bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dysphagia screening among stroke patients in a tertiary hospital: a best practice implementation project
Authors: Shen Guojing , Xia Qingyi , Zhang XiaoLing , Xue Ping , Wang Ying , Wang Jue 
Published: February 2024

ABSTRACT

Objectives:
The study aimed to promote nurses’ compliance with best practices for dysphagia screening in patients with stroke.

Introduction:
Dysphagia can significantly increase the risk of complications, especially aspiration pneumonia, leading to increased risk of disability, death, and high medical expenses. Dysphagia screening can reduce aspiration risk and is recommended as a crucial step in dysphagia management; however, not all patients with stroke undergo dysphagia screening in the neurology ward.

Methods:
The JBI Evidence Implementation Framework was used in this study. A baseline audit was conducted by interviewing 22 nurses and reviewing 48 medical records to evaluate current practice against best practice recommendations. The JBI Getting Research into Practice (GRiP) tool was used to identify barriers and strategies for practice change. A follow-up audit of 19 nurses and 48 medical records was conducted after implementation of improvement strategies.

Results:
The follow-up audit results showed improvement in three criteria compared with the baseline audit: for Criterion 1, compliance increased by 27.3%, rising from 72.7% to 100%; for Criteria 3 and 4, compliance increased by 77.1%, rising from 20.8% to 97.9%. The difference in nurses’ knowledge, attitude, and behavior scores for dysphagia screening between the baseline and follow-up audits was statistically significant (all p < 0.05).

Conclusions:
The project showed improvements in evidence-based practice in the dysphagia screening of stroke patients in a neurology ward. However, more work needs to be done to ensure the sustainability of best practices, such as regular training for nurses, supervision from managers, and regular audits of dysphagia screening.
Large-Scale Evaluation of Spatial Metabolomics Protocols and Technologies
Authors: Saharuka Veronika , Vieira Lucas M. , Stuart Lachlan , Ekelöf Måns , Molenaar Martijn R. , Bailoni Alberto , Ovchinnikova Katja , Soltwisch Jens , Bausbacher Tobias , Jakob Dennis , King Mary , Müller Max A. , Oetjen Janina , Pace Crystal , Pinto Fernanda E. , Strittmatter Nicole , Velickovic Dusan , Spengler Bernhard , Muddiman David C. , Liebeke Manuel , Janfelt Christian , Goodwin Richard , Eberlin Livia S. , Anderton Christopher R. , Hopf Carsten , Dreisewerd Klaus , Alexandrov Theodore 
Published: February 2024

AbstractSpatial metabolomics using imaging mass spectrometry (MS) enables untargeted and label-free metabolite mapping in biological samples. Despite the range of available imaging MS protocols and technologies, our understanding of metabolite detection under specific conditions is limited due to sparse empirical data and predictive theories. Consequently, challenges persist in designing new experiments, and accurately annotating and interpreting data. In this study, we systematically measured the detectability of 172 biologically-relevant metabolites across common imaging MS protocols using custom reference samples. We evaluated 24 MALDI-imaging MS protocols for untargeted metabolomics, and demonstrated the applicability of our findings to complex biological samples through comparison with animal tissue data. We showcased the potential for extending our results to further analytes by predicting metabolite detectability based on molecular properties. Additionally, our interlaboratory comparison of 10 imaging MS technologies, including MALDI, DESI, and IR-MALDESI, showed extensive metabolite coverage and comparable results, underscoring the broad applicability of our findings within the imaging MS community. We share our results and data through a new interactive web application integrated with METASPACE. This resource offers an extensive catalogue of detectable metabolite ions, facilitating protocol selection, supporting data annotation, and benefiting future untargeted spatial metabolomics studies.
Aggregating Residue-Level Protein Language Model Embeddings with Optimal Transport
Authors: NaderiAlizadeh Navid , Singh Rohit 
Published: February 2024

