Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromatin remodelers HELLS and UHRF1 mediate the epigenetic deregulation of genes that drive retinoblastoma tumor progression

The retinoblastoma (Rb) family of proteins are key regulators of cell cycle exit during development and their deregulation is associated with cancer. Rb is critical for normal retinal development and germline mutations lead to retinoblastoma making retinae an attractive system to study Rb family signaling. Rb coordinates proliferation and differentiation through the E2f family of transcription factors, a critical interaction for the role of Rb in retinal development and tumorigenesis. However, whether the roles of the different E2fs are interchangeable in controlling development and tumorigenesis in the retina or if they have selective functions remains unknown. In this study, we found that E2f family members play distinct roles in the development and tumorigenesis. In Rb;p107-deficient retinae, E2f1 and E2f3 inactivation rescued tumor formation but only E2f1 rescued the retinal development phenotype. This allowed the identification of key target genes for Rb/E2f family signaling contributing to tumorigenesis and those contributing to developmental defects. We found that Sox4 and Sox11 genes contribute to the developmental phenotype and Hells and Uhrf1 contribute to tumorigenesis. Using orthotopic human xenografts, we validated that upregulation of HELLS and UHRF1 is essential for the tumor phenotype. Also, these epigenetic regulators are important for the regulation of SYK.
Semiparametric nonhomogeneity analysis

Let ~(x,~)) be a 'piecewise stationary' random field, defined as an embedding of stationary random fields ? ,'(x,(~)) via the polytomous field m(x,~J). The domain of definition is partitioned into disjoint regions R ~. Denote the marginals for each ~i(x,(J)) by ~'(~) so that ~(x,~,)) ~ ~'(~) for x ~ R s. Define homogeneity as the situation in which all the :(are identical versus nonhomo-geneity in which there exist at least two regions with differing marginals. To perform a test of these hypotheses without assuming parametric structure for the ~' or choosing a specific type of nonhomogeneity in the alternative requires estimates ~, for each region. However, the competing requirements of estimation without restrictive assumptions versus small-area investigation to determine the unknown locations of potential nonhomogeneities lead to an impasse which cannot easily be overcome and has led to a dichotomy of approaches-parametric versus nonparamet-ric. This paper develops a borrowed strength methodology which can be used to improve upon the local estimates which are obtainable by either fully nonparametric methods or by simple parametric procedures. The approach involves estimating the marginals as a generalized mixture model, and the improvement derives from using all the observed data, borrowing strength l? om potentially dissimilar regions, to impose constraints on the local estimation problems.
ImageNotion as a Mashup Service for a Semantic Image Web ?

While the amount of multimedia content on the Web is continuously growing, reuse of multimedia content remains low and automated processing of content remains hard. An increased reuse of content however would result in a greater consistency, quality and lowered cost of the production of new content. The retrieval of multimedia content on the Web is a continuous challenge which is due to the lack of (formal) descriptions and generic multimedia analysis algorithms. We present a model and a set of ontologies to mark up multimedia content embedded in web pages which can be used to deploy its descriptions on the Semantic Web and which in turn can be used to reason about the contents of multimedia resources. This model is part of a method to raise the reusability potential of content which in turn is expected to lower production costs of new content.
Dysregulated Serum MiRNA Profile and Promising Biomarkers in Dengue-infected Patients

