Miracle-dz/UniFAR-FTUs huggingface dataset:
Inactivation of Dnmt3b in Mouse Embryonic Fibroblasts Results in DNA Hypomethylation, Chromosomal Instability, and Spontaneous Immortalization*

DNA hypomethylation is a hallmark of many types of solid tumors. However, it remains elusive how DNA hypomethylation may contribute to tumorigenesis. In this study, we have investigated how targeted disruption of the DNA methyltransferases Dnmt3a and Dnmt3b affects the growth of mouse embryonic fibroblasts (MEFs). Our studies led to the following observations. 1) Constitutive or conditional deletion of Dnmt3b, but not Dnmt3a, resulted in partial loss of DNA methylation throughout the genome, suggesting that Dnmt3b, in addition to the major maintenance methyltransferase Dnmt1, is required for maintaining DNA methylation in MEF cells. 2) Dnmt3b-deficient MEF cells showed aneuploidy and polyploidy, chromosomal breaks, and fusions. 3) Inactivation of Dnmt3b resulted in either premature senescence or spontaneous immortalization of MEF cells. 4) The G1 to S-phase checkpoint was intact in primary and spontaneously immortalized Dnmt3b-deficient MEFs because the p53 protein was inducible by DNA damage. Interestingly, protein levels of the cyclindependent kinase inhibitor p21 were increased in immortalized Dnmt3b-deficient MEFs even in the absence of p53 induction. These results suggest that DNA hypomethylation may induce genomic instability, which in turn leads to spontaneous immortalization or premature senescence of Dnmt3b-deficient MEFs via a p53-independent mechanism.
A novel method for efficient amplification of whole hepatitis B virus genomes permits rapid functional analysis and reveals deletion mutants in immunosuppressed patients

Current knowledge of hepatitis B virus (HBV) sequence heterogeneity is based mainly on sequencing of amplified subgenomic HBV fragments. Here, we describe a method which allows sensitive amplification and simplified functional analysis of full-length HBV genomes with or without prior cloning. By this method, a large number of HBV genomes were cloned from sera of six immunosuppressed kidney transplant patients. Two size classes of HBV genomes, one 3.2 kb and another about 2.0 kb in size, were found in all patients. The genome population from one serum sample was studied in detail by size analysis of subgenomic PCR fragments and sequencing. Regions with deletions and insertions were mapped in the C gene and pre-S region. Up to 100% of HBV genomes in all other immunosuppressed patients also had deletions in the C gene. Our results demonstrate the potential of the established method for the structural and functional characterization of heterogeneous populations of complete virion-encapsidated HBV DNAs and suggest that HBV genomes with C gene deletions can have a selective advantage in immunosuppressed patients.
Static and Dynamic Big Data Partitioning on Apache Spark

Many of today’s large datasets are organized as a graph. Due to their size it is often infeasible to process these graphs using a single machine. Therefore, many software frameworks and tools have been proposed to process graph on top of distributed infrastructures. This software is often bundled with generic data decomposition strategies that are not optimised for specific algorithms. In this paper we study how a specific data partitioning strategy affects the performances of graph algorithms executing on Apache Spark. To this end, we implemented different graph algorithms and we compared their performances using a naive partitioning solution against more elaborate strategies, both static and dynamic.
Effect of green tea polyphenols on the genes with atherosclerotic potential

The genomics of atherosclerosis can arise as a result of cross‐talk between the genes coding for the LDL‐receptor (LDL‐R), LXR‐α, PPARs (α, γ), CD36 and C‐myc because these genes control lipid metabolism, cytokine production and cellular activity within the arterial wall. The effect of green tea polyphenols (GTPs) upon such genomics revealed their ability to down‐regulate genes coding for PPAR‐γ, CD36, LXR‐α, C‐myc coupled with up‐regulation of genes coding for LDL‐R and PPAR‐α at the transcriptional level. Based upon these results, it is proposed that GTPs have the inherent capacity to inhibit the development of atherosclerotic lesions. Copyright © 2004 John Wiley & Sons, Ltd.
Tunable whispering gallery mode resonance structure for millimeter-wave/sub-THz applications

