julilili42/papers huggingface dataset:
Image content matched directional filters for image coding based on contourlet transform
2013-12-01

Due to the separability of its filters, the wavelet transform is suboptimal for transform coding of natural images. The contourlet transform is an approach to overcome this problem by employing directional filters. In contrast to the great number of filters available for the wavelet transform, few filters exist for use with contourlets. We describe a method for the design of directional filters, which can be tailored to specific image contents. The method numerically optimizes the coding gain of directional filters within the lifting framework. Thereto, a link is derived between the coefficients of directional filters and coding gain. An example of an optimized filter is presented and its superiority over a standard filter for contourlet based image coding is shown.
Linking metabolomics with quality traits in crop plants
2013-12-01

Metabolomics is a field that aims to develop technologies for the comprehensive profiling of metabolites, the intermediates and products of metabolism, in biological samples. While the coverage of the entire metabolome is presently impractical, approaches involving nontargeted analyses of suitable metabolome subsets have been very successful in the basic plant sciences to support gene discovery, metabolic engineering and pathway modeling efforts. It is increasingly recognized that metabolomics also bears the potential to contribute to the applied agricultural sciences. The appearance, texture, aroma and potential health benefits of fruits and vegetables contribute substantially to their attractiveness to consumers. These distinguishing characteristics, or quality traits, are ultimately determined by the metabolome. In this chapter, the experimental evidence for the use of metabolomics data to predict quality traits in crop plants will be highlighted.
PReS-FINAL-2224: Canakinumab treatment regimens in CAPS-patients
2013-12-01

Canakinumab is a recombinant monoclonal fully human antibody against Interleukin-1β and approved for the treatment of CAPS in many countries including Europe and the US. Current dose recommendations are 150 mg (body weight >40 kg) respectively 2 mg/kg body weight (15 to 40 kg) every 8 weeks but yield insufficient response in some individuals, especially in children and patients with severe phenotypes [1].
Indirect NFC-Login on a Non-NFC Device using an NFC-Smartphone
2013-12-01

Smartcard based authentication on web services stays a niche application because of the lack of smartcard readers on the vast majority of internet devices.In this paper we discuss a method that uses an NFC-enabled Smartphone in order to login via NFC-enabled smartcard on basically any internet device.We explain the details of this method and analyze its security, deployability, and usability aspects.The Smartphone here acts as a mere communication device.It communicates with the web browser (via camera), with the smartcard via NFC (back and forth), with the server via mobile internet, and with the user via display, see Fig. 3.
On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications
2013-12-01

Summary The similarity search in theoretical mass spectra generated from protein sequence databases is a widely accepted approach for identification of peptides from query mass spectra produced by shotgun proteomics. Growing protein sequence databases and noisy query spectra demand database indexing techniques and better similarity measures for the comparison of theoretical spectra against query spectra. We employ a modification of previously proposed parameterized Hausdorff distance for comparisons of mass spectra. The new distance outperforms the original distance, the angle distance and state-of-the-art peptide identification tools OMSSA and X!Tandem in the number of identified peptides even though the q-value is only 0.001. When a precursor mass filter is used as a database indexing technique, our method outperforms OMSSA in the speed of search. When variable modifications are not searched, the search time is similar to X!Tandem. We show that the precursor mass filter is an efficient database indexing technique for high-accuracy data even though many variable modifications are being searched. We demonstrate that the number of identified peptides is bigger when variable modifications are searched separately by more search runs of a peptide identification engine. Otherwise, the false discovery rates are affected by mixing unmodified and modified spectra together resulting in a lower number of identified peptides. Our method is implemented in the freely available application SimTandem which can be used in the framework TOPP based on OpenMS.
Trade and the Environment: The Role of Firm Heterogeneity
2013-12-02

Abstract In this paper, we derive a new effect of trade liberalization on the quality of the environment. We show that in the presence of heterogeneous firms, the aggregate volume of emissions is influenced by a reallocation effect resulting from an increase in the relative size of more productive firms. The relative importance of this reallocation effect and the scale effect well‐known from the literature is affected by the emission intensity at the firm level. Domestic emissions decrease as a result of a unilateral tariff reduction if and only if firm‐specific emission intensity decreases strongly with increasing firm productivity. As a result of the induced change in foreign emissions, domestic pollution can increase even if domestic emissions decrease.
3D Chemical Mapping: Application of Scanning Transmission (Soft) X-ray Microscopy (STXM) in Combination with Angle-Scan Tomography in Bio-, Geo-, and Environmental Sciences
2013-12-02

