The Fe and Zn isotope composition of deep mantle source regions: Insights from Baffin Island picrites

Young (61 Ma) unaltered picrites from Baffin Island, northwest Canada, possess some of the highest 3He/4He (up to 50 Ra) seen on Earth, and provide a unique opportunity to study primordial mantle that has escaped subsequent chemical modification. These high-degree partial melts also record anomalously high 182W/184W ratios, but their Sr-Nd-Hf-Pb isotopic compositons (including 142Nd) are indistinguishable from those of North Atlantic mid-ocean ridge basalts. New high precision Fe and Zn stable isotope analyses of Baffin Island picrites show limited variability with δ56Fe ranging from −0.03‰ to 0.13‰ and δ66Zn varying from 0.18‰ to 0.28‰. However, a clear inflection is seen in both sets of isotope data around the composition of the parental melt (MgO = 21 wt %; δ56Fe = 0.08 ± 0.04‰; and δ66Zn = 0.24 ± 0.03‰), with two diverging trends interpreted to reflect the crystallisation of olivine and spinel in low-MgO samples and the accumulation of olivine at higher MgO. Olivine mineral separates are significantly isotopically lighter than their corresponding whole rocks (δ56Fe ≥ −0.62‰ and δ66Zn ≥ −0.22‰), with analyses of individual olivine phenocrysts having extremely variable Fe isotope compositions (δ56Fe = −0.01‰ to −0.80‰). By carrying out modelling in three-isotope space, we show that the very negative Fe isotope compositions of olivine phenocryst are the result of kinetic isotope fractionation from disequilibrium diffusional processes. An excellent correlation is observed between δ56Fe and δ66Zn, demonstrating that Zn isotopes are fractionated by the same processes as Fe in simple systems dominated by magmatic olivine. The incompatible behaviour of Cu during magmatic evolution is consistent with the sulfide-undersaturated nature of these melts. Consequently Zn behaves as a purely lithophile element, and estimates of the bulk Earth Zn isotope composition based on Baffin Island should therefore be robust. The ancient undegassed lower mantle sampled at Baffin Island possesses a δ56Fe value that is within error of previous estimates of bulk mantle δ56Fe, however, our estimate of the Baffin mantle δ66Zn (0.20 ± 0.03‰) is significantly lower than some previous estimates. Comparison of our new data with those for Archean and Proterozoic komatiites is consistent with the Fe and Zn isotope composition of the mantle remaining constant from at least 3 Ga to the present day. By focusing on large-degree partial melts (e.g. komatiites and picrites) we are potenitally biasing our record to samples that will inevitably have interacted with, entrained and melted the ambient shallow mantle during ascent. For a major element such as Fe, that will continuosly participate in melting as it rises through the mantle, the final isotopic compositon of the magama will be a weighted average of the complete melting column. Thus it is unsuprising that minimal Fe isotope variation are seen between localities. In contrast, the unique geochemical signatures (e.g. He and W) displayed by the Baffin Island picrites are inferred to solely originate from the lowermost mantle and will be continuously diluted upon magma ascent

Proteomic analysis of total cellular proteins of human neutrophils

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Peptide characterization of mature fluorotic and control human enamel

Exposure to high fluoride levels during amelogenesis causes enamel fluorosis. This study aimed to determine and compare the amino acid sequences in the enamel of fluorotic and control teeth. This investigation included enamel samples obtained from erupted and non-erupted third molars with either TF grade 4-6 (n=7) fluorosis or no sign of fluorosis (controls, n=7). The samples were kept frozen at -20 °C until protein extraction. Samples were etched and processed with a cocktail of proteinase inhibitors and immediately analyzed. Matrix Assisted Laser Desorption/Ionization-Time-Of-Flight/Time-of-Flight Mass Spectrometry (MALDI-TOF/TOF) followed by MASCOT search aided the peptides analysis. The more abundant peptides bore the N-terminal amelogenin sequences WYQSIRPPYP (which is specific for the X-encoded amelogenin) and MPLPPHPGHPGYINF (which does not show sexual dimorphism) were not different in control or fluorotic enamel. There was no missing proteolytic cleavage in the fluorotic samples, which suggested that the increased amount of protein described in fluorotic enamel did not stem from the decreased ability of proteinases to cleave the proteins in humans. This study showed how to successfully obtain peptide from superficial enamel. A relatively low number of teeth was sufficient to provide good data on the actual peptides found in mature enamel2716671CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPSem informaçãoSem informaçãoExposição a altos níveis de flúor durante a amelogênese causa fluorose no esmalte. Este estudo tem como objetivo determinar e comparar as sequências de aminoácidos presentes no esmalte de dentes controles e fluoróticos. A investigação incluiu amostras de esmalte obtidas de terceiros molares erupcionados e não erupcionados, ambas ou com grau de fluorose TF 4-6 (n=7) ou sem sinais de fluorose (controles, n=7), congelados a -20 oC até a extração das proteínas. As amostras sofreram ataque ácido e foram processadas utilizando um coquetel de inibidores de proteinases, sendo imediatamente analisadas. MALDI-TOF/TOF seguido pela pesquisa com MASCOT foram utilizados para a análise dos peptídeos. Os peptídeos mais abundantes foram das amelogeninas com sequências N-terminal WYQSIRPPYP (que é codificada especificamente pela amelogenina X) e MPLPPHPGHPGYINF (que não apresenta dimorfismo sexual algum), não havendo diferenças entre dentes fluoróticos e controles. Nenhuma alteração na proteólise ocorreu nas amostras fluoróticas, o que sugere que o aumento na quantidade de proteínas existentes nas amostras fluoróticas não está correlacionada a habilidade das proteinases em clivar as proteínas em humanos. Este estudo mostrou como extrair com sucesso peptídeos do esmalte superficial. Um número relativamente baixo de dentes foram suficientes para se obter ótimos dados a respeito de peptídeos encontrados no esmalte madur

