Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Memory CD4+ T Cell Immune Responses against Giardia lamblia

ABSTRACT The intestinal protozoan parasite Giardia lamblia may cause severe prolonged diarrheal disease or pass unnoticed as an asymptomatic infection. T cells seem to play an important role in the immune response to Giardia infection, and memory responses may last years. Recently, TH17 responses have been found in three animal studies of Giardia infection. The aim of this study was to characterize the human CD4+ T cell responses to Giardia. Peripheral blood mononuclear cells (PBMCs) were obtained from 21 returning travelers with recent or ongoing giardiasis and 12 low-risk healthy controls and stimulated in vitro with Giardia lamblia proteins. Production of tumor necrosis factor alpha (TNF-α), gamma interferon, interleukin-17A (IL-17A), IL-10, and IL-4 was measured in CD4+ effector memory (EM) T cells after 24 h by flow cytometry. After 6 days of culture, activation and proliferation were measured by flow cytometry, while an array of inflammatory cytokine levels in supernatants were measured with multiplex assays. We found the number of IL-17A-producing CD4+ EM T cells, as well as that of cells simultaneously producing both IL-17A and TNF-α, to be significantly elevated in the Giardia-exposed individuals after 24 h of antigen stimulation. In supernatants of PBMCs stimulated with Giardia antigens for 6 days, we found inflammation-associated cytokines, including 1L-17A, as well as CD4+ T cell activation and proliferation, to be significantly elevated in the Giardia-exposed individuals. We conclude that symptomatic Giardia infection in humans induces a CD4+ EM T cell response of which IL-17A production seems to be an important component.
Innocent Strategies as Presheaves and Interactive Equivalences for CCS

Seeking a general framework for reasoning about and comparing programming languages, we derive a new view of Milner's CCS. We construct a category E of 'plays', and a subcategory V of 'views'. We argue that presheaves on V adequately represent 'innocent' strategies, in the sense of game semantics. We equip innocent strategies with a simple notion of interaction. We then prove decomposition results for innocent strategies, and, restricting to presheaves of finite ordinals, prove that innocent strategies are a final coalgebra for a polynomial functor derived from the game. This leads to a translation of CCS with recursive equations. Finally, we propose a notion of 'interactive equivalence' for innocent strategies, which is close in spirit to Beffara's interpretation of testing equivalences in concurrency theory. In this framework, we consider analogues of fair testing and must testing. We show that must testing is strictly finer in our model than in CCS, since it avoids what we call 'spatial unfairness'. Still, it differs from fair testing, and we show that it coincides with a relaxed form of fair testing.
Tersoff potential with improved accuracy for simulating graphene in molecular dynamics environment

Graphene is an elementary unit for various carbon based nanostructures. The recent technological developments have made it possible to manufacture hybrid and sandwich structures with graphene. In order to model these nanostructures in atomistic scale, a compatible interatomic potential is required to successfully model these nanostructures. In this article, an interatomic potential with modified cut-off function for Tersoff potential was proposed to avoid overestimation and also to predict the realistic mechanical behavior of single sheet of graphene. In order to validate the modified form of cut-off function for Tersoff potential, simulations were performed with different set of temperatures and strain rates, and results were made to compare with available experimental data and molecular dynamics simulation results obtained with the help of other empirical interatomic potentials.
Comparative Study on Recent Development of Heuristic Optimization Methods

In engineering and design problems, various noisy non-linear mathematical optimization problems can't be efficaciously solved by using conventional optimization techniques. But metaheuristic algorithms seem very efficient to approach in these problems and became very popular such as Genetic Algorithm (GA), Particle Swarm Optimization (PSO). Recently, many new metaheuristic algorithms were proposed, but the performance of these algorithms in solving noisy non-linear optimization problems when compared with popular methods still need more of verifications. In this context, two popular algorithms called GA and PSO will be compared with some recent metaheuristic algorithms such as Grey Wolf Optimizer, Firefly Algorithm, and Brain Storm Optimization algorithm in finding optimal solutions of noisy non-linear optimization problems. The results will be compared in terms of accuracy of the best solutions found and the execution time.
PECVD silicon-rich nitride and low stress nitride films mechanical characterization using membrane point load deflection

