Near-Infrared Classification Spectroscopy: H-band Spectra of Fundamental MK Standards

We present a catalogue of H-band spectra for 85 stars of approximately solar abundance observed at a resolving power of 3000 with the KPNO Mayall 4m FTS. The atlas covers spectral types O7-M5 and luminosity classes I-V as defined on the MK system. We identify both atomic and molecular indices and line-ratios which are temperature and luminosity sensitive allowing spectral classification to be carried out in the H-band. The line ratios permit spectral classification in the presence of continuum excess emission, which is commonly found in pre-main sequence and evolved stars. We demonstrate that with spectra of R = 1000 obtained at SNR > 50 it is possible to derive spectral types within +- 2 subclasses for late-type stars. These data are available electronically through the Astronomical Data Center in addition to being served on the World-Wide-Web.Comment: To appear in the November 20, 1998 issue of ApJ (Volume 508, #1

Carbon and nitrogen stable isotope values in freshwater, brackish and marine fish bone collagen from Mesolithic and Neolithic sites in central and northern Europe

The aim of this research is to examine the isotopic characterisation of archaeological fish species as it relates to freshwater, brackish and marine environments, trophic level and migration patterns, and to determine intraspecies variation within and between fish populations in different locations within central and northern Europe. Carbon and nitrogen stable isotope analysis was undertaken on collagen extracted from 72 fish bone samples from eight Mesolithic and Neolithic archaeological sites in this region. Thirty-six (50%) of the specimens analysed produced results with acceptable carbon to nitrogen atomic ratios (2·9–3·6). The fish remains encompassed a wide spectrum of freshwater, brackish and marine taxa (n = 12), which were reflected in the δ13C values (−24·5 to −7·8‰). The freshwater/brackish fish (pike, Esox lucius; perch, Perca fluviatilis; zander, Sander lucioperca) had δ13C values that ranged from −24·2 to −19·3‰, whereas the brackish/marine fish (spurdog, Squalus acanthias; flatfish, Pleuronectidae; codfish, Gadidae; garfish, Belone belone; mackerel, Scomber scombrus) ranged from −14·9 to −9·4‰. Salmonidae, an anadromous taxon, and eel (Anguilla anguilla), a catadromous species, had carbon isotope values consistent with marine origin, and no evidence of freshwater residency (−12·7 to −11·7‰). The δ15N values had a range of 6·2‰ (6·5–12·7‰) indicating that these fish were on average feeding at 1·7 trophic levels higher than their producers in these diverse aquatic environments. These results serve as an important ecological baseline for the future isotopic reconstruction of the diet of human populations dating to the late Mesolithic and early Neolithic of the region

Pharmacogenomics of statin-related myopathy:Meta-analysis of rare variants from whole-exome sequencing

AIMS:Statin-related myopathy (SRM), which includes rhabdomyolysis, is an uncommon but important adverse drug reaction because the number of people prescribed statins world-wide is large. Previous association studies of common genetic variants have had limited success in identifying a genetic basis for this adverse drug reaction. We conducted a multi-site whole-exome sequencing study to investigate whether rare coding variants confer an increased risk of SRM. METHODS AND RESULTS:SRM 3-5 cases (N = 505) and statin treatment-tolerant controls (N = 2047) were recruited from multiple sites in North America and Europe. SRM 3-5 was defined as symptoms consistent with muscle injury and an elevated creatine phosphokinase level >4 times upper limit of normal without another likely cause of muscle injury. Whole-exome sequencing and variant calling was coordinated from two analysis centres, and results of single-variant and gene-based burden tests were meta-analysed. No genome-wide significant associations were identified. Given the large number of cases, we had 80% power to identify a variant with minor allele frequency of 0.01 that increases the risk of SRM 6-fold at genome-wide significance. CONCLUSIONS:In this large whole-exome sequencing study of severe statin-related muscle injury conducted to date, we did not find evidence that rare coding variants are responsible for this adverse drug reaction. Larger sample sizes would be required to identify rare variants with small effects, but it is unclear whether such findings would be clinically actionable

Predicted risks of radiogenic cardiac toxicity in two pediatric patients undergoing photon or proton radiotherapy

