Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between Hepatitis C Virus and Very-Low-Density Lipoprotein (VLDL)/LDL Analyzed in Iodixanol Density Gradients

ABSTRACT Hepatitis C virus (HCV) RNA circulates in the blood of persistently infected patients in lipoviroparticles (LVPs), which are heterogeneous in density and associated with host lipoproteins and antibodies. The variability and lability of these virus-host complexes on fractionation has hindered our understanding of the structure of LVP and determination of the physicochemical properties of the HCV virion. In this study, HCV from an antibody-negative immunodeficient patient was analyzed using three fractionation techniques, NaBr gradients, isotonic iodixanol, and sucrose gradient centrifugation. Iodixanol gradients were shown to best preserve host lipoprotein-virus complexes, and all HCV RNA was found at densities below 1.13 g/ml, with the majority at low density, ≤1.08 g/ml. Immunoprecipitation with polyclonal antibodies against human ApoB and ApoE precipitated 91.8% and 95.0% of HCV with low density, respectively, suggesting that host lipoprotein is closely associated with HCV in a particle resembling VLDL. Immunoprecipitation with antibodies against glycoprotein E2 precipitated 25% of HCV with low density, providing evidence for the presence of E2 in LVPs. Treatment of serum with 0.5% deoxycholic acid in the absence of salt produced HCV with a density of 1.12 g/ml and a sedimentation coefficient of 215S. The diameters of these particles were calculated as 54 nm. Treatment of serum with 0.18% NP-40 produced HCV with a density of 1.18 g/ml, a sedimentation coefficient of 180S, and a diameter of 42 nm. Immunoprecipitation analysis showed that ApoB remained associated with HCV after treatment of serum with deoxycholic acid or NP-40, whereas ApoE was removed from HCV with these detergents.
Intelligent Visual Analytics Queries

Visualizations of large multi-dimensional data sets, occurring in scientific and commercial applications, often reveal interesting local patterns. Analysts want to identify the causes and impacts of these interesting areas, and they also want to search for similar patterns occurring elsewhere in the data set. In this paper we introduce the Intelligent Visual Analytics Query (IVQuery) concept that combines visual interaction with automated analytical methods to support analysts in discovering the special properties and relations of identified patterns. The idea of IVQuery is to interactively select focus areas in the visualization. Then, according to the characteristics of the selected areas, such as the data dimensions and records, IVQuery employs analytical methods to identify the relationships to other portions of the data set. Finally, IVQuery generates visual representations for analysts to view and refine the results. IVQuery has been applied successfully to different real-world data sets, such as data warehouse performance, product sales, and sever performance analysis, and demonstrates the benefits of this technique over traditional filtering and zooming techniques. The visual analytics query technique can be used with many different types of visual representation. In this paper we show how to use IVQuery with parallel coordinates, visual maps, and scatter plots.
Efficient Parallel Simulation of Mobile Wireless Networks by Run-time Prediction of Multi-hop Propagation Delay

In this paper, we propose a method to improve the performance of parallel and distributed simulation of multi-hop mobile wireless networks. We assume that the simulation field is divided into several pieces and is simulated by multiple parallel processes which synchronize conservatively, i.e., without violation of causality. The basic idea of our approach is to predict the lower bounds of timestamps of "potential" upcoming events which cause inter-process messages based on the timestamps of the currently scheduled events plus minimum multi-hop propagation delay estimated in run-time. By this prediction method, we are able to enlarge the lookahead of parallel processes, and their concurrency can be enhanced. We have implemented the parallel and distributed version of our network simulator MobiREAL, and have also implemented this mechanism. The experimental results have shown that we could achieve 50% speed up in average compared with the version using static lookahead in the simulation of end-to-end communications over 1,200 nodes.
Serological responses of adult dogs to revaccination against distemper, parvovirus and rabies

