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PubMed1984

Competitor analysis in health care marketing.

Health care providers increasingly are relying upon marketing as a means of overcoming growing competition. Competition-oriented marketing necessitates a comprehensive analysis of the competitive setting, a task which the health care marketing literature has generally given little attention. Herein the concept, perspective and tools of competitor analysis are borrowed from strategic planning and adapted for use in health care marketing.

Economic Competition↗
PubMed1994

The graphical analysis of tooth width discrepancy.

The standard tooth width ratio tables currently do not provide an overall indication of the final interdigitation of teeth. To provide a comprehensive analysis of inter-arch tooth width discrepancy, this study has developed a combination of cumulative percentage tooth width ratios and a method to visually determine the harmony between maxillary and mandibular tooth widths. Mesiodistal tooth widths from the first permanent molar to the corresponding first permanent molar were measured from 60 sets of pretreatment study models which were selected consecutively. Cumulative percentage ratios relating mandibular teeth to maxillary teeth were calculated utilising the mesiodistal tooth width measurements. The 13 mean cumulative percentage ratios developed in this study were plotted on graph paper showing plus and minus two standard deviations from the mean. These ratios provide a standard from which cumulative percentage ratios obtained from any new case may be compared graphically. Deviations from the mean cumulative percentage ratios are immediately recognised. No simple graphical method of assessment on the final interdigitation of anterior and posterior teeth has previously been devised. The graphical analysis of tooth width discrepancy is invaluable as an aid in localising any tooth width discrepancy and ensuring that incompatible maxillary-to-mandibular tooth widths are recognised prior to orthodontic treatment.

Humans↗
PubMed2026

Machine learning-based integration develops a novel lysosome-related prognostic signature associated with prognosis and immune infiltration landscape in acute myeloid leukemia.

BACKGROUND: Lysosomes are essential for intracellular degradation and recycling, and changes in their function significantly contribute to tumor growth. Nonetheless, the exact role of lysosome-related genes (LRGs) in the pathogenesis of acute myeloid leukemia (AML) is still inadequately comprehended. METHODS: Differentially expressed LRGs (DE-LRGs) between AML and control groups were identified using AML-related data extracted from the Gene Expression Omnibus (GEO). The LRGs-related prognostic genes were identified and the risk model was established using univariate COX regression analysis and machine learning algorithms, based on the data obtained from The Cancer Genome Atlas (TCGA). Subsequently, we performed comprehensive analyses regarding clinical features, functional pathways, immune microenvironment, and chemotherapeutic drugs sensitivity between the high- and low-risk groups. Reverse transcription Quantitative polymerase chain reaction (RT-qPCR) and western blot were adopted to validate the expression of prognostic genes in human bone marrow-derived cell line HS-27 A and human AML cell line MOLM-13. RESULTS: Through comprehensive analysis, a risk model was developed utilizing ten LRGs (ATP6V0E2, CALCRL, TMEM165, GZMB, HCK, TCIRG1, CD1D, GPRASP1, ABCA1, and NAGA), and this model was further validated using GEO datasets. Significant differences in clinical characteristics, functional pathways, immune microenvironment characteristics, and chemotherapeutic drug sensitivity were observed between the two risk groups In vitro validation experiment illustrated that the expression trends of ATP6V0E2, TMEM165, and ABCA1 were consistent with our bioinformatics analysis. CONCLUSION: Our study demonstrates that lysosome-associated signature might forecast the prognosis of AML patients and offer guidance for subsequent immunotherapy and chemotherapy strategies.

Acute myeloid leukemia↗
PubMed2005

The future of post-genomic biology at the proteomic level: an outlook.

