Miracle-dz/UniFAR-FTUs huggingface dataset:
LplR, a Repressor Belonging to the TetR Family, Regulates Expression of the l-Pantoyl Lactone Dehydrogenase Gene in Rhodococcus erythropolis

ABSTRACT The l-pantoyl lactone (l-PL) dehydrogenase (LPLDH) gene (lpldh) has been cloned from Rhodococcus erythropolis AKU2103, and addition of 1,2-propanediol (1,2-PD) was shown to be required for lpldh expression in this strain. In this study, based on an exploration of the nucleotide sequence around lpldh, a TetR-like regulator gene, which we designated lplR, was found upstream of lpldh, and three putative open reading frames existed between the two genes. Disruption of lplR led to 22.8 times higher lpldh expression, even without 1,2-PD induction, than that in wild-type R. erythropolis AKU2103 without 1,2-PD addition. Introduction of a multicopy vector carrying lplR (multi-lplR) into the wild-type and ΔlplR strains led to no detectable LPLDH activity even in the presence of 1,2-PD. The results of an electrophoretic mobility shift assay revealed that purified LplR bound to a 6-bp inverted-repeat sequence located in the promoter/operator region of the operon containing lpldh. These results indicated that LplR is a negative regulator in lpldh expression. Based on the clarification of the expression mechanism of lpldh, recombinant cells showing high LPLDH activity were constructed and used as a catalyst for the conversion of l-PL to ketopantoyl lactone. Finally, a promising production process of d-PL from dl-PL was constructed.
A Topographical Atlas of Shiga Toxin 2e Receptor Distribution in the Tissues of Weaned Piglets

Shiga toxin (Stx) 2e of Stx-producing Escherichia coli (STEC) is the primary virulence factor in the development of pig edema disease shortly after weaning. Stx2e binds to the globo-series glycosphingolipids (GSLs) globotriaosylceramide (Gb3Cer, Galα1-4Galβ1-4Glcβ1-1Cer) and globotetraosylceramide (Gb4Cer, GalNAcβ1-3Galα1-4Galβ1-4Glcβ1-1Cer), the latter acting as the preferential Stx2e receptor. We determined Stx receptor profiles of 25 different tissues of a male and a female weaned piglet using immunochemical solid phase binding assays combined with mass spectrometry. All probed tissues harbored GSL receptors, ranging from high (category I) over moderate (category II) to low content (category III). Examples of Gb4Cer expression in category I tissues are small intestinal ileum, kidney pelvis and whole blood, followed by colon, small intestinal duodenum and jejunum belonging to category II, and kidney cortex, cerebrum and cerebellum as members of category III organs holding true for both genders. Dominant Gb3Cer and Gb4Cer lipoforms were those with ceramides carrying constant sphingosine (d18:1) and a variable C16:0, C22:0 or C24:1/C24:0 fatty acid. From the mapping data, we created a topographical atlas for Stx2e receptors in piglet tissues and organs, which might be helpful to further investigations on the molecular and cellular mechanisms that underlie infections of Stx2e-producing STEC in pigs and their zoonotic potential for humans.
Impaired emotional processing in a patient with a left posterior insula-SII lesion

The present case-report investigated the influence of a lesion in the left posterior insula-SII cortices on the processing of emotions. MB and 16 normal controls explicitly rated the valence and the intensity of both facial expressions and emotional words. In addition, they had to perform a number comparison task and a lexical decision task without focusing their attention on emotional components of stimuli. MB identified the valence of emotional words as well as the control group. Nevertheless, she provided higher intensity scores for disgusted words and her responses in the lexical decision task were significantly delayed for these stimuli. In addition, MB’s response times were not differently influenced by the presence of irrelevant emotional faces. However, she explicitly identified fewer facial expressions of disgust and she assessed them as significantly less intense. This pattern of results contributes to highlight the psychological and behavioral disorders observed after a left posterior insular stroke.
Deep community detection based on memetic algorithm

Deep community can be detected by removing noise nodes or edges from a network. A centrality measure, named local Fiedler vector centrality is proposed for deep community detection. Algorithms to optimize local Fiedler vector centrality are either with high computation complexity or difficult to find the optimal solution of local Fiedler vector centrality. In this paper, a novel memetic algorithm is proposed to maximize local Fiedler vector centrality for deep community detection. Experiments of our proposed memetic algorithm on four real world networks demonstrate that our algorithm can find optimal solution of local Fiedler vector centrality and is effective to discover deep communities.
Exploiting ad space of long tail queries through concept-based bidding in sponsored search

