Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient and Scalable Algorithms for Smoothed Particle Hydrodynamics on Hybrid Shared/Distributed-Memory Architectures

This paper describes a new fast and implicitly parallel approach to neighbour-finding in multi-resolution Smoothed Particle Hydrodynamics (SPH) simulations. This new approach is based on hierarchical cell decompositions and sorted interactions, within a task-based formulation. It is shown to be faster than traditional tree-based codes, and to scale better than domain decomposition-based approaches on hybrid shared/distributed-memory parallel architectures, e.g. clusters of multi-cores, achieving a $40\times$ speedup over the Gadget-2 simulation code.
Nested Markov chain — A novel approach to model network-induced constraints

During the past a few years, control systems are greatly influenced by the evolution of networked control systems (NCSs). However, challenges such as time-delay and packet dropouts in NCSs are still breaking its stride. To analyse and tackle those constraints, Markov chains had been widely used to model time-delay and packet dropouts, and a set of controllers had been designed thereafter. Nevertheless, none of those models considered the relation between those constraints, which will be investigated in this paper. In this proposed system model, nested Markov chain (NMC) with one main Markov chain used to model packet dropouts and two sub-Markov chains responsible for the time-delays is exploited. Furthermore, the difference between Markov chain model and NMC model is discussed in detail. The modeled process and evaluation results illustrate the effectiveness of this NMC model.
An After-School Physical Activity Program for Obesity Prevention in Children

This article describes the process of setting up a 3-year, school-based after-school physical activity intervention in elementary schools. The primary aim of the study is to determine whether adiposity and fitness will improve in children who are exposed to a fitogenic versus an obesogenic environment. Eighteen schools were randomized to the control (obesogenic) or intervention (fitogenic) group. The study design, program components, and evaluation of the intervention are described in detail. The intervention consists of (a) academic enrichment, (b) a healthy snack, and (c) physical activity in a mastery-oriented environment. Successful implementation would show the feasibility of schools’ being able to provide a fitogenic environment. Significant differences between the groups would provide evidence that a fitogenic environment after school has positive health benefits. If feasibility and efficacy are demonstrated, implementing an after-school program like this one in elementary schools could play a major role in preventing and reducing childhood obesity.
Photoresponse characteristics and daily dynamic analysis of photosynthetic physiology for three kind of bamboo

Three-year old bamboo species of Bitter bamboo, Bambusa officinalis, Chimonobambusa communis were selected as the experimental material for testing physiological characteristics with Licor-6400. The results indicated that in the light saturation point, the value of Bambusa officinalis and Chimonobambusa communis were the same (1800µmol·m<sup>−2</sup>s<sup>−1</sup>), which was larger than that of Bitter bamboo. The sequence of LCP was in an order of Bitter bamboo (8.04µmol·m<sup>−2</sup>s<sup>−1</sup>) &#60; Bambusa officinalis (10.2µmol·m<sup>−2</sup>s<sup>−1</sup>) &#60; Chimonobambusa communis (29.81µmol·m<sup>−2</sup>s<sup>−1</sup>). The diurnal change of net photosynthetic rate of these three bamboo species could be expressed as double-peek curve, exhibiting a clear midday depression respectively. Bambusa officinalis displayed the highest daily average value in net photosynthetic rate (6.47µmol·mol<sup>−1</sup>), and then Chimonobambusa communis (6.16µmol·mol<sup>−1</sup>), finally Bitter bamboo (4.93µmol·mol<sup>−1</sup>).
Integrins in point contacts mediate cell spreading: factors that regulate integrin accumulation in point contacts vs. focal contacts

We have studied the function and distribution of the alpha 1 beta 1, alpha 5 beta 1 and alpha 6 beta 1 heterodimers on type-1 astrocytes with antibodies specific for integrin subunits (alpha 1, alpha 5, alpha 6, and beta 1). The alpha 1 beta 1 heterodimer mediates adhesion to laminin and collagen, the alpha 5 beta 1 to fibronectin in an RGD- dependent manner. The alpha 5 beta 1 integrin is found in focal contacts in long-term cultures of well-spread astrocytes colocalizing with vinculin and the termini of actin stress fibers. alpha 1 beta 1 heterodimers can occasionally be found as small aggregates within focal contacts but they do not accumulate there. Instead, alpha 1 beta 1 integrins are found in punctate deposits called point contacts which are distributed over the upper and the lower cell surfaces whether laminin, collagen, fibronectin or polylysine is used as a substratum. Unlike focal contacts, point contacts contain clathrin but rarely codistribute with actin or vinculin. Two observations indicate that these point contacts are functional. First, mAb 3A3, directed against the rat alpha 1 subunit, inhibits the attachment of astrocytes to laminin and collagen. Second, during the spreading of astrocytes, a band of point contacts forms around the cell perimeter at a time when no focal contacts are visible. While alpha 1 beta 1 integrins are found only in point contacts in astrocytes, the alpha 6 beta 1 integrin, another laminin receptor, is localized within focal contacts. Moreover, alpha 1 beta 1 heterodimers accumulate in focal contacts in fibroblasts. Thus, the alpha subunit contributes, independent of its ligand, to functional integrin heterodimer accumulation in focal contacts or in point contacts. This accumulation varies among different cell types with apparently identical heterodimers as well as with the motile state (spreading vs. flattened) of the same cells.
Grow Rich While You Sleep: Selection in Experiments with Voluntary Participation