Objectives: Pathological biomarkers and mechanisms of dengue infection are poorly understood. We investigated a new serum biomarker using miRNAs and performed further correlation analysis in dengue-infected patients. Methods: Expression levels of broad-spectrum miRNAs in serum samples from three patients with dengue virus type 1 (DENV-1) and three healthy volunteers were separately analyzed using miRNA PCR arrays. The expressions of the five selected miRNAs were verified by qRT-PCR in the sera of 40 DENV-1 patients and compared with those from 32 healthy controls. Receiver operating characteristic (ROC) curve and correlation analyses were performed to evaluate the potential of these miRNAs for the diagnosis of dengue infection. Results: MiRNA PCR arrays revealed that 41 miRNAs were upregulated, whereas 12 miRNAs were down-regulated in the sera of DENV-1 patients compared with those in healthy controls. Among these miRNAs, qRT-PCR validation showed that serum hsa-miR-21-5p, hsa-miR-590-5p, hsa-miR-188-5p, and hsa-miR-152-3p were upregulated, whereas hsa-miR-146a-5p was down-regulated in dengue-infected patients compared with healthy controls. ROC curves showed serum hsa-miR-21-5p and hsa-miR-146a-5p could distinguish dengue-infected patients with preferable sensitivity and specificity. Correlation analysis indicated that expression levels of serum hsa-miR-21-5p and hsa-miR-146a-5p were negative and positively correlated with the number of white blood cells and neutrophils, respectively. Functional analysis of target proteins of these miRNAs in silico indicated their involvement in inflammation and cell proliferation. Conclusion: Dengue-infected patients have a broad “fingerprint” profile with dysregulated serum miRNAs. Among these miRNAs, serum hsa-miR-21-5p, hsa-miR-146a-5p, hsa-miR-590-5p, hsa-miR-188-5p, and hsa-miR-152-3p were identified as promising serum indicators for dengue infection.
CONTINUUM MONTE CARLO SIMULATION ATCONSTANT PRESSURE OF STIFF CHAIN MOLECULESAT

Continuum Monte-Carlo simulations at constant pressure are performed on short chain molecules at surfaces. The rodlike chains, consisting of seven eeective monomers, are attached at one end to a at twodimensional sub-strate. It is found that the model exhibits phases similar to the liquid condensed and liquid expanded phases of Langmuir monolayers. The model is investigated here for a wide range of pressures and temperatures using a special form of constant pressure simulation compatible with the symmetry breaking during tilting transitions in the liquid condensed phases. At low pressures the chains undergo a tilting transition exhibiting tilt directions towards nearest and also next nearest neighbours depending on temperature. At elevated temperatures and low pressure the lm enters a uidlike phase similar to the liquid expanded phase observed in experiment.
Climatologies of streamer events derived from a transport model and a coupled chemistry-climate model

Climatologies of streamer events derived from a transport model and a coupled chemistry-climate model V. Eyring, M. Dameris, V. Grewe, I. Langbein, and W. Kouker DLR Institut für Physik der Atmosphäre, Oberpfaffenhofen, D-82234 Wessling, Germany Forschungszentrum Karlsruhe, Institut für Meteorologie und Klimaforschung, 76344 Eggenstein-Leopoldshafen, Germany Received: 17 October 2002 – Accepted: 14 November 2002 – Published: 2 December 2002 Correspondence to: V. Eyring (Veronika.Eyring@dlr.de)
The Australasian Hepatology Association consensus guidelines for the provision of adherence support to patients with hepatitis C on direct acting antivirals

Background Hepatitis C is a blood-borne virus primarily spread through sharing of drug-injecting equipment. Approximately 150 million people worldwide and 230,000 Australians are living with chronic hepatitis C infection. In March 2016, the Australian government began subsidizing direct acting antivirals (DAAs) for the treatment of hepatitis C, which are highly effective (95% cure rate) and have few side effects. However, there is limited evidence to inform the provision of adherence support to people with hepatitis C on DAAs including the level of medication adherence required to achieve a cure. Methodology In February 2016, a steering committee comprising four authors convened an expert panel consisting of six hepatology nurses, a hepatologist, a pharmacist, a consumer with hepatitis C and treatment experience, and a consumer advocate. The expert panel focused on the following criteria: barriers and enablers to DAA adherence; assessment and monitoring of DAA adherence; components of a patient-centered approach to DAA adherence; patients that may require additional adherence support; and interventions to support DAA adherence. The resultant guidelines underwent three rounds of consultation with the expert panel, Australasian Hepatology Association (AHA) members (n=12), and key stakeholders (n=7) in June 2016. Feedback was considered by the steering committee and incorporated if consensus was achieved. Results Twenty-four guidelines emerged from the evidence synthesis and expert panel discussion. The guidelines focus on the pretreatment assessment and education, assessment of treatment readiness, and monitoring of medication adherence. The guidelines are embedded in a patient-centered approach which highlights that all patients are at risk of nonadherence. The guidelines recommend implementing interventions focused on identifying patients’ memory triggers and hooks; use of nonconfrontational and nonjudgmental language by health professionals; and objectively monitoring adherence. Conclusion These are the first guidelines to support patients and health professionals in the delivery of clinical care by identifying practical adherence support interventions for patients taking DAAs.
A Systematic Literature Review on Architectures for Cyber-Foraging Systems

