julilili42/papers huggingface dataset:
Influence of Pre-Sintered Zirconia Surface Conditioning on Shear Bond Strength to Resin Cement
2016-06-25

This study analyzed the shear bond strength (SBS) of resin composite on zirconia surface to which a specific conditioner was applied before sintering. After sintering of either conditioner-coated or uncoated specimens, both groups were divided into three subgroups by their respective surface modifications (n = 10 per group): no further treatment; etched with hydrofluoric acid; and sandblasted with 50 μm Al2O3 particles. Surfaces were characterized by measuring different surface roughness parameters (e.g., Ra and Rmax) and water contact angles. Half of the specimens underwent thermocycling (10,000 cycles, 5–55 °C) after self-adhesive resin cement build-up. The SBSs were measured using a universal testing machine, and the failure modes were analyzed by microscopy. Data were analyzed by nonparametric and parametric tests followed by post-hoc comparisons (α = 0.05). Conditioner-coated specimens increased both surface roughness and hydrophilicity (p &lt; 0.01). In the non-thermocycled condition, sandblasted surfaces showed higher SBSs than other modifications, irrespective of conditioner application (p &lt; 0.05). Adhesive fractures were commonly observed in the specimens. Thermocycling favored debonding and decreased SBSs. However, conditioner-coated specimens upon sandblasting showed the highest SBS (p &lt; 0.05) and mixed fractures were partially observed. The combination of conditioner application before sintering and sandblasting after sintering showed the highest shear bond strength and indicated improvements concerning the failure mode.
Frequency of BRAF V600E mutations in 969 central nervous system neoplasms
2016-06-27

Our data suggest routine screening for BRAF V600E mutations for glioblastomas WHO grade IV below the age of 30, especially in glioblastomas with epithelioid features and in all rhabdoid meningiomas WHO grade III. For colorectal carcinoma, thyroid cancer, malignant melanoma and gliomas BRAF V600E immunostaining is sufficient for screening purposes. We also recommend routine immunohistochemical staining followed by sequencing validation in rare CNS metastases or metastases of unknown primary. Immunohistochemical analysis using mutation-specific antibodies on tissue microarrays is a feasible, time- and cost-efficient approach to high-throughput screening for specific mutations in large tumor series but sequencing validation is necessary in unexpected cases.
Cross‐reactivity to fish and chicken meat – a new clinical syndrome
2016-06-27

Abstract Background Fish is one of the most allergenic foods. While clinical cross‐reactivity among different fishes is a widely accepted feature of fish allergy, associations with other food allergies are not well understood. This study aims at analyzing the relevance of clinical cross‐reactivity between fish and chicken meat in patients with allergy to chicken meat without sensitization to hen's eggs. Methods Patients with food allergy to fish and chicken meat ( n = 29) or chicken meat only ( n = 7) were recruited. IgE‐reactive chicken proteins were identified (Edman, MS analysis) and quantified ( ELISA ). Allergens were used in IgE ELISA and skin testing. Results Chicken parvalbumin and two new allergens, aldolase and enolase, were identified at 12, 40, and 50 kDa, respectively. They were recognized by sIgE of 61%, 75%, and 83% of all patient sera which were in the majority of the cases positive for the fish homologues as well. Fish and chicken meat allergens were highly cross‐reactive while high inhibition rates with fish or chicken allergens correlated with the patients' primary sensitization to fish or chicken. In cooked or roasted foods, enolase and aldolase were detectable in chicken breast while parvalbumin was detectable in chicken legs and wings. Conclusions Fish and chicken meat are cross‐reactive foods; both fish‐allergic and chicken meat‐allergic patients might be at risk of developing a food allergy to chicken meat or to fish, respectively. This clinical phenomenon is proposed to be termed ‘fish–chicken syndrome’ with cross‐reactive allergens involved being parvalbumins, enolases, and aldolases.
Long‐term fore‐arc basin evolution in response to changing subduction styles in southern Alaska
2016-06-27

