Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathogenesis of Human Papillomaviruses in Differentiating Epithelia

SUMMARY Human papillomaviruses (HPV) are the etiological agents of cervical and other anogenital malignancies. Over 100 different types of HPVs have been identified to date, and all target epithelial tissues for infection. One-third of HPV types specifically infect the genital tract, and a subset of these are the causative agents of anogenital cancers. Other HPV types that infect the genital tract induce benign hyperproliferative lesions or genital warts. The productive life cycle of HPVs is linked to epithelial differentiation. Papillomaviruses are thought to infect cells in the basal layer of stratified epithelia and establish their genomes as multicopy nuclear episomes. In these cells, viral DNA is replicated along with cellular chromosomes. Following cell division, one of the daughter cells migrates away from the basal layer and undergoes differentiation. In highly differentiated suprabasal cells, vegetative viral replication and late-gene expression are activated, resulting in the generation of progeny virions. Since virion production is restricted to differentiated cells, infected basal cells can persist for up to several decades or until the immune system clears the infection. The E6 and E7 genes encode viral oncoproteins that target Rb and p53, respectively. During the viral life cycle, these proteins facilitate stable maintenance of episomes and stimulate differentiated cells to reenter the S phase. The E1 and E2 proteins act as origin recognition factors as well as regulators of early viral transcription. The functions of the E5 and E1^E4 proteins are still largely unknown, but these proteins have been implicated in modulating late viral functions. The L1 and L2 proteins form icosahedral capsids for progeny virion generation. The characterization of the cellular targets of these viral proteins and the mechanisms regulating the differentiation-dependent viral life cycle remain active areas for the study of these important human pathogens.
A Generalized Fuzzy Clustering Regularization Model With Optimality Tests and Model Complexity Analysis

In this paper, we propose a generalized fuzzy clustering regularization (GFCR) model and then study its theoretical properties. GFCR unifies several fuzzy clustering algorithms, such as fuzzy c-means (FCM), maximum entropy clustering (MEC), fuzzy clustering based on Fermi-Dirac entropy, and fuzzy bidirectional associative clustering network, etc. The proposed GFCR becomes an alternative model of the generalized FCM (GFCM) that was recently proposed by Yu and Yang. To advance theoretical study, we have the following three considerations. 1) We give an optimality test to monitor if GFCR converges to a local minimum. 2) We relate the GFCR optimality tests to Occam's razor principle, and then analyze the model complexity for fuzzy clustering algorithms. 3) We offer a general theoretical method to evaluate the performance of fuzzy clustering algorithms. Finally, some numerical experiments are used to demonstrate the validity of our theoretical results and complexity analysis.
Human skin color code recognition: A case study

Human skin color has been studied as biometric indicator, most of previous researches studies focused in using skin color to detect the face, human and human motion. The objective of this article is to evaluate the variation in human skin color as a unique code for identification purpose. Fifty picture of the nose were captured using a mobile camera with a resolution of 3 mega pixel. Part of the nose area has been the region of interest to represent a region of less direct exposure to the sun light as the rest of the face. The color images were converted from RGB to HSI format in order to isolate the effect of the light intensity during shots. The images were analyzed using mathematical and statistical methods (Mean, Median, standard deviation, kurtosis, skewness, and gray level co-occurrence matrices (GLCM). This algorithm found that the variation in skin color from one person to another is statistically remarkable when implementing this technique.
A Research of the Relationship between Childhood Maltreatment and Suicide: Does Support Increase The Risk of Suicide in Maltreated Children?

