High early failure rate for a new unicondylar knee system.

Background: This single-center retrospective study evaluated early failure rates for an unicompartmental knee arthroplasty (UKA) system with an anti-allergic surface. Methods: We studied 87 consecutive joints received an UKA at a single center between 2017 and 2020. All patients received a fully cemented anti-allergic Univation-Aesculap partial knee replacement implant with a corundum blasting surface. All joints had precise indication of unicompartmental arthroplasty according to the current criteria of this procedure. The current series was restricted to patients undergoing medial cemented UKA. Medial compartment osteoarthritis was the main indication. Results: We found early failure (aseptic loosening) was documented in 20 of the 87 joints (23%). The time to failure ranged from 7 weeks to 3 years, for an estimated 33% (15-46%) cumulative hazard rate for implant loosening over three years. No cases of periprosthetic joint infection were found. On average, the patients began complaining about first symptoms during the third month after surgery. In most cases (66.66%), the cement remained fixed to the bone. Conclusions: Based on these early results, the manufacturer of this implant stopped all further distribution. Continued efforts should be made to understand the clinical and radiographic outcomes of alternative and anti-allergic surface coatings in knee arthroplasty.

Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature.

BACKGROUND: Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSD provenance, scientific use, and reuse in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level. FINDINGS: We extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. We constructed flat data tables and a data warehouse with an interactive web application to enable ad hoc exploration of NSD use and summary statistics. CONCLUSIONS: The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enable scientists worldwide to join literature and sequence databases in a multidimensional fashion. As a concrete use case, we visualized statistics of country clusters concerning NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.

Myth-busting the provider-user relationship for digital sequence information.

BACKGROUND: The United Nations Convention on Biological Diversity (CBD) formally recognized the sovereign rights of nations over their biological diversity. Implicit within the treaty is the idea that mega-biodiverse countries will provide genetic resources and grant access to them and scientists in high-income countries will use these resources and share back benefits. However, little research has been conducted on how this framework is reflected in real-life scientific practice. RESULT: Currently, parties to the CBD are debating whether digital sequence information (DSI) should be regulated under a new benefit-sharing framework. At this critical time point in the upcoming international negotiations, we test the fundamental hypothesis of provision and use of DSI by looking at the global patterns of access and use in scientific publications. CONCLUSION: Our data reject the provider-user relationship and suggest a far more complex information flow for DSI. Therefore, any new policy decisions on DSI should be aware of the high level of use of DSI across low- and middle-income countries and seek to preserve open access to this crucial common good.

KRAS, EGFR, PDGFR-α, KIT and COX-2 status in carcinoma showing thymus-like elements (CASTLE).

BACKGROUND: CASTLE (Carcinoma showing thymus-like elements) is a rare malignant neoplasm of the thyroid resembling lymphoepithelioma-like and squamous cell carcinoma of the thymus with different biological behaviour and a better prognosis than anaplastic carcinoma of the thyroid. METHODS: We retrospectively investigated 6 cases of this very rare neoplasm in order to investigate the mutational status of KRAS, EGFR, PDGFR-α and KIT, as well as the immunohistochemical expression pattern of CD117, EGFR and COX-2, and possibly find new therapeutic targets. RESULTS: Diagnosis was confirmed by a moderate to strong expression of CD5, CD117 and CK5/6, whereas thyroglobulin, calcitonin and TTF-1 were negative in all cases. Tumors were also positive for COX-2 and in nearly all cases for EGFR. In four cases single nucleotide polymorphisms (SNPs) could be detected in exon 12 of the PDGFR-α gene (rs1873778), in three cases SNPs were found in exon 20 of the EGFR gene (rs1050171). No mutations were found in the KIT and KRAS gene. CONCLUSIONS: All tumors showed a COX-2 expression as well as an EGFR expression except for one case and a wild-type KRAS status. No activating mutations in the EGFR, KIT and PDGFR-α gene could be detected. Our data may indicate a potential for targeted therapies, but if these therapeutic strategies are of benefit in CASTLE remains to be determined. VIRTUAL SLIDES: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1658499296115016.

