Miracle-dz/UniFAR-FTUs huggingface dataset:
Applying effective feature selection techniques with hierarchical mixtures of experts for spam classification

E-mail abuse has been steadily increasing during the last decade. E-mail users find themselves targeted by massive quantities of unsolicited bulk e-mail, which often contains offensive language or has fraudulent intentions. Internet Service Providers (ISPs) on the other hand, have to face a considerable system overloading as the incoming mail consumes network and storage resources. Among the plethora of solutions, the most prominent in terms of cost efficiency and complexity are the text filtering approaches. Most of the approaches model the problem using linear statistical models. Despite their popularity - due both to their simplicity and relative ease of interpretation - the non-linearity assumption of data samples is inappropriate in practice. This is mainly due to the inability of other approaches to capture the apparent non-linear relationships, which characterize these samples. In this paper, we propose a margin-based feature selection approach integrated with a Hierarchical Mixtures of Experts (HME) system, which attempts to overcome limitations common to other machine-learning based approaches. By reducing the data dimensionality using effective algorithms for feature selection we evaluated our system with publicly available corpora of e-mails, characterized by very high similarity between legitimate and bulk e-mail (and thus low discriminative potential). We experimented with two different architectures, a hierarchical HME and a perceptron HME. As a result, we confirm the domination of our Spam Filtering (SF) - HME method against other machine learning approaches, which present lesser degree of recall, as well as against traditional rule-based approaches, which lack considerably in the achieved degrees of precision.
Obatoclax Regulates the Proliferation and Fusion of Osteoclast Precursors through the Inhibition of ERK Activation by RANKL

Obatoclax, a pan-Bcl2 inhibitor, shows antitumor activities in various solid malignancies. Bcl2-deficient mice have shown the importance of Bcl2 in osteoclasts, as the bone mass of the mice was increased by the induced apoptosis of osteoclasts. Despite the importance of Bcl2, the effects of obatoclax on the proliferation and differentiation of osteoclast precursors have not been studied extensively. Here, we describe the anti-proliferative effects of obatoclax on osteoclast precursors and its negative role on fusion of the cells. Stimulation with low doses of obatoclax significantly suppressed the proliferation of osteoclast precursors in a dose-dependent manner while the apoptosis was markedly increased. Its stimulation was sufficient to block the activation of ERK MAP kinase by RANKL. The same was true when PD98059, an ERK inhibitor, was administered to osteoclast precursors. The activation of JNK1/2 and p38 MAP kinase, necessary for osteoclast differentiation, by RANKL was not affected by obatoclax. Interestingly, whereas the number of TRAP-positive mononuclear cells was increased by both obatoclax and PD98059, fused, multinucleated cells larger than 100 μm in diameter containing more than 20 nuclei were completely reduced. Consistently, obatoclax failed to regulate the expression of osteoclast marker genes, including c-Fos, TRAP, RANK and CtsK. Instead, the expression of DC-STAMP and Atp6v0d2, genes that regulate osteoclast fusion, by RANKL was significantly abrogated by both obatoclax and PD98059. Taken together, these results suggest that obatoclax down-regulates the proliferation and fusion of osteoclast precursors through the inhibition of the ERK1/2 MAP kinase pathway.
A Systematic Review on the Implication of Minerals in the Onset, Severity and Treatment of Periodontal Disease

Periodontal disease is an inflammatory disease with high prevalence in adults that leads to destruction of the teeth-supporting tissues. Periodontal therapy has been traditionally directed at reduction of the bacterial load to a level that encourages health-promoting bacteria and maintenance of oral-hygiene. The role of nutrition in different chronic inflammatory diseases has been the subject of an increasing body of research in the last decades. In this sense, there has been an important increase in the volume of research on role of nutrition in periodontitis since the diet has known effects on the immune system and inflammatory cascades. Minerals play a key role in all these processes due to the multiple pathways where they participate. To clarify the role of the different minerals in the establishment, progression and/or treatment of this pathology, a systemically review of published literature cited in PubMed until May 2016 was conducted, which included research on the relationship of these elements with the onset and progression of periodontal disease. Among all the minerals, calcium dietary intake seems important to maintain alveolar bone. Likewise, dietary proportions of minerals that may influence its metabolism also can be relevant. Lastly, some observations suggest that all those minerals with roles in immune and/or antioxidant systems should be considered in future research.
Risk factors associated with Salmonella prevalence on swine farms

Summary This article reviews on-farm risk factors that have been associated with the prevalence status of Salmonella in swine. Salmonellosis is the second most common etiological cause of bacterial human foodborne illness in the United States, and most cases can be attributed to contaminated food products. Reduction of human foodborne salmonellosis has become a public health priority both nationally and internationally. Public health concerns, increased stringency of regulatory limits at slaughter, and competition for international market share are likely to increase interest in on-farm Salmonella control.
Antioxidant Micronutrients and Biomarkers of Oxidative Stress and Inflammation in Colorectal Adenoma Patients: Results from a Randomized, Controlled Clinical Trial

