julilili42/papers huggingface dataset:
Quantum reflection of ultracold atoms from thin films, graphene and semiconductor heterostructures
2011-08-16

We show that thin dielectric films can be used to enhance the performance of\\npassive atomic mirrors by enabling quantum reflection probabilities of over 90%\\nfor atoms incident at velocities ~1 mm/s, achieved in recent experiments. This\\nenhancement is brought about by weakening the Casimir-Polder attraction between\\nthe atom and the surface, which induces the quantum reflection. We show that\\nsuspended graphene membranes also produce higher quantum reflection\\nprobabilities than bulk matter. Temporal changes in the electrical resistance\\nof such membranes, produced as atoms stick to the surface, can be used to\\nmonitor the reflection process, non-invasively and in real time. The resistance\\nchange allows the reflection probability to be determined purely from\\nelectrical measurements without needing to image the reflected atom cloud\\noptically. Finally, we show how perfect atom mirrors may be manufactured from\\nsemiconductor heterostructures, which employ an embedded two-dimensional\\nelectron gas to tailor the atom-surface interaction and so enhance the\\nreflection by classical means.\\n
Identifying associations between amino acid changes and meta information in alignments
2011-08-16

Abstract Motivation: We present a method that identifies associations between amino acid changes in potentially significant sites in an alignment (taking into account several amino acid properties) with phenotypic data, through the phylogenetic mixed model. The latter accounts for the dependency of the observations (organisms). It is known from previous studies that the pathogenic aspect of many organisms may be associated with a single or just few changes in amino acids, which have a strong structural and/or functional impact on the protein. Discovering these sites is a big step toward understanding pathogenicity. Our method is able to discover such sites in proteins responsible for the pathogenic character of a group of bacteria. Results: We use our method to predict potentially significant sites in the RpoS protein from a set of 209 bacteria. Several sites with significant differences in biological relevant regions were found. Availability: Our tool is publicly available on the CRAN network at http://cran.r-project.org/ Contact: naya@pasteur.edu.uy Supplementary information: Supplementary data are available at Bioinformatics online.
Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis
2011-08-17

Abstract Objective: Several studies have suggested an increased frequency of variants in the gene encoding angiogenin ( ANG ) in patients with amyotrophic lateral sclerosis (ALS). Interestingly, a few ALS patients carrying ANG variants also showed signs of Parkinson disease (PD). Furthermore, relatives of ALS patients have an increased risk to develop PD, and the prevalence of concomitant motor neuron disease in PD is higher than expected based on chance occurrence. We therefore investigated whether ANG variants could predispose to both ALS and PD. Methods: We reviewed all previous studies on ANG in ALS and performed sequence experiments on additional samples, which allowed us to analyze data from 6,471 ALS patients and 7,668 controls from 15 centers (13 from Europe and 2 from the USA). We sequenced DNA samples from 3,146 PD patients from 6 centers (5 from Europe and 1 from the USA). Statistical analysis was performed using the variable threshold test, and the Mantel‐Haenszel procedure was used to estimate odds ratios. Results: Analysis of sequence data from 17,258 individuals demonstrated a significantly higher frequency of ANG variants in both ALS and PD patients compared to control subjects ( p = 9.3 × 10 −6 for ALS and p = 4.3 × 10 −5 for PD). The odds ratio for any ANG variant in patients versus controls was 9.2 for ALS and 6.7 for PD. Interpretation: The data from this multicenter study demonstrate that there is a strong association between PD, ALS, and ANG variants. ANG is a genetic link between ALS and PD. ANN NEUROL 2011;70:964–973
The Asilomar Survey: Stakeholders’ Opinions on Ethical Issues Related to Brain-Computer Interfacing
2011-08-17

Brain-Computer Interface (BCI) research and (future) applications raise important ethical issues that need to be addressed to promote societal acceptance and adequate policies. Here we report on a survey we conducted among 145 BCI researchers at the 4<sup>th</sup> International BCI conference, which took place in May-June 2010 in Asilomar, California. We assessed respondents' opinions about a number of topics. First, we investigated preferences for terminology and definitions relating to BCIs. Second, we assessed respondents' expectations on the marketability of different BCI applications (BCIs for healthy people, BCIs for assistive technology, BCIs-controlled neuroprostheses and BCIs as therapy tools). Third, we investigated opinions about ethical issues related to BCI research for the development of assistive technology: informed consent process with locked-in patients, risk-benefit analyses, team responsibility, consequences of BCI on patients' and families' lives, liability and personal identity and interaction with the media. Finally, we asked respondents which issues are urgent in BCI research.
β-Catenin Signaling Increases during Melanoma Progression and Promotes Tumor Cell Survival and Chemoresistance
2011-08-17

