Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular marker based genetic diversity analysis in rice (Oryza sativaL.) using SSR markers

Assessment of genetic diversity is very important in rice breeding from the standpoint of selection, conservation and proper utilization. The role of a broad genetic base and systematically characterized germplasm in the crop improvement of cultivated plants has been well recognized. To meet the continuously expanding needs of varietal improvements, the evaluation and characterization of all existing germplasm are required. Genetic variability studies are important in selection of parents for hybridization as sound crop improvement depends upon the magnitude of variability in the base population. In the present investigation 36 rice genotypes were studied for diversity studies using polymorphic SSR markers. These rice genotypes were grouped into two main clusters that is cluster I and II with similarity coefficient (0.00). Cluster I can be sub divided into two minor sub-groups IA, IB, and with similarity coefficient (0.15). Cluster IA consisted of 12 genotypes, whereas cluster IB consisted of 13 genotypes. The second main cluster can be also sub divided into two minor sub-groups that is IIA and IIB (0.25). This indicated presence of considerable diversity in the genotypes studied. Through diversity analysis, highest similarity was observed between cultivar URG-5 and URG-8 followed by NDR-359 and Pusa-6-B. The most diverse cultivars were Akshaya dhan and URG-24.
Transcorneal Electrical Stimulation Inhibits Retinal Microglial Activation and Enhances Retinal Ganglion Cell Survival After Acute Ocular Hypertensive Injury

Purpose To investigate the effect of transcorneal electrical stimulation (TcES) on retinal ganglion cell (RGC) function and survival after acute ocular hypertension-related retinal injury in gerbil eyes. Methods Gerbil eyes were subjected to acute ocular hypertensive injury (80 mm Hg for 60 minutes). In the treatment group, TcES was applied to the surgical eye immediately and then twice weekly for a total of 1 month. In the control group, sham TcES was given to the surgical eye at the same time points. Retinal function was assessed and compared between groups using flash electroretinography. For histological analysis, the number of RGC and microglial cells were counted by immunofluorescence staining after the gerbils were sacrificed on day 7 and day 28. Real-time polymerase chain reaction and western blot analysis were conducted to compare expression of interleukin (IL)-10, IL-6, COX-2, tumor necrosis factor (TNF)-α, and NF-κB phosphorylation among groups. Results TcES-treated eyes had significantly higher RGC survival at 1 month compared to controls. This was associated with RGC function. Furthermore, TcES-treated eyes were shown to have increased IL-10 expression, with a corresponding reduction in IL-6 and COX-2 expression as well as reduction in NF-κB phosphorylation. This was associated with a suppression in microglial cell activation in TcES-treated eyes. Conclusions Early treatment with TcES in gerbils protected the RGC from secondary damage and preserved retinal function in acute ocular hypertensive injury through modulation of the microglial-cell activated local inflammatory response. Translational Relevance Our study strengthens the argument for translating TcES as a viable treatment in acute glaucoma.
Enhancement of Immunoregulatory Function of Modified Bone Marrow Mesenchymal Stem Cells by Targeting SOCS1

