Miracle-dz/UniFAR-FTUs huggingface dataset:
A fluid-structure-interaction tool by coupling of existing codes

Fluid-Structure-Interaction (FSI), as a sub-discipline of computational mechanics, has been gaining relevance since the growth in clusters capacity has made it possible to simulate high resolution models. Although some commercial tools already present certain capabilities for coupled simulations, the lack of efficiency of these general purpose programs is still an issue. Moreover, the high cost of commercial licenses - on a per processor basis - hampers the computation of high resolution models for academic research. Instead, a coupled software solution that resorts to well established existent programs proves a good alternative to preserve the value of decades-long development and associated know-how. However, since such codes were mostly conceived for standalone run, an elegant software implementation is not easily achieved. In this work our CFD code SPARC has been coupled with the open-source structural solver CalculiX by means of the in-house developed software packet FSiM. FSiM stands for Fluid-Structure-Interaction Simulation Manager and is in charge of the communication between the fluid and structure solver using the Dynamic Process Management of the MPI-2 standard. This approach facilitates that the parallelization strategies of both part-solvers be used with minimal modifications and no risk of mutual interference. Results of a simple two-dimensional test case of the panel flutter problem are presented to show the capabilities of the new coupling tool.
Comparing the Quality of Life of Patients With Hemophilia and Juvenile Idiopathic Arthritis in Which Chronic Arthropathy Is a Common Complication

Introduction: Hemophilia is a genetic disorder in which recurrent joint bleeding causes arthropathy. Inflammation and degeneration play roles in the pathogenesis of hemophilic arthropathy. Patients with juvenile idiopathic arthritis (JIA) experience a similar inflammatory degenerative joint disease. A comparison of different patients with common pathogenetic features may identify unique features helpful in terms of the follow-up. Aim: We compared the quality of life (QoL) of patients with hemophilia and JIA, and healthy controls, using a generic QoL scale, Kidscreen and Disabkids Questionnaires (KINDL). Differences among groups were evaluated in terms of sociodemographic characteristics and clinical parameters affecting the QoL. Methods: We included 33 hemophilia patients, 19 JIA patients, and 32 healthy individuals aged 4 to 18 years. Sociodemographic characteristics (the age, the maternal educational status, the place of residence, the size of the household, the household income, divorced parents) were noted, and the KINDL was administered to all participants. Clinical parameters associated with arthropathy (the functional independence score [FISH], the hemophilia joint health score [HJHS], the arthropathic joint count, and the painful joint count) were documented. Differences in frequencies and medians among the groups were evaluated using the &khgr;2, the Mann-Whitney U, and the Kruskal-Wallis tests. Results: All KINDL dimensions were above 50, reflecting “good conditions” in the 2 patient groups. No difference between patients with hemophilia and JIA was evident in terms of the clinical parameters of FISH, the HJHS, or the arthropathic or painful joint counts (P>0.05). Sociodemographically, only the frequency of literate mothers was lower in patients with hemophilia than in those with JIA and healthy controls (P=0.03). Patients with JIA scored more higher on the KINDL dimension of chronic illness than those with hemophilia (P=0.02). The FISH score correlated with the total QoL score in both patients with hemophilia and JIA (r=0.39, P=0.03 and r=0.48, P=0.04, respectively). Conclusions: Although no difference was evident between the patient groups in terms of clinical parameters associated with arthropathy, JIA patients coped better with illness than those with hemophilia. JIA patients had a higher proportion of literate mothers than hemophilia patients; this may affect a patient’s ability to cope with issues relating to chronic illness. Implementation of an educational program for mothers of hemophilia patients, during follow-up, may improve the patient’s QoL. Also, hemophilia patients should be assisted to improve their QoL in the dimensions of self-esteem and schooling. Lastly, the evaluation of functional disability by FISH in hemophilia patients is important because the FISH score correlated with the total QoL score, as revealed by KINDL. In JIA patients also, functional disabilities caused by arthropathy affected the QoL.
Les Invariants du n-cube

