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Do we still need supertrees?
Arndt von Haeseler
BMC Biology , 2012, DOI: 10.1186/1741-7007-10-13
Abstract: See research article http://www.biomedcentral.com/1741-7007/10/12 webciteAfter more than two centuries of intensive research the phylogeny of such important groups as the carnivores, let alone deeper phylogenetic relationships, is still not satisfactorily settled. Recently, Nyakatura and Bininda-Emonds [1] published an up-dated phylogeny of all 286 carnivore species. The new phylogeny is an extension of a study 12 years ago [2], which needed revision due to better methodologies and more data, especially DNA sequence data.However, the reconstruction of the carnivore tree is not as straightforward as one may expect. Typically, DNA or protein sequence data or phylogenies are available for only a subset of the carnivores. Thus, the major challenge is to construct one phylogeny for a taxonomic group from multiple sources. To this end the authors analyzed 241 trees available from the literature and additionally 74 gene trees generated from sequence data. The total of 341 so-called source trees was then combined into one supertree, assumed to mirror the phylogeny of the carnivore species. Combining trees derived from different data sets falls into the realm of supertree methods [3]. Alternatively one may also apply the so-called supermatrix method to combine data [4]. Here, the character data are pooled and then followed by a tree reconstruction. Both methods are in wide use and it is still an open question which method is preferable.Supertree methods combine source-trees, or trees obtained from the literature, with overlapping species sets into one tree. Nyakatura and Bininda-Emonds [1] selected matrix representation with parsimony (MRP) [5] as the method of choice for generating a supertree of carnivore species. The workflow is illustrated in Figure 1: MRP constructs a new data matrix (MRP-matrix), where each species in the source-trees is represented in a row. The columns of the MRP-matrix are built by encoding the source-trees. Species sharing a common node in the root
Ramadan fasting and transplantation: Current knowledge and what we still need to know  [cached]
Khedmat Hossein,Taheri Saeed
Saudi Journal of Kidney Diseases and Transplantation , 2010,
Abstract: Ramadan fasting is one of the most appreciated Islamic rituals in Islamic culture. Although non-healthy as well as weak people are allowed not to fast in this month, some trans-plant recipient patients are willing to fast but are concerned about adverse effects on their health. Due to answering this question, a number of studies have been conducted. In this literature review we review the existing data on this issue and attempt to reach to a conclusion on what we know and what we still need to know.
Do we still need a permanent colostomy in XXI-st century?  [PDF]
Szezepkowski M.
Acta Chirurgica Iugoslavica , 2002, DOI: 10.2298/aci0202045s
Abstract: The aim of this paper is to answer the question: do we still need a permanent colostomy and present the quality of life of patients operated on for rectal cancer. A comparative analysis of patients after abdomino-perineal resection of the rectum vs. patients after low anterior resection of the rectum with preservation of sphincters is presented. When assessing the quality of life of patients, the following issues were considered: a) function of the whole organism and general condition (physical function); b) psychological well-being (psychological function); c) professional activity, relations with relatives and friends, leisure activities (social function) and d) intimate relations (sexual function). In both groups of patients, both after abdomino-perineal resection of the rectum and after low-anterior resection, a significant deterioration in the quality of life was noted. In spite of a good general health condition in the majority of cases (over 60% in both groups), frequent are irregular stools and diarrhea. Stomy patients complain about uncontrolled passing of gas and urologic problems, while patients with preserved sphincter complain about constipation. Stomy patients significantly more often suffer depression, loneliness and even despair due to low self-esteem and feeling of unfavorable change in body appearance. This feeling is present more often in younger patients and in women. Rectal cancer may cause social dysfunction, like reluctance to resume professional activity after surgery, limitation of social contacts, change of model of rest and leisure activities towards more passive forms and forms which do not require the attendance of many people. These phenomena apply to both groups but are more prominent among stomy patients. As stomy patients are usually older, some of these alterations may be due to age. Sexual dysfunction is significantly more frequent in stomy patients. Age may be one of the causes thereof. These problems are significantly more frequent in males. In some cases of colorectal cancer, the best way of management is colostomy. Further studies are needed to elaborate more clear criteria for optimal management of patients with colorectal cancer.
Thiopurines in inflammatory bowel disease revisited  [cached]
Florian B?r,Christian Sina,Klaus Fellermann
World Journal of Gastroenterology , 2013, DOI: 10.3748/wjg.v19.i11.1699
Abstract: Although a great variety of new drugs have been introduced for the therapy of inflammatory bowel diseases so far, a definite cure of the disease is still out of scope. An anti-inflammatory approach to induce remission followed by maintenance therapy with immunosupressants is still the mainstay of therapy. Thiopurines comprising azathioprine and its active metabolite mercaptopurine as well as tioguanine, are widely used in the therapy of chronic active inflammatory bowel disease (IBD). Their steroid sparing potential and efficacy in remission maintenance are out of doubt. Unfortunately, untoward adverse events are frequently observed and may preclude further administration or be life threatening. This review will focus on new aspects of thiopurine therapy in IBD, its efficacy and safety.
We still need to operate at night!
