julilili42/papers huggingface dataset:
MRI Findings in Psoriatic Arthritis of the Hands
2010-10-21

The MRI findings of psoriatic arthritis include enthesitis, bone marrow edema, and periostitis accompanying articular or flexor tendon sheath synovitis in the early stage accompanied by destructive and proliferative bony changes, subluxation, and ankylosis in the late stage.
Mass spectrometry at the interface of proteomics and genomics
2010-10-21

With the onset of modern DNA sequencing technologies, genomics is experiencing a revolution in terms of quantity and quality of sequencing data. Rapidly growing numbers of sequenced genomes and metagenomes present a tremendous challenge for bioinformatics tools that predict protein-coding regions. Experimental evidence of expressed genomic regions, both at the RNA and protein level, is becoming invaluable for genome annotation and training of gene prediction algorithms. Evidence of gene expression at the protein level using mass spectrometry-based proteomics is increasingly used in refinement of raw genome sequencing data. In a typical "proteogenomics" experiment, the whole proteome of an organism is extracted, digested into peptides and measured by a mass spectrometer. The peptide fragmentation spectra are identified by searching against a six-frame translation of the raw genomic assembly, thus enabling the identification of hitherto unpredicted protein-coding genomic regions. Application of mass spectrometry to genome annotation presents a range of challenges to the standard workflows in proteomics, especially in terms of proteome coverage and database search strategies. Here we provide an overview of the field and argue that the latest mass spectrometry technologies that enable high mass accuracy at high acquisition rates will prove to be especially well suited for proteogenomics applications.
Human SAP18 mediates assembly of a splicing regulatory multiprotein complex via its ubiquitin-like fold
2010-10-21

RNPS1, Acinus, and SAP18 form the apoptosis- and splicing-associated protein (ASAP) complex, which is also part of the exon junction complex. Whereas RNPS1 was originally identified as a general activator of mRNA processing, all three proteins have been found within functional spliceosomes. Both RNPS1 and Acinus contain typical motifs of splicing regulatory proteins including arginine/serine-rich domains. Due to the absence of such structural features, however, a function of SAP18 in splicing regulation is completely unknown. Here we have investigated splicing regulatory activities of the ASAP components. Whereas a full-length Acinus isoform displayed only limited splicing regulatory activity, both RNPS1 and, surprisingly, SAP18 strongly modulated splicing regulation. Detailed mutational analysis and three-dimensional modeling data revealed that the ubiquitin-like fold of SAP18 was required for efficient splicing regulatory activity. Coimmunoprecipitation and immunofluorescence experiments demonstrated that SAP18 assembles a nuclear speckle-localized splicing regulatory multiprotein complex including RNPS1 and Acinus via its ubiquitin-like fold. Our results therefore suggest a novel function of SAP18 in splicing regulation.
Variants in the CD36 Gene Locus Determine Whole‐Body Adiposity, but Have No Independent Effect on Insulin Sensitivity
2010-10-21

CD36 variants have been associated with type 2 diabetes, features of the metabolic syndrome, and alterations in lipid metabolism. In contrast, the effect of single‐nucleotide polymorphisms (SNPs) in CD36 on insulin resistance is controversial in literature. Therefore, we investigated whether genetic variation within the CD36 gene locus affects insulin resistance in a well‐phenotyped cohort of white European subjects at increased risk for type 2 diabetes. We genotyped 1,790 subjects (1,174 women, 616 men) for six SNPs tagging 100% of common variants (minor allele frequency ≥0.05) within the CD36 gene locus with an r 2 ≥ 0.8. All subjects underwent an oral glucose tolerance test (OGTT) and a subset additionally a hyperinsulinemic‐euglycemic clamp ( n = 523). Ectopic hepatic lipids ( n = 346) were assessed by magnetic resonance spectroscopy. After appropriate adjustment and Bonferroni correction for multiple comparisons, the four CD36 SNPs rs9784998, rs3211883, rs3211908, and rs3211956 significantly associated with BMI and rs3211883 and rs3211908 significantly associated with waist circumference (all P &lt; 0.0042). In contrast, CD36 SNPs rs3211816 and rs3211960 were not associated with measures of adiposity (all P ≥ 0.11). No reliable association was detected between the six CD36 SNPs and insulin sensitivity or ectopic hepatic lipid accumulation after adjustment for age, gender, and BMI. In the long run, genetic variation within the CD36 locus may contribute to metabolic disease via its effect on body adiposity, but not via an independent effect on insulin sensitivity.
Serum levels of a subset of cytokines show high interindividual variability and are not altered in rats transgenic for Huntington´s disease
2010-10-21

