Dataset for the reporting of urinary tract carcinoma-biopsy and transurethral resection specimen: recommendations from the International Collaboration on Cancer Reporting (ICCR)

The International Collaboration on Cancer Reporting (ICCR) is an alliance of major pathology organisations in Australasia, Canada, Europe, United Kingdom, and United States of America that develops internationally standardised, evidence-based datasets for the pathology reporting of cancer specimens. This dataset was developed by a multidisciplinary panel of international experts based on previously published ICCR guidelines for the production of cancer datasets. It is composed of Required (core) and Recommended (noncore) elements identified on the basis of literature review and expert consensus. The document also includes an explanatory commentary explaining the rationale behind the categorization of individual data items and provides guidance on how these should be collected and reported. The dataset includes nine required and six recommended elements for the reporting of cancers of the urinary tract in biopsy and transurethral resection (TUR) specimens. The required elements include specimen site, operative procedure, histological tumor type, subtype/variant of urothelial carcinoma, tumor grade, extent of invasion, status of muscularis propria, noninvasive carcinoma, and lymphovascular invasion (LVI). The recommended elements include clinical information, block identification key, extent of T1 disease, associated epithelial lesions, coexistent pathology, and ancillary studies. The dataset provides a structured template for globally harmonized collection of pathology data required for management of patients diagnosed with cancer of the urinary tract in biopsy and TUR specimens. It is expected that this will facilitate international collaboration, reduce duplication of effort in updating current national/institutional datasets, and be particularly useful for countries that have not developed their own datasets.

Effect of fluoride mouthrinses and stannous ions on the erosion protective properties of the in situ pellicle

The particular feature of this study is the investigation of effects of pure fluoride- or stannous ions based mouthrinses on the erosion protective properties and the ultrastructure of the in situ pellicle (12 volunteers). Experimental solutions were prepared either from 500 ppm NaF, SMFP, AmF or SnF₂ or 1563 ppm SnCl₂, respectively. After 1 min of in situ pellicle formation on bovine enamel slabs, rinses with one of the preparations were performed for 1 min and intraoral specimens’ exposure was continued for 28 min. Native enamel slabs and rinses with bidestilled water served as controls. After oral exposure, slabs were incubated in HCl (pH 2; 2.3; 3) for 120 s and kinetics of calcium- and phosphate release were measured photometrically; representative samples were analysed by TEM and EDX. All mouthrinses reduced mineral loss compared to the native 30-min pellicle. The effect was pH-dependent and significant at all pH values only for the tin-containing mouthrinses. No significant differences were observed between the SnF₂- and the SnCl₂-containing solutions. TEM/EDX confirmed ultrastructural pellicle modifications. SnF₂ appears to be the most effective type of fluoride to prevent erosive enamel demineralisation. The observed effects primarily have to be attributed to the stannous ions’ content.

The killer cell lectin-like receptor B1 (KLRB1) 503T>C polymorphism (rs1135816) and acute rejection after liver transplantation

The killer cell lectin-like receptor B1 (KLRB1) gene encodes for CD161 expressed by different subsets of leukocytes involved in the development of acute liver transplant rejection. The single nucleotide polymorphism (SNP) 503T>C (rs1135816) in the KLRB1 gene represents a missense mutation modifying functional properties of CD161. The aim of our study is to determine whether the SNP 503T>C is associated with acute liver transplant rejection. We genotyped the SNP for 163 liver recipients without acute rejection, 125 recipients with a single acute rejection, and 53 recipients with multiple acute rejections. The genotype frequencies within the groups did not show any significant difference. Our data suggest that the SNP 503T>C has no impact on the susceptibility of acute liver transplant rejection.

[Treatment goals in patients with post-stroke upper limb spasticity following injection of botulinum toxin A : Results of the German-Austrian subgroup of the ULIS-II study]

BACKGROUND

The ULIS-II was an international cohort study (NCT01020500) evaluating current treatment of upper limb spasticity in post-stroke adult patients with botulinum toxin A (BoNT-A) in real-life practice.

OBJECTIVE

Post hoc analysis to compare current management of post-stroke adult patients regarding goal setting and attainment with BoNT-A in Germany (D) and Austria (A) with the full cohort of ULIS-II.

MATERIAL AND METHODS

The ULIS-II was a global, open-label, prospective, multicenter observational study with 2 visits conducted in 84 centers worldwide. A total of 468 patients aged ≥18 years with post-stroke upper limb spasticity were included. The primary outcome measure was the responder rate defined as achievement of a goal attainment scale (GAS) score of 0, 1 or 2 after 1 cycle of BoNT-A.