On etudie divers problemes concernant le n-cube. On decrit les exemples connus de (0,2) graphes (bipartis de diametre 2 ou 3). On presente des constructions de (0,2) graphes. On etudie les (0,2) graphes avec des triangles. On montre comment construire certains des (0,2) graphes comme graphes de Cayley de groupes. On etudie les invariants immediats du n-cube.
Chloroform anaesthesia in Liverpool

The introduction of chloroform into anaesthesia is described, together with an account of the parts played by Simpson and Waldie and their connexions with Liverpool. An account of the first chloroform anaesthetics administered in Liverpool is also given; David Waldie, who suggested the use of chloroform, was one of the administrators at the first demonstration.
Associations between Intakes of Fluoride from Beverages during Infancy and Dental Fluorosis of Primary Teeth

Objective: We describe associations between primary tooth fluorosis status and intakes of beverages and fluoride from these beverages during infancy. Methods: Subjects (n = 677) are members of the Iowa Fluoride Study, a cohort of young children followed from birth. Food and nutrient intakes were obtained from 3-day diet records. Diets were analyzed at 6 weeks, 3, 6, 9, 12 and 16 months and cumulatively for 6 weeks through 16 months of age. Primary tooth fluorosis was assessed at 4.5–6.9 years of age and defined as present or absent. Multiple logistic regression analyses were used to develop models to predict fluorosis status. Results: Water-based beverage intakes were higher in subjects with fluorosis than in those without. Specifically, higher intakes of water used to reconstitute formulas at 3, 6 and 9 months; any intake of water as a beverage at 16 months; and higher intakes of combined 100% juice and miscellaneous beverages at 16 months were positively associated with fluorosis (p < 0.05). Fluoride intakes from water sources were also higher in subjects with fluorosis than in those without. Specifically, higher intakes of fluoride from water used to reconstitute formulas at 3, 6, 9 and 12 months and for 6 weeks through 16 months, and higher intakes of fluoride from water as a beverage at 16 months and for 6 weeks through 16 months were positively associated with fluorosis (p < 0.05). Conclusion: Infant beverages, particularly infant formulas prepared with fluoridated water, can increase the risk of fluorosis in primary teeth.
An internet-based food frequency questionnaire for a large Chinese population.

BACKGROUND AND OBJECTIVES National dietary surveys are needed and difficult to conduct in China. The current study aims to develop and validate an internet-based diet questionnaire for Chinese (IDQC) to assess intakes in Northern China. METHODS AND STUDY DESIGN We recruited 292 city residents by email and telephone in Harbin to obtain the IDQC and 3-day diet diaries. The food group and nutrient intakes from the IDQC were validated against those from the 3-day diet diaries. Paired sample t-tests were used to compare the methodological differences, and repeatability was estimated using Pearson's correlations. Cross-classification was used to calculate the percentage agreement in quartiles for all food groups and nutrients. RESULTS Positive correlations were found between the IDQC and 3-day diet diaries for all food groups after energy adjustment (from 0.28 for seeds and nuts to 0.63 for dairy products). Positive correlations were observed for all nutrients between the IDQC and 3-day diet diaries, with correlations ranging from 0.37 for folic acid to 0.98 for iodine. The overall agreements for food groups and nutrients were above 69.2%, indicating satisfactory consistency between the IDQC and 3-day diet diaries. CONCLUSIONS The IDQC can be used to estimate the food and nutrient intakes in a Northern China population for both clinical nutrition epidemiological and public health nutritional purposes. The questionnaire system IDQC (v1.0) is freely available at http://www.yyjy365. org/diet/.
Growth of Listeria monocytogenes and Yersinia enterocolitica on Cooked Modified-Atmosphere-Packaged Poultry in the Presence and Absence of a Naturally Occurring Microbiota

