Miracle-dz/UniFAR-FTUs huggingface dataset:
SASS: Self-Adaptation Using Stochastic Search

Future-generation self-adaptive systems will need to be able to optimize for multiple interrelated, difficult-to-measure, and evolving quality properties. To navigate this complex search space, current self-adaptive planning techniques need to be improved. In this position paper, we argue that the research community should more directly pursue the application of stochastic search techniques -- search techniques, such as hill climbing or genetic algorithms, that incorporate an element of randomness -- to self-adaptive systems research. These techniques are well-suited to handling multi-dimensional search spaces and complex problems, situations which arise often for self-adaptive systems. We believe that recent advances in both fields make this a particularly promising research trajectory. We demonstrate one way to apply some of these advances in a search-based planning prototype technique to illustrate both the feasibility and the potential of the proposed research. This strategy informs a number of potentially interesting research directions and problems. In the long term, this general technique could enable sophisticated plan generation techniques that improve domain specific knowledge, decrease human effort, and increase the application of self-adaptive systems.
Integrated Synthetic, Pharmacological, and Computational Investigation of cis‐2‐(3,5‐Dichlorophenylcarbamoyl)cyclohexanecarboxylic Acid Enantiomers As Positive Allosteric Modulators of Metabotropic Glutamate Receptor Subtype 4

2‐(3,5‐Dichlorophenylcarbamoyl)cyclohexanecarboxylic acid (1) is a potent and selective positive allosteric modulator of metabotropic glutamate receptor subtype 4 (mGluR4). The activity of 1 was reported to reside in the cis diastereomer with equal potency between its enantiomeric forms (Niswender et al., Mol. Pharmacol. 2008, 74, 1345–1358). In the present study, the asymmetric synthesis of each of the cis enantiomers was performed, and their activities were compared with that of the racemic trans. In our assays, the cis enantiomers differ in potency, with one of them (1R,2S) higher and the other (1S,2R) lower than the racemic trans. High‐level quantum chemical calculations were carried out to characterize the structures of minimum energy in all‐isomer conformational space as well as particular intermediates between conformational transitions. Computational analysis identified structural features of 1 that can play a role in mGluR4 functionality and establish the basis for subsequent work, in which molecular chirality constructed on conformations derived from those found for the active (1R,2S) enantiomer can provide new ideas for drug discovery. Comparison between experimental and theoretical circular dichroism spectra confirmed both the absolute configuration of the (1R,2S) compound and its calculated most stable conformation, thereby supporting experimental and theoretical work.
Resilin: Elastic MapReduce over Multiple Clouds

The MapReduce programming model offers a simple and efficient way of performing distributed computation over large data sets. To enable the usage of MapReduce in the cloud, Amazon Web Services offers Elastic MapReduce (EMR), a web service enabling users to easily run MapReduce jobs by leveraging Amazon resources (i.e. compute and storage). EMR takes care of tasks such as resource provisioning, performance tuning, and fault tolerance thus allowing the users to concentrate on the problem to be solved. However, EMR is restricted to Amazon's resources and is provided at an additional cost. In this paper, we present the design, implementation, and evaluation of Resilin, a novel EMR API-compatible system to perform distributed MapReduce computations. Resilin goes one step beyond Amazon's proprietary EMR solution and allows users (e.g. companies, scientists) to leverage resources from one or multiple public and/or private clouds. This gives Resilin users the opportunity to perform MapReduce computations over a large number of potentially geographically distributed resources. An extensive experimental evaluation conducted on multiple clusters of the Grid'5000 experimentation test bed shows that Resilin enables the use of geographically distributed resources with only limited impact on MapReduce jobs execution time.
Thermodynamics and Kinetics of Sulfide Oxidation by Oxygen: A Look at Inorganically Controlled Reactions and Biologically Mediated Processes in the Environment

The thermodynamics for the first electron transfer step for sulfide and oxygen indicates that the reaction is unfavorable as unstable superoxide and bisulfide radical ions would need to be produced. However, a two-electron transfer is favorable as stable S(0) and peroxide would be formed, but the partially filled orbitals in oxygen that accept electrons prevent rapid kinetics. Abiotic sulfide oxidation kinetics improve when reduced iron and/or manganese are oxidized by oxygen to form oxidized metals which in turn oxidize sulfide. Biological sulfur oxidation relies on enzymes that have evolved to overcome these kinetic constraints to affect rapid sulfide oxidation. Here we review the available thermodynamic and kinetic data for H2S and HS• as well as O2, reactive oxygen species, nitrate, nitrite, and NOx species. We also present new kinetic data for abiotic sulfide oxidation with oxygen in trace metal clean solutions that constrain abiotic rates of sulfide oxidation in metal free solution and agree with the kinetic and thermodynamic calculations. Moreover, we present experimental data that give insight on rates of chemolithotrophic and photolithotrophic sulfide oxidation in the environment. We demonstrate that both anaerobic photolithotrophic and aerobic chemolithotrophic sulfide oxidation rates are three or more orders of magnitude higher than abiotic rates suggesting that in most environments biotic sulfide oxidation rates will far exceed abiotic rates due to the thermodynamic and kinetic constraints discussed in the first section of the paper. Such data reshape our thinking about the biotic and abiotic contributions to sulfide oxidation in the environment.
Conformally Invariant Operators via Curved Casimirs: Examples

