Miracle-dz/UniFAR-FTUs huggingface dataset:
Transposition genes of the Bacteroides mobilizable transposon Tn4555: role of a novel targeting gene

Conjugative transposons have been identified in several bacterial species, most notably the Gram‐positive Enterococci and the Gram‐negative Bacteroides. In Bacteroides species, these elements encode a complete conjugative machinery, which mediates their own intercellular transfer, and they can mobilize in trans co‐resident elements. One such mobilizable element is the antibiotic resistance transposon, Tn4555, which was previously found to integrate into a specific genome target site via a site‐specific recombination mechanism. In this work, we demonstrate that three Tn4555 genes were involved in integration of the element. These were int encoding a lambda‐type integrase, which was absolutely required for integration of the transposon, and two accessory genes, which increased the frequency of integration. Interestingly, one of these accessory gene products, TnpA, directed the insertion of Tn4555 into the genome target site; in the absence of tnpA, the insertion pattern was essentially random. This is the first example of a site‐specific recombinase that uses a specific targeting protein.
Heart-rate reduction by If-channel inhibition with ivabradine restores collateral artery growth in hypercholesterolemic atherosclerosis.

AIMS Collateral arteries protect tissue from ischaemia. Heart rate correlates with vascular events in patients with arterial obstructive disease. Here, we tested the effect of heart-rate reduction (HRR) on collateral artery growth. METHODS AND RESULTS The I(f)-channel inhibitor ivabradine reduced heart rate by 11% in wild-type and 15% in apolipoprotein E (ApoE)(-/-) mice and restored endothelium-dependent relaxation in aortic rings of ApoE(-/-) mice. Microsphere perfusion and angiographies demonstrated that ivabradine did not change hindlimb perfusion in wild-type mice but improved perfusion in ApoE(-/-) mice from 40.5 ± 15.8-60.2 ± 18.5% ligated/unligated hindlimb. Heart rate reduction (13%) with metoprolol failed to improve endothelial function and perfusion. Protein expression of endothelial nitric oxide synthase (eNOS), phosphorylated eNOS, and eNOS activity were increased in collateral tissue following ivabradine treatment of ApoE(-/-) mice. Co-treatment with nitric oxide-inhibitor N (G)-nitro-L-arginine methyl ester abolished the effects of ivabradine on arteriogenesis. Following ivabradine, classical inflammatory cytokine expression was lowered in ApoE(-/-) circulating mononuclear cells and in plasma, but unaltered in collateral-containing hindlimb tissue, where numbers of perivascular macrophages also remained unchanged. However, ivabradine reduced expression of anti-arteriogenic cytokines CXCL10and CXCL11 and of smooth muscle cell markers smoothelin and desmin in ApoE(-/-) hindlimb tissue. Endothelial nitric oxide synthase and inflammatory cytokine expression were unchanged in wild-type mice. Ivabradine did not affect cytokine production in HUVECs and THP1 mononuclear cells and had no effect on the membrane potential of HUVECs in patch-clamp experiments. CONCLUSION Ivabradine-induced HRR stimulates adaptive collateral artery growth. Important contributing mechanisms include improved endothelial function, eNOS activity, and modulation of inflammatory cytokine gene expression.
A comparative study of sampling analysis in scene classification of high-resolution remote sensing imagery

Scene classification is a key problem in the interpretation of high-resolution remote sensing imagery. The state-of-the-art methods, e.g. bag-of-visual-words model and its various extensions as well as the topic models, share similar procedures: patch sampling, feature description/learning and classification. Patch sampling is the first and the key procedure which has a great influence on the results. In this paper, we focus on the effects of different sampling strategies used in the literature sa as to find a suitable sampling strategy for the scene classification of high-resolution remote sensing images. We divide the existing sampling methods into two types: random sampling and saliency-based sampling, and embed them in the bag-of-visual-words framework for comparison owing to its simplicity, robustness and efficiency. Moreover, we compare it using another framework - Fisher kernel, to validate our conclusions. The experimental results on two commonly used datasets using two different frameworks both show that random sampling can give better or comparable results than other sampling methods.
The PHQ-9 as a brief assessment of lifetime major depression.

