Miracle-dz/UniFAR-FTUs huggingface dataset:
Contributions of maternal and paternal adiposity and smoking to adult offspring adiposity and cardiovascular risk: the Midspan Family Study

Objective Obesity has some genetic basis but requires interaction with environmental factors for phenotypic expression. We examined contributions of gender-specific parental adiposity and smoking to adiposity and related cardiovascular risk in adult offspring. Design Cross-sectional general population survey. Setting Scotland. Participants 1456 of the 1477 first generation families in the Midspan Family Study: 2912 parents (aged 45–64 years surveyed between 1972 and 1976) who had 1025 sons and 1283 daughters, aged 30–59 years surveyed in 1996. Main measures Offspring body mass index (BMI), waist circumference (WC), cardiometabolic risk (lipids, blood pressure and glucose) and cardiovascular disease as outcome measures, and parental BMI and smoking as determinants. All analyses adjusted for age, socioeconomic status and family clustering and offspring birth weight. Results Regression coefficients for BMI associations between father–son (0.30) and mother–daughter (0.33) were greater than father–daughter (0.23) or mother–son (0.22). Regression coefficient for the non-genetic, shared-environment or assortative-mating relationship between BMIs of fathers and mothers was 0.19. Heritability estimates for BMI were greatest among women with mothers who had BMI either <25 or ≥30 kg/m2. Compared with offspring without obese parents, offspring with two obese parents had adjusted OR of 10.25 (95% CI 6.56 to 13.93) for having WC ≥102 cm for men, ≥88 cm women, 2.46 (95% CI 1.33 to 4.57) for metabolic syndrome and 3.03 (95% CI 1.55 to 5.91) for angina and/or myocardial infarct (p<0.001). Neither parental adiposity nor smoking history determined adjusted offspring individual cardiometabolic risk factors, diabetes or stroke. Maternal, but not paternal, smoking had significant effects on WC in sons (OR=1.50; 95% CI 1.13 to 2.01) and daughters (OR=1.42; 95% CI 1.10 to 1.84) and metabolic syndrome OR=1.68; 95% CI 1.17 to 2.40) in sons. Conclusions There are modest genetic/epigenetic influences on the environmental factors behind adverse adiposity. Maternal smoking appears a specific hazard on obesity and metabolic syndrome. A possible epigenetic mechanism linking maternal smoking to obesity and metabolic syndrome in offspring is proposed. Individuals with family histories of obesity should be targeted from an early age to prevent obesity and complications.
Sociodemographic Characteristics and Coronary Calcium Levels by Sex and Race / Ethnicity : MESA 2000 – 2002

Background—Coronary calcium has recently emerged as a marker of subclinical coronary heart disease. Although there has been much interest in race differences in calcification, heterogeneity within race or ethnic groups has not been investigated. Methods and Results—Data from the Multi-Ethnic Study of Atherosclerosis (MESA), a population-based study of coronary calcification, were used to investigate acculturation and socioeconomic position as predictors of coronary calcification within 2553 non-Hispanic whites, 1734 non-Hispanic blacks, 1457 Hispanics, and 797 Chinese residing in the United States. Coronary calcium was assessed by chest CT. Relative risk regression and linear regression were used to estimate adjusted associations of sociodemographic variables with the presence and amount of calcium. Not being born in the United States was associated with a lower prevalence of calcification in blacks (relative prevalence [RP], 0.75; 95% confidence limit [CL], 0.61 to 0.94) and Hispanics (RP, 0.89; 95% CL, 0.81 to 0.98) after adjustment for age, sex, income, and education. Years in the United States was positively associated with prevalence of calcification in non–US-born Chinese (adjusted RP per 10 years in United States, 1.06; 95% CL, 1.01 to 1.11) and non–US-born blacks (RP, 1.59; 95% CL, 1.22 to 2.06). Low education was associated with a higher prevalence of calcification in whites (adjusted RP for no high school versus complete college, 1.17; 95% CL, 1.05 to 1.32) but with lower prevalence of calcification in Hispanics (RP, 0.91; 95% CL, 0.77 to 1.09) (P for interaction 0.02). US birth and time in the United States were also positively associated with the extent of calcification in persons with detectable calcium. These differences did not appear to be accounted for by smoking, body mass index, LDL and HDL cholesterol, hypertension, and diabetes. Conclusions—Acculturation and socioeconomic factors are associated with differences in the prevalence and amount of coronary calcification within whites, Chinese, blacks, and Hispanics. The presence of this heterogeneity needs to be acknowledged in the quantification and investigation of race/ethnic differences. (Circulation. 2005;112:1557-1565.)
Parthenolide inhibits pro-inflammatory cytokine production and exhibits protective effects on progression of collagen-induced arthritis in a rat model

