bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning
Authors: Vitsios Dimitrios , Dhindsa Ryan S. , Middleton Lawrence , Gussow Ayal B. , Petrovski Slavé 
Published: March 2021

AbstractElucidating functionality in non-coding regions is a key challenge in human genomics. It has been shown that intolerance to variation of coding and proximal non-coding sequence is a strong predictor of human disease relevance. Here, we integrate intolerance to variation, functional genomic annotations and primary genomic sequence to build JARVIS: a comprehensive deep learning model to prioritize non-coding regions, outperforming other human lineage-specific scores. Despite being agnostic to evolutionary conservation, JARVIS performs comparably or outperforms conservation-based scores in classifying pathogenic single-nucleotide and structural variants. In constructing JARVIS, we introduce the genome-wide residual variation intolerance score (gwRVIS), applying a sliding-window approach to whole genome sequencing data from 62,784 individuals. gwRVIS distinguishes Mendelian disease genes from more tolerant CCDS regions and highlights ultra-conserved non-coding elements as the most intolerant regions in the human genome. Both JARVIS and gwRVIS capture previously inaccessible human-lineage constraint information and will enhance our understanding of the non-coding genome.
Oxidation inhibits autophagy protein deconjugation from phagosomes to sustain MHC class II restricted antigen presentation
Authors: Ligeon Laure-Anne , Pena-Francesch Maria , Vanoaica Liliana Danusia , Núñez Nicolás Gonzalo , Talwar Deepti , Dick Tobias P. , Münz Christian 
Published: March 2021

AbstractLC3-associated phagocytosis (LAP) contributes to a wide range of cellular processes and notably to immunity. The stabilization of phagosomes by the macroautophagy machinery in human macrophages can maintain antigen presentation on MHC class II molecules. However, the molecular mechanisms involved in the formation and maturation of the resulting LAPosomes are not completely understood. Here, we show that reactive oxygen species (ROS) produced by NADPH oxidase 2 (NOX2) stabilize LAPosomes by inhibiting LC3 deconjugation from the LAPosome cytosolic surface. NOX2 residing in the LAPosome membrane generates ROS to cause oxidative inactivation of the protease ATG4B, which otherwise releases LC3B from LAPosomes. An oxidation-insensitive ATG4B mutant compromises LAP and thereby impedes sustained MHC class II presentation of exogenousCandida albicansantigens. Redox regulation of ATG4B is thereby an important mechanism for maintaining LC3 decoration of LAPosomes to support antigen processing for MHC class II presentation.
Flexible thermoelectric generator with liquid metal interconnects and low thermal conductivity silicone filler
Authors: Padmanabhan Ramesh Viswanath , Sargolzaeiaval Yasaman , Neumann Taylor , Misra Veena , Vashaee Daryoosh , Dickey Michael D. , Ozturk Mehmet C. 
Published: March 2021

AbstractHarvesting body heat using thermoelectricity provides a promising path to realizing self-powered, wearable electronics that can achieve continuous, long-term, uninterrupted health monitoring. This paper reports a flexible thermoelectric generator (TEG) that provides efficient conversion of body heat to electrical energy. The device relies on a low thermal conductivity aerogel–silicone composite that secures and thermally isolates the individual semiconductor elements that are connected in series using stretchable eutectic gallium-indium (EGaIn) liquid metal interconnects. The composite consists of aerogel particulates mixed into polydimethylsiloxane (PDMS) providing as much as 50% reduction in the thermal conductivity of the silicone elastomer. Worn on the wrist, the flexible TEGs present output power density figures approaching 35 μWcm−2 at an air velocity of 1.2 ms−1, equivalent to walking speed. The results suggest that these flexible TEGs can serve as the main energy source for low-power wearable electronics.
How COVID-19 will boost remote exercise-based treatment in Parkinson’s disease: a narrative review
Authors: Langer Agnes , Gassner Lucia , Flotz Anna , Hasenauer Sebastian , Gruber Jakob , Wizany Laurenz , Pokan Rochus , Maetzler Walter , Zach Heidemarie 
Published: March 2021

