julilili42/papers huggingface dataset:
High prevalence of BRAF V600E mutations in Erdheim-Chester disease but not in other non-Langerhans cell histiocytoses
2012-08-10

Abstract Histiocytoses are rare disorders of unknown origin with highly heterogeneous prognosis. BRAF mutations have been observed in Langerhans cell histiocytosis (LCH). We investigated the frequency of BRAF mutations in several types of histiocytoses. Histology from 127 patients with histiocytoses were reviewed. Detection of BRAFV600 mutations was performed by pyrosequencing of DNA extracted from paraffin embedded samples. Diagnoses of Erdheim-Chester disease (ECD), LCH, Rosai-Dorfman disease, juvenile xanthogranuloma, histiocytic sarcoma, xanthoma disseminatum, interdigitating dendritic cell sarcoma, and necrobiotic xanthogranuloma were performed in 46, 39, 23, 12, 3, 2, 1, and 1 patients, respectively. BRAF status was obtained in 93 cases. BRAFV600E mutations were detected in 13 of 24 (54%) ECD, 11 of 29 (38%) LCH, and none of the other histiocytoses. Four patients with ECD died of disease. The high frequency of BRAFV600E in LCH and ECD suggests a common origin of these diseases. Treatment with vemurafenib should be investigated in patients with malignant BRAFV600E histiocytosis.
Spectral formation in accreting X-ray pulsars: bimodal variation of the cyclotron energy with luminosity
2012-08-10

Context. Accretion-powered X-ray pulsars exhibit significant variability of the cyclotron resonance scattering feature (CRSF) centroid energy on pulse-to-pulse timescales, and also on much longer timescales. Two types of spectral variability are observed. For sources in group 1, the CRSF energy is negatively correlated with the variable source luminosity, and for sources in group 2, the opposite behavior is observed. The physical basis for this bimodal behavior is currently not well understood. Aims. We explore the hypothesis that the accretion dynamics in the group 1 sources is dominated by radiation pressure near the stellar surface, and that Coulomb interactions decelerate the gas to rest in the group 2 sources. Methods. We derive a new expression for the critical luminosity, Lcrit, such that radiation pressure decelerates the matter to rest in sources with X-ray luminosity LX > Lcrit. The formula for Lcrit is based on a simple physical model for the structure of the accretion column in luminous X-ray pulsars that takes into account radiative deceleration, the energy dependence of the cyclotron cross section, the thermodynamics of the accreting gas, the dipole structure of the pulsar magnetosphere, and the diffusive escape of radiation through the column walls. We show that for typical neutron star parameters, \\hbox{ }, where B12 is the surface magnetic field strength in units of 1012 G. Results. The formula for the critical luminosity is evaluated for five sources, using the maximum value of the CRSF centroid energy to estimate the surface magnetic field strength B12. The results confirm that the group 1 sources are supercritical (LX > Lcrit) and the group 2 sources are subcritical (LX < Lcrit), although the situation is less clear for those highly variable sources that cross over the line LX = Lcrit. We also explain the variation of the CRSF energy with luminosity as a consequence of the variation of the characteristic emission height. The sign of this dependence is opposite in the supercritical and subcritical cases, hence creating the observed bimodal behavior. Conclusions. We have developed a new model for the critical luminosity in accretion-powered X-ray pulsars that explains the bimodal dependence of the CRSF centroid energy on the X-ray luminosity LX. Our model provides a physical basis for the observed variation of the CRSF energy as a function of LX for both the group 1 (supercritical) and the group 2 (subcritical) sources as a result of the variation of the emission height in the column.
Role of KCNMA1 in Breast Cancer
2012-08-10

KCNMA1 encodes the α-subunit of the large conductance, voltage and Ca(2+)-activated (BK) potassium channel and has been reported as a target gene of genomic amplification at 10q22 in prostate cancer. To investigate the prevalence of the amplification in other human cancers, the copy number of KCNMA1 was analyzed by fluorescence-in-situ-hybridization (FISH) in 2,445 tumors across 118 different tumor types. Amplification of KCNMA1 was restricted to a small but distinct fraction of breast, ovarian and endometrial cancer with the highest prevalence in invasive ductal breast cancers and serous carcinoma of ovary and endometrium (3-7%). We performed an extensive analysis on breast cancer tissue microarrays (TMA) of 1,200 tumors linked to prognosis. KCNMA1 amplification was significantly associated with high tumor stage, high grade, high tumor cell proliferation, and poor prognosis. Immunofluorescence revealed moderate or strong KCNMA1 protein expression in 8 out of 9 human breast cancers and in the breast cancer cell line MFM223. KCNMA1-function in breast cancer cell lines was confirmed by whole-cell patch clamp recordings and proliferation assays, using siRNA-knockdown, BK channel activators such as 17ß-estradiol and the BK-channel blocker paxilline. Our findings revealed that enhanced expression of KCNMA1 correlates with and contributes to high proliferation rate and malignancy of breast cancer.
Robust Surface Nano-Architecture by Alkali–Carboxylate Ionic Bonding
2012-08-10

