The Matheny Manifesto

The book is written by former Major League Manager Mike Matheny and takes a dive into the Matheny Manifesto, which was a letter he wrote to the parents of his son\u27s travel team before he began coaching them. A slide deck is also included from the class presentation of the material

Inferring gene ontologies from pairwise similarity data.

MotivationWhile the manually curated Gene Ontology (GO) is widely used, inferring a GO directly from -omics data is a compelling new problem. Recognizing that ontologies are a directed acyclic graph (DAG) of terms and hierarchical relations, algorithms are needed that: analyze a full matrix of gene-gene pairwise similarities from -omics data; infer true hierarchical structure in these data rather than enforcing hierarchy as a computational artifact; and respect biological pleiotropy, by which a term in the hierarchy can relate to multiple higher level terms. Methods addressing these requirements are just beginning to emerge-none has been evaluated for GO inference.MethodsWe consider two algorithms [Clique Extracted Ontology (CliXO), LocalFitness] that uniquely satisfy these requirements, compared with methods including standard clustering. CliXO is a new approach that finds maximal cliques in a network induced by progressive thresholding of a similarity matrix. We evaluate each method's ability to reconstruct the GO biological process ontology from a similarity matrix based on (a) semantic similarities for GO itself or (b) three -omics datasets for yeast.ResultsFor task (a) using semantic similarity, CliXO accurately reconstructs GO (>99% precision, recall) and outperforms other approaches (<20% precision, <20% recall). For task (b) using -omics data, CliXO outperforms other methods using two -omics datasets and achieves ∼30% precision and recall using YeastNet v3, similar to an earlier approach (Network Extracted Ontology) and better than LocalFitness or standard clustering (20-25% precision, recall).ConclusionThis study provides algorithmic foundation for building gene ontologies by capturing hierarchical and pleiotropic structure embedded in biomolecular data

Protective mechanisms and current clinical evidence of hypothermic oxygenated machine perfusion (HOPE) in preventing post-transplant cholangiopathy

The development of cholangiopathies after liver transplantation impacts on the quality and duration of graft and patient survival, contributing to higher costs as numerous interventions are required to treat strictures and infections at the biliary tree. Prolonged donor warm ischaemia time in combination with additional cold storage are key risk factors for the development of biliary strictures. Based on this, the clinical implementation of dynamic preservation strategies is a current hot topic in the field of donation after circulatory death (DCD) liver transplantation. Despite various retrospective studies reporting promising results, also regarding biliary complications, there are only a few randomised-controlled trials on machine perfusion. Recently, the group from Groningen has published the first randomised-controlled trial on hypothermic oxygenated perfusion (HOPE), demonstrating a significant reduction of symptomatic ischaemic cholangiopathies with the use of a short period of HOPE before DCD liver implantation. The most likely mechanism for this important effect, also shown in several experimental studies, is based on mitochondrial reprogramming under hypothermic aerobic conditions, e.g. exposure to oxygen in the cold, with a controlled and slow metabolism of ischaemically accumulated succinate and simultaneous ATP replenishment. This unique feature prevents mitochondrial oxidative injury and further downstream tissue inflammation. HOPE treatment therefore supports livers by protecting them from ischaemia-reperfusion injury (IRI), and thereby also prevents the development of post-transplant biliary injury. With reduced IRI-associated inflammation, recipients are also protected from activation of the innate immune system, with less acute rejections seen after HOPE

Tumore des biliären Trakts: Häufigkeit, Diagnostik und Therapie

Die malignen Tumoren des biliären Trakts, unterteilt in Gallenblasen- und Gallengangskarzinome, sind eher selten. Dennoch wurden in den vergangenen Jahren Fortschritt in Diagnostik und Therapie erzielt. Neben Verbesserung der operativen Techniken als einzige kurative Option konnte auch ein chemotherapeutischer Standard bei fortgeschrittenen Tumoren etabliert werden. Multimodal Konzepte stehen im Fokus des Forschungsinteresses

Delimitacja obszarów metropolitalnych w Polsce jako historycznie i globalnie uwarunkowane zagadnienie polityczne