BACKGROUND: Hodgkin disease (HD) and medulloblastoma (MB) are common malignancies found in children and young adults, and radiotherapy is part of the standard treatment. It was reported that these patients who received radiation therapy have an increased risk of cardiovascular late effects. We compared the predicted risk of developing radiogenic cardiac toxicity after photon versus proton radiotherapies for a pediatric patient with HD and a pediatric patient with MB. METHODS: In the treatment plans, each patient’s heart was contoured in fine detail, including substructures of the pericardium and myocardium. Risk calculations took into account both therapeutic and stray radiation doses. We calculated the relative risk (RR) of cardiac toxicity using a linear risk model and the normal tissue complication probability (NTCP) values using relative seriality and Lyman models. Uncertainty analyses were also performed. RESULTS: The RR values of cardiac toxicity for the HD patient were 7.27 (proton) and 8.37 (photon), respectively; the RR values for the MB patient were 1.28 (proton) and 8.39 (photon), respectively. The predicted NTCP values for the HD patient were 2.17% (proton) and 2.67% (photon) for the myocardium, and were 2.11% (proton) and 1.92% (photon) for the whole heart. The predicted ratios of NTCP values (proton/photon) for the MB patient were much less than unity. Uncertainty analyses revealed that the predicted ratio of risk between proton and photon therapies was sensitive to uncertainties in the NTCP model parameters and the mean radiation weighting factor for neutrons, but was not sensitive to heart structure contours. The qualitative findings of the study were not sensitive to uncertainties in these factors. CONCLUSIONS: We conclude that proton and photon radiotherapies confer similar predicted risks of cardiac toxicity for the HD patient in this study, and that proton therapy reduced the predicted risk for the MB patient in this study

A FRUITFULL-like gene is associated with genetic variation for fruit flesh firmness in apple (Malus domestica Borkh.)

The FRUITFULL (FUL) and SHATTERPROOF (SHP) genes are involved in regulating fruit development and dehiscence in Arabidopsis. We tested the hypothesis that this class of genes are also involved in regulating the development of fleshy fruits, by exploring genetic and phenotypic variation within the apple (Malus domestica) gene pool. We isolated and characterised the genomic sequences of two candidate orthologous FUL-like genes, MdMADS2.1 and MdMADS2.2. These were mapped using the reference population ‘Prima x Fiesta’ to loci on Malus linkage groups LG14 and LG06, respectively. An additional MADS-box gene, MdMADS14, shares high amino acid identity with the Arabidopsis SHATTERPROOF1/2 genes and was mapped to Malus linkage group LG09. Association analysis between quantitative fruit flesh firmness estimates of ‘Prima x Fiesta’ progeny and the MdMADS2.1, MdMADS2.2 and MdMADS14 loci was carried out using a mixed model analysis of variance. This revealed a significant association (P < 0.01) between MdMADS2.1 and fruit flesh firmness. Further evidence for the association between MdMADS2.1 and fruit flesh firmness was obtained using a case–control population-based genetic association approach. For this, a polymorphic repeat, (AT)n, in the 3′ UTR of MdMADS2.1 was used as a locus-specific marker to screen 168 apple accessions for which historical assessments of fruit texture attributes were available. This analysis revealed a significant association between the MdMADS2.1 and fruit flesh firmness at both allelic (χ 2 = 34, df = 9, P < 0.001) and genotypic (χ 2 = 57, df = 32, P < 0.01) levels

Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren’s syndrome

Sjögren’s syndrome is a common autoimmune disease (~0.7% of European Americans) typically presenting as keratoconjunctivitis sicca and xerostomia. In addition to strong association within the HLA region at 6p21 (Pmeta=7.65×10−114), we establish associations with IRF5-TNPO3 (Pmeta=2.73×10−19), STAT4 (Pmeta=6.80×10−15), IL12A (Pmeta =1.17×10−10), FAM167A-BLK (Pmeta=4.97×10−10), DDX6-CXCR5 (Pmeta=1.10×10−8), and TNIP1 (Pmeta=3.30×10−8). Suggestive associations with Pmeta<5×10−5 were observed with 29 regions including TNFAIP3, PTTG1, PRDM1, DGKQ, FCGR2A, IRAK1BP1, ITSN2, and PHIP amongst others. These results highlight the importance of genes involved in both innate and adaptive immunity in Sjögren’s syndrome