Abstract Detrital zircon U‐Pb and fission track double‐dating and Hf isotopes from the Mesozoic and Cenozoic strata in the southern Alaska fore‐arc basin system reveal the effects of two different modes of flat‐slab subduction on the evolution of the overriding plate. The southern margin of Alaska has experienced subduction of a spreading‐ridge (~62–50 Ma) and an oceanic plateau (~40–0 Ma). When a subducting spreading ridge drives slab flattening, our data suggest that after the ridge has moved along strike retro‐arc sediment sources to the fore arc become more predominant over more proximal arc sources. Spreading‐ridge subduction also results in thermal resetting of rocks in the upper plate that is revealed by thermochronologic data that record the presence of young age peaks found in subsequent, thin sedimentary strata in the fore‐arc basin. When a subducting oceanic plateau drives slab flattening, our data suggest that basin catchments get smaller and local sediment sources become more predominant. Crustal thickening due to plateau subduction drives widespread surface uplift and significant vertical uplift in rheologically weak zones that, combined, create topography and increase rock exhumation rates. Consequently, the thermochronologic signature of plateau subduction has generally young age peaks that generate short lag times indicating rapid exhumation. The cessation of volcanism associated with plateau subduction limits the number of syndepositional volcanic grains that produce identical geochronologic and thermochronologic ages. This study demonstrates the merit of double‐dating techniques integrated with stratigraphic studies to expose exhumational age signatures diagnostic of large‐scale tectonic processes in magmatic regions.
The German IVF Register as an Instrument to Document Assisted Reproductive Technologies
2016-06-27

The German IVF Register (Deutsches IVF-Register [D.I.R]) has been collecting and publishing data on the use of IVF and related methods in Germany since 1982. It is the only institution which provides information for all of Germany on procedures and their success rates. For this reason it plays an important role in the provision of information to the public, to patients, political decision-makers and the scientific community. However, the register does not have the data of all centers offering treatment in Germany nor does it have complete datasets on all reported treatments. The register accepts retrospective data entries, it does not publish the success rates of individual centers and up until 2015 it did not provide a summary of information which was suitable for non-specialists. The D.I.R has been the focus of criticism in the past. Even today, the information it provides to the scientific community, the public, political decision-makers and potential patients on the outcomes of assisted reproduction is insufficient. The documentation of reproductive medicine procedures in other countries is much more meaningful.
Limitations of the TheraMon®‐microsensor in monitoring occlusion therapy
2016-06-27

Abstract Purpose A proof of principle study showed that the TheraMon ® ‐microsensor can reliably measure wearing times of glasses and occlusion patches while having no discomfort for the bearer. The goal of this study was to identify specific temperature profiles in a larger patient group wearing the microsensor with an occlusion patch on the eye, the forehead or in the trouser pocket. Methods Temperature measurements with microsensors were performed at the orbital rim of the eye, at the forehead and in a trousers pocket of 20 healthy adults. The temperature measurements were analysed comparing the three locations using a repeated‐measures anova with a 0.050 two‐sided significance level. Results There was no significant temperature difference in wearing the microsensors at the orbital rim compared to forehead (p = 0.507). A significant difference could be detected if the microsensors had been in trousers pockets as compared to being positioned at orbital rim/forehead (p = 0.001). The study participants reported easy handling and comfortable wearing. Conclusion This study demonstrates for the first time that TheraMon ® ‐microsensors are fully operational in monitoring occlusion therapy in a larger group of patients (20 adult study participants). Because of the microsensor's ease of handling further studies in a larger group of children is recommended.
Response to the Comment by the Board of the German IVF Register
2016-06-27

Comment on: Comment by the Board of the German IVF Register on the Article “The German IVF Register as an Instrument to Document Assisted Reproductive Technologies” by S. Kadi and U. WiesingGeburtshilfe Frauenheilkd 2016; 76(06): 685-687DOI: 10.1055/s-0042-108695 Comment on: The German IVF Register as an Instrument to Document Assisted Reproductive TechnologiesGeburtshilfe Frauenheilkd 2016; 76(06): 680-684DOI: 10.1055/s-0042-108576
Eye Movement Training and Suggested Gaze Strategies in Tunnel Vision - A Randomized and Controlled Pilot Study
2016-06-28