Mobile devices have become for many the preferred way of interacting with the Internet, social media and the enterprise. However, mobile devices still do not have the computing power and battery life that will allow them to perform effectively over long periods of time, or for executing applications that require extensive communication, computation, or low latency. Cyber-foraging is a technique to enable mobile devices to extend their computing power and storage by offloading computation or data to more powerful servers located in the cloud or in single-hop proximity. This article presents the protocol that was followed in the execution of a systematic literature review (SLR) on software architectures that support cyber-foraging. It is an online companion for the article titled Architectural Tactics for Cyber-Foraging: Results of a Systematic Literature Review published by the Journal of Systems and Software.
Minor Physical Anomalies in Patients with Schizophrenia, Unaffected First-Degree Relatives, and Healthy Controls: A Meta-Analysis

Background Minor physical anomalies (MPAs) have been found to be more prevalent in schizophrenia than control participants in numerous studies and may index a potential endophenotype for schizophrenia. Aim To quantitatively define the magnitude of the difference in total MPA scores between patients with schizophrenia and healthy controls; to determine the degree of manifestation in unaffected first-degree relatives compared to patients and controls; and to investigate the degree of sensitivity among individual MPA items. Methods A systematic search was conducted on the literature pertaining to MPAs in patients with schizophrenia and unaffected relatives. Effect sizes (Cohen's d and odds ratios) and corresponding confidence intervals were combined using the Comprehensive Meta-Analysis software package. Results A large difference was found when examining 14 studies comprising 1207 patients with schizophrenia and 1007 healthy controls (d = 0.95, 95% CI = 0.63, 1.27). Six studies involving relatives of individuals with schizophrenia showed a medium effect size (d = 0.45, 95% CI = 0.29,0.62) between patients and relatives, but a small and non-significant effect size (d = 0.32, 95% CI = −0.08, 0.73) between relatives and controls. The majority of MPAs items showed significant odds ratios (1.26–9.86) in comparing patients and controls. Conclusions The findings indicate that medium effect size of MPAs have been demonstrated in patients with schizophrenia as compared to healthy controls, and to a lesser extent in unaffected relatives. These findings are consistent with the idea that MPAs may represent a putative endophenotype for schizophrenia. However, more research including first-degree family members is warranted.
ON LONG-RANGE-DEPENDENCE SYNTHETIC DATA GENERATION THROUGH HEAVY-TAILED DISTRIBUTIONS

Comprehensive analysis of the Internet traffic conducted over the last decade revealed the concept of longrange dependence (LRD) in the collected data traces. Some of this analysis work proved that this property is a result of the heavy tailed distribution of the packet inter-arrival time, which is a result of the heavy tailed distribution of packet size of the traffic sources. In this paper, we use this fact to build a traffic generator model that is based on multiplexing sources of heavy-tailed inter-arrival times and then counting the number of arrivals in the successive periods of length T. To come up with a parameterized model, we also study the effect of the heavy tailed distribution parameters (i.e. the Pareto distribution), and the time scale along with the number of multiplexed sources on the LRD of the generated traffic. Our model is different from the on/off models proposed in the literature that need to multiplex a very large number of sources, while we need only a few sources. Our findings are; 1. The LRD level is higher for sources with heavier tails; 2. There is a need to multiplex only a few sources; 3. The LRD level is higher for larger time scales; 4. Fixing the time scale and tuning the tail of the distribution helps us to come up with a parameterized linear model that only has one parameter, which is the Hurst parameter.
NoPhish App Evaluation: Lab and Retention Study

