Miracle-dz/UniFAR-FTUs huggingface dataset:
The Generalised Colouring Numbers on Classes of Bounded Expansion

The generalised colouring numbers $\mathrm{adm}_r(G)$, $\mathrm{col}_r(G)$, and $\mathrm{wcol}_r(G)$ were introduced by Kierstead and Yang as generalisations of the usual colouring number, also known as the degeneracy of a graph, and have since then found important applications in the theory of bounded expansion and nowhere dense classes of graphs, introduced by Nesetřil and Ossona de Mendez. In this paper, we study the relation of the colouring numbers with two other measures that characterise nowhere dense classes of graphs, namely with uniform quasi-wideness, studied first by Dawar et al. in the context of preservation theorems for first-order logic, and with the splitter game, introduced by Grohe et al. We show that every graph excluding a fixed topological minor admits a universal order, that is, one order witnessing that the colouring numbers are small for every value of $r$. Finally, we use our construction of such orders to give a new proof of a result of Eickmeyer and Kawarabayashi, showing that the model-checking problem for successor-invariant first-order formulas is fixed-parameter tractable on classes of graphs with excluded topological minors.
Helicobacter pylori HopH (OipA) and bacterial pathogenicity: genetic and functional genomic analysis of hopH gene polymorphisms.

BACKGROUND Expression of the Helicobacter pylori outer membrane protein HopH is regulated by phase variation within a CT dinucleotide repeat motif of the hopH gene. METHODS To investigate the importance of HopH for bacterial pathogenicity, we performed a detailed functional genomic and population-based genetic characterization of this contingency locus. RESULTS Sequencing of hopH in H. pylori strains from 58 patients revealed that the hopH "on" genotype is linked to bacterial virulence determinants, such as the vacAs1, vacAm1, babA2, and, most strongly, cagA genotypes. hopH mutagenesis resulted in reduced bacterial adherence to gastric epithelia in vitro. Complementation of hopH in trans restored the adherence properties of hopH mutants. Although HopH has been previously linked to proinflammatory epithelial signaling, hopH mutagenesis did not alter epithelial interleukin-8 secretion in vitro. Comparative epithelial gene-expression profiling by cDNA microarrays revealed no significant differences between the wild-type-specific and hopH mutant-specific transcriptomes. By contrast, a large set of genes was differentially regulated in a cag pathogenicity island-dependent manner. CONCLUSION An in-frame hopH gene may be linked to gastroduodenal diseases because of its association with other virulence factors or increased bacterial adherence and colonization. The strong linkage with cagA indicates that HopH may contribute to the fitness of cagA-positive strains in vivo.
Moments of zeta and correlations of divisor-sums: I

We examine the calculation of the second and fourth moments and shifted moments of the Riemann zeta-function on the critical line using long Dirichlet polynomials and divisor correlations. Previously, this approach has proved unsuccessful in computing moments beyond the eighth, even heuristically. A careful analysis of the second and fourth moments illustrates the nature of the problem and enables us to identify the terms that are missed in the standard application of these methods.
Influence of Type and Level of Water-Soluble Additives on Drug Release and Surface and Mechanical Properties of Surelease® Films

Ethylcellulose in combination with water-soluble additives has been used in the development of microporous membrane-coated dosage forms. In the present study, application of three types of water-soluble additives, namely polyethylene glycols (PEG 400, 3350, and 8000), maltodextrins (Maltrin M150, M100, and M040 in the order of lower to higher average polymer size and molecular weight; dextrose equivalence 16.9, 11.1, and 4.8, respectively), and xylitol, as porosity modifiers in the films of a commercially available aqueous ethylcellulose dispersion (Surelease/E-7-7060 plasticized with glyceryl tricaprylate/caprate) was investigated. The effect of type and level of these additives on drug release characteristics and surface and mechanical properties of the polymeric films was studied. Each additive was incorporated at 20 and 30% levels in the polymeric dispersion based on its solids content. Ibuprofen tablets were coated using the polymeric dispersion with and without additive at 3% w/w coat level in a fluid-bed equipment. The coated tablets were evaluated for their drug release rate, coat reflectivity (gloss), Brinell hardness, and elastic modulus. Differential scanning calorimetric analysis of the films was performed to determine the physico-chemical changes in the applied film-coats. The rate of drug release, hence film porosity, was observed to be dependent on the type and level of the additive added. The molecular weight of the additive and its concentration in the polymeric dispersion had significant influence on the rate of drug release, hardness, and elasticity of the film-coats.
Fibroblast migration is mediated by CD44-dependent TGFβ activation

