bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data
Authors: Yones Sara A. , Annett Alva , Stoll Patricia , Diamanti Klev , Holmfeldt Linda , Barrenäs Carl Fredrik , Meadows Jennifer R. S. , Komorowski Jan 
Published: May 2022

AbstractTranscriptomic analyses are commonly used to identify differentially expressed genes between patients and controls, or within individuals across disease courses. These methods, whilst effective, cannot encompass the combinatorial effects of genes driving disease. We applied rule-based machine learning (RBML) models and rule networks (RN) to an existing paediatric Systemic Lupus Erythematosus (SLE) blood expression dataset, with the goal of developing gene networks to separate low and high disease activity (DA1 and DA3). The resultant model had an 81% accuracy to distinguish between DA1 and DA3, with unsupervised hierarchical clustering revealing additional subgroups indicative of the immune axis involved or state of disease flare. These subgroups correlated with clinical variables, suggesting that the gene sets identified may further the understanding of gene networks that act in concert to drive disease progression. This included roles for genes (i) induced by interferons (IFI35 and OTOF), (ii) key to SLE cell types (KLRB1 encoding CD161), or (iii) with roles in autophagy and NF-κB pathway responses (CKAP4). As demonstrated here, RBML approaches have the potential to reveal novel gene patterns from within a heterogeneous disease, facilitating patient clinical and therapeutic stratification.
Modulation of the autophagic pathway inhibits HIV-1 infection in human lymphoid tissue cultured ex vivo
Authors: Pedreño-López Sònia , García Elisabet , Guerrero Dolores , Gómez-Mora Elisabet , Molina Mateu Laura , Orera Pérez Fernando , Senserrich Jordi , Clotet Bonaventura , Cabrera Cecilia 
Published: May 2022

AbstractA complex link exists between HIV-1 and autophagy, and discordant results have been reported in different in vitro models regarding the way HIV and autophagy modulate each other. Despite this, there is very limited knowledge about the interplay between HIV and autophagy in vivo in lymphoid tissue, due in part by the lack of cell models that recapitulate the in vivo setting. Here, we evaluate the interrelationship between HIV and autophagy using human ex vivo lymphoid tissue cultures as an HIV infection model. Our results showed that human lymphoid aggregated cultures (HLACs) from tonsillar tissue displayed fully functional autophagic activity. In this system, HIV infection resulted in an increase in autophagy. Notably, we observed that both, autophagy-enhancing (rapamycin) or blocking drugs (3-methyladenine, chloroquine and bafilomycin), were able to decrease HIV-DNA levels and HIV replication. Therefore, efficient HIV-1 replication requires a fine-tuned level of autophagy, so modifications of this balance will have a negative impact on its replication. Therefore, targeting the autophagic pathway could be a new therapeutic approach to be explored to treat HIV-1 infection. Ex vivo cultures of human lymphoid tissue are a suitable model to obtain further insights into HIV and its intricate relationship with autophagy.
Unveiling the dynamics of ultra high velocity droplet impact on solid surfaces
Authors: Tretola Giovanni , Vogiatzaki Konstantina 
Published: May 2022

AbstractThe impact of a liquid droplet onto a solid surface is a phenomenon present in a wide range of natural processes and technological applications. In this study, we focus on impact conditions characterised by ultra high velocities (up to 500 m/s), to investigate—for the first time—how the impact dynamics change when the compressibility of the liquid in the droplet is no longer negligible. A water droplet impacting a dry substrate at four different velocities, from 50 to 500 m/s, is simulated. Such conditions are particularly relevant to aviation as well as industrial gas turbine engine risk management. Thus, numerical investigations as the one we present here provide a powerful tool to analyse the process. We find that increasing the impact velocity changes the flow field within and outside the droplet the moment that the compressibility can no longer be neglected, with the rise of pressure fronts in both regions. Increasing the impact velocity, the compressibility affects also the lamella formed and changes its ejection velocity observed over time (and thus the wetting behaviour) when the region shift from incompressible to compressible. Moreover, it is found that the maximum pressure observed at the wall during the impact is located at the corner of the impact, where the lamella is ejected, not in the centre, and it is influenced by the initial velocity. To predict the maximum pressure experienced by the surface during the high velocity impact, we propose a correlation based on the initial Weber and Reynolds number of the droplet. The complexity and the scales of the dynamics involved in the ultra-high velocity impact is limiting the experimental and analytical studies. To the best of our knowledge there are no experimental data currently available at such conditions. In this study, through numerical simulations, new insights about the impact dynamics at such conditions are provided.
Shock wave formation from head-on collision of two subsonic vortex rings
Authors: Bauer Rachel L. , Thomas Cody J. , Baker Everett V. P. , Johnson Emily M. , Williams Kelly R. , Langenderfer Martin J. , Johnson Catherine E. 
Published: May 2022