We discuss a general scheme for a construction of linear conformally invariant differential operators from curved Casimir operators; we then explicitly carry this out for several examples. Apart from demonstrating the efficacy of the approach via curved Casimirs, this shows that this method applies both in regular and in singular infinitesimal character, and also that it can be used to construct standard as well as non--standard operators. The examples treated include conformally invariant operators with leading term, in one case, a square of the Laplacian, and in another case, a cube of the Laplacian.
Brain Reorganization After Stroke

Abstract After a stroke, recovery that continues beyond 3 or 4 weeks has been attributed to plasticity, a reorganization of the brain in which functions previously performed by the ischemic area are assumed by other ipsilateral or contralateral brain areas. Neuronal plasticity has been variously attributed to redundancy (parallel distributed pathways), changes in synaptic strength, axonal sprouting with formation of new synapses, assumption of function by contralateral homologous cortex, and substitution of uncrossed pathways. Transcranial magnetic stimulation, positron emission tomography (PET), functional magnetic resonance imaging (fMRI), and 128-electrode high-resolution electroencephalography have been successfully applied to demonstrate cortical reorganization after hemiplegia. Recording the motor potential is a promising noninvasive method for the localization of motor control after hemispheric lesions. Most patients with hemiparetic stroke show some improvement, usually during the first 3 to 6 months after the ictus. Improvement and prognosis depend on a number of variables including volume and location of the infarction, age of the patient, and the elimination of risk factors to avoid future episodes (i.e., dietary control of lipids, the elimination of tobacco, and the control of diabetes and hypertension). Currently, emphasis has been placed on fibrinolytic treatment in the first 3 hours to prevent or minimize neurological deficit. Aside from the above listed factors, improvement after stroke may be due to reorganization of the brain, particularly the cerebral cortex, and repair of damaged tissue and recanalization. It is also important to relate such changes to functional improvement and successful rehabilitation.
Essential and desirable characteristics of ecotoxicity quantitative structure–activity relationships

Quantitative structure–activity relationships (QSAR) developed and applied in the prediction of ecotoxic potencies far out number those in other areas, such as health effects. There are yet to be any formal guidelines for the development of ecotoxicological QSARs. Despite this, the depth and breadth of our knowledge of QSARs as they apply to ecotoxicology, especially short‐term aquatic toxicity, allow for the formulation of characteristics that appear to be essential and/or desirable for high‐quality QSARs. The three components of a QSAR are the biological activity, the property/structural descriptors, and the statistical methodology. Problems may arise from all three components and may be compounded by interactions between them. In an effort to minimize any tribulations associated with development and application of ecotoxic QSARs, a number of essential or desirable characteristics have been identified. Ecotoxicological data used in formulating the QSAR must be reliable, of high quality, and reflect a well‐defined and continuous endpoint; this dataset should be diverse both in terms of potency and chemical structure (i.e., property). Descriptors used in formulating the QSAR should be of high quality, reproducible, of a number and type consistent with the endpoint being modeled, and when possible allow for a mechanistic interpretation of the QSAR. The statistical process used in formulating a QSAR should be as rigorous as possible, appropriate for the endpoint being modeled, and allow for the development of as easily interpretable (i.e., transparent) QSARs as possible. The resultant QSAR should be validated, only used within the descriptor space and chemical domain of the model, and relied on in relation to the total weight of evidence; precision of the QSAR and expectations from its application need to be related to the error in the original ecotoxicological and descriptor measurements. Finally, development of QSARs should be through the interaction of a group of multidisciplinary experts.
The pharmacoeconomic picture in Saudi Arabia

Saudi Arabia is the largest country in the region and it is the largest oil producing country in the world. It is one of the few countries in the world which was not affected significantly by the global economic crisis. Health care spending is led mainly by governmental expenditure. Private sector share of the health care services is supported by the government and increasing. The demands for pharmaceutical products, medical devices and health care services is fueled by the rapidly growing population and the wide spread of chronic diseases. Publications and expertise in the field of pharmacoeconomics is scarce within the country. There is an urgent need to establish a national center for pharmacoeconomics to lead the country efforts in controlling the cost of health care services. Such a center is needed to promote pharmacoeconomics research and train health care professionals in this field.
A Critical Examination of Community-Based Responses to Household Food Insecurity in Canada

