and visualization. At the same time, the software supports multiple input and output results, such as GFF3, FASTA, CSV, PNG, JPG, JSON, and TXT, etc. Besides, to improve the efficiency for users, MicroWorldOmics supports being deployed in three mainstream systems: Windows, Linux, and Mac and also sets the demo/example data for users to test the benchmark easily. In summary, the development of MicroWorldOmics greatly facilitates the process of analyzing microbiome and virome data for researchers who have no programming foundation and are devoted to life science and biomedicine data analysis.
A role for condensin-mediator interaction in mitotic chromosomal organization
Authors: Iwasaki Osamu , Tashiro Sanki , Chung Claire , Hayashi Tomomi , Tanizawa Hideki , Wang Xuebing , Ohta Shinya , Fujioka Yuko , Han Joseph , Tabor Gabrielle , Kawagoe Mikihiro , Marmorstein Ronen , Noda Nobuo N , Noma Ken-ichi
Published: June 2024

Eukaryotic genomes are organized by condensin into 3D chromosomal architectures suitable for chromosomal segregation during mitosis. However, molecular mechanisms underlying the condensin-mediated chromosomal organization remain largely unclear. Here, we investigate the role of newly identified interaction between the Cnd1 condensin and Pmc4 mediator subunits in fission yeast, Schizosaccharomyces pombe. We develop a condensin mutation, cnd1-K658E, that impairs the condensin-mediator interaction and find that this mutation diminishes condensinmediated chromatin domains during mitosis and causes chromosomal segregation defects. The condensin-mediator interaction is involved in recruiting condensin to highly transcribed genes and mitotically activated genes, the latter of which demarcate condensin-mediated domains. Furthermore, this study predicts that mediator-driven transcription of mitotically activated genes contributes to forming domain boundaries via phase separation. This study provides a novel insight into how genome-wide gene expression during mitosis is transformed into the functional chromosomal architecture suitable for chromosomal segregation.
Peripheral glia and neurons jointly regulate activity-induced synaptic remodeling at theDrosophilaneuromuscular junction
Authors: Chang Yen-Ching , Peng Yi-Jheng , Lee Joo Yeun , Chang Karen T.
Published: July 2024

In the nervous system, reliable communication depends on the ability of neurons to adaptively remodel their synaptic structure and function in response to changes in neuronal activity. While neurons are the main drivers of synaptic plasticity, glial cells are increasingly recognized for their roles as active modulators. However, the underlying molecular mechanisms remain unclear. Here, usingDrosophilaneuromuscular junction as a model system for a tripartite synapse, we show that peripheral glial cells collaborate with neurons at the NMJ to regulate activity-induced synaptic remodeling, in part through a protein called shriveled (Shv). Shv is an activator of integrin signaling previously shown to be released by neurons during intense stimulation at the fly NMJ to regulate activity-induced synaptic remodeling. We demonstrate that Shv is also present in peripheral glia, and glial Shv is both necessary and sufficient for synaptic remodeling. However, unlike neuronal Shv, glial Shv does not activate integrin signaling at the NMJ. Instead, it regulates synaptic plasticity in two ways: 1) maintaining the extracellular balance of neuronal Shv proteins to regulate integrin signaling, and 2) controlling ambient extracellular glutamate concentration to regulate postsynaptic glutamate receptor abundance. Loss of glial cells showed the same phenotype as loss of Shv in glia. Together, these results reveal that neurons and glial cells homeostatically regulate extracellular Shv protein levels to control activity-induced synaptic remodeling. Additionally, peripheral glia maintains postsynaptic glutamate receptor abundance and contribute to activity-induced synaptic remodeling by regulating ambient glutamate concentration at the fly NMJ.
Genome-wide DNA Methylation Patterns inDaphnia magnaare Not Significantly Associated with Age
Authors: Liu Ruoshui , Morselli Marco , Yampolsky Lev Y. , Peshkin Leonid , Pellegrini Matteo
Published: June 2024

