Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic detection of safety and security vulnerabilities in open source software

Growing software quality requirements have raised the stakes on software safety and security. Building secure software focuses on techniques and methodologies of design and implementation in order to avoid exploitable vulnerabilities. Unfortunately, coding errors have become common with the inexorable growth tendency of software size and complexity. According to the US National Institute of Standards and Technology (NIST), these coding errors lead to vulnerabilities that cost the US economy $60 billion each year. Therefore, tracking security and safety errors is considered as a fundamental cornerstone to deliver software that are free from severe vulnerabilities. The main objective of this thesis is the elaboration of efficient, rigorous, and practical techniques for the safety and security evaluation of source code. To tackle safety errors related to the misuse of type and memory operations, we present a novel type and effect discipline that extends the standard C type system with safety annotations and static safety checks. We define an inter-procedural, flow-sensitive, and alias-sensitive inference algorithm that automatically propagates type annotations and applies safety checks to programs without programmers' interaction. Moreover, we present a dynamic semantics of our C core language that is compliant with the ANSI C standard. We prove the consistency of the static semantics with respect to the dynamic semantics. We show the soundness of our static analysis in detecting our targeted set of safety errors. To tackle system-specific security properties, we present a security verification framework that combines static analysis and model-checking. We base our approach on the GCC compiler and its GIMPLE representation of source code to extract model-checkable abstractions of programs. For the verification process, we use an off-the-shelf pushdown system model-checker, and turn it into a fully-fledged security verification framework. We also allow programmers to define a wide range of security properties using an automata-based specification approach. To demonstrate the efficiency and the scalability of our approach, we conduct extensive experiments and case studies on large scale open-source software to verify their compliance with a representative set of the CERT standard secure coding rules.
Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc (N̂c) and ENCprime (N̂′c) measures

Effective number of codons ( N^c ) and its variant N^′c (effective number of codons prime) are the two widely used methods for measuring unequal usage of synonymous codons in coding sequences, known as the codon usage bias (CUB). The mathematical formula used in calculating N^c and N^′c values is giving inappropriate measures of CUB in case of low abundance of amino acids. In addition, the magnitude of error also varies according to codon degeneracy. In this study, a modified formula for N^c and N^′c has been developed to measure the CUB more accurately. Online implementations of the modified formula are available in the web portal at http://agnigarh.tezu. ernet.in/~ssankar/cub.php.
Apparent metabolisable energy and digestibility of shea (Vitellaria paradoxa) fat, cocoa (Theobroma cacao) fat and soybean oil in broiler chicks

1. The objective of this experiment was to determine and compare the apparent lipid digestibility coefficient and apparent metabolisable energy (AME) value of shea nut (Vitellaria paradoxa, Gaertn.) fat in broiler chickens with that of soybean oil and cocoa fat. 2. One hundred and sixty 13-d-old male broiler chicks were used in a randomised complete block design. The fats were added at 30, 60 and 90 g/kg to a basal diet. A tenth dietary treatment was the basal feed with no added fats or oils. The birds were fed on the diets for 8 d and all droppings were collected for the final 4 d. 3. The mean coefficient of apparent lipid digestibility for shea fat (0·58) was similar to that of cocoa fat (0·54) but lower than that of soybean oil (0·95). There was evidence of a lipid × concentration interaction with the 90 g/kg shea fat diet having low lipid digestibility (0·43). 4. There was an interaction between the effects of dietary lipid concentration and test lipid on AME but, at dietary levels of 60 g/kg and below, the AME of shea fat (22·0 MJ/kg DM) and cocoa fat (26·4 MJ/kg DM) was significantly lower than that of soybean oil (39·8 MJ/kg DM).
A Fast Overlapping Community Detection Algorithm Based on Weak Cliques for Large-Scale Networks