Objective The study aim to investigate the role of microRNA-155 (miR-155) on the immunoregulatory function of bone marrow mesenchymal stem cells (MSCs). Methods MSCs were isolated from 2-week-old Sprague-Dawley rats and identified by flow cytometry using anti-CD29, anti-CD44, anti-CD34, and anti-CD45 antibodies. MSCs were transfected with miR155-mimics, miR155-inhibitor, and control oligos, respectively, and then cocultured with spleen mononuclear cells (SMCs). The mRNA levels of Th1, Th2, Th17, and Treg cell-specific transcription factors (Tbx21, Gata3, Rorc, and Foxp3, resp.) and the miR-155 target gene SOCS1 were detected by quantitative real-time PCR (qPCR) in SMCs. The proportion of CD4+ FOXP3+ Treg cells was detected by flow cytometry. In addition, the effects of MSCs transfected with miR-155 on the migration of rat SMCs were investigated by transwell chamber. Results CD29 and CD44 were expressed in MSCs, while CD34 and CD45 were negative. The percentage of CD4+ FOXP3+ Treg cells in the SMC population was significantly higher compared with that noted in SMCs control group (p < 0.001) following 72 hours of coculture with miR155-mimics-transfected SMCs. In contrast, the percentage of CD4+ FOXP3+ Treg cells in the SMCs cocultured with miR155-inhibitor-transfected MSCs was significantly lower compared with that noted in SMCs control group (p < 0.001). MiR155-mimics-transfected MSCs inhibited the expression of Tbx21, Rorc, and SOCS1, while the expression of Gata3 and Foxp3 was increased. In contrast to the downregulation of the aforementioned genes, miR155-inhibitor-transfected MSCs resulted in upregulation of Tbx21, Rorc, and SOCS1 expression levels and inhibition of Gata3 and Foxp3. In the transwell assay, miR155-mimics-transfected MSCs exhibited lower levels of SMCs migration, while the miR155-inhibitor-transfected MSCs demonstrated significantly higher levels of migration, compared with the blank control group (p < 0.01, resp.). Conclusion miR-155 favors the differentiation of T cells into Th2 and Treg cells in MSCs, while it inhibits the differentiation to Th1 and Th17 cells.
Real Time Online Facial Expression Transfer with Single Video Camera

Facial expression transfer is currently an active research field. However, 2D image wrapping based methods suffer from depth ambiguity and specific hardware is required for depth-based methods to work. We present a novel markerless, real time online facial transfer method that requires only a single video camera. Our method adapts a model to user specific facial data, computes expression variances in real time and rapidly transfers them to another target. Our method can be applied to videos without prior camera calibration and focal adjustment. It enables realistic online facial expression editing and performance transferring in many scenarios, such as: video conference; news broadcasting; lip-syncing for song performances; etc. With a low computational demand and hardware requirement, our method tracks a single user at an average of 38 fps. Our tracking method runs smoothly in web browsers despite their slower execution speed.
Robust hydraulic actuator force control through relief discharge

Actuator force control in servo-hydraulic systems has numerous applications in machinery and industrial settings. The prevalent hydraulic configuration for force control utilizes a proportional directional control valve to properly route the supplied hydraulic fluid toward the chambers of the actuator. It is well known that this configuration imposes certain physical limitations on force-tracking performance. In this article, a different configuration is utilized to improve the hydraulic force control performance. This is done by replacing the proportional directional control valve with a proportional double-stage relief valve. It is shown that this new setting is superior in its achievable force-tracking performance. This comes at the cost of a more challenging control problem compared to the proportional directional control valve case, due to the presence of un-modeled dynamics and unknown parameters. A robust H ∞ control approach has been followed as the main solution to address uncertainty problems. However, conservative robust design imposes its own limitations on force-tracking performance. To address this issue, a combination of additional switched-proportional–integral–derivative and Prandtl–Ishlinskii hysteresis compensation control loops is proposed. Conditions are derived under which the additional loops improve the performance of the robust H ∞ controller. The effectiveness of the proposed configuration and control method is demonstrated by the experimental results.
Dual-Task Walking in Challenging Environments in People with Stroke: Cognitive-Motor Interference and Task Prioritization

Cognitive-motor interference may contribute to the risk of falling in people with stroke, as may be the associated phenomenon of inappropriate task prioritization. Examining dual-task walking could provide valuable insights as to how to best evaluate and treat walking in people with stroke. This study aimed to examine the effect of different walking environments on cognitive-motor interference and task prioritization in dual-task walking in people with stroke. Using a repeated-measures design, cognitive-motor interference and task prioritization were assessed in 30 stroke survivors, while walking in a plain environment and in two challenging environments that were enriched with either stationary physical context or suddenly appearing projector-augmented context. All three walking environment conditions were performed with and without a concurrent serial-3 subtraction task. We found stronger cognitive-motor interference for the two challenging environments than for the plain walking environment. Cognitive-motor interference did not differ between challenging walking environments, but task prioritization did: motor performance was prioritized more in the environment with physical context than in the environment with projector-augmented context and vice versa for cognitive-task performance. In conclusion, walking environment strongly influenced cognitive-motor interference and task prioritization during dual-task walking in people with stroke.
Decreased Oxidative Stress in Male Patients with Active Phase Ankylosing Spondylitis Who Underwent Whole-Body Cryotherapy in Closed Cryochamber

