julilili42/papers huggingface dataset:
Taking forward the World TB Day 2016 theme ‘Unite to End Tuberculosis’ for the WHO Africa Region
2016-03-08

Tuberculosis (TB) remains a global emergency, with an estimated 9.6 million new TB cases worldwide reported in 2014. Twenty-eight percent of these cases were in the World Health Organization (WHO) Africa Region, where the annual case detection rate was 281 per 100000 population-more than double the global average of 133 per 100000. Of the 9.6 million people who developed TB, an estimated 1.2 million (12%) were HIV-positive, and the Africa Region accounted for 74% of these cases. Three million people with TB remain undiagnosed and untreated. Globally, an estimated 480000 had multidrug-resistant TB (MDR-TB). Whilst of the African countries, only South Africa has reported a high prevalence of MDR-TB, it is likely that all of Sub-Saharan Africa has an unreported high load of drug-resistant TB. Tragically, in 2014, only 48% of individuals diagnosed with MDR-TB had successful treatment and an estimated 190000 people died of MDR-TB. Of the global TB funding gap of US 0.4 billion in 2015. The MDR-TB pandemic in particular now threatens to devastate entire regions and may fundamentally alter the life-expectancy and demographic profile of many countries in Sub-Saharan Africa. The theme designated for this year's World TB Day, March 24, 2016, is 'Unite to End TB'. From the Africa Region, there is an urgent need to seriously address the political, economic, and social factors that influence host-Mycobacterium tuberculosis interactions and result in disease. Recent political and funder initiatives that provide renewed hope for the alleviation of Africa's TB and TB/HIV problems are discussed.
Rendering refraction and reflection of eyeglasses for synthetic eye tracker images
2016-03-08

While for the evaluation of robustness of eye tracking algorithms the use of real-world data is essential, there are many applications where simulated, synthetic eye images are of advantage. They can generate labelled ground-truth data for appearance based gaze estimation algorithms or enable the development of model based gaze estimation techniques by showing the influence on gaze estimation error of different model factors that can then be simplified or extended. We extend the generation of synthetic eye images by a simulation of refraction and reflection for eyeglasses. On the one hand this allows for the testing of pupil and glint detection algorithms under different illumination and reflection conditions, on the other hand the error of gaze estimation routines can be estimated in conjunction with different eyeglasses. We show how a polynomial function fitting calibration performs equally well with and without eyeglasses, and how a geometrical eye model behaves when exposed to glasses.
On the necessity of adaptive eye movement classification in conditionally automated driving scenarios
2016-03-08

Algorithms for eye movement classification are separated into threshold-based and probabilistic methods. While the parameters of static threshold-based algorithms usually need to be chosen for the particular task (task-individual), the probabilistic methods were introduced to meet the challenge of adjusting automatically to multiple individuals with different viewing behaviors (inter-individual). In the context of conditionally automated driving, especially while the driver is performing various secondary tasks, these two requirements of task- and inter-individuality fuse to an even greater challenge. This paper shows how the combination of task- and inter-individual differences influences the viewing behavior of a driver during conditionally automated drives and that state-of-the-art algorithms are not able to sufficiently adapt to these variances. To approach this challenge, an extended version of a Bayesian online learning algorithm is introduced, which is not only able to adapt its parameters to upcoming variances in the viewing behavior, but also has real-time capability and lower computational overhead. The proposed approach is applied to a large-scale driving simulator study with 74 subjects performing secondary tasks while driving in an automated setting. The results show that the eye movement behavior of drivers performing different secondary tasks varies significantly while remaining approximately consistent for idle drivers. Furthermore, the data shows that only a few of the parameters used for describing the eye movement behavior are responsible for these significant variations indicating that it is not necessary to learn all parameters in an online-fashion.
Applications of Immunochemistry in Human Health: Advances in Vaccinology and Antibody Design
2016-03-08

