Approach to risk stratification for papillary thyroid carcinoma based on molecular profiling: institutional analysis

BACKGROUND

Currently, treatment recommendations for papillary thyroid carcinoma are not based on the genetic background causing tumourigenesis. The aim of the present study was to correlate the mutational profile of papillary thyroid carcinoma with clinical parameters of tumour aggressiveness, to establish recommendations for risk-stratified surgical treatment.

METHOD

Papillary thyroid carcinoma tumour tissue of patients undergoing thyroid surgery at the University Medical Centre Mainz underwent analysis of BRAF, TERT promoter and RAS mutational status as well as potential RET and NTRK rearrangements. Mutation status was correlated with clinical course of disease.

RESULTS

One hundred and seventy-one patients operated for papillary thyroid carcinoma were included. The median age was 48 years (range 8-85) and 69 per cent (118/171) of patients were females. One hundred and nine papillary thyroid carcinomas were BRAF-V600E mutant, 16 TERT promotor mutant and 12 RAS mutant; 12 papillary thyroid carcinomas harboured RET rearrangements and two papillary thyroid carcinomas showed NTRK rearrangements. TERT promoter mutant papillary thyroid carcinomas had a higher risk of distant metastasis (OR 51.3, 7.0 to 1048.2, P < 0.001) and radioiodine-refractory disease (OR 37.8, 9.9 to 169.5, P < 0.001). Concomitant BRAF and TERT promoter mutations increased the risk of radioiodine-refractory disease in papillary thyroid carcinoma (OR 21.7, 5.6 to 88.9, P < 0.001). RET rearrangements were associated with a higher count of tumour-affected lymph nodes (OR 7950.9, 233.7 to 270495.7, P < 0.001) but did not influence distant metastasis or radioiodine-refractory disease.

CONCLUSIONS

Papillary thyroid carcinoma with concomitant BRAF-V600E and TERT promoter mutations demonstrated an aggressive course of disease, suggesting the need for a more extensive surgical strategy. RET rearrangement-positive papillary thyroid carcinoma did not affect the clinical outcome, potentially obviating the need for prophylactic lymphadenectomy.

Gene expression variability in long-term survivors of childhood cancer and cancer-free controls in response to ionizing irradiation

BACKGROUND

Differential expression analysis is usually adjusted for variation. However, most studies that examined the expression variability (EV) have used computations affected by low expression levels and did not examine healthy tissue. This study aims to calculate and characterize an unbiased EV in primary fibroblasts of childhood cancer survivors and cancer-free controls (N0) in response to ionizing radiation.

METHODS

Human skin fibroblasts of 52 donors with a first primary neoplasm in childhood (N1), 52 donors with at least one second primary neoplasm (N2 +), as well as 52 N0 were obtained from the KiKme case-control study and exposed to a high (2 Gray) and a low dose (0.05 Gray) of X-rays and sham- irradiation (0 Gray). Genes were then classified as hypo-, non-, or hyper-variable per donor group and radiation treatment, and then examined for over-represented functional signatures.

RESULTS

We found 22 genes with considerable EV differences between donor groups, of which 11 genes were associated with response to ionizing radiation, stress, and DNA repair. The largest number of genes exclusive to one donor group and variability classification combination were all detected in N0: hypo-variable genes after 0 Gray (n = 49), 0.05 Gray (n = 41), and 2 Gray (n = 38), as well as hyper-variable genes after any dose (n = 43). While after 2 Gray positive regulation of cell cycle was hypo-variable in N0, (regulation of) fibroblast proliferation was over-represented in hyper-variable genes of N1 and N2+. In N2+, 30 genes were uniquely classified as hyper-variable after the low dose and were associated with the ERK1/ERK2 cascade. For N1, no exclusive gene sets with functions related to the radiation response were detected in our data.

CONCLUSION

N2+ showed high degrees of variability in pathways for the cell fate decision after genotoxic insults that may lead to the transfer and multiplication of DNA-damage via proliferation, where apoptosis and removal of the damaged genome would have been appropriate. Such a deficiency could potentially lead to a higher vulnerability towards side effects of exposure to high doses of ionizing radiation, but following low-dose applications employed in diagnostics, as well.

Replication stress drives chromosomal instability in fibroblasts of childhood cancer survivors with second primary neoplasms

New development and optimization of oncologic strategies are steadily increasing the number of long-term cancer survivors being at risk of developing second primary neoplasms (SPNs) as a late consequence of genotoxic cancer therapies with the highest risk among former childhood cancer patients. Since risk factors and predictive biomarkers for therapy-associated SPN remain unknown, we examined the sensitivity to mild replication stress as a driver of genomic instability and carcinogenesis in fibroblasts from 23 long-term survivors of a pediatric first primary neoplasm (FPN), 22 patients with the same FPN and a subsequent SPN, and 22 controls with no neoplasm (NN) using the cytokinesis-block micronucleus (CBMN) assay. Mild replication stress was induced with the DNA-polymerase inhibitor aphidicolin (APH). Fibroblasts from patients with the DNA repair deficiency syndromes Bloom, Seckel, and Fanconi anemia served as positive controls and for validation of the CBMN assay supplemented by analysis of chromosomal aberrations, DNA repair foci (γH2AX/53BP1), and cell cycle regulation. APH treatment resulted in G2/M arrest and underestimation of cytogenetic damage beyond G2, which could be overcome by inhibition of Chk1. Basal micronuclei were significantly increased in DNA repair deficiency syndromes but comparable between NN, FPN, and SPN donors. After APH-induced replication stress, the average yield of micronuclei was significantly elevated in SPN donors compared to FPN (p = 0.013) as well as NN (p = 0.03) donors but substantially lower than for DNA repair deficiency syndromes. Our findings suggest that mild impairment of the response to replication stress induced by genotoxic impacts of DNA-damaging cancer therapies promotes genomic instability in a subset of long-term cancer survivors and may drive the development of an SPN. Our study provides a basis for detailed mechanistic studies as well as predictive bioassays for clinical surveillance, to identify cancer patients at high risk for SPNs at first diagnosis.

Self-administered questionnaire assessing childhood cancer treatments and associated risks for adverse health outcomes - The KiKme study

Background

Childhood cancer survivors (CCS) are at particularly high risk for therapy-related late sequelae, with secondary primary neoplasms (SPN) being the most detrimental. Since there is no standardized questionnaire for retrospective assessment of associations between prior cancer treatments and late health effects, we developed a self-administered questionnaire and validated it in a cohort of CCS.

Methods

CCS of a first primary neoplasm (FPN, N=340) only or with a subsequent SPN (N=101) were asked whether they had received cancer therapies. Self-reports were compared to participants' medical records on cancer therapies from hospitals and clinical studies (N=242). Cohen's Kappa (κ) was used to measure their agreement and logistic regression was used to identify factors influencing the concordance. Associations between exposure to cancer therapies and late health effects (overweight/obesity, diseases of the lipid metabolism and the thyroid gland, cardiovascular diseases, occurrence of SPN) were analyzed in all participants by applying generalized linear mixed models to calculate odds ratios (OR) and 95% confidence intervals (95%CI).