Chromosomal imbalances in carcinoma showing thymus-like elements (CASTLE).

Carcinoma showing thymus-like elements (CASTLE) is a rare neoplasm of the thyroid gland resembling lymphoepithelioma-like and squamous cell carcinoma of the thymus and is thought to arise from ectopic thymic tissue within the thyroid gland or rudimentary branchial pouches along the thymic line. Using comparative genomic hybridization (CGH), chromosomal imbalances have been detected in several types of thymomas and thymic carcinomas. To evaluate whether there are hints of an underlying sequence in the pathogenesis of CASTLE analogue to those found in thymomas and thymic carcinomas, we evaluated four of these rare neoplasms for chromosomal imbalances using CGH. The most frequent gains were seen on chromosomal arm 1q (3/4), and losses were most frequently detected on 6p (4/4), 6q (3/4) and 16q (3/4). These CGH data show that CASTLE is characterized by chromosomal imbalances similar to those found in thymomas and thymic carcinomas and indicate a similar sequence in tumour development.

Teaching (and learning from) metabolomics: the 2006 PlantMetaNet ETNA Metabolomics Research School.

Under the auspices of the European Training and Networking Activity programme of the European Union, a 'Metabolic Profiling and Data Analysis' Plant Genomics and Bioinformatics Summer School was hosted in Potsdam, Germany between 20 and 29 September 2006. Sixteen early career researchers were invited from the European Union partner nations and the so-called developing nations (Appendix). Lectures from invited leading European researchers provided an overview of the state of the art of these fields and seeded discussion regarding major challenges for their future advancement. Hands-on experience was provided by an example experiment - that of defining the metabolic response of Arabidopsis to treatment of a commercial herbicide of defined mode of action. This experiment was performed throughout the duration of the course in order to teach the concepts underlying extraction and machine handling as well as to provide a rich data set with which the required computation and statistical skills could be illustrated. Here we review the state of the field by describing both key lectures given at and practical aspects taught at the summer school. In addition, we disclose results that were obtained using the four distinct technical platforms at the different participating institutes. While the effects of the chosen herbicide are well documented, this study looks at a broader number of metabolites than in previous investigations. This allowed, on the one hand, not only to characterise further effects of the herbicide than previously observed but also to detect molecules other than the herbicide that were obviously present in the commercial formulation. These data and the workshop in general are all discussed in the context of the teaching of metabolomics.

Transcriptome analysis of sulfur depletion in Arabidopsis thaliana: interlacing of biosynthetic pathways provides response specificity.

Higher plants assimilate inorganic sulfate into cysteine, which is subsequently converted to methionine, and into a variety of other sulfur-containing organic compounds. To resist sulfur deficiency, plants must demonstrate physiological flexibility: the expression of an extensive set of genes and gene regulators that act in the affected pathways or signalling cascades must be delicately tuned in response to environmental challenges. To elucidate this network of interactions, we have applied an array hybridisation/transcript profiling method to Arabidopsis plants subjected to 6, 10 and 13 days of constitutive and induced sulfur starvation. The temporal expression behaviour of approximately 7200 non-redundant genes was analysed simultaneously. The experiment was designed in a way to identify statistically significant changes of gene expression based on sufficient numbers of repeated hybridisations performed with five uniform pools of plant material. The expression profiles were processed to select differentially expressed genes. Among the 1507 sulfur-responsive clones implicated in this way, 632 genes responded specifically to sulfur deficiency by significant over-expression. The sulfur-responsive genes were grouped according to functional categories or biosynthetic pathways. As expected, genes of the sulfur assimilation pathway were altered in expression. Furthermore, genes involved in flavonoid, auxin, and jasmonate biosynthesis pathways were upregulated in conditions of sulfur deficiency. Based on the correlative analysis of gene expression patterns, we suggest that a complex co-ordination of systematic responses to sulfur depletion is provided via integration of flavonoid, auxin and jasmonate pathway elements. Plait concept for transduction of specificity via the main non-specific signalling stream is proposed.