This report discusses the history and mechanisms of vaccination of humans as well as the engineering of therapeutic antibodies. Deeper understanding of the molecular interactions involved in both acquired and innate immunity is allowing sophistication in design of modified and even synthetic vaccines. Recombinant DNA technologies are facilitating development of DNA-based vaccines, for example, with the recognition that unmethylated CpG sequences in plasmid DNA will target Toll-like receptors on antigen-presenting cells. Formulations of DNA vaccines with increased immunogenicity include engineering into plasmids with “genetic adjuvant” capability, incorporation into polymeric or magnetic nanoparticles, and formulation with cationic polymers and other polymeric and non-polymeric coatings. Newer methods of delivery, such as particle bombardment, DNA tattooing, electroporation, and magnetic delivery, are also improving the effectiveness of DNA vaccines. RNA-based vaccines and reverse vaccinology based on gene sequencing and bioinformatic approaches are also considered. Structural vaccinology is an approach in which the detailed molecular structure of viral epitopes is used to design synthetic antigenic peptides. Virus-like particles are being designed for vaccine deliveries that are based on structures of viral capsid proteins and other synthetic lipopeptide building blocks. A new generation of adjuvants is being developed to further enhance immunogenicity, based on squalene and other oil–water emulsions, saponins, muramyl dipeptide, immunostimulatory oligonucleotides, Toll-like receptor ligands, and lymphotoxins. Finally, current trends in engineering of therapeutic antibodies including improvements of antigen-binding properties, pharmacokinetic and pharmaceutical properties, and reduction of immunogenicity are discussed. Taken together, understanding the chemistry of vaccine design, delivery and immunostimulation, and knowledge of the techniques of antibody design are allowing targeted development for the treatment of chronic disorders characterized by continuing activation of the immune system, such as autoimmune disorders, cancer, or allergies that have long been refractory to conventional approaches.
Glucose Augments Killing Efficiency of Daptomycin Challenged Staphylococcus aureus Persisters
2016-03-09

Treatment of Staphylococcus aureus in stationary growth phase with high doses of the antibiotic daptomycin (DAP) eradicates the vast majority of the culture and leaves persister cells behind. Despite resting in a drug-tolerant and dormant state, persister cells exhibit metabolic activity which might be exploited for their elimination. We here report that the addition of glucose to S. aureus persisters treated with DAP increased killing by up to five-fold within one hour. This glucose-DAP effect also occurred with strains less sensitive to the drug. The underlying mechanism is independent of the proton motive force and was not observed with non-metabolizable 2-deoxy-glucose. Our results are consistent with two hypotheses on the glucose-DAP interplay. The first is based upon glucose-induced carbohydrate transport proteins that may influence DAP and the second suggests that glucose may trigger the release or activity of cell-lytic proteins to augment DAP's mode of action.
The Influence of Human Body Orientation on Distance Judgments
2016-03-09

People maintain larger distances to other peoples' front than to their back. We investigated if humans also judge another person as closer when viewing their front than their back. Participants watched animated virtual characters (avatars) and moved a virtual plane toward their location after the avatar was removed. In Experiment 1, participants judged avatars, which were facing them as closer and made quicker estimates than to avatars looking away. In Experiment 2, avatars were rotated in 30 degree steps around the vertical axis. Observers judged avatars roughly facing them (i.e., looking max. 60 degrees away) as closer than avatars roughly looking away. No particular effect was observed for avatars directly facing and also gazing at the observer. We conclude that body orientation was sufficient to generate the asymmetry. Sensitivity of the orientation effect to gaze and to interpersonal distance would have suggested involvement of social processing, but this was not observed. We discuss social and lower-level processing as potential reasons for the effect.
Immunological Effects of Mercury
2016-03-09

Various chemical species of mercury differ considerably with regard to their route of absorption and their distribution in the body, yet many of them and their metabolites exhibit high-affinity binding to sulfanyl groups of proteins. Among all metals, mercury appears to have the most diverse effects on the immune system. Depending on the animal species and experimental conditions, mercury compounds may cause immunosuppression or immunostimulation, autoimmune reactions, or hypersensitivity. Mercury-sensitive strains of rats and mice are often used as model organisms to study the time course and events in autoimmunity. Within about 14 days after onset of oral mercury(II) exposure, levels of immunoglobulins E and G (IgE and IgG) increase, including autoantibodies to biomolecules such as laminin and fibrillarin. Antigen-antibody complexes are formed and are the cause of subsequent autoimmune diseases of blood vessels and organs. Mercury may induce local mercury hypersensitivity in humans, but the evidence for a role of mercury in autoimmune disease of humans is at best weak. Models for the immune effects of mercury are presented on the basis of current knowledge.
Comparison of Tumor Uptake Heterogeneity Characterization Between Static and Parametric 18F-FDG PET Images in Non–Small Cell Lung Cancer
2016-03-10

In NSCLC primary tumors, parametric and static baseline (18)F-FDG PET images provided strongly correlated quantitative features for both standard (MATV, SUVmax, SUVmean) and heterogeneity quantification. Consequently, heterogeneity quantification on parametric images does not seem to provide significant complementary information compared with static SUV images.
Inhibition of Plexin C1 Protects Against Hepatic Ischemia-Reperfusion Injury*
2016-03-10