We use data from a promotion campaign of NH-Hoteles to study self-selection of participants in a gift-exchange experiment. The promotion campaign allowed guests to pay any non negative amount of money for a stay in one of 36 hotels in Belgium and the Netherlands. The data allow us to distinguish between `regular guests', who booked prior to the announcement of the promotion campaign and guests who booked after the campaign was announced. During the promotion campaign we varied the posted price of a room that was communicated to the guests. Only the regular guests respond to the exogenous variation in the posted price and they pay substantially more on average. This different behavior cannot be explained by differences in satisfaction or observed compositional differences between both groups. We argue that the promotion campaign mainly attracted individuals who find it relatively unimportant to be viewed of as prosocial.
TGFβ regulates epithelial-mesenchymal interactions through WNT signaling activity to control muscle development in the soft palate

Clefting of the soft palate occurs as a congenital defect in humans and adversely affects the physiological function of the palate. However, the molecular and cellular mechanism of clefting of the soft palate remains unclear because few animal models exhibit an isolated cleft in the soft palate. Using three-dimensional microCT images and histological reconstruction, we found that loss of TGFβ signaling in the palatal epithelium led to soft palate muscle defects in Tgfbr2fl/fl;K14-Cre mice. Specifically, muscle mass was decreased in the soft palates of Tgfbr2 mutant mice, following defects in cell proliferation and differentiation. Gene expression of Dickkopf (Dkk1 and Dkk4), negative regulators of WNT-β-catenin signaling, is upregulated in the soft palate of Tgfbr2fl/fl;K14-Cre mice, and WNT-β-catenin signaling is disrupted in the palatal mesenchyme. Importantly, blocking the function of DKK1 and DKK4 rescued the cell proliferation and differentiation defects in the soft palate of Tgfbr2fl/fl;K14-Cre mice. Thus, our findings indicate that loss of TGFβ signaling in epithelial cells compromises activation of WNT signaling and proper muscle development in the soft palate through tissue-tissue interactions, resulting in a cleft soft palate. This information has important implications for prevention and non-surgical correction of cleft soft palate.
Magnetoencephalography in Stroke Recovery and Rehabilitation

Magnetoencephalography (MEG) is a non-invasive neurophysiological technique used to study the cerebral cortex. Currently, MEG is mainly used clinically to localize epileptic foci and eloquent brain areas in order to avoid damage during neurosurgery. MEG might, however, also be of help in monitoring stroke recovery and rehabilitation. This review focuses on experimental use of MEG in neurorehabilitation. MEG has been employed to detect early modifications in neuroplasticity and connectivity, but there is insufficient evidence as to whether these methods are sensitive enough to be used as a clinical diagnostic test. MEG has also been exploited to derive the relationship between brain activity and movement kinematics for a motor-based brain–computer interface. In the current body of experimental research, MEG appears to be a powerful tool in neurorehabilitation, but it is necessary to produce new data to confirm its clinical utility.
Protein Complexes Prediction Method Based on Core—Attachment Structure and Functional Annotations

Recent advances in high-throughput laboratory techniques captured large-scale protein–protein interaction (PPI) data, making it possible to create a detailed map of protein interaction networks, and thus enable us to detect protein complexes from these PPI networks. However, most of the current state-of-the-art studies still have some problems, for instance, incapability of identifying overlapping clusters, without considering the inherent organization within protein complexes, and overlooking the biological meaning of complexes. Therefore, we present a novel overlapping protein complexes prediction method based on core–attachment structure and function annotations (CFOCM), which performs in two stages: first, it detects protein complex cores with the maximum value of our defined cluster closeness function, in which the proteins are also closely related to at least one common function. Then it appends attach proteins into these detected cores to form the returned complexes. For performance evaluation, CFOCM and six classical methods have been used to identify protein complexes on three different yeast PPI networks, and three sets of real complexes including the Munich Information Center for Protein Sequences (MIPS), the Saccharomyces Genome Database (SGD) and the Catalogues of Yeast protein Complexes (CYC2008) are selected as benchmark sets, and the results show that CFOCM is indeed effective and robust for achieving the highest F-measure values in all tests.
A Quantitative Analysis of Variability Warnings in Linux

