Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning Probabilistic Relational Models Using Non-Negative Matrix Factorization

Probabilistic Relational Models (PRMs) are directed probabilistic graphical models representing a factored joint distribution over a set of random variables for relational datasets. While regular PRMs define probabilistic dependencies be- tween classes’ descriptive attributes, an extension called PRM with Reference Uncertainty (PRM-RU) allows in addition to manage link uncertainty between them, by adding random variables called selectors. In order to avoid variables with large domains, selectors are associated with partition functions, mapping objects to a set of clusters, and selectors’ distributions are defined over the set of clusters. In PRM-RU, the definition of partition functions constrains us to learn them only from concerned individuals entity attributes and to assign the same cluster to a pair of individuals having the same attributes values. This constraint is actually based on a strong assumption which is not generalizable and can lead to an under usage of relationship data for learning. For these reasons, we relax this constraint in this paper and propose a different partition function learning approach based on relationship data clustering. We empirically show that this approach provides better results than attribute-based learning in the case where relationship topology is independent from involved entity attributes values, and that it gives close results whenever the attributes assumption is correct.
Abstract-recently, We Observed Zero Phase and Undershoot Patterns in Data Processed by a Minimum-variance Deconvolution (mvd) Fiiter

These observations motivated a careful analysis of the MVD fiiter, which, as we demonstrate in this paper, explains both the zero phase and under-shoot patterns. This analysis also connects the MVD fiiter with the well-known prediction-error filter [6], and Berkhout's two-sided least-squares inverse filter [7]. We show that the performance of the MVD filter depends heavily on the bandwidth of the source wavelet and signd-to-noise ratio, and only slightly on data length.
Pathway and network-based strategies to translate genetic discoveries into effective therapies

One way to design a drug is to attempt to phenocopy a genetic variant that is known to have the desired effect. In general, drugs that are supported by genetic associations progress further in the development pipeline. However, the number of associations that are candidates for development into drugs is limited because many associations are in noncoding regions or difficult to target genes. Approaches that overlay information from pathway databases or biological networks can expand the potential target list. In cases where the initial variant is not targetable or there is no variant with the desired effect, this may reveal new means to target a disease. In this review we discuss recent examples in the domain of pathway and network-based drug repositioning from genetic associations. We highlight important caveats and challenges for the field, and we discuss opportunities for further development.
Cross-Lingual Information Retrieval based on LSI with Multiple Word Spaces

In this paper, we report the utilization of a largescaled bilingual corpus in Cross-Language Latent Semantic Indexing(CL-LSI). When we construct one monolithic word space with a large-scaled corpus, we encounter problems such as the increase in ambiguity of word translation, the difficulty in singular value decomposition, which is the important process in LSI. In order to cope with the problems, we introduce the method in which the large bilingual corpus is divided into smaller sub-corpora according to the similarity among documents in it, and from each of them one word sub-space is created. By placing each document in the word sub-space, which is made from the sub-corpus most similar to the document, ambiguity of translation is expected to decrease. In the searching process, the query is placed into every word subspaces, and similarity between the query and the documents are calculated.
Decomposing combinatorial auctions and set packing problems

Combinatorial auctions allow bidders to bid on bundles of items rather than just on single items. The winner determination problem in combinatorial auctions is the problem of determining the allocation of items to bidders such that the sum of the accepted bid prices is maximized. This problem is equivalent to the well-known maximum-weight set packing problem. Even though these problems are NP-hard in general, they can be solved in polynomial time on instances whose associated item graphs have bounded treewidth (called structured item graphs). However, the tractability of determining whether for a given problem instance a structured item graph of fixed treewidth exists (and if so, computing one efficiently) was an open problem. In this article, we solve this problem by proving that deciding the existence of structured item graphs is computationally intractable, even for treewidth 3. Motivated by this unfavorable complexity result, we investigate other structural restrictions, and we show that the notion of hypertree decomposition, a well-studied measure of hypergraph cyclicity, turns out to be most useful here. Indeed, we show that the winner determination problem is solvable in polynomial time on instances whose dual auction hypergraphs have bounded hypertree width. Our solution method is based on encoding winner determination via a constraint satisfaction optimization problem and on exhibiting an algorithm to solve this latter problem efficiently for such structurally restricted instances. The class of tractable instances identified by our approach, while being efficiently recognizable, properly contains the class of instances having a structured item graph. Moreover, on the larger class, our method solves winner determination with the same asymptotic complexity as the best algorithm proposed in the literature for the subclass of structured item graphs. Hypertree decompositions can equally profitably be applied to the maximum-weight independent set problem, which is the dual problem of maximum-weight set packing.
Governing the Commons