Results

For CCS of SPN, a perfect agreement was found between self-reports and medical records for chemotherapy (CT, κ=1.0) while the accordance for radiotherapy (RT) was lower but still substantial (κ=0.8). For the CCS of FPN the accordance was less precise (CT: κ=0.7, RT: κ=0.3). Cancer status, tumors of the central nervous system, sex, age at recruitment, vocational training, follow-up time, and comorbidities had no impact on agreement. CCS with exposure to CT were found to be less often overweight or obese compared to those without CT (OR=0.6 (95%CI 0.39; 0.91)). However, they were found to suffer more likely from thyroid diseases excluding thyroid cancers (OR=9.91 (95%CI 4.0; 24.57)) and hypercholesterolemia (OR=4.45 (95%CI 1.5; 13.23)). All other analyses did not show an association.

Conclusion

Our new questionnaire proved reliable for retrospective assessment of exposure to CT and RT in CCS of SPN. For the CCS of FPN, self-reported RT was very imprecise and should not be used for further analyses. We revealed an association between late health outcomes occurring as hypercholesterolemia and thyroid diseases, excluding thyroid cancer, and the use of CT for the treatment of childhood cancer.

Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls

Introduction

Long non-coding ribonucleic acids (lncRNAs) are involved in the cellular damage response following exposure to ionizing radiation as applied in radiotherapy. However, the role of lncRNAs in radiation response concerning intrinsic susceptibility to late effects of radiation exposure has not been examined in general or in long-term survivors of childhood cancer with and without potentially radiotherapy-related second primary cancers, in particular.

Methods

Primary skin fibroblasts (n=52 each) of long-term childhood cancer survivors with a first primary cancer only (N1), at least one second primary neoplasm (N2+), as well as tumor-free controls (N0) from the KiKme case-control study were matched by sex, age, and additionally by year of diagnosis and entity of the first primary cancer. Fibroblasts were exposed to 0.05 and 2 Gray (Gy) X-rays. Differentially expressed lncRNAs were identified with and without interaction terms for donor group and dose. Weighted co-expression networks of lncRNA and mRNA were constructed using WGCNA. Resulting gene sets (modules) were correlated to the radiation doses and analyzed for biological function.

Results

After irradiation with 0.05Gy, few lncRNAs were differentially expressed (N0: AC004801.4; N1: PCCA-DT, AF129075.3, LINC00691, AL158206.1; N2+: LINC02315). In reaction to 2 Gy, the number of differentially expressed lncRNAs was higher (N0: 152, N1: 169, N2+: 146). After 2 Gy, AL109976.1 and AL158206.1 were prominently upregulated in all donor groups. The co-expression analysis identified two modules containing lncRNAs that were associated with 2 Gy (module1: 102 mRNAs and 4 lncRNAs: AL158206.1, AL109976.1, AC092171.5, TYMSOS, associated with p53-mediated reaction to DNA damage; module2: 390 mRNAs, 7 lncRNAs: AC004943.2, AC012073.1, AC026401.3, AC092718.4, MIR31HG, STXBP5-AS1, TMPO-AS1, associated with cell cycle regulation).

Discussion

For the first time, we identified the lncRNAs AL158206.1 and AL109976.1 as involved in the radiation response in primary fibroblasts by differential expression analysis. The co-expression analysis revealed a role of these lncRNAs in the DNA damage response and cell cycle regulation post-IR. These transcripts may be targets in cancer therapy against radiosensitivity, as well as provide grounds for the identification of at-risk patients for immediate adverse reactions in healthy tissues. With this work we deliver a broad basis and new leads for the examination of lncRNAs in the radiation response.

Real-world EUROCRINE® registry data challenge the reliability of Bethesda cytopathology for thyroid surgery indication

Objectives

Fine-needle aspiration cytology (FNAC) is recommended by international guidelines for the preoperative evaluation of suspicious thyroid nodules >1 cm. Despite robust evidence from endocrine centers demonstrating the key role of FNAC results for the indication of surgery, the method is not routinely used in European clinics. The database EUROCRINE^®, which was introduced in 2015 with the scope of registering operations of the endocrine system, allows for a large-scale analysis of the current service reality in Europe concerning FNAC use and associated accuracy.

Methods

Operations performed to "exclude malignancy", registered from January 2015 to December 2018 in EUROCRINE^®, were analyzed. Parameters of accuracy were calculated for FNAC. FNAC results were considered "test positive" in the case of Bethesda category IV, V, and VI, since these categories usually prompt surgical interventions in European centers for thyroid surgery. Bethesda category II and III were considered "test negative".

Results

Of 8,791 operations, 5,780 had preoperative FNAC (65.7%). The overall malignancy rate was 28.3% (2,488/8,791). Malignancy rates were 68.8% for Bethesda VI, 69.9% for Bethesda V, 32.6% for Bethesda IV, 28.2% for III, 20.2% for Bethesda II, and 24.5% for Bethesda I. After exclusion of papillary microcarcinomas (PTMCs), the sensitivity of FNAC was 71.7% and specificity 43.5%, the positive predictive value was 29.1% and the negative predictive value 82.7%.

Conclusions

Although the indication to "exclude malignancy" was the predominant reason that prompted thyroid resection in the present cohort, FNAC was only used in about 65.7% of cases. When performed, FNAC was associated with unexpectedly low accuracy. Interestingly, in Bethesda II, 20.2% of malignant entities were present (13.3% after the exclusion of PTMCs).

Late health effects and changes in lifestyle factors after cancer in childhood with and without subsequent second primary cancers – the KiKme case-control study

Background

Improved treatments for childhood cancer result in a growing number of long-term childhood cancer survivors (CCS). The diagnosis and the prevalence of comorbidities may, however, influence their lifestyle later in life. Nonetheless, little is known about differences in late effects between CCS of a first primary neoplasm (FPN) in childhood and subsequent second primary neoplasms (SPN) and their impact on lifestyle. Therefore, we aim to investigate associations between the occurrence of FPN or SPN and various diseases and lifestyle in the later life of CCS.

Methods

CCS of SPN (n=101) or FPN (n=340) and cancer-free controls (n=150) were matched by age and sex, and CCS additionally by year and entity of FPN. All participants completed a self-administered questionnaire on anthropometric and socio-economic factors, medical history, health status, and lifestyle. Mean time between FPN diagnosis and interview was 27.3 years for SPN and 26.2 years for FPN CCS. To confirm results from others and to generate new hypotheses on late effects of childhood cancer as well as CCS´ lifestyles, generalized linear mixed models were applied.

Results

CCS were found to suffer more likely from diseases compared to cancer-free controls. In detail, associations with cancer status were observed for hypercholesterinemia and thyroid diseases. Moreover, CCS were more likely to take regular medication compared to controls. A similar association was observed for CCS of SPN compared to CCS of FPN. In contrast to controls, CCS rarely exercise more than 5 hours per week, consumed fewer soft and alcoholic drinks, and were less likely to be current, former, or passive smokers. Additionally, they were less likely overweight or obese. All other exploratory analyses performed on cardiovascular, chronic lung, inflammatory bone, allergic, and infectious diseases, as well as on a calculated health-score revealed no association with tumor status.

Conclusion

CCS were more affected by pathologic conditions and may consequently take more medication, particularly among CCS of SPN. The observed higher disease burden is likely related to the received cancer therapy. To reduce the burden of long-term adverse health effects in CCS, improving cancer therapies should therefore be in focus of research in this area.

