julilili42/papers huggingface dataset:
In vivo analysis of the vascular pattern of the superficial temporal artery based on digital subtraction angiography
2014-11-03

Background Existing anatomic descriptions of the superficial temporal artery (STA) are mainly based on cadaver studies and do not accurately reflect the in vivo situation. In this study, the anatomical course and branching pattern of the STA were analyzed with digital subtraction angiographies (DSAs). Methods DSAs of 93 Caucasian individuals between 16‐ and 79‐years old were retrospectively analyzed regarding the course and branching pattern of the STA as well as surgically relevant inner diameters and lengths of its main branches. Results In total, 11 variations in the branching pattern of the terminal STA were found. About 89% of the examined individuals demonstrated the classic variation in which the main trunk of the STA bifurcates into a single frontal and parietal branch. In 60% of cases with an existing bifurcation, the division of the main trunk of the STA was located above the zygoma. The mean inner diameters of the STA main trunk, the frontal branch and the parietal branch were 2.4 ± 0.6 mm, 1.3 ± 0.6 mm and 1.2 ± 0.4 mm, respectively. The surgically relevant “working lengths” of the frontal and parietal branches above the upper margin of the zygoma up to an inner diameter of 1 mm were 106.4 ± 62.1mm and 99.7 ± 40.9 mm, respectively. Conclusions The common variations of the branching pattern of the STA are described in this study. Furthermore, surgically relevant inner diameters and lengths of the main branches of the STA are determined. These findings should improve our understanding of the suitability and usefulness of the STA for various surgical procedures. © 2014 Wiley Periodicals, Inc. Microsurgery 35:380–386, 2015.
EIF4G1 is neither a strong nor a common risk factor for Parkinson's disease: evidence from large European cohorts
2014-11-03

Background Missense mutations in the eukaryotic translation initiation factor 4-γ 1 ( EIF4G1 ) gene have previously been implicated in familial Parkinson's disease (PD). A large PD family with autosomal-dominant segregation showed a heterozygous missense mutation and additional patients were found to have unique sequence variants that have not been observed in controls. Subsequent studies have reported contradictory findings. Methods We assessed the relevance of EIF4G1 mutations in a European cohort of 2146 PD patients. Of these, 2051 sporadic PD patients were screened for the reported p.Ala502Val and p.Arg1205His mutations. In addition, the complete coding region of EIF4G1 was directly sequenced in 95 familial PD patients with autosomal-dominant inheritance. Moreover, we imputed the p.Arg1205His substitution and tested for association with PD in the Icelandic population (93 698 samples). Results We did not observe the presence of the p.Ala502Val substitution in our cohort; however, the p.Arg1205His mutation was identified in one sporadic PD patient. The same mutation was also found in 76 Icelandic subjects older than 65 years using haplotype imputing. Only five of these subjects reported PD symptoms (OR 1.3, p =0.50). Thus, if causal, the p.Arg1205His EIF4G1 mutation has a low penetrance or a late onset manifestation. A novel variant p.Arg566Cys found in a patient with familial PD did not cosegregate with PD in all three affected siblings. All further recently published EIF4G1 mutations found in our cohort are likely to be benign polymorphisms. Conclusions This is the largest genetic study of EIF4G1 mutations in PD. Our data do not support the EIF4G1 gene as a high-risk PD locus, neither for the familial nor the sporadic condition. Furthermore, the p.Arg1205His mutation is not significantly associated with increased risk of PD in the Icelandic population. Therefore, caution should be exercised when interpreting EIF4G1 genotyping results in isolated patients and PD families. In summary, diagnostic testing of EIF4G1 should not be recommended in clinical settings.
How Structure Shapes Dynamics: Knowledge Development in Wikipedia - A Network Multilevel Modeling Approach
2014-11-03

