julilili42/papers huggingface dataset:
A blind deconvolution approach for pseudo CT prediction from MR image pairs
2012-09-01

Predicting a CT image or a map of the linear attenuation coefficients from the information provided by magnetic resonance imaging (MRI) is a challenging task. This problem is of significant importance for combined positron emission tomography (PET)/MRI scanners, as quantitative PET image reconstruction requires an attenuation map. In PET/CT this attenuation map is derived from the CT scan or from a rotating source, however, current PET/MR systems can not directly measure attenuation images - and indeed it is desirable to save the patient from the additional radiation exposure. Recent approaches tackle this problem by using MR sequences with ultra-short echo times (UTE). At the price of lower effective image resolution, the UTE image yields signal from bone and therefore provides valuable information for calculating the attenuation map. We propose a novel approach to this problem based on nonnegative blind deconvolution and present the first method that explicitly models the image degradation of the UTE image. Incorporating prior knowledge such as smoothness and a novel orthogonality constraint alleviates the deconvolution process. Due to its probabilistic formulation our approach allows hyperparameter estimation and is therefore parameter-free.
Massive intra and extracranial benign meningioma metastasizing to the lung and spine: the problem of meningiomas classification and iatrogenic metastasizing
2012-09-01

Abstract Meningioma is a common CNS tumor and metastasis in these tumours is a rare occurrence. Malignant meningiomas are more prone to metastase. However, there are frequent case reports of metastases in atypical (grade II) and even benign (grade I), which demonstrates the somehow unsatisfying prognostic power of the current classification system. We describe an extraordinary case of a patient with a massive intra and extra-cranial, benign meningioma, metastasizing to both lung and spine. Following the report we discuss 1) some of the problems of classifying meningioma, 2) massive meningiomas and 3) the possibility of intra-operative iatrogenic metastasizing. This case is unique due to its combination of different sites of metastases, massiveness, invasive growth and benign histology. Thus it ranks among those rare but not uncommon complicated courses in meningioma which is otherwise a common benign tumor. Unfortunately the existing classification-criteria do not have sufficient power to predict such complicated courses.
Stable discretization of a diffuse interface model for liquid-vapor flows with surface tension
2012-09-03

\\n The isothermal Navier–Stokes–Korteweg system is used to model dynamics of a compressible\\n fluid exhibiting phase transitions between a liquid and a vapor phase in the presence of\\n capillarity effects close to phase boundaries. Standard numerical discretizations are\\n known to violate discrete versions of inherent energy inequalities, thus leading to\\n spurious dynamics of computed solutions close to static equilibria (e.g.,\\n parasitic currents). In this work, we propose a time-implicit discretization of the\\n problem, and use piecewise linear (or bilinear), globally continuous finite element spaces\\n for both, velocity and density fields, and two regularizing terms where corresponding\\n parameters tend to zero as the mesh-size h &gt; 0 tends to zero.\\n Solvability, non-negativity of computed densities, as well as conservation of mass, and a\\n discrete energy law to control dynamics are shown. Computational experiments are provided\\n to study interesting regimes of coefficients for viscosity and capillarity.\\n
A Note on Phrasal Comparatives
2012-09-03

This paper investigates the various comparative operators that a language might employ and provides arguments for choosing a particular one. In particular, different phrasal comparatives are contrasted. We argue that Schoenfinkelization of the operator matters and reflects different crosslinguistic possibilities.
Reveal—visual eQTL analytics
2012-09-03

Abstract Motivation: The analysis of expression quantitative trait locus (eQTL) data is a challenging scientific endeavor, involving the processing of very large, heterogeneous and complex data. Typical eQTL analyses involve three types of data: sequence-based data reflecting the genotypic variations, gene expression data and meta-data describing the phenotype. Based on these, certain genotypes can be connected with specific phenotypic outcomes to infer causal associations of genetic variation, expression and disease. To this end, statistical methods are used to find significant associations between single nucleotide polymorphisms (SNPs) or pairs of SNPs and gene expression. A major challenge lies in summarizing the large amount of data as well as statistical results and to generate informative, interactive visualizations. Results: We present Reveal, our visual analytics approach to this challenge. We introduce a graph-based visualization of associations between SNPs and gene expression and a detailed genotype view relating summarized patient cohort genotypes with data from individual patients and statistical analyses. Availability: Reveal is included in Mayday, our framework for visual exploration and analysis. It is available at http://it.inf.uni-tuebingen.de/software/reveal/. Contact: guenter.jaeger@uni-tuebingen.de
Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
2012-09-04

