Miracle-dz/UniFAR-FTUs huggingface dataset:
Blood glutathione redox status and global methylation of peripheral blood mononuclear cell DNA in Bangladeshi adults

Oxidative stress and DNA methylation are metabolically linked through the relationship between one-carbon metabolism and the transsulfuration pathway, but possible modulating effects of oxidative stress on DNA methylation have not been extensively studied in humans. Enzymes involved in DNA methylation, including DNA methyltransferases and histone deacetylases, may show altered activity under oxidized cellular conditions. Additionally, in vitro studies suggest that glutathione (GSH) depletion leads to global DNA hypomethylation, possibly through the depletion of S-adenosylmethionine (SAM). We tested the hypothesis that a more oxidized blood GSH redox status is associated with decreased global peripheral blood mononuclear cell (PBMC) DNA methylation in a sample of Bangladeshi adults. Global PBMC DNA methylation and whole blood GSH, glutathione disulfide (GSSG), and SAM concentrations were measured in 320 adults. DNA methylation was measured by using the [3H]-methyl incorporation assay; values are inversely related to global DNA methylation. Whole blood GSH redox status (Eh) was calculated using the Nernst equation. We found that a more oxidized blood GSH Eh was associated with decreased global DNA methylation (B ± SE, 271 ± 103, p = 0.009). Blood SAM and blood GSH were associated with global DNA methylation, but these relationships did not achieve statistical significance. Our findings support the hypothesis that a more oxidized blood GSH redox status is associated with decreased global methylation of PBMC DNA. Furthermore, blood SAM does not appear to mediate this association. Future research should explore mechanisms through which cellular redox might influence global DNA methylation.
Intercomparison of Six Upscaling Evapotranspiration Methods: From Site to the Satellite Pixel

Land surface evapotranspiration (ET) is an important component of the surface energy budget and water cycle. To solve the problem of the spatial‐scale mismatch between in situ observations and remotely sensed ET, it is necessary to find the most appropriate upscaling approach for acquiring ground truth ET data at the satellite pixel scale. Based on a data set from two flux observation matrices in the middle stream and downstream of the Heihe River Basin, six upscaling methods were intercompared via direct validation and cross validation. The results showed that the area‐weighted method performed better than the other five upscaling methods introducing auxiliary variables (the integrated Priestley‐Taylor equation, weighted area‐to‐area regression kriging [WATARK], artificial neural network, random forest [RF], and deep belief network methods) over homogeneous underlying surfaces. Over moderately heterogeneous underlying surfaces, the WATARK method performed better. However, the RF method performed better over highly heterogeneous underlying surfaces. A combined method (using the area‐weighted and WATARK methods for homogeneous and moderately heterogeneous underlying surfaces, respectively, and using the RF method for highly heterogeneous underlying surfaces) was proposed to acquire the daily ground truth ET data at the satellite pixel scale, and the errors in the ground truth ET data were evaluated. The Dual Temperature Difference (DTD) and ETMonitor were validated using ground truth ET data, which solve the problem of the spatial‐scale mismatch and quantify uncertainties in the validation process.
Are droughts becoming more frequent or severe in China based on the Standardized Precipitation Evapotranspiration Index: 1951–2010?

The Standardized Precipitation Evapotranspiration Index (SPEI) was computed based on the monthly precipitation and air temperature values at 609 locations over China during the period 1951–2010.Various characteristics of drought across China were examined including: long‐term trends, percentage of area affected, intensity, duration, and drought frequency. The results revealed that severe and extreme droughts have become more serious since late 1990s for all of China (with dry area increasing by ∼3.72% per decade); and persistent multi‐year severe droughts were more frequent in North China, Northeast China, and western Northwest China; significant drying trends occurred over North China, the southwest region of Northeast China, central and eastern regions of Northwest China, the central and southwestern parts of Southwest China and southwestern and northeastern parts of western Northwest mainly due to a decrease in precipitation coupled with a general increase in temperature. In addition, North China, the western Northwest China, and the Southwest China had their longest drought durations during the 1990s and 2000s. Droughts also affected western Northwest, eastern Northwest, North, and Northeast regions of China more frequently during the recent three decades. The results of this article could provide certain references and triggers for establishing a drought early warning system in China. © 2013 Royal Meteorological Society
Lentiviral silencing of GSK-3β in adult dentate gyrus impairs contextual fear memory and synaptic plasticity

