Miracle-dz/UniFAR-FTUs huggingface dataset:
Scalable Collectives for Distributed Asynchronous Many-Task Runtimes

Global collectives (reductions/aggregations) are ubiquitous and feature in nearly every application of distributed high-performance computing (HPC). While it is advisable to devise algorithms by placing collectives off the critical path of execution, they are sometimes unavoidable for correctness, numerical convergence and analyses purposes. Scalable algorithms for distributed collectives are well studied and have become an integral part of MPI, but new and emerging distributed computing frameworks and paradigms such as Asynchronous Many-Task (AMT) models lack the same sophistication for distributed collectives. Since the central promise of AMT runtimes is that they automatically discover, and expose, task dependencies in the underlying program and can schedule work optimally to minimize idle time and hide data movement, a naively designed collectives protocol can completely offset any gains made from asynchronous execution. In this study we demonstrate that scalable distributed collectives are indispensable for performance in AMT models. We design, implement and test the performance of a scalable collective algorithm in Legion, an exemplar data-centric AMT programming model. Our results show that AMT systems contain the necessary primitives that allow for fully scalable collectives without breaking the transparent data movement abstractions. Scalability tests of an integrated Legion 1D stencil mini-application show the clear benefit of implementing scalable collectives and the performance degradation when a naïve collectives alternative is used instead.
Soft-Actuator-Based Robotic Joint for Safe and Forceful Interaction With Controllable Impact Response

Impact safety and response are critical challenges for robots working under dynamic environments and with close proximity to humans. State-of-the-art rigid robots and soft robots both have limitations and tradeoffs due to their characteristics. In this letter, we introduced a hybrid-antagonistic-pneumatic joint (HAP-joint) with soft actuators and rigid structures, achieving safe and forceful interaction. Due to the hybrid approach and the wide working range of the proprietary soft actuators, the HAP-joint could achieve controllable impact responses both predetermined by control parameters and regulated online by real-time feedback. The design, modeling, control, and experimental validation of HAP-joint are presented in detail. Based on the excellent features and performances of HAP-joint, a controller framework is formulated on impact response shaping, combining passive compliance, and online regulating. The controller could achieve both excellent tracking behavior while handling accidental impacts following a desired manner, demonstrating the vast potentials of soft robots for safe and forceful interactive tasks toward various applications.
Markov Differential Game for Network Defense Decision-Making Method

While network attack and defense are experiencing a rapid change, the current research achievements of network security based on traditional game theory fail to characterize the real-time performance of the actual network attack–defense process accurately. Furthermore, all kinds of disturbance and accidental factors would affect the evolution of the network security state. Therefore, to tackle with the randomness of network security state and the high dynamic of network defense decision making, we analyzed the attack–defense behaviors from the perspectives of dynamic and real-time confrontation. Then we constructed the Markov attack–defense differential game model for the dynamic analysis to predict multi-stage continuous attack–defense process by combining differential game models and the Markov decision-making method. In addition, according to the discounted total payoffs of attack–defense game, we designed the objective function of the game. Based on previous statements, we proposed the multi-stage game equilibrium solution and designed the optimal defense strategy selection algorithm. Finally, we conducted simulations to demonstrate that the proposed model and method could shed some light to the real-time interplay of decision making between attack and defense.
Profiles of empathic sensitivity in students of the last year of medicine.

