julilili42/papers huggingface dataset:
Prenasal Thickness, Prefrontal Space Ratio and Other Facial Profile Markers in First-Trimester Fetuses with Aneuploidies, Cleft Palate, and Micrognathia
2016-11-17

&lt;b&gt;&lt;i&gt;Objective:&lt;/i&gt;&lt;/b&gt; To investigate the feasibility and reproducibility of the prenasal thickness (PNT)/nasal bone length (NBL) ratio, maxilla-nasion-mandible (MNM) angle, facial profile line, profile line distance, and prefrontal space ratio (PFSR) in the first trimester of pregnancy, develop normal ranges, and evaluate these markers in abnormal fetuses. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; All measurements were performed on stored images by two operators. Feasibility, interoperator agreement, and prediction intervals were calculated for all measurements. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; Feasibility was the highest for the NBL (74.3-79.7%) and the MNM angle (75.7-79.05%). Correlation was good for the NBL, the PNT, and the MNM angle (intraclass correlation coefficient 0.706-0.835). Mean difference between operators was the lowest for the PNT and PFSR (0.03-0.08). Measurements in abnormal fetuses showed that the majority of trisomy 21 fetuses had either an absent nasal bone or a shorter NBL. The PNT and PNT/NBL ratio were above the 97.5th centile in one third of the cases. Fetuses with facial clefts or micrognathia showed on average a large MNM angle (multiple of the median 0.96-5.15). &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; First-trimester facial markers are feasible. The PNT and PNT/NBL ratio were increased in one third of the trisomic fetuses, and the MNM angle in the majority of fetuses with micrognathia and facial clefts.
QCD compositeness as revealed in exclusive vector boson reactions through double-photon annihilation: e+e−→γγ⁎→γV0 and e+e−→γ⁎γ⁎→V0V0
2016-11-17

We study the exclusive double-photon annihilation processes, e&lt;sup&gt;+&lt;/sup&gt;e&lt;sup&gt;-&lt;/sup&gt; →γγ* → γV&lt;sup&gt;0&lt;/sup&gt; and e&lt;sup&gt;+&lt;/sup&gt;e&lt;sup&gt;-&lt;/sup&gt; γ*γ* V V , where the V is a neutral vector meson produced in the forward kinematical region: s&gt;&gt; -t and -t &gt;&gt; Λ . We show how the differential cross sections , as predicted by QCD, have additional falloff in the momentum transfer squared t due to the QCD compositeness of the hadrons, consistent with the leading-twist fixed-θ&lt;sub&gt;CM&lt;/sub&gt; scaling laws, both in terms of conventional Feynman diagrams and by using the AdS/QCD holographic model to obtain the results more transparently. However, even though they are exclusive channels and not associated with the conventional electron–positron annihilation process e&lt;sup&gt;+&lt;/sup&gt;e&lt;sup&gt;-&lt;/sup&gt;→γ*→ , these total cross sections σ(e&lt;sup&gt;+&lt;/sup&gt;e&lt;sup&gt;-&lt;/sup&gt;→γV&lt;sup&gt;0&lt;/sup&gt;)and σ(e&lt;sup&gt;+&lt;/sup&gt;e&lt;sup&gt;-&lt;/sup&gt;→V V ), integrated over the dominant forward-and backward-θ&lt;sub&gt;CM&lt;/sub&gt; angular domains, scale as 1/s, and thus contribute to the leading-twist scaling behavior of the ratio R&lt;sub&gt;e&lt;sup&gt;+&lt;/sup&gt;e&lt;sup&gt;-&lt;/sup&gt;&lt;/sub&gt;. We generalize these results to exclusive double-electroweak vector-boson annihilation processes accompanied by the forward production of hadrons, such as e&lt;sup&gt;+&lt;/sup&gt;e&lt;sup&gt;-&lt;/sup&gt;→Z&lt;sup&gt;0&lt;/sup&gt;V&lt;sup&gt;0&lt;/sup&gt;and e&lt;sup&gt;+&lt;/sup&gt;e&lt;sup&gt;-&lt;/sup&gt;→W&lt;sup&gt;-&lt;/sup&gt;ρ&lt;sup&gt;+&lt;/sup&gt;. These results can also be applied to the exclusive production of exotic hadrons such as tetraquarks, where the cross-section scaling behavior can reveal their multiquark nature.
Debates—Stochastic subsurface hydrology from theory to practice: The relevance of stochastic subsurface hydrology to practical problems of contaminant transport and remediation. What is characterization and stochastic theory good for?
2016-11-18