Serum antibody titres to canine distemper virus (cdv), canine parvovirus (cpv) and rabies were measured in dogs that had not been revaccinated annually and compared with the titres in a control group of regularly vaccinated animals; 83 per cent (171 of 207) of the dogs vaccinated against cdv one or more years earlier had serum neutralising antibody titres equal to or greater than 16; 64 per cent (136 of 213) of the dogs vaccinated against cpv one or more years earlier had haemagglutination inhibiting titres equal to or greater than 80; and 59 per cent (46 of 78) of the dogs vaccinated against rabies two or more years earlier had serum neutralising antibody titres equal to or greater than 0·5 iu/ml. Three weeks after a single booster vaccination the dogs' antibody titres against cdv had increased above the threshold level in 94 per cent of the dogs, against cpv in 68 per cent, and against rabies in 100 per cent.
Paediatric Care in General Practice: an Experiment in Collaboration

A project of joint consultation between a paediatrician and several general practitioners serving a group practice of 15,000 patients has shown that outpatient clinics held at a group-practice centre (when 36 children were seen at 78 consultations over 18 months) reduced the overall work-load, eliminated dual care, and directly benefited the doctors, the children, and their families.
Genetic demography at the leading edge of the distribution of a rabies virus vector

Abstract The common vampire bat, Desmodus rotundus, ranges from South America into northern Mexico in North America. This sanguivorous species of bat feeds primarily on medium to large‐sized mammals and is known to rely on livestock as primary prey. Each year, there are hotspot areas of D. rotundus‐specific rabies virus outbreaks that lead to the deaths of livestock and economic losses. Based on incidental captures in our study area, which is an area of high cattle mortality from D. rotundus transmitted rabies, it appears that D. rotundus are being caught regularly in areas and elevations where they previously were thought to be uncommon. Our goal was to investigate demographic processes and genetic diversity at the north eastern edge of the range of D. rotundus in Mexico. We generated control region sequences (441 bp) and 12‐locus microsatellite genotypes for 602 individuals of D. rotundus. These data were analyzed using network analyses, Bayesian clustering approaches, and standard population genetic statistical analyses. Our results demonstrate panmixia across our sampling area with low genetic diversity, low population differentiation, loss of intermediate frequency alleles at microsatellite loci, and very low mtDNA haplotype diversity with all haplotypes being very closely related. Our study also revealed strong signals of population expansion. These results follow predictions from the leading‐edge model of expanding populations and supports conclusions from another study that climate change may allow this species to find suitable habitat within the U.S. border.
Effects of Nonlamellar-prone Lipids on the ATPase Activity of SecA Bound to Model Membranes*

The effect of nonlamellar-prone lipids, diacylglycerol (DG) and phosphatidylethanolamine (PE), on the ATPase activity of SecA was examined. When Escherichia coli PE of the standard vesicles composed of 60 mol% of this lipid and 40 mol% of dioleoylphosphatidylglycerol (DOPG) is gradually replaced with either dioleoylglycerol (DOG) or dioeloyl PE (DOPE), the ATPase activity of SecA present together increased appreciably. On the other hand, when E. coli PE of the standard vesicles was replaced with DOG analogs, the SecA ATPase activity decreased slightly, and when replaced with phosphatidylcholine the decrease in the ATPase activity was more appreciable. When DOPE or E. coli PE was added to PC vesicles, the SecA ATPase activity was enhanced only slightly, suggesting that the hexagonal II structure per se is not important for the ATPase activity increase. It was observed that DOG induced phase separation of PG, and the lamellar-hexagonal II (L-HII) transition temperature of vesicles decreased by about 10 °C. The DOG analogs had no effect on these properties, suggesting the importance of the phase separation of PG and the decrease of L-HIItransition temperature of lipid bilayers to the SecA ATPase activity. The phase separation of PG by Ca2+ also brought about increased ATPase activity of SecA, underlining the importance of phase separation of PG for the enzyme activity. The incorporation of DOG or DOPE in the vesicle also increased the amount of SecA bound to model membranes and the extent of SecA penetration into the membrane. Studies with vesicles without SecA showed increased exposure of hydrophobic acyl chains when the DOG was present. Taken together, these observations suggest that the phase separation of PG and/or the bilayer penetration of SecA are mainly responsible for the enhanced SecA-vesicle interaction with concomitant increase in SecA ATPase activity.
Stress-Strain Responses of Multi-Phase CoCrCuMnNi and CoCrMnFeCu Alloys