Community detection is an important tool to analyze hidden information such as functional module and topology structure in complex networks. Compared with traditional community detection, it is more challenging to find overlapping communities in complex networks, especially when the networks are of large scales. Among various overlapping community detection techniques, the well-known clique percolation method (CPM) has shown promising performance in terms of quality of found communities, but suffers from serious curse of dimensionality due to its high computational complexity, which makes it very unlikely to be applied to large-scale networks. To address this issue, in this paper, we propose a weak-CPM for overlapping community detection in large-scale networks. A new measure for characterizing the similarity between weak cliques is also suggested to check whether the weak cliques can be merged into a community. Experimental results on synthetic and real-world networks demonstrate the competitive performance of the proposed method over six popular overlapping community detection algorithms in terms of both computational efficiency and quality of found communities. In addition, the proposed method is also suitable for detecting large-scale networks with an unclear community structure under different levels of overlapping density and overlapping diversity, which is an important property of many real-world complex networks.
Are Migraine and Bipolar Disorders Comorbid Phenomena?: Findings From a Pharmacoepidemiological Study Using the Norwegian Prescription Database

Objectives: Clinical, epidemiological, and, recently, genome-wide linkage and genome-wide association studies suggest migraine and bipolar disorder are comorbid phenomena. The objective of this study was to determine whether there is also evidence that this comorbidity exists by virtue of there being a positive relationship between the prescription of medications used to treat migraine and mood-stabilizing agents using the National Norwegian Prescription Database. Methods: Data allowing ascertainment of the concurrence of prescriptions for migraine and mood-stabilizing agents were gleaned from the Norwegian Prescription Database for calendar year 2006, covering the total population (N = 4,640,219). Results were obtained using logistic regression analyses and were expressed by odds ratios (ORs). Results: A total of 81,225 persons (1.8% of the population) received medications for migraine and 19,517 (0.45%) received a mood-stabilizing agent for a bipolar disorder; 843 persons received both types of medications. The OR expressing the relationship between the concurrent use of both categories of medications was 2.55 (95% confidence interval [CI], 2.38-2.73, P < 0.001, z score = 26.44), significant for all mood stabilizers (lithium: OR = 1.82 [95% CI, 1.58-2.10], P < 0.001, z score = 8.31; carbamazepine: OR = 2.48 [95% CI, 2.01-3.06], P < 0.001, z score = 8.42; valproic acid: OR = 2.26 [95% CI, 1.89-2.70], P < 0.001, z score = 8.96; and lamotrigine: OR = 3.50 [95% CI, 3.14-3.90], P < 0.001, z score = 22.68). The association was significantly higher for men (OR = 3.16 [95% CI, 2.74-3.66], P < 0.001, z score = 15.53) than for women (OR = 2.21 [95% CI, 2.04-2.39], P < 0.001, z score = 19.61) and was most pronounced in younger age groups and for lamotrigine. Conclusions: There was a strong positive association between the prescription of medications used to treat migraine and mood-stabilizing agents. This is compatible with the hypothesis that migraine and bipolar disorders are associated with one another.
Living in a World of Our Own: The Experience of Parents Who Have a Child With Autism

In this article, we discuss findings of a hermeneutic phenomenological study that sought to describe the experiences of parents who have a child with autism. Qualitative interviews were conducted with parents from 16 families of children with autism residing in a western Canadian province. “Living in a world of our own” emerged as the essence of the parents' experiences. In “living in a world of our own,” parents described a world of isolation. Three themes representing the essential challenging elements of the parents' experiences included vigilant parenting, sustaining the self and family, and fighting all the way. Although much is known about the fundamental importance of support to parents of children with chronic conditions and/or disabilities, findings from this study indicate that knowledge has not been adequately transferred to the care of children with autism.
A kinematic description of the trajectories of Listeria monocytogenes propelled by actin comet tails