Abstract The emergence of stochastic subsurface hydrology stemmed from the realization that the random spatial variability of aquifer properties has a profound impact on solute transport. The last four decades witnessed a tremendous expansion of the discipline, many fundamental processes and principal mechanisms being identified. However, the research findings have not impacted significantly the application in practice, for several reasons which are discussed. The paper discusses the current status of stochastic subsurface hydrology, the relevance of the scientific results for applications and it also provides a perspective to a few possible future directions. In particular, we discuss how the transfer of knowledge can be facilitated by identifying clear goals for characterization and modeling application, relying on recent recent advances in research in these areas.
Debates—Stochastic subsurface hydrology from theory to practice: Does stochastic subsurface hydrology help solving practical problems of contaminant hydrogeology?
2016-11-18

Abstract While stochastic subsurface hydrology has been tremendously successful in understanding how the spatial variability of hydraulic conductivity affects conservative solute transport in idealized settings, it has gained little impact in practice. This is the case because typical assumptions needed for the derivation of analytical expressions are too restrictive for practical applications and often geologically implausible, small‐scale variation of hydraulic conductivity is by far not the only cause of uncertainty when considering the fate and remediation of pollutants, and the research community has not developed enough methods that can directly be used by practitioners. To overcome these shortcomings, we propose putting more emphasis on providing easy‐to‐use tools to generate realistic realizations of subsurface properties that are conditioned on all data measured at a site, extending the focus from hydraulic conductivity only to all parameters and processes relevant for reactive transport, making use of self‐organizing principles of reactive transport to conceptually simplify the problem, and addressing conceptual uncertainty by stochastic methods.
The Systematic Investigation of the Quorum Sensing System of the Biocontrol Strain Pseudomonas chlororaphis subsp. aurantiaca PB-St2 Unveils aurI to Be a Biosynthetic Origin for 3-Oxo-Homoserine Lactones
2016-11-18

The shoot endophytic biocontrol strain Pseudomonas chlororaphis subsp. aurantiaca PB-St2 produces a wide range of exoproducts, including enzymes and antibiotics. The production of exoproducts is commonly tightly regulated. In order to get a deeper insight into the regulatory network of PB-St2, the strain was systematically investigated regarding its quorum sensing systems, both on the genetic and metabolic level. The genome analysis of PB-St2 revealed the presence of four putative acyl homoserine lactone (AHL) biosynthesis genes: phzI, csaI, aurI, and hdtS. LC-MS/MS analyses of the crude supernatant extracts demonstrated that PB-St2 produces eight AHLs. In addition, the concentration of all AHL derivatives was quantified time-resolved in parallel over a period of 42 h during the growth of P. aurantiaca PB-St2, resulting in production curves, which showed differences regarding the maximum levels of the AHLs (14.6 nM- 1.75 μM) and the production period. Cloning and heterologous overexpression of all identified AHL synthase genes in Escherichia coli proved the functionality of the resulting synthases PhzI, CsaI, and AurI. A clear AHL production pattern was assigned to each of these three AHL synthases, while the HdtS synthase did not lead to any AHL production. Furthermore, the heterologous expression study demonstrated unequivocally and for the first time that AurI directs the synthesis of two 3-oxo-AHLs.
The impact of physicians' communication styles on evaluation of physicians and information processing: A randomized study with simulated video consultations on contraception with an intrauterine device
2016-11-18

Abstract Objective This study aimed at examining the impact of different types of physicians' communication styles on people's subsequent evaluation of physician attributes as well as on their information processing, attitude and decision making. Method In a between‐group experiment, 80 participants watched one of three videos in which a gynaecologist displayed a particular communication style in a consultation situation on contraception with an intrauterine device. We compared doctor‐centred communication ( DCC ) vs patient‐centred communication ( PCC ) vs patient‐centred communication with need‐orientation ( PCC ‐N). Results In the PCC condition, participants perceived the physician to be more empathetic and more competent than in the DCC condition. In the DCC condition, participants showed less attitude change compared to the other conditions. In the PCC ‐N condition, the physician was perceived as more empathetic and more socially competent than in the other conditions. However, participants acquired less knowledge in the PCC ‐N condition. Conclusion We conclude that appropriate application of particular communication styles depends on specific consultation goals. Our results suggest that patients' needs should be addressed if the main goal is to build a good relationship, whereas a traditional PCC style appears to be more effective in communicating factual information.
Delineating baseflow contribution areas for streams – A model and methods comparison
2016-11-18