Developing the empathic attitude is one of the tasks of medical education as it affects the quality of therapeutic contact in the relationship between the doctor and the participant, conditioning the treatment process. According to Davis's concept, empathy is defined as an affective-cognitive reaction in the context of the other person's experience. AIM Analysis of profiles of empathic sensitivity in students of medicine. Group: Male and female students of the fifth year of medicine who agreed to participate in an anonymous study (n = 153; M = 57, F = 96; mean age: 23 years). Tools: The Empathetic Sensitivity Scale (EES), which is the Polish tool for Davis's Interpersonal Reactivity Index (IRI) was used. The ESS includes three sub-scales: Empathic Care (EC), Personal Distress (PD) and Adopting Perspective (AP). RESULTS The raw results were converted into sten scores and for sten scores for all three dimensions of empathetic sensitivity no differences were found between male and female students. Three clusters (1: n = 33%, 2: n = 39%, 3: n = 28%), which differ in terms of each distinguished indicator, were identified. CONCLUSIONS The first cluster characterizes empathetic people, both in the affective and cognitive spheres, and those dealing well with unpleasant emotions in situations difficult to others. The second cluster characterizes participants with the ability to recognize the needs of others and to take into account their perspectives; the third cluster includes participants with a tendency to focus on own experiences emerging in response to other people's suffering but with the ability to understand a situation and show empathic concern for the other person. The most favourable profile - for a future doctor as well as for his participants - is the first cluster because the doctor, with his empathic sensitivity directed towardsthe other man, can deal with his own unpleasant emotions.
Magnetic resonance (MR) spectroscopic measurement of γ-aminobutyric acid (GABA) in major depression before and after electroconvulsive therapy

Abstract Objective Prior studies suggest that a dysregulation of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) is involved in the pathophysiology of major depression. We aimed to elucidate changes in cortical GABA content in relation to depression and electroconvulsive therapy (ECT) using magnetic resonance spectroscopy (MRS). Methods In total, 11 patients with major depression or depressive episode of bipolar disorder (mean pre-ECT Ham-17 of 26) and 11 healthy subjects were recruited. GABA was quantified using short-TE MRS in prefrontal and occipital cortex. Other neurometabolites such as glutathione (GSH), N-acetylaspartate (NAA) and glutamate (Glu) were secondary outcome measures. Results No significant differences in GABA/Cr levels were observed between patients at baseline and healthy subjects in prefrontal cortex, t(20)=0.089, p=0.93 or occipital cortex t(21)=0.37, p=0.72. All patients improved on Ham-17 (mean post-ECT Ham-17 of 9). No significant difference was found in GABA, Glu, glutamine, choline or GSH between pre- and post-ECT values. However, we observed a significant decrease in NAA levels following ECT t(22)=3.89, p=0.0038, and a significant correlation between the NAA decline and the number of ECT sessions p=0.035. Conclusions Our study does not support prior studies arguing for GABA as a key factor in the treatment effect of ECT on major depression. The reduction in NAA levels following ECT could be due to neuronal loss or a transient dysfunction in prefrontal cortex. As no long-term follow-up scan was performed, it is unknown whether NAA levels will normalise over time.
Test-retest reliability of the Life Satisfaction Questionnaire (LiSat-11) and association between items in individuals with chronic stroke.

OBJECTIVE To evaluate the test-retest reliability of the Life Satisfaction Questionnaire (LiSat-11) and the association between items in individuals with chronic stroke. DESIGN Test-retest design. SUBJECTS Forty-five individuals (mean age 65 years) with mild to moderate disability at least 6 months post-stroke. METHODS LiSat-11, which includes 1 global item "Life as a whole" and 10 domain-specific items, was rated on 2 occasions, one week apart. Test-retest reliability was evaluated by kappa statistics, the percent agreement (PA) and the Svensson rank-invariant method. The association between items was evaluated with the Spearman's rank correlation coefficient (rho). RESULTS The kappa coefficients showed good to excellent agreement (0.59-0.97) and the PA ≤ 1 point was high (> 89%) for all items. According to the Svensson method, a small systematic disagreement was found for "Partner relationship". The other items showed no systematic or random disagreements. All domain-specific items, except one ("Sexual life") were significantly correlated with "Life as a whole" (rhos 0.29-0.80). CONCLUSION LiSat-11 is considered reliable and can be recommended for assessing life satisfaction after stroke. The association between items indicates that LiSat-11 measures various aspects that can impact on an individual's life satisfaction.
Passivity Analysis and Control of Humanoid Robots on Movable Ground

Reliable and robust balancing controllers are key elements of whole-body control frameworks for humanoid robots. Passivity-based balancing controllers have been proposed and tested successfully in various scenarios involving different types of ground surfaces. This letter extends the passivity considerations for covering not only the robot and the controller but also the ground floor in order to guarantee an appropriate behavior, even when the underlying ground surface is not stable. The proposed extension is validated with experiments using the humanoid robot TOrque-controlled humanoid RObot (TORO).
The State of Practice on Virtual Reality (VR) Applications: An Exploratory Study on Github and Stack Overflow