Studying DNA methylation inDaphnia magna, a model organism in ecological and evolutionary research, offers valuable insights into pharmaceutical toxicity and behavioral ethology. In this study, we characterized DNA methyltransferases and mapped DNA methylation across theD. magnagenome using whole-genome bisulfite sequencing. Our analysis revealed a highly expressed, nonfunctionalde novomethyltransferase (DNMT3.1) alongside lowly expressed functionalde novomethyltransferase DNMT3.2 and maintenance methyltransferase DNMT1.D. magnadisplays overall low DNA methylation, targeting primarily CpG dinucleotides. Methylation is sparse at promoters but elevated in the first exons downstream of transcription start sites, with these exons showing hypermethylation relative to adjacent introns. In contrast to prior studies, we observed minimal age-related changes in DNA methylation patterns that were not sufficiently robust to build an accurate epigenetic clock. These findings expand our understanding of the epigenetic landscape inD. magna.
Assessing the predictive value of peak alpha frequency for the sensitivity to pain
Authors: May Elisabeth S. , Tiemann Laura , Gil Ávila Cristina , Bott Felix S. , Hohn Vanessa , Gross Joachim , Ploner Markus
Published: July 2024

Pain perception varies considerably between and within individuals. How the brain determines these variations has yet to be fully understood. The peak frequency of alpha oscillations (PAF) has recently been shown to predict an individual’s sensitivity to longer-lasting experimental and clinical pain. PAF is, thus, discussed as a potential biomarker and novel target for neuromodulatory treatments of pain. Here, we scrutinized the generalizability of the relation between PAF and pain. We applied brief painful laser stimuli to 159 healthy participants and related inter- and intra-individual variations of pain perception to PAF measured with electroencephalography. Comprehensive multiverse analyses across two sessions did not provide consistent evidence for a predictive role of PAF for brief experimental pain. This indicates that the relationship between PAF and pain does not generalize to all types of pain and calls for a systematic exploration of the relationship between PAF, pain perception, and other neuropsychiatric symptoms.
Joint and tissue mechanics in post-traumatic osteoarthritis: insights from the rat model
Authors: Piet Judith , Esrafilian Amir , Elahi Seyed Ali , Mielke Falk , Van Nuffel Maarten , Orozco Gustavo , Vancleef Sanne , Lories Rik , Korhonen Rami K. , Aerts Peter , Van Wassenbergh Sam , Jonkers Ilse
Published: July 2024

Objective

Altered mechanical loading is a known risk factor for osteoarthritis. Destabilization of the medial meniscus (DMM) is a preclinical gold standard model for post-traumatic osteoarthritis and is thought to induce instability and locally increased loading. However, the joint- and tissue-level mechanical environment underlying cartilage degeneration remains poorly documented.

Design

Using a custom multiscale modeling approach, we assessed joint and tissue biomechanics in rats undergoing sham surgery and DMM. High-fidelity experimental gait data were collected in a setup combining biplanar fluoroscopy and a ground reaction force plate. Knee poses and joint-level loading were estimated through musculoskeletal modeling, using bony landmarks, semi-automatically tracked via deep learning on fluoroscopic images, and ground reaction forces. A musculoskeletal model of the rat hindlimb was adapted to represent knee flexion-extension, valgus-varus, and internal-external rotation. The tissue-level cartilage mechanical environment was then spatially estimated, using the musculoskeletal modeling parameters as inputs into a dedicated finite element (FE) model of the rat knee, comprising cartilage and meniscal tissues. Experimental gait data and modeling workflows, including musculoskeletal models and FE meshes, are openly shared through a data repository.

Results

In rats with DMM, the frontal plane knee pose was altered, yet there was no indication of joint-level overloading. Tissue-level mechanical cues typically linked with cartilage degeneration were not increased in the medial tibial cartilage, despite evidence of tissue structural changes.