The bacterial pathogen Listeria monocytogenes propels itself in the cytoplasm of the infected cells by forming a filamentous comet tail assembled by the polymerization of the cytoskeletal protein actin. Although a great deal is known about the molecular processes that lead to actin-based movement, most macroscale aspects of motion, including the nature of the trajectories traced out by the motile bacteria, are not well understood. Here, we present 2D trajectories of Listeria moving between a glass-slide and coverslip in a Xenopus frog egg extract motility assay. We observe that the bacteria move in a number of fascinating geometrical trajectories, including winding S curves, translating figure eights, small- and large-amplitude sine curves, serpentine shapes, circles, and a variety of spirals. We then develop a dynamic model that provides a unified description of these seemingly unrelated trajectories. A key ingredient of the model is a torque (not included in any microscopic models of which we are aware) that arises from the rotation of the propulsive force about the body axis of the bacterium. We show that a large variety of trajectories with a rich mathematical structure are obtained by varying the rate at which the propulsive force moves about the long axis. The trajectories of bacteria executing both steady and saltatory motion are found to be in excellent agreement with the predictions of our dynamic model. When the constraints that lead to planar motion are removed, our model predicts motion along regular helical trajectories, observed in recent experiments.
Culturally competent interventions in Type 2 diabetes mellitus management: an equity-oriented literature review

Objectives. Although, culturally competent (CC) interventions aim to reduce health inequalities for ethnic minorities, they have been criticized on the grounds that they increase prejudice and stereotyping. It remains unclear whether CC interventions really can reduce health inequalities among ethnic minorities. The purpose of this review is to assess whether CC interventions in the management of Type 2 diabetes mellitus (T2DM) match the recommendations to reduce health inequalities. Design. We identified CC interventions relating to T2DM among ethnic minority patients in the literature published between 2005 and 2011. Data were analyzed according to an equity-oriented framework. Each study was given a score based on its congruence with the reduction of health inequalities amongst ethnic minorities. Results. We reviewed 137 papers and found 61 studies that met the inclusion criteria. Most interventions focused on the individual level and the modification of patients' health behavior. Very few addressed the sociopolitical level. A minority of the studies acknowledged the role of socioeconomic deprivation in ethnic health inequalities. Half of the studies contained no information about the socioeconomic status of the patients. The patients receiving the interventions were socioeconomically deprived. Only 10 studies compared ethnic minority groups to majority groups. Thirty-three studies had a very low average congruence score. The highest score of congruence was achieved by one study. Conclusion. Overall, CC interventions addressing T2DM are not congruent with the reduction of ethnic health inequalities. The future of CC interventions may involve going one step further and going back to basic tenets of cultural competence: the integration of difference, whatever its source, into the delivery of fair health care for patients.
Outpatient pulmonary rehabilitation

Educational aims To consider the fundamental aims of pulmonary rehabilitation. To give an overview of the outcome measures used and how they can be applied To review the content of a course of rehabilitation and methods by which it can be delivered. To review the structure and format of rehabilitation including setting, location and duration. Summary Pulmonary rehabilitation provides a package of education, nutritional support and physical training that promotes the skills required for patients to successfully self manage their respiratory condition. Improvements in quality of life, exercise tolerance, physical activity and function are key outcomes for the individual. There are many tools available which measure these changes and can be used to identify individual deficits and needs. Most of the literature describes the intervention in chronic obstructive pulmonary disease (COPD), but there is emerging evidence that the benefits translate to other respiratory conditions, and improvements are achievable regardless of disease severity, smoking status, gender or age. To maintain the benefits from rehabilitation it is critical to identify barriers and address behaviour change that will provoke better lifestyle choices.
[Evaluation of the dose of endotoxin to produce endotoxin shock models in dogs].