This research focuses on the relationship between childhood maltreatment and suicide. The types of maltreatment that were included are physical abuse, sexual abuse, emotional maltreatment and physical neglect, and suicide was operationalized by the factors suicidal thoughts, suicide attempts and a combination of both. It was hypothesized that the types of maltreatment were all related to the suicide variables, and that these relationships are influenced by the variables negative self-concept, social support, teacher support, family support, relationship with parents, and present contact with parents. Results showed that there was hardly any significant direct relationship between the maltreatment types and suicide variables. Only sexual abuse was related with suicide attempts and suicide (total), and emotional maltreatment with suicide (total). When several risk/protective factors were added in a logistic regression analysis, ‘negative self-concept’ and teacher support were the most important risk factors, and ‘present contact with parents’ was the biggest protective factor of suicide in maltreated persons. Utrecht University, Netherlands Videnscenter for Psykotraumatologi Master Clinical and Health Psychology Odense, Denmark Supervisor: Prof. Dr. R. Kleber Supervisor: Prof. A. Elklit
Simulated capacitor method for difficult region dynamic boosting in changing environments

This paper presents a novel method to identify and boost difficult regions of in the configuration space (C-space) in changing environments. Difficult regions, especially narrow passages, change their shapes frequently in changing environments, which result in challenging problems to find valid and safe paths. Although a lot of research has been done to identify difficult regions, seldom methods provide robust paths. Moreover, they depend on frequent replanning which wastes a lot of resources. In this paper, a bridge test method based on workspace to configuration space (W-C) nodes mapping is invoked to identify difficult regions dynamically. Consequently, not only difficult regions are identified efficiently, but safe regions which are less likely to be occupied temporarily, are flagged for boosting. Furthermore, the calculated simulated capacitance, which represents the local difficulty level is used to lead boosting procedure. Specifically, boosting nodes would be activated or re-closed according to the changing capacitance, so that calculation resources are concentrate on current difficult regions. As a result, both the total planning time and replanning times are descended a lot. Finally, the simulation experiment with two manipulators shows the proposed method is efficient even in difficult changing environments.
Representing interests as a hyperlinked document collection

We describe a latent variable model for representing a user's interests as a hyperlinked document collection. By collecting hyper-text documents that a user views, creates or updates whilst at their computer, we are able to use not only the content of these documents but also the inter-connectivity of the collection to model the user's interests. The model uses Probabilistic Latent Semantic Analysis and Probabilistic Hypertext Induced Topic Selection and decomposes the user's document collection into a set of factors each of which represents a user's interest. This model can be used to personalise information access tasks such as a personalised search engine or a personalised news service. Our latent variable model's performance is compared with that of a more conventional vector space clustering algorithm.
Association of T CD4 lymphocyte levels and chronic periodontitis in HIV-infected brazilian patients undergoing highly active anti-retroviral therapy: clinical results.

BACKGROUND Controversial data regarding the association between immunosuppression and prevalence/ severity of periodontal diseases in HIV infection have been reported. Thus, the aim of this study was to test the hypothesis that lower T CD4 lymphocyte levels are not related to a higher prevalence of chronic periodontitis in HIV-infected Brazilians undergoing highly active anti-retroviral therapy (HAART). METHODS Sixty-four HIV-infected patients under HAART were classified as having chronic periodontitis; i.e., > or = three sites with probing depth (PD) and/or clinical attachment level (CAL) > or = 5 mm or periodontal healthy (no sites with PD > 3 mm and/or CAL > 4 mm). All subjects received conventional periodontal therapy. Bleeding on probing, plaque accumulation, PD, and CAL were registered at six sites/tooth at baseline and 4 months after therapy. Epidemiological features and levels of T CD4 lymphocytes were obtained from medical records. Significance of differences in periodontal clinical parameters within and between groups were determined using Wilcoxon signed-rank and Mann-Whitney or independent sample t tests. Associations between T CD4 levels and clinical parameters were determined using the chi square test. RESULTS Sixty-one percent of the HIV-infected patients represented AIDS cases, although 69% of them were periodontally healthy. The overall T CD4 lymphocyte mean levels was 333 +/- 254 cells/mm3 and viral load was 12,815 +/- 24,607 copies/mm3. Yet the prevalence of chronic periodontitis was relatively low (36%). In addition, patients with periodontitis presented a moderate disease (mean PD = 2.2 +/- 0.10; mean CAL = 2.6 +/- 0.13) and responded successfully to periodontal therapy. These subjects showed higher levels of T CD4 cells, but lower counts of neutrophils than periodontally healthy patients. Among periodontally healthy and chronic periodontitis patients, 41.7% and 22.9%, respectively, had low levels of T CD4 lymphocytes. No significant differences between periodontal status and epidemiological and immunological parameters were observed. CONCLUSION Based on these results, the hypothesis that lower T CD4 lymphocyte levels are not associated with higher prevalence of chronic periodontitis in HIV-infected Brazilians under HAART cannot be rejected.
Task Scheduling in an Asynchronous Distributed Memory Multifrontal Solver

