Representing and querying disease networks using graph databases

BACKGROUND: Systems biology experiments generate large volumes of data of multiple modalities and this information presents a challenge for integration due to a mix of complexity together with rich semantics. Here, we describe how graph databases provide a powerful framework for storage, querying and envisioning of biological data. RESULTS: We show how graph databases are well suited for the representation of biological information, which is typically highly connected, semi-structured and unpredictable. We outline an application case that uses the Neo4j graph database for building and querying a prototype network to provide biological context to asthma related genes. CONCLUSIONS: Our study suggests that graph databases provide a flexible solution for the integration of multiple types of biological data and facilitate exploratory data mining to support hypothesis generation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13040-016-0102-8) contains supplementary material, which is available to authorized users

Effect of shot size in surface improvement via shot peening; analytical, modeling and experimental approaches

This paper discusses about the surface engineering improvement by means of shot peening. Shot peening improves the surface engineering quality by eliminating the tool marks, such as machining, grinding, stamping and other surface defects. Most importantly, the improvements of shot peening are produced by combination of compressive stress and cold work. Compressive stresses are beneficial in increasing resistances to fatigue failures, while the cold work effects of shot peening treatments can increase the surface hardness. It employs a steel shot media running at high speed to smash the material’s surfaces systematically, which results in a compressed and condensed surface. Several factors influence the effectiveness of shot peening. They are namely shot nature, shot size, shot hardness, Almen intensity, shot angle and coverage. The focus of this research is finding the influence of the shot size. The approaches used are analytical, computational, and experimental studies. The center of the study is the influence of shot size in the generation of the compressive residual stress. Through analytical, computational and experimental approaches, it is confirmed that the shot size has influence on the depth of the peak residual stress rather than the surface residual stress. This research reaffirms the qualitative understanding with quantitative and comprehensive approaches that can also be used for further in depth research in surface engineering improvement especially via shot peening

EpiGeNet : A graph database of interdependencies between genetic and epigenetic events in colorectal cancer

The development of colorectal cancer (CRC)—the third most common cancer type—has been associated with deregulations of cellular mechanisms stimulated by both genetic and epigenetic events. StatEpigen is a manually curated and annotated database, containing information on interdependencies between genetic and epigenetic signals, and specialized currently for CRC research. Although StatEpigen provides a well-developed graphical user interface for information retrieval, advanced queries involving associations between multiple concepts can benefit from more detailed graph representation of the integrated data. This can be achieved by using a graph database (NoSQL) approach. Data were extracted from StatEpigen and imported to our newly developed EpiGeNet, a graph database for storage and querying of conditional relationships between molecular (genetic and epigenetic) events observed at different stages of colorectal oncogenesis. We illustrate the enhanced capability of EpiGeNet for exploration of different queries related to colorectal tumor progression; specifically, we demonstrate the query process for (i) stage-specific molecular events, (ii) most frequently observed genetic and epigenetic interdependencies in colon adenoma, and (iii) paths connecting key genes reported in CRC and associated events. The EpiGeNet framework offers improved capability for management and visualization of data on molecular events specific to CRC initiation and progression

Age and sexual features of stomatologic incidence at patients of clinics of various forms of ownership

Preservation of stomatologic health at persons of able-bodied age extremely topical issue. Today the competition of the state and private odontology became objective reality. During research of the stomatologic status of inhabitants of the monotown of Chelyabinsk region it is confirmed that higher appealability of the patients preferring treatment in paid clinic, is not a consequence of their inferior stomatologic status. But it is accompanied by improvement of this status, at the expense of well-timed sanitation of a painful teeth.Сохранение стоматологического здоровья у лиц трудоспособного возраста чрезвычайно актуальный вопрос. Сегодня объективной реальностью стала конкуренция государственной и частной стоматологии. В ходе исследования стоматологического статуса жителей моногорода Челябинской области подтверждено, что более высокая обращаемость пациентов, предпочитающих лечение в платной клинике, не является следствием их худшего стоматологического статуса. Но сопровождается улучшением этого статуса, за счёт своевременной санации больных зубов

Evaluation of the morphonctional status and a series of biochemical parameters of thromboconcentrate during storage

The purpose of the study is to establish whether there are changes in the morphofunctional status and biochemical parameters during the storage of thromboconcentrate.Цель исследования – установить имеются ли изменения морфофункционального статуса и биохимических параметров при хранении тромбоконцентрата

A model of flux regulation in the cholesterol biosynthesis pathway:Immune mediated graduated flux reduction versus statin-like led stepped flux reduction

10.1016/j.biochi.2012.05.024Biochimie953613-621BICM

Clinical and diagnostic significance of some laboratory analysis of pericardial fluid

The aim of the study – identify differential laboratory characteristic of pericardial fluid examination in exudative and metastatic pericarditis.Цель исследования – установить дифференциальные лабораторные признаки исследования ПЖ при воспалительном и метастатическом перикардите

Sociological assessment of the quality of medical care in the clinic of the municipal formation

Quality assurance of medical care is the most urgent problem of the national healthcare system. The aim of the work was the estimation of the quality of medical care in municipal polyclinic by questioning patients. Prepared the original form with 9 questions. On completing the substantial and the General part of the questionnaire can be noted that most of the patients were often visited by the medical institution and have an understanding of his work and a fully formed opinion about the quality of medical assistance it received. Conducted by the sociological survey, the analysis of its results were an important channel of information for managers of health care institutions allows a quick assessment of the activities of the organization; measure the ratio of patients to health workers, conditions of delivery and services provided. The changes taking place in the health care system at the present time, have a positive response among the population.Обеспечение качества оказания медицинской помощи является актуальнейшей проблемой отечественного здравоохранения. Целью работы явилась оценка качества медицинской помощи в муниципальной поликлинике путем анкетирования пациентов. Подготовлен оригинальный бланк с 9 вопросами. По заполнению констатирующей и общей части анкеты можно отметить, что основная часть пациентов достаточно часто посещают исследуемое медицинское учреждение и имеют представление о его работе и вполне сложившееся мнение о качестве медицинской помощи в ней получаемой. Проведенное социологическое исследование, анализ его результатов явились важным информационным каналом для руководителей учреждения здравоохранения позволяющий оперативно получить оценку деятельности организации; измерить отношение пациентов к медработникам, условиям предоставления и предоставляемым услугам. Изменения, происходящие в системе здравоохранения в настоящее время, имеют положительный отклик у обслуживаемого населения

Sterols and oxysterols in plasma from Smith-Lemli-Opitz syndrome patients

Smith-Lemli-Opitz syndrome (SLOS) is a severe autosomal recessive disorder resulting from defects in the cholesterol synthesising enzyme 7-dehydrocholesterol reductase (Δ7-sterol reductase, DHCR7, EC 1.3.1.21) leading to a build-up of the cholesterol precursor 7-dehydrocholesterol (7-DHC) in tissues and blood plasma. Although the underling enzyme deficiency associated with SLOS is clear there are likely to be multiple mechanisms responsible for SLOS pathology. In an effort to learn more of the aetiology of SLOS we have analysed plasma from SLOS patients to search for metabolites derived from 7-DHC which may be responsible for some of the pathology. We have identified a novel hydroxy-8-dehydrocholesterol, which is either 24- or 25-hydroxy-8-dehydrocholesterol and also the known metabolites 26-hydroxy-8-dehydrocholesterol, 4-hydroxy-7-dehydrocholesterol, 3β,5α-dihydroxycholest-7-en-6-one and 7α,8α-epoxycholesterol. None of these metabolites are detected in control plasma at quantifiable levels (0.5 ng/mL)