AbstractVortex ring collisions have attracted intense interest in both water and air studies (Baird in Proc R Soc Lond Ser Math Phys Sci 409:59–65, 1987, Poudel et al. in Phys Fluids 33:096105, 2021, Lim and Nickels in Nature 357:225, 1992, New et al. in Exp Fluids 57:109, 2016, Suzuki et al. in Geophys Res Lett 34, 2007, Yan et al. in J Fluids Eng 140:054502, 2018, New et al. in J Fluid Mech 899, 2020, Cheng et al. in Phys Fluids 31:067107, 2019, Hernández and Reyes in 29:103604, 2017, Mishra et al. in Phys Rev Fluids, 2021, Zednikova et al. in Chem Eng Technol 42:843–850, 2019, Kwon et al. in Nature 600:64–69, 2021). These toroidal structures spin around a central axis and travel in the original direction of impulse while spinning around the core until inertial forces become predominant causing the vortex flow to spontaneously decay to turbulence (Vortex Rings, https://projects.iq.harvard.edu/smrlab/vortex-rings). Previous studies have shown the collision of subsonic vortex rings resulting in reconnected vortex rings, but the production of a shock wave from the collision has not been demonstrated visibly (Lim and Nickels in Nature 357:225, 1992, Cheng et al. in Phys Fluids 31:067107, 2019). Here we present the formation of a shock wave due to the collision of explosively formed subsonic vortex rings. As the vortex rings travel at Mach 0.66 toward the collision point, they begin to trap high pressure air between them. Upon collision, high pressure air was imploded and released radially away from the axis of the collision, generating a visible shock wave traveling through and away from the colliding vortices at Mach 1.22. Our results demonstrate a pressure gradient with high pressure release creating a shock wave. We anticipate our study to be a starting point for more explosively formed vortex collisions. For example, explosives with different velocities of detonation could be tested to produce vortex rings of varying velocities.
Numerical and experimental analysis of Lagrangian dispersion in two-dimensional chaotic flows
Authors: Forgia Giovanni La , Cavaliere Davide , Espa Stefania , Falcini Federico , Lacorata Guglielmo 
Published: May 2022

AbstractWe present a review and a new assessment of the Lagrangian dispersion properties of a 2D model of chaotic advection and diffusion in a regular lattice of non stationary kinematic eddies. This model represents an ideal case for which it is possible to analyze the same system from three different perspectives: theory, modelling and experiments. At this regard, we examine absolute and relative Lagrangian dispersion for a kinematic flow, a hydrodynamic model (Delft3D), and a laboratory experiment, in terms of established dynamical system techniques, such as the measure of (Lagrangian) finite-scale Lyapunov exponents (FSLE). The new main results concern: (i) an experimental verification of the scale-dependent dispersion properties of the chaotic advection and diffusion model here considered; (ii) a qualitative and quantitative assessment of the hydro-dynamical Lagrangian simulations. The latter, even though obtained for an idealized open flow configuration, contributes to the overall validation of the computational features of the Delft3D model.
Rearrangements in the musculature correlate with jumping behaviour in legless Mediterranean fruit fly larvae Ceratitis capitata (Tephritidae)
Authors: Diesner Max , Brenner Marcel , Azarsa Amin , Heymann Caroline , Aberle Hermann 
Published: May 2022

