julilili42/papers huggingface dataset:
Partonic description of the transverse target single-spin asymmetry in inclusive deep-inelastic scattering
2013-02-04

The single-spin asymmetry of unpolarized leptons scattering\\ndeep-inelastically off transversely polarized nucleons is studied in a partonic\\npicture within a collinear twist-3 framework. Since this observable is\\ngenerated by multi-photon exchanges between lepton and nucleon a partonic\\ndescription of the asymmetry contains essential elements of a full\\nnext-to-leading order calculation for single-spin asymmetries in perturbative\\nQuantum Chromodynamics. In particular it is shown how nontrivial cancellations\\nbetween kinematical and dynamical twist-3 contributions lead to a well-behaved\\nand finite formula. This final result can be expressed in terms of\\nmultipartonic quark-gluon and quark-photon correlation functions. Hence, a\\nmeasurement of the transverse target single-spin asymmetry may provide new\\nconstraints on these multipartonic correlations.\\n
Smoking, apolipoprotein E genotypes, and mortality (the Ludwigshafen RIsk and Cardiovascular Health study)
2013-02-04

In persons undergoing coronary angiography, there is a significant interaction between APOE-genotype and smoking. The presence of the ε4 allele in current smokers increases cardiovascular and all-cause mortality.
‐mapping with the transient phase of unbalanced steady‐state free precession
2013-02-04

Purpose A novel ‐mapping technique (B1‐TRAP) is presented, which derives the actual flip angle from the frequency of signal oscillations, observed in the transient phase of unbalanced steady‐state free precession sequences. Theory For short repetition times (TR), the angular frequency of distinct oscillations in the transient phase of steady‐state free precession sequences is proven to be approximately proportional to the actual flip angle: . The result is not influenced by off‐resonance and it can be shown that deviations are only of second order in the small parameter . Methods B1‐TRAP makes use of this effect through a frequency analysis of the transient phase of a train of steady‐state free precession signals. Results In terms of reliability and time efficiency, a two‐dimensional multislice implementation was found to be optimal. Unlike many steady‐state ‐mapping methods, the accuracy of B1‐TRAP was not impaired by imperfect slice profiles. Conclusion Simulations, phantom, and in vivo measurements showed that B1‐TRAP offers a good compromise with respect to speed, robustness, and accuracy. Magn Reson Med 70:1515–1523, 2013. © 2013 Wiley Periodicals, Inc.
Fact or artefact: an item response theory analysis of median split based repressor classification
2013-02-04

Objective Many studies have investigated the phenomenon of repression. Repressors are defined as individuals who deny or avoid the experience of negative affect. A common method for the identification of repressors is a median split approach using questionnaires that measure anxiety and social desirability. The present study aimed to evaluate this most frequently used procedure using a psychometric model. Design We applied item response theory using model assumptions comparable with those of the median split approach to detect repressors and examine the appropriateness of the median split procedure. Methods A mixed sample of 655 students and members of the general public completed the two scales usually used to identify repressors, namely the T aylor M anifest A nxiety S cale and the Marlowe‐Crowne S ocial D esirability S cale. Results Employing item response theory mixture‐model analyses, we were unable to replicate the median split solution on a latent level. Conclusions Our results did not support the identification of repressors via dichotomization of the two scales. The median split approach does not appear to detect repressors satisfactorily. The implications of the results for the conceptualization and assessment of repressors are discussed. Statement of contribution What is already known on this subject? Repression is a construct describing the suppression, denial or failure to exhibit negative emotions, and has been associated with many health outcomes. In much of the literature, two self‐report scales are used to identify repressors, one measuring manifest anxiety and the other measuring social desirability. Median splits on these scales identify people low in manifest anxiety and high in self‐reported social desirability as repressors. What does this study add? Using item‐response theory we examined whether median splits are an appropriate method to identify repressors. We found that the latent classes did not show the characteristic pattern suggested by the median split approach and concluded that the psychometric model did not support the classification of individuals via median splits. Our findings have implications for future work using the repression construct and median splits to identify repressors.
Preanalytical Aspects and Sample Quality Assessment in Metabolomics Studies of Human Blood
2013-02-05

