Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant fecundity and DNA methylation Individual variation in size and fecundity is correlated with differences in global DNA cytosine methylation in the perennial herb Helleborus foetidus ( Ranunculaceae ) 1

• Premise of the study Few studies have examined how epigenetic modifications of DNA may influence individual plant phenotypes and ecological processes in wild plant populations. We investigated natural variation in global DNA cytosine methylation and its phenotypic correlates in the perennial herb Helleborus foetidus. • Methods We focused specifically on individual differences in sizeand fecundity-related traits and use HPLC to quantify percent of total cytosines in the genome of young fullgrown leaves that were methylated. • Key Results About one third of all cytosines in H. foetidus genome were methylated. Methylation level differed significantly among individual plants (range = 26.4–36.6%; n = 60 plants), and this variation was significantly related to most sizeand fecundityrelated traits considered. Relatively hypomethylated plants bore more vegetative, reproductive and total ramets, produced more flowers, larger inflorescences and more seed-bearing follicles, and their ramets remained vegetative for fewer years before reproducing sexually, than relatively hypermethylated ones. Taken together, results revealed that individual differences in size and reproductive output were inversely related to global cytosine methylation. • Conclusions Results confirm, in a natural scenario, the association between DNA methylation and sizeand fecundity-related traits previously found by experimental studies. Variations in global cytosine methylation were predictably related to individual differences in sexual reproduction through significant effects on flower and fruit production, which might ultimately influence patterns of selection and population dynamics in this species. This study provides novel insights on the potential ecological significance of epigenetic heterogeneity in wild plant populations.
Can Order of Access to Learning Resources Predict Success?

Learning management systems capture student’s interactions with the course contents in the form of event logs, including the order in which resources are accessed. We build on past research which indicates there are learning benefits if students determine their own ordering of use of learning materials. We report our exploration of sequential data mining that aims to help teachers determine whether some patterns of access to learning resources are predictive of performance, especially where this may signal the need for remediation. We report first explorations of the data in a graphics course and these indicate that sequence of resource access varied between the low, medium and high achieving student groups.
Polymorphisms of Homocysteine Metabolism Are Associated with Intracranial Aneurysms

Background: Impaired homocysteine metabolism is associated with a number of vasculopathies including extracranial aneurysms. We analyzed the possible association of nine genetic variants of homocysteine metabolism with the occurrence of intracranial aneurysms. Methods: Caucasian patients (n = 255) treated at two German hospitals for intracranial aneurysms and local controls (n = 348) were genotyped for the following polymorphisms: methionine synthase (MTR) c.2756A→G, methylenetetrahydrofolate reductase (MTHFR) c.677C→T, MTHFR c.1298A→C, cystathionine β-synthase (CBS) c. 844_855ins68, CBS c.833T→C, dihydrofolate reductase (DHFR) c.594 + 59del19bp, glutathione S-transferase Ω-1 (GSTO1) c.428C→A, reduced folate carrier 1 (RFC1) c.80G→A and transcobalamin 2 (Tc2) c.776C→G. Results: The G-allele of the missense polymorphism Tc2 c.777C→G was found to be underrepresented in patients, suggesting that this variant may protect from the formation of cerebral aneurysms [odds ratio per two risk alleles (OR) 0.48; 95% confidence interval (CI) 0.30–0.77; p = 0.002]. We obtained borderline results for the G-allele of RFC1 c.80G→A (OR 1.64; 95% CI 1.01–2.65; p = 0.051) and the insertion allele of DHFR c.594 + 59del19bp (OR 1.61; 95% CI 1.00–2.60; p = 0.059), which were found to be overrepresented in patients. Conclusion: Polymorphisms of homocysteine metabolism are possible risk factors for the formation of intracranial aneurysms.
Social Distance and Reciprocity