Sponsored search is one of the most dominant modes of online advertising on the web. In sponsored search, advertisers bid on relevant keywords to advertise their product. For an incoming search query, advertisements from the ad campaigns containing the query keywords are shown along with the search results. If multiple advertisers demand to be shown on the same query’s results page, they are ranked for the allocation of ad space. The ranking is determined by multiple factors including the bid amount of the advertiser on the query keywords, relevance of ad content to the search query, Click-Through-Rate (CTR) and budget of the advertiser. The ecosystem of sponsored search has three main stakeholders search engine, advertisers and users. Search engines aim to maximize the revenue by showing ads. Advertisers want to maximize the reach of their service or increase the sales. Users see advertisements on the search results page. Some of the key research challenges in sponsored search are query-ad relevance, click-through-rate prediction, optimal auction design, optimum utilization of ad space of rare (tail) queries and click-fraud detection. In this thesis, related to sponsored search, we have investigated approaches to exploit the ad space of tail queries. It is well established that search queries tend to follow a heavy-tailed Zipf distribution wherein a large fraction of queries occur too infrequently. Such infrequent query set is called long tail. Advertising on long tail queries is challenging as long tail queries are encountered rarely which makes them hard to interpret for sponsored search. Also, it has been observed that during keyword auctions, advertisers tend to bid for the head keywords to reach more users. This creates a high demand for the head query keywords and little or no demand for the tail query keywords. The long tail phenomenon also makes it quite difficult for an advertiser to capture the relevant keywords from the long tail. The above stated factors result in under-utilization of a significant amount of the ad space provided by tail queries in sponsored search which is identified as the research issue. We propose two approaches for the utilization of ad space of tail queries by proposing that instead of bidding on keywords, advertisers should bid upon high level concepts. In the first approach, we propose bidding on concepts by organizing concepts into a two level taxonomy. In the second approach, we propose a generalized approach by considering organization of concepts into a multi-level taxonomy. In the first approach, we have proposed an improved framework to cover more advertisers by exploiting the notions of coverage and concept taxonomy based on the log data of search queries. The proposed framework allows to form the distinct groups of keywords such that each group of keywords could be allocated to meet the demands of the advertiser. We model each search session as a transaction
Aortic Stiffness in Prediabetic Adults: Relationship to Insulin Resistance

Background A decrease in the compliance of the arterial system, termed arterial stiffness, results in increased cardiac workload. Several studies have shown that arterial stiffness is increased in individuals with type 2 diabetes. Also, insulin resistance is generally considered to be of major importance in the pathophysiology of type 2 diabetes mellitus given that glucose intolerance and insulin resistance precede the development of overt diabetes, these factors would be associated with arterial stiffness. This study was to evaluate the state of aortic elasticity in prediabetic adults in relation to insulin resistance. Methods A case-control study was performed. A total of 113 consecutive adults with prediabetes were enrolled for the study, 32 adults had insulin resistance (group A) and 81 had insulin sensitive (group B). Forty-five healthy (with normal fasting glucose) adults matched for age and gender were considered as control. All were subjected to full medical history and clinical examination including blood pressure and body mass index. Biochemical studies including lipids profile, fasting glucose and homeostasis model assessment of insulin resistance (HOMA IR) test. Echocardiographic studies were done for assessment of the aortic stiffness index. Results Significant increase in mean aortic stiffness index was seen in group A than group B. Stiffness was correlated with insulin resistance and the correlation appeared to be independent of glucose tolerance status and obesity. Similar correlations were observed with age, triglycerides and waist circumference. Conclusions Prediabetic subjects have an aortic stiffness which represent pattern of cardiovascular risk factors. These changes are predominantly observed in prediabetic subjects with increased HOMA IR and visceral obesity independent of glucose levels. Keywords Prediabetes; Insulin resistance; Aortic stiffness index
Amorphous Silica Particles Relevant in Food Industry Influence Cellular Growth and Associated Signaling Pathways in Human Gastric Carcinoma Cells

Nanostructured silica particles are commonly used in biomedical and biotechnical fields, as well as, in cosmetics and food industry. Thus, their environmental and health impacts are of great interest and effects after oral uptake are only rarely investigated. In the present study, the toxicological effects of commercially available nano-scaled silica with a nominal primary diameter of 12 nm were investigated on the human gastric carcinoma cell line GXF251L. Besides the analysis of cytotoxic and proliferative effects and the comparison with effects of particles with a nominal primary diameter of 200 nm, emphasis was also given to their influence on the cellular epidermal growth factor receptor (EGFR) and mitogen-activated protein kinases (MAPK) signaling pathways—both of them deeply involved in the regulation of cellular processes like cell cycle progression, differentiation or proliferation. The investigated silica nanoparticles (NPs) were found to stimulate cell proliferation as measured by microscopy and the sulforhodamine B assay. In accordance, the nuclear level of the proliferation marker Ki-67 was enhanced in a concentration-dependent manner. At high particle concentrations also necrosis was induced. Finally, silica NPs affected the EGFR and MAPK pathways at various levels dependent on concentration and time. However, classical activation of the EGFR, to be reflected by enhanced levels of phosphorylation, could be excluded as major trigger of the proliferative stimulus. After 45 min of incubation the level of phosphorylated EGFR did not increase, whereas enhanced levels of total EGFR protein were observed. These results indicate interference with the complex homeostasis of the EGFR protein, whereby up to 24 h no impact on the transcription level was detected. In addition, downstream on the level of the MAP kinases ERK1/2 short term incubation appeared to affect total protein levels without clear increase in phosphorylation. Depending on the concentration range, enhanced levels of ERK1/2 phosphorylation were only observed after 24 h of incubation. Taken together, the present study demonstrates the potential of the tested silica particles to enhance the growth of gastric carcinoma cells. Although interference with the EGFR/MAPK cascade is observed, additional mechanisms are likely to be involved in the onset of the proliferative stimulus.
Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock*