BACKGROUND Metabolomics is a powerful tool that is increasingly used in clinical research. Although excellent sample quality is essential, it can easily be compromised by undetected preanalytical errors. We set out to identify critical preanalytical steps and biomarkers that reflect preanalytical inaccuracies. METHODS We systematically investigated the effects of preanalytical variables (blood collection tubes, hemolysis, temperature and time before further processing, and number of freeze–thaw cycles) on metabolomics studies of clinical blood and plasma samples using a nontargeted LC-MS approach. RESULTS Serum and heparinate blood collection tubes led to chemical noise in the mass spectra. Distinct, significant changes of 64 features in the EDTA-plasma metabolome were detected when blood was exposed to room temperature for 2, 4, 8, and 24 h. The resulting pattern was characterized by increases in hypoxanthine and sphingosine 1-phosphate (800% and 380%, respectively, at 2 h). In contrast, the plasma metabolome was stable for up to 4 h when EDTA blood samples were immediately placed in iced water. Hemolysis also caused numerous changes in the metabolic profile. Unexpectedly, up to 4 freeze–thaw cycles only slightly changed the EDTA-plasma metabolome, but increased the individual variability. CONCLUSIONS Nontargeted metabolomics investigations led to the following recommendations for the preanalytical phase: test the blood collection tubes, avoid hemolysis, place whole blood immediately in ice water, use EDTA plasma, and preferably use nonrefrozen biobank samples. To exclude outliers due to preanalytical errors, inspect the biomarker signal intensities reflecting systematic as well as accidental and preanalytical inaccuracies before processing the bioinformatics data.
Determination of Organ-Specific Anemia Tolerance*
2013-02-05

Heart, brain, kidneys, liver, small intestine, and skeletal muscle experience tissue hypoxia at different degrees of acute anemia, as assessed by the pimonidazole method and vascular endothelial growth factor expression. Further studies are needed to elucidate the mechanisms that determine organ-specific anemia tolerance.
Time Series Analysis as a Tool To Predict the Impact of Antimicrobial Restriction in Antibiotic Stewardship Programs Using the Example of Multidrug-Resistant Pseudomonas aeruginosa
2013-02-05

ABSTRACT The association between antimicrobial consumption and resistance in nonfermentative Gram-negative bacteria is well-known. Antimicrobial restriction, implemented in clinical routines by antibiotic stewardship programs (ASPs), is considered a means to reduce resistance rates. Whether and how antimicrobial restriction can accomplish this goal is still unknown though. This leads to an element of uncertainty when designing strategies for ASPs. From January 2002 until December 2011, an observational study was performed at the University Hospital Tübingen, Tübingen, Germany, to investigate the association between antimicrobial use and resistance rates in Pseudomonas aeruginosa . Transfer function models were used to determine such associations and to simulate antimicrobial restriction strategies. Various positive associations between antimicrobial consumption and resistance were observed in our setting. Surprisingly, impact estimations of different antimicrobial restriction strategies revealed relatively low intervention expenses to effectively attenuate the observed increase in resistance. For example, a simulated intervention of an annual 4% reduction in the use of meropenem over 3 years from 2009 until 2011 yielded a 62.5% attenuation (95% confidence interval, 15% to 110%) in the rising trend of multidrug-resistant Pseudomonas aeruginosa (three- and four-class-resistant P. aeruginosa [34MRGN-PA]). Time series analysis models derived from past data may be a tool to predict the outcome of antimicrobial restriction strategies, and could be used to design ASPs.
Examination of the interplay between glacial processes and exhumation in the Saint Elias Mountains, Alaska
2013-02-05