Using a longitudinal network analysis approach, we investigate the structural development of the knowledge base of Wikipedia in order to explain the appearance of new knowledge. The data consists of the articles in two adjacent knowledge domains: psychology and education. We analyze the development of networks of knowledge consisting of interlinked articles at seven snapshots from 2006 to 2012 with an interval of one year between them. Longitudinal data on the topological position of each article in the networks is used to model the appearance of new knowledge over time. Thus, the structural dimension of knowledge is related to its dynamics. Using multilevel modeling as well as eigenvector and betweenness measures, we explain the significance of pivotal articles that are either central within one of the knowledge domains or boundary-crossing between the two domains at a given point in time for the future development of new knowledge in the knowledge base.
Orbitally tuned age model for the late Pliocene–Pleistocene lacustrine succession of drill core SG-1 from the western Qaidam Basin (NE Tibetan Plateau)
2014-11-03

The availability of accurate and reliable age control is a crucial prerequisite for palaeoclimate studies, particularly when different archives are to be compared. Here we present a detailed depth-to-time transformation for the lacustrine sediments of a ∼940-m-long drill core (SG-1) from the western Qaidam Basin (NE Tibetan Plateau). To establish a more precise age model than the one previously available, which was based solely on magnetostratigraphic dating using polarity boundaries as tie points, we applied time-series analysis on magnetic susceptibility (χ) variation. The χ data are available in high resolution and are considered to be closely linked to orbital forcing. Since the sediment accumulation rate (SAR) varies strongly throughout the succession of core SG-1, conventional cyclostratigraphy by bandpass filtering cannot be applied. We present two alternative age models based on spectral characteristics and orbital tuning. The first age model (TPspec) is based on the assumption that changes in SAR occurred when the frequency spectra revealed obviously different characteristics in the spectral pattern. For the second age model (SARA), SAR was adjusted every 2 m by comparing observed with expected orbital cycles in accordance with the age of magnetic reversals. This age model appears more robust and shows the most convincing spectral results in the frequency and wavelet power spectrum of χ. According to the SARA age model, SAR varies between 14 and 73 cm kyr–1, and the bottom of SG-1 has an age of 2.69 Ma. Our results show that orbital tuning can be successfully applied for sequences with strongly variable SAR. The age model SARA can be used for a more detailed analysis of the existing multiproxy data set in terms of palaeoclimate evolution. The most prominent feature of χ spectra using the SARA age model is the identification of the middle Pleistocene transition.
Nic1 Inactivation Enables Stable Isotope Labeling with 13C615N4-Arginine in Schizosaccharomyces pombe
2014-11-03

Stable Isotope Labeling by Amino Acids (SILAC) is a commonly used method in quantitative proteomics. Because of compatibility with trypsin digestion, arginine and lysine are the most widely used amino acids for SILAC labeling. We observed that Schizosaccharomyces pombe (fission yeast) cannot be labeled with a specific form of arginine, (13)C(6) (15)N(4)-arginine (Arg-10), which limits the exploitation of SILAC technology in this model organism. We hypothesized that in the fission yeast the guanidinium group of (13)C(6) (15)N(4)-arginine is catabolized by arginase and urease activity to (15)N1-labeled ammonia that is used as a precursor for general amino acid biosynthesis. We show that disruption of Ni(2+)-dependent urease activity, through deletion of the sole Ni(2+) transporter Nic1, blocks this recycling in ammonium-supplemented EMMG medium to enable (13)C(6) (15)N(4)-arginine labeling for SILAC strategies in S. pombe. Finally, we employed Arg-10 in a triple-SILAC experiment to perform quantitative comparison of G1 + S, M, and G2 cell cycle phases in S. pombe.
Reply to Maxwell et al.: Stable isotopes and their potential for interpreting archaeobotanical remains
2014-11-03

We thank Maxwell et al. (1) for their interest in our study and agree that multielement isotopic analysis helps interpret ancient agricultural systems. Measurements of δ15N on archaeobotanical crop seeds have corroborated hypotheses of Near Eastern cultivation under gradually less-fertile soil conditions (2) and that early farmers used livestock manure to enhance crop yields (3). It is also understood that soil fertility along with salinity, evapotranspiration, and crop density causes variation in δ13C.
Model selection on solid ground: Rigorous comparison of nine ways to evaluateBayesian model evidence
2014-11-04