Objective The aim of the study was to estimate the impact of whole body cryotherapy (WBC) on oxidative stress when performed in a closed cryochamber on patients with ankylosing spondylitis (AS). Material and methods The effect of ten WBC procedures lasting 3 minutes a day with a subsequent 60-minute session kinesiotherapy on oxidative stress in male AS patients (WBC group n = 16) was investigated. To assess the disease activity, the Bath Ankylosing Spondylitis Diseases Activity Index (BASDAI) and Bath Ankylosing Spondylitis Functional Index (BASFI) were calculated. The WBC group was compared to the kinesiotherapy only (KT; n = 16) group. The routine parameters of oxidative stress (antioxidant enzymatic and nonenzymatic antioxidant status, lipid peroxidation products, total oxidative status (TOS), and oxidative stress index (OSI)) were estimated one day before the beginning and one day after the completion of the research program. Results After the completion of the treatment in the WBC group, a significant decrease of oxidative stress markers (TOS and OSI) and a significant increase of total antioxidant status were observed. The erythrocyte activity of glutathione peroxidase, glutathione reductase decreased significantly in both groups, but the differences of activity of that enzymes prior to post treatment values (Δ) in the KT group were significantly higher as compared to the WBC group. The activity of erythrocyte catalase and plasma ZnCu isoenzyme of superoxide dismutase showed a decreased tendency; erythrocyte total superoxide dismutase activity showed an increased tendency in the WBC group after the completion of the treatment. The BASDAI and BASFI decreased significantly in both groups, but the differences of value indexes prior to post treatment (Δ) were significantly higher in the WBC than KT group. Conclusion WBC performed in a closed cryochamber decreases oxidative stress and improves BASDAI and BASFI indexes in male patients during the active phase of ankylosing spondylitis.
Sparsity-Constrained Controllability Maximization With Application to Time-Varying Control Node Selection

In this letter, we consider the maximization of a quantitative metric of controllability with a constraint of $L^{0}$ norm of the control input. Since the optimization problem contains a combinatorial structure, we introduce a convex relaxation problem for the sake of reducing computation burden. We prove the existence of solutions to the main problem and also give a simple condition under which the relaxed problem gives a solution to the main problem. It should be emphasized that the main problem can formulate time-varying control node selection, which attempts to extract when and where exogenous inputs should be provided in order to achieve high controllability of multi-agent systems.
Molecular Docking of Potential Inhibitors of Broccoli Myrosinase

Glucosinolates are secondary metabolites occurring in Brassicaceae plants whose hydrolysis may yield isothiocyanates, widely recognized as health-promoting compounds. Myrosinase catalyzes this conversion. The chemical mechanism involves an unstable intermediary (thiohydroxamate-O-sulfonate) that spontaneously decomposes into isothiocyanates or other non-bioactive compounds depending on pH and cofactors. At acidic pH, non-bioactive compounds such as nitriles and thiocyanates are formed, while at neutral pH isothiocyanates are obtained. Broccoli myrosinase has been poorly studied so far. Recently, its amino acidic sequence was elucidated, and a structural model was built. The aim of this work was to study the molecular interaction of broccoli myrosinase with different ligands at acidic pH to propose possible inhibitors that prevent formation of undesirable compounds at acidic pH, and that at neutral pH dissociate from the enzyme, allowing formation of isothiocyanates. The interaction between broccoli myrosinase and 40 ligands was studied by molecular docking simulations. Both the enzyme and each inhibitor were set at pH 3.0. Amygdaline and arbutin showed the highest affinity to broccoli myrosinase in this condition. The residues that stabilize the complexes agree with those that stabilize the substrate (Gln207, Glu429, Tyr352, and Ser433). Accordingly, amygdaline and arbutin would perform as competitive inhibitors of myrosinase at pH 3.0.
Response of brain-derived neurotrophic factor to combining cognitive and physical exercise