Drug discovery and early-stage drugs and biomarkers development is a continuous adaptation and maturation process. The cycle of changes based on new findings is coupled with shifts in research priorities and make this part of pharmaceutical research a challenging endeavour. Over the last years, the emphasis on genomics has shifted to proteomics, the science of understanding how proteins translate gene information into function, and metabonomics, the science of small metabolites that are further apart from genomic projects. Proteomics describes the analysis of the protein complement of a biological sample with respect to temporal and spatial resolution. This technology is based on separation of complex protein mixtures by 2D gel-electrophoresis, in gel digest and mass spectrometric analysis of the protein fragments. Proteomics has been recently flanked by peptidomics, a new research direction aimed at the comprehensive analysis of small (1-20 kDa) polypeptides, thus covering the gap between proteomics and metabonomics. The refinement of peptidomics is based on an essential paradigm related to modularity and diversity. Peptides are a paramount example of how one single gene can release multiple functionalities. We can expect fast progress in understanding protein and peptide networks from a systems biology approach ending in the discovery of new peptide targets. However, the way from a complex sample to potential diagnostic and therapeutic targets will depend on technological developments and from the ability to discriminate true disease-related signals from false positive and negative signals, and the way from target discovery to target validation will not be short.

Aged↗
PubMed1994

The comparison of limited resection to lobectomy for T1N0 non-small cell lung cancer. LCSG 821.

The Lung Cancer Study Group, in order to investigate lesser resection within the community as definitive management for T1N0 lung cancers, in 1982 began a prospective trial of limited resection compared to lobectomy for these patients. First reported results demonstrated no significant differences for stratification and other prognostic variables, and no differences in postoperative complication rates. Interim analysis 3 years later suggested a higher local recurrence rate in the limited resection arm of the study. Further comprehensive analysis will be forthcoming.

Carcinoma, Non-Small-Cell Lung↗
PubMed1993

Establishing a physician incentive system.

The increasing complexity of managed care is changing the need for better information on medical costs and utilization. Because most claims systems have limited reporting and analysis capabilities, a better alternative is to transfer the data into the reporting systems described herein, in which a comprehensive analysis is conducted faster and at a lower cost. Virtually any type of analysis is possible.

Adult↗
PubMed2002

MIPS: a database for genomes and protein sequences.

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz-Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91-93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155-158; Barker et al. (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

Amino Acid Sequence↗
PubMed2005

The molecular signature of normal squamous esophageal epithelium identifies the presence of a field effect and can discriminate between patients with Barrett's esophagus and patients with Barrett's-associated adenocarcinoma.

BACKGROUND AND AIM: Genetic alterations in the normal tissues surrounding various cancers have been described, but a comprehensive analysis of this carcinogenic field effect in Barrett's-associated adenocarcinoma of the esophagus disease has not been reported. The aim of this study was to analyze the gene expression profile of a panel of highly selected genes in the normal squamous esophagus epihelium of patients with Barrett's esophagus, patients with Barrett's-associated adenocarcinoma, and a healthy control group to define the existence of a carcinogenic field effect, and to investigate the clinical importance of such a field effect in the management of Barrett's disease. METHODS: Forty-nine histologic normal squamous esophageal epithelia collected from 19 patients with Barrett's esophagus, 20 patients with Barrett's-associated esophageal adenocarcinoma, and a healthy control group of 10 patients were studied. A quantitative real-time reverse transcription-PCR method (TaqMan) was used to measure the expression of a panel of genes with known associations with gastrointestinal carcinogenesis. RESULTS: A widespread carcinogenic field effect was detected for more than 50% of the genes analyzed including Bax, BFT, CDX2, COX2, DAPK, DNMT1, GSTP1, RARalpha, RARgamma, RXRalpha, RXRbeta, SPARC, TSPAN, and VEGF. Based on the expression signature of the normal appearing squamous esophagus, a linear discriminant analysis was able to distinguish between the three groups of patients with an error rate of 0%. CONCLUSION: This study provides the first comprehensive investigation of a carcinogenic field effect in Barrett's esophagus disease. Based on the gene expression signature of the normal esophagus, patients could be correctly characterized according to their pathologic classification by applying a linear discriminant analysis. Our results provide evidence that a molecular classification might have clinical importance for the diagnosis and treatment of patients with Barrett's esophagus disease.