We conclude that the exploratory saccade training was beneficial for RP patients and resulted in shorter fixation durations after the training. We also found a significant improvement in relative walking speed during navigation in a real-world like controlled environment.
Faces on Her and His Mind: Female and Likable
2016-06-28

Faces are a valuable source of non-verbal information for daily life social interaction. Mounting evidence points to gender specificity in face perception. Here we search for the factors that can potentially trigger gender differences in tuning to faces. By using a set of Face-n-Food images slightly bordering on the Giuseppe Arcimboldo style, we examine: (i) whether face resemblance is linked to gender specific face impression, and, if so, whether this association is perceiver gender specific; and (ii) whether images most resembling a face are also most likable for female and male perceivers. First, in a spontaneous recognition task, participants were shown a set of Face-n-Food images in a predetermined order from the least to most resembling a face. Then in a two-alternative forced-choice (2AFC) task, participants judged whether each face appeared for them (i) either female or male (Exp. 1); or (ii) either likable or unlikable (Exp. 2). Remarkably, face resemblance is closely connected to gender specific impressions: images more resembling a face elicit also more female-face responses. This link is not perceiver gender specific as it occurs for both females and males. Moreover, face resemblance is positively linked to face likability, but this holds true only for female perceivers. The findings shed light on gender specificity in tuning to faces, and help to clarify abnormalities of the social brain in neurodevelopmental, psychiatric and psychosomatic disorders.
TGF-β Contributes to Impaired Exercise Response by Suppression of Mitochondrial Key Regulators in Skeletal Muscle
2016-06-29

A substantial number of people at risk of developing type 2 diabetes could not improve insulin sensitivity by physical training intervention. We studied the mechanisms of this impaired exercise response in 20 middle-aged individuals at high risk of developing type 2 diabetes who performed 8 weeks of controlled cycling and walking training at 80% individual Vo2 peak. Participants identified as nonresponders in insulin sensitivity (based on the Matsuda index) did not differ in preintervention parameters compared with high responders. The failure to increase insulin sensitivity after training correlates with impaired upregulation of mitochondrial fuel oxidation genes in skeletal muscle, and with the suppression of the upstream regulators PGC1α and AMPKα2. The muscle transcriptomes of the nonresponders are further characterized by the activation of transforming growth factor (TGF)-β and TGF-β target genes, which is associated with increases in inflammatory and macrophage markers. TGF-β1 as inhibitor of mitochondrial regulators and insulin signaling is validated in human skeletal muscle cells. Activated TGF-β1 signaling downregulates the abundance of PGC1α, AMPKα2, the mitochondrial transcription factor TFAM, and mitochondrial enzymes. Thus, the data suggest that increased TGF-β activity in skeletal muscle can attenuate the improvement of mitochondrial fuel oxidation after training and contribute to the failure to increase insulin sensitivity.
A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil
2016-06-29

Abstract In soils halogens (fluorine, chlorine, bromine, iodine) are cycled through the transformation of inorganic halides into organohalogen compounds and vice versa. There is evidence that these reactions are microbially driven but the key enzymes and groups of microorganisms involved are largely unknown. Our aim was to uncover the diversity, abundance and distribution of genes encoding for halogenating and dehalogenating enzymes in a German forest soil by shotgun metagenomic sequencing. Metagenomic libraries of three soil horizons revealed the presence of genera known to be involved in halogenation and dehalogenation processes such as Bradyrhizobium or Pseudomonas . We detected a so far unknown diversity of genes encoding for (de)halogenating enzymes in the soil metagenome including specific and unspecific halogenases as well as metabolic and cometabolic dehalogenases. Genes for non-heme, no-metal chloroperoxidases and haloalkane dehalogenases were the most abundant halogenase and dehalogenase genes, respectively. The high diversity and abundance of (de)halogenating enzymes suggests a strong microbial contribution to natural halogen cycling. This was also confirmed in microcosm experiments in which we quantified the biotic formation of chloroform and bromoform. Knowledge on microorganisms and genes that catalyze (de)halogenation reactions is critical because they are highly relevant to industrial biotechnologies and bioremediation applications.
The influence of chronotype on the academic achievement of children and adolescents – evidence from Russian Karelia
2016-06-29

