bluuebunny/crossref_metadata_2025_split huggingface dataset:
FRISTS: Interpretable Time Series-Based Heart Failure Risk Prediction
Authors: Lin Sophia , Dong Xinyu , Wang Fusheng 
Published: December 2023

AbstractHeart failure is an incurable medical condition that affects millions of people globally. Developing prediction models is crucial to prevent patients from progressing to heart failure. Current heart failure prediction models struggle with achieving interpretability, a mandatory trait that allows the model to be applied in healthcare, while possessing high real-world accuracy. We introduce FRISTS, a novel HF prediction approach leveraging sequential times series-based modeling, such as long short-term memory (LSTM) networks, and feature selection. Our study utilized an extensive electronic health record (EHR) database and found that FRISTS outperformed traditional AI models (e.g., Random Forest Classifier, Logistic Regression, and Decision Tree) and more complex machine learning techniques (e.g., XGBoost, LSTM), yielding an average F1 score of 0.805 and receiver operating characteristic area under the curve (ROC AUC) value of 0.990. Our SHAP-inspired permutation method enables interpretation of the feature ranking, enhancing the result transparency and paving the way for a new class of interpretable models. This approach holds promise in enhancing clinical decision-making and patient care in the context of heart failure prevention.
Is metacarpophalangeal joint restriction an indicator of blood pressure?
Authors: Shah Rohan , Phatak Sanat , Jadhav Sarita , Bhalerao Aboli , Mehra Shreya , Dhadge Smita , Ingram Jennifer , Yajnik Chittaranjan 
Published: December 2023

AbstractArterial wall stiffness is implicated in the etiopathogenesis of hypertension, reflecting medial stiffness and atherosclerotic plaques. In individuals with diabetes, musculoskeletal phenotypes like limited joint mobility (LJM) in the hands suggests soft tissue fibrosis and could mirror internal organ fibrosis including arterial stiffness.In Quantifying hand stiffness, mean extension at the metacarpophalangeal (MCP) joint emerges as a promising metric. In a type 1 diabetes cohort, this correlated with structural fibrotic changes on MRI. The study introduces a clinically scalable methodology for measuring joint stiffness, with implications for community screening programs for hypertension.In an ongoing study with 1885 participants, MCP extension showed a significant association with SBP (p <0.001). Linear regression, adjusted for age, gender, and diabetes status, reveals a negative correlation between average MCP extension and SBP. These pilot findings support earlier associations with an easier methodology. Future work involves establishing cutoffs in mean MCP extension for optimized screening algorithms, considering potential confounders like physical activity.
Effects of interval treadmill training on spatiotemporal parameters in children with cerebral palsy: a machine learning approach
Authors: Caskey Charlotte D. , Shrivastav Siddhi R. , Spomer Alyssa M. , Bjornson Kristie F. , Roge Desiree , Moritz Chet T. , Steele Katherine M. 
Published: December 2023

AbstractBackgroundChildren with cerebral palsy (CP) have reduced step length, reduced symmetry, and greater step width compared to their peers. Short-burst interval locomotor treadmill training (SBLTT) is a novel rehabilitation paradigm for children with CP that may improve spatiotemporal outcomes. However, for interventions like SBLTT, quantifying rehabilitation responses and optimizing therapy parameters remains challenging. Machine learning and causal modeling provide a platform to quantify step-by-step changes during gait training to understand mechanisms driving individual responses.Research questionWhat is the direct effect of SBLTT on step length, asymmetry, and step width in children with CP?MethodsWe recruited four children with spastic CP, ages 4-13. Each participant received 24 sessions of SBLTT over 8-12 weeks, with spatiotemporal outcomes monitored with an instrumented treadmill. We used Bayesian Additive Regression Trees (BART) to model the direct effect of therapy parameters on step length, step length asymmetry, and step width. Additionally, we generatedin silicodata for 150 virtual participants to quantify the quality of BART models to capture rehabilitation progression.ResultsAfter SBLTT, participants’ step lengths increased by 26 ± 13% (pre-post effect). Controlling for treadmill speed, time in session, limb, and treadmill incline with BART demonstrated that SBLTT directly increased step length for three participants (direct effect: 13.5 ± 4.5%), while one participant decreased step length (−11.6%). SBLTT had minimal effects on step length asymmetry and step width. Virtual datasets demonstrated that BART could accurately predict step length progression (R2= 0.73) and plateaus in progression (R2= 0.87), with better model fit for participants with less step-to-step variability.SignificanceTools such as BART can leverage step-by-step data collected during gait training to monitor progression and optimize rehabilitation protocols. This work can help personalize rehabilitation and understand the causal mechanisms driving individual responses.
A 17-month longitudinal environmental sampling study carried out on public transport vehicles operating in England during the COVID-19 pandemic identified low levels of SARS-CoV-2 RNA contamination
Authors: Aranega-Bou Paz , Pottage Thomas , Fenwick Abigail , D’Costa Wilhemina , Brown Natalie F. , Yaxley Nicola , King Marco-Felipe , Parker Simon T. , Miller Daniel , López-García Martín , Noakes Catherine J. , Moore Ginny , Bennett Allan 
Published: December 2023