Contrary to the predictions of non-cooperative game theory, trust and reciprocity are commonly reported in simple games. We conduct a one-shot investment game to examine how social distance affects behavior in two-person exchanges. Two aspects of social distance are examined: ex post revelation of complete information on the second playerA¢? s choice set and ex post revelation of information regarding the second playerA¢? s identity. The results indicate that reciprocity is not affected by knowledge of the choice set, but depends critically on the possible revelation of the decision makerA¢? s identity. That is, the possibility that the second playerA¢? s identity (picture) is revealed to his/her counterpart has a profound effect on the degree of reciprocity extended.
Mechanism of Photosignaling by Drosophila Cryptochrome

Background: It is not known whether the redox status of cryptochrome affects circadian clock resetting. Results: Blocking cryptochrome photoreduction does not impair cryptochrome-mediated Timeless degradation and light can induce a conformational change in cryptochrome with oxidized flavin. Conclusion: Cryptochrome can mediate its function in either oxidized or reduced form. Significance: This study provides novel insight into cryptochrome photosignaling. Cryptochrome (CRY) is the primary circadian photoreceptor in Drosophila. Upon light absorption, dCRY undergoes a conformational change that enables it to bind to Timeless (dTIM), as well as to two different E3 ligases that ubiquitylate dTIM and dCRY, respectively, resulting in their proteolysis and resetting the phase of the circadian rhythm. Purified dCRY contains oxidized flavin (FADox), which is readily photoreduced to the anionic semiquinone through a set of 3 highly conserved Trp residues (Trp triad). The crystal structure of dCRY has revealed a fourth Trp (Trp-536) as a potential electron donor. Previously, we reported that the Trp triad played no role in photoinduced proteolysis of dCRY in Drosophila cells. Here we investigated the role of the Trp triad and Trp-536, and the redox status of the flavin on light-induced proteolysis of both dCRY and dTIM and resetting of the clock. We found that both oxidized (FADox) and reduced (FAD⨪) forms of dCRY undergo light-induced conformational change in vitro that enable dCRY to bind JET and that Trp triad and Trp-536 mutations that block known or presumed intraprotein electron transfer reactions do not affect dCRY phototransduction under bright or dim light in vivo as measured by light-induced proteolysis of dCRY and dTIM in Drosophila S2R+ cells. We conclude that both oxidized and reduced forms of dCRY are capable of photosignaling.
Charcot‐Marie‐Tooth disease: molecular characterization of patients from Central and Southern Italy

The syndrome of peroneal muscular atrophy, or Charcot‐Marie‐Tooth (CMT), disease represents the most common inherited peripheral neuropathy, with a prevalence of about 1 per 2500. The disease is usually transmitted in an autosomal dominant fashion, although it can display all the mendelian patterns of inheritance. The chromosome 17‐linked form (CMT1a) appears to be the most common form of the disease in all the ethnic groups studied so far, Italians included, and is due to a tandem duplication in 17p11.2. In order to study the distribution of CMT types and to establish a genotype‐phenotype correlation in patients from Central and Southern Italy, we collected 19 CMT pedigrees diagnosed in the years 1992–1993. Simple tandem repeats (STR) polymorphism analysis with the marker RM11‐GT and Southern blotting with the probes pVAW409R3 and pVAW412 were performed, demonstrating a high prevalence (about 60%) or 17p duplication in the families studied. No clinical or electrophysiological differences were noted between CMT1 patients with or without 17p duplication, respectively. Two families affected by CMT2 showed no evidence of rearrangement at the D17S122 locus. These data are consistent with the hypothesis of a different molecular basis for CMT2.
Colorectal cancer in Russian-speaking Jewish emigrés: community-based screening