ABSTRACT Cooked poultry cuts were inoculated with five-strain composite mixtures of either Listeria monocytogenes or Yersinia enterocolitica (1,000 CFU/150-g piece), packaged in 44:56 CO2-N2, and stored at 3.5, 6.5, or 10°C for up to 5 weeks. Both L. monocytogenes and Y. enterocolitica grew under all test conditions. The presence of a naturally occurring microbiota did not influence the growth of either pathogen. Addition of lactate with the shelf life extender ALTA 2341 lengthened the lag phases of L. monocytogenes and Y. enterocolitica but did not prevent their growth.
Word Sense Disambiguation of Adjectives Using Probabilistic Networks

In this paper, word sense disambiguation (WSD) accuracy achievable by a probabilistic classifier, using very minimal training sets, is investigated. We made the assumption that there are no tagged corpora available and identified what information, needed by an accurate WSD system, can and cannot be automatically obtained. The lesson learned can then be used to focus on what knowledge needs manual annotation. Our system, named Bayesian Hierarchical Disambiguator (BHD), uses the Internet, arguably the largest corpus in existence, to address the sparse data problem, and uses WordNet's hierarchy for semantic contextual features. In addition, Bayesian networks are automatically constructed to represent knowledge learned from training sets by modeling the selectional preference of adjectives. These networks are then applied to disambiguation by performing inferences on unseen adjective-noun pairs. We demonstrate that this system is able to disambiguate adjectives in unrestricted text at good initial accuracy rates without the need for tagged corpora. The learning and extensibility aspects of the model are also discussed, showing how tagged corpora and additional context can be incorporated easily to improve accuracy, and how this technique can be used to disambiguate other types of word pairs, such as verb-noun and adverb-verb pairs.
Lightweight, robust adaptivity for software transactional memory

When a program uses Software TransactionalMemory (STM) to synchronize accesses to shared memory, the performance often depends on which STM implementation is used. Implementation vary greatly in their underlying mechanisms, in the features they provide, and in the assumptions they make about the common case. Consequently, the best choice of algorithm is workload-dependent. Worse yet, for workload composed of multiple phases of execution, the "best choice of implementation may change during execution. We present a low-overhead system for adapting between STM implementations. Like previous work, our system enable adaptivity between different parameterizations of a given algorithm, and it allows adapting between the use of transactions and coarse-grained locks. In addition, we support dynamic switching between fundamentally different STM implementations. We also explicitly support irrevocability retry-based condition synchronization, and privatization. Through a series of experiments, we show that our system introduces negligible overhead. We also present a candidate use of dynamic adaptivity, as a replacement for contention management. When using adaptivity in this manner, STM implementations can be simplified to a great degree without lowering throughput or introducing a risk of pathological slowdown, even for challenging workloads.
Neonatal Screening for Medium-Chain Acyl-CoA Deficiency—Insights and Unexpected Challenges

With the implementation of tandem mass spectrometry (MS/MS), neonatal screening for medium-chain acyl-CoA dehydrogenase (MCADD) has been introduced in many screening programs worldwide. Together with phenylketonuria, MCADD is the disorder most frequently diagnosed. Despite undeniable beneficial effects on morbidity and mortality, neonatal screening for MCADD effectively exemplifies the unexpected challenges of increased diagnosis by screening programs. MS/MS-based screening revealed an at least 2-fold higher incidence than expected with a considerable share of individuals showing mild biochemical alterations and/or novel mutations with unknown clinical significance. Whether these individuals are at lower risk to experience metabolic decompensations is a matter of ongoing debate. Defining patients, stratifying them according to their clinical risk, and adopting treatment protocols is an as yet unmet challenge in neonatal screening for MCADD.
Functions of Rab Proteins at Presynaptic Sites