To evaluate whether cytokines are altered in peripheral blood of rats transgenic for the human Huntington ́s disease mutation we investigated serum levels of GRO/KC, IL-1β, IL-13 and TNF-α at a symptomatic stage at 12 months of age. Overall serum levels of these cytokines were not significantly changed between transgenic HD rats and controls. Moreover, we observed a high interindividual variability. Our results indicate that these cytokines will be difficult to pursue as biomarkers in at least this rat model of HD.
Peripherally Applied Aβ-Containing Inoculates Induce Cerebral β-Amyloidosis
2010-10-22

Infectious Amyloid? Patients with Alzheimer's disease have characteristic lesions in the brains associated with masses of polymerized protein called β-amyloid. Recently, evidence from mouse models of Alzheimer's disease shows that brain extracts containing β-amyloid can “infect” otherwise healthy animals when injected directly into their brains. Eisele et al. (p. 980 , published online 21 October; see the Perspective by Kim and Holtzman ) extend these findings to show that when mice are injected in other parts of their bodies with similar brain extracts after several months, they also develop amyloidosis within their brains.
Significance of Cuscutain, a cysteine protease from Cuscuta reflexa, in host-parasite interactions
2010-10-22

Abstract Background Plant infestation with parasitic weeds like Cuscuta reflexa induces morphological as well as biochemical changes in the host and the parasite. These modifications could be caused by a change in protein or gene activity. Using a comparative macroarray approach Cuscuta genes specifically upregulated at the host attachment site were identified. Results One of the infestation specific Cuscuta genes encodes a cysteine protease. The protein and its intrinsic inhibitory peptide were heterologously expressed, purified and biochemically characterized. The haustoria specific enzyme was named cuscutain in accordance with similar proteins from other plants, e.g. papaya. The role of cuscutain and its inhibitor during the host parasite interaction was studied by external application of an inhibitor suspension, which induced a significant reduction of successful infection events. Conclusions The study provides new information about molecular events during the parasitic plant - host interaction. Inhibition of cuscutain cysteine proteinase could provide means for antagonizing parasitic plants.
Identification of Epidermal Pdx1 Expression Discloses Different Roles of Notch1 and Notch2 in Murine KrasG12D-Induced Skin Carcinogenesis In Vivo
2010-10-22

Our results provide strong evidence for epidermal expression of Pdx1 as of yet not identified function. In addition, this finding may be relevant for research using Pdx1-Cre transgenic strains. Additionally, our study confirms distinctive expression and functions of Notch1 and Notch2 in the skin supporting the importance of careful dissection of the contribution of individual Notch receptors.
Are Treatment Preferences Relevant in Response to Serotonergic Antidepressants and Cognitive-Behavioral Therapy in Depressed Primary Care Patients? Results from a Randomized Controlled Trial Including a Patients’ Choice Arm
2010-10-23

&lt;i&gt;Background:&lt;/i&gt; Little is known about the influence of depressed patients’ preferences and expectations about treatments upon treatment outcome. We investigated whether better clinical outcome in depressed primary care patients is associated with receiving their preferred treatment. &lt;i&gt;Methods:&lt;/i&gt; Within a randomized placebo-controlled single-centre 10-week trial with 5 arms (sertraline; placebo; cognitive-behavioral group therapy, CBT-G; moderated self-help group control; treatment with sertraline or CBT-G according to patients’ choice), outcomes for 145 primary care patients with mild-to-moderate depressive disorders according to DSM-IV criteria were investigated. Preference for medication versus psychotherapy was assessed at screening using a single item. Post-baseline difference scores for the Hamilton Depression Rating Scale (HAMD-17) were used to assess treatment outcome (mixed-model repeated-measures regression analysis). &lt;i&gt;Results:&lt;/i&gt; Depressed patients receiving their preferred treatment (n = 63), whether sertraline or CBT-G, responded significantly better than those who did not receive their preferred therapy (n = 54; p = 0.001). The difference in outcome between both groups was 8.0 points on the HAMD-17 for psychotherapy and 2.9 points on the HAMD-17 for treatment with antidepressants. Results were not explained by differences in depression severity or dropout rates. &lt;i&gt;Conclusions:&lt;/i&gt; Patients’ relative preference for medication versus psychotherapy should be considered when offering a treatment because receiving the preferred treatment conveys an additional and clinically relevant benefit (HAMD-17: +2.9 points for drugs; +8.0 points for CBT-G) in outcome.
Right and Left Ventricular Myocardial Perfusion Reserves Correlate with Right Ventricular Function and Pulmonary Hemodynamics in Patients with Pulmonary Arterial Hypertension
2010-10-23