Objectives: Hepatic ischemia-reperfusion injury is a disease pattern that is associated with an acute inflammatory reaction. It is well known that neutrophils play an essential role in the early phase of hepatic ischemia-reperfusion injury and determine the extent of tissue damage. Hepatic ischemia-reperfusion injury can result in organ failure, which is linked to high mortality. Recent data indicate that the neuronal guidance receptor Plexin C1 is involved in the control of the acute inflammatory response and, as such, modulates the transmigration of neutrophils. Hence, we investigated the functional role of Plexin C1 in a mouse model of early hepatic ischemia-reperfusion injury. Design: Animal study. Setting: University experimental laboratory. Subjects: Wild-type, PLXNC1 −/− and chimeric mice. Interventions: Hepatic ischemia-reperfusion injury or sham operation. Measurements and Main Results: We found that the functional inhibition of Plexin C1 in wild-type mice treated with an anti-Plexin C1 antibody and a Semaphorin 7A peptide reduced hepatic ischemia-reperfusion injury, as measured by the levels of lactate dehydrogenase, aspartate, and alanine aminotransferase. This reduction in ischemia-reperfusion injury was accompanied by reduced numbers of neutrophils in ischemic hepatic tissue and reduced serum levels of inflammatory cytokines. Experiments using Plexin C1 receptor–deficient ( PLXNC1 −/− ) mice also demonstrated decreased hepatic ischemia-reperfusion injury. Studies of chimeric mice revealed that the hematopoietic Plexin C1 knockout is crucial for reducing the extent of hepatic ischemia-reperfusion injury. Conclusions: These results describe a role for Plexin C1 during ischemia-reperfusion injury, highlight the role of hematopoietic Plexin C1 in the development of hepatic ischemia-reperfusion injury, and suggest that Plexin C1 is a potential drug target.
Desynchronization of Cartesian k‐space sampling and periodic motion for improved retrospectively self‐gated 3D lung MRI using quasi‐random numbers
2016-03-10

Purpose To demonstrate that desynchronization between Cartesian k‐space sampling and periodic motion in free‐breathing lung MRI improves the robustness and efficiency of retrospective respiratory self‐gating. Methods Desynchronization was accomplished by reordering the phase (k y ) and partition (k z ) encoding of a three‐dimensional FLASH sequence according to two‐dimensional, quasi‐random (QR) numbers. For retrospective respiratory self‐gating, the k‐space center signal (DC signal) was acquired separately after each encoded k‐space line. QR sampling results in a uniform distribution of k‐space lines after gating. Missing lines resulting from the gating process were reconstructed using iterative GRAPPA. Volunteer measurements were performed to compare quasi‐random with conventional sampling. Patient measurements were performed to demonstrate the feasibility of QR sampling in a clinical setting. Results The uniformly sampled k‐space after retrospective gating allows for a more stable iterative GRAPPA reconstruction and improved ghost artifact reduction compared with conventional sampling. It is shown that this stability can either be used to reduce the total scan time or to reconstruct artifact‐free data sets in different respiratory phases, both resulting in an improved efficiency of retrospective respiratory self‐gating. Conclusion QR sampling leads to desynchronization between repeated data acquisition and periodic respiratory motion. This results in an improved motion artifact reduction in shorter scan time. Magn Reson Med 77:787–793, 2017. © 2016 International Society for Magnetic Resonance in Medicine
Single-Inclusive Leptoproduction of Hadrons and Jets at NLO
2016-03-10

In these proceedings we discuss next-to-leading order (NLO) perturbative-QCD calculations of the cross section for the process N → hX.We briefly present the main features of the calculation and in particular analyze the role of quasi-real photons that enter the processes because the scattered lepton is not observed.We find that the NLO corrections are sizable for the spin-averaged cross section.In order to quantify this statement we present the K-factors of the cross sections for fixed target experiments HERMES, JLab12 and COMPASS.
Toward NNLL Resummation for Single- and Di-Hadron Production in Hadronic Collisions
2016-03-10

We present results relevant for the extension of threshold resummation beyond the next-to-leading logarithmic (NLL) order for QCD hard-scattering processes.As an example, we consider dihadron production H 1 H 2 → h 1 h 2 X, where the produced pair has a large invariant mass.Taking into account the non-trivial color structure of the partonic hard-scattering process, we determine the hard and soft matrices in color space.In our numerical studies we find a significant improvement compared to previous results at NLL accuracy.In particular, the scale dependence of the resummed cross section is greatly reduced.In addition, we comment on the extension of the techniques developed in this work to other observables relevant for hadronic collisions.
Twist-3 spin Asymmetries in $\\ell N \\to h X$ Studied in Collinear Factorization
2016-03-10

