Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence Similarity of Clostridium difficile Strains by Analysis of Conserved Genes and Genome Content Is Reflected by Their Ribotype Affiliation

PCR-ribotyping is a broadly used method for the classification of isolates of Clostridium difficile, an emerging intestinal pathogen, causing infections with increased disease severity and incidence in several European and North American countries. We have now carried out clustering analysis with selected genes of numerous C. difficile strains as well as gene content comparisons of their genomes in order to broaden our view of the relatedness of strains assigned to different ribotypes. We analyzed the genomic content of 48 C. difficile strains representing 21 different ribotypes. The calculation of distance matrix-based dendrograms using the neighbor joining method for 14 conserved genes (standard phylogenetic marker genes) from the genomes of the C. difficile strains demonstrated that the genes from strains with the same ribotype generally clustered together. Further, certain ribotypes always clustered together and formed ribotype groups, i.e. ribotypes 078, 033 and 126, as well as ribotypes 002 and 017, indicating their relatedness. Comparisons of the gene contents of the genomes of ribotypes that clustered according to the conserved gene analysis revealed that the number of common genes of the ribotypes belonging to each of these three ribotype groups were very similar for the 078/033/126 group (at most 69 specific genes between the different strains with the same ribotype) but less similar for the 002/017 group (86 genes difference). It appears that the ribotype is indicative not only of a specific pattern of the amplified 16S–23S rRNA intergenic spacer but also reflects specific differences in the nucleotide sequences of the conserved genes studied here. It can be anticipated that the sequence deviations of more genes of C. difficile strains are correlated with their PCR-ribotype. In conclusion, the results of this study corroborate and extend the concept of clonal C. difficile lineages, which correlate with ribotypes affiliation.
Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.

The biological role, biochemical function, and structure of uncharacterized protein sequences is often inferred from their similarity to known proteins. A constant goal is to increase the reliability, sensitivity, and accuracy of alignment techniques to enable the detection of increasingly distant relationships. Development, tuning, and testing of these methods benefit from appropriate benchmarks for the assessment of alignment accuracy.Here, we describe a benchmark protocol to estimate sequence-to-sequence and sequence-to-structure alignment accuracy. The protocol consists of structurally related pairs of proteins and procedures to evaluate alignment accuracy over the whole set. The set of protein pairs covers all the currently known fold types. The benchmark is challenging in the sense that it consists of proteins lacking clear sequence similarity. Correct target alignments are derived from the three-dimensional structures of these pairs by rigid body superposition. An evaluation engine computes the accuracy of alignments obtained from a particular algorithm in terms of alignment shifts with respect to the structure derived alignments. Using this benchmark we estimate that the best results can be obtained from a combination of amino acid residue substitution matrices and knowledge-based potentials.
Sesar security 2020: How to embed and assure security in system-of-systems engineering?

Significant efforts are underway to modernise global air traffic management systems. This will result in a level of connectivity between different systems that has never before been achieved, creating a `system of systems' that requires a very high level of dependability. To achieve this dependability, security must be designed-in rather than relying on hardening of systems post implementation. This is also expected to minimise the costs of security. The European ATM modernisation programme, SESAR, has been taking a systems engineering approach to ensure that R&D is rapidly transferred to industrialisation and then deployment. This approach has been applied to security, organised around `operational focus areas' that represent discrete operational improvements. In such a complex programme, traditional risk analysis and mitigation was thought to be limited when attempting a system wide coherence for security. Hence the SESAR programme is adopting a `security case' approach, drawing on lessons learned in safety cases, validation & verification of ATM R&D, and aligned to the system engineering approach.
TactileTape: low-cost touch sensing on curved surfaces

TactileTape is a one-dimensional touch sensor that looks and behaves like regular tape. It can be constructed from everyday materials (a pencil, tin foil, and shelf liner) and senses single-touch input on curved and deformable surfaces. It is used as a roll of touch sensitive material from which designers cut pieces to quickly add touch sensitive strips to physical prototypes. TactileTape is low-cost, easy to interface, and, unlike current non-planar touch solutions [2,7,11], it is better adapted for the rapid exploration and iteration in the early design stage.
Index-based approximate XML joins

XML data integration tools are facing a variety of challenges for their efficient and effective operation. Among these is the requirement to handle a variety of inconsistencies or mistakes present in the data sets. We study the problem of integrating XML data sources through index assisted join operations, using notions of approximate match in the structure and content of XML documents as the join predicate. We show how a well known and widely deployed index structure, namely the R-tree, can be adopted to improve the performance of such operations. We propose novel search and join algorithms for R-trees adopted to index XML document collections. We also propose novel optimization objectives for R-tree construction, making R-trees better suited for this application.
Heterogeneous Chromosomal Aberrations in Intraductal Breast Lesions Adjacent to Invasive Carcinoma

