Miracle-dz/UniFAR-FTUs huggingface dataset:
Nanomedicines in the treatment of patients with hepatitis C co-infected with HIV – focus on pegylated interferon-alpha

In immuno-competent individuals, the natural course of chronic hepatitis C virus (HCV) infection is highly variable and 5%–30% of patients develop cirrhosis over 20 years. Co-infection with HCV and human immunodeficiency virus (HIV) is an important prognostic factor and associated with more frequent and accelerated progression to cirrhosis. Until recently HIV/AIDS-related complications were life limiting in patients co-infected with HCV; the introduction of highly active antiretroviral treatment (HAART) and the better prognosis of HIV infection has made HCV-related complications an emerging health problem in HCV/HIV co-infected individuals. Treatment of chronic HCV infection has also evolved since the introduction of interferon-alpha. Recently, introduction of pegylated interferon-alpha (peginterferon-alpha) has resulted in an increase in sustained virus clearance rates of up to 80% in selected genotypes and patient populations. The safety and efficacy of modern anti HCV treatment regimens – based on peginterferon-alpha in combination with ribavirin – was evaluated in 4 controlled trials. Sustained clearance of hepatitis C virus can be achieved in up to 35% of patients with HIV/HCV co-infection, and novel HCV treatment regimens based on peginterferon-alpha have no negative effect on the control of HIV disease. In conclusion, if HIV infection is well controlled and CD4+ cell counts >100/mm3, treatment of chronic hepatitis C with peginterferon in combination with ribavirin is safe and should be given for 48 weeks regardless of the HCV genotype. Introduction of peginterferon-alpha has significantly improved adherence to treatment and treatment efficacy; in particular sustained virologic response in patients with HCV genotype 1 or 4 infection improved, but sustained viral clearance in only 7%–38% of patients infected with genotype 1 and 4 cannot be the final step in development of effective treatments in patients with HCV/HIV co-infection.
Executive Functioning in Criminal Behavior: Differentiating between Types of Crime and Exploring the Relation between Shifting, Inhibition, and Anger

ABSTRACT The study of executive functioning in prisoner populations is important to the task of elucidating underlying neuropsychological causes of criminal behavior; these deficits should also be considered in offender rehabilitation efforts. A general sample of offenders (N = 42), further divided into three subtypes of crimes (violent, property, and drug trafficking), was tested using a battery of executive functioning measures and compared with a group of non-offenders (N = 28). Offenders performed worse than non-offenders on mental flexibility and planning measures, and pairwise analysis revealed differences in the executive functioning of the offender subgroups – the property offenders had poorer performance on mental flexibility measures, while the violent offenders performed worse on planning measures. The relationship between executive functions and anger in the criminal subgroups was further explored. Preliminary results revealed strong significant correlations between mental flexibility, interference resistance, and anger control in the subgroup of violent offenders. Further investigation of the relation between executive functions and anger in violent offenders is recommended.
Evaluation of Gene Therapy as an Intervention Strategy to Treat Brain Injury from Stroke

Stroke is a leading cause of death and disability, with a lack of treatments available to prevent cell death, regenerate damaged cells and pathways, or promote neurogenesis. The extended period of hours to weeks over which tissue damage continues to occur makes this disorder a candidate for gene therapy. This review highlights the development of gene therapy in the area of stroke, with the evolution of viral administration, in experimental stroke models, from pre-injury to clinically relevant timeframes of hours to days post-stroke. The putative therapeutic proteins being examined include anti-apoptotic, pro-survival, anti-inflammatory, and guidance proteins, targeting multiple pathways within the complex pathology, with promising results. The balance of findings from animal models suggests that gene therapy provides a viable translational platform for treatment of ischemic brain injury arising from stroke.
Track Me If You Can: On the Effectiveness of Context-based Identifier Changes in Deployed Mobile Networks

Location privacy is a major concern in an increasingly connected and highly pervasive network of mobile users. Novel location-based applications and device-to-device services (on these mobile devices) are gaining popularity, but at the same time, these services allow curious service providers and eavesdroppers to track users and their movements. Earlier research efforts on location-privacy preservation, which were mostly based on identifier-change mechanisms in spatio-temporal de-correlation regions called mix-zones, show that coordinated identifier-change techniques are reasonably effective in a simulation setting, although some smart attacks are still possible. However, a thorough analysis of these mechanisms that takes into consideration communication patterns and mobility from a real-life deployment is missing from these results. In this paper, we evaluate in a real-life setting the effectiveness of standard mix-zone-based privacy protection mechanisms against probabilistic tracking attacks. Our exper- iments involved 80 volunteers carrying smartphones for 4 months and being constantly eavesdropped on an adversarial mesh network of standard wireless Access Points (APs). To the best of our knowledge, this is the first study that provides empirical evidence about the effectiveness of mix-zone-based privacy-preserving mechanisms against practical adversaries in upcoming wireless and mobile systems.
Automaticity of walking: functional significance, mechanisms, measurement and rehabilitation strategies