This paper presents a novel approach to realize a low-cost wide tunable Whispering Gallery Mode (WGM) resonance-based structure at Millimeter-wave and sub-THz range of frequencies. The tunability is achieved by moving a metallic structure over the WGM resonator using a micro-positioner. Perturbing the WGM resonance causes shift in the resonance frequency and the coupling. Two types of perturbation are tested for two different structures: grounded Alumina-based WGM resonance structure and Silicon-On-Glass (SOG) WGM resonance structure, operating in D-band (110-170 GHz) and G-band (140-220 GHz), respectively. The experimental results reveal the SOG-based resonator has tuning range of 4.5 GHz at 154 GHz and resonance depth better than -20 dB over the tuning range.
Downregulation of NANOG Induces Differentiation of Human Embryonic Stem Cells to Extraembryonic Lineages

The homeobox transcription factor Nanog has been proposed to play a crucial role in the maintenance of the undifferentiated state of murine embryonic stem cells. A human counterpart, NANOG, has been identified, but its function and localization have not hitherto been described. We have used a combination of RNA interference and quantitative real‐time polymerase chain reaction to study NANOG in human embryonic stem and embryonic carcinoma cells. Transfection of NANOG‐specific small interfering RNAs reduced levels of NANOG transcript and protein and induced activation of the extraembryonic endoderm‐associated genes GATA4, GATA6, LAMININ B1, and AFP as well as upregulation of trophectoderm‐associated genes CDX2, GATA2, hCG‐alpha, and hCG‐beta. Immunostaining of preimplantation human embryos showed that NANOG was expressed in the inner cell mass of expanded blastocysts but not in earlier‐stage embryos, consistent with a role in the maintenance of pluripotency. Taken together, our findings suggest that NANOG acts as a gatekeeper of pluripotency in human embryonic stem and carcinoma cells by preventing their differentiation to extraembryonic endoderm and trophectoderm lineages.
Effect of high-efficient electric motors on efficiency improvement and electric energy saving

In this paper, advantages of energy-efficient motors over standard-motors in terms of electrical energy saving and demand reduction in a tire-rubber factory are thoroughly evaluated. Energy-efficient motors reduce losses because of their better design, materials, and manufacturing. These motors are 2 to 8% more efficient than standard ones. Lengthening the core and using lower- electrical-loss steel, thinner stator laminations, and more copper in the windings reduce electrical losses. Because a motor consumes energy worth 4 to 10 times its own cost each year, energy-efficient motors often make economic sense in a wide variety of applications. At the end of this study, the amount of energy savings, demand reductions, dollar savings and pay-back time when replacing the existing or failed motors with high-efficient models are determined.
Mining Frequent Trajectory Patterns From GPS Tracks

The aim of this paper is mining frequent trajectory patterns from GPS tracks collected from birds. Mining is done using DBSCAN (Density-Based Spatial Clustering of Applications with Noise)[1] clustering algorithm that is based on density and finds most common stay points along the trajectory. As a result, it is possible to see frequent patterns in birds’ trajectories and estimate birds’ behavior. The result is shown on QGIS [2] maps.
La récidive des premiers placés sous surveillance électronique

Le placement sous surveillance electronique a fait l'objet d'une recherche au long cours des sa mise en place en 2000 1 . Si les profils des places ont ete plusieurs fois analyses, de nombreux questionnements subsistent quant a l'evaluation de la mesure au regard de la recidive. Cinq annees apres le placement sous surveillance electronique, 6 condamnes sur 10 (58 %) n'ont pas de nouvelle condamnation inscrite sur leur casier judiciaire. Moins d'un quart (23 %) ont une nouvelle affaire sanctionnee par une peine de prison ferme. Ces resultats placent a priori la surveillance electronique dans une position plus favorable, en termes de recidive, que la detention. Les differences selon la nature de l'infraction, le passe judiciaire et l'âge entre les places, et les detenus expliquent en partie les taux de recidive plus faibles des PSE.
Effects of the Inducible Nitric-Oxide Synthase Inhibitor l-N6-(1-Iminoethyl)-lysine on Microcirculation and Reactive Nitrogen Species Generation in the Kidney following Lipopolysaccharide Administration in Mice