Sergey N. Kolomeichuka*, Christoph Randlerb, Irina Shabalinac, Ludmila Fradkovad & Mikhail Borisenkovea Russian Academy of Sciences, Institute of Biology, Karelian Research Centre, Petrozavodsk, Russiab Department of Biology, University of Tübingen, Tübingen, Germanyc Department of Applied Mathematics and Cybernetics, Petrozavodsk State University, Russiad Centre for Development of Education, Petrozavodsk, Russiae Ural Branch of Russian Academy of Sciences, Institute of Physiology, Komi Science Centre, Syktyvkar, Russia
Pharmacological targeting of glucose-6-phosphate dehydrogenase in human erythrocytes by Bay 11–7082, parthenolide and dimethyl fumarate
2016-06-29

Abstract In mature erythrocytes, glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6PGDH) yield NADPH, a crucial cofactor of the enzyme glutathione reductase (GR) converting glutathione disulfide (GSSG) into its reduced state (GSH). GSH is essential for detoxification processes in and survival of erythrocytes. We explored whether the anti-inflammatory compounds Bay 11–7082, parthenolide and dimethyl fumarate (DMF) were able to completely deplete a common target (GSH), and to impair the function of upstream enzymes of GSH recycling and replenishment. Treatment of erythrocytes with Bay 11–7082, parthenolide or DMF led to concentration-dependent eryptosis resulting from complete depletion of GSH. GSH depletion was due to strong inhibition of G6PDH activity. Bay 11–7082 and DMF, but not parthenolide, were able to inhibit the GR activity. This approach “Inhibitors, Detection of their common target that is completely depleted or inactivated when pharmacologically relevant concentrations of each single inhibitor are applied, Subsequent functional analysis of upstream enzymes for this target” (IDS), can be applied to a broad range of inhibitors and cell types according to the selected target. The specific G6PDH inhibitory effect of these compounds may be exploited for the treatment of human diseases with high NADPH and GSH consumption rates, including malaria, trypanosomiasis, cancer or obesity.
Gyroid phase of fluids with spherically symmetric competing interactions
2016-06-29

We study the phase diagram of a fluid with spherically symmetric competing pair interactions that consist of a short-ranged attraction and a longer-ranged repulsion in addition to a hard core. To this end we perform free minimizations of three-dimensional triple periodic structures within the framework of classical density functional theory. We compare our results to those from Landau theory. Our main finding is that the double gyroid phase can exist as a thermodynamically stable phase.
Tuberculosis Treatment Outcome and Drug Resistance in Lambaréné, Gabon: A Prospective Cohort Study
2016-06-29

Despite overall global progress in tuberculosis (TB) control, TB remains one of the deadliest communicable diseases. This study prospectively assessed TB epidemiology in Lambaréné, Gabon, a Central African country ranking 10th in terms of TB incidence rate in the 2014 World Health Organization TB report. In Lambaréné, between 2012 and 2014, 201 adult and pediatric TB patients were enrolled and followed up; 66% had bacteriologically confirmed TB and 95% had pulmonary TB. The human immunodeficiency virus (HIV) coinfection rate was 42% in adults and 16% in children. Mycobacterium tuberculosis and Mycobacterium africanum were identified in 82% and 16% of 108 culture-confirmed TB cases, respectively. Isoniazid (INH) and streptomycin yielded the highest resistance rates (13% and 12%, respectively). The multidrug resistant TB (MDR-TB) rate was 4/91 (4%) and 4/13 (31%) in new and retreatment TB cases, respectively. Treatment success was achieved in 53% of patients. In TB/HIV coinfected patients, mortality rate was 25%. In this setting, TB epidemiology is characterized by a high rate of TB/HIV coinfection and low treatment success rates. MDR-TB is a major public health concern; the need to step-up in-country diagnostic capacity for culture and drug susceptibility testing as well as access to second-line TB drugs urgently requires action.
Integrative Systems Biology Visualization with MAYDAY
2016-06-29