Automaticity is a hallmark feature of walking in adults who are healthy and well-functioning. In the context of walking, “automaticity” refers to the ability of the nervous system to successfully control typical steady state walking with minimal use of attention-demanding executive control resources. Converging lines of evidence indicate that walking deficits and disorders are characterized in part by a shift in the locomotor control strategy from healthy automaticity to compensatory executive control. This is potentially detrimental to walking performance, as an executive control strategy is not optimized for locomotor control. Furthermore, it places excessive demands on a limited pool of executive reserves. The result is compromised ability to perform basic and complex walking tasks and heightened risk for adverse mobility outcomes including falls. Strategies for rehabilitation of automaticity are not well defined, which is due to both a lack of systematic research into the causes of impaired automaticity and to a lack of robust neurophysiological assessments by which to gauge automaticity. These gaps in knowledge are concerning given the serious functional implications of compromised automaticity. Therefore, the objective of this article is to advance the science of automaticity of walking by consolidating evidence and identifying gaps in knowledge regarding: (a) functional significance of automaticity; (b) neurophysiology of automaticity; (c) measurement of automaticity; (d) mechanistic factors that compromise automaticity; and (e) strategies for rehabilitation of automaticity.
CYCLIC VARIATIONS IN HYPOTHALAMIC TEMPERATURE IN UNANESTHETIZED RATS.

Male and female rats, equipped with stainless steel re-entrant tubes implanted in the brain adjacent to one preoptic area, were placed in cages with accessible activity wheels. Brain temperatures were recorded continuously for periods up to 48 hr by means of thermocouples inserted into the tubes. The activities of running, feeding, and drinking were recorded simultaneously. About 90% of feeding and drinking activity occurred irregularly during three to nine periods of running activity at night. Active periods at night were associated with brain temperatures 1.0–2.5 C higher than inactive periods during the night or day. Moderate restraint with absence of food abolished these cyclic temperature variations whereas absence of food alone did not. During the night of estrus (9 pm–3 am), marked increases in activity frequently were associated with elevated mean preoptic temperatures.
Statistical methods for assessing observer variability in clinical measures.

The lack of consistency ofmuch medical judgment and decision making has long been appreciated. This is now recognised as an important source of error, and attempts to quantify it have been enhanced by an increasingly sophisticated statistical toolbox at the disposal of the clinical investigator. Variability in measurement and classification may arise from two sources, (a) a lack of consistency within an individual observer (or measuring process) when carrying out successive recordings, and (b) a lack of consistency between observers. Assessing lack of consistency between observers is important for two reasons. Firstly, in any single study using more than one observer an assessment of the variation between them is essential in interpreting the data derived. Secondly, the observer variation seen in one study may be extrapolated to other studies of the same technique but using different observers-that is, the origin of the variation may be inherent in the method itself. This review attempts to summarise in simple terms the statistical techniques available to quantify the variation within and between observers.
Evaluating the heritability explained by known susceptibility variants: a survey of ten complex diseases

Recently, an increasing number of susceptibility variants have been identified for complex diseases. At the same time, the concern of “missing heritability” has also emerged. There is however no unified way to assess the heritability explained by individual genetic variants for binary outcomes. A systemic and quantitative assessment of the degree of “missing heritability” for complex diseases is lacking. In this study, we measure the variance in liability explained by individual variants, which can be directly interpreted as the locus‐specific heritability. The method is extended to deal with haplotypes, multi‐allelic markers, multi‐locus genotypes, and markers in linkage disequilibrium. Methods to estimate the standard error and confidence interval are proposed. To assess our current level of understanding of the genetic basis of complex diseases, we conducted a survey of 10 diseases, evaluating the total variance explained by the known variants. The diseases under evaluation included Alzheimer's disease, bipolar disorder, breast cancer, coronary artery disease, Crohn's disease, prostate cancer, schizophrenia, systemic lupus erythematosus (SLE), type 1 diabetes and type 2 diabetes. The median total variance explained across the 10 diseases was 9.81%, while the median variance explained per associated SNP was around 0.25%. Our results suggest that a substantial proportion of heritability remains unexplained for the diseases under study. Programs to implement the methodologies described in this paper are available at http://sites.google. com/site/honcheongso/software/varexp. Genet. Epidemiol. 2011. © 2011 Wiley‐Liss, Inc. 35:310‐317, 2011
A clinical study of risk factors related to malware infections

