julilili42/papers huggingface dataset:
Quality Control of Serum and Plasma by Quantification of (4E,14Z)-Sphingadienine-C18-1-Phosphate Uncovers Common Preanalytical Errors During Handling of Whole Blood
2018-03-22

Abstract BACKGROUND Nonadherence to standard operating procedures (SOPs) during handling and processing of whole blood is one of the most frequent causes affecting the quality of serum and plasma. Yet, the quality of blood samples is of the utmost importance for reliable, conclusive research findings, valid diagnostics, and appropriate therapeutic decisions. METHODS UHPLC-MS-driven nontargeted metabolomics was applied to identify biomarkers that reflected time to processing of blood samples, and a targeted UHPLC-MS analysis was used to quantify and validate these biomarkers. RESULTS We found that (4E,14Z)-sphingadienine-C18-1-phosphate (S1P-d18:2) was suitable for the reliable assessment of the pronounced changes in the quality of serum and plasma caused by errors in the phase between collection and centrifugation of whole blood samples. We rigorously validated S1P-d18:2, which included the use of practicality tests on &amp;gt;1400 randomly selected serum and plasma samples that were originally collected during single- and multicenter trials and then stored in 11 biobanks in 3 countries. Neither life-threatening disease states nor strenuous metabolic challenges (i.e., high-intensity exercise) affected the concentration of S1P-d18:2. Cutoff values for sample assessment were defined (plasma, ≤0.085 μg/mL; serum, ≤0.154 μg/mL). CONCLUSIONS Unbiased valid monitoring to check for adherence to SOP-dictated time for processing to plasma or serum and/or time to storage of whole blood at 4 °C is now feasible. This novel quality assessment step could enable scientists to uncover common preanalytical errors, allowing for identification of serum and plasma samples that should be excluded from certain investigations. It should also allow control of samples before long-term storage in biobanks.
Real-Time Structural and Optical Study of Growth and Packing Behavior of Perylene Diimide Derivative Thin Films: Influence of Side-Chain Modification
2018-03-22

We study the growth of two n-type small-molecule organic semiconductors from the perylene diimide family: <em>N,N</em>′-bis-(2-ethylhexyl)-dicyanoperylene-3,4:9,10-bis(dicarboximide) (PDIR-CN<sub>2</sub>) and <em>N,N</em>′-1<em>H</em>,1<em>H</em>-perfluorobutyl-dicyanoperylene-3,4:9,10-bis(dicarboximide) (PDIF-CN<sub>2</sub>) whose chemical structures differ only in the imide substituents, branched alkyl chains -C<sub>8H16</sub> and linear fluoroalkyl chains -C<sub>4</sub>F<sub>7</sub>H<sub>2</sub>, respectively. Both types of substituents introduce some degree of steric hindrance for intermolecular interactions, affecting solid-state packing during thin film formation, and thus induce specific structure-dependent optoelectronic properties in thin films. The transition from an amorphous structure to crystalline domains with strong intermolecular coupling was followed in situ and in real time during growth. We investigated the structural and morphological properties by X-ray diffraction and atomic force microscopy as a function of the substrate temperature and chemical structure. We examined the relationship between the structural properties and thin film optical signatures probed via differential reflectance spectroscopy, ellipsometry, and temperature-dependent photoluminescence. A new crystalline PDIR-CN<sub>2</sub> polymorph at high temperatures emerges. In addition, we observed in PDIF-CN<sub>2</sub> that the fluorinated chains contribute to crystallization inhibition because of the higher overall steric hindrance compared to the alkyl chains.
Symbiosis-related genes sustain the development of a downy mildew pathogen onArabidopsis thaliana
2018-03-22

A bstract The interfaces through which nutrients are transferred from plant cells to arbuscular mycorrhiza fungi and biotrophic hyphal pathogens are structurally similar. We report that in Arabidopsis thaliana , mutations in homologs of common symbiosis genes (CSGs) encoding homologs of the symbiosis receptor kinase SYMRK, the nucleoporins NUP133 and SEC13 or the cation channel POLLUX reduce the reproductive success of Hyaloperonospora arabidopsidis (Hpa). Analysis of the multiplication of extracellular bacterial pathogens, Hpa -induced cell death or callose accumulation, as well as Hpa -or flg22-induced defence marker gene expression, did not reveal any traces of constitutive or exacerbated defence responses. We discovered an age-dependent, possibly senescence-related transition of haustorial shape that occurred significantly earlier and at higher frequency in the CSG mutants. These findings point to a function of the homologs of common symbiosis genes in haustorial maintenance thus revealing an overlapping gene set for the intracellular accommodation of hyphal symbionts and pathogens.
Mid-term development of the right ventricle in competitive athletes
2018-03-22