The identification of environmental processes and mechanisms often requires information on the organochemical and inorganic composition of specimens at high spatial resolution. X-ray spectroscopy (XAS) performed in the soft X-ray range (100-2,200 eV) provides chemical speciation information for elements that are of high biogeochemical relevance such as carbon, nitrogen, and oxygen but also includes transition metals such as iron, manganese, or nickel. Synchrotron-based scanning transmission X-ray microscopy (STXM) combines XAS with high resolution mapping on the 20-nm scale. This provides two-dimensional (2D) quantitative information about the distribution of chemical species such as organic macromolecules, metals, or mineral phases within environmental samples. Furthermore, the combination of STXM with angle-scan tomography allows for three-dimensional (3D) spectromicroscopic analysis of bio-, geo-, or environmental samples. For the acquisition of STXM tomography data, the sample is rotated around an axis perpendicular to the X-ray beam. Various sample preparation approaches such as stripes cut from TEM grids or the preparation of wet cells allow for preparing environmentally relevant specimens in a dry or in a fully hydrated state for 2D and 3D STXM measurements. In this chapter we give a short overview about the principles of STXM, its application to environmental sciences, different preparation techniques, and the analysis and 3D reconstruction of STXM tomography data.
Impact of Type 2 Diabetes Susceptibility Variants on Quantitative Glycemic Traits Reveals Mechanistic Heterogeneity
2013-12-03

Patients with established type 2 diabetes display both β-cell dysfunction and insulin resistance. To define fundamental processes leading to the diabetic state, we examined the relationship between type 2 diabetes risk variants at 37 established susceptibility loci, and indices of proinsulin processing, insulin secretion, and insulin sensitivity. We included data from up to 58,614 nondiabetic subjects with basal measures and 17,327 with dynamic measures. We used additive genetic models with adjustment for sex, age, and BMI, followed by fixed-effects, inverse-variance meta-analyses. Cluster analyses grouped risk loci into five major categories based on their relationship to these continuous glycemic phenotypes. The first cluster (PPARG, KLF14, IRS1, GCKR) was characterized by primary effects on insulin sensitivity. The second cluster (MTNR1B, GCK) featured risk alleles associated with reduced insulin secretion and fasting hyperglycemia. ARAP1 constituted a third cluster characterized by defects in insulin processing. A fourth cluster (TCF7L2, SLC30A8, HHEX/IDE, CDKAL1, CDKN2A/2B) was defined by loci influencing insulin processing and secretion without a detectable change in fasting glucose levels. The final group contained 20 risk loci with no clear-cut associations to continuous glycemic traits. By assembling extensive data on continuous glycemic traits, we have exposed the diverse mechanisms whereby type 2 diabetes risk variants impact disease predisposition.
The Effect of Dosing Regimens on the Antimalarial Efficacy of Dihydroartemisinin-Piperaquine: A Pooled Analysis of Individual Patient Data
2013-12-03

DP demonstrates excellent efficacy in a wide range of transmission settings; however, treatment failure is associated with a lower dose of piperaquine, particularly in young children, suggesting potential for further dose optimisation.
Effects of Stimulus Order on Discrimination Processes in Comparative and Equality Judgements: Data and Models
2013-12-03

In typical discrimination experiments, participants are presented with a constant standard and a variable comparison stimulus and their task is to judge which of these two stimuli is larger (comparative judgement). In these experiments, discrimination sensitivity depends on the temporal order of these stimuli (Type B effect) and is usually higher when the standard precedes rather than follows the comparison. Here, we outline how two models of stimulus discrimination can account for the Type B effect, namely the weighted difference model (or basic Sensation Weighting model) and the Internal Reference Model. For both models, the predicted psychometric functions for comparative judgements as well as for equality judgements, in which participants indicate whether they perceived the two stimuli to be equal or not equal, are derived and it is shown that the models also predict a Type B effect for equality judgements. In the empirical part, the models’ predictions are evaluated. To this end, participants performed a duration discrimination task with comparative judgements and with equality judgements. In line with the models’ predictions, a Type B effect was observed for both judgement types. In addition, a time-order error, as indicated by shifts of the psychometric functions, and differences in response times were observed only for the equality judgement. Since both models entail distinct additional predictions, it seems worthwhile for future research to unite the two models into one conceptual framework.
Gαi2 Signaling Is Required for Skeletal Muscle Growth, Regeneration, and Satellite Cell Proliferation and Differentiation
2013-12-03