Stress-strain responses and microstructure of multi-phase CoCrCuMnNi and CoCrMnFeCu alloys in which Fe or Ni was replaced by Cu from Cantor alloy were studied. The deformation mechanisms of CoCrCuMnNi and CoCrMnFeCu were observed to be influenced by the presence of brittle sigma phase and the separated Cu-rich and the matrix phase. CoCrCuMnNi exhibited the relatively lower strength and excellent deformability, while CrMnFeCoCu alloy exhibited higher strength and lower ductility. The higher strength and the lower ductility of CoCrCuMnNi is associated with the presence more frequent and coarser sigma phase than those in CoCrCuMnNi.
Feature Pairs Connected by Lines for Object Recognition

In this paper we exploit image edges and segmentation maps to build features for object category recognition. We build a parametric line based image approximation to identify the dominant edge structures. Line ends are used as features described by histograms of gradient orientations. We then form descriptors based on connected line ends to incorporate weak topological constraints which improve their discriminative power. Using point pairs connected by an edge assures higher repeatability than a random pair of points or edges. The results are compared with state-of-the-art, and show significant improvement on challenging recognition benchmark Pascal VOC 2007. Kernel based fusion is performed to emphasize the complementary nature of our descriptors with respect to the state-of-the-art features.
On the power efficiency for cognitive radio networks with multiple relays

In this paper, we study and analyze cooperative cognitive radio networks with multiple secondary users (SUs). Each SU is considered a prospective relay for the primary user (PU) besides having its own data demand. The proposed scheme leverages the spectral efficiency of the system via allowing two SUs to transmit simultaneously thanks to dirty-paper coding. We propose a power allocation policy that minimizes the average transmitted power at each SU. Moreover, we are concerned with enhancing the throughput of both primary and secondary links. Towards this objective, we investigate multiple opportunistic relay selection policies. We develop a mathematical framework for deriving stability conditions for the queues involved in the system using outage probabilities. Results reveal that we achieve better performance in terms of average power and throughput as compared to uniform power allocation schemes proposed earlier in literature. Extensive numerical simulations are conducted to validate our theoretical findings.
Matrilinear phylogeography of Atlantic salmon (Salmo salar L.) in Europe and postglacial colonization of the Baltic Sea area

Sixty‐four samples from 46 salmon populations totalling 2369 specimens were used for polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis of the mitochondrial ND1 region. The final analyses included 3095 specimens from 60 populations in Northern Europe. A subsample was analysed by RFLP of ND3/4/5/6. Representative RFLP haplotypes from different parts of the distribution area were sequenced and the phylogeny of European haplotypes and their relations to the North American lineage was described. The four common European haplotypes derive from the ancestral ND1‐BBBA (rooting the European clade to the North American) by one‐step substitutions: AAAA < AABA < BBBA > BBBB. The Swedish west‐coast populations differ from the geographically close southern Baltic, indicating absence of inward and limited outward gene flow through the Danish straits during the last 8000 years. Within the Baltic Sea, only three ND1 haplotypes were detected and there was no variation for ND3/4/5/6. In the whole southern Baltic and in lakes Vänern, Ladoga and Onega the haplotype AABA dominated. Proposed postglacial colonization routes to the Baltic Sea are discussed in relation to the haplotype distribution pattern.
Computation of Alias Sets from Shape Graphs for Comparison of Shape Analysis Precision

Various shape analysis algorithms have been introduced but their relation in terms of precision often remains unclear as different analyses use different representations of analysis results. The aim of our work is to extract alias sets from shape analysis results to compute a relative precision factor that expresses for a given program how much more precise one analysis is than the other. We present a significant improvement over an existing algorithm based on 3-valued logic to compute alias sets from shape graphs. Instead of looking only at the final nodes in pointer access paths, our common tail algorithm takes sequences of selectors into account. The common tail algorithm is strictly more precise than the existing algorithm by Reps, Sagiv, and Wilhelm, for our benchmarks we can reduce the number of conservative results by a factor of up to 5 in the best case while incurring an additional analysis overhead that is below 10% even in the worst case of our benchmarks. We selected two well-known graph-based shape analyses that use different representations of analysis results to demonstrate the usefulness of our approach. The shape analysis proposed by Nielson, Nielson & Hankin (NNH) and the analysis by Sagiv, Reps & Wilhelm (SRW) were implemented for a subset of C++ in the SATIrE program analysis framework. We are thus able to determine that NNH is more precise than SRW by a factor of 1.62 on average for our set of benchmarks.
From multilingual to polyglot speech synthesis