Genetic generalized epilepsies (GGEs) have a lifetime prevalence of 0.3% and account for 20-30% of all epilepsies. Despite their high heritability of 80%, the genetic factors predisposing to GGEs remain elusive. To identify susceptibility variants shared across common GGE syndromes, we carried out a two-stage genome-wide association study (GWAS) including 3020 patients with GGEs and 3954 controls of European ancestry. To dissect out syndrome-related variants, we also explored two distinct GGE subgroups comprising 1434 patients with genetic absence epilepsies (GAEs) and 1134 patients with juvenile myoclonic epilepsy (JME). Joint Stage-1 and 2 analyses revealed genome-wide significant associations for GGEs at 2p16.1 (rs13026414, P(meta) = 2.5 × 10(-9), OR[T] = 0.81) and 17q21.32 (rs72823592, P(meta) = 9.3 × 10(-9), OR[A] = 0.77). The search for syndrome-related susceptibility alleles identified significant associations for GAEs at 2q22.3 (rs10496964, P(meta) = 9.1 × 10(-9), OR[T] = 0.68) and at 1q43 for JME (rs12059546, P(meta) = 4.1 × 10(-8), OR[G] = 1.42). Suggestive evidence for an association with GGEs was found in the region 2q24.3 (rs11890028, P(meta) = 4.0 × 10(-6)) nearby the SCN1A gene, which is currently the gene with the largest number of known epilepsy-related mutations. The associated regions harbor high-ranking candidate genes: CHRM3 at 1q43, VRK2 at 2p16.1, ZEB2 at 2q22.3, SCN1A at 2q24.3 and PNPO at 17q21.32. Further replication efforts are necessary to elucidate whether these positional candidate genes contribute to the heritability of the common GGE syndromes.
Radiative exciton recombination and defect luminescence observed in single silicon nanocrystals
2012-09-04

The role of quantum confinement (QC) and surface-related defect centers (DCs) on the photoluminescence (PL) of individual silicon nanocrystals (Si NCs) is investigated using confocal microscopy with radially and azimuthally polarized laser beams. It is shown that the multiple-peak PL spectra of single Si NCs revealing SiO phonon side bands are associated with a linear transition dipole moment (TDM) and a short lifetime of 4 ns, indicating that the PL originates from defect centers. In a new study applied to free-standing single Si NCs obtained by Si cluster beam deposition, we could discriminate between PL centers with one- and more-dimensional TDM. Nanoparticles revealing a three-dimensional TDM are characterized by a significantly weaker and structureless Gaussian PL band at larger wavelengths and by s lifetimes. These PL features are attributed to the radiative recombination of quantum-confined excitons generated in the Si cores. Within the same sample, we found coexistence of Si NCs exhibiting QC PL and others showing DC PL.
Improving behavioral performance under full attention by adjusting response criteria to changes in stimulus predictability
2012-09-04

One of the key features of active perception is the ability to predict critical sensory events. Humans and animals can implicitly learn statistical regularities in the timing of events and use them to improve behavioral performance. Here, we used a signal detection approach to investigate whether such improvements in performance result from changes of perceptual sensitivity or rather from adjustments of a response criterion. In a regular sequence of briefly presented stimuli, human observers performed a noise-limited motion detection task by monitoring the stimulus stream for the appearance of a designated target direction. We manipulated target predictability through the hazard rate, which specifies the likelihood that a target is about to occur, given it has not occurred so far. Analyses of response accuracy revealed that improvements in performance could be accounted for by adjustments of the response criterion; a growing hazard rate was paralleled by an increasing tendency to report the presence of a target. In contrast, the hazard rate did not affect perceptual sensitivity. Consistent with previous research, we also found that reaction time decreases as the hazard rate grows. A simple rise-to-threshold model could well describe this decrease and attribute predictability effects to threshold adjustments rather than changes in information supply. We conclude that, even under conditions of full attention and constant perceptual sensitivity, behavioral performance can be optimized by dynamically adjusting the response criterion to meet ongoing changes in the likelihood of a target.
The influence of ibandronate treatment on bone density and biochemical bone markers in patients with osteogenesis imperfecta
2012-09-04