Biventricular vasoreactivity is significantly reduced with PAH and inversely correlated with RV workload and ejection fraction, suggesting that reduced myocardial perfusion reserve may contribute to RV dysfunction in patients with PAH.
Partner Knowledge Awareness in Knowledge Communication: Learning by Adapting to the Partner
2010-10-25

Abstract Awareness of the knowledge of learning partners is not always sufficiently available in collaborative learning scenarios. To compensate, the authors propose to provide collaborators with partner knowledge awareness by means of a visualization tool. Partner knowledge awareness can be used to adapt messages toward the partner. This study investigated the cognitive consequences of message adaptation on producers. The authors chose a simulated collaboration scenario in order to dissociate the producer effect from recipient and collaboration effects. Results on 42 participants that had been randomly assigned to either the partner knowledge awareness condition (partner and own knowledge visualized) or the control condition (only own knowledge visualized) are reported here. Participants in the partner knowledge awareness condition adapted their contributions according to the visualized partner's knowledge and benefited with regard to the acquisition of elaborated knowledge. Keywords: awareness toolsgroup awarenessknowledge awarenessknowledge communicationlearning by explainingremote collaboration
An automatic layout algorithm for BPEL processes
2010-10-25

The Business Process Execution Language (BPEL) is the standard execution language for business workflows. BPEL is an XML-based, verbose and complex language, consisting of block- and graph-oriented control structures, which makes it hard to generate intuitive visualizations.
Light and heavy mesons in a soft-wall holographic approach
2010-10-26

We study the mass spectrum and decay constants of light and heavy mesons in a\\nsoft-wall holographic approach, using the correspondence of string theory in\\nAnti-de Sitter space and conformal field theory in physical space-time.\\n
Cyclic GMP Kinase I Modulates Glucagon Release From Pancreatic α-Cells
2010-10-26

OBJECTIVE The physiologic significance of the nitric oxide (NO)/cGMP signaling pathway in islets is unclear. We hypothesized that cGMP-dependent protein kinase type I (cGKI) is directly involved in the secretion of islet hormones and glucose homeostasis. RESEARCH DESIGN AND METHODS Gene-targeted mice that lack cGKI in islets (conventional cGKI mutants and cGKIα and Iβ rescue mice [α/βRM] that express cGKI only in smooth muscle) were studied in comparison to control (CTR) mice. cGKI expression was mapped in the endocrine pancreas by Western blot, immuno-histochemistry, and islet-specific recombination analysis. Insulin, glucagon secretion, and cytosolic Ca2+ ([Ca2+]i) were assayed by radioimmunoassay and FURA-2 measurements, respectively. Serum levels of islet hormones were analyzed at fasting and upon glucose challenge (2 g/kg) in vivo. RESULTS Immunohistochemistry showed that cGKI is present in α- but not in β-cells in islets of Langerhans. Mice that lack α-cell cGKI had significantly elevated fasting glucose and glucagon levels, whereas serum insulin levels were unchanged. High glucose concentrations strongly suppressed the glucagon release in CTR mice, but had only a moderate effect on islets that lacked cGKI. 8-Br-cGMP reduced stimulated [Ca2+]i levels and glucagon release rates of CTR islets at 0.5 mmol/l glucose, but was without effect on [Ca2+]i or hormone release in cGKI-deficient islets. CONCLUSIONS We propose that cGKI modulates glucagon release by suppression of [Ca2+]i in α-cells.
Probing the Influence of an Allylic Methyl Group in Zearalenone Analogues on Binding to Hsp90
2010-10-27

Abstract By the replacement of an acetate with propionate by means of organic synthesis, a range of zearalenone analogues were prepared that feature an allylic methyl group. For the synthesis of the aliphatic region of the analogues, we used an asymmetric alkylation to yield pentenol derivatives 16 and ent ‐ 16 . By means of hydroboration the corresponding aldehydes were secured. These were coupled with 2‐pentynol derivate 23 by means of a Carreira acetylide addition. Further routine steps led to the sulfones 29 and 45 , respectively. After merging them with 2‐bromobenzaldehyde 9 in a Julia–Kocienski reaction, metalation, carboxylation, and protecting‐group manipulations gave the seco acids 35 and 49 . By means of lactonization under Mitsunobu (alcohol activation) or Trost–Kita conditions (carboxyl activation), all four possible macrocyclic ketone stereoisomers were accessible. In all, considering various protecting‐group decorations, 16 analogues were obtained and tested for cytotoxicity (L929 mouse fibroblast cell line). Whereas most of the analogues were less active than zearalenone (IC 50 =9.4 μ M ), the resorcinol derivatives were comparable, with one stereoisomer ( 40 b ) being slightly more active (IC 50 =6.6 μ M ). These results were also reflected in the binding assays to Hsp90 in which 40 b showed a dissociation constant ( K d ) value of 130 n M .
Corrosion of Single Crystal Cordierite by Model Diesel Particulate Filter Ashes: Mechanisms and Orientation Dependence
2010-10-27

Cordierite Mg2Al4Si5O18 is a material for diesel particulate filters (DPF) with high potential. Its resistance to a simplified model ash has been tested on single crystals at temperatures up to 1050°C, which are realistic for use under ‘worst case’ conditions. A mixture of Ca, Mg and Zn phosphates, which are typical main constituents of many DPF ashes, was used as model ash. Single crystals were examined in order to investigate the orientation dependence of attack due to the strongly anisotropic nature of the Cordierite crystal lattice. Strong corrosion by the ash occurs at 1050 °C, connected to excessive ash melting. The molten ash attacks Cordierite by fast dissolution of the substrate with melt (super)saturation within minutes. Anisotropy of the dissolution process could not be detected. The initial kinetics are dominated by saturation effects, which slow down corrosion. The saturated melt attacks Cordierite by reaction processes leading to the formation of new crystalline phases. This process is much slower than the initial dissolution process but may significantly contribute to the destruction of Cordierite substrates if large contact areas between ash melt and Cordierite exist.
Discovery and follow-up studies of the extended, off-plane, VHE gamma-ray source HESS J1507-622
2010-10-28

Context. The detection of gamma-rays in the very-high-energy (VHE) range (100 GeV−100 TeV) offers the possibility of studying the parent population of ultrarelativistic particles found in astrophysical sources, so it is useful for understanding the underlying astrophysical processes in nonthermal sources.&#13;\\n&#13;\\nAims. The discovery of the VHE gamma-ray source HESS J1507-622 is reported and possibilities regarding its nature are investigated.&#13;\\n&#13;\\nMethods. The H.E.S.S. array of imaging atmospheric Cherenkov telescopes (IACTs) has a high sensitivity compared with previous instruments (~1% of the Crab flux in 25 h observation time for a 5σ point-source detection) and has a large field of view (~5° in diameter). HESS J1507-622 was discovered within the ongoing H.E.S.S. survey of the inner Galaxy, and the source was also studied by means of dedicated multiwavelength observations.&#13;\\n&#13;\\nResults. A Galactic gamma-ray source, HESS J1507-622, located ~3.5° from the Galactic plane was detected with a statistical significance &gt;9σ. Its energy spectrum is well fitted by a power law with spectral index Γ = 2.24 ± 0.16stat ± 0.20sys and a flux above 1 TeV of (1.5 ± 0.4stat ± 0.3sys) × 10-12 cm-2 s-1. Possible interpretations (considering both hadronic and leptonic models) of the VHE gamma-ray emission are discussed in the absence of an obvious counterpart.
Bead‐based protein–protein interaction assays for the analysis of Rho GTPase signaling
2010-10-28

Abstract Bead‐based interaction assays are excellently suited to study protein–protein interactions, as they require only minimal amounts of sample material. Miniaturized protein–protein interaction assays were designed to analyze Rho GTPase activation based on its interaction with Rho GDI or p21‐activated kinase (PAK). Rho GDI plays a key role in the regulation of a variety of cellular functions through its interaction with Rho GTPases. Rho GDI is frequently overexpressed in many human cancers. Therefore, there is a growing and as yet unfulfilled demand for screening assays to identify biologically active compounds that may inhibit the Rho GTPase–Rho GDI interaction. Bead‐based interaction assays provide an interesting alternative that facilitate such assays to be performed faster with only small amounts of material compared to routinely used co‐immunoprecipitation followed by Western Blot analysis. Bead‐based protein interaction assays for overexpressed HA‐tagged Rho GTPases were established to study the GTP γ S‐dependent interaction of five different Rho GTPases with the regulatory protein Rho GDI α and the downstream effector PAK1. In addition, it was demonstrated that the ability of Rho GTPases to interact with Rho GDI in this experimental system was markedly, but differentially sensitive to post‐translational modification of their carboxyl terminus. Importantly, this modification also notably affected the ability of Rac1 and Rac2, but not of Cdc42, to interact with PAK1. Copyright © 2010 John Wiley &amp; Sons, Ltd.
New fin-line devices for radiofrequency exposure of small biological samples in vitro allowing whole-cell patch clamp recordings
2010-10-28