Abstract Purpose: Brain-derived neurotrophic factor (BDNF) is well known for its potential to promote brain plasticity. It has been proposed that combining cognitive and physical exercise (CCPE) may have the potential to generate more synergistic benefits in cognitive function than either cognitive exercise (CE) or physical exercise (PE) alone. The purpose of this study was to examine acute responses of peripheral BDNF levels and cognitive performance to CE, PE, and CCPE. Methods: Thirteen healthy adult men participated in four experimental sessions; a 30-min CE, a 30-min cycling PE at an intensity of 60% peak oxygen uptake, a 30-min CCPE at the same intensity as PE, and a 30-min session of complete rest. Plasma BDNF levels and cognitive performance were measured before and after each session. Results: Both PE and CCPE significantly increased plasma BDNF levels (p < .05). CE led to no significant increase (p ≥ .05), and there was no significant difference in peripheral BDNF levels between PE and CCPE (p ≥ .05). No session induced a significant change in cognitive performance (p ≥ .05). Conclusions: Our study suggests that CE and PE have different responses of peripheral BDNF levels and that CCPE had no additional or synergistic effect on peripheral BDNF levels compared with PE alone. This study offers further insights into the potential mechanisms underlying the respective roles of CE, PE, and CCPE for peripheral BDNF levels and cognitive performance.
Rapid registration of multimodal images using a reduced number of voxels

Rapid registration of multimodal cardiac images can improve image-guided cardiac surgeries and cardiac disease diagnosis. While mutual information (MI) is arguably the most suitable registration technique, this method is too slow to converge for real time cardiac image registration; moreover, correct registration may not coincide with a global or even local maximum of MI. These limitations become quite evident when registering three-dimensional (3D) ultrasound (US) images and dynamic 3D magnetic resonance (MR) images of the beating heart. To overcome these issues, we present a registration method that uses a reduced number of voxels, while retaining adequate registration accuracy. Prior to registration we preprocess the images such that only the most representative anatomical features are depicted. By selecting samples from preprocessed images, our method dramatically speeds up the registration process, as well as ensuring correct registration. We validated this registration method for registering dynamic US and MR images of the beating heart of a volunteer. Experimental results on in vivo cardiac images demonstrate significant improvements in registration speed without compromising registration accuracy. A second validation study was performed registering US and computed tomography (CT) images of a rib cage phantom. Two similarity metrics, MI and normalized crosscorrelation (NCC) were used to register the image sets. Experimental results on the rib cage phantom indicate that our method can achieve adequate registration accuracy within 10% of the computation time of conventional registration methods. We believe this method has the potential to facilitate intra-operative image fusion for minimally invasive cardio-thoracic surgical navigation.
Hand Recognition Obtained by Simulation of Hand Regard

Eye-hand coordination of an infant is observed during the early months of their development. Hand regard, which is an example of this coordination, occurs at about 2 months. It is considered that after experiencing hand regard, an infant may recognize their own hands. However, it is unknown how an infant recognizes their hands through hand regard. Accordingly, the process by which an infant recognizes their hands and distinguishes between their hands and other objects was simulated. A simple neural network was trained with a modified real-time recurrent learning (RTRL) algorithm to deal with time-varying input and output during hand regard. The simulation results show that information about recognition of the modeled hands of an infant is stored in cell assemblies, which were self-organized. Cell assemblies appear during the phase of U-shaped developments of hand regard, and the configuration of the cell assemblies changes with each U-shaped development. Furthermore, movements like general movements (GMs) appear during the phase of U-shaped developments of hand regard.
Outcomes of acute kidney injury depend on initial clinical features: a national French cohort study