Attempts have been made to use glycogen synthase kinase-3 beta (GSK3β) inhibitors for prophylactic treatment of neurocognitive conditions. However the use of lithium, a non-specific inhibitor of GSK3β results in mild cognitive impairment in humans. The effects of global GSK3β inhibition or knockout on learning and memory in healthy adult mice are also inconclusive. Our study aims to better understand the role of GSK3β in learning and memory through a more regionally, targeted approach, specifically performing lentiviral-mediated knockdown of GSK3β within the dentate gyrus (DG). DG-GSK3β-silenced mice showed impaired contextual fear memory retrieval. However, cue fear memory, spatial memory, locomotor activity and anxiety levels were similar to control. These GSK3β-silenced mice also showed increased induction and maintenance of DG long-term potentiation (DG-LTP) compared to control animals. Thus, this region-specific, targeted knockdown of GSK3β in the DG provides better understanding on the role of GSK3β in learning and memory.
Predictors of Contraceptive Use Among Married Youths and Their Husbands in a Rural Area of Myanmar

This study aimed to determine the predictors of contraceptive use among married female youths and their husbands using the behavioral theory of the Health Belief Model (HBM). A community-based survey was conducted in a rural area of Myanmar in 2008. A total of 444 respondents (222 couples) were interviewed separately using a pretested, structured questionnaire. Significant predictors of contraceptive use were determined by univariate and multivariate analysis. Wife’s HBM perception was a highly significant predictor of contraceptive use in married youths (adjusted odds ratio = 10; 95% confidence interval = 2.7, 37.6). Wives aged 20 to 24 years and having their own income, experience of spousal communication, and shorter distance from home to health center were also significant predictors of contraceptive use. A poor agreement on HBM perception between wife and husband was noted. This study highlights the importance of HBM perceptions, wife’s income, spousal communication, and geographic barriers in contraceptive use among married youths in rural Myanmar.
Haptic Detection of Sine-Wave Gratings

We studied human haptic perception of sine-wave gratings. In the first experiment we measured the dependence of amplitude detection thresholds on the number of cycles and on the wavelength of the gratings. In haptic perception of sine-wave gratings, the results are in agreement with neural summation. The rate at which detection thresholds decrease with increasing number of cycles is much higher than can be accounted for by probability summation alone. Further, neural summation mechanisms describe the detection thresholds accurately over the whole spatial range probed in the experiment, that is wavelengths from 14 mm up to 225 mm. Earlier, we found a power-law dependence of thresholds on the spatial width of Gaussian profiles (Louw et al, 2000 Experimental Brain Research 132 369–374). The current results extend these findings; the power-law dependence holds not only for Gaussian profiles, but also for a broad range of sine-wave gratings with the number of cycles varying between 1 and 8. Haptic perception involves tactual scanning combined with an active, dynamic exploration of the environment. We measured characteristics of the velocity and force with which stimuli were scanned while performing a psychophysical task. One particularly surprising finding was that, without being instructed, participants maintained an almost constant scanning velocity during each 45-min session. A constant velocity in successive trials of the experiment might facilitate or even be necessary for discrimination. Further, a large systematic dependence of velocity on scanning length was found. An eightfold increase in scanning length resulted in about a fourfold increase in scanning velocity. A second experiment was conducted to study the influence of scanning velocity on psychophysical detection thresholds. This was done by systematically imposing specific scanning velocities to the participants while the thresholds were measured. The main result of the second experiment was that psychophysical detection thresholds are constant over a relatively broad range of scanning velocities.
A Survey of the FDA's AERS Database Regarding Muscle and Tendon Adverse Events Linked to the Statin Drug Class

