Miracle-dz/UniFAR-FTUs huggingface dataset:
Search Engines in Website Security Leak

4 Abstract: Search engines should access certain website directories and specific information through queries; some of these queries can be used by hackers to access private sites information without the permission of their owners. Many websites have security leaks that allow search engines to penetrate into them and have access to critical information that are classified as private or secure. This paper aims at investigating the leaks in websites' secured information that the search engine can access through many queries, it also shows how these leaks and security gaps are prune to the danger of website security and shows the suggested solutions to avoid website vulnerability in order to overcome these issues.
Escherichia coli Induces DNA Double-Strand Breaks in Eukaryotic Cells

Transient infection of eukaryotic cells with commensal and extraintestinal pathogenic Escherichia coli of phylogenetic group B2 blocks mitosis and induces megalocytosis. This trait is linked to a widely spread genomic island that encodes giant modular nonribosomal peptide and polyketide synthases. Contact with E. coli expressing this gene cluster causes DNA double-strand breaks and activation of the DNA damage checkpoint pathway, leading to cell cycle arrest and eventually to cell death. Discovery of hybrid peptide-polyketide genotoxins in E. coli will change our view on pathogenesis and commensalism and open new biotechnological applications.
LASTA: large scale topic assignment on multiple social networks

Millions of people use social networks everyday to talk about a variety of subjects, publish opinions and share information. Understanding this data to infer user's topical interests is a challenging problem with applications in various data-powered products. In this paper, we present 'LASTA' (Large Scale Topic Assignment), a full production system used at Klout, Inc., which mines topical interests from five social networks and assigns over 10,000 topics to hundreds of millions of users on a daily basis. The system continuously collects streams of user data and is reactive to fresh information, updating topics for users as interests shift. LASTA generates over 50 distinct features derived from signals such as user generated posts and profiles, user reactions such as comments and retweets, user attributions such as lists, tags and endorsements, as well as signals based on social graph connections. We show that using this diverse set of features leads to a better representation of a user's topical interests as compared to using only generated text or only graph based features. We also show that using cross-network information for a user leads to a more complete and accurate understanding of the user's topics, as compared to using any single network. We evaluate LASTA's topic assignment system on an internal labeled corpus of 32,264 user-topic labels generated from real users.
Infectious Tolerance

Regulatory CD4+CD25+ T cells (Treg) are mandatory for maintaining immunologic self-tolerance. We demonstrate that the cell-cell contact–mediated suppression of conventional CD4+ T cells by human CD25+ Treg cells is fixation resistant, independent from membrane-bound TGF-β but requires activation and protein synthesis of CD25+ Treg cells. Coactivation of CD25+ Treg cells with Treg cell–depleted CD4+ T cells results in anergized CD4+ T cells that in turn inhibit the activation of conventional, freshly isolated CD4+ T helper (Th) cells. This infectious suppressive activity, transferred from CD25+ Treg cells via cell contact, is cell contact–independent and partially mediated by soluble transforming growth factor (TGF)-β. The induction of suppressive properties in conventional CD4+ Th cells represents a mechanism underlying the phenomenon of infectious tolerance. This explains previously published conflicting data on the role of TGF-β in CD25+ Treg cell–induced immunosuppression.
Changing trends in gastrointestinal disease in the Asia–Pacific region

