Miracle-dz/UniFAR-FTUs huggingface dataset:
Neighborhood based fast graph search in large networks

Complex social and information network search becomes important with a variety of applications. In the core of these applications, lies a common and critical problem: Given a labeled network and a query graph, how to efficiently search the query graph in the target network. The presence of noise and the incomplete knowledge about the structure and content of the target network make it unrealistic to find an exact match. Rather, it is more appealing to find the top-k approximate matches. In this paper, we propose a neighborhood-based similarity measure that could avoid costly graph isomorphism and edit distance computation. Under this new measure, we prove that subgraph similarity search is NP hard, while graph similarity match is polynomial. By studying the principles behind this measure, we found an information propagation model that is able to convert a large network into a set of multidimensional vectors, where sophisticated indexing and similarity search algorithms are available. The proposed method, called Ness (Neighborhood Based Similarity Search), is appropriate for graphs with low automorphism and high noise, which are common in many social and information networks. Ness is not only efficient, but also robust against structural noise and information loss. Empirical results show that it can quickly and accurately find high-quality matches in large networks, with negligible cost.
Problems, problems, problems: The social construction of ‘leadership’

The invasion of Iraq was premised upon accounts of the situation that have proved unsustainable, but that has not generated a change in the strategy of the coalition forces. Conventional contingency accounts of leadership suggest that accurate accounts of the context are a critical element of the decision-making apparatus but such accounts appear incapable of explaining the decisions of those engaged. An alternative model is developed that adapts the Tame and Wicked problem analysis of Rittell and Webber, in association with Etzioni’s typology of compliance, to propose an alternative analysis that is rooted in social constructivist approaches. This is then applied to three asymmetric case studies which suggest that decision-makers are much more active in the constitution of the context than conventional contingency theories allow, and that a persuasive rendition of the context then legitimizes a particular form of action that often relates to the decision-maker’s preferred mode of engagement, rather than what ‘the situation’ apparently demands. In effect, the context is reconstructed as a political arena not a scientific laboratory.
Frailty measures, inflammatory biomarkers and post-operative complications in older surgical patients.

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In Vivo RNAi Screen Reveals Neddylation Genes as Novel Regulators of Hedgehog Signaling

Hedgehog (Hh) signaling is highly conserved in all metazoan animals and plays critical roles in many developmental processes. Dysregulation of the Hh signaling cascade has been implicated in many diseases, including cancer. Although key components of the Hh pathway have been identified, significant gaps remain in our understanding of the regulation of individual Hh signaling molecules. Here, we report the identification of novel regulators of the Hh pathway, obtained from an in vivo RNA interference (RNAi) screen in Drosophila. By selectively targeting critical genes functioning in post-translational modification systems utilizing ubiquitin (Ub) and Ub-like proteins, we identify two novel genes (dUba3 and dUbc12) that negatively regulate Hh signaling activity. We provide in vivo and in vitro evidence illustrating that dUba3 and dUbc12 are essential components of the neddylation pathway; they function in an enzyme cascade to conjugate the ubiquitin-like NEDD8 modifier to Cullin proteins. Neddylation activates the Cullin-containing ubiquitin ligase complex, which in turn promotes the degradation of Cubitus interruptus (Ci), the downstream transcription factor of the Hh pathway. Our study reveals a conserved molecular mechanism of the neddylation pathway in Drosophila and sheds light on the complex post-translational regulations in Hh signaling.
Sub-tropical seagrass ecosystem metabolism measured by eddy covariance

The metabolism of seagrass ecosystems was examined at 4 sites in south Florida, USA, using the eddy covariance technique under in situ conditions. Three sites were located across a phosphorus-driven productivity gradient to examine the combined effects of dynamic variables (irradiance, flow velocity) and state variables (sediment phosphorus and organic content, seagrass biomass) on ecosystem metabolism and trophic status. Gross primary production and re - spiration rates varied significantly across Florida Bay in the summer of 2012 with the lowest rates (64 and −53 mmol O2 m −2 d −1 , respectively) in low-phosphorus sediments in the northeast and the highest (287 and −212 mmol O2 m −2 d −1 , respectively) in the southwest where sediment phospho- rus, organic matter, and seagrass biomass are higher. Seagrass eco systems offshore of the Florida Keys had similar large daily production and respiration rates (397 and −217 mmol O2 m −2 d −1 , respectively) and were influenced by flow through the permeable offshore sediments. Across all sites, net ecosystem metabolism rates indicated that the seagrass ecosystems were autotrophic in the summertime. Substantial day-to-day variability in metabolic rates was found due to variations in irradiance and flow velocity. At all sites the relationship between photosynthesis and irradiance was linear and did not show any sign of saturation over the entire irradiance range (up to 1400 µmol photons m −2 s −1 ). This was likely due to the efficient use of light by the large photosyn- thetic surface area of the seagrass canopy, an effect which can only be examined by in situ mea- surements that integrate across all autotrophs in the seagrass ecosystem.
Structural basis of end-stage failure in ischemic cardiomyopathy in humans.