Abstract Bayesian model selection or averaging objectively ranks a number of plausible, competing conceptual models based on Bayes' theorem. It implicitly performs an optimal trade‐off between performance in fitting available data and minimum model complexity. The procedure requires determining Bayesian model evidence (BME), which is the likelihood of the observed data integrated over each model's parameter space. The computation of this integral is highly challenging because it is as high‐dimensional as the number of model parameters. Three classes of techniques to compute BME are available, each with its own challenges and limitations: (1) Exact and fast analytical solutions are limited by strong assumptions. (2) Numerical evaluation quickly becomes unfeasible for expensive models. (3) Approximations known as information criteria (ICs) such as the AIC, BIC, or KIC (Akaike, Bayesian, or Kashyap information criterion, respectively) yield contradicting results with regard to model ranking. Our study features a theory‐based intercomparison of these techniques. We further assess their accuracy in a simplistic synthetic example where for some scenarios an exact analytical solution exists. In more challenging scenarios, we use a brute‐force Monte Carlo integration method as reference. We continue this analysis with a real‐world application of hydrological model selection. This is a first‐time benchmarking of the various methods for BME evaluation against true solutions. Results show that BME values from ICs are often heavily biased and that the choice of approximation method substantially influences the accuracy of model ranking. For reliable model selection, bias‐free numerical methods should be preferred over ICs whenever computationally feasible.
Knowing your friends and foes – plant receptor‐like kinases as initiators of symbiosis or defence
2014-11-04

Summary The decision between defence and symbiosis signalling in plants involves alternative and modular plasma membrane‐localized receptor complexes. A critical step in their activation is ligand‐induced homo‐ or hetero‐oligomerization of leucine‐rich repeat ( LRR )‐ and/or lysin motif (LysM) receptor‐like kinases ( RLK s). In defence signalling, receptor complexes form upon binding of pathogen‐associated molecular patterns ( PAMP s), including the bacterial flagellin‐derived peptide flg22, or chitin. Similar mechanisms are likely to operate during the perception of microbial symbiont‐derived (lipo)‐chitooligosaccharides. The structurally related chitin‐oligomer ligands chitooctaose and chitotetraose trigger defence and symbiosis signalling, respectively, and their discrimination involves closely related, if not identical, LysM‐ RLK s. This illustrates the demand for and the challenges imposed on decision mechanisms that ensure appropriate signal initiation. Appropriate signalling critically depends on abundance and localization of RLK s at the cell surface. This is regulated by internalization, which also provides a mechanism for the removal of activated signalling RLK s. Abundance of the malectin‐like domain ( MLD )‐ LRR ‐ RLK Symbiosis Receptor‐like Kinase ( SYMRK ) is additionally controlled by cleavage of its modular ectodomain, which generates a truncated and rapidly degraded RLK fragment. This review explores LRR ‐ and LysM‐mediated signalling, the involvement of MLD ‐ LRR ‐ RLK s in symbiosis and defence, and the role of endocytosis in RLK function.
Fetal facial profile markers of Down syndrome in the second and third trimesters of pregnancy
2014-11-04

Abstract Objectives To investigate the use of the maxilla–nasion–mandible ( MNM ) angle and fetal profile ( FP ) line to assess the degree of midfacial hypoplasia in Down‐syndrome fetuses in the second and third trimesters of pregnancy. Methods The MNM angle and FP line were measured retrospectively in stored two‐dimensional images or three‐dimensional volumes of fetuses with Down syndrome. Data collected from January 2006 to July 2013 were retrieved from the digital databases of participating units. The MNM angle was expressed as a continuous variable (degrees) and the FP line as positive, negative or zero. Measurements were obtained from stored images in the midsagittal plane by two experienced examiners and compared with our previously reported normal ranges for euploid fetuses. A MNM angle below the 5 th centile of the reference range and a positive or negative FP line were considered as abnormal. Results A total of 133 fetuses with Down syndrome were available for analysis, eight of which were subsequently excluded because of inadequate images. The MNM angle was not influenced by gestational age ( P = 0.48) and was significantly smaller in Down‐syndrome fetuses than in euploid fetuses (mean, 12.90° vs 13.53°, respectively; P = 0.015). The MNM angle was below the 5 th centile for euploid fetuses in 16.8% of fetuses with Down syndrome ( P &lt; 0.01). In the cohort of Down‐syndrome fetuses, a positive FP line was present in 41.6% of cases (with a false‐positive rate ( FPR ) of 6.3%) and was positively correlated with Down syndrome and gestational age ( P &lt; 0.01). There was no case with a negative FP line. In cases of Down syndrome, a positive FP line was correlated with a small MNM angle ( P &lt; 0.01). Conclusions A small MNM angle and a positive FP line can be regarded as novel markers for Down syndrome. The FP line is an easy marker to measure, has a low FPR , does not require knowledge of normal reference values and has the potential to differentiate between Down syndrome and trisomy 18, as, in the latter, the FP line is often negative. Copyright © 2014 ISUOG. Published by John Wiley &amp; Sons Ltd.
Bacterial infections in childhood: A risk factor for gastrointestinal and other diseases?
2014-11-04