Virtual Reality (VR) is a computer technology that holds the promise of revolutionizing the way we live. The release in 2016 of new-generation headsets from Facebook-owned Oculus and HTC has renewed the interest in that technology. Thousands of VR applications have been developed over the past years, but most software developers lack formal training on this technology. In this paper, we propose descriptive information on the state of practice of VR applications' development to understand the level of maturity of this new technology from the perspective of Software Engineering (SE). To do so, we focused on the analysis of 320 VR open source projects from Github to determine which are the most popular languages and engines used in VR projects, and evaluate the quality of the projects from a software metric perspective. To get further insights on VR development, we also manually analyzed nearly 300 questions from Stack Overflow. Our results show that (1) VR projects on GitHub are currently mostly small to medium projects, and (2) the most popular languages are JavaScript and C#. Unity is the most used game engine during VR development and the most discussed topic on Stack Overflow. Overall, our exploratory study is one of the very first of its kind for VR projects and provides material that is hopefully a starting point for further research on challenges and opportunities for VR software development.
Inhibitory effects of quail egg on mast cells degranulation by suppressing PAR2-mediated MAPK and NF-kB activation

Background Quail egg (QE) has been reported to possess an anti-allergic and anti-inflammatory activity. We have demonstrated that whole QE was able to attenuate the allergic symptoms in food allergy–induced EoE murine model, but whether QE albumen or QE yolk plays a more important role still remains unclear. Objective In this current study, we investigated the suppressive role of QE in mast cell degranulation and cytokine production of the effect phase response. Method A passive cutaneous anaphylaxis (PCA) mouse model was used to confirm the anti-allergic effect of QE. Besides, HMC-1 cell model was used to study its suppressive role in more detail. In this in vitro study, we divided QE into three groups: whole QE, QE albumen, and QE yolk. The effect of QE treatment on mast cell degranulation and intracellular calcium influx was investigated. Moreover, the effect of QE allergy– related mediators, genes, and proteins were also assessed by ELISA, RT-PCR, and western blotting. Results and discussion Our data showed that the extent of mast cell degranulation–mediated ear vascular permeability in IgE-mediated PCA mice treated with whole QE (17 mg/kg) was decreased significantly up to 43.31 ± 0.42% reduction. HMC-1 cell–based immunological assay in vitro indicated that QE, particularly its albumen, acted as a ‘mast cell stabilizer’. Under the concentration of 70 μg/mL, QE albumen effectively suppressed the releases of β-hexosaminidase, histamine, and tryptase, as well as Th2 and pro-inflammatory cytokine production; reached 30 up to 50% reduction. Besides, QE albumen was also able to significantly modulate the upregulation of IL-10 up to 58.30 ± 5.9%. Interestingly, our data indicated that QE yolk still had a significant inhibitory effect on modulating Th2 cytokines in its highest concentration (100 μg/mL), while QE albumen showed no inhibitory effect. Western blot analysis showed QE albumen effectively down-regulated the expressions of calcium-related protein (TRPC1, Orai1, STIM1, PLC-γ and IP3R), facilitated the reduction of PAR-2 and induced the reduction of phosphorylation of JNK, IKKα, p50 and p65 protein expressions. Conclusion As confirmed by PCA and HMC-1 cell-based immunology assay, QE albumen and QE yolk may work together through exerting anti-allergy activity and can be used as a potential anti-allergic nutrient in the future.
A Parallel, Energy Efficient Hardware Architecture for the merAligner on FPGA Using Chisel HCL