AbstractAimsTo monitor severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA contamination in vehicles operating in England during the pandemic, to better understand transmission risk of SARS-CoV-2 on public transport.Methods and ResultsWe collected 1,314 surface samples between December 2020 and April 2022 on trains and buses managed by five different transport operators. The presence of SARS-CoV-2 RNA was investigated through reverse transcription polymerase chain reaction (RT-PCR). SARS-CoV-2 RNA was found on 197 (15%) of the 1,314 surfaces sampled, including seat head rests, handholds, and air extract grilles, but the levels of RNA recovered on those samples (median value of 23.4, inter-quartile range: 14.3-35.4,Ngene copies per extraction) made the presence of infectious virus at the time of sampling extremely unlikely. However, detection rates varied over time with peaks broadly coinciding with times of high community transmission, suggesting that people infected with SARS-CoV-2 when travelling on public transport could create opportunities for transmission.ConclusionDuring the pandemic, and as in other public spaces, low levels of SARS-CoV-2 RNA were found on surfaces associated with public transport.Impact statementThe results of this study will inform modelling approaches and the implementation of mitigation strategies to minimise the risk of transmission of respiratory viruses in public transport.
Age- and disease severity-associated changes in the nasopharyngeal microbiota of COVID-19 patients
Authors: Pérez-Sanz Fernando , Tyrkalska Sylwia D. , Álvarez-Santacruz Carmen , Moreno-Docón Antonio , Mulero Victoriano , Cayuela María L. , Candel Sergio 
Published: December 2023

ABSTRACTDysbiosis has been linked to the pathogenesis of multiple diseases. Although dozens of publications have associated changes in the nasopharyngeal microbiota to patient’s susceptibility to COVID-19, results from these studies are highly variable and contradictory in many cases. Addressing the limitations in previous research responsible for that variability, this study uses 16S rRNA gene sequencing to analyse the nasopharyngeal microbiota of 395 subjects, 117 uninfected controls and 278 COVID-19 patients, of different age groups that cover the entire lifespan and across varying disease severities. Importantly, our results reveal that bacterial diversity decreases progressively throughout life but only in severely ill COVID-19 patients, in whose nasopharynx, moreover, the opportunistic pathogen bacterial generaStaphylococcus,Corynebacterium,Streptococcus,Prevotella,Acinetobacter, andPseudomonasare overrepresented. Notably,Scardovia wiggsiaeappears only in severe COVID-19 patients over 60 years of age, suggesting a potential utility of this bacterial species as a COVID-19 severity biomarker in the elderly, who are the most susceptible individuals to suffer from serious forms of the disease and the age group that presents more differences in comparison with the other age groups according to the majority of the parameters analysed in this study. Our results provide valuable insights into age-associated dynamics within nasopharyngeal microbiota during severe COVID-19, offering potential avenues for further exploration and therapeutic interventions.
Gazing Down Has benefits Unrelated To Visual Input
Authors: Koren Yogev , Goldhamer Noy , Shmuelof Lior , Bar-Haim Simona 
Published: December 2023

