bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Convolutional Neural Networks for the Classification of Suboptimal Chest Radiographs
Authors: Liu Emily , Carrion D , Badawy MK 
Published: November 2024

AbstractBackgroundChest X-rays (CXR) rank among the most conducted X-ray examinations. They often require repeat imaging due to inadequate quality, leading to increased radiation exposure and delays in patient care and diagnosis. This research assesses the efficacy of DenseNet121 and YOLOv8 neural networks in detecting suboptimal CXRs, which may minimise delays and enhance patient outcomes.MethodThe study included 3,587 patients with a median age of 67 (0-102). It utilised an initial dataset comprising 10,000 CXRs randomly divided into a training subset (4,000 optimal and 4,000 suboptimal) and a validation subset (400 optimal and 400 suboptimal). The test subset (25 optimal and 25 suboptimal) was curated from the remaining images to provide adequate variation. DenseNet121 and YOLOv8 were chosen due to their capabilities in image classification. Their performance was assessed via the area under the receiver operating curve (AUROC) and compared to radiologist classification, utilising the chi-squared test.ResultsDenseNet121 attained an AUROC of 0.97, while YOLOv8 recorded a score of 0.95, indicating a strong capability in differentiating between optimal and suboptimal CXRs. The alignment between radiologists and models exhibited variability partly due to the lack of clinical indications. However, the performance was not statistically significant.ConclusionBoth AI models effectively classified chest X-ray quality, demonstrating the potential for providing radiographers with feedback to improve image quality. Notably, this was the first study to include both PA and lateral CXRs, as well as pediatric cases, and the first to evaluate YOLOv8 for this application.
Association between biomarkers of environmental enteric dysfunction and growth and neurodevelopment in Guatemalan infants
Authors: Connery Amy K. , Calvimontes Diva M. , Bucardo Filemon , Olson Daniel , Colbert Alison M. , Bartelt Luther , Asturias Edwin J. , Lamb Molly M. , Becker-Dreps Sylvia 
Published: November 2024

ABSTRACTBACKGROUNDThere is growing evidence that environmental enteric dysfunction (EED) is a driver of poor growth and neurodevelopment (ND) in early childhood. To further investigate this, we measured the associations between biomarkers reflecting various domains of EED and growth and ND in Guatemalan infants. METHODS. A subset of 114 cohort infants were randomly selected for inclusion from a 2017-2019 population-based cohort study of 499 young infants in rural southwest Guatemala. Growth and neurodevelopmental performance using the Mullen Scales of Early Learning (MSEL) were assessed at a household visit around 12 months of age. Serum samples collected at the visit were analyzed for concentrations of α-1 acid glycoprotein (AGP), glucagon-like peptide-2 (GLP-2), and anti-flagellin IgA (Anti-FliC IgA), Multivariable regression analyses adjusted for relevant confounders were conducted to define associations between these EED biomarkers and length-for-age z-score (LAZ) and neurodevelopmental performance. We planneda priorito conduct analyses with and without excluding infants who had acute infectious disease symptoms (fever, cough, vomiting, diarrhea) at the 12-month visit.RESULTSNo significant association between biomarkers representing different domains of EED and LAZ or MSEL scores at 12-14 months of age was found. However, removing children with acute infectious symptoms uncovered an association between Anti-FliC IgA and MSEL. Specifically, an increase in 10ng/L in Anti-FliC IgA concentration was associated in a decrease in the MSEL Early Learning Composite (ELC) raw score of 3.2 points, which equates to approximately a 9-point decrease in the ELC standard score.CONCLUSIONSIn this study, having increased levels of Anti-FliC IgA was associated with lower ND in the first year of life and may represent an important risk to long-term health and development.AUTHOR SUMMARYThere is growing evidence that a key driver of stunting and poor neurodevelopment in low-resource settings is environmental enteric dysfunction. Environmental enteric dysfunction is a subclinical condition of the small intestine that may include chronic mucosal inflammation and/or increased intestinal permeability; it is common in children experiencing repeated infections with fecal-oral pathogens. In this preliminary study, we examined the link between biomarkers of environmental enteric dysfunction and neurodevelopment in 114 infants. After excluding children with acute infectious symptoms (which could transiently modify biomarker levels), we found a strong link between one marker of EED and poor neurodevelopment, independent of child growth. Further research is warranted to explore the associations between EED and ND to guide future interventions to reduce these risks.
An implementation-effectiveness trial investigating feasibility, safety and efficacy of Best pRacticE guideline cAre physioTHErapy with addition of protocolised ventilator hyperinflation on patient-important outcomes for critically ill adults intUbated and ventilated with Pneumonia. (BREATHE UP)
Authors: van der Lee Lisa , Regli Adrian , Allen Christopher , Anstey Matthew , Blakeman Robert , Denehy Linda , Dennis Diane , Elliott Mercedes , Hill Anne-Marie , Ho Kwok-Ming , Jacob Wendy , Jacques M Angela , Marsh Lisa , Palermo Mark , Wibrow Bradley , Ntoumenopoulos George 
Published: November 2024