Recently, three twist-3 spin asymmetries for single-inclusive hadron production in deep-inelastic lepton-nucleon scattering have been computed using collinear factorization and the leading order approximation.Here we summarize the main findings of these studies.
A systematic review of the characteristics and validity of monitoring technologies to assess Parkinson’s disease
2016-03-11

Seventy-three devices were identified, 22 were wearable, 38 were non-wearable, and 13 were hybrid devices. In accordance with our classification method, 9 devices were 'recommended', 34 devices were 'suggested', and 30 devices were classified as 'listed'. Within the wearable devices group, the Mobility Lab sensors from Ambulatory Parkinson's Disease Monitoring (APDM), Physilog®, StepWatch 3, TriTrac RT3 Triaxial accelerometer, McRoberts DynaPort, and Axivity (AX3) were classified as 'recommended'. Within the non-wearable devices group, the Nintendo Wii Balance Board and GAITRite® gait analysis system were classified as 'recommended'. Within the hybrid devices group only the Kinesia® system was classified as 'recommended'.
Testing models of peripheral encoding using metamerism in an oddity paradigm
2016-03-11

Most of the visual field is peripheral, and the periphery encodes visual input with less fidelity compared to the fovea. What information is encoded, and what is lost in the visual periphery? A systematic way to answer this question is to determine how sensitive the visual system is to different kinds of lossy image changes compared to the unmodified natural scene. If modified images are indiscriminable from the original scene, then the information discarded by the modification is not important for perception under the experimental conditions used. We measured the detectability of modifications of natural image structure using a temporal three-alternative oddity task, in which observers compared modified images to original natural scenes. We consider two lossy image transformations, Gaussian blur and Portilla and Simoncelli texture synthesis. Although our paradigm demonstrates metamerism (physically different images that appear the same) under some conditions, in general we find that humans can be capable of impressive sensitivity to deviations from natural appearance. The representations we examine here do not preserve all the information necessary to match the appearance of natural scenes in the periphery.
Is It Possible to Detect Activated Brown Adipose Tissue in Humans Using Single-Time-Point Infrared Thermography under Thermoneutral Conditions? Impact of BMI and Subcutaneous Adipose Tissue Thickness
2016-03-11

We conclude that supraclavicular SCAT thickness influences supraclavicular skin temperature and thus makes a specific detection of activated BAT using single-time-point thermography difficult. Further studies are necessary to evaluate the possibility of BAT detection using alternative thermographic methods, e.g. dynamic thermography or MR-based thermometry taking into account BMI as a confounding factor.
MR spectroscopy for in vivo assessment of the oncometabolite 2‐hydroxyglutarate and its effects on cellular metabolism in human brain gliomas at 9.4T
2016-03-11

Purpose To examine in vivo metabolic alterations in the isocitrate dehydrogenase (IDH) mutated gliomas using magnetic resonance spectroscopy (MRS) at magnetic field 9.4T. Materials and Methods Spectra were acquired with a 9.4T whole‐body scanner with the use of a custom‐built head coil (16 channel transmit and 31 channel receive). A modified stimulated echo acquisition mode (STEAM) sequence was used for localization. Eighteen patients with brain tumors of probable glial origin participated in this study. The study was performed in accordance with the guidelines of the local Ethics Committee. Results The increased spectral resolution allowed us to directly address metabolic alterations caused by the specific pathophysiology of IDH mutations including the presence of the oncometabolite 2‐hydroxglutarate (2HG) and a significant decrease of the pooled glutamate and glutamine (20%, P = 0.024), which probably reflects an attempt to replenish α‐ketoglutarate lost by conversion to 2HG. We also observed significantly reduced glutathione (GSH) levels (39%, P = 0.019), which could be similarly caused by depletion of dihydronicotinamide‐adenine dinucleotide phosphate (NADPH) during this conversion in IDH mutant gliomas. Conclusion We demonstrate that MRS at 9.4T provides a noninvasive measure of 2HG in vivo, which may be used for therapy planning and prognostication, and may provide insights into related pathophysiologic metabolic alterations associated with IDH mutations. J. MAGN. RESON. IMAGING 2016;44:823–833.
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data
2016-03-11

Abstract Background Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. Results We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. Conclusions GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.