BACKGROUND Ischemic cardiomyopathy is characterized by myocyte loss, reactive cellular hypertrophy, and ventricular scarring. However, the relative contribution of these tissue and cellular processes to late failure remains to be determined. METHODS AND RESULTS Ten hearts were obtained from individuals undergoing cardiac transplantation as a result of chronic coronary artery disease in its terminal stage. An identical number of control hearts were collected at autopsy from patients who died from causes other than cardiovascular disease, and morphometric methodologies were applied to the analysis of the left and right ventricular myocardium. Left ventricular hypertrophy evaluated as a change in organ weight, aggregate myocyte mass, and myocyte cell volume per nucleus showed increases of 85%, 47%, and 103%, respectively. Corresponding increases in the right ventricle were 75%, 74%, and 112%. Myocyte loss, which accounted for 28% and 30% in the left and right ventricles, was responsible for the difference in the assessment of myocyte hypertrophy at the ventricular, tissue, and cellular levels. Left ventricular muscle cell hypertrophy was accomplished through a 16% and 51% increase in myocyte diameter and length, whereas right ventricular myocyte hypertrophy was the consequence of a 13% and 67% increase in these linear dimensions, respectively. Moreover, a 36% reduction in the number of myocytes included in the thickness of the left ventricular wall was found. Collagen accumulation in the form of segmental, replacement, and interstitial fibrosis comprised an average 28% and 13% of the left and right ventricular myocardia, respectively. The combination of cell loss and myocardial fibrosis, myocyte lengthening, and mural slippage of cells resulted in 4.6-fold expansion of left ventricular cavitary volume and a 56% reduction in the ventricular mass-to-chamber volume ratio. CONCLUSIONS These results are consistent with the contention that both myocyte and collagen compartments participate in the development of decompensated eccentric ventricular hypertrophy in the cardiomyopathic heart of ischemic origin.
Composite Dirac liquids: parent states for symmetric surface topological order

We introduce exotic gapless states---`composite Dirac liquids'---that can appear at a strongly interacting surface of a three-dimensional electronic topological insulator. Composite Dirac liquids exhibit a gap to all charge excitations but nevertheless feature a single massless Dirac cone built from emergent electrically neutral fermions. These states thus comprise electrical insulators that, interestingly, retain thermal properties similar to those of the non-interacting topological insulator surface. A variety of novel fully gapped phases naturally descend from composite Dirac liquids. Most remarkably, we show that gapping the neutral fermions via Cooper pairing---which crucially does not violate charge conservation---yields symmetric non-Abelian topologically ordered surface phases captured in several recent works. Other (Abelian) topological orders emerge upon alternatively gapping the neutral Dirac cone with magnetism. We establish a hierarchical relationship between these descendant phases and expose an appealing connection to paired states of composite Fermi liquids arising in the half-filled Landau level of two-dimensional electron gases. To controllably access these states we exploit a quasi-1D deformation of the original electronic Dirac cone that enables us to analytically address the fate of the strongly interacting surface. The algorithm we develop applies quite broadly and further allows the construction of symmetric surface topological orders for recently introduced bosonic topological insulators.
Empirical Study of Usage and Performance of Java Collections

Collection data structures have a major impact on the performance of applications, especially in languages such as Java, C#, or C++. This requires a developer to select an appropriate collection from a large set of possibilities, including different abstractions (e.g. list, map, set, queue), and multiple implementations. In Java, the default implementation of collections is provided by the standard Java Collection Framework (JCF). However, there exist a large variety of less known third-party collection libraries which can provide substantial performance benefits with minimal code changes. In this paper, we first study the popularity and usage patterns of collection implementations by mining a code corpus comprised of 10,986 Java projects. We use the results to evaluate and compare the performance of the six most popular alternative collection libraries in a large variety of scenarios. We found that for almost every scenario and JCF collection type there is an alternative implementation that greatly decreases memory consumption while offering comparable or even better execution time. Memory savings range from 60% to 88% thanks to reduced overhead and some operations execute 1.5x to 50x faster. We present our results as a comprehensive guideline to help developers in identifying the scenarios in which an alternative implementation can provide a substantial performance improvement. Finally, we discuss how some coding patterns result in substantial performance differences of collections.
Mechanisms of noradrenaline release in the anoxic heart of the rat.