Objectives: Progressive destruction of synovial joint cartilage and bone occurs in pathological conditions such as rheumatoid arthritis (RA) because of the overproduction of pro-inflammatory cytokines and activation of nuclear factor kappa B (NF-κB). Through the screening of NF-κB inhibitors by a luciferase reporter gene assay, we identified parthenolide (PAR) as the most potent NF-κB inhibitor, among several PAR analogue compounds. This study was undertaken to determine whether PAR inhibits pro-inflammatory cytokine production, cartilage degradation, and inflammatory arthritis. Method: The mRNA levels of pro-inflammatory cytokines were examined by real-time polymerase chain reaction (PCR). Proteoglycan content and release were determined by measuring glycosaminoglycan (GAG) levels using the dimethylmethylene blue (DMMB) dye-binding assay. The potential role of PAR in treatment of arthritis was studied using a collagen-induced arthritis (CIA) model. Results: We established that PAR, as a prototype compound, suppressed lipopolysaccharide (LPS)- and tumour necrosis factor (TNF)-α-induced increases in matrix metalloproteinase (MMP)-1, MMP-3, inducible nitric oxide synthase (iNOS), and interleukin (IL)-1β mRNA in chondrocytes. In addition, PAR prevented proteoglycan degradation triggered by pro-inflammatory cytokines. PAR treatment at the onset of CIA symptoms significantly reduced synovitis, inflammation, and pannus formation scores. Reduced synovial inflammation after PAR treatment was also reflected in significantly less bone erosion and cartilage damage. Conclusions: These data indicate a protective effect of PAR on the catabolic insults of pro-inflammatory cytokines on chondrocyte metabolism and GAG release in vitro and in CIA. PAR had anti-inflammatory and structure-modifying effects on experimental arthritis, suggesting that PAR may be useful as a potential alternative or adjunct therapy for inflammatory arthritis.
Expanded impact of protein N-myristoylation in plants

N-MYR controls the function of the plant protein complex SnRK1, described as one of the most important plant regulatory protein in stress and energy signalling. In plant cells, N-MYR is involved in a significantly higher number of metabolic pathways than in yeast or human. Some N-myristoylated protein families are solely encountered in plant cells. This lipid modification could be involved in the control of the redox imbalances originating from different stresses in plants. This prevalence of N-MYR in such proteins is unique to the plant kingdom. We hypothesize that this expansion of the mechanism in plants improves the control of the damages induced by environmental changes. Addendum to: Pierre M, Traverso JA, Boisson B, Domenichini S, Bouchez D, Giglione C, Meinnel T. N-myristoylation regulates the SnRK1 pathway in Arabidopsis. Plant Cell 2007; 19:2804-21.
Determining the spatial reader scopes of news sources using local lexicons

Information sources on the Internet (e.g., Web versions of newspapers) usually have an implicit spatial reader scope, which is the geographical location for which the content has been primarily produced. Knowledge of the spatial reader scope facilitates the construction of a news search engine that provides readers a set of news sources relevant to the location in which they are interested. In particular, it plays an important role in disambiguating toponyms (e.g., textual specifications of geographical locations) in news articles, as the process of selecting an interpretation for the toponym often reduces to one of selecting an interpretation that seems natural in the context of the spatial reader scope. The key to determining the spatial reader scope of news sources is the notion of local lexicon, which for a location s is a set of concepts such as, but not limited to, names of people, landmarks, and historical events, that are spatially related to s. Techniques to automatically generate the local lexicon of a location by using the link structure of Wikipedia are described and evaluated. A key contribution is the improvement of existing methods used in the semantic relatedness domain to extract concepts spatially related to a given location from the Wikipedia. Results of experiments are presented that indicate that the knowledge of the spatial reader scope significantly improves the disambiguation of textually specified locations in news articles and that using local lexicons is an effective method to determine the spatial reader scopes of news sources.
Detecting epistatic effects in association studies at a genomic level based on an ensemble approach

