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Formalin‐fixed, paraffin‐embedded (FFPE ), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here, we developed a pressure cycling technology (PCT )‐SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PC a) and diffuse large B‐cell lymphoma (DLBCL ) samples. We show that the proteome patterns of FFPE PC a tissue samples and their analogous fresh‐frozen (FF ) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PC a tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between 1 and 15 years in a biobank and show a high degree of the proteome pattern similarity between two types of histological regions in small FFPE samples, that is, punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of a certain degree of biological variations. Applying the method to two independent DLBCL cohorts, we identified myeloperoxidase, a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PC a and DLBCL have been discovered.
Introduction: Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) occurs approximately 1 in 3.500 live births representing the most common malformation of the upper digestive tract. Only half a century ago, EA/TEF was fatal among affected newborns suggesting that the steady birth prevalence might in parts be due to mutational de novo events in genes involved in foregut development.
Methods: To identify mutational de novo events in EA/TEF patients, we surveyed the exome of 30 case-parent trios. Identified and confirmed de novo variants were prioritized using in silico prediction tools. To investigate the embryonic role of genes harboring prioritized de novo variants we performed targeted analysis of mouse transcriptome data of esophageal tissue obtained at the embryonic day (E) E8.5, E12.5, and postnatal.
Results: In total we prioritized 14 novel de novo variants in 14 different genes (APOL2, EEF1D, CHD7, FANCB, GGT6, KIAA0556, NFX1, NPR2, PIGC, SLC5A2, TANC2, TRPS1, UBA3, and ZFHX3) and eight rare de novo variants in eight additional genes (CELSR1, CLP1, GPR133, HPS3, MTA3, PLEC, STAB1, and PPIP5K2). Through personal communication during the project, we identified an additional EA/TEF case-parent trio with a rare de novo variant in ZFHX3. In silico prediction analysis of the identified variants and comparative analysis of mouse transcriptome data of esophageal tissue obtained at E8.5, E12.5, and postnatal prioritized CHD7, TRPS1, and ZFHX3 as EA/TEF candidate genes. Re-sequencing of ZFHX3 in additional 192 EA/TEF patients did not identify further putative EA/TEF-associated variants.
Conclusion: Our study suggests that rare mutational de novo events in genes involved in foregut development contribute to the development of EA/TEF.
Background: Due to constantly rising air pollution levels as well as an increasing awareness of the hazardousness of air pollutants, new laws and rules have recently been passed. Although there has been a large amount of research on this topic, bibliometric data is still to be collected. Thus this study provides a scientometric approach to the material published on this subject so far.
Methods: For this purpose, data retrieved from the "Web of Science" provided by the Thomson Scientific Institute was analyzed and visualized both with density-equalizing methods and classic data-processing methods such as tables and charts.
Results: For the time span between 1955 and 2006, 26,253 items were listed and related to the topic of air pollution, published by 124 countries in 24 different languages. General citation activity has been constantly increasing since the beginning of the examined period. However, beginning with the year 1991, citation levels have been rising exponentially each year, reaching 39,220 citations in the year 2006. The United States, the UK and Germany were the three most productive countries in the area, with English and German ranked first and second in publishing languages, followed by French. An article published by Dockery, Pope, Xu et al. was both the most cited in total numbers and in average citation rate. J. Schwartz was able to claim the highest total number of citations on his publications, while D.W. Dockery has the highest citation rate per publication. As to the subject areas the items are assigned with, the most item were published in Environmental Sciences, followed by Meteorology & Atmospheric Sciences and Public, Environmental & Occupational Health. Nine out of the ten publishing journals with more than 300 entries dealt with environmental interests and one dealt with epidemiology.
Conclusions: Using the method of density-equalizing mapping and further common data processing procedures, it can be concluded that scientific work concerning air pollution and related topics enjoys unbrokenly growing scientific interest. This can be observed both in publication numbers and in citation activity.