The mortality rate for septic patients with acute renal failure is approximately doubled compared with patients with sepsis alone. Unfortunately, the treatment for sepsis-induced renal failure has advanced little during the last several decades. Because sepsis is often caused by lipopolysaccharide (LPS), a mouse model of LPS challenge was used to study the development of kidney injury. We hypothesized that inducible nitric-oxide synthase (iNOS)-catalyzed nitric oxide production and that generation of reactive nitrogen species (RNS) might play a role in the microcirculatory defect and resulting tubular injury associated with LPS administration. Fluorescent intravital videomicroscopy was used to assess renal peritubular capillary perfusion and document RNS generation by renal tubules in real time. As early as 6 h after LPS administration (10 mg/kg i.p.), RNS generation (rhodamine fluorescence), redox stress [NAD(P)H autofluorescence], and the percentage of capillaries without flow were each significantly increased compared with saline-treated mice (p < 0.05). The generation of RNS was supported by the detection of nitrotyrosine-protein adducts in the kidney using immunohistochemistry. The iNOS inhibitor l-N6-(1-iminoethyl)-lysine (l-NIL; 3 mg/kg i.p.) completely blocked the increase in rhodamine fluorescence and NAD(P)H autofluorescence and prevented the capillary defects at 6 h after LPS administration. These results suggest that iNOS-derived RNS is an important contributor to the peritubular capillary perfusion defects and RNS generation that occur during sepsis and emphasize that pharmacological inhibition of iNOS may provide beneficial effects during sepsis by improving renal capillary perfusion and reducing RNS generation in the kidney.
Molecular Diagnosis of Ewing Sarcoma Family of Tumors: A Comparative Analysis of 560 Cases With FISH and RT-PCR

Aims To compare the sensitivity and specificity of fluorescence in situ hybridization (FISH) with reverse transcription polymerase chain reaction (RT-PCR) in the diagnosis of Ewing sarcoma family of tumors (ESFTs) and other small round-cell tumors (SRCTs) in formalin-fixed paraffin-embedded tissue assembled in tissue microarrays (TMAs). The second objective is to confirm the value of molecular methods and immunohistochemical (IHC) assays, to perform a differential diagnosis between ESFTs and SRCTs with similar or overlapping morphology. Materials and Methods A total of 560 cases were selected for the present study out the 806 cases collected from the PROgnosis and THerapeutic Targets in the Ewing's Family of TumorS project. Case selection bias included only the cases with enough material to enable the TMA construction, as FISH analysis and the majority of IHC studies were performed in TMAs. Histopathologic, IHC, and molecular assays were carried out. Results Of the 560 total cases, 411 (73.4%) were considered informative (with results by FISH and/or RT-PCR assays). From the informative cases, 382 (92.9%) were diagnosed as ESFT, 23 cases (5.6%) as non-ESFT but with specific diagnosis for another established entity, and 6 cases (1.5%) as small round cell tumors not otherwise specified. Sensitivity and specificity for the FISH assays was 96.3% and 95.2%, respectively, whereas RT-PCR presented a sensitivity of 97.5% and specificity of 92.9%. In concordant cases, both methods showed a sensitivity and specificity of 99.2% and 100%, respectively. Twenty-nine cases (7.1%) initially interpreted at morphologic level as atypical ESFTs were finally reclassified, with the support of molecular methods and IHC, as either non-ESFT with another specific histologic type or as small round cell tumors not otherwise specified. Conclusions FISH and RT-PCR are ancillary techniques possessing high sensitivity in the diagnosis of ESFT; nevertheless, FISH is more specific than RT-PCR in the diagnosis of formalin-fixed paraffin-embedded tissue. Both methods in combination displayed the highest sensitivity and specificity. The combination of histopathologic, IHC, and molecular findings is the method of choice for the diagnosis of ESFT, as well as for the differential diagnosis with other SRCTs.
Haemophilus ducreyi Strain ATCC 27722 Contains a Genetic Element with Homology to the Vibrio RS1 Element That Can Replicate as a Plasmid and Confer NAD Independence on Haemophilus influenzae

ABSTRACT The nucleotide sequence of pNAD1, a plasmid from Haemophilus ducreyi identified on the basis of its ability to confer NAD independence on Actinobacillus pleuropneumoniae and H. influenzae, has been determined. In addition to containing the nadV gene, the plasmid contains homologues of the rstR and rstA genes, genes encoding repressor and replication proteins, respectively, in the Vibrio CTXφ and the Vibrio RS1 element, suggesting a single-stranded bacteriophage origin for pNAD1. Tandem copies of the plasmid are integrated into the H. ducreyi 35000HP genome.
Improved prognostic stratification using NCCN- and GELTAMO-international prognostic index in patients with diffuse large B-cell lymphoma