Radiation-response in primary fibroblasts of long-term survivors of childhood cancer with and without second primary neoplasms: the KiKme study

Background

The etiology and most risk factors for a sporadic first primary neoplasm in childhood or subsequent second primary neoplasms are still unknown. One established causal factor for therapy-associated second primary neoplasms is the exposure to ionizing radiation during radiation therapy as a mainstay of cancer treatment. Second primary neoplasms occur in 8% of all cancer survivors within 30 years after the first diagnosis in Germany, but the underlying factors for intrinsic susceptibilities have not yet been clarified. Thus, the purpose of this nested case–control study was the investigation and comparison of gene expression and affected pathways in primary fibroblasts of childhood cancer survivors with a first primary neoplasm only or with at least one subsequent second primary neoplasm, and controls without neoplasms after exposure to a low and a high dose of ionizing radiation.

Methods

Primary fibroblasts were obtained from skin biopsies from 52 adult donors with a first primary neoplasm in childhood (N1), 52 with at least one additional primary neoplasm (N2+), as well as 52 without cancer (N0) from the KiKme study. Cultured fibroblasts were exposed to a high [2 Gray (Gy)] and a low dose (0.05 Gy) of X-rays. Messenger ribonucleic acid was extracted 4 h after exposure and Illumina-sequenced. Differentially expressed genes (DEGs) were computed using limma for R, selected at a false discovery rate level of 0.05, and further analyzed for pathway enrichment (right-tailed Fisher’s Exact Test) and (in-) activation (z ≥|2|) using Ingenuity Pathway Analysis.

Results

After 0.05 Gy, least DEGs were found in N0 (n = 236), compared to N1 (n = 653) and N2+ (n = 694). The top DEGs with regard to the adjusted p-value were upregulated in fibroblasts across all donor groups (SESN1, MDM2, CDKN1A, TIGAR, BTG2, BLOC1S2, PPM1D, PHLDB3, FBXO22, AEN, TRIAP1, and POLH). Here, we observed activation of p53 Signaling in N0 and to a lesser extent in N1, but not in N2+. Only in N0, DNA (excision-) repair (involved genes: CDKN1A, PPM1D, and DDB2) was predicted to be a downstream function, while molecular networks in N2+ were associated with cancer, as well as injury and abnormalities (among others, downregulation of MSH6, CCNE2, and CHUK). After 2 Gy, the number of DEGs was similar in fibroblasts of all donor groups and genes with the highest absolute log₂ fold-change were upregulated throughout (CDKN1A, TIGAR, HSPA4L, MDM2, BLOC1SD2, PPM1D, SESN1, BTG2, FBXO22, PCNA, and TRIAP1). Here, the p53 Signaling-Pathway was activated in fibroblasts of all donor groups. The Mitotic Roles of Polo Like Kinase-Pathway was inactivated in N1 and N2+. Molecular Mechanisms of Cancer were affected in fibroblasts of all donor groups. P53 was predicted to be an upstream regulator in fibroblasts of all donor groups and E2F1 in N1 and N2+. Results of the downstream analysis were senescence in N0 and N2+, transformation of cells in N0, and no significant effects in N1. Seven genes were differentially expressed in reaction to 2 Gy dependent on the donor group (LINC00601, COBLL1, SESN2, BIN3, TNFRSF10A, EEF1AKNMT, and BTG2).

Conclusion

Our results show dose-dependent differences in the radiation response between N1/N2+ and N0. While mechanisms against genotoxic stress were activated to the same extent after a high dose in all groups, the radiation response was impaired after a low dose in N1/N2+, suggesting an increased risk for adverse effects including carcinogenesis, particularly in N2+.

Supplementary Information

The online version contains supplementary material available at 10.1186/s10020-022-00520-6.

Quantitative proteomics analysis reveals core and variable tick salivary proteins at the tick-vertebrate host interface

Few studies have examined tick proteomes, how they adapt to their environment, and their roles in the parasite-host interactions that drive tick infestation and pathogen transmission. Here we used a proteomics approach to screen for biologically and immunologically relevant proteins acting at the tick-host interface during tick feeding and, as proof of principle, measured host antibody responses to some of the discovered candidates. We used a label-free quantitative proteomic workflow to study salivary proteomes of (i) wild Ixodes ricinus ticks fed on different hosts; (ii) wild or laboratory ticks fed on the same host; and (iii) adult ticks co-fed with nymphs. Our results reveal high and stable expression of several protease inhibitors and other tick-specific proteins under different feeding conditions. Most pathways functionally enriched in sialoproteomes were related to proteolysis, endopeptidase, and amine-binding activities. The generated catalog of tick salivary proteins enabled the selection of six candidate secreted immunogenic peptides for rabbit immunizations, three of which induced strong and durable antigen-specific antibody responses in rabbits. Furthermore, rabbits exposed to ticks mounted immune responses against the candidate peptides/proteins, confirming their expression at the tick-vertebrate interface. Our approach provides insights into tick adaptation strategies to different feeding conditions and promising candidates for developing anti-tick vaccines or markers of exposure of vertebrate hosts to tick bites.

Hypermethylation of RAD9A intron 2 in childhood cancer patients, leukemia and tumor cell lines suggest a role for oncogenic transformation

Most childhood cancers occur sporadically and cannot be explained by an inherited mutation or an unhealthy lifestyle. However, risk factors might trigger the oncogenic transformation of cells. Among other regulatory signals, hypermethylation of RAD9A intron 2 is responsible for the increased expression of RAD9A protein, which may play a role in oncogenic transformation. Here, we analyzed the RAD9A intron 2 methylation in primary fibroblasts of 20 patients with primary cancer in childhood and second primary cancer (2N) later in life, 20 matched patients with only one primary cancer in childhood (1N) and 20 matched cancer-free controls (0N), using bisulfite pyrosequencing and deep bisulfite sequencing (DBS). Four 1N patients and one 2N patient displayed elevated mean methylation levels (≥ 10 %) of RAD9A. DBS revealed ≥ 2 % hypermethylated alleles of RAD9A, indicative for constitutive mosaic epimutations. Bone marrow samples of NHL and AML tumor patients (n=74), EBV (Epstein Barr Virus) lymphoblasts (n=6), tumor cell lines (n=5) and FaDu subclones (n=13) were analyzed to substantiate our findings. We find a broad spectrum of tumor entities with an aberrant methylation of RAD9A. We detected a significant difference in mean methylation of RAD9A for NHL versus AML patients (p ≤0.025). Molecular karyotyping of AML samples during therapy with hypermethylated RAD9A showed an evolving duplication of 1.8 kb on Chr16p13.3 including the PKD1 gene. Radiation, colony formation assays, cell proliferation, PCR and molecular karyotyping SNP-array experiments using generated FaDu subclones suggest that hypermethylation of RAD9A intron 2 is associated with genomic imbalances in regions with tumor-relevant genes and survival of the cells. In conclusion, this is the very first study of RAD9A intron 2 methylation in childhood cancer and Leukemia. RAD9A epimutations may have an impact on leukemia and tumorigenesis and can potentially serve as a biomarker.

Preoperative calcitonin testing improves the diagnosis of medullary thyroid carcinoma in female and male patients

AIM

Calcitonin (Ctn) measurement in patients with thyroid disease could potentially increase the detection rates of medullary thyroid carcinoma (MTC) but remains a controversial issue. The aim of this study was to evaluate routine preoperative Ctn measurements.

METHODS

All patients with thyroid surgery documented in the prospective StuDoQ|Thyroid registry between March 2017 and September 2020 were included. Cutoff levels for Ctn were determined with receiver-operating characteristic analyses to assess the preoperative diagnosis of MTC in subgroups for females and males.

