Miracle-dz/UniFAR-FTUs huggingface dataset:
Determinism at Standard Library Level in Transactional Memory Based Applications

Deterministic execution of a multi-threaded application guarantees that threads access shared memory in the same order and the application gives the same output when it runs with the same input parameters. Determinism provides repeatability, which helps a programmer in testing and debugging. Additionally, Transactional Memory (TM) simpliﬁes development of applications that use transactions (instead of locks) to synchronize accesses to shared memory. However, transactions that call standard library functions have to be serialized, and the serialization causes a deadlock when applications run with the deterministic systems proposed so far. In this paper, we present DeTrans-lib, the ﬁrst standard C library that provides deterministic execution of TM-based applications at user and standard-library level. DeTrans-lib avoids deadlocks by performing transaction serialization in deterministic order. We evaluate DeTrans-lib using benchmarks that perform I/O operations.
The family journey-to-diagnosis with systemic juvenile idiopathic arthritis: a cross-sectional study of the changing social media presence

Background Children with systemic juvenile idiopathic arthritis (SJIA) often encounter a delay between symptom onset and disease diagnosis, partly due to the broad differential of fever and lack of symptom recognition by providers. Families often seek multiple medical opinions and post on social media about their frustrations. This linguistic analysis observed the changing language patterns and social media posting behaviors of parents in the time leading to, during, and after SJIA diagnosis. Methods Public social media sites were manually reviewed by a linguistic team to evaluate posts about SJIA from US-based parents. Results A total of 3,979 posts between July 2001 and January 2015 were reviewed from 108 sites. Pre-SJIA diagnosis parents sought answers and shared status updates on social media, focusing primarily on the following three site types: alternative/natural lifestyle forums (39%), Facebook (27%), and disease-specific forums (17%). Posts during early prediagnosis phases were characterized by expressive language showing confidence in health care providers and trust in parental instincts. At later prediagnosis stages, parents continued to use social media, but the posts demonstrated increased frustration with delays in diagnosis and gaps in communication with providers. More objective symptom descriptions and a greatly reduced child-centered emotional focus were observed as parents shifted into caregiving roles. Once the diagnosis of SJIA was confirmed, parents used straightforward, less expressive language, and Facebook (47%) to make “announcement” posts and increased their use of SJIA websites (30%). With treatment initiation, the posts demonstrated a slow return of expressive language and an increased parental understanding of the “new normal”. Conclusion Parents use different language styles, frames of reference, and websites before and after SJIA diagnosis. Gaps in parent–provider communication, especially before diagnosis, and their new roles as caregivers lead to parental use of social media to express frustration with the health care process. Providers should tailor their discussions with parents to address these issues.
Mindful Connections: The Role of a Peer Support Group on the Psychosocial Adjustment for Adults Recovering From Brain Injury

ABSTRACT How does participating in a peer support group impact an adult’s psychosocial adjustment following brain injury? This question was investigated using a qualitative approach, interviewing patients recruited from an ambulatory care program. Data analysis guided by Bury’s sociological framework, biographical disruption and biographical repair, revealed participants’ pregroup disrupted sense of self, including subthemes related to intrinsic losses and uncertainty. Enhanced psychosocial adjustment including subthemes described participants’ reorientation through shared experience. Finally, a postgroup adapted sense of self including subthemes was characterized by heightened purpose, self-awareness, and acceptance. Findings lend weight to using tailored peer interventions to optimize psychosocial adjustment for this population.
Resonance wave pumping with surface waves

In this paper, we present a novel extension of impedance (Liebau) wave pumping to a free-surface condition where resonance pumping could be used for hydraulic energy harvesting. Similar pumping behaviours are reported. Surface envelopes of the free surface are shown and outline two different dynamics: U-tube oscillator and wave/resonance pumping. The latter is particularly interesting, since, from an oscillatory motion, a unidirectional flow with small to moderate oscillations is generated. A linear theory is developed to evaluate pseudo-analytically the resonance frequencies of the pump using eigenfunction expansions, and a simplified model is proposed to understand the main pumping mechanism in this type of pump. It is found that the Stokes mass transport is driving the pump. The conversion of energy from paddle oscillation to mean flow is evaluated. Efficiency up to 22 % is reported.
A priori error estimates for the Arbitrary Lagrangian Eulerian formulation with finite elements

Abstract The Arbitrary Lagrangian Eulerian formulation is widely used when problems in moving domains have to be approximated. Here we consider a time dependent linear advection–diffusion problem in a moving two-dimensional domain and discretize it by linear finite elements in space and a modification of the implicit Euler scheme, based on the mid point rule, in time. The resulting space–time discretization satisfies the so called Geometric Conservation Laws which prevent from numerical instabilities due to inaccurate calculations of geometric quantities. We derive a priori error estimates which are optimal both in space and time using slightly more regularity than that necessary for the case of non moving domains.
Repetitive memorization mobile application development for elderly memory recall