Background Long-term intensive training induces physiological, morphological, and functional adaption of the athlete’s heart. Purpose To evaluate the development of athlete’s heart during a mid-term follow-up of competitive athletes using cardiac magnetic resonance (CMR). Material and Methods Eighteen competitive long-distance runners and triathletes (age 43 ± 13 years, 3 women) were prospectively examined in a longitudinal follow-up study 5.05 ± 0.6 years after baseline. CMR at 1.5-T was performed for functional and late gadolinium enhancement (LGE) imaging. Left ventricular (LV) and right ventricular (RV) end-diastolic volume (LVEDV, RVEDV) as well as ejection fraction (LVEF, RVEF), LV myocardial mass (LVMM), and atrial sizes were determined and compared to baseline in matched pairs statistics for paired difference. Results LVEDV (197 ± 38 mL vs. 196 ± 38 mL, paired difference −0.9 mL, P = 0.7) and LVEF (62 ± 7% vs. 62 ± 5%, paired difference 0.1%, P = 0.9) did not change during the follow-up period, whereas LVMM increased significantly (149 ± 31 g vs.164 ± 32 g, paired difference 14 g, P &lt; 0.0001). RVEDV significantly increased from 221 ± 47 mL at baseline to 230 ± 52 mL (paired difference 10 mL, P = 0.0033). RVEF decreased from baseline 57 ± 8% to 53 ± 7% (paired difference −3%, P = 0.0234). Left atrial size showed no significant changes (24 ± 5 cm 2 vs. 25 ± 6 cm 2 , paired difference 0.5 cm 2 , P = 0.17) and right atrial size increased significantly (30 ± 5 cm 2 vs. 32 ± 4 cm 2 , paired difference 2 cm 2 , P = 0.0054). Conclusion This study supports the theory of ongoing remodeling in an athlete’s heart. Predominantly the right heart can further enlarge in a mid-term period. This response seems not linearly dependent on a steady, decreased, or increased training volume.
Preclinical evaluation of NUDT15-guided thiopurine therapy and its effects on toxicity and antileukemic efficacy
2018-03-23

Key Points We established a Nudt15 knockout mouse model with which to evaluate individualized thiopurine therapy. Preemptive NUDT15 genotype–guided thiopurine dosing can effectively prevent drug toxicity without compromising antileukemic efficacy.
Re‐irradiation of recurrent gliomas: pooled analysis and validation of an established prognostic score—report of the Radiation Oncology Group (ROG) of the German Cancer Consortium (DKTK)
2018-03-23

Abstract The heterogeneity of high‐grade glioma recurrences remains an ongoing challenge for the interdisciplinary neurooncology team. Response to re‐irradiation (re‐ RT ) is heterogeneous, and survival data depend on prognostic factors such as tumor volume, primary histology, age, the possibility of reresection, or time between primary diagnosis and initial RT and re‐ RT . In the present pooled analysis, we gathered data from radiooncology centers of the DKTK Consortium and used it to validate the established prognostic score by Combs et al. and its modification by Kessel et al. Data consisted of a large independent, multicenter cohort of 565 high‐grade glioma patients treated with re‐ RT from 1997 to 2016 and a median dose of 36 Gy. Primary RT was between 1986 and 2015 with a median dose of 60 Gy. Median age was 54 years; median follow‐up was 7.1 months. Median OS after re‐ RT was 7.5, 9.5, and 13.8 months for WHO IV , III , and I/ II gliomas, respectively. All six prognostic factors were tested for their significance on OS . Aside from the time from primary RT to re‐ RT ( P = 0.074) and the reresection status ( P = 0.101), all factors (primary histology, age, KPS , and tumor volume) were significant. Both the original and new score showed a highly significant influence on survival with P &lt; 0.001. Both prognostic scores successfully predict survival after re‐ RT and can easily be applied in the routine clinical workflow. Now, further prognostic features need to be found to even improve treatment decisions regarding neurooncological interventions for recurrent glioma patients.
Age‐ and sex‐related heterogeneity in prodromal Parkinson's disease
2018-03-23