Individuals, communities and nations in all regions of the world are experiencing the effects of climate and human induced changes in their physical and social environments. The highest and the most direct impact of these changes are seen in the case of commons (e.g., fisheries, shellfish beds, coastal spaces, lagoons, mangroves, range lands, forests, groundwater, freshwater systems, irrigation systems, urban spaces, etc.) upon which humans depend for their social, cultural and economic needs. When impacted by a variety of drivers, commons not only go through a process of change in their biophysical characteristics, but the resulting impacts linger on to the social, cultural, political and economic lives (e.g., loss of livelihoods, subsistence, institutions, disempowerment, loss of rights, cultural identity) of the commons-dependent population. In a similar sense we all, as humans, are linked to some form of commons in our daily lives we either impact the commons or get impacted by it or experience the both. Given this background, sustaining the commons remains an ongoing challenge that requires enhanced understanding and innovative governance approaches at all levels of society. The aim of this course is exactly to do this, i.e., creatively engage students in furthering their understanding and knowledge on commons and deliberate on novel governance approaches though which commons can be sustained.
A Saturated Light Correction Method for DMSP/OLS Nighttime Satellite Imagery

Several studies have clarified that electric power consumption can be estimated from the Defense Meteorological Satellite Program/Operational Linescan System (DMSP/OLS) stable light imagery. As digital numbers (DNs) of stable light images are often saturated in the center of city areas, we developed a saturated light correction method for the DMSP/OLS stable light image using the nighttime radiance calibration image of the DMSP/OLS. The comparison between the nonsaturated part of the stable light image for 1999 and the radiance calibration image for 1996-1997 in major areas of Japan showed a strong linear correlation (R2 = 92.73) between the DNs of both images. Saturated DNs of the stable light image could therefore be corrected based on the correlation equation between the two images. To evaluate the new saturated light correction method, a regression analysis is performed between statistic data of electric power consumption from lighting and the cumulative DNs of the stable light image before and after correcting for the saturation effects by the new method, in comparison to the conventional method, which is, the cubic regression equation method. The results show a stronger improvement in the determination coefficient with the new saturated light correction method (R2 = 0.91, P = 1.7 ·10-6 <; 0.05) than with the conventional method (R2 = 0.81, P = 2.6 ·10-6 <; 0.05) from the initial correlation with the uncorrected data (R2 = 0.70, P = 4.5 · 10-6 <; 0.05). The new method proves therefore to be very efficient for saturated light correction.
The effects of preconditioning on the oxidative stress in small-bowel autotransplantation.

BACKGROUND One determining factor in intestinal transplantation is the extreme sensitivity of the small bowel to ischemia-reperfusion injury. This study investigated the effect of ischemic preconditioning prior to autotransplantation. METHODS Total orthotopic intestinal autotransplantation was performed in 40 mongrel dogs. In 4 groups (GI-GIV), grafts were stored for 3 hours in cold Euro Collins (GI,GIII) and University of Wisconsin (GII,GIV) solutions. In GIII and GIV, before preservation, preconditioning was induced by 4 cycles (5-min ischemia + 10-min reperfusion). Bowel samples were collected after laparotomy (control), at the end of preservation and reperfusion periods. We determined oxidative stress markers (reduced glutathione [GSH], superoxide dismutase [SOD]), production of oxygen free radicals, activity of nuclear factor-kappaB (NF-kappaB), and DNA damage. RESULTS In the non-preconditioned groups, GSH concentration increased slightly, while SOD activity decreased significantly during reperfusion. In the preconditioned groups, GSH increased markedly, and better preservation of SOD was observed. The number of oxygen free radicals increased during reperfusion mainly in non-preconditioned groups. Activation of NF-kappaB peaked by 1 hour, and decreased 3 hours after preconditioning. We observed DNA-damaged cells in all groups. CONCLUSIONS Our findings confirm that preconditioning prior to preservation can moderate the severity of oxidative stress and activate the endogenous cellular adaptation in bowel tissue.
Edinburgh Research Explorer Intelligence and personality as predictors of illness and death: How researchers in differential psychology and chronic disease epidemiology are collaborating to understand and address health inequalities

We describe the research findings that link intelligence and personality traits with health outcomes: health behaviors, morbidity, and mortality. The former field is called cognitive epidemiology, and the latter is known as personological epidemiology. However, intelligence and personality traits are the principal research topics studied by differential psychologists, and so the combined field might be termed differential epidemiology. The importance of bringing this field to wider attention lies in the facts that: the findings overviewed here are relatively new, often known neither to researchers or practitioners; the effect sizes are on a par with better-known, traditional risk factors for illness and death, so they should be broadcast as important; mechanisms of the associations are largely unknown, so they must be explored further; and the findings have yet to be applied, so we write this to encourage diverse interested parties to consider how this might be done.
Obesity did not diminish the efficacy of percutaneous ablation for hepatocellular carcinoma

