A framework for philosophical biology

Advances in biology have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. Theoretical biology used to primarily provide a basis to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. This could in part be explained by a relatively recent tendency in which a "data first", rather than a "theory first", approach is preferred. Moreover, generating hypotheses has at times become procedural rather than theoretical. This situation leaves our understanding enmeshed in data, which should be disentangled from much noise. Given the many unresolved questions in biology and medicine, it seems apt to revive the role of pure theory in the biological sciences. This paper makes the case for a "philosophical biology" (philbiology), distinct from but quite complementary to philosophy of biology (philobiology), which would entail biological investigation through philosophical approaches. Philbiology would thus be a reincarnation of theoretical biology, adopting the true sense of the word "theory" and making use of a rich tradition of serious philosophical approaches in the natural sciences. A philbiological investigation, after clearly defining a given biological problem, would aim to propose a set of empirical questions, along with a class of possible solutions, about that problem. Importantly, whether or not the questions can be tested using current experimental paradigms would be secondary to whether the questions are inherently empirical or not. The final goal of a philbiological investigation would be to develop a theoretical framework that can lead observational and/or interventional experimental studies of the defined problem

Comparison of three with six regions of interest analyses in patients with idiopathic constipation undertaking colon transit scintigraphy using 67Ga-citrate

OBJECTIVE AND INTRODUCTION: Preparation of data from 6 geometric regions of interest in the colon is time consuming, and can become impractical in the environment of busy Nuclear Medicine Departments. Therefore, we have investigated and demonstrated an alternative method for obtaining the same diagnostic information from an analysis of patients with idiopathic constipation who underwent colon transit scintigraphy using 67Ga-citrate. Data analysis methods using three regions of interest are compared to the results obtained using the more time consuming 6 regions of interest method to analyze the data. MATERIALS AND METHODS: In this study, we report our results of the comparative reanalysis of data obtained by more traditional methods. We compare 3 regions of interest (ROI) which were taken from areas including the right colon, left colon and the rectosigmoid colon, with original work using our alternative 6 (ROI) diagnostic methodology. In addition, the proximal colonic emptying (PCE) was determined at 24 hr post ingestion among members of 3 identified subject groups. RESULTS: The distribution of activity as the ingested 67Ga-citrate passes through the colon constitutes an activity profile. The mean activity position in the colon can be determined from subsequent radiographic images and from this the mean clearance time can be calculated. In quantitative assessment, this represents the time at which half of activity was eliminated from colon (mean half clearance time - MCT) which did not appear different in the reanalysis. There is no significant difference in the current study in GMC 24h, GMC 48h and GMC 72h between two groups using the Man Whitney u test (p > 0.05), while in the previous work the results were statistically significant for the two later time periods GMC (GMC 48h and GMC 72h) (p = 0.016 and p = 0.027 respectively). The PCE in the group 1 was = 2.50 (0.37); group 2, 1.57 (0.47) and group 3, 2.97. The PCE was not different between the two groups (p = 0.21). CONCLUSIONS: This investigation demonstrated that the radionuclide colon transit study using 67Ga-citrate is a safe, physiologic, and quantitative method for evaluating the transit of fecal material from cecum to rectum. Although, the visual assessment of diagnosis of the subjects in the two analyses is the same, it was not completely supported by quantitative measurements. Therefore, further studies need to be done

Comparison evaluation of Curcumin(Curcuma longa extract)with the application of expressed breast milk in the treatment of nipple cracks in lactating primiparous women: A randomized clinical trial

زمینه و هدف: شقاق پستان مشکل شایعی در زنان شیرده می باشد که می تواند باعث قطع زودهنگام شیردهی گردد. زردچوبه یکی از قدیمی ترین گیاهان دارویی است که به دلیل دارا بودن کورکومین، اثر ترمیم کننده روی زخم ها دارد. این مطالعه با هدف تعیین تأثیر عصاره آبی الکلی کورکومین و مقایسه آن با باقی گذاردن قطره شیر مادر در درمان شقاق پستان انجام گردید. روش بررسی: پژوهش حاضر به صورت کارآزمایی بالینی تصادفی در سال 1392 بر روی زنان نخست زای مراجعه کننده به مراکز بهداشتی غرب اهواز انجام گردید. 88 مادر شیرده مبتلا به شقاق پستان، به شکل تصادفی به دو گروه مساوی درمان با کورکومین و گروه باقی گذاردن قطره شیر مادر تقسیم شدند. به منظور بررسی روند بهبود زخم و عوارض جانبی کورکومین، قبل ازدرمان، روز سوم و روز هفتم پس از شروع درمان، مقیاس استور توسط پژوهشگر تکمیل گردید. یافته ها: قبل از مطالعه و همچنین در روز هفتم تفاوت معنی دار بین میانگین نمره شقاق پستان در دو گروه مشاهده نشد؛ اما در روز سوم میانگین نمره شقاق در گروه کورکومین (267/0±761/)0 در مقایسه با گروه باقی گذاردن قطره شیر مادر (426/0±23/1) به طور معنی داری کمتر بود. همچنین اختلاف میانگین نمره شقاق قبل از درمان با روز سوم و همچنین با روز هفتم پس از شروع درمان، در هر دو گروه، معنی دار بود. نتیجه گیری: کورکومین و شیر مادر هر دو در درمان شقاق پستان موثر هستند؛ ولی باتوجه به عوارض جانبی محدود، فعالیت ضد میکروبی و اثر بیشتر کورکومین در کوتاه مدت، پیشنهاد می گردد از این دارو برای درمان شقاق پستان استفاده شود

The IDIP framework for assessing protein function and its application to the prion protein