Chimeric antigen receptor (CAR) T cells are a novel class of anti-cancer therapy in which autologous or allogeneic T cells are engineered to express a CAR targeting a membrane antigen. In Europe, tisagenlecleucel (Kymriah™) is approved for the treatment of refractory/relapsed acute lymphoblastic leukemia in children and young adults as well as relapsed/refractory diffuse large B-cell lymphoma, while axicabtagene ciloleucel (Yescarta™) is approved for the treatment of relapsed/refractory high-grade B-cell lymphoma and primary mediastinal B-cell lymphoma. Both agents are genetically engineered autologous T cells targeting CD19. These practical recommendations, prepared under the auspices of the European Society of Blood and Marrow Transplantation, relate to patient care and supply chain management under the following headings: patient eligibility, screening laboratory tests and imaging and work-up prior to leukapheresis, how to perform leukapheresis, bridging therapy, lymphodepleting conditioning, product receipt and thawing, infusion of CAR T cells, short-term complications including cytokine release syndrome and immune effector cell-associated neurotoxicity syndrome, antibiotic prophylaxis, medium-term complications including cytopenias and B-cell aplasia, nursing and psychological support for patients, long-term follow-up, post-authorization safety surveillance, and regulatory issues. These recommendations are not prescriptive and are intended as guidance in the use of this novel therapeutic class.
Nep1 (Emg1) is a highly conserved nucleolar protein with an essential function in ribosome biogenesis. A mutation in the human Nep1 homolog causes Bowen–Conradi syndrome—a severe developmental disorder. Structures of Nep1 revealed a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases suggesting that Nep1 acts as a methyltransferase in ribosome biogenesis. The target for this putative methyltransferase activity has not been identified yet. We characterized the RNA-binding specificity of Methanocaldococcus jannaschii Nep1 by fluorescence- and NMR-spectroscopy as well as by yeast three-hybrid screening. Nep1 binds with high affinity to short RNA oligonucleotides corresponding to nt 910–921 of M. jannaschii 16S rRNA through a highly conserved basic surface cleft along the dimer interface. Nep1 only methylates RNAs containing a pseudouridine at a position corresponding to a previously identified hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in eukaryotic 18S rRNAs. Analysis of the methylated nucleoside by MALDI-mass spectrometry, HPLC and NMR shows that the methyl group is transferred to the N1 of the pseudouridine. Thus, Nep1 is the first identified example of an N1-specific pseudouridine methyltransferase. This enzymatic activity is also conserved in human Nep1 suggesting that Nep1 is the methyltransferase in the biosynthesis of m1acp3-Psi in eukaryotic 18S rRNAs.
Background: Hepatitis delta frequently leads to liver cirrhosis and hepatic decompensation. As treatment options are limited, there is a need for biomarkers to determine disease activity and to predict the risk of disease progression. We hypothesized that anti-HDV IgM could represent such a marker.
Methods: Samples of 120 HDV-infected patients recruited in an international multicenter treatment trial (HIDIT-2) were studied. Anti-HDV IgM testing was performed using ETI-DELTA-IGMK-2-assay (DiaSorin). In addition, fifty cytokines, chemokines and angiogenetic factors were measured using multiplex technology (Bio-Plex System). A second independent cohort of 78 patients was studied for the development of liver-related clinical endpoints (decompensation, HCC, liver transplantation or death; median follow up of 3.0 years, range 0.6–12).
Results: Anti-HDV IgM serum levels were negative in 18 (15%), low (OD<0.5) in 76 (63%), and high in 26 (22%) patients of the HIDIT-2 cohort. Anti-HDV IgM were significantly associated with histological inflammatory (p<0.01) and biochemical disease activity (ALT, AST p<0.01). HDV replication was independent from anti-HDV IgM, however, low HBV-DNA levels were observed in groups with higher anti-HDV IgM levels (p<0.01). While high IP-10 (CXCL10) levels were seen in greater groups of anti-HDV IgM levels, various other antiviral cytokines were negatively associated with anti-HDV IgM. Associations between anti-HDV IgM and ALT, AST, HBV-DNA were confirmed in the independent cohort. Clinical endpoints occurred in 26 anti-HDV IgM positive patients (39%) but in only one anti-HDV IgM negative individual (9%; p = 0.05).
Conclusions: Serum anti-HDV IgM is a robust, easy-to-apply and relatively cheap marker to determine disease activity in hepatitis delta which has prognostic implications. High anti-HDV IgM levels may indicate an activated interferon system but exhausted antiviral immunity.