Osteogenesis imperfecta (OI) is characterized by different signs including increased bone fragility, short stature, blue sclera, abnormal tooth growth and often secondary immobility. No curative therapy has been found for this rare disease up to now, and different pharmacological substances have been tried as treatment for severe forms of OI. Promising results were seen with intravenous bisphosphonates in the treatment of patients with OI. The aim of present study was to show the effect of intravenous ibandronate therapy on bone density and bone metabolism markers. We analyzed the data of 27 patients with the diagnosis of OI who were treated off-label with intravenous ibandronate. Ibandronate was administered by intravenous infusion every three months at a dosage of 0.3-2 mg. Bone turnover markers and bone density were measured before starting therapy and every three months during treatment. Bone density was measured by using an ultrasound imaging system providing an accurate image of the calcaneus and by evaluating broadband ultrasound attenuation (BUA). Twenty-seven patients were treated with intravenous ibandronate during the observation period. 18 were female. The mean age of all patients was 23.9 years ± 19.6 (range 4-63). Seventeen patients were categorized to have OI Type I, 5 patients to have OI Type III and 5 patients to have OI Type IV. There was a statistically significant decrease in total alkaline phosphatase (P<0.0001). We detected also a statistically significant decrease in the ratio urinary deoxypyridinoline/urinary creatinine (P=0.0048) and the ratio urinary pyridinoline/urinary creatinine (P<0.0001) respectively. There was also a statistically significant increase in serum magnesium (P=0.034) and BUA (P=0.0071). No statistically significant changes were seen for total serum calcium (P=0.16), the ratio of urine calcium/urine creatinine (P=0.29), alkaline phosphatase (isoform bone) (P=0.3), procollagen-I-peptide (P=0.5), osteocalcin (P=0.9), serum phosphatase (P=0.71), parathormone (P=0.11) and the ratio urine phosphatase/urine creatinine (P=0.58) Therapy with ibandronate in patients with OI leads to a normalisation of bone turnover markers and increasing bone density. Therefore serum alkaline phosphatase and bone density are possible parameters to monitor bisphosphonate treatment in patients with OI.
Identification of two-component system elements downstream of AHK5 in the stomatal closure response of Arabidopsis thaliana
2012-09-05

To optimize water use efficiency, plants regulate stomatal closure through a complex signaling process. Hydrogen peroxide (H2O2) is produced in response to several environmental stimuli, and has been identified as a key second messenger involved in the regulation of stomatal aperture. The Arabidopsis histidine kinase 5 (AHK5) has been shown to regulate stomatal closure in response to H2O2 and other stimuli that depend on H2O2. AHK5 is a member of the two-component system (TCS) in Arabidopsis. The plant TCS comprises three different protein types: the hybrid histidine kinases (HKs), the phosphotransfer proteins (HPs) and the response regulators (RRs). Here we determined TCS elements involved in H2O2- and ethylene-dependent stomatal closure downstream of AHK5. By yeast and in planta interaction assays and functional studies, AHP1, 2 and 5 as well as the response regulators ARR4 and ARR7 were identified acting downstream of AHK5 in the ethylene and H2O2 response pathways of guard cells. Furthermore, we demonstrate that aspartate phosphorylation of ARR4 is only required for the H2O2- but not for the ethylene-induced stomatal closure response. Our data suggest the presence of a complex TCS signaling network comprising of at least AHK5, several AHPs and response regulators, which modulate stomatal closure in response to H2O2 and ethylene.
A Frozen Analogue Approach to Aminopyridinylimidazoles Leading to Novel and Promising p38 MAP Kinase Inhibitors
2012-09-06

In this study we report the design, synthesis, and biological evaluation of constrained aminopyridinylimidazoles as p38α MAP kinase inhibitors. The frozen analogue approach focused on the pyridinyl unit, using purine bioisosteres as constrained structure analogues. The identification of the most potent bioisostere was followed by a further derivatization to address hydrophobic region II. In combination with C-2 modifications of the imidazole core, we were able to design highly active inhibitors on the p38α MAP kinase. The inhibitor design presented herein represents a promising and highly efficient advancement of recent stages of development in this class of p38 MAP kinase inhibitors. In combination with the highly flexible synthetic strategy, directions toward further investigations of complex C-5 modifications of diarylimidazoles are indicated.
Sphingomyelinase-induced adhesion of eryptotic erythrocytes to endothelial cells
2012-09-07