Background Cholesterol management drugs known as statins are widely used and often well tolerated; however, a variety of muscle-related side effects can arise. These adverse events (AEs) can have serious impact, and form a significant barrier to therapy adherence. Surveillance of post-marketing AEs is of vital importance to understand real-world AEs and reporting differences between individual statin drugs. We conducted a review of post-approval muscle and tendon AE reports in association with statin use, to assess differences within the drug class. Methods We analyzed all case reports from the FDA AE Reporting System (AERS) database linking muscle-related AEs to statin use (07/01/2005–03/31/2011). Drugs examined were: atorvastatin, simvastatin, lovastatin, pravastatin, rosuvastatin, and fluvastatin. Results Relative risk rates for rosuvastatin were consistently higher than other statins. Atorvastatin and simvastatin showed intermediate risks, while pravastatin and lovastatin appeared to have the lowest risk rates. Relative risk of muscle-related AEs, therefore, approximately tracked with per milligram LDL-lowering potency, with fluvastatin an apparent exception. Incorporating all muscle categories, rates for atorvastatin, simvastatin, pravastatin, and lovastatin were, respectively, 55%, 26%, 17%, and 7.5% as high, as rosuvastatin, approximately tracking per milligram potency (Rosuvastatin>Atorvastatin>Simvastatin>Pravastatin≈Lovastatin) and comporting with findings of other studies. Relative potency, therefore, appears to be a fundamental predictor of muscle-related AE risk, with fluvastatin, the least potent statin, an apparent exception (risk 74% vs rosuvastatin). Interpretation AE reporting rates differed strikingly for drugs within the statin class, with relative reporting aligning substantially with potency. The data presented in this report offer important reference points for the selection of statins for cholesterol management in general and, especially, for the rechallenge of patients who have experienced muscle-related AEs (for whom agents of lower expected potency should be preferred).
Thought Beyond Language

A central question in cognitive science is whether natural language provides combinatorial operations that are essential to diverse domains of thought. In the study reported here, we addressed this issue by examining the role of linguistic mechanisms in forging the hierarchical structures of algebra. In a 3-T functional MRI experiment, we showed that processing of the syntax-like operations of algebra does not rely on the neural mechanisms of natural language. Our findings indicate that processing the syntax of language elicits the known substrate of linguistic competence, whereas algebraic operations recruit bilateral parietal brain regions previously implicated in the representation of magnitude. This double dissociation argues against the view that language provides the structure of thought across all cognitive domains.
Control of a Family of Phosphatase Regulatory Genes (phr) by the Alternate Sigma Factor Sigma-H ofBacillus subtilis

ABSTRACT A family of 11 phosphatases can help to modulate the activity of response regulator proteins in Bacillus subtilis. Downstream of seven of the rap (phosphatase) genes arephr genes, encoding secreted peptides that function as phosphatase regulators. By using fusions to lacZ and primer extension analysis, we found that six of the sevenphr genes are controlled by the alternate sigma factor sigma-H. These results expand the potential of sigma-H to contribute to the output of several response regulators by controlling expression of inhibitors of phosphatases.
Scalable and systematic detection of buggy inconsistencies in source code