Background: Overweight and hepatic steatosis can increase the risk of hepatocarcinogenesis. In addition, overweight may affect the treatment efficacy of ultrasound‐guided percutaneous ablation. We evaluated the impact of overweight on the safety and efficacy of percutaneous ablation to hepatocellular carcinoma (HCC).
FATORES DE RISCO E PROTEÇÃO ASSOCIADOS AO DECLÍNIO COGNITIVO NO ENVELHECIMENTO - REVISÃO SISTEMÁTICA DE LITERATURA Risk and protective factors associated with cognitive decline in aging - a systematic review of literature

RESUMO Objetivo: Realizar uma revisao bibliografica sistematica nas bases de dados SciELO e PubMed sobre as alteracoes cognitivas e linguisticas associadas ao processo de envelhecimento, focalizando fatores de risco e protecao. Metodos: Foram pesquisados artigos em ingles, portugues e espanhol, publicados entre 2002 e 2008, realizados com pessoas de 60 anos ou mais. Resultados: Foram revisados 72 trabalhos de 38 periodicos diferentes, 7 (9,7%) nacionais e 65 (90,3%) internacionais, sendo 10 (26,3%) da area de Neurologia; 9 (23,7%) de Geriatria e Envelhecimento; 5 (13,2%) de Epidemiologia e Saude Coletiva; 4 (10,5%) de Psiquiatria; e o restante de revistas de diferentes temas em saude. O delineamento longitudinal foi utilizado em 37 (51,3%) e o transversal, em 26 (36,1%). Quanto aos instrumentos de coleta de dados, 35 (48,6%) trabalhos utilizaram o Miniexame do Estado Mental; 11 (15,1%) usaram testes de Fluencia Verbal; 9 (12,5%) usaram a Escala de Inteligencia Wechsler para Adulto; 7 (9,7%) usaram o Teste de Nomeacao de Boston; e 10 (13,8%) utilizaram a Escala de Depressao Geriatrica. Foram identificadas relacoes entre a cognicao no envelhecimento e fatores biologicos em 50 (69,4%) trabalhos. Estudos apontaram maior probabilidade de deficit cognitivo entre idosos com sintomas depressivos e entre tabagistas, outros mostraram um efeito positivo da escolaridade e da participacao em atividades fisicas e sociais sobre a cognicao. Conclusao: Os estudos analisados investigaram especialmente a relacao entre fatores de risco biologicos e declinio cognitivo. Pouca atencao foi dada as alteracoes linguisticas e aos fatores de protecao associados ao envelhecimento. Descritores: Envelhecimento; Fatores de Risco; Idoso; Cognicao, Linguagem.
The Enigmatic Origin of Bovine mtDNA Haplogroup R: Sporadic Interbreeding or an Independent Event of Bos primigenius Domestication in Italy?

Background When domestic taurine cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of cattle domestication occurred. Methodology The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. These mtDNAs were then integrated in a phylogenetic tree encompassing all available P, Q and R complete mtDNA sequences. Conclusions Phylogenetic analyses of 28 mitochondrial genomes belonging to haplogroups P (N = 2), Q (N = 16) and R (N = 10) together with an extensive survey of all previously published mtDNA datasets revealed major similarities between haplogroups Q and T. Therefore, Q most likely represents an additional minor lineage domesticated in the Near East together with the founders of the T subhaplogroups. Whereas, haplogroup R is found, at least for the moment, only in Italy and nowhere else, either in modern or ancient samples, thus supporting an origin from European aurochsen. Haplogroup R could have been acquired through sporadic interbreeding of wild and domestic animals, but our data do not rule out the possibility of a local and secondary event of B. primigenius domestication in Italy.
Design and analysis of a model-based Covert Timing Channel for Skype traffic

In a model-based Covert Timing Channel (CTC), the (covert) sender modulates the inter-packet delays (IPDs) of the packet stream generated by the overt application (source) by following a well-known statistical model of the application traffic. Implementing a CTC system that operates on real application traffic such as Skype requires addressing several challenges. First, packets generated by Skype must meet a maximum end-to-end delay requirement which imposes limits on how long a packet can be buffered by the sender. Second, buffer overrun and underrun may occur due to transient mis-matches between the rate at which packets are generated by the source and the rate at which the sender can service the covert buffer. As a single IPD of Skype traffic is small and has a small delay spread, we propose to use delay of multiple IPDs (m-IPDs) to modulate the encoded symbols. To minimize buffer overruns and underruns, we partition the delay of m-IPDs so that each encoded symbol can be mapped to multiple partitions of the delay distribution. We then provide a mathematical model to choose the appropriate partition for a given encoded symbol based on the state of the buffer. We evaluate the performance of an users-space implementation of the CTC system in real network settings for Skype traffic. We show that the covert channel based on the proposed design can be established even when the source is connected to a public WiFi network and it is largely non-detectable under well-known statistical tests including the entropy test, the Kolmogorov-Smirnov test, and the Kullback-Leibler divergence test.
AN IMPROVED GENETIC ALGORITHM FOR RECTANGLES CUTTING & PACKING PROBLEM