CD44 contributes to inflammation and fibrosis in response to injury. As fibroblast recruitment is critical to wound healing, we compared cytoskeletal architecture and migration of wild-type (CD44WT) and CD44-deficient (CD44KO) fibroblasts. CD44KO fibroblasts exhibited fewer stress fibers and focal adhesion complexes, and their migration was characterized by increased velocity but loss of directionality, compared with CD44WT fibroblasts. Mechanistically, we demonstrate that CD44WT cells generated more active TGFβ than CD44KO cells and that CD44 promotes the activation of TGFβ via an MMP-dependent mechanism. Reconstitution of CD44 expression completely rescued the phenotype of CD44KO cells whereas exposure of CD44KO cells to exogenous active TGFβ rescued the defect in stress fibers and migrational velocity, but was not sufficient to restore directionality of migration. These results resolve the TGFβ-mediated and TGFβ-independent effects of CD44 on fibroblast migration and suggest that CD44 may be critical for the recruitment of fibroblasts to sites of injury and the function of fibroblasts in tissue remodeling and fibrosis.
Amlodipine attenuates oxidative stress in the heart and blood of high-cholesterol diet rabbits

Introduction Oxidative stress is a key component of atherosclerosis. It has been suggested that amlodipine inhibits oxidative stress. In this study, we evaluated the effects of amlodipine on the total antioxidant capacity of heart tissue and blood in 36 control and cholesterol-fed male New Zealand white rabbits. Methods The rabbits were divided into four groups (n = 9). Group 1 rabbits were fed a regular diet, group 2 were fed a diet with 2% cholesterol, group 3 were fed a regular diet plus 5 mg/kg/day oral amlodipine, and group 4 were fed 2% cholesterol diet plus amlodipine 5 mg/kg/day. At the end of eight weeks, blood samples were drawn and at the same time heart tissue was isolated and frozen in liquid nitrogen. After homogenisation, the solution was centrifuged and the light supernatant was stored at –80˚C. This was used for determination of glutathione peroxidase (GPX), superoxide dismutase (SOD) and (MDA) levels. Results Eight weeks of amlodipine treatment significantly reduced the levels of total cholesterol, low-density lipoprotein cholesterol and triglycerides in the group on the hypercholesterolaemic diet (p < 0.05). In the blood, the level of thiobarbituric acid-reactive substances increased in the rabbits on the 2% cholesterol diet (group 2) and 2% cholesterol-plusamlodipine diet (group 4) and decreased in the amlodipineonly group (group 3) (p < 0.05). Lipid peroxidation in the heart tissue was similar to that in the blood, except in the amlodipine-only group (group 3). In the blood, the activity of total SOD (tSOD) decreased in the group on the 2% cholesterol diet (group 2) (p < 0.05) and markedly increased in the amlodipine-only (group 3) and 2% cholesterol-plusamlodipine groups (group 4) (p < 0.05). Conclusion Amlodipine decreased oxidative stress in the heart and blood and improved the lipid profile in cholesterolfed rabbits. Therefore, it may be considered a useful tool for the reduction of oxidative stress and improvement of lipid profiles in diseases related to atherosclerosis.
Trust-Based Requirements Traceability