Adenocarcinoma↗
PubMed2004

An mRNA amplification procedure with directional cDNA cloning and strand-specific cRNA synthesis for comprehensive gene expression analysis.

We developed an integrated system suitable for comprehensive gene expression studies including construction and analysis of cDNA microarrays starting from a small amount of mRNA. We amplified total mRNA first as cDNA mixtures by polymerase chain reaction and then as strand-specific cRNA mixtures by in vitro transcription. These amplified cDNA and cRNA enabled determination of mRNA levels by hybridization analyses such as Southern, Northern, reverse-Northern macroarray, and cDNA microarray analyses, as well as construction of the cDNA library with a unidirectional cDNA insert. By using strand-specific cRNA derived from rat primary-cultured hepatocytes, we detected putative antisense transcripts for the metallothionein gene. cDNA microarray analysis for genes regulated by glucocorticoids and glucagon in the hepatocytes revealed that a number of genes involved in signal transduction and transcriptional regulation were up- or down-regulated. The present system is widely applicable to gene expression analysis with limited amounts of RNA samples.

Animals↗
PubMed1999

Design and analysis issues in case-control studies addressing genetic susceptibility.

Case-control studies are among the main study designs for investigating the effect of environmental exposures on disease etiology and are now becoming more frequently used to examine the influence of genetic susceptibility. Incorporating a case-control design to examine genetic exposure would seem appropriate as the main problems of case-control studies, those of bias and confounding, are more easily avoided. However, they do not have a strong image and are thought to provide too many spurious findings as a result of chance, bias or confounding. This criticism has often been valid, especially for many early studies based on small numbers of poorly defined cases that were compared to convenient groups of local controls. New family-based study designs that account for these problems have been suggested, including the transmission disequilibrium test. However, the traditional format of case-control studies may be improved by incorporating methodological refinements developed over the past 30 years in environmental epidemiology. The present chapter attempts to outline these issues and to provide guidelines for the selection of cases and controls and for the analysis of genetic data from case-control studies. Alternative, family-based study designs will also be discussed. Finally, a comprehensive analysis approach to gene-environment and gene-gene interaction is proposed.

Bias↗
PubMed1992

[A frontal cephalometric analysis].

A comprehensive frontal cephalometric analysis was developed and its normal values for Chinese adults were established in this study. This analysis includes two parts: width proportional analysis and symmetry analysis. Most linear width values of males were significantly greater than those of females as expected. However, there were no significant sex differentials in the most width ratios. Among these, the ratio Go/Z reached ca. 75%, Mx/Zy ca. 50%, L6/Go ca. 50% and the Mx/Go ca. 66.6% (2/3). Width problems and possible expansion at canine and molar areas could be evaluated through proportional analysis. To determine the locations as well as extents of dentofacial asymmetry is of great clinical value especially in orthodontic treatment. In symmetry analysis, linear differences between both side structures in vertical and horizontal directions could be calculated.

Adult↗
PubMed1996

Genomic localization of novel candidate tumor suppressor gene loci in human parathyroid adenomas.