We have previously shown that activation of Gαi2, an α subunit of the heterotrimeric G protein complex, induces skeletal muscle hypertrophy and myoblast differentiation. To determine whether Gαi2 is required for skeletal muscle growth or regeneration, Gαi2-null mice were analyzed. Gαi2 knockout mice display decreased lean body mass, reduced muscle size, and impaired skeletal muscle regeneration after cardiotoxin-induced injury. Short hairpin RNA (shRNA)-mediated knockdown of Gαi2 in satellite cells (SCs) leads to defective satellite cell proliferation, fusion, and differentiation ex vivo. The impaired differentiation is consistent with the observation that the myogenic regulatory factors MyoD and Myf5 are downregulated upon knockdown of Gαi2. Interestingly, the expression of microRNA 1 (miR-1), miR-27b, and miR-206, three microRNAs that have been shown to regulate SC proliferation and differentiation, is increased by a constitutively active mutant of Gαi2 [Gαi2(Q205L)] and counterregulated by Gαi2 knockdown. As for the mechanism, this study demonstrates that Gαi2(Q205L) regulates satellite cell differentiation into myotubes in a protein kinase C (PKC)- and histone deacetylase (HDAC)-dependent manner.
Wild-growing lignicolous mushroom species as sources of novel agents with antioxidative and antibacterial potentials
2013-12-03

Crude extracts of two edible and two medicinal lignicolous mushroom species: Meripilus giganteus, Agrocybe aegerita, Fomes fomentarius and Xylaria polymorpha, growing wild in Serbia, were analyzed for their antioxidative and antibacterial potentials. Free radical scavenging capacity (RSC) on DPPH(•) and (•)OH was evaluated both by spectrophotometer and by Electron Spin Resonance (ESR) spectroscopy against DPPH(•). The highest antioxidant and antibacterial bioactivity was obtained with F. fomentarius extracts (IC50 ≈ 10.7 μg/ml in DPPH(•) assay; 136.6 mg ascorbic acid equivalents (AAE)/g dry weight (d.w.) for ferric reducing antioxidant power FRAP). It also showed the highest total phenol (TP) (82.54 mg gallic acid equivalents (GAE)/g dry weight (d.w.)) and total flavonoid (TF) content (76.8 μg rutin equivalents (RE)/g dry weight (d.w.)). A. aegerita showed the best antioxidant activity (IC50 = 0.87 mg/ml) against DPPH(•) in ESR analysis. Total redox potential of extracts was in direct positive correlation with TP content (r(2 )= 0.98) and TF content (r(2 )= 0.58). GC/MS analysis detected major constituents of extracts, confirming the presence of the following organic and phenolic acids: fumaric, succinic, mallic, 4-hydroxy benzoic, gentisic, protocatechuic, vanillic, gallic and p-coumaric acid.
The small GTPase Rac1 is required for smooth muscle contraction
2013-12-03