The new millennium has seen distinct changes in the pattern of gastrointestinal disease in the Asia–Pacific region. These changes are important as more than half of the world's population come from the region and therefore impact significantly on the global disease burden. The highest incidence of gastric cancer (GCA) has been reported from Asia and GCA remains a very important cancer. However time‐trend studies have shown a decrease in GCA incidence in several countries in Asia. A rise in cardio‐esophageal cancers as seen in the West has not been reported. On the other hand, colorectal cancer has been steadily increasing in Asia with age‐standardized incidence rates of some countries approaching that of the West. The pattern of acid‐related diseases has also changed. Gastroesophageal reflux disease is a fast emerging disease with an increasing prevalence of reflux esophagitis and reflux symptoms. The prevalence of peptic ulcer disease has at the same time declined in step with a decrease in H. pylori infection. Many of the changes taking place mirror the Western experience of several decades ago. Astute observation of the epidemiology of emerging diseases combined with good scientific work will allow a clearer understanding of the key processes underlying these changes. With rapid modernization, lifestyle changes have been blamed for an increase in several diseases including gastroesophageal reflux disease, nonalcoholic fatty liver disease and colorectal cancer. A worrying trend has been the increase in obesity among Asians, which has been associated with an increase in metabolic diseases and various gastrointestinal cancers. Conversely, an improvement in living conditions has been closely linked to the decrease in GCA and H. pylori prevalence.
Giga-scale exhaustive points-to analysis for Java in under a minute

Computing a precise points-to analysis for very large Java programs remains challenging despite the large body of research on points-to analysis. Any approach must solve an underlying dynamic graph reachability problem, for which the best algorithms have near-cubic worst-case runtime complexity, and, hence, previous work does not scale to programs with millions of lines of code. In this work, we present a novel approach for solving the field-sensitive points-to problem for Java with the means of (1) a transitive-closure data-structure, and (2) a pre-computed set of potentially matching load/store pairs to accelerate the fix-point calculation. Experimentation on Java benchmarks validates the superior performance of our approach over the standard context-free language reachability implementations. Our approach computes a points-to index for the OpenJDK with over 1.5 billion tuples in under a minute.
Effect of Limonene and 1,8 Cineole on the Skin Penetration of Fluorescein Sodium Deformable Liposomes

The aim of this study was to develop fluorescein sodium (NaFl) deformable liposomes with two different terpenes, d-limonene and 1,8 cineole, as skin penetration enhancer. NaFl was used as the model drug as it is a hydrophilic diagnostic agent, and has low skin penetration. The liposomes were prepared by reverse phase evaporation method. Their particle size, surface charge, and shape were characterized, in vitro skin penetration of NaFl through porcine skin were investigated. The obtained deformable liposomes were small particle size (<100 nm), negative charge and spherical shape. The liposome containing d-limonene provided the highest amount of NaFl followed by deformable liposomes with 1,8 cineole and conventional liposomes, repectively. The enhancement ratio of formulations containing terpenes were about 18-38fold compared with the conventional liposomes. These results indicated that the obtained deformable liposomes could be used as transdermal delivery of NaFl and incorporation of terpenes into deformable liposomes provided high efficiency for NaFl delivery through the skin.
Pairwise Preferences Based Matrix Factorization and Nearest Neighbor Recommendation Techniques

Many recommendation techniques rely on the knowledge of preferences data in the form of ratings for items. In this paper, we focus on pairwise preferences as an alternative way for acquiring user preferences and building recommendations. In our scenario, users provide pairwise preference scores for a set of item pairs, indicating how much one item in each pair is preferred to the other. We propose a matrix factorization (MF) and a nearest neighbor (NN) prediction techniques for pairwise preference scores. Our MF solution maps users and items pairs to a joint latent features vector space, while the proposed NN algorithm leverages specific user-to-user similarity functions well suited for comparing users preferences of that type. We compare our approaches to state of the art solutions and show that our solutions produce more accurate pairwise preferences and ranking predictions.
Megx.net: integrated database resource for marine ecological genomics

Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB), which is subdivided to hold both sequence and habitat data and global environmental data layers. The extended system provides access to several hundreds of genomes and metagenomes from prokaryotes and phages, as well as over a million small and large subunit ribosomal RNA sequences. With the refined Genes Mapserver, all data can be interactively visualized on a world map and statistics describing environmental parameters can be calculated. Sequence entries have been curated to comply with the proposed minimal standards for genomes and metagenomes (MIGS/MIMS) of the Genomic Standards Consortium. Access to data is facilitated by Web Services. The updated megx.net portal offers microbial ecologists greatly enhanced database content, and new features and tools for data analysis, all of which are freely accessible from our webpage http://www.megx.net.
A Fast Iterative Algorithm for Recovery of Sparse Signals from One-Bit Quantized Measurements