Over the past two decades, household food insecurity has emerged as a significant social problem and serious public health concern in the “First World. ” In Canada, communities initially responded by establishing ad hoc charitable food assistance programs, but the programs have become institutionalized. In the quest for more appropriate and effective responses, a variety of community development programs have recently been initiated. Some are designed to foster personal empowerment through self-help and mutual support; others promote community-level strategies to strengthen local control over food production. The capacity of current initiatives to improve household food security appears limited by their inability to overcome or alter the poverty that under-pins this problem. This may relate to the continued focus on food-based responses, the ad hoc and communitybased nature of the initiatives, and their origins in publicly funded health and social service sectors.
Enhancement of Antineoplastic Action of 5-Aza-2′-deoxycytidine by Phenylbutyrate on L1210 Leukemic Cells

Epigenetic changes, such as aberrant DNA methylation that silences tumor suppressor genes (TSGs), can play an important role in the development of leukemia. The DNA methylation inhibitor, 5-aza-2′-deoxycytidine (5-AZA-CdR), can reactivate these silent TSGs and is an interesting agent to investigate for therapy of leukemia. It has been reported that the effectiveness of 5-AZA-CdR to reactivate TSG can be enhanced by inhibitors of histone deacetylase (HDIs). HDIs can convert a compact chromatin structure to an open configuration that facilitates gene expression. An interesting HDI is phenylbutyrate (PB), which has shown some clinical activity for the therapy of leukemia. In this report we have investigated the antineoplastic activity of 5-AZA-CdR and PB alone and in combination on murine L1210 lymphoid leukemic cells. The in vitro treatment of 5-AZA-CdR and PB in combination produced a greater inhibition of growth, DNA synthesis, and also a greater reduction on colony formation on both L1210 and human HL-60 leukemic cells as compared to either drug alone. The combination also produced a synergistic activation of the TSG, p15CDN2B, in the L1210 cells. In mice with L1210 leukemia the combination showed enhanced antineoplastic activity. We also observed an enhancement of the antineoplastic activity of this combination in mice with L1210 leukemia. These data provide a rationale to investigate 5-AZA-CdR and PB in patients with advanced leukemia.
AsseSQL: an online, browser-based SQL skills assessment tool

AsseSQL is an online, browser-based SQL query assessment tool, developed in-house and designed to assess students' SQL query design and construction skills in a manner that more authentically mirrors how these skills are applied in professional practice. A few thousand students have now used this assessment tool over ten years. Student feedback is still overwhelmingly positive, primarily for the reason that they are assessed as they will use their SQL skills in professional practice. AsseSQL has been a successful way of assessing students' skills. The Tips, Techniques and Courseware session is an opportune time to reflect on its use, the challenges and possible changes.
Culture of the surfaces of urinary catheters to sample urethral flora and study the effect of antimicrobial therapy

At the time indwelling urinary catheters were removed, the urethral flora was sampled by rolling the catheters onto culture plates. Cultures were obtained from 398 patients with sterile urine. Catheter surfaces were colonized less often in males than in females (16.8 and 67.0%, respectively) and yielded correspondingly fewer bacterial species per catheter. In both sexes, gram-positive species were isolated more frequently than gram-negative species (428 and 131 isolates, respectively). The bacteria most commonly isolated were Staphylococcus epidermidis and Streptococcus faecalis. Staphylococcus saprophyticus was not recovered despite the large proportion of young, sexually active women in the study population. Gram-negative bacteria, mainly Escherichia coli, gradually colonized the catheters over time but at all times were recovered in lower amounts the gram-positive organisms and less often in males than in females. Slime production by coagulase-negative staphylococci did not relate to the density of organisms recovered from the catheters or influence the presence of gram-negative bacteria. Despite frequent use of antibiotics in this population, the urethral flora remained highly susceptible to these drugs. Antibacterial activity was not detected on the catheters despite high concentrations in the urine. This suggests that systemic antibiotics have a very limited effect on resident urethral flora. Despite relatively small numbers in the urethra, gram-negative bacteria readily produce urinary tract infections in catheterized patients.
Introduction to the Bootstrap 1 Motivation

The traditional approach to statistical inference relies on idealized models and assumptions. Often expressions for measures of accuracy such as the standard error are based on asymptotic theory and are not available for small samples. A modern alternative to the traditional approach is the bootstrapping method, introduced by Efron (1979). The bootstrap is a computer-intensive resampling method, which is widely applicable and allows the treatment of more realistic models. As a motivation, we first discuss four examples of situations in which the exact sampling distribution of the statistic of interest is intractable. We will use these examples later to illustrate the application of the bootstrapping method. Example The accuracy of the sample mean Data: Mouse data • Survival times of 16 mice after a test surgery • 7 mice in treatment group (new medical treatment) • 9 mice in control group (no treatment) Question: Did treatment prolong survival? This question can be addressed by comparing the means for the two groups: • ¯ X − ¯ Y = 30.63 indicates a life prolonging effect of the new treatment. • Problem: samples show high fluctuation need to assess accuracy of estimates Statistical theory for sample means:
The Role of Inventories and Speculative Trading in the Global Market for Crude Oil