Phishing is a prevalent issue of today’s Internet. Previous approaches to counter phishing do not draw on a crucial factor to combat the threat - the users themselves. We believe user education about the dangers of the Internet is a further key strategy to combat phishing. For this reason, we developed an Android app, a game called –NoPhish–, which educates the user in the detection of phishing URLs. It is crucial to evaluate NoPhish with respect to its effectiveness and the users’ knowledge retention. Therefore, we conducted a lab study as well as a retention study (five months later). The outcomes of the studies show that NoPhish helps users make better decisions with regard to the legitimacy of URLs immediately after playing NoPhish as well as after some time has passed. The focus of this paper is on the description and the evaluation of both studies. This includes findings regarding those types of URLs that are most difficult to decide on as well as ideas to further improve NoPhish.
RELEASE OF DNA IN CIRCULATING BLOOD AND INDUCTION OF ANTI-DNA ANTIBODIES AFTER INJECTION OF BACTERIAL LIPOPOLYSACCHARIDES

The present data demonstrate the induction of antisingle-stranded (SS) DNA and antidouble-stranded DNA antibodies in various strains of mice, including athymic C57BL/6 nude mice, after the injection of bacterial lipopolysaccharide (LPS). This anti-DNA response is dose dependent and varies quantitatively according to the strain of the injected mice. It is not correlated to the H-2 histocompatibility locus nor to the immune response to LPS. The lipid A fraction appears to be the active part of the LPS molecule for this particular effect. In addition, it was found that DNA is released in circulating blood a few hours after the injection of LPS. Most of the DNA released has physicochemical and immunochemical characteristics of SS DNA. Therefore, the anti-DNA response induced by injections of LPS may be the result of a release of DNA in a particularly immunogenic form at a time when the immune system, in particular the B lymphocytes, is rendered capable by LPS of developing an immune response to such a soluble antigen. These effects of LPS may account for the triggering or the exacerbation of ante-DNA antibodies during infections with gram-negative bacteria, and a similar mechanism may be involved in the pathogenesis of systemic lupus erythematosus.
Modeling human decisions in coupled human and natural systems : Review of agent-based models

Coupled human and natural systems (CHANS) manifest various complexities such as heterogeneity, nonlinearity, feedback, and emergence. Humans play a critical role in affecting such systems and in giving rise to various environmental consequences, which may in turn affect future human decisions and behavior. In light of complexity theory and its application in CHANS, this paper reviews various decision models used in agent based simulations of CHANS dynamics, discussing their strengths and weaknesses. This paper concludes by advocating development of more process-based decision models as well as protocols or architectures that facilitate better modeling of human decisions in various CHANS. © 2011 Elsevier B.V. All rights reserved.
Deletions within the 3′ Non-Translated Region of Alfalfa mosaic virus RNA4 Do Not Affect Replication but Significantly Reduce Long-Distance Movement of Chimeric Tobacco mosaic virus

Alfalfa mosaic virus (AlMV) RNAs 1 and 2 with deletions in their 3′ non‑translated regions (NTRs) have been previously shown to be encapsidated into virions by coat protein (CP) expressed from RNA3, indicating that the 3′ NTRs of RNAs 1 and 2 are not required for virion assembly. Here, we constructed various mutants by deleting sequences within the 3′ NTR of AlMV subgenomic (sg) RNA4 (same as of RNA3) and examined the effect of these deletions on replication and translation of chimeric Tobacco mosaic virus (TMV) expressing AlMV sgRNA4 from the TMV CP sg promoter (Av/A4) in tobacco protoplasts and Nicotiana benthamiana plants. While the Av/A4 mutants were as competent as the wild-type Av/A4 in RNA replication in protoplasts, their encapsidation, long-distance movement and virus accumulation varied significantly in N. benthamiana. These data suggest that the 3′ NTR of AlMV sgRNA4 contains potential elements necessary for virus encapsidation.
Characterization of Human Immunodeficiency Virus (HIV)-Infected Cells in Infiltrates Associated With CNS Opportunistic Infections in Patients With HIV Clade C Infection