FINDINGS

In 29 590 of 39 679 patients (75%) participating in the registry, routine preoperative Ctn testing was performed. In 357 patients (227 females and 130 males), histopathology confirmed MTC with a mean tumor size of 14.7 mm (±12.43). Biochemical cure was achieved in 71.4% of the patients. Ctn levels between 11 and 20 pg/mL were seen in 2.6% of the patients, and only 0.7% of the patients had Ctn levels above 21 pg/mL. Cutoff levels for the diagnosis of MTC were 7.9 pg/mL for females and 15 pg/mL for males (P < 0.001). The sensitivity and specificity for females were 95 and 98%, and 96 and 97% for males, respectively.

CONCLUSION

Routine Ctn testing is a reliable predictor for MTC and provides the opportunity for earlier thyroidectomy before lymph node metastases occur, resulting in a better prognosis. Females with Ctn levels >7.9 pg/mL and males >15 pg/mL without any other extrathyroidal sources for an elevated Ctn should be monitored. Thyroid surgery should be considered if Ctn levels are increasing or ultrasound detects suspicious thyroid lesions.

Identification of Genetic Predispositions Related to Ionizing Radiation in Primary Human Skin Fibroblasts From Survivors of Childhood and Second Primary Cancer as Well as Cancer-Free Controls: Protocol for the Nested Case-Control Study KiKme

BACKGROUND

Therapy for a first primary neoplasm (FPN) in childhood with high doses of ionizing radiation is an established risk factor for second primary neoplasms (SPN). An association between exposure to low doses and childhood cancer is also suggested; however, results are inconsistent. As only subgroups of children with FPNs develop SPNs, an interaction between radiation, genetic, and other risk factors is presumed to influence cancer development.

OBJECTIVE

Therefore, the population-based, nested case-control study KiKme aims to identify differences in genetic predisposition and radiation response between childhood cancer survivors with and without SPNs as well as cancer-free controls.

METHODS

We conducted a population-based, nested case-control study KiKme. Besides questionnaire information, skin biopsies and saliva samples are available. By measuring individual reactions to different exposures to radiation (eg, 0.05 and 2 Gray) in normal somatic cells of the same person, our design enables us to create several exposure scenarios for the same person simultaneously and measure several different molecular markers (eg, DNA, messenger RNA, long noncoding RNA, copy number variation).

RESULTS

Since 2013, 101 of 247 invited SPN patients, 340 of 1729 invited FPN patients, and 150 of 246 invited cancer-free controls were recruited and matched by age and sex. Childhood cancer patients were additionally matched by tumor morphology, year of diagnosis, and age at diagnosis. Participants reported on lifestyle, socioeconomical, and anthropometric factors, as well as on medical radiation history, health, and family history of diseases (n=556). Primary human fibroblasts from skin biopsies of the participants were cultivated (n=499) and cryopreserved (n=3886). DNA was extracted from fibroblasts (n=488) and saliva (n=510).

CONCLUSIONS

This molecular-epidemiological study is the first to combine observational epidemiological research with standardized experimental components in primary human skin fibroblasts to identify genetic predispositions related to ionizing radiation in childhood and SPNs. In the future, fibroblasts of the participants will be used for standardized irradiation experiments, which will inform analysis of the case-control study and vice versa. Differences between participants will be identified using several molecular markers. With its innovative combination of experimental and observational components, this new study will provide valuable data to forward research on radiation-related risk factors in childhood cancer and SPNs.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/32395.

Virtual reality and 3D printing improve preoperative visualization of 3D liver reconstructions-results from a preclinical comparison of presentation modalities and user's preference

Background

Preoperative three-dimensional (3D) reconstructions for liver surgery planning have been shown to be effective in reduction of blood loss and operation time. However, the role of the ‘presentation modality’ is not well investigated. We present the first study to compare 3D PDFs, 3D printed models (PR) and virtual reality (VR) 3D models with regard to anatomical orientation and personal preferences in a high volume liver surgery center.

Methods

Thirty participants, 10 medical students, 10 residents, 5 fellows and 5 hepatopancreatobiliary (HPB) experts, assigned the tumor-bearing segments of 20 different patient’s individual liver reconstructions. Liver models were presented in a random order in all modalities. Time needed to specify the tumor location was recorded. In addition, a score was calculated factoring in correct, wrong and missing segment assignments. Furthermore, standardized test/questionnaires for spatial thinking and seeing, vegetative side effects and usability were completed.

Results

Participants named significantly more correct segments in VR (P=0.040) or PR (P=0.036) compared to PDF. Tumor assignment was significantly shorter with 3D PR models compared to 3D PDF (P<0.001) or VR application (P<0.001). Regardless of the modality, HPB experts were significantly faster (24±8 vs. 35±11 sec; P=0.014) and more often correct (0.87±0.12 vs. 0.83±0.15; P<0.001) than medical students. Test results for spatial thinking and seeing had no influence on time but on correctness of tumor assignment. Regarding usability and user experience the VR application achieved the highest scores without causing significant vegetative symptoms and was also the most preferred method (n=22, 73.3%) because of the multiple functions like scaling and change of transparency. Ninety percent (n=27) stated that this application can positively influence the operation planning.

Conclusions

3D PR models and 3D VR models enable a better and partially faster anatomical orientation than reconstructions presented as 3D PDFs. User’s preferred the VR application over the PR models and PDF. A prospective trial is needed to evaluate the different presentation modalities regarding intra- and postoperative outcomes.

Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis

Development of primary liver cancer is a multi-stage process. Detailed understanding of sequential epigenetic alterations is largely missing. Here, we performed Infinium Human Methylation 450k BeadChips and RNA sequencing analyses for genome-wide methylome and transcriptome profiling of cirrhotic liver (n=7), low- (n=4) and high-grade (n=9) dysplastic lesions, early (n=5) and progressed (n=3) hepatocellular carcinomas (HCC) synchronously detected in eight HCC patients with chronic hepatitis B infection. Integrative analyses of epigenetically driven molecular changes were identified and validated in two independent cohorts comprising 887 HCC. Mitochondrial DNA sequencing was further employed for clonality analyses and indicates multi-clonal origin in the majority of investigated HCC. Alterations in DNA methylation progressively increased from CL to dysplastic lesions and reached a maximum in early HCC. Associated early alterations identified by IPA pathway analyses involved apoptosis, immune regulation and stemness pathways, while late changes centered on cell survival, proliferation and invasion. We further validated putative 23 epi-drivers with concomitant expression changes and associated with overall survival. Functionally, Striatin 4 (STRN4) was demonstrated to be epigenetically regulated and inhibition of STRN4 significantly suppressed tumorigenicity of HCC cell lines.Overall, application of integrative genomic analyses defines epigenetic driver alterations and provides promising targets for novel therapeutic approaches.

