Miracle-dz/UniFAR-FTUs huggingface dataset:
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content

Intrinsically unstructured/disordered proteins and domains (IUPs) lack a well-defined three-dimensional structure under native conditions. The IUPred server presents a novel algorithm for predicting such regions from amino acid sequences by estimating their total pairwise interresidue interaction energy, based on the assumption that IUP sequences do not fold due to their inability to form sufficient stabilizing interresidue interactions. Optional to the prediction are built-in parameter sets optimized for predicting short or long disordered regions and structured domains.
Monitoring of toxic metals (cadmium, lead, arsenic and mercury) in vegetables of Sindh, Pakistan

A monitoring study was carried out with the aim to assess the level of toxic metals i.e., lead (Pb), cadmium (Cd), arsenic (As) and mercury (Hg) in different vegetables grown in Sindh province of Pakistan during 2007-2008. Two hundred ten samples of twenty one vegetables were collected from farmers’ field of Sindh and exporters at Karachi. These samples were grouped into four categories viz., leafy, root and tuberous, cucurbits and fruity. The samples in duplicate were digested with nitric and perchloric acid mixture with 3:1 ratio. Cadmium and Pb were analyzed with Graphite Furnace Atomic Absorption Spectrophotometer and As and Hg on Atomic Absorption using Vapor and Hydride Generation Assembly. Average concentration of Cd, Pb, As and Hg in leafy vegetables was found 0.083 µgg -1 , 0.05 µgg -1 , 0.042 µgg -1 and 0.008 µgg -1 respectively, in roots and tuberous vegetables was 0.057 µgg -1 , 0.03 µgg -1 , 0.045 µgg -1 & 0.004 µgg -1 respectively, in cucurbit vegetables was 0.021 µgg -1 , 0.051 µgg -1 , 0.056 µgg -1 and 0.0089 µgg -1 respectively and in fruity vegetables was 0.035 µgg -1 , 0.067 µgg -1 , 0.054 µgg -1 and 0.007 µgg -1 respectively. In leafy vegetables, the concentration of cadmium, lead and mercury were found comparatively higher than other three groups of vegetables. However, concentration of heavy metals found in the samples of all four categories of vegetables, was within the permissible limits and safe to consume.
Venous thrombosis in an ALS population over four years

We conducted a retrospective chart review of all ALS patients seen at our institution over four years to determine the incidence of venous thromboembolism and to identify risk factors in this population. Events occurred in 13 of 438 patients (2.97%), yielding an annual incidence rate of 33.1 events per 1000 patients (95% CI 17.5–55.3). ALS patients have a risk of venous thromboembolism that is higher than the general population but lower than the population of patients with acute stroke or spinal cord injury. Immobility was significantly associated with increased risk of venous thrombosis (RR = 4.96; 95% CI 1.39–17.78).
Impaired Initiation But Not Execution of Contralesional Saccades in Hemispatial Neglect

Patients with unilateral neglect are impaired at making saccades to contralesional targets. Whether this problem arises from a deficit in perception, in planning the saccade or in executing the eye movement or some combination thereof remains unclear. We measured several variables related to the initiation and execution of saccades in an experiment which crossed two factors: target side (left, right) and direction of saccade (leftwards, rightwards). Relative to control subjects, patients with left-sided neglect were impaired in planning but not executing the contralesional saccade; while the latency to move their eyes following the onset of the target was increased, the duration and velocity to reach the target were normal. In addition, there were also no directional differences for saccades that were hypometric or inaccurate in the patients, further ruling out an execution impairment. Interestingly, this directional initiation deficit was exaggerated for leftward saccades to left targets, compared with all other conditions. We suggest that the disadvantage for contralesional saccades in neglect patients is attributable to a deficit not only in perceiving contralateral targets but also in planning leftward saccades. Once the saccade is initiated, however, execution apparently proceeds unimpaired.
Does Kindness Matter? Diabetes, Depression, and Self-Compassion: A Selective Review and Research Agenda