The National Comprehensive Cancer Network (NCCN)-International Prognostic Index (IPI) and GELTAMO (Grupo Español de Linfomas/Trasplante Autólogo de Médula Ósea)-IPI were developed to enable better risk prediction of patients with diffuse large B-cell lymphoma (DLBCL). The present study compared the effectiveness of risk prediction between IPI, NCCN-IPI, and GELTAMO-IPI in patients with DLBCL particularly in terms of determining high-risk patients. Among 439 patients who were enrolled to a prospective DLBCL cohort treated with R-CHOP immunochemotherapy, risk groups were classified according to the three IPIs and the prognostic significance of individual IPI factors and IPI models were analyzed and compared. All three IPI effectively separated the analyzed patients into four risk groups according to overall survival (OS). Estimated 5-year OS of patients classified as high-risk according to the IPI was 45.7%, suggesting that the IPI is limited in the selection of patients who are expected to have a poor outcome. In contrast, the 5-year OS of patients stratified as high-risk according to NCCN- and GELTAMO-IPI was 31.4% and 21.9%, respectively. The results indicate that NCCN- and GELTAMO-IPI are better than the IPI in predicting patients with poor prognosis, suggesting the superiority of enhanced, next-generation IPIs for DLBCL.
Tracking Events in Social Media

Tracking topical events in social media streams, such as Twitter, provides a means for users to keep up-to-date on topics of interest to them. This tracking may last a period of days, or even weeks. These events and topics might be provided by users explicitly, or generated for users from selected news articles. Push notification from social media provides a method to push the updates directly to the users on their mobile devices or desktops. In this thesis, we start with a lexical comparison between carefully edited prose and social media posts, providing an improved understanding of word usage within social media. Compared with carefully edited prose, such as news articles and Wikipedia articles, the language of social media is informal in the extreme. By using word embeddings, we identify words whose usage differs greatly between a Wikipedia corpus and a Twitter corpus. Following from this work, we explore a general method for developing succinct queries, reflecting the topic of a given news article, for the purpose of tracking the associated news event within a social media stream. A series of probe queries are generated from an initial set of candidate keywords extracted from the article. By analyzing the results of these probes, we rank and trim the candidate set to create a succinct query. The method can also be used for linking and searching among different collections. Given a query for topical events, push notification to users directly from social media streams provides a method for them to keep up-to-date on topics of personal interest. We determine that the key to effective notification lies in controlling of update volume, by establishing and maintaining appropriate thresholds for pushing updates. We explore and evaluate multiple threshold setting strategies. Push notifications should be relevant to the personal interest, and timely, with pushes occurring as soon as after the actual event occurrence as possible and novel for providing non-duplicate information. An analysis of existing evaluation metrics for push notification reflects different assumptions regarding user requirements. This analysis leads to a framework that places different weights and penalties on different behaviours and can guide the future development of a family of evaluation metrics that more accurately models user needs. Throughout the thesis, rank similarity measures are applied to compare rankings generated by various experiments. As a final component, we develop a family of rank similarity metrics based
[Expression analysis of different collagens and cytokines in cartilage cells derived from arthrotic hip and knee joints].