Identification of Potential Distinguishing Markers for the Use of Cannabis-Based Medicines or Street Cannabis in Serum Samples

Increasing prescription numbers of cannabis-based medicines raise the question of whether uptake of these medicines can be distinguished from recreational cannabis use. In this pilot study, serum cannabinoid profiles after use of cannabis-based medicines were investigated, in order to identify potential distinguishing markers. Serum samples after use of Sativex^®, Dronabinol or medical cannabis were collected and analyzed for 18 different cannabinoids, using a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. Analytes included delta-9-tetrahydrocannabinol, 11-hydroxy-tetrahydrocannabinol, 11-nor-9-carboxy-tetrahydrocannabinol, cannabidiol, cannabinol, cannabigerol, cannabichromene, cannabicyclol, tetrahydrocannabivarin, cannabidivarin, tetrahydocannabinolic acid A, cannabidiolic acid, cannabinolic acid, cannabigerolic acid, cannabichromenic acid, cannabicyclolic acid, tetrahydrocannabivarinic acid and cannabidivarinic acid. Cannabinoid profiles of study samples were compared to profiles of street cannabis user samples via principal component analysis and Kruskal–Wallis test. Potential distinguishing markers for Dronabinol and Sativex^® intake were identified, including 11-hydroxy-tetrahydrocannabinol/delta-9-tetrahydrocannabinol ratios ≥1 and increased concentrations of 11-nor-9-carboxy-tetrahydrocannabinol, cannabidiol or cannabichromene. Larger quantities of minor cannabinoids suggested use of cannabis. Use of medical and street cannabis could not be distinguished, except for use of a cannabidiol-rich strain with higher cannabidiol/delta-9-tetrahydrocannabinol and cannabichromene/delta-9-tetrahydrocannabinol ratios. Findings of the study were used to classify forensic serum samples with self-reported use of cannabis-based medicines.

Timeout procedure in paediatric surgery: effective tool or lip service? A randomised prospective observational study

Background

For over a decade, the preoperative timeout procedure has been implemented in most paediatric surgery units. However, the impact of this intervention has not been systematically studied. This study evaluates whether purposefully introduced errors during the timeout routine are detected and reported by the operating team members.

Methods

After ethics board approval and informed consent, deliberate errors were randomly and clandestinely introduced into the timeout routine for elective surgical procedures by a paediatric surgery attending. Errors were randomly selected among wrong name, site, side, allergy, intervention, birthdate and gender items. The main outcome measure was how frequent an error was reported by the team and by whom.

Results

Over the course of 16 months, 1800 operations and timeouts were performed. Errors were randomly introduced in 120 cases (6.7%). Overall, 54% of the errors were reported; the remainder went unnoticed. Errors were pointed out most frequently by anaesthesiologists (64%), followed by nursing staff (28%), residents-in-training (6%) and medical students (1%).

Conclusion

Errors in the timeout routine go unnoticed by the team in almost half of cases. Therefore, even if preoperative timeout routines are strictly implemented, mistakes may be overlooked. Hence, the timeout procedure in its current form appears unreliable. Future developments may be useful to improve the quality of the surgical timeout and should be studied in detail.

Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries

Primary open-angle glaucoma (POAG), is a heritable common cause of blindness world-wide. To identify risk loci, we conduct a large multi-ethnic meta-analysis of genome-wide association studies on a total of 34,179 cases and 349,321 controls, identifying 44 previously unreported risk loci and confirming 83 loci that were previously known. The majority of loci have broadly consistent effects across European, Asian and African ancestries. Cross-ancestry data improve fine-mapping of causal variants for several loci. Integration of multiple lines of genetic evidence support the functional relevance of the identified POAG risk loci and highlight potential contributions of several genes to POAG pathogenesis, including SVEP1, RERE, VCAM1, ZNF638, CLIC5, SLC2A12, YAP1, MXRA5, and SMAD6. Several drug compounds targeting POAG risk genes may be potential glaucoma therapeutic candidates.

Self-reported cardiovascular health of teachers: results from the 5-year follow-up of the Gutenberg Health Study cohort

Objectives

Following an exploratory approach, we examined cardiovascular disease risk factors at baseline and the 5-year incidence proportion of self-reported doctor-diagnosed cardiovascular diseases (CVD) in teachers and other occupational groups of the Gutenberg Health Study.

Methods

Study participants lived in the region of Mainz, Germany. Data from 6510 working participants without prevalent CVD at baseline (2007–2012) were analyzed. Participants were teachers (n = 215), other professionals from the health, social or educational (HSE) fields (n = 1061) or worked outside the HSE fields (n = 5234). For occupational comparisons, we estimated prevalence ratios (PR) for each CVD risk factor at baseline with robust Poisson regression analyses. We calculated crude CVD incidence rates based on the observed 5-year CVD cumulative incidence at follow-up and estimated age-weighted incidence proportions. All analyses were stratified by sex.

Results

Male non-HSE workers showed a higher prevalence of smoking and physical inactivity than male teachers (PR 2.26; 95%-CI: 1.06–4.82/PR 1.89; 95%-CI: 1.24–2.87). In contrast, non-HSE workers and other HSE professionals were less likely to have reported an unhealthy alcohol intake than teachers. Differences were attenuated after SES-adjustment. We did not detect occupational group-specific differences in CVD incidence. However, there were only two cases of CVD among the teachers.

Conclusion

Particularly male teachers showed a healthier lifestyle regarding physical inactivity and smoking. Nevertheless, occupational-medical care practitioners and researchers need to be aware of the relatively heightened prevalence of unhealthy alcohol intake in female and male teachers, and in absolute terms, the high hypertension prevalence in male teachers.

Correction to: Molecular karyotyping and gene expression analysis in childhood cancer patients

The correct Author names are presented in this paper.

Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease

BACKGROUND

Advanced age-related macular degeneration (AMD) is a leading cause of blindness. While around half of the genetic contribution to advanced AMD has been uncovered, little is known about the genetic architecture of early AMD.

METHODS

To identify genetic factors for early AMD, we conducted a genome-wide association study (GWAS) meta-analysis (14,034 cases, 91,214 controls, 11 sources of data including the International AMD Genomics Consortium, IAMDGC, and UK Biobank, UKBB). We ascertained early AMD via color fundus photographs by manual grading for 10 sources and via an automated machine learning approach for > 170,000 photographs from UKBB. We searched for early AMD loci via GWAS and via a candidate approach based on 14 previously suggested early AMD variants.

RESULTS

Altogether, we identified 10 independent loci with statistical significance for early AMD: (i) 8 from our GWAS with genome-wide significance (P < 5 × 10- 8), (ii) one previously suggested locus with experiment-wise significance (P < 0.05/14) in our non-overlapping data and with genome-wide significance when combining the reported and our non-overlapping data (together 17,539 cases, 105,395 controls), and (iii) one further previously suggested locus with experiment-wise significance in our non-overlapping data. Of these 10 identified loci, 8 were novel and 2 known for early AMD. Most of the 10 loci overlapped with known advanced AMD loci (near ARMS2/HTRA1, CFH, C2, C3, CETP, TNFRSF10A, VEGFA, APOE), except two that have not yet been identified with statistical significance for any AMD. Among the 17 genes within these two loci, in-silico functional annotation suggested CD46 and TYR as the most likely responsible genes. Presence or absence of an early AMD effect distinguished the known pathways of advanced AMD genetics (complement/lipid pathways versus extracellular matrix metabolism).

CONCLUSIONS

Our GWAS on early AMD identified novel loci, highlighted shared and distinct genetics between early and advanced AMD and provides insights into AMD etiology. Our data provide a resource comparable in size to the existing IAMDGC data on advanced AMD genetics enabling a joint view. The biological relevance of this joint view is underscored by the ability of early AMD effects to differentiate the major pathways for advanced AMD.