AbstractThe lack of physical exercise during the COVID-19 pandemic-related quarantine measures is challenging, especially for patients with Parkinson’s disease (PD). Without regular exercise not only patients, but also nursing staff and physicians soon noticed a deterioration of motor and non-motor symptoms. Reduced functional mobility, increased falls, increased frailty, and decreased quality of life were identified as consequences of increased sedentary behavior. This work overviews the current literature on problems of supplying conventional physiotherapy and the potential of telerehabilitation, allied health services, and patient-initiated exercise for PD patients during the COVID-19 period. We discuss recent studies on approaches that can improve remote provision of exercise to patients, including telerehabilitation, motivational tools, apps, exergaming, and virtual reality (VR) exercise. Additionally, we provide a case report about a 69-year-old PD patient who took part in a 12-week guided climbing course for PD patients prior to the pandemic and found a solution to continue her climbing training independently with an outdoor rope ladder. This case can serve as a best practice example for non-instructed, creative, and patient-initiated exercise in the domestic environment in difficult times, as are the current. Overall, many recent studies on telemedicine, telerehabilitation, and patient-initiated exercises have been published, giving rise to optimism that facilitating remote exercise can help PD patients maintain physical mobility and emotional well-being, even in phases such as the COVID-19 pandemic. The pandemic itself may even boost the need to establish comprehensive and easy-to-do telerehabilitation programs.
A profile of a major trauma centre of North West England between 2011 and 2018
Authors: Lunevicius Raimundas , Mesri Mina 
Published: March 2021

AbstractThis study examined the trends and patterns of major trauma (MT) activities, causes, mortality and survival at the Aintree Major Trauma Centre (MTC), Liverpool, between 2011 and 2018. The number of trauma team activations (TTAs) rose sharply over time (n = 699 in 2013; n = 1522 in 2018). The proportion of TTAs that involved MT patients decreased from 75.1% in 2013 to 67.4% in 2018. The leading cause of MT was a fall from less than 2 m (36%). There has been a fivefold increase in the overall number of trauma procedures between 2011 and 2018. Orthopaedic surgeons have performed 80% of operations (n = 7732), followed by neurosurgeons, oral and maxillofacial surgeons, and general trauma surgeons. Both types of fall (> 2 m and < 2 m) and road traffic accidents were the three leading causes of death during the study period. The observed mortality rates exceeded that of expected rates in years 2012, 2014, 2016 and 2017. The all-cause observed to expected mortality ratio was 1.08 between 2012 and 2018. A change in care for MT patients was not directly associated with improved survival, although the marginally ascending trend line in survival rates between 2012 and 2018 reflects a gradual positive change.
Robust icephobic coating based on the spiky fluorinated Al2O3 particles
Authors: Starostin Anton , Strelnikov Vladimir , Valtsifer Viktor , Lebedeva Irina , Legchenkova Irina , Bormashenko Edward 
Published: March 2021

AbstractOmniphobic and icephobic twin-scale surfaces based on the “urchin”-like fluorinated Al2O3 particles are presented. Combined effect of hierarchical topography and fluorination supplied to the surfaces omniphobic and icephobic properties. The study of the stability of the Cassie wetting state is reported. High apparent contact angles were accompanied with the low contact angle hysteresis and high stability of the Cassie air trapping wetting state. Time delay of the ice crystallization as high as $$88\pm 5$$

88
±
5

min was established when compared to the ice formation on flat aluminum and non-fluorinated “urchin”-like surfaces. Crystallized water droplets formed on the reported nano-structured surfaces were easily blown out by the air jet with the velocity of $$v=3.0\pm 1.0$$

v
=
3.0
±
1.0

m/s, (which is markedly lower than that common for exploitation of aircrafts and turbines). Heated “urchin”-like surfaces completely restored their omniphobic and icephobic surfaces after thawing. Qualitative analysis of water freezing is supplied.
High genomic diversity of novel phages infecting the plant pathogen Ralstonia solanacearum, isolated in Mauritius and Reunion islands
Authors: Trotereau Angélina , Boyer Claudine , Bornard Isabelle , Pécheur Max Jean Bernard , Schouler Catherine , Torres-Barceló Clara 
Published: March 2021

AbstractBacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is among the most important plant diseases worldwide, severely affecting a high number of crops and ornamental plants in tropical regions. Only a limited number of phages infecting R. solanacearum have been isolated over the years, despite the importance of this bacterium and the associated plant disease. The antibacterial effect or morphological traits of these R. solanacearum viruses have been well studied, but not their genomic features, which need deeper consideration. This study reports the full genome of 23 new phages infecting RSSC isolated from agricultural samples collected in Mauritius and Reunion islands, particularly affected by this plant bacterial pathogen and considered biodiversity hotspots in the Southwest Indian Ocean. The complete genomic information and phylogenetic classification is provided, revealing high genetic diversity between them and weak similarities with previous related phages. The results support our proposal of 13 new species and seven new genera of R. solanacearum phages. Our findings highlight the wide prevalence of phages of RSSC in infected agricultural settings and the underlying genetic diversity. Discoveries of this kind lead more insight into the diversity of phages in general and to optimizing their use as biocontrol agents of bacterial diseases of plants in agriculture.
Impact of ambient sound on risk perception in humans: neuroeconomic investigations
Authors: Payzan-LeNestour Elise , Pradier Lionnel , Doran James , Nave Gideon , Balleine Bernard 
Published: March 2021

AbstractResearch in the field of multisensory perception shows that what we hear can influence what we see in a wide range of perceptual tasks. It is however unknown whether this extends to the visual perception of risk, despite the importance of the question in many applied domains where properly assessing risk is crucial, starting with financial trading. To fill this knowledge gap, we ran interviews with professional traders and conducted three laboratory studies using judgments of financial asset risk as a testbed. We provide evidence that the presence of ambient sound impacts risk perception, possibly due to the combination of facilitatory and synesthetic effects of general relevance to the perception of risk in many species as well as humans. We discuss the implications of our findings for various applied domains (e.g., financial, medical, and military decision-making), and raise new questions for future research.
Disruption of pathways regulated by Integrator complex in Galloway–Mowat syndrome due to WDR73 mutations
Authors: Tilley F. C. , Arrondel C. , Chhuon C. , Boisson M. , Cagnard N. , Parisot M. , Menara G. , Lefort N. , Guerrera I. C. , Bole-Feysot C. , Benmerah A. , Antignac C. , Mollet G. 
Published: March 2021

AbstractSeveral studies have reported WDR73 mutations to be causative of Galloway–Mowat syndrome, a rare disorder characterised by the association of neurological defects and renal-glomerular disease. In this study, we demonstrate interaction of WDR73 with the INTS9 and INTS11 components of Integrator, a large multiprotein complex with various roles in RNA metabolism and transcriptional control. We implicate WDR73 in two Integrator-regulated cellular pathways; namely, the processing of uridylate-rich small nuclear RNAs (UsnRNA), and mediating the transcriptional response to epidermal growth factor stimulation. We also show that WDR73 suppression leads to altered expression of genes encoding cell cycle regulatory proteins. Altogether, our results suggest that a range of cellular pathways are perturbed by WDR73 loss-of-function, and support the consensus that proper regulation of UsnRNA maturation, transcription initiation and cell cycle control are all critical in maintaining the health of post-mitotic cells such as glomerular podocytes and neurons, and preventing degenerative disease.
Clinical evidence of the role of Methanobrevibacter smithii in severe acute malnutrition
Authors: Camara Aminata , Konate Salimata , Tidjani Alou Maryam , Kodio Aly , Togo Amadou Hamidou , Cortaredona Sebastien , Henrissat Bernard , Thera Mahamadou Ali , Doumbo Ogobara K. , Raoult Didier , Million Matthieu 
Published: March 2021