We describe the improvements to the task scheduling for MUMPS, an asynchronous distributed memory direct solver for sparse linear systems. In the new approach, we determine, during the analysis of the matrix, candidate processes for the tasks that will be dynamically scheduled during the subsequent factorization. This approach significantly improves the scalability of the solver in terms of execution time and storage. By comparison with the previous version of MUMPS, we demonstrate the efficiency and the scalability of the new algorithm on up to 512 processors. Our test cases include matrices from regular three-dimensional grids and irregular grids from real-life applications.
Déterminants, modalités et performance des stratégies collectives en PME : le cas du syndicat de producteurs de vin du Pic Saint-Loup

Dans un contexte economique mondialise, hyperconcurrentiel, en situation de crise, les entreprises initient des strategies collectives (Astley et Fombrun, 1983). Les strategies collectives (Le Roy, 2006) caracterisent des relations horizontales de grand nombre, au sein desquelles des concurrents creent une structure federative de coordination. Elles s’observent particulierement sur des secteurs ou evoluent de nombreuses PME, ces entreprises restant plus vulnerables aux forces de l’environnement et devant lier leur destin pour survivre. L’etude de cas du syndicat de vignerons du Pic Saint-Loup, qui a conduit a realiser quarante-cinq entretiens semi-directifs, combines a de l’observation directe confortee par une position de professionnel du secteur, a mis en lumiere un certain nombre de resultats. D’une part, des determinants psychologiques influent sur la capacite des dirigeants a s’impliquer dans des strategies collectives. D’autre part, des groupes d’acteurs, dont les instigateurs de la strategie, occupent une place centrale au sein du reseau de dirigeants et en retirent une performance economique superieure. Enfin, concernant les modalites, principalement la gestion du paradoxe par le dirigeant implique dans la strategie collective, l’analyse des phases de concurrence et de collaboration met en evidence une discontinuite des flux qui engendre un processus d’alternance de fonctions.
Checkpoints and continuations instead of nested transactions

We present a mechanism for partially aborting transactions through the use of data structure checkpoints and control-flow continuations. In particular, we show that boosted transactions [9] already have built-in restoration points and afford a simple, efficient implementation. Our mechanism is far simpler than previous work, which relied on complex nesting schemes to establish checkpoints. We demonstrate syntactic advantages and we quantify the overhead of checkpoints and explore several examples, illustrating the utility of partially aborting transactions. We additionally present a novel queue-based spin lock which allows threads to timeout and differ in priority. Unlike the known lock due to Craig [5], our lock is more efficient for priority schemes of few levels.
Educating Moral People: A Caring Alternative to Character Education

In this collection of essential essays, Nel Noddings examines alternatives to prevailing models of character education - a sympathetic approach based on an ethic of care. Covering both stories in the classroom and controversial issues in education, Noddings describes the similarities and differences between character education and care ethics.examines how moral education might be infused throughout the curriculum.and calls for greater cooperation across fields and more attention to the practical problems of everyday teaching.
Variance estimation in high dimensional regression models

We treat the problem of variance estimation of the least squares estimate of the parameter in high dimensional linear regression models by using the Uncor- related Weights Bootstrap ( UBS ). We find a representation of the UBS dispersion matrix and show that the bootstrap estimator is consistent if p 2 /n → 0w herep is the dimension of the parameter and n is the sample size. For fixed dimension we show that the UBS belongs to the R-class as defined in Liu and Singh (1992).
Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals

In mammals, the circadian clock allows them to anticipate and adapt physiology around the 24 hours. Conversely, metabolism and food consumption regulate the internal clock, pointing the existence of an intricate relationship between nutrient state and circadian homeostasis that is far from being understood. The Sterol Regulatory Element Binding Protein 1 (SREBP1) is a key regulator of lipid homeostasis. Hepatic SREBP1 function is influenced by the nutrient-response cycle, but also by the circadian machinery. To systematically understand how the interplay of circadian clock and nutrient-driven rhythm regulates SREBP1 activity, we evaluated the genome-wide binding of SREBP1 to its targets throughout the day in C57BL/6 mice. The recruitment of SREBP1 to the DNA showed a highly circadian behaviour, with a maximum during the fed status. However, the temporal expression of SREBP1 targets was not always synchronized with its binding pattern. In particular, different expression phases were observed for SREBP1 target genes depending on their function, suggesting the involvement of other transcription factors in their regulation. Binding sites for Hepatocyte Nuclear Factor 4 (HNF4) were specifically enriched in the close proximity of SREBP1 peaks of genes, whose expression was shifted by about 8 hours with respect to SREBP1 binding. Thus, the cross-talk between hepatic HNF4 and SREBP1 may underlie the expression timing of this subgroup of SREBP1 targets. Interestingly, the proper temporal expression profile of these genes was dramatically changed in Bmal1 −/− mice upon time-restricted feeding, for which a rhythmic, but slightly delayed, binding of SREBP1 was maintained. Collectively, our results show that besides the nutrient-driven regulation of SREBP1 nuclear translocation, a second layer of modulation of SREBP1 transcriptional activity, strongly dependent from the circadian clock, exists. This system allows us to fine tune the expression timing of SREBP1 target genes, thus helping to temporally separate the different physiological processes in which these genes are involved.
CupCarbon: a multi-agent and discrete event wireless sensor network design and simulation tool

This paper presents the first version of a Wireless Sensor Network simulator, called CupCarbon. It is a multi-agent and discrete event Wireless Sensor Network (WSN) simulator. Networks can be designed and prototyped in an ergonomic user-friendly interface using the OpenStreetMap (OSM) framework by deploying sensors directly on the map. It can be used to study the behaviour of a network and its costs. The main objectives of CupCarbon are both educational and scientific. It can help trainers to explain the basic concepts and how sensor networks work and it can help scientists to test their wireless topologies, protocols, etc. The current version can be used only to study the power diagram of each sensor and the overall network. The power diagrams can be calculated and displayed as a function of the simulated time. Prototyping networks is more realistic compared to existing simulators.
CHRONIC OBSTRUCTIVE PULMONARY DISEASE Reduction in sputum neutrophil and eosinophil numbers by the PDE4 inhibitor roflumilast in patients with COPD

Background: Roflumilast is a targeted oral once-daily administered phosphodiesterase 4 (PDE4) inhibitor with clinical efficacy in chronic obstructive pulmonary disease (COPD). Results from in vitro studies with roflumilast indicate that it has anti-inflammatory properties that may be applicable for the treatment of COPD. Methods: In a crossover study, 38 patients with COPD (mean (SD) age 63.1 (7.0) years, post-bronchodilator forced expiratory volume in 1 s (FEV1) 61.0 (12.6)% predicted) received 500 mg roflumilast or placebo once daily for 4 weeks. Induced sputum samples were collected before and after 2 and 4 weeks of treatment. Differential and absolute cell counts were determined in whole sputum samples. Markers of inflammation were determined in sputum supernatants and blood. Spirometry was performed weekly. Results: Roflumilast significantly reduced the absolute number of neutrophils and eosinophils/g sputum compared with placebo by 35.5% (95% CI 15.6% to 50.7%; p = 0.002) and 50.0% (95% CI 26.8% to 65.8%; p,0.001), respectively. The relative proportion of sputum neutrophils and eosinophils was not affected by treatment (p.0.05). Levels of soluble interleukin-8, neutrophil elastase, eosinophil cationic protein and a2macroglobulin in sputum and the release of tumour necrosis factor a from blood cells were significantly reduced by roflumilast compared with placebo treatment (p,0.05 for all). Post-bronchodilator FEV1 improved significantly during roflumilast compared with placebo treatment with a mean difference between treatments of 68.7 ml (95% CI 12.9 to 124.5; p = 0.018). Conclusion: PDE4 inhibition by roflumilast treatment for 4 weeks reduced the number of neutrophils and eosinophils, as well as soluble markers of neutrophilic and eosinophilic inflammatory activity in induced sputum samples of patients with COPD. This anti-inflammatory effect may in part explain the concomitant improvement in post-bronchodilator FEV1.
Electrocardiographic Left Ventricular Hypertrophy and Outcome in Hemodialysis Patients