Visualization is pivotal for gaining insight in systems biology data. As the size and complexity of datasets and supplemental information increases, an efficient, integrated framework for general and specialized views is necessary. MAYDAY is an application for analysis and visualization of general 'omics' data. It follows a trifold approach for data visualization, consisting of flexible data preprocessing, highly customizable data perspective plots for general purpose visualization and systems based plots. Here, we introduce two new systems biology visualization tools for MAYDAY. Efficiently implemented genomic viewers allow the display of variables associated with genomic locations. Multiple variables can be viewed using our new track-based ChromeTracks tool. A functional perspective is provided by visualizing metabolic pathways either in KEGG or BioPax format. Multiple options of displaying pathway components are available, including Systems Biology Graphical Notation (SBGN) glyphs. Furthermore, pathways can be viewed together with gene expression data either as heatmaps or profiles. We apply our tools to two 'omics' datasets of Pseudomonas aeruginosa. The general analysis and visualization tools of MAYDAY as well as our ChromeTracks viewer are applied to a transcriptome dataset. We furthermore integrate this dataset with a metabolome dataset and compare the activity of amino acid degradation pathways between these two datasets, by visually enhancing the pathway diagrams produced by MAYDAY.
A Two-Step Clustering for 3-D Gene Expression Data Reveals the Main Features of the Arabidopsis Stress Response
2016-06-29

We developed an integrative approach for discovering gene modules, i.e. genes that are tightly correlated under several experimental conditions and applied it to a threedimensional Arabidopsis thaliana microarray dataset. The dataset consists of approximately 23000 genes responding to 9 abiotic stress conditions at 6-9 different points in time. Our approach aims at finding relatively small and dense modules lending themselves to a specific biological interpretation. In order to detect gene modules within this dataset, we employ a two-step clustering process. In the first step, a k-means clustering on one condition is performed, which is subsequently used in the second step as a seed for the clustering of the remaining conditions. To validate the significance of the obtained modules, we performed a permutation analysis and determined a null hypothesis to compare the module scores against, providing a p-value for each module. Significant modules were mapped to the Gene Ontology (GO) in order to determine the participating biological processes.&lt;br /&gt;As a result, we isolated modules showing high significance with respect to the p-values obtained by permutation analysis and GO mapping. In these modules we identified a number of genes that are either part of a general stress response with similar characteristics under different conditions (coherent modules), or part of a more specific stress response to a single stress condition (single response modules). We also found genes clustering within several conditions, which are, however, not part of a coherent module. These genes have a distinct temporal response under each condition. We call the modules they are contained in individual response modules (IR).
Carcinogenesis of renal cell carcinoma reflected in HLA ligands: A novel approach for synergistic peptide vaccination design
2016-06-30

Despite recent advances in immunotherapy of renal cell carcinoma (RCC), peptide vaccination strategies still lack an approach for personalized peptide vaccination that takes intra- and inter-tumoral heterogeneity and biological characteristics into account. In this study, we use an immunoprecipitation and mass spectrometry-based approach supplemented by network analysis of HLA ligands to target this goal. By analyzing HLA-presented peptides for HLA class I and II of 11 malignant and 6 non-malignant kidney tissue samples, more than 2,700 peptides and 1,600 corresponding source proteins were identified. A high overlap with HLA ligands derived from peripheral blood mononuclear cells (PBMCs) was detected most likely due to tumor-infiltrating inflammatory cells and therefore excluded from network analysis. Subsequent biological function analysis of HLA ligands by the GeneMANIA online platform showed enrichment for well established, but also novel, pathways and biological processes involved in carcinogenesis of RCC almost exclusively in malignant tissue samples. By exploring source proteins involved in these overrepresented pathways, we verified various known tumor-associated antigens (TAAs) for RCC (e.g., CA9, EGLN3, IGFBP3, MMP7, PAX2, VEGFA, or EGFR) but could also detect novel TAAs for RCC (e.g., PLOD2, LOX, ENPEP, or TGFBI). Some of these new TAAs had already been shown to elicit a T cell response in cancer patients. Thus, network analysis of HLA ligands provided a new platform for implementing personalized, multipeptide vaccines with potentially synergistic antitumor effects.