Miracle-dz/UniFAR-FTUs huggingface dataset:
Vibrio cholerae OmpU and OmpT Porins Are Differentially Affected by Bile

ABSTRACT OmpT and OmpU are pore-forming proteins of the outer membrane of Vibrio cholerae, a pathogen that colonizes the intestine and produces cholera. Expression of the ompU and ompT genes is under the regulation of ToxR, a transmembrane transcriptional activator that also controls expression of virulence factors. It was recently shown that bile stimulates the ToxR-mediated transcription of ompU and that ompU-expressing strains are more resistant to bile and anionic detergents than ompT-expressing cells. In order to further understand the role of the OmpT and OmpU porins in the ability of V. cholerae to survive and colonize the host intestine, we examined the outer membrane permeability of cells expressing only ompU or only ompT or both genes in the absence and in the presence of bile. By comparing various strains in terms of the rate of degradation of the β-lactam antibiotic cephaloridine by the periplasmic β-lactamase, we found that the permeation of the antibiotic through the outer membrane of OmpU-containing cells was slower than the permeation in OmpT-containing cells. In addition, the OmpU-mediated outer membrane permeability was not affected by external bile, while the OmpT-mediated antibiotic flux was reduced by bile in a concentration-dependent manner. Our results confirm that OmpT and OmpU provide a passageway for hydrophilic solutes through the outer membrane and demonstrate that bile might interfere with this traffic in OmpT-producing cells by functionally inhibiting the OmpT pore. The insensitivity of OmpU to bile may be due to its small pore size and may provide an explanation for the resistance of OmpU-producing cells to bile in vivo.
Practically relevant research: capturing real world tasks, environments, and outcomes.

PURPOSE Development of strategies to optimize the functional performance of older adults requires understanding the behavior of older people doing tasks in real-world settings and capturing these interactions in research protocols. This is a major challenge as there is some degree of tension between capturing the contextual variables and constraints that operate in the real world and the scale of research that can be realistically conducted within controlled experimental settings. This article presents a research approach that can be used to help ensure the ecological validity of research protocols. The intent is to demonstrate how an ecologically valid approach affords greater insight into the performance of older adults in real world settings. METHODS The approach involves techniques such as task analysis and simulation. Examples from two research projects examining aging and the performance of real-world computer-based work tasks are used to demonstrate the application of this approach. RESULTS The article demonstrates how an ecologically valid research approach yields information about human performance that can be translated into solutions for real-world problems. IMPLICATIONS Ecologically valid research protocols offer the potential for providing answers to real-world problems and advancing theory regarding aging and functional performance.
Gene Dosage in the Dysbindin Schizophrenia Susceptibility Network Differentially Affect Synaptic Function and Plasticity

Neurodevelopmental disorders arise from single or multiple gene defects. However, the way multiple loci interact to modify phenotypic outcomes remains poorly understood. Here, we studied phenotypes associated with mutations in the schizophrenia susceptibility gene dysbindin (dysb), in isolation or in combination with null alleles in the dysb network component Blos1. In humans, the Blos1 ortholog Bloc1s1 encodes a polypeptide that assembles, with dysbindin, into the octameric BLOC-1 complex. We biochemically confirmed BLOC-1 presence in Drosophila neurons, and measured synaptic output and complex adaptive behavior in response to BLOC-1 perturbation. Homozygous loss-of-function alleles of dysb, Blos1, or compound heterozygotes of these alleles impaired neurotransmitter release, synapse morphology, and homeostatic plasticity at the larval neuromuscular junction, and impaired olfactory habituation. This multiparameter assessment indicated that phenotypes were differentially sensitive to genetic dosages of loss-of-function BLOC-1 alleles. Our findings suggest that modification of a second genetic locus in a defined neurodevelopmental regulatory network does not follow a strict additive genetic inheritance, but rather, precise stoichiometry within the network determines phenotypic outcomes.
Environmental Effects of Soil Salt in the Arid Area under the Human Beings' Interference

This paper mainly discussed the relations about the environmental effects of soil salt in the arid area in the west China,especially under the human being activity.Based on soil sampling and chemical analysis,some features are fund out. From the beginning of soil physical and chemical properties,the spacial distribution features and temporal change characteristics of soil salt are pointed out. Furthormore,the complexity of environmental effects of soil salt are revealed in a sense.In order to improve environmental quality,human beings should pay attention to the coupling between water and soil as well as the water resource,vegetation resource and land resource management in the arid area.
A no-reference blocking artifact measure for adaptive video processing