ABSTRACTPneumonia is a common cause for intensive care unit (ICU) admission for breathing support from a mechanical ventilator, resulting in high morbidity, mortality, and healthcare costs. Physiotherapists working in ICU treat patients with critical pneumonia using a range of respiratory treatments to improve breathing, hasten weaning from the ventilator, and restore functional independence. Evidence supports the short-term benefits of these treatments, however currently no standard of physiotherapy practice exists for these ICU patients. Despite a plethora of studies which have shown that physiotherapy treatments, such as ventilator lung hyperinflation (VHI), aid the lungs to work better short-term, there are no studies to date which investigate the effect of these important treatments on meaningful patient-important outcomes, such as earlier weaning from the ventilator, earlier hospital discharge, less breathlessness and lung secretions, short- and longer-term disability, health- related quality of life and survival. Through previous multiphase mixed-methods research, a clinical practice guideline was developed outlining best physiotherapy practice for this ICU patient cohort. This proposed research involves conducting a multicentre hybrid implementation-effectiveness randomised, controlled trial which aims to: evaluate implementation of physiotherapy guideline care for management of pneumonia in ICU regarding feasibility, safety and acceptability; and to determine the safety and effectiveness of a standardised dosage of daily ventilator hyperinflation in addition to standard guideline care on patient-important outcomes, health system outcomes; and cost effectiveness. This study will address critical knowledge gaps in the ICU physiotherapy evidence base regarding the impact of a course of standardised, best practice respiratory physiotherapy intervention during the ICU stay for patients with critical pneumonia requiring invasive mechanical ventilation, provide valuable information for clinicians to inform clinical practice regarding treatable traits and streamlining care to promote clinical efficiency, and determine the impact of respiratory physiotherapy care on patient-important and health service outcomes.Trial registrationANZ Clinical trials Registry number ACTRN12624001130550.
REMINDer randomized controlled study: Feasibility and impact of an online multimodal mind-body intervention in older adults
Authors: Wirth Miranka , Stamer Selina , Podolski Odile , Maßalsky Annemarie , Koch Sabine C. , Klimecki Olga 
Published: November 2024