Previous epidemiologic observational and experimental studies investigated the potential of antioxidant micronutrients to modulate cancer risk, but these studies produced inconsistent results. In this pilot, randomized, double-blind, placebo-controlled clinical trial (n = 47), we assessed the effects of an antioxidant micronutrient combination (800 mg dl-α-tocopherol acetate, 24 mg β-carotene, 1.0 g vitamin C, 200 μg l-selenomethionine, 7.2 mg riboflavin, 80 mg niacin, 60 mg zinc, 5 mg manganese) given daily over 4 months on oxidative and inflammatory biomarkers in patients with a history of sporadic colorectal adenoma. Plasma tumor necrosis factor-α (TNF-α), interleukin-6, and F2-isoprostane concentrations were measured using ELISAs, and cystine (CySS) was measured using high-performance liquid chromatography. Plasma TNF-α concentration decreased in the active treatment group by 37% relative to the placebo group (P = 0.002), and CySS decreased by 19% (P = 0.03); however, interleukin-6 and F2-isoprostane concentrations decreased in antioxidant-treated nonsmokers but increased in smokers, although these findings were not statistically significant. The decreases of TNF-α and CySS were more pronounced in nonsmokers. These data suggest that (a) an antioxidant micronutrient cocktail can modulate biomarkers of oxidative stress and inflammation in humans and (b) the effects of antioxidant micronutrient supplementation on biomarkers of inflammation and oxidative stress may differ according to smoking status. Cancer Epidemiol Biomarkers Prev; 19(3); 850–8
Quality Score Based Identification and Correction of Pyrosequencing Errors

Massively-parallel DNA sequencing using the 454/pyrosequencing platform allows in-depth probing of diverse sequence populations, such as within an HIV-1 infected individual. Analysis of this sequence data, however, remains challenging due to the shorter read lengths relative to that obtained by Sanger sequencing as well as errors introduced during DNA template amplification and during pyrosequencing. The ability to distinguish real variation from pyrosequencing errors with high sensitivity and specificity is crucial to interpreting sequence data. We introduce a new algorithm, CorQ (Correction through Quality), which utilizes the inherent base quality in a sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion (indel) errors. CorQ also takes uneven read mapping into account for correcting pyrosequencing miscall errors and it identifies and corrects carry forward errors. We tested the ability of CorQ to correctly call SNPs on a set of pyrosequences derived from ten viral genomes from an HIV-1 infected individual, as well as on six simulated pyrosequencing datasets generated using non-zero error rates to emulate errors introduced by PCR. When combined with the AmpliconNoise error correction method developed to remove ambiguities in signal intensities, we attained a 97% reduction in indel errors, a 98% reduction in carry forward errors, and >97% specificity of SNP detection. When compared to four other error correction methods, AmpliconNoise+CorQ performed at equal or higher SNP identification specificity, but the sensitivity of SNP detection was consistently higher (>98%) than other methods tested. This combined procedure will therefore permit examination of complex genetic populations with improved accuracy.
Lifestyle changes are related to reductions in depression in persons with elevated coronary risk factors

This observational study investigates whether persons with elevated coronary risk factors (CRFs >3 and/or diabetes) and depression [i.e., ≥16 on the Center for Epidemiological Scale – Depression (CES-D)] can make changes in health behaviours over 3 months and improve depressive symptoms and other CRFs. Analyses were based on data from 310 men and 687 women enrolled in the high-risk arm of the Multisite Cardiac Lifestyle Intervention Program, targeting diet (10% fat), exercise (3 h per week) and stress management (7 h per week). As expected, at study entry, depressed persons had a more adverse medical status, consumed more dietary fat and practiced less stress management than non-depressed persons. To examine 3-month changes, participants were grouped into (1) depressed persons who became non-depressed (CES-D ≤ 16, n = 248; 73%), (2) persons who remained or became depressed (CES-D >16, n = 76) and (3) non-depressed persons who remained non-depressed (n = 597). All persons, regardless of group, met program goals. The greatest improvements (i.e., diet, exercise, perceived stress, hostility and mental health) were observed in Group 1 relative to Groups 2 and 3, which did not differ from each other. Comprehensive lifestyle changes appear to be feasible and beneficial for initially depressed persons with elevated CRFs.
Gender Differences in Risk Aversion and Ambiguity Aversion