Objective:To determine the prevalence and impact on mortality of delays in initiation of effective antimicrobial therapy from initial onset of recurrent/persistent hypotension of septic shock. Design:A retrospective cohort study performed between July 1989 and June 2004. Setting:Fourteen intensive care units (four medical, four surgical, six mixed medical/surgical) and ten hospitals (four academic, six community) in Canada and the United States. Patients:Medical records of 2,731 adult patients with septic shock. Interventions:None. Measurements and Main Results:The main outcome measure was survival to hospital discharge. Among the 2,154 septic shock patients (78.9% total) who received effective antimicrobial therapy only after the onset of recurrent or persistent hypotension, a strong relationship between the delay in effective antimicrobial initiation and in-hospital mortality was noted (adjusted odds ratio 1.119 [per hour delay], 95% confidence interval 1.103–1.136, p < .0001). Administration of an antimicrobial effective for isolated or suspected pathogens within the first hour of documented hypotension was associated with a survival rate of 79.9%. Each hour of delay in antimicrobial administration over the ensuing 6 hrs was associated with an average decrease in survival of 7.6%. By the second hour after onset of persistent/recurrent hypotension, in-hospital mortality rate was significantly increased relative to receiving therapy within the first hour (odds ratio 1.67; 95% confidence interval, 1.12–2.48). In multivariate analysis (including Acute Physiology and Chronic Health Evaluation II score and therapeutic variables), time to initiation of effective antimicrobial therapy was the single strongest predictor of outcome. Median time to effective antimicrobial therapy was 6 hrs (25–75th percentile, 2.0–15.0 hrs). Conclusions:Effective antimicrobial administration within the first hour of documented hypotension was associated with increased survival to hospital discharge in adult patients with septic shock. Despite a progressive increase in mortality rate with increasing delays, only 50% of septic shock patients received effective antimicrobial therapy within 6 hrs of documented hypotension.
Bounds for Maximum Likelihood Regular and Non-Regular DoA Estimation in $K$-Distributed Noise

We consider the problem of estimating the direction of arrival of a signal embedded in K-distributed noise, when secondary data which contains noise only are assumed to be available. Based upon a recent formula of the Fisher information matrix (FIM) for complex elliptically distributed data, we provide a simple expression of the FIM with the two data sets framework. In the specific case of K-distributed noise, we show that, under certain conditions, the FIM for the deterministic part of the model can be unbounded, while the FIM for the covariance part of the model is always bounded. In the general case of elliptical distributions, we provide a sufficient condition for unboundedness of the FIM. Accurate approximations of the FIM for K-distributed noise are also derived when it is bounded. Additionally, the maximum likelihood estimator of the signal DoA and an approximated version are derived, assuming known covariance matrix: the latter is then estimated from secondary data using a conventional regularization technique. When the FIM is unbounded, an analysis of the estimators reveals a rate of convergence much faster than the usual T-1. Simulations illustrate the different behaviors of the estimators, depending on the FIM being bounded or not.
Emergent Design and learning environments: Building on indigenous knowledge

The empirical basis of this paper is a two-year project to bring new learning environments and methodologies to rural Thailand. Pilot projects were mounted outside of the education system, with the specific purpose of breaking "educational mind-sets" that have been identified as blocks to educational reform. A salient example of such a mind-set is the assumption that the population and teachers of rural areas lack the cognitive foundations for modern technological education. The work required a flexible approach to the design of digitally based educational interventions. Analysis of design issues led to a theoretical framework, Emergent Design, for investigating how choice of design methodology contributes to the success or failure of education reforms. A practice of "applied epistemological anthropology," which consists of probing for skills and knowledge resident in a community and using these as bridges to new content, was developed. Analysis of learning behaviors led to the identification of an "engine culture" in rural Thailand as an unrecognized source of "latent learning potential. " This discovery has begun to spawn a theoretical inquiry with significant promise for assessment of the learning potential of developing countries.
An Approach : Constructing the Grammar from Security Pattern