The aging process in human being will eventually develop some degree of decline in cognitive capacity and show a variety of symptoms associated with it such as forgetfulness. Forgetfulness might lead to frustration as it hinders elderly from carrying out their daily life activities. Living a healthy aging life, the spiritual aspect is considered essential by older adults. Muslims believe that their spirituality could be improved through some of their religious practices, one of it is prayer. During prayer, a Muslim recite short chapter from the Quran which they learn to memorize since they were children. As they grow older, they experience cognitive decline and forget the verses that they used to remember. This lead to frustration among the Muslim elderly as they are unable to perform their religious practice. Therefore, we studied the most suitable memorization technique and apply it in the development of mobile application that could help elderly in memorizing Quranic Verses. We interviewed an expert to understand the memorizing process. Based on these findings, we designed the system processes of the mobile application and implement the repetitive memorization technique using the rule based expert system to suggest what the user need to memorize based on the usage history. The rule based expert system should be able to optimize the memorization process that the user experienced and subsequently help elderly to memorize the Quranic Verses. This would eventually enhance their spirituality and also improve their memory.
Mesoscale geographical patterns in the distribution of pandalid shrimps Plesionika spp. in the Western Mediterranean

Six bottom-trawl cruises, undertaken in spring 1994 to 1999 along the Spanish Mediter- ranean coastline, sampled pandalid shrimps from 30 to 800 m depth. Data analysis yielded a descrip- tion of the distribution patterns of the 4 most common species (Plesionika heterocarpus, P. martia, P. gigliolii, P. edwardsi) over an area of 45 331 km 2 . We analysed abundance of juveniles and adults by partial correspondence analysis (pCCA) in order to determine the effect on distribution of depth (as an overall estimate of temperature, salinity, turbidity and other variables), time (among-survey vari- ability) and space (geographical location). The main null hypothesis we explicitly evaluated is that species composition remains constant along the Spanish Mediterranean coastline after controlling for depth and time. A significant (8.2%) effect of geographical location was found. Hauls located in the central zone of the sampling cruises (Valencia: Ibiza Channel) showed an intermediate relative abun- dance of all species. By contrast, the samples from northern and southern zones showed a large rela- tive abundance of P. martia and P. heterocarpus, respectively. This pattern may be related to envi- ronmental specificity of the hydrodynamic conditions in the Ibiza Channel, dynamic topography characteristics linked to the canyons in the North Catalan zone, and surface production inputs, as found in the North Alboran zone (southern zone), where the main species (P. heterocarpus) exhibited the shallowest bathymetric distribution. Although discrimination between depth preferences of juve- niles and adults (with adults being located deeper) is already known on a local scale, our results extend this pattern to the entire Spanish Mediterranean coastline and across all the species studied.
Relating the Type of Ambiguity of Finite Automata to the Succinctness of Their Representation

We consider the problem of how the size of a nondeterministic finite automaton (nfa) representing a regular language depends on the degree of ambiguity of the nfa. We obtain results for the unary and bounded inputs, and partial results for the unrestricted inputs. One of the main results of this paper shows that for unrestricted inputs, deterministic, unambiguous and nondeterministic machines form a hierarchy with respect to the number of states, solving an open problem of Stearns and Hunt. We also propose a new approach to the study of the succinctness of representation through regularity preserving closure properties and obtain some results in this direction.
DELAYED HYPERSENSITIVITY IN VITRO. II. EFFECT OF SENSITIVE CELLS ON NORMAL CELLS IN THE PRESENCE OF ANTIGEN.

Summary Peritoneal exudate cells from guinea pigs exhibiting delayed hypersensitivity to tuberculin and from normal animals were mixed in varying proportions, and their migration in the presence of specific antigens was studied. The results indicate that only a few cells in a mixed population need be specifically sensitive to influence the behavior of the whole population. Killing the sensitive cells abolishes their effect on normal cells. Some questions raised by these results are discussed.
A Physical Model for the Statistics of the Set Switching Time of Resistive RAM Measured With the Width-Adjusting Pulse Operation Method

The correlation between the set time (t<sub>set</sub>) and the initial off-state resistance (R<sub>OFF</sub>) statistics for a Ti/ZrO<sub>2</sub>/Pt bipolar resistive random access memory device was investigated. The width-adjusting pulse operation method, which can significantly improve the switching uniformity, was used to accurately measure t<sub>set</sub>, and the gathered statistical data were analyzed using Weibull distributions. Both the Weibull slope (β<sub>t</sub>) and the scale factor (t<sub>set63%</sub>) of tset distributions were found to increase logarithmically with R<sub>OFF</sub>. The observed t<sub>set</sub> - R<sub>OFF</sub> interdependence provides a guideline in improving the switching uniformity and optimizing the tradeoff between set speed and disturb immunity. An analytical cell-based model was developed to explain the R<sub>OFF</sub>-dependent t<sub>SET</sub> statistics, which can be implemented in statistical compact models and circuit simulators for improving RRAM cell design and memory performances.
Venous thromboembolism and coagulation activity in patients with immune thrombocytopenia treated with thrombopoietin receptor agonists