OBJECTIVE The aim was to examine the time course of exocytotic and "spontaneous" noradrenaline overflow and the influence of an Uptake1 inhibitor, desipramine, in rat hearts subjected to anoxic and substrate-free perfusion. METHODS Hearts were perfused with a constant flow and exocytotic noradrenaline overflow was elicited either by electrical stimulation of the left stellate ganglion or by K+ depolarisation. Noradrenaline overflow was measured by HPLC. RESULTS Energy depletion for a period of 30 min resulted in an enhanced spontaneous noradrenaline overflow and a progressive decline in the nerve stimulation induced noradrenaline overflow. However, noradrenaline overflow induced by 40 mM K+ was enhanced by three- to fourfold in the energy depleted conditions. During anoxia, desipramine (0.3 microM) inhibited the spontaneous noradrenaline overflow and partly increased, in the early phase of anoxia, noradrenaline overflow by nerve stimulation, but showed no effect on K+ induced overflow. Further experiments showed that K+ at 10 mM failed to evoke noradrenaline overflow in normoxic hearts but induced a significant overflow in energy depleted hearts, either in the presence or absence of desipramine; quantities of noradrenaline overflow in response to 10-40 mM K+ were substantially higher in anoxia. This difference in noradrenaline overflow caused by K+ during normoxia and anoxia was partly narrowed by desipramine which enhanced overflow in normoxia. CONCLUSIONS "Spontaneous" and exocytotic noradrenaline release coexist within the 30 min period of anoxia but their responses to Uptake1 inhibitor differ. K(+)-induced noradrenaline overflow was markedly augmented by energy depletion due to a combination of failed neuronal reuptake and enhanced exocytosis.
The relevance of minor histocompatibility antigens in solid organ transplantation

Purpose of reviewDisparities in minor histocompatibility antigens between HLA-matched organ and hematopoietic stem cell donors and recipients create the risks of graft failure and graft-versus-host disease (GvHD) respectively. A decade ago, technical advances combined with genomic information resulted in the identification of the chemical nature of the first series of minor histocompatibility antigens, facilitating their molecular typing. A new era of research had begun in exploring the role of minor histocompatibility antigens in physiological and nonphysiological settings. Here we summarize, to the best of our knowledge, human studies on the relevance of minor histocompatibility antigens in solid organ transplantation with a main focus on renal allografting. Recent findingsThe minor histocompatibility antigen HY is associated with acute rejection, and male grafts in female recipients have reduced graft survival; both cellular and humoral responses are observed. Studies on autosomal minor histocompatibility antigens on graft rejection are less conclusive; their role in transplant tolerance, however, offers perspective. SummaryInformation on the clinical relevance of minor histocompatibility antigen allo-immune responses in solid organ allografting is still scarce. The possible implications of the minor histocompatibility allo-immune responses for future clinical practice in solid organ transplantation are discussed in relation to their possible detrimental or beneficial effects on the host.
The importance of quality of primary studies in producing unbiased systematic reviews.

BACKGROUND Traditional and largely qualitative reviews of evidence are now giving way to much more structured systematic overviews that use a quantitative method to calculate the overall effect of treatment. The latter approach is dependent on the quality of primary studies, which may introduce bias if they are of poor methodologic quality. OBJECTIVE To test the hypothesis that the inclusion of poor-quality trials in meta-analyses would bias the conclusions and produce incorrect estimates of treatment effect. METHODS An overview of randomized trials of antiestrogen therapy in subfertile men with oligospermia was performed to test the hypothesis. Data sources included online searching of MEDLINE and Science Citation Index databases between 1966 and 1994, scanning the bibliography of known primary studies and review articles, and contacting experts in the field. After independent, blind assessment, nine of 149 originally identified studies met the inclusion criteria and were selected. We assessed study quality independently. Outcome data from each study were pooled and statistically summarized. RESULTS There was a marginal improvement in pregnancy rate with antiestrogen treatment (odds ratio, 1.6; 95% confidence interval, 0.9 to 2.6). Sensitivity analyses on the basis of methodologic quality demonstrated that poor-quality studies produced a positive effect with treatment, whereas no benefit was observed with high-quality studies. CONCLUSION The results of a meta-analysis are influenced by the quality of the primary studies included. Methodologically, poor studies tend to exaggerate the overall estimate of treatment effect and may lead to incorrect inferences.
On Multiplicative Integration with Recurrent Neural Networks

We introduce a general and simple structural design called Multiplicative Integration (MI) to improve recurrent neural networks (RNNs). MI changes the way in which information from difference sources flows and is integrated in the computational building block of an RNN, while introducing almost no extra parameters. The new structure can be easily embedded into many popular RNN models, including LSTMs and GRUs. We empirically analyze its learning behaviour and conduct evaluations on several tasks using different RNN models. Our experimental results demonstrate that Multiplicative Integration can provide a substantial performance boost over many of the existing RNN models.
Mediterranean diet and weight loss: meta-analysis of randomized controlled trials.