The combination of large, temperate glaciers and rapid crustal convergence in the Saint Elias Mountains (southeastern Alaska, USA, and Yukon Territory and British Colombia, Canada) provides an exceptional opportunity to study the interactions between the tectonic and surface processes that have shaped most active orogens on Earth during much of the Quaternary. This research first provides a review of thermochronometric data sets recording exhumation under two major glacier systems of the Saint Elias Mountains, the Bagley-Bering and the Seward-Malaspina systems. These data sets are integrated over the single glacier systems and used in conjunction with glaciological data to investigate the interactions of glacial erosion and tectonics. Despite their proximity, the glaciological processes and geological settings of these two glacial systems differ significantly. On the east side of the orogen, sediments eroded from bedrock underneath the Malaspina Glacier reflect regions of rapid erosion under the slowly moving Seward Ice Field. Because the Seward Ice Field overlies a localized zone of major faulting and rapid exhumation, the strained and fractured bedrock is primed for erosion. On the west side, the Bering Glacier is the primary outlet for the Bagley Ice Field, which covers half of the crest of the orogen; however, few if any of the sediments at its terminus originate from under the Bagley Ice Field. Sediment transport is likely hindered by subglacial freeze-on processes that reduce the sediment-carrying capacity of subglacial rivers, though glacial surges are likely exceptions that deposit sediment far beyond the active margin of the glacier. Our study concludes that the widely invoked concepts of glacial erosion should be used with caution, as oversimplification can fail to account for important site-specific differences in geologic and glacial conditions.
Metabolic Changes in Synechocystis PCC6803 upon Nitrogen-Starvation: Excess NADPH Sustains Polyhydroxybutyrate Accumulation
2013-02-06

Polyhydroxybutyrate (PHB) is a common carbon storage polymer among heterotrophic bacteria. It is also accumulated in some photoautotrophic cyanobacteria; however, the knowledge of how PHB accumulation is regulated in this group is limited. PHB synthesis in Synechocystis sp. PCC 6803 is initiated once macronutrients like phosphorus or nitrogen are limiting. We have previously reported a mutation in the gene sll0783 that impairs PHB accumulation in this cyanobacterium upon nitrogen starvation. In this study we present data which explain the observed phenotype. We investigated differences in intracellular localization of PHB synthase, metabolism, and the NADPH pool between wild type and mutant. Localization of PHB synthase was not impaired in the sll0783 mutant; however, metabolome analysis revealed a difference in sorbitol levels, indicating a more oxidizing intracellular environment than in the wild type. We confirmed this by directly measuring the NADPH/NADP ratio and by altering the intracellular redox state of wild type and sll0783 mutant. We were able to physiologically complement the mutant phenotype of diminished PHB synthase activity by making the intracellular environment more reducing. Our data illustrate that the NADPH pool is an important factor for regulation of PHB biosynthesis and metabolism, which is also of interest for potential biotechnological applications.
Control of matter-wave superradiance with a high-finesse ring cavity
2013-02-06

We experimentally investigate light scattering from a Bose-Einstein condensate which is positioned inside an optical ring cavity. With a cavity linewidth at the recoil limit, the resulting superradiant scattering behavior is strongly influenced by the cavity detuning. The experimental observations are interpreted with a quantum mean-field description and with a rate-equation model. We discuss applications in the context of quantum phase transitions, Dicke subradiance, and nonconventional superfluidity.
Regulation of Hematopoietic Stem Cell Behavior by the Nanostructured Presentation of Extracellular Matrix Components
2013-02-06

Hematopoietic stem cells (HSCs) are maintained in stem cell niches, which regulate stem cell fate. Extracellular matrix (ECM) molecules, which are an essential part of these niches, can actively modulate cell functions. However, only little is known on the impact of ECM ligands on HSCs in a biomimetic environment defined on the nanometer-scale level. Here, we show that human hematopoietic stem and progenitor cell (HSPC) adhesion depends on the type of ligand, i.e., the type of ECM molecule, and the lateral, nanometer-scaled distance between the ligands (while the ligand type influenced the dependency on the latter). For small fibronectin (FN)-derived peptide ligands such as RGD and LDV the critical adhesive interligand distance for HSPCs was below 45 nm. FN-derived (FN type III 7-10) and osteopontin-derived protein domains also supported cell adhesion at greater distances. We found that the expression of the ECM protein thrombospondin-2 (THBS2) in HSPCs depends on the presence of the ligand type and its nanostructured presentation. Functionally, THBS2 proved to mediate adhesion of HSPCs. In conclusion, the present study shows that HSPCs are sensitive to the nanostructure of their microenvironment and that they are able to actively modulate their environment by secreting ECM factors.
Mutation detection in cholestatic patients using microarray resequencing of ATP8B1 and ABCB11
2013-02-06