AbstractRecent reports have revealed that downward gazing enhances postural control. The mechanism underlying this phenomenon is currently unknown, yet there are several plausible explanations. In this study, we attempt to provide evidence to support the hypothesis that this effect is primarily derived from altered visual flow caused by gazing down.To this end, we quantified standing postural sway of 20 healthy participants and 20 people with stroke who were instructed to stand as still as possible under different conditions: while gazing forward and gazing down, with their eyes open and eyes closed.Both the horizontal gaze angle and the lack of visual input had a negative effect on participants’ ability to attenuate their body sway. Yet, the effect of gaze angle was constant regardless of the presence or absence of visual input. Also, people with stroke swayed more than their healthy counterparts and were more sensitive to the effect of gaze angle, but not to that of visual input.The results of this study indicate that downward gazing enhances postural control even in the absence of visual input and do not support our main hypothesis. Also, it seems that the effect of downward gazing on postural control is greater in unstable people (people with stroke) than that observed in healthy adults, which might explain less stable individuals’ tendency to gaze down while walking. Furthermore, these results might suggest that downward gazing behavior does not necessarily indicate an attempt to acquire visual information of any kind but instead serves to modulate some other sensory input helpful for postural control.
Rare disease gene association discovery from burden analysis of the 100,000 Genomes Project data
Authors: Cipriani Valentina , Vestito Letizia , Magavern Emma F , Jacobsen Julius OB , Arno Gavin , Behr Elijah R , Benson Katherine A , Bertoli Marta , Bockenhauer Detlef , Bowl Michael R , Burley Kate , Chan Li F , Chinnery Patrick , Conlon Peter , Costa Marcos , Davidson Alice E , Dawson Sally J , Elhassan Elhussein , Flanagan Sarah E , Futema Marta , Gale Daniel P , García-Ruiz Sonia , Corcia Cecilia Gonzalez , Griffin Helen R , Hambleton Sophie , Hicks Amy R , Houlden Henry , Houlston Richard S , Howles Sarah A , Kleta Robert , Lekkerkerker Iris , Lin Siying , Liskova Petra , Mitchison Hannah , Morsy Heba , Mumford Andrew D , Newman William G , Neatu Ruxandra , O’Toole Edel A , Ong Albert CM , Pagnamenta Alistair T , Rahman Shamima , Rajan Neil , Robinson Peter N , Ryten Mina , Sadeghi-Alavijeh Omid , Sayer John A , Shovlin Claire L , Taylor Jenny C , Teltsh Omri , Tomlinson Ian , Tucci Arianna , Turnbull Clare , van Eerde Albertien M , Ware James S , Watts Laura M , Webster Andrew R , Westbury Sarah K , Zheng Sean L , Caulfield Mark , Smedley Damian 
Published: December 2023

AbstractTo discover rare disease-gene associations, we developed a gene burden analytical framework and applied it to rare, protein-coding variants from whole genome sequencing of 35,008 cases with rare diseases and their family members recruited to the 100,000 Genomes Project (100KGP). Followingin silicotriaging of the results, 88 novel associations were identified including 38 with existing experimental evidence. We have published the confirmation of one of these associations, hereditary ataxia withUCHL1, and independent confirmatory evidence has recently been published for four more. We highlight a further seven compelling associations: hypertrophic cardiomyopathy withDYSFandSLC4A3where both genes show high/specific heart expression and existing associations to skeletal dystrophies or short QT syndrome respectively; monogenic diabetes withUNC13Awith a known role in the regulation of β cells and a mouse model with impaired glucose tolerance; epilepsy withKCNQ1where a mouse model shows seizures and the existing long QT syndrome association may be linked; early onset Parkinson’s disease withRYR1with existing links to tremor pathophysiology and a mouse model with neurological phenotypes; anterior segment ocular abnormalities associated withPOMKshowing expression in corneal cells and with a zebrafish model with developmental ocular abnormalities; and cystic kidney disease withCOL4A3showing high renal expression and prior evidence for a digenic or modifying role in renal disease. Confirmation of all 88 associations would lead to potential diagnoses in 456 molecularly undiagnosed cases within the 100KGP, as well as other rare disease patients worldwide, highlighting the clinical impact of a large-scale statistical approach to rare disease gene discovery.
Heat stress-induced heat shock protein 70 (HSP70) expressions among vulnerable populations in urban and rural areas Klang Valley, Malaysia
Authors: Muhamad Siti Nurfahirah , Akim Abdah Md , Lim Fang Lee , Mohd Shabri Nur Shabrina Azreen , How Vivien 
Published: December 2023