Beta-catenin plays an important role in embryogenesis and carcinogenesis by controlling either cadherin-mediated cell adhesion or transcriptional activation of target gene expression. In many types of cancers nuclear translocation of beta-catenin has been observed. Our data indicate that during melanoma progression an increased dependency on the transcriptional function of beta-catenin takes place. Blockade of beta-catenin in metastatic melanoma cell lines efficiently induces apoptosis, inhibits proliferation, migration and invasion in monolayer and 3-dimensional skin reconstructs and decreases chemoresistance. In addition, subcutaneous melanoma growth in SCID mice was almost completely inhibited by an inducible beta-catenin knockdown. In contrast, the survival of benign melanocytes and primary melanoma cell lines was less affected by beta-catenin depletion. However, enhanced expression of beta-catenin in primary melanoma cell lines increased invasive capacity in vitro and tumor growth in the SCID mouse model. These data suggest that beta-catenin is an essential survival factor for metastatic melanoma cells, whereas it is dispensable for the survival of benign melanocytes and primary, non-invasive melanoma cells. Furthermore, beta-catenin increases tumorigenicity of primary melanoma cell lines. The differential requirements for beta-catenin signaling in aggressive melanoma versus benign melanocytic cells make beta-catenin a possible new target in melanoma therapy.
Cryobiopsy increases the diagnostic yield of endobronchial biopsy: a multicentre trial
2011-08-18

Forceps, brushes or needles are currently the standard tools used during flexible bronchoscopy when diagnosing endobronchial malignancies. The new biopsy technique of cryobiopsy appears to provide better diagnostic samples. The aim of this study was to evaluate cryobiopsy over conventional endobronchial sampling. A total of 600 patients in eight centres with suspected endobronchial tumours were included in a prospective, randomised, single-blinded multicentre study. Patients were randomised to either sampling using forceps or the cryoprobe. After obtaining biopsy samples, a blinded histological evaluation was performed. According to the definitive clinical diagnosis, the diagnostic yield for malignancy was evaluated by a Chi-squared test. A total of 593 patients were randomised, of whom 563 had a final diagnosis of cancer. 281 patients were randomised to receive endobronchial biopsies using forceps and 282 had biopsies performed using a flexible cryoprobe. A definitive diagnosis was achieved in 85.1% of patients randomised to conventional forceps biopsy and 95.0% of patients who underwent cryobiopsy (p&lt;0.001). Importantly, there was no difference in the incidence of significant bleeding. Endobronchial cryobiopsy is a safe technique with superior diagnostic yield in comparison with conventional forceps biopsy.
Compound-Specific Chlorine Isotope Analysis: A Comparison of Gas Chromatography/Isotope Ratio Mass Spectrometry and Gas Chromatography/Quadrupole Mass Spectrometry Methods in an Interlaboratory Study
2011-08-18

Chlorine isotope analysis of chlorinated hydrocarbons like trichloroethylene (TCE) is of emerging demand because these species are important environmental pollutants. Continuous flow analysis of noncombusted TCE molecules, either by gas chromatography/isotope ratio mass spectrometry (GC/IRMS) or by GC/quadrupole mass spectrometry (GC/qMS), was recently brought forward as innovative analytical solution. Despite early implementations, a benchmark for routine applications has been missing. This study systematically compared the performance of GC/qMS versus GC/IRMS in six laboratories involving eight different instruments (GC/IRMS, Isoprime and Thermo MAT-253; GC/qMS, Agilent 5973N, two Agilent 5975C, two Thermo DSQII, and one Thermo DSQI). Calibrations of (37)Cl/(35)Cl instrument data against the international SMOC scale (Standard Mean Ocean Chloride) deviated between instruments and over time. Therefore, at least two calibration standards are required to obtain true differences between samples. Amount dependency of δ(37)Cl was pronounced for some instruments, but could be eliminated by corrections, or by adjusting amplitudes of standards and samples. Precision decreased in the order GC/IRMS (1σ ≈ 0.1‰), to GC/qMS (1σ ≈ 0.2-0.5‰ for Agilent GC/qMS and 1σ ≈ 0.2-0.9‰ for Thermo GC/qMS). Nonetheless, δ(37)Cl values between laboratories showed good agreement when the same external standards were used. These results lend confidence to the methods and may serve as a benchmark for future applications.
Associations of common variants at 1p11.2 and 14q24.1 (RAD51L1) with breast cancer risk and heterogeneity by tumor subtype: findings from the Breast Cancer Association Consortium†
2011-08-18