Key points The role of the small G‐protein Rac1 was investigated in smooth muscle, using a smooth muscle‐specific knockout mouse and pharmacological blockers. Inhibition of the interaction between Rac1 and upstream regulators inhibited the α‐receptor contractions and potentiated prostaglandin F2α contractions in vascular tissue. The inhibition was mediated via an attenuation of the Ca 2+ transient. A global inhibition of Rac1 activity inhibited contractions in response to several agonists in a range of smooth muscle tissues. The results demonstrate a novel Rac1‐associated signalling pathway for regulation of smooth muscle contraction. Abstract The role of the small GTP‐binding protein Rac1 in smooth muscle contraction was examined using small molecule inhibitors (EHT1864, NSC23766) and a novel smooth muscle‐specific, conditional, Rac1 knockout mouse strain. EHT1864, which affects nucleotide binding and inhibits Rac1 activity, concentration‐dependently inhibited the contractile responses induced by several different modes of activation (high‐K + , phenylephrine, carbachol and protein kinase C activation by phorbol‐12,13‐dibutyrate) in several different visceral (urinary bladder, ileum) and vascular (mesenteric artery, saphenous artery, aorta) smooth muscle tissues. This contractile inhibition was associated with inhibition of the Ca 2+ transient. Knockout of Rac1 (with a 50% loss of Rac1 protein) lowered active stress in the urinary bladder and the saphenous artery consistent with a role of Rac1 in facilitating smooth muscle contraction. NSC23766, which blocks interaction between Rac1 and some guanine nucleotide exchange factors, specifically inhibited the α 1 receptor responses (phenylephrine) in vascular tissues and potentiated prostaglandin F2α and thromboxane (U46619) receptor responses. The latter potentiating effect occurred at lowered intracellular [Ca 2+ ]. These results show that Rac1 activity is required for active contraction in smooth muscle, probably via enabling an adequate Ca 2+ transient. At the same time, specific agonists recruit Rac1 signalling via upstream modulators, resulting in either a potentiation of contraction via Ca 2+ mobilization (α 1 receptor stimulation) or an attenuated contraction via inhibition of Ca 2+ sensitization (prostaglandin and thromboxane receptors).
Nanosphere Lithography: Parallel Fabrication of Plasmonic Nanocone Sensing Arrays (Small 23/2013)
2013-12-03

Ordered arrays of nanocones and nanopyramids are fabricated in a fully parallel approach by M. Fleischer and co-workers, as reported on page 3987. Single or double layers of self-assembled nanospheres are directly modified or used as templates for the creation of etch masks. Nanocones with sharp tips form when the masks are transferred into a gold or silver layer. Under optical excitation, narrowly confi ned hotspots are created near the cone tips. These structures have interesting properties for nano-optical applications and are evaluated as substrates for surface enhanced Raman spectroscopy using a thin film of pentacene molecules.
Membrane-Anchored Aβ Accelerates Amyloid Formation and Exacerbates Amyloid-Associated Toxicity in Mice
2013-12-04

Pathological, genetic, and biochemical hallmarks of Alzheimer's disease (AD) are linked to amyloid-β (Aβ) peptide aggregation. Especially misfolded Aβ 42 peptide is sufficient to promote amyloid plaque formation. However, the cellular compartment facilitating the conversion of monomeric Aβ to aggregated toxic Aβ species remains unknown. In vitro models suggest lipid membranes to be the driving force of Aβ conversion. To this end, we generated two novel mouse models, expressing either membrane-anchored or nonanchored versions of the human Aβ 42 peptide. Strikingly, membrane-anchored Aβ 42 robustly accelerated Aβ deposition and exacerbated amyloid-associated toxicity upon crossing with Aβ precursor protein transgenic mice. These in vivo findings support the hypothesis that Aβ–membrane interactions play a pivotal role in early-onset AD as well as neuronal damage and provide evidence to study Aβ–membrane interactions as therapeutic targets.
Both Terminal Oxidases Contribute to Fitness and Virulence during Organ-Specific Staphylococcus aureus Colonization
2013-12-04

ABSTRACT In their recent article, Hammer et al. (N. D. Hammer, M. L. Reniere, J. E. Cassat, Y. Zhang, A. O. Hirsch, M. Indriati Hood, and E. P. Skaar, mBio 4 :e00241-13, 2013) described the dual functions of the two terminal oxidases encoded by cydBA and qoxABCD in Staphylococcus aureus . The aerobic growth of cydB or qoxB single mutant bacteria was barely affected. However, a cydB qoxB double mutant was completely unable to respire and exhibited the small-colony variant phenotype that is typical of menaquinone and heme biosynthesis mutants. The authors found that the two terminal oxidases play a role in pathogenesis. In a systemic mouse infection model, it turned out that in the cydB mutant the bacterial burden was significantly decreased in the heart, kidneys, and liver, while in the qoxB mutant it was decreased only in the liver. These results illustrate that both terminal oxidases contribute to fitness and virulence, representing promising candidates for the development of antimicrobials.
Right Temporoparietal Gray Matter Predicts Accuracy of Social Perception in the Autism Spectrum
2013-12-04

