Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance engineering of hybrid message passing + shared memory programming on multi-core clusters

The hybrid message passing + shared memory programming model combines two parallel programming styles within the same application in an effort to improve the performance and efficiency of parallel codes on modern multi-core clusters. This thesis presents a performance study of this model as it applies to two Molecular Dynamics (MD) applications. Both a large scale production MD code and a smaller scale example MD code have been adapted from existing message passing versions by adding shared memory parallelism to create hybrid message passing + shared memory applications. The performance of these hybrid applications has been investigated on different multi-core clusters and compared with the original pure message passing codes. This performance analysis reveals that the hybrid message passing + shared memory model provides performance improvements under some conditions, while the pure message passing model provides better performance in others. Typically, when running on small numbers of cores the pure message passing model provides better performance than the hybrid message passing + shared memory model, as hybrid performance suffers due to increased overheads from the use of shared memory constructs. However, when running on large numbers of cores the hybrid model performs better as these shared memory overheads are minimised while the pure message passing code suffers from increased communication overhead. These results depend on the interconnect used. Hybrid message passing + shared memory molecular dynamics codes are shown to exhibit different communication profiles from their pure message passing versions and this is revealed to be a large factor in the performance difference between pure message passing and hybrid message passing + shared memory codes. An extension of this result shows that the choice of interconnection fabric used in a multi-core cluster has a large impact on the performance difference between the pure message passing and the hybrid code. The factors affecting the performance of the applications have been analytically examined in an effort to describe, generalise and predict the performance of both the pure message passing and hybrid message passing + shared memory codes.
Denosumab for the treatment of osteoporosis

Introduction: Low trauma fractures due to osteoporosis are a major health concern worldwide. Despite the availability of many therapeutic compounds to reduce fracture risk, osteoporosis remains undertreated and the burden of osteoporotic fractures remains high. Denosumab is a novel agent that acts to reduce bone turnover, improve bone mineral density, and reduce fracture risk, offering a favorable efficacy and safety profile. Areas covered: This review covers the pharmacology and major clinical trials with extension/post-marketing follow-up, including trials for all FDA-approved indications of denosumab to date. Expert opinion: Denosumab is an efficacious and safe osteoporosis treatment option, with current data from up to 8 years of continued use showing continued improvement in bone density with sustained fracture risk reduction. Safety profiles overall are similar to placebo, with no new safety concerns in extension trials, though a theoretical increased risk of infection exists with RANKL inhibition. Future considerations include safety of prolonged treatment beyond 8 years, and efficacy/fracture risk after discontinuation or with non-adherence, given the characteristic pharmacodynamic profile of denosumab.
Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities

MOTIVATION The computational evaluation of candidate genes for hereditary disorders is a non-trivial task. Several excellent methods for disease-gene prediction have been developed in the past 2 decades, exploiting widely differing data sources to infer disease-relevant functional relationships between candidate genes and disorders. We have shown recently that spatially mapped, i.e. 3D, gene expression data from the mouse brain can be successfully used to prioritize candidate genes for human Mendelian disorders of the central nervous system. RESULTS We improved our previous work 2-fold: (i) we demonstrate that condition-independent transcription factor binding affinities of the candidate genes' promoters are relevant for disease-gene prediction and can be integrated with our previous approach to significantly enhance its predictive power; and (ii) we define a novel similarity measure-termed Relative Intensity Overlap-for both 3D gene expression patterns and binding affinity profiles that better exploits their disease-relevant information content. Finally, we present novel disease-gene predictions for eight loci associated with different syndromes of unknown molecular basis that are characterized by mental retardation.
Presentation, management, and outcome of out of hospital cardiopulmonary arrest: comparison by underlying aetiology

Objective: To describe and compare presentation, management, and survival by aetiology of cardiopulmonary arrest. Design, setting, and patients: A retrospective cohort study was undertaken of all 21 175 first out of hospital cardiopulmonary arrests in Scotland between May 1991 and March 1998. Main outcome measure: Discharge alive from hospital. Results: Presumed cardiac disease accounted for 17 451 cases (82%), other internal aetiologies for 1814 (9%), and external aetiologies for 1910 (9%). Arrests caused by presumed cardiac disease had a better risk profile in terms of presence of a witness, bystander cardiopulmonary resuscitation, call–response interval, and use of defibrillation; 1265 (7%) of those who arrested from presumed cardiac disease were discharged alive, compared with only 77 (2%) of those with non-cardiac disorders (p < 0.001). Among those defibrillated, call–response interval was associated with survival following arrests from both presumed cardiac and non-cardiac causes (p < 0.001). Conclusions: Out of hospital cardiopulmonary arrests from non-cardiac causes were associated with worse crude survival than arrests from cardiac causes. Improvements in call–response interval and basic life support skills in the community would improve survival irrespective of the aetiology and should therefore be encouraged.
ProcSimity: an experimental tool for processor allocation and scheduling in highly parallel systems