AbstractGut microbial dysbiosis has been shown to be an instrumental factor in severe acute malnutrition (SAM) and particularly, the absence of Methanobrevibacter smithii, a key player in energy harvest. Nevertheless, it remains unknown whether this absence reflects an immaturity or a loss of the microbiota. In order to assess that, we performed a case–control study in Mali using a propensity score weighting approach. The presence of M. smithii was tested using quantitative PCR on faeces collected from SAM children at inclusion and at discharge when possible or at day 15 for controls. M. smithii was highly significantly associated with the absence of SAM, detected in 40.9% controls but only in 4.2% cases (p < 0.0001). The predictive positive value for detection of M. smithii gradually increased with age in controls while decreasing in cases. Among children providing two samples with a negative first sample, no SAM children became positive, while this proportion was 2/4 in controls (p = 0.0015). This data suggests that gut dysbiosis in SAM is not an immaturity but rather features a loss of M. smithii. The addition of M. smithii as a probiotic may thus represent an important addition to therapeutic approaches to restore gut symbiosis.
Disrupted metabolic connectivity in dopaminergic and cholinergic networks at different stages of dementia from 18F-FDG PET brain persistent homology network
Authors: Hsu Tun-Wei , Fuh Jong-Ling , Wang Da-Wei , Chen Li-Fen , Chang Chia-Jung , Huang Wen-Sheng , Wu Hsiu-Mei , Guo Wan-Yuo 
Published: March 2021

AbstractDementia is related to the cellular accumulation of β-amyloid plaques, tau aggregates, or α-synuclein aggregates, or to neurotransmitter deficiencies in the dopaminergic and cholinergic pathways. Cellular and neurochemical changes are both involved in dementia pathology. However, the role of dopaminergic and cholinergic networks in metabolic connectivity at different stages of dementia remains unclear. The altered network organisation of the human brain characteristic of many neuropsychiatric and neurodegenerative disorders can be detected using persistent homology network (PHN) analysis and algebraic topology. We used18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) imaging data to construct dopaminergic and cholinergic metabolism networks, and used PHN analysis to track the evolution of these networks in patients with different stages of dementia. The sums of the network distances revealed significant differences between the network connectivity evident in the Alzheimer’s disease and mild cognitive impairment cohorts. A larger distance between brain regions can indicate poorer efficiency in the integration of information. PHN analysis revealed the structural properties of and changes in the dopaminergic and cholinergic metabolism networks in patients with different stages of dementia at a range of thresholds. This method was thus able to identify dysregulation of dopaminergic and cholinergic networks in the pathology of dementia.
Key factors in a rigorous longitudinal image-based assessment of retinopathy of prematurity
Authors: Rosenblatt Tatiana R. , Ji Marco H. , Vail Daniel , Ludwig Cassie A. , Al-Moujahed Ahmad , Pasricha Malini Veerappan , Callaway Natalia F. , Kumm Jochen , Moshfeghi Darius M. 
Published: March 2021

AbstractTo describe a database of longitudinally graded telemedicine retinal images to be used as a comparator for future studies assessing grader recall bias and ability to detect typical progression (e.g. International Classification of Retinopathy of Prematurity (ICROP) stages) as well as incremental changes in retinopathy of prematurity (ROP). Cohort comprised of retinal images from 84 eyes of 42 patients who were sequentially screened for ROP over 6 consecutive weeks in a telemedicine program and then followed to vascular maturation or treatment, and then disease stabilization. De-identified retinal images across the 6 weekly exams (2520 total images) were graded by an ROP expert based on whether ROP had improved, worsened, or stayed the same compared to the prior week’s images, corresponding to an overall clinical “gestalt” score. Subsequently, we examined which parameters might have influenced the examiner’s ability to detect longitudinal change; images were graded by the same ROP expert by image view (central, inferior, nasal, superior, temporal) and by retinal components (vascular tortuosity, vascular dilation, stage, hemorrhage, vessel growth), again determining if each particular retinal component or ROP in each image view had improved, worsened, or stayed the same compared to the prior week’s images. Agreement between gestalt scores and view, component, and component by view scores was assessed using percent agreement, absolute agreement, and Cohen’s weighted kappa statistic to determine if any of the hypothesized image features correlated with the ability to predict ROP disease trajectory in patients. The central view showed substantial agreement with gestalt scores (κ = 0.63), with moderate agreement in the remaining views. Of retinal components, vascular tortuosity showed the most overall agreement with gestalt (κ = 0.42–0.61), with only slight to fair agreement for all other components. This is a well-defined ROP database graded by one expert in a real-world setting in a masked fashion that correlated with the actual (remote in time) exams and known outcomes. This provides a foundation for subsequent study of telemedicine’s ability to longitudinally assess ROP disease trajectory, as well as for potential artificial intelligence approaches to retinal image grading, in order to expand patient access to timely, accurate ROP screening.
Assessment of trunk flexion in arm reaching tasks with electromyography and smartphone accelerometry in healthy human subjects
Authors: Castillo-Escario Yolanda , Kumru Hatice , Valls-Solé Josep , García-Alen Loreto , Vidal Joan , Jané Raimon 
Published: March 2021