RESULTS

A total of 57 patients from D/A were included in the efficacy analysis. The number of patients in D/A and the full cohort achieving the primary (78.9% vs. 79.6%) and secondary treatment goal (76.8% vs. 75.6%), respectively, was comparable. Deviating from the full cohort, the most common primary treatment goal in D/A was related to impairment (33.3%). Compared to baseline there was a marked reduction in concomitant therapies at the follow-up visit after 3-5 months in the D/A group: patients receiving oral anti-spastic medication 61.4% vs. 40.4%, positioning 50.9% vs. 36.8% and splinting 43.9% vs. 31.6%. Injection control techniques were less frequently used in the D/A group compared to the global study cohort (electrical stimulation: 26.3% vs. 45.8% and electromyography: 12.3% vs. 29.2%). No adverse events were documented in the D/A cohort.

CONCLUSION

A single injection of BoNT-A in adult patients with post-stroke spasticity of the arm led to a high response rate of approximately 80% in both cohorts. The BoNT-A injections in post-stroke adult patients contributed to an improvement in the daily life of patients and their carers beyond simple reduction of muscle tone or spasticity.

Progress in modelling agricultural impacts of and adaptations to climate change

Modelling is a key tool to explore agricultural impacts of and adaptations to climate change. Here we report recent progress made especially referring to the large project initiatives MACSUR and AgMIP; in particular, in modelling potential crop impacts from field to global using multi-model ensembles. We identify two main fields where further progress is necessary: a more mechanistic understanding of climate impacts and management options for adaptation and mitigation; and focusing on cropping systems and integrative multi-scale assessments instead of single season and crops, especially in complex tropical and neglected but important cropping systems. Stronger linking of experimentation with statistical and eco-physiological crop modelling could facilitate the necessary methodological advances.

The distribution of mycotoxins in a heterogeneous wheat field in relation to microclimate, fungal and bacterial abundance

AIM

To observe the variation in accumulation of Fusarium and Alternaria mycotoxins across a topographically heterogeneous field and tested biotic (fungal and bacterial abundance) and abiotic (microclimate) parameters as explanatory variables.

METHODS AND RESULTS

We selected a wheat field characterized by a diversified topography, to be responsible for variations in productivity and in canopy-driven microclimate. Fusarium and Alternaria mycotoxins where quantified in wheat ears at three sampling dates between flowering and harvest at 40 points. Tenuazonic acid (TeA), alternariol (AOH), alternariol monomethyl ether (AME), tentoxin (TEN), deoxynivalenol (DON), zearalenone (ZEN) and deoxynivalenol-3-Glucoside (DON.3G) were quantified. In canopy temperature, air and soil humidity were recorded for each point with data-loggers. Fusarium spp. as trichothecene producers, Alternaria spp. and fungal abundances were assessed using qPCR. Pseudomonas fluorescens bacteria were quantified with a culture based method. We only found DON, DON.3G, TeA and TEN to be ubiquitous across the whole field, while AME, AOH and ZEN were only occasionally detected. Fusarium was more abundant in spots with high soil humidity, while Alternaria in warmer and drier spots. Mycotoxins correlated differently to the observed explanatory variables: positive correlations between DON accumulation, tri 5 gene and Fusarium abundance were clearly detected. The correlations among the others observed variables, such as microclimatic conditions, varied among the sampling dates. The results of statistical model identification do not exclude that species coexistence could influence mycotoxin production.

CONCLUSIONS

Fusarium and Alternaria mycotoxins accumulation varies heavily across the field and the sampling dates, providing the realism of landscape-scale studies. Mycotoxin concentrations appear to be partially explained by biotic and abiotic variables.

SIGNIFICANCE AND IMPACT OF THE STUDY

We provide a useful experimental design and useful data for understanding the dynamics of mycotoxin biosynthesis in wheat.

[Early bilateral nephrectomy in neonatal autosomal recessive polycystic kidney disease : Improved prognosis or unnecessary effort?]

BACKGROUND

Neonatal autosomal recessive polycystic kidney disease (ARPKD) is associated with giant kidneys, lung hypoplasia, pulmonal hypertension, and end-stage renal failure. Depending on the study, mortality is reported to range between 20 and 80%.

OBJECTIVES

Does bilateral nephrectomy improve survival?

PATIENTS AND METHODS

Between 2010 and 2016, we treated 7 children with prenatally diagnosed ARPKD. All had a planned delivery by cesarean section. After birth, oscillated ventilation with nitrogen enrichment was initiated to achieve maximum oxygenation and to decrease pumonary hypertension. All children had bilateral massive kidney hyperplasia (length 13-16 cm).

RESULTS

Nephrectomy on one side was performed within 72 h together with placement of a peritoneal dialysis catheter in the intensive care unit. Contralateral nephrectomy was performed after 1-2 weeks when the child was stabilized by dialysis. In 2 children, kidney transplantation has already been performed and they are doing fine. One child died after 10 months due to infection. The other children are stable on home peritoneal dialysis awaiting transplantation.

