bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overground gait adaptability in older adults with diabetes in response to virtual targets and physical obstacles
Authors: Martin Suzanne , Taylor Simon B. , Shideler Blynn L. , Ogrin Rajna , Begg Rezaul 
Published: October 2022

BackgroundTo step over an unexpected obstacle, individuals adapt gait; they adjust step length in the anterior-posterior direction prior to the obstacle and minimum toe clearance height in the vertical direction. Inability to adapt gait may lead to falls in older adults with diabetes. Therefore, this study aimed to investigate gait adaptability in older adults with diabetes.Research questionDoes diabetes impair gait adaptability and increase sagittal foot adjustment errors?MethodsThree cohorts of 16 people were recruited: young adults (Group I), healthy older adults (Group II), and older adults with diabetes (Group III). Participants walked in baseline at their comfortable speeds. They then walked and responded to what was presented in gait adaptability tests which included 40 trials with four random conditions: step shortening, step lengthening, obstacle avoiding, and walking through. Virtual step length targets were 40% of the baseline step length longer or shorter than the mean baseline step length; the actual obstacle was a 5-cm height across the walkway. A Vicon three-dimensional motion capture system and four A.M.T.I force plates were used to quantify spatiotemporal parameters of a gait cycle and sagittal foot adjustment errors (differences between desired and actual responses in the second step of the gait cycle). Analyses of variance (ANOVA) repeated measured tests were used to investigate group and condition effects on dependent gait parameters at a significance level of 0.05.ResultsStatistical analyses of Group I (n = 16), Group II (n = 14) and Group III (n = 13) revealed that gait parameters did not differ between groups in baseline. However, they were significantly different in adaptability tests. Group III significantly increased their stance and double support times in adaptability tests, but these adaptations did not improve their foot adjustments. They had the greatest step length errors and the lowest toe-obstacle clearance which might cause them to touch the obstacle the most.SignificanceThe presented gait adaptability tests may serve as entry tests for falls prevention programs.
Persistence of the ecological niche in pond damselflies underlies a stable adaptive zone despite varying selection
Authors: Gupta Anjali , Svensson Erik I. , Frietsch Henrik , Tsuboi Masahito 
Published: October 2022

AbstractFollowing the development of regression-based methods to estimate natural and sexual selection, evolutionary biologists have quantified the strength, mode and direction of selection in natural populations. Although this approach has been successful, its limitations include lack of replication across species, compromising the generality of the inferences beyond microevolutionary time scales. Here, we carried out a comparative study of selection on wing shape and body size across multiple populations of two closely related and ecologically similar pond damselflies:Enallagma cyathigerumandIschnura elegans(Odonata: Coenagrionidae). We found weak stabilizing selection on wing shape in both sexes, and no evidence that selection on this trait differed between the species. In contrast, selection on body size was curvilinear in males and directional in females, and they differed in form (males) and intensity (females) between these two species. By analyzing selection on the fine-grained spatial scale, we found that selection on male body size was shaped by the local mating system, and the relationship between mating system characteristics and directional selection was remarkably consistent across these species. Finally, we present a graphical model that links contemporary selection and macroevolution. Based on this model, we conclude that the persistence in ecological modes of life in pond damselflies offers a plausible explanation for why varying selection in nature may still result in a stable adaptive zone lasting millions of years.
GrapHiC: An integrative graph based approach for imputing missing Hi-C reads
Authors: Murtaza Ghulam , Wagner Justin , Zook Justin M. , Singh Ritambhara 
Published: October 2022