After reviewing the background and description of cutting & packing problem and packing algorithms, this paper proposed an improved genetic algorithm for non-guillotine rectangles packing problem. First, self-adaptive mutation probability is adopted to avoid pre-maturity, some commonly used crossover operators are compared, and a stochastic hill-climbing operator is designed to improve the local searching ability. Second, the greedy mechanism is introduced to acquire good packing pattern after packing order is determined by the GA. Computational results show the effectiveness of these improvements. Copyright © 2002 IFAC
Air Pollution and Inflammation (Interleukin-6, C-Reactive Protein, Fibrinogen) in Myocardial Infarction Survivors

Background Numerous studies have found that ambient air pollution has been associated with cardiovascular disease exacerbation. Objectives Given previous findings, we hypothesized that particulate air pollution might induce systemic inflammation in myocardial infarction (MI) survivors, contributing to an increased vulnerability to elevated concentrations of ambient particles. Methods A prospective longitudinal study of 1,003 MI survivors was performed in six European cities between May 2003 and July 2004. We compared repeated measurements of interleukin 6 (IL-6), fibrinogen, and C-reactive protein (CRP) with concurrent levels of air pollution. We collected hourly data on particle number concentrations (PNC), mass concentrations of particulate matter (PM) < 10 μm (PM10) and < 2.5 μm (PM2.5), gaseous pollutants, and meteorologic data at central monitoring sites in each city. City-specific confounder models were built for each blood marker separately, adjusting for meteorology and time-varying and time-invariant covariates. Data were analyzed with mixed-effects models. Results Pooled results show an increase in IL-6 when concentrations of PNC were elevated 12–17 hr before blood withdrawal [percent change of geometric mean, 2.7; 95% confidence interval (CI), 1.0–4.6]. Five day cumulative exposure to PM10 was associated with increased fibrinogen concentrations (percent change of arithmetic mean, 0.6; 95% CI, 0.1–1.1). Results remained stable for smokers, diabetics, and patients with heart failure. No consistent associations were found for CRP. Conclusions Results indicate an immediate response to PNC on the IL-6 level, possibly leading to the production of acute-phase proteins, as seen in increased fibrinogen levels. This might provide a link between air pollution and adverse cardiac events.
HIV type 1 superinfection with a dual-tropic virus and rapid progression to AIDS: a case report.

BACKGROUND The occurrence of human immunodeficiency virus type 1 (HIV-1) superinfection has implications for vaccine development and our understanding of HIV pathogenesis and transmission. METHODS AND RESULTS We describe a subject from the Multicenter AIDS Cohort Study who was superinfected with a dual-tropic (CXCR4/CCR5-utilizing) HIV-1 subtype B strain between 0.8 and 1.3 years after seroconversion who had rapid progression to AIDS; the subject developed Pneumocystis pneumonia 3.4 years after seroconversion, as well as multiple other opportunistic infections. The superinfecting strain rapidly became the predominant population virus, suggesting that the initial and superinfecting viruses in this individual differed in virulence. However, we found no molecular epidemiological evidence in the HIV database to suggest that this strain had been found in other individuals. In addition, this subject's HIV-1 viral load and pattern of human leukocyte antigen and coreceptor polymorphisms only partially explained his rapid disease progression. CONCLUSIONS Additional studies are needed to determine whether superinfection itself and/or infection with a dual-tropic virus causes rapid disease progression, or whether certain individuals who are innately more susceptible to rapid disease progression also lack the ability to resist the challenge of a second infection. This case appears to support the latter hypothesis.
Fiber Type-Specific Effects of Dietary Nitrate

Dietary nitrate supplementation increases circulating nitrite concentration, and the subsequent reduction of nitrite to nitric oxide is promoted in hypoxic environments. Given that PO2 is lower in Type II compared with Type I muscle, this article examines the hypothesis that the ergogenicity of nitrate supplementation is linked to specific effects on vascular, metabolic, and contractile function in Type II muscle.
Complete Genome Sequences of Two Escherichia coli O157:H7 Phages Effective in Limiting Contamination of Food Products

ABSTRACT We previously demonstrated that application of bacteriophages significantly reduced Escherichia coli O157:H7 contamination in spinach and ground beef. Here, we present the genomic sequences of two bacteriophages, vB_EcoS_FFH_1, a T5-like phage, and vB_EcoM_FFH_2, an rV5-like phage, used in those treatments.