Strenuous and unaccustomed exercise frequently lead to what has been coined “delayed onset muscle soreness” (DOMS). As implied by this term, it has been proposed that the associated pain and stiffness stem from micro-lesions, inflammation, or metabolite accumulation within the skeletal muscle. However, recent research points towards a strong involvement of the connective tissue. First, according to anatomical studies, the deep fascia displays an intimate structural relationship with the underlying skeletal muscle and may therefore be damaged during excessive loading. Second, histological and experimental studies suggest a rich supply of algogenic nociceptors whose stimulation evokes stronger pain responses than muscle irritation. Taken together, the findings support the hypothesis that DOMS originates in the muscle-associated connective tissue rather than in the muscle itself. Sports and fitness professionals designing exercise programs should hence consider fascia-oriented methods and techniques (e.g., foam rolling, collagen supplementation) when aiming to treat or prevent DOMS.
Background: Second hand smoke (ETS)-associated particulate matter (PM) contributes considerably to indoor air contamination and constitutes a health risk for passive smokers. Easy to measure, PM is a useful parameter to estimate the dosage of ETS that passive smokers are exposed to. Apart from its suitability as a surrogate parameter for ETS-exposure, PM itself affects human morbidity and mortality in a dose-dependent manner. We think that ETS-associated PM should be considered an independent hazard factor, separately from the many other known harmful compounds of ETS. We believe that brand-specific and tobacco-product-specific differences in the release of PM matter and that these differences are of public interest. Methods: To generate ETS of cigarettes and cigarillos as standardized and reproducible as possible, an automatic second hand smoke emitter (AETSE) was developed and placed in a glass chamber. L&M cigarettes ("without additives", "red label", "blue label"), L&M filtered cigarillos ("red") and 3R4F standard research cigarettes (as reference) were smoked automatically according to a self-developed, standardized protocol until the tobacco product was smoked down to 8 mm distance from the tipping paper of the filter. Results: Mean concentration (Cmean) and area under the curve (AUC) in a plot of PM2.5 against time were measured, and compared. CmeanPM2.5 were found to be 518 μg/m3 for 3R4F cigarettes, 576 μg/m3 for L&M "without additives" ("red"), 448 μg/m3 for L&M "blue label", 547 μg/m3 for L&M "red label", and 755 μg/m3 for L&M filtered cigarillos ("red"). AUCPM2.5-values were 208,214 μg/m3·s for 3R4F reference cigarettes, 204,629 μg/m3·s for L&M "without additives" ("red"), 152,718 μg/m3·s for L&M "blue label", 238,098 μg/m3·s for L&M "red label" and 796,909 μg/m3·s for L&M filtered cigarillos ("red"). Conclusion: Considering the large and significant differences in particulate matter emissions between cigarettes and cigarillos, we think that a favorable taxation of cigarillos is not justifiable.
Background: Classical dance comprises gender specific movement tasks. There is a lack of studies which investigate work related traumatic injuries in terms of gender specific differences in detail.
Objective: To define gender related differences of occupational accidents.
Methods: Basis for the evaluation were occupational injuries of professional dancers from three (n = 785; f: n = 358, m: n = 427) state theatres.
Results: The incidence rate (0.36 per year) was higher in males (m: 0.45, f: 0.29). There were gender specific differences as to the localizations of injuries, particularly the spine region (m: 17.3%, f: 9.8%, p = 0.05) and ankle joint (m: 23.7%, f: 35.5%, p = 0.003). Compared to male dancers, females sustained more injuries resulting from extrinsic factors. Significant differences could specifically be observed with dance floors (m: 8.8%, f: 15.1%, p = 0.02). There were also significant gender differences observed with movement vocabulary.
Conclusion: The clearly defined gender specific movement activities in classical dance are reflected in occupational accidents sustained. Organisational structures as well as work environment represent a burden likewise to male and female dancers. The presented differences support the development of gender specific injury prevention measures.
We have studied one-proton-removal reactions of about 500MeV/u 17Ne beams on a carbon target at the R3B/LAND setup at GSI by detecting beam-like 15O-p and determining their relative-energy distribution. We exclusively selected the removal of a 17Ne halo proton, and the Glauber-model analysis of the 16F momentum distribution resulted in an s2 contribution in the 17Ne ground state of about 40%.