julilili42/papers huggingface dataset:
An open-source computational and data resource to analyze digital maps of immunopeptidomes
2015-07-08

We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies.
Face-n-Food: Gender Differences in Tuning to Faces
2015-07-08

Faces represent valuable signals for social cognition and non-verbal communication. A wealth of research indicates that women tend to excel in recognition of facial expressions. However, it remains unclear whether females are better tuned to faces. We presented healthy adult females and males with a set of newly created food-plate images resembling faces (slightly bordering on the Giuseppe Arcimboldo style). In a spontaneous recognition task, participants were shown a set of images in a predetermined order from the least to most resembling a face. Females not only more readily recognized the images as a face (they reported resembling a face on images, on which males still did not), but gave on overall more face responses. The findings are discussed in the light of gender differences in deficient face perception. As most neuropsychiatric, neurodevelopmental and psychosomatic disorders characterized by social brain abnormalities are sex specific, the task may serve as a valuable tool for uncovering impairments in visual face processing.
{Ge9[Si(SiMe3)2(SiPh3)]3}−: Ligand Modification in Metalloid Germanium Cluster Chemistry
2015-07-08

The influence of the stabilizing ligand on the physical and chemical properties of a metalloid cluster compound is important for nanotechnology as metalloid clusters are ideal model compounds for metal nanoparticles. Here we present the synthesis of a differently substituted metalloid {Ge9R3}(-) cluster: {Ge9[Si(SiMe3)2(SiPh3)]3}(-) 1, which is obtained in good yield by the reaction of K4Ge9 with ClSi(SiMe3)2(SiPh3). 1 is characterized via NMR and mass spectrometry, but crystallization is hindered. However, the reaction with HgCl2 gives the neutral compound HgGe18[Si(SiMe3)2(SiPh3)]6 2, which can be crystallized and structurally characterized. The presented results are a first step for the investigation of the ligand's influence on the properties of a metalloid germanium cluster compound.
TheCACNA1BR1389H variant is not associated with myoclonus-dystonia in a large European multicentric cohort
2015-07-08

Myoclonus-dystonia (M-D) is a very rare movement disorder, caused in ∼30-50% of cases by mutations in SGCE. The CACNA1B variant c.4166G>A; (p.R1389H) was recently reported as the likely causative mutation in a single 3-generation Dutch pedigree with five subjects affected by a unique dominant M-D syndrome and cardiac arrhythmias. In an attempt to replicate this finding, we assessed by direct sequencing the frequency of CACNA1B c.4166G>A; (p.R1389H) in a cohort of 520 M-D cases, in which SGCE mutations had been previously excluded. A total of 146 cases (28%) had a positive family history of M-D. The frequency of the variant was also assessed in 489 neurologically healthy controls and in publicly available data sets of genetic variation (1000 Genomes, Exome Variant Server and Exome Aggregation Consortium). The variant was detected in a single sporadic case with M-D, but in none of the 146 probands with familial M-D. Overall, the variant was present at comparable frequencies in M-D cases (1 out of 520; 0.19%) and healthy controls (1 out of 489; 0.2%). A similar frequency of the variant was also reported in all publicly available databases. These results do not support a causal association between the CACNA1B c.4166G>A; (p.R1389H) variant and M-D.
PROSAIKA: A prospective multicenter registry with the first programmable gravitational device for hydrocephalus shunting
2015-07-08

This is the first clinical report on the implantation of the adjustable gravitational valve proSA with a follow-up of 12 months in a substantial number of patients. Irrespective of different hydrocephalus etiologies and indications for shunt surgery, the overall results after 12 months were very satisfying. The high frequency of valve readjustments underlines the fact that preoperative selection of the appropriate valve opening pressure is difficult. The low number of revisions and complications compared to other valves proves that proSA implantation adds no further risk; this valve is reliable, helpful and safe.
Different Coordination Modes of the Ph2PCsp3PPh2 Pincer Ligand in Rhodium Complexes as a Consequence of Csp3–H Metal Interaction
2015-07-08

Starting from commercially available 4,4′-di-tert-butyldiphenylmethane the pincer ligand bis(4-tert-butyl-2-(diphenylphosphino)phenyl)methane (PCP) was prepared in two steps in moderate yield. Treatment of a solution of RhCl3·3H2O in a mixture of isopropyl alcohol and toluene with equimolar amounts of PCP gave the dimeric rhodium complex 1. In an electrophilic metalation a facially coordinated pincer complex is formed. When PCP is treated with [CODRhCl]2 in a solution of pyridine, the square-pyramidal complex 2 is generated where the bis-phosphine PCP acts as bidentate ligand that coordinates in a cis fashion. SnCl2 inserts into the Rh–Cl bond of 2, which results in an oxidative addition of one of the methylene C–H bonds to form the Rh(III) complex 3, where the PCP ligand coordinates in a meridional way. A 2 equiv portion of PCP reacts with 1 equiv of [CODRhCl]2 in the presence of the electron-donating ligands HPhPC6H4NMe2, PPh2Py, and PPh3, respectively, as well as with stanna- and germa-closo-dodecaborate to give the octahedral Rh(III) complexes 4–8. Attempts to remove the HCl with KOtBu from complexes 4–6 produces the planar Rh(I) compounds 9 and 10. No carbene formation has been observed.
Impact of the radius of the injector system on the cell viability in descemet membrane endothelial keratoplasty: an ex vivo experimental study
2015-07-08