Background and Aims Electrocardiography (ECG) is the most widely used initial screening test for the assessment of left ventricular hypertrophy (LVH), an independent predictor of cardiovascular mortality in patients with end-stage renal disease (ESRD). However, traditional ECG criteria based only on voltage to detect LVH have limited clinical utility for the detection of LVH because of their poor sensitivity. Methods This prospective observational study was undertaken to compare the prognostic significance of commonly used ECG criteria for LVH, namely Sokolow-Lyon voltage (SV) or voltage-duration product (SP) and Cornell voltage (CV) or voltage-duration product (CP) criteria, and to investigate the association between echocardiographic LV mass index (LVMI) and ECG-LVH criteria in ESRD patients, who consecutively started maintenance hemodialysis (HD) between January 2006 and December 2008. Results A total of 317 patients, who underwent both ECG and echocardiography, were included. Compared to SV and CV criteria, SP and CP criteria, respectively, correlated more closely with LVMI. In addition, CP criteria provided the highest positive predictive value for echocardiographic LVH. The 5-year cardiovascular survival rates were significantly lower in patients with ECG-LVH by each criterion. In multivariate analyses, echocardiographic LVH [adjusted hazard ratio (HR): 11.71; 95% confidence interval (CI): 1.57–87.18; P = 0.016] and ECG-LVH by SP (HR: 3.43; 95% CI: 1.32–8.92; P = 0.011) and CP (HR: 3.07; 95% CI: 1.16–8.11; P = 0.024) criteria, but not SV and CV criteria, were significantly associated with cardiovascular mortality. Conclusions The product of QRS voltage and duration is helpful in identifying the presence of LVH and predicting cardiovascular mortality in incident HD patients.
Mex3a expression and survival analysis of bladder urothelial carcinoma.

OBJECTIVE Bladder urothelial carcinoma is a common tumor in humans and a multifactorial disease. The gene mex3a is associated with tumor formation and may promote cell proliferation and migration. Therefore, this study aimed to determine the relationship between mex3a and bladder urothelial carcinoma. METHODS The clinical and RNA sequencing expression data in patients with bladder urothelial carcinoma were downloaded from the The Cancer Genome Atlas data portal. A total of 412 bladder urothelial carcinoma samples were available in the database, for which the clinical information was acquired, of which 412 are RNA sequencing samples with a total of 19 paired samples. Univariate and multivariate Cox analyses and univariate logistic regression analysis were conducted using the software SPSS version 22.0 and P<0.05 was considered statistically significant. RESULTS The results of the independent t-test of 19 paired samples indicated that the expression level of mex3a was significantly higher in tumor tissues compared with adjacent normal tissues. Mex3a expression as a categorical dependent variable was not associated with overall survival, and the overall survival of bladder urothelial carcinoma was associated with the group of age, cancer status, lymphatic vascular invasion, pathological stage, pathological size, and pathological lymph metastasis. The multivariable Cox model adjusted for the group of mex3a expression level, age, gender, tumor status, and pathological stage showed that only the age and cancer status groups were associated with the overall survival. CONCLUSION Mex3a expression was not a poor prognostic factor of bladder urothelial carcinoma. Moreover, the expression levels of mex3a in the papillary type of bladder urothelial carcinoma were higher than those of the non-papillary type.