Depression and severe psychological distress are frequently comorbid with diabetes and are associated with reduced adherence to medication and healthy lifestyle regimens, poorer glycemic control, and increased complications. The mixed success of existing treatments for depression in diabetes patients suggests a need for supplementary approaches to this common problem. This article reviews recent evidence for the benefits of self-compassion in chronically ill patients, suggesting its utility as a clinical tool for improving self-care, depression, and glycemic control in diabetes. Possible physical and psychological pathways by which self-compassion may promote better outcomes in diabetes patients are considered, with particular attention given to reductions in negative self-judgment and improved motivation to undertake self-care.
Natural Attenuation of BTEX Compounds: Model Development and Field‐Scale Application

Benzene, toluene, ethyl benzene and xylene (BTEX) dissolved into ground water and migrated from a light nonaqueous phase liquid (LNAPL) source in a sandy aquifer near a petroleum, oil, and lubricants (POL) facility at Hill Air Force Base (AFB), Utah. Field observations indicated that microbially mediated BTEX degradation using multiple terminal electron‐accepting processes including aerobic respiration, denitrification, Fe(III) reduction, sulfate reduction, and methanogenesis has occurred in the aquifer. To study the transport and transformation of dissolved BTEX compounds under natural conditions, a reactive flow and transport model incorporating biochemical multispecies interactions and BTEX was developed. The BTEX, oxygen, nitrate, Fe(II), sulfate, and methane plumes calculated by the model agree reasonably well with field observations. The first‐order biodegrada‐tion rate constants, estimated based on model calibration are 0.051, 0.031, 0.005, 0.004, and 0.002 day−1 for aerobic respiration, denitrification, Fe(III), sulfate reduction, and methanogenesis, respectively. The results of a sensitivity analysis show that the saturated aquifer thickness, hydraulic conductivity, and reaction rate constants are the most critical parameters controlling the natural attenuation of BTEX at this site. The hydraulic conductivity and aquifer thickness were found to be the key factors affecting the restoration of oxygen, nitrate, and sulfate after their interaction with the BTEX plume. The multispecies reactive transport modeling effort, describing BTEX degradation mediated by multiple electron‐accepting processes, represents one of the few attempts to date to quantify a complete sequence of natural attenuation processes with a detailed field data set. Because the case study is representative of many petroleum‐product contaminated sites, the results and insights obtained from this study are of general interest and relevance to other fuel‐hydrocarbon natural attenuation sites
Slow Rates of Rock Surface Erosion and Sediment Production across the Namib Desert and Escarpment, Southern Africa

Slow erosion has characterized the Namib Desert, the Namibian escarpment, and the adjacent Namibian highlands over the Pleistocene. Paired analyses (n566) of in-situ-produced Be and Al in quartz-bearing samples of bedrock primarily from inselbergs, of sediment from dry river and stream channels, and of clasts from desert surfaces reveal large inventories of these cosmogenic nuclides indicating significant landscape stability over at least the past million years. Bedrock samples (n 5 47) collected in three transects from the coast, across the escarpment, and into the highlands, show no spatial pattern in elevation-normalized nuclide abundance despite a difference in mean annual precipitation (MAP) between sample sites at the coast (MAP 400 mm yr). Average model erosion rates inland of the escarpment (3.2 6 1.5, n 5 9) are indistinguishable from average rates seaward of the escarpment (3.6 6 1.9, n 5 38) indicating that rock on the pedimented coastal plain is eroding at the same rate as rock in the highlands. Sediment samples (n 5 3) from small streams suggest that the landscape as a whole is eroding more rapidly than the bedrock outcrops and that a basin in the steep escarpment zone is eroding several times faster (16 m my) than either a basin in the highlands (5 m my) or a basin in the coastal plain (8 m my). Data from large rivers (n 5 4) constrain erosion rates, averaged over 10 yrs and 10 to 10 km, between 3 and 9 m my. Small quartz clasts (n 5 12) collected from four desert surfaces record extraordinarily long, variable, and in some cases complex exposure histories. Simple Be model ages are as high as 1.8 my; some minimum total histories, considering both Be and Al and including both burial and exposure, exceed 2.7 my. As a group, the Namibian cosmogenic data do not support the model of significant and on-going escarpment retreat. The similarity of erosion rates calculated from Be analysis of fluvial sediments and longer-term (10 yr), average mass removal rates estimated by others using fission track analysis of rock suggests that Namibian erosion rates have reached a steady state and are changing little over time. At outcrop scales, the concordance of Be and Al in most bedrock samples suggests that the model of steady, uniform bedrock erosion is valid; there is no indication of intermittent burial, shedding of thick rock slabs, or stripping of previous cover. At an intermediate scale, a transect of bedrock samples north of Gobabeb demonstrates that the northern boundary of the massive Namib Sand Sea has been steady and unshifting. Similarly low cosmogenically estimated erosion rates across west and central Namibia suggest that the landscape is in geomorphic steady state, its overall appearance changing only slowly through time.
Evaluation of Fluticasone Propionate and Fluticasone Propionate/Salmeterol Combination on Exercise in Pediatric and Adolescent Patients with Asthma