P. A. Mehta and J. Svahn – designed the study, performed the research, analysed the data and wrote the paper. S. M. Davies and C. Dufour – designed the research study, analysed the data and reviewed the paper. Q. Pang – provided preclinical animal data, contributed to analysis of correlative studies and reviewed the paper. R. Harris – participated in performance of research and reviewed the paper. P. Ghezzi – performed the research and Pharmacokinetics and reviewed the paper. P. Barabino – performed the research and reviewed the paper, R. Mueller – coordinated patient enrollment and follow-up, and reviewed the paper. T. Lanza – performed the experiments and data management. E. Ferretti – performed the experiments and data management.
Climate change and plant health: designing research spillover from plant genomics for understanding the role of microbial communities

Abstract Climate change presents new challenges for managing plant health. Simultaneously, the revolution in sequencing technologies offers an exciting new perspective on whole microbial communities – and on both microbial responses to climate and microbial effects on plant health. There is still the need for a comparable revolution in experimental approaches to understand the functional roles of microbial taxa within these communities. Two approaches leveraging advances in genomics tools and analyses may contribute. First, new soil mixing experiments may be developed, where analyses of quantitative trait taxa (QTT) may be analogous to analyses of quantitative trait loci (QTL). Second, new approaches for characterizing the extended phenotype or phenome of soil microbial communities may be developed, leveraging genomic tools for Arabidopsis and other model plant species through the construction of plant genotype panels in an ‘Arabidopsitron’.
Luteal phase estrogen is decreased in regularly menstruating older women compared with a reference population of younger women

Objective: To compare daily reproductive hormone secretion in regularly menstruating older versus younger women. Design: This was a prospective cohort study. Results: Daily morning urine samples were obtained from 106 women, 28 of whom were aged between 20 and 34 years (mean: 27.8 ± 3.7 y) and 78 of whom were aged between 35 and 50 years (mean: 40.3 ± 3.7 y). Lower luteal estrone-3-glucuronide levels were seen in the older versus the younger group (82.7 vs 93.5 ng/ml, P = 0.035). The pregnanediol-3-glucuronide levels in the older group were lower than those in the younger group throughout the entire cycle. The median length of the follicular phase was shorter in the older versus younger women (13 vs 14.5 d, P = 0.005). There was no significant difference in the median luteal phase lengths between groups. Conclusions: We report the new finding that regularly menstruating older women not only have lower pregnanediol-3-glucuronide levels but also have a significant reduction in luteal phase estrone-3-glucuronide compared with a contemporaneous cohort of younger women. This combined deficit may play a key role during the luteal-follicular transition, potentially affecting follicle recruitment and decreasing fecundity in the subsequent cycle.
Comprehensively designed consensus of standalone secondary structure predictors improves Q3 by over 3%

Protein fold is defined by a spatial arrangement of three types of secondary structures (SSs) including helices, sheets, and coils/loops. Current methods that predict SS from sequences rely on complex machine learning-derived models andprovide the three-state accuracy (Q3) at about 82%. Further improvements in predictive quality could be obtained with a consensus-based approach, which so far received limited attention. We perform first-of-its-kind comprehensive design of a SS consensus predictor (SScon), in which we consider 12 modern standalone SS predictors and utilize Support Vector Machine (SVM) to combine their predictions. Using a large benchmark data-set with 10 random training-test splits, we show that a simple, voting-based consensus of carefully selected base methods improves Q3 by 1.9% when compared to the best single predictor. Use of SVM provides additional 1.4% improvement with the overall Q3 at 85.6% and segment overlap (SOV3) at 83.7%, when compared to 82.3 and 80.9%, respectively, obtained by the best individual methods. We also show strong improvements when the consensus is based on ab-initio methods, with Q3 = 82.3% and SOV3 = 80.7% that match the results from the best template-based approaches. Our consensus reduces the number of significant errors where helix is confused with a strand, provides particularly good results for short helices and strands, and gives the most accurate estimates of the content of individual SSs in the chain. Case studies are used to visualize the improvements offered by the consensus at the residue level. A web-server and a standalone implementation of SScon are available at http://biomine.ece. ualberta.ca/SSCon/.
Acidic citrate stabilizes blood samples for assay of total homocysteine.