Ionic bonding in supramolecular surface networks is a promising strategy to self-assemble nanostructures from organic building blocks with atomic precision. However, sufficient thermal stability of such systems has not been achieved at metal surfaces, likely due to partial screening of the ionic interactions. We demonstrate excellent stability of a self-assembled ionic network on a metal surface at elevated temperatures. The structure is characterized directly by atomic resolution scanning tunneling microscopy (STM) experiments conducted at 165 °C showing intact domains. This robust nanometer-scale structure is achieved by the on-surface reaction of a simple and inexpensive compound, sodium chloride, with a model system for carboxylate interactions, terephthalic acid (TPA). Rather than distinct layers of TPA and NaCl, angle resolved X-ray photoelectron spectroscopy experiments indicate a replacement reaction on the Cu(100) surface to form Na-carboxylate ionic bonds. Chemical shifts in core level electron states confirm a direct interaction and a +1 charge state of the Na. High-temperature STM imaging shows virtually no fluctuation of Na-TPA island boundaries, revealing a level of thermal stability that has not been previously achieved in noncovalent organic-based nanostructures at surfaces. Comparable strength of intermolecular ionic bonds and intramolecular covalent bonds has been achieved in this surface system. The formation of these highly ordered structures and their excellent thermal stability is dependent on the interplay of adsorbate-substrate and ionic interactions and opens new possibilities for ionic self-assemblies at surfaces with specific chemical function. Robust ionic surface structures have potential uses in technologies requiring high thermal stability and precise ordering through self-assembly.
Very late stent thrombosis 5 years after IVUS-guided drug-eluting stent implantation
2012-08-10

It is well accepted that drug-eluting stents (DES) are effective in reducing restenosis, although implantation of DES may result in increased occurrence of stent thrombosis. The study describes the case of a patient with very late stent thrombosis (VLST) despite intravascular ultrasound (IVUS) control after implantation of a paclitaxel-eluting stent, an adequate response to antiplatelet therapy, and the lack of distinct risk factors for VLST. Stent thrombosis remains a serious complication after stent implantation even after prolonged time, and studies are urgently needed to optimize diagnosis and treatment of VLST.
Introduction to the Issue on Emerging Techniques in 3-D
2012-08-10

The fifteen papers in this special section that focus on three dimensional content (3D), with particular emphasis on the fusion of conventional camera outputs with those captured by other modalities, such as active sensors, multi-spectral data or dynamic range images as well as applications that support the measurement and improvement of 3-D content.
Discriminating emotions from point-light walkers in persons with Schizophrenia
2012-08-10

The visual system is well adapted to recognize human motion from point lights attached to the major joints of an actor. Moreover, individuals are able to recognize emotions based on the visual information in such dynamic point-light displays. This ability is important because humans utilize both biological motion and affect recognition for understanding the intentions of people in the environment. It is not clear, however, whether atypical observers, including people with schizophrenia, also process visual information about emotion in point-light walkers in the same way. There is evidence that people with schizophrenia are impaired in recognizing emotional expressions. Furthermore, people with schizophrenia are known to have deficits in social perception. For these reasons, we investigated whether the ability to recognize emotions from point-light displays is altered in people with schizophrenia. In the current study, groups of healthy community-based controls (N=33) and people with schizophrenia (N=33) were asked to discriminate the emotions of four types of affective point-light walkers: upright, inverted, scrambled (which contained only local form information), and random-position (which contained only global form information). The point-light walkers were presented in three emotional conditions: happy, sad, and angry. Both healthy controls and people with schizophrenia were able to discriminate emotions from point-light walkers, where performance was best for upright walkers, worst with scrambled walkers, and intermediate with random-position and inverted walkers. Overall, performance was worse for people with schizophrenia compared to healthy observers. These results suggest that both healthy controls and people with schizophrenia are able to recognize emotions from point-light walkers on the basis of local motion or global form information alone. However, performance is best when both form and motion information are presented simultaneously, and, although they do perform above chance, people with schizophrenia are relatively impaired in all conditions. Meeting abstract presented at VSS 2012
Neural theories for the recognition of dynamic faces in monkey cortex
2012-08-10