The behavior of iron and zinc stable isotopes accompanying the subduction of mafic oceanic crust: A case study from Western Alpine ophiolites

Arc lavas display elevated Fe3+/ΣFe ratios relative to MORB. One mechanism to explain this is the mobilization and transfer of oxidized or oxidizing components from the subducting slab to the mantle wedge. Here we use iron and zinc isotopes, which are fractionated upon complexation by sulfide, chloride, and carbonate ligands, to remark on the chemistry and oxidation state of fluids released during prograde metamorphism of subducted oceanic crust. We present data for metagabbros and metabasalts from the Chenaillet massif, Queyras complex, and the Zermatt-Saas ophiolite (Western European Alps), which have been metamorphosed at typical subduction zone P-T conditions and preserve their prograde metamorphic history. There is no systematic, detectable fractionation of either Fe or Zn isotopes across metamorphic facies, rather the isotope composition of the eclogites overlaps with published data for MORB. The lack of resolvable Fe isotope fractionation with increasing prograde metamorphism likely reflects the mass balance of the system, and in this scenario Fe mobility is not traceable with Fe isotopes. Given that Zn isotopes are fractionated by S-bearing and C-bearing fluids, this suggests that relatively small amounts of Zn are mobilized from the mafic lithologies in within these types of dehydration fluids. Conversely, metagabbros from the Queyras that are in proximity to metasediments display a significant Fe isotope fractionation. The covariation of δ56Fe of these samples with selected fluid mobile elements suggests the infiltration of sediment derived fluids with an isotopically light signature during subduction

Expression of human protein S100A7 (psoriasin), preparation of antibody and application to human larynx squamous cell carcinoma

Background\ud Up-regulation of S100A7 (Psoriasin), a small calcium-binding protein, is associated with the development of several types of carcinomas, but its function and possibility to serve as a diagnostic or prognostic marker have not been fully defined. In order to prepare antibodies to the protein for immunohistochemical studies we produced the recombinant S100A7 protein in E. coli. mRNA extracted from human tracheal tumor tissue which was amplified by RT-PCR to provide the region coding for the S100A7 gene. The amplified fragment was cloned in the vector pCR2.1-TOPO and sub-cloned in the expression vector pAE. The protein rS100A7 (His-tag) was expressed in E. coli BL21::DE3, purified by affinity chromatography on an Ni-NTA column, recovered in the 2.0 to 3.5 mg/mL range in culture medium, and used to produce a rabbit polyclonal antibody anti-rS100A7 protein. The profile of this polyclonal antibody was evaluated in a tissue microarray.\ud \ud \ud Results\ud The rS100A7 (His-tag) protein was homogeneous by SDS-PAGE and mass spectrometry and was used to produce an anti-recombinant S100A7 (His-tag) rabbit serum (polyclonal antibody anti-rS100A7). The molecular weight of rS100A7 (His-tag) protein determined by linear MALDI-TOF-MS was 12,655.91 Da. The theoretical mass calculated for the nonapeptide attached to the amino terminus is 12,653.26 Da (delta 2.65 Da). Immunostaining with the polyclonal anti-rS100A7 protein generated showed reactivity with little or no background staining in head and neck squamous cell carcinoma cells, detecting S100A7 both in nucleus and cytoplasm. Lower levels of S100A7 were detected in non-neoplastic tissue.\ud \ud \ud Conclusions\ud The polyclonal anti-rS100A7 antibody generated here yielded a good signal-to-noise contrast and should be useful for immunohistochemical detection of S100A7 protein. Its potential use for other epithelial lesions besides human larynx squamous cell carcinoma and non-neoplastic larynx should be explored in future.FAPESP doctoral fellowship n°. 05/50781-2CTC/CEPID/FAPESP [grant n. 1998/14247-6

Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer.