Nowadays science has made great progress in extracting information from DNA and the huge amounts of data that is being produced need new ways and architectures to carry on the computation in an efficient way. Among the different analysis performed on the DNA, one of the most compute intensive concerns the task of aligning a set of strings (reads) to specific targets. In these regards, Lawrence Berkeley National Laboratory (LBNL) and the University of California Berkeley (UCB) developed the merAligner: a fully parallel sequence aligner that uses a seed-and-extend algorithm to perform the alignment. This aligner is able to scale up efficiently to thousands of cores on a Cray XC30 supercomputer. Despite the high computational power, this architecture consumes a significant amount of power, reducing considerably its power efficiency. To this end, reconfigurable hardware architectures have demonstrated to be able to deliver high performances, while keeping a relatively low power profile. In this work, we propose an FPGA architecture for the alignment step of the merAligner. The architecture has been designed using Chisel HCL, while the final architecture has been synthesized using Xilinx SDAccel targeting a Xilinx Kintex Ultrascale board. Final results are capable of outperforming merAligner alignment step on a test dataset by a factor of up to 7x in performance and 66x in power efficiency.
Is the History of Substance Abuse Correlated with Neuropsychiatric Disorders and Co-morbid HIV Infection? An Urban Population Study.

Background Human immunodeficiency virus (HIV) infection remains a serious immunological disease with new infections in the U.S. disproportionately reported in minority populations. For many years, the District of Columbia (DC) has reported the highest HIV infection rate in the nation. Drug abuse and addiction is also prevalent in DC and has traditionally been linked to HIV/AIDS because of the likelihood for opportunistic infections. Despite this data, the relationship between HIV status, drugs of abuse, and the incidence of neurological disorders are scarcely reported for minority populations. Method We carried out a retrospective study on the prevalence of substance abuse in HIV and their association with neuropsychiatric comorbidities in an African American subpopulation in Washington DC. Findings Our data suggests an 86 percent prevalence of drug use in the HIV patients with neuropsychiatric comorbidities, with cocaine use being significantly higher in patients with major depressive disorder (MDD) and bipolar disorder (BD), whereas PCP use was associated with patients with schizophrenia. The mean CD4 count was elevated in patients with neuropsychiatric disease, and specifically in MDD patients. CD8 counts were elevated as expected for HIV status but were not influenced by disease diagnosis. A majority (2/3) of patients were on HAART therapy, however the records did not account for adherence. Conclusion These data suggest that neuropsychiatric comorbidities are independent of HIV disease progression but are correlated with certain illicit drugs of abuse.
Resilient Filtering for Linear Time-Varying Repetitive Processes Under Uniform Quantizations and Round-Robin Protocols

In this paper, the resilient filtering problem is investigated for a class of linear time-varying repetitive processes with communication constraints. The communication between the sensors and the remote filter, which is subject to uniform quantizations, is carried out through a shared communication medium where only one sensor has access to the network at each transmission time. To prevent data from collisions, the Round-Robin (R-R) protocol scheduling is applied to orchestrate the transmission order of sensor nodes in a periodic manner. Moreover, stochastic perturbations on the gain parameters are taken into account in the course of the actual filter implementation. The main purpose of the addressed problem is to design a resilient filter such that, in the presence of the uniform quantization, the R-R protocol, and the filter gain perturbation, a certain upper bound is guaranteed on the filtering error variance and subsequently minimized at each time instant. By means of intensive stochastic analysis and mathematical induction, sufficient condition is provided to ensure the local minimization of certain upper bound on the filtering error variance. Furthermore, the boundedness issue is also discussed with respect to the filtering error variance. Finally, a numerical example is employed to demonstrate the effectiveness of the proposed filter strategy.
Long-term results of photodynamic therapy or ranibizumab for polypoidal choroidal vasculopathy in LAPTOP study