Motivation: Most complex diseases involve multiple genes and their interactions. Although genome-wide association studies (GWAS) have shown some success for identifying genetic variants underlying complex diseases, most existing studies are based on limited single-locus approaches, which detect single nucleotide polymorphisms (SNPs) essentially based on their marginal associations with phenotypes. Results: In this article, we propose an ensemble approach based on boosting to study gene–gene interactions. We extend the basic AdaBoost algorithm by incorporating an intuitive importance score based on Gini impurity to select candidate SNPs. Permutation tests are used to control the statistical significance. We have performed extensive simulation studies using three interaction models to evaluate the efficacy of our approach at realistic GWAS sizes, and have compared it with existing epistatic detection algorithms. Our results indicate that our approach is valid, efficient for GWAS and on disease models with epistasis has more power than existing programs. Contact: jingli@case.edu
Structure of the Arginine Methyltransferase PRMT5-MEP50 Reveals a Mechanism for Substrate Specificity

The arginine methyltransferase PRMT5-MEP50 is required for embryogenesis and is misregulated in many cancers. PRMT5 targets a wide variety of substrates, including histone proteins involved in specifying an epigenetic code. However, the mechanism by which PRMT5 utilizes MEP50 to discriminate substrates and to specifically methylate target arginines is unclear. To test a model in which MEP50 is critical for substrate recognition and orientation, we determined the crystal structure of Xenopus laevis PRMT5-MEP50 complexed with S-adenosylhomocysteine (SAH). PRMT5-MEP50 forms an unusual tetramer of heterodimers with substantial surface negative charge. MEP50 is required for PRMT5-catalyzed histone H2A and H4 methyltransferase activity and binds substrates independently. The PRMT5 catalytic site is oriented towards the cross-dimer paired MEP50. Histone peptide arrays and solution assays demonstrate that PRMT5-MEP50 activity is inhibited by substrate phosphorylation and enhanced by substrate acetylation. Electron microscopy and reconstruction showed substrate centered on MEP50. These data support a mechanism in which MEP50 binds substrate and stimulates PRMT5 activity modulated by substrate post-translational modifications.
Distribution and Seasonal Variation in Hypothalamic RF‐amide Peptides in a Semi‐Desert Rodent, the Jerboa

The jerboa is a semi‐desert rodent, in which reproductive activity depends on the seasons, being sexually active in the spring–summer. The present study aimed to determine whether the expression of two RF‐amide peptides recently described to regulate gonadotrophin‐releasing hormone neurone activity, kisspeptin (Kp) and RF‐amide‐related peptide (RFRP)‐3, displays seasonal variation in jerboa. Kp and/or RFRP‐3 immunoreactivity was investigated in the hypothalamus of jerboas captured in the field of the Middle Atlas mountain (Morocco), either in the spring or autumn. As in other rodents, the Kp‐immunoreactive (‐IR) neurones were found in the anteroventro‐periventricular and arcuate nuclei. RFRP‐3 neurones were noted within the dorso/ventromedial hypothalamus. A marked sexual dimorphism in the expression of Kp (but not RFRP‐3) was observed. The number of Kp‐IR neurones was nine‐fold higher, and the density of Kp‐IR fibres and terminal‐like elements in the median eminence was two‐fold higher in females than in males. Furthermore, a significant seasonal variation in peptide expression was obtained with an increase in both Kp‐ and RFRP‐3‐IR cell bodies in sexually active male jerboas captured in the spring compared to sexually inactive autumn animals. In the arcuate nucleus, the level of Kp‐IR cells and fibres was significant higher during the sexually active period in the spring than during the autumnal sexual quiescence. Similarly, the number of RFRP‐3‐IR neurones in the ventro/dorsomedial hypothalamus was approximately three‐fold higher in sexually active jerboa captured in the spring compared to sexually inactive autumn animals. Altogether, the present study reports the distribution of Kp and RFRP‐3 neurones in the hypothalamus of a desert species and reveals a seasonal difference in their expression that correlates with sexual activity. These findings suggest that these two RF‐amide peptides may act in concert to synchronise the gonadotrophic activity of jerboas with the seasons.
The roles of information deficits and identity threat in the prevalence of misperceptions

