Miracle-dz/UniFAR-FTUs huggingface dataset:
Card15 mutations and gastric cancer in a Portuguese population

Abstract Background. CARD15 is involved in the innate immune response and mutations of this gene have been linked with increased risk of Crohn's disease and colorectal cancer. The relation between CARD15 mutations and gastric cancer (GC) remains controversial. Aims. To assess whether CARD15 mutations are risk factors for GC in Portugal and whether there are genotype–phenotype correlations in these patients. Methods. The 3 main CARD15 mutations (3020insC, R702W and G908R) were searched in 150 patients with GC and in 202 healthy controls. Results. Overall, CARD15 mutations were found in 28 patients (18.7%) and in 27 controls (13.4%) (p = 0.176). Individually, the incidence of 3020insC was significantly higher in patients than in controls (6.0% vs. 1.0%, p = 0.021). This polymorphism was linked with an increased risk for the intestinal-type of GC (p = 0.002), while no association was found with the diffuse and/or mixed types. Genotype frequencies for R702W (10.0% vs. 7.9%) and G908R (4.0% vs. 4.0%) were not statistically different between the two groups. Similarly, no significant associations were detected between these two polymorphisms and the different histological GC types. No correlations were observed between CARD15 mutations and family history, mean age at diagnosis or GC stage. Conclusions. The CARD15 3020insC variant is a risk factor for intestinal GC in Portugal. CARD15 variants are not correlated with age of diagnosis or family aggregation of the disease neither with the GC stage.
On Toughness and Hamiltonicity of 2K2‐Free Graphs

The toughness of a (noncomplete) graph G is the minimum value of t for which there is a vertex cut A whose removal yields |A|/t components. Determining toughness is an NP‐hard problem for general input graphs. The toughness conjecture of Chvátal, which states that there exists a constant t such that every graph on at least three vertices with toughness at least t is hamiltonian, is still open for general graphs. We extend some known toughness results for split graphs to the more general class of 2K2‐free graphs, that is, graphs that do not contain two vertex‐disjoint edges as an induced subgraph. We prove that the problem of determining toughness is polynomially solvable and that Chvátal's toughness conjecture is true for 2K2‐free graphs.
Growth of mature boreal Norway spruce was not affected by elevated [CO(2)] and/or air temperature unless nutrient availability was improved.

The growth responses of mature Norway spruce (Picea abies (L.) Karst. ) trees exposed to elevated [CO(2)] (CE; 670-700 ppm) and long-term optimized nutrient availability or elevated air temperature (TE; ±3.9 °C) were studied in situ in northern Sweden in two 3 year field experiments using 12 whole-tree chambers in ca. 40-year-old forest. The first experiment (Exp. I) studied the interactions between CE and nutrient availability and the second (Exp. II) between CE and TE. It should be noted that only air temperature was elevated in Exp. II, while soil temperature was maintained close to ambient. In Exp. I, CE significantly increased the mean annual height increment, stem volume and biomass increment during the treatment period (25, 28, and 22%, respectively) when nutrients were supplied. There was, however, no significant positive CE effect found at the low natural nutrient availability. In Exp. II, which was conducted at the natural site fertility, neither CE nor TE significantly affected height or stem increment. It is concluded that the low nutrient availability (mainly nitrogen) in the boreal forests is likely to restrict their response to the continuous rise in [CO(2)] and/or TE.
The sample complexity of revenue maximization

In the design and analysis of revenue-maximizing auctions, auction performance is typically measured with respect to a prior distribution over inputs. The most obvious source for such a distribution is past data. The goal of this paper is to understand how much data is necessary and sufficient to guarantee near-optimal expected revenue. Our basic model is a single-item auction in which bidders' valuations are drawn independently from unknown and nonidentical distributions. The seller is given m samples from each of these distributions "for free" and chooses an auction to run on a fresh sample. How large does m need to be, as a function of the number k of bidders and ε 0, so that a (1 -- ε)-approximation of the optimal revenue is achievable? We prove that, under standard tail conditions on the underlying distributions, m = poly(k, 1/ε) samples are necessary and sufficient. Our lower bound stands in contrast to many recent results on simple and prior-independent auctions and fundamentally involves the interplay between bidder competition, non-identical distributions, and a very close (but still constant) approximation of the optimal revenue. It effectively shows that the only way to achieve a sufficiently good constant approximation of the optimal revenue is through a detailed understanding of bidders' valuation distributions. Our upper bound is constructive and applies in particular to a variant of the empirical Myerson auction, the natural auction that runs the revenue-maximizing auction with respect to the empirical distributions of the samples. To capture how our sample complexity upper bound depends on the set of allowable distributions, we introduce α-strongly regular distributions, which interpolate between the well-studied classes of regular (α = 0) and MHR (α = 1) distributions. We give evidence that this definition is of independent interest.
Running head : EFFECTS OF DISTRACTION ON ENUMERATION 1 Brief Report Effects of Distraction on Visual Enumeration in Children and Adults