ProcSimity is a software tool that supports research in processor allocation and scheduling for highly parallel systems. ProcSimity's multicomputer simulator supports experimentation with selected allocation and scheduling algorithms on architectures with a range of network topologies and for several current routing and flow control mechanisms. Message-passing can be simulated in detail at the flit level or at a higher level of modeling. Our tool supports both stochastic job streams as well as communication patterns from actual parallel applications, including several of the NAS parallel benchmarks. ProcSimity's visualisation and performance analysis tool allows the user to view a dynamic animation of the selected algorithms as well as a variety of system and job level performance metrics. ProcSimity has been successfully used in experiments investigating the feasibility of non-contiguous processor allocation in meshes and k-ary n-cubes. <<ETX>>
Preoperative Determinants of Patient-reported Pain and Physical Function Levels Following Total Knee Arthroplasty: A Systematic Review

Background: A sound knowledge of the determinants of total knee arthroplasty (TKA) outcomes could help in patient selection, preparation and education. We aimed to assess the current status of the literature evaluating preoperative determinants of early and medium term patient-reported pain and disability following TKA. Method: A search in Medline, Pubmed, Embase and CINAHL until October 2014 was undertaken. Selection criteria included: 1- participants undergoing primary unilateral TKA with a follow-up from 6 months to 2 years, 2- validated disease-specific patient-reported outcome measures assessing pain and/or function used as outcome measure and 3- identification of preoperative determinants obtained via multivariate analyses. Risk of bias was assessed using a modified version of the Methodology checklist for prognostic studies. Results: Thirty-three prognostic explanatory studies were included. Mean total score of the methodological quality was 80.7±12.2 %. Sociodemographic and psychosocial determinants included greater socioeconomic deprivation (both studies), greater levels of depression and/or anxiety (7 out of 10 studies) and greater preoperative pain catastrophizing (all 3 studies). Significant clinical determinants included worse pre-operative knee related pain or disability (20 out of 22 studies), presence or greater levels of comorbidity (12 out of 23 studies), back pain (4 out of 5 studies) and lower general health (all 11 studies). Conclusion: Several significant determinants of short to medium-term pain and functional outcomes following TKA have been summarized by studies with moderate-to-high methodological quality. No conclusions can be reached regarding the strength of the associations between significant determinants and TKA results because of heterogeneity of study methodologies and results. Further high-quality research is required.
Transnational practices of Albanian families during the Greek crisis: unemployment, de-regularization and return

The outbreak of economic crisis in Greece in 2010 and the austerity measures adopted have dramatically altered the economic and social conditions throughout the country and consequently deeply impacted the migrant families. With Albanian regular migrants losing the legal status and lapsing back into irregularity due to the high unemployment rates, the reverse process of de-regularization and social disintegration has emerged. As a result, many migrants drew on family and social networks to pursue work opportunities either back home or elsewhere, while maintaining their formal ties/residence in Greece. This article explores the impact of the Greek crisis and de-regularization phenomenon on the transnational practices among Albanian families. Our aim is to go beyond the general theories on transnationalism and look at what exactly is the impact of the crisis on the families, as well as individuals' dilemmas of return and negotiations between transnational mobility and staying put, between different levels of belonging and their orientation to the present and future. The empirical analysis is based on in-depth interviews with 70 Albanians of first and second generation living in Greece.
Involving the hard to reach: developing and evaluating a sexual health programme for early school leavers in Hong Kong