In order to get insight into challenges with quality in highly-configurable software, we analyze one of the largest open source projects, the Linux kernel, and quantify basic properties of configuration-related warnings. We automatically analyze more than 20 thousand valid and distinct random configurations, in a computation that lasted more than a month. We count and classify a total of 400,000 warnings to get an insight in the distribution of warning types, and the location of the warnings. We run both on a stable and unstable version of the Linux kernel. The results show that Linux contains a significant amount of configuration-dependent warnings, including many that appear harmful. In fact, it appears that there are no configuration-independent warnings in the kernel at all, adding to our knowledge about relevance of family-based analyses.
Toward Text-to-Picture Synthesis

It is estimated that more that 2 million people in the United States have significant communication impairments that result in them relying on methods other than natural speech alone for communication [2]. One type of commonly used augmentative and alternative communication (AAC) system is pictorial communication software such as SymWriter [8], which uses a lookup table to transliterate each word (or common phrase) in a sentence into an icon. This is an example of converting information between modalities. However, the resulting sequence of icons can be difficult to understand.
DARE: High-Performance State Machine Replication on RDMA Networks

The increasing amount of data that needs to be collected and analyzed requires large-scale datacenter architectures that are naturally more susceptible to faults of single components. One way to offer consistent services on such unreliable systems are replicated state machines (RSMs). Yet, traditional RSM protocols cannot deliver the needed latency and request rates for future large-scale systems. In this paper, we propose a new set of protocols based on Remote Direct Memory Access (RDMA) primitives. To asses these mechanisms, we use a strongly consistent key-value store; the evaluation shows that our simple protocols improve RSM performance by more than an order of magnitude. Furthermore, we show that RDMA introduces various new options, such as log access management. Our protocols enable operators to fully utilize the new capabilities of the quickly growing number of RDMA-capable datacenter networks.
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes. DOI: http://dx.doi. org/10.7554/eLife.08490. 001
Solution structure of a DNA decamer duplex containing the stable 3' T.G base pair of the pyrimidine(6-4)pyrimidone photoproduct [(6-4) adduct]: implications for the highly specific 3' T --> C transition of the (6-4) adduct.

The pyrimidine(6-4)pyrimidone photoproduct [(6-4) adduct] is one of the major photoproducts induced by UV irradiation of DNA and occurs at TpT sites. The (6-4) adduct is highly mutagenic and leads most often to a 3' T --> C transition with 85% replicating error frequency [LeClerc, J. E. , Borden, A. & Lawrence, C. W. (1991) Proc. Natl. Acad. Sci. USA 88, 9685-9689]. To determine the origin of the specific 3' T --> C transition of the (6-4) adduct, we have used experimental NMR restraints and molecular dynamics to determine the solution structure of a (6-4)-lesion DNA decamer duplex that contains a mismatched base pair between the 3' T residue and an opposed G residue. Normal Watson-Crick-type hydrogen bonding is retained at the 5' T of the lesion site. The O2 carbonyl of the 3' T residue forms hydrogen bonds with the imino and amino protons of the opposed G residue. This potential hydrogen bonding stabilizes the overall helix and restores the highly distorted conformation of the (6-4) adduct to the typical B-form-like DNA structure. This structural feature can explain the marked preference for the insertion of an A residue opposite the 5' T and a G residue opposite the 3' T of the (6-4) lesion during trans-lesion synthesis. Thus these insertions yield the predominant 3' T --> C transition.
Efficacy of Coordinated Distributed Multiple Attacks (A Proactive Approach to Cyber Defense)

The goal of the proposed coordinated distributed multiple attack (CDMA) is to strike a selected adversarial network and render its services useless. In this attack a number of compromised systems are used as facilitators in a coordinated manner to launch an attack on a victim's host or network. By distributing the attack and varying the type of attack the source attacker exhibits a decreased intensity of activity; therefore, the attack becomes harder to detect. Meanwhile, the concentrated effect on the victim is sufficient to overload network peripherals and systems, resulting in denial of service. In CDMAs an adversary can target a wide range of vulnerabilities present in victims' operating systems, protocol stacks, applications, network infrastructure, etc
Assessment of myocardial viability in rats: Evaluation of a new method using superparamagnetic iron oxide nanoparticles and Gd‐DOTA at high magnetic field