Information retrieval (IR) approaches have proven useful in recovering traceability links between free-text documentation and source code. IR-based traceability recovery approaches produce ranked lists of traceability links between pieces of documentation and source code. These traceability links are then pruned using various strategies and, finally, validated by human experts. In this paper we propose two contributions to improve the precision and recall of traceability links and, thus, reduces the required human experts' manual validation effort. First, we propose a novel approach, Trust race, inspired by Web trust models to improve the precision and recall of traceability links: Trust race uses intractability recovery approach to obtain a set of traceability links, which rankings are then re-evaluated using a set of other traceability recovery approaches. Second, we propose a novel traceability recovery approach, His trace, to identify traceability links between requirements and source code through CVS/SVN change logs using a Vector Space Model (VSM). We combine a traditional recovery traceability approach with His trace to build Trust race in which we use Histraceas one expert adding knowledge to the traceability links extracttedfrom CVS/SVN change logs. We apply Trustrace on two case studies to compare its traceability links with those recovered using only the VSM-based approach, in terms of precision and recall. We show that Trustrace improves with statistical significance the precision of the traceability links while also improving recall but without statistical significance.
Mortality in multiple sclerosis: a review

This work was undertaken to evaluate studies on mortality caused by multiple sclerosis (MS), to evaluate if useful inferences can be drawn from survival studies that can be applied to clinical practice. A literature search was carried out to find epidemiological studies on MS prognosis, survival, mortality and causes of death relevant to our aim. The World Health Organization (WHO) reports on worldwide cause‐specific mortality were also considered. Studies were evaluated according to the duration of the follow‐up study, the year of publication and the methodology used. We evaluated MS survival from a methodological point of view and considered if time trends could be drawn from study results. We conclude that mortality is only slightly higher in MS patients when compared with that in the general population. Mortality is higher particularly for older patients and those with longer disease duration.
Influence of fat crystals in the oil phase on stability of oil-in-water emulsions.

Coalescence at rest and during flow was studied in emulsions of paraffin oil in water with several surfactants and with crystals of solid paraffin or tristearate in the oil phase. Solid fat in the oil phase was estimated by pulsed nuclear magnetic resonance. Without crystals, oil-in-water emulsions were mostly stable and flow hardly influenced coalescence, even of unstable emulsions. Emulsions with crystals in the dispersed oil phase were less stable if crystals appeared at the interface. The contact angle indicated that crystals could be oriented in the interface; if so, instability was promoted by creaming, Couette flow, turbulence or flow with Taylor vortices. Coalescence in such systems could be caused by crystals sticking through the interface and piercing the film between the globule and a second approaching globule. The effect of variables such as type of surfactant, type of crystal, amount of crystalline fat, globule size, volume fraction of fat and ionic strength fitted this view. Natural cream with part of the globular fat crystallised behaved to some degree like the model systems but there were deviations.
Latency coding in POm: importance of parametric regimes.

to the editor: In a recent Epub issue of the Journal of Neurophysiology , a paper ([Masri et al. 2008][1]) appeared in which the authors claim to replicate experiments, but not results, previously obtained in our laboratory ([Ahissar et al. 2000][2]; [Sosnik et al. 2001][3]). We maintain that Masri
Solvent exposure and cognitive ability at age 67: a follow-up study of the 1947 Scottish Mental Survey

Objectives Organic solvent exposure may be associated with cognitive impairment in later life although the evidence for this association is inconsistent. This study sought to examine the association between organic solvent exposure and cognitive function in later life. Methods A prospective longitudinal study set in Aberdeen, Scotland examined 336 men and women born in 1936 who participated in the 1947 Scottish Mental Survey. Cognitive function at age 67 years was measured using the Trail Making Test B (TMT B), the Digit Symbol (DS) test, and the Auditory Verbal Learning Test (AVLT). Occupational hygienists reviewed occupational histories, blind to cognitive function, and estimated lifetime solvent exposures. Multiple regression analyses were employed to explore the association between solvent exposure and cognitive performance after adjustment for confounders. Results After adjusting for childhood IQ, smoking, alcohol and sex, the solvent exposed group took on average almost 10 s longer than the unexposed group to complete the TMT B, a highly significant difference. For the DS test, after adjusting for childhood IQ, smoking and gender, the exposed group scored on average two points lower than the unexposed group, which was again highly significant. There was no evidence of an effect for cumulative solvent exposure on the TMT B or DS test. For the AVLT there were no significant differences associated with exposure. Conclusions This study of subjects with generally low exposures, found no clear evidence of an association between solvent exposure and cognitive function.
New clinical investigations with selective angiotensin II receptor blocker therapy in diabetes and renal disease