Intravenous bolus administration of purified endotoxin (ET) is one of the most popular methods of producing experimental ET shock. In an attempt to evaluate the dose of ET in these experimental models, the kinetics of ET was assessed in various doses (1-0.002 mg.kg-1), and dose response study was performed, measuring chronological changes in hemodynamic (mean arterial pressure & cardiac output) and hematological (leucocyte & platelet counts) parameters. It was demonstrated that plasma ET concentrations were sustained extraordinarily high (greater than 5000 pg.ml-1) in doses of 0.2-1 mg.kg-1 during the observation period of several hours, while they were measurable in doses of 0.02 and 0.002 mg.kg-1, showing a biphasic decrease pattern after ET administration. In particular, plasma ET levels of low dose group (0.002 mg.kg-1) were similar to those of clinical gram negative septic patients. We conclude that the empirically used ET doses of more than 1 mg.kg-1 produce extremely severe endotoxemia and that milder degree of ET shock models produced by low dose of ET (0.002 mg.kg-1) would be more applicable for a pathophysiological study of ET shock.
Intermittent exercises reduce the hypertension syndromes and improve the quality of life.

BACKGROUND Hypertension is one of the most common causes for cardiovascular mortality in China and physical exercises have been well recognized for its prevention and treatment. Recent studies indicated that the methods of exercise differed in improving cardiorespiratory fitness, endothelial function, etc. METHODS In the present study, we compared the effects of high-intensity intermittent exercise and moderate-intensity continuous exercise on the blood pressure, plasma CRAMP level and living quality of hypertensive patients. We measured the basic characteristics of all the individuals and made intermittent/continuous exercise plans according to each of their conditions. RESULTS The whole training lasted for 16 weeks and the CRAMP level of each patient was recorded by blood sampling and ELISA test. The patients' quality of life (QoL) was also surveyed to determine their physical and psychological health. Our result suggested that the intermittent exercise significantly reduced the blood pressure and the CRAMP level of the hypertensive patients. Although the physical pain and social function were not improved by either exercises training, the other six dimensions of QoL, including physical function, physical role, general health condition, vitality, emotional role and mental health, were significant improved by exercises, especially by intermittent exercises. CONCLUSIONS To sum up, the high-intensity intermittent exercise and moderate-intensity continuous exercise could both improve the living quality of hypertensive patients, but the effect of intermittent exercise was more obvious that it reduced the blood pressure and the CRAMP level of hypertensive patients and improve the living quality in a higher level.
Estimation of overall survival in an ‘illness–death’ model with application to the vertical transmission of HIV‐1

We derive a nonparametric maximum likelihood estimate of the overall survival distribution in an illness–death model from interval censored observations with unknown status of the nonfatal event. This expanded model is applied to the re‐analysis of data from a randomized trial where infants, born to women infected with HIV‐1 that were randomly assigned to breastfeeding or counseling for formula feeding, were followed for 24 months for HIV‐1 positivity, HIV‐1‐free survival, and overall survival. HIV‐1 positivity, assessed by postpartum venous blood tests, is the interval censored nonfatal event, and HIV‐1 positivity status is unknown for a subset of infants due to periodic assessment. The analysis demonstrates that estimation of the overall and the pre‐ and post‐nonfatal event survival distributions with the proposed methods provide novel insights into how overall survival is influenced by the occurrence of the nonfatal event. More generally, it suggests the usefulness of this expanded illness–death model when evaluating composite endpoints as potential surrogates for overall survival in a given disease setting. Copyright © 2010 John Wiley & Sons, Ltd.
Results of Penetrating Keratoplasty In CHED: Congenital Hereditary Endothelial Dystrophy

Congenital hereditary endothelial dystrophy is characterized by a diffuse bilateral corneal opacity (edema). Its inheritance has been reported to be both autosomal recessive and dominant. All our cases seemed to be autosomal recessive. There seems to be a prevalence of the recessive gene in the Iranian population. The dystrophy might be misdiagnosed as congenital glaucoma, as in several of our cases. We have operated on 37 eyes of 21 patients during the past 10 years. Our visual and anatomical success rate has been very good, with 92% clear grafts and only an 8% rejection rate, in contrast to poor prognosis that has been previously reported. In children, suture removal should be started 3 months postoperatively. Partial amblyopia was preexistent in all cases, but deep amblyopia was not common.
Enforcing experimentally stochastic techniques in uncertain electromagnetic environments