BACKGROUND: There is a need to improve prediction of response to chemotherapy in breast cancer in order to improve clinical management and this may be achieved by harnessing computational metrics of tissue pathology. We investigated the association between quantitative image metrics derived from computational analysis of digital pathology slides and response to chemotherapy in women with breast cancer who received neoadjuvant chemotherapy. METHODS: We digitised tissue sections of both diagnostic and surgical samples of breast tumours from 768 patients enrolled in the Neo-tAnGo randomized controlled trial. We subjected digital images to systematic analysis optimised for detection of single cells. Machine-learning methods were used to classify cells as cancer, stromal or lymphocyte and we computed estimates of absolute numbers, relative fractions and cell densities using these data. Pathological complete response (pCR), a histological indicator of chemotherapy response, was the primary endpoint. Fifteen image metrics were tested for their association with pCR using univariate and multivariate logistic regression. RESULTS: Median lymphocyte density proved most strongly associated with pCR on univariate analysis (OR 4.46, 95 % CI 2.34-8.50, p < 0.0001; observations = 614) and on multivariate analysis (OR 2.42, 95 % CI 1.08-5.40, p = 0.03; observations = 406) after adjustment for clinical factors. Further exploratory analyses revealed that in approximately one quarter of cases there was an increase in lymphocyte density in the tumour removed at surgery compared to diagnostic biopsies. A reduction in lymphocyte density at surgery was strongly associated with pCR (OR 0.28, 95 % CI 0.17-0.47, p < 0.0001; observations = 553). CONCLUSIONS: A data-driven analysis of computational pathology reveals lymphocyte density as an independent predictor of pCR. Paradoxically an increase in lymphocyte density, following exposure to chemotherapy, is associated with a lack of pCR. Computational pathology can provide objective, quantitative and reproducible tissue metrics and represents a viable means of outcome prediction in breast cancer. TRIAL REGISTRATION: ClinicalTrials.gov NCT00070278 ; 03/10/2003.We acknowledge funding from Cancer Research UK and NIHR Cambridge Biomedical Research Centre. HRA is an NIHR Academic Clinical Lecturer supported by a Career Development Fellowship from the Pathological Society of Great Britain and Northern Ireland and a Starter Grant for Clinical Lecturers from the Academy of Medical Sciences.This is the final version of the article. It first appeared from BioMed Central via https://doi.org 10.1186/s13058-016-0682-

Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel

To date, most BC GWASs have been performed Background Polygenic risk score (PRS), calculated in individuals of European (EUR) ancestry, and based on genome-wide association studies (GWASs), the generalisation of EUR-based PRS to other can improve breast cancer (BC) risk assessment. populations is a major challenge. In this study, we examined the performance of EUR-based BC PRS models in Ashkenazi Jewish (AJ) women. Methods We generated PRSs based on data on EUR women from the Breast Cancer Association Consortium (BCAC). We tested the performance of the PRSs in a cohort of 2161 AJ women from Israel (1437 cases and 724 controls) from BCAC (BCAC cohort from Israel (BCAC-IL)). In addition, we tested the performance of these EUR-based BC PRSs, as well as the established 313-SNP EUR BC PRS, in an independent cohort of 181 AJ women from Hadassah Medical Center (HMC) in Israel. Results In the BCAC-IL cohort, the highest OR per 1 SD was 1.56 (±0.09). The OR for AJ women at the top 10% of the PRS distribution compared with the middle quintile was 2.10 (±0.24). In the HMC cohort, the OR per 1 SD of the EUR-based PRS that performed best in the BCAC-IL cohort was 1.58±0.27. The OR per 1 SD of the commonly used 313-SNP BC PRS was 1.64 (±0.28). Conclusions Extant EUR GWAS data can be used for generating PRSs that identify AJ women with markedly elevated risk of BC and therefore hold promise for improving BC risk assessment in AJ women.</p

Obstetric Outcomes in Women with Rheumatic Disease and COVID-19 in the Context of Vaccination Status