An analysis of the mechanical properties of plasma enhanced chemical vapor (PECVD) silicon nitrides is presented, using micro fabricated silicon nitride membranes under point load deflection. The membranes are made of PECVD silicon-rich nitride and low stress nitride films. The mechanical performance of the bended membranes is examined both with analytical models and finite element simulation in order to extract the elastic modulus and residual stress values. The elastic modulus of low stress silicon nitride is calculated using stress free analytical models, while for silicon-rich silicon nitride and annealed low stress silicon nitride it is estimated with a pre-stressed model of point-load deflection. The effect of annealing both in nitrogen and hydrogen atmosphere is evaluated in terms of residual stress, refractive index and thickness variation. It is demonstrated that a hydrogen rich annealing atmosphere induces very little change in low stress silicon nitride. Nitrogen annealing effects are measured and shown to be much higher in silicon-rich nitride than in low stress silicon nitride. An estimate of PECVD silicon-rich nitride elastic modulus is obtained in the range between 240–320 GPa for deposited samples and 390 GPa for samples annealed in nitrogen atmosphere. PECVD low stress silicon nitride elastic modulus is estimated to be 88 GPa as deposited and 320 GPa after nitrogen annealing.
A bone substitute with high affinity for vitamin D-binding protein―relationship with niche of osteoclasts

The biological activity of osteoblasts and osteoclasts is regulated not only by hormones but also by local growth factors, which are expressed in neighbouring cells or included in bone matrix. Previously, we developed hydroxyapatite (HA) composed of rod‐shaped particles using applied hydrothermal methods (HHA), and it revealed mild biodegradability and potent osteoclast homing activity. Here, we compared serum proteins adsorbed to HHA with those adsorbed to conventional HA composed of globular‐shaped particles (CHA). The two ceramics adsorbed serum albumin and γ‐globulin to similar extents, but affinity for γ‐globulin was much greater than that to serum albumin. The chemotactic activity for macrophages of serum proteins adsorbed to HHA was significantly higher than that of serum proteins adsorbed to CHA. Quantitative proteomic analysis of adsorbed serum proteins revealed preferential binding of vitamin D‐binding protein (DBP) and complements C3 and C4B with HHA. When implanted with the femur of 8‐week‐old rats, HHA contained significantly larger amount of DBP than CHA. The biological activity of DBP was analysed and it was found that the chemotactic activity for macrophages was weak. However, DBP‐macrophage activating factor, which is generated by the digestion of sugar chains of DBP, stimulated osteoclastogenesis. These results confirm that the microstructure of hydroxyapatite largely affects the affinity for serum proteins, and suggest that DBP preferentially adsorbed to HA composed of rod‐shaped particles influences its potent osteoclast homing activity and local bone metabolism.
Delayed platelet recovery after allogeneic hematopoietic stem cell transplantation: Association with chronic graft‐versus‐host disease and survival outcome

Delayed platelet recovery (DPR) despite prompt neutrophil engraftment is frequently observed after allogeneic hematopoietic stem cell transplantation (HSCT). However, few studies have evaluated the risk factors and long‐term outcome. Therefore, we retrospectively analysed 219 adult patients who underwent their first allogenic HSCT with neutrophil engraftment. Of these 219 patients, 50 (22.8%) had DPR that was defined as relapse‐free survival at day 60 after HSCT without primary platelet recovery despite neutrophil engraftment. The results of a multivariate analysis showed that a high‐risk underlying disease (odds ratio [OR], 2.38; 95% confidence interval [CI], 1.04‐5.48; P = .041) and human leukocyte antigen–mismatched HSCT (OR, 2.63; 95% CI, 1.28‐5.43; P = .009) were associated with an increased risk of DPR. In univariate analyses, the occurrence of DPR was significantly associated with inferior overall survival, high nonrelapse mortality, and a low incidence of chronic graft‐versus‐host disease (GVHD), despite a comparable relapse rate. In multivariate analyses, DPR was associated with inferior overall survival (hazard ratio [HR], 2.00; 95% CI, 1.23‐3.27; P = .005) and a low incidence of chronic GVHD (HR, 0.42; 95% CI, 0.22‐0.78; P = .002). In conclusion, DPR was a strong predictor of shorter survival but also less frequent chronic GVHD.
Plastic Moment of Intermediate Horizontal Boundary Elements of Steel Plate Shear Walls