Presynaptic neurotransmitter release is dominated by the synaptic vesicle (SV) cycle and entails the biogenesis, fusion, recycling, reformation or turnover of synaptic vesicles—a process involving bulk movement of membrane and proteins. As key mediators of membrane trafficking, small GTPases from the Rab family of proteins play critical roles in this process by acting as molecular switches that dynamically interact with and regulate the functions of different sets of macromolecular complexes involved in each stage of the cycle. Importantly, mutations affecting Rabs, and their regulators or effectors have now been identified that are implicated in severe neurological and neurodevelopmental disorders. Here, we summarize the roles and functions of presynaptic Rabs and discuss their involvement in the regulation of presynaptic function.
Intrusion-tolerant group management in Enclaves

Groupware applications require secure communication and group-management services. Participants in such applications may have divergent interests and may not fully trust each other. The services provided must then be designed to tolerate possibly misbehaving participants. Enclaves is a software framework for building such group applications. We discuss how the protocols used by Enclaves can be modified to guarantee proper service in the presence of nontrustworthy group members. We show how the improved protocol was formally specified and proven correct.
Next Generation Sequencing: Potential and Application in Drug Discovery

The world has now entered into a new era of genomics because of the continued advancements in the next generation high throughput sequencing technologies, which includes sequencing by synthesis-fluorescent in situ sequencing (FISSEQ), pyrosequencing, sequencing by ligation using polony amplification, supported oligonucleotide detection (SOLiD), sequencing by hybridization along with sequencing by ligation, and nanopore technology. Great impacts of these methods can be seen for solving the genome related problems of plant and animal kingdom that will open the door of a new era of genomics. This may ultimately overcome the Sanger sequencing that ruled for 30 years. NGS is expected to advance and make the drug discovery process more rapid.
A second black hole candidate in a M31 globular cluster is identified with XMM–Newton

We use arguments developed in previous work to identify a second black hole candidate associated with an M31 globular cluster (GC), Bo 144, on the basis of X-ray spectral and timing properties. The 2002 XMM–Newton observation of the associated X-ray source (hereafter XBo 144) revealed behaviour that is common to all low-mass X-ray binaries (LMXBs) in the low-hard state. Studies have shown that neutron star LMXBs exhibit this behaviour at 0.01–1000 keV luminosities ≤10 per cent of the Eddington limit ( L Edd ). However, the unabsorbed 0.3–10 keV luminosity of XBo 144 was ~0.30 L Edd for a 1.4 M ⊚ neutron star, and the 0.01–1000 keV luminosity is expected to be ≳3–7 times higher. We therefore identify XBo 144 as a black hole candidate. Furthermore, it is the second black hole candidate to be consistent with formation via tidal capture of a main sequence donor in a GC; such systems were previously thought non-existent, because the donor was thought to be disrupted during the capture process.
ntracardiac and extracardiac markers of inflammation during trial fibrillation

547-5271/$ -see front matter © 2010 Heart Rhythm Society. All rights reserved ersisted after adjusting for potential confounders. AF ablation atients in AF exhibited a positive median left atrial minus coroary sinus gradient CRP (0.3 mg/dL, IQR 0.03–1.1), whereas hose in sinus rhythm had a negative median left atrial minus oronary sinus gradient CRP ( 0.2, IQR 0.8–[ 0.02], P .01). emoral artery minus femoral vein gradients in AF versus sinus hythm did not show any differences.
Reading words in Spanish and English: Mapping orthography to phonology in two languages

English-Spanish bilinguals named visually presented words aloud in each language. The words included cognates (e.g., fruit-fruta) and non-cognate translations (e.g., pencil-ládpiz). The cognates were selected so that the orthographic and phonological similarity of their lexical form in each language varied orthogonally. Cognate naming latencies were influenced by the cross-language match of the orthographic and phonological codes. When the orthographic forms were similar in the two languages, naming latencies were slowed by dissimilar phonology, providing evidence for feed-forward activation from orthography to phonology across languages. When the orthographic forms were dissimilar, the effects of the corresponding phonological match were not statistically reliable. The results suggest that lexical access is non-selective across bilinguals' two languages, and that the degree of consistency between orthographic and phonological codes influences the manner in which cross-language competition is manifest. Findings are discussed in terms of feed-forward and feed-backward activation dynamics across languages.
Exploiting dendritic cells to improve vaccine efficacy.