Objective image quality metrics offer the prospect of adapting video processing algorithms to the quality of the incoming signal. In the context of image enhancement, such as peaking, contrast enhancement or color mapping, the original image does not necessarily correspond to the subjective optimum. There is, therefore, a compelling need for reliable quality metrics that are based exclusively on the characteristics of the processed images (no-reference). In this paper, we illustrate the design and application of no-reference quality metrics for the case of blocking artifacts that commonly degrade the quality of block-based DCT encoded video. We outline a simple cost-effective method that allows the grid position and its visibility to be determined without the need for access to the coding parameters. This information, in turn, is used to effectively suppress blocking artifacts while preserving the sharpness of object edges.
AIS Electronic

Trying to understand how laymen search for information, we have studied ordinary employees’ use of their intranets for work-related information seeking. Based on 267 responses to our web-based survey we have examined the use of various information sources in three different organisations, with a particular focus on the intranets. We have found that employees prefer to use menus to navigate to information and that a poor structure thus results in difficulties finding the right information. We have also found that gender appears to have an effect on people’s preferences for choosing one information source over another. This is a novel finding that organisations with an uneven gender distribution should consider when investing in IT support for information seeking.
A Robust Algorithm for Text String Separation from Mixed Text/Graphics Images

The development and implementation of an algorithm for automated text string separation that is relatively independent of changes in text font style and size and of string orientation are described. It is intended for use in an automated system for document analysis. The principal parts of the algorithm are the generation of connected components and the application of the Hough transform in order to group components into logical character strings that can then be separated from the graphics. The algorithm outputs two images, one containing text strings and the other graphics. These images can then be processed by suitable character recognition and graphics recognition systems. The performance of the algorithm, both in terms of its effectiveness and computational efficiency, was evaluated using several test images and showed superior performance compared to other techniques. >
Reliability Cost/Worth Assessment of Distribution Systems Incorporating Time Varying Weather Conditions and Restoration Resources

This paper presents a time sequential simulation technique incorporating the effects of weather conditions and restoration resources in reliability cost/worth evaluation of distribution systems. Time varying weight factors (TVWF) are introduced to represent the effects on component failure rates and restoration times of weather and available restoration resources. The average failure rate is combined with the TVWF to create time varying failure rates (TVFR) for each component. The average restoration time is combined with the TVWF to create time varying restoration times (TVRT). Studies conducted in a test distribution system show that the TVFR have large impacts on the interruption costs of frequency sensitive customers and slight effects on others. The TVRT have significant effects on the indices for all the customers. It is therefore important to consider TVRT in evaluating reliability cost/worth of network reinforcement.
Exemplar based metric learning for robust visual localization

This paper presents an exemplar based metric learning framework dedicated to robust visual localization in complex scenes, e.g. street images. The proposed framework learns off-line a specific (local) metric for each image of the database, so that the distance between a database image and a query image representing the same scene is smaller than the distance between the current image and other images of the database. To achieve this goal, we generate geometric and photometric transformations as proxies for query images. From the generated constraints, the learning problem is cast as a convex optimization problem over the cone of positive semi-definite matrices, which is efficiently solved using a projected gradient descent scheme. Successful experiments, conducted using a freely available geo-referenced image database, reveal that the proposed method significantly improves results over the metric in the input space, while being as efficient at test time. In addition, we show that the model learns discriminating features for the localization task, and is able to gain invariance to meaningful transformations.
Steady-shear rheology of concentrated chitosan solutions

The rheological properties of 0.5 - 2.0% (wt/wt) chitosan solutions in steady-shear were investigated as a function of temperature (25C - 45C), acid type (acetic, lactic, and hydrochloric), and ionic strength (0 and 0.2 M NaCI) to determine their flow behavior. Viscosity and normal forces have been determined over a wide range of shear rates and the results are presented using appropriate master curves for the temperature and concentration effects. For the experimental conditions studied, chitosan solutions behaved like non-Newtonian viscoelastic shear-thinning fluids. They show a low-shear rate Newtonian plateau and a high-shear rate non-Newtonian region. All material functions (viscosity and primary normal stress) decrease with an increase in temperature and a decrease in chitosan concentration. The most important parameter affecting the rheology of the solutions has been found to be salt addition, particularly for chitosans dissolved in weak acids where electrostatic effects are believed to be important.
How are decisions on care services for people with dementia made and experienced? A systematic review and qualitative synthesis of recent empirical findings