This paper presents results of an analytical study of plastic moment in horizontal boundary elements (HBEs) in steel plate shear walls. To account for the effect of shear and vertical stresses in HBE web, the reduced axial yield strength was studied using the von Mises yield criterion. In the spirit of classic plastic analysis, analytical procedures for estimating plastic moment of the intermediate HBE under equal top and bottom tension fields are developed. Those analytical procedures are then extended for intermediate HBE under unequal top and bottom tension fields. Both positive and negative flexures are considered. Results from the analytical procedures are shown to agree well with those from finite element analysis. Simplified models for estimating plastic moment of HBEs are also developed for design and shown to be accurate.
Short-term effects of physiotherapy combining repetitive facilitation exercises and orthotic treatment in chronic post-stroke patients

[Purpose] This study investigated the short-term effects of a combination therapy consisting of repetitive facilitative exercises and orthotic treatment. [Subjects and Methods] The subjects were chronic post-stroke patients (n=27; 24 males and 3 females; 59.3 ± 12.4 years old; duration after onset: 35.7 ± 28.9 months) with limited mobility and motor function. Each subject received combination therapy consisting of repetitive facilitative exercises for the hemiplegic lower limb and gait training with an ankle-foot orthosis for 4 weeks. The Fugl-Meyer assessment of the lower extremity, the Stroke Impairment Assessment Set as a measure of motor performance, the Timed Up & Go test, and the 10-m walk test as a measure of functional ambulation were evaluated before and after the combination therapy intervention. [Results] The findings of the Fugl-Meyer assessment, Stroke Impairment Assessment Set, Timed Up & Go test, and 10-m walk test significantly improved after the intervention. Moreover, the results of the 10-m walk test at a fast speed reached the minimal detectible change threshold (0.13 m/s). [Conclusion] Short-term physiotherapy combining repetitive facilitative exercises and orthotic treatment may be more effective than the conventional neurofacilitation therapy, to improve the lower-limb motor performance and functional ambulation of chronic post-stroke patients.
BchY-Based Degenerate Primers Target All Types of Anoxygenic Photosynthetic Bacteria in a Single PCR

ABSTRACT To detect anoxygenic bacteria containing either type 1 or type 2 photosynthetic reaction centers in a single PCR, we designed a degenerate primer set based on the bchY gene. The new primers were validated in silico using the GenBank nucleotide database as well as by PCR on pure strains and environmental DNA.
Influence of atmospheric stability on wind-turbine wakes: A large-eddy simulation study

In this study, large-eddy simulation is combined with a turbine model to investigate the influence of atmospheric thermal stability on wind-turbine wakes. The simulation results show that atmospheric stability has a significant effect on the spatial distribution of the mean velocity deficit and turbulence statistics in the wake region as well as the wake meandering characteristics downwind of the turbine. In particular, the enhanced turbulence level associated with positive buoyancy under the convective condition leads to a relatively larger flow entrainment and, thus, a faster wake recovery. For the particular cases considered in this study, the growth rate of the wake is about 2.4 times larger for the convective case than for the stable one. Consistent with this result, for a given distance downwind of the turbine, wake meandering is also stronger under the convective condition compared with the neutral and stable cases. It is also shown that, for all the stability cases, the growth rate of the wake and wake meandering in the vertical direction is smaller compared with the ones in the lateral direction. This is mainly related to the different turbulence levels of the incoming wind in the different directions, together with the anisotropy imposed by the presence of the ground. It is also found that the wake velocity deficit is well characterized by a modified version of a recently proposed analytical model that is based on mass and momentum conservation and the assumption of a self-similar Gaussian distribution of the velocity deficit. Specifically, using a two-dimensional elliptical (instead of axisymmetric) Gaussian distribution allows to account for the different lateral and vertical growth rates, particularly in the convective case, where the non-axisymmetry of the wake is stronger. Detailed analysis of the resolved turbulent kinetic energy budget in the wake reveals also that thermal stratification considerably affects the magnitude and spatial distribution of the turbulence production, dissipation, and transport terms.
Secure Linear Regression on Vertically Partitioned Datasets

