julilili42/papers huggingface dataset:
Quantum Galvanometer by Interfacing a Vibrating Nanowire and Cold Atoms
2011-11-23

We evaluate the coupling of a Bose-Einstein condensate (BEC) of ultracold, paramagnetic atoms to the magnetic field of the current in a mechanically vibrating carbon nanotube within the frame of a full quantum theory. We find that the interaction is strong enough to sense quantum features of the nanowire current noise spectrum by means of hyperfine-state-selective atom counting. Such a nondestructive measurement of the electric current via its magnetic field corresponds to the classical galvanometer scheme, extended to the quantum regime of charge transport. The calculated high sensitivity of the interaction in the nanowire-BEC hybrid systems opens up the possibility of quantum control, which may be further extended to include other relevant degrees of freedom.
Piriformospora indica —a mutualistic basidiomycete with an exceptionally large plant host range
2011-11-24

SUMMARY Piriformospora indica is a basidiomycete of the order Sebacinales, representing a model for the study of mutualistic symbiosis and, beyond that, the plant immune system. The fungus colonizes the roots of a wide range of vascular plants, increasing their growth, seed yield and adaptation to abiotic and biotic stresses. The fungal colonization of roots begins with a biotrophic growth phase, in which living cells are colonized, and continues with a cell death‐dependent phase, in which root cells are actively killed by the fungus. The complexity of sebacinalean symbiosis is further enhanced by the presence of endocellular bacteria which may represent significant determinants for a successful outcome of the symbioses. Molecular ecological analyses have revealed an exceptional relevance of sebacinoid fungi in natural ecosystems worldwide. This natural competence could be rooted in their phenotypic adaptability, which, for instance, allows P. indica to grow readily on various synthetic media and to colonize distinct hosts. In molecular and genetic studies, P. indica 's mutualistic colonization strategy has been partly unravelled, showing that the jasmonate pathway is exploited for immune suppression and successful development in roots. Research on P. indica supports efforts to make the bioprotective potential of the fungus accessible for agricultural plant production. The decoding of P. indica's genome has revealed its potential for application as bioagent and for targeted improvement of crop plants in biotechnology‐based approaches.
Cleavage of Annexin A1 by ADAM10 during Secondary Necrosis Generates a Monocytic “Find-Me” Signal
2011-11-24

Abstract Annexin A1 is an intracellular calcium/phospholipid-binding protein that is involved in membrane organization and the regulation of the immune system. It has been attributed an anti-inflammatory role at various control levels, and recently we could show that annexin A1 externalization during secondary necrosis provides an important fail-safe mechanism counteracting inflammatory responses when the timely clearance of apoptotic cells has failed. As such, annexin A1 promotes the engulfment of dying cells and dampens the postphagocytic production of proinflammatory cytokines. In our current follow-up study, we report that exposure of annexin A1 during secondary necrosis coincided with proteolytic processing within its unique N-terminal domain by ADAM10. Most importantly, we demonstrate that the released peptide and culture supernatants of secondary necrotic, annexin A1-externalizing cells induced chemoattraction of monocytes, which was clearly reduced in annexin A1- or ADAM10-knockdown cells. Thus, altogether our findings indicate that annexin A1 externalization and its proteolytic processing into a chemotactic peptide represent final events during apoptosis, which after the transition to secondary necrosis contribute to the recruitment of monocytes and the prevention of inflammation.
TDP-43 regulates global translational yield by splicing of exon junction complex component SKAR
2011-11-25

TDP-43 is linked to neurodegenerative diseases including frontotemporal dementia and amyotrophic lateral sclerosis. Mostly localized in the nucleus, TDP-43 acts in conjunction with other ribonucleoproteins as a splicing co-factor. Several RNA targets of TDP-43 have been identified so far, but its role(s) in pathogenesis remains unclear. Using Affymetrix exon arrays, we have screened for the first time for splicing events upon TDP-43 knockdown. We found alternative splicing of the ribosomal S6 kinase 1 (S6K1) Aly/REF-like target (SKAR) upon TDP-43 knockdown in non-neuronal and neuronal cell lines. Alternative SKAR splicing depended on the first RNA recognition motif (RRM1) of TDP-43 and on 5'-GA-3' and 5'-UG-3' repeats within the SKAR pre-mRNA. SKAR is a component of the exon junction complex, which recruits S6K1, thereby facilitating the pioneer round of translation and promoting cell growth. Indeed, we found that expression of the alternatively spliced SKAR enhanced S6K1-dependent signaling pathways and the translational yield of a splice-dependent reporter. Consistent with this, TDP-43 knockdown also increased translational yield and significantly increased cell size. This indicates a novel mechanism of deregulated translational control upon TDP-43 deficiency, which might contribute to pathogenesis of the protein aggregation diseases frontotemporal dementia and amyotrophic lateral sclerosis.
Significant impact of different oxygen breathing conditions on noninvasive in vivo tumor-hypoxia imaging using [18F]-fluoro-azomycinarabino-furanoside ([18F]FAZA)
2011-11-25