ABSTRACT Why do so many Americans hold misperceptions? We examine two factors that contribute to the prevalence of these beliefs. First, presenting correct information should reduce misperceptions, especially if provided in a clear and compelling format. We therefore test the effect of graphical information, which may be especially effective in facilitating belief updating about changes in quantities over time. In some cases, though, people may reject information because it threatens their worldview or self-concept – a mechanism that can be revealed by affirming individuals’ self-worth, which could make them more willing to acknowledge uncomfortable facts. We test both mechanisms jointly. In three experiments, we find that providing information in graphical form reduces misperceptions. A third study shows that this effect is greater than for equivalent textual information. Our findings for self-affirmation are more equivocal. We find limited evidence that self-affirmation can help diminish misperceptions when no other information is provided, but it does not consistently increase willingness to accept corrective information as previous research in social psychology would suggest. These results suggest that misperceptions are caused by a lack of information as well as psychological threat, but that these factors may interact in ways that are not yet well understood.
A Practical Investigation into Acoustic Wave Propagation in Concrete Structures

Acoustic Emission (AE) testing in concrete structures shows great potential for monitoring and assessing the health condition of structures. Source location is normally based on the arrival times of transient signals, the simplest method is known as the Time of Arrival (TOA) method, where the location of the damage can be determined from the arrival time of the event at two or more sensors. When using this method, the wave velocity of the signals that propagate through the material needs to be determined. Homogenous materials, such as steel, have welldefined velocities, but in non-homogeneous materials such as concrete the wave velocity is more difficult to predict. This makes the use of a single wave velocity as required in the TOA method very difficult due to the variety of wave velocities obtained, especially for large structures. This paper explores wave propagation in concrete structures over a variety of source to sensor distances. Experiments were performed on a reinforced concrete beam and a reinforced concrete slab, using an Hsu-Nelsen (H-N) Source. It is found that, in general, as the source to sensor distance increases, the wave velocity decreases. The presence of longitudinal and transverse waves is demonstrated and the influence of the part of the waveform used for temporal measurement is explored. In order to provide a practical approach to velocity determination, different thresholds are investigated and the results are discussed in relation to the wave modes present.
Ablation of AMP-Activated Protein Kinase α2 Activity Exacerbates Insulin Resistance Induced by High-Fat Feeding of Mice

OBJECTIVE—We determined whether muscle AMP-activated protein kinase (AMPK) has a role in the development of insulin resistance. RESEARCH DESIGN AND METHODS—Muscle-specific transgenic mice expressing an inactive form of the AMPK α2 catalytic subunit (α2i TG) and their wild-type littermates were fed either a high-fat (60% kcal fat) or a control (10% kcal fat) diet for 30 weeks. RESULTS—Compared with wild-type mice, glucose tolerance in α2i TG mice was slightly impaired on the control diet and significantly impaired on the high-fat diet. To determine whether the whole-body glucose intolerance was associated with impaired insulin sensitivity in skeletal muscle, glucose transport in response to submaximal insulin (450 μU/ml) was measured in isolated soleus muscles. On the control diet, insulin-stimulated glucose transport was reduced by ∼50% in α2i TG mice compared with wild-type mice. High-fat feeding partially decreased insulin-stimulated glucose transport in wild-type mice, while high-fat feeding resulted in a full blunting of insulin-stimulated glucose transport in the α2i TG mice. High-fat feeding in α2i TG mice was accompanied by decreased expression of insulin signaling proteins in gastrocnemius muscle. CONCLUSIONS—The lack of skeletal muscle AMPK α2 activity exacerbates the development of glucose intolerance and insulin resistance caused by high-fat feeding and supports the thesis that AMPK α2 is an important target for the prevention/amelioration of skeletal muscle insulin resistance through lifestyle (exercise) and pharmacologic (e.g., metformin) treatments.
Classifying Phishing Emails Using Confidence-Weighted Linear Classifiers

