Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transformation_of can facilitate the integration of such ontologies in ways which have (...) the potential to support new kinds of automated reasoning. We here extend this approach to the treatment of pathologies, focusing especially on those pathological continuant entities which arise when organs become affected by carcinomas. (shrink)

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a (...) way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population. (shrink)

Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records (...) in such a way that real time conclusions can be drawn. In this paper we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma. (shrink)

Serum lmmunglobulin and Complement Levels in the Patients With Head and Neck Carcinoma and the Evaluation of Autoantibody Positivity Ratein this study, smooth muscle antibody (SMA), anti-nücleer antibody (ANA) anti- mitochondrial antibody (AMA), anti-parietal cell antibody (PA), antiglomerular basal membrane antibody (GM), serum immunglobulins and complement-C3 levels have been searched. The positivity rate of ANA (31.91 %) and SMA (38.29 %) were found high in sera of the patients with head and neck carcinoma which had been diagnosed histopathologically. (...) But the positivity rate of AMA (4.25 %) PA (12.76 %) and GM (2.12 %) were low in the same group. ANA and SMA were detected in 1 O of 30 patients with laryngeal carcinoma; ANA were detected in 5 of 9 patients (55.5 %) and SMA were found in 4 of 9 patients (44.5 %) with nasopharyngeal carcinoma. There was no significant deviation in the levels of immunglobulins and complement-C3. The highest levels of immunoglobulins have been detected in patients with laryngeal carcinoma. Finding of high positivity rate of ANA and SMA in the patients with head and neck carcinoma showed an accordance with the other investigators' results. (shrink)

Objective: This study aimed to investigate and compare the effects of tubular gastroesophageal anastomosis and traditional gastroesophageal supra-arch anastomosis on the postoperative lung function of patients with esophageal carcinoma. -/- Methods: A total of 90 patients with middle-lower segmental esophageal cancer admitted in our hospital from August 2014 to August 2016 were recruited to our study. They were randomly divided into two groups. The observation group underwent tubular gastroesophageal anastomosis, whereas the control group underwent traditional gastroesophageal supra-arch anastomosis. Changes (...) in the postoperative pulmonary function were compared between the two groups. -/- Results: The numbers of CD4 cells (27.45 ± 5.48), CD8 cells (35.97 ± 7.16), and natural killer cells (20.79 ± 2.49), as well as the CH4/CD8 ratio (0.69 ± 0.18), of the patients in the observation group were significantly higher than the (38.45 ± 5.98), (20.45 ± 6.41), (39.44 ± 3.49), and (1.31 ± 0.48), respectively, of the patients in the control group. The differences between the two groups were statistically significant (P<0.05). By contrast, the preoperative forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), and maximum voluntary ventilation (MVV) did not significantly differ between the two groups (P>0.05). The FEV1 (1.76 ± 0.41 L), FVC (2.33 ± 0.32 L), and MVV (33.7 ± 5.2 L/min) of the observation group were significantly higher than those of the control group (P<0.05). Meanwhile, the complication rate of the observation group was 42.2%, which was significantly lower than that of the control group (75.6%) (P<0.05). -/- Conclusion: Tubular gastroesophageal anastomosis can benefit patients with esophageal cancer by significantly reducing the adverse effects on their postoperative pulmonary function and control the occurrence of postoperative complications. (shrink)

Transoral laser microsurgery applies to the piecemeal removal of malignant tumours of the upper aerodigestive tract using the CO2 laser under the operating microscope. This method of surgery is being increasingly popularised as a single modality treatment of choice in early laryngeal cancers (T1 and T2) and occasionally in the more advanced forms of the disease (T3 and T4), predomi- nantly within the supraglottis. Thomas Kuhn, the American physicist turned philosopher and historian of science, coined the phrase ‘paradigm shift’ in (...) his groundbreaking book The Structure of Scientific Revolutions. He argued that the arrival of the new and often incompatible idea forms the core of a new paradigm, the birth of an entirely new way of thinking. This article discusses whether Steiner and col- leagues truly brought about a paradigm shift in oncological surgery. By rejecting the principle of en block resection and by replacing it with the belief that not only is it oncologically safe to cut through the substance of the tumour but in doing so one can actually achieve better results, Steiner was able to truly revolutionise the man- agement of laryngeal cancer. Even though within this article the repercussions of his insight are limited to the upper aerodigestive tract oncological surgery, his willingness to question other peoples’ dogma makes his contribution truly a genuine paradigm shift. (shrink)

I argue that ductal carcinoma in situ (DCIS), the tumor most commonly diagnosed by breast mammography, cannot be confidently classified as cancer, that is, as pathological. This is because there may not be dysfunction present in DCIS—as I argue based on its high prevalence and the small amount of risk it conveys—and thus DCIS may not count as a disease by dysfunction-requiring approaches, such as Boorse’s biostatistical theory and Wakefield’s harmful dysfunction account. Patients should decide about treatment for DCIS (...) based on the risks it poses and the risks and benefits of treatment, not on its disease status. (shrink)

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is (...) worth investigating whether, by overcoming some of its weaknesses from the point of view of formal-ontological principles, we might not be able to enhance a version of GO which can come even closer to serving the needs of the various communities of biomedical researchers and practitioners. It is accepted that clinical and bioinformatics need to find common ground if the results of data-intensive biomedical research are to be harvested to the full. It is also widely accepted that no single method will be sufficient to create the needed common framework. We believe that the principles-based approach to life-science data integration and knowledge representation must be one of the methods applied. Indeed in dealing with the ontological representation of carcinomas, and specifically of colon carcinomas, we have established that, had GO (and related biomedical ontologies) followed some of the basic formal-ontological principles we have identified (Smith et al. 2004, Ceusters et al. 2004), then the effort required to navigate successfully between clinical and bioinformatics systems would have been reduced. We point here to the sources of ontologically-related errors in GO, and also provide arguments as to why and how such errors need to be resolved. (shrink)

Lung cancer is still a detrimental problem for physicians and surgeons. Because of having no standard treatment and poor survival, enforces us to find new approaches for its eradication. However, we have a so long way to this purpose. Genetic and cell researches to find out its real etiology and pathway are developing. But today, patients with lung cancer are waiting for some treatment methods which ease and give hope themselves immediately. Surgery is the most hopeful way for radical solution (...) of lung cancer. Recently, new anesthetic and surgical technics give us some important advantages that were very frightfully before. In this issue, we aimed to emphasize the new researches, interventions and experimental studies about pulmonary carcinoma. All authors worked hard for this purpose. I appreciate all of them and the editor in chief Prof. Murat Sucu. I hope all articles will help us thinking and researching lung cancer in all ways. -/- Prof. A. Feridun Işık. (shrink)