This paper considers the problem of reconstructing sparse or compressible signals from one-bit quantized measurements. We study a new method that uses a log-sum penalty function, also referred to as the Gaussian entropy, for sparse signal recovery. Also, in the proposed method, sigmoid functions are introduced to quantify the consistency between the acquired one-bit quantized data and the reconstructed measurements. A fast iterative algorithm is developed by iteratively minimizing a convex surrogate function that bounds the original objective function, which leads to an iterative reweighted process that alternates between estimating the sparse signal and refining the weights of the surrogate function. Connections between the proposed algorithm and other existing methods are discussed. Numerical results are provided to illustrate the effectiveness of the proposed algorithm.
Human Cytochrome P450 1A1 Structure and Utility in Understanding Drug and Xenobiotic Metabolism*

Background: Human cytochrome P450 1A1 (CYP1A1) activates procarcinogens, but the basis of their binding is unknown. Results: A 2.6 Å structure with the inhibitor α-naphthoflavone and docking simulations suggest key active site features. Conclusion: CYP1A1 has a planar active site that restricts ligand orientations. Significance: This provides a useful framework for understanding CYP1A1 interactions with a variety of substrates and inhibitors. Cytochrome P450 (CYP) 1A1 is an extrahepatic monooxygenase involved in the metabolism of endogenous substrates and drugs, as well as the activation of certain toxins and environmental pollutants. CYP1A1 is particularly well known for its ability to biotransform polycyclic aromatic hydrocarbons, such as benzo[a]pyrene in tobacco smoke, into carcinogens. CYP1A1 possesses functional similarities and differences with human CYP1A2 and CYP1B1 enzymes, but the structural basis for this has been unclear. We determined a 2.6 Å structure of human CYP1A1 with the inhibitor α-naphthoflavone. α-Naphthoflavone binds within an enclosed active site, with the planar benzochromen-4-one core packed flat against the I helix that composes one wall of the active site, and the 2-phenyl substituent oriented toward the catalytic heme iron. Comparisons with previously determined structures of the related cytochrome P450 1A2 and 1B1 enzymes reveal distinct features among the active sites that may underlie the functional variability of these enzymes. Finally, docking studies probed the ability of CYP1A structures to assist in understanding their known in vitro interactions with several typical substrates and inhibitors.
Final results from a multicenter, international, pivotal study of romidepsin in refractory cutaneous T-cell lymphoma.

PURPOSE The primary objective of this study was to confirm the efficacy of romidepsin in patients with treatment refractory cutaneous T-cell lymphoma (CTCL). PATIENTS AND METHODS This international, pivotal, single-arm, open-label, phase II study was conducted in patients with stage IB to IVA CTCL who had received one or more prior systemic therapies. Patients received romidepsin as an intravenous infusion at a dose of 14 mg/m(2) on days 1, 8, and 15 every 28 days. Response was determined by a composite assessment of total tumor burden including cutaneous disease, lymph node involvement, and blood (Sézary cells). RESULTS Ninety-six patients were enrolled and received one or more doses of romidepsin. Most patients (71%) had advanced stage disease (≥ IIB). The response rate was 34% (primary end point), including six patients with complete response (CR). Twenty-six of 68 patients (38%) with advanced disease achieved a response, including five CRs. The median time to response was 2 months, and the median duration of response was 15 months. A clinically meaningful improvement in pruritus was observed in 28 (43%) of 65 patients, including patients who did not achieve an objective response. Median duration of reduction in pruritus was 6 months. Drug-related adverse events were generally mild and consisted mainly of GI disturbances and asthenic conditions. Nonspecific, reversible ECG changes were noted in some patients. CONCLUSION Romidepsin has significant and sustainable single-agent activity (including improvement in pruritus) and an acceptable safety profile, making it an important therapeutic option for treatment refractory CTCL.
Research on Structured Programming: An Empiricist's Evaluation