Early school leavers cannot access school-based sex education programmes, increasing their vulnerability to sexual health issues. This study evaluated a culturally-sensitive and target-orientated sex education programme involving this group. Early school leavers were recruited from two branches of the Chinese Young Men's Christian Association in Hong Kong. These potential peer educators (PEs) attended five three-hour workshops providing comprehensive sex and sexuality education. They then provided peers with sex education, whilst receiving continuing support and attending additional training and activities. The Safer Choice Student Health Questionnaire, Mathtech Student Course Evaluation and Student Assessment of Course Impact questionnaires and Behavioral Intent Questionnaire were used to assess attitudes towards the programme and changes in knowledge, attitudes, practices regarding sex and sexual health. Of 60 PEs, 97% completed the workshop course. Seven months post intervention, changes in attitude towards contraception (p = 0.01) and a lower likelihood of having sex (p < 0.001) were found amongst PEs. At 14 months, PEs were less likely to have sex (p < 0.001) and were more comfortable talking about sex with friends and family (p = 0.01) but no difference was observed in pre-training and post-training tests among 545 targeted peers. The intervention successfully engaged the heavily involved PEs, and had some positive effects on their willingness to discuss sexual health issues, their perceived likelihood of having and their attitude towards sexual intercourse.
Metabolic changes underlying 31P MR spectral alterations in human hepatic tumours

Magnetic resonance spectroscopy (MRS) remains the technique of choice for observing tumour metabolism non‐invasively. Although initially 31P MR spectroscopy showed much promise as a non‐invasive diagnostic tool, studies of a wide range of hepatic tumours have conclusively shown that this technique cannot be utilized to distinguish between different tumour types. This lack of specificity and sensitivity appears to be a consequence of the fact that hepatic tumours develop with a range of modalities and not as a single abnormal disease process, and also because of the limited availability of MR detectable metabolic markers. This has led, in recent years, to a re‐evaluation of the role of 31P MR spectroscopy, re‐emerging as a non‐invasive tool to follow the efficacy of the treatment regime. Furthermore, since the principal changes observed in tumours by 31P MRS appear to be an elevation in the concentration of phosphorylcholine (PCho) and phosphoethanolamine (PEth), new research using a combination of MRS and tissue culture of cell lines which carry a combination of known inducible oncogenes, are helping to elucidate some of the metabolic pathways that give rise to these metabolic alterations. © 1998 John Wiley & Sons, Ltd.
Northern bald ibises follow others’ gaze into distant space but not behind barriers

Gaze following is the ability to use the visual orientation of others as a trigger to look in the same direction. Thereby, animals may either align their head and eye orientation with others (gaze following into distant space) or may even reposition themselves to look behind barriers impairing their perception (geometrical gaze following). It has been proposed that these two different modes are functionally and cognitively distinct, but experimental evidence for this claim is lacking. We here, to our knowledge, demonstrate for the first time, that adult animals may be capable of following gaze into distant space, but not geometrically around barriers. We tested Northern bald ibises (Geronticus eremita) for their ability to follow a conspecific's gaze in two standard tasks. The birds readily looked up after seeing a model bird looking up; however, when seeing a model looking behind a barrier, they responded by looking at the barrier instead of walking around. These findings are in stark contrast to results obtained with great apes and corvids and provide the first experimental evidence, to our knowledge, for cognitive differences in gaze following tasks.
EMWIN:: emulating a mobile wireless network using a wired network

Test and performance evaluation of protocols and algorithms in mobile wireless networks is known to be challenging. Due to the highly varying characteristics of mobile wireless networks, one cannot merely rely on either network simulation or a testbed. Network emulation provides a controllable and reproducible environment, yet it generally lacks the support for the emulation of network topology and mobility, which are extremely critical in mobile wireless network research. We introduce EMWIN, a new IP-based mobile wireless emulation system that can overcome those drawbacks. In EMWIN, a target mobile wireless network is precisely mapped to an emulation configuration in a laboratory private network consisting of several emulator nodes, each of which is able to emulate multiple mobile hosts. Moreover, the emulator node can be flexibly configured such that predefined network conditions and traffic dynamics can be generated in an automatic manner. With EMWIN, the mobility of the target mobile wireless network with a number of mobile nodes can be faithfully emulated in a wired network environment.
Acoustic Correlates of Word Stress as A Cue to Accent Strength

Abstract Due to the clear interference of their mother tongue prosody, many Czech learners produce their English with a conspicuous foreign accent. The goal of the present study is to investigate the acoustic cues that differentiate stressed and unstressed syllabic nuclei and identify individual details concerning their contribution to the specific sound of Czech English. Speech production of sixteen female non-professional Czech and British speakers was analysed with the sounds segmented on a word and phone level and with both canonical and actual stress positions manually marked. Prior to analyses the strength of the foreign accent was assessed in a perception test. Subsequently, stressed and unstressed vowels were measured with respect to their duration, amplitude, fundamental frequency and spectral slope. Our results show that, in general, Czech speakers use much less acoustic marking of stress than the British subjects. The difference is most prominent in the domains of fundamental frequency and amplitude. The Czech speakers also deviate from the canonical placement of stress, shifting it frequently to the first syllable. On the other hand, they seem to approximate the needed durational difference quite successfully. These outcomes support the concept of language interference since they correspond with the existing linguistic knowledge about Czech and English word stress. The study adds specific details concerning the extent of this interference in four acoustic dimensions.
THE USE OF COLLOCATIONS BY ADVANCED LEARNERS OF ENGLISH AND SOME IMPLICATIONS FOR TEACHING