Only one oncogene, cyclin D1/PRAD1, has an established role in parathyroid tumorigenesis, and parathyroid tumor suppressor genes on chromosome arms 1p and 11q, which still have not been identified, have also been implicated by loss of heterozygosity analysis. To investigate whether other putative tumor suppressor genes are involved in the pathogenesis of parathyroid adenomas, we performed a more comprehensive analysis of allelic losses in these tumors. Using 39 polymorphic markers, we examined each chromosome arm, excluding the short arms of the acrocentric chromosomes. In 25 parathyroid adenomas, frequent loss of heterozygosity, in > 25% of the informative cases, was observed on chromosome arms 6q (30%), 11p (27%), and 15q (35%), in addition to previously reported 1p (30%) and 11q (38%) allelic losses. To more specifically localize the smallest shared regions of molecular genetic deletion, we examined the following chromosomes in greater detail: chromosome 6 (9 additional markers), chromosome 11 (8 additional markers), and chromosome 15 (15 additional markers). The regions most commonly deleted in these tumors were 6q22-23, 6q26-27, 11q13, 15q11-21, and 15q26-qter. All tumors with 11p loss had patterns consistent with monosomy for chromosome 11. These findings provide novel evidence for the existence of tumor suppressor genes on chromosome arms 6q and 15q that contribute commonly to the pathogenesis of parathyroid adenomas.

Adenoma↗
PubMed1994

Integrin expression by human articular chondrocytes.

OBJECTIVE: To perform a comprehensive analysis of the integrin forms expressed by normal human articular chondrocytes. METHODS: Cartilage sections and collagenase-released chondrocytes were probed with a comprehensive panel of integrin isoform-specific monoclonal antibodies (MAb), using in situ immunohistochemistry techniques, indirect immunofluorescence and flow cytometry, and immunoprecipitation/sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). RESULTS: Chondrocytes in cartilage sections reacted with MAb specific for the alpha 5, alpha v, and beta 1 integrin subunits and the alpha v beta 3 and alpha v beta 5 heterodimers. They also reacted with a polyclonal antibody specific for the intracytoplasmic portion of the alpha 1 subunit. MAb specific for the alpha v subunit reacted more strongly with chondrocytes near the articular surface than with those in deeper layers of cartilage, and the alpha v beta 3-specific MAb reacted exclusively with chondrocytes within the most superficial 30 microns of cartilage. Flow cytometric analysis and SDS-PAGE analysis of immunoprecipitates prepared from extracts of cell-surface radioiodinated chondrocytes confirmed the above observations, and additionally revealed the presence of the alpha 3 beta 1 integrin. CONCLUSION: Normal human articular chondrocytes prominently display substantial quantities of the alpha 1 beta 1, alpha 5 beta 1, and alpha v beta 5 integrin heterodimers, as well as lesser quantities of the alpha 3 beta 1 and alpha v beta 3 heterodimers. The alpha v subunit-containing integrins are detected more readily on the more superficial chondrocytes than on chondrocytes deep within cartilage. These observations provide the basis for analysis of the role of chondrocyte integrins in cartilage homeostasis and in the pathogenesis of joint diseases.

Adult↗
PubMed2006

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

BACKGROUND: Pigment epithelium derived factor (PEDF), a member of the serpin family, regulates cell proliferation, promotes survival of neurons, and blocks growth of new blood vessels in mammals. Defining the molecular phylogeny of PEDF by bioinformatic analysis is one approach to understanding the link between its gene structure and its function in these biological processes. RESULTS: From a comprehensive search of available DNA databases we identified a single PEDF gene in all vertebrate species examined. These included four mammalian and six non-mammalian vertebrate species in which PEDF had not previously been described. A five gene cluster around PEDF was found in an approximate 100 kb region in mammals, birds, and amphibians. In ray-finned fish these genes are scattered over three chromosomes although only one PEDF gene was consistently found. The PEDF gene is absent in invertebrates including Drosophila melanogaster (D. melanogaster), Caenorhabditis elegans (C. elegans), and sea squirt (C. intestinalis). The PEDF gene is transcribed in all vertebrate phyla, suggesting it is biologically active throughout vertebrate evolution. The multiple actions of PEDF are likely conserved in evolution since it has the same gene structure across phyla, although the size of the gene ranges from 48.3 kb in X. tropicalis to 2.9 kb in fugu, with human PEDF at a size of 15.6 kb. A strong similarity in the proximal 200 bp of the PEDF promoter in mammals suggests the existence of a possible regulatory region across phyla. Using a non-synonymous/synonymous substitution rate ratio we show that mammalian and fish PEDFs have similar ratios of <0.13, reflecting a strong purifying selection of PEDF gene. A large number of repetitive transposable elements of the SINE and LINE class were found with random distribution in both the promoter and introns of mammalian PEDF. CONCLUSION: The PEDF gene first appears in vertebrates and our studies suggest that the regulation and biological actions of this gene are preserved across vertebrates. This comprehensive analysis of the PEDF gene across phyla provides new information that will aid further characterization of common functional motifs of this serpin in biological processes.