Security requirement is one of essential requirements for the currently information system. Since, the system without security is risk to attack or fail. Consequently, stakeholders and developers must concern with security requirements. However, the security requirement is rather difficult to define correctly and completely because it requires experience and knowledge from stakeholders and developers with security background. In order to avoid the miss-configuration of system from requirements that gather from stakeholders. One of alternative solutions is security patterns which are guidance that include security requirements of a common security system. We propose an approach to construct a grammar in an extended-BNF form which helps to create security requirements of a system. A prototyping tool based on our proposed grammar is also presented.
Swirling Combustor Energy Converter: H2/Air Simulations of Separated Chambers

This work reports results related to the “EU-FP7-HRC-Power” project aiming at developing micro-meso hybrid sources of power. One of the goals of the project is to achieve surface temperatures up to more than 1000 K, with a ∆ T ≤ 100 K, in order to be compatible with a thermal/electrical conversion by thermo-photovoltaic cells. The authors investigate how to reach that goal adopting swirling chambers integrated in a thermally-conductive and emitting element. The converter consists of a small parallelepiped brick inside two separated swirling meso-combustion chambers, which heat up the parallelepiped, emitting material by the combustion of H 2 and air at ambient pressure. The overall dimension is of the order of cm. Nine combustion simulations have been carried out assuming detailed chemistry, several length/diameter ratios ( Z / D = 3, 5 and 11) and equivalence ratios (0.4, 0.7 and 1); all are at 400 W of injected chemical power. Among the most important results are the converter surfaces temperatures, the heat loads, provided to the environment, and the chemical efficiency. The high chemical efficiency, h > 99.9%, is due to the relatively long average gas residence time coupled with the fairly good mixing due to the swirl motion and the impinging air/fuel jets that provide heat and radicals to the flame.
Diffusion-limited kinetics of the solution–solid phase transition of molecular substances

For critical tests of whether diffusion-limited kinetics is an option for the solution–solid phase transition of molecular substances or whether they are determined exclusively by a transition state, we performed crystallization experiments with ferritin and apoferritin, a unique pair of proteins with identical shells but different molecular masses. We find that the kinetic coefficient for crystallization is identical (accuracy ≤7%) for the pair, indicating diffusion-limited kinetics of crystallization. Data on the kinetics of this phase transition in systems ranging from small-molecule ionic to protein and viri suggest that the kinetics of solution-phase transitions for broad classes of small-molecule and protein materials are diffusion-limited.
Scheduling Multilayer Divisible Computations

We analyze scheduling multilayer divisible computations. Multilayer computations consist of a chain of parallel applications, such that one application produces input for the next one. A simple form of multilayer computations are MapReduce parallel applications. The operations of mapping and reducing are two divisible applications with precedence constraints. We propose a divisible load model and give an algorithm for scheduling multilayer divisible computations. The algorithm is tested in a series of computational experiments. We draw conclusions on schedule patterns and determinants of the performance.
Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes

Many Saccharomyces cerevisiae duplicate genes that were derived from an ancient whole-genome duplication (WGD) unexpectedly show a small synonymous divergence (KS), a higher sequence similarity to each other than to orthologues in Saccharomyces bayanus, or slow evolution compared with the orthologue in Kluyveromyces waltii, a non-WGD species. This decelerated evolution was attributed to gene conversion between duplicates. Using ≈300 WGD gene pairs in four species and their orthologues in non-WGD species, we show that codon-usage bias and protein-sequence conservation are two important causes for decelerated evolution of duplicate genes, whereas gene conversion is effective only in the presence of strong codon-usage bias or protein-sequence conservation. Furthermore, we find that change in mutation pattern or in tDNA copy number changed codon-usage bias and increased the KS distance between K. waltii and S. cerevisiae. Intriguingly, some proteins showed fast evolution before the radiation of WGD species but little or no sequence divergence between orthologues and paralogues thereafter, indicating that functional conservation after the radiation may also be responsible for decelerated evolution in duplicates.
Synthesis from Recursive-Components Libraries

Synthesis is the automatic construction of a system from its specification. In classical synthesis algorithms it is always assumed that the system is "constructed from scratch" rather than composed from reusable components. This, of course, rarely happens in real life. In real life, almost every non-trivial commercial software system relies heavily on using libraries of reusable components. Furthermore, other contexts, such as web-service orchestration, can be modeled as synthesis of a system from a library of components. In 2009 we introduced LTL synthesis from libraries of reusable components. Here, we extend the work and study synthesis from component libraries with "call and return"' control flow structure. Such control-flow structure is very common in software systems. We define the problem of Nested-Words Temporal Logic (NWTL) synthesis from recursive component libraries, where NWTL is a specification formalism, richer than LTL, that is suitable for "call and return" computations. We solve the problem, providing a synthesis algorithm, and show the problem is 2EXPTIME-complete, as standard synthesis.