Although it is widely acknowledged that collocations are both indispensable and problematic for language learners and that they therefore should play an important part in second language teaching, especially at an advanced level, learners' difficulties with collocations have not been investigated in much detail so far. This paper reports on an exploratory study that analyses the use of verb-noun collocations such as take a break or shake one's head by advanced German-speaking learners of English in free written production. First, an attempt is made to define 'collocations' as precisely as possible, and the methodology that has been developed for analysing learner collocations in free production is described. Then, the types of mistakes that the learners make when producing collocations are identified and the influence of the degree of restriction of a combination and of the learners' L1 on the production of collocations is investigated. While the degree of restriction emerges to have some, but comparatively little, impact on the difficulty of combinations for the learners, the learners' L1 turns out to have a degree of influence that goes far beyond what earlier (small-scale) studies have predicted. Finally, the implications of these results for teaching are discussed, most importantly the role of L1-L2 differences.
Rules Placement Problem in OpenFlow Networks: A Survey

Software-defined networking (SDN) abstracts low-level network functionalities to simplify network management and reduce costs. The OpenFlow protocol implements the SDN concept by abstracting network communications as flows to be processed by network elements. In OpenFlow, the high-level policies are translated into network primitives called rules that are distributed over the network. While the abstraction offered by OpenFlow allows to potentially implement any policy, it raises the new question of how to define the rules and where to place them in the network while respecting all technical and administrative requirements. In this paper, we propose a comprehensive study of the so-called OpenFlow rules placement problem with a survey of the various proposals intending to solve it. Our study is multifold. First, we define the problem and its challenges. Second, we overview the large number of solutions proposed, with a clear distinction between solutions focusing on memory management and those proposing to reduce signaling traffic to ensure scalability. Finally, we discuss potential research directions around the OpenFlow rules placement problem.
Brazilian natural dietary components (annatto, propolis and mushrooms) protecting against mutation and cancer

Considering the high number of new cancer cases in Brazil (approximately 470 000 cases in 2005) and the remarkable differences in the incidence of this disease around the world, the development of chemopreventive strategies using foods widely consumed would have a huge impact, both medically and economically. This review summarizes some of our studies conducted to verify the anti-mutagenic and anti-carcinogenic potential of some Brazilian natural dietary constituents (annatto, mushrooms, and propolis). Overall data have shown a clear role for these compounds in preventing mutation and specific preneoplastic lesions. Taken together, these agents indicate a favorable side-effect profile and may prove to be a promising alternative for cancer prevention strategies, although more investigation is needed to fully explore this issue.
Dense Graphlet Statistics of Protein Interaction and Random Networks

Understanding evolutionary dynamics from a systemic point of view crucially depends on knowledge about how evolution affects size and structure of the organisms' functional building blocks (modules). It has been recently reported that statistics over sparse PPI graphlets can robustly monitor such evolutionary changes. However, there is abundant evidence that in PPI networks modules can be identified with highly interconnected (dense) and/or bipartite subgraphs. We count such dense graphlets in PPI networks by employing recently developed search strategies that render related inference problems tractable. We demonstrate that corresponding counting statistics differ significantly between prokaryotes and eukaryotes as well as between "real" PPI networks and scale free network emulators. We also prove that another class of emulators, the low-dimensional geometric random graphs (GRGs) cannot contain a specific type of motifs, complete bipartite graphs, which are abundant in PPI networks.
Generalized multilevel inverter topology with stacked coupled inductors

In this paper a generalized multilevel inverter topology with stacked-coupled-inductors (SCI) is proposed. It is based on two cascaded stages controlled at different switching frequencies and two stacked groups of coupled-inductors. The high-frequency stage is specific to a parallel connection of at least two groups of stacked switching cells, while the low-frequency stage is composed by a basic switching cell. The operation principle of the proposed SCI generalization is verified by numerical simulations both for single- and three-phase VSI topologies.