The aim of this study was to detect salvageable peri‐infarction myocardium by MRI in rats after infarction, using with a double contrast agent (CA) protocol at 7 Tesla. Intravascular superparamagnetic iron oxide (SPIO) nanoparticles and an extracellular paramagnetic CA (Gd‐DOTA) were used to characterize the peri‐infarction zone, which may recover function after reperfusion occurs. Infarcted areas measured from T1‐weighted (T1‐w) images post Gd‐DOTA administration were overestimated compared to histological TTC staining (52% ± 3% of LV surface area vs. 40% ± 3%, P = 0.03) or to T2‐w images post SPIO administration (41% ± 4%, P = 0.04), whereas areas measured from T2‐w images post SPIO administration were not significantly different from those measured histologically (P = 0.7). Viable and nonviable myocardium portions of ischemically injured myocardium were enhanced after diffusive Gd‐DOTA injection. The subsequent injection of vascular SPIO nanoparticles enables the discrimination of viable peri‐infarction regions by specifically altering the signal of the still‐vascularized myocardium. Magn Reson Med 52:932–936, 2004. © 2004 Wiley‐Liss, Inc.
Sanctions and moral judgments: The moderating effect of sanction severity and trust in authorities

In order to induce people to follow rules, sanctions are often introduced. In this paper we argue for the importance of studying the positive influence of sanctioning systems on people's moral convictions regarding the rule advocated by the sanction and of studying factors that moderate this influence. In three experiments we tested the influence of sanction severity and showed that severe sanctions evoke stronger moral judgments with regard to rule-breaking behavior and stronger social disapproval towards rule-breakers than mild sanctions. This was particularly the case when trust in authorities is high rather than low. Implications of these findings are discussed. Also, a framework is proposed to understand the possible circumstances that determine whether sanctions either increase or decrease moral norms.
The pharmacology of vascular smooth muscle.

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Universal Schubert polynomials

We introduce polynomials that represent general degeneracy loci for maps of vector bundles. These polynomials specialize to the known classical and quantum forms of single and double Schubert polynomials. This is the final version of the paper, to appear in Duke Math. J. The results are strengthened because Lakshmibai and Magyar have proved a conjecture from the previous version: in the universal case, these loci are Cohen-Macaulay.
Sentinel Lymph Node Identification in Breast Cancer - Comparison of Planar Scintigraphy and SPECT/CT

Aim: Assess the role of planar lymphoscintigraphy and fusion imaging of SPECT/CT in sentinel lymph node (SLN) identification in patients with breast cancer. Methods: Planar scintigraphy and hybrid modality SPECT/CT were performed in 223 consecutive women with breast cancer (mean age 59,5 yrs with range 25 - 82 years). In 190 women with a palpable mass radiocolloid was injected in four peritumoral sites and one subdermal injection above the tumour (GROUP A), in 33 women with nonpalpable tumour radiotracer was injected in four subareolar sites (GROUP B). Planar and SPECT/CT images were interpreted separately by two nuclear medicine physicians. Ability of these two techniques to image SLN was compared. Results: In GROUP A the overall hot LN detection rate by planar and SPECT-CT lymphoscintigraphy was 87,9 % (167 patients). In 10 patients (5,3 %), hot LNs were detected only by SPECT-CT. 18 (5,3 %) foci of uptake in 13 (6,8 %) patients interpreted on planar images as hot LNs were found to be false positive non-nodal sites of uptake when further assessed on SPECT/CT. In GROUP B the overall hot LN detection rate on planar and SPECT-CT was 97 % (32 patients). In one (3,0 %) patient hot LNs were identified only on SPECT/CT. Four (6,6 %) foci of uptake in four (12,1 %) patients were found to be false positive when further correlated with SPECT/CT. Differences in detection of SLNs between planar and SPECT/CT imaging in all 223 patients were statistically significant (P< 0.001). Conclusion: In some patients with breast cancer SPECT/CT improves the detection of sentinel lymph nodes. It can image nodes not visible on planar scintigrams, exclude false positive uptake and exactly localize axillary and non-axillary SLN.
An interactional approach to emergent interorganizational fields

Collaboration among community organizations is considered an important strategy for addressing the challenges posed by complex problems and turbulent environments. Indeed, there has been a proliferation of research on factors influencing the formation of interorganizational relationships (IORs), including a marked emphasis on transaction costs, resource dependence, and strategic choice. Far less attention has been focused on interest convergence, communal will, and mutuality, all of which are central to Wilkinson’s social field theory. A pilot study (n = 30) was conducted to explore community development practitioners’ views concerning the involvement of field-theoretic processes in community-oriented IORs. Participants rated a series of Likert-format statements based on an interactional approach to emergent IORs among local development agencies. Non-parametric Mokken analysis of the item responses identified six hierarchically ordered scales reflecting core tenets of social field theory. This research was undertaken to advance contemporary methods of investigating field-interactional interpretations of community and organizational development.