Animals↗
PubMed2002

Analysis of the proteome in the human pituitary.

The pituitary is the master endocrine gland responsible for the regulation of various physiologic and metabolic processes. Proteomics offers an efficient means for a comprehensive analysis of pituitary protein expression. This paper reports on the application of proteomics for the mapping of major proteins in a normal (control) pituitary. Pituitary proteins were separated by two-dimensional gel electrophoresis with immobilized pH 3-10 gradient strips. Major protein spots that were visualized in the two-dimensional gel by silver staining were excised, and the proteins in these spots were digested with trypsin. The tryptic digests were analyzed by mass spectrometry, and the mass spectrometric data were used to identify the proteins through searches of the SWISS-PROT or NCBInr protein sequence databases. The majority of the proteins were identified on the basis of peptide mass fingerprinting data obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Several proteins were also characterized based on product-ion spectra measured by post-source decay analysis and/or liquid chromatography-electrospray-quadrupole ion trap mass spectrometry. To date, 62 prominent protein spots, corresponding to 38 different proteins, were identified. The identified proteins include important pituitary hormones, structural proteins, enzymes, and other proteins. The protein identification data were used to establish a two-dimensional reference database of the human pituitary, which can be accessed over the Internet (http://www.utmem.edu/proteomics). This database will serve as a tool for further proteomics studies of pituitary protein expression in health and disease.

Computational Biology↗
PubMed2024

Exploring Regulatory Roles of Transposable Elements in EMT and MET through Data-Driven Analysis: Insights from regulaTER.

Gene expression is regulated at the transcriptional and translational levels and a plethora of epigenetic mechanisms. Regulation of gene expression by transposable elements is well documented. However, a comprehensive analysis of their regulatory roles is challenging due to the lack of dedicated approaches to define their contribution. Here, we present regulaTER, a new R library dedicated to deciphering the regulatory potential of transposable elements in a given phenotype. regulaTER utilizes a variety of genomics data of any origin and combines gene expression level information to predict the regulatory roles of transposable elements. We further validated its capabilities using data generated from an epithelial-mesenchymal and mesenchymal-epithelial transition cellular model. regulaTER stands out as an essential asset for uncovering the impact of transposable elements on the regulation of gene expression, with high flexibility to perform a range of transposable element-focused analyses. Our results also provided insights on the contribution of the MIR and B element subfamilies in regulating EMT and MET through the FoxA transcription factor family. regulaTER is publicly available and can be downloaded from https://github.com/karakulahg/regulaTER.

DNA Transposable Elements↗
PubMed2002

Tools for comparative analysis of alternatives: competing or complementary perspectives?

A third generation of environmental policy making and risk management will increasingly impose environmental measures, which may give rise to analyzing countervailing risks. Therefore, a comprehensive analysis of all risks associated with the decision alternatives will aid decision-makers in prioritizing alternatives that effectively reduce both target and countervailing risks. Starting with the metaphor of the ripples caused by a stone that is thrown into a pond, we identify 10 types of ripples that symbolize, in our case, risks that deserve closer examination: direct, upstream, downstream, accidental risks, occupational risks, risks due to offsetting behavior, change in disposable income, macro-economic changes, depletion of natural resources, and risks to the manmade environment. Tools to analyze these risks were developed independently and recently have been applied to overlapping fields of application. This suggests that either the tools should be linked in a