We propose multi-party computation protocols for securely computing a linear regression model from a training dataset whose columns are distributed among several parties. Our solution enables organizations to collaborate in the construction of a predictive model while keeping their training data private. Our approach is based on a hybrid MPC protocol combining garbled circuits with an offline phase enabled by a semi-trusted external party. As part of our contribution, we evaluate several algorithms and implementations for solving systems of linear equations using garbled circuts. Experiments conducted with an implementation of our protocols show that our approach leads to highly scalable solutions that can solve data analysis problems with one million records and one hundred features in less than one hour.
Piezoresistance in Polymer Nanocomposites

Piezoresistivity in conductive polymer nanocomposites occurs because of the disturbance of particle networks in the polymer matrix. The piezoresistance effect becomes more prominent if the matrix material is compliant making these materials attractive for applications that require flexible force and displacement sensors such as e‐textiles and biomechanical measurement devices. However, the exact mechanisms of piezoresistivity including the relationship between the matrix polymer, conductive particle, internal structure and the composite’s piezoresistance need to be better understood before it can be applied for such applications. The objective of this thesis is to report on the development of conductive polymer nanocomposites for use as flexible sensors and electrodes. Electrically conductive and piezoresistive nanocomposites were fabricated by a scalable melt compounding process. Particular attention was given to elucidating the role of matrix and filler materials, plastic deformation and porosity on the electrical conduction and piezoresistance. These effects were parametrically investigated through characterizing the morphology, electrical properties, rheological properties, and
Tunable Bandgap and Optical Properties of Black Phosphorene Nanotubes

Black phosphorus (BP), a new two-dimensional material, has been the focus of scientists’ attention. BP nanotubes have potential in the field of optoelectronics due to their low-dimensional effects. In this work, the bending strain energy, electronic structure, and optical properties of BP nanotubes were investigated by using the first-principles method based on density functional theory. The results show that these properties are closely related to the rolling direction and radius of the BP nanotube. All the calculated BP nanotube properties show direct bandgaps, and the BP nanotubes with the same rolling direction express a monotone increasing trend in the value of bandgap with a decrease in radius, which is a stacking effect of the compression strain on the inner atoms and the tension strain on the outer atoms. The bending strain energy of the zigzag phosphorene nanotubes (zPNTs) is higher than that of armchair phosphorene nanotubes (aPNT) with the same radius of curvature due to the anisotropy of the BP’s structure. The imaginary part of the dielectric function, the absorption range, reflectivity, and the imaginary part of the refractive index of aPNTs have a wider range than those of zPNTs, with higher values overall. As a result, tunable BP nanotubes are suitable for optoelectronic devices, such as lasers and diodes, which function in the infrared and ultra-violet regions, and for solar cells and photocatalysis.
Low Power Link Layer Security for Internet of Things : Implementation and Performance Analysis

In this paper we present the implementation and performance evaluation of security functionalities at the link layer of IEEE 802.15. 4-compliant IoT devices. Specifically, we implement the required encryption and authentication mechanisms entirely in software and as well exploit the hardware ciphers that are made available by our IoT platform. Moreover, we present quantitative results on the memory footprint, the execution time and the energy consumption of selected implementation modes and discuss some relevant tradeoffs. As expected, we find that hardware-based implementations are not only much faster, leading to latencies shorter than two orders of magnitude compared to software-based security suites, but also provide substantial savings in terms of ROM memory occupation, i.e. up to six times, and energy consumption. Furthermore, the addition of hardware-based security support at the link layer only marginally impacts the network lifetime metric, leading to worst-case reductions of just 2% compared to the case where no security is employed. This is due to the fact that energy consumption is dominated by other factors, including the transmission and reception of data packets and the control traffic that is required to maintain the network structures for routing and data collection. On the other hand, entirely software-based implementations are to be avoided as the network lifetime reduction in this case can be as high as 25%.
Person Name Disambiguation based on Topic Model

