Miracle-dz/UniFAR-FTUs huggingface dataset:
The Lipopolysaccharide Export Pathway in Escherichia coli: Structure, Organization and Regulated Assembly of the Lpt Machinery

The bacterial outer membrane (OM) is a peculiar biological structure with a unique composition that contributes significantly to the fitness of Gram-negative bacteria in hostile environments. OM components are all synthesized in the cytosol and must, then, be transported efficiently across three compartments to the cell surface. Lipopolysaccharide (LPS) is a unique glycolipid that paves the outer leaflet of the OM. Transport of this complex molecule poses several problems to the cells due to its amphipatic nature. In this review, the multiprotein machinery devoted to LPS transport to the OM is discussed together with the challenges associated with this process and the solutions that cells have evolved to address the problem of LPS biogenesis.
Measuring capital market integration

The convergence of European economies in the wake of European monetary union, together with increasingly common dynamics in currency and equity returns, suggests that capital markets are at least partially integrated. We impose a dynamic factor analytical model for the returns on currency and stock portfolios on eight European markets, taking into account predictability by forward premia and dividend yields. The resulting asset pricing model is characterised by time-varying risk premia, and constant betas and return variances. We propose a measure of the degree of integration and examine its evolution from 1979 until 1997. We find that the degree of integration for equity markets increased in the 1990s but that this was mainly due to an increase in the premium for extra-European currency risk. We also find that the sources of co-movement lie only in part in the US equity markets.
Biomechanical stress‐induced apoptosis in vein grafts involves p38 mitogen‐activated protein kinases

The present study was designed to investigate whether apoptosis occurs in early‐stage vein grafts and to determine the mechanisms by which mechanical stress contributes to apoptosis in vascular smooth muscle cells (SMCs). Apoptosis in vessel walls of mouse vein grafts was confirmed by morphological changes and by terminal deoxynucleotidyl transferase‐mediated dUTP‐biotin nick end labeling (TUNEL). TUNEL+ cells in vein grafts 1, 4, and 8 wk postoperatively was 13%, 29%, and 21%, respectively, and apoptosis occurred mainly in veins grafted to arteries, remaining unchanged in vein‐to‐vein grafts. When mouse, rat, and human arterial SMCs were cultured on a flexible membrane and subjected to cyclic strain stress, apoptosis was observed in a time‐ and strength‐dependent manner. All three types of SMCs showed apoptotic death as confirmed by TUNEL, propidium iodide, and annexin V staining. To further study the signal pathways leading to apoptosis, activities of p38, a subfamily of mitogen‐activated protein kinases (MAPKs), were determined. Mechanical stress resulted in p38 MAPK activation, reaching high levels within 8 min. SB 202190, a specific inhibitor for p38 MAPKs, prevented SMC apoptosis in response to mechanical stress. SMC lines stably transfected with a dominant negative rac, an upstream signal transducer, or overexpressing MAPK phosphatase‐1, a negative regulator for MAPKs, completely inhibited mechanical stress stimulated p38 activation and abolished mechanical stress‐induced apoptosis. Thus, we provide solid evidence that one of the earliest events in venous bypass grafts is apoptosis, in which mechanical stress‐induced p38‐MAPK activation is responsible for transducing signals leading to apoptosis. —Mayr, M. , Li, C. , Zou, Y. , Huemer, U. , Hu, Y. , Xu, Q. Biomechanical stress‐induced apoptosis in vein grafts involves p38 mitogen‐activated protein kinases. FASEB J. 15, 261–270 (2000)
Dynamics of a rigid body in a Stokes fluid

We demonstrate that the dynamics of a rigid body falling in an infinite viscous fluid can, in the Stokes limit, be reduced to the study of a three-dimensional system of ordinary differential equations ${\dot\Grav} \,{=}\, \Grav\times M_2\Grav$ where $M_2\,{\in}\,{{\mathbb R}^{3\times 3}}$ is a generally non-symmetric matrix containing certain hydrodynamic mobility coefficients. We further show that all steady states and their stability properties can be classified in terms of the Schur form of $M_2$. Steady states correspond to screw motions (or limits thereof) in which the centre of mass traces a helical path, while the body spins uniformly about the vertical. All rigid bodies have at least one such stable screw motion. Bodies for which $M_2$ has exactly one real eigenvalue have a unique globally attracting asymptotically stable screw motion, while other bodies can have multiple, stable and unstable steady motions. One application of our theory is to the case of rigid filaments, which in turn is a first step in modelling the sedimentation rate of flexible polymers such as DNA. For rigid filaments the matrix $M_2$ can be approximated using the Rotne–Prager theory, and we present various examples corresponding to certain ideal shapes of knots which illustrate the various possible multiplicities of steady states. Our simulations of rigid ideal knots in a Stokes fluid predict an approximate linear relation between sedimentation speed and average crossing number, as has been observed experimentally for the much more complicated system of real DNA knots in gel electrophoresis.
Species Identification of Marine Fishes in China with DNA Barcoding

DNA barcoding is a molecular method that uses a short standardized DNA sequence as a species identification tool. In this study, the standard 652 base-pair region of the mitochondrial cytochrome oxidase subunit I gene (COI) was sequenced in marine fish specimens captured in China. The average genetic distance was 50-fold higher between species than within species, as Kimura two parameter (K2P) genetic distances averaged 15.742% among congeners and only 0.319% for intraspecific individuals. There are no overlaps of pairwise genetic variations between conspecific and interspecific comparisons apart from the genera Pampus in which the introgressive hybridization was detected. High efficiency of species identification was demonstrated in the present study by DNA barcoding. Due to the incidence of cryptic species, an assumed threshold is suggested to expedite discovering of new species and biodiversity, especially involving biotas of few studies.
Optimal Aggregation Policy for Reducing Tail Latency of Web Search

A web search engine often employs partition-aggregate architecture, where an aggregator propagates a user query to all index serving nodes (ISNs) and collects the responses from them. An aggregation policy determines how long the aggregators wait for the ISNs before returning aggregated results to users, crucially affecting both query latency and quality. Designing an aggregation policy is, however, challenging: Response latency among queries and among ISNs varies significantly, and aggregators lack of knowledge about when ISNs will respond. In this paper, we propose aggregation policies that minimize tail latency of search queries subject to search quality service level agreements (SLAs), combining data-driven offline analysis with online processing. Beginning with a single aggregator, we formally prove the optimality of our policy: It achieves the offline optimal result without knowing future responses of ISNs. We extend our policy for commonly-used hierarchical levels of aggregators and prove its optimality when messaging times between aggregators are known. We also present an empirically-effective policy to address unknown messaging time. We use production traces from a commercial search engine, a commercial advertisement engine, and synthetic workloads to evaluate the aggregation policy. The results show that compared to prior work, the policy reduces tail latency by up to 40% while satisfying same quality SLAs.
Association between childhood feeding problems and maternal eating disorder: role of the family environment

Background There is a strong relationship between feeding problems in childhood and eating disorder in the mother. The mechanisms responsible for this relationship are not understood. Aims To elucidate family-environmental factors that could mediate this association. Method A general population sample of children with feeding problems (n=35), other problems (shyness, fears or behavioural problems; n=58), or no problems (n=23) was identified. The mental state of their mothers was evaluated, including an assessment of current and past eating disorder. Video recordings were made in the families' homes of a mealtime and of the mothers and children participating in a standardised exploratory task. Results Two family-environmental variables significantly distinguished the children with feeding problems from the other two groups: ‘mealtime disorganisation’ and ‘maternal strong control and disharmony’. Path analysis revealed the importance of these two environmental variables in mediating the association between child and maternal disturbance. Conclusions The degree of mealtime disorganisation and the level of maternal strong control and disharmony mediate the association between maternal eating disorder and child feeding disturbance.
Two distinct nuclear receptor-interaction domains and CREB-binding protein-dependent transactivation function of activating signal cointegrator-2.

ASC-2 is a recently isolated transcriptional cointegrator molecule, which is amplified in human cancers and stimulates transactivation by nuclear receptors, AP-1, nuclear factor kappaB (NFkappaB), serum response factor (SRF), and numerous other transcription factors. ASC-2 contained two nuclear receptor-interaction domains, both of which are dependent on the integrity of their core LXXLL sequences. Surprisingly, the C-terminal LXXLL motif specifically interacted with oxysterol receptor LXRss, whereas the N-terminal motif bound a broad range of nuclear receptors. These interactions appeared to be essential because a specific subregion of ASC-2 including the N- or C-terminal LXXLL motif acted as a potent dominant negative mutant with transactivation by appropriate nuclear receptors. In addition, the autonomous transactivation domain (AD) of ASC-2 was found to consist of three separable subregions; i.e. AD1, AD2, and AD3. In particular, AD2 and AD3 were binding sites for CREB binding protein (CBP), and CBP-neutralizing E1A repressed the autonomous transactivation function of ASC-2. Furthermore, the receptor transactivation was not enhanced by ASC-2 in the presence of E1A and significantly impaired by overexpressed AD2. From these results, we concluded that ASC-2 directly binds to nuclear receptors and recruits CBP to mediate the nuclear receptor transactivation in vivo.
Cardiorespiratory fitness as a mediator of the relationship between birth weight and cognition in school children

Objectives: To examine differences in cognition parameters by birth weight categories and to analyze whether the relationships between birth weight and cognitive functions are mediated by cardiorespiratory fitness (CRF) in schoolchildren. Methods: A cross-sectional study using a sample of 664 school children from the MOVI-Kids study. Variables: i) cognitive function measured by the Battery of General and Differential Aptitudes (BADyG); ii) birth weight, reported by parents; and iii) CRF (20-m shuttle run test). ANCOVA models were estimated to assess differences in cognitive function categories across birth weight and CRF categories. Mediation analysis was conducted with Hayes’ PROCESS macro. Results: CRF is a full mediator of the association between birth weight with the verbal and numerical factors, and general intelligence; and is a partial mediator when logical reasoning and the spatial factor were the dependent variables. The available data suggest that, in schoolchildren, the influence of birth weight on cognitive function is mediated by CRF. Conclusions: These findings highlight that children with lower birth weight values and lower fitness levels should be target subgroups to improve children’s cognition, in which long-life physical activity interventions at early ages are a priority.
Liquid Publications: Scientific Publications meet the Web

The world of scientific publications has been largely oblivious to the advent of the Web and to advances in ICT. Scientific knowledge dissemination is still based on the traditional notion of “paper” publication and on peer review as quality assessment method. The current approach encourages authors to write many (possibly incremental) papers to get more “tokens of credit”, generating often unnecessary dissemination overhead for themselves and for the community of reviewers. Furthermore, it does not encourage or support reuse and evolution of publications: whenever a (possibly small) progress is made on a certain subject, a new paper is written, reviewed, and published, often after several months. We propose a paradigm shift in the way scientific knowledge is created, disseminated, evaluated and maintained. This shift is enabled by the notion of Liquid publications, which are evolutionary, collaborative, and composable scientific contributions. Many Liquid Publication concepts in this document are based on a parallel between scientific knowledge artifacts and software artifacts, and hence on lessons learned in (agile, collaborative, open source) software development. Liquid Publications concepts are reified by a model based on i) Scientific Knowledge Objects (SKOs), which are the digital instantiation of liquid publications, by ii) the processes involved in their creation, evolution, and quality assessment, and by iii) the people and roles that contribute to knowledge creation (authors, reviewers, bloggers.). Various models (including social reputation models) are developed to analyze and improve publication quality assessment and the process for attributing credit to and measuring reputation for individuals.
Object co-labeling in multiple images

We introduce a new problem called object co-labeling where the goal is to jointly annotate multiple images of the same scene which do not have temporal consistency. We present an adaptive framework for joint segmentation and recognition to solve this problem. We propose an objective function that considers not only appearance but also appearance and context consistency across images of the scene. A relaxed form of the cost function is minimized using an efficient quadratic programming solver. Our approach improves labeling performance compared to labeling each image individually. We also show the application of our co-labeling framework to other recognition problems such as label propagation in videos and object recognition in similar scenes. Experimental results demonstrates the efficacy of our approach.
A Simple Algorithm for Information Clustering in Network Attached Storage

Network attached storage (NAS) is both used by and is an application of massively parallel computing. The increasing scale of networked storage has exposed issues such as data integrity and access latency to distributed data and computation. One of the approaches to reduce the wasted network bandwidth is, following the classic localityof-data principle, to partition interrelated data objects between networked storage nodes. The paper describes an algorithm for data clustering based on the relative interconnectivity between data objects. Because of its simplicity, the method could be incorporated in network attached hard disk storage with all range of complexity from embedded controllers to complex network file servers.
Evidence for bipolar jets from the optical spectra of the prototypical symbiotic star Z Andromedae

Aims. We have studied optical spectra of the symbiotic star Z And, obtained during its latest outburst started in April 2006, wi th the aim of finding changes in the spectrum yielding clues to the na ture of the hot component and its outbursts. Methods. The spectroscopic observations of Z And have been made using the 1.5-meter telescope at the Tartu Observatory, Estonia, and processed in a standard way. Results. We have found high velocity satellites to the hydrogen Balmer emission lines. Starting from July 30, 2006, weak additional emission components at velocities of about± 1150 km s −1 were detected. Their appearance near the outburst maximum and similarity to the emission features in another symbiotic star Hen 3-1341 imply fast collimated outflows from the hot component of Z An d. This finding is consistent with the earlier results by severa l authors that symbiotic stars can emit bipolar jets at certa in stages of their outbursts. A significant decrease in the temperature o f the hot component in initial stages of the outburst was detected by the disappearance of the high excitation emission lines from the spectrum.
A framework to foster problem-solving in STEM and computing education

ABSTRACT Background: Recent developments in STEM and computer science education put a strong emphasis on twenty-first-century skills, such as solving authentic problems. These skills typically transcend single disciplines. Thus, problem-solving must be seen as a multidisciplinary challenge, and the corresponding practices and processes need to be described using an integrated framework. Purpose: We present a fine-grained, integrated, and interdisciplinary framework of problem-solving for education in STEM and computer science by cumulatively including ways of problem-solving from all of these domains. Thus, the framework serves as a tool box with a variety of options that are described by steps and processes for students to choose from. The framework can be used to develop competences in problem-solving. Sources of evidence: The framework was developed on the basis of a literature review. We included all prominent ways of domain-specific problem-solving in STEM and computer science, consisting mainly of empirically orientated approaches, such as inquiry in science, and solely theory-orientated approaches, such as proofs in mathematics. Main argument: Since there is an increasing demand for integrated STEM and computer science education when working on natural phenomena and authentic problems, a problem-solving framework exclusively covering the natural sciences or other single domains falls short. Conclusions: Our framework can support both practice and research by providing a common background that relates the ways, steps, processes, and activities of problem-solving in the different domains to one single common reference. In doing so, it can support teachers in explaining the multiple ways in which science problems can be solved and in constructing problems that reflect these numerous ways. STEM and computer science educational research can use the framework to develop competences of problem-solving at a fine-grained level, to construct corresponding assessment tools, and to investigate under what conditions learning progressions can be achieved.
Cognitive and behavioural environmental concern among university students in a Canadian city: Implications for institutional interventions

Abstract Informed by Stern and colleagues’ value-belief-norm theory and their earlier empirical work, we examined levels and predictors of cognitive and behavioural environmental concern (EC) of university students in a Canadian postsecondary context. Data for this study were obtained through completion of self-administered questionnaires from a sample of 421 undergraduate students attending a public university in Saskatchewan, a province heavily focused on expanding resource extraction. The study used a descriptive, correlational, and cross-sectional methodology. Statistical analysis was performed in three parts: (a) univariate description of students’ cognitive and behavioural EC indicators; (b) bivariate associations to assess the nature and direction of the relationships between EC measures; and (c) multivariate analyses to test the causal structure of the theoretical model. Results showed no widespread acceptance of the ‘New Ecological Paradigm’. Students were slightly more prone to place responsibility for environmental protection at the door of government and industry than themselves. Respondents practised a range of environmentally supportive behaviours (ESB) with varying intensities. Hierarchical multiple regression analyses provided support for several of the theory’s propositions in predicting generalised and specific environmental beliefs and ESB. Findings highlighted the complex relationships between personal background, academic and cognitive variables and ESB. That formal instruction on the environment influenced cognitive and behavioural EC, both directly and indirectly, suggests it is essential universities have formal curricula that expose students to the types of environmental knowledge, awareness, and critical thinking skills to promote environmental literacy and address unsustainable lifestyles and attitudes. Institutional interventions, including universities’ role as ‘effective change agents’, are discussed.
Perceptual optimization of DCT color quantization matrices

The JPEG baseline standard for image compression employs a block discrete cosine transform (DCT) and uniform quantization. For a monochrome image, a single quantization matrix is allowed, while for a color image, distinct matrices are allowed for each color channel. We describe a method, called DCTune, for the design of color quantization matrices that is based on a model of the visibility of quantization artifacts. The model describes the artifact visibility as a function of DCT frequency, color channel, and display resolution and brightness. The model also describes the summation of artifacts over space and frequency, and masking of artifacts by the image itself. The DCTune matrices are different from the de facto JPEG matrices, and appear to provide superior visual quality at equal bit-rates. <<ETX>>
Real Time Forecasts of Inflation: The Role of Financial Variables

We present a mixed-frequency model for daily forecasts of euro area inflation. The model combines a monthly index of core inflation with daily data from financial markets; estimates are carried out with the MIDAS regression approach. The forecasting ability of the model in real-time is compared with that of standard VARs and of daily quotes of economic derivatives on euro area inflation. We find that the inclusion of daily variables helps to reduce forecast errors with respect to models that consider only monthly variables. The mixed-frequency model also displays superior predictive performance with respect to forecasts solely based on economic derivatives.
School Adoption by School-University Partnerships – an example from Germany

ABSTRACT The partnership model ‘School Adoption’ was developed in Norway as a part of teacher education and in the meantime, is being implemented in several European countries as an internship concept. The core element is the so-called ‘adoption week’, during which student teachers teach all the lessons at a school, while the teachers attend a professional development course. University teacher educators work intensively together with student teachers and teachers. The student teachers who participate in the School Adoption experience their future professional field under increasingly real conditions and also in its entire complexity. How the complex internship is processed cognitively by student teachers, has not yet been examined. This study at the German University of Flensburg, is designed to evaluate student teachers’ concerns and stress experiences, and determine which factors are relevant for being able to deal with the high level of complexity. Content analyses show that student teachers’ biggest concerns are classroom management and recognition as a teacher, as well as an increase in the workload. The findings also indicate that internship settings with a high level of complexity, can be perceived as a positive challenge in the context of sufficiently structured preparation and support.