This contribution deals with the advanced integration of uncertainties in electromagnetic interferences (EMI) and electromagnetic compatibility (EMC) measures. Among the diversity of EMC topics that may be encountered in aerospace, this work focuses on the importance of metallic box with apertures and varying enclosures. The aim of this paper is to present the precise and reliable experimental setup developed ex nihilo to model such an issue. Statistical assessments are obtained using the reference but expensive Monte Carlo formalism and other advanced stochastic methods. The presented results will lay emphasis on the efficiency of these latter stochastic formalisms applied on experimental data.
p53: Guardian of reprogramming

The reprogramming of somatic cells to induced pluripotent stem (iPS) cells is one of the major discoveries of recent years. The development and application of patient specific iPS lines could potentially revolutionize cell-based therapy, facilitating the treatment of a wide range of diseases. Despite the numerous technological advancements in the field, an in-depth mechanistical understanding of the pathways involved in reprogramming is still lacking. Several groups have recently provided a mechanistical insight into the role of the p53 tumor suppressor pathway in reprogramming. The repercussions of these findings are profound and reveal an unexpected role of p53 as a "guardian of reprogramming", ensuring genomic integrity during reprogramming at the cost of a reduced efficiency of the process. Here we analyze the latest findings in the field and discuss their relevance for future applications of iPS cell technology.
Variation of quantitative composition of phenolic compounds in rowan (Sorbus aucuparia L.) leaves during the growth season

The aim of our study was to explore variation peculiarities of qualitative and quantitative composition of phenolic compounds in leaf samples of rowan (Sorbus aucuparia L.) plants growing in natural habitats of Lithuania during their growth season using the HPLC method. In rowan leaf samples, collected during different phenological stages, qualitative and quantitative estimation of neochlorogenic acid, chlorogenic acid, caffeic acid, hyperoside, isoquercitrin, rutin, astragalin, ( − )-epicatechin, procyanidin B1 and procyanidin B2 was performed. Analysis of the qualitative and quantitative composition of phenolic compounds in ethanol extracts of leaf samples of S. aucuparia growing in natural habitats of Lithuania revealed a close relationship between the content of phenolic compounds in S. aucuparia raw plant material and different growth stages.
Boundary conditions in quantum cosmology.

The problem of boundary conditions for the cosmological wave function \ensuremath{\psi} is analyzed using a simple model as an example. The model has two degrees of freedom: the scale factor and a homogeneous scalar field. A tunneling wave function is found for this model which describes an ensemble of universes tunneling from ``nothing'' to a de Sitter space, then evolving along the lines of an inflationary scenario and eventually collapsing to a singularity. A boundary condition in superspace is proposed which selects the tunneling solution for \ensuremath{\psi}. This boundary condition can be thought of as a quantum version of the Penrose condition in classical general relativity. The probability current, the concept of time, and the possibility of an experimental test of quantum cosmology are also discussed.
Influence of Stress on Individual Lag Time Distributions of Listeria monocytogenes

ABSTRACT The effects of nine common food industry stresses on the times to the turbidity (Td) distribution of Listeria monocytogenes were determined. It was established that the main source of the variability of Td for stressed cells was the variability of individual lag times. The distributions of Td revealed that there was a noticeable difference in response to the stresses encountered by the L. monocytogenes cells. The applied stresses led to significant changes of the shape, the mean, and the variance of the distributions. The variance of Td of wells inoculated with single cells issued from a culture in the exponential growth phase was multiplied by at least 6 and up to 355 for wells inoculated with stressed cells. These results suggest stress-induced variability may be important in determining the reliability of predictive microbiological models.