Abstract Background [ 18 F]FAZA is a PET biomarker with great potential for imaging tumor hypoxia. Aim of our study was to compare [ 18 F]FAZA uptake in mice with subcutaneous exogenous CT26 colon carcinomas and endogenous polyoma middle-T (PyV-mT) mammary carcinomas and to analyze the influence of different breathing protocols in CT26 colon carcinomas as well as the reversibility or irreversibility of [ 18 F]FAZA uptake. Methods We injected subcutaneous CT26 colon carcinoma or polyomavirus middle-T (PyV-mT) mammary carcinoma-bearing mice intravenously with 18 F-FAZA and performed PET scans 1-3 h post injection ( p.i. ). To analyze the impact of oxygen supply in CT26 carcinomas we used three different breathing protocols: (P0) air; (P1) 100% oxygen 1 h prior injection until 3 h p.i. ; (P2) 100% oxygen breathing starting 2 min prior tracer injection until 1 h p.i. and during the PET scans; mice were breathing air between the 2 h and 3 h 10 min static scans. Normalized PET images were analyzed by using defined regions of interest. Finally, some mice were dissected for pimonidazole immunohistochemistry. Results There was no difference in 18 F-FAZA uptake 1-3 h p.i. between the two carcinoma types (CT26: 1.58 ± 0.45%ID/cc; PyV-mT: 1.47 ± 0.89%ID/cc, 1 h p.i. , tumor size &lt; 0.5 cm 3 ). We measured a significant tracer clearance, which was more pronounced in muscle tissue (P0). The [ 18 F]FAZA tumor-to-muscle-ratios in CT26 colon carcinoma-bearing mice 2 h and 3 h, but not 1 h p.i. were significantly higher when the mice breathed air (P0: 3.56 ± 0.55, 3 h) compared to the oxygen breathing protocols (P1: 2.45 ± 0.58; P2: 2.77 ± 0.42, 3 h). Surprisingly, the breathing protocols P1 and P2 showed no significant differences in T/M ratios, thus indicating that the crucial [ 18 F]FAZA uptake phase is during the first hour after [ 18 F]FAZA injection. Importantly, the muscle clearance was not affected by the different oxygen breathing conditions while the tumor clearance was lower when mice were breathing air. Conclusion Exogenous CT26 colon carcinomas and endogenous polyoma middle-T (PyV-mT) mammary carcinomas showed no differences in [ 18 F]FAZA uptake 1-3 h p.i. Our analysis using various breathing protocols with air (P0) and with pure oxygen (P1, P2) clearly indicate that [ 18 F]FAZA is an appropriate PET biomarker for in vivo analysis of hypoxia revealing an enhanced tracer uptake in tumors with reduced oxygen supply. [ 18 F]FAZA uptake was independent of tumor-type.
Suzaku Observation of the Unidentified Very High Energy Gamma-Ray Source HESS J1702−420
2011-11-25

Abstract A deep X-ray observation of the unidentified very high energy (VHE) gamma-ray source HESS J1702 420, for the first time, was carried out by Suzaku. No bright sources were detected in the XIS field of view (FOV), except for two faint point-like sources. The two sources, however, are considered not to be related to HESS J1702 420, because their fluxes in the 2–10 keV band ( 10 erg s cm ) are 3 orders of magnitude smaller than the VHE gamma-ray flux in the 1–10 TeV band ( 2.7 10 erg s cm in the 2–10 keV band for an assumed power-law spectrum of $\\Gamma = F_{\\rm TeV}/F_{\\rm X} - \\ \\mu \\ \\mu -$ 420 and a significant fraction of the VHE gamma-rays may originate from protons.
Epidemiology of Major Eye Diseases Leading to Blindness in Europe: A Literature Review
2011-11-26

The objective of this work was to study the epidemiology of major eye diseases leading to blindness in Europe through a systematic literature review. The literature search was performed using the Medline database (PubMed), with MeSH and free text search terms. Inclusion criteria for the studies were: (a) performed on a healthy population of Caucasian origin aged between 50 and 75 years; (b) diagnosed by ophthalmological examination in accordance with the &lt;i&gt;International Classification of Diseases 10&lt;/i&gt;; (c) contained a detailed description of the sampling and diagnostic procedures and data resources; (d) sample size &gt;500, and (e) published between 1990 and 2008. The results of 57 studies on the prevalence and incidence of age-related macular degeneration, diabetic retinopathy and glaucoma are reported, providing an up-to-date and comprehensive overview of these diseases in Europe from an epidemiological perspective.
Retinal degeneration modulates intracellular localization of CDC42 in photoreceptors
2011-11-26

Retinal degeneration induces the accumulation of CDC42 in the perinuclear region of photoreceptors. In contrast to RAC1, however, lack of CDC42 does not affect the progression of degeneration. CDC42 is also dispensable for normal morphology and function of adult rod photoreceptor cells. RECEIVED: May 25, 2011 ACCEPTED: November 10, 2011.
Khuff Sequence 5 (KS5), Oman Mountains: Lateral Facies and Sequence Variability – a Record of Differential Subsidence?
2011-11-28

This study focuses on the sequence stratigraphy and 3-D modelling of the Khuff Sequence 5 (KS5) in the Oman Mountains (Al Jabal al-Akhdar), Sultanate of Oman. The Lower Khuff sequences (KS5 and KS6) are at this stage poorly understood, since most of the reservoir units are located in the Upper and Middle Khuff sequences (KS1 to KS4). Previous studies (Koehrer et al., 2010, 2011) revealed layer-cake geometries of grainstone bodies in the Middle and Upper Khuff sequences (KS1 to KS4) on outcrop to exploration scales. The key question of this study was if the layer-cake geometries continue to be present or are different in the KS5.
Khuff Sequence KS4: High-resolution Anatomy of a Middle Khuff Grainstone Package, Oman Mountains, Sultanate of Oman
2011-11-28

This outcrop study is part of a larger-scale project on the Saiq Formation in the Oman Mountains (outcrop analog of Khuff Formation), and focussed on the small-scale heterogeneities of the lower part of Khuff Sequence 4 (KS4). This interval is dominated by massive grainstones that at first glance seem extremely homogenous with distinct trough cross-bedding detectable in spite of strong dolomitization. Serrated gamma-ray patterns made small-scale cycle interpretations difficult. Therefore a very detailed facies and sequence analysis was necessary to decipher the vertical microfacies make-up of the grainstones and link it with potential pore types.
Khuff Sequence KS6: Paleorelief-influenced Facies and Sequence Patterns in the Lower Khuff Formation, Sultanate of Oman
2011-11-28

This outcrop analog study of Lower Khuff Sequence KS6 (Saiq Formation) aims to capture lateral reservoir facies distribution during the initial phase of basin-fill. The Hercynian tectonic event triggered the erosion of Cambrian to Carboniferous strata in Oman and formed the topography of the Sub-Khuff Unconformity. When the Neo-Tethys Ocean flooded the Arabian Shield clastic sediments, the so-called "Basal Khuff Clastics" became preferentially deposited in possible paleo-lows. One main objective of this study was to unravel the effect of this paleo-relief on reservoir facies distribution within the overlying sediments.
Na+-d-glucose Cotransporter SGLT1 is Pivotal for Intestinal Glucose Absorption and Glucose-Dependent Incretin Secretion
2011-11-29

To clarify the physiological role of Na+-d-glucose cotransporter SGLT1 in small intestine and kidney, Sglt1−/− mice were generated and characterized phenotypically. After gavage of d-glucose, small intestinal glucose absorption across the brush-border membrane (BBM) via SGLT1 and GLUT2 were analyzed. Glucose-induced secretion of insulinotropic hormone (GIP) and glucagon-like peptide 1 (GLP-1) in wild-type and Sglt1−/− mice were compared. The impact of SGLT1 on renal glucose handling was investigated by micropuncture studies. It was observed that Sglt1−/− mice developed a glucose-galactose malabsorption syndrome but thrive normally when fed a glucose-galactose–free diet. In wild-type mice, passage of d-glucose across the intestinal BBM was predominantly mediated by SGLT1, independent the glucose load. High glucose concentrations increased the amounts of SGLT1 and GLUT2 in the BBM, and SGLT1 was required for upregulation of GLUT2. SGLT1 was located in luminal membranes of cells immunopositive for GIP and GLP-1, and Sglt1−/− mice exhibited reduced glucose-triggered GIP and GLP-1 levels. In the kidney, SGLT1 reabsorbed ∼3% of the filtered glucose under normoglycemic conditions. The data indicate that SGLT1 is 1) pivotal for intestinal mass absorption of d-glucose, 2) triggers the glucose-induced secretion of GIP and GLP-1, and 3) triggers the upregulation of GLUT2.
Molecular outcomes of neuromyelitis optica (NMO)-IgG binding to aquaporin-4 in astrocytes
2011-11-29

The astrocytic aquaporin-4 (AQP4) water channel is the target of pathogenic antibodies in a spectrum of relapsing autoimmune inflammatory central nervous system disorders of varying severity that is unified by detection of the serum biomarker neuromyelitis optica (NMO)-IgG. Neuromyelitis optica is the most severe of these disorders. The two major AQP4 isoforms, M1 and M23, have identical extracellular residues. This report identifies two novel properties of NMO-IgG as determinants of pathogenicity. First, the binding of NMO-IgG to the ectodomain of astrocytic AQP4 has isoform-specific outcomes. M1 is completely internalized, but M23 resists internalization and is aggregated into larger-order orthogonal arrays of particles that activate complement more effectively than M1 when bound by NMO-IgG. Second, NMO-IgG binding to either isoform impairs water flux directly, independently of antigen down-regulation. We identified, in nondestructive central nervous system lesions of two NMO patients, two previously unappreciated histopathological correlates supporting the clinical relevance of our in vitro findings: ( i ) reactive astrocytes with persistent foci of surface AQP4 and ( ii ) vacuolation in adjacent myelin consistent with edema. The multiple molecular outcomes identified as a consequence of NMO-IgG interaction with AQP4 plausibly account for the diverse pathological features of NMO: edema, inflammation, demyelination, and necrosis. Differences in the nature and anatomical distribution of NMO lesions, and in the clinical and imaging manifestations of disease documented in pediatric and adult patients, may be influenced by regional and maturational differences in the ratio of M1 to M23 proteins in astrocytic membranes.
Critical Review of Low-Density Polyethylene’s Partitioning and Diffusion Coefficients for Trace Organic Contaminants and Implications for Its Use As a Passive Sampler
2011-11-29

Polyethylene (PE)-water equilibrium partitioning constants, K(PEw), were reviewed for trace hydrophobic organic contaminants (HOCs). Relative standard deviations were <30% for phenanthrene, anthracene, fluoranthene, and pyrene implying excellent reproducibility of K(PEw) across laboratories and PE sources. Averaged K(PEw) values of various HOCs were best correlated with aqueous solubility, logC(w)(sat)(L): logK(PEw) = -0.99(±0.029)logC(w)(sat)(L) + 2.39(±0.096) (r(2) = 0.92, SE = 0.35, n = 100). For 80% of analytes, this equation predicted logK(PEw) within a factor of 2. A first-order estimation of K(PEw) can be obtained assuming constant solubility of the compounds in the PE, such that the variation in C(w)(sat)(L) determines the differences in K(PEw). For PE samplers, K(PEw) values do not change with the thickness of the PE sampler. The influence of temperature on K(PEw) seems dominated by solubility-changes of the compound in water, not in PE. The effect of salt is rather well understood, using a Schetschenow-style approach. The air-PE partitioning constant, K(PEa), can be approximated as the ratio of K(PEw)/K(aw) (the air-water partitioning constant). A critical review of diffusivities in PE, D(PE), suggests that best results are obtained when using the film-stacking method. A good correlation is then found between D(PE) and molar volume, V(m) (Ǻ(3)/mol): logD(PE) (m(2)/s) = 0.0145(±0.001)V(m) + 10.1(±0.20) (r(2) = 0.76, SE = 0.24, n = 74).
Visceral Leishmaniasis in the Indian Subcontinent: Modelling Epidemiology and Control
2011-11-29

Treatment of Kala-azar is necessary on the level of the individual patient but may have little effect on transmission of parasites. In contrast, vector control or exposure prophylaxis has the potential to efficiently reduce transmission of parasites. Based on these findings, control of VL should pay more attention to vector-related interventions. Cases of PKDL may appear after years and may initiate a new outbreak of disease; interventions should therefore be long enough, combined with an active case detection and include effective treatment.
Homologues and Bioengineered Derivatives of LtnJ Vary in Ability to Form d -Alanine in the Lantibiotic Lacticin 3147
2011-11-29

ABSTRACT Ltnα and Ltnβ are individual components of the two-peptide lantibiotic lacticin 3147 and are unusual in that, although ribosomally synthesized, they contain d -amino acids. These result from the dehydration of l -serine to dehydroalanine by LtnM and subsequent stereospecific hydrogenation to d -alanine by LtnJ. Homologues of LtnJ are rare but have been identified in silico in Staphylococcus aureus C55 (SacJ), Pediococcus pentosaceus FBB61 (PenN), and Nostoc punctiforme PCC73102 (NpnJ, previously called NpunJ [P. D. Cotter et al., Proc. Natl. Acad. Sci. U. S. A. 102:18584–18589, 2005]). Here, the ability of these enzymes to catalyze d -alanine formation in the lacticin 3147 system was assessed through heterologous enzyme production in a Δ ltnJ mutant. PenN successfully incorporated d -alanines in both peptides, and SacJ modified Ltnα only, while NpnJ was unable to modify either peptide. Site-directed mutagenesis was also employed to identify residues of key importance in LtnJ. The most surprising outcome from these investigations was the generation of peptides by specific LtnJ mutants which exhibited less bioactivity than those generated by the Δ ltnJ strain. We have established that the reduced activity of these peptides is due to the inability of the associated LtnJ enzymes to generate d -alanine residues in a stereospecific manner, resulting in the presence of both d - and l -alanines at the relevant locations in the lacticin 3147 peptides.
The Nubian Complex of Dhofar, Oman: An African Middle Stone Age Industry in Southern Arabia
2011-11-30

Despite the numerous studies proposing early human population expansions from Africa into Arabia during the Late Pleistocene, no archaeological sites have yet been discovered in Arabia that resemble a specific African industry, which would indicate demographic exchange across the Red Sea. Here we report the discovery of a buried site and more than 100 new surface scatters in the Dhofar region of Oman belonging to a regionally-specific African lithic industry--the late Nubian Complex--known previously only from the northeast and Horn of Africa during Marine Isotope Stage 5, ∼128,000 to 74,000 years ago. Two optically stimulated luminescence age estimates from the open-air site of Aybut Al Auwal in Oman place the Arabian Nubian Complex at ∼106,000 years ago, providing archaeological evidence for the presence of a distinct northeast African Middle Stone Age technocomplex in southern Arabia sometime in the first half of Marine Isotope Stage 5.
Viscosity and diffusion: crowding and salt effects in protein solutions
2011-11-30

We report on a joint experimental-theoretical study of collective diffusion\\nin, and static shear viscosity of solutions of bovine serum albumin (BSA)\\nproteins, focusing on the dependence on protein and salt concentration. Data\\nobtained from dynamic light scattering and rheometric measurements are compared\\nto theoretical calculations based on an analytically treatable spheroid model\\nof BSA with isotropic screened Coulomb plus hard-sphere interactions. The only\\ninput to the dynamics calculations is the static structure factor obtained from\\na consistent theoretical fit to a concentration series of small-angle X-ray\\nscattering (SAXS) data. This fit is based on an integral equation scheme that\\ncombines high accuracy with low computational cost. All experimentally probed\\ndynamic and static properties are reproduced theoretically with an at least\\nsemi-quantitative accuracy. For lower protein concentration and low salinity,\\nboth theory and experiment show a maximum in the reduced viscosity, caused by\\nthe electrostatic repulsion of proteins. The validity range of a generalized\\nStokes-Einstein (GSE) relation connecting viscosity, collective diffusion\\ncoefficient, and osmotic compressibility, proposed by Kholodenko and Douglas\\n[PRE 51, 1081 (1995)] is examined. Significant violation of the GSE relation is\\nfound, both in experimental data and in theoretical models, in semi-dilute\\nsystems at physiological salinity, and under low-salt conditions for arbitrary\\nprotein concentrations.\\n
Evolutionary Relationships of Microbial Aromatic Prenyltransferases
2011-11-30

The linkage of isoprenoid and aromatic moieties, catalyzed by aromatic prenyltransferases (PTases), leads to an impressive diversity of primary and secondary metabolites, including important pharmaceuticals and toxins. A few years ago, a hydroxynaphthalene PTase, NphB, featuring a novel ten-stranded β-barrel fold was identified in Streptomyces sp. strain CL190. This fold, termed the PT-barrel, is formed of five tandem ααββ structural repeats and remained exclusive to the NphB family until its recent discovery in the DMATS family of indole PTases. Members of these two families exist only in fungi and bacteria, and all of them appear to catalyze the prenylation of aromatic substrates involved in secondary metabolism. Sequence comparisons using PSI-BLAST do not yield matches between these two families, suggesting that they may have converged upon the same fold independently. However, we now provide evidence for a common ancestry for the NphB and DMATS families of PTases. We also identify sequence repeats that coincide with the structural repeats in proteins belonging to these two families. Therefore we propose that the PT-barrel arose by amplification of an ancestral ααββ module. In view of their homology and their similarities in structure and function, we propose to group the NphB and DMATS families together into a single superfamily, the PT-barrel superfamily.