Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeled urea distribution volume and mortality in the HEMO Study.

BACKGROUND AND OBJECTIVES In the Hemodialysis (HEMO) Study, observed small decreases in achieved equilibrated Kt/V(urea) were noncausally associated with markedly increased mortality. Here we examine the association of mortality with modeled volume (V(m)), the denominator of equilibrated Kt/V(urea). DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Parameters derived from modeled urea kinetics (including V(m)) and blood pressure (BP) were obtained monthly in 1846 patients. Case mix-adjusted time-dependent Cox regressions were used to relate the relative mortality hazard at each time point to V(m) and to the change in V(m) over the preceding 6 months. Mixed effects models were used to relate V(m) to changes in intradialytic systolic BP and to other factors at each follow-up visit. RESULTS Mortality was associated with V(m) and change in V(m) over the preceding 6 months. The association between change in V(m) and mortality was independent of vascular access complications. In contrast, mortality was inversely associated with V calculated from anthropometric measurements (V(ant)). In case mix-adjusted analysis using V(m) as a time-dependent covariate, the association of mortality with V(m) strengthened after statistical adjustment for V(ant). After adjustment for V(ant), higher V(m) was associated with slightly smaller reductions in intradialytic systolic BP and with risk factors for mortality including recent hospitalization and reductions in serum albumin concentration and body weight. CONCLUSIONS An increase in V(m) is a marker for illness and mortality risk in hemodialysis patients.
Immunomodulation of RA Patients' PBMC with a Multiepitope Peptide Derived from Citrullinated Autoantigens

Citrullinated peptides are used for measuring anticitrullinated protein antibodies (ACPA) in rheumatoid arthritis (RA). Accumulation of citrullinated proteins in the inflamed synovium suggests that they may be good targets for inducing peripheral tolerance. In view of the multiplicity of citrullinated autoantigens described as ACPA targets, we generated a multiepitope citrullinated peptide (Cit-ME) from the sequences of major citrullinated autoantigens: filaggrin, β-fibrinogen, vimentin, and collagen type II. We assessed the ability of Cit-ME or the citrullinated β60-74 fibrinogen peptide (β60-74-Fib-Cit) which bears immunodominant citrullinated epitopes (i) to modify cytokine gene expression and (ii) to modulate Treg and Th17 subsets in PBMC derived from newly diagnosed untreated RA patients. RA patient's PBMC incubated with Cit-ME or β60-74-Fib-Cit, showed upregulation of TGF-β expression (16% and 8%, resp.), and increased CD4+Foxp3+ Treg (22% and 19%, resp.). Both peptides were shown to downregulate the TNF-α and IL-1β expression; in addition, Cit-ME reduced CD3+IL17+ T cells. We showed that citrullinated peptides can modulate the expression of anti- and proinflammatory cytokines in PBMC from RA patients as well as the proportions of Treg and Th17 cells. These results indicate that citrullinated peptides could be active in vivo and therefore might be used as immunoregulatory agents in RA patients.
Two-channel analysis of QUELL experimental results

We have improved the model presently used in the thermo-hydraulic code Gandalf, adapting it to cable-in-conduit conductors with central cooling channel such as those developed for the model coils of ITER. In particular the helium flow in an arbitrary number of parallel channels have now independent velocity and thermodynamic state (pressure and temperature). We demonstrate the capability of the new model by means of comparison to measurements taken during the QUELL experiment in SULTAN. We compare in particular data on heat slug at zero current and field in a broad range of energy inputs, as well as data on quench propagation, to simulation results obtained with the single channel approximation and the newly implemented two-channel model. The latter achieves significantly better agreement with experimental data, in particular in the case of slow heating transients such as in heat slug propagation tests.
Spectool 2.4 Beta: A research tool for modular modeling, analysis, and synthesis of discrete event systems.

