Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling transport mode decisions using hierarchical logistic regression models with spatial and cluster effects

This work is motivated by a mobility study conducted in the city of Munich, Germany. The variable of interest is a binary response, which indicates whether public transport has been utilized or not. One of the central questions is to identify areas of low/high utilization of public transport after adjusting for explanatory factors such as trip, individual and household attributes. For the spatial effects a modification of a class of Markov random fields (MRF) models with proper joint distributions introduced by Pettitt et al. (2002) is developed. It contains the intrinsic MRF in the limit and allows for efficient Markov Chain Monte Carlo (MCMC) algorithms. Further cluster effects using group and individual approaches are taken into consideration. The first one models heterogeneity between clusters, while the second one models heterogeneity within clusters. A naive approach to include individual cluster effects results in an unidentifiable model. It is shown how a re-parametrization gives identifiable parameters. This provides a new approach for modeling heterogeneity within clusters. Finally, the proposed model classes are applied to the mobility study.
High HIV, HPV, and STI Prevalence Among Young Western Cape, South African Women: EVRI HIV Prevention Preparedness Trial

Background:This study sought to assess the feasibility of conducting a phase III HIV prevention trial using a multivalent human papillomavirus (HPV) vaccine (Gardasil; Merck, Whitehouse Station, NJ). Methods:A total of 479 sexually active women aged 16–24 years in the Western Cape, South Africa, were enrolled in the Efficacy of HPV Vaccine to Reduce HIV Infection (EVRI) Trial. Of these, 402 were HIV negative, nonpregnant, and randomized 1:1 to receive Gardasil or a saline placebo vaccine. Vaccine doses were administered at enrollment, month 2, and month 6, and participants were followed for 1 month after the third dose. Enrollment HIV, HPV, other sexually transmitted infections (STIs), and cervical cytology were evaluated. Rates of accrual, vaccine compliance, and adherence to protocol were monitored. Results:High rates of accrual of eligible females to study (93%) and completion of the 3-dose vaccine series (91%) were noted, with few protocol violations. Ineligibility due to reported HIV positivity was 19%, and another 12% of those enrolled tested HIV positive. STI prevalence was high, with 6.2%, 10.9%, and 32.8% testing positive for syphilis, gonorrhea, and chlamydia, respectively. Cervical prevalence of ≥1 of 37 HPV types was 71%. STI and HPV prevalence was highest among the youngest women (<19 years). Conclusions:Feasibility (successful accrual, retention, and vaccination) of conducting randomized placebo-controlled trials of HPV vaccines among HIV high-risk women in South Africa was demonstrated. This work demonstrates that phase III HIV prevention trials need to intervene at young ages and screen and treat multiple STIs concurrently to have a measurable impact on HIV acquisition.
Randomized Bidirectional B-Spline Parameterization Motion Planning

This paper presents a motion planner tailored for particular requirements for robotic car navigation. We leverage B-spline curve properties to include vehicle's constraint requirements, thus lowering the search dimensionality. An algorithm, which combines competent exploratory nature of the randomized search methods with vector-valued parameterization steering, is developed here. Vehicle's limitations, along with obstacle's constraints, are satisfied without being hindered by numerical integration and control space discretization of traditional randomized kinodynamic planners. We rely on newly developed theoretical underpinnings to overcome performance issues in rapidly exploring random tree (RRT) solutions. Rigorous simulations and analysis demonstrate that this new approach outperforms recently proposed planners by using an efficient bidirectional RRT-based search, by maintaining continuous state and control spaces, and generating C2 continuous paths, which are realistic inputs suited for mobile robotic applications and passenger vehicles.
On Quasi-Cyclic Repeat-Accumulate Codes

Repeat-Accumulate (RA) codes, consisting of a simple binary repetition followed by a permutation and an accumulator, are converting into quasi-cyclic codes with multiple cross-linked cycles. The algebraic heuristics are used to design codes with an explicit algebraic permutation yielding desirable graph properties. Recursive graph constructions techniques are given for the construction of very long codes. Simulation results for codes of rate 1/3 and 1/4 demonstrate that these algebraic RA codes can compete with RA codes using pseudo-random permutations and outperform the random codes at high SNR.
SEMANTIC DATA INTEGRATION ACROSS DIFFERENT SCALES: AUTOMATIC LEARNING OF GENERALIZATION RULES