The Patient Health Questionnaire-9 (PHQ-9; R. L. Spitzer, K. Kroenke, J. B. W. Williams, & The Patient Health Questionnaire Primary Care Study Group, 1999), modified to ask about the worst period of depression lifetime, was validated against lifetime mood disorder diagnoses established by the Structured Clinical Interview for DSM-IV (SCID; M. B. First, R. L. Spitzer, M. Gibbon, & J. B. W. Williams, 2001) in 526 participants. PHQ-9 dichotomous scores corresponded highly with major depressive episode (MDE) Criterion A, MDE, and major depressive disorder (MDD), odds ratios >or= 9.5, and area under the receiver operating characteristic curve (AUC) >or= 0.84. The continuous scale score was higher in participants who did (M=17.14, SD=7.36) than in those who did not (M=6.05, SD=6.29) meet MDE Criterion A, t(524)=18.09, p<. 001; was correlated with number of MDE Criterion A symptoms, r(525)=. 67, p<. 001; and detected MDE Criterion A (AUC=0.88). The PHQ-9 as a lifetime measure may be used to complement or replace more costly interview assessments.
Role of electrostriction on the electrical aging of polymers

It is shown that the major parameters affecting most electrical properties of dielectrics, especially aging, are more poorly known than believed. This paper points out three major problems: the real values of the field-induced stress and strain, the strain saturation under high fields and the exact role of the sample size. One mechanism allowing to take those difficulties into account is electrostriction and although it is limited in low dielectric constant dielectrics, it appears to be significant in the cases studied here. The influence of sample size requires further work but it is already clear that many parameters involved in electrostriction are depending on sample thickness and possibly also on volume. Application to conduction and breakdown is briefly evoked.
Role of the host cell in bacteriophage T4 development. II. Characterization of host mutants that have pleiotropic effects on T4 growth

Mutant host-defective Escherichi coli that fail to propagate bacteriophage T4 and have a pleiotropic effect on T4 development have been isolated and characterized. In phage-infected mutant cells, specific early phage proteins are absent or reduced in amount, phage DNA synthesis is depressed by about 50%, specific structural phage proteins, including some tail and collar components, are deficient or missing, and host-cell lysis is delayed and slow. Almost all phage that can overcome the host block carry mutantions that map in functionally undefined 'nonessential' regions of the T4 genome, most near gene 39. The mutant host strains are temperature sensitive for growth and show simultaneous reversion of the ts phenotype and the inability to propagate T4+. The host mutations are cotransduced with ilv (83 min) and may lie in the gene for transcription termination factor rho.
Enhancing mobile video streaming by lookahead rate allocation in wireless networks

Developing novel video delivery mechanisms have become imperative to cope with the unprecedented growth in mobile video traffic. In this paper, we present video transmission schemes that improve the streaming experience by looking ahead at the future rates users are expected to face. Such an approach is useful for the delivery of stored videos that can be strategically buffered in advance at the users' devices. For instance, if it is known a user is entering a low coverage area, content can be prebuffered to support smooth streaming. Therefore, the Base Stations (BSs) can now plan long-term multi-user rate allocations based not only on current channel states, but also on future conditions. To provide a performance benchmark we first develop a lookahead multi-objective Linear Program (LP) that offers a trade-off between minimizing overall network video degradation, and providing fairness in individual user degradation. Then, to efficiently solve the problem, we present a polynomial-time algorithm that closely follows the pareto-optimal trade-off of the multi-objective LP. We provide an extensive performance analysis of the proposed methods by simulations, and numerical results demonstrate that significant improvements in video streaming are achievable by the lookahead rate allocation strategies.
Involvement of Rhodocyclus-Related Organisms in Phosphorus Removal in Full-Scale Wastewater Treatment Plants