Spontaneous and Radiation-Induced Chromosome Aberrations in Primary Fibroblasts of Patients With Pediatric First and Second Neoplasms

The purpose of the present study was to investigate whether former childhood cancer patients who developed a subsequent secondary primary neoplasm (SPN) are characterized by elevated spontaneous chromosomal instability or cellular and chromosomal radiation sensitivity as surrogate markers of compromised DNA repair compared to childhood cancer patients with a first primary neoplasm (FPN) only or tumor-free controls. Primary skin fibroblasts were obtained in a nested case-control study including 23 patients with a pediatric FPN, 22 matched patients with a pediatric FPN and an SPN, and 22 matched tumor-free donors. Clonogenic cell survival and cytogenetic aberrations in Giemsa-stained first metaphases were assessed after X-irradiation in G1 or on prematurely condensed chromosomes of cells irradiated and analyzed in G2. Fluorescence in situ hybridization was applied to investigate spontaneous transmissible aberrations in selected donors. No significant difference in clonogenic survival or the average yield of spontaneous or radiation-induced aberrations was found between the study populations. However, two donors with an SPN showed striking spontaneous chromosomal instability occurring as high rates of numerical and structural aberrations or non-clonal and clonal translocations. No correlation was found between radiation sensitivity and a susceptibility to a pediatric FPN or a treatment-associated SPN. Together, the results of this unique case-control study show genomic stability and normal radiation sensitivity in normal somatic cells of donors with an early and high intrinsic or therapy-associated tumor risk. These findings provide valuable information for future studies on the etiology of sporadic childhood cancer and therapy-related SPN as well as for the establishment of predictive biomarkers based on altered DNA repair processes.

Effect of intraoperative nerve monitoring on postoperative vocal cord palsy rates after thyroidectomy: European multicentre registry-based study

Background

Intraoperative nerve monitoring (IONM) of the recurrent laryngeal nerve (RLN) predicts the risk of vocal cord palsy (VCP). IONM can be used to adapt the surgical strategy in order to prevent bilateral VCP and associated morbidity. Controversial results have been reported in the literature for the effect of IONM on rates of VCP, and large multicentre studies are required for elucidation.

Methods

Patients undergoing first‐time thyroidectomy for benign thyroid disease between May 2015 and January 2019, documented prospectively in the European registry EUROCRINE®, were included in a cohort study. The influence of IONM and other factors on the development of postoperative VCP was analysed using multivariable regression analysis.

Results

Of 4598 operations from 82 hospitals, 3542 (77·0 per cent) were performed in female patients. IONM was used in 4182 (91·0 per cent) of 4598 operations, independent of hospital volume. Postoperative VCP was diagnosed in 50 (1·1 per cent) of the 4598 patients. The use of IONM was associated with a lower risk of postoperative VCP in multivariable analysis (odds ratio (OR) 0·34, 95 per cent c.i. 0·16 to 0·73). Damage to the RLN noted during surgery (OR 24·77, 12·91 to 48·07) and thyroiditis (OR 2·03, 1·10 to 3·76) were associated with an increased risk of VCP. Higher hospital volume correlated with a lower rate of VCP (OR 0·05, 0·01 to 0·13).

Conclusion

Use of IONM was associated with a low rate of postoperative VCP.

EndoPredict® in early hormone receptor-positive, HER2-negative breast cancer

Purpose

Evaluating consecutive early breast cancer patients, we analyzed both the impact of EndoPredict^® on clinical decisions as well as clinico-pathological factors influencing the decision to perform this gene expression test.

Methods

Hormone receptor (HR)-positive and human epidermal growth factor receptor 2 (HER2)-negative early breast cancer patients treated between 2011 and 2016 were included in this study to investigate the role of EndoPredict^® (EPclin) in the treatment of early breast cancer. A main study aim was to analyze the changes in therapy recommendations with and without EPclin. In addition, the impact of clinico-pathological parameters for the decision to perform EPclin was examined by Pearson's chi-squared test (χ²-test) and Fisher's exact test as well as univariate and multivariate logistic regressions.

Results

In a cohort of 869 consecutive early HR-positive, HER-negative breast cancer patients, EPclin was utilized in 156 (18.0%) patients. EPclin led to changes in therapy recommendations in 33.3% (n = 52), with both therapy escalation in 19.2% (n = 30) and de-escalation in 14.1% (n = 22). The clinico-pathological factors influencing the use of EPclin were age (P < 0.001, odds ratio [OR] 0.498), tumor size (P = 0.011, OR 0.071), nodal status (P = 0.021, OR 1.674), histological grade (P = 0.043, OR 0.432), and Ki-67 (P < 0.001, OR 3.599).

Conclusions

EPclin led to a change in therapy recommendations in one third of the patients. Clinico-pathological parameters such as younger age, smaller tumor size, positive nodal status, intermediate histological grade and intermediate Ki-67 had a significant influence on the use of EndoPredict^®.

Electronic supplementary material

The online version of this article (10.1007/s10549-020-05688-1) contains supplementary material, which is available to authorized users.

Local, semi-automatic, three-dimensional liver reconstruction or external provider? An analysis of performance and time expense

PURPOSE

In hepatobiliary surgery, preoperative three-dimensional reconstruction based on CT or MRI can be provided externally or by local, semi-automatic software. We analyzed the time expense and quality of external versus local three-dimensional reconstructions.

METHODS

Three first-year residents reconstructed data from 20 patients with liver pathologies using a local, semi-automatic, server-based program. Initially, five randomly selected patient datasets were segmented, with the visualization of an established external company available for comparison at all times (learning phase). The other fifteen cases were compared with the external datasets after completing local reconstruction (control phase). Total time expense/case and for specific manual and semi-automated reconstruction steps were recorded. Segmentation quality was analyzed by testing the equivalence for liver and tumor volumes, portal vein sectors, and hepatic vein territories.

RESULTS

The median total reconstruction time was reduced from 2.5 h (learning phase) to 1.5 h (control phase) (- 42%; p < 0.001). Comparing the total and detailed liver volumes (sectors and territories) as well as the tumor volumes in the control phase equivalence was proven. In addition, a highly significant correlation between the external and local analysis was obtained over all analyzed segments with a very high ICC (median [IQR]: 0.98 [0.97; 0.99]; p < 0.01).

CONCLUSION

Local, semi-automatic reconstruction performed by inexperienced residents was feasible with an expert level time expense and the quality of the three-dimensional images was comparable with those from an external provider.

[Effect of different training methods on the use of the i-gel laryngeal mask by lay persons on a manikin]

BACKGROUND

Several studies have described the successful application of extraglottic airways by lay people to a phantom.

OBJECTIVES

This study examined the influence of the training method on the success of the application.

METHODS

A total of 150 visitors of a shopping mall were asked to place an i‑gel laryngeal mask (Intersurgical GmbH, Sankt Augustin, Germany) on a manikin. The short instruction was randomized and performed either as a practical demonstration or through the self-study of an illustrated manual.

RESULTS

Application success in the first attempt was 95.8 % for the practical demonstration group and 78.5 % for the written instruction group (p = 0.001). Placement times were also significantly different (median 11.5 s vs. 22.5 s, p < 0.001).

CONCLUSIONS

Learning success can be achieved with both training methods. Initially, a hands-on training should be carried out with a practical demonstration.

Access to an online video enhances the consent process, increases knowledge, and decreases anxiety of caregivers with children scheduled for inguinal hernia repair: A randomized controlled study

BACKGROUND

There is limited time within the clinical workflow of most pediatric surgeons to obtain a comprehensive, well informed consent. This study evaluates whether ad-lib access to an online video on the consent dialogue enhances the consent process for inguinal hernia repair (IHR) in children.