Background : Neonatal cholestasis is a common presentation of childhood liver diseases and can be a feature of various conditions including disorders of bile acid biogenesis and transport, various inborn errors of metabolism and perinatal infections. Some inherited metabolic diseases can be easily screened using biochemical assays, however many can only be accurately diagnosed by DNA sequencing. Fluorescent capillary Sanger sequencing (FS) is the gold standard method used by clinical laboratories for genetic diagnosis of many inherited conditions; however, it does have limitations. Recently microarray resequencing (MR) has been introduced into research and clinical practice as an alternative method for genetic diagnosis of heterogeneous conditions. In this report we compared the accuracy of mutation detection for MR with FS in a group of patients with 'low-normal' gamma glutamyl transpeptidase (gGT) cholestasis without known molecular diagnoses. Methods : 29 patient DNA samples were tested for mutations in the ATP8B1 and ABCB11 genes using both FS and MR. Other known causes of "low gGT cholestasis" such as ARC syndrome and bile acid biosynthesis disorders were excluded. Results : Mutations were identified in 13/29 samples. In 3/29 samples FS and MR gave discordant results: MR had a false positive rate of 3.4% and a false negative rate of 7%. Conclusions : The major advantage of MR over FS is that multiple genes can be screened in one experiment, allowing rapid and cost-effective diagnoses. However, we have demonstrated that MR technology is limited in sensitivity. We therefore recommend that MR be used as an initial evaluation, with FS deployed when genetic and clinical or histopathological findings are discordant.
Small changes—Huge influences: NMR chemical shifts of Ni(II) complexes with polar substrates
2013-02-06

Abstract Neutral Ni(II) complexes have been shown to be highly valuable as robust and versatile catalysts in olefin polymerization. But they show reduced reactivity when the polar monomers methyl acrylate and vinyl acetate are incorporated. To get further insight into this behavior, NMR chemical shift calculations were performed on the system [(N,O) Ni (H) (PMe3)] 1 (N,O = ‐N,O‐{2,6‐(3,5‐(F3C)2C6H3)2C6H3)NC(H)‐3,5‐I2‐2‐O‐C6H2}). The chemical shifts show reasonable agreement with experiment but are also extremely influenced by geometrical features of the complex as well as the inserted substrate. The first prominent feature, the low‐field shift of the C carbonyl in the incorporated monomer, can only be reproduced when it is in close proximity to the Ni and in this way hinders the attack of a new monomer. Second, the almost 100 ppm difference in the chemical shift of the carbon of the two substrates directly bound to Ni can be reasoned by the different directionality of polarization as disclosed by natural bond orbital (NBO) analysis. © 2013 Wiley Periodicals, Inc.
Retinitis pigmentosa: rapid neurodegeneration is governed by slow cell death mechanisms
2013-02-07

For most neurodegenerative diseases the precise duration of an individual cell's death is unknown, which is an obstacle when counteractive measures are being considered. To address this, we used the rd1 mouse model for retinal neurodegeneration, characterized by phosphodiesterase-6 (PDE6) dysfunction and photoreceptor death triggered by high cyclic guanosine-mono-phosphate (cGMP) levels. Using cellular data on cGMP accumulation, cell death, and survival, we created mathematical models to simulate the temporal development of the degeneration. We validated model predictions using organotypic retinal explant cultures derived from wild-type animals and exposed to the selective PDE6 inhibitor zaprinast. Together, photoreceptor data and modeling for the first time delineated three major cell death phases in a complex neuronal tissue: (1) initiation, taking up to 36 h, (2) execution, lasting another 40 h, and finally (3) clearance, lasting about 7 h. Surprisingly, photoreceptor neurodegeneration was noticeably slower than necrosis or apoptosis, suggesting a different mechanism of death for these neurons.
Characterization of peripheral hematopoietic stem cells and monocytes in Parkinson's disease
2013-02-07