AbstractBackgroundThe increase in life expectancy and age-related diseases, such as Alzheimer’s disease, is a global challenge. Given the drawbacks of pharmacological treatments, it is important to pursue non-pharmacological strategies for dementia risk reduction. To effectively promote health and well-being in later life, multimodal, low-threshold, and cost-effective lifestyle interventions are needed.MethodsREMINDeris a monocentric, outcome assessor-blinded, randomized controlled pilot study to assess the feasibility and impact of an online (home-based and live-streamed) multimodal intervention. The 6-week (two one-hour sessions/week) mind-body group intervention will be compared to a 6-week passive control (waitlist with delayed intervention) using a cross-over (AB-BA) design. The intervention was designed for older adults and includes music, dance-based movement, and mindfulness. A total ofN=50 cognitively unimpaired older adults will be enrolled and randomized into the two intervention arms using a block randomization with a 1:1 allocation ratio.ResultsOutcomes will be assessed at pre-intervention, post-intervention, and follow-up using digital assessments of online questionnaires. Primary outcomes include feasibility, operationalized by adherence rates, and preliminary effectiveness of the intervention. The latter will be assessed by changes in self-reported mental and physical well-being, operationalized by the Short-Form Health Survey (SF-12). Secondary outcomes will include changes in cognitive, motor, sensory, emotional/affective, social, and lifestyle health behaviors.DiscussionThe study will provide evidence of the feasibility and preliminary effectiveness of an online multimodal mind-body intervention based on “Arts for Health” activities. If successful, the study may inform accessible lifestyle strategies to improve mental health and well-being and other risk factors for dementia in older adults.Trail RegistrationClinicalTrials.gov,NCT06530277ProtocolSR-EK-477112023
ComFB, a new widespread family of c-di-NMP receptor proteins
Authors: Samir Sherihan , Elshereef Abdalla A. , Alva Vikram , Hahn Jeanette , Dubnau David , Galperin Michael Y. , Selim Khaled A. 
Published: November 2024

ABSTRACTCyclic dimeric GMP (c-di-GMP) is a widespread bacterial second messenger that controls a variety of cellular functions, including protein and polysaccharide secretion, motility, cell division, cell development, and biofilm formation, and contributes to the virulence of some important bacterial pathogens. While the genes for diguanylate cyclases and c-di-GMP hydrolases (active or mutated) can be easily identified in microbial genomes, the list of c-di-GMP receptor domains is quite limited, and only two of them, PliZ and MshEN, are found across multiple bacterial phyla. Recently, a new c-di-GMP receptor protein, named CdgR or ComFB, has been identified in cyanobacteria and shown to regulate their cell size and, more recently, natural competence. Sequence and structural analysis indicated that CdgR is part of a widespread ComFB protein family, named after the “late competence development protein ComFB” fromBacillus subtilis. This prompted the suggestion that ComFB and ComFB-like proteins could also be c-di-GMP receptors. Indeed, we revealed that ComFB proteins from Gram-positiveB. subtilisandThermoanaerobacter brockiiwere able to bind c-di-GMP with high-affinity. The ability to bind c-di-GMP was also demonstrated for the ComFB proteins from clinically relevant Gram-negative bacteriaVibrio choleraeandTreponema denticola. These observations indicate that the ComFB family serves as yet another widespread family of bacterial c-di-GMP receptors. Incidentally, some ComFB proteins were also capable of c-di-AMP binding, identifying them as a unique family of c-di-NMP receptor proteins. The overexpression ofcomFBinB. subtilis,combined with an elevated concentration of c-di-GMP, suppressed motility, attesting to the biological relevance of ComFB as a c-di-GMP binding protein.IMPORTANCEThe cellular content of the bacterial second messenger c-di-GMP is controlled by c-di-GMP synthases (GGDEF domains) and hydrolases (EAL or HD-GYP domains), whose activities, in turn, respond to the signals perceived by their upstream sensory domains. Cyclic-di-GMP transmits the signals to a variety of its targets, which may contain inactivated GGDEF, EAL, or HD-GYP domains, widespread PilZ or MshEN domains, or various lineage-specific c-di-GMP receptors. Many organisms encode multiple GGDEF domains but few c-di-GMP-binding proteins, suggesting the existence of still unidentified c-di-GMP receptors. Here, we demonstrate that the ComFB family proteins, which include the recently characterized cyanobacterial CdgR/ComFB, constitute yet another widespread family of bacterial c-di-NMP receptors. We additionally show that ComFB controls bacillar motility in a c-di-GMP-dependent manner.
Mass flowering and flowering asynchrony characterise a seasonal herbaceous community in the Western Ghats
Authors: Shrotri Saket , Kaur Sukhraj , Dhargalkar Rahul , Najla PV , Gowda Vinita 
Published: November 2024