OBJECTIVES:Colorectal cancer (CRC) screening by fecal occult blood testing and flexible sigmoidoscopy is recommended by many authorities for those older than age 50. Ashkenazi Jews have been shown to have a higher level of CRC and polyps than the general population. A subset of Ashkenazi Jews, Russian-speaking Jewish immigrants to the United States (RJIs), have not been studied extensively for CRC and may have additional risk factors not found in other Ashkenazi populations.METHODS:A retrospective chart review was undertaken of fecal occult blood tests, endoscopy reports, and pathology reports of 132 RJIs and 124 non-RJI controls over age 50 between 1987 and 1999 at the Jewish Hospital of Cincinnati Medical Outpatient Clinic.RESULTS:Mean ages at the time of diagnosis or flexible sigmoidoscopy were 68 yr for RJIs and 66 yr for the non-RJI patients. Of the RJI patients, 38.7% had positive findings: 37 (28.0%) with lesions < 2 cm, five (3.8%) with lesions > 2 cm, and nine (6.8%) with CRC. Of the non-RJI control group patients, 16.9% had positive findings: 16 (12.9%) with lesions < 2 cm, three (2.4%) with lesions > 2 cm, and two (1.6%) with CRC. Age- and sex-matched statistical analysis revealed significantly greater CRC and significantly more polyps > 2 cm for the RJI patients (p < 0.003). This is higher than in other studies of Ashkenazis, which show a 2.3% incidence, and in statistics from the National Cancer Institute, which reveal a national CRC incidence rate for those over age 65 to be 0.30%. CONCLUSIONS:RJIs in our study have polyps > 2 cm and CRC at a rate of 10.6%, as compared with 4.0% for in-clinic controls and a national average of 0.30% for patients over age 65. This suggests a need for more aggressive screening of this patient population for CRC.
Performance-related completions for software specifications

To evaluate a software specification for its performance potential, it is necessary to supply additional information, not required for functional specification. Examples range from the execution cost of operations and details of deployment, up to missing subsystems and layers. The term "completions" is used here to include all such additions, including annotations, component insertions, environment infrastructure, deployment, communication patterns, design refinements and scenario or design transformations which correspond to a given deployment style. Completions are related to the purpose of evaluation, so they are tailored to describing the performance at a suitable level of detail. Completions for evaluating other attributes such as reliability or security are also possible. The paper describes how completions are added to a specification regardless of the language used (provided that it describes the system behaviour as well as its structure), and experience with completions in Use Case Maps.
Design and Implementation of jAHP: A Java-based Analytic Hierarchy Process Application

a multiple criteria decision making problem by a group of decision makers in different geographical locations could be hard. Analytic Hierarchy Process is a mathematical model capable of dealing with such type of problems. However, the lack of geographical support is the major drawback of a traditional standalone Analytic Hierarchy Process tool. To address this issue, this paper proposes to adopt Java programming language to design and implement jAHP, a Java-based Analytic Hierarchy Process application available over the Internet. External validity is accessed by comparing jAHP results with both manual approach and commercial software. KeywordsHierarchy Process (AHP), Java Programming, JTree
Associations of Sedentary Time with Fat Distribution in a High-Risk Population.

PURPOSE The effect of sedentary behavior on regional fat deposition, independent of physical activity, remains equivocal. We examined the cross-sectional associations between objectively measured sedentary time and markers of regional fat distribution (heart, liver, visceral, subcutaneous, and total body fat) in a population at a high risk of type 2 diabetes mellitus (T2DM). METHODS Participants were recruited from primary care to two diabetes prevention programs. Sedentary time (<25 counts per 15 s) was measured using ActiGraph GT3X accelerometers. Heart, liver, visceral, subcutaneous, and total body fat were quantified using magnetic resonance images. Fat volumes were calculated by multiplying the cross-sectional areas of the fat-containing pixels by the slice thickness. The liver fat percentage was measured using a representative region of interest created in the right lobe of the liver, avoiding the main portal veins. Linear regression models examined the association of sedentary time with markers of regional fat deposition. RESULTS Sixty-six participants (age, 47.9 ± 16.2 yr; male, 50.0%) were included. After adjustment for several covariates, including glycemia, whole-body fat, and moderate-to-vigorous physical activity, each 30 min of sedentary time was associated with 15.7 cm higher heart fat (P = 0.008), 1.2% higher liver fat (P = 0.026), and 183.7 cm higher visceral fat (P = 0.039). CONCLUSIONS This study provides new evidence suggesting that objectively measured sedentary behavior may have an independent association with heart, liver, and visceral fat in individuals at a high risk of T2DM.
Major joint replacement. A model for antithrombotic drug development: from proof-of-concept to clinical use.