In this paper we describe our participation in the SIGHAN 2010 Task-3 (Person Name Disambiguation) and detail our approaches. Person Name Disambiguation is typically viewed as an unsupervised clustering problem where the aim is to partition a name’s contexts into different clusters, each representing a real world people. The key point of Clustering is the similarity measure of context, which depends upon the features selection and representation. Two clustering algorithms, HAC and DBSCAN, are investigated in our system. The experiments show that the topic features learned by LDA outperforms token features and more robust.
Cramér-Rao Bound for Circular and Noncircular Complex Independent Component Analysis

Despite an increased interest in complex independent component analysis (ICA) during the last two decades, a closed form expression for the Cramér-Rao bound (CRB) for the demixing matrix is not known yet. In this paper, we fill this gap by deriving a closed-form expression for the CRB of the demixing matrix for instantaneous noncircular complex ICA. It contains the CRB for circular complex ICA and noncircular complex Gaussian ICA as two special cases. We also study the CRB numerically for the family of noncircular complex generalized Gaussian distributions and compare it to simulation results of two ICA estimators. Furthermore, we show how to extend the CRB to the case where the source signals are not temporally independent and identically distributed.
Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo

The ability of grand canonical Monte Carlo (GCMC) to create and annihilate molecules in a given region greatly aids the identification of water sites and water binding free energies in protein cavities. However, acceptance rates without the application of biased moves can be low, resulting in large variations in the observed water occupancies. Here, we show that replica-exchange of the chemical potential significantly reduces the variance of the GCMC data. This improvement comes at a negligible increase in computational expense when simulations comprise of runs at different chemical potentials. Replica-exchange GCMC is also found to substantially increase the precision of water binding free energies as calculated with grand canonical integration, which has allowed us to address a missing standard state correction.
Cognitive Behavioral Therapy for Depression, Anxiety, and Stress in Caregivers of Dementia Patients: A Systematic Review and Meta-Analysis.

Background and Objectives There is limited evidence for the efficacy of cognitive behavioral therapy (CBT) in managing psychological morbidities in caregivers of dementia patients. To evaluate changes in dementia caregivers' depression, anxiety, and stress following CBT. Also to assess quality of life, intervention adherence/satisfaction and therapy effectiveness using different formats, frequencies, and delivery methods. Research Design and Methods Studies were identified through electronic bibliographic searches (MEDLINE, EMBASE, CINAHL, PsycINFO, and the Cochrane Library) and from gray literature (Conference Proceedings Citation Index and clinicaltrials.gov). Data were pooled for meta-analysis. Results Twenty-five studies were included. Depression (standardized mean difference [SMD] = -0.34; 95% confidence interval [CI] -0.47 to -0.21; p < .001) and stress (SMD = -0.36; 95% CI: -0.52 to -0.20; p < .001) were significantly reduced after CBT, relative to comparator groups, while anxiety was not (SMD = 0.10; 95% CI: -0.18 to 0.39; p = .47). A subgroup analysis demonstrated that statistically significant reductions in depression and stress were limited to group, but not individual, formats. An additional subgroup analysis revealed that eight CBT sessions or fewer were equally effective as more than eight sessions at significantly reducing depression and stress, relative to comparator groups. Furthermore, analysis with independent samples t-tests demonstrated no statistically significant differences between mean changes in depression (MD = 0.79; 95% CI: -0.45 to 2.03; p = .21) and stress (MD = 0.21; 95% CI: -1.43 to 1.85; p = .80) when directly comparing CBT groups of ≤8 and >8 sessions. Discussion and Implications Group CBT provides small but significant benefits to caregivers' depression and stress. Therapy cost-effectiveness may be improved by limiting therapy to group formats and eight sessions.