Background/aim We previously reported that ranibizumab performed better on visual prognosis than photodynamic therapy (PDT) in a Ranibizumab (Lucentis) And Photodynamic Therapy On Polypoidal choroidal vasculopathy (LAPTOP) study. To determine if the first-choice treatment, either PDT or intravitreal ranibizumab, has a long-term effect in patients with polypoidal choroidal vasculopathy (PCV). Methods We reviewed medical records of patientsrandomised to either PDT (29 eyes) or ranibizumab (27 eyes) from July 2009 to June 2011 in LAPTOP study. Retreatment or switching to other treatments were at the investigator’s discretion after release from the 2-year LAPTOP study up to 5years. We evaluated visual acuity (VA), continuity of initial treatment, percentage of dry macula achievement and macular atrophy at 5 years. Results The logarithm of minimal angle of resolution VA was 0.56 in the PDT and 0.44 in the ranibizumab groups at baseline (p=0.101) and was 0.55 and 0.28 at 5years, respectively (p<0.05). More than 70% of the patients converted to aflibercept in following years. Achievement percentages of dry macula were 74% (PDT) and 63% (ranibizumab) at 5years, and macular atrophy was detected in 78% (PDT) and 60% (ranibizumab) with a mean area of 7.7 and 3.5 mm2, respectively (p=0.155). Conclusions The better VA in the initial ranibizumab group compared with the PDT group at 2 years was retained at the 5-year follow-up.
The effects of a workplace intervention on employees’ cortisol awakening response

ABSTRACT Work-related stressors are known to adversely affect employees’ stress physiology, including the cortisol awakening response (CAR) – or the spike in cortisol levels shortly after people wake up that aids in mobilizing energy. A flat or blunted CAR has been linked to chronic stress and burnout. This daily diary study tested the effects of a workplace intervention on employed parents’ CAR. Specifically, we tested whether the effects of the intervention on CAR were moderated by the type of days (workday versus non-work day). Data came from 94 employed parents from an information technology firm who participated in the baseline and 12-month diurnal cortisol components of the Work, Family, and Health Study, a group-randomized field experiment. The workplace intervention was designed to reduce work-family conflict (WFC) and implemented after the baseline data collection. Diurnal salivary cortisol was collected on 4 days at both baseline and 12 months. Multilevel modeling revealed that the intervention significantly increased employees’ CAR at 12 months on non-workdays, but this was not evident on workdays or for employees in the usual practice condition. The results provide evidence that the intervention was effective in enhancing employees’ biological stress physiology particularly during opportunities for recovery that are more likely to occur on non-work days.
Antibacterial effects and resistance induction of silver and gold nanoparticles against Staphylococcus aureus‐induced mastitis and the potential toxicity in rats

Staphylococcus aureus (S. aureus) is one of the prevalent mastitis‐inducing pathogens worldwide. The resistance of S. aureus to antibiotics is a common issue for dairy farms. Recently, nanoparticles (NPs) have been used for treating antibiotic‐resistant bacteria. We therefore aimed to investigate the antimicrobial effect of silver and gold NPs (AgNPs and AuNPs, respectively) and the resistance developed by S. aureus as well as the toxic effects of both NPs in rats. We used 198 S. aureus strains to determine the antibacterial effects of AgNPs and AuNPs. The microdilution method was used to establish the minimum inhibitory concentrations (MICs) of both NPs. To induce resistance, 20 S. aureus strains were passaged 10 times in broth medium with sublethal doses of NPs and an additional 10 times without NPs to examine the stability of resistance. Histopathology was performed after oral administration to the rats with the study doses of 0.25, 0.5, 1, and 2 mg/kg of NPs for 30 days. The MICs of 10‐nm AgNPs, 20‐nm AgNPs, 10‐nm AuNPs, and 20‐nm AuNPs against S. aureus were 14.70 ± 1.19 μg/ml, 9.15 ± 0.13 μg/ml, 24.06 ± 2.36 μg/ml, and 18.52 ± 1.26 μg/ml, respectively. Most strains developed strong resistance when treated with 20‐nm or 10‐nm AgNPs, whereas only two strains were resistant to 10‐nm AuNPs and three strains to 20‐nm AuNPs. No cross‐resistance between NPs and various antibiotics was identified in any of the adapted S. aureus strains. Organ histopathology revealed that 0.25, 0.5, and 1 mg/kg doses of AgNPs and AuNPs were not toxic to rat tissue. In contrast, a higher dose (2 mg/kg) of NPs impaired all organs tested. This study demonstrates the antibacterial effects of NPs. S. aureus strains develop resistance less frequently against AuNPs than AgNPs, and neither AuNPs nor AgNPs was toxic to rats at low doses.