julilili42/papers huggingface dataset:
Ultrashort‐TE stimulated echo acquisition mode (STEAM) improves the quantification of lipids and fatty acid chain unsaturation in the human liver at 7 T
2015-08-27

Ultrahigh‐field, whole‐body MR systems increase the signal‐to‐noise ratio (SNR) and improve the spectral resolution. Sequences with a short TE allow fast signal acquisition with low signal loss as a result of spin–spin relaxation. This is of particular importance in the liver for the precise quantification of the hepatocellular content of lipids (HCL). In this study, we introduce a spoiler Gradient‐switching Ultrashort STimulated Echo AcqUisition (GUSTEAU) sequence, which is a modified version of a stimulated echo acquisition mode (STEAM) sequence, with a minimum TE of 6 ms. With the high spectral resolution at 7 T, the efficient elimination of water sidebands and the post‐processing suppression of the water signal, we estimated the composition of fatty acids (FAs) via the detection of the olefinic lipid resonance and calculated the unsaturation index (UI) of hepatic FAs. The performance of the GUSTEAU sequence for the assessment of UI was validated against oil samples and provided excellent results in agreement with the data reported in the literature. When measuring HCL with GUSTEAU in 10 healthy volunteers, there was a high correlation between the results obtained at 7 and 3 T ( R 2 = 0.961). The test–retest measurements yielded low coefficients of variation for HCL (4 ± 3%) and UI (11 ± 8%) when measured with the GUSTEAU sequence at 7 T. A negative correlation was found between UI and HCL ( n = 10; p &lt; 0.033). The ultrashort TE MRS sequence (GUSTEAU; TE = 6 ms) provided high repeatability for the assessment of HCL. The improved spectral resolution at 7 T with the elimination of water sidebands and the offline water subtraction also enabled an assessment of the unsaturation of FAs. This all highlights the potential use of this MRS acquisition scheme for studies of hepatic lipid composition in vivo . Copyright © 2015 John Wiley &amp; Sons, Ltd.
Coulomb versus physical string tension on the lattice
2015-08-27

From continuum studies it is known that the Coulomb string tension gives an upper bound for the physical (Wilson) string tension [D. Zwanziger, Phys. Rev. Lett. 90, 102001 (2003)]. How does however such relationship translate to the lattice? In this paper we give evidence that there, while the two string tensions are related at zero temperature, they decouple at finite temperature. More precisely, we show that on the lattice the Coulomb gauge confinement scenario is always tied to the spatial string tension, which is known to survive the deconfinement phase transition and to cause screening effects in the quark-gluon plasma. Our analysis is based on the identification and elimination of center vortices which allows to control the physical string tension and study its effect on the Coulomb gauge observables. We also show how alternative definitions of the Coulomb potential may sense the deconfinement transition; however a true static Coulomb gauge order parameter for the phase transition is still elusive on the lattice.
Phenotypic characterization and prognostic impact of circulating γδ and αβ T‐cells in metastatic malignant melanoma
2015-08-27

Human T cells carrying γδ T‐cell receptors (TCRs) represent a minor population relative to those with αβ TCRs. There has been much interest recently in the possibility of using these γδ T‐cells in cancer therapy because they can kill tumor cells in vitro in an MHC‐unrestricted manner, and possess potential regulatory capability and antigen‐presenting capacity. The presence of γδ T‐cells in late‐stage melanoma patients and their relationship with survival has not been extensively explored, although relatively lower percentages of total γδ T‐cells and Vδ2+ cells have been reported. Here, we present a detailed analysis of associations of γδ T‐cell subsets and differentiation stages with survival in Stage IV patients, compared with CD4+ and CD8+ αβ T‐cells. We found an increased Vδ1:Vδ2‐ratio and a decreased CD4:CD8‐ratio in patients compared to healthy controls, on the basis both of relative frequencies and absolute cell counts per μL blood. Nonetheless, Kaplan–Meier analyses showed that a higher than median frequency of Vδ1+ cells was negatively associated with survival, whereas there were no positive or negative associations with frequencies of Vδ2+ cells. Correlations of cell differentiation status with survival revealed a negative association of early‐differentiated Vδ1+ T cells with survival, both on the basis of relative frequencies and absolute counts. There was also a positive correlation between the frequencies of early‐differentiated CD8+ αβ T‐cells and survival. Our findings suggest peripheral blood frequencies of Vδ1+ T‐cells as a potential prognostic marker in melanoma. The mechanisms by which higher abundance of Vδ1+ cells are associated with poorer survival require determination.
Talented football players' development of achievement motives, volitional components, and self‐referential cognitions: A longitudinal study†
2015-08-27