The success of malicious software (malware) depends upon both technical and human factors. The most security conscious users are vulnerable to zero-day exploits; the best security mechanisms can be circumvented by poor user choices. While there has been significant research addressing the technical aspects of malware attack and defense, there has been much less research reporting on how human behavior interacts with both malware and current malware defenses. In this paper we describe a proof-of-concept field study designed to examine the interactions between users, anti-virus (anti-malware) software, and malware as they occur on deployed systems. The 4-month study, conducted in a fashion similar to the clinical trials used to evaluate medical interventions, involved 50 subjects whose laptops were instrumented to monitor possible infections and gather data on user behavior. Although the population size was limited, this initial study produced some intriguing, non-intuitive insights into the efficacy of current defenses, particularly with regards to the technical sophistication of end users. We assert that this work shows the feasibility and utility of testing security software through long-term field studies with greater ecological validity than can be achieved through other means.
The J6JFH1 strain of hepatitis C virus infects human B-cells with low replication efficacy.

Abstract Hepatitis C virus (HCV) infection is a serious health problem worldwide that can lead to hepatocellular carcinoma or end-stage liver disease. Current treatment with pegylated interferon, ribavirin, and NS3/4A protease inhibitor would lead to a good prognosis in a large population of patients, but there is still no effective vaccine for HCV. HCV robustly infects hepatocytes in the liver. However, extrahepatic manifestations such as mixed cryoglobulinemia, a systemic immune complex-mediated disorder characterized by B-cell proliferation, which may evolve into overt B-cell non-Hodgkin's lymphoma, have been demonstrated. HCV-RNA is often found to be associated with peripheral blood lymphocytes, suggesting a possible interaction with peripheral blood mononuclear cells (PBMCs), especially B-cells with HCV. B-cell HCV infection was a matter of debate for a long time, and the new advance in HCV in vitro infectious systems suggest that exosome can transmit HCV genome to support "infection. " We aimed to clarify the susceptibility of primary B-cells to HCV infection, and to study its functional effect. In this article, we found that the recombinant HCV J6JFH1 strain could infect human B-cells isolated from the peripheral blood of normal volunteers by the detection of both HCV-negative-strand RNA by reverse transcription polymerase chain reaction, and NS5A protein. We also show the blocking of HCV replication by type I interferon after B-cell HCV infection. Although HCV replication in B-lymphocytes showed lower efficiency, in comparison with hepatocyte line (Huh7) cells, our results clearly demonstrate that human B-lymphocytes without other non-B-cells can actually be infected with HCV, and that this interaction leads to the induction of B-cells' innate immune response, and change the response of these cells to apoptosis.
GRENITS: Gene Regulatory Network Inference Using Time Series

Overview GRENITS o(cid:27)ers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection. A linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) and a non-linear interaction model ([1] and [2]). The package is intended to be used by both users with a background in Bayesian Inference, as well as casual users. To this end, prior parameters and MCMC (Markov chain Monte Carlo) parameters have been set by default to values that in our experience are adequate for a large range of data sets. As well as this, some basic diagnostic and analysis plots are provided. The example contained in this document shows how to run the Linear Network model, as well as how to analyse the output and how to make an explicit network prediction
An Adjusted Likelihood Ratio Approach Analysing Distribution of Food Products to Assist the Investigation of Foodborne Outbreaks

In order to facilitate foodborne outbreak investigations there is a need to improve the methods for identifying the food products that should be sampled for laboratory analysis. The aim of this study was to examine the applicability of a likelihood ratio approach previously developed on simulated data, to real outbreak data. We used human case and food product distribution data from the Norwegian enterohaemorrhagic Escherichia coli outbreak in 2006. The approach was adjusted to include time, space smoothing and to handle missing or misclassified information. The performance of the adjusted likelihood ratio approach on the data originating from the HUS outbreak and control data indicates that the adjusted approach is promising and indicates that the adjusted approach could be a useful tool to assist and facilitate the investigation of food borne outbreaks in the future if good traceability are available and implemented in the distribution chain. However, the approach needs to be further validated on other outbreak data and also including other food products than meat products in order to make a more general conclusion of the applicability of the developed approach.
Optimisation des horaires des agents et du routage des appels dans les centres d’appels