Speeded enumeration of visual stimuli typically produces a bilinear function, with a shallow subitizing rate (<100 ms/item) up to 3-4 items (subitizing span) and a steeper counting rate (~300 ms/item) thereafter. FINST theory (Trick & Pylyshyn, 1993, 1994) suggests that subitizing of targets is possible in the presence of distractors if attention is not required for target detection, but this has not been tested in children. The present study explored enumeration without distractors (Os alone) and with distractors (Os among Xs) in 35 children aged 6-11 years and 17 adults. Subitizing span increased significantly from childhood to adulthood, and counting rate increased significantly with age. Bilinear functions were significantly better than linear fits to the data for most children and adults both without distractors (97% and 100%, respectively) and with distractors (89% and 94%), consistent with their efficient visual search for a single O among multiple Xs. These findings are discussed in comparison with those from new modeling of earlier enumeration data from young and older adults, revealing striking asymmetries in subitizing with distractors between development and aging.
Greenhouse Gas Emissions from Food and Garden Waste Composting Effects of Management and Process Conditions

Composting is a robust waste treatment technology. Use of finished compost enables plant nutrient recycling, carbon sequestration, soil structure improvement and mineral fertiliser replacement. However, composting also emits greenhouse gases (GHG) such as methane (CH4) and nitrous oxide (N2O) with high global warming potential (GWP). This thesis analysed emissions of CH4 and N2O during composting as influenced by management and process conditions and examined how these emissions could be reduced. The GHG emissions from home-scale, large-scale and reactor composting were determined. At small scale, 18 home compost units were analysed over one year. At large scale, the effects of aeration strategies on emissions were studied in 10-20 m long windrow composts. Finally, reactor composting was studied in two sets of experiments under a controlled laboratory environment to investigate the influence of specific process conditions on CH4 and N2O emissions. Methane emissions increased almost 1000-fold when moisture content in the compost substrate increased from about 44% to 66% in the reactor. Moreover, CH4 emissions increased 100-fold as a result of poor aeration. In home composting CH4 emissions were low, but increased with temperature, mixing frequency and moisture. In windrow composting, high CH4 emissions were associated with thermophilic temperatures and large moisture gradients. Moisture content from about 44% to 59% significantly affected N2O emissions in the reactor studies, with N2O emissions increasing at lower moisture. The presence of nitrate in the initial substrate resulted in an early N2O emissions peak in reactor composting. Extended composting period during some reactor runs resulted in higher total GHG emissions due to continued production of both CH4 and N2O late in the process, after 50% of initial carbon had been mineralised. Total direct GHG emissions from home and windrow composting systems, assessed based on their GWP, were similar to or lower than those reported by others, while emissions from most composting reactor runs were lower. To reduce CH4 emissions, composting at a combination of high moisture and high temperature should be avoided. To reduce N2O emissions, extremes of moisture content in the compost matrix should be avoided.
Chinese Metabolic Syndrome Risk Score