Abstract Purpose To evaluate the impact of the radius of the injector system on the viability of the endothelial cells in Descemet membrane endothelial keratoplasty ( DMEK ). Methods Descemet membranes ( DM s) of 30 corneoscleral rims were used in a paired design and divided into three groups (A, B, C). The right corneas were used as control (without shooting through the injector after DM preparation) and the left cornea for simulation of the implantation step (shooting through a glass injector of different radii). The injector in Group A had a diameter of 0.5 mm, group B 0.9 mm and group C 1.4 mm. Prior to preparation, endothelial cell count was measured and endothelial cell quality assessed. Quantification of potential damage was achieved by staining with a viability bioassay (calcein acetoxymethyl and ethidium homodimer‐1) and DAPI . Apoptosis was evaluated by TUNEL (terminal dUTP nick‐end labelling) staining. Results The average percentage of the endothelial cell death ratios was 4.9 ± 3.3% in group A ( n = 5), 3.7 ± 3.7% in group B ( n = 5) and 3.9 ± 3.6% in group C ( n = 5) with no significant difference compared to the control. The average percentage of apoptotic endothelial cells was 0.05 ± 0.05%, 0.60 ± 0.53% and 0.15 ± 0.26% in groups A, B and C, respectively, with no significant difference compared to the control. Conclusions Prepared grafts for transplantation in DMEK procedures may be injected through a smaller sized injector system of up to 0.5 mm with no significant increase in cell loss. Clinical studies are necessary to draw a final conclusion.
Relational Contracts and Global Sourcing
2015-07-08

Relational contracts – informal agreements sustained by the value of future relationships – are integral parts of global production processes. This paper develops a repeated-game model of global sourcing in which final goods producers decide whether to engage with their suppliers in relational contracting and whether to integrate a supplier into a firm’s boundaries or deal with the latter at arm’s length. The model predicts that the likelihood of vertical integration increases in the long-term orientation of cooperation parties. Combining data from the U.S. Census Bureau’s Related Party Trade database with measures for long-term orientation from Hofstede et al. (2010) and World Values Survey, I find empirical evidence supportive of this paper’s key prediction. To better understand if the relationship is causal, I apply instrumental variables approach using genetic proxies and inherited components of long-term orientation as instruments. Taken together, the evidence suggests that the level of long-term orientation of the home and host country has a positive effect on the relative prevalence of vertical integration.
Epigenetic activities of flavonoids in the prevention and treatment of cancer
2015-07-09

Aberrant epigenetic modifications are described in an increasing number of pathological conditions, including neurodegenerative diseases, cardiovascular diseases, diabetes mellitus type 2, obesity and cancer. The general reversibility of epigenetic changes makes them an attractive and promising target e.g. in the treatment of cancer. Thus, a growing number of epigenetically active compounds are currently tested in clinical trials for their therapeutic potential. Interestingly, many phytochemicals present in plant foods, particularly flavonoids, are suggested to be able to alter epigenetic cellular mechanisms. Flavonoids are natural phenol compounds that form a large group of secondary plant metabolites with interesting biological activities. They can be categorized into six major subclasses, which display diverse properties affecting the two best characterized epigenetic mechanisms: modulation of the DNA methylation status and histone acetylation. High dietary flavonoid intake has strongly been suggested to reduce the risk of numerous cancer entities in a large body of epidemiological studies. Established health-promoting effects of diets rich in fruit and vegetables are faced by efforts to use purified flavonoids as supplements or pharmaceuticals, whereupon data on the latter applications remain controversial. The purpose of this review is to give an overview of current research on flavonoids to further elucidate their potential in cancer prevention and therapy, thereby focusing on their distinct epigenetic activities.
Information Structure and Discourse Particles
2015-07-09

Abstract Focusing on German as its object language, this chapter explores the interactions between discourse particles (e.g. ja, doch) and information structure. The first half of the chapter explores the traditional idea that discourse particles form a watershed between thematic (old) and rhematic (new) information. Concerning the ‘theme’, it is argued that unstressed elements to the left of discourse particles (in the ‘middle field’ between C0 and the verbal complex) must be aboutness topics. Concerning the ‘rheme’, it is shown that the focus exponent generally has to follow discourse particles. The second half of the chapter discusses current issues relating to the interactions of discourse particles and focus. Specifically, it investigates ‘relational’ discourse particles (e.g. doch and schon), which operate on a contextually salient alternative proposition q, giving rise to a discussion of the potential role that focus may play in the interpretation of such particles.
Regulation of the epithelial Na+ channel by the mTORC2/SGK1 pathway
2015-07-09