AbstractLarvae of holometabolic insects evolved different crawling strategies depending on the presence or absence of larval legs or life style. A rather unusual mode of locomotion has independently evolved in legless larvae of several dipteran species. Maggots of the Mediterranean fruit flyCeratitis capitatadeveloped an effective jumping mechanism to increase locomotion speed or to deter predators during the search for suitable pupation sites. Here, we use high-speed videography to visualize even the fastest movements during jump preparation and take-off. Quantification of kinetic and biometric parameters reveal that maggots jump up to 15-fold of their body length from a standing position and gain speed with 27 times the acceleration of gravity. Videos at high spatial resolution show the mechanism of latch formation and release in unprecedented detail. Mouth hooks insert in the caudal segment and raise a cuticular fold that serves as a handle to pressurize the body prior to launch. Since locomotion behaviour should be intrinsically linked to neuromuscular systems, we dissected third instar larvae and determined the precise pattern of abdominal muscles fibres. Compared to non-jumping dipteran larvae, such asDrosophila melanogaster, the overall arrangement is highly similar, but a few muscle fibres show characteristic re-arrangements in orientation and strength that are consistent with a role in bending and jumping. These results suggest that body wall muscles show adaptations to jumping behaviour inCeratitislarvae, and possibly also in other species with different jumping techniques.
Daily prosocial actions during the COVID-19 pandemic contribute to giving behavior in adolescence
Authors: Sweijen Sophie W. , van de Groep Suzanne , Green Kayla H. , te Brinke Lysanne W. , Buijzen Moniek , de Leeuw Rebecca N. H. , Crone Eveline A. 
Published: May 2022

AbstractProsocial actions are a building block for developing mature and caring social relations. However, the global pandemic may hamper adolescents’ prosocial actions. In this preregistered study, we examined the extent to which adolescents provided daily emotional support during the COVID-19 pandemic. In total, 10–25-year-old high school and university students participated at three timepoints (N = 888 at the first timepoint (May 2020); 494 at the second timepoint (Nov 2020) and 373 at the third timepoint (May 2021)). At the first and second timepoint, participants completed 2 weeks of daily diaries on providing emotional support. At all timepoints, participants performed Dictator Games to measure giving to peers, friends and COVID-19 targets (medical doctors, COVID-19 patients, individuals with a poor immune system). Across the three timepoints, adolescents gave more to COVID-19 targets than peers and friends, but giving to COVID-19 target was highest in the beginning of the pandemic (first timepoint relative to second and third timepoint). Results from the first timepoint showed that emotional support directed to friends peaked in mid-adolescence, whereas emotional support towards family members showed a gradual increase from childhood to young adulthood. Furthermore, daily emotional support increased between the first and second timepoint. Daily emotional support to friends predicted giving behavior to all targets, whereas emotional support to family was specifically associated with giving to COVID-19 targets. These findings elucidate the relation between daily actions and prosocial giving to societally-relevant targets in times of crisis, underlying the importance of prosocial experiences during adolescence.
Detection of balance disorders using rotations around vertical axis and an artificial neural network
Authors: Kamiński Marek , Marciniak Paweł , Tylman Wojciech , Kotas Rafał , Janc Magdalena , Józefowicz-Korczyńska Magdalena , Gawrońska Anna , Zamysłowska-Szmytke Ewa 
Published: May 2022

AbstractVestibular impairments affect patients' movements and can result in difficulties with daily life activities. The main aim of this study is to answer the question whether a simple and short test such as rotation about a vertical axis can be an objective method of assessing balance dysfunction in patients with unilateral vestibular impairments. A 360˚ rotation test was performed using six MediPost devices. The analysis was performed in three ways: (1) the analytical approach based only on data from one sensor; (2) the analytical approach based on data from six sensors; (3) the artificial neural network (ANN) approach based on data from six sensors. For approaches 1 and 2 best results were obtained using maximum angular velocities (MAV) of rotation and rotation duration (RD), while approach 3 used 11 different features. The following sensitivities and specificities were achieved: for approach 1: MAV—80% and 60%, RD—69% and 74%; for approach 2: 61% and 85% and RD—74% and 56%; for approach 3: 88% and 84%. The ANN-based six-sensor approach revealed the best sensitivity and specificity among parameters studied, however one-sensor approach might be a simple screening test used e.g. for rehabilitation purposes.
Spatial distribution and identification of potential risk regions to rice blast disease in different rice ecosystems of Karnataka
Authors: Amoghavarsha Chittaragi , Pramesh Devanna , Sridhara Shankarappa , Patil Balanagouda , Shil Sandip , Naik Ganesha R. , Naik Manjunath K. , Shokralla Shadi , El-Sabrout Ahmed M. , Mahmoud Eman A. , Elansary Hosam O. , Nayak Anusha , Prasannakumar Muthukapalli K. 
Published: May 2022