AbstractHi-C experiments allow researchers to study and understand the 3D genome organization and its regulatory function. Unfortunately, sequencing costs and technical constraints severely restrict access to high-quality Hi-C data for many cell types. Existing frameworks rely on a sparse Hi-C dataset or cheaper-to-acquire ChIP-seq data to predict Hi-C contact maps with high read coverage. However, these methods fail to generalize to sparse or cross-cell-type inputs because they do not account for the contributions of epigenomic features or the impact of the structural neighborhood in predicting Hi-C reads. We propose GrapHiC, which combines Hi-C and ChIP-seq in a graph representation, allowing more accurate embedding of structural and epigenomic features. Each node represents a binned genomic region, and we assign edge weights using the observed Hi-C reads. Additionally, we embed ChIP-seq and relative positional information as node attributes, allowing our representation to capture structural neighborhoods and the contributions of proteins and their modifications for predicting Hi-C reads. Our evaluations show that GrapHiC generalizes better than the current state-of-the-art on cross-cell-type settings and sparse Hi-C inputs. Moreover, we can utilize our framework to impute Hi-C reads even when no Hi-C contact map is available, thus making high-quality Hi-C data more accessible for many cell types.Availabilityhttps://github.com/rsinghlab/GrapHiCACM Reference FormatGhulam Murtaza, Justin Wagner, Justin M. Zook, and Ritambhara Singh. 2018. GrapHiC: An integrative graph based approach for imputing missing Hi-C reads. InProceedings of 22nd International Workshop on Data Mining in Bioinformatics (BioKDD ‘23). ACM, New York, NY, USA, 16 pages. https://doi.org/XXXXXXX.XXXXXXX
Targeted Vibration-Induced Necrosis in Cancer Cells using Paramagnetic Microrobots
Authors: Mallick Sudipta , Sokolich Max , Rivas David , Das Sambeeta 
Published: October 2022

AbstractTherapeutic delivery of anti-cancer drugs is a major goal of modern medicine. In particular, microrobots (MRs) have recently been studied for their ability to navigate difficult-to-reach regions in the human body to deliver therapeutics for microscopically localized interventions. However, the control of individual and swarms of MRs to precisely target localized cellular regions remains a significant challenge, preventing their applications as delivery systems in cancer research. In this study, magnetic MRs were used to target cancer cells and create localized magnetic oscillations which resulted in magnetolysis of cancer cells. The magnetic MRs were selectively steered towards Hepatocarcinoma cells (HepG2 cells) using our custom-built magnetic controller under a rotating magnetic field at different frequencies. After internalization of the microrobots by cancer cells, magnetic oscillation of varying dosages was applied to disrupt the internal structure of cancer cells which leads to subsequent cell death.
Associations of microbial diversity with age and other clinical variables among pediatric chronic rhinosinusitis (CRS) patients
Authors: Lim Shen Jean , Jithpratuck Warit , Wasylik Kathleen , Sriaroon Panida , Dishaw Larry J. 
Published: October 2022

AbstractChronic rhinosinusitis (CRS) is a heterogenous disease that causes persistent paranasal sinus inflammation in children. Microorganisms are thought to contribute to the etiology and progression of CRS. Culture-independent microbiome analysis offers deeper insights on sinonasal microbial diversity and microbe-disease associations than culture-based methods. To date, CRS-related microbiome studies have mostly focused on the adult population, and only one study has characterized the pediatric CRS microbiome. In this study, we analyzed the bacterial diversity of adenoid tissue, adenoid swab, maxillary sinus, and sinus wash samples from 45 pediatric CRS patients recruited from the Johns Hopkins All Children’s Hospital (JHACH) in St Petersburg, FL, USA. The alpha diversity in these samples was associated with baseline nasal steroid use, leukotriene receptor antagonist (LTRA) use, and total serum immunoglobulin (Ig) E (IgE) level.Streptococcus, Moraxella, andHaemophilusspp. were most frequently identified from sinus cultures and the sequenced 16S rRNA gene content. Comparative analyses combining our samples with the samples from the previous microbiome study revealed differentially abundant genera between patients with pediatric CRS and healthy controls, includingCutibacteriumandMoraxella. Additionally, the abundances ofStreptobacillusandStaphylococcuswere consistently correlated with age in both adenoid- and sinus-derived samples. Our study uncovers new associations of alpha diversity with clinical parameters, as well as associations of specific genera with disease status and age, that can be further investigated.
Bayesian linear models with unknown design over finite alphabets
Authors: Wang Yuexuan , Futschik Andreas , Dutta Ritabrata 
Published: October 2022