Facial expressions are essentially dynamic. However, most research on faces has entirely focused on static pictures of faces. While it is clear that neurons with selectivity for dynamic facial expressions are located in the superior temporal sulcus, the underlying neural circuits and computational mechanisms are completely unknown. As a first step towards a systematic electrophysiological study of these mechanisms in monkey cortex we devised a quantitative physiologically plausible model for the processing of dynamic faces. METHODS: The model combines mechanisms from a hierarchical neural model for the norm-referenced encoding of static faces (Giese & Leopold, Neurocomputing, 2005) and different mechanisms for the integration of information over time. We tested two mechanisms: 1) 'snapshot neurons' that are selective for the temporal order of the stimuli, and 2) a completely novel mechanism that recognizes dynamic facial expressions by the detection of the temporal changes of the activity of neurons, encode faces in a norm-referenced framework. These neurons encode the distance between the actual face shape and the neutral facial expression in face space. RESULTS: Both models successfully recognize facial expressions of monkeys (e.g. coo call, or threat) from real videos, while they make fundamentally different predictions at the single-cell level. These predictions are straight-forward to test in single-cell studies. CONCLUSIONS: The proposed mechanisms are compatible with the known electrophysiological data about the encoding of dynamic faces. They result in predictions that are straight-forward to test in the context of single cell recordings: 1) sequence-selective neurons tuned to specific intermediate frames of facial movies, and 2) neurons changing their activity monotonically with the distance between stimuli and the neutral expressions in face space, and its temporal derivative. These predictions will help to structure electrophysiological experiments unraveling the cortical mechanisms of the processing of dynamic faces. Meeting abstract presented at VSS 2012
When luminance increment thresholds depend on apparent lightness
2012-08-10

p { margin-bottom: 0.08in; } The just noticeable difference (JND) between two stimulus intensities increases proportional to the background intensity (Weber's law). It is less clear, however, whether the JND is a function of the proximal or perceptual stimulus intensity. In the domain of achromatic surface colors the question would translate to whether the JND depends on local luminance or surface lightness. In the laboratory using simple stimuli such as uniform patches, proximal (luminance) and perceived intensity (lightness) often coincide. Reports that tried to disentangle the two factors yielded inconsistent results (e.g. Heinemann, 1961 JEP 61 389-399; Cornsweet and Teller, 1965 JOSA 55(10) 1303-1308; Zaidi and Krauskopf, 1985 Vision Res 26 759-62; McCourt and Kingdom, 1996 Vision Res 36 2563-73; Henning, Millar and Hill, 2000 JOSA 17(7) 1147-1159; Hillis and Brainard, 2007 CurrBiol 17 1714-1719). Following a previous experiment (Maertens and Wichmann, 2010 JVis 10 424) we measured discrimination thresholds in the Adelson checkerboard pattern for two equiluminant checks which differed in lightness (black vs. white). Discrimination performance was measured in two conditions: in the 'blob' condition, the increment was a two-dimensional gaussian centered on the check, in the 'check' condition, the increment was a constant that was added to the entire check. Performance was assessed in a 2-interval forced-choice and a yes-no task. In the 'blob' condition thresholds were indistinguishable between equiluminant checks and did not differ between the tasks. In the 'check' condition thresholds differed between equiluminant checks and were elevated for the lighter one. This was true for the yes-no task and to a lesser extent in the 2-IFC task. We think that these results require discussion beyond the question for the appropriate type of increment. We believe that the visual system might respond fundamentally different to light emanating from meaningful surfaces and to isolated spots of light. Meeting abstract presented at VSS 2012
Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils
2012-08-12

ABSTRACT In soil, Acidobacteria constitute on average 20% of all bacteria, are highly diverse, and are physiologically active in situ . However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1 Acidobacteria . The analysis of a large number of sites ( n = 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed that Acidobacteria diversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations of Acidobacteria subpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters with Acidobacteria , individual populations within subgroups have to be considered.
Using genome-wide complex trait analysis to quantify 'missing heritability' in Parkinson's disease
2012-08-13

Genome-wide association studies (GWASs) have been successful at identifying single-nucleotide polymorphisms (SNPs) highly associated with common traits; however, a great deal of the heritable variation associated with common traits remains unaccounted for within the genome. Genome-wide complex trait analysis (GCTA) is a statistical method that applies a linear mixed model to estimate phenotypic variance of complex traits explained by genome-wide SNPs, including those not associated with the trait in a GWAS. We applied GCTA to 8 cohorts containing 7096 case and 19 455 control individuals of European ancestry in order to examine the missing heritability present in Parkinson's disease (PD). We meta-analyzed our initial results to produce robust heritability estimates for PD types across cohorts. Our results identify 27% (95% CI 17-38, P = 8.08E - 08) phenotypic variance associated with all types of PD, 15% (95% CI -0.2 to 33, P = 0.09) phenotypic variance associated with early-onset PD and 31% (95% CI 17-44, P = 1.34E - 05) phenotypic variance associated with late-onset PD. This is a substantial increase from the genetic variance identified by top GWAS hits alone (between 3 and 5%) and indicates there are substantially more risk loci to be identified. Our results suggest that although GWASs are a useful tool in identifying the most common variants associated with complex disease, a great deal of common variants of small effect remain to be discovered.
Cherish yourself: Longitudinal patterns and conditions of self-esteem change in the transition to young adulthood.
2012-08-13