Polycomb Target Genes Are Silenced in Multiple Myeloma

Multiple myeloma (MM) is a genetically heterogeneous disease, which to date remains fatal. Finding a common mechanism for initiation and progression of MM continues to be challenging. By means of integrative genomics, we identified an underexpressed gene signature in MM patient cells compared to normal counterpart plasma cells. This profile was enriched for previously defined H3K27-tri-methylated genes, targets of the Polycomb group (PcG) proteins in human embryonic fibroblasts. Additionally, the silenced gene signature was more pronounced in ISS stage III MM compared to stage I and II. Using chromatin immunoprecipitation (ChIP) assay on purified CD138+ cells from four MM patients and on two MM cell lines, we found enrichment of H3K27me3 at genes selected from the profile. As the data implied that the Polycomb-targeted gene profile would be highly relevant for pharmacological treatment of MM, we used two compounds to chemically revert the H3K27-tri-methylation mediated gene silencing. The S-adenosylhomocysteine hydrolase inhibitor 3-Deazaneplanocin (DZNep) and the histone deacetylase inhibitor LBH589 (Panobinostat), reactivated the expression of genes repressed by H3K27me3, depleted cells from the PRC2 component EZH2 and induced apoptosis in human MM cell lines. In the immunocompetent 5T33MM in vivo model for MM, treatment with LBH589 resulted in gene upregulation, reduced tumor load and increased overall survival. Taken together, our results reveal a common gene signature in MM, mediated by gene silencing via the Polycomb repressor complex. The importance of the underexpressed gene profile in MM tumor initiation and progression should be subjected to further studies

Anticoagulants and the Propagation Phase of Thrombin Generation

The view that clot time-based assays do not provide a sufficient assessment of an individual's hemostatic competence, especially in the context of anticoagulant therapy, has provoked a search for new metrics, with significant focus directed at techniques that define the propagation phase of thrombin generation. Here we use our deterministic mathematical model of tissue-factor initiated thrombin generation in combination with reconstructions using purified protein components to characterize how the interplay between anticoagulant mechanisms and variable composition of the coagulation proteome result in differential regulation of the propagation phase of thrombin generation. Thrombin parameters were extracted from computationally derived thrombin generation profiles generated using coagulation proteome factor data from warfarin-treated individuals (N = 54) and matching groups of control individuals (N = 37). A computational clot time prolongation value (cINR) was devised that correlated with their actual International Normalized Ratio (INR) values, with differences between individual INR and cINR values shown to derive from the insensitivity of the INR to tissue factor pathway inhibitor (TFPI). The analysis suggests that normal range variation in TFPI levels could be an important contributor to the failure of the INR to adequately reflect the anticoagulated state in some individuals. Warfarin-induced changes in thrombin propagation phase parameters were then compared to those induced by unfractionated heparin, fondaparinux, rivaroxaban, and a reversible thrombin inhibitor. Anticoagulants were assessed at concentrations yielding equivalent cINR values, with each anticoagulant evaluated using 32 unique coagulation proteome compositions. The analyses showed that no anticoagulant recapitulated all features of warfarin propagation phase dynamics; differences in propagation phase effects suggest that anticoagulants that selectively target fXa or thrombin may provoke fewer bleeding episodes. More generally, the study shows that computational modeling of the response of core elements of the coagulation proteome to a physiologically relevant tissue factor stimulus may improve the monitoring of a broad range of anticoagulants

Shiga Toxin 1 Induces on Lipopolysaccharide-Treated Astrocytes the Release of Tumor Necrosis Factor-alpha that Alter Brain-Like Endothelium Integrity

The hemolytic uremic syndrome (HUS) is characterized by hemolytic anemia, thrombocytopenia and renal dysfunction. The typical form of HUS is generally associated with infections by Gram-negative Shiga toxin (Stx)-producing Escherichia coli (STEC). Endothelial dysfunction induced by Stx is central, but bacterial lipopolysaccharide (LPS) and neutrophils (PMN) contribute to the pathophysiology. Although renal failure is characteristic of this syndrome, neurological complications occur in severe cases and is usually associated with death. Impaired blood-brain barrier (BBB) is associated with damage to cerebral endothelial cells (ECs) that comprise the BBB. Astrocytes (ASTs) are inflammatory cells in the brain and determine the BBB function. ASTs are in close proximity to ECs, hence the study of the effects of Stx1 and LPS on ASTs, and the influence of their response on ECs is essential. We have previously demonstrated that Stx1 and LPS induced activation of rat ASTs and the release of inflammatory factors such as TNF-α, nitric oxide and chemokines. Here, we demonstrate that rat ASTs-derived factors alter permeability of ECs with brain properties (HUVECd); suggesting that functional properties of BBB could also be affected. Additionally, these factors activate HUVECd and render them into a proagregant state promoting PMN and platelets adhesion. Moreover, these effects were dependent on ASTs secreted-TNF-α. Stx1 and LPS-induced ASTs response could influence brain ECs integrity and BBB function once Stx and factors associated to the STEC infection reach the brain parenchyma and therefore contribute to the development of the neuropathology observed in HUS