AbstractOur topic is the reconstruction of the unknown matricesSandωfor the multivariate linear modelY=Sω+εunder the assumption that the entries ofSare drawn from the finite alphabet 𝔄 = 0, 1 andωis a weight matrix. While a frequentist method has recently been proposed for this purpose, a Bayesian approach seems also desirable. We therefore provide a new hierarchical Bayesian method for this inferential task. Our approach provides estimates of the posterior that may be used to quantify uncertainty. Since matching permutations in bothSandωlead to the same reconstructionSω, we introduce an order-preserving shrinkage prior to establish identifiability with respect to permutations.
Revisiting Macromolecular Hydration with HullRadSAS
Authors: Fleming Patrick J. , Correia John J. , Fleming Karen G. 
Published: October 2022

AbstractHydration of biological macromolecules is important for their stability and function. Historically, attempts have been made to describe the degree of macromolecular hydration using a single parameter over a narrow range of values. Here, we describe a method to calculate two types of hydration: surface shell water and entrained water. A consideration of these two types of hydration helps to explain the “hydration problem” in hydrodynamics. The combination of these two types of hydration allows accurate calculation of hydrodynamic volume and related macromolecular properties such as sedimentation and diffusion coefficients, intrinsic viscosities, and the concentration dependent non-ideality identified with sedimentation velocity experiments.
Glutarate regulates T cell function and metabolism
Authors: Minogue Eleanor , Cunha Pedro P. , Quaranta Alessandro , Zurita Javier , Teli Shiv Sah , Wadsworth Brennan J. , Hughes Rob , Grice Guinevere L. , Velica Pedro , Bargiela David , Barbieri Laura , Wheelock Craig E. , Nathan James A. , Koivunen Peppi , Foskolou Iosifina P. , Johnson Randall S. 
Published: October 2022

AbstractT cell function is influenced by several metabolites; some acting through enzymatic inhibition of α-KG-dependent dioxygenases (αKGDDs), others, through post-translational modification of lysines in important targets. We show here that glutarate, a product of amino acid catabolism, has the capacity to do both, with effects on T cell function and differentiation. Glutarate exerts those effects through αKGDD inhibition and through direct regulation of T cell metabolism via post-translational modification of the pyruvate dehydrogenase E2 subunit. Diethyl-glutarate, a cell-permeable form of glutarate, alters CD8+T cell differentiation and increases cytotoxicity against target cells.In vivoadministration of the compound reduces tumor growth and is correlated with increased levels of both peripheral and intratumoral cytotoxic CD8+T cells. These results demonstrate that glutarate regulates both T cell metabolism and differentiation, with a potential role in the improvement of T cell immunotherapy.
DGH-GO: Dissecting the Genetic Heterogeneity of complex diseases using Gene Ontology
Authors: Asif M , Martiniano Hugo F. , Lamurias Andre , Kausar Samina , Couto Francisco M. 
Published: October 2022

AbstractComplex diseases such as neurodevelopmental disorders (NDDs) lack biological markers for their diagnosis and are phenotypically heterogeneous, which makes them difficult to diagnose at early-age. The genetic heterogeneity corresponds to their clinical phenotype variability and, because of this, complex diseases exhibit multiple etiologies. The multi-etiological aspects of complex-diseases emerge from distinct but functionally similar group of genes. Different diseases sharing genes of such groups show related clinical outcomes that further restrict our understanding of disease mechanisms, thus, limiting the applications of personalized medicine or systems biomedicine approaches to complex genetic disorders.Here, we present an interactive and user-friendly application, DGH-GO that allows biologists to dissect the genetic heterogeneity of complex diseases by stratifying the putative disease-causing genes into clusters that may lead to or contribute to a specific disease traits development. The application can also be used to study the shared etiology of complex-diseases.DGH-GO creates a semantic similarity matrix of putative disease-causing genes or known-disease genes for multiple disorders using Gene Ontology (GO). The resultant matrix can be visualized in a 2D space using different dimension reduction methods (T-SNE, Principal component analysis and Principal coordinate analysis). Functional similarities assessed through GO and semantic similarity measure can be used to identify clusters of functionally similar genes that may generate a disease specific traits. This can be achieved by employing four different clustering methods (K-means, Hierarchical, Fuzzy and PAM). The user may change the clustering parameters and see their effect on stratification results immediately.DGH-GO was applied to genes disrupted by rare genetic variants in Autism Spectrum Disorder (ASD) patients. The analysis confirmed the multi-etiological nature of ASD by identifying the four clusters that were enriched for distinct biological mechanisms and phenotypic terms. In the second case study, the analysis of genes shared by different NDDs showed that genes involving in multiple disorders tend to aggregate in similar clusters, indicating a possible shared etiology. In summary, functional similarities, dimension reduction and clustering methods, coupled with interactive visualization and control over analysis allows biologists to explore and analyze their datasets without requiring expert knowledge on these methods.The source code of proposed application is available athttps://github.com/Muh-Asif/DGH-GOGraphical abstract
Structure and mechanics of the human Nuclear Pore Complex basket
Authors: Vial Anthony , Costa Luca , Dosset Patrice , Rosso Pietro , Boutières Gaëlle , Faklaris Orestis , Haschke Heiko , Milhiet Pierre-Emmanuel , Doucet Christine M. 
Published: October 2022

AbstractNuclear pore complexes (NPCs) are the only gateways between the nucleus and cytoplasm in eukaryotic cells. They restrict free diffusion to molecules below 5 nm while facilitating the active transport of selected cargoes, sometimes as large as the pore itself. This versatility implies an important pore plasticity. Recently, cryo-EM and AI-based protein modeling revealed with acute precision how most NPC constituents are arranged. But the basket, a fish trap-like structure capping the nucleoplasmic side of the pore, remains the missing piece in this puzzle. Here by Atomic Force Microscopy (AFM) coupled to Single Molecule Localization Microscopy (SMLM) we revealed that the basket is very soft and explores a large conformational landscape: apart from its canonical shape, it dives into the central pore channel or opens, with filaments reaching to the pore sides. Our observations enlighten how this structure can adapt and let morphologically diverse cargoes shuttling through NPCs.
Intra-V1 functional networks predict observed stimuli
Authors: Ontivero-Ortega Marlis , Iglesias-Fuster Jorge , Perez-Hidalgo Jhoanna , Marinazzo Daniele , Valdes-Sosa Mitchell , Valdes-Sosa Pedro 
Published: October 2022

AbstractSeveral studies suggest that the pattern of co-fluctuations of neural activity within V1 (measured with fMRI) changes with variations in attention/perceptual organization of observed stimuli. Here we used multivariate pattern analysis of intra-V1 correlation matrices to predict the level and shape of the observed Navon letters. We examined the inter-individual stability of network topologies and then tested if they contained intra-individual information about stimulus shape or level that was tolerant to changes in the irrelevant feature. The inter-individual classification was accurate for all specific level and letter-shape tests. These results indicate that the association of V1 topologies and perceptual states is stable across participants. Intra-participant cross-classification of level (ignoring shape) was accurate but failed for shape (ignoring level). Cross-classification of stimulus level was more accurate when the stimulus-evoked response was suppressed in the fMRI time series and not present for correlations based on raw time series, stimulus-evoked beta-series, or simulations of the effects of eye movements measured in a control group. Furthermore, cross-classification weight maps evinced asymmetries of link strengths across the visual field that mirrored perceptual asymmetries. We hypothesize that feedback about level information drives the intra-V1 networks based on fMRI background activity. These intra-V1 networks can shed light on the neural basis of attention and perceptual organization.
Cell Surface-localized CsgF Condensate is a Gatekeeper in Bacterial Curli Subunit Secretion
Authors: Swasthi Hema M. , Basalla Joseph L. , Dudley Claire E. , Vecchiarelli Anthony G. , Chapman Matthew R. 
Published: October 2022