BACKGROUND The epidemiological evidence supporting a causal link between Mediterranean diets and body weight is contrasting. We evaluated the effect of Mediterranean diets on body weight in randomized controlled trials (RCTs) using a meta-analysis. METHODS We searched English and non-English publications in PubMed, Embase, Scopus, and the Cochrane Central Register of Controlled Trials from inception to January, 2010. Two evaluators independently selected and reviewed eligible studies. Sixteen randomized controlled trials, with 19 arms and 3,436 participants (1,848 assigned to a Mediterranean diet and 1,588 assigned to a control diet) were included. RESULTS In a random-effects meta-analysis of all 19 arms, the Mediterranean diet group had a significant effect on weight [mean difference between Mediterranean diet and control diet, -1.75 kg; 95% confidence interval (CI), -2.86 to -0.64 kg] and body mass index (mean difference, -0.57 kg/m², -0.93 to -0.21 kg/m²). The effect of Mediterranean diet on body weight was greater in association with energy restriction (mean difference, -3.88 kg, -6.54 to -1.21 kg), increased physical activity (-4.01 kg, -5.79 to -2.23 kg), and follow up longer than 6 months (-2.69 kg, -3.99 to -1.38 kg). No study reported significant weight gain with a Mediterranean diet. CONCLUSIONS Mediterranean diet may be a useful tool to reduce body weight, especially when the Mediterranean diet is energy-restricted, associated with physical activity, and more than 6 months in length. Mediterranean diet does not cause weight gain, which removes the objection to its relatively high fat content. These results may be useful for helping people to lose weight.
C-Reactive Protein: Risk Marker or Mediator in Atherothrombosis?

Abstract—Inflammation appears to be pivotal in all phases of atherosclerosis from the fatty streak lesion to acute coronary syndromes. An important downstream marker of inflammation is C-reactive protein (CRP). Numerous studies have shown that CRP levels predict cardiovascular disease in apparently healthy individuals. This has resulted in a position statement recommending cutoff levels of CRP <1.0, 1.0 to 3.0, and >3.0 mg/L equating to low, average, and high risk for subsequent cardiovascular disease. More interestingly, much in vitro data have now emerged in support of a role for CRP in atherogenesis. To date, studies largely in endothelial cells, but also in monocyte-macrophages and vascular smooth muscle cells, support a role for CRP in atherogenesis. The proinflammatory, proatherogenic effects of CRP that have been documented in endothelial cells include the following: decreased nitric oxide and prostacyclin and increased endothelin-1, cell adhesion molecules, monocyte chemoattractant protein-1 and interleukin-8, and increased plasminogen activator inhibitor-1. In monocyte-macrophages, CRP induces tissue factor secretion, increases reactive oxygen species and proinflammatory cytokine release, promotes monocyte chemotaxis and adhesion, and increases oxidized low-density lipoprotein uptake. Also, CRP has been shown in vascular smooth muscle cells to increase inducible nitric oxide production, increase NFκb and mitogen-activated protein kinase activities, and, most importantly, upregulate angiotensin type-1 receptor resulting in increased reactive oxygen species and vascular smooth muscle cell proliferation. Future studies should be directed at delineating the molecular mechanisms for these important in vitro observations. Also, studies should be directed at confirming these findings in animal models and other systems as proof of concept. In conclusion, CRP is a risk marker for cardiovascular disease and, based on future studies, could emerge as a mediator in atherogenesis.
Eradication of H pylori infection in a rural population: one-day quadruple therapy versus 7-day triple therapy.

AIM To compare the one-day quadruple therapy with a standard 7-d triple therapy for H pylori eradication in a rural population of China. METHODS A total of 396 patients with (13)C-urea breath test positive for H pylori were assigned into two groups: 239 patients received one-day quadruple therapy (amoxicillin 2000 mg qid; metronidazole 500 mg qid; bismuth citrate 900 mg qid and lansoprazole 60 mg once daily) and 157 patients received 7-d standard triple therapy (amoxicillin 1000 mg bid; clarithromycin 500 mg bid and lansoprazole 30 mg bid). All the patients underwent a (13)C-UBT to assess the eradication of H pylori infection six weeks after treatment. RESULTS Two hundred and twenty-nine patients completed the one-day therapy (95.8%) and 148 patients completed the 7-d therapy (94.2%). The one-day therapy eradicated H pylori infection in 64 patients (27.95%). In contrast, 103 patients (69.59%) were H pylori negative after the 7-d therapy (P < 0.01). CONCLUSION This pilot study suggests there is no beneficial effect of the one-day therapy in treatment of H pylori infection compared with the 7-d standard therapy.