This study addresses the delineation of areas that contribute baseflow to a stream reach, also known as stream capture zones. Such areas can be delineated using standard well capture zone delineation methods, with three important differences: (1) natural gradients are smaller compared to those produced by supply wells and are therefore subject to greater numerical errors, (2) stream discharge varies seasonally, and (3) stream discharge varies spatially. This study focuses on model-related uncertainties due to model characteristics, discretization schemes, delineation methods, and particle tracking algorithms. The methodology is applied to the Alder Creek watershed in southwestern Ontario. Four different model codes are compared: HydroGeoSphere, WATFLOW, MODFLOW, and FEFLOW. In addition, two delineation methods are compared: reverse particle tracking and reverse transport, where the latter considers local-scale parameter uncertainty by using a macrodispersion term to produce a capture probability plume. The results from this study indicate that different models can calibrate acceptably well to the same data and produce very similar distributions of hydraulic head, but can produce different capture zones. The stream capture zone is found to be highly sensitive to the particle tracking algorithm. It was also found that particle tracking by itself, if applied to complex systems such as the Alder Creek watershed, would require considerable subjective judgement in the delineation of stream capture zones. Reverse transport is an alternative and more reliable approach that provides probability intervals for the baseflow contribution areas, taking uncertainty into account. The two approaches can be used together to enhance the confidence in the final outcome.
Distinct transcriptional changes in non-small cell lung cancer patients associated with multi-antigenic RNActive® CV9201 immunotherapy
2016-11-18

We recently completed a phase I/IIa trial of RNActive® CV9201, a novel mRNA-based therapeutic vaccine targeting five tumor-associated antigens in non-small cell lung cancer (NSCLC) patients. The aim of the study presented here was to comprehensively analyze changes in peripheral blood during the vaccination period and to generate hypotheses facilitating the identification of potential biomarkers correlating with differential clinical outcomes post RNActive® immunotherapy. We performed whole-genome expression profiling in a subgroup of 22 stage IV NSCLC patients before and after initiation of treatment with CV9201. Utilizing an analytic approach based on blood transcriptional modules (BTMs), a previously described, sensitive tool for blood transcriptome data analysis, patients segregated into two major clusters based on transcriptional changes post RNActive® treatment. The first group of patients was characterized by the upregulation of an expression signature associated with myeloid cells and inflammation, whereas the other group exhibited an expression signature associated with T and NK cells. Patients with an enrichment of T and NK cell modules after treatment compared to baseline exhibited significantly longer progression-free and overall survival compared to patients with an upregulation of myeloid cell and inflammatory modules. Notably, these gene expression signatures were mutually exclusive and inversely correlated. Furthermore, our findings correlated with phenotypic data derived by flow cytometry as well as the neutrophil-to-lymphocyte ratio. Our study thus demonstrates non-overlapping, distinct transcriptional profiles correlating with survival warranting further validation for the development of biomarker candidates for mRNA-based immunotherapy.
Rare Earth Element Determination in Olivine by Laser Ablation‐Quadrupole‐ICP‐MS: An Analytical Strategy and Applications
2016-11-18

Olivine offers huge, largely untapped, potential for improving our understanding of magmatic and metasomatic processes. In particular, a wealth of information is contained in rare earth element ( REE ) mass fractions, which are well studied in other minerals. However, REE data for olivine are scarce, reflecting the difficulty associated with determining mass fractions in the low ng g −1 range and with controlling the effects of LREE contamination. We report an analytical procedure for measuring REE s in olivine using laser ablation quadrupole‐ ICP ‐ MS that achieved limits of determination (LOD) at sub‐ng g −1 levels and biases of ~ 5–10%. Empirical partition coefficients ( D values) calculated using the new olivine compositions agree with experimental values, indicating that the measured REE s are structurally bound in the olivine crystal lattice, rather than residing in micro‐inclusions. We conducted an initial survey of REE contents of olivine from mantle, metamorphic, magmatic and meteorite samples. REE mass fractions vary from 0.1 to double‐digit ng g −1 levels. Heavy REE s vary from low mass fractions in meteoritic samples, through variably enriched peridotitic olivine to high mass fractions in magmatic olivines, with fayalitic olivines showing the highest levels. The variable enrichment in HREE s demonstrates that olivine REE patterns have petrological utility.
Improved Delineation of Pulmonary Embolism and Venous Thrombosis Through Frequency Selective Nonlinear Blending in Computed Tomography
2016-11-18

Objective The aim of this study was to test the hypothesis that a novel frequency selective nonlinear blending (NLB) algorithm increases the delineation of pulmonary embolism and venous thrombosis in portal-venous phase whole-body staging computed tomography (CT). Materials and Methods A cohort of 67 patients with incidental pulmonary embolism and/or venous thrombosis in contrast-enhanced oncological staging CT were retrospectively selected. Computed tomography data sets were acquired 65 to 90 seconds after intravenous iodine contrast administration using state-of-the-art multi-detector CT scanners. A novel frequency selective NLB postprocessing technique was applied to reconstructed standard CT images. Two readers determined the most suitable settings to increase the delineation of pulmonary embolism and venous thrombosis. Outcome measure included region of interest and contrast-to-noise ratio (CNR) analyses, image noise, overall image quality, subjective delineation, as well as number and size of emboli and thrombi. Statistical testing included quantitative comparisons of Hounsfield units of thrombus and vessel, image noise and related CNR values and subjective image analyses of image noise, image quality and thrombus delineation, number and size in standard, and NLB images. Results Using frequency selective NLB settings with a center of 100 HU, delta of 40 HU, and a slope of 5, CNR values of pulmonary embolism (Standard CNR , 10 [6, 16]; NLB CNR , 22 [15, 30]; P &lt; 0.001) and venous thrombosis (Standard CNR , 8 [5, 15]; NLB CNR , 12 [7, 19]; P = 0.0007) increased. Mean vascular enhancement using NLB was significantly higher than in standard images for pulmonary arteries (Standard, 138 [118, 191] HU; NLB, 269 [176, 329] HU; P &lt; 0.0001) and veins (Standard, 120 [103, 162] HU; NLB, 169 [132, 217] HU; P &lt; 0.0001), respectively. Image noise was not significantly different between standard and NLB images ( P = 0.64-0.88). There was substantial to almost perfect interrater agreement as well as a significant increase of overall image quality ( P &lt; 0.004) and subjective delineation of the thrombotic material ( P &lt; 0.0001) in both subgroups. Nonlinear blending images revealed 8 additional segmental and 13 subsegmental emboli. Thrombus sizes were not significantly different, but subjective accuracy of the measurement could be significantly increased using NLB ( P = 0.03). Conclusions Postprocessing of standard whole-body staging CT images with frequency selective NLB improves image quality and the delineation of pulmonary embolism and venous thrombosis.
Gröbner fans of x-homogeneous ideals in R〚t〛[x]
2016-11-21

We generalise the notion of a Gröbner fan to ideals in R 〚 t 〛 [ x 1 , ... , x n ] for certain classes of coefficient rings R and give a constructive proof that the Gröbner fan is a rational polyhedral fan. For this we introduce the notion of initially reduced standard bases and show how these can be computed in finite time. We deduce algorithms for computing the Gröbner fan, implemented in the computer algebra system Singular . The problem is motivated by the wish to compute tropical varieties over the p -adic numbers.
Trifluoromethanesulfonic Anhydride
2016-11-21

[358-23-6] C2F6O5S2 (MW 282.16) InChI = 1S/C2F6O5S2/c3-1(4,5)14(9,10)13-15(11,12)2(6,7)8 InChIKey = WJKHJLXJJJATHN-UHFFFAOYSA-N (preparation of triflates;1 mild dehydrating reagent; promoter for coupling reactions in carbohydrates2) Alternate Name: triflic anhydride. Physical Data: bp 81–83 °C/745 mmHg; d 1.677 g cm−3; n20D 1.3210. Solubility: soluble in dichloromethane; insoluble in hydrocarbons. Form Supplied in: colorless liquid in ampules. Once opened it should be immediately used. Analysis of Reagent Purity: IR, NMR. Preparative Methods: by distillation of Trifluoromethanesulfonic Acid with an excess of Phosphorus (V) Oxide.1 Purity: by redistillation with a small amount of P2O5. It is advisable to freshly distill the reagent from a small quantity of P2O5 before use. Handling, Storage, and Precautions: the pure reagent is a colorless liquid that does not fume in air and is stable for a long period. It is not soluble in water and hydrolyzes only very slowly to triflic acid over several days at room temperature. Preferably stored under N2 in a stoppered flask. Dangerously exothermic reactions have been reported when attempting to triflate hindered alcohols.67
Formation of N-Nitrosodimethylamine during Chloramination of Secondary and Tertiary Amines: Role of Molecular Oxygen and Radical Intermediates
2016-11-22