Though Internet users are generally becoming more aware of phishing emails and phishing websites, cyber scammers are able to come up with novel schemes constantly that circumvent phishing filters and often succeed in fooling even savvy users. Using heuristic approaches and knowledge about the phishing techniques, researchers have developed several phishing specific unique features to detect phishing emails. In this paper, we propose a new and simple methodology to detect phishing emails utilizing Confidence- Weighted Linear Classifiers. We use the contents of the emails as features without applying any heuristic based phishing specific features and obtain highly accurate results compared to the best that have been published in the literature.
Hepatitis D Virus Genotypes in Intravenous Drug Users in Taiwan: Decreasing Prevalence and Lack of Correlation with Hepatitis B Virus Genotypes

ABSTRACT Of 368 hepatitis B virus (HBV)-infected intravenous drug users, 144 (39%) were positive for antibody to hepatitis D virus (anti-HDV). Anti-HDV-positive HBV carriers had a lower rate of positivity for HBV DNA than did anti-HDV-negative carriers (52 versus 73%, respectively). From 1986 to 1997, the average rate of decrease in the prevalence of HDV infection in this population was 4.7%/year.
Finite Element Nonlinear Random Response of Composite Panels of Arbitrary Shape to Acoustic and Thermal Loads

Abstract : A finite element formulation in modal coordinates is presented for postbuckling of thin laminated composite plates subjected to combined thermal and mechanical loads. The mechanical load considered is a uniformly distributed transverse load which is to simulate the static pressure differential applied to the aircraft skin panel. A modal participation value is defined and the minimum number of modes for convergence and accurate postbuckling solution can be determined. The modal formulation reduces the number of coupled nonlinear equations in the structure nodal degrees of freedom of hundreds, if not thousands, to a number of coupled nonlinear equations in the modal coordinates of usually ten. This greatly reduces the computation costs. Deflection shape change for a long rectangular plate is observed and investigated. Three multiple postbuckling solutions or branches are obtained from the modal formulation. The total potential energy and its second variation indicate that there exist only two stable, primary and secondary branches and the third is an unstable peak.
Detection and characterization of buried landmines using infrared thermography

The application of infrared (IR) thermography to the detection and characterization of buried landmines (more generally, buried objects) is introduced. The problem is aimed at detecting the presence of objects buried under the ground and characterizing them by estimating their thermal and geometrical properties using IR measurements on the soil surface. Mathematically, this problem can be stated as an inverse problem for reconstructing a piecewise constant coefficient of a three-dimensional heat equation in a parallelepiped from only one measurement taken at one plane of its boundary (the air-soil interface). Due to the lack of spatial information in the observed data, this problem is extremely ill-posed. In order to reduce its ill-posedness, keeping in mind the application of detecting buried landmines we make use of some simplification steps and propose a two-step method for solving it. The performance of the proposed algorithm is illustrated with numerical examples.
DeepWalk: online learning of social representations

We present DeepWalk, a novel approach for learning latent representations of vertices in a network. These latent representations encode social relations in a continuous vector space, which is easily exploited by statistical models. DeepWalk generalizes recent advancements in language modeling and unsupervised feature learning (or deep learning) from sequences of words to graphs. DeepWalk uses local information obtained from truncated random walks to learn latent representations by treating walks as the equivalent of sentences. We demonstrate DeepWalk's latent representations on several multi-label network classification tasks for social networks such as BlogCatalog, Flickr, and YouTube. Our results show that DeepWalk outperforms challenging baselines which are allowed a global view of the network, especially in the presence of missing information. DeepWalk's representations can provide F1 scores up to 10% higher than competing methods when labeled data is sparse. In some experiments, DeepWalk's representations are able to outperform all baseline methods while using 60% less training data. DeepWalk is also scalable. It is an online learning algorithm which builds useful incremental results, and is trivially parallelizable. These qualities make it suitable for a broad class of real world applications such as network classification, and anomaly detection.