Nous etudions la gestion de centres d'appels multi-competences, ayant plusieurs types d'appels et groupes d'agents. Un centre d'appels est un systeme de files d'attente tres complexe, ou il faut generalement utiliser un simulateur pour evaluer ses performances. Tout d'abord, nous developpons un simulateur de centres d'appels base sur la simulation d'une chaine de Markov en temps continu (CMTC), qui est plus rapide que la simulation conventionnelle par evenements discrets. A l'aide d'une methode d'uniformisation de la CMTC, le simulateur simule la chaine de Markov en temps discret imbriquee de la CMTC. Nous proposons des strategies pour utiliser efficacement ce simulateur dans l'optimisation de l'affectation des agents. En particulier, nous etudions l'utilisation des variables aleatoires communes. Deuxiemement, nous optimisons les horaires des agents sur plusieurs periodes en proposant un algorithme base sur des coupes de sous-gradients et la simulation. Ce probleme est generalement trop grand pour etre optimise par la programmation en nombres entiers. Alors, nous relaxons l'integralite des variables et nous proposons des methodes pour arrondir les solutions. Nous presentons une recherche locale pour ameliorer la solution finale. Ensuite, nous etudions l'optimisation du routage des appels aux agents. Nous proposons une nouvelle politique de routage base sur des poids, les temps d'attente des appels, et les temps d'inoccupation des agents ou le nombre d'agents libres. Nous developpons un algorithme genetique modifie pour optimiser les parametres de routage. Au lieu d'effectuer des mutations ou des croisements, cet algorithme optimise les parametres des lois de probabilite qui generent la population de solutions. Par la suite, nous developpons un algorithme d'affectation des agents base sur l'agregation, la theorie des files d'attente et la probabilite de delai. Cet algorithme heuristique est rapide, car il n'emploie pas la simulation. La contrainte sur le niveau de service est convertie en une contrainte sur la probabilite de delai. Par apres, nous proposons une variante d'un modele de CMTC base sur le temps d'attente du client a la tete de la file. Et finalement, nous presentons une extension d'un algorithme de coupe pour l'optimisation stochastique avec recours de l'affectation des agents dans un centre d'appels multi-competences.
The Academic Achievement Gap Between Blacks and Whites

ABSTRACT This paper considers the academic achievement gap between African American and White students at the elementary and high school levels. It attempts to determine if race or lower socioeconomic status impact results of standardized test results at high performing and low performing schools. It presents research involving regression analysis of data for the state of Illinois. Results indicate race is not a negative factor at high performing or low performing schools for both elementary or high school years, given the samples. Also, low socioeconomic status is not a negative factor at high performing or low performing schools for both the elementary and high school years. High performing schools had low to moderate quantities of the identified variables, while low performing schools had high levels of the identified variables. Societal biases toward Blacks-rich or poor-are challenged in this paper.
Indexing HDFS Data in PDW: Splitting the data from the index

There is a growing interest in making relational DBMSs work synergistically with MapReduce systems. However, there are interesting technical challenges associated with figuring out the right balance between the use and co-deployment of these systems. This paper focuses on one specific aspect of this balance, namely how to leverage the superior indexing and query processing power of a relational DBMS for data that is often more cost-effectively stored in Hadoop/HDFS. We present a method to use conventional B+-tree indices in an RDBMS for data stored in HDFS and demonstrate that our approach is especially effective for highly selective queries.
Collagen Synthesis Is Upregulated in Mitral Valves Subjected to Altered Stress

Mitral regurgitation (MR) and abnormal ventricular wall motion (AVWM) are two cardiac conditions that may increase mitral valve (MV) stresses. Theoretically, increased stress could induce damaging MV tissue alterations. These alterations may impair the preferred option of repair, and mandate replacement. It is hypothesized that MV collagen synthesis is upregulated in response to MR and AVWM. To test this hypothesis in a pilot study, an ischemic sheep model (n = 8) was employed. Four sheep underwent selective coronary artery ligation to infarct a papillary muscle, which resulted in MR. Two other sheep underwent similar coronary ligation to create AVWM. As controls, two sheep underwent sham surgery (no ligation), Sheep were killed 4 or 8 weeks post operatively and their MVs were sectioned. Sections were stained with an antibody (SP1.D8, University of lowa) to procollagen I (precursor to collagen I). The percent area of procollagen stain present was measured by image analysis (Optimas Corporation) and used as an indicator of collagen synthesis. Procollagen results indicated that MV collagen synthesis was upregulated by a factor of 1.8 in both the MR and AVWM groups versus controls. In addition, results showed greater upregulation in anterior leaflets compared with posterior leaflets in both infarct groups. These results indicate that MV collagen synthesis is upregulated in response to MR and AVWM.
Current distribution of a pyrethroid resistance gene (kdr) in Anopheles gambiae complex from west Africa and further evidence for reproductive isolation of the Mopti form.

In the field, the kdr mutation, involved in pyrethroid resistance, has been found widely distributed in the Savanna form of Anopheles gambiae s.s. , but never in wild populations of the Mopti form or An. arabiensis, even in areas where both occur in sympatry with resistant Savanna populations. Under laboratory conditions, Mopti and Savanna forms were fully able to interbreed and the kdr mutation was transmissible from one form to the other. Both forms appeared to be exposed to pyrethroid selection pressure in the field. The absence of the kdr mutation in the Mopti form and the total lack of Mopti-Savanna heterozygotes in field populations provides further evidence of a pre-copulatory barrier to gene flow between these two forms. Molecular markers, including kdr, are powerful tools for studying population genetics and circulation of resistance genes, and should be used through an integrated approach for a better understanding of the speciation process.