Eryptosis, the suicidal erythrocyte death, leads to cell shrinkage and cell membrane scrambling with phosphatidylserine exposure at the cell surface. Eryptotic erythrocytes adhere to the vascular wall by binding of phosphatidylserine to the CXC chemokine ligand 16 (CXCL16). Stimulators of eryptosis include increased cytosolic Ca 2+ activity, energy depletion, and activation of ceramide-producing sphingomyelinase. The present study explored whether sphingomyelinase triggers erythrocyte adhesion to endothelial cells. To this end, human erythrocytes were exposed for 6 h to bacterial sphingomyelinase (1–10 mU/ml) and phosphatidylserine exposure was estimated from fluorescent annexin-V-binding, cell volume from forward scatter in FACS-analysis, erythrocyte adhesion to human umbilical vein endothelial cells (HUVEC) from trapping of labeled erythrocytes in a flow chamber under flow conditions at arterial shear rates, and CXCL16 protein abundance utilizing Western blotting and FACS analysis of fluorescent antibody binding. As a result, sphingomyelinase (≥1 mU/ml) triggered cell shrinkage, phosphatidylserine exposure and erythrocyte adhesion to HUVEC, effects blunted by Ca 2+ removal. Adhesion was significantly blunted by phosphatidylserine-coating annexin-V (5 μl/ml), following addition of neutralizing antibodies against endothelial CXCL16 (4 μg/ml) and following silencing of the CXCL16 gene with small interfering RNA. Pretreatment of HUVEC with sphingomyelinase upregulated CXCL16 protein abundance. Six hours pretreatment of HUVEC with sphingomyelinase (10 mU/ml) or C6-ceramide (50 μM) augmented erythrocyte adhesion following a 30-min treatment with Ca 2+ ionophore ionomycin (1 μM) or following energy depletion by 48-h glucose removal. Thus exposure to sphingomyelinase or C6-ceramide triggers eryptosis followed by phosphatidylserine- and CXCL16-sensitive adhesion of eryptotic erythrocytes to HUVEC.
Experimental Evidence of aφJosephson Junction
2012-09-07

We demonstrate experimentally the existence of Josephson junctions having a doubly degenerate ground state with an average Josephson phase ψ=±φ. The value of φ can be chosen by design in the interval 0<φ<π. The junctions used in our experiments are fabricated as 0-π Josephson junctions of moderate normalized length with asymmetric 0 and π regions. We show that (a) these φ Josephson junctions have two critical currents, corresponding to the escape of the phase ψ from -φ and +φ states, (b) the phase ψ can be set to a particular state by tuning an external magnetic field, or (c) by using a proper bias current sweep sequence. The experimental observations are in agreement with previous theoretical predictions.
Aerosol‐Assisted Molten Salt Synthesis of NaInS2 Nanoplates for Use as a New Photoanode Material
2012-09-07

NaInS(2) , a H(2) -evolving photocatalyst, is synthesized as single-crystalline hexagonal plates by coupling a molten salt synthesis with ultrasonic spray pyrolysis (USP) for the first time. USP NaInS(2) films are used as a new photoanode material and have an initial photocurrent of ≈37 μA/cm(2) upon illumination and activities 25 times greater than films made from a standard non-aerosol NaInS(2) sample.
Simulations of the x-ray imaging capabilities of the silicon drift detectors (SDD) for the LOFT wide-field monitor
2012-09-07

The Large Observatory For X-ray Timing (LOFT), selected by ESA as one of the four Cosmic Vision M3 candidate missions to undergo an assessment phase, will revolutionize the study of compact objects in our galaxy and of the brightest supermassive black holes in active galactic nuclei. The Large Area Detector (LAD), carrying an unprecedented effective area of 10 m2, is complemented by a coded-mask Wide Field Monitor, in charge of monitoring a large fraction of the sky potentially accessible to the LAD, to provide the history and context for the sources observed by LAD and to trigger its observations on their most interesting and extreme states. In this paper we present detailed simulations of the imaging capabilities of the Silicon Drift Detectors developed for the LOFT Wide Field Monitor detection plane. The simulations explore a large parameter space for both the detector design and the environmental conditions, allowing us to optimize the detector characteristics and demonstrating the X-ray imaging performance of the large-area SDDs in the 2–50 keV energy band.
Potent Melanin Production Enhancement of Human Tyrosinase Gene by Tat and an Entrapment in Elastic Cationic Niosomes: Potential Application in Vitiligo Gene Therapy
2012-09-07