Software developers often duplicate source code to replicate functionality. This practice can hinder the maintenance of a software project: bugs may arise when two identical code segments are edited inconsistently. This paper presents DejaVu, a highly scalable system for detecting these general syntactic inconsistency bugs. DejaVu operates in two phases. Given a target code base, a parallel /inconsistent clone analysis/ first enumerates all groups of source code fragments that are similar but not identical. Next, an extensible /buggy change analysis/ framework refines these results, separating each group of inconsistent fragments into a fine-grained set of inconsistent changes and classifying each as benign or buggy. On a 75+ million line pre-production commercial code base, DejaVu executed in under five hours and produced a report of over 8,000 potential bugs. Our analysis of a sizable random sample suggests with high likelihood that at this report contains at least 2,000 true bugs and 1,000 code smells. These bugs draw from a diverse class of software defects and are often simple to correct: syntactic inconsistencies both indicate problems and suggest solutions.
Implementation and Feasibility of Electronic Patient-Reported Outcome (ePRO) Data Entry in the PRAEGNANT Real-Time Advanced and Metastatic Breast Cancer Registry

Abstract Purpose Patient-reported outcomes (PROs) have been incorporated into clinical trials for many symptoms and medical conditions. A transition from paper-based capture of PROs to electronic PROs (ePROs) has recently started. This study reports on the feasibility of ePRO assessment in a prospective registry including molecular data for patients with advanced breast cancer. Methods As part of the PRAEGNANT network, patients were invited by clinical trial staff, physicians, and nurses to complete three standardized Internet-based questionnaires (EQ 5D 5 L, CES-D and IPAQ). Feasibility was assessed by the staff members who assigned the user accounts by the patients. The completeness of the questionnaires was also assessed. Results Fifteen of 17 patients who were asked agreed to participate to complete the PRO questionnaires (EQ-5D-5L and CES-D). However, the IPAQ (physical activity) questionnaire was only validly completed by 9 patients. Feasibility was ranked better by the physicians and dedicated clinical trial staff than by the nursing staff. Conclusions Incorporating ePRO questionnaires into an advanced breast cancer registry is feasible, and no major hurdles were reported. Involving stakeholders from the start, the application is tailored to the capacities and abilities of both patients and clinical staff. The patientsʼ compliance was better with some questionnaires, but others may present difficulties.
Dynamic force distribution in multifingered grasping by decomposition and positive combination

This paper presents a general algorithm for computing the optimal dynamic force distribution in multifingered grasping. It consists of two phases. In the offline phase, we select a spanning set for the required dynamic resultant wrench and find a corresponding spanning set for the total contact force. Then, in the online phase, the total contact force is obtained by decomposition of the resultant wrench into the former spanning set and a coefficient vector followed by positive combination of the latter spanning set with the vector. To make the online computation as simple as possible, iterative operation is executed offline and only arithmetic operation is employed online. To improve the grasping quality, the two spanning sets are selected elaborately.
Chronically Injured Posterior Cruciate Ligament Magnetic Resonance Imaging

Magnetic resonance imaging has been said to be highly reliable for diagnosis of acute posterior cruciate ligament insufficiency. In the present study, 13 patients whose posterior cruciate ligament insufficiency had been documented by magnetic resonance imaging within 10 weeks of the acute injury were recalled for a followup examination and magnetic resonance imaging. The followup interval ranged from 5 months to 4 years. In only 23% of the cases did the posterior cruciate ligament still appear discontinuous on followup magnetic resonance imaging. In the remaining 77%, the posterior cruciate ligament was continuous from tibia to femur, although it appeared abnormally arcuate or hyperbuckled. Conventional interpretation of these magnetic resonance images would suggest that the posterior cruciate ligament had healed. Nevertheless, by clinical examination results, these same patients all were judged to have posterior cruciate ligament insufficiency. Thus, it was concluded that although magnetic resonance imaging may be reliable for evaluation of acute posterior cruciate ligament injury, magnetic resonance imaging findings should not be used to infer functional status in chronic cases.
Lifelong Physical Activity Regardless of Dose Is Not Associated With Myocardial Fibrosis