AbstractAs climate change raises global temperatures, there remains a notable gap in understanding the body’s mechanism of the heat stress defense exhibited by Heat Shock Protein (HSP) within the populations. This study aims to evaluate the expression of heat shock protein 70 (HSP70) in vulnerable populations living in urban and rural areas in response to heat exposure. A comparative cross-sectional study involved 54 urban and 54 rural participants from Klang Valley, Malaysia. This study comprises four methods: Part I involves conducting face-to-face interviews questionnaire; Part II involves monitoring indoor heat exposure and classifying thermal stress using the Universal Thermal Climate Index (UTCI); Part III involves using the reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and Part IV involves using the HSP70 High Sensitivity Enzyme-linked Immunosorbent Assay (ELISA). The findings revealed that urban areas have a higher heat level, classified as strong UTCI thermal stress (32.1°C), whereas rural areas have moderate UTCI thermal stress (31.0°C). In response to heat stress, the urban vulnerable populations exhibited higher HSP70 gene expression (0.167 ± 0.86) compared to the rural (0.154 ± 0.28). A significant difference (p<0.001) in HSP70 protein expression was observed in the plasma of urban compared to rural vulnerable populations. There was a strong association between UTCI heat exposure level and the expression of the HSP70 gene and protein in both vulnerable population groups (p<0.001). Although susceptible to vulnerabilities, the populations demonstrated HSP70 expressions in response to varying levels of heat exposure as a coping mechanism at the cellular level.
Neural Activity Shaping in Visual Prostheses with Deep Learning
Authors: Castro Domingos , Grayden David B. , Meffin Hamish , Spencer Martin 
Published: December 2023

AbstractObjectiveThe visual perception provided by retinal prostheses is poor and limited to images constructed of phosphenes generated by the electrodes. One limiting factor has been the conventional strategy used to encode the target image into a stimulation pattern. Under this strategy, if the electrode density is high, the current spread of neighbouring unipolar stimuli overlaps, leading to blurred images. Simultaneous multipolar stimulation guided by the measured neural responses can attenuate excessive spread of excitation and allows for a more precise electrical input to the retina. However, it is far from trivial to predict what multipolar stimulus pattern will elicit the desired retinal response for a given target image. Here, we propose to solve this problem using an Artificial Neural Network (ANN) that could be trained with data acquired from the implant itself.ApproachOur method consists of two ANNs trained sequentially. The Measurement Predictor Network (MPN) is trained on data from the implant and is used to predict how the retina responds to multipolar stimulation by learning the forward model. The Stimulus Generator Network (STG) is trained on a large dataset of natural images and uses the trained MPN to determine efficient multipolar stimulus patterns by learning the inverse model. We validate our methodin silicousing a realistic model of retinal response to multipolar stimulation.Main ResultsWe show that the simulated retinal activations elicited with our ANN-based approach are considerably sharper when compared with the conventional method used in existing devices. The SGN finds multipolar stimulation patterns that are tuned to a specific retina, thus providing patient-specific stimuli. Also, due to its small computational cost, the SGN can output stimulation patterns at a very high rate.SignificanceOur novel protocol opens the door to personalized multipolar retinal stimulation, which may improve the visual experience and quality of life of retinal prosthesis users.
Identification of a short, single site matriglycan that maintains neuromuscular function in the mouse
Authors: Yang Tiandi , Chandel Ishita , Gonzales Miguel , Okuma Hidehiko , Prouty Sally J. , Zarei Sanam , Joseph Soumya , Garringer Keith W. , Ocampo Landa Saul , Yonekawa Takahiro , Walimbe Ameya S. , Venzke David P. , Anderson Mary E. , Hord Jeffery M. , Campbell Kevin P. 
Published: December 2023