: In this paper we present an approach realizing the integration of data sets of different origin and with different resolution levels. The underlying idea is to reveal semantic correspondences between object classes of different geo-ontologies only by analysis of spatial and geometrical characteristics of instances of the data sets. As a result we derive transformation rules with Data Mining methods, which subsequently allow the semantic connection between data sets. For our case study we use data sets with similar thematic focus, but different semantic and geometric resolution: on the one hand building objects from cadastral data in a scale about 1:1K (detailed data set) and on the other hand settlement areas from topographic data in a scale about 1:25K (less detailed data set). To derive links between instances from the detailed data set to the more general one by geometric overlay it is required that the data sets are available in the same geographical extent. Then we generalize the detailed data set by using the object boundaries in the less detailed data set as a constraint for the generalization and generate an ’intermediate data set’ that is in a similar spatial resolution. We enrich the given information with additional attributes representing spatial relations and implicit or intrinsic given instance properties (e.g. object size), in order to derive transformation rules. These rules can be further used for classiﬁcation of settlement areas of unknown regions in the target data set.
A cross-layer optimization of gnutella for mobile ad hoc networks

In recent years, the Internet has witnessed the introduction of many peer-to-peer systems designed to realize large-scale data sharing. These platforms exhibit interesting features like self-configuration, self-healing and complete decentralization, which make them appealing for employment in ad hoc environments as well. However, the impact of ad hoc dynamics on the performance of these protocols, and the different set of constraints which this emerging networking paradigm imposes, haven't been yet carefully evaluated. This paper investigates the performance of Gnutella, one of the most widely used peer-to-peer systems, when put through typical ad hoc conditions like node mobility, frequent network partitioning, etc. We show that a straightforward implementation of the protocol is not satisfactory under the point of view of the produced overhead and the average overlay connectivity. Finally, we propose a cross-layer optimization of Gnutella, which enhances its performance up to the expectations and makes it more suitable to the degree of self-organization and self-healing required in ad hoc environments.
Overexpression of the CTLA-4 Isoform Lacking Exons 2 and 3 Causes Autoimmunity

CTLA-4 is a potent inhibitor of T cell activation, primarily upon binding to its costimulatory ligands (B7.1 and B7.2) expressed on APCs. However, variants of CTLA-4 can also function independently of B7 molecules. 1/4CTLA-4 is a highly conserved isoform encoded by exons 1 and 4 of the Ctla4 gene that lacks the ligand-binding and the transmembrane domains, and as yet, its function is not known. To investigate the function of 1/4CTLA-4, we generated transgenic (Tg) mice overexpressing this variant. Cytokine production by 1/4CTLA-4 Tg T cells was elevated compared with wild type T cells. The frequency of CD44high memory T cells in 1/4CTLA-4 Tg mice was increased, and as the mice aged, the frequency further increased. 1/4CTLA-4 Tg mice >1 y old had increased expression of T cell activation markers and developed spontaneous autoimmunity, including elevated production of autoantibodies. In contrast with young 1/4CTLA-4 Tg mice, aged 1/4CTLA-4 Tg mice had elevated frequencies of Foxp3+ regulatory T cells, but the regulatory T cells from these mice were not able to inhibit colitis development. Collectively, these data suggest that the function of the 1/4CTLA-4 isoform is distinct from that of CTLA-4 in that it enhances T cell activation and promotes autoimmunity rather than inhibiting immune responses.
Outcome Improvement for Hypothermic Machine Perfusion Versus Cold Storage for Kidneys From Cardiac Death Donors

Organ shortage has led to an increased use of kidneys from cardiac death donors (DCDs), but controversies about the methods of organ preservation still exist. This study aims to compare the effect of machine perfusion (MP) and cold storage (CS) in protecting kidneys harvested from DCDs. 141 kidney pairs from DCDs between July 2010 and July 2015 were included in this randomized controlled study. One kidney from each donor was randomly assigned to MP and the contralateral kidney was assigned to CS. Delayed graft function (DGF) rate, resistance index of renal arteries, early renal function, and survival rates were used to estimate the effect of preservation. The results showed that MP decreased the rate of DGF from 33.3 to 22.0% (P = 0.033). Ultrasound of the kidneys within 48 h after transplantation showed that the resistance index of renal main artery (0.673 ± 0.063 vs. 0.793 ± 0.124, P < 0.001), sub segmental artery (0.66 ± 0.062 vs. 0.764 ± 0.077, P < 0.001) and interlobular artery (0.648 ± 0.056 vs. 0.745 ± 0.111, P = 0.023) were all significantly lower in the MP group than those in the CS group. Furthermore, compared to the CS group, in the first 7 days following transplantation, the median urine volume was significantly higher (4080 mL vs. 3000 mL, P = 0.047) in kidneys sustained using MP and the median serum creatinine was remarkably lower (180 µmol/L vs. 390 µmol/L, P = 0.024). More importantly, MP group had higher 1- and 3-year graft survival rates (98% vs. 93%, P = 0.026; 93% vs. 82%, P = 0.036, respectively). Hypothermic MP improved the outcomes of DCD kidney transplantation.
Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is in MXL, in CLM, and in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas thousand years ago (kya), supports that the MXL Ancestors split kya, with a subsequent split of the ancestors to CLM and PUR kya. The model also features effective populations of in Mexico, in Colombia, and in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations.
Peroxisomal ATP-binding cassette transporters form mainly tetramers