A genome-wide association study (GWAS) identified single-nucleotide polymorphisms (SNPs) at 1p11.2 and 14q24.1 (RAD51L1) as breast cancer susceptibility loci. The initial GWAS suggested stronger effects for both loci for estrogen receptor (ER)-positive tumors. Using data from the Breast Cancer Association Consortium (BCAC), we sought to determine whether risks differ by ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), grade, node status, tumor size, and ductal or lobular morphology. We genotyped rs11249433 at 1p.11.2, and two highly correlated SNPs rs999737 and rs10483813 (r(2)= 0.98) at 14q24.1 (RAD51L1), for up to 46 036 invasive breast cancer cases and 46 930 controls from 39 studies. Analyses by tumor characteristics focused on subjects reporting to be white women of European ancestry and were based on 25 458 cases, of which 87% had ER data. The SNP at 1p11.2 showed significantly stronger associations with ER-positive tumors [per-allele odds ratio (OR) for ER-positive tumors was 1.13, 95% CI = 1.10-1.16 and, for ER-negative tumors, OR was 1.03, 95% CI = 0.98-1.07, case-only P-heterogeneity = 7.6 × 10(-5)]. The association with ER-positive tumors was stronger for tumors of lower grade (case-only P= 6.7 × 10(-3)) and lobular histology (case-only P= 0.01). SNPs at 14q24.1 were associated with risk for most tumor subtypes evaluated, including triple-negative breast cancers, which has not been described previously. Our results underscore the need for large pooling efforts with tumor pathology data to help refine risk estimates for SNP associations with susceptibility to different subtypes of breast cancer.
Proinflammatory and regulatory cytokines and chemokines in infants with uncomplicated and severePlasmodium falciparummalaria
2011-08-18

Summary Cytokine and chemokine levels were studied in infants (&amp;lt;5 years) with uncomplicated (MM) and severe malaria tropica (SM), and in Plasmodium falciparum infection-free controls (NEG). Cytokine plasma levels of interleukin (IL)-10, IL-13, IL-31 and IL-33 were strongly elevated in MM and SM compared to NEG (P &amp;lt; 0·0001). Inversely, plasma concentrations of IL-27 were highest in NEG infants, lower in MM cases and lowest in those with SM (P &amp;lt; 0·0001, NEG compared to MM and SM). The levels of the chemokines macrophage inflammatory protein (MIP3)-α/C–C ligand 20 (CCL20), monokine induced by gamma interferon (MIG)/CXCL9 and CXCL16 were enhanced in those with MM and SM (P &amp;lt; 0·0001 compared to NEG), and MIP3-α/CCL20 and MIG/CXCL9 were correlated positively with parasite density, while that of IL-27 were correlated negatively. The levels of 6Ckine/CCL21 were similar in NEG, MM and SM. At 48–60 h post-anti-malaria treatment, the plasma concentrations of IL-10, IL-13, MIG/CXCL9, CXCL16 and MIP3-α/CCL20 were clearly diminished compared to before treatment, while IL-17F, IL-27, IL-31 and IL-33 remained unchanged. In summary, elevated levels of proinflammatory and regulatory cytokines and chemokines were generated in infants during and after acute malaria tropica. The proinflammatory type cytokines IL-31 and IL-33 were enhanced strongly while regulatory IL-27 was diminished in those with severe malaria. Similarly, MIP3-α/CCL20 and CXCL16, which may promote leucocyte migration into brain parenchyma, displayed increased levels, while CCL21, which mediates immune surveillance in central nervous system tissues, remained unchanged. The observed cytokine and chemokine production profiles and their dynamics may prove useful in evaluating either the progression or the regression of malarial disease.
Rebound excitation triggered by synaptic inhibition in cerebellar nuclear neurons is suppressed by selective T-type calcium channel block
2011-08-18