The development and analysis of three waveguides for the exposure of small biological in vitro samples to mobile communication signals at 900 MHz (GSM, Global System for Mobile Communications), 1.8 GHz (GSM), and 2 GHz (UMTS, Universal Mobile Telecommunications System) is presented. The waveguides were based on a fin-line concept and the chamber containing the samples bathed in extracellular solution was placed onto two fins with a slot in between, where the exposure field concentrates. Measures were taken to allow for patch clamp recordings during radiofrequency (RF) exposure. The necessary power for the achievement of the maximum desired specific absorption rate (SAR) of 20 W/kg (average over the mass of the solution) was approximately Pin = 50 mW, Pin = 19 mW, and Pin = 18 mW for the 900 MHz, 1800 MHz, and 2 GHz devices, respectively. At 20 W/kg, a slight RF-induced temperature elevation in the solution of no more than 0.3 °C was detected, while no thermal offsets due to the electromagnetic exposure could be detected at the lower SAR settings (2, 0.2, and 0.02 W/kg). A deviation of 10% from the intended solution volume yielded a calculated SAR deviation of 8% from the desired value. A maximum ±10% variation in the local SAR could occur when the position of the patch clamp electrode was altered within the area where the cells to be investigated were located. Bioelectromagnetics 32:102–112, 2011. © 2010 Wiley-Liss, Inc.
Separation of Enantiomers by Gas Chromatography on Chiral Stationary Phases
2010-10-28

This chapter contains sections titled: Introduction Chiral Stationary Phases Based on α-Amino Acid Derivatives for Hydrogen-Bonding GC Chiral Stationary Phases Based on Metal Chelates for Complexation GC Chiral Stationary Phases Based on Modified Cyclodextrins for Inclusion GC Thermodynamic Parameters of Enantioseparation by GC: The Isoenantioselective Temperature TISO Applications Mixed Chiral Stationary Phases Comprising Diamides and Modified Cyclodextrins in Enantioselective GC Unified Enantioselective Capillary Chromatography Miniaturization Hyphenated Approaches in Enantioselective GC Method of Enantiomer Labeling Chiral Test Mixtures Data Retrieval for Enantioselective GC Miscellaneous Topics Some Statistics Preparative-Scale Gas Chromatographic Enantioseparation Conclusions References
ChemInform Abstract: Tetrahydrofurans from Substituted Hex‐5‐yne‐1,4‐diols.
2010-10-28

Abstract It is discovered that hex‐5‐yne‐1,4‐diols of type (I) undergo metal‐catalyzed Meyer—Schuster rearrangement followed by an intramolecular Michael addition to yield 2,5‐disubstituted tetrahydrofurans.
Independent and joint effects of the MAPT and SNCA genes in Parkinson disease
2010-10-29

Abstract Objective: We studied the independent and joint effects of the genes encoding alpha‐synuclein ( SNCA ) and microtubule‐associated protein tau ( MAPT ) in Parkinson disease (PD) as part of a large meta‐analysis of individual data from case–control studies participating in the Genetic Epidemiology of Parkinson's Disease (GEO‐PD) consortium. Methods: Participants of Caucasian ancestry were genotyped for a total of 4 SNCA (rs2583988, rs181489, rs356219, rs11931074) and 2 MAPT (rs1052553, rs242557) single nucleotide polymorphism (SNPs). Individual and joint effects of SNCA and MAPT SNPs were investigated using fixed‐ and random‐effects logistic regression models. Interactions were studied on both a multiplicative and an additive scale, and using a case–control and case‐only approach. Results: Fifteen GEO‐PD sites contributed a total of 5,302 cases and 4,161 controls. All 4 SNCA SNPs and the MAPT H1‐haplotype–defining SNP (rs1052553) displayed a highly significant marginal association with PD at the significance level adjusted for multiple comparisons. For SNCA , the strongest associations were observed for SNPs located at the 3′ end of the gene. There was no evidence of statistical interaction between any of the 4 SNCA SNPs and rs1052553 or rs242557, neither on the multiplicative nor on the additive scale. Interpretation: This study confirms the association between PD and both SNCA SNPs and the H1 MAPT haplotype. It shows, based on a variety of approaches, that the joint action of variants in these 2 loci is consistent with independent effects of the genes without additional interacting effects. ANN NEUROL 2011