Potent melanin production enhancement of human tyrosinase plasmid (pAH7/Tyr, P) in mouse melanoma cells (B 16 F 10 ) by Tat peptide (T) and an entrapment in elastic cationic niosomes (E) was described. The E composed of Tween 61/cholesterol/dodecyl dimethyl ammonium bromide at 1:1:0.5 molar ratio was prepared by freeze‐dried emptying liposomes method. PE at P/E ratio of 1:160 w/w and TPE at T/P/E ratio of 0.125:1:160, 0.25:1:160, and 0.5:1:160 w/w/w were prepared. The final concentration of the plasmid in the study was 4 ng/μL. By sulforhodamine B assay, PE and TPE complexes showed slight or no cytotoxic effect. The cells transfected with TPE (0.5:1:160) exhibited the highest enhancement of tyrosinase enzyme activity of 11.82‐, 7.67‐, 5.07‐, and 6.29‐folds of control, P, PE, and TP (0.5:1) and melanin production of 13.03‐, 8.46‐, 5.36‐, and 6.58‐folds of control, P, PE, and TP (0.5:1), respectively. The elastic cationic niosomes demonstrated an increase in thermal stability of P at 4 ± 2, 25 ± 2, and 45 ± 2 °C. The vesicular size and the zeta potential values of PE and TPE complexes were slightly increased but still in the range of stable dispersion (out of ±30 mV). These results indicated the high potential application of the TPE complexes for further investigation for vitiligo gene therapy.
Calibration strategies for the LAD instrument on-board LOFT
2012-09-07

The Scientific objectives of the LOFT mission, e.g., the study of the Neutron\\nStar equation of state and of the Strong Gravity, require accurate energy, time\\nand flux calibration for the 500k channels of the SDD detectors, as well as the\\nknowledge of the detector dead-time and of the detector response with respect\\nto the incident angle of the photons. We report here the evaluations made to\\nasses the calibration issues for the LAD instrument. The strategies for both\\nground and on-board calibrations, including astrophysical observations, show\\nthat the goals are achievable within the current technologies.\\n
Accelerator experiments with soft protons and hyper-velocity dust particles: application to ongoing projects of future x-ray missions
2012-09-07

We report on our activities, currently in progress, aimed at performing\\naccelerator experiments with soft protons and hyper-velocity dust particles.\\nThey include tests of different types of X-ray detectors and related components\\n(such as filters) and measurements of scattering of soft protons and\\nhyper-velocity dust particles off X-ray mirror shells. These activities have\\nbeen identified as a goal in the context of a number of ongoing space projects\\nin order to assess the risk posed by environmental radiation and dust and\\nqualify the adopted instrumentation with respect to possible damage or\\nperformance degradation. In this paper we focus on tests for the Silicon Drift\\nDetectors (SDDs) used aboard the LOFT space mission. We use the Van de Graaff\\naccelerators at the University of T\\\\"ubingen and at the Max Planck Institute\\nfor Nuclear Physics (MPIK) in Heidelberg, for soft proton and hyper-velocity\\ndust tests respectively. We present the experimental set-up adopted to perform\\nthe tests, status of the activities and some very preliminary results achieved\\nat present time.\\n
An introduction to the World Space Observatory-Ultraviolet spectrographs
2012-09-07

The World Space Observatory Ultraviolet (WSO-UV) is a multinational mission under the leadership of Russia with contributions of Spain and Germany. The mission is part of the Spektrum series and launch is currently scheduled for 2016. It consists of a 1.7 m mirror focusing on spectrographs in the range of 102-310 nm with a resolution of R ≥ 55,000 for high resolution spectral observations, a long-slit-spectrograph for spatially resolved observations and an imager. According to the Phase-B-Study all spectrographs will use the same detectors built by the IAAT. These spectrographs are designed to observe cosmic plasma with temperatures of several ten thousands Kelvin and atomic transition lines of all important atoms and molecules like H<SUB>2</SUB>, CO, OH etc. In the core program the community wants to determine the amount of baryonic matter in the universe, extend the knowledge about the formation of galaxies and analyze the atmospheres of extrasolar planets and protoplanetary discs. To achieve these goals the IAAT designed in cooperation with the Leibniz-Institute for Analytical Sciences (ISAS Berlin) the spectrographs. In addition Tscopy,ubingen develops and builds a new type of microchannel plate detector based on gallium nitride cathodes and a cross-strip-Anode.