AbstractProtein language models (PLMs) have emerged as powerful approaches for mapping protein sequences into embeddings suitable for various applications. As protein representation schemes, PLMs generate per-token (i.e., per-residue) representations, resulting in variable-sized outputs based on protein length. This variability poses a challenge for protein-level prediction tasks that require uniform-sized embeddings for consistent analysis across different proteins. Previous work has typically used average pooling to summarize token-level PLM outputs, but it is unclear whether this method effectively prioritizes the relevant information across token-level representations. We introduce a novel method utilizing optimal transport to convert variable-length PLM outputs into fixed-length representations. We conceptualize per-token PLM outputs as samples from a probabilistic distribution and employ sliced-Wasserstein distances to map these samples against a reference set, creating a Euclidean embedding in the output space. The resulting embedding is agnostic to the length of the input and represents the entire protein. We demonstrate the superiority of our method over average pooling for several downstream prediction tasks, particularly with constrained PLM sizes, enabling smaller-scale PLMs to match or exceed the performance of average-pooled larger-scale PLMs. Our aggregation scheme is especially effective for longer protein sequences by capturing essential information that might be lost through average pooling.
The CoLab-score rapidly and efficiently excludes COVID-19 at the emergency department without need for SARS-CoV-2 testing: a multicenter case-control study
Authors: Boer Arjen-Kars , Deneer Ruben , Maas Maaike , Ammerlaan Heidi S. M. , van Balkom Roland H. H. , Leers Mathie P. G. , Martens Remy J.H. , Buijs Madelon M. , Kerremans Jos J. , Messchaert Muriël , van Suijlen Jeroen D.E. , van Riel Natal A.W. , Scharnhorst Volkher 
Published: February 2024

AbstractBackgroundRapid identification of emergency department (ED) patients with a possible COVID-19 infection is needed. PCR-testing all ED patients is neither feasible nor effective in most centers, therefore a rapid, objective, low-cost screening tool to triage ED patients is necessary.MethodsResults from all routine lab tests from ED patients at the Catharina Hospital were collected from July 2019 to July 2020 and used in a statistical model to obtain the CoLab-score. The score was validated temporally and externally in three independent centers.ResultsThe CoLab-score consists of 10 routine lab results and can be used to safely rule-out a COVID-19 infection in more than one third of ED presentations with a negative predictive value of 0.997 (95% CI: 0.994 – 0.999).ConclusionsThe CoLab-score is a valuable tool to rule out COVID-19, guide PCR testing and is available to any center with access to routine laboratory tests.
Determination of prevalence of HLA-B27 in patients with backache at Armed Forces Institute of Pathology (AFIP), Rawalpindi
Authors: Haris Abdul Rehman , Maqsood Furqan , Tipu Hamid Nawaz , Ahmed Dawood 
Published: February 2024

AbstractBackgroundHLA-B27 is a class I MHC protein that is associated with different diseases collectively called, spondyloarthropathies. It includes;2.Ankylosing spondylitis, which causes inflammation of the bones in your spine3.Reactive arthritis, which causes inflammation of your joints, urethra, and eyes, and in some cases lesions on your skin4.Juvenile rheumatoid arthritis5.Anterior Uveitis, which causes swelling and irritation in the middle layer of your eyeObjectivesTo determine the prevalence of HLA-B27 in patients with backache at the Armed Forces Institute of Pathology in Rawalpindi. This descriptive cross-sectional study was conducted between June 2020 and Nov 2020.Material and methodsOf the 243 patients, 167 males and 76 females were tested for HLA-B27 during the study period. Venous blood samples (3 mL) were collected in EDTA tubes and processed for HLA-B27 gene identification on the cell surface. A two-color flow cytometry panel was used to analyze samples using a BD FACS Canto II flow cytometer on BD FACS Diva software. The dot plot was created using an isotype control in four quadrants, and positive and negative populations of cells were identified.ResultsA total of 243 patients were analyzed for the presence of HLA-B27 using flow cytometry. Of the 243 patients, 167 were male and 76 were female patient.51 male patients tested positive, with a positivity rate of 30.53% among the male population and 20.98% among the general population. In contrast to the male population, 12 female patients tested positive for the HLA-B27 gene, with a positivity rate of 15.78% among the female population and 4.93% among the general population. The total positivity rate was 25.92%, with a higher prevalence in the male population included in this study.ConclusionAll individuals tested for HLA B27 were included in this study. This study showed that positivity rate of HLA-B27 is more in males with a percentage of 20.98% as compared to female population (4.93%).
A novel and efficient machine learning Mendelian randomization estimator applied to predict the safety and efficacy of sclerostin inhibition
Authors: Legault Marc-André , Hartford Jason , Arsenault Benoît J. , Yang Archer Y. , Pineau Joelle 
Published: February 2024