In spite of the widespread acceptance by academics and practitioners of structured programming precepts, relatively few formal empirical studies have been conducted to obtain evidence that either supports or refutes the theory. This paper reviews the empirical studies that have been undertaken and critiques them from the viewpoints of the soundness of their methodology and their ability to contribute to scientific understanding. In general, the evidence supporting programming precepts is weak. A framework for an ongoing research program is outlined.
EFFECT OF ADDITIONAL LENGTH ON PARTIAL COMPRESSION PERPENDICULAR TO THE GRAIN OF WOOD

It is known that apparent mechanical performance improve on partial compression perpendicular to the grain. The equation in the construction standard follows the assumption that the surface deformation at additional area is exponential shape. However the factor to determine its shape has not been investigated.In this research the influence of supporting condition was studied. It was suggested by FEM analysis that the factor is different among them and was confirmed by the experiments. Consequently, three different factors were proposed instead of 1.5/Zo (height of specimen) in current standard, 2.5/Zo for normal, 3/Zo for triangle and 5.5/Zo for double triangle.
Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets

Objective LC-MS/MS phospho-proteomics is an essential technology to help unravel the complex molecular events that lead to and propagate cancer. We have developed a global phospho-proteomic workflow to determine activity of signaling pathways and drug targets in pancreatic cancer tissue for clinical application. Methods Peptides resulting from tryptic digestion of proteins extracted from frozen tissue of pancreatic ductal adenocarcinoma and background pancreas (n = 12), were labelled with tandem mass tags (TMT 8-plex), separated by strong cation exchange chromatography, then were analysed by LC-MS/MS directly or first enriched for phosphopeptides using IMAC and TiO2, prior to analysis. In-house, commercial and freeware bioinformatic platforms were used to identify relevant biological events from the complex dataset. Results Of 2,101 proteins identified, 152 demonstrated significant difference in abundance between tumor and non-tumor tissue. They included proteins that are known to be up-regulated in pancreatic cancer (e.g. Mucin-1), but the majority were new candidate markers such as HIPK1 & MLCK. Of the 6,543 unique phosphopeptides identified (6,284 unique phosphorylation sites), 635 showed significant regulation, particularly those from proteins involved in cell migration (Rho guanine nucleotide exchange factors & MRCKα) and formation of focal adhesions. Activator phosphorylation sites on FYN, AKT1, ERK2, HDAC1 and other drug targets were found to be highly modulated (≥2 fold) in different cases highlighting their predictive power. Conclusion Here we provided critical information enabling us to identify the common and unique molecular events likely contributing to cancer in each case. Such information may be used to help predict more bespoke therapy suitable for an individual case.
Prevalence of oral HPV infection in the United States, 2009-2010.

CONTEXT Human papillomavirus (HPV) infection is the principal cause of a distinct form of oropharyngeal squamous cell carcinoma that is increasing in incidence among men in the United States. However, little is known about the epidemiology of oral HPV infection. OBJECTIVE To determine the prevalence of oral HPV infection in the United States. DESIGN, SETTING, AND PARTICIPANTS A cross-sectional study was conducted as part of the National Health and Nutrition Examination Survey (NHANES) 2009-2010, a statistically representative sample of the civilian noninstitutionalized US population. Men and women aged 14 to 69 years examined at mobile examination centers were eligible. Participants (N = 5579) provided a 30-second oral rinse and gargle with mouthwash. For detection of HPV types, DNA purified from oral exfoliated cells was evaluated by polymerase chain reaction and type-specific hybridization. Demographic and behavioral data were obtained by standardized interview. Statistical analyses used NHANES sample weights to provide weighted prevalence estimates for the US population. MAIN OUTCOME MEASURES Prevalence of oral HPV infection. RESULTS The prevalence of oral HPV infection among men and women aged 14 to 69 years was 6.9% (95% CI, 5.7%-8.3%) and of HPV type 16 was 1.0% (95% CI, 0.7%-1.3%). Oral HPV infection followed a bimodal pattern with respect to age, with peak prevalence among individuals aged 30 to 34 years (7.3%; 95% CI, 4.6%-11.4%) and 60 to 64 years (11.4%; 95% CI, 8.5%-15.1%). Men had a significantly higher prevalence than women for any oral HPV infection (10.1% [95% CI, 8.3%-12.3%] vs 3.6% [95% CI, 2.6%-5.0%], P < .001; unadjusted prevalence ratio [PR], 2.80 [95% CI, 2.02-3.88]). Infection was less common among those without vs those with a history of any type of sexual contact (0.9% [95% CI, 0.4%-1.8%] vs 7.5% [95% CI, 6.1%-9.1%], P < .001; PR, 8.69 [95% CI, 3.91-19.31]) and increased with number of sexual partners (P < .001 for trend) and cigarettes smoked per day (P < .001 for trend). Associations with age, sex, number of sexual partners, and current number of cigarettes smoked per day were independently associated with oral HPV infection in multivariable models. CONCLUSION Among men and women aged 14 to 69 years in the United States, the overall prevalence of oral HPV infection was 6.9%, and the prevalence was higher among men than among women.
Immature and Maturation-Resistant Human Dendritic Cells Generated from Bone Marrow Require Two Stimulations to Induce T Cell Anergy In Vitro

Immature dendritic cells (DC) represent potential clinical tools for tolerogenic cellular immunotherapy in both transplantation and autoimmunity. A major drawback in vivo is their potential to mature during infections or inflammation, which would convert their tolerogenicity into immunogenicity. The generation of immature DC from human bone marrow (BM) by low doses of GM-CSF (lowGM) in the absence of IL-4 under GMP conditions create DC resistant to maturation, detected by surface marker expression and primary stimulation by allogeneic T cells. This resistence could not be observed for BM-derived DC generated with high doses of GM-CSF plus IL-4 (highGM/4), although both DC types induced primary allogeneic T cell anergy in vitro. The estabishment of the anergic state requires two subsequent stimulations by immature DC. Anergy induction was more profound with lowGM-DC due to their maturation resistance. Together, we show the generation of immature, maturation-resistant lowGM-DC for potential clinical use in transplant rejection and propose a two-step-model of T cell anergy induction by immature DC.
Effects of water hardness on toxicological responses to chronic waterborne silver exposure in early life stages of rainbow trout (Oncorhynchus mykiss)

Rainbow trout embryos and larvae were exposed to 0, 0.1, and 1 μg/L total silver (as AgNO3) in water of three different hardnesses (soft water [2 mg/L as CaCO3], moderately hard water [150 mg/L], and hard water [400 mg/L]) in a flow‐through system from fertilization to swim‐up (64 d). The objective of the study was to investigate the effects of water hardness on chronic silver toxicity. In the absence of silver, elevating hardness had a positive effect on early life stage survival and development, significantly decreasing mortality and accelerating time to 50% swim‐up. Following hatch, exposure to 1 μg/L Ag significantly increased mortality relative to exposure to 0 μg/L Ag. No significant effects of silver on time to 50% hatch were observed; however, time to 50% swim‐up was delayed, and 50% swim‐up was not achieved over the course of the experiment during some exposures to 1 μg/L Ag. These results suggest that the current Canadian Water Quality Guideline (http://www.ccme.ca/assets/pdf/el_062.pdf) of 0.1 μg/L Ag is sufficient in preventing mortality and altered development in early life stages of rainbow trout. Increasing water hardness from 2 to 150 or 400 mg/L was modestly protective against the mortality and delays in time to 50% swim‐up associated with exposure to 1 μg/L Ag. The 150‐ and 400‐mg/L hardnesses were equally protective against mortality, but 150‐mg/L was more protective than 400‐mg/L hardness against the delays in time to 50% swim‐up. Overall, the protective effects of hardness on chronic silver toxicity in early life stages of rainbow trout are modest but similar to the protection afforded to acute silver toxicity in juvenile and adult rainbow trout.