OBJECTIVE: To describe obstetric outcomes based on COVID-19 vaccination status, in women with rheumatic and musculoskeletal diseases (RMDs) who developed COVID-19 during pregnancy. METHODS: Data regarding pregnant women entered into the COVID-19 Global Rheumatology Alliance registry from 24 March 2020-25 February 2022 were analysed. Obstetric outcomes were stratified by number of COVID-19 vaccine doses received prior to COVID-19 infection in pregnancy. Descriptive differences between groups were tested using the chi -square or Fisher's exact test. RESULTS: There were 73 pregnancies in 73 women with RMD and COVID-19. Overall, 24.7% (18) of pregnancies were ongoing, while of the 55 completed pregnancies 90.9% (50) of pregnancies resulted in livebirths. At the time of COVID-19 diagnosis, 60.3% (n = 44) of women were unvaccinated, 4.1% (n = 3) had received one vaccine dose while 35.6% (n = 26) had two or more doses. Although 83.6% (n = 61) of women required no treatment for COVID-19, 20.5% (n = 15) required hospital admission. COVID-19 resulted in delivery in 6.8% (n = 3) of unvaccinated women and 3.8% (n = 1) of fully vaccinated women. There was a greater number of preterm births (PTB) in unvaccinated women compared with fully vaccinated 29.5% (n = 13) vs 18.2%(n = 2). CONCLUSION: In this descriptive study, unvaccinated pregnant women with RMD and COVID-19 had a greater number of PTB compared with those fully vaccinated against COVID-19. Additionally, the need for COVID-19 pharmacological treatment was uncommon in pregnant women with RMD regardless of vaccination status. These results support active promotion of COVID-19 vaccination in women with RMD who are pregnant or planning a pregnancy

Encorafenib plus binimetinib versus vemurafenib or encorafenib in patients with BRAF-mutant melanoma (COLUMBUS): a multicentre, open-label, randomised phase 3 trial

BACKGROUND Combined BRAF-MEK inhibitor therapy is the standard of care for BRAF-mutant advanced melanoma. We investigated encorafenib, a BRAF inhibitor with unique target-binding properties, alone or in combination with the MEK inhibitor binimetinib, versus vemurafenib in patients with advanced BRAF-mutant melanoma. METHODS COLUMBUS was conducted as a two-part, randomised, open-label phase 3 study at 162 hospitals in 28 countries. Eligible patients were aged 18 years or older and had histologically confirmed locally advanced (American Joint Committee on Cancer [AJCC] stage IIIB, IIIC, or IV), unresectable or metastatic cutaneous melanoma, or unknown primary melanoma; a BRAF or BRAF mutation; an Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1; and were treatment naive or had progressed on or after previous first-line immunotherapy. In part 1 of the study, patients were randomly assigned (1:1:1) via interactive response technology to receive either oral encorafenib 450 mg once daily plus oral binimetinib 45 mg twice daily (encorafenib plus binimetinib group), oral encorafenib 300 mg once daily (encorafenib group), or oral vemurafenib 960 mg twice daily (vemurafenib group). The primary endpoint was progression-free survival by blinded independent central review for encorafenib plus binimetinib versus vemurafenib. Efficacy analyses were by intention-to-treat. Safety was analysed in patients who received at least one dose of study drug and one postbaseline safety assessment. The results of part 2 will be published separately. This study is registered with ClinicalTrials.gov, number NCT01909453, and EudraCT, number 2013-001176-38. FINDINGS Between Dec 30, 2013, and April 10, 2015, 577 of 1345 screened patients were randomly assigned to either the encorafenib plus binimetinib group (n=192), the encorafenib group (n=194), or the vemurafenib group (n=191). With a median follow-up of 16·6 months (95% CI 14·8-16·9), median progression-free survival was 14·9 months (95% CI 11·0-18·5) in the encorafenib plus binimetinib group and 7·3 months (5·6-8·2) in the vemurafenib group (hazard ratio [HR] 0·54, 95% CI 0·41-0·71; two-sided p<0·0001). The most common grade 3-4 adverse events seen in more than 5% of patients in the encorafenib plus binimetinib group were increased γ-glutamyltransferase (18 [9%] of 192 patients), increased creatine phosphokinase (13 [7%]), and hypertension (11 [6%]); in the encorafenib group they were palmoplantar erythrodysaesthesia syndrome (26 [14%] of 192 patients), myalgia (19 [10%]), and arthralgia (18 [9%]); and in the vemurafenib group it was arthralgia (11 [6%] of 186 patients). There were no treatment-related deaths except for one death in the combination group, which was considered possibly related to treatment by the investigator. INTERPRETATION Encorafenib plus binimetinib and encorafenib monotherapy showed favourable efficacy compared with vemurafenib. Overall, encorafenib plus binimetinib appears to have an improved tolerability profile compared with encorafenib or vemurafenib. Encorafenib plus binimetinib could represent a new treatment option for patients with BRAF-mutant melanoma. FUNDING Array BioPharma, Novartis

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas