julilili42/papers huggingface dataset:
Financial Market Spillovers Around the Globe
2011-06-10

Financial market spillovers around the globeThis paper investigates the transmission of return and volatility spillovers around the globe. It draws on index futures of three representative indices, namely the Dow Jones Euro Stoxx 50, the S&amp;P 500 and the Nikkei 225. Devolatised returns and realised volatilities are modeled separately using a structural vector autoregressive model, thereby accounting for the particular sequential time structure of the trading venues. Within this framework, we test hypotheses in the spirit of Granger causality tests, investigate the short-run dynamics in the three markets using impulse response functions, and identify leadership effects through variance decomposition. Our key results are as follows. We find weak and shortlived return spillovers, in particular from the USA to Japan. Volatility spillovers are more pronounced and persistent. The information from the home market is most important for both returns and volatilities; the contribution from foreign markets is less pronounced in the case of returns than in the case of volatility. Possible gains in terms of forecasting precision when applying our modelling strategy are illustrated by a forecast evaluation.
Tumor Biology Influences the Prognosis of Nephroblastoma Patients With Primary Pulmonary Metastases
2011-06-11

The prognosis of children with primary Wilms' tumor lung metastases mainly depends on the biology of primary tumors and metastases and is excellent with adequate treatment. Pulmonary metastasectomy is indicated if complete remission can be achieved to avoid lung irradiation. In the future a standardized local approach to nonresponding lung metastases (metastasectomy, irradiation, or both) will have to be prospectively evaluated regarding outcome, acute toxicity, and late effects.
MGV: a generic graph viewer for comparative omics data
2011-06-11

Abstract Motivation: High-throughput transcriptomics, proteomics and metabolomics methods have revolutionized our knowledge of biological systems. To gain knowledge from comparative omics studies, strong data integration and visualization features are required. Knowledge gained from these studies is often available in the form of graphs, and their visualization is especially useful in a wide range of systems biology topics, including pathway analysis, interaction networks or gene models. Especially, it is necessary to compare biological models with measured data. This allows the identification of new models and new insights into existing ones. Results: We present MGV, a versatile generic graph viewer for multiomics data. MGV is integrated into Mayday (Battke et al., 2010). It extends Mayday's visual analytics capabilities by integrating a wide range of biological models, high-throughput data and meta information to display enriched graphs that combine data and models. A wide range of tools is available for visualization of nodes, data-aware graph layout as well as automatic and manual aggregation and refinement of the data. We show the usefulness of MGV applied to several problems, including differential expression of alternative transcripts, transcription factor interaction, cross-study clustering comparison and integration of transcriptomics and metabolomics data for pathway analysis. Availability: MGV is a open-source software implemented in Java and freely available as a part of Mayday at www.microarray-analysis.org/mayday. Contact: symons@informatik.uni-tuebingen.de Supplementary information: Supplementary data are available at Bioinformatics online.
Treatment of recurrent vaginal eversion after previous Le Fort colpocleisis
2011-06-12

An 89-year-old woman was referred to the Department of Obstetrics and Gynecology, University Hospital Tuebingen, Tuebingen, Germany, with extreme discomfort and voiding problems due to a large mass protruding through the introitus, which had significantly limited her physical and social activities. She had undergone vaginal hysterectomy in 1966, followed by 2 operations for prolapse: an anterior and posterior colporrhaphy with perineorrhaphy and sacrospinous vaginal vault suspension in 2003; and a modified Le Fort colpocleisis in 2004, which was performed using the technique described by LeFort [1] but without a perineorrhaphy. Recurrent vaginal eversion following the second operation was treated unsuccessfully via multiple pessaries. The women herself applied topical estrogens for 3 months. Clinical examination revealed a vault prolapse at stage IV of the International Continence Society pelvic organ prolapse quantification system (Fig. 1), with a loss of all 3 levels of support, nonfunctioning pelvic floor muscles, and 320 mL of postvoid residual urine at catheterization. Recurrent vaginal eversion after previous prolapse surgeries, including Le Fort colpocleisis. It was agreed that the woman would undergo further surgery to repair the vaginal eversion. She was placed in the lithotomy position and prepared aseptically. The bladder was emptied using a urethral catheter, and a circumscribing incision was made through the vaginal mucosa. Anteriorly, the incision was made approximately 3 cm from the urethral meatus at the level of the urethrovesical junction. Posteriorly, the incision ran along the perineum 2 cm below the hymen and laterally at the level of the hymenal ring. Colpectomy was performed via sharp and blunt dissection of all 4 quadrants of the vagina. The surfaces of the denuded anterior and posterior vaginal prolapse were connected using horizontal rows of interrupted sutures with nonresorbable material (Ethibond 2–0; Johnson & Johnson, Norderstedt, Germany) and the denuded vaginal prolapse was simultaneously repositioned into the pelvis. Concurrent levator myorrhaphy and perineorrhaphy were performed using resorbable sutures (Vicryl 0; Johnson & Johnson, Norderstedt, Germany). Postoperative urethrocystoscopy revealed no damage to the bladder, urethra, or urethrovesical junction. To enable a suburethral sling to be inserted in the event of postoperative stress urinary incontinence, special care was taken not to involve the area beneath the urethra. Following surgery, the vagina was reduced to a length of 2 cm. On the first postoperative day, the catheter was removed and the woman was able to empty her bladder. She was discharged on the third postoperative day in a stable medical condition. Five years after the surgery, prolapse had not recurred and the 94-year-old woman was continent and in good health. The present case highlights an additional option for individualized treatment of vaginal eversion. The authors have no conflicts of interest.
Nanoscale Order and Structure in Organic Materials: Diindenoperylene on Gold as a Model System
2011-06-13

Device performances in organic electronics are strongly influenced by the structure and morphology of the active layer. We investigated the thin film of diindenoperylene, a promising candidate for electronics, deposited on polycrystalline gold, and Au(100) and Au(111) single crystals using X-ray absorption and photoemission together with atomic force microscopy. The results show the influence of the substrate morphology, in this case via the roughness, on the structure of the obtained films. This affects the intermolecular interactions as evidenced by different details in X-ray absorption comparing the three cases. A further source of influence is the surface lattice geometry of the substrate that affects the shape of the islands. This behavior mimics very closely the behavior of atoms on metal growth, showing a general pattern in matter organization in the nanoscale regime.
Pontine Reference Frames for the Sensory Guidance of Movement
2011-06-13

The pontine nuclei (PN) are the major intermediary elements in the corticopontocerebellar pathway. Here we asked if the PN may help to adapt the spatial reference frames used by cerebrocortical neurons involved in the sensory guidance of movement to a format potentially more appropriate for the cerebellum. To this end, we studied movement-related neurons in the dorsal PN (DPN) of monkeys, most probably projecting to the cerebellum, executing fixed vector saccades or, alternatively, fixed vector hand reaches from different starting positions. The 83 task-related neurons considered fired movement-related bursts before saccades (saccade-related) or before hand movements (hand movement-related). About 40% of the SR neurons were "oculocentric," whereas the others were modulated by eye starting position. A third of the HMR neurons encoded hand reaches in hand-centered coordinates, whereas the remainder exhibited different types of dependencies on starting positions, reminiscent in general of cortical responses. All in all, pontine reference frames for the sensory guidance of movement seem to be very similar to those in cortex. Specifically, the frequency of orbital position gain fields of SR neurons is identical in the DPN and in one of their major cortical inputs, lateral intraparietal area (LIP).
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
2011-06-14

Bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs. To find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide variety of microbes. However, rapidly and reliably pinpointing all the potential gene clusters for secondary metabolites in dozens of newly sequenced genomes has been extremely challenging, due to their biochemical heterogeneity, the presence of unknown enzymes and the dispersed nature of the necessary specialized bioinformatics tools and resources. Here, we present antiSMASH (antibiotics & Secondary Metabolite Analysis Shell), the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides, aminocoumarins, indolocarbazoles, lantibiotics, bacteriocins, nucleosides, beta-lactams, butyrolactones, siderophores, melanins and others). It aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view. antiSMASH is available at http://antismash.secondarymetabolites.org.
Proceedings of the 8th ACM international conference on Autonomic computing
2011-06-14