Abstract Adolescence is regarded as a key developmental phase in the course of talented football players' careers. The present study focuses on early adolescent players' development of achievement motives, volitional components, and self‐referential cognitions. Based on the multidimensional and dynamic nature of talent, the development of multifaceted personality characteristics is an important issue in the context of sports talent research. According to previous findings in psychology, personality characteristics' development is defined by both stability and change, and the current study analyses four different types: differential stability (I), mean‐level change (II), individual‐level change (III), and structural stability (IV). The sample consists of 151 male players in the talent development programme of the German Football Association. Psychological diagnostics of the personality characteristics are implemented across longitudinal sections over a time period of three seasons, from the U12 to U14 age classes. The results reveal that the personality characteristics show (I) moderate test–retest correlations over one‐year intervals (.43 ≤ r tt ≤ .62), and lower coefficients for a two‐year period (.26 ≤ r tt ≤ .53). (II) Most of the personality characteristics' mean values differ significantly across the age classes with small effect sizes (.01 ≤ ≤ .03). (III) Only minor individual‐level changes in the football players' development are found. (IV) The personality characteristics' associations within a two‐factor structure do not stay invariant over time. From the results of the present study, conclusions are drawn regarding the talent identification and development process.
Comparative Genomics Including the Early-Diverging Smut FungusCeraceosorus bombacisReveals Signatures of Parallel Evolution within Plant and Animal Pathogens of Fungi and Oomycetes
2015-08-27

Ceraceosorus bombacis is an early-diverging lineage of smut fungi and a pathogen of cotton trees (Bombax ceiba). To study the evolutionary genomics of smut fungi in comparison with other fungal and oomycete pathogens, the genome of C. bombacis was sequenced and comparative genomic analyses were performed. The genome of 26.09 Mb encodes for 8,024 proteins, of which 576 are putative-secreted effector proteins (PSEPs). Orthology analysis revealed 30 ortholog PSEPs among six Ustilaginomycotina genomes, the largest groups of which are lytic enzymes, such as aspartic peptidase and glycoside hydrolase. Positive selection analyses revealed the highest percentage of positively selected PSEPs in C. bombacis compared with other Ustilaginomycotina genomes. Metabolic pathway analyses revealed the absence of genes encoding for nitrite and nitrate reductase in the genome of the human skin pathogen Malassezia globosa, but these enzymes are present in the sequenced plant pathogens in smut fungi. Interestingly, these genes are also absent in cultivable oomycete animal pathogens, while nitrate reductase has been lost in cultivable oomycete plant pathogens. Similar patterns were also observed for obligate biotrophic and hemi-biotrophic fungal and oomycete pathogens. Furthermore, it was found that both fungal and oomycete animal pathogen genomes are lacking cutinases and pectinesterases. Overall, these findings highlight the parallel evolution of certain genomic traits, revealing potential common evolutionary trajectories among fungal and oomycete pathogens, shaping the pathogen genomes according to their lifestyle.
A statistical concept to assess the uncertainty in Bayesian model weights and its impact on model ranking
2015-08-28

