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DNA microarray technology produces large amounts of data. For data mining of these datasets, background information on genes can be helpful. Unfortunately most information is stored in free text. Here, we present an approach to use this information for DNA microarray data mining.
OBJECTIVES: The objective of this work was to contribute to the development, validation and application of data mining methods for prediction in decision support systems in medicine. The particular focus was on the prediction of cardiovascular risk factors in hemodialysis patients, specifically the interventricular septum (IVS) thickness of the heart of individual patients as an important quantitative indicator to diagnose left ventricular hypertrophy. The work was based on data from 63 long-term hemodialysis patients of the KfH Dialysis Centre in Jena, Germany. METHODS: The approach applied is based on data mining methods and involves four major steps: data based clustering, cluster based rule extraction, rulebase construction and cluster and rule based prediction. The methods employed include crisp and fuzzy algorithms. At each step, logical and medical validation of results was carried out. Different sets of randomly selected patient data were used to train, test and optimize the clusterbases and rulebases for prediction. RESULTS: Using the best clusterbase/rulebase combination designed, the IVS thickness cluster ('small' or 'large') was predicted correctly for 30 of the 35 patients with known IVS values in the training data set; no patient was predicted incorrectly and 5 were parity predicted. For the test data set, 4 of the 6 patients with known IVS values were predicted correctly, no patient incorrectly and 2 parity. These results did not substantially differ from those obtained using the second best clusterbase/rulebase combination which was finally recommended for use based on further performance criteria. The prediction of the IVS thickness clusters of the 22 patients with unknown IVS values also yielded good results that were (and could only be) validated by a medical individual risk assessment of these patients. CONCLUSIONS: The approach applied proved successful for the cluster and rule based prediction of a quantitative variable, such as IVS thickness, for individual patients from other variables relevant to the problem. The results obtained demonstrate the high potential of the approach and the methods developed and validated to support decision-making in hemodialysis and other fields of medicine by individual risk prediction.
Since the Aha Lake, located in Guizhou Province, China, was enlarged in 1982, a great amount of iron and manganese were input into it owing to the uninterrupted pollution from acidic mining drainage of coal mines (AMD). The results show that dissolved Fe2+ and Mn2+, mainly from AMD, were markedly separated each other as water flowed from inlet to downstream. The Aha lake water, with the average pH equal to 7.28, was not acidified just because the lake is developed in the karst area and people continuously put lime in it in recent years. Fe2 + and Mn2 + deposit in the different locations in lake because of the difference of oxidizing rate between Fe2+ and Mn2+ during water flowing from inlet to downstream, and also forming the horizontal separation along the lake water flowing direction. Manganese tends to be obviously enriched in the upper of sediment in lake's deep locations, presenting the remarkable separation with iron in the vertical section. After normalized by Ti content in sediment, it is obvious that the remarkable separation between iron and manganese corresponds with the enlargement of lake in 1982. As shown in the concentration profile of pore water in sediment, iron was remobilized weakly while manganese reduction mainly happens in the upper of sediment, indicating its strong remobilization. Based on the studies, a mechanism for environment and fractionation of Fe2+ /Mn2 + during water flowing in the lake was also demonstrated.
Teleost fish genome projects involving model species are resulting in a rapid accumulation of genomic and expressed DNA sequences in public databases. The expressed sequence tags (ESTs) collected in the databases can be mined for the analysis of both structural and functional genomics. In this study, we in silico analyzed 49,430 unigenes representing a total of 692,654 ESTs from four model fish for their potential use in developing simple sequence repeats (SSRs), or microsatellites. After bioinformatical mining, a total of 3,018 EST derived SSRs (EST-SSRs) were identified for 2,335 SSR containing ESTs (SSR-ESTs). The frequency of identified SSR-ESTs ranged from 1.5% for Xiphophorus to 7.3% for zebrafish. The dinucleotide repeat motif is the most abundant SSR, accounting for 47%, 52%, 64%, and 78% for medaka, Fundulus, zebrafish, and Xiphophorus, respectively. Simulation analysis suggests that a majority of these EST-SSRs have sufficient flanking sequences for polymerase chain reaction (PCR) primer design. Comparative DNA sequence analyses of SSR-ESTs identified several cross-species SSRs and sequences that may be used as cross-reference genes in comparative studies. For example, the flanking sequences of one SSR (CTG)n within the pituitary tumor-transforming gene (PTTG) 1 interacting protein (PTTGIP), showed conservation spanning the medaka, Fundulus, human, and mouse genomes. This study provides a large body of information on EST-SSRs that can be useful for the development of polymorphic markers, gene mapping, and comparative genome analysis. Functional analysis of these SSR-ESTs may reveal their role in metabolism and gene evolution of these model species.