Abstract The epithelial Na+ channel (ENaC) is decisive for sodium reabsorption by the aldosterone-sensitive distal nephron (ASDN) of the kidney. ENaC is regulated by the serum- and glucocorticoid-inducible kinase 1 (SGK1), a kinase genomically upregulated by several hormones including glucocorticoids and mineralocorticoids. SGK1 is activated by the serine/threonine kinase mammalian target of rapamycin (mTOR) isoform mTORC2. SGK1 knockout (sgk1−/− mice) impairs renal Na+ retention during salt depletion. The mTOR catalytic site inhibitor, PP242, but not mTORC1 inhibitor rapamycin, inhibits ENaC, decreases Na+ flux in isolated perfused tubules and induces natriuresis in wild-type mice. PP242 does not lead to further impairment of Na+ reabsorption in sgk1−/− mice. The mTORC2/SGK1 sensitive renal Na+ retention leads to extracellular volume expansion with increase of blood pressure. A SGK1 gene variant (prevalence ∼3–5% in Caucasians, ∼10% in Africans) predisposes to hypertension, stroke, obesity and type 2 diabetes. Future studies will be required to define the role of mTORC2 in the regulation of further SGK1 sensitive transport proteins, such as further ion channels, carriers and the Na+/K+-ATPase. Moreover, studies are required disclosing the impact of mTORC2 on SGK1 sensitive disorders, such as hypertension, obesity, diabetes, thrombosis, stroke, inflammation, autoimmune disease, fibrosis and tumour growth.
Hydrological model comparison and assessment: criteria from catchment scales and temporal resolution
2015-07-09

This study examines the performance of three hydrological models, namely the artificial neural network (ANN) model, the Hydrologiska Byråns Vattenbalansavdelning-D (HBV-D) model, and the Soil and Water Integrated Model (SWIM) over the upper reaches of the Huai River basin. The assessment is done by using databases of different temporal resolution and by further examining the applicability of SWIM for different catchment sizes. The results show that at monthly scale the performance of the ANN model is better than that of HBV-D and SWIM. The ANN model can be applied at any temporal scale as it establishes an artificial precipitation–runoff relationship for various time scales by only using monthly precipitation, temperature and runoff data. However, at daily scale the performance of both HBV-D and SWIM are similar or even better than the ANN model. In addition, the performance of SWIM at a small catchment size (less than 10 000 km2) is much better than at a larger catchment size. In view of climate change modelling, HBV-D and SWIM might be integrated in a dynamical atmosphere-water-cycle modelling rather than the ANN model due to their use of observed physical links instead of artificial relations within a black box.Editor D. Koutsoyiannis; Associate editor D. Hughes
Modality and Mood in Formal Syntactic Approaches
2015-07-09

The chapter discusses a selection of major approaches to modality and mood in generative syntax. The primary focus lies on the representation of modal auxiliaries and verbs. Key issues relating to modal adverbs and a selection of aspects pertaining to mood are reviewed. Central points addressed are the structural options for different types of modality including the raising vs control debate and the possible structural correlates of epistemic modality addressed in the literature. The chapter incorporates a discussion of “coherent constructions” following a tradition established for German modals. The latter serves as an illustration of a different type of possible syntactic analysis and, in virtue of its data coverage, also of points of variation even between closely related languages like English and German.
RNA sequencing analysis identifies novel spliced transcripts but does not indicate quantitative or qualitative changes of viral transcripts during progression of cottontail rabbit papillomavirus-induced tumours
2015-07-09

Persistent infections with high-risk human papillomaviruses (HPVs) can result in the development of cancer of the cervix uteri and other malignancies. The underlying molecular mechanisms leading to the progression of HPV-induced lesions are, however, not well understood. Cottontail rabbit papillomavirus (CRPV) induces papillomas in domestic rabbits which progress at a very high rate to cancer. Using this model, we compared the transcriptional patterns of CRPV in papillomas and carcinomas by RNA sequencing (RNA-seq). The most abundant transcripts can encode E7, short E6 and E1^E4, followed by full-length E6, E2, E1 and E9^E2C. In addition, we identified two rare, novel splice junctions 7810/3714 and 1751/3065 in both papillomas and carcinomas which have been described for other papillomaviruses. Neither RNA-seq nor quantitative real-time PCR-based assays identified qualitative or quantitative changes of viral transcription between papillomas and carcinomas. In summary, our analyses confirmed that papillomaviruses have highly similar transcriptional patterns, but they do not suggest that changes in these patterns contribute to the progression of CRPV-induced tumours.
Alzheimer Disease: Approaches to Early Diagnosis and High-Accuracy Imaging
2015-07-09