AbstractTrunk stability is essential to maintain upright posture and support functional movements. In this study, we aimed to characterize the muscle activity and movement patterns of trunk flexion during an arm reaching task in sitting healthy subjects and investigate whether trunk stability is affected by a startling acoustic stimulus (SAS). For these purposes, we calculated the electromyographic (EMG) onset latencies and amplitude parameters in 8 trunk, neck, and shoulder muscles, and the tilt angle and movement features from smartphone accelerometer signals recorded during trunk bending in 33 healthy volunteers. Two-way repeated measures ANOVAs were applied to examine the effects of SAS and target distance (15 cm vs 30 cm). We found that SAS markedly reduced the response time and EMG onset latencies of all muscles, without changing neither movement duration nor muscle recruitment pattern. Longer durations, higher tilt angles, and higher EMG amplitudes were observed at 30 cm compared to 15 cm. The accelerometer signals had a higher frequency content in SAS trials, suggesting reduced movement control. The proposed measures have helped to establish the trunk flexion pattern in arm reaching in healthy subjects, which could be useful for future objective assessment of trunk stability in patients with neurological affections.
People prefer joint outcome prosocial resource distribution towards future others
Authors: Inoue Yukako , Himichi Toshiyuki , Mifune Nobuhiro , Saijo Tatsuyoshi 
Published: March 2021

AbstractToday, developing and maintaining sustainable societies is becoming a notable social concern, and studies on altruism and prosociality toward future generations are increasing in importance. Although altruistic behaviors toward future generations have previously been observed in some experimental situations, it remains unknown whether prosocial preferences toward future others are based on equality or joint outcome orientations. In the present research, we exploratorily investigated preferences regarding resource distribution by manipulating the time points (i.e., present/future) of the participants and their imaginary partners. The results indicate that prosocial preference toward future others was as strong as that toward present others and seemed to be based on a joint outcome prosocial preference. Notably, when participants and their partners were at different time points, participants preferred to leave resources for the persons in the future. The findings indicate that the type of altruistic preference toward future others may differ from that toward present others, which is mainly equality.
Phenotypic and environmental correlates of natal dispersal in a long-lived territorial vulture
Authors: Serrano David , Cortés-Avizanda Ainara , Zuberogoitia Iñigo , Blanco Guillermo , Benítez José Ramón , Ponchon Cecile , Grande Juan Manuel , Ceballos Olga , Morant Jon , Arrondo Eneko , Zabala Jabi , Montelío Eugenio , Ávila Enrique , González José L. , Arroyo Bernardo , Frías Óscar , Kobierzycki Erick , Arenas Rafael , Tella José Luis , Donázar José Antonio 
Published: March 2021

AbstractNatal dispersal, the movement between the birth and the first breeding site, has been rarely studied in long-lived territorial birds with a long-lasting pre-breeding stage. Here we benefited from the long-term monitoring programs of six populations of Egyptian vultures (Neophron percnopterus) from Spain and France to study how the rearing environment determines dispersal. For 124 vultures, we recorded a median dispersal distance of 48 km (range 0–656 km). Linear models were used to assess the effect of population and individual traits on dispersal distance at two spatial scales. Dispersal distances were inversely related to vulture density in the natal population, suggesting that birds perceive the abundance of conspecifics as a signal of habitat quality. This was particularly true for declining populations, so increasing levels of opportunistic philopatry seemed to arise in high density contexts as a consequence of vacancies created by human-induced adult mortality. Females dispersed further than males, but males were more sensitive to the social environment, indicating different dispersal tactics. Both sexes were affected by different individual attributes simultaneously and interactively with this social context. These results highlight that complex phenotype-by-environment interactions should be considered for advancing our understanding of dispersal dynamics in long-lived organisms.