This paper demonstrates gender differences in risk aversion and ambiguity aversion. It also contributes to a growing literature relating economic preference parameters to psychological measures by asking whether variations in preference parameters among persons, and in particular across genders, can be accounted for by differences in personality traits and traits of cognition. Women are more risk averse than men. Over an initial range, women require no further compensation for the introduction of ambiguity but men do. At greater levels of ambiguity, women have the same marginal distaste for increased ambiguity as men. Psychological variables account for some of the interpersonal variation in risk aversion. They explain none of the differences in ambiguity.
Identification of Intermediate-Size Non-Coding RNAs Involved in the UV-Induced DNA Damage Response in C. elegans

Background A network of DNA damage response (DDR) mechanisms functions coordinately to maintain genome integrity and prevent disease. The Nucleotide Excision Repair (NER) pathway is known to function in the response to UV-induced DNA damage. Although numbers of coding genes and miRNAs have been identified and reported to participate in UV-induced DNA damage response (UV-DDR), the precise role of non-coding RNAs (ncRNAs) in UV-DDR remains largely unknown. Methodology/Principal Findings We used high-throughput RNA-sequencing (RNA-Seq) to discover intermediate-size (70–500 nt) ncRNAs (is-ncRNAs) in C. elegans, using the strains of L4 larvae of wild-type (N2), UV-irradiated (N2/UV100) and NER-deficient mutant (xpa-1), and 450 novel non-coding transcripts were initially identified. A customized microarray assay was then applied to examine the expression profiles of both novel transcripts and known is-ncRNAs, and 57 UV-DDR-related is-ncRNA candidates showed expression variations at different levels between UV irradiated strains and non- irradiated strains. The top ranked is-ncRNA candidates with expression differences were further validated by qRT-PCR analysis, of them, 8 novel is-ncRNAs were significantly up-regulated after UV irradiation. Knockdown of two novel is-ncRNAs, ncRNA317 and ncRNA415, by RNA interference, resulted in higher UV sensitivity and significantly decreased expression of NER-related genes in C. elegans. Conclusions/Significance The discovery of above two novel is-ncRNAs in this study indicated the functional roles of is-ncRNAs in the regulation of UV-DDR network, and aided our understanding of the significance of ncRNA involvement in the UV-induced DNA damage response.
Comparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships

In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59 and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C) and environmental (E), all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins) were present in all human pathogenic strains (both biotype 3 and non-biotype 3) and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS) proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and formed a genetically distinct group within the E-cluster. The unique epidemiological circumstances facilitated disease outbreak and brought this genotype to the attention of the scientific community.
Liver resection for intrahepatic stones.

HYPOTHESIS Long-term outcome is good for a selected group of patients with hepatolithiasis treated with liver resection. Liver resection should also be offered to patients with complex hepatolithiasis such as bilateral stones or those with strictures. DESIGN Retrospective study. SETTING Regional hospital. PATIENTS A total of 174 patients with hepatolithiasis (201 procedures) treated between January 1, 1989, and September 30, 2003. INTERVENTIONS Liver resection (52 procedures) or removal of stones primarily by percutaneous choledochoscopy (149 procedures). MAIN OUTCOME MEASURE Recurrence of cholangitis. RESULTS Most patients in the liver resection group had stones localized to the left side. The overall success rate in this group was 98.0% (49 of 50 patients, excluding 2 patients found to have cholangiocarcinoma). The chance of biliary sepsis at 5 years after resection was 13.3%. The overall success rate of stone removal primarily by percutaneous choledochoscopy was 70.5%. The bilaterality of stones, the presence of stricture, and the presence of atrophy were found to be significant risk factors for a poor long-term outcome after stone removal alone. The chance of biliary sepsis at 5 years was 26.4% and 43.2% for those without and with stricture, respectively. CONCLUSIONS The long-term outcome after liver resection for hepatolithiasis was excellent for a selected group of patients. Poor outcomes were recorded for patients whose intrahepatic stones were removed primarily by percutaneous choledochoscopy, especially those with strictures. The indication for liver resection for hepatolithiasis should be extended to patients with strictures and those with bilateral stones. A combination of different treatment modalities is necessary to improve the outcome of these patients.
Agpat6—a novel lipid biosynthetic gene required for triacylglycerol production in mammary epithelium Published, JLR Papers in Press, January 31, 2006.