Summary Halting the reduction in glomerular filtration rate (GFR) is the primary aim of any treatment of patients presenting with progressive chronic renal failure, a very common corollary to diabetes. To improve GFR, the high blood pressure (BP) and proteinuria often seen in these patients must both be controlled. These symptoms lead not only to progressive loss of renal function, but also to an increase in cardiovascular risk. Use of angiotensin-converting enzyme (ACE) inhibitors in these patients has been reported to control BP and reduce protein excretion and cardiovascular risk. Complete blockade of angiotensin II (Ang II) action with the highly selective Ang II receptor blocker (ARB) valsartan, both as monotherapy and in combination with ACE inhibitors, is well-tolerated and efficacious in patients with renal failure. Unlike ACE inhibition, ARB treatment leads to no initial reduction in GFR, thus valsartan may be a better agent for the control of BP, with greater renal protection.
Prevalence of and Risk Factors for Peripheral Arterial Disease in the United States: Results From the National Health and Nutrition Examination Survey, 1999–2000

Background—Peripheral arterial disease (PAD) is associated with significant morbidity and mortality and is an important marker of subclinical coronary heart disease. However, estimates of PAD prevalence in the general US population have varied widely. Methods and Results—We analyzed data from 2174 participants aged 40 years and older from the 1999–2000 National Health and Nutrition Examination Survey. PAD was defined as an ankle-brachial index <0.90 in either leg. The prevalence of PAD among adults aged 40 years and over in the United States was 4.3% (95% CI 3.1% to 5.5%), which corresponds to ≈5 million individuals (95% CI 4 to 7 million). Among those aged 70 years or over, the prevalence was 14.5% (95% CI 10.8% to 18.2%). In age- and gender-adjusted logistic regression analyses, black race/ethnicity (OR 2.83, 95% CI 1.48 to 5.42) current smoking (OR 4.46, 95% CI 2.25 to 8.84), diabetes (OR 2.71, 95% CI 1.03 to 7.12), hypertension (OR 1.75, 95% CI 0.97 to 3.13), hypercholesterolemia (OR 1.68, 95% CI 1.09 to 2.57), and low kidney function (OR 2.00, 95% CI 1.08 to 3.70) were positively associated with prevalent PAD. More than 95% of persons with PAD had 1 or more cardiovascular disease risk factors. Elevated fibrinogen and C-reactive protein levels were also associated with PAD. Conclusions—This study provides nationally representative prevalence estimates of PAD in the United States, revealing that PAD affects more than 5 million adults. PAD prevalence increases dramatically with age and disproportionately affects blacks. The vast majority of individuals with PAD have 1 or more cardiovascular disease risk factors that should be targeted for therapy.
Biogeographical Survey Identifies Consistent Alternative Physiological Optima and a Minor Role for Environmental Drivers in Maintaining a Polymorphism

The contribution of adaptive mechanisms in maintaining genetic polymorphisms is still debated in many systems. To understand the contribution of selective factors in maintaining polymorphism, we investigated large-scale (>1000 km) geographic variation in morph frequencies and fitness-related physiological traits in the damselfly Nehalennia irene. As fitness-related physiological traits, we investigated investment in immune function (phenoloxidase activity), energy storage and fecundity (abdomen protein and lipid content), and flight muscles (thorax protein content). In the first part of the study, our aim was to identify selective agents maintaining the large-scale spatial variation in morph frequencies. Morph frequencies varied considerably among populations, but, in contrast to expectation, in a geographically unstructured way. Furthermore, frequencies co-varied only weakly with the numerous investigated ecological parameters. This suggests that spatial frequency patterns are driven by stochastic processes, or alternatively, are consequence of highly variable and currently unidentified ecological conditions. In line with this, the investigated ecological parameters did not affect the fitness-related physiological traits differently in both morphs. In the second part of the study, we aimed at identifying trade-offs between fitness-related physiological traits that may contribute to the local maintenance of both colour morphs by defining alternative phenotypic optima, and test the spatial consistency of such trade-off patterns. The female morph with higher levels of phenoloxidase activity had a lower thorax protein content, and vice versa, suggesting a trade-off between investments in immune function and in flight muscles. This physiological trade-off was consistent across the geographical scale studied and supports widespread correlational selection, possibly driven by male harassment, favouring alternative trait combinations in both female morphs.
The auto-inhibitory domain and ATP-independent microtubule-binding region of Kinesin heavy chain are major functional domains for transport in the Drosophila germline