CONCLUSIONS

Early bilateral nephrectomy in neonatal ARPKD is feasible, but requires distinctive care at a pediatric intensive care unit and a high amount of organizational efforts to treat these children adequately in the first few days. In our experience, the procedure is a promising approach to improve ventilation and enable dialysis. However, kidney transplantation, best from a living donor, is required within the first years of life.

Enhanced Absorption by Linewidth Narrowing in Optically Excited Type-II Semiconductor Heterostructures

We experimentally report a surprising linewidth narrowing of the direct exitonic 1  s heavy-hole transition in a type-II quantum well system. This narrowing, which builds up on a pico- to nanosecond timescale, causes a transient enhanced absorption at the spectral peak position of the excitonic resonance. We discuss how this effect depends on experimental parameters such as excitation density, temperature, and barrier width. We cannot attribute this effect to known physical mechanisms.

Salivary duct stenosis: diagnosis and treatment

The management of stenoses of the major salivary glands had undergone a significant change during the last 15-20 years. Accurate diagnosis forms the basis of adapted minimal invasive therapy. Conventional sialography and MR-sialography are useful examination tools, and ultrasound seems to be a first-line investigational tool if salivary duct stenosis is suspected as cause of gland obstruction. Sialendoscopy is the best choice to establish final diagnosis and characterise the stenosis in order to plan accurate treatment. In all major salivary glands, inflammatory stenosis can be distinguished from fibrotic stenosis. In the parotid duct system, an additional stenosis associated with various abnormalities of the duct system has been reported. Conservative therapy is not sufficient in the majority of cases. The development of a minimally invasive treatment regime, in which sialendoscopy plays a major role, has made the preservation of the gland and its function possible in over 90% of cases. Ductal incision procedures are the most important measure in submandibular duct stenoses, but sialendoscopy becomes more important in the more centrally located stenoses. Sialendoscopic controlled opening and dilation is the dominating method in parotid duct stenoses. In 10-15% of cases, success can be achieved after a combined treatment regime had been applied. This review article aims to give an overview on the epidemiology, diagnostics and current state of the art of the treatment of salivary duct stenoses.

Remodeling of muscle fibers approaching the human myotendinous junction

The myotendinous junction (MTJ) is at high risk of strain injuries, due to high amounts of energy that is transferred through this structure. The risk of strain injury is significantly reduced by heavy resistance training (HRT), indicating a remodeling capacity of MTJ. We investigated the degree of remodeling of muscle fibers near the human MTJ. In 8 individuals, samples were taken from the semitendinosus and gracilis MTJ and they were stained immunohistochemically for myonuclei (DAPI), fibroblasts (TCF7L2), and satellite cells (CD56). A high portion of the muscle fibers adjacent to the MTJ contained a centrally located myonucleus (47 ± 8%, mean ± SD) and half of the muscle fibers were CD56 positive. The number of satellite cells and fibroblasts were not higher than what has previously been reported from muscle bellies. The immunohistochemical findings suggest that the rate of remodeling of muscle fibers near the MTJ is very high. The finding that there was no increased number of satellite cells and fibroblasts could be explained as a dynamic phenomenon. The effect of HRT should be evaluated in a randomized setting.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

BACKGROUND

Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes.

RESULTS

The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal.

CONCLUSIONS

PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.

Hemodialysis-Related Induction of β2-Microglobulin Synthesis and Release by Mononuclear Phagocytes

We have investigated β2-microglobulin (β2M) synthesis and release by blood leukocytes and isolated mononuclear phagocytes. Since β2M was discovered to form amyloid fibrils in patients undergoing long term, chronic hemodialysis and monomeric β2M levels in plasma of these patients are highly elevated, and since hemodialysis-related factors that increase β2M production are unknown, we evaluated β2M production by mononuclear phagocytes under a variety of conditions. We utilized a novel enzyme-lined immunoabsorbant assay to quantitate β2M release. Adherence of macrophages onto polystyrene or Cuprophan membranes does not induce β2M synthesis or release. In contrast, interaction of macrophages with lipopolysaccharide, gamma-interferon, tumor necrosis factor, or interleukin 1 induces synthesis or release. In contrast, interaction of macrophages with lipopolysaccharide, gamma-interferon, tumor necrosis factor, or interleukin 1 induces synthesis and release of β2M, indicating that β2M synthesis is increased during macrophage activation. Exposing leukocytes or macrophages to changes in osmotic or oncotic pressure induces a rapid release of β2M and interleukin 1 into the cellular medium. These results suggest that during hemodialysis, β2M production is more likely to result from endotoxin contamination, or osmotic and oncotic changes, rather than direct interaction of mononuclear phagocytes with cellulosic membranes.

JAMI: a Java library for molecular interactions and data interoperability

Background

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types.

Results

A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats.

Conclusion

Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI’s model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.