AbstractCurli are functional amyloids present on the outer membrane ofE. coli. Cell-surface aggregation of CsgA, the major subunit of curli, is a well-orchestrated process. CsgB, the minor subunit of curli, nucleates the aggregation of CsgA while CsgF, a curli accessory protein, ensures proper anchoring of CsgB to the cell surface. The molecular basis of the interactions between CsgF and curli subunits is unclear. Here, we show that CsgF undergoes phase separationin vitroand that the ability of CsgF variants to phase separate tightly correlated with CsgF function in cells during curli biogenesis. Substitution of phenylalanine residues in the CsgF N-terminus both reduced the propensity of CsgF to phase-separate and impaired curli biogenesis. Exogenous addition of purified CsgF complementedcsgF−cells. This exogenous addition assay was used to assess the ability of CsgF variants to complementcsgF−cells. The presence of CsgF on the cell surface modulated the secretion of CsgA to the cell surface. We also found that the CsgB nucleator protein is a CsgF client. CsgB can form SDS-insoluble aggregates within the dynamic CsgF condensate, and we propose that these multi-component CsgF-B condensates form a nucleation-competent complex that templates CsgA amyloid formation on the cell surface. Together, our study provides insight into the ability of CsgF to phase separate, regulate CsgA secretion, and promote CsgB aggregation in curli assembly.
Comparison of the risk of hospitalisation among BA.1 and BA.2 COVID-19 cases treated with Sotrovimab in the community in England
Authors: Harman Katie , Nash Sophie G , Webster Harriet H , Groves Natalie , Hardstaff Jo , Bridgen Jessica , Blomquist Paula B , Hope Russell , Ashano Efejiro , Myers Richard , Rokadiya Sakib , Hopkins Susan , Brown Colin S , Chand Meera , Dabrera Gavin , Thelwall Simon 
Published: October 2022

AbstractObjectivesSotrovimab is one of several therapeutic agents that have been licensed to treat people at risk of severe outcomes following COVID-19 infection. However, there are concerns that it has reduced efficacy to treat people with the BA.2 sub-lineage of the Omicron (B.1.1.529) SARS-CoV-2 variant. We compared individuals with the BA.1 or BA.2 sub-lineage of the Omicron variant treated Sotrovimab in the community to assess their risk of hospital admission.MethodsWe performed a retrospective cohort study of individuals treated with Sotrovimab in the community and either had BA.1 or BA.2 variant classification.ResultsUsing a Stratified Cox regression model it was estimated that the hazard ratios (HR) of hospital admission with a length of stay of two or more days was 1.17 for BA.2 compared to BA.1 (95% CI 0.74-1.86) and for such admissions where COVID-19 ICD-10 codes was recorded the HR was 0.98 (95% CI 0.58-1.65).ConclusionThese results suggest that the risk of hospital admission is similar between BA.1 and BA.2 cases treated with Sotrovimab in the community.
Exploring the Gut-Brain Connection in Gastroparesis with Autonomic and Gastric Myoelectric Monitoring
Authors: Subramanian Sandya , Kunkel David C. , Nguyen Linda , Coleman Todd P. 
Published: October 2022

AbstractObjectiveThe goal of this study was to identify autonomic and gastric myoelectric biomarkers from throughout the day that differentiate patients with gastroparesis, diabetics without gastroparesis, and healthy controls, while providing insight into etiology.MethodsWe collected 19 24-hour recordings of electrocardiogram (ECG) and electrogastrogram (EGG) data from healthy controls and patients with diabetic or idiopathic gastroparesis. We used physiologically and statistically rigorous models to extract autonomic and gastric myoelectric information from the ECG and EGG data respectively. From these, we constructed quantitative indices which differentiated the different groups and demonstrated their application in automatic classification paradigms and as quantitative summary scores.ResultsWe identified several differentiators that separate healthy controls from gastroparetic patient groups, specifically around sleep and meals. We also demonstrated the downstream utility of these differentiators in automatic classification and quantitative scoring paradigms. Even with this small pilot dataset, automated classifiers achieved an accuracy of 79% separating autonomic phenotypes and 65% separating gastrointestinal phenotypes. We also achieved 89% accuracy separating controls from gastroparetic patients in general and 90% accuracy separating diabetics with and without gastroparesis. These differentiators also suggested varying etiologies for different phenotypes.ConclusionThe differentiators we identified were able to successfully distinguish between several autonomic and gastrointestinal (GI) phenotypes using data collected while at-home with non-invasive sensors.SignificanceAutonomic and gastric myoelectric differentiators, obtained using at-home recording of fully non-invasive signals, can be the first step towards dynamic quantitative markers to track severity, disease progression, and treatment response for combined autonomic and GI phenotypes.