AbstractRice is a globally important crop and highly vulnerable to rice blast disease (RBD). We studied the spatial distribution of RBD by considering the 2-year exploratory data from 120 sampling sites over varied rice ecosystems of Karnataka, India. Point pattern and surface interpolation analyses were performed to identify the spatial distribution of RBD. The spatial clusters of RBD were generated by spatial autocorrelation and Ripley’s K function. Further, inverse distance weighting (IDW), ordinary kriging (OK), and indicator kriging (IK) approaches were utilized to generate spatial maps by predicting the values at unvisited locations using neighboring observations. Hierarchical cluster analysis using the average linkage method identified two main clusters of RBD severity. From the Local Moran’s I, most of the districts were clustered together (at I > 0), except the coastal and interior districts (at I < 0). Positive spatial dependency was observed in the Coastal, Hilly, Bhadra, and Upper Krishna Project ecosystems (p > 0.05), while Tungabhadra and Kaveri ecosystem districts were clustered together at p < 0.05. From the kriging, Hilly ecosystem, middle and southern parts of Karnataka were found vulnerable to RBD. This is the first intensive study in India on understanding the spatial distribution of RBD using geostatistical approaches, and the findings from this study help in setting up ecosystem-specific management strategies against RBD.
Peanut triacylglycerols activate innate immunity both in insects and mammals
Authors: Li Wenyuan , Miyashita Atsushi , Sekimizu Kazuhisa 
Published: May 2022

AbstractIn this study, we investigated immunoreactivity of peanut (Arachis hypogaea) oil using the silkworm (Bombyx mori) model. The peanut oil induced melanin formation when injected to the silkworm hemocoel. We then purified the active substance and identified the triacylglycerols (TAGs) as the responsible molecule for the melanin-forming effect of peanut oil. Also, the peanut TAGs induced the muscle contraction of the silkworm (i.e., cleavage of the insect cytokine BmPP) and the TNF-α production by cultured mouse macrophage cells. The muscle contraction activity of the peanut TAGs was reduced by saponification reaction, indicating that the TAG (not the degraded fatty acids) moiety is responsible for the activity. The muscle contraction effects of other TAGs of olive, lard, and beef oil were comparable with that of peanut TAGs. Nevertheless, for the melanin formation, the effect of peanut TAGs was outstanding. The fatty acid composition of peanut TAGs was distinct from that of olive TAGs. These results suggest that TAGs are immunoreactive and induces cytokines both in insect and mammalian immune systems. Also, the differential effects of peanut and olive TAGs for the melanin formation may suggest that TAGs with different fatty acid compositions are distinguished by the immune system.
End-of-life discussions reduce the utilization of life-sustaining treatments during the last three months of life in cancer patients
Authors: Chan Shang-Yih , Lai Yun-Ju , Chen Yu-Yen , Chiang Shuo-Ju , Tsai Yi-Fan , Hsu Li-Fei , Chuang Pei-Hung , Chen Chu-Chieh , Yen Yung-Feng 
Published: May 2022

AbstractStudies to examine the impact of end-of-life (EOL) discussions on the utilization of life-sustaining treatments near death are limited and have inconsistent findings. This nationwide population-based cohort study determined the impact of EOL discussions on the utilization of life-sustaining treatments in the last three months of life in Taiwanese cancer patients. From 2012 to 2018, this cohort study included adult cancer patients, which were confirmed by pathohistological reports. Life-sustaining treatments during the last three months of life included cardiopulmonary resuscitation, intubation, and defibrillation. EOL discussions in cancer patients were confirmed by their medical records. Association of EOL discussions with utilization of life-sustaining treatments were assessed using multiple logistic regression. Of 381,207 patients, the mean age was 70.5 years and 19.4% of the subjects received life-sustaining treatments during the last three months of life. After adjusting for other covariates, those who underwent EOL discussions were less likely to receive life-sustaining treatments during the last three months of life compared to those who did not (Adjusted odds ratio [AOR] 0.87; 95% confidence interval [CI] 0.85–0.89). Considering the type of treatments, EOL discussions correlated with a lower likelihood of receiving cardiopulmonary resuscitation (AOR = 0.45, 95% CI 0.43–0.47), endotracheal intubation (AOR = 0.92, 95%CI 0.90–0.95), and defibrillation (AOR = 0.54, 95%CI 0.49–0.59). Since EOL discussions are associated with less aggressive care, our study supports the importance of providing these discussions to cancer patients during the EOL treatment.
A Bayesian network structure learning approach to identify genes associated with stress in spleens of chickens
Authors: Videla Rodriguez E. A. , Mitchell John B. O. , Smith V. Anne 
Published: May 2022