The challenges to vaccine biology are dramatized by the current situation with an AIDS vaccine (see Letvin, this Perspective series, ref. 1). For years, data have been available on the HIV-1 genome and its proteins, as well as numerous antigens recognized by the immune system. Still, this information has not been readily translated into candidate vaccines that induce the broad and long-lasting T cell–mediated immunity thought to be necessary to protect people from acquiring AIDS (2–5). Vaccines are also lacking for many other serious infections in which T cell–mediated immunity should be protective. These include pathogens whose genomic sequences and antigenic proteins are well characterized: tuberculosis, malaria, and the herpes simplex, papilloma, Epstein-Barr, and hepatitis C viruses. In essence, the identification of foreign antigens is necessary but not sufficient for producing vaccines that are effective in the T cell sphere. Better vaccine delivery and vaccine adjuvants, or enhancers of immunity, are required (6, 7). We propose that dendritic cell (DC) physiology should be considered and exploited in meeting each of the challenges in vaccine biology that lie ahead (see Table ​Table1). 1). DCs act as nature’s adjuvants for regulating antigen-specific immunity. As antigen-presenting cells, DCs capture antigens, process them into peptides, and present them on products of the MHC to T cells. DCs are both efficient and specialized in antigen presentation, and they control the magnitude, quality, and memory of the ensuing immune response. DCs have been used successfully as cellular adjuvants in mice to elicit protective T cell–mediated immunity against pathogens and tumors (8, 9). These cells are now being used to prime and expand T cells specific for human cancers (refs. 10–12; see also Yu and Restifo, this Perspective series, ref. 13). The responding T cells include helper cells, especially Th1 CD4+ cells, which produce IFN-γ; and killer cells, especially CD8+ cytolytic T lymphocytes (CTLs), which exocytose granules rich in perforin and granzyme. New information indicates that DCs control responses by other classes of lymphocytes (B, NK, and NKT cells) and elicit T cell memory, a critical goal of vaccination. Table 1 Challenges in vaccine biology requiring improved control of antigen presentation Developing the capacity to harness DCs for vaccination seems particularly urgent in confronting infectious agents that, like HIV-1, pose unusual demands with respect to safety; the time-honored approach of microbial attenuation is now being set aside as vaccine biologists turn to defined antigens, poorly replicating vectors, and DNA. Although these vaccines introduce foreign microbial products, they often generate weak immunity, especially T cell–mediated immunity. Consequently, greater emphasis on underlying immunologic processes is needed, notably the strong adjuvant roles of DCs. Interestingly, as we discuss below, even the classical vaccine approach of microbial attenuation, used successfully for smallpox and measles, may have unknowingly exploited the adjuvant roles of DCs.
Minimization of a Large-Scale Quadratic FunctionSubject to a Spherical Constraint

An important problem in linear algebra and optimization is the trust-region subproblem: minimize a quadratic function subject to an ellipsoidal or spherical constraint. This basic problem has several important large-scale applications including seismic inversion and forcing convergence in optimization methods. Existing methods to solve the trust-region subproblem require matrix factorizations, which are not feasible in the large-scale setting. This paper presents an algorithm for solving the large-scale trust-region subproblem that requires a fixed-size limited storage proportional to the order of the quadratic and that relies only on matrix-vector products. The algorithm recasts the trust-region subproblem in terms of a parameterized eigenvalue problem and adjusts the parameter with a superlinearly convergent iteration to find the optimal solution from the eigenvector of the parameterized problem. Only the smallest eigenvalue and corresponding eigenvector of the parameterized problem needs to be computed. The implicitly restarted Lanczos method is well suited to this subproblem.