Homocysteine is a sulfhydryl-containing amino acid, formed by demethylation of the essential amino acid methionine. Homocysteine is either transsulfurated to cysteine or is remethylated to methionine by methionine synthase. Excess intracellular homocysteine is likely to be transported to the extracellular compartment (1). Increasing evidence indicates that homocysteine is implicated in the pathogenesis of thromboembolic diseases. Several case control studies have shown a relationship between increased total plasma homocysteine (tHcy) concentrations and an increased risk of arterial (2)(3)(4) and venous thrombosis (5)(6)(7)(8). An increase of the tHcy concentration of 5 μmol/L is associated with 1.5–1.9 times increased risk for coronary artery or cerebrovascular disease (9). These values indicate that small differences might be of clinical importance. Therefore, practical standardized conditions for handling blood specimens for tHcy determination are required. In most studies, blood is drawn in tubes containing K3EDTA. The whole-blood sample is immediately put on crushed ice and then centrifuged as soon as possible to prevent an increase of tHcy concentrations. This tHcy increase is caused by ongoing homocysteine metabolism in blood cells, the majority of which are red blood cells (10)(11). This blood handling procedure is not practical, particularly when larger studies are conducted outside a hospital setting; even in a routine clinical setting, this protocol might be hard to put into practice. To find an alternative, more suitable blood-collection medium, we investigated the effect of different blood-collection media on tHcy production when whole blood is kept at room temperature for 6 h. Blood was drawn by venipuncture of the antecubital vein from laboratory coworkers or from consecutive patients who visited the outpatient clinics of the Leyenburg Hospital in The Hague for various reasons, unknown to the authors. Informed consent was obtained in accordance …
The Effect of the Section Thickness Used for 2- and 3-Dimensional Quantification of Dual-Energy Perfusion Computed Tomography

Purpose To retrospectively investigate the effect of the section thickness used for quantifying dual-energy perfusion computed tomography (DEpCT) during 2- and 3-dimensional evaluation. Methods Sixty-six patients (22 males and 44 females; mean age, 59.3 years) suspected of having an acute pulmonary embolism underwent DEpCT, and 15patients were diagnosed to have intrapulmonary clots (IPCs). Two-dimensional DEpCT images were reconstructed into various section thicknesses from 1 to 10 mm at the main pulmonary artery, and the ratios of the low attenuation area (LAA) ranging from 1 to 5 HU (%LAA5) and 10 HU (%LAA10) on DEpCT were compared with the relative areas of the lung with attenuation coefficients lower than –950 HU (RA−950) using the lung CT images of each section thickness. Three-dimensional values of DEpCT were reconstructed with 3 different section thicknesses (1, 3, and 10 mm) and were analyzed for the presence of IPC burden using the factors suggesting IPC burden, including the right/left ventricular diameter ratio and CT obstruction index. Results The mean attenuation and image noise were decreased as the section thickness increased. In the 2-dimensional analysis, the %LAA5 and %LAA10 had the smallest value at 1-mm section, and DEpCT with thinner sections had a correlation with the RA−950 (r = 0.22–0.23, P < 0.05). The 3-dimensional values of DEpCT reconstructed with a 1- or 3-mm section thickness had a correlation with the CT obstruction index (r = 0.52–0.59, P < 0.05) and right/left ventricular diameter ratio (r = 0.60–0.68, P < 0.01). Conclusions The thinner images should be used for 2- and 3-dimensional quantification of DEpCT.
Research participants' high expectations of benefit in early-phase oncology trials: are we asking the right question?

PURPOSE To determine whether patients' expectations of benefit in early-phase oncology trials depend on how patients are queried and to explore whether expectations are associated with patient characteristics. PATIENTS AND METHODS Participants were 171 patients in phase I or II oncology trials in the United States. After providing informed consent for a trial but before receiving the investigational therapy, participants answered questions about expectations of benefit. We randomly assigned participants to one of three groups corresponding to three queries about expectations: frequency type, belief type, or both. Main outcomes were differences in expectations by question type and the extent to which expectations were associated with demographic characteristics, numeracy, dispositional optimism, religiousness/spirituality, understanding of research, and other measures. RESULTS The belief-type group had a higher mean expectation of benefit (64.4 of 100) than the combination group (51.6; P = .01) and the frequency-type group (43.1; P < .001). Mean expectations in the combination and frequency groups were not significantly different (P = .06). Belief-type expectations were associated with a preference for nonquantitative information (r = -0.19; 95% CI, -0.19 to -0.36), knowledge about research (r = -0.21; 95% CI, -0.38 to -0.03), dispositional optimism (r = 0.20; 95% CI, 0.01 to 0.37), and spirituality (r = 0.22; 95% CI, 0.03 to 0.38). Frequency-type expectations were associated with knowledge about clinical research (r = -0.27; 95% CI, -0.27 to -0.51). CONCLUSION In early-phase oncology trials, patients' reported expectations of benefit differed according to how patients were queried and were associated with patient characteristics. These findings have implications for how informed consent is obtained and assessed.