Explosion barotraumas of the middle ear and neurosensory hypoacusis were observed in all examinees with ENT contusion. Acute neurosensory hypoacusis of any etiology is accompanied with stress which stimulates secretion of beta-endorphine showing adaptogenic, immunomodulating and anti-inflammatory properties. In patients with mine explosion trauma beta-endorphine was 2-2.5-fold higher than the basal concentration. Pharmacoacupuncture followed by electrostimulation of biologically active points improves acoustic function. Further target studies of current aspects of complex mine explosion trauma of the brain, acoustic and vestibular systems must be done.
The Medical Quality Improvement Consortium data warehouse contains de-identified data on more than 3.6 million patients including their problem lists, test results, procedures and medication lists. This study uses reconstructability analysis, an information-theoretic data mining technique, on the MQIC data warehouse to empirically identify risk factors for various complications of diabetes including myocardial infarction and microalbuminuria. The risk factors identified match those risk factors identified in the literature, demonstrating the utility of the MQIC data warehouse for outcomes research, and RA as a technique for mining clinical data warehouses.
While recent technological advances have made available large datasets of experimentally-detected pairwise protein-protein interactions, there is still a lack of experimentally-determined protein complex data. To make up for this lack of protein complex data, we explore the mining of existing protein interaction graphs for protein complexes. This paper proposes a novel graph mining algorithm to detect the dense neighborhoods (highly connected regions) in an interaction graph which may correspond to protein complexes. Our algorithm first locates local cliques for each graph vertex (protein) and then merge the detected local cliques according to their affinity to form maximal dense regions. We present experimental results with yeast protein interaction data to demonstrate the effectiveness of our proposed method. Compared with other existing techniques, our predicted complexes can match or overlap significantly better with the known protein complexes in the MIPS benchmark database. Novel protein complexes were also predicted to help biologists in their search for new protein complexes.
Korea has National Health Insurance Program operated by the government-owned National Health Insurance Corporation, and diagnostic services are provided every two year for the insured and their family members. Developing a customer relationship management (CRM) system using data mining technology would be useful to improve the performance of diagnostic service programs. Under these circumstances, this study developed a model for diagnostic service management taking into account the characteristics of subjects using a data mining approach. This study could be further used to develop an automated CRM system contributing to the increase in the rate of receiving diagnostic services.
Spirographic examinations have been performed in 20-25-year-old healthy men randomized into two groups. Group I subjects underwent a 24-day adaptation to the climate of moderate altitudes (2100 m above the sea level). In addition, group II subjects spent a few hours daily (day 5-23, altogether 170 hours) in a salt mine Chon-Tuz. It was found that in healthy men microclimate of a salt mine potentiated the adaptive changes of external respiration in moderate altitudes as shown by increased bronchial permeability and vital capacity indicating growing functional reserves of external respiration.
During a 3 month period 94 patients, injured by anti-personnel mines on the Thailand-Cambodian border, underwent emergency surgical treatment in the ICRC (International Committee of the Red Cross) hospital in Khao-I-Dang, Thailand. As a result of difficult evacuation facilities at the border, the mean time between injury caused by an anti-personnel mine and admission to the hospital was 8.3 hours (range: 2.5 to 14 hours). However, in 14 patients a penetrating vessel injury was sustained, and these underwent surgical treatment. Peripheral vascular repair was performed in 10 patients. The vessels involved in these reconstructions were: popliteal artery: 4, femoral artery: 2, anterior tibial artery: 3, femoral vein: 1. Vascular repair of the iliac artery and vein was performed in 1 patient. Limb amputation had to be performed in 3 patients, due to the long duration of tourniquet application in these cases. In the field conditions at Khao-I-Dang hospital many surgical facilities normally present in Western hospitals were unavailable. However, our series shows that satisfactory results could be obtained, despite adverse working conditions.