Objective: This study was designed to demonstrate that four weeks of fluticasone propionate (FP) 100 micrograms (mcg) combined with salmeterol 50 mcg twice daily (BID) via DISKUS® resulted in protection against bronchospasm induced by activity, as measured by standardized exercise challenge testing in pediatric and adolescent subjects who required regular use of inhaled corticosteroids for the treatment of persistent asthma. Methods: Prior to study entry, all patients reported regular use of inhaled corticosteroids (ICS). During screening all patients demonstrated ≥20% fall in FEV1 following exercise. Results: A total of 231 subjects aged 4 to 17 were randomized to the two study treatments: 113 to the FP/salmeterol combination group (FSC) and 118 to receive FP 100 mcg BID. Of the subjects randomized, 106 (94%) subjects in the FSC 100/50 group and 108 (92%) subjects in the FP 100 group completed the study. At the end of treatment (Week 4), both FSC and FP protected against a fall in FEV1 following exercise in patients who at baseline experienced ≥20% fall in FEV1 following exercise. A mean decrease in FEV1 of 9.9% was observed in the FSC 100/50 group as compared with a mean decrease of 11.1% in the FP 100 group; there was no statistical difference between treatments. Conclusion: Both FSC 100/50 and FP 100 provided protection against an exercised-induced fall in FEV1; but statistically significant differences we not noted. Both treatments were well-tolerated over four weeks and FSC 100/50 had an adverse event profile comparable to that observed with FP 100.
Comparison of 2 frailty indexes for prediction of falls, disability, fractures, and death in older women.

BACKGROUND Frailty, as defined by the index derived from the Cardiovascular Health Study (CHS index), predicts risk of adverse outcomes in older adults. Use of this index, however, is impractical in clinical practice. METHODS We conducted a prospective cohort study in 6701 women 69 years or older to compare the predictive validity of a simple frailty index with the components of weight loss, inability to rise from a chair 5 times without using arms, and reduced energy level (Study of Osteoporotic Fractures [SOF index]) with that of the CHS index with the components of unintentional weight loss, poor grip strength, reduced energy level, slow walking speed, and low level of physical activity. Women were classified as robust, of intermediate status, or frail using each index. Falls were reported every 4 months for 1 year. Disability (> or =1 new impairment in performing instrumental activities of daily living) was ascertained at 4(1/2) years, and fractures and deaths were ascertained during 9 years of follow-up. Area under the curve (AUC) statistics from receiver operating characteristic curve analysis and -2 log likelihood statistics were compared for models containing the CHS index vs the SOF index. RESULTS Increasing evidence of frailty as defined by either the CHS index or the SOF index was similarly associated with an increased risk of adverse outcomes. Frail women had a higher age-adjusted risk of recurrent falls (odds ratio, 2.4), disability (odds ratio, 2.2-2.8), nonspine fracture (hazard ratio, 1.4-1.5), hip fracture (hazard ratio, 1.7-1.8), and death (hazard ratio, 2.4-2.7) (P < .001 for all models). The AUC comparisons revealed no differences between models with the CHS index vs the SOF index in discriminating falls (AUC = 0.61 for both models; P = .66), disability (AUC = 0.64; P = .23), nonspine fracture (AUC = 0.55; P = .80), hip fracture (AUC = 0.63; P = .64), or death (AUC = 0.72; P = .10). Results were similar when -2 log likelihood statistics were compared. CONCLUSION The simple SOF index predicts risk of falls, disability, fracture, and death as well as the more complex CHS index and may provide a useful definition of frailty to identify older women at risk of adverse health outcomes in clinical practice.
Investigating the Effect of Growth Phase on the Surface-Layer Associated Proteome of Lactobacillus acidophilus Using Quantitative Proteomics