1AbstractMendelian Randomization (MR) enables estimation of causal effects while controlling for unmeasured confounding factors. However, traditional MR’s reliance on strong parametric assumptions can introduce bias if these are violated. We introduce a new machine learning MR estimator named Quantile Instrumental Variable (IV) that achieves low estimation error in a wide range of plausible MR scenarios. Quantile IV is distinctive in its ability to estimate nonlinear and heterogeneous causal effects and offers a flexible approach for subgroup analysis. Applying Quantile IV, we investigate the impact of circulating sclerostin levels on heel bone mineral density, osteoporosis, and cardiovascular outcomes in the UK Biobank. Employing various MR estimators and colocalization techniques that allow multiple causal variants, our analysis reveals that a genetically predicted reduction in sclerostin levels significantly increases heel bone mineral density and reduces the risk of osteoporosis, while showing no discernible effect on ischemic cardiovascular diseases. Quantile IV contributes to the advancement of MR methodology, and the case study on the impact of circulating sclerostin modulation contributes to our understanding of the on-target effects of sclerostin inhibition.
Toward a more comprehensive understanding of network centrality disruption in amnestic Mild Cognitive Impairment: a MEG multilayer approach
Authors: Taguas Ignacio , Doval Sandra , Maestú Fernando , López-Sanz David 
Published: February 2024

AbstractAlzheimer’s Disease (AD) is the most common form of dementia. Its early stage, amnestic Mild Cognitive Impairment (aMCI), is characterized by disrupted information flow in the brain. Previous studies using electrophysiological techniques to investigate AD’s functional connectivity changes have yielded inconsistent results; contributing factors may include the specific metric employed and the separate study of brain activity in each frequency band. Our study addresses this by employing a cross-frequency approach to compare functional networks in 172 healthy subjects and 105 aMCI patients. Using magnetoencephalography, we constructed source-based multilayer graphs considering both intra- and inter-band functional connectivity across the five classical frequency bands. We assessed network changes through three centrality measures (strength, eigenvector centrality, and betweenness centrality), and combined them into a unified centrality score for a comprehensive assessment of centrality disruption in aMCI. Results revealed a notable shift in centrality distribution in aMCI patients spatially and across frequencies. Posterior brain regions decrease synchrony between high-frequency oscillations and other regions’ activity across all frequencies, while anterior regions increase synchrony between low-frequency oscillations and other regions’ activity across all bands. Thus, posterior regions reduce their relative importance in favor of anterior regions. This study demonstrates that considering the interplays between different frequency bands enhances understanding of AD network dynamics and sets a precedent for multilayer functional network studies. Our findings provide valuable insights into the intricate changes that occur in functional brain networks during the early stages of AD, offering a framework for developing interventions aimed at modifying the disease trajectory.Significance statementOver 55 million people worldwide suffer from Alzheimer’s Disease. The brain changes causing the symptoms begin around 20 years before their onset, so characterizing these changes in the early stage, mild cognitive impairment, is of utmost importance. Magnetoencephalography and electroencephalography (M/EEG) are two commonly used techniques to assess changes in functional networks; however, the existing studies yield inconsistent results. Our study applies a novel methodology for the analysis of M/EEG data that addresses two factors contributing to this effect: the metric employed to assess network changes and the use of a cross-frequency approach. Results show that posterior regions reduce their relative importance in favor of anterior regions. This study sets a precedent for the functional study of all brain disorders.
Age-Related RPE changes in Wildtype C57BL/6J Mice between 2 and 32 Months
Authors: Shelton Debresha A. , Gefke Isabelle , Summers Vivian , Kim Yong-Kyu , Yu Hanyi , Getz Yana , Ferdous Salma , Donaldson Kevin , Liao Kristie , Papania Jack T. , Chrenek Micah A. , Boatright Jeffrey H. , Nickerson John M. 
Published: February 2024