There is evidence that breast cancer is a heterogeneous disease phenotypically as well as molecular biologically. So far, heterogeneity on the molecular biological level has not been investigated in potential precursor lesions, such as ductal hyperplasia (DH) and ductal carcinoma in situ (DCIS). In this study we applied comparative genomic hybridization (CGH) to formalin‐fixed, paraffin‐embedded breast tissue with DH and DCIS, adjacent to invasive ductal carcinoma (IDC), to screen these potential precursor lesions for whole genomic chromosomal imbalances. Laser‐microdissection was used to select pure cell populations from the sections. Isolated DNA was amplified by degenerate oligonucleotide primed PCR (DOP‐PCR) and further processed for CGH analysis. Investigating multiple samples (n=25) from four patients we found an average of 5.6 ± 0.9 (mean ± SEM) chromosomal imbalances already present in DH. In the twelve DCIS lesions an average of 10.8 (±0.9) aberrations was identified with 14.8 (±0.8) aberrations in the four adjacent IDC lesions. The increasing number of chromosomal changes in parallel with the histopathological sequence corroborate the hypothesis, that the carcinomas may have developed through a sequential progression from normal to proliferative epithelium and eventually into carcinoma. However, heterogeneous results were identified in the multiple samples per entity from the same patient, demonstrated mainly in the DCIS samples in the chromosomal regions 6p, 9p, 11q, 16p and 17q, in the DH samples by 3p, 16p and 17q. This heterogeneous findings were most pronounced within the DH and was less in the DCIS and IDC samples. The only aberration consistently found in all samples – even in all DH samples – was amplification of the 20q13 region. Our results demonstrate, that the applied combination of laser‐microdissection, DOP‐PCR and CGH, may serve to analyse breast carcinogenesis pathways in suitable histological material. However, so far, it is unclear how to handle heterogeneous results and these make identification of relevant changes more difficult. Setting a threshold and valuating only those chromosomal changes which are present in a majority of samples may be one possibility. This involves however, the risk that infrequent but possibly significant aberrations may be missed. Figures on http://www.esacp. org/acp/2000/20‐1/aubele.htm.
The Pathway Logic Assistant

Pathway Logic [6, 7, 23] is an approach to modeling cellular processes based on formal methods. In particular, formal executable models of processes such as signal transduction, metabolic pathways, and immune system cell-cell signaling are developed using the rewriting logic language Maude [3, 4] and a variety of formal tools are used to query these models. An important objective of Pathway logic is to reflect the ways that biologists think about problems using informal models, and to provide bench biologists with tools for computing with and analyzing these models that are natural. This paper describes an interface, representation, and reasoning system for Pathway Logic that is a substantial step towards achieving these goals. Using the reflective capabilities of Maude, several alternative representations are derived to support use of different tools for visualization and analysis. The Pathway Logic Assistant (PLA) manages these different representations and, using the IOP+IMaude framework [14], provides a user interface that supports visualization and interaction with the models, and access to tools such as the Pathalyzer for carrying out in silico experiments. In particular, PLA uses Petri nets which provide visual representations and algorithms for answering reachability queries interactively, displaying the results in a way that is natural for biologists. Being able to use alternative representations with different expressive capabilities and tools for analysis is important both for scaling and being able to focus on different properties. In the presence of multiple representations it is crucial to be able move between representations in semantically meaningful ways, preserving relevant properties. In this paper we define mappings between a class of rewriting logic models of biological processes and Petri net models, and transformations that specialize Petri net models to specific queries, and sketch correctness proofs. We begin with a brief overview of Pathway Logic and the ways that biologists can compute with and query these models to motivate the mappings.
The Outbursts of Dwarf Novae

We present a numerical scheme for the evolution of an accretion disc through a dwarf nova outburst. We introduce a time-varying artificial viscosity into an existing smoothed particle hydrodynamics code optimised for two and three-dimensional simulations of accretion discs. The technique gives rise to coherent outbursts and can easily be adapted to include a complete treatment of thermodynamics. We apply a two-dimensional isothermal scheme to the system SS Cygni and present a wide range of observationally testable results.
Gridlan: a Multi-purpose Local Grid Computing Framework