ABSTRACT Background: During recent decades, there has been a growing recognition that people cannot be assumed incapable of making decisions about their own care solely on the basis of a dementia diagnosis and international agreements and legislative changes have strengthened the formal right for people with dementia to participate in decisions on care services. This raises important questions about how these decisions are currently made and experienced in practice. In this review, we address this question and highlight directions for further research. Methods: We searched CINAHL, PsycINFO, ASSIA, Social Services Abstracts, Science Direct, Academic Search Premier, and PubMed. Twenty-four pertinent articles were identified, all representing qualitative studies. Relevant findings were extracted and synthesized along dimensions of involvement of the person with dementia in decisions on care services, using an integrative approach to qualitative synthesis. Results: We identified three overarching ways in which people with dementia are involved, primarily, in the informal part of a process of decisions: excluded, prior preferences taken into account, and current preferences respected. Several (10) articles seemed to be based on the assumption that decisions on care services are invariably and solely made within the family and without participation of the person with dementia. Conclusions: The review emphasizes the need for more updated research about international debates and agreements concerning capabilities and rights of people with dementia and about the (potential) formal contexts of care decisions in the country concerned. This, we argue, is vital for future knowledge production in the area.
Links between plant litter chemistry, species diversity, and below-ground ecosystem function

Decomposition is a critical source of plant nutrients, and drives the largest flux of terrestrial C to the atmosphere. Decomposing soil organic matter typically contains litter from multiple plant species, yet we lack a mechanistic understanding of how species diversity influences decomposition processes. Here, we show that soil C and N cycling during decomposition are controlled by the composition and diversity of chemical compounds within plant litter mixtures, rather than by simple metrics of plant species diversity. We amended native soils with litter mixtures containing up to 4 alpine plant species, and we used 9 litter chemical traits to evaluate the chemical composition (i.e., the identity and quantity of compounds) and chemical diversity of the litter mixtures. The chemical composition of the litter mixtures was the strongest predictor of soil respiration, net N mineralization, and microbial biomass N. Soil respiration and net N mineralization rates were also significantly correlated with the chemical diversity of the litter mixtures. In contrast, soil C and N cycling rates were poorly correlated with plant species richness, and there was no relationship between species richness and the chemical diversity of the litter mixtures. These results indicate that the composition and diversity of chemical compounds in litter are potentially important functional traits affecting decomposition, and simple metrics like plant species richness may fail to capture variation in these traits. Litter chemical traits therefore provide a mechanistic link between organisms, species diversity, and key components of below-ground ecosystem function.
Visual search in hunting archerfish shares all hallmarks of human performance

SUMMARY Archerfish are renowned for shooting down aerial prey with water jets, but nothing is known about how they spot prey items in their richly structured mangrove habitats. We trained archerfish to stably assign the categories ‘target’ and ‘background’ to objects solely on the basis of non-motion cues. Unlike many other hunters, archerfish are able to discriminate a target from its background in the complete absence of either self-motion or relative motion parallax cues and without using stored information about the structure of the background. This allowed us to perform matched tests to compare the ways fish and humans scan stationary visual scenes. In humans, visual search is seen as a doorway to cortical mechanisms of how attention is allocated. Fish lack a cortex and we therefore wondered whether archerfish would differ from humans in how they scan a stationary visual scene. Our matched tests failed to disclose any differences in the dependence of response time distributions, a most sensitive indicator of the search mechanism, on number and complexity of background objects. Median and range of response times depended linearly on the number of background objects and the corresponding effective processing time per item increased similarly – approximately fourfold – in both humans and fish when the task was harder. Archerfish, like humans, also systematically scanned the scenery, starting with the closest object. Taken together, benchmark visual search tasks failed to disclose any difference between archerfish – who lack a cortex – and humans.
Copper micro and nano particles mixture for 3D interconnections application