ABSTRACT The participation of organisms related to Rhodocyclus in full-scale enhanced biological phosphorus removal (EBPR) was investigated. By using fluorescent in situ hybridization techniques, the communities of Rhodocyclus-related organisms in two full-scale wastewater treatment plants were estimated to represent between 13 and 18% of the total bacterial population. However, the fractions of these communities that participated in polyphosphate accumulation depended on the type of treatment process evaluated. In a University of Cape Town EBPR process, the percentage of Rhodocyclus-related cells that contained polyphosphate was about 20% of the total bacterial population, but these cells represented as much as 73% of the polyphosphate-accumulating organisms (PAOs). In an aerated-anoxic EBPR process, Rhodocyclus-related PAOs were less numerous, accounting for 6% of the total bacterial population and 26% of the total PAO population. In addition, 16S ribosomal DNA sequences 99.9% similar to the sequences of Rhodocyclus-related organisms enriched in acetate-fed bench-scale EBPR reactors were recovered from both full-scale plants. These results confirmed the involvement of Rhodocyclus-related organisms in EBPR and demonstrated their importance in full-scale processes. In addition, the results revealed a significant correlation between the type of EBPR process and the PAO community.
Leveraging 'The Crowd': An Exploration of how Solver Brokerages enhance Knowledge Mobility

The concept of open innovation has drawn considerable interest from both researchers and practitioners in recent years. We conceptualize the emerging phenomenon of Open Innovation intermediaries (or ‘Solver Brokerages’) as intermediaries that facilitate innovation exchanges between organizations and crowds. The study presents a theoretical model based on extant research, which is refined through a field study consisting of elite interviewing, with representatives from four solver brokerages as well as stakeholders from an innovation-seeking organisation and a solution provider. In exploring how Solver Brokerages enhance knowledge mobility, the paper examines the ways in which providing access to a knowledgeable and diverse solution community, facilitating problem decomposition and articulation, and mechanisms for increasing appropriability affect knowledge mobility. In addition, the paper examines the ways in which filters and rewards affect appropriability as well as the roles played by collaborative mechanisms in mediating these effects.
Factor XI–Dependent Reciprocal Thrombin Generation Consolidates Blood Coagulation when Tissue Factor Is Not Available

Objective—Feedback activation of factor XI by thrombin is a likely alternative for tissue factor-dependent propagation of thrombus formation. However, the hypothesis that thrombin can initiate and propagate its formation in a factor XI-dependent and platelet-dependent manner has not been tested in a plasma milieu. Methods and Results—We investigated thrombin generation in recalcified platelet-rich plasma activated with varying amounts of thrombin or factor VIIa. Thrombin initiates and propagates dose-dependently thrombin generation only when platelets and plasma factor XI are present. Incubation of thrombin-activated platelets with a tissue factor neutralizing antibody had no effect on thrombin formation, indicating that platelet-associated tissue factor, if present at all, is not involved. In the absence of factor VIII, thrombin could not initiate its own formation, whereas factor VIIa-induced thrombin generation was reduced. Collagen strongly stimulated both thrombin-initiated and factor VIIa-initiated thrombin generation. Conclusions—These findings support the notion that platelet-localized feedback activation of factor XI by thrombin plays an important role in maintaining normal hemostasis as well as in sustaining thrombus formation when the TF pathway is inhibited by tissue factor pathway inhibitor.
Perceived social support from family, school, and peers: relationship with emotional and behavioral problems among adolescents.

OBJECTIVE To examine (1) the extent to which negative perceptions of support from family, school, and peers differ with regard to their impact on emotional and behavioral problems and (2) the extent to which negative perceptions of multiple social support systems are related to the presence of multiple emotional and behavioral problems in adolescence. METHOD The sample comprised 476 high school students, aged 16 to 18 years: 119 without any emotional and behavioral problems, 119 with emotional problems only, 119 with behavioral problems only, and 119 with emotional and behavioral problems. Possible differences between the subgroups were tested with regard to the perceived social support from family, school, and peers, and with regard to the number of negatively perceived support systems. RESULTS Whereas a negative perception of school was shown to be specifically related to behavioral problems and a negative perception of peers specifically to emotional problems, a negative perception of the family appeared to be strongly related both to emotional and behavioral dysfunction. A strong accumulating effect was found for multiple negatively perceived social environments. CONCLUSIONS The results suggest a dominant role of negatively perceived family support. Therefore, to prevent emotional and behavioral problems in adolescence it is of paramount importance to identify families at risk at the earliest possible stage and to provide training and support for the parents involved.
Cell–extracellular matrix versus cell–cell interactions during the development of the cochlear‐vestibular ganglion

Cells destined to become the neurones of the cochlear‐vestibular ganglion (CVG) originate within the otic epithelium. Early in development they detach from their neighbors and migrate out of the epithelium, where they coalesce to form the CVG. To accomplish this process, the neuroblasts must modify their interactions with other cells within the epithelium and with proteins in the extracellular matrix to allow for repositioning. The aim of this study was to investigate the roles of the major families of adhesion molecules that mediate cellular interactions with the extracellular matrix, the integrins, and with other cells, the cadherins, in neuroblast segregation from the otic epithelium. The expression of classical cadherins increased in migrating neuroblasts compared with the otic epithelium. Quantitative RT‐PCR revealed that this was concomitant with down‐regulation of E‐cadherin and up‐regulation of N‐cadherin in the migrating cells. In contrast, the level of β1 integrin expression by the epithelium was maintained in migrating neuroblasts. However, although multiple integrin ligands were expressed within the otic basement membrane at this stage of development, only fibronectin (FN) supported neuroblast migration along the substrate in vitro. Inhibition of β1 integrins resulted in significantly reduced linear migration on FN. Importantly, neuroblasts retained the ability to segregate from the epithelium but remained compacted immediately adjacent to the originating tissue, suggesting dominance of cell–cell over cell–matrix interactions. These data suggest that the balance between cell–cell and cell–substratum interactions directs otic neuroblast migration and gangliogenesis. © 2011 Wiley‐Liss, Inc.
Leptin directly promotes T‐cell glycolytic metabolism to drive effector T‐cell differentiation in a mouse model of autoimmunity

Upon activation, T cells require energy for growth, proliferation, and function. Effector T (Teff) cells, such as Th1 and Th17 cells, utilize high levels of glycolytic metabolism to fuel proliferation and function. In contrast, Treg cells require oxidative metabolism to fuel suppressive function. It remains unknown how Teff/Treg‐cell metabolism is altered when nutrients are limited and leptin levels are low. We therefore examined the role of malnutrition and associated hypoleptinemia on Teff versus Treg cells. We found that both malnutrition‐associated hypoleptinemia and T cell‐specific leptin receptor knockout suppressed Teff‐cell number, function, and glucose metabolism, but did not alter Treg‐cell metabolism or suppressive function. Using the autoimmune mouse model EAE, we confirmed that fasting‐induced hypoleptinemia altered Teff‐cell, but not Treg‐cell, glucose metabolism, and function in vivo, leading to decreased disease severity. To explore potential mechanisms, we examined HIF‐1α, a key regulator of Th17 differentiation and Teff‐cell glucose metabolism, and found HIF‐1α expression was decreased in T cell‐specific leptin receptor knockout Th17 cells, and in Teff cells from fasted EAE mice, but was unchanged in Treg cells. Altogether, these data demonstrate a selective, cell‐intrinsic requirement for leptin to upregulate glucose metabolism and maintain function in Teff, but not Treg cells.
The scope for Online Social Network aided caching in web CDNs

With Online Social Networking (OSN) services coming to prominence as a major platform for the popularization of Web content, recent research has focused on using information gleaned from these services to improve the performance of Content Distribution Networks (CDN). In this paper we find that contrary to popular belief, the simple cache replacement policy LRU outperforms methods based on OSN input. To establish this we propose an OSN-assisted caching strategy which we evaluate using a large Twitter dataset and through simulation. Our results show that vanilla LRU mostly outperforms the OSN-aided mechanisms. We study the reasons for this and find that if at any time there is a large enough percentage of highly popular content, which becomes popular within a short enough time span, CDN can do well by just following an LRU principle. While we do not claim generalizability to other workloads, or other caching architectures on the Internet, our results are important as they apply to the common use-case and show that simple algorithms do quite well.
Forced Lordosis on the Thoracolumbar Junction Can Correct Coronal Plane Deformity in Adolescents With Double Major Curve Pattern Idiopathic Scoliosis

Study Design. A prospective radiographic study was conducted. Objective. To support our hypothesis that correction of the scoliosis may benefit from a lordotic fulcrum force in the sagittal plane on the thoracolumbar spine. Summary of Background Data. Adolescent idiopathic scoliosis is an important spinal deformity. Correction can be achieved with limited options by current bracing techniques. Lateral bending radiographs are used to assess flexibility and predict treatment outcome. The corrective potential of a lordotic fulcrum force in the sagittal plane has not been addressed. Methods. Anterioposterior spine radiographs of patients with a double major curve pattern scoliosis were obtained in 2 groups of patients. In group A radiographs in 3 positions: standing, and supine with and without fulcrum (n = 12), and group B radiographs in 2 positions (n = 28): standing, and supine with lordotic fulcrum. Cobb angles were determined and evaluated statistically. The sagittal contour of the thoracolumbar junction in standing position was measured. Results. In group A with the patients lying supine a correction of the Cobb angle was obtained at the thoracic level of 15.4% and the lumbar level of 27.5% (P < 0.001). Adding in supine position a lordotic fulcrum on the thoracolumbar junction resulted in a coupled further correction at the thoracic level of 15.7% and lumbar 18.1% (P < 0.001). Comparing in group A the thoracic and lumbar curvatures in standing position with that on a lordotic fulcrum in supine position revealed a total reduction of 31% and 45.6%, respectively. For the independent group B this reduction in 1 step is 38% and 44.4%, respectively. Conclusion. Scoliotic deformities are significantly reduced in supine position by a lordotic fulcrum force on the thoracolumbar junction. These findings may have consequences on bracing techniques.
Seroprevalence of antibody to mumps virus in the US population, 1999-2004.

BACKGROUND In 2006, the largest mumps outbreak in the United States in 20 years occurred. To understand prior mumps seroprevalence and factors associated with the presence of antibody to mumps virus, data from the 1999-2004 National Health and Nutrition Examination Survey (NHANES) were analyzed. METHODS A mumps virus-specific enzyme immunoassay was used to measure the seroprevalence of serum immunoglobulin G (IgG) antibody among NHANES participants aged 6-49 years. Participants were grouped on the basis of 10-year birth cohorts, 95% confidence intervals (CIs) were calculated using SUDAAN software, and logistic regression was used to identify independent predictors. RESULTS The overall age-adjusted seroprevalence of IgG antibody to mumps virus during 1999-2004 was 90.0% (95% CI, 88.8%-91.1%). Seroprevalence was higher among US-born non-Hispanic blacks (96.4% [95% CI, 95.5%-97.2%]) and non-US-born Mexican Americans (93.7% [95% CI, 92.0%-95.2%]). Seroprevalence was significantly lower in the 1967-1976 birth cohort (85.7% [95% CI, 83.5%-87.8%]). The variables sex, education, and race/ethnicity/birthplace were independent predictors in at least 1 of the birth cohorts. CONCLUSIONS The overall estimate of 90.0% is at the lower end of the estimated population immunity (90%-92%) needed to achieve herd immunity. Lower seroprevalence among groups suggest that they represent populations at an increased risk. For mumps control, high vaccine coverage and high population immunity must be achieved and maintained.
The canonical FEP construction

A class K of algebras has the finite embeddability property (FEP) if every finite partial subalgebra of some member of K can be embedded into some finite member of K. We prove the FEP for varieties of decreasing residuated lattice-ordered algebras using a construction based on the canonical extension. This construction produces a (generally) different finite member of the class from alternative FEP constructions for similar classes of algebras. Additionally, the constructed algebra is internally compact, in contrast to other FEP constructions. We give a description of the σ and π -extensions of operations that do not rely on the notions of closed and open elements and we use this to obtain a syntactic description of a class of inequalities s≤ t that are preserved by the construction.