Background There is evidence for post‐infectious irritable bowel syndrome (PI‐IBS) in adults, but little is known about PI‐IBS in children. The nationwide representative German Health Interview and Examination Survey for Children and Adolescents (KiGGS) assessed children's health. Objective and methods We identified 643 children (50.1% males) in the KiGGS cohort ( N = 15,878, 51% males) with a history of Salmonella infection. The number was validated comparing this group with the known infection statistics from the Robert Koch‐Institute registry. We compared this group to the remaining KiGGS cohort ( n = 12,951) with respect to sociodemographic characteristics, pain and quality of life. To check for specificity, we repeated the comparisons with a group with a history of scarlet fever. Results Infection statistics predicted 504 cases of Salmonella infection in the KiGGS cohort, indicating high validity of the data. In children between 3 and 10 years with a history of Salmonella infection, significantly more abdominal pain (31.7% versus 21.9%, p &lt; 0.001) and headache (27.2% versus 15.1%, p &lt; 0.001) were reported. This group showed lower quality of life ( p &lt; 0.001). Comparison to a group of scarlet fever‐infected children revealed poor specificity of the data. Conclusion Differences found between children with and without Salmonella infection reveal the role of gastrointestinal infection in the development of post‐infectious abdominal problems, but poor specificity may point toward a psychosocial (“somatization”) rather than a Salmonella ‐specific mechanism.
Numerical Integrators for Motion under a Strong Constraining Force
2014-11-04

This paper deals with the numerical integration of Hamiltonian systems in which a stiff anharmonic potential causes highly oscillatory solution behavior with solution-dependent frequencies. The impulse method, which uses micro- and macro-steps for the integration of fast and slow parts, respectively, does not work satisfactorily on such problems. Here it is shown that variants of the impulse method with suitable projection preserve the actions as adiabatic invariants and yield accurate approximations, with macro-stepsizes that are not restricted by the stiffness parameter.
Crystal structure of 1,3-dicyclohexyl-4,5-dimethyl-1H-imidazol-3-ium-2-carbodithioate chloroform monosolvate
2014-11-04

The title compound, C 18 H 28 N 2 S 2 ·CHCl 3 , crystallizes as a zwitterion. The C—S bonds are almost equivalent, with lengths of 1.666 (3) and 1.657 (3) Å. The S—C—S bond angle is expanded to 129.54 (16)° and the N—C—N angle is reduced to the tetrahedal value of 108.8 (2)°. In the crystal, adjacent molecules are linked via C—H...S hydrogen bonds, forming chains along [100]. The chloroform solvent molecule, which is disordered over two positions [occupancy ratio = 0.51 (2):0.49 (2)], is linked to the chain by bifurcated C—H...(S,S) hydrogen bonds.
Impaired Action Potential Initiation in GABAergic Interneurons Causes Hyperexcitable Networks in an Epileptic Mouse Model Carrying a Human NaV1.1 Mutation
2014-11-05