Additional Supporting Information may be found in the online version of this article at the publisher's website. Supplementary figure 1: Prodromal PD probabilities in incident PD cases and individuals who remained PD-free. Supplementary figure 2: Age- and sex-dependencies of predictive values of markers indicating prodromal Parkinson's disease. Supplementary figure 3: Marker profiles of incident PD cases in the five cohorts Supplementary table 1: Marker differences between incident PD and PD-free individuals in the full sample of the five DPG cohorts Supplementary table 2: Logistic regressions Supplementary table 3: The diagnostic accuracy of prodromal PD Supplementary table 4: Sensitivity and specificity of risk and prodromal markers Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A multilevel study of position effects in PISA achievement tests: student- and school-level predictors in the German tracked school system
2018-03-23

Position effects (PE) cause decreasing probabilities of correct item responses towards the end of a test. We analysed PEs in science, mathematics and reading tests administered in the German extension to the PISA 2006 study with respect to their variability at the student- and school-level. PEs were strongest in reading and weakest in mathematics. Variability in PEs was found at both levels of analysis. PEs were stronger for male students, for students with a migration background (science and mathematics), and for students with a less favourable socio-economic background (reading). At the school level, PEs were stronger in lower school tracks and in schools with a high proportion of students with a migration background. The relationships of the test scores with the covariates partly reflected the covariates’ relationships with PEs. Our findings suggest that PEs should be taken seriously in large-scale assessments as they have an undesirable impact on the results.
Hierarchical Mesoporous Organosilica–Silica Core–Shell Nanoparticles Capable of Controlled Fungicide Release
2018-03-23

Abstract A new class of hierarchically structured mesoporous silica core–shell nanoparticles (HSMSCSNs) with a periodic mesoporous organosilica (PMO) core and a mesoporous silica (MS) shell is reported. The applied one‐pot, two‐step strategy allows rational control over the core/shell chemical composition, topology, and pore/particle size, simply by adjusting the reaction conditions in the presence of cetyltrimethylammonium bromide (CTAB) as structure‐directing agent under basic conditions. The spherical, ethylene‐ or methylene‐bridged PMO cores feature hexagonal ( p 6 mm ) or cage‐like cubic symmetry ( Pm n ) depending on the organosilica precursor. The hexagonal MS shell was obtained by n ‐hexane‐induced controlled hydrolysis of TEOS followed by directional co‐assembly/condensation of silicate/CTAB composites at the PMO cores. The HSMSCSNs feature a hierarchical pore structure with pore diameters of about 2.7 and 5.6 nm in the core and shell domains, respectively. The core sizes and shell thicknesses are adjustable in the ranges of 90–275 and 15–50 nm, respectively, and the surface areas (max. 1300 m 2 g −1 ) and pore volumes (max. 1.83 cm 3 g −1 ) are among the highest reported for core–shell nanoparticles. The adsorption and controlled release of the fungicide propiconazole by the HSMSCSNs showed a three‐stage release profile.
Induction of IL‐10‐balanced immune profiles following exposure to LTA from Staphylococcus epidermidis
2018-03-23