TO THE EDITOR: The development and application of ligands for PET imaging of Alzheimer disease (AD) has evolved into an important tool for the clinical diagnosis of AD. Among the promising ligands, Pittsburgh compound B (PiB), developed by Mathis et al. ([1][1]) and Klunk et al. ([2][2]), is one
Intraoperative model based identification of tissue properties using a multimodal and multiscale elastographic measurement approach
2015-07-09

During minimally invasive surgery the visual (3 dimensional) and mechanical (haptic) feedback is restricted or even non-existing, which imposes a serious loss of important information for decision making. Information about the mechanical properties of the biological tissue helps the surgeon to localize tissue abnormalities (benign vs. malign tissue). The work described here is directed towards assisting the surgeon during minimally invasive surgery, which in particular relates to the segmentation and navigation based on the recovery of mechanical properties. Besides the development of noninvasive elastographic measurement techniques, a reliable constitutive FE-model of the organ (describing its mechanical properties) is generated resulting in a further improvement of the segmentation and localization process. At first silicon phantoms, with and without foreign bodies have been generated for the purpose of testing the transfer of information (delivery and processing of data). The stress-strain curve was recorded and embedded in the FE-model (Arruda-Boyce). Two dimensional (2D) displacement maps have experimentally been obtained from the phantom, which were in good agreement with the FE simulation.
Evolution of circumbinary planets around eccentric binaries: The case of Kepler-34
2015-07-10

The existence of planets orbiting a central binary star system immediately raises questions regarding their formation and dynamical evolution. Recent discoveries of circumbinary planets by the Kepler space telescope has shown that some of these planets reside close to the dynamical stability limit where it is very difficult to form planets in situ. For binary systems with nearly circular orbits, such as Kepler-38, the observed proximity of planetary orbits to the stability limit can be understood by an evolutionary process in which planets form farther out in the disk and migrate inward to their observed position. The Kepler-34 system has a high orbital eccentricity of 0.52. Here, we analyse evolutionary scenarios for the planet observed around this system using two-dimensional hydrodynamical simulations. The highly eccentric binary opens a wide inner hole in the disk which is also eccentric, and displays a slow prograde precession. As a result of the large, eccentric inner gap, an embedded planet settles in a final equilibrium position that lies beyond the observed location of Kepler-34 b, but has the correct eccentricity. In this configuration the planetary orbit is aligned with the disk in a state of apsidal corotation.To account for the closer orbit of Kepler-34 b to the central binary, we considered a two-planet scenario and examined the evolution of the system through joint inward migration and capture into mean-motion resonances. When the inner planet orbits inside the gap of the disk, planet-planet scattering ensues. While often one object is thrown into a large, highly eccentric orbit, at times the system is left with a planet close to the observed orbit, suggesting that Kepler 34 might have had two circumbinary planets where one might have been scattered out of the system or into an orbit where it did not transit the central binary during the operation of Kepler.
Facial Affect Recognition in Violent and Nonviolent Antisocial Behavior Subtypes
2015-07-13

Prior studies provide evidence for impaired recognition of distress cues in individuals exhibiting antisocial behavior. However, it remains unclear whether this deficit is generally associated with antisociality or may be specific to violent behavior only. To examine whether there are meaningful differences between the two behavioral dimensions rule-breaking and aggression, violent and nonviolent incarcerated offenders as well as control participants were presented with an animated face recognition task in which a video sequence of a neutral face changed into an expression of one of the six basic emotions. The participants were instructed to press a button as soon as they were able to identify the emotional expression, allowing for an assessment of the perceived emotion onset. Both aggressive and nonaggressive offenders demonstrated a delayed perception of primarily fearful facial cues as compared to controls. These results suggest the importance of targeting impaired emotional processing in both types of antisocial behavior.
Leveraging Qualitative Reasoning to Learning Manipulation Tasks
2015-07-13

Learning and planning are powerful AI methods that exhibit complementary strengths. While planning allows goal-directed actions to be computed when a reliable forward model is known, learning allows such models to be obtained autonomously. In this paper we describe how both methods can be combined using an expressive qualitative knowledge representation. We argue that the crucial step in this integration is to employ a representation based on a well-defined semantics. This article proposes the qualitative spatial logic QSL, a representation that combines qualitative abstraction with linear temporal logic, allowing us to represent relevant information about the learning task, possible actions, and their consequences. Doing so, we empower reasoning processes to enhance learning performance beyond the positive effects of learning in abstract state spaces. Proof-of-concept experiments in two simulation environments show that this approach can help to improve learning-based robotics by quicker convergence and leads to more reliable action planning.