AbstractMatriglycan (−1,3-β-glucuronic acid-1,3-α-xylose-) is a polysaccharide that is synthesized on α-dystroglycan, where it functions as a high-affinity glycan receptor for extracellular proteins, such as laminin, perlecan and agrin, thus anchoring the plasma membrane to the extracellular matrix. This biological activity is closely associated with the size of matriglycan. Using high-resolution mass spectrometry and site-specific mutant mice, we show for the first time that matriglycan on the T317/T319 and T379 sites of α-dystroglycan are not identical. T379-linked matriglycan is shorter than the previously characterized T317/T319-linked matriglycan, although it maintains its laminin binding capacity. Transgenic mice with only the shorter T379-linked matriglycan exhibited mild embryonic lethality, but those that survived were healthy. The shorter T379-linked matriglycan exists in multiple tissues and maintains neuromuscular function in adult mice. In addition, the genetic transfer of α-dystroglycan carrying just the short matriglycan restored grip strength and protected skeletal muscle from eccentric contraction-induced damage in muscle-specific dystroglycan knock-out mice. Due to the effects that matriglycan imparts on the extracellular proteome and its ability to modulate cell-matrix interactions, our work suggests that differential regulation of matriglycan length in various tissues optimizes the extracellular environment for unique cell types.
Physiological constraints limiting the growth ofDrosophilalarvae
Authors: Schönborn Jürgen , Akhtar Irfan , Droste Andrea , Wesemann Stephanie , Beller Mathias 
Published: December 2023

AbstractThe phenotype of organisms is the result of complex interactions between physiology, developmental conditions, and intra-organismic processes, such as metabolism and genetic adaptation. Organisms pursue various developmental strategies that depend on factors such as available resources. How organisms regulate and control critical developmental principles is not fully understood. In this study, we investigated the dynamic development ofDrosophila melanogasterlarvae throughin vitroandin silicoexperiments. First, we enhanced the larval metabolic network FlySilico and its parameters using growth and metabolite measurements. Subsequently, we established a dynamic flux balance analysis approach and incorporated spatial physiological information from the larval gut to improve the prediction results. We successfully predicted larval growth on different media and developmental critical processes, such as the emergence of larval metamorphosis. This expands the ability to investigate and understand the process of the larval critical weight and, furthermore, the influence of critical developmental processes of multicellular organisms on metabolism. Thus, we present an approach to understand the development, metabolism, and the role of physiology in the development of multicellular organisms.Graphical Abstract
Tactile Adaptation to Orientation Produces a Robust Tilt Aftereffect and Exhibits Crossmodal Transfer When Tested in Vision
Authors: Wang Guandong , Alais David 
Published: December 2023

ABSTRACTOrientation processing is one of the most fundamental functions in both visual and somatosensory perception. Converging findings suggest that orientation processing in both modalities is closely linked: somatosensory neurons share a similar orientation organisation as visual neurons, and the visual cortex has been found to be heavily involved in tactile orientation perception. The tilt aftereffect (TAE) is a demonstration of orientation adaptation and is used widely in behavioural experiments to investigate orientation mechanisms in vision. By testing the classic TAE paradigm in both tactile and crossmodal orientation tasks between vision and touch we were able to show that tactile perception of orientation shows a very robust TAE, similar to its visual counterpart. We further show that orientation adaptation in touch transfers to produce a TAE when tested in vision, but not vice versa. We also observed a similar asymmetricity in the intramodal serial dependence effect within the test sequence. These findings provide concrete evidence that vision and touch engage a similar orientation processing mechanism, but the asymmetry in the crossmodal transfer of TAE and serial dependence provides more insights into the underlying mechanism of this link.