On behalf of the steering committee and the program committee, it is our great pleasure to welcome you to the 8th ACM International Conference on Computing -- ICAC 2011. We are pleased to hold this established conference at Karlsruhe, Germany. About ten years ago, the research area of autonomic computing has been initiated by Paul Horn, IBM's senior vice president of research. This conference series is demonstrating the impressive and lasting impact of the Computing Initiative. We are delighted that one of the authors of the seminal paper on Jeff Kephart, will reflect in his keynote on Autonomic Computing: The First Decade. Independently, another research initiative evolved in Germany started by a joint position paper of the German Informatics Society (GI) and the Information Technology Society (ITG) on Computing, which is driven by similar insights as Computing. The sixth and final year of the resulting priority research program of the German Research Foundation (DFG) has been a motivation for having ICAC 2011 in Germany. We are pleased that Christian Muller-Schloer, one of the founders of Organic Computing will share his thoughts on the future of this research area in his keynote on Computing: Quo Vadis? Both keynote talks will inspire thoughts on future directions of these fascinating research initiatives which have found widespread use in a broad range of application areas. We are looking forward to an attractive conference program: Out of 89 submissions, 20 papers were accepted as full papers and 7 as short papers. We also welcome the participants of the five workshops that complement the main conference with topics from economics (ACE), bio-inspired methods in distributed system (BADS), feedback control of computer networks (FeBID), an eenergy market challenge (IEEMC), and organic computing (OC).
Potential role of probiotic bacteria in the treatment and prevention of localised candidosis
2011-06-14

Summary The extensive use of immunosuppressive therapies in recent years has increased the number of patients prone to or actually suffering from localised candidosis. As Candida species gain increasing resistance towards common antifungal drugs, new strategies are needed to prevent and treat infections caused by these pathogens. Probiotic bacteria have been in vogue in the past two decades. More and more dairy products containing such organisms offer promising potential beneficial effects on human health and well‐being. Because of the ability of probiotic bacteria to inhibit the growth of pathogens and to modulate human immune responses, these bacteria could provide new possibilities in antifungal therapy. We summarise the recent findings concerning the usefulness of probiotic treatment in localised candidosis, as well as discussing possible risks of probiotic treatment and highlighting the molecular mechanisms that are believed to contribute to probiotic effects.
Influence of Calcium-Induced Aggregation on the Sensitivity of Aminobis(methylenephosphonate)-Containing Potential MRI Contrast Agents
2011-06-14

A novel class of 1,4,7,10-tetraazacyclododecane-1,4,7-tris(methylenecarboxylic) acid (DO3A)-based lanthanide complexes with relaxometric response to Ca(2+) was synthesized, and their physicochemical properties were investigated. Four macrocyclic ligands containing an alkyl-aminobis(methylenephosphonate) side chain for Ca(2+)-chelation have been studied (alkyl is propyl, butyl, pentyl, and hexyl for L(1), L(2), L(3), and L(4), respectively). Upon addition of Ca(2+), the r(1) relaxivity of their Gd(3+) complexes decreased up to 61% of the initial value for the best compounds GdL(3) and GdL(4). The relaxivity of the complexes was concentration dependent (it decreases with increasing concentration). Diffusion NMR studies on the Y(3+) analogues evidenced the formation of agglomerates at higher concentrations; the aggregation becomes even more important in the presence of Ca(2+). (31)P NMR experiments on EuL(1) and EuL(4) indicated the coordination of a phosphonate to the Ln(3+) for the ligand with a propyl chain, while phosphonate coordination was not observed for the analogue bearing a hexyl linker. Potentiometric titrations yielded protonation constants of the Gd(3+) complexes. log K(H1) values for all complexes lie between 6.12 and 7.11 whereas log K(H2) values are between 4.61 and 5.87. Luminescence emission spectra recorded on the Eu(3+) complexes confirmed the coordination of a phosphonate group to the Ln(3+) center in EuL(1). Luminescence lifetime measurements showed that Ca-induced agglomeration reduces the hydration number which is the main cause for the change in r(1). Variable temperature (17)O NMR experiments evidenced high water exchange rates on GdL(1), GdL(2), and GdL(3) comparable to that of the aqua ion.
Ex vivoimaging of injured arteries in rabbits using fluorescence-labelled glycoprotein VI-Fc
2011-06-14

Vascular lesion formation and collagen presentation are key events leading to the development of vulnerable plaques. Glycoprotein VI (GPVI) significantly contributes to plaque-associated collagen binding and thrombus formation. The aim of this study was to image endothelial injury using fluorescence-labelled GPVI-Fc (Fc, fragment crystallized), a soluble form of GPVI that was generated by cloning and fusing GPVI to an Fc-domain, in an ex-vivo rabbit model. This study serves as a proof-of-principle study to demonstrate that GPVI-Fc is a useful tool for detecting endothelial damage. The carotid and femoral arteries and the aorta abdominalis were isolated from rabbits and perfused with phosphate buffered saline (PBS) to remove all blood, and a catheter was placed into the vessels in situ. Endothelial damage was achieved by pulling an inflated balloon approximately 1 inch through the vessels, while control vessels were not balloon-treated. After balloon deflation, the catheter was removed. Fluorescence-labelled GPVI-Fc (50 μg/mL) was injected into the injured and control intact vessels, and the opened vessels were sealed by clamps. After incubation, the vessels were rinsed with PBS, and optical imaging was performed to measure GPVI-Fc binding to injured endothelium. The optical data corresponding to the mean detected optical signal of the regions of interest were corrected by subtracting the mean data of the background fluorescence (arbitrary units). After denudation, fluorescence was enhanced in injured femoral and carotid arteries when compared to intact femoral (41.1 ± 17.5 vs. 14.6 ± 6.5; P = 0.021) and carotid (30.2 ± 7.6 vs. 7.9 ± 3.9; P = 0.005) arteries. This preclinical GPVI-Fc-based vascular lesion imaging approach may be the first step towards a method that allows identification of vascular lesions in vivo.
Higher order heavy quark Green’s functions in Coulomb gauge
2011-06-14

The Dyson-Schwinger equation for the 4-point quark Green's functions is\\nstudied. In the limit of the heavy quark mass and with the truncation to\\ninclude only the dressed two point functions for the Yang-Mills sector, we\\nprovide an exact solution for the 4-point quark Green's functions, in both\\nquark-antiquark and diquark channels, and show that the corresponding poles\\nrelate to the bound state energy of the heavy quark systems. Moreover, a\\nnatural separation between physical and unphysical poles in the Green's\\nfunctions emerges.\\n
Osteopenia Due to Enhanced Cathepsin K Release by BK Channel Ablation in Osteoclasts
2011-06-14

Our findings suggest that the BK channel controls resorptive osteoclast activity by regulating Cathepsin K release. Targeted deletion of BK channel in mice resulted in an osteoclast-autonomous osteopenia, becoming apparent in juvenile females. Thus, the BK(-/-) mouse-line represents a new model for juvenile osteopenia, and revealed the BK channel as putative new target for therapeutic controlling of osteoclast activity.
Streptomyces staurosporininus sp. nov., a staurosporine-producing actinomycete
2011-06-14

The taxonomic position of a staurosporine-producing actinomycete isolated from a hay meadow soil was determined using a polyphasic approach. The organism had chemical and morphological characteristics consistent with its classification in the genus Streptomyces and formed a distinct branch between the Streptomyces lydicus and Streptomyces noursei clades in the 16S rRNA Streptomyces gene tree. DNA–DNA relatedness values between the isolate and its nearest phylogenetic neighbours, namely Streptomyces lydicus NBRC 13058 T and Streptomyces chattanoogensis NBRC 12754 T , were 53 % and 40 %, respectively. The isolate was also readily distinguished from the type strains of these species using a combination of morphological and other phenotypic properties. On the basis of these results, it is proposed that isolate BK179 T ( = KACC 20912 T = NRRL B-24850 T ) be classified as the type strain of Streptomyces staurosporininus sp. nov.
No evidence of viral genomes in whole‐transcriptome sequencing of three melanoma metastases
2011-06-14

Abstract: Several viruses are known to cause cancer, such as human herpes virus 8 in Kaposi sarcoma and human papilloma viruses in cervical cancer. Recently, Merkel cell polyoma virus (MCPyV) has been described in 80% of Merkel cell carcinomas (MCC). Similarly to MCC and Kaposi sarcoma, melanoma incidence is increased in immunosuppressed patients. We asked whether infection by known or yet unknown viruses may play a role in melanoma development as well. To detect viral sequences expressed in melanoma cells, we analysed three melanoma metastases by whole‐transcriptome sequencing and digital transcriptome subtraction. None of the samples investigated harboured viral sequences. In contrast, artificial viral sequences and MCPyV transcripts used as a positive control for the bioinformatics analysis were detected. This renders it less likely that viruses are frequently involved in melanoma induction. A larger number of melanoma transcriptome sequencings are required to rule out viruses as a relevant pathogen.
Gain and Loss of Extracellular Molecules in Sporadic Inclusion Body Myositis and Polymyositis—A Proteomics‐Based Study
2011-06-14

Abstract Sporadic inclusion body myositis (sIBM) contains non‐necrotic myofibers that are surrounded and/or invaded by inflammatory cells. In this study we aimed to identify selective molecules that are present at this site. Myofibers of four biopsies of sIBM that were surrounded and/or invaded by inflammatory cells were microdissected, pooled and profiled by proteomic studies using mass spectrometry. Normal skeletal muscle tissue served as control. Based on the table of proteins that were detected in sIBM only, we selected nine extracellular matrix molecules and validated the results performing immunofluorescence. Seven out of nine proteins that were detected in sIBM by mass spectrometry showed different immunohistochemical results in myositis and normal controls. Of these, the small leucine‐rich repeat proteins proline arginine‐rich end leucine‐rich repeat protein (PRELP) and biglycan were deposited precisely at myofibers surrounded and/or invaded by inflammatory cells both in sIBM and polymyositis. The basement membrane (BM) molecules merosin, perlecan, nidogen‐2 and collagen IV were variably destroyed or increased at these sites. P component, which ensheathed all myofibers in normal controls, was absent from invaded myofibers. Similar to BM remodeling, the specific deposition of PRELP and biglycan may represent a mechanism to defend against immune attack. Loss of P component may affect the anchorage of the myofiber in the endomysium.
Autonomous multi-processor-SoC optimization with distributed learning classifier systems XCS
2011-06-14

We present a methodology for autonomous optimization of multi-processor system-on-chips (MPSoC) using distributed learning classifier systems (LCS). The methodology promises to offer a high design reuse rate and to reduce design complexity. The distributed LCS autonomously optimize each core of an MPSoC and, by exchanging classifiers, help each other in achieving their individual goals, compensating reciprocal heating of the cores. We validate our methodology with a realistic simulation of an MPSoC inspired by the Cell processor, where the LCSs set the frequency and voltage of the cores to maximize each core's performance while minimizing temperature-dependent timing errors. In our example application, selecting emigrants by fitness, communicating along a complete graph, and deleting by prediction error results in the highest performance for each core that allows operation with almost no temperature-dependent timing errors but retains self-adaptation capabilities. The results show how distributed LCS autonomously optimize the cores of an MPSoC, greatly reducing design efforts through a reusable self-adaptation component and an according design methodology.
Modulating the Acidity: Highly Acidic Brønsted Acids in Asymmetric Catalysis
2011-06-15

Abstract Recently, chiral highly acidic Brønsted acids have emerged as powerful catalysts for enantioselective CC and CX bond‐forming reactions. Their strong acidity renders them valuable tools for the activation of imines, carbonyl compounds, and other weakly basic substrates. As a result, new perspectives are opened and highly stereoselective transformations based on the concept of chiral contact‐ion‐pair catalysis can be realized. This Minireview gives an overview of the design and application of these new organocatalysts and presents recent results in this rapidly growing field.