Condition systems are an excellent choice for the modeling and analysis of distributed systems. A condition system is a distributed Petri net where the distributed models communicate via state-based condition signals. In this paper the salient points of Spectool 2.4 Beta are presented. Spectool 2.4 Beta is a new release of our condition system modeling, analysis, and control synthesis tool. The paper begins with a brief review of our work using condition systems. We then present the features of this tool
A Graph Laplacian Approach to Coordinate-Free Formation Stabilization for Directed Networks

This paper concentrates on coordinate-free formation control for directed networks, for which the dynamic motion of each agent is assumed to be governed only by a local control. We develop a graph Laplacian approach to solve the global and exponential formation stabilization problem using merely relative position measurements between neighbors. First, to capture the sensing and control architectures that are needed to maintain the shape of a formation, a necessary and sufficient topological condition is proposed. Second, a Laplacian-based control law is developed for the stabilization problem of a group of mobile agents to a desired formation shape under both fixed and switching topologies due to temporal node failures. Simulation results are provided to demonstrate that our Laplacian-based formation control strategy is inherently fault-tolerant and robust to node failures.
A Novel Way to Compare Health Care Systems and to Assess Their Potential Competitiveness

Traditionally, health care systems have been compared mainly in terms of their finance, that is, Beveridge‐type vs Bismarck‐type arrangements. This article adopts a novel approach permitting not only comparisons of a broader range of systems but also assessments of their potential competitiveness. This will become an issue at the latest when citizens of the European Union obtain the right to choose their health insurance. Systems are characterised by their so‐called dominant complementary agents, who promise to correct an important failure in the physician–patient relationship but differ in their incentives and their capacity to deal with a number of emerging challenges.
Effects of Simultaneous Deletion of pUL11 and Glycoprotein M on Virion Maturation of Herpes Simplex Virus Type 1

ABSTRACT The conserved membrane-associated tegument protein pUL11 and envelope glycoprotein M (gM) are involved in secondary envelopment of herpesvirus nucleocapsids in the cytoplasm. Although deletion of either gene had only moderate effects on replication of the related alphaherpesviruses herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PrV) in cell culture, simultaneous deletion of both genes resulted in a severe impairment in virion morphogenesis of PrV coinciding with the formation of huge inclusions in the cytoplasm containing nucleocapsids embedded in tegument (M. Kopp, H. Granzow, W. Fuchs, B. G. Klupp, and T. C. Mettenleiter, J. Virol. 78:3024-3034, 2004). To test whether a similar phenotype occurs in HSV-1, a gM and pUL11 double deletion mutant was generated based on a newly established bacterial artificial chromosome clone of HSV-1 strain KOS. Since gM-negative HSV-1 has not been thoroughly investigated ultrastructurally and different phenotypes have been ascribed to pUL11-negative HSV-1, single gene deletion mutants were also constructed and analyzed. On monkey kidney (Vero) cells, deletion of either pUL11 or gM resulted in ca. -fivefold-reduced titers and 40- to 50%-reduced plaque diameters compared to those of wild-type HSV-1 KOS, while on rabbit kidney (RK13) cells the defects were more pronounced, resulting in ca. -50-fold titer and 70% plaque size reduction for either mutant. Electron microscopy revealed that in the absence of either pUL11 or gM virion formation in the cytoplasm was inhibited, whereas nuclear stages were not visibly affected, which is in line with the phenotypes of corresponding PrV mutants. Simultaneous deletion of pUL11 and gM led to additive growth defects and, in RK13 cells, to the formation of large intracytoplasmic inclusions of capsids and tegument material, comparable to those in PrV-ΔUL11/gM-infected RK13 cells. The defects of HSV-1ΔUL11 and HSV-1ΔUL11/gM could be partially corrected in trans by pUL11 of PrV. Thus, our data indicate that PrV and HSV-1 pUL11 and gM exhibit similar functions in cytoplasmic steps of virion assembly.
A Novel Design of Gap-Coupled Sectoral Patch Antenna

Using gap coupling between the elements, an antenna of four sectors by cutting the slots through and through from a circular patch is designed for application in X-band. The bandwidth enhancement along with reduced sidelobes is obtained by marginally or fully moving one of the feeding sectoral patches diagonally away. The results are analyzed for different positions of the slot. A bandwidth of 1.2 GHz in X-band along with a reduced sidelobe level of -15.0 dB and a gain of 12.0 dBi is obtained. An analysis of mutual coupling and parasitic patch effect is also presented and discussed in this letter.
DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis

UNLABELLED DnaSP is a Windows integrated software package for the analysis of the DNA polymorphism from nucleotide sequence data. DnaSP version 3 incorporates several methods for estimating the amount and pattern of DNA polymorphism and divergence, and for conducting neutrality tests. AVAILABILITY For academic uses, DnaSP is available free of charge from: http://www.bio. ub.es/julio/DnaSP.html CONTACT julio@porthos.bio. ub.es
Analysis of urban and vegetation growing in NW Senegal during the last 25 years using medium resolution imagery

Land use and land cover information are key information for Governments in developing countries. In this context, remote sensing satellites like Landsat or SPOT can provide valuable data covering several decades. We have developed a methodology to generate land cover maps with the aim to analyze changes in the last 25 years in the NW region of Senegal. In particular, we have applied the radiometric and atmospheric corrections prior to the classification algorithm or to the generation of vegetation indexes and, finally, to analyze the spatial and temporal variability, post-classification change detection techniques have been applied, providing valuable quantitative information.
Glucose tolerance in pregnancy in South India: relationships to neonatal anthropometry

Background. The incidence of type 2 diabetes is increasing worldwide, most rapidly in developing countries such as India. Exposure as a fetus to maternal gestational diabetes is thought to be a risk factor for developing the disease. This study was set up to determine the incidence of gestational diabetes mellitus in one urban maternity unit in South India and to examine its effect on the offspring's neonatal anthropometry, childhood growth, and glucose/insulin metabolism. This paper reports neonatal outcomes.
The dynamic properties of the Hepatitis C Virus E2 envelope protein unraveled by molecular dynamics

Hepatitis C Virus (HCV) is one of the most persistent human viruses. Although effective therapeutic approaches have been recently discovered, their use is limited by the elevated costs. Therefore, the development of alternative/complementary strategies is an urgent need. The E2 glycoprotein, the most immunogenic HCV protein, and its variants represent natural candidates to achieve this goal. Here we report an extensive molecular dynamics (MD) analysis of the intrinsic properties of E2. Our data provide interesting clues on the global and local intrinsic dynamic features of the protein. Present MD data clearly indicate that E2 combines a flexible structure with a network of covalent bonds. Moreover, the analysis of the two most important antigenic regions of the protein provides some interesting insights into their intrinsic structural and dynamic properties. Our data indicate that a fluctuating β-hairpin represents a populated state by the region E2412−423. Interestingly, the analysis of the epitope E2427−446 conformation, that undergoes a remarkable rearrangement in the simulation, has significant similarities with the structure that the E2430−442 fragment adopts in complex with a neutralizing antibody. Present data also suggest that the strict conservation of Gly436 in E2 protein of different HCV genotypes is likely dictated by structural restraints. Moreover, the analysis of the E2412−423 flexibility provides insights into the mechanisms that some antibodies adopt to anchor Trp437 that is fully buried in E2. Finally, the present investigation suggests that MD simulations should systematically complement crystallographic studies on flexible proteins that are studied in combination with antibodies.
Deep Learning for Environmentally Robust Speech Recognition

Eliminating the negative effect of non-stationary environmental noise is a long-standing research topic for automatic speech recognition but still remains an important challenge. Data-driven supervised approaches, especially the ones based on deep neural networks, have recently emerged as potential alternatives to traditional unsupervised approaches and with sufficient training, can alleviate the shortcomings of the unsupervised methods in various real-life acoustic environments. In this light, we review recently developed, representative deep learning approaches for tackling non-stationary additive and convolutional degradation of speech with the aim of providing guidelines for those involved in the development of environmentally robust speech recognition systems. We separately discuss single- and multi-channel techniques developed for the front-end and back-end of speech recognition systems, as well as joint front-end and back-end training frameworks. In the meanwhile, we discuss the pros and cons of these approaches and provide their experimental results on benchmark databases. We expect that this overview can facilitate the development of the robustness of speech recognition systems in acoustic noisy environments.
Timing of C-arm drape contamination.