Background Emerging evidence has highlighted the pivotal role of the immune system in neurodegenerative diseases. This study investigated the impact of progressive neurodegeneration on the differentiation and development of hematopoietic stem cells in the peripheral blood of Parkinson's patients. Methods: A colony‐forming cell assay was established to study hematopoietic stem cells from venous blood of Parkinson's patients, and flow cytometry was used to analyze the expression of chemokine receptors on monocytes. Results We demonstrate that there is strong upregulation in the percentage of monocyte precursors in the peripheral blood of Parkinson's patients and asymptomatic high‐risk individuals. We identify the receptor CCR2 as undergoing strong upregulation on the surface of classical monocytes in Parkinson's patients. Conclusions The association between blood cell development and progressive cell death in the brain of Parkinson's patients should be further investigated as a potential dynamic biomarker and indicator of disease progression. © 2013 Movement Disorder Society
Mucosal Improvement in Patients With Moderate to Severe Postoperative Endoscopic Recurrence of Crohn’s Disease and Azathioprine Metabolite Levels
2013-02-07

Our post hoc analysis from a double-blind, randomized trial suggests that higher RBC 6-TGN levels are associated with endoscopic improvement in patients with severe postoperative endoscopic recurrence of CD. Thus, our study provides first evidence on the utility of monitoring of thiopurine metabolites to achieve mucosal response in CD.
An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics
2013-02-08

We present a computational pipeline for the quantification of peptides and proteins in label-free LC-MS/MS data sets. The pipeline is composed of tools from the OpenMS software framework and is applicable to the processing of large experiments (50+ samples). We describe several enhancements that we have introduced to OpenMS to realize the implementation of this pipeline. They include new algorithms for centroiding of raw data, for feature detection, for the alignment of multiple related measurements, and a new tool for the calculation of peptide and protein abundances. Where possible, we compare the performance of the new algorithms to that of their established counterparts in OpenMS. We validate the pipeline on the basis of two small data sets that provide ground truths for the quantification. There, we also compare our results to those of MaxQuant and Progenesis LC-MS, two popular alternatives for the analysis of label-free data. We then show how our software can be applied to a large heterogeneous data set of 58 LC-MS/MS runs.
Modified Foxp3 mRNA protects against asthma through an IL-10–dependent mechanism
2013-02-08

Chemically modified mRNA is capable of inducing therapeutic levels of protein expression while circumventing the threat of genomic integration often associated with viral vectors. We utilized this novel therapeutic tool to express the regulatory T cell transcription factor, FOXP3, in a time- and site-specific fashion in murine lung, in order to prevent allergic asthma in vivo. We show that modified Foxp3 mRNA rebalanced pulmonary T helper cell responses and protected from allergen-induced tissue inflammation, airway hyperresponsiveness, and goblet cell metaplasia in 2 asthma models. This protection was conferred following delivery of modified mRNA either before or after the onset of allergen challenge, demonstrating its potential as both a preventive and a therapeutic agent. Mechanistically, FOXP3 induction controlled Th2 and Th17 inflammation by regulating innate immune cell recruitment through an IL-10-dependent pathway. The protective effects of FOXP3 could be reversed by depletion of IL-10 or administration of recombinant IL-17A or IL-23. Delivery of Foxp3 mRNA to sites of inflammation may offer a novel, safe therapeutic tool for the treatment of allergic asthma and other diseases driven by an imbalance in helper T cell responses.
Experimental Hyperleptinemia Acutely Increases Vasoconstrictory Sympathetic Nerve Activity in Healthy Humans
2013-02-08

Acute experimental hyperleptinemia has significant central nervous excitatory effects on vasoconstrictory sympathetic outflow as measured by MSNA in healthy men. These results suggest that leptin acts as an important mediator linking obesity to elevated MSNA and potentially to the development of hypertension.
QCD resummation for semi-inclusive hadron production processes
2013-02-08

We investigate the resummation of large logarithmic perturbative corrections\\nto hadron production in electron-positron annihilation and semi-inclusive\\ndeep-inelastic scattering. We find modest, but significant, enhancements of\\nhadron multiplicities in the kinematic regimes accessible in present\\nhigh-precision experiments. Our results are therefore relevant for the\\ndetermination of hadron fragmentation functions from data for these processes.\\n