The major motor Kinesin-1 provides a key pathway for cell polarization through intracellular transport. Little is known about how Kinesin works in complex cellular surroundings. Several cargos associate with Kinesin via Kinesin light chain (KLC). However, KLC is not required for all Kinesin transport. A putative cargo-binding domain was identified in the C-terminal tail of fungal Kinesin heavy chain (KHC). The tail is conserved in animal KHCs and might therefore represent an alternative KLC-independent cargo-interacting region. By comprehensive functional analysis of the tail during Drosophila oogenesis we have gained an understanding of how KHC achieves specificity in its transport and how it is regulated. This is, to our knowledge, the first in vivo structural/functional analysis of the tail in animal Kinesins. We show that the tail is essential for all functions of KHC except Dynein transport, which is KLC dependent. These tail-dependent KHC activities can be functionally separated from one another by further characterizing domains within the tail. In particular, our data show the following. First, KHC is temporally regulated during oogenesis. Second, the IAK domain has an essential role distinct from its auto-inhibitory function. Third, lack of auto-inhibition in itself is not necessarily detrimental to KHC function. Finally, the ATP-independent microtubule-binding motif is required for cargo localization. These results stress that two unexpected highly conserved domains, namely the auto-inhibitory IAK and the auxiliary microtubule-binding motifs, are crucial for transport by Kinesin-1 and that, although not all cargos are conserved, their transport involves the most conserved domains of animal KHCs.
Microsatellite markers for the analysis of genotypic of Phytophthora infestans in north of China

In this study, a total of 255 isolates of Phytophthora infestans were collected from potato in Hebei, Liaoning, Jilin and Heilongjiang in 2008 and 2009. Twelve types of SSR genotypes were identified from 200 strains of P. infestans using two pairs of SSR primers, Pi4B and Pi4G. Among them, Genotype F-01 dominated population and accounted for 72.00%. Genotypes in Hebei were the most abundant, including eight genotypes of A-03, A-09, F-01, F-05, F-06, F-07, F-08 and I-01. Heilongjiang had six genotypes of F-01, F-06, F-07, F-08, G-03 and K-01. There were genotypes of F-01, F-06 and L-01 in Jilin and genotypes of F-01, F-06 and J-01 in Liaoning. In addition, Genotypes A-09, F-07, F-08, I-01, J-01, K-01 and L-01 were firstly reported at home and abroad. The genetic diversity of P. infestans in four provinces of northern China was less than that in Europe, as well as Jinlin and Liaoning were less than in Hebei and Heilongjiang.
Relationship between paraoxonase and homocysteine: crossroads of oxidative diseases

Homocysteine (Hcy) is an accepted independent risk factor for several major pathologies including cardiovascular disease, birth defects, osteoporosis, Alzheimer's disease, and renal failure. Interestingly, many of the pathologies associated with homocysteine are also linked to oxidative stress. The enzyme paraoxonase (PON1) – so named because of its ability to hydrolyse the toxic metabolite of parathion, paraoxon – was also shown early after its identification to manifest arylesterase activity. Although the preferred endogenous substrate of PON1 remains unknown, lactones comprise one possible candidate class. Homocysteine-thiolactone can be disposed of by enzymatic hydrolysis by the serum Hcy-thiolactonase/paraoxonase carried on high-density lipoprotein (HDL). In this review, Hcy and the PON1 enzyme family were scrutinized from different points of view in the literature and the recent articles on these subjects were examined to determine whether these two molecular groups are related to each other like a coin with two different sides, so close and yet so different and so opposite.