BACKGROUND Surgical site infection remains a concern in orthopedic surgery, and contamination of C-arm covers is a potentially modifiable risk factor. METHODS A single-cohort study was conducted using 30 consecutive patients undergoing operative fracture fixation. Cultures were obtained from the C-arm cover after initial draping and every 20 min thereafter. The total number of persons in the operating room (person-hours/h of study time) and the number of door openings were recorded. The C-arm position changes and the time to contamination were monitored. RESULTS The median time from the start of the operation to contamination was 20 min. There was a 17% contamination rate on initial draping, 50% at 20 min, 57% at 40 min, and 80% by 80 min. The C-arms in five cases were not contaminated during the surgery. Time to contamination correlated significantly with lateral position changes (correlation [r]=0.64; p=0.003) but was not related to C-arm position changes (r=0.22; p=0.34), number of door openings (r=0.20; p=0.39), or person-hours/h (r=0.04; p=0.85). CONCLUSIONS Contamination of the C-arm drape occurs often and early during surgery for orthopedic fractures. We recommend minimal contact with the C-arm to avoid contamination of the surgical field.
Decision support in healthcare: determining provider influence on treatment outcomes with robust risk adjustment

Abstract Recent advances in decision support offer a powerful toolkit to monitor, benchmark and improve healthcare quality. Since the underlying demography and prior illness of patients vary across hospitals, performance should be risk-adjusted to allow for fair comparison of providers. While previous research has proposed risk-standardisation models, their estimation still remains a non-trivial task. As a remedy, this paper utilises the least absolute shrinkage operator, LASSO for short, as a Bayesian method as part of a framework to propose a robust technique for estimating the risk-adjusted performance of hospitals. We compare our robust estimation to existing approaches (namely, the case mix approach and hierarchical generalised linear models) and demonstrate its advantages with real data. Our findings show that our method, which is robust and fully automated, can yield useful findings even with small data sets.
Vertex-neighboring multilevel force-directed graph drawing

We introduce a new force-directed graph drawing algorithm for large undirected graphs with at least a few hundreds of vertices. Our algorithm falls into the class of multilevel force-directed graph drawing algorithms. Unlike other multilevel algorithms it has no pre-processing step and it also ignores repulsion forces between pairs of non-adjacent vertices. As a result, our algorithm demonstrably outperforms known multilevel algorithms in terms of running time while keeping the quality of the layout sufficiently good.
Sexual behaviors and sexual risk in a prospective cohort of HIV-positive men and women in New York City, 1994-2002: implications for prevention.

As an ever-increasing number of people infected with HIV are living longer, healthier lives, concerns about continued transmission are growing along with an awareness of the need to develop "prevention for positives. " This study of HIV-positive adults in New York City is the first examination of patterns of sexual behavior in a large, representative cohort of HIV-infected individuals followed over an extended time period. A total of 968 HIV-positive adults were interviewed every 6-12 months between 1994 and 2002 and reported considerable variability in sexual behaviors over time. Many persons were not sexually active at all for months at a time; some continued to have multiple partners. Over one third of the cohort had one or more periods when they had engaged in unprotected sex with a partner who was HIV-negative or status unknown (unsafe sex) and one in five reported exchanging sex. Periods of unsafe sex alternated with periods of safer sex. Predictors of sexual risk varied by gender, and among men who had sex with men, and men sexually active with women only. Contextual factors such as partner relations, housing status, and receipt of HIV services were as important as individual attributes as predictors of unsafe sex and sex exchange. The variability observed in sexual risk behavior reported over time provides new insight into the importance of engaging persons living with HIV in ongoing prevention programs.
Topological analysis of NHE 1 , the ubiquitous Na 1 / H 1 exchanger using chymotryptic cleavage

Shrode, Lamara D. , Bing Siang Gan, Sudhir J. A. D’Souza, John Orlowski, and Sergio Grinstein. Topological analysis of NHE1, the ubiquitous Na1/H1 exchanger, using chymotryptic cleavage. Am. J. Physiol. 275 (Cell Physiol. 44): C431–C439, 1998. —Proteases, glycosidases, and impermeant biotin derivatives were used in combination with antibodies to analyze the subcellular distribution and transmembrane disposition of the Na1/H1 exchanger NHE1. Both native human NHE1 in platelets and epitope-tagged rat NHE1 transfected into antiport-deficient cells were used for these studies. The results indicated that 1) the entire population of exchangers is present on the surface membrane of unstimulated platelets, ruling out regulation by recruitment of internal stores of NHE1; 2) the putative extracellular loops near the NH2 terminus are exposed to the medium and contain all the Nand O-linked carbohydrates; 3) by contrast, the putative extracellular loops between transmembrane domains 9–10 and 11–12 are not readily accessible from the outside and may be folded within the protein, perhaps contributing to an aqueous ion transport pathway; 4) the extreme COOH terminus of the protein was found to be inaccessible to extracellular proteases, antibodies, and other impermeant reagents, consistent with a cytosolic localization; and 5) detachment of ,150 amino acids from the NH2terminal end of the protein had little effect on the transport activity of NHE1.
Evolution of Microcin V and Colicin Ia Plasmids in Escherichia coli

ABSTRACT Survey results and genotypic characterization of Escherichia coli strains demonstrate that the bacteriocins colicin Ia and microcin V coassociate in a strain more often than would be expected by chance. When these two bacteriocins co-occur, they are encoded on the same conjugative plasmid. Plasmids encoding colicin Ia and microcin V are nonrandomly distributed with respect to the genomic background of the host strain. Characterization of microcin V and colicin Ia nucleotide variation, together with the backbone of plasmids encoding these bacteriocins, indicates that the association has evolved on multiple occasions and involves the movement of the microcin V operon, together with the genes iroNEDCB and iss, onto a nonrandom subset of colicin Ia plasmids. The fitness advantage conferred on cells encoding both colicin Ia and microcin V has yet to be determined.
Two-dimensional FEM Analysis of Brillouin Gain Spectra in Acoustic Guiding and Antiguiding Single Mode Optical Fibers

The analysis of optical and acoustic properties of optical fibers is required for accurate Brillouin gain spectrum (BGS) determination. We present a full modal-analysis of the guided optical and acoustic modes based on a two-dimensional finite-element method (2D-FEM) for BGS calculation using COMSOL Multiphysics. We believe that this method will be helpful in analyzing and designing special fibers for applications, such as fiber amplifiers with significant SBS (Stimulated Brillouin Scattering) suppression or Brillouin-based fibersensors. The model is adapted for BGS evaluation of any single mode fiber (in term of optical mode) based on its profile, namely its geometry, and its doping composition. Compared to standard multi-layer methods limited to axially-symmetric fibers [1], the 2D-FEM analysis enables the BGS computation even for more complicated geometries, such as PANDA polarization-maintaining fiber where the optical index and the material stress are azimuthally dependant. The results of numerical modeling have shown good agreement with measured Brillouin spectra for different types of silica fibers. Examples are given for a standard GeO2-doped core fiber (standard fiber for telecommunication applications), Fluor-doped cladding fiber (acoustic anti-waveguide) and PANDA fiber.
Bayesian linear discriminant analysis with hybrid ABC-PSO classifier for classifying epilepsy from EEG signals

One of the serious neurological disorders affecting millions of people in the world is epilepsy. Epilepsy is a disease of the brain where the neurons behave in an abnormal fashion thereby leading to seizures. To monitor the activities of the brain, Electroencephalography (EEG) signals play a vital role especially for the analysis and diagnosis of epilepsy. The neurophysiologist visually examines the signals of the brain for the identification of epileptic seizures and abnormalities in it. It is quite a difficult procedure because of its prolonging time consumption and erroneous decisions made by humans and so automatic seizure detection and classification systems came into existence. In this paper, the epilepsy classification was done in two stages, firstly with Bayesian Linear Discriminant Analysis (BLDA) and the output obtained from it is further optimized and classified with Hybrid Artificial Bee Colony - Particle Swarm Optimization (ABC-PSO) classifier. Results show that an average classification accuracy of 94% is obtained when classified with BLDA classifier and on further optimization and classification, an average classification accuracy of 97.91% is obtained when classified with ABC-PSO classifier.