METHODS

The study was approved by the state ethics board. A 6-min video of a consent speech on IHR was produced and uploaded to a nonpublic online channel, explaining the condition, procedure, complications, and postoperative expectations. A total of 50 families were randomized to conventional, face-to-face consenting in clinic either with (intervention) or without (control) access to the online video. During their child's IHR, the parents were asked to complete the State-Trait-Anxiety Inventory (STAI), a modified Friedlander questionnaire on assessing knowledge sufficient to provide informed consent, and a validated satisfaction survey. Scores of the intervention and control group were statistically compared.

RESULTS

The intervention group demonstrated significantly decreased anxiety measured with the STAI (p = 0,026) and increased knowledge (p = 0,016) compared to controls. There was no difference in satisfaction (p = 0,557).

CONCLUSION

Preoperatively providing access to an online consent video regarding IHR reduces anxiety and enhances knowledge without altering satisfaction level. Adjunct online videos are a useful tool to enhance the consent process.

TYPE OF STUDY

Prospective randomized controlled trial.

LEVEL OF EVIDENCE

Level I.

Intrathecal B-cell accumulation and axonal damage distinguish MRI-based benign from aggressive onset in MS

Objective

We explored the incremental value of adding multiple disease activity biomarkers in CSF and serum for distinguishing MRI-based benign from aggressive MS in early disease course.

Methods

Ninety-three patients diagnosed with clinically isolated syndrome (CIS) or early MS were divided into 3 nonoverlapping severity groups defined by objective MRI criteria. Ninety-seven patients with noninflammatory neurologic disorders and 48 patients with other inflammatory neurologic diseases served as controls. Leukocyte subsets in the CSF were analyzed by flow cytometry. CSF neurofilament light chain (NfL) and chitinase-3-like protein 1 (CHI3L1) levels were measured by ELISA. Serum NfL levels were examined using single molecule array technology.

Results

CSF CD20+/CD14+ ratios and NfL levels in CSF and serum were significantly different between high and low MRI severity groups, whereas no difference was found for CSF CHI3L1 levels. NfL levels in CSF and serum highly correlated. Receiver operating characteristic analysis demonstrated that the cumulative sums combining CSF CD20+/CD14+ ratios and NfL levels in serum or CSF considerably improved diagnostic accuracy. A composite score built from these 2 cumulative sums best distinguished MRI severity. These findings were validated by support vector machine analysis, which confirmed that the accuracy of the cumulative sums and composite score outperforms single biomarkers.

Conclusion

Patients with extreme manifestations of CIS or early MS defined by strict MRI parameters can be best distinguished by combining markers of intrathecal B-cell accumulation and axonal damage. This could stratify individual treatment decisions toward a more personalized immunotherapy.

Feasibility of sample size calculation for RNA-seq studies

Sample size calculation is a crucial step in study design but is not yet fully established for RNA sequencing (RNA-seq) analyses. To evaluate feasibility and provide guidance, we evaluated RNA-seq sample size tools identified from a systematic search. The focus was on whether real pilot data would be needed for reliable results and on identifying tools that would perform well in scenarios with different levels of biological heterogeneity and fold changes (FCs) between conditions. We used simulations based on real data for tool evaluation. In all settings, the six evaluated tools provided widely different answers, which were strongly affected by FC. Although all tools failed for small FCs, some tools can at least be recommended when closely matching pilot data are available and relatively large FCs are anticipated.

Central Venous Access Devices (CVAD) in Pediatric Oncology Patients-A Single-Center Retrospective Study Over More Than 9 Years

Background: Central venous access devices (CVAD) provide important benefits in the management of oncological pediatric patients. However, these catheters are responsible for severe complications. Methods: In this context, we aimed to analyze all patients receiving a CVAD in the Department of Pediatric Hematology and Oncology of the University hospital of Mainz over a period of 9 years, focused on CVAD related complications. Data on demographics, as well as intraoperative and postoperative complications were extracted. Results: A total of 296 patients with a mean age 93.2 ± 62.4 months were analyzed. The majority suffered from leukemia (n = 91, 30.7%), lymphomas (n = 50, 16.9%), and brain tumors (n = 48, 16.2%). In 63 (21.3) patients, complications were observed. No death caused by complications of CVADs was found in our series. Catheter-related blood stream infections (BSI) (7.4%) were most prevalent, followed by dislodgements (5.4%), occlusions (2.7%), thrombosis (2.4%), and catheter leakage (2.4%). Insertion site infections were observed in three patients (1.0%). Fifty-nine percent of all patients with catheter-related BSI suffered from Leukemia. In patients with Catheter-related BSIs we detected the condition leukemia as the underlying disease as a risk factor compared to solid tumors as the underlying disease. Overall, totally implanted devices (ports) have a lower complication rate than tunneled catheter. Conclusion: Implantation of CVADs seems to be safe and reliable in this large pediatric patient cohort. Even if complications occur in the long-term management of CVADs, they can be treated successfully and long-term catheter survival rates are excellent.

Method for Determining Antiheparin Activity of Platelets and Erythrocytes

A method for determining antiheparin activity of platelets and erythrocytes is described. The neutralization of various concentrations of heparin by various amounts of protamine sulphate or tested material is measured simultaneously. Results are expressed in mean equivalent of protamine sulphate (PS) standard solution. The normal values of antiheparin activity of platelets and erythrocytes in human and in various animals are given.

Intravascular Coagulation and Fibrinolysis by Stapliylocoagiilase. Comparison with Thrombin

Intravascular clotting in rabbits after intravenous injection of 30 N.I.H. units of thrombin/kg and 5/mg/kg of staphylocoagulase were studied. Following determinations were made : clotting time, thrombin time, fibrinogen, factors V, VII, VIII, X, XI and XII, “true prothrombin”, two stage prothrombin, P-P test, prothrombin consumption, fibrinolysis in serum euglobulins, plasminogen, antithrombin III and VI, and coagulase reacting factor. Intravenous staphylocoagulase produced in rabbits precipitous drop of fibrinogen level in a very short time, which was not observed with the dose of thrombin used. Activity of staphylocoagulase in vivo was very much higher than of thrombin, as it could be expected on basis of the in vitro comparison. Together with defibrination caused by staphylocoagulase, fibrinogen breakdown products, identified as antithrombin VI, appear in plasma. There were no such changes observed when thrombin was used. Slight decrease of prothrombin and antithrombin III levels, together with a lack of significant changes in factors V, VII, VIII, X, XI and XII content, were observed after staphylocoagulase injection. Slight increase of CRF content in staphylo co agulase clotted plasma was noted. Fibrinolytic system was not activated during clotting process caused by staphylo-coagulase. Significance of the data obtained is discussed.

Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective

RNA-sequencing (RNA-seq) has become an established way for measuring gene expression in model organisms and humans. While methods development for refining the corresponding data processing and analysis pipeline is ongoing, protocols for typical steps have been proposed and are widely used. Several user interfaces have been developed for making such analysis steps accessible to life scientists without extensive knowledge of command line tools. We performed a systematic search and evaluation of such interfaces to investigate to what extent these can indeed facilitate RNA-seq data analysis. We found a total of 29 open source interfaces, and six of the more widely used interfaces were evaluated in detail. Central criteria for evaluation were ease of configuration, documentation, usability, computational demand and reporting. No interface scored best in all of these criteria, indicating that the final choice will depend on the specific perspective of users and the corresponding weighting of criteria. Considerable technical hurdles had to be overcome in our evaluation. For many users, this will diminish potential benefits compared with command line tools, leaving room for future improvement of interfaces.