The quest to determine the function of a protein can represent a profound challenge. Although this task is the mandate of countless research groups, a general framework for how it can be approached is conspicuously lacking. Moreover, even expectations for when the function of a protein can be considered to be ‘known’ are not well defined. In this review, we begin by introducing concepts pertinent to the challenge of protein function assignments. We then propose a framework for inferring a protein's function from four data categories: ‘inheritance’, ‘distribution’, ‘interactions’ and ‘phenotypes’ (IDIP). We document that the functions of proteins emerge at the intersection of inferences drawn from these data categories and emphasise the benefit of considering them in an evolutionary context. We then apply this approach to the cellular prion protein (PrP^{C}), well known for its central role in prion diseases, whose function continues to be considered elusive by many investigators. We document that available data converge on the conclusion that the function of the prion protein is to control a critical post-translational modification of the neural cell adhesion molecule in the context of epithelial-to-mesenchymal transition and related plasticity programmes. Finally, we argue that this proposed function of PrP^{C} has already passed the test of time and is concordant with the IDIP framework in a way that other functions considered for this protein fail to achieve. We anticipate that the IDIP framework and the concepts analysed herein will aid the investigation of other proteins whose primary functional assignments have thus far been intractable

Comparative antibacterial effects of essential oils of Melissa officinalis and Deracocephalum moldavica L. against some pathogenic bacteria in food in vitro

زمینه و هدف: استفاده از نگهدارنده‌های شیمیایی و مضرات آنها، سبب شده که تولید کنندگان مواد غذایی اخیرا گرایش به استفاده از نگهدارنده‌های طبیعی در مواد غذایی پیدا کنند. اسانس‌های گیاهی که همان روغن‌های فرار (volatile oils) می باشند، روغن‌های مایع و معطر گیاهان اند. گیاهان معطر حاوی اسانس هایی با خواص ضد میکروبی هستند. در این مطالعه اثرات ضدباکتریایی اسانس‌های بادرنجبویه (Melissa officinalis) و بادرشبو (Dracocephalum moldavica) علیه 4 باکتری بیماریزای مواد غذایی در شرایط آزمایشگاهی بررسی شد. روش بررسی: در این مطالعه تجربی پس از تهیه باکتری های مورد بررسی، با روش انتشار بر روی دیسک قطر هاله ممانعت از رشد و با روش میکرودایلوشن حداقل غلظت ممانعت از رشد و حداقل غلظت کشندگی برای هر دو اسانس بادرنجبویه و بادرشبو تعیین شد و جهت مقایسه نتایج از نرم افزار SPSS با آزمون T test استفاده گردید و سطح اختلاف معنی دار کمتر از 0/05 انتخاب شد(P< 0/05). یافته ها: نتایج این مطالعه بیانگر تاثیر ضد میکروبی قوی دو اسانس فوق روی این باکتری ها بود. باکتری استافیلوکوکوس اورئوس با حداقل غلظت ممانعت کنندگی mg/mL 1/2 (برای هر دو اسانس) حساس‌ترین باکتری در مقابل اسانس‌های بادرنجبویه و بادرشبو بود. در این میان اسانس بادرنجبویه اثرات ضد باکتریایی قوی‌تری علیه باکتری‌های مورد آزمایش در مقایسه با اسانس بادرشبو داشت. نتیجه گیری: نتایج حاصل بیانگر توان مهارکنندگی و ضد باکتریایی اسانس های بادرنجبویه و بادرشبو علیه این میکروارگانیسم های بیماریزا می باشد که می تواند بعنوان یک ماده ضد میکروبی گیاهی، جایگزینی مناسب برای ترکیبات شیمیایی ضد باکتری باشد و در صنایع غذایی و داروسازی مورد استفاده قرار گیرد

On a Bounded Budget Network Creation Game

We consider a network creation game in which each player (vertex) has a fixed budget to establish links to other players. In our model, each link has unit price and each agent tries to minimize its cost, which is either its local diameter or its total distance to other players in the (undirected) underlying graph of the created network. Two versions of the game are studied: in the MAX version, the cost incurred to a vertex is the maximum distance between the vertex and other vertices, and in the SUM version, the cost incurred to a vertex is the sum of distances between the vertex and other vertices. We prove that in both versions pure Nash equilibria exist, but the problem of finding the best response of a vertex is NP-hard. We take the social cost of the created network to be its diameter, and next we study the maximum possible diameter of an equilibrium graph with n vertices in various cases. When the sum of players' budgets is n-1, the equilibrium graphs are always trees, and we prove that their maximum diameter is Theta(n) and Theta(log n) in MAX and SUM versions, respectively. When each vertex has unit budget (i.e. can establish link to just one vertex), the diameter of any equilibrium graph in either version is Theta(1). We give examples of equilibrium graphs in the MAX version, such that all vertices have positive budgets and yet the diameter is Omega(sqrt(log n)). This interesting (and perhaps counter-intuitive) result shows that increasing the budgets may increase the diameter of equilibrium graphs and hence deteriorate the network structure. Then we prove that every equilibrium graph in the SUM version has diameter 2^O(sqrt(log n)). Finally, we show that if the budget of each player is at least k, then every equilibrium graph in the SUM version is k-connected or has diameter smaller than 4.Comment: 28 pages, 3 figures, preliminary version appeared in SPAA'1

Potential Application of Electrical Conductivity (EC) Map for Variable Rate Seeding

Rosana G. Moreira, Editor-in-Chief; Texas A&M UniversityThis is a paper from International Commission of Agricultural Engineering (CIGR, Commission Internationale du Genie Rural) E-Journal Volume 7 (2005): Potential Application of Electrical Conductivity (EC) Map for Variable Rate Seeding by M. R. Ehsani, C. D. Durairaj, S. Woods, M. Sulliva