AbstractPurposeThis study provides a systematic evaluation of age-related changes in RPE cell structure and function using a morphometric approach. We aim to better capture nuanced predictive changes in cell heterogeneity that reflect loss of RPE integrity during normal aging. Using C57BL6/J mice ranging from P60-P730, we sought to evaluate how regional changes in RPE shape reflect incremental losses in RPE cell function with advancing age. We hypothesize that tracking global morphological changes in RPE is predictive of functional defects over time.MethodsWe tested three groups of C57BL/6J mice (young: P60-180; Middle-aged: P365-729; aged: 730+) for function and structural defects using electroretinograms, immunofluorescence, and phagocytosis assays.ResultsThe largest changes in RPE morphology were evident between the young and aged groups, while the middle-aged group exhibited smaller but notable region-specific differences. We observed a 1.9-fold increase in cytoplasmic alpha-catenin expression specifically in the central-medial region of the eye between the young and aged group. There was an 8-fold increase in subretinal, IBA-1-positive immune cell recruitment and a significant decrease in visual function in aged mice compared to young mice. Functional defects in the RPE corroborated by changes in RPE phagocytotic capacity.ConclusionsThe marked increase of cytoplasmic alpha-catenin expression and subretinal immune cell deposition, and decreased visual output coincide with regional changes in RPE cell morphometrics when stratified by age. These cumulative changes in the RPE morphology showed predictive regional patterns of stress associated with loss of RPE integrity.
Structural dynamics and immunogenicity of the recombinant and outer membrane vesicle-embedded Meningococcal antigen NadA
Authors: Calvaresi Valeria , Dello Iacono Lucia , Borghi Sara , Luzzi Enrico , Biolchi Alessia , Benucci Barbara , Ferlenghi Ilaria , Peschiera Ilaria , Giusti Fabiola , Fontana Lucia E. , Kan Zhong-Yuan , Spinello Zaira , Merola Marcello , Delany Isabel , Rand Kasper D. , Norais Nathalie 
Published: February 2024

AbstractThe structure and conformation adopted by protein vaccine antigens significantly influence the exposure of their antigenic determinants. Structural knowledge of antigens in native state could drive the design of recombinant vaccines that resemble their cognate native forms, although such information is often difficult to obtain, particularly for membrane proteins. Here, we assessed the structural and functional features of the native Neisseria Adhesin A (NadA), a meningococcal trimeric outer membrane protein included as soluble recombinant antigen in the 4CMenB vaccine. We used hydrogen-deuterium exchange mass spectrometry (HDX-MS) to generate a structural model of NadA and to compare the fold and structural dynamics of the recombinant NadA as soluble vaccine form, and the native NadAin situ, as embedded in meningococcal outer membrane vesicles (OMVs), complementing the HDX data with electron microscopy imaging. While their overall structures are similar, conformational differences between the two forms were observed. Especially, OMV- embedded NadA appears more susceptible to trimer opening than its cognate soluble antigen, suggesting that NadA in its native membrane could display a larger antigenic surface. Accordingly, we show that mice immunized with OMV-embedded NadA elicited antibodies with superior bactericidal activity and capable of better preventing bacterial adhesion compared to the soluble antigen. Collectively, these data support the hypothesis that protein vaccine antigens presented in native-like environments can elicit a more potent immune response than recombinant forms.
3D-ARM-Gaze: a public dataset of 3D Arm Reaching Movements with Gaze information in virtual reality
Authors: Lento Bianca , Segas Effie , Leconte Vincent , Doat Emilie , Danion Frederic , Péteri Renaud , Benois-Pineau Jenny , de Rugy Aymar 
Published: February 2024

ABSTRACT3D-ARM-Gaze is a public dataset designed to provide natural arm movements together with visual and gaze information when reaching objects in a wide reachable space from a precisely controlled, comfortably seated posture. Participants were involved in picking and placing objects in various positions and orientations in a virtual environment, whereby a specific procedure maximized the workspace explored while ensuring a consistent seated posture. The dataset regroups more than 2.5 million samples recorded from 20 healthy participants performing 14 000 single pick-and-place movements (700 per participant). While initially designed to explore novel prosthesis control strategies based on natural eye-hand and arm coordination, this dataset will also be useful to researchers interested in core sensorimotor control, humanoid robotics, human-robot interactions, as well as for the development and testing of associated solutions in gaze-guided computer vision.
Gastric microbiomes ofCassiopeain the Florida Keys are low diversity andEndozoicomonas-,Vibrio-andMycoplasma-dominated
Authors: Muffett Kaden M , Labonté Jessica M , Miglietta Maria Pia 
Published: February 2024