Infection with human immunodeficiency virus (HIV) clade C is the most common HIV infection worldwide, yet its impact on the nervous system remains largely unknown. Autopsy studies from regions affected by this virus are scarce, and HIV dementia has only rarely been reported from these countries. Most patients who develop neurologic complications die of opportunistic infections. We thus conducted a neuropathologic study from a single institution in India to characterize the HIV-infected cells in the inflammatory infiltrates in a total of 15 cases (5 patients each who died of either CNS toxoplasmosis, tuberculosis, or cryptococcal meningitis). Nearly, all patients had HIV-infected cells in the brain, although these cells were most abundant in patients with toxoplasma encephalitis. Interestingly, none of the patients had any multinucleated giant cells. HIV-infected cells were found in the parenchyma, perivascular regions, and choroid plexus and found infiltrating the parenchyma from the meninges, suggesting multiple portals of entry into the brain. These findings suggest the possibility that patients, even if successfully treated for an opportunistic inflection, may be at high risk of developing HIV encephalitis and subsequent dementia.
First record of larvae of Chironomidae (Insecta, Diptera) as prey of Temnocephala sp. (Platyhelminthes, Temnocephalidae), an ectosymbiont on larvae of Corydalidae (Megaloptera)

First record of larvae of Chironomidae (Insecta, Diptera) as prey of Temnocephala sp. (Platyhelminthes, Temnocephalidae), an ectosymbiont on larvae of Corydalidae (Megaloptera). This study constitutes the first record of Temnocephala Blanchard, an ectosymbiont on Corydalidae, as a possible predator of chironomid larvae. Twenty-eight Corydalidae larvae (Corydalus and Protochauliodes) were examined under stereomicroscopic in search for Temnocephala and Chironomidae larvae, of which five megalopteran larvae had 24 Temnocephala sp. associated. Furthermore, eight of these Temnocephala worms had chironomid larvae in their gut contents, an interaction previously unknown. Gut content analyses revealed Corynoneura as the commonest chironomid, but larvae of Larsia, Rheotanytarsus and Tanytarsus were recorded as well. This study included Corydalus and Protochauliodes as hosts for Temnocephala, which might be important for this worm dispersion and population dynamics.
A-deficient rat liver by exogenous androgen

Down-regulation of microsomal androgen-dependent CYP2C1 1 is produced in male rat liver by dietary vitamin A deficiency. Decreased circulating androgen concentrations also occur in vitamin A-deficient male rats. Both effects are prevented by addition of all-trans-retinoic acid to the diet. The present study evaluated directly whether androgen deficiency may be responsible for the down-regulation of 2C1 1 in vitamin A-deficient male rats. The major finding was that subcutaneous administration of the androgen methyltrienolone (MT) during the final week of the study restored CYP2C 11 protein and its associated steroid 1 6u-hydroxylation activities to control levels; CYP2C 11 mRNA was also restored. Despite the efficient restoration of CYP2C 11 at a pretranslational level, no alteration in vitamin A status was apparent and animals remained vitamin A deficient after MT treatment. The possibility was assessed that vitamin A can maintain the microsomal content of CYP2C11 in normal liver. However, in contrast to MT, administration of ATRA to gonadectomized male rats did not restore 2C11 in liver. These findings establish that the major effect of vitamin A deficiency on CYP2C1 1 in male rat liver is mediated indirectly by androgen deficiency. -Murray, M. , Butler, A. M. , Agus, C. Restoration of cytochrome P450 2C11 in vitamin A-deficient rat liver by exogenous androgen. FASEB J. 10, 1058-1063 (1996)
A Numerical Simulation of Cyclic Mesocyclogenesis

Abstract A three-dimensional nonhydrostatic numerical model, the Advanced Regional Prediction System, is used to study the process of cyclic mesocyclogenesis in a classic supercell thunderstorm. During the 4-h simulation, the storm’s mesocyclone undergoes two distinct occlusions, with the beginning of a third indicated at the end of the simulation. The occlusion process exhibits a period of approximately 60 min and is qualitatively similar in each case. Initial midlevel (3–7 km) mesocyclogenesis proceeds according to the “classic” picture, that is, via tilting of streamwise environmental vorticity. The development of an evaporatively driven rear-flank downdraft (RFD) signals the beginning of the occlusion process. The developing RFD wraps cyclonically around the mesocyclone, causing the gust front to surge outward. Simultaneously, the occluding mesocyclone rapidly intensifies near the surface. Trajectory analyses demonstrate that this intensification follows from the tilting and stretching of near-ground .