AIM Development of antithrombotic compounds has traditionally been performed in patients undergoing total hip and knee replacement surgery. A high number of asymptomatic deep-vein thromboses are radiologically detectable, and bleeding and other adverse events (AE) are easy to observe. However, standardization of study procedures and endpoints in early proof-of-concept studies and late pure clinical endpoint studies has been lacking. This has made comparison between studies difficult, economic analyses speculative and potential benefits of applying the drug regimen in non-selected patients uncertain. In this paper, the International Surgical Thrombosis Forum proposes a strategy for the clinical investigation of new pharmacological agents for the prophylaxis of postoperative thrombotic events. METHODS First, dose titration safety studies of short duration, in highly selected patients using objective venographic endpoints are recommended. Bleeding should be divided into the quantified volume of surgical bleeding and other adjudicated clinical bleeding events. The number of AE should be described for each dose step and classified according to International Coding of Diagnoses (ICD). Second, a dose confirmatory study of moderate exposure period and sufficient follow-up time is recommended. The exclusion criteria should be restricted to contraindications of the compared drugs and technical procedure. RESULTS The efficacy, bleeding and AE should be similar to those used in dose-titration studies. In addition, the failure rate of the drug to exert its effect and the net clinical benefit should be calculated. CONCLUSION Finally, trials with simple clinical endpoints and long follow-up should be conducted to evaluate the potential benefits of the drug-regimen in non-selected populations.
Driver Reaction Time to Tactile and Auditory Rear-End Collision Warnings While Talking on a Cell Phone

Objective: This study examined the effectiveness of rear-end collision warnings presented in different sensory modalities while drivers were engaged in cell phone conversations in a driving simulator. Background: Tactile and auditory collision warnings have been shown to improve braking response time (RT) in rear-end collision situations. However, it is not clear how effective these warnings are when the driver is engaged in attentionally demanding secondary tasks, such as talking on a cell phone. Method: Sixteen participants in a driving simulator experienced three collision warning conditions (none, tactile, and auditory) in three conversation conditions (none, simple hands free, complex hands free). Driver RT was captured from warning onset to brake initiation (WON2B). Results: WON2B times for auditory warnings were significantly larger for simple conversations compared with no conversation (+148 ms), whereas there was no significant difference between these conditions for tactile warnings (+53 ms). For complex conversations, WON2B times for both tactile (+146 ms) and auditory warnings (+221 ms) were significantly larger than during no conversation. During complex conversations, tactile warnings produced significantly shorter WON2B times than no warning (—141 ms). Conclusion: Tactile warnings are more effective than auditory warnings during both simple and complex conversations. Application: These results indicate that tactile rear-end collision warnings have the potential to offset some of the driving impairments caused by cell phone conversations.
Prevention through Design Adoption Readiness Model (PtD ARM): An integrated conceptual model.

BACKGROUND Prevention through Design (PtD), eliminating hazards at the design-stage of tools and systems, is the optimal method of mitigating occupational health and safety risks. A recent National Institute of Safety and Health initiative has established a goal to increase adoption of PtD innovation in industry. The construction industry has traditionally lagged behind other sectors in the adoption of innovation, in general; and of safety and health prevention innovation, in particular. Therefore, as a first step toward improving adoption trends in this sector, a conceptual model was developed to describe the parameters and causal relationships that influence and predict construction stakeholder "adoption readiness" for PtD technology innovation. METHODS This model was built upon three well-established theoretical frameworks: the Health Belief Model, the Diffusion of Innovation Model, and the Technology Acceptance Model. Earp and Ennett's model development methodology was employed to build a depiction of the key constructs and directionality and magnitude of relationships among them. Key constructs were identified from the literature associated with the three theoretical frameworks, with special emphasis given to studies related to construction or OHS technology adoption. RESULTS A conceptual model is presented. Recommendations for future research are described and include confirmatory structural equation modeling of model parameters and relationships, additional descriptive investigation of barriers to adoption in some trade sectors, and design and evaluation of an intervention strategy.
Adaptive Modulation Technique for cooperative diversity in Wireless Fading Channels

