A new charge-transfer complex in UHV co-deposited tetramethoxypyrene and tetracyanoquinodimethane

UHV-deposited films of the mixed phase of tetramethoxypyrene and tetracyanoquinodimethane (TMP1-TCNQ1) on gold have been studied using ultraviolet photoelectron spectroscopy (UPS), X-ray-diffraction (XRD), infrared (IR) spectroscopy and scanning tunnelling spectroscopy (STS). The formation of an intermolecular charge-transfer (CT) compound is evident from the appearance of new reflexes in XRD (d1= 0.894 nm, d2= 0.677 nm). A softening of the CN stretching vibration (red-shift by 7 cm-1) of TCNQ is visible in the IR spectra, being indicative of a CT of the order of 0.3e from TMP to TCNQ in the complex. Characteristic shifts of the electronic level positions occur in UPS and STS that are in reasonable agreement with the prediction of from DFT calculations (Gaussian03 with hybrid functional B3LYP). STS reveals a HOMO-LUMO gap of the CT complex of about 1.25 eV being much smaller than the gaps (>3.0 eV) of the pure moieties. The electron-injection and hole-injection barriers are 0.3 eV and 0.5 eV, respectively. Systematic differences in the positions of the HOMOs determined by UPS and STS are discussed in terms of the different information content of the two methods.Comment: 20 pages, 6 figure

MATSim Model Vienna: Analyzing the Socioeconomic Impacts for Different Fleet Sizes and Pricing Schemes of Shared Autonomous Electric Vehicles

Shared Autonomous Electric Vehicles (SAEVs) are expected to enter the transportation market in the upcoming decades. In this paper, we describe the preparation of a MATSim model for Vienna in which we add this new service as a new transportation mode. We simulate different pricing schemes for various SAEV fleet sizes and analyze their impacts. Our focus is on the impacts in regards of socioeconomic heterogeneity. One main finding of our paper is that the number of SAEV trips does not necessarily decrease for higher fares. It is instead the average travel time of SAEV rides which decreases if the service gets more expensive. Our simulation results for higher pricing schemes show that many people switch from bike or walk mode to SAEV. Public transport is also highly cannibalized by this new service regardless of the price, whereas SAEVs would always replace no more than 10% of car trips. SAEVs help reduce travel times significantly. People who do not have a car available in their household experience the greatest savings in travel time. A similar high share of SAEV trips is done by people older than 35 years. In regards of gender, our results reveal that women tend to use SAEVs for shorter trips

A lack of close binaries among hot horizontal branch stars in globular clusters. II. NGC\,2808

Models based on their binary origin have been very successful in reproducing the properties of field subdwarf-B stars, but the observations of their analogues in globular clusters has posed new problems, while the discovery of multiple populations offered an appealing alternative scenario for the formation of these stars. We search for binaries of period P<200 days among a sample of blue horizontal branch stars (Teff=12000-22000 K) in NGC2808, a cluster known to host three distinct stellar populations and a multimodal horizontal branch. The final sample consists of 64 targets. The radial velocity of the targets was measured in fourteen epochs, spanning a temporal interval of about 75 days. We detect no RV variable object among stars cooler than the photometric G1 gap at 17000 K, while two close (P<10 days) and two intermediate-period (P=10-50 days) systems are found among hotter targets. The close and intermediate-period binary fraction for stars cooler than the gap are fc<5% and fip<10%, respectively, with 95% confidence. The most probable values among hotter stars are fc~20% and fip~30%, but the 90%- confidence level intervals are large (6-42% and 11-72%, respectively). The G1 gap appears as a discontinuity in the binary faction, with a higher incidence of binaries among hotter stars, but a constant increase in f with temperature rather than a discontinuity cannot be excluded from our observations. We find that intermediate-period binaries, never investigated before among cluster HB stars, could play an important role, being more than ~15-20% of the hottest stars of our sample. Our results indicate that fc among hot HB stars is most probably higher for younger clusters, confirming the recently proposed age-fc relation. However, the large observed difference in binary fraction between clusters (e.g. NGC2808 and NGC6752) is still not reproduced by binary population synthesis models

Associations of CDH1 germline variant location and cancer phenotype in families with hereditary diffuse gastric cancer (HDGC)