Background—Recent reports have suggested that long-term, intensive physical training may be associated with adverse cardiovascular effects, including the development of myocardial fibrosis. However, the dose–response association of different levels of lifelong physical activity on myocardial fibrosis has not been evaluated. Methods and Results—Seniors free of major chronic illnesses were recruited from predefined populations based on the consistent documentation of stable physical activity over >25 years and were classified into 4 groups by the number of sessions/week of aerobic activities ≥30 minutes: sedentary (group 1), <2 sessions; casual (group 2), 2 to 3 sessions; committed (group 3), 4 to 5 sessions; and Masters athletes (group 4), 6 to 7 sessions plus regular competitions. All subjects underwent cardiopulmonary exercise testing and cardiac magnetic resonance imaging, including late gadolinium enhancement assessment of fibrosis. Ninety-two subjects (mean age 69 years, 27% women) were enrolled. No significant differences in age or sex were seen between groups. Median peak oxygen uptake was 25, 26, 32, and 40 mL/kg/min for groups 1, 2, 3, and 4, respectively. Cardiac magnetic resonance imaging demonstrated increasing left ventricular end-diastolic volumes, end-systolic volumes, stroke volumes, and masses with increasing doses of lifelong physical activity. One subject in group 2 had late gadolinium enhancement in a noncoronary distribution, and no subjects in groups 3 and 4 had evidence of late gadolinium enhancement. Conclusions—A lifelong history of consistent physical activity, regardless of dose ranging from sedentary to competitive marathon running, was not associated with the development of focal myocardial fibrosis.
Factors Influencing Crop Tolerance to Herbicides

Herbicides are amazing chemicals. Ideally, we expect herbicides to kill weeds and protect our crops from weed competition, without harming the crop. Fortunately, this is the typical case, but herbicides can damage our crops on occasion. To minimize the risk of herbicide-injured crops, we need to understand how herbicides function and factors that affect their activity. We can use this information to make better decisions regarding the risk of crop injury when selecting or applying herbicides.
Prescribing of oral nutritional supplements in Primary Care: can guidelines supported by education improve prescribing practice?

BACKGROUND AND AIMS With increasing resources being spent on nutritional supplements, this study sought to evaluate the effect of introducing guidelines on prescribing of supplements, by auditing practice, prior to, and after the implementation of guidelines. METHODS Prescribing practice was evaluated from patient interviews, and knowledge of health professionals examined from questionnaires from 50 GP practices. Training on the use of guidelines on prescribing supplements was implemented, incorporating a Nutritional Screening Tool and practical application of high-energy dietary advice, targeting GPs and Community Nurses. RESULTS Education to GPs and Community Nurses significantly reduced total prescribing by 15% and reduced the levels of inappropriate prescribing from 77% to 59% due to an improvement in monitoring of patients prescribed supplements. Although knowledge regarding high-energy dietary advice for nutritionally 'at risk' patients did improve as a result of the training, this was not demonstrated in practice. This lack of relevant dietary advice remained the main reason that inappropriate supplement prescriptions remained high. CONCLUSION Education on guidelines incorporating a Nutritional Screening Tool has proved to be an effective method of achieving more appropriate prescribing of supplements, suggesting the need for ongoing training of health professionals in Primary Care.
Mining Sequential Patterns Across Data Streams

There are extensive endeavors toward mining frequent items or itemsets in a single data stream, but rare efforts have been made to explore sequential patterns among literals in different data streams. In this paper, we define a challenging problem of mining frequent sequential patterns across multiple data streams. We propose an efficient algorithm MILE to manage the mining process. The proposed algorithm recursively utilizes the knowledge of existing patterns to make new patterns’ mining fast. We also apply a state-of-the-art sequential pattern mining algorithm PrefixSpan which was designed for transaction databases to solve our problem. Extensive empirical results show that MILE is significantly faster than PrefixSpan. One unique feature of our algorithm is when some prior knowledge of the data distribution in the data streams is available, it can be incorporated into the mining process to further improve the performance of MILE. As MILE consumes more memory than PrefixSpan, we also propose a solution to balance the memory usage and time efficiency in memory limited environments.