Abstract Staphylococcus epidermidis colonises human skin without apparent inflammation, but a dominance of S. epidermidis and S. aureus is characteristic of cutaneous microbial dysbiosis in atopic dermatitis ( AD ). While S. aureus can trigger AD , the role of S. epidermidis is less understood. We characterised consequences of innate immune sensing of lipoteichoic acid ( LTA ) preparations derived from S. epidermidis (epi‐ LTA ) or S. aureus (aureus‐ LTA ). Therefore, dendritic cell ( DC ) activation and consecutive priming of antigen‐specific T cells following exposure of DC to epi‐ LTA or aureus‐ LTA were investigated. Mimicking acute AD , exposure of DC to IL ‐4 and LTA s was analysed. Exposure to epi‐ LTA or aureus‐ LTA activated human immune cells and murine dendritic cells ( DC s) via TLR 2/MyD88, however, resulting in divergent immune profiles. Differences between LTA s were significant for IL ‐6, IL ‐12p40 and IL ‐12p70 but not for IL ‐10, which was best reflected by the IL ‐12p70‐to‐ IL ‐10 ratio being IL ‐10‐balanced for epi‐ LTA but pro‐inflammatory for aureus‐ LTA . LTA ‐exposed DC s activated CD 4+ T cells; however, while T‐cell‐derived IL ‐10 was equivalent between LTA s, IFN ‐γ and IL ‐17 were significantly higher for aureus‐ LTA . Mimicking acute AD by exposing DC s to IL ‐4 and LTA s revealed that IL ‐4 significantly and uniformly suppressed epi‐ LTA ‐induced cytokine production, keeping the IL ‐12p70‐to‐ IL ‐10 ratio balanced. In contrast, exposure of DC s to aureus‐ LTA and IL ‐4 enhanced IL ‐12p70 but suppressed IL ‐10 levels, further unbalancing the IL ‐12p70‐to‐ IL ‐10 ratio. These data demonstrate opposing immune consequences following exposure to staphylococcal LTA s. Epi‐ LTA induced IL ‐10‐balanced, aureus‐ LTA pro‐inflammatory immune profiles.
Low hair cortisol concentration and emerging attention‐deficit/hyperactivity symptoms in preschool age
2018-03-23

Abstract Previous research demonstrated hypoactivity of the HPA axis in children with attention‐deficit/hyperactivity disorder (ADHD) or externalizing symptoms. We analyzed the predictive association between the long‐term HPA axis activity and increasing symptoms of ADHD in the preschool period. The sample consisted of n = 125 4‐year‐old children and their families (including n = 64 children with elevated ADHD symptoms). ADHD symptoms were assessed by a structured clinical interview with the mother and by parent‐ and teacher‐report questionnaires. The long‐term HPA axis activity was assessed by the hair cortisol concentration (HCC) (over a 3‐month period). After controlling for potential confounders, low HCC predicted an increase in ADHD symptoms between the age of 4 and 5 years. Exploration of gender effects revealed that cross‐sectional and predictive associations were significant in boys but not in girls. Low HCC might thus be regarded as an early marker of a possibly gender‐related developmental pathway to ADHD.
Diagnostic accuracy of dermatofluoroscopy in cutaneous melanoma detection: results of a prospective multicentre clinical study in 476 pigmented lesions
2018-03-23

Dermatofluoroscopy is a safe and accurate diagnostic method to aid physicians in diagnosing cutaneous melanoma. Limitations arise from largely amelanotic or regressing lesions lacking sufficient melanin fluorescence.
Macro-SICM: A Scanning Ion Conductance Microscope for Large-Range Imaging
2018-03-23

The scanning ion conductance microscope (SICM) is a versatile, high-resolution imaging technique that uses an electrolyte-filled nanopipet as a probe. Its noncontact imaging principle makes the SICM uniquely suited for the investigation of soft and delicate surface structures in a liquid environment. The SICM has found an ever-increasing number of applications in chemistry, physics, and biology. However, a drawback of conventional SICMs is their relatively small scan range (typically 100 μm × 100 μm in the lateral and 10 μm in the vertical direction). We have developed a Macro-SICM with an exceedingly large scan range of 25 mm × 25 mm in the lateral and 0.25 mm in the vertical direction. We demonstrate the high versatility of the Macro-SICM by imaging at different length scales: from centimeters (fingerprint, coin) to millimeters (bovine tongue tissue, insect wing) to micrometers (cellular extensions). We applied the Macro-SICM to the study of collective cell migration in epithelial wound healing.
Miocene snakes from northeastern Kazakhstan: new data on the evolution of snake assemblages in Siberia
2018-03-23