N-Nitrosodimethylamine (NDMA) is a carcinogenic disinfection byproduct from water chloramination. Despite the identification of numerous NDMA precursors, essential parts of the reaction mechanism such as the incorporation of molecular O<sub>2</sub> are poorly understood. In laboratory model systems for the chloramination of secondary and tertiary amines, we investigated the kinetics of precursor disappearance and NDMA formation, quantified the stoichiometries of monochloramine (NH<sub>2</sub>Cl) and aqueous O<sub>2</sub> consumption, derived <sup>18</sup>O-kinetic isotope effects (<sup>18</sup>O-KIE) for the reactions of aqueous O<sub>2</sub>, and studied the impact of radical scavengers on NDMA formation. Although the molar NDMA yields from five N,N-dimethylamine-containing precursors varied between 1.4% and 90%, we observed the stoichiometric removal of one O<sub>2</sub> per N,N-dimethylamine group of the precursor indicating that the oxygenation of N atoms did not determine the molar NDMA yield. Small <sup>18</sup>O-KIEs between 1.0026 ± 0.0003 and 1.0092 ± 0.0009 found for all precursors as well as completely inhibited NDMA formation in the presence of radical scavengers (ABTS and trolox) imply that O<sub>2</sub> reacted with radical species. Our study suggests that aminyl radicals from the oxidation of organic amines by NH<sub>2</sub>Cl and N-peroxyl radicals from the reaction of aminyl radicals with aqueous O<sub>2</sub> are part of the NDMA formation mechanism.
Cellular Senescence, Immunosenescence and HIV
2016-11-22

Aging is a complex biological process that leads to several physiological changes. Among these changes, the most striking are those involving the innate and adaptive parts of the immune system. Furthermore, these changes are associated with a low-grade inflammation called inflamm-aging, which is the result of several lifelong antigenic stimulations, including chronic viral infections such as cytomegalovirus. Immunosenescence, concomitantly with inflamm-aging, is considered as the leading cause of age-related diseases including cardiovascular, neurodegenerative and metabolic diseases, and cancer. HIV infection, once considered a unique deadly infectious disease, has now become a chronic disease with efficacious highly active antiretroviral therapy. This signifies that the treatment transforms HIV infection from a chronic infection to a chronic inflammatory disease. Most people with HIV infection become aged, and older adults have been contracting HIV infection. Thus, there is a great interest to study HIV infection in relation to immunosenescence and inflamm-aging to determine whether immunosenescence contributes to HIV infection, or if HIV is causing immunosenescence and, as such, represents a premature immunosenescence and accelerated aging. Although there are many similarities in the immune and inflammatory changes and the occurrence of age-related chronic diseases between normal aging and HIV infection, the interaction between these processes is not well understood, and consequently the concept that HIV infection is an accelerated aging model is questioned. Future studies are needed to effectively answer this question for the better care of HIV-infected elderly patients.
Comparing Methods to Assess Intraobserver Measurement Error of 3D Craniofacial Landmarks Using Geometric Morphometrics Through a Digitizer Arm
2016-11-22

Abstract Intraobserver error ( INTRA ‐ OE ) is the difference between repeated measurements of the same variable made by the same observer. The objective of this work was to evaluate INTRA ‐ OE from 3D landmarks registered with a Microscribe, in different datasets: (A) the 3D coordinates, (B) linear measurements calculated from A, and (C) the six‐first principal component axes. INTRA ‐ OE was analyzed by digitizing 42 landmarks from 23 skulls in three events two weeks apart from each other. Systematic error was tested through repeated measures ANOVA ( ANOVA ‐ RM ), while random error through intraclass correlation coefficient. Results showed that the largest differences between the three observations were found in the first dataset. Some anatomical points like nasion, ectoconchion, temporosphenoparietal, asterion, and temporomandibular presented the highest INTRA ‐ OE . In the second dataset, local distances had higher INTRA ‐ OE than global distances while the third dataset showed the lowest INTRA ‐ OE .
Multimodal Body Representation of Obese Children and Adolescents before and after Weight-Loss Treatment in Comparison to Normal-Weight Children
2016-11-22

Although OBE children and adolescents generally perceived their body size and internal status of the body accurately, weight reduction improved their heartbeat detection accuracy and body dissatisfaction.