ABSTRACTSeasonally flowering communities often exhibit higher flowering synchrony than what can be attributed to environmental factors alone. Flowering synchrony can either increase competition for pollinators or improve pollination through facilitation. Consequently, analysing a community’s flowering patterns can help identify its ecological constraints. In this study, we characterised the flowering phenology of a seasonal, herbaceous community (Kaas plateau) in Western Ghats, India, known for its endemic flora and mass flowering displays. Over three years, we addressed the following questions: (a) Is flowering seasonality shaped by environmental factors? (b) Is there evidence for flowering synchrony within the community? (c) Are plant-pollinator interactions specialised?Our results show that flowering seasonality was shaped by long dry seasons and subsequent rainfall patterns. Based on the floral abundance, we categorised the flora into mass flowering and non-mass flowering species. To incorporate flowering abundance in defining flowering synchrony, we introduced two novel synchrony indices, which identified community-wide flowering asynchrony, despite having mass flowering species. Finally, the plant-pollinator networks identified native bees as dominant pollinators and the prominence of generalised interactions. We also noted sub-seasonal temporal shifts in pollination networks that matched flowering abundances within the community.This is the first study to exhaustively characterise the flowering phenology of plants from a laterite plateau in the Western Ghats. We show that despite seasonality, both mass flowering and flowering asynchrony emerged as the defining characteristics of this habitat. Our results suggest that competition for pollinators probably drives flowering asynchrony within these seasonal herbaceous communities, rather than pollination facilitation.
A Watershed Algorithm GUI for Personalized fMRI-guided rTMS Target
Authors: Feng Zi-Jian , Wei Ziyu , Hong Liquan , Fang Hongli , Han Yu , Yang Peifeng , Dongsheng Lv , Zang Yu-Feng 
Published: November 2024

AbstractThe FDA approved personalized resting-state functional connectivity for precise target localization in rTMS. However, objective methods for pinpointing optimal connectivity clusters have remained limited. This study proposed a watershed-based approach with a graphical user interface, offering threshold-independent segmentation that outperformed traditional threshold-based methods. Demonstrated in the context of Alzheimer’s disease, this approach enabled precise targeting within the default mode network, specifically the posterior cingulate cortex and inferior parietal lobule. By facilitating more accurate and individualized localization, this method holds promise for refining the precision of personalized rTMS treatment.
Assessing Conformation Validity and Rationality of Deep Learning-Generated 3D Molecules
Authors: Fan Fan , Xi Bin , Meng Xianghu , Wang Han , Zhang Bowen , Xu Qingbo , Feng Wei , Wang Xiaoman , Zhang Hongbo , Zhou Feng , Liu Zhenming , Zhou Wenbiao , Huang Bo 
Published: November 2024

AbstractRecent advancements in artificial intelligence (AI) have revolutionized the field of 3D molecule generation. However, the lack of effective evaluation methods for 3D conformations limits further improvements. Current techniques, in order to achieve the necessary speed for evaluating large numbers of AI-generated molecules, often rely on empirical geometric metrics that do not adequately capture various conformational anomalies, or on molecular mechanics (MM) energy metrics that exhibit low accuracy and lack atomic or torsional details. To address this gap, we propose a two-stage approach that achieves both high speed and quantum mechanical (QM) level accuracy. The first stage, termed the validity test, employs an AI-derived force field to identify atoms with elevated energy resulting from implausible neighboring environments. The second stage, known as the rationality test, utilizes a deep learning network trained on data with density functional theory (DFT) accuracy to detect rotatable bonds with high torsional energies. To demonstrate the functionality of our evaluation system, we applied our approach to five recently reported 3D molecule generation AI models across 102 targets in Directory of Useful Decoys-Enhanced (DUD-E) dataset. To facilitate accessibility for the academic community, our method is available as an open-source package.
ROSIE: AI generation of multiplex immunofluorescence staining from histopathology images
Authors: Wu Eric , Bieniosek Matthew , Wu Zhenqin , Thakkar Nitya , Charville Gregory W. , Makky Ahmad , Schürch Christian , Huyghe Jeroen R , Peters Ulrike , Li Christopher I , Li Li , Giba Hannah , Behera Vivek , Raman Arjun , Trevino Alexandro E. , Mayer Aaron T. , Zou James 
Published: November 2024