Bacterial surface-layers (S-layers) are semi-porous crystalline arrays that self-assemble to form the outermost layer of some cell envelopes. S-layers have been shown to act as scaffolding structures for the display of auxiliary proteins externally. These S-layer associated proteins have recently gained attention in probiotics due to their direct physical contact with the intestinal mucosa and potential role in cell proliferation, adhesion, and immunomodulation. A number of studies have attempted to catalog the S-layer associated proteome of Lactobacillus acidophilus NCFM under a single condition. However, due to the versatility of the cell surface, we chose to employ a multiplexing-based approach with the intention of accurately contrasting multiple conditions. In this study, a previously described lithium chloride isolation protocol was used to release proteins bound to the L. acidophilus S-layer during logarithmic and early stationary growth phases. Protein quantification values were obtained via TMT (tandem mass tag) labeling combined with a triple-stage mass spectrometry (MS3) method. Results showed significant growth stage-dependent alterations to the surface-associated proteome while simultaneously highlighting the sensitivity and reproducibility of the technology. Thus, this study establishes a framework for quantifying condition-dependent changes to cell surface proteins that can easily be applied to other S-layer forming bacteria.
Innovative program and course outcomes' assessment tools

This paper describes in details innovative course outcomes' assessment tools used by the Department of Electrical & Computer Engineering at Sultan Qaboos University. A course outcomes' assessment program, developed in house, is used to evaluate the contributions of a given course, training, or any other item in the curriculum to the design, delivery and achievement of program outcomes. The program is an Excel Workbook which includes many sheets for input, calculation, and analysis and interpretation of student scores in relation to preset assessment tools outcome standards. For instance student scores for activities such as the final exam are fed in where the relevance of the final exam questions to the course outcomes is also entered. Upon input of all the course activities in the data entry sheets the students' final grades and reports on the assessment of individual activities are generated automatically. Reports showing results of course outcomes' assessments and degree of outcomes achievements are also generated automatically based on student performance (scores) in the specific course outcomes.
Oral apixaban for the treatment of acute venous thromboembolism.

BACKGROUND Apixaban, an oral factor Xa inhibitor administered in fixed doses, may simplify the treatment of venous thromboembolism. METHODS In this randomized, double-blind study, we compared apixaban (at a dose of 10 mg twice daily for 7 days, followed by 5 mg twice daily for 6 months) with conventional therapy (subcutaneous enoxaparin, followed by warfarin) in 5395 patients with acute venous thromboembolism. The primary efficacy outcome was recurrent symptomatic venous thromboembolism or death related to venous thromboembolism. The principal safety outcomes were major bleeding alone and major bleeding plus clinically relevant nonmajor bleeding. RESULTS The primary efficacy outcome occurred in 59 of 2609 patients (2.3%) in the apixaban group, as compared with 71 of 2635 (2.7%) in the conventional-therapy group (relative risk, 0.84; 95% confidence interval [CI], 0.60 to 1.18; difference in risk [apixaban minus conventional therapy], -0.4 percentage points; 95% CI, -1.3 to 0.4). Apixaban was noninferior to conventional therapy (P<0.001) for predefined upper limits of the 95% confidence intervals for both relative risk (<1.80) and difference in risk (<3.5 percentage points). Major bleeding occurred in 0.6% of patients who received apixaban and in 1.8% of those who received conventional therapy (relative risk, 0.31; 95% CI, 0.17 to 0.55; P<0.001 for superiority). The composite outcome of major bleeding and clinically relevant nonmajor bleeding occurred in 4.3% of the patients in the apixaban group, as compared with 9.7% of those in the conventional-therapy group (relative risk, 0.44; 95% CI, 0.36 to 0.55; P<0.001). Rates of other adverse events were similar in the two groups. CONCLUSIONS A fixed-dose regimen of apixaban alone was noninferior to conventional therapy for the treatment of acute venous thromboembolism and was associated with significantly less bleeding (Funded by Pfizer and Bristol-Myers Squibb; ClinicalTrials.gov number, NCT00643201).
Timed Bromocriptine-QR Therapy Reduces Progression of Cardiovascular Disease and Dysglycemia in Subjects with Well-Controlled Type 2 Diabetes Mellitus