AIM Osteoarthritis (OA) is characterized by an irreversible destruction of articular cartilage. This is associated with a multiplicity of factors, causing an increased catabolic metabolism in cartilage. However, the prevalence of the OA is very variable in different joints. Therefore , we conducted a comparative analysis of chondrocytes derived from knee and hip joints with respect to their expression of inflammatory factors, such as IL-1beta, IL-1beta-receptorantagonist, iNOS, components of cartilage matrix (collagen I, II, and VI) as well as vimentin. METHODS Different cytokines and proteins were detected by immune-histochemical staining of cartilage samples ex vivo. Further, chondrocytes were isolated from OA knee and hip joints, expanded in vitro and gene expression patterns were investigated by quantitative RT-PCR. RESULTS Chondrocytes from knee and hip joints of OA patients express collagenes I, II and VI, IL-1beta and IL-1beta-RA, iNOS as well as Vimentin. A significant difference in gene expression patterns was not found in chondrocytes from the hip joints versus the knee joint ex vivo or in primary culture cells in vitro. However, in vitro the expression of type I collagen exceeded the expression of type II collagen. The IL-1beta-expression was high ex vivo, remained low during primary culture but was significantly elevated after primary culture in hip chondrocytes. CONCLUSION Osteoarthritic gene expression patterns in cells derived from hip or knee joints ex vivo and in primary culture were not significantly different. We conclude that the rather frequent occurrence of OA in these joints in comparison to the ankle joint may be associated with a close physiological relation of cells in these joints. However, future studies which will include ankle cartilage must be investigated in further detail.
Information Privacy: The Attitudes and Behaviours of Internet Users

The rise of electronic commerce and the Internet have created new technologies and capabilities, which increase concern for privacy online. This study reports on the results of an investigation of Internet users attitudes towards concern for privacy online, online behaviours adopted under varying levels of concern for privacy (high, moderate and low) and the types of information Internet users are protective of. Methodological triangulation was used, whereby both quantitative and qualitative research was conducted. A questionnaire and semi-structured individual interviews were used as the data collection methods. The results of a cross-sectional survey of 104 Internet users suggest a lack of control over personal information online, a lack of privacy rights online, a dislike of government regulation and other privacy concerns. Concern was decreased if personal information was provided for customisation or if there was the ability to opt-out. Anonymity also decreased concern. The qualitative results reveal five areas of concern for privacy, namely the role of Internet Service Providers, online businesses, Internet shopping, government regulation and general Internet privacy problems. This study attempts to add something of value to the body of knowledge regarding concern for privacy on the Internet in the context of South African environment.
Using HOG-LBP features and MMP learning to recognize imaging signs of lung lesions

This paper proposes an approach to recognize Common Imaging Signs of Lesions (CISLs) in lung CT images. We combine the bag-of-visual-words based on the Histograms of Oriented Gradients (HOG) and the Local Binary Pattern (LBP) to represent regions of interest (ROIs) in lung CT images. Then the Max-Min posterior Pseudo-probabilities (MMP) learning method is applied to recognize the category of the imaging sign contained in each ROI. We conducted the 5-fold cross validation experiments on a set of 696 ROIs captured from real lung CT images. The proposed approach achieved the average sensitivity of 91.8%, the average specificity of 98.5% and the average accuracy of 98%. Furthermore, the HOG-LBP features surpassed individual HOG or LBP as well as the hybrid of LBP and intensity histograms, and the MMP behaved better than the Support Vector Machines (SVMs). These experimental results confirm the effectiveness of our approach.
Addressing Physician Concerns About Performance Profiling: Experience With a Local Veterans Affairs Quality Evaluation Program

The Authors investigated the addition of novel quality indicators, patient risk adjustment, and simple statistics in an ongoing clinician feedback initiative that profiles diabetes care for 13 Veterans Affairs (VA) clinics. Data were extracted from a computerized database for calendar years 2004 to 2005. Performance was assessed with 4 monitoring measures, 3 intermediate outcomes, and 3 appropriate treatment measures. Attainment rates for each indicator were calculated by clinic. The effect of risk adjustment and the significance of clinic performance variation were determined with multivariate logistic models. Analysis of the 10 quality measures revealed lower attainment and greater clinic-level variation for the less familiar indicators. Statistically significant performance variations were detected among clinics, with several being of a clinically important magnitude. Risk adjustment did not substantially change performance. The addition of clinically relevant quality measures and simple statistics appeared to enhance the characterization of performance by this profiling program. (Am J Med Qual 2009;24:123-131)
Initiation and Maintenance of Online Sexual Compulsivity: Implications for Assessment and Treatment

Sexually compulsive behavior on the Internet is now a widely recognized problem. Factors unique to the Internet environment that initiate online compulsive sexual behavior include accessibility, affordability, and anonymity, also known as the Triple A Engine. Factors that serve to maintain compulsive online sexual behavior include classical conditioning and operant conditioning. This article elucidates these factors and explores how they can be countered and harnessed in treatment. Future directions for research are suggested.