ABCD1 and its homolog ABCD2 are peroxisomal ATP-binding cassette (ABC) half-transporters of fatty acyl-CoAs with both distinct and overlapping substrate specificities. Although it is established that ABC half-transporters have at least to dimerize to generate a functional unit, functional equivalents of tetramers (i.e. dimers of full-length transporters) have also been reported. However, oligomerization of peroxisomal ABCD transporters is incompletely understood but is of potential significance because more complex oligomerization might lead to differences in substrate specificity. In this work, we have characterized the quaternary structure of the ABCD1 and ABCD2 proteins in the peroxisomal membrane. Using various biochemical approaches, we clearly demonstrate that both transporters exist as both homo- and heterotetramers, with a predominance of homotetramers. In addition to tetramers, some larger molecular ABCD assemblies were also found but represented only a minor fraction. By using quantitative co-immunoprecipitation assays coupled with tandem mass spectrometry, we identified potential binding partners of ABCD2 involved in polyunsaturated fatty-acid metabolism. Interestingly, we identified calcium ATPases as ABCD2-binding partners, suggesting a role of ABCD2 in calcium signaling. In conclusion, we have shown here that ABCD1 and its homolog ABCD2 exist mainly as homotetramers in the peroxisomal membrane.
Comparing Results of Algorithms Implementing Blind Source Separation of EEG Data

to electroencephalographic (EEG) data, has proven capable of separating artifacts and brain sources. Of the variety of ICA and blind source separation algorithms now available, which are more efficient at processing EEG data? Here, we defined efficiency to mean blind separation of the data into near " dipolar " components having scalp maps consistent with synchronous activity in a single cortical region. We applied 20 ICA algorithms as well as PCA, whitening, and PROMAX decomposition to 71-channel data from 14 subjects, and ranked the resulting decompositions by the number of near-dipolar components they identified. By this measure, Infomax and Pearson ICA ranked highest, though similar near-dipolar components were returned by most of the ICA-based algorithms.
Uncertainty and Reproducibility of Quantitative DTI and Fiber Tracking of the Human Brain

Introduction. Diffusion tensor imaging (DTI) techniques like fiber tracking (FT) or quantification of DTI related parameters have the potential to identify major white matter tracts afflicted by an individual pathology or tracts at risk for a given surgical approach. However, the reliability and reproducibility of these techniques are known to be limited by the quality of acquired data, the underlying models and algorithms, and by the methods for reporting and displaying the results. We show how different image resolutions of the acquired data influence the quantification and fiber tracking process, derive a relationship between the diffusion anisotropy (DA) and the orientation uncertainty (OU) by considering image noise, and present methods to assess and visualize the uncertainty of fiber reconstructions. As a consequence, we are able to develop and evaluate robust preprocessing, fiber tracking, and quantification algorithms which take partial volume effects into account and which are able to compute DTI parameters along fiber bundles automatically. Our optimized color-coding scheme for DTI data as well as our fiber clustering algorithm address the problem of presenting the results to the clinicians in such a way that uncertainties in the interpretation are reduced and the perception of the visualization is enhanced.
Implementation of Points and Edges Technique

This paper describes an implementation of Points and Edges Technique (Bala et al. 2003). Algorithms and data structures are described in sufficient detail for an informed reader to perform similar implementation without going into unnecessary details about low-level implementation issues. Also a couple of other approaches to accomplish similar results are introduced. Finally, performance issues and the problems of the method are discussed.
The PCI Interface for GRAPE Systems: PCI-HIB

We developed a PCI interface for GRAPE systems. GRAPE (GRAvity piPE) is a special-purpose computer for gravitational N-body simulations. The newest of the GRAPE machines, GRAPE-4, has achieved a peak performance of 1.08 Tflops. The new host interface board we have developed adopts the PCI bus to connect GRAPE-4 to a wide variety of host computers. In test runs with a Barnes-Hut treecode, we found that the performance of the new system with the PCI interface is 40% better than that of the original system.
AF‐353, a novel, potent and orally bioavailable P2X3/P2X2/3 receptor antagonist

