Miracle-dz/UniFAR-FTUs huggingface dataset:
Brucella Peptide Cross-Reactive Major Histocompatibility Complex Class I Presentation Activates SIINFEKL-Specific T Cell Receptor-Expressing T Cells

ABSTRACT Brucella spp. are intracellular pathogenic bacteria remarkable in their ability to escape immune surveillance and therefore inflict a state of chronic disease within the host. To enable further immune response studies, Brucella was engineered to express the well-characterized chicken ovalbumin (OVA). Surprisingly, we found that CD8 T cells bearing T cell receptors (TCR) nominally specific for the OVA peptide SIINFEKL (OT-1) reacted to parental Brucella-infected targets as well as OVA-expressing Brucella variants in cytotoxicity assays. Furthermore, splenocytes from Brucella-immunized mice produced gamma interferon (IFN-γ) and exhibited cytotoxicity in response to SIINFEKL-pulsed target cells.To determine if the SIINFEKL-reactive OT-1 TCR could be cross-reacting to Brucella peptides, we searched the Brucella proteome using an algorithm to generate a list of near-neighbor nonamer peptides that would bind to H2Kb. Selecting five Brucella peptide candidates, along with controls, we verified that several of these peptides mimicked SIINFEKL, resulting in T cell activation through the “SIINFEKL-specific” TCR. Activation was dependent on peptide concentration as well as sequence. Our results underscore the complexity and ubiquity of cross-reactivity in T cell recognition. This cross-reactivity may enable microbes such as Brucella to escape immune surveillance by presenting peptides similar to those of the host and may also lead to the activation of autoreactive T cells.
Prediction of Return-to-original-work after an Industrial Accident Using Machine Learning and Comparison of Techniques

Background Many studies have tried to develop predictors for return-to-work (RTW). However, since complex factors have been demonstrated to predict RTW, it is difficult to use them practically. This study investigated whether factors used in previous studies could predict whether an individual had returned to his/her original work by four years after termination of the worker's recovery period. Methods An initial logistic regression analysis of 1,567 participants of the fourth Panel Study of Worker's Compensation Insurance yielded odds ratios. The participants were divided into two subsets, a training dataset and a test dataset. Using the training dataset, logistic regression, decision tree, random forest, and support vector machine models were established, and important variables of each model were identified. The predictive abilities of the different models were compared. Results The analysis showed that only earned income and company-related factors significantly affected return-to-original-work (RTOW). The random forest model showed the best accuracy among the tested machine learning models; however, the difference was not prominent. Conclusion It is possible to predict a worker's probability of RTOW using machine learning techniques with moderate accuracy.
Effects of age, gender and menstrual cycle on platelet function assessed by impedance aggregometry

Abstract Platelets are needed to prevent or arrest bleeding and aggregate at the site of injury upon vascular damage. Platelets express receptors for estrogens which might affect the function of the platelets and their hemostatic ability. The aim was to identify possible differences in platelet function related to age, gender, and phases of the menstrual cycle by use of impedance aggregometry with Multiplate. In the first part of the study, platelet function was assessed in 60 healthy individuals (30 men and 30 women) in each of three age groups (20–25, 40–45, and 60–65 years). In the second part of the study, the platelet function was analyzed on four occasions during the menstrual cycle in women without oral contraceptives (OCs) (n = 17) and compared to 19 women on OCs and 18 men of similar age (20–40 years). For the women on OCs, aggregation was analyzed once during the tablet-free week and once late during the period with OCs. The men were sampled once. Women of younger age (<45 years) had significantly higher agonist-induced aggregation response than both men and post-menopausal women (60–65 years). The agonist-induced aggregation response did not differ between phases of the menstrual cycle or OC use. The results suggest that estradiol and/or progesterone affect spontaneous aggregation since it was found to be lowest in the mid-luteal phase. Spontaneous aggregation was significantly lower in women on OCs than in both men and women without OCs. Our findings indicate that fertile age is associated with higher aggregation response capacity of the platelets, possibly to prevent excessive bleeding during menstruation, but this response capacity is not altered during the menstrual cycle or by use of OCs.
COMPARATIVE STUDY ON BIOACTIVE COATING OF Ti-6 Al-4 V ALLOY AND 316 L STAINLESS STEEL