This paper proposes a distinction between existing multilingual synthesis systems and mixed-lingual or polyglot synthesis systems. The latter should be capable of synthesising with the same voice utterances which contain foreign language words or word groups. As a first step towards polyglot synthetic speech, the design and realisation of a 4-lingual single-speaker diphone inventory is detailed. The first results show that mixedlingual sentences can be synthesised using this inventory. Further work will focus on multilingual text analysis and prosodic modelling in order to create a complete polyglot TTS system.
Data-driven design of a cascaded observer for battery state of health estimation

The design of an observer for battery state of charge (SoC) and state of health (SoH) using data-driven models is addressed. SoH estimation is an important issue in battery management system design for (hybrid) electrical vehicles. Without SoH correction, the accuracy of the SoC indication system will decrease progressively with battery age/degradation. In order to take the battery degradation into account, ageing data analysis using data-driven models and the associated model adaptation is addressed. Furthermore, a cascaded observer structure for combined SoC and SoH estimation is presented and preliminary results using real measurement data demonstrate the performance of the proposed concepts.
An Ensemble Approach for Expanding Queries

Abstract : In our TREC participation, we used an ensemble approach in query expansion. Query expansion, such as synonym expansion, had shown promising results in medical literature search. On the other hand, some of the 2011 papers reported worse results from expansion. Since there are multiple knowledge sources available and each resource has clear strengths and weaknesses, we tested the combination of three expansion methods versus each individual method. We found that the ensemble approach performed better (in terms of average infAP, infNDCG, R-prec, and P10) than the individual methods and better than the Lucene baseline. The individual expansion methods, however, did not improve the baseline Lucene performance. We also performed an unofficial run using a concept index to boost the query performance, which led to small improvements in infAP, infNDCG, and R-prec.
Rationally designed meta-implants: a combination of auxetic and conventional meta-biomaterials

Rationally designed meta-biomaterials present unprecedented combinations of mechanical, mass transport, and biological properties favorable for tissue regeneration. Here we introduce hybrid meta-biomaterials with rationally-distributed values of negative (auxetic) and positive Poisson's ratios, and use them to design meta-implants that unlike conventional implants do not retract from the bone under biomechanical loading. We rationally design and additively manufacture six different types of meta-biomaterials (three auxetic and three conventional), which then serve as the parent materials to six hybrid meta-biomaterials (with or without transitional regions). Both single and hybrid meta-biomaterials are mechanically tested to reveal their full-field strain distribution by digital image correlation. The best-performing hybrid meta-biomaterials are then selected for the design of meta-implants (hip stems), which are tested under simulated-implantation conditions. Full-field strain measurements clearly show that, under biomechanical loading, hybrid meta-implants press onto the bone on both the medial and lateral sides, thereby improving implant–bone contact and potentially implant longevity.
Nosocomial outbreak caused by antibiotic-resistant strain of Salmonella typhimurium acquired from dairy cattle.

Lung biopsy showed parenchymal, peribronchial and alveolar septal infiltration without any vascular congestion. Evidently the patient needed an alternative form of therapy, one directed specifically at the pulmonary lesions. Following the first course of radiotherapy, 200 rad to the entire lung field, a remarkable improveme.nt was noted in the patient's respiratory status. A total of 600 rad was given over 3 days. The pulmonary capillary diffusion defect lessened dramatically, such that respiratory support was no longer necessary at the end of the radiotherapy. Chest roentgenograms then showed remarkable clearing of the infiltration, which had completely resolved 1 week later. There was no recurrence of the pulmonary problems for the subsequent 30 days that the patient lived. We hope that this case helps to bring to light a seemingly forgotten complication of leirkemia and a new dimension in therapy for leukemic lung infiltration. The response to this relatively simple treatment may be dramatic.
Seroprevalence and Associated Factors of 9-Valent Human Papillomavirus (HPV) Types among Men in the Multinational HIM Study