In scientific computing, more computational power generally implies faster and possibly more detailed results. The goal of this study was to develop a framework to submit computational jobs to powerful workstations underused by nonintensive tasks. This is achieved by using a virtual machine in each of these workstations, where the computations are done. This group of virtual machines is called the Gridlan. The Gridlan framework is intermediate between the cluster and grid computing paradigms. The Gridlan is able to profit from existing cluster software tools, such as resource managers like Torque, so a user with previous experience in cluster operation can dispatch jobs seamlessly. A benchmark test of the Gridlan implementation shows the system's suitability for computational tasks, principally in embarrassingly parallel computations.
An Efficient State-Space Model for Joint Tempo and Meter Tracking

Dynamic Bayesian networks (e.g., Hidden Markov Models) are popular frameworks for meter tracking in music because they are able to incorporate prior knowledge about the dynamics of rhythmic parameters (tempo, meter, rhythmic patterns, etc.). One popular example is the bar pointer model, which enables joint inference of these rhythmic parameters from a piece of music. While this allows the mutual dependencies between these parameters to be exploited, it also increases the computational complexity of the models. In this paper, we propose a new state-space discretisation and tempo transition model for this class of models that can act as a drop-in replacement and not only increases the beat and downbeat tracking accuracy, but also reduces time and memory complexity drastically. We incorporate the new model into two state-of-the-art beat and meter tracking systems, and demonstrate its superiority to the original models on six datasets.
Trade Union Membership and Works Councils in West Germany

The fraction of works councillors belonging to a trade union in Germany is much higher than union density among employees. If works councils represent the face of unions, union membership of employees should be related positively to the existence of works councils and their proximity to unions. Using data from the German Socio-Economic-Panel SOEP for West Germany we find that (a) works councillors exhibit a higher probability of being a union member, (b) the mere existence of a works council within an establishment has no significant impact on union membership and (c) a ten percent decrease in the average share of unionised works councillors coincides with a ten percent fall in the probability of being a union member. Hence, the decline in the unionisation of works councillors and the fall in union density in West Germany are closely linked.
High frequency preserving fast compressive sensing based on wavelet block orthogonal matching pursuit

Due to large data set, block processing is usually applied for fast compressive sensing (CS) reconstruction; however, it gives the undesired blocking artifact in reconstructed data. In order to reduce blocking artifact and preserve high frequency, this paper proposes a novel block processing on wavelet domain instead of spatial domain. No post-processing nor special mapping is included. CS is applied only on blocks where the data are really sparse. An enhancing process, often included for artifact reduction, is no longer necessary. Our algorithm was evaluated by reconstructing three standard images (Lena, Mandrill and Peppers) and then compared with scrambled block hadamard ensemble (SBHE) and block-based CS sampling with a smoothed PL variant using directional discrete wavelet transform (BCS-SPL-DDWT). In the experiment, it provided better reconstruction both objectively (PSNR) and subjectively at low measurement rate. It gave the sharpest image in all cases. Details were preserved and blocking artifact was not detectable.
Development and validation of a system for clinical assessment of gait cycle parameter in patients with idiopathic normal pressure hydocephalus

A number of parameters have been identified as characteristic of the walking pattern in patients with INPH. Most of these have been identified through qualitative surveys and manually conducted test batteries. In order to obtain quantitative, standardized and objective measures, which enable studies based on larger patient populations and comparable results, there is a need for a user-friendly system that can measure specific key parameters over time in a reliable manner in everyday clinical work. Step height, width and the variability in the gait cycle are such parameters which are interesting research areas for this group of patient.Problems with balance and gait are very common in other patient groups as well, particularly in neurological diseases such as Parkinson's disease, multiple sclerosis and stroke.This is the reason that the development of this gait analyzer is performed. Giving access to a simple and objective method for estimating gait and balance ability in clinical routine investigations would increase the ability to provide the right kind of treatment, confirm treatment results, and conducting larger research studies. Therefore, this equipment can contribute to the assessment of diseases which contain impaired gait. As a first test of the usability and for the validation of accuracy and repeatability of the equipment a group of healthy volunteers was used. Results from tests on healthy subjects show god repeatability between measurements, for step width at normal gait the difference was -0,2 ±0,34 cm (mean, ±SD) and step height 0,69 ±3,34 cm. The stride time variability in the healthy group where very small 0,00048 ±0,00028 s2 with a difference between test of 0,000019 ±0,00038 s2. Three pilot patients have been tested where we have clearly seen indications of increased stride time variability and reduced step height.
SUBMISSION IDENTIFICATION AND TRACKING NUMBER CREATED : 14001 3 2