The Neogene snake fauna from the central and eastern regions of Eurasia is still largely unknown. This paper reports on a unique snake fauna from the late middle Miocene of the Baikadam and Malyi Kalkaman 1 and 2 localities, northeastern Kazakhstan, which represents the best-documented Miocene snake assemblage in Central Asia. Previous studies admitted that snake fauna could be homogeneous over a large part of Eurasia during the Miocene, with the late middle to early late Miocene assemblages similar to snake assemblages that inhabited Europe in the late early and early middle Miocene. This assumption is partially supported by the presence of Texasophis bohemiacus and Coluber cf. hungaricus, as well as vipers of the ‘V. aspis’ complex. However, the presence of taxa which are (1) probably not related to European representatives (‘Colubrinae’ A and B), (2) probably never occurred in Central and Western Europe and (3) are closely related to species recently inhabiting southern Siberia (Elaphe aff. dione, Gloydius sp.) indicates that faunal dissimilarity was relatively high within Eurasia during the late middle Miocene. This assumption is in accordance with studies of small mammal assemblages which show a decreasing homogenity in the Eurasia in the course of the middle Miocene.
Variational and Dyson-Schwinger equations of Hamiltonian quantum chromodynamics
2018-03-23

The variational Hamiltonian approach to Quantum Chromodynamics in Coulomb\\ngauge is investigated within the framework of the canonical recursive\\nDyson--Schwinger equations. The dressing of the quark propagator arising from\\nthe variationally determined non-perturbative kernels is expanded and\\nrenormalized at one-loop order, yielding a chiral condensate compatible with\\nthe observations.\\n
Peptide-Based Sandwich Immunoassay for the Quantification of the Membrane Transporter Multidrug Resistance Protein 1
2018-03-23

Multitransmembrane proteins are notoriously difficult to analyze. To date, rapid, and cost-efficient detection methods are lacking and only mass spectrometry-based systems allow reliable quantification of these proteins. Here, we present a novel type of sandwich immunoassay that is capable of sensitively detecting multidrug resistance protein 1 (MDR1), a prototypic 12-transmembrane-domains transporter. In a first assay step, complex samples are enzymatically fragmented into peptides as routinely done for mass spectrometry. A proteotypic peptide derived from MDR1 was chosen and antibodies targeting this peptide were used to build a sandwich immunoassay. Validation of the optimized assay showed good sensitivity, reproducibility and it allowed reliable quantification of MDR1; cross-validation by mass spectrometry demonstrated the applicability for routine analyses in clinical and pharmaceutical research. MDR1 was quantified in primary human renal cell carcinoma and corresponding normal tissue and down-regulation or expression loss was found in tumor tissue corroborating its importance in drug resistance and efficacy.
Methods in Psychophysics
2018-03-23

Abstract Typically researchers in psychology are interested in substantive issues about the mind—how we see, hear, categorize, or reason about the world. To answer the multitude of yet unanswered substantive questions about the mind, one typically conducts experiments to collect data, analyzes the data obtained, and then interprets them in the context of current theories and models. Here we look at some of the aspects of the first two steps, the collection and analysis of behavioral data from psychophysical experiments. We concentrate on the various experimental designs for experiments of the threshold or just noticeable difference (JND) type. Subsequent to data acquistion, we suggest to use Bayesian inference to estimate the psychometric function of a beta‐binomial model as the default data analysis if there is a single independent variable. For multidimensional data and exploratory data analyses, we briefly introduce multidimensional psychometric function estimation techniques, making use of regularization techniques from machine learning. We conclude our chapter with a discussion of the timeliness of the two commandments of psychophysics: Know thy stimulus by Wilson Geisler and Thou shalt not be lazy (when gathering data) , which we attribute to Karl Dallenbach.
No Evidence for Communication in the Complete Locked-in State
2018-03-24

Enabling communication for patients in the complete locked-in state (CLIS) has been a major goal for Brain-Computer Interface (BCI) research over the past 20 years. Last year, two papers were published that claim to have reached this goal: (Chaudhary et al., 2017) were the first to report communication in CLIS using a method based on fNRIS. Few month later, (Guger et al., 2017) claimed that their EEG-based BCI system is able to restore communication in CLIS. This manuscript demonstrates methodological flaws in the analysis of both papers and that their conclusions are invalid. Further, the data from (Chaudhary et al., 2017) is reanalyzed to demonstrate that their results cannot be reproduced and that there is currently no scientifically sound evidence that demonstrates communication in CLIS.