AbstractInteractions with microbial communities fundamentally shape metazoans’ physiology, development, and health across marine ecosystems. This is especially true in zooxanthellate (symbiotic algae-containing) cnidarians. In photosymbiotic anthozoans (eg. shallow water anemones and corals), the key members of the associated microbiota are increasingly well studied, however there is limited data on photosymbiotic scyphozoans (true jellyfish). Using 16S rRNA barcoding, we sampled the internal and external mucus of the zooxanthellate Upside- Down Jellyfish,Cassiopea xamachanathroughout eight sites covering the full length of the Florida Keys. We find that across sites, these medusae to have low-diversity internal microbial communities distinct from the communities of their external surfaces and their environment.These internal communities are dominated by only three taxa:Endozoicomonascf.atrinae, an uncultured novelMycoplasma, andVibriocf. coralliilyticus.Cassiopeabell mucosal samples conform largely to the communities of surrounding sediment with the addition ofEndozoicomonascf.atrinae. The microbial taxa we identify associated with wild Florida KeysCassiopeabear a strong resemblance to those found within photosymbiotic anthozoans, increasing the known links in ecological position between these groups.
Structural basis of the Integrator complex assembly and association with transcription factors
Authors: Razew Michal , Fraudeau Angelique , Pfleiderer Moritz M. , Galej Wojciech P. 
Published: February 2024

SummaryIntegrator is a multi-subunit protein complex responsible for premature transcription termination of coding and non-coding RNAs in Metazoans. This is achieved via Integrator’s two enzymatic activities, RNA endonuclease and protein phosphatase, acting on the promoter-proximally paused RNA Polymerase II (RNAPII). Yet, it remains unclear how Integrator assembly and recruitment are regulated and what are the functions of many of its core subunits. Here we report two cryo-EM reconstructions of large Integrator sub-complexes: INTS10/13/14/15 (Arm module) and INTS5/8/10/15, which allowed integrative modelling of the fully-assembled Integrator bound to the RNAPII paused elongating complex (PEC). INTS13/14 are positioned near the DNA upstream from the transcription pause site, suggesting a potential role in the chromatin context. Anin silicoprotein interaction screen of over 1500 transcription factors (TFs), identified Zinc Finger Protein 655 (ZNF655) as a direct interacting partner of INTS13 that associates with a fully assembled, 17-subunit Integrator complex. We propose a model wherein the Arm module acts as a platform for the recruitment of TFs that could modulate the stability of the Integrator’s association at specific loci and modulate transcription attenuation of the target genes.
Cell-material interactions in 3D bioprinted plant cells
Authors: Madison Imani , Tahir Maimouna , Van den Broeck Lisa , Phan Linh , Horn Timothy , Sozzani Rosangela 
Published: February 2024

Abstract3D bioprinting is an additive manufacturing technology with promise towards facilitating tissue engineering and single-cell investigations of cellular development and microenvironment responses. 3D bioprinting is still a new technology in the field of plant biology so its optimization with plant cells is still widely needed. Here, we present a study in which 3D bioprinting parameters, such as needle gauge, extrusion pressure, and scaffold type, were all tested in 3D bioprinted Tobacco BY-2 cells to evaluate how cell viability is responsive to each parameter. As a result, this study revealed an optimal range of extrusion pressures and needle gauges that resulted in an optimum cell viability. Furthermore, this study applied the identified optimal 3D bioprinting parameters to a different cell line,Arabidopsisroot protoplasts, and stress condition, phosphate starvation, to confirm that the identified parameters were optimal in a different species, cell type, and cellular microenvironment. This suggested that phosphate-starved bioprintedArabidopsiscells were less viable by 7 days, which was consistent with whole root phosphate starvation responses. As a result, the 3D bioprinter optimization yielded optimal cell viabilities in both BY-2 and Arabidopsis cells and facilitated an applied investigation into phosphate starvation stress.