Background Human papillomavirus (HPV) is one of the most common sexually transmitted infections worldwide. Recently a 9-valent HPV (9vHPV) prophylactic vaccine was licensed. Seroprevalence prior to vaccine dissemination is needed for monitoring vaccine effectiveness over time. Few studies have assessed the seroprevalence of 9vHPV types in men. Objectives To investigate the seroprevalence of 9vHPV vaccine types and associated risk factors among men residing in Brazil, Mexico, and the United States. Methods Six hundred men were randomly selected from the HPV Infection in Men (HIM) Study. Archived serum specimens collected at enrollment were tested for antibodies against nine HPV types (6, 11, 16, 18, 31, 33, 45, 52 and 58) using a glutathione S-transferase (GST) L1-based multiplex serologic assay. Socio-demographic, lifestyle and sexual behavior data at enrollment were collected through a questionnaire. Binomial proportions were used to estimate seroprevalence and logistic regression was used to examine factors associated with seropositivity of type-specific and grouped (i.e. 9vHPV, high-risk 9vHPV, low risk 9vHPV, and five-additional) HPV types. Results Overall, 28.3% of men were seropositive for at least one of the 9vHPV vaccine types, 14.0% for at least one of the seven high-risk types (16, 18, 31, 33, 45, 52 and 58) and 11.2% for at least one of the five high-risk types (31, 33, 45, 52 and 58) not included in the quadrivalent HPV vaccine, and 17.4% for at least one of the low-risk types (6/11). In multivariate analyses, odds ratios adjusted (AOR) for country of residence, age, marital status, smoking, number of anal sex lifetime partners, compared to men with no anal sex lifetime partners, men with ≥2 partners were more likely to be seropositive for grouped HPV [(9vHPV: AOR 2.52; 95% confidence interval (CI) 1.40–4.54), (high-risk 9vHPV: AOR 2.18; 95%CI: 1.05–4.50) and (low-risk 9vHPV: AOR 2.12; 95%CI: 1.12–4.03)], and individual HPV types 6, 16, 33 and 58 with AORs ranging from 2.19 to 7.36. Compared to men aged 18–30 years, men older than 30 years were significantly more likely to be seropositive for any high-risk 9vHPV, in addition to individual types 18 and 45; and compared to never smokers, current smokers were more likely to be seropositive to 9vHPV, low-risk 9vHPV and HPV 6. In contrast, married men were less likely to be seropositive to any high-risk 9vHPV and individual HPV types 18 and 31 when compared to single men. Conclusions These data indicate that exposure to the nine HPV types included in the 9vHPV vaccine is common in men and that seropositivity to 9vHPV vaccine types is associated with older age and the lifetime number of anal sex partners. Nine valent HPV vaccination of males and females has the potential to prevent HPV related diseases and transmission in both sexes.
Cardiovascular Risk Assessment in Prediabetes and Undiagnosed Diabetes Mellitus Study: International Collaboration Research Overview

The study aims to develop a screening protocol for the risk of future cardiovascular disease and diabetes mellitus in people with prediabetes and undiagnosed diabetes; and to establish a framework for early identification and intervention of prediabetes including strategies for holistic management and monitoring of progression. The first phase is to identify prediabetes and undiagnosed diabetes in volunteers who are ≥18-years-old for 5 years. Point-of-care testing and questionnaire will be used to screen for prediabetes and cardiovascular disease. We anticipate screening more than 2000 individuals of both genders by the end of first phase. The second and third phases which shall run for 5-10 years will be longitudinal study involving participants identified in the first phase as having prediabetes without dyslipidaemia, or clinically established cardiovascular disease. The second phase shall focus on preventive management of risk of progress to diabetes with explicit diagnosis of cardiovascular disease. Oxidative stress measurements will be performed cum evaluation of the use of antioxidants, exercise, and nutrition. The third phase will include probing the development of diabetes and cardiovascular disease. Binomial logistic regression would be performed to generate and propose a model chart for the assessment of cardiovascular disease risk in prediabetes.