Following hyperpolarizing inputs, many neurons respond with an increase in firing rate, a phenomenon known as rebound excitation. Rebound excitation has been proposed as a mechanism to encode and process inhibitory signals and transfer them to target structures. Activation of low-voltage-activated T-type calcium channels and the ensuing low-threshold calcium spikes is one of the mechanisms proposed to support rebound excitation. However, there is still not enough evidence that the hyperpolarization provided by inhibitory inputs, particularly those dependent on chloride ions, is adequate to deinactivate a sufficient number of T-type calcium channels to drive rebound excitation on return to baseline. Here, this issue was investigated in the deep cerebellar nuclear neurons (DCNs), which receive the output of the cerebellar cortex conveyed exclusively by the inhibitory Purkinje cells and are also known to display rebound excitation. Using cerebellar slices and whole cell recordings of large DCNs, we show that a novel piperidine-based compound that selectively antagonizes T-type calcium channel activity, 3,5-dichloro- N-[1-(2,2-dimethyl-tetrahydropyran-4-ylmethyl)-4-fluoro-piperidin-4-ylmethyl]-benzamide (TTA-P2), suppressed rebound excitation elicited by current injection as well as by synaptic inhibition, whereas other electrophysiological properties of large DCNs were unaltered. Furthermore, TTA-P2 suppressed transient high-frequency rebounds found in DCNs with low-threshold spikes as well as the slow rebounds present in DCNs without low-threshold spikes. These findings demonstrate that chloride-dependent synaptic inhibition effectively triggers T-type calcium channel-mediated rebounds and that the latter channels may support slow rebound excitation in neurons without low-threshold spikes.
Probing the Nanoscale Phase Separation and Photophysics Properties of Low‐Bandgap Polymer:Fullerene Blend Film by Near‐Field Spectroscopic Mapping
2011-08-18

Abstract The effect of the additive 1,8‐octanedithiol (ODT) on the nanometer‐scale morphology and local photophysical properties of low‐bandgap polymer blends of poly[2,6‐(4,4‐bis(2‐ethylhexyl)‐4 H ‐cyclopenta[2,1‐b;3,4‐b′] dithiophene)‐ alt ‐4,7(2,1,3‐benzothiadiazole)] (PCPDTBT) and [6,6]‐phenyl C 61 ‐butyric acid methyl ester (PCBM) is investigated. Phase separations of the PCPDTBT:PCBM blend film induced by ODT are visualized by the morphological changes from fibril‐shaped features to spherical bumps, by the dramatically increased photoluminescence emission from PCPDTBT that was originally largely quenched, and by the fluctuations of spectral features at different locations of the sample surface. The correlations between the morphology and the local photophysical properties of the blend film with/without ODT at both the micrometer and nanometer scales are revealed by confocal and high‐resolution near‐field spectroscopic mapping techniques.
Promiscuous survivin peptide induces robust CD4+ T‐cell responses in the majority of vaccinated cancer patients
2011-08-19

Abstract CD4 + T cells have been shown to be crucial for the induction and maintenance of cytotoxic T cell responses and to be also capable of mediating direct tumor rejection. Therefore, the anticancer therapeutic efficacy of peptide‐based vaccines may be improved by addition of HLA class II epitopes to stimulate T helper cells. Survivin is an apoptosis inhibiting protein frequently overexpressed in tumors. Here we describe the first immunological evaluation of a survivin‐derived CD4 + T cell epitope in a multipeptide immunotherapy trial for prostate carcinoma patients. The survivin peptide is promiscuously presented by several human HLA‐DRB1 molecules and, most importantly, is naturally processed by dendritic cells. In vaccinated patients, it was able to induce frequent, robust and multifunctional CD4 + T cell responses, as monitored by IFN‐γ ELISPOT and intracellular cytokine staining. Thus, this HLA‐DR restricted epitope is broadly immunogenic and should be valuable for stimulating T helper cells in patients suffering from a wide range of tumors.
Nephron Sparing Surgery for Synchronous Bilateral Nephroblastoma Involving the Renal Hilus
2011-08-19

Surgery for central stage V nephroblastoma is possible with good functional and oncologic outcomes. The single stage approach is safe, provided that operating and treating physicians have sufficient expertise with such conditions. The ultimate goal is to avoid tumor nephrectomy.
Transanal Endoscopic Microsurgery–Based Transanal Access for Colorectal Surgery: Experience on Human Cadavers
2011-08-19

Transanal endoscopic microsurgery (TEM) was described in 1983 for local excision of rectal tumors. In the context of natural orifice translumenal endoscopic surgery, we have modified the original TEM system and developed a new set of instruments. These are more curved and, in addition, steerable. After extensive studies in an ex-vivo model, we developed a novel technique for transanal rectosigmoid resection and colorectal anastomosis. The technique comprises closure of the rectal lumen by purse-string suture, transection of the rectal wall distal to the closure, circumferential mobilization of rectum and mesorectal tissue in the anatomical plane from below upward, control of the inferior mesenteric vessel, removal of mobilized colorectum through the anus, and, finally, the colorectal anastomosis by either stapled or hand-sutured technique. This procedure was performed on three alcohol-glycerol preserved well-built human cadavers (M:F=2:1). The average operating time was 190 minutes. The average length of the resected specimen was 23 cm. There was no fecal contamination or injury to the resected specimen. Postprocedure laparotomy revealed adequate mesorectal resection and no inadvertent injury to other viscera. During dissection in the pelvis, as the resected rectum was pushed upward, an unobstructed "empty pelvis" situation was developed in the operating site, thus facilitating the mesorectal resection. Transanal access for colorectal surgery seems feasible. It provides a precise definition of the distal safety margin, good view of the pelvis for meticulous mesorectal resection, and reduces the abdominal wall trauma. These may enhance the outcome of colorectal resection. However, further clinical studies can only substantiate these findings.
Highlights of the Second International Conference on “Immunotherapy in Pediatric Oncology”
2011-08-19

The third International Conference on Immunotherapy in Pediatric Oncology was held in Frankfurt/Main, Germany, October 1-2, 2012. Major topics of the conference included (i) cellular therapies using antigen-specific and gene-modified T cells for targeting leukemia and pediatric solid tumors; (ii) overcoming hurdles and barriers with regard to immunogenicity, immune escape, and the role of tumor microenvironment; (iii) vaccine strategies and antigen presentation; (iv) haploidentical transplantation and innate immunity; (v) the role of immune cells in allogeneic transplantation; and (vi) current antibody/immunoconjugate approaches for the treatment of pediatric malignancies. During the past decade, major advances have been made in improving the efficacy of these modalities and regulatory hurdles have been taken. Nevertheless, there is still a long way to go to fully exploit the potential of immunotherapeutic strategies to improve the cure of children and adolescents with malignancies. This and future meetings will support new collaborations and insights for further translational and clinical immunotherapy studies.
Modelling the Extensive Margin of World Trade: New Evidence on GATT and WTO Membership
2011-08-19

This chapter contains sections titled: Introduction State of the Literature: Open Issues A Simple Model of the Extensive Margin An Empirical Model Data and Econometric Strategy Estimation Results Conclusion References
Circulating and Disseminated Tumor Cells in the Management of Advanced Prostate Cancer
2011-08-21

Management of prostate cancer is recognized as one of the most important medical problems. Latest findings concerning the role of circulating (CTC) and disseminated tumor cells (DTC) have provided new insights into the biology of metastasis with important implications for the clinical management of prostate cancer patients. Most of the established methods of circulating/disseminated tumor cell enrichment use density-gradient centrifugation and immunomagnetic procedures. Reverse transcriptase polymerase chain reaction is another used detection technique. Novel methods, the CTC-chip and the epithelial immunospot assay already showed promising results. For localized and metastatic prostate cancer, significant correlations between spreading tumor cells and well-established indicators of disease activity have been demonstrated. Careful randomized prospective trials will be required to justify the routine use of CTCs/DTCs for therapy decision making.
Complete three-dimensional optical characterization of single gold nanorods
2011-08-21

We present a powerful technique to fully characterize individual gold nanorods by using confocal microscopy in combination with higher order laser modes. We obtain topological information far beyond the optical resolution limit, although the used method is diffraction limited. We perform, for the first time, the imaging of gold nanorods by recording simultaneously their scattering and luminescence signal. In the future, this might permit to extent the results achieved already in [1] to a 3D system. Moreover, the scattering pattern is strongly dependent on the phase relation between the light scattered and reflected at the sample interface, while the luminescence pattern does not depend on this phase relation. By exploiting an index matched sample geometry, we were able to omit the phase relation and therefore detect the pure scattering signal and qualitatively compare it with the luminescence one. Furthermore, as previously shown [2, 3], our technique is capable to track the rotation of single noble metal nanorods. We show that measuring the rotation rate of gold nanorods might be useful to estimate the local viscosity of the surrounding medium.