AbstractHematoxylin and eosin (H&E) is a common and inexpensive histopathology assay. Though widely used and information-rich, it cannot directly inform about specific molecular markers, which require additional experiments to assess. To address this gap, we presentROSIE,a deep-learning framework that computationally imputes the expression and localization of dozens of proteins from H&E images. Our model is trained on a dataset of over 1000 paired and aligned H&E and multiplex immunofluorescence (mIF) samples from 20 tissues and disease conditions, spanning over 16 million cells. Validation of ourin silico mIFstaining method on held-out H&E samples demonstrates that the predicted biomarkers are effective in identifying cell phenotypes, particularly distinguishing lymphocytes such as B cells and T cells, which are not readily discernible with H&E staining alone. Additionally,ROSIEfacilitates the robust identification of stromal and epithelial microenvironments and immune cell subtypes like tumor-infiltrating lymphocytes (TILs), which are important for understanding tumor-immune interactions and can help inform treatment strategies in cancer research.
Ligand binding characteristics of an NAD+ riboswitch revealed by FRET and biolayer interferometry
Authors: Conoan Nieves Nico E. , Widom Julia R. 
Published: November 2024

AbstractThe Class II NAD+riboswitch is a bacterial RNA that binds ligands containing nicotinamide. Herein, we report a fluorescence and biolayer interferometry study of riboswitch interactions with β-NMN. The results reveal a shift in the prevalence of a pseudoknot structure in the presence of ligand and Mg2+.
Contrast-Enhanced Micro-CT Imaging of a Foetal Female Pelvic Floor Reveals Anatomical Details
Authors: Aaldijk Dea , Halm Sebastian , Liashchenko Diana N. , Haberthür David 
Published: November 2024

AbstractBackgroundThe pelvic floor is a highly important structure for the stability of the pelvis, providing support for the organs that lie within it. Until today, the detailed anatomy of the female perineal centre and the exact course of surrounding muscles remain controversial. This paper demonstrated a method to non-destructively obtain high-resolution contrast-enhanced x-ray microtomography images from a long-fixed sample and thereby aimed to contribute to the detailed anatomical knowledge about the female pelvic floor.Materials and MethodsA human foetal pelvis of 20-21 weeks gestational age, formalin-fixed for 4 years, was immersed in Lugol solution and tomographically scanned periodically to document the staining process. The influence of the former fixation time was addressed by comparison with a short time fixed mouse pelvis. High-resolution imaging was performed by µCT, and the detailed analysis of the anatomy was supported by segmentation and 3D reconstruction.ResultsLugol staining of long-fixed tissue worked well and showed no disadvantages compared to short-fixed tissue. Lugol staining and high-resolution µCT images provided a nicely stained image- stack with clearly identifiable tissue types. The anatomy of the foetal pelvis and its structures were resolved in detail. Interconnections between the external anal sphincter, the bulbospongiosus muscle and the superficial transverse perineal muscle could be shown within the perineal centre. There was no evidence for a skeletal muscle that corresponded to the formerly described deep transverse perineal muscle, instead there was cloudy-looking tissue, most likely smooth muscle fibres dispersed in connective tissue in a 3-D arrangement.ConclusionsX-ray microtomography of Lugol-stained tissue is an excellent method to gain anatomical details in high resolution, in a non-invasive and non-destructive way, independently of the fixation time. Using this method, the topographical relationships of the pelvic floor muscles could be illustrated, showing their linkage within the perineal centre.