AbstractDifferences in the expression patterns of genes have been used to measure the effects of non-stress or stress conditions in poultry species. However, the list of genes identified can be extensive and they might be related to several biological systems. Therefore, the aim of this study was to identify a small set of genes closely associated with stress in a poultry animal model, the chicken (Gallus gallus), by reusing and combining data previously published together with bioinformatic analysis and Bayesian networks in a multi-step approach. Two datasets were collected from publicly available repositories and pre-processed. Bioinformatics analyses were performed to identify genes common to both datasets that showed differential expression patterns between non-stress and stress conditions. Bayesian networks were learnt using a Simulated Annealing algorithm implemented in the software Banjo. The structure of the Bayesian network consisted of 16 out of 19 genes together with the stress condition. Network structure showed CARD19 directly connected to the stress condition plus highlighted CYGB, BRAT1, and EPN3 as relevant, suggesting these genes could play a role in stress. The biological functionality of these genes is related to damage, apoptosis, and oxygen provision, and they could potentially be further explored as biomarkers of stress.
Enhancement of backscattering cross section from an equivalent human cylinder under oblique incidence
Authors: Awan Zeeshan A. , Seetharamdoo Divitha 
Published: May 2022

AbstractAn analysis about the enhancement of backscattering radar cross section from an equivalent human body cylinder using a specific type of coating is presented. The types of coatings considered for the human body are taken to inductive meta surface (MS), inductive MS followed by a dielectric layer and an epsilon negative (ENG) metamaterial. An eigenfunction expansion method has been used to derive analytical expressions for the scattered electric and magnetic fields. It is investigated that inductive MS and inductive MS followed by a dielectric layer type of coatings cannot be used to enhance the backscattering radar cross section from the human body. It is found that an ENG metamaterial coating having specific permittivity and coating thickness can be used to significantly enhance the back‐scattering radar cross section from the human body under oblique incidence. Therefore, an ENG metamaterial coating is selected for the proposed model and finally, the modelling of the proposed design is suggested.
Investigating dust properties in AGB wind-ISM interaction regions
Authors: Maercker M. , Khouri T. , Mecina M. , De Beck E. 
Published: May 2022

Aims.In this paper, we aim to constrain the dust mass and grain sizes in the interaction regions between the stellar winds and the interstellar medium (ISM) around asymptotic giant branch (AGB) stars. By describing the dust in these regions, we aim to shed light on the role of evolved low-mass stars in the origin of dust in galaxies.Methods.We use images in the far-infrared (FIR) at 70 and 160 µm to derive dust temperatures and dust masses in the wind-ISM interaction regions around a sample of carbon-rich and oxygen-rich AGB stars. The dust temperature and mass are determined in two ways: first, directly from the data using the ratio of the measured fluxes and assuming opacities for dust with a constant grain size of 0.1 µm, and then using three-dimensional dust-radiative transfer models spatially constrained by the observations. Each of the radiative transfer models contains one constant grain size, which is varied between 0.01 and 5.0 µm.Results.We find that the observed dust mass in the wind-ISM interaction regions is consistent with mass accumulated from the stellar winds. For the carbon-rich sources, adding the spatial constraints in the radiative transfer models results in preferentially larger grain sizes (≈2 µm). For the oxygen-rich sources, the spatial constraints result in overly high temperatures in the models, making it impossible to fit the observed FIR ratio irrespective of the grain size used, indicating a more complex interplay of grain properties and the stellar radiation field.Conclusions.Our results have implications for how likely it is for the grains to survive the transition into the ISM, and the properties of dust particles that later act as seeds for grain growth in the ISM. However, our results for the oxygen-rich sources show that the derivation of dust properties is not straight forward, requiring more complex modelling.