Speleotherapy was conducted in 216 children with bronchial asthma treated in conditions of salt mines situated near the town of Nakhichevan. The assessment of clinical, immunological and functional parameters showed that the best results had been achieved in atopic asthma running a light or moderate course. Speleotherapy courses noticeably diminished broncho-obstructive syndrome, improved pulmonary ventilation. The improvement proved stable in the majority of the patients. It is recommended to include speleotherapy in salt mines into combined rehabilitation treatment of pediatric asthmatics.
This is a review of the literature concerning the epidemiology and natural history of land mine deaths and injuries among civilian as well as military populations. Included is a case report involving the wounding and treatment of a member of the Croatian armed forces who stepped on and detonated a 100-g PMA-II anti-personnel plastic land mine. The explosive properties of PMA II is described.
Data mining is a recent development in computer science that combines artificial intelligence algorithms and relational databases to discover patterns automatically, without the use of traditional statistical methods. Work with data mining tools in health care is in a developmental stage that holds great promise, given the combination of demographic and diagnostic information.
The wide use of the mine-explosive weapon in modern military conflicts is accompanied by high specific weight of mine-explosive traumas (MET), which achieve 30-40% of all traumas. In the departments of the hospital in 21.3-35.8% of the wounded with MET accompanying defeat of acoustical system with probable subsequent development of neurosensory hypoacusis and invalidism of the injured is established. It defines necessity of early ENT-inspections of all injured with such traumas. Steady up to 1-6 months reduction of hearing is accompanied by biochemical infringements of a cerebrospinal liquid.
Correlation between the sequential, structural, and functional features of proteins is one of the most important open questions in the field of molecular biology. To this problem, we apply a technique known as data mining for discovering associations across protein sequence, structure, and function. We were able to find various association rules on the substructures essential to some protein functions. Moreover, structure-structure associations were found between proteins having different functions. The results suggest that data mining might be a powerful tool in protein analysis.
Clinical databases have accumulated large quantities of information about patients and their medical conditions. Relationships and patterns within this data could provide new medical knowledge. Unfortunately, few methodologies have been developed and applied to discover this hidden knowledge. In this study, the techniques of data mining (also known as Knowledge Discovery in Databases) were used to search for relationships in a large clinical database. Specifically, data accumulated on 3,902 obstetrical patients were evaluated for factors potentially contributing to preterm birth using exploratory factor analysis. Three factors were identified by the investigators for further exploration. This paper describes the processes involved in mining a clinical database including data warehousing, data query and cleaning, and data analysis.
In most hereditary cancer syndromes, finding a correspondence between various genetic mutations within a gene (genotype) and a patient's clinical cancer history (phenotype) is challenging; to date there are few clinically meaningful correlations between specific DNA intragenic mutations and corresponding cancer types. To define possible genotype and phenotype correlations, we evaluated the application of data mining methodology whereby the clinical cancer histories of gene-mutation-positive patients were used to define valid or "true" patterns for a specific DNA intragenic mutation. The clinical histories of patients with their corresponding detailed attributes without the same oncologic intragenic mutation were labeled incorrect or "false" patterns. The results of data mining technology yielded characterizing rules for the true cases that constituted clinical features which predicted the intragenic mutation. Some of the initial results derived correlations already independently known in the literature, adding to the confidence of using this methodological approach.
In recent years, more effective and less toxic treatment protocols have been developed to increase the cure rates in intermediate and high grade non-Hodgkin's lymphoma (NHL). This study was undertaken to investigate the efficacy and toxicity of MINE (ifosfamide, mesna, mitoxantrone and etoposide) combination chemotherapy in patients with intermediate and high grade NHL. Twenty-one patients (16 male, 5 female; age between 26 and 70 years) with NHL were included in the study. An overall response rate of 73% and complete response rate of 56% were achieved and survival rate for responding patients was 80% at the 48th month. Side effects including mild myelosuppression, nausea/vomiting and alopecia were observed. MINE combination seems to be effective and well tolerated without significant toxicity as a first-line therapy in patients with intermediate or high grade NHL.