In recent years, cooperative diversity techniques have gained increased attention as a new way to combat degrading effects of fading. Cooperation among two or more single antenna users generates a virtual diverse multiple-antenna transmission system in the wireless network. In this paper, we investigate the application of adaptive modulation concept to the performance of cooperative techniques. We consider the adaptation of rate and power allocation with M-QAM modulation, and study the performance of amplify & forward scenarios in Rayleigh fading channels. We compare these systems with their comparable adaptive non-cooperative scenario and evaluate the energy saving achieved through cooperation
Deep Brain Stimulation for Obsessive-Compulsive Disorder: A Meta-Analysis of Treatment Outcome and Predictors of Response

Background Deep brain stimulation (DBS) has been proposed as an alternative to ablative neurosurgery for severe treatment-resistant Obsessive-Compulsive Disorder (OCD), although with partially discrepant results probably related to differences in anatomical targetting and stimulation conditions. We sought to determine the efficacy and tolerability of DBS in OCD and the existence of clinical predictors of response using meta-analysis. Methods We searched the literature on DBS for OCD from 1999 through January 2014 using PubMed/MEDLINE and PsycINFO. We performed fixed and random-effect meta-analysis with score changes (pre-post DBS) on the Yale-Brown Obsessive Compulsive Scale (Y-BOCS) as the primary-outcome measure, and the number of responders to treatment, quality of life and acceptability as secondary measures. Findings Thirty-one studies involving 116 subjects were identified. Eighty-three subjects were implanted in striatal areas—anterior limb of the internal capsule, ventral capsule and ventral striatum, nucleus accumbens and ventral caudate—27 in the subthalamic nucleus and six in the inferior thalamic peduncle. Global percentage of Y-BOCS reduction was estimated at 45.1% and global percentage of responders at 60.0%. Better response was associated with older age at OCD onset and presence of sexual/religious obsessions and compulsions. No significant differences were detected in efficacy between targets. Five patients dropped out, but adverse effects were generally reported as mild, transient and reversible. Conclusions Our analysis confirms that DBS constitutes a valid alternative to lesional surgery for severe, therapy-refractory OCD patients. Well-controlled, randomized studies with larger samples are needed to establish the optimal targeting and stimulation conditions and to extend the analysis of clinical predictors of outcome.
Trade Liberalisation and Poverty in Nepal: A Computable General Equilibrium Micro Simulation Analysis

Concern is growing regarding the poverty impacts of trade liberalization. The strong general equilibrium effects of trade liberalization can only be properly analysed in a CGE model. However, the aggregate nature of CGE models is not suited to detailed poverty analysis. We bridge this gap by constructing a CGE model that explicitly models all households from a nationally representative household survey. We find complex income and consumption effects that would be missed in standard CGE models. Urban poverty falls and rural poverty increases as initial tariffs were highest for agriculture. Impacts increase with income level, resulting in rising income inequality.
An experimental framework for the derivation of perceptually-optimal noise suppression functions

This paper presents a novel experimental framework designed to derive, through subjective testings, noise suppression functions which are perceptually optimal under specific experimental conditions. Noisy speech sequences are continuously processed according to a gain curve function of the a priori SNR that listeners are required to adjust two points at a time with respect to specified perceptual criteria. An experiment based on this framework is reported testing one specific combination of speech and noise signals. The specified perceptual criterion was the suitability for a phone conversation. The resulting mean experimental gain function shows a statistically significant deviation from an ideal Wiener filter. Experiments based on this framework are repeatable, suit untrained listeners and are considerably faster than conventional subjective testing methods, without the necessity to place restrictive assumptions on the assessed noise suppression function.