Background. Type 2 diabetes (T2DM) patients, including those in good glycemic control, have an increased risk of cardiovascular disease (CVD). Maintaining good glycemic control may reduce long-term CVD risk. However, other risk factors such as elevated vascular sympathetic tone and/or endothelial dysfunction may be stronger potentiators of CVD. This study evaluated the impact of bromocriptine-QR, a sympatholytic dopamine D2 receptor agonist, on progression of metabolic disease and CVD in T2DM subjects in good glycemic control (HbA1c ≤7.0%). Methods. 1834 subjects (1219 bromocriptine-QR; 615 placebo) with baseline HbA1c ≤7.0% derived from the Cycloset Safety Trial (this trial is registered with ClinicalTrials.gov Identifier: NCT00377676), a 12-month, randomized, multicenter, placebo-controlled, double-blind study in T2DM, were evaluated. Treatment impact upon a prespecified composite CVD endpoint (first myocardial infarction, stroke, coronary revascularization, or hospitalization for angina/congestive heart failure) and the odds of losing glycemic control (HbA1c >7.0% after 52 weeks of therapy) were determined. Results. Bromocriptine-QR reduced the CVD endpoint by 48% (intention-to-treat; HR: 0.52 [0.28−0.98]) and 52% (on-treatment analysis; HR: 0.48 [0.24−0.95]). Bromocriptine-QR also reduced the odds of both losing glycemic control (OR: 0.63 (0.47−0.85), p = 0.002) and requiring treatment intensification to maintain HbA1c ≤7.0% (OR: 0.46 (0.31−0.69), p = 0.0002). Conclusions. Bromocriptine-QR therapy slowed the progression of CVD and metabolic disease in T2DM subjects in good glycemic control.
A Unified Framework for Efficiently Processing Ranking Related Queries

The computation of k-lower envelope is a classical problem and has been very well studied for main memory non-indexed data. In this paper, we study the problem from the database perspective and present the first algorithm which utilizes the presence of the index and achieves access optimality, i.e., it accesses a node of the index only if the correctness of the results cannot be guaranteed without accessing this node. We also demonstrate the applications of k-lower envelope in ranking systems. Let an object be called valuable if it is one of the top-k objects according to at least one linear scoring function. In this paper, we answer the following important questions that may be asked by different users: 1) I am not sure what scoring function I should use, therefore, return me the set of valuable objects so that I can select an object I like the most; 2) How can I modify the attributes (e.g., price) of my product such that it becomes a valuable object; 3) What are the preference functions for which a given object is among the top-k objects. These three questions are formalized and called k-snippet, k-depth contour and reverse top-k query, respectively. We propose a unified framework to solve these queries by utilizing k-lower envelope as a common foundation. Our main algorithm is access optimal for k-snippet and k-lower envelope computation. We also demonstrate its access optimality for the k-depth contour problem when k is smaller than the minimum number of objects in any leaf node of the index structure. Our algorithms outperform state-of-the-art algorithms by more than an order of magnitude in terms of both CPU and I/O cost.
The Relationship between Entrepreneur Psychological Capital and Employee’s Innovative Behavior: The Strategic Role of Transformational Leadership and Knowledge Sharing

This research is to explore the relationships among entrepreneur psychological capital; innovative behavior; transformational leadership and knowledge sharing. Chinese enterprises participated in this investigation. We found that entrepreneur psychological capital influenced transformational leadership, while transformational leadership influenced employee’s innovative behavior positively. Besides, entrepreneur psychological capital influenced employee’s knowledge sharing positively while knowledge sharing influenced employee’s innovative behavior positively, but the direct influence between entrepreneur psychological capital and employee’s innovative behavior wasn’t exist. As anticipated, the intervening effect of transformational leadership and knowledge sharing between entrepreneur psychological capital and employee’s innovative behavior was significant. Implications, limitations and future research directions for the study are discussed.