Omar Faiz, Saswata Banerjee, Paris Tekkis, Savvas Papagrigoriadis, John Rennie, Andrew Leather
World Journal of Emergency Surgery , 2007, DOI: 10.1186/1749-7922-2-29
Abstract: All general surgical and vascular emergency operations recorded prospectively on the theatre database between 1997 and 2004 were included in the study. Operations were categorised according to whether they commenced during the daytime(08:01–18:00 hours), evening(18:01–00:00 hours) or night-time(00:01–08:00 hours). The procedure type and grade of the participating surgical personnel were also recorded. Bivariate correlation was used to analyse changing trends in the emergency workload.In total 5,316 emergency operations were performed over the study period. The numbers of daytime, evening and night-time emergency procedures performed were 2,963(55.7%), 1,832(34.5%), and 521(9.8%) respectively. Laparotomies and complex vascular procedures collectively accounted for half of all cases performed after midnight whereas they represented only 30% of the combined daytime and evening emergency workload. Thirty-two percent (n = 166) of all night-time operations were supervised or performed by a consultant surgeon. The annual volume of emergency cases performed increased significantly throughout the study period. Enhanced daytime (r = 0.741, p < 0.01) and evening (r = 0.548, p < 0.01) operating absorbed this increase in workload. There was no significant change in the absolute number of cases performed at night but the proportion of the emergency workload that took place after midnight decreased significantly throughout the study (r = -0.742, p < 0.01).A small but consistent volume of complex cases require emergency surgery after midnight. Provision of an emergency general surgical service must incorporate this need.Over the last decade significant change has occurred to the provision of the emergency service in many hospitals. The principal factors underlying this change have been the influence of recommendations made by the 'National Confidential Enquiry into Peri-operative Deaths' (NCEPOD) [1,2] as well as a mandatory reduction in junior doctor working hours brought about by
Do we really understand what the immunological disturbances in inflammatory bowel disease mean?
Epameinondas V Tsianos, Konstantinos Katsanos
World Journal of Gastroenterology , 2009,
Abstract: The gastrointestinal tract uses a system of tolerance and controlled inflammation to limit the response to dietary or bacteria-derived antigens in the gut. When this complex system breaks down, either by a chemical or pathogenic insult in a genetically predisposed individual the resulting immune response may lead to inflammatory bowel disease. Although the aetiopathogenesis of inflammatory bowel disease remains unsolved current evidence indicates that defective T-cell apoptosis and impairment of intestinal epithelial barrier function play important roles. In inflammatory bowel disease, it has been reported that activation of macrophages seems to be as important as increased production of the macrophage-derived cytokines such as TNF-α, IL-1 and IL-6. The triggering factor for this cascade is still to be elucidated as to whether it represents an auto-antigen or a hetero-antigen. It has been also demonstrated that a serologic anti-microbial response exists. This response includes antibodies against saccharomyces cerevisiae (ASCA), E. coli outer membrane porin C (Omp-C), flagelin (cBir1) and pseudomonas aeroginosa (I2). Host response to microbial pathogens includes self-defense mechanisms including defensins, pattern recognition receptors and Toll-like receptors. Neuroimmunomodulation in inflammatory bowel disease (IBD) is another interesting approach with implications on the influence of brain-gut axis on intestinal inflammation and its perpetuation. It is probable that inflammatory bowel disease represents a heterogenic group of diseases that share similar mechanisms of tissue damage but have different initiating events and immunoregulatory abnormalities. A better understanding of all these events will hopefully provide new insights into the mechanisms of epithelial responses to microorganisms and ideas for therapies.
INTERSEPT study: we still need more clarity
Flavia R Machado, Milton Caldeira-Filho, Rubens Costa-Filho, Ciro Mendes, Suzana Lobo, Eduardo da Rocha, Jose Telles, Glauco Westphal
Critical Care , 2012, DOI: 10.1186/cc11192
Abstract: We served as the principal investigators of this trial and come from sites that did not successfully include any patients or that included only a small number of patients. From this vantage point, we believe that Pontes-Arruda's reply to Machado's comments [2] did not clarify several important points.As stated in the article [1], only five of the 12 sites successfully enrolled patients. However, the first author's site was responsible for the inclusion of about 100 of the 106 patients. We believe that this imbalance is relevant and that readers of Critical Care need to be aware of it. We disagree with Pontes-Arruda's response [2] that all relevant limitations were already mentioned in the Discussion [1]. We found it difficult to understand his affirmation that the results were unaffected by the unbalanced distribution pattern of the patients, as any statistical analysis of the few patients from the other four sites would obviously be underpowered. We also think he should clearly state the strategies that were used at his site to successfully enroll patients given that the 11 other sites, most of which are very skilled at performing intervention studies, failed to enroll similar numbers of patients.The author's explanation [2] of the Sequential Organ Failure Assessment (SOFA) findings is also not clear. We agree that it is perfectly possible for some patients to have a high SOFA score that may be insufficient to fulfill the inclusion criteria. However, the median and interquartile values shown in Table 3 [1] indicate that 75% of all patients had a SOFA score of more than 4. This would be a very unusual finding in sepsis patients without significant organ dysfunction. Moreover, the interquartile interval in Table 3 indicates that at least 75% of the patients had platelet levels of more than 144 × 109 cells per liter, a bilirubin level of less than 1.5 mg/dL, and a creatinine level of less than 1.6 mg/dL; as stated in the text [1], no patients had an arterial partial p
Are we giving azathioprine too much time?  [cached]
Fernando Gomollón, Santiago García López
World Journal of Gastroenterology , 2008,
Abstract: Azathioprine is currently the key drug in the maintenance treatment of inflammatory bowel diseases. However, there are still some practical issues to be resolved: one is how long we must maintain the drug. Given that inflammatory bowel diseases are to date chronic, non-curable conditions, treatment should be indefinite and only the loss of efficacy or the appearance of serious side effects may cause withdrawal. As regards to efficacy and their maintenance over time, evidence supports the continuous usefulness of the drug in the long term: in fact its withdrawal very substantially increases the risk of relapse. About side effects, azathioprine is a relatively well tolerated drug and even indefinite use seems safe. The main theoretical risks of prolonged use would be the myelotoxicity, hepatotoxicity, and the development of cancer. In fact, serious bone marrow suppression or serious liver damage are uncommon, and can be minimized with proper use of the drug. Recent metanalysis suggests that the risk of lymphoma is real, but the individual risk is rather low, and decision analysis suggests a favorable benefit/risk ratio in the long term. Therefore, in patients with inflammatory bowel diseases in whom azathioprine is effective and well tolerated, the drug should not be stopped. This recommendation concerns the use of azathioprine as a single maintenance drug, and is not necessarily applicable to patients receiving concomitant biological therapy.
Recent results of laparoscopic surgery in inflammatory bowel disease  [cached]
Hermann Kessler, Jonas Mudter, Werner Hohenberger
World Journal of Gastroenterology , 2011,
Abstract: Inflammatory bowel diseases are an ideal indication for the laparoscopic surgical approach as they are basically benign diseases not requiring lymphadenectomy and extended mesenteric excision; well-established surgical procedures are available for the conventional approach. Inflammatory alterations and fragility of the bowel and mesentery, however, may demand a high level of laparoscopic experience. A broad spectrum of operations from the rather easy enterostomy formation for anal Crohn’s disease (CD) to restorative proctocolectomies for ulcerative colitis (UC) may be managed laparoscopically. The current evidence base for the use of laparoscopic techniques in the surgical therapy of inflammatory bowel diseases is presented. CD limited to the terminal ileum has become a common indication for laparoscopic surgical therapy. In severe anal CD, laparoscopic stoma formation is a standard procedure with low morbidity and short operative time. Studies comparing conventional and laparoscopic bowel resections, have found shorter times to first postoperative bowel movements and shorter hospital stays as well as lower complication rates in favour of the laparoscopic approach. Even complicated cases with previous surgery, abscess formation and enteric fistulas may be operated on laparoscopically with a low morbidity. In UC, restorative proctocolectomy is the standard procedure in elective surgery. The demanding laparoscopic approach is increasingly used, however, mainly in major centers; its feasibility has been proven in various studies. An increased body mass index and acute inflammation of the bowel may be relative contraindications. Short and long-term outcomes like quality of life seem to be equivalent for open and laparoscopic surgery. Multiple studies have proven that the laparoscopic approach to CD and UC is a safe and successful alternative for selected patients. The appropriate selection criteria are still under investigation. Technical considerations are playing an important role for the complexity of both diseases.
Pharmacological Nutrition in Inflammatory Bowel Diseases
Campos,F. G.; Waitzberg,D. L.; Teixeira,M. G.; Mucerino,D. R.; Kiss,D. R.; Habr-Gama,A.;
Nutrición Hospitalaria , 2003,
Abstract: inflammatory bowel diseases - ulcerative colitis and crohn?s disease- are chronic gastrointestinal inflammatory diseases of unknown etiology. decreased oral intake, malabsorption, accelerated nutrient losses, increased requirements, and drug-nutrient interactions cause nutritional and functional deficiencies that require proper correction by nutritional therapy. the goals of the different forms of nutritional therapy are to correct nutritional disturbances and to modulate inflammatory response, thus influencing disease activity. nutritional intervention may improve outcome in certain individuals; however, because of the costs and complications of such therapy, careful selection is warranted. total parenteral nutrition has been used to correct and prevent nutritional disturbances and to promote bowel rest during active disease, mainly in cases of digestive fistulae with a high output. its use should be reserved for patients who cannot tolerate enteral nutrition. enteral nutrition is effective in inducing clinical remission of disease in adults and promoting growth in children. recent research has focused on the use of specific nutrients as primary treatment agents. although some reports have indicated that glutamine, short-chain fatty acids, antioxidants and immunonutrition with omega-3 fatty acids are an important therapeutic alternative in the management of inflammatory bowel diseases, the beneficial reported effects have yet to be translated into the clinical practice. the real efficacy of these nutrients still need further evaluation through prospective and randomized trials.
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