Bayesian model averaging (BMA) ranks the plausibility of alternative conceptual models according to Bayes' theorem. A prior belief about each model's adequacy is updated to a posterior model probability based on the skill to reproduce observed data and on the principle of parsimony. The posterior model probabilities are then used as model weights for model ranking, selection, or averaging. Despite the statistically rigorous BMA procedure, model weights can become uncertain quantities due to measurement noise in the calibration data set or due to uncertainty in model input. Uncertain weights may in turn compromise the reliability of BMA results. We present a new statistical concept to investigate this weighting uncertainty, and thus, to assess the significance of model weights and the confidence in model ranking. Our concept is to resample the uncertain input or output data and then to analyze the induced variability in model weights. In the special case of weighting uncertainty due to measurement noise in the calibration data set, we interpret statistics of Bayesian model evidence to assess the distance of a model's performance from the theoretical upper limit. To illustrate our suggested approach, we investigate the reliability of soil-plant model selection following up on a study by Wöhling et al. (2015). Results show that the BMA routine should be equipped with our suggested upgrade to (1) reveal the significant but otherwise undetected impact of measurement noise on model ranking results and (2) to decide whether the considered set of models should be extended with better performing alternatives.
Energy Sensing versus 2-Oxoglutarate Dependent ATPase Switch in the Control of Synechococcus PII Interaction with Its Targets NAGK and PipX
2015-08-28

PII proteins constitute a superfamily of highly conserved signaling devices, common in all domains of life. Through binding of the metabolites ATP, ADP and 2-oxoglutarate (2-OG), they undergo conformational changes which allow them to regulate a variety of target proteins including enzymes, transport proteins and transcription factors. But, in reverse, these target proteins also modulate the metabolite sensing properties of PII, as has been recently shown. We used this effect to refine our PII based Förster resonance energy transfer (FRET) sensor and amplify its sensitivity towards ADP. With this enhanced sensor setup we addressed the question whether the PII protein from the model organism Synechococcus elongatus autonomously switches into the ADP conformation through ATPase activity as proposed in a recently published model. The present study disproves ATPase activity as a relevant mechanism for the transition of PII into the ADP state. In the absence of 2-OG, only the ATP/ADP ratio and concentration of ADP directs the competitive interaction of PII with two targets, one of which preferentially binds PII in the ATP-state, the other in the ADP-state.
Automatic refunctionalization to a language with copattern matching: with applications to the expression problem
2015-08-29

Defunctionalization and refunctionalization establish a correspondence between first-class functions and pattern matching, but the correspondence is not symmetric: Not all uses of pattern matching can be automatically refunctionalized to uses of higher-order functions. To remedy this asymmetry, we generalize from first-class functions to arbitrary codata. This leads us to full defunctionalization and refunctionalization between a codata language based on copattern matching and a data language based on pattern matching. We observe how programs can be written as matrices so that they are modularly extensible in one dimension but not the other. In this representation, defunctionalization and refunctionalization correspond to matrix transposition which effectively changes the dimension of extensibility a program supports. This suggests applications to the expression problem.
Modeling diffusion in colloidal suspensions by dynamical density functional theory using fundamental measure theory of hard spheres
2015-08-31

We study the dynamics of colloidal suspensions of hard spheres that are subject to Brownian motion in the overdamped limit. We obtain the time evolution of the self- and distinct parts of the van Hove function by means of dynamical density functional theory. The free-energy model for the hard-sphere fluid that we use is the very accurate White Bear II version of Rosenfeld's fundamental measure theory. However, in order to remove interactions within the self-part of the van Hove function, a nontrivial modification has to be applied to the free-energy functional. We compare our theoretical results with data that we obtain from dynamical Monte Carlo simulations, and we find that the latter are well described by our approach even for colloid packing fractions as large as 40%.
Callus massage after distraction osteogenesis using the concept of lengthening then dynamic plating
2015-08-31

Correction of complex deformities is a challenging procedure. Long-term wearing of a fixator after correction and lengthening are inconvenient and has a high rate of complication. The goals of the surgical treatment in the presented case were: (1) correction of the deformity and lengthening of the left leg by the Taylor spatial frame (TSF, Smith and Nephew, Marl, Germany); (2) reduction in the time the patient wears the TSF by changing the fixation system to a plate (lengthening then plating-LTP) and using a locking compression plate in conjunction with the 5.0 dynamic locking screws in order to accelerate bone healing.
Explanation of “Silver Effects” in Gold(I)-Catalyzed Hydroalkoxylation of Alkynes
2015-09-01

An extensive experimental NMR study of gold-catalyzed hydroalkoxylation was conducted to explain the influence of a silver salt additive on the gold-catalyzed process (silver effect). Addition of silver salt may have no effect or a negative or positive effect on gold-catalyzed hydroalkoxylation. However, silver was shown to be essentially innocent (plays no role) with regard to the mechanism of the catalytic process itself. The effect occurs only if silver induces variations in the fraction of in-cycle organogold intermediates and H+. This is associated with the formation of the argento vinyl gold species G, which was shown to be an off-cycle intermediate. This species is formed by trapping the vinyl gold species B with Ag+; in the same way, the diaurated species D (another possible off-cycle intermediate) is formed by trapping B with LAu+. The argento vinyl gold species G1 was extensively characterized in solution by various NMR techniques at different temperatures. Furthermore, bringing together our results and the topical research of others, we introduced classification of silver effects to eliminate the confusion around the interpretation of erratic effects. Reactions that are separately catalyzed either by silver or by gold were beyond the scope of this study (for those reactions a "true" silver effect would take place).
Driver-Activity Recognition in the Context of Conditionally Autonomous Driving
2015-09-01

This paper presents a novel approach to automated recognition of the driver's activity, which is a crucial factor for determining the take-over readiness in conditionally autonomous driving scenarios. Therefore, an architecture based on head-and eye-tracking data is introduced in this study and several features are analyzed. The proposed approach is evaluated on data recorded during a driving simulator study with 73 subjects performing different secondary tasks while driving in an autonomous setting. The proposed architecture shows promising results towards in-vehicle driver-activity recognition. Furthermore, a significant improvement in the classification performance is demonstrated due to the consideration of novel features derived especially for the autonomous driving context.
What's Wrong With Recalcitrant Emotions? From Irrationality to Challenge of Agential Identity
2015-09-01

I argue that, in experiencing a recalcitrant emotion, one does not violate a rational requirement of any sort. Rational requirements, as the expression has come to be used, are requirements of coherence (for instance, the requirements to be consistent in your beliefs and in your intentions). Accordingly, my argument is that there is nothing incoherent in any way about experiencing a recalcitrant emotion. One becomes incoherent (i.e., irrational) only if one allows the emotion to influence one's reasoning and/or action, in which case one violates the 'consistency principle' and/or the 'enkratic principle'. From the standpoint of rationality, it would even be counterproductive to put subjects under the obligation that their emotional experiences and their evaluative judgements must always fit together. When we nevertheless intuitively sense that the subject is irrational in experiencing a recalcitrant emotion this is in cases in which the emotion challenges the subject's agential identity. However, emotions can, but need not, challenge one's agential identity, and, furthermore, perceptions can do so as well. In any case, challenges of this kind do not involve the violation of a rational requirement.
In Vitro Cytotoxicity and Adaptive Stress Responses to Selected Haloacetic Acid and Halobenzoquinone Water Disinfection Byproducts
2015-09-01

The process of disinfecting drinking water inadvertently leads to the formation of numerous disinfection byproducts (DBPs). Some of these are mutagenic, genotoxic, teratogenic, and cytotoxic, as well as potentially carcinogenic both in vivo and in vitro. We investigated the in vitro biological activity of five DBPs: three monohaloacetic acids (monoHAAs) [chloroacetic acid (CAA), bromoacetic acid (BAA), and iodoacetic acid (IAA)] and two novel halobenzoquinones (HBQs) [2,6-dichloro-p-benzoquinone (DCBQ) and 2,6-dibromo-p-benzoquinone]. We focused particularly on cytotoxicity and induction of two adaptive stress response pathways: the oxidative stress responsive Nrf2/ARE and DNA-damage responsive p53 pathways. All five DBPs were cytotoxic to the Caco-2 cell line after a 4 h exposure, and all DBPs induced both of the adaptive stress response pathways, Nrf2/ARE and p53, in the micromolar range, as measured by two β-lactamase-based reporter gene assays. The decreasing order of potency for all three endpoints for the five DBPs was IAA ∼ BAA > DCBQ ∼ DBBQ > CAA. Induction of oxidative stress was previously proposed to be the molecular initiating event (MIE) for both classes of DBPs. However, comparing the levels of activation of the two pathways uncovered that the Nrf2/ARE pathway was the more sensitive endpoint for HAAs, whereas the p53 pathway was more sensitive in the case of HBQs. Therefore, the DNA damage-responsive p53 pathway may be an important piece of information to fill in a gap in the adverse outcome pathway framework for the assessment of HBQs. Finally, we cautiously compared the potential risk of the two novel HBQs using a benchmarking approach to that of the well-studied CAA, which suggested that their relative risk may be lower than that of BAA and IAA.
Neural correlates of math anxiety – an overview and implications
2015-09-01

Math anxiety is a common phenomenon which can have a negative impact on numerical and arithmetic performance. However, so far little is known about the underlying neurocognitive mechanisms. This mini review provides an overview of studies investigating the neural correlates of math anxiety which provide several hints regarding its influence on math performance: while behavioral studies mostly observe an influence of math anxiety on difficult math tasks, neurophysiological studies show that processing efficiency is already affected in basic number processing. Overall, the neurocognitive literature suggests that (i) math anxiety elicits emotion- and pain-related activation during and before math activities, (ii) that the negative emotional response to math anxiety impairs processing efficiency, and (iii) that math deficits triggered by math anxiety may be compensated for by modulating the cognitive control or emotional regulation network. However, activation differs strongly between studies, depending on tasks, paradigms, and samples. We conclude that neural correlates can help to understand and explore the processes underlying math anxiety, but the data are not very consistent yet.
The Influence of Sub-Unit Composition and Expression System on the Functional Antibody Response in the Development of a VAR2CSA Based Plasmodium falciparum Placental Malaria Vaccine
2015-09-01

The disease caused by Plasmodium falciparum (Pf) involves different clinical manifestations that, cumulatively, kill hundreds of thousands every year. Placental malaria (PM) is one such manifestation in which Pf infected erythrocytes (IE) bind to chondroitin sulphate A (CSA) through expression of VAR2CSA, a parasite-derived antigen. Protection against PM is mediated by antibodies that inhibit binding of IE in the placental intervillous space. VAR2CSA is a large antigen incompatible with large scale recombinant protein expression. Vaccines based on sub-units encompassing the functionally constrained receptor-binding domains may, theoretically, circumvent polymorphisms, reduce the risk of escape-mutants and induce cross-reactive antibodies. However, the sub-unit composition and small differences in the borders, may lead to exposure of novel immuno-dominant antibody epitopes that lead to non-functional antibodies, and furthermore influence the folding, stability and yield of expression. Candidate antigens from the pre-clinical development expressed in High-Five insect cells using the baculovirus expression vector system were transitioned into the Drosophila Schneider-2 cell (S2) expression-system compliant with clinical development. The functional capacity of antibodies against antigens expressed in High-Five cells or in S2 cells was equivalent. This enabled an extensive down-selection of S2 insect cell-expressed antigens primarily encompassing the minimal CSA-binding region of VAR2CSA. In general, we found differential potency of inhibitory antibodies against antigens with the same borders but of different var2csa sequences. Likewise, we found that subtle size differences in antigens of the same sequence gave varying levels of inhibitory antibodies. The study shows that induction of a functional response against recombinant subunits of the VAR2CSA antigen is unpredictable, demonstrating the need for large-scale screening in order to identify antigens that induce a broadly strain-transcending antibody response.
GM-CSF stimulates granulopoiesis in a congenital neutropenia patient with loss-of-function biallelic heterozygous CSF3R mutations
2015-09-01

To the editor: Severe congenital neutropenia (CN) is a heterogeneous disease characterized by an absolute neutrophil count (ANC) below 500 cells per microliter and recurrent, life-threatening bacterial infections. Treatment with recombinant human granulocyte colony-stimulating factor (rhG-CSF) was