Background: The metabolic syndrome (MetS) was first proposed to predict the occurrence of cardiovascular disease and type 2 diabetes. However, it is difficult to identify subjects with MetS early. No previous studies designed to develop a predictive model for MetS in the Chinese population exists; this study was designed to fill that gap. Methods: A middle-aged Chinese cohort of 198 men and 154 women were followed for two years. The binary logistic regression and receiver operation characteristic (ROC) curve were used to develop a predictive model for the future development of MetS. Results: Over two years of follow up, 30 of the 352 subjects (8.52%) without MetS at baseline subsequently developed MetS. Triglycerides (TG) had the highest area under the curve (AUC), while diastolic blood pressure had the lowest. In order to increase the prediction power, MetS components were arranged in the ROC model according to their AUC. After adding waist circumference (WC) to TG (model 1), the AUC was significantly higher than for TG alone. Adding other components into the model did not increase the AUC significantly. A risk score cutoff (0.078) was selected for the best predictive power of model 1 (sensitivity of 76.7%, specificity of 63.4%, with AUC of 76.8%). Conclusions: These results imply that WC and TG are related to the pathophysiologies of MetS, and model 1 could also be used clinically for screening subjects at high risks for MetS.
Book selection behavior in the physical library: implications for ebook collections

Little is known about how readers select books, whether they be print books or ebooks. In this paper we present a study of how people select physical books from academic library shelves. We use the insights gained into book selection behavior to make suggestions for the design of ebook-based digital libraries in order to better facilitate book selection behavior.
Factorial Invariance of the Physical Activity Neighborhood Environment Survey Among Single- Versus Multi-Family Housing Residents

Purpose: Individual perceptions of one's neighborhood environment influence decisions about physical activity participation. Differences between single-family housing neighborhoods versus multi-family housing neighborhoods may affect perceptions and lead to varying responses on surveys designed to assess perceptions of the neighborhood environment for physical activity. This study tested the factorial invariance for the Physical Activity Neighborhood Environment Survey (PANES) between residents of single-family versus multi-family housing neighborhoods. Method: This study was a secondary data analysis of PANES ratings from African American and Hispanic or Latina women (n = 324) who participated in the Health Is Power study (NCI R01CA109403), a multi-site, community-based trial to investigate the relationship between neighborhood factors and physical activity adoption and maintenance. Factorial invariance was tested using a series of nested confirmatory factor analysis models. Results: The final model was a 2nd-order factor structure with partial invariance of item intercepts. The 2nd-order factor structure and the relationships of the PANES items to the 1st-order factors (amenable, unsafe, and walkable) and of the 1st-order factors to the 2nd-order factor (environment) were invariant between the single-family and multi-family housing neighborhood groups. Conclusion: These findings support the construct validity of PANES, which can be considered valid for measuring neighborhood perceptions among residents of neighborhoods with different housing types.
Nucleic acid reactivity: Challenges for next‐generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next‐generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self‐consistent density‐functional tight‐binding semiempirical models are evaluated against high‐level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density‐functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d‐PhoT model is the most robust at predicting proton affinities. AM1/d‐PhoT and DFTB3‐3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear‐scaling “modified divide‐and‐conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next‐generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.
Analysis of the c‐myc P2 promoter

The cis‐acting elements governing transcription from the murine c‐myc P2 promoter have not been well defined. To gain a better understanding of the nature of the protein‐DNA interactions that take place on the P2 promoter, protein binding assays were performed. The ME1a2 and E2F factors appear to be the predominant proteins bound to a region spanning positions −140 to −24 relative to the P2 transcription start site. By a number of criteria, these factors appear to be distinct. When c‐myc promoter sequences were coupled to the chloramphenicol acetyltransferase gene (CAT) and transiently transfected into tissue culture cells it was found that optimal transcription from P2 was heavily dependent on the ME1a2 element.
Effective Anomaly based Intrusion Detection using Rough Set Theory and Support Vector Machine

detection system is used to discover illegitimate and unnecessary behavior at accessing or manipulating computer systems. Subsequently, these behaviors are checked as an attack or normal behavior. Intrusion detection systems aim to identify attacks with a high detection rate and a low false positive. Most of the earlier IDs make use of all the features in the packet to analyze and look for well-known intrusive models. Some of these features are unrelated and superfluous. The disadvantage of these methods is degrading the performance of IDs. The proposed Rough Set Support Vector Machine (RSSVM) approach is extensively decreases the computer resources like memory and CPU utilization which are required to identify an attack. The approach uses rough set to find out feature reducts sets. Then reduct sets are sent to SVM to train and test data. The results showed that the proposed approach gives better and robust representation of data.
DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome

The Cdc45/Mcm2-7/GINS (CMG) helicase separates DNA strands during replication in eukaryotes. How the CMG is assembled and engages DNA substrates remains unclear. Using electron microscopy, we have determined the structure of the CMG in the presence of ATPγS and a DNA duplex bearing a 3′ single-stranded tail. The structure shows that the MCM subunits of the CMG bind preferentially to single-stranded DNA, establishes the polarity by which DNA enters into the Mcm2-7 pore, and explains how Cdc45 helps prevent DNA from dissociating from the helicase. The Mcm2-7 subcomplex forms a cracked-ring, right-handed spiral when DNA and nucleotide are bound, revealing unexpected congruencies between the CMG and both bacterial DnaB helicases and the AAA+ motor of the eukaryotic proteasome. The existence of a subpopulation of dimeric CMGs establishes the subunit register of Mcm2-7 double hexamers and together with the spiral form highlights how Mcm2-7 transitions through different conformational and assembly states as it matures into a functional helicase. DOI: http://dx.doi. org/10.7554/eLife.03273. 001
Trauma-Informed Care: A Paradigm Shift Needed for Services With Homeless Veterans

Purpose of Study: Exposure to traumatic events is a highly prevalent, although often overlooked, aspect in the lives of homeless veterans. In this study, the prevalence and correlates of potentially traumatic events, including posttraumatic stress disorder, in the homeless veteran population are presented. Findings/Conclusions: Presently, there exists a lack of trauma-informed case management services for homeless veterans. Failing to recognize the association between trauma and homelessness may lead to further victimization, exacerbate mental health symptomology, and hinder a provider's ability to effectively intervene on behalf of homeless veterans. Implications for Case Management: Subgroups of homeless veterans such as those who served in the Vietnam and post-Vietnam era, more recent returnees from Iraq and Afghanistan, women, rural-residing veterans, and those who are justice involved, are discussed for unique trauma histories and service needs. Barriers to receiving trauma-informed care among homeless veterans are reviewed. Information to assist providers in assessing trauma histories and current best practices in the treatment of posttraumatic stress disorder are noted. Suggestions for how this document can be used in varied organizational settings are made.
Assessing contamination and compliance in the prostate component of the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial

Background Recently, the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial published 7-year complete prostate cancer mortality results, which showed no benefit of screening with prostate specific antigen (PSA) and digital rectal examination (DRE). An issue of concern was the substantial level of ‘contamination’, or use of PSA and DRE in control arm men. Purpose To provide a detailed description of contamination in PLCO. Methods Surveys inquiring about the most recent PSA and DRE use were given to a sample of control arm men throughout the screening phase of PLCO (years 0—5). A probability model was utilized to translate survey results into actual frequency counts of tests. To assess the impact of contamination, Surveillance, Epidemiology, and End Results (SEER) incidence rates from the pre-screening era (1985—1987) as well as contemporaneous rates, were applied to PLCO person-years of observation. Results Of 38,350 control arm men, 2427 were surveyed. Pre-trial screening and college education were statistically significantly associated with increased contamination rates. The estimated mean number of screening PSAs (DREs) in the control arm was 2.7 (1.1); this compares to 5.0 (3.5) in the screened arm. 1984 and 2538 prostate cancers were observed in the control and screened arms, respectively, during the screening phase. In the absence of screening, 960 and 949 would have been expected; with contemporaneous incidence rates, 1630 and 1611 were expected. Limitations Due to the limitations of the surveys, in terms of both reach and scope, the exact level of PSA and DRE use in control arm men cannot be known. Conclusions Use of prostate screening by control arm men was substantial, but also substantially less than in screened arm men. Detailed quantitative analyses of screening use across arms are critical for understanding current and future findings from the prostate component of PLCO. Clinical Trials 2010; 7: 303—311. http:// ctj.sagepub. com
Sensitivity of critical transmission ranges to node placement distributions

We consider the geometric random graph where n points are distributed independently on the unit interval [0, 1] according to some probability distribution function F with density f. Two nodes are adjacent (i.e., communicate with each other) if their distance is less than some transmission range. We survey results, some classical and some recently obtained by the authors, concerning the existence of zero-one laws for graph connectivity, the type of zero-one laws under the specific assumptions made, the form of its critical scaling and its dependence on the density f. We also present results and conjectures concerning the width of the corresponding phase transition. Engineering implications are discussed for power allocation.