Conclusion

DMM did not increase joint and tissue mechanical responses in the knee medial compartment, suggesting that mechanical loading alone does not explain the observed osteoarthritis-like structural changes.
Dispersal history of SARS-CoV-2 variants Alpha, Delta, and Omicron (BA.1) in Spain
Authors: Gallego-García Pilar , Hong Samuel L , Bollen Nena , Dellicour Simon , Baele Guy , Suchard Marc A , Lemey Philippe , Posada David
Published: July 2024

Different factors influence the spread of SARS-CoV-2, from the inherent transmission capabilities of the different variants to the control measurements put in place. Here we studied the introduction of the Alpha, Delta, and Omicron-BA.1 variants of concern (VOCs) into Spain. For this, we collected genomic data from the GISAID database and combined it with connectivity data from different countries with Spain to perform a phylodynamic Bayesian analysis of the introductions. Our findings reveal that the introductions of these VOCs predominantly originated from France, especially in the case of Alpha. As travel restrictions were eased during the Delta and Omicron-BA.1 waves, the number of introductions from distinct countries increased, with the United Kingdom and Germany becoming significant sources of the virus. The largest number of introductions detected corresponded to the Delta wave, which was associated with fewer restrictions and the summer period, when Spain receives a considerable number of tourists. This research underscores the importance of monitoring international travel patterns and implementing targeted public health measures to manage the spread of SARS-CoV-2.
In VitroGeneration and Characterization of The Wu Syndrome Model That Causes Mental Retardation in Neural Cell Lines
Authors: Karaman Sumeyye Seher , Sevik Tuba , Akdemir Selin , Bilgin Burak , Karadeli Esra , Yalcin Dilay , Baran Buse , Gelsin Beste , Budaklar Buket , Sert Berranur , Gulden Gamze , Tastan Cihan
Published: July 2024

Wu Syndrome, also known as X-Linked Wu Type Intellectual Developmental Disorder, is caused by a mutation in the GRIA3 (Glutamate Ionotropic Receptor AMPA Type Subunit 3) gene located at position 25 on the X chromosome. GRIA3 encodes iGluR3, a subunit of the AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, which plays a critical role in rapid excitatory synaptic transmission in the central nervous system. This receptor is essential for learning, memory, and the processes of long-term depression (LTD) and long-term potentiation (LTP). Despite its significance, Wu Syndrome remains under-researched and lacks effective treatments. Notably, some genetic variants have been identified, but many, including the W637S variant, are still unstudied. This study pioneers the development of a Wu Syndrome model in neural cell lines using genetic modification techniques to identify and characterize new GRIA3 variants. By focusing on variants such as G833R and W637S, this research provides novel insights into their effects on GRIA3 function, paving the way for potential therapeutic strategies. This is the first study to explore the responses of neural cells to these mutations in vitro, thereby contributing valuable knowledge toward understanding and treating Wu Syndrome.
Knowledge systems, behaviours and organizational tasks for hospital effectiveness: mixed effects on quality of care
Authors: Gonçalves Tiago Rodrigues , Curado Carla
Published: June 2024

Purpose

The healthcare sector relies on knowledge management systems to improve knowledge flows and effectively capture, leverage and share knowledge with several organizational stakeholders. However, knowledge as a resource represents a social construct that involves additional managerial complexities and challenges, including undesirable knowledge behaviours. The aim of the current study is to provide insight on how knowledge management systems, knowledge hoarding, knowledge hiding and task conflict shape the quality of care provided by hospitals. We propose and test an original revealing model.

Design/methodology/approach

We follow a quantitative approach to address the structural relationship between variables using a combination of factor analysis and multiple regression analysis. The model is tested adopting a structural equation modelling approach and using survey data conducted to 318 healthcare professionals working in Portuguese hospitals.

Findings

The main findings suggest that knowledge hiding is positively related to task conflict in hospitals, and task conflict negatively influences quality of care. Knowledge management systems directly and indirectly (via knowledge hoarding) promote quality of care. Moreover, knowledge management systems also mitigate the negative influence of task conflict over quality of care. We propose a final corollary on the relevant role of HRM as the backstage for the model.

Practical implications

Our research offers a novel insight into an overlap of organizational behaviour and healthcare management research. It provides an original framework on knowledge management systems, counterproductive knowledge behaviours and task conflict in hospital settings.

Originality/value

Our research offers a novel insight into an overlap of organizational behaviour and healthcare management research. It provides an original framework on knowledge management systems, counterproductive knowledge behaviours and task conflict in hospital settings.