Several recent studies have illustrated a general increase in self-esteem from after adolescence until midlife. However, the specific pattern and possible conditions of self-esteem development from the important transition out of high school into young adulthood are still not well understood. In a longitudinal study (Transformation of the Secondary School System and Academic Careers; TOSCA), German students were interviewed 4 times beginning with their senior high school year (at Time 1 [T1]: N = 4,532; age: M = 19.6 years, SD = 0.9; 55% female). Conditional latent change models were applied and established 3 main findings. First, self-esteem showed a gradual increase across the transition, with both the self-esteem intercept and slope indicating substantial interindividual variability in the transition to young adulthood. Second, structural (having a partnership) as well as personality (Big Five) characteristics were substantially related to self-esteem development in emerging adulthood. Third, there were gender-specific associations between self-esteem and partnership status as well as between self-esteem and neuroticism and agreeableness. Findings point to a general upward development of self-esteem yet show interdependencies with the accomplishment of age-specific challenges in the transition to young adulthood.
Paleontological and developmental evidence resolve the homology and dual embryonic origin of a mammalian skull bone, the interparietal
2012-08-13

The homologies of mammalian skull elements are now fairly well established, except for the controversial interparietal bone. A previous experimental study reported an intriguing mixed origin of the interparietal: the medial portion being derived from the neural crest cells, whereas the lateral portion from the mesoderm. The evolutionary history of such mixed origin remains unresolved, and contradictory reports on the presence or absence and developmental patterns of the interparietal among mammals have complicated the question of its homology. Here we provide an alternative perspective on the evolutionary identity of the interparietal, based on a comprehensive study across more than 300 extinct and extant taxa, integrating embryological and paleontological data. Although the interparietal has been regarded as being lost in various lineages, our investigation on embryos demonstrates its presence in all extant mammalian “orders.” The generally accepted paradigm has regarded the interparietal as consisting of two elements that are homologized to the postparietals of basal amniotes. The tabular bones have been postulated as being lost during the rise of modern mammals. However, our results demonstrate that the interparietal consists not of two but of four elements. We propose that the tabulars of basal amniotes are conserved as the lateral interparietal elements, which quickly fuse to the medial elements at the embryonic stage, and that the postparietals are homologous to the medial elements. Hence, the dual developmental origin of the mammalian interparietal can be explained as the evolutionary consequence of the fusion between the crest-derived “postparietals” and the mesoderm-derived “tabulars.”
Fertility preservation in women with vasculitis: experiences from the FertiPROTEKT network.
2012-08-13

Regarding the experiences from the registry and the literature gonadotropin releasing hormone analogues are evaluated best and recommended to most of the patients with AID. Cryoconservation of ovarian tissue is a promising option. Stimulation for oocyte cryopreservation can be offered to patients with vasculitis. A combination of the methods might have the biggest preservative effect.
Phylogenetic diversity and structure of sebacinoid fungi associated with plant communities along an altitudinal gradient
2012-08-14

To study the diversity and phylogenetic structure of Sebacinales communities from eight vegetation communities along an altitudinal gradient in the Bavarian Alps (Germany), we analysed 456 thalli or roots of plants. We detected 264 sebacinoid sequences, spanning the intergenic transcribed spacer region, 5.8S and D1/D2 regions of the nuclear rRNA gene, mostly using a nested PCR approach. Based on 97% sequence similarity, 73 Sebacinales molecular taxonomic units were found from 70 host species belonging to 44 plant families. Twenty-six molecular taxonomic units represented singletons, the most frequent of these being restricted exclusively to either wooded or grassland habitats. Although Sebacinales appear to occur in low abundance in plant roots, these microorganisms are phylogenetically diverse and widely spread in the ecosystems studied. Ordination analyses showed that land use, pH and humus content strongly influence the diversity and assembly of Sebacinales. In most cases, Sebacinales communities in ecosystems with extreme soil conditions or intensive land use exhibited significant phylogenetic clustering, whereas in undisturbed plant communities no trend was observed. These results suggest that ecosystem disturbance and environmental forces have an influence on the diversity and structure of Sebacinales community assembly over local and spatial scales.