Mutations in SCN1A and other ion channel genes can cause different epileptic phenotypes, but the precise mechanisms underlying the development of hyperexcitable networks are largely unknown. Here, we present a multisystem analysis of an SCN1A mouse model carrying the Na V 1.1-R1648H mutation, which causes febrile seizures and epilepsy in humans. We found a ubiquitous hypoexcitability of interneurons in thalamus, cortex, and hippocampus, without detectable changes in excitatory neurons. Interestingly, somatic Na + channels in interneurons and persistent Na + currents were not significantly changed. Instead, the key mechanism of interneuron dysfunction was a deficit of action potential initiation at the axon initial segment that was identified by analyzing action potential firing. This deficit increased with the duration of firing periods, suggesting that increased slow inactivation, as recorded for recombinant mutated channels, could play an important role. The deficit in interneuron firing caused reduced action potential-driven inhibition of excitatory neurons as revealed by less frequent spontaneous but not miniature IPSCs. Multiple approaches indicated increased spontaneous thalamocortical and hippocampal network activity in mutant mice, as follows: (1) more synchronous and higher-frequency firing was recorded in primary neuronal cultures plated on multielectrode arrays; (2) thalamocortical slices examined by field potential recordings revealed spontaneous activities and pathological high-frequency oscillations; and (3) multineuron Ca 2+ imaging in hippocampal slices showed increased spontaneous neuronal activity. Thus, an interneuron-specific generalized defect in action potential initiation causes multisystem disinhibition and network hyperexcitability, which can well explain the occurrence of seizures in the studied mouse model and in patients carrying this mutation.
The Importance of Spectral Separation
2014-11-05

Dual-source CT systems enable DE data to be acquired using a variety of voltage combinations. Combined (or mixed) DE images provide an image impression similar to standard 120 kV images, yet the noise level depends on the DE voltage combination that is selected. Noise in decomposed VNC images is strongly influenced by the DE ratio, and it improves substantially with tin filtration of the high-voltage beam.
The SEURAT-1 approach towards animal free human safety assessment
2014-11-05

SEURAT-1 is a European public-private research consortium that is working towards animal-free testing of chemical compounds and the highest level of consumer protection. A research strategy was formulated based on the guiding principle to adopt a toxicological mode-of-action framework to describe how any substance may adversely affect human health.The proof of the initiative will be in demonstrating the applicability of the concepts on which SEURAT-1 is built on three levels:(i) Theoretical prototypes for adverse outcome pathways are formulated based on knowledge already available in the scientific literature on investigating the toxicological mode-of-actions leading to adverse outcomes (addressing mainly liver toxicity);(ii)adverse outcome pathway descriptions are used as a guide for the formulation of case studies to further elucidate the theoretical model and to develop integrated testing strategies for the prediction of certain toxicological effects (i.e., those related to the adverse outcome pathway descriptions);(iii) further case studies target the application of knowledge gained within SEURAT-1 in the context of safety assessment. The ultimate goal would be to perform ab initio predictions based on a complete understanding of toxicological mechanisms. In the near-term, it is more realistic that data from innovative testing methods will support read-across arguments. Both scenarios are addressed with case studies for improved safety assessment. A conceptual framework for a rational integrated assessment strategy emerged from designing the case studies and is discussed in the context of international developments focusing on alternative approaches for evaluating chemicals using the new 21st century tools for toxicity testing.
Communication: Non-Hadwiger terms in morphological thermodynamics of fluids
2014-11-05

We demonstrate that the Hadwiger form of the free energy of a fluid in contact with a wall is insufficient to describe the low-density behavior of a hard-sphere fluid. This implies that morphological thermodynamics of the hard-sphere fluid is an approximate theory if only four geometric measures are included. In order to quantify deviations from the Hadwiger form we extend standard fundamental measure theory of the bulk fluid by introducing additional scaled-particle variables which allow for the description of non-Hadwiger coefficients. The theory is in excellent agreement with recent computer simulations. The fact that the leading non-Hadwiger coefficient is one order of magnitude smaller than the smallest Hadwiger coefficient lends confidence to the numerous results that have been previously obtained within standard morphological thermodynamics.
Analysis of island shape evolution from diffuse x-ray scattering of organic thin films and implications for growth
2014-11-05

Understanding the growth of organic semi-conducting molecules with shape anisotropy is of high relevance to the processing of optoelectronic devices. This work provides insight into the growth of thin films of the prototypical rodlike organic semiconductor diindenoperylene on a microscopic level, by analyzing in detail the film morphology. We model our data, which were obtained by high-resolution grazing incidence small angle x-ray scattering (GISAXS), using a theoretical description from small angle scattering theory derived for simple liquids. Based on form factor calculations for different object types we determine how the island shapes change in the respective layers. Atomic force microscopy measurements approve our findings.