INTRODUCTION: Hereditary diffuse gastric cancer (HDGC) is a cancer syndrome associated with variants in E-cadherin (CDH1), diffuse gastric cancer and lobular breast cancer. There is considerable heterogeneity in its clinical manifestations. This study aimed to determine associations between CDH1 germline variant status and clinical phenotypes of HDGC. METHODS: One hundred and fifty-two HDGC families, including six previously unreported families, were identified. CDH1 gene-specific guidelines released by the Clinical Genome Resource (ClinGen) CDH1 Variant Curation Expert Panel were applied for pathogenicity classification of truncating, missense and splice site CDH1 germline variants. We evaluated ORs between location of truncating variants of CDH1 and incidence of colorectal cancer, breast cancer and cancer at young age (gastric cancer at \u3c40 or breast cancer \u3c50 years of age). RESULTS: Frequency of truncating germline CDH1 variants varied across functional domains of the E-cadherin receptor gene and was highest in linker (0.05785 counts/base pair; p=0.0111) and PRE regions (0.10000; p=0.0059). Families with truncating CDH1 germline variants located in the PRE-PRO region were six times more likely to have family members affected by colorectal cancer (OR 6.20, 95% CI 1.79 to 21.48; p=0.004) compared with germline variants in other regions. Variants in the intracellular E-cadherin region were protective for cancer at young age (OR 0.2, 95% CI 0.06 to 0.64; p=0.0071) and in the linker regions for breast cancer (OR 0.35, 95% CI 0.12 to 0.99; p=0.0493). Different CDH1 genotypes were associated with different intracellular signalling activation levels including different p-ERK, p-mTOR and β-catenin levels in early submucosal T1a lesions of HDGC families with different CDH1 variants. CONCLUSION: Type and location of CDH1 germline variants may help to identify families at increased risk for concomitant cancers that might benefit from individualised surveillance and intervention strategies

Prognostic significance of tumor-infiltrating lymphocytes in ductal carcinoma in situ of the breast

Tumor-infiltrating lymphocytes (TILs) provide prognostic value in invasive breast cancer and guidelines for their assessment have been published. This study aims to evaluate: (a) methods of TILs assessment, and (b) their prognostic significance in breast ductal carcinoma in situ (DCIS). Hematoxylin and eosin sections from two clinically annotated DCIS cohorts; a training set (n = 150 pure DCIS) and a validation set (n = 666 comprising 534 pure DCIS and 132 cases wherein DCIS and invasive breast carcinoma were co-existent) were assessed. Seven different scoring methods were applied to the training set to identify the most optimal reproducible method associated with strongest prognostic value. Among different methods, TILs touching ducts' basement membrane or away from it by one lymphocyte cell thickness provided the strongest significant association with outcome and highest concordance rate [inter-cluster correlation coefficient = 0.95]. Assessment of periductal TILs at increasing distances from DCIS (0.2 , 0.5 , and 1 mm) as well as percent of stromal TILs were practically challenging and showed lower concordance rates than touching TILs. TILs hotspots and lymphoid follicles did not show prognostic significance. Within the pure DCIS validation set, dense TILs were associated with younger age, symptomatic presentation, larger size, higher nuclear grade, comedo necrosis and estrogen receptor negativity as well as shorter recurrence-free interval (p = 0.002). In multivariate survival analysis, dense TILs were independent predictor of shorter recurrence-free interval (p = 0.002) in patients treated with breast conservation. DCIS associated with invasive carcinoma showed denser TILs than pure DCIS (p = 9.0 × 10-13). Dense TILs is an independent prognostic variable in DCIS. Touching TILs provides a reproducible method for their assessment that can potentially be used to guide management

GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all

The EMBRACE web service collection

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions

Transcriptome Profiling of Bovine Milk Oligosaccharide Metabolism Genes Using RNA-Sequencing

This study examines the genes coding for enzymes involved in bovine milk oligosaccharide metabolism by comparing the oligosaccharide profiles with the expressions of glycosylation-related genes. Fresh milk samples (n = 32) were collected from four Holstein and Jersey cows at days 1, 15, 90 and 250 of lactation and free milk oligosaccharide profiles were analyzed. RNA was extracted from milk somatic cells at days 15 and 250 of lactation (n = 12) and gene expression analysis was conducted by RNA-Sequencing. A list was created of 121 glycosylation-related genes involved in oligosaccharide metabolism pathways in bovine by analyzing the oligosaccharide profiles and performing an extensive literature search. No significant differences were observed in either oligosaccharide profiles or expressions of glycosylation-related genes between Holstein and Jersey cows. The highest concentrations of free oligosaccharides were observed in the colostrum samples and a sharp decrease was observed in the concentration of free oligosaccharides on day 15, followed by progressive decrease on days 90 and 250. Ninety-two glycosylation-related genes were expressed in milk somatic cells. Most of these genes exhibited higher expression in day 250 samples indicating increases in net glycosylation-related metabolism in spite of decreases in free milk oligosaccharides in late lactation milk. Even though fucosylated free oligosaccharides were not identified, gene expression indicated the likely presence of fucosylated oligosaccharides in bovine milk. Fucosidase genes were expressed in milk and a possible explanation for not detecting fucosylated free oligosaccharides is the degradation of large fucosylated free oligosaccharides by the fucosidases. Detailed characterization of enzymes encoded by the 92 glycosylation-related genes identified in this study will provide the basic knowledge for metabolic network analysis of oligosaccharides in mammalian milk. These candidate genes will guide the design of a targeted breeding strategy to optimize the content of beneficial oligosaccharides in bovine milk