In analyzing the sequence tags for mutant mouse embryonic stem (ES) cell lines in BayGenomics (a mouse gene-trapping resource), we identified a novel gene, 1-acylglycerol-3-phosphate O-acyltransferase (Agpat6), with sequence similarities to previously characterized glycerolipid acyltransferases. Agpat6's closest family member is another novel gene that we have provisionally designated Agpat8. Both Agpat6 and Agpat8 are conserved from plants, nematodes, and flies to mammals. AGPAT6, which is predicted to contain multiple membrane-spanning helices, is found exclusively within the endoplasmic reticulum (ER) in mammalian cells. To gain insights into the in vivo importance of Agpat6, we used the Agpat6 ES cell line from BayGenomics to create Agpat6-deficient (Agpat6−/−) mice. Agpat6−/− mice lacked full-length Agpat6 transcripts, as judged by northern blots. One of the most striking phenotypes of Agpat6−/− mice was a defect in lactation. Pups nursed by Agpat6−/− mothers die perinatally. Normally, Agpat6 is expressed at high levels in the mammary epithelium of breast tissue, but not in the surrounding adipose tissue. Histological studies revealed that the aveoli and ducts of Agpat6−/− lactating mammary glands were underdeveloped, and there was a dramatic decrease in the size and number of lipid droplets within mammary epithelial cells and ducts. Also, the milk from Agpat6−/− mice was markedly depleted in diacylglycerols and triacylglycerols. Thus, we identified a novel glycerolipid acyltransferase of the ER, AGPAT6, which is crucial for the production of milk fat by the mammary gland.
The role of the large intestine in post-ruminal digestion of feeds as measured by the mobile-bag method in cattle

To study the importance of site of recovery and other factors related to mobile-bag (MB) digestion values, two consecutive experiments in which diets were applied in a 3 × 3 Latin square design, were carried out with cannulated growing heifers. In Expt 1, several types of experimental feed were exposed to intestinal digestion in mobile bags made of two cloth types and filled with intact or rumen-undegradable (RUD) feed material to be recovered either from the ileum (IB) or faeces (FB). In Expt 2, mean retention time (MRT) of Yb-labelled digesta particles within the intestine and in vivo digestibility of diets were measured. With vegetable concentrates, FB resulted generally in slight overestimation of small-intestinal dry matter and N digestion, while with meat-and-bone meal no difference between FB and IB was found. The respective N digestibility of RUD late-cut silage was clearly underestimated as measured from FB. The disappearance of neutral-detergent fibre (NDF) of all feeds under test was higher from FB than from IB. It was not possible to isolate the influence of the large intestine on the MB values by changing bag cloth type. Irrespective of the longer retention time of bags and longer MRT of Yb in the intestine on a low as compared with a high level of feeding, only NDF disappearance of feeds increased due to lower feeding level. Altering the diet type to increase large-intestinal fermentation, as indicated in vivo, usually had no effect on the MB values. It is concluded that the site of collection of bags does not practically affect small-intestinal digestion values of feed N, unless the feed is rich in fibre.
Collector-base junction avalanche multiplication effects in advanced UHV/CVD SiGe HBTs

The collector-base junction avalanche multiplication factor (M-1) in SiGe HBTs is investigated using a new technique better tolerant to self-heating and collector-base leakage. The new technique provides higher accuracy at low current densities and enables M-1 to be measured at high current densities typically used in circuits. Comparisons with identically processed silicon control devices show that M-1 is not inadvertently increased by the incorporation of SiGe, despite its smaller bandgap. With cooling, M-1 first increases, and then saturates when T<117 K. A 2.3 V critical reverse CB voltage at which base current reversal occurs is observed down to 83 K, which is sufficiently high for today's bipolar and BiCMOS logic applications.
Association between Agent Orange and birth defects: systematic review and meta-analysis.

BACKGROUND The association between parental exposure to Agent Orange or dioxin and birth defects is controversial, due to inconsistent findings in the literature. The principal aim of this study was to conduct a meta-analysis of relevant epidemiological studies that examined this association and to assess the heterogeneity among studies. METHODS Relevant studies were identified through a computerized literature search of Medline and Embase from 1966 to 2002; reviewing the reference list of retrieved articles and conference proceedings; and contacting researchers for unpublished studies. A specified protocol was followed to extract data on study details and outcomes. Both fixed-effects and random-effects models were used to synthesize the results of individual studies. The Cochrane Q test and index of heterogeneity (I2) were used to evaluate heterogeneity, and a funnel plot and Egger's test were used to evaluate publication bias. RESULTS In total, 22 studies including 13 Vietnamese and nine non-Vietnamese studies were identified. The summary relative risk (RR) of birth defects associated with exposure to Agent Orange was 1.95 [95% confidence interval (95% CI) 1.59-2.39], with substantial heterogeneity across studies. Vietnamese studies showed a higher summary RR (RR = 3.00; 95% CI 2.19-4.12) than non-Vietnamese studies (RR = 1.29; 95% CI 1.04-1.59). Sub-group analyses found that the magnitude of association tended to increase with greater degrees of exposure to Agent Orange, rated on intensity and duration of exposure and dioxin concentrations measured in affected populations. CONCLUSION Parental exposure to Agent Orange appears to be associated with an increased risk of birth defects.