We develop a structural model of the global market for crude oil that for the first time explicitly allows for shocks to the speculative demand for oil as well as shocks to the flow demand and flow supply. The forward-looking element of the real price of oil is identified with the help of data on oil inventories. The model estimates rule out explanations of the 2003-08 oil price surge based on unexpectedly diminishing oil supplies and based on speculative trading. Instead, we find that this surge was caused by fluctuations in the flow demand for oil driven by the global business cycle. There is evidence, however, that speculative demand shifts played an important role during earlier oil price shock episodes including 1979, 1986, and 1990. Recently, it has been suggested that it is possible for speculative trading to occur even without any change in oil inventories, if the short-run price elasticity of oil demand is zero. Our structural model allows us to obtain an estimate of this elasticity based on shifts of the supply curve along the demand curve. We show that, even after accounting for the role of inventories in smoothing oil consumption, our estimate of the price elasticity of oil demand is not close to zero and much higher than traditional estimates from dynamic models that do not account for price endogeneity. This eliminates speculation as an explanation of the 2003-08 oil price surge.
Angiogenesis, vascular endothelial growth factor and its receptors in human surgical wounds

Angiogenesis plays an essential role in tissue repair. Vascular endothelial growth factor (VEGF) mediates angiogenesis through receptor kinases VEGF‐R1 and VEGF‐R2, and co‐receptors, neuropilins Np1 and Np2. This study examined the spatial and temporal expression of these factors in relation to angiogenesis in surgical wounds.
Radiometric traceability diagnosis and bias correction for the Suomi NPP VIIRS long‐wave infrared channels during blackbody unsteady states

The Suomi National Polar‐orbiting Partnership Program (NPP) Visible Infrared Imaging Radiometer Suite (VIIRS) Thermal Emissive Bands (TEBs) have been performing well since the data became available on 20 January 2012, and the Sensor Data Record data reached validated maturity on 18 March 2014. While overall the validation has shown that these channels have an estimated absolute uncertainty on the order of 0.1 K based on extensive comparisons, there is a remaining issue that persisted over the years. A calibration bias on the order of 0.1 K is introduced in channels such as M15 during the quarterly blackbody temperature warm‐up/cooldown, and the bias is further amplified by the sea surface temperature (SST) retrieval algorithm up to 0.3 K in the global daily‐averaged products which causes an apparent spike in the SST time series. Our investigation reveals that this bias is caused by a fundamental but flawed theoretical assumption in the VIIRS calibration equation, which states that the shape of the calibration curve is assumed unchanged from prelaunch to postlaunch without any constrains. While the assumption may work to account for long‐term degradation, it has a shortcoming during the blackbody unsteady state. In this study, we present a diagnostic and correction method with a compensatory term (Ltrace) to reconcile the assumption such that it removes the calibration bias during the blackbody temperature changes. The methodology has been tested using historical data, and the results are very positive. The implementation has minimal impacts on the operational data processing system and is readily available for use in operations.
Quality of life in patients with coronary heart disease after myocardial infarction and with ischemic heart failure

Introduction Quality of life measures are useful when interventions or treatments are indicated for several reasons such as improvement of physical functioning, pain relief, to estimate the effectiveness of therapies or to predict mortality. The aim of the current study was to describe quality of life in patients with stable coronary artery disease, myocardial infarction and heart failure and to evaluate the relationship between depression and health-related quality of life. Material and methods Patients after STEMI, with stable coronary artery disease, and heart failure (n = 332) completed the MacNew Heart Disease Health-related Quality of Life Questionnaire and the Hospital Anxiety and Depression Scale. Results Patients with myocardial infarction had significantly higher scores than patients with stable coronary artery disease or heart failure on the MacNew global scale (p < 0.001) and the physical (p < 0.001), emotional (p < 0.001) and social (p < 0.001) subscales. The anxiety scores were significantly higher in the group of patients with stable coronary artery disease than in patients with myocardial infarction (p < 0.05). The depression scores were significantly higher in patients with heart failure (p < 0.01). Conclusions In patients with stable CAD, anxiety correlated mainly with symptoms, i.e. angina, than with the history of MI. Patients with symptoms of angina react to the illness with anxiety more than depression, whereas patients with heart failure with dyspnea react to the illness with depressive symptoms more than anxiety. In patients after MI and with stable CAD, cognitive-behavioral techniques could be useful to quickly reduce the level of anxiety, while patients with heart failure require long-term support therapy to reduce the risk of depressive symptoms.