Individuals with an autism spectrum disorder (ASD) show hallmark deficits in social perception. These difficulties might also reflect fundamental deficits in integrating visual signals. We contrasted predictions of a social perception and a spatial-temporal integration deficit account. Participants with ASD and matched controls performed two tasks: the first required spatiotemporal integration of global motion signals without social meaning, the second required processing of socially relevant local motion. The ASD group only showed differences to controls in social motion evaluation. In addition, gray matter volume in the temporal-parietal junction correlated positively with accuracy in social motion perception in the ASD group. Our findings suggest that social-perceptual difficulties in ASD cannot be reduced to deficits in spatial-temporal integration.
Development of a GEM based detector for the CBM Muon Chamber (MUCH)
2013-12-04

ABSTRACT: The characteristics of triple GEM detectors have been studied systematically by using cosmic ray muons. The minimum ionizing particle (MIP) spectra has been taken for different GEM voltage setting. Efficiency of GEM detector has been measured for cosmic ray. At high rate operation of GEMs the value of the protection resistor influences the gain and the stability. This feature has been investigated varying both the rate and the value of the protection resistor. This measurement has been performed using both X-ray generator and Fe55 source. The ageing and long-term stability of GEM based detectors has been studied employing both X-ray generator and Fe55 source. The ageing study of one GEM module is performed by using a 8 keV Cu X-ray generator to verify the stability and integrity of the GEM detectors over a longer period of time. The accumulated charge on the detector is calculated from the rate of the X-ray and the average gain of the detector. The details of the measurement and results has been described in this article.
An Association between External Hydrocephalus in Infants and Reversible Collapse of the Venous Sinuses
2013-12-04

The etiology of external hydrocephalus is usually ascribed to either a delay in maturation or obstruction of the arachnoid granulations, but the arachnoid granulations are absent in neonates. Venous outflow stenoses, similar to those seen in idiopathic intracranial hypertension (IIH), have been described in external hydrocephalus. A reversible collapse of the sinuses is known to operate in IIH, but collapsible sinuses have not been previously described in infants with external hydrocephalus. Three infants with external hydrocephalus had magnetic resonance venography at differing time points during their illness. The venous sinuses varied in size depending on the cerebrospinal fluid pressure similar to IIH in adults. External hydrocephalus may be analogous to IIH in adults.
Synthesis of Pladienolide B and Its 7‐Epimer with Insights into the Role of the Allylic Acetate
2013-12-04

Abstract Diastereomeric macrolactones 41 and 48 , which are epimeric at C‐7, were both prepared by a synthesis based on our previously developed route to the macrolactone core of pladienolide B. Both compounds contain all the functionality of the macrolactone core plus the vinyl iodide unit in the side chain. The key step to construct the seco acid for the macrolactonization was a Horner–Wadsworth–Emmons (HWE) reaction to produce acyclic enone 17 . The required keto phosphonate for the HWE reaction was originally obtained from ( R )‐(–)‐linalool. The derived macrolactone underwent a reduction of the enone function to give 7‐ epi ‐alcohol 20 , and its acetylation, either under Mitsunobu or classical acylation conditions, produced allylic acetate 40 . This represents a rare case in which a Mitsunobu reaction occurred with retention of configuration. The complete side chain that contains all the functionality was attached by a Stille cross‐coupling reaction to lead to 7‐ epi ‐pladienolide B ( 42 ). To obtain pladienolide B ( 1 ), the reduction of acyclic enone 17 under chelation‐controlled conditions [Zn(BH 4 ) 2 , Et 2 O] gave allylic alcohol 43 with the correct configuration at C‐7 with regard to the natural product. Conversion of this allylic alcohol to seco acid 46 followed by a Shiina macrolactonization afforded vinyl iodide 48 . Its Stille coupling with vinylstannane 39 provided pladienolide B ( 1 ). Preliminary testing for cytotoxicity against the L929 cell line showed 7‐ epi ‐pladienolide B ( 42 ) to be completely inactive, which is in contrast to pladienolide B ( 1 ) that displayed an IC 50 (half maximal inhibitory concentration) value of 7.5 nM. These results point to the importance of the correct configuration of the OAc functional group at C‐7 of pladienolide B.