In the article the problem of delimitation of metropolitan areas in Poland is discussed in two aspects. On the one hand, in the context of global and historical processes of industrialization, servitization and metropolization of big cities, and, on the other hand, in the light of the various concepts of the region (structural, functional and territorial). Most of the Polish big cities suffer from deindustrialization caused by systemic change. The service economy is developing rapidly, but only in some of them (Warsaw, Krakow, Wroclaw, Poznan) and much slower in other big cities. Everywhereit causes the intensive suburbanization (sprawl). Metropolitan functions are rather in initial stage, concentrated mainly in the capital city Warsaw. So, the notion "metropolitan area” should be in the Polish context understood rather as "big city with their suburbs”. In the era of globalization, the public control of functioning and development of metropolitan areas in Poland is necessary in order to ensure their future metropolization. Functional linkages inside metropolitan areas are, however, nor necessary, nor sufficient condition of the efficiency of such a control. It is necessary to restore the territorial principle. In conclusion shows that the metropolitan areas in Poland, which are in fact regions, should be defined as the territories, that is areas ruled by sovereign, but democratically controlled power. The only imaginable such territorial unit is in Poland the metropolitan county (metropolis). It moves the problem of their delimitation from research and planning agenda to political agenda.W artykule przedstawiono i przedyskutowano problem delimitacji obszarów metropolitalnych w Polsce w dwóch aspektach. Z jednej strony w kontekście globalnych i historycznych procesów industrializacji, serwicyzacji i metropolizacji wielkich miast, a z drugiej strony w świetle różnych koncepcji regionu (strukturalnego, funkcjonalnego i terytorialnego). W warunkach globalizacji sterowanie funkcjonowaniem i rozwojem wielkich miast w Polsce jest niezbędne dla zapewnienia ich prawidłowej metropolizacji. Powiązania funkcjonalne wewnątrz obszarów metropolitalnych nie są jednak ani koniecznym, ani wystarczającym warunkiem sprawności takiego sterowania. Niezbędne jest natomiast przywrócenie zasady terytorialnej. W konkluzji wykazuje się, że obszary metropolitalne w Polsce, będące w istocie regionami, powinny być definiowane jako terytoria, czyli obszary władztwa podmiotu suwerennego, choć podlegającego demokratycznej kontroli. Jedyną obecnie jednostką terytorialną tego rodzaju wyobrażalną w ramach porządku prawnego w Polsce jest powiat metropolitalny, o odmiennych kompetencjach niż istniejące powiaty i miasta na prawach powiatu. Przenosi to problem ich delimitacji z płaszczyzny naukowej i planistycznej na polityczną. Pochodną ewentualnej decyzji o utworzeniu powiatów metropolitalnych jest konieczność ich delimitacji. W tym przypadku również, wbrew rozpowszechnionym poglądom, najważniejsze są kryteria polityczne, a wtórne naukowe i planistyczne

Model of an integrated ecological system nature-man-technology-culture

PURPOSE: The aim of this article is to propose a synthetic approach in the form of a model of an integrated ecological system Nature-Man-Technology-Culture.DESIGN/METHODOLOGY/APPROACH: The article is theoretical. To achieve the research goal, six studies were carried out: 1. Analysis of the vast philosophical literature and the achievements of the natural, social, humanistic, technical, medical sciences and others 2. Formulation of partial conclusions in the form of identification of individual ecological relationships 3. Adoption of a systemic methodology assuming distinguishing system components and relations between them based on flows 4. Formulating ecological relations in a systemic approach - distinguishing energy-material and information flows 5. Specifying energy-material relations as flows of energy and animate and inanimate matter 6. Specifying information relations as flows human sensory information as well as economic, scientific, technical and other social information.FINDINGS: They are presented in the summary. It can be added that the proposed model of an integrated ecological system Nature-Man-Technology-Culture is real and complete and includes all the components and relationships among them that are conducted in scientific research.PRACTICAL IMPLICATIONS: A novelty is the joint approach to the relationship between man and the environment and artificial and natural. A novelty is the distinction of the Human component, covering all living people - their bodies and minds - senses, knowledge, memory and emotions. The intangible effects of the work of people's minds and their mutual communication create Culture.ORIGINALITY/VALUE: The proposed model of an integrated ecological system Nature-ManTechnology-Culture takes into account the four components of the reality of the earth's shell and all 12 ecological relations between them. Due to the multi-disciplinarity of disciplines dealing with human impact on the environment, there is a need for synthetic approaches enabling their mutual understanding. So far, the proposed approaches are incomplete and do not take into account the separate divisions rooted in philosophy and science into man and his environment, and into what is natural and what is artificial.The project is financed within the framework of the program of the Minister of Science and Higher Education under the name “Regional Excellence Initiative” in the years 2019 – 2022; project number 001/RID/2018/19; the amount of financing PLN 10,684,000.00.peer-reviewe

The pre-modern, modern, and post-modern metaphors of nature

PURPOSE: The question in the title of this paper determines the paper’s contents. It will be considered whether the numerous metaphors of nature can be ordered according to the scheme: pre-modern – modern – postmodern, oeconomia naturae and natura lapsa, colors of metaphors. Throughout the centuries these colors were used by philosophical and scientific schools (thinking collectives), according to their own mental rules, for painting different images of nature. Then it will be discussed two main thinking styles concerning the human-environment relationship: oeconomia naturae and natura lapsa. Subsequently, it will be showed that metaphors of nature which are used in research and scientific explanations (i.e., outside of the sphere of everyday life and common language) can on one hand be joined into families of metaphors around the root metaphors and living words, and on the other be referred to as colors (also a metaphor). Throughout the centuries these colors were used by philosophical and scientific schools (thinking collectives), according to their own mental rules, for painting different images of nature.DESIGN/METHODOLOGY/APPROACH: The article is theoretical. To achieve the research goal, five desktop studies were carried out. They involved a critical analysis of texts on metaphors created in various scientific disciplines, mainly connected with the man-nature studies.FINDINGS: The social and cultural context of the past or strange thinking styles cannot be fully recognized. Only the metaphors–colors enable the general understanding of these images, and as a result many metaphors of nature, irrespective of the time that they came into being. This is also the main, original result of the study guarantee the continuity of the cognitive process. That is, the main reason why we need and use in our postmodern times so.ORIGINALITY/VALUE: The research approach presented in this article is one of the few attempts at a scientific approach to the metaphorical understanding of nature. It allows you to better understand research concepts, practical activities, as well as the reflection of nature in literature, art, and everyday life. Numerous ecological conflicts take place in the form of diametrically different metaphors and understandings of nature. Therefore, this article is also relevant to ecological policy.Subsidy for research activities in the discipline of socio-economic geography and spatial management, no. 503-0003-230000-01.peer-reviewe