Conversion coefficients for the estimation of effective doses in intraoral and panoramic dental radiology from dose-area product values

Conversion coefficients for the estimation of effective doses in intraoral and panoramic dental radiology from dose-area product (DAP) values were determined by measuring organ-absorbed doses and the corresponding DAP values. Measurements were performed for all standard intraoral radiological projections and standard panoramic examination at different exposure parameters. Organ-absorbed doses were measured using thermoluminescent detectors and an adult anthropomorphic phantom specially designed for dosimetric study in dental radiology. Different techniques for the calculation of effective doses were evaluated. Conversion coefficients derived from this study range from 0.008 to 0.132 microSv mGy(-1) cm(-2) for intraoral radiography and 0.055 to 0.238 microSv mGy(-1) cm(-2) for panoramic radiography.

Dose-area product measurements in panoramic dental radiology

In this study, dose-area product (DAP) measurements in panoramic dental radiology have been performed in Germany. The results obtained in this study were proposed as diagnostic reference levels (DRLs). A representative number of dental panoramic units, both with digital and conventional image receptors, have been chosen. Common statistical parameters such as mean, standard deviation and 3rd quartile have been calculated. For four different standard programmes, 'large adult', 'adult male', 'adult female' and 'child', the proposed DRLs are 101, 87, 84 and 75 mGy cm(2), respectively. No clear tendency to a generalised dose reduction from the transition to digital techniques has been observed. Effective doses have been calculated from E/DAP conversion factors published in literature. Even though these values differ by a factor of approximately 3, upper limits of 15.8-21.2 microSv for the four different exposure settings were derived from the data.

Dose-area product measurements and determination of conversion coefficients for the estimation of effective dose in dental lateral cephalometric radiology

A study has been carried out to propose diagnostic reference levels (DRLs) for lateral cephalometric radiology in Germany based on the dose-area product (DAP). DRLs were proposed separately for child and adult exposure settings which are 26.4 and 32.6 mGy cm2, respectively. Organ absorbed doses from lateral cephalometric radiology were also measured using thermoluminescence detectors (TLDs) and an adult anthropomorphic phantom specially design for dosimetric study in dental radiology. Effective doses were then calculated using three different techniques where the salivary gland and brain tissue were given different weighting factors. Conversion coefficients for estimating effective dose from DAP value derived in this study range from 0.042 to 0.149 microSv/mGy cm2.

Radiation exposure and dose evaluation in intraoral dental radiology

In this study, dose area product measurements have been performed to propose diagnostic reference levels (DRLs) in intraoral dental radiology. Measurements were carried out at 60 X-ray units for all types of intraoral examinations performed in clinical routine. The third quartile values calculated range from 26.2 to 87.0 mGy cm(2). The results showed that there exists a large difference between the patient exposures among different dental facilities. It was also observed that dentists working with faster film type or higher tube voltage are not always associated with lower exposure. The study demonstrated the necessity to have the DRLs laid out as guidelines in dental radiology.

Radiation exposure to children in intraoral dental radiology

In this study, dose area product (DAP) measurements have been performed aiming at establishing diagnostic reference levels (DRLs) in paediatric intraoral dental radiology. Measurements were carried out at 52 X-ray units for all types of intraoral examinations performed in clinical routine. Not all X-ray units have pre-set child exposure settings with reduced exposure time or in some cases lower tube voltage. Child examinations are carried out using adult exposure settings at these units, which increases the DAP third quartile values by up to 50%. For example, third quartile values for periapical examination ranges from 14.4 to 40.9 mGy cm(2) for child settings and 20.6 to 48.8 mGy cm(2) when the adult settings are included. The results show that there exists a large difference between the patient exposures among different dental facilities. It was also observed that clinics working with faster film type or higher tube voltage are not always associated with lower exposure.

The zinc finger domain of the archaeal minichromosome maintenance protein is required for helicase activity

The minichromosome maintenance (MCM) proteins, a family of six conserved polypeptides found in all eukaryotes, are essential for DNA replication. The archaeon Methanobacterium thermoautotrophicum Delta H contains a single homologue of MCM with biochemical properties similar to those of the eukaryotic enzyme. The amino acid sequence of the archaeal protein contains a putative zinc-binding domain of the CX(2)CX(n)CX(2)C (C(4)) type. In this study, the roles of the zinc finger domain in MCM function were examined using recombinant wild-type and mutant proteins expressed and purified from Escherichia coli. The protein with a mutation in the zinc motif forms a dodecameric complex similar to the wild-type enzyme. The mutant enzyme, however, is impaired in DNA-dependent ATPase activity and single-stranded DNA binding, and it does not possess helicase activity. These results illustrate the importance of the zinc-binding domain for archaeal MCM function and suggest a role for zinc binding in the eukaryotic MCM complex as well, since four out of the six eukaryotic MCM proteins contain a similar zinc-binding motif.

The ftsZ gene of Haloferax mediterranei: sequence, conserved gene order, and visualization of the FtsZ ring

We sequenced the ftsZ gene region of the halophilic archaeon Haloferax mediterranei and mapped the transcription start sites for the ftsZ gene. The gene encoded a 363-amino-acid long FtsZ protein with a predicted molecular mass of 38 kDa and an isoelectric point of 4.2. A high level of similarity to the FtsZ protein of Haloferax volcanii was apparent, with 97 and 90% identity at the amino acid and nucleotide levels, respectively. Structural conservation at the protein level was shown by visualization of the FtsZ ring structure in H. mediterranei cells using an antiserum raised against FtsZ of H. volcanii. FtsZ rings were observed in cells in different stages of division, including cells with pleomorphic shapes and cells that appeared to be undergoing asymmetric division. Cells were also observed that displayed constriction-like invaginations in the absence of an FtsZ ring, indicating that morphological data are not sufficient to determine whether pleomorphic Haloferax cells are undergoing cell division. Both the upstream and downstream gene order in the ftsZ region was found to be conserved within the genus Haloferax. Furthermore, the downstream gene order, which includes the secE and nusG genes, is conserved in almost all euryarchaea sequenced to date. The secE and nusG genes are likely to be transcriptionally and translationally coupled in Haloferax, and this co-expression may have been a selective force that has contributed to keeping the gene cluster intact.

Cell cycle characteristics of thermophilic archaea

We have performed a cell cycle analysis of organisms from the Archaea domain. Exponentially growing cells of the thermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius were analyzed by flow cytometry, and several unusual cell cycle characteristics were found. The cells initiated chromosome replication shortly after cell division such that the proportion of cells with a single chromosome equivalent was low in the population. The postreplication period was found to be long; i.e., there was a considerable time interval from termination of chromosome replication until cell division. A further unusual feature was that cells in stationary phase contained two genome equivalents, showing that they entered the resting stage during the postreplication period. Also, a reduction in cellular light scatter was observed during entry into stationary phase, which appeared to reflect changes not only in cell size but also in morphology and/or composition. Finally, the in vivo organization of the chromosome DNA appeared to be different from that of eubacteria, as revealed by variation in the relative binding efficiency of different DNA stains.