A novel copper paste with copper micro particles mixed with copper nanoparticles is proposed in this study. The mixed ratio between the two kinds of particles is simulated based on the Monte Carlo method. The copper micro particles are assumed to have a Face-Centered-Cubic (FCC) structure and the nanoparticles are filled randomly in the interstices between micro particles. The nanoparticles arrangement with maximum occupancy in the interstitial space is calculated, which enable its weight percentage estimation. Based on the simulation results, experiments are carried out to examine the micro paste, nano paste and mixed paste quality by optical microscope, contact angle measurements and thermogravimetric analysis (TGA). The experimental results reveal that the mixed paste is denser in structure and has a lower transition temperature.
Understanding linux feature distribution

Managing variability is hard. This applies both to feature modeling itself as well as the maintenance of the corresponding feature implementations which poses additional challenges. Especially in embedded systems and system software that are developed using the tools CPP, GCC and MAKE, feature realizations happen on different levels of abstractions, concepts and implementation languages. This particularly applies to Linux, which exposes over 11000 features on over two dozen different architectures. While features are modeled centrally with the Kconfig tool, feature-code is realized in various source-files and managed by the Kbuild build-system. In this article, we identify and relate levels of variability on which feature-code is implemented. The quantification of variability on the different levels in Linux disproves two common beliefs about the amount of implemented variability.
A Bayesian Analysis of Unobserved Component Models Using Ox

This article details a Bayesian analysis of the Nile river flow data, using a similar state space model as other articles in this volume. For this data set, Metropolis-Hastings and Gibbs sampling algorithms are implemented in the programming language Ox. These Markov chain Monte Carlo methods only provide output conditioned upon the full data set. For filtered output, conditioning only on past observations, the particle filter is introduced. The sampling methods are flexible, and this advantage is used to extend the model to incorporate a stochastic volatility process. The volatility changes both in the Nile data and also in daily S&P 500 return data are investigated. The posterior density of parameters and states is found to provide information on which elements of the model are easily identifiable, and which elements are estimated with less precision.
Multi-system neurological disease is common in patients with OPA1 mutations

Additional neurological features have recently been described in seven families transmitting pathogenic mutations in OPA1, the most common cause of autosomal dominant optic atrophy. However, the frequency of these syndromal ‘dominant optic atrophy plus’ variants and the extent of neurological involvement have not been established. In this large multi-centre study of 104 patients from 45 independent families, including 60 new cases, we show that extra-ocular neurological complications are common in OPA1 disease, and affect up to 20% of all mutational carriers. Bilateral sensorineural deafness beginning in late childhood and early adulthood was a prominent manifestation, followed by a combination of ataxia, myopathy, peripheral neuropathy and progressive external ophthalmoplegia from the third decade of life onwards. We also identified novel clinical presentations with spastic paraparesis mimicking hereditary spastic paraplegia, and a multiple sclerosis-like illness. In contrast to initial reports, multi-system neurological disease was associated with all mutational subtypes, although there was an increased risk with missense mutations [odds ratio = 3.06, 95% confidence interval = 1.44–6.49; P = 0.0027], and mutations located within the guanosine triphosphate-ase region (odds ratio = 2.29, 95% confidence interval = 1.08–4.82; P = 0.0271). Histochemical and molecular characterization of skeletal muscle biopsies revealed the presence of cytochrome c oxidase-deficient fibres and multiple mitochondrial DNA deletions in the majority of patients harbouring OPA1 mutations, even in those with isolated optic nerve involvement. However, the cytochrome c oxidase-deficient load was over four times higher in the dominant optic atrophy + group compared to the pure optic neuropathy group, implicating a causal role for these secondary mitochondrial DNA defects in disease pathophysiology. Individuals with dominant optic atrophy plus phenotypes also had significantly worse visual outcomes, and careful surveillance is therefore mandatory to optimize the detection and management of neurological disability in a group of patients who already have significant visual impairment.
Relaxation on a mesh: a formalism for generalized localization

This paper considers two problems which at first sight appear to be quite distinct: localizing a robot in an unknown environment and calibrating an embedded sensor network. We show that both of these can be formulated as special cases of a generalized localization problem. In the standard localization problem, the aim is to determine the pose of some object (usually a mobile robot) relative to a global coordinate system. In our generalized version, the aim is to determine the pose of all elements in a network (both fixed and mobile) relative to an arbitrary global coordinate system. We have developed a physically inspired 'mesh-based' formalism for solving such problems. This paper outlines the formalism, and describes its application to the concrete tasks of multirobot mapping and calibration of a distributed sensor network. The paper presents experimental results for both tasks obtained using a set of Pioneer mobile robots equipped with scanning laser range-finders.