Background and purpose: Purinoceptors containing the P2X3 subunit (P2X3 homotrimeric and P2X2/3 heterotrimeric) are members of the P2X family of ion channels gated by ATP and may participate in primary afferent sensitization in a variety of pain‐related diseases. The current work describes the in vitro pharmacological characteristics of AF‐353, a novel, orally bioavailable, highly potent and selective P2X3/P2X2/3 receptor antagonist.
Acquisition of Obstacle Avoidance Behaviors for a Quadruped Robot Using Visual and Ultrasonic Sensors

In this paper, an obstacle avoidance method is described for a quadruped walking robot by using camera image and ultrasonic sensors. A single camera is used to acquire the rough information of three-dimensional obstacle, while some ultrasonic sensors are used to obtain the accurate information of the obstacle. Thus, the obstacle is efficiently measured by combining these sensors properly. The effectiveness of the proposed method is verified for several experiments, in which TITAN-VIII is adopted as an experimental setup. The quadruped robot can arrives at the target with repeat of these actions. The effectiveness of the presented method is verified through some experiments
The development of the family and marriage in Europe: ‘Bilaterality’ and the development of English kin terminology

List of figures, maps and tables Preface 1. Perspectives 2. Two sides to the Mediterranean 3. Change in the German lands 4. Cousins and widows, adoptees and concubines 5. From sect to Church 6. Church, land and family in the West 7. Reformation and reform 8. The hidden economy of kinship 9. The spiritual and the natural Appendices References and bibliography Glossary Index.
Characterization of the induced effects on electronic boards placed in metal enclosures with loaded apertures

The paper investigates the EMI induced on electronic boards placed inside rectangular metallic enclosure having thin or thick apertures illuminated by a plane wave. The effects of optically-transparent thin films loading the apertures are also considered. The analysis is carried out through an integral-equation formulation which is able of dealing with micro/nano thin films. The investigation is aimed at assessing the level of the interference induced on the victim with open or loaded apertures.
Proteomic Profiling and Neurodegeneration in West-Nile-Virus-Infected Neurons

West Nile virus, a mosquito-borne flavivirus, is a human, equine, and avian pathogen. High-resolution two-dimensional differential-gel electrophoresis (2D-DIGE) was used to characterize protein expression in primary rat neurons and to examine the proteomic profiling to understand the pathogenesis of West-Nile-associated meningoencephalitis. Three pH ranges, 3–10, 4–7, and 5–6, were used to analyze the protein spots. The proteins are labeled with fluorescent dyes Cy3 and Cy5 before being separated on the basis of charge and size respectively on a two-dimensional platform. About 55 proteins showed altered expression levels. These were then subsequently digested and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis using peptide mass fingerprinting and database searching. These cellular proteins could represent distinct roles during infection related to apoptosis. Our findings show that two-dimensional differential gel electrophoresis combined with mass spectrometry is a powerful approach that permits the identification of proteins whose expression was altered due to West Nile virus infection.
Impact of rosiglitazone treatment on the bioavailability of antiretroviral compounds in HIV-positive patients.

OBJECTIVES The insulin-sensitizer rosiglitazone is under investigation for therapy of HIV-associated lipodystrophy syndrome (LDS). Little is known about pharmacological interactions with antiretroviral (ARV) drugs. METHODS Therapeutic drug monitoring (TDM) of ARV drugs was performed in a prospective study before and at day 28 after start of treatment with 4 mg of rosiglitazone for combined LDS. Drug levels were measured in the morning fasting, and 0.5, 1, 2, 4, 6 and 8 h after standardized drug intake. Values were log-transformed for analysis. RESULTS Twelve males and six females were assessed; mean age was 50.7 years and mean CD4 cell count was 496 cells/mm(3). All patients had a viral load below 50 copies/mL, and backbone ARV therapy consisted of two or three nucleoside reverse transcriptase inhibitors in all cases. After administration of rosiglitazone, no significant differences in Cmax, Cmin and AUC were found in cases treated with efavirenz (n = 10) and lopinavir (n = 4). Mean Cmax of nevirapine (n = 4) was reduced significantly [-0.44; 95% confidence interval (CI) -0.86 to -0.01]. Furthermore, there was a consistent trend to a reduction in the geometric mean ratio (GMR) of Cmax, Cmin and AUC (GMR of Cmax 0.95; 95% CI 0.9-1.0; GMR of Cmin 0.89; 95% CI 0.65-1.13; GMR of AUC 0.96; 95% CI 0.91-1.01). CONCLUSIONS Treatment with 4 mg of rosiglitazone for HIV-associated LDS is likely to reduce the bioavailability of nevirapine. Thus, routine TDM is recommended for patients treated with rosiglitazone and nevirapine. A therapy consisting of efavirenz or lopinavir seems to be without negative impact. Further studies on the interaction of rosiglitazone with ARV drugs are necessary.