julilili42/papers huggingface dataset:
Lowered Serum Amyloid-β1-42 Autoantibodies in Individuals with Lifetime Depression
2012-09-25

Reduced levels of naturally occurring autoantibodies against amyloid-β (Aβ) have been described in Alzheimer's disease (AD). Lifetime depression doubles the risk of AD, thus these autoantibodies may also be reduced in this group. We measured serum IgG autoantibody titers against Aβ1-42, S100b and α-synuclein in 214 individuals with depression and 419 controls. Titers against Aβ1-42 were lower in individuals with lifetime depression (5544.6 ± 389.3) compared to controls (7208.7 ± 482.4; p = 0.048). Titers against S100b and α-synuclein were comparable between the cohorts. These data suggest an AD-like impairment of the humoral immune response in a relevant proportion of individuals with depression.
Mixing, entropy and reactive solute transport
2012-09-26

Mixing processes significantly affect reactive solute transport in fluids. For example, contaminant degradation in environmental aquatic systems can be limited either by the availability of one or more reactants, brought into contact by physical mixing, or by the kinetics of the (bio)chemical transformations. Appropriate metrics are needed to accurately quantify the interplay between mixing and reactive processes. The exponential of the Shannon entropy of the concentration probability distribution has been proposed and applied to quantify the dilution of conservative solutes either in a given volume (dilution index) or in a given water flux (flux‐related dilution index). In this work we derive the transport equation for the entropy of a reactive solute. Adopting a flux‐related framework, we show that the degree of uniformity of the solute mass flux distribution for a reactive species and its rate of change are informative measures of physical and (bio)chemical processes and their complex interaction.
Urothelial Carcinoma of the Bladder and the Upper Tract: Disparate Twins
2012-09-27

While urothelial carcinoma of the bladder and upper tract urothelial carcinoma share many characteristics, they represent 2 distinct diseases. There are practical, anatomical, biological and molecular differences that warrant consideration when risk stratifying and treating patients with these disparate twin diseases. To overcome the challenges that impede progress toward evidence-based medicine in upper tract urothelial carcinoma, we believe that focused collaborative efforts will best augment our understanding of this rare disease and ultimately improve the care we deliver to our patients.
Coordination Chemistry of Gold Catalysts in Solution: A Detailed NMR Study
2012-09-27

Abstract Coordination chemistry of gold catalysts bearing eight different ligands [L=PPh 3 , JohnPhos ( L2 ), Xphos ( L3 ), DTBP, IMes, IPr, dppf, S ‐tolBINAP ( L8 )] has been studied by NMR spectroscopy in solution at room temperature. Cationic or neutral mononuclear complexes LAuX (L= L2 , L3 , IMes, IPr; X=charged or neutral ligand) underwent simple ligand exchange without giving any higher coordinate complexes. For L2 AuX the following ligand strength series was determined: MeOH≪hex‐3‐yne &lt;MeCN≈OTf − ≪Me 2 S&lt;2,6‐lutidine&lt;4‐picoline&lt;CF 3 CO 2 − ≈DMAP&lt;TMTU&lt;PPh 3 &lt;OH − ≈Cl − . Some heteroligand complexes DTBPAuX exist in solution in equilibrium with the corresponding symmetrical species. Binuclear complexes dppf(AuOTf) 2 and S ‐tolBINAP(AuOTf) 2 showed different behavior in exchange reactions with ligands depending on the ligand strength. Thus, PPh 3 causes abstraction of one gold atom to give mononuclear complexes LLAuPPh 3 + and (Ph 3 P) n Au + , but other N and S ligands give ordinary dicationic species LL(AuNu) 2 2+ . In reactions with different bases, LAu + provided new oxonium ions whose chemistry was also studied: (DTBPAu) 3 O + , ( L2 Au) 2 OH + , ( L2 Au) 3 O + , ( L3 Au) 2 OH + , and (IMesAu) 2 OH + . Ultimately, formation of gold hydroxide LAuOH (L= L2 , L3 , IMes) was studied. Ligand‐ or base‐assisted interconversions between ( L2 Au) 2 OH + , ( L2 Au) 3 O + , and L2 AuOH are described. Reactions of dppf(AuOTf) 2 and S ‐tolBINAP(AuOTf) 2 with bases provided more interesting oxonium ions, whose molecular composition was found to be [dppf(Au) 2 ] 3 O 2 2+ , L8 (Au) 2 OH + , and [ L8 (Au) 2 ] 3 O 2 2+ , but their exact structure was not established. Several reactions between different oxonium species were conducted to observe mixed heteroligand oxonium species. Reaction of L2 AuNCMe + with S 2− was studied; several new complexes with sulfide are described. For many reversible reactions the corresponding equilibrium constants were determined.
High Hepatic SCD1 Activity Is Associated with Low Liver Fat Content in Healthy Subjects under a Lipogenic Diet
2012-09-27

DNL is closely linked with hepatic steatosis under dietary conditions rich in monosaccharides. Our data suggest that the individual hepatic SCD1 activity is a determinant of liver fat accumulation under lipogenic dietary conditions.
Serum- and glucocorticoid-inducible kinase SGK1 regulates reorganization of actin cytoskeleton in mast cells upon degranulation
2012-09-27

Aggregation of the high-affinity IgE receptor (FcεRI) on mast cells (MCs) causes MC degranulation, a process that involves cortical F-actin disassembly. Actin depolymerization may be triggered by increase of cytosolic Ca 2+ . Entry of Ca 2+ through the Ca 2+ release-activated Ca 2+ (CRAC) channels is under powerful regulation by the serum- and glucocorticoid-inducible kinase SGK1. Moreover, FcεRI-dependent degranulation is decreased in SGK1-deficient ( sgk1 −/− ) MCs. The present study addressed whether SGK1 is required for actin cytoskeleton rearrangement in MCs and whether modulation of actin architecture could underlie decreased degranulation of sgk1 −/− MCs. Confirming previous results, release of β-hexosaminidase reflecting FcεRI-dependent degranulation was impaired in sgk1 −/− MCs compared with sgk1 +/+ MCs. When CRAC channels were inhibited by 2-aminoethoxydiphenyl borate (2-APB; 50 μM), MC degranulation was strongly decreased in both sgk1 +/+ and sgk1 −/− MCs and the difference between genotypes was abolished. Moreover, degranulation was impaired by actin-stabilizing (phallacidin) and enhanced by actin-disrupting (cytochalasin B) agents to a similar extent in sgk1 +/+ MCs and sgk1 −/− MCs, implying a regulatory role of actin reorganization in this event. In line with this, measurements of monomeric (G) and filamentous (F) actin content by FACS analysis and Western blotting of detergent-soluble and -insoluble cell fractions indicated an increase of the G/F-actin ratio in sgk1 +/+ MCs but not in sgk1 −/− MCs upon FcεRI ligation, an observation reflecting actin depolymerization. In sgk1 +/+ MCs, FcεRI-induced actin depolymerization was abolished by 2-APB. The observed actin reorganization was confirmed by confocal laser microscopic analysis. Our observations uncover SGK1-dependent Ca 2+ entry in mast cells as a novel mechanism regulating actin cytoskeleton.
Photoisomerization of 1,2‐Dihydro‐1,2‐Azaborine: A Matrix Isolation Study
2012-09-28

Closing the loop: Photoisomerization of 1,2-dihydro-1,2-azaborine in neon, argon, or xenon at 4 K with UV light (253.7 nm) as part of a matrix isolation study led to the Dewar form as the only photoproduct, in agreement with the vibrational spectra computed for possible isomers of 1,2-dihydro-1,2-azaborine. Detailed facts of importance to specialist readers are published as "Supporting Information". Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Germa- and Stanna-closo-dodecaborate in Reaction with [PdCl2(Xantphos)]: P–C and B–H Bond Activation
2012-09-28

The two nucleophilic heteroborates germa-closo-dodecaborate and stanna-closo-dodecaborate show different reactivity toward the electrophile [PdCl2(Xantphos)]: In the case of the germanium ligand we found straightforward substitution of one chloride ligand and formation of a Ge–Pd bond. The tin ligand also reacts to give the substitution products [PdCl(SnB11H11)(Xantphos)]− and [Pd(SnB11H11)(Xantphos)], but the complexes exhibit a subsequent reaction under activation of a B–H and P–C bond. A dinuclear Pd(I)–Pd(I) complex featuring a P–B bond was characterized, and during its formation the evolution of benzene was detected. The respective germanium derivative does not show an activation reaction even at elevated temperature.
Observations of the post-shock break-out emission of SN 2011dh withXMM-Newton
2012-09-28

After the occurrence of the type cIIb SN 2011dh in the nearby spiral galaxy M 51 numerous observations were performed with different telescopes in various bands ranging from radio to gamma-rays. We analysed the XMM-Newton and Swift observations taken 3 to 30 days after the SN explosion to study the X-ray spectrum of SN 2011dh. We extracted spectra from the XMM-Newton observations, which took place ~7 and 11 days after the SN. In addition, we created integrated Swift/XRT spectra of 3 to 10 days and 11 to 30 days. The spectra are well fitted with a power-law spectrum absorbed with Galactic foreground absorption. In addition, we find a harder spectral component in the first XMM-Newton spectrum taken at t ~ 7 d. This component is also detected in the first Swift spectrum of t = 3 - 10 d. While the persistent power-law component can be explained as inverse Compton emission from radio synchrotron emitting electrons, the harder component is most likely bremsstrahlung emission from the shocked stellar wind. Therefore, the harder X-ray emission that fades away after t ~ 10 d can be interpreted as emission from the shocked circumstellar wind of SN 2011dh.
OSR1-sensitive small intestinal Na+ transport
2012-09-28

The oxidative stress responsive kinase 1 (OSR1) contributes to WNK (with no K)-dependent regulation of renal tubular salt transport, renal salt excretion, and blood pressure. Little is known, however, about a role of OSR1 in the regulation of intestinal salt transport. The present study thus explored whether OSR1 is expressed in intestinal tissue and whether small intestinal Na + /H + exchanger (NHE), small intestinal Na + -glucose cotransport (SGLT1), and/or colonic epithelium Na + channel (ENaC) differ between knockin mice carrying one allele of WNK-resistant OSR1 ( osr1 +/KI ) and wild-type mice ( osr1 +/+ ). OSR1 protein abundance was determined by Western blotting, cytosolic pH from BCECF fluorescence, NHE activity from Na + -dependent realkalinization following an ammonium pulse, SGLT1 activity from glucose-induced current, and colonic ENaC activity from amiloride-sensitive transepithelial current in Ussing chamber experiments. As a result, OSR1 protein was expressed in small intestine of both osr1 +/KI mice and osr1 +/+ mice. Daily fecal Na + , K + , and H 2 O excretion and jejunal SGLT1 activity were lower, whereas small intestinal NHE activity and colonic ENaC activity were higher in osr1 +/KI mice than in osr1 +/+ mice. NHE3 inhibitor S-3226 significantly reduced NHE activity in both genotypes but did not abrogate the difference between the genotypes. Plasma osmolarity, serum antidiuretic hormone, plasma aldosterone, and plasma corticosterone concentrations were similar in both genotypes. Small intestinal NHE3 and colonic α-ENaC protein abundance were not significantly different between genotypes, but colonic phospho-β-ENaC (ser633) was significantly higher in osr1 +/KI mice. In conclusion, OSR1 is expressed in intestine and partial WNK insensitivity of OSR1 increases intestinal NHE activity and colonic ENaC activity.
Shell colouration and antioxidant defence capacity in Theba pisana (O.F. Müller, 1774)
2012-09-28

Theba pisana (Müller, 1774), a Mediterranean snail, is known for its heat tolerance and its remarkable shell colour polymorphism ranging from pale white to darkly striped, although darker morphs are considered less vital in hot habitats due to presumably stronger absorption of radiation. Melanin, the black pigment of these snails, is known as an effective antioxidant, and elevated temperatures can increase oxidative stress. By analysing oxidative waste products via the ferrous oxidation xylenol orange (FOX) assay as a marker for the lipid peroxidation level, we aimed at investigating possible links between heat stress, colouration and antioxidant defence capacity in T. pisana. Although we found increasing levels of peroxidation products with increasing heat exposure duration, there was no difference in antioxidant defence capacity observable between different morphs of T. pisana. Hence the avoidance of lipid peroxidation as an environmentally relevant factor for the maintenance of melanistic morphs in strongly illuminated habitats can be considered improbable.
Pedagogic Corpora for Content and Language Integrated Learning. Insights from the BACKBONE Project
2012-09-29

BACKBONE is a European LLP/Languages project (1) (Jan 2009 - Feb 2011), whose overall objective is to provide foreign language teachers in CLIL settings with innovative language learning solutions. To achieve this goal, pedagogic corpora of spoken interviews are combined with corpus-related e-learning activities in blended learning scenarios. The seven BACKBONE corpora contain video interviews in English, German, French, Polish, Spanish and Turkish as well as in European manifestations of English as a Lingua Franca (ELF). The interviews have been transcribed and pedagogically annotated with regard to thematic and linguistic features; additional enrichment resources include ready-made language learning modules as well as suggestions and instructions for exploratory and communicative learning activities. The BACKBONE search interface provides free online access to the interviews and enrichment resources. It supports pedagogically motivated searches using thematic and linguistic categories as well as lexical searches with words and phrases. 24 CLIL-related pilot courses have been implemented and evaluated in secondary, higher and vocational education; they demonstrate how BACKBONE search results can be used to facilitate individual and collaborative learning in Moodle-based blended learning activities. A suite of pedagogic corpus tools covering transcription, annotation, management of enrichment resources and corpus search is available under a GNU General Public License. The customization and flexibility these tools offer enables teachers to cater to diverse language learning and teaching needs in CLIL contexts or in connection with lesser taught languages and varieties. To facilitate exploitation, the BACKBONE website serves as a ‘one-stop-shop’ for an ensemble of teacher support facilities including web support for the development and hosting of “guest” corpora and courses.
Molecule-Dependent Plasmonic Enhancement of Fluorescence and Raman Scattering near Realistic Nanostructures
2012-09-30

The enhancement of fluorescence and Raman scattering by plasmonic nanostructures is studied theoretically with special focus on the effects of the observed molecule's properties and the realistic geometry of the plasmonic nanostructure. Numerical experiments show that the enhancement factor may vary by many orders of magnitude depending on a fluorophore's transition rates or intrinsic quantum yield. For different molecules, boosting fluorescence enhancement means optimizing different factors, leading to a different ideal geometric and spectral configuration. This framework, coupled with powerful new simulation tools, will facilitate the design and characterization of fluorescence-enhancing plasmonic nanostructures as well as yield experimental access to the intrinsic properties of the molecules under study.
Tentative Reference Acts? ‘Recognitional Demonstratives’ as Means of Suggesting Mutual Knowledge – or Overriding a Lack of It
2012-09-30

In an explorative study on German oral corpus data we investigate recognitional use of proximal demonstratives as a means of explicit speaker-hearer interaction shaping the discourse structure. We show that recognitionals mark tentative reference acts in that speakers suggest - or pretend - mutual knowledge of the referent, at the same time appealing to the hearers to accept the reference. Hearers may tacitly or explicitly accept the referential act or deny it asking for clarification, in the latter case making speakers change the intended local discourse topic. On these grounds we argue against a differentiation between recognitional and indefinite demonstratives, subsuming both as kinds of recognitional use under ‘pretended’ cognitive proximity.
Methicillin resistance in Staphylococcus aureus requires glycosylated wall teichoic acids
2012-10-01

Staphylococcus aureus peptidoglycan (PG) is densely functionalized with anionic polymers called wall teichoic acids (WTAs). These polymers contain three tailoring modifications: d -alanylation, α- O -GlcNAcylation, and β- O -GlcNAcylation. Here we describe the discovery and biochemical characterization of a unique glycosyltransferase, TarS, that attaches β- O -GlcNAc (β- O - N -acetyl- d -glucosamine) residues to S. aureus WTAs. We report that methicillin resistant S. aureus (MRSA) is sensitized to β-lactams upon tarS deletion. Unlike strains completely lacking WTAs, which are also sensitive to β-lactams, Δ tarS strains have no growth or cell division defects. Because neither α- O -GlcNAc nor β- O -Glucose modifications can confer resistance, the resistance phenotype requires a highly specific chemical modification of the WTA backbone, β- O -GlcNAc residues. These data suggest β- O -GlcNAcylated WTAs scaffold factors required for MRSA resistance. The β- O -GlcNAc transferase identified here, TarS, is a unique target for antimicrobials that sensitize MRSA to β-lactams.
Probing the extent of the non-thermal emission from the Vela X region at TeV energies with H.E.S.S.
2012-10-01

Vela X is a region of extended radio emission in the western part of the Vela\\nconstellation: one of the nearest pulsar wind nebulae (PWNe), and associated\\nwith the energetic Vela pulsar (PSR B0833-45). Extended very-high-energy (VHE)\\n -ray emission (HESS ) was discovered using\\nthe H.E.S.S. experiment in 2004. The VHE -ray emission was found to be\\ncoincident with a region of X-ray emission discovered with above\\n1.5 keV (the so-called \\\\textit{Vela X cocoon}): a filamentary structure\\nextending southwest from the pulsar to the centre of Vela X. A deeper\\nobservation of the entire Vela X nebula region, also including larger offsets\\nfrom the cocoon, has been performed with H.E.S.S. This re-observation was\\ncarried out in order to probe the extent of the non-thermal emission from the\\nVela X region at TeV energies and to investigate its spectral properties. In\\norder to increase the sensitivity to the faint -ray emission from the\\nvery extended Vela X region, a multivariate analysis method combining three\\ncomplementary reconstruction techniques of Cherenkov-shower images is applied\\nfor the selection of -ray events. The analysis is performed with the\\nOn/Off background method, which estimates the background from separate\\nobservations pointing away from Vela X; towards regions free of -ray\\nsources but with comparable observation conditions. The -ray surface\\nbrightness over the large Vela X region reveals that the detection of\\nnon-thermal VHE -ray emission from the PWN HESS is statistically significant over a region of radius 1.2 around\\nthe position = 08 35 00 ,\\n = -45 36 \\n00 (J2000).\\n
Survival in Duchenne muscular dystrophy.
2012-10-01

our study provides survival data for a cohort of DMD patients in Germany stratified by year of death. Median survival was 24.0 years in patients confirmed by molecular testing. Ventilated patients had a median survival of 27 years. We consider this piece of information helpful in the medical care of DMD patients.
Deubiquitinase USP9x Confers Radioresistance through Stabilization of Mcl-1
2012-10-01

Myeloid cell leukemia sequence 1 (Mcl-1), an antiapoptotic member of the Bcl-2 family, is often overexpressed in tumor cells limiting the therapeutic success. Mcl-1 differs from other Bcl-2 members by its high turnover rate. Its expression level is tightly regulated by ubiquitylating and deubiquitylating enzymes. Interaction of Mcl-1 with certain Bcl-2 homology domain 3 (BH3)-only members of the Bcl-2 family can limit the access to Mcl-1 ubiquitin ligase E3 and stabilizes the antiapoptotic protein. In addition, the overexpression of the deubiquitinase ubiquitin-specific protease 9x (USP9x) can result in the accumulation of Mcl-1 by removing poly-ubiquitin chains from Mcl-1 preventing its proteasomal degradation. Analyzing radiation-induced apoptosis in Jurkat cells, we found that Mcl-1 was downregulated more efficiently in sensitive parental cells than in a resistant subclone. The decline of Mcl-1 correlated with cell death induction and clonogenic survival. Knockdown of BH3-only proteins Bim, Puma, and Noxa did not affect Mcl-1 level or radiation-induced apoptosis. However, ionizing radiation resulted in activation of USP9x and enhanced deubiquitination of Mcl-1 in the radioresistant cells preventing fast Mcl-1 degradation. USP9x knockdown enhanced radiation-induced decrease of Mcl-1 and sensitized the radioresistant cells to apoptosis induction, whereas USP9x knockdown alone did not change Mcl-1 level in unirradiated cells. Together, our results indicate that radiation-induced activation of USP9x inhibits Mcl-1 degradation and apoptosis resulting in increased radioresistance.
Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins. 3. Conformational Sampling and Explicit Solvents Model
2012-10-01

Fragment-based quantum chemical calculations are able to accurately calculate NMR chemical shifts even for very large molecules like proteins. But even with systematic optimization of the level of theory and basis sets as well as the use of implicit solvents models, some nuclei like polar protons and nitrogens suffer from poor predictions. Two properties of the real system, strongly influencing the experimental chemical shifts but almost always neglected in the calculations, will be discussed here in great detail: (1) conformational averaging and (2) interactions with first-shell solvent molecules. Classical molecular dynamics simulations in explicit water were carried out for obtaining a representative ensemble including the arrangement of neighboring solvent molecules, which was then subjected to quantum chemical calculations. We could demonstrate with the small test system N-methyl acetamide (NMA) that the calculated chemical shifts show immense variations of up to 6 ppm and 50 ppm for protons and nitrogens, respectively, depending on the snapshot taken from a classical molecular dynamics simulation. Applying the same approach to the HA2 domain of the influenza virus glycoprotein hemagglutinin, a 32-amino-acid-long polypeptide, and comparing averaged values to the experiment, chemical shifts of nonpolar protons and carbon atoms in proteins were calculated with unprecedented accuracy. Additionally, the mean absolute error could be reduced by a factor of 2.43 for polar protons, and reasonable correlations were obtained for nitrogen and carbonyl carbon in contrast to all other studies published so far.