Background Acute kidney injury (AKI) is a common condition that is associated with poor short- and long-term outcomes. The aim of this nationwide cohort study was to profile the long-term outcome of patients admitted for AKI in France. Methods Based on the comprehensive French hospital discharge database, all hospitalizations for an AKI episode were categorized in four groups according to the presence of at least one dialysis session [renal replacement therapy (RRT)] and according to the coding of AKI as the principal or associated diagnosis (PRINC_DIAG or ASS_DIAG). Results In this nationwide cohort of 989 974 patients (median age 77 years) hospitalized with AKI during the 2009-16 period, 422 739 (43%) patients died (235 572 during the first hospitalization) and 40 015 (4%) patients reached end-stage renal disease (ESRD) (5962 during first hospitalization) up to 31 December 2016. Patients without RRT and discharged from hospital had a cumulative incidence of ESRD that ranged from 5.3% (5.2-5.4) in the ASS_DIAG group to 28.7% (27.9-29.5) in the RRT-PRINC_DIAG group at 60 months. The cumulative incidence of death ranged from 31.0% (30.2-32.2) in the RRT-ASS_DIAG group to 45.5% (45.3-45.7) in the ASS_DIAG group. Initial clinical features were associated with outcome independent of comorbidities and age. Conclusions The death penalty of AKI is abysmal and AKI was an important predisposing factor to chronic ESRD. Our study strengthens the current recommendations for long-term follow-up of patients with AKI. The novelty of this study is to propose a clinical classification of AKI episodes that is easy to detect in administrative medical databases and that is strongly associated with immediate and long-term outcomes.
Speech and social network dynamics in a constrained vocabulary game : design and hypotheses

This paper describes the design of a longitudinal speech study and the general hypotheses associated with the study. Simply put, the general hypotheses are that some variation over time in how people speak is caused by their interactions with other people, that the nature of this variation is related to the social attitudes people have toward each other, and that social dynamics are the main source of instability in speech patterns. While these hypotheses may seem straightforward, and perhaps obviously true, testing them rigorously is complicated. I should confess that in testing these hypotheses I have a parallel agenda, which is to promote a research paradigm in which we attend more carefully to the physical grounding of our analytical categories. Because the hypotheses refer to variation over time, I start by considering possible patterns and causes of temporal variation:
Evaluation of person-level heterogeneity of treatment effects in published multiperson N-of-1 studies: systematic review and reanalysis

Objective Individual patients with the same condition may respond differently to similar treatments. Our aim is to summarise the reporting of person-level heterogeneity of treatment effects (HTE) in multiperson N-of-1 studies and to examine the evidence for person-level HTE through reanalysis. Study design Systematic review and reanalysis of multiperson N-of-1 studies. Data sources Medline, Cochrane Controlled Trials, EMBASE, Web of Science and review of references through August 2017 for N-of-1 studies published in English. Study selection N-of-1 studies of pharmacological interventions with at least two subjects. Data synthesis Citation screening and data extractions were performed in duplicate. We performed statistical reanalysis testing for person-level HTE on all studies presenting person-level data. Results We identified 62 multiperson N-of-1 studies with at least two subjects. Statistical tests examining HTE were described in only 13 (21%), of which only two (3%) tested person-level HTE. Only 25 studies (40%) provided person-level data sufficient to reanalyse person-level HTE. Reanalysis using a fixed effect linear model identified statistically significant person-level HTE in 8 of the 13 studies (62%) reporting person-level treatment effects and in 8 of the 14 studies (57%) reporting person-level outcomes. Conclusions Our analysis suggests that person-level HTE is common and often substantial. Reviewed studies had incomplete information on person-level treatment effects and their variation. Improved assessment and reporting of person-level treatment effects in multiperson N-of-1 studies are needed.