The impact of customer satisfaction on results and competitiveness of firms and countries has been the focus of studies around the world. This paper attempts to test a model that measures satisfaction and the nomological net of this construct with loyalty, expectations, value and quality level perceived in service organizations, specifically at institutions for higher education. With a sample of 604 respondents, this research applies structural equation modeling and shows that satisfaction and service quality have a great impact on loyalty. The study also raises questions about the relation among expectations, satisfaction and value, contributing for competitiveness of organizations through quality, value and satisfaction delivered to customers.
A FRAX Experience in Korea: Fracture Risk Probabilities with a Country-specific Versus a Surrogate Model

Background Recently, a Korean fracture-risk assessment tool (FRAX) model has become available, but large prospective cohort studies, which are needed to validate the model, are still lacking, and there has been little effort to evaluate its usefulness. This study evaluated the clinical usefulness of the FRAX model, a FRAX developed by the World Health Organization, in Korea. Methods In 405 postmenopausal women and 139 men with a proximal femoral fracture, 10-year predicted fracture probabilities calculated by the Korean FRAX model (a country-specific model) were compared with the probabilities calculated with a FRAX model for Japan, which has a similar ethnic background (surrogate model). Results The 10-year probabilities of major osteoporotic and hip fractures calculated by the Korean model were significantly lower than those calculated by the Japanese model in women and men. The fracture probabilities calculated by each model increased significantly with age in both sexes. In patients aged 70 or older, however, there was a significant difference between the two models. In addition, the Korean model led to lower probabilities for major osteoporotic fracture and hip fracture in women when BMD was excluded from the model than when it was included. Conclusions The 10-year fracture probabilities calculated with FRAX models might differ between country-specific and surrogate models, and caution is needed when applying a surrogate model to a new population. A large prospective study is warranted to validate the country-specific Korean model in the general population.
Internet Secure Communications Between Citizens and Public Administrations

The increasing number of Internet users forecasts a great importance of this communication mechanism in the near future, and both the Public Administrations and the citizens can substantially benefit from it. Although there are already some working experiences that try to make use of Internet to communicate them, two are the main technological issues that prevent the Public Administrations from extensively making use of Internet for interacting with the citizens. First, the lack of mechanisms that guarantee the security and privacy of the communications; and second, the lack of a mature software technology for the development of applications over this kind of open, distributed and evolving system. This paper presents the fundamentals of the Project “Development of a Software Framework for the Secure Communication between the Public Administrations and the Citizens using Internet”. This Project, whose main objective is to design a security-oriented software architecture for AdministrationCitizens communication, was recently accepted to be included in the Spanish R&D Programme.
Effects of Hydrostatic Pressure on Carcinogenic Properties of Epithelia

The relationship between chronic inflammation and cancer is well known. The inflammation increases the permeability of blood vessels and consequently elevates pressure in the interstitial tissues. However, there have been only a few reports on the effects of hydrostatic pressure on cultured cells, and the relationship between elevated hydrostatic pressure and cell properties related to malignant tumors is less well understood. Therefore, we investigated the effects of hydrostatic pressure on the cultured epithelial cells seeded on permeable filters. Surprisingly, hydrostatic pressure from basal to apical side induced epithelial stratification in Madin-Darby canine kidney (MDCK) I and Caco-2 cells, and cavities with microvilli and tight junctions around their surfaces were formed within the multi-layered epithelia. The hydrostatic pressure gradient also promoted cell proliferation, suppressed cell apoptosis, and increased transepithelial ion permeability. The inhibition of protein kinase A (PKA) promoted epithelial stratification by the hydrostatic pressure whereas the activation of PKA led to suppressed epithelial stratification. These results indicate the role of the hydrostatic pressure gradient in the regulation of various epithelial cell functions. The findings in this study may provide clues for the development of a novel strategy for the treatment of the carcinoma.
Potential Use of Proximate and Fatty Acid Composition to Distinguish Between Cultured and Wild Largemouth Bass (Micropterus salmoides)

Cultured largemouth bass (LMB) cannot be sold as food in some lucrative markets due to regulatory restric- tions that protect wild LMB. Distinguishing between cultured and wild fish could open food markets for cultured fish. Wild LMB eat freshwater fish and cultured LMB eat diets high in marine fish meal and oil, which should produce differ- ences in flesh composition. We analyzed the proximate and fatty acid composition of wild and cultured LMB muscle to determine the potential for distinguishing fish origin analytically. Protein and moisture were higher in wild fish, while lipid was higher in cultured fish. The n-3 and n-6 fatty acids, long-chain polyunsaturated fatty acids (LC-PUFA), and the ratio of n-3 to n-6 fatty acids all differed between cultured and wild fish. The n-3 to n-6 ratio and n-3 LC-PUFA were higher in cultured fish, while elevated arachidonic acid (20:4n-6) in wild fish was a key distinguishing feature.