In the present investigation, hydroxyapatite (HA) bioactive coating is deposited with sol-gel method on the surface of 316 L stainless steel and Ti-6Al-4V alloy as the most important biomaterials. Biocompatible additives such as P2O5, Na2CO3, KH2PO4 and HA commercial powder have been used for preparation of HA sol-gel. Characterization of the coated specimens was performed using SEM, XRD, EDS, AFM and optical microscopy. Substrates mechanical properties, e.g. micro hardness and bonding strength, were evaluated in respect to the substrates sintering temperature after completion of the coating process. The results show that denser structure of HA can be obtained by increasing the sintering temperature. In addition, pores volume fraction and size decreased by increasing the sintering temperature. It is shown that surface roughness of the HA decreased when the sintering temperature was incresed to 800 °C. However, growth of the HA grains for the coated alloys sintered at 800 oC is attributed to the slight increase in roughness. Hardness and bonding strength of the biomaterials increased for the metals sintered at the higher temperatures. Different responses to the mechanical tests have been seen for in the titanium alloy sintered at 800 °C.
Hierarchical Structured Model for Fine-to-Coarse Manifesto Text Analysis

Election manifestos document the intentions, motives, and views of political parties. They are often used for analysing a party’s fine-grained position on a particular issue, as well as for coarse-grained positioning of a party on the left–right spectrum. In this paper we propose a two-stage model for automatically performing both levels of analysis over manifestos. In the first step we employ a hierarchical multi-task structured deep model to predict fine- and coarse-grained positions, and in the second step we perform post-hoc calibration of coarse-grained positions using probabilistic soft logic. We empirically show that the proposed model outperforms state-of-art approaches at both granularities using manifestos from twelve countries, written in ten different languages.
La representación de servicios de salud en la televisión mexicana: potenciales consecuencias en las subjetividades en salud

RESUMEN El objetivo de este trabajo es analizar la representacion de los servicios de salud en la television mexicana, considerando su participacion en la produccion y reproduccion de significados sociales sobre salud. Se realizo un estudio descriptivo que analizo los contenidos de 672 horas de television continuas (flujos mediaticos) en Mexico, emitidas en el ano 2011, y reviso publicidad, programas de television y noticiarios. Como resultado del analisis del conjunto de mensajes se observo que en los contenidos se representan principalmente servicios privados de salud; cuando aparecen servicios publicos, predomina la comunicacion sobre el Seguro Popular de Salud; y el modelo de servicios menos representado es el de la seguridad social. Se concluye que la television favorece a los dos primeros tipos de servicios de salud y diluye la importancia de la seguridad social. Este tipo de representaciones de los servicios tiene potenciales consecuencias en las subjetividades en salud.
Recovery of effective HIV-specific CD4+ T-cell activity following antiretroviral therapy in paediatric infection requires sustained suppression of viraemia

Background: The success of increasing access to antiretroviral therapy (ART) in paediatric HIV infection prompts the question of the potential for eradication of HIV infection in this age group. ‘Shock-and-kill’ HIV cure approaches, currently in development, may depend upon an effective antiviral T-cell response to eradicate virus-infected cells. Method: We here investigate the ability of HIV-infected children receiving ART from early childhood (median 24 months’ age) to generate effective HIV-specific CD4+ and CD8+ T-cell immune responses that would facilitate future immune-based cure therapies. Results: Initial analysis of ART-naive HIV-infected children demonstrated that maintenance of normal-for-age absolute CD4+ T-cell counts was strongly linked to high IL-2 production and polyfunctional HIV-specific CD4+ T-cell responses (P < 0.0001 in each case). Low viral load was, similarly, strongly associated with markedly low IFN-&ggr; and high IL-2 HIV-specific CD4+ T-cell responses (P < 0.0001). In children receiving ART, establishment of this immune profile (high IL-2 and low IFN-&ggr; HIV-specific T-cell production) was strongly related to the duration of viraemic suppression. Failure to suppress viraemia on ART, and even the successful suppression of viraemia interrupted by the occurrence of transient viraemia of more than 1000 HIV copies/ml, was associated with an immune profile of high IFN-&ggr; and low IL-2 HIV-specific T-cell responses and low polyfunctionality. Conclusion: These data are consistent with recovery of functional CD4+ T-cell responses in ART-treated children, in contrast to relative lack of CD4+ T-cell function recovery described in ART-treated adults. However, the challenges of achieving long-term suppression of viraemia in ART-treated children through adolescence remain daunting.
Steady/Unsteady Reynolds-Averaged Navier–Stokes and Large Eddy Simulations of a Turbine Blade at High Subsonic Outlet Mach Number

Reynolds-averaged Navier–Stokes (RANS), unsteady RANS (URANS), and large eddy simulation (LES) numerical approaches are clear candidates for the understanding of turbine blade flows. For such blades, the flow unsteady nature appears critical in certain situations and URANS or LES should provide more physical understanding as illustrated here for a laboratory high outlet subsonic Mach blade specifically designed to ease numerical validation. Although RANS offers good estimates of the mean isentropic Mach number and boundary layer thickness, LES and URANS are the only approaches that reproduce the trailing edge flow. URANS predicts the mean trailing edge wake but only LES offers a detailed view of the flow. Indeed, LESs identify flow phenomena in agreement with the experiment, with sound waves emitted from the trailing edge separation point that propagate upstream and interact with the lower blade suction side. [DOI: 10.1115/1.4028493]
Convergence to equilibrium in the free Fokker–Planck equation with a double-well potential

We consider the one-dimensional free Fokker-Planck equation $\frac{\partial \mu\_t}{\partial t} = \frac{\partial}{\partial x} \left[ \mu\_t \left( \frac12 V' - H\mu\_t \right) \right]$, where $H$ denotes the Hilbert transform and $V$ is a particular double-well quartic potential, namely $V(x) = \frac14 x^4 + \frac{c}{2} x^2$, with $-2 \le c < 0$. We prove that the solution $(\mu\_t)\_{t \ge 0}$ of this PDE converges to the equilibrium measure $\mu\_V$ as $t$ goes to infinity, which provides a first result of convergence in a non-convex setting. The proof involves free probability and complex analysis techniques.
Testing for periodicity in functional time series

We derive several tests for the presence of a periodic component in a time series of functions. We consider both the traditional setting in which the periodic functional signal is contaminated by functional white noise, and a more general setting of a contaminating process which is weakly dependent. Several forms of the periodic component are considered. Our tests are motivated by the likelihood principle and fall into two broad categories, which we term multivariate and fully functional. Overall, for the functional series that motivate this research, the fully functional tests exhibit a superior balance of size and power. Asymptotic null distributions of all tests are derived and their consistency is established. Their finite sample performance is examined and compared by numerical studies and application to pollution data.
Several Tunable GMM Kernels

While tree methods have been popular in practice, researchers and practitioners are also looking for simple algorithms which can reach similar accuracy of trees. In 2010, (Ping Li UAI'10) developed the method of "abc-robust-logitboost" and compared it with other supervised learning methods on datasets used by the deep learning literature. In this study, we propose a series of "tunable GMM kernels" which are simple and perform largely comparably to tree methods on the same datasets. Note that "abc-robust-logitboost" substantially improved the original "GDBT" in that (a) it developed a tree-split formula based on second-order information of the derivatives of the loss function; (b) it developed a new set of derivatives for multi-class classification formulation. In the prior study in 2017, the "generalized min-max" (GMM) kernel was shown to have good performance compared to the "radial-basis function" (RBF) kernel. However, as demonstrated in this paper, the original GMM kernel is often not as competitive as tree methods on the datasets used in the deep learning literature. Since the original GMM kernel has no parameters, we propose tunable GMM kernels by adding tuning parameters in various ways. Three basic (i.e., with only one parameter) GMM kernels are the "$e$GMM kernel", "$p$GMM kernel", and "$\gamma$GMM kernel", respectively. Extensive experiments show that they are able to produce good results for a large number of classification tasks. Furthermore, the basic kernels can be combined to boost the performance.
Confidence Modeling for Neural Semantic Parsing

In this work we focus on confidence modeling for neural semantic parsers which are built upon sequence-to-sequence models. We outline three major causes of uncertainty, and design various metrics to quantify these factors. These metrics are then used to estimate confidence scores that indicate whether model predictions are likely to be correct. Beyond confidence estimation, we identify which parts of the input contribute to uncertain predictions allowing users to interpret their model, and verify or refine its input. Experimental results show that our confidence model significantly outperforms a widely used method that relies on posterior probability, and improves the quality of interpretation compared to simply relying on attention scores.
Granulomatous Lobular Mastitis: Clinicopathologic Presentation of 90 Cases

OBJECTIVE Granulomatous lobular mastitis is a rare benign chronic breast disease first described by Milward in 1970, and then by Kessler and Wolloch in 1972. In this study, we aimed to present clinicopathologic features of granulomatous lobular mastitis with literature data. MATERIAL AND METHOD In this study, the archives of Uludag University Medical Faculty Department of Pathology were screened for granulomatous lobular mastitis cases between 2005 and 2017. RESULTS A total of 90 patients with granulomatous lobular mastitis diagnosed between 2005 and 2017 were identified. All of the cases were female. The mean age was 34+8.3 (range 21-60 years). There was sarcoidosis in one case and tuberculosis in another case, but no systemic disease was found in the charts of the other cases. Histopathological evaluation of 90 cases revealed non-necrotizing granulomas involving lobule-restricted, epithelioid histiocytes and Langhans-type multinuclear giant cells. There was no case of necrosis, including our only case with a history of tuberculosis. CONCLUSION We conclude that our granulomatous lobular mastitis cases have similar characteristics with the series reported earlier, when all features are taken into consideration.
Fast Feature Extraction with CNNs with Pooling Layers

In recent years, many publications showed that convolutional neural network based features can have a superior performance to engineered features. However, not much effort was taken so far to extract local features efficiently for a whole image. In this paper, we present an approach to compute patch-based local feature descriptors efficiently in presence of pooling and striding layers for whole images at once. Our approach is generic and can be applied to nearly all existing network architectures. This includes networks for all local feature extraction tasks like camera calibration, Patchmatching, optical flow estimation and stereo matching. In addition, our approach can be applied to other patch-based approaches like sliding window object detection and recognition. We complete our paper with a speed benchmark of popular CNN based feature extraction approaches applied on a whole image, with and without our speedup, and example code (for Torch) that shows how an arbitrary CNN architecture can be easily converted by our approach.
Canonical correlation coefficients of high-dimensional Gaussian vectors: Finite rank case

Consider a Gaussian vector $\mathbf{z}=(\mathbf{x}',\mathbf{y}')'$, consisting of two sub-vectors $\mathbf{x}$ and $\mathbf{y}$ with dimensions $p$ and $q$ respectively, where both $p$ and $q$ are proportional to the sample size $n$. Denote by $\Sigma_{\mathbf{u}\mathbf{v}}$ the population cross-covariance matrix of random vectors $\mathbf{u}$ and $\mathbf{v}$, and denote by $S_{\mathbf{u}\mathbf{v}}$ the sample counterpart. The canonical correlation coefficients between $\mathbf{x}$ and $\mathbf{y}$ are known as the square roots of the nonzero eigenvalues of the canonical correlation matrix $\Sigma_{\mathbf{x}\mathbf{x}}^{-1}\Sigma_{\mathbf{x}\mathbf{y}}\Sigma_{\mathbf{y}\mathbf{y}}^{-1}\Sigma_{\mathbf{y}\mathbf{x}}$. In this paper, we focus on the case that $\Sigma_{\mathbf{x}\mathbf{y}}$ is of finite rank $k$, i.e. there are $k$ nonzero canonical correlation coefficients, whose squares are denoted by $r_1\geq\cdots\geq r_k>0$. We study the sample counterparts of $r_i,i=1,\ldots,k$, i.e. the largest $k$ eigenvalues of the sample canonical correlation matrix $\S_{\mathbf{x}\mathbf{x}}^{-1}\S_{\mathbf{x}\mathbf{y}}\S_{\mathbf{y}\mathbf{y}}^{-1}\S_{\mathbf{y}\mathbf{x}}$, denoted by $\lambda_1\geq\cdots\geq \lambda_k$. We show that there exists a threshold $r_c\in(0,1)$, such that for each $i\in\{1,\ldots,k\}$, when $r_i\leq r_c$, $\lambda_i$ converges almost surely to the right edge of the limiting spectral distribution of the sample canonical correlation matrix, denoted by $d_{+}$. When $r_i>r_c$, $\lambda_i$ possesses an almost sure limit in $(d_{+},1]$. We also obtain the limiting distribution of $\lambda_i$'s under appropriate normalization. Specifically, $\lambda_i$ possesses Gaussian type fluctuation if $r_i>r_c$, and follows Tracy-Widom distribution if $r_i
Effect of probiotic supplements in women with gestational diabetes mellitus on inflammation and oxidative stress biomarkers: a randomized clinical trial.

BACKGROUND AND OBJECTIVES Very little is known about the use of probiotics among pregnant women with gestational diabetes mellitus (GDM) especially its effect on oxidative stress and inflammatory indices. The aim of present study was to measure the effect of a probiotic supplement capsule on inflammation and oxidative stress biomarkers in women with newly-diagnosed GDM. METHODS AND STUDY DESIGN 64 pregnant women with GDM were enrolled in a double-blind placebo controlled randomized clinical trial in the spring and summer of 2014. They were randomly assigned to receive either a probiotic containing four bacterial strains of Lactobacillus acidophilus LA-5, Bifidobacterium BB-12, Streptococcus Thermophilus STY-31 and Lactobacillus delbrueckii bulgaricus LBY-27 or placebo capsule for 8 consecutive weeks. Blood samples were taken pre- and post-treatment and serum indices of inflammation and oxidative stress were assayed. The measured mean response scales were then analyzed using mixed effects model. All statistical analysis was performed using Statistical Package for Social Sciences (SPSS) software (version 16). RESULTS Serum high-sensitivity C-reactive protein and tumor necrosis factor-α levels improved in the probiotic group to a statistically significant level over the placebo group. Serum interleukin-6 levels decreased in both groups after intervention; however, neither within group nor between group differences interleukin-6 serum levels was statistically significant. Malondialdehyde, glutathione reductase and erythrocyte glutathione peroxidase levels improved significantly with the use of probiotics when compared with the placebo. CONCLUSIONS The probiotic supplement containing L.acidophilus LA- 5, Bifidobacterium BB- 12, S.thermophilus STY-31 and L.delbrueckii bulgaricus LBY-2 appears to improve several inflammation and oxidative stress biomarkers in women with GDM.
Effects of dietary protein levels and 2‐methylbutyrate on ruminal fermentation, nutrient degradability, bacterial populations and urinary purine derivatives in Simmental steers

The objective of this study was to evaluate the effects of dietary crude protein (CP) levels and 2-methylbutyrate (MB) supplementation on ruminal fermentation, bacterial populations, microbial enzyme activity and urinary excretion of purine derivatives (PD) in Simmental steers. Eight ruminally cannulated Simmental steers, averaging 18 months of age and 465 ± 8.6 kg of body weight (BW), were used in a replicated 4 × 4 Latin square design by a 2 × 2 factorial arrangement. Low protein (98.5 g CP/kg dry matter [LP] or high protein (128.7 g CP/kg dry matter [HP]) diets were fed with MB supplementation (0 g [MB-] or 16.8 g steer-1 day-1 [MB+]). Steers were fed a total mixed ration with dietary corn straw to concentrate ratio of 50:50 (dry matter [DM] basis). The CP × MB interaction was observed for ruminal total VFA, molar proportions of acetate and propionate, acetate to propionate ratio, ammonia-N, effective degradability of neutral detergent fibre (NDF) and CP, microbial enzyme activity, bacterial populations and total PD excretion (p < .05). Ruminal pH decreased (p < .05), but ruminal total VFA concentration increased (p < .05) with increasing dietary CP level or MB supplementation. Acetate molar proportion increased (p = .043) with MB supplementation, but was not affected by dietary CP level. Propionate molar proportion decreased (p < .05) with increasing dietary CP level or MB supplementation. Consequently, acetate-to-propionate ratio increased (p = .001) with MB supplementation, but was not affected by dietary CP level. Ruminal ammonia-N content increased (p = .034) with increasing dietary CP level, but decreased (p = .012) with MB supplementation. The effective degradability of NDF and CP increased (p < .05) with increasing dietary CP level or MB supplementation. Microbial enzyme activity, bacterial populations and total PD excretion also increased (p < .05) with increasing dietary CP level or MB supplementation. The results indicated that ruminal fermentation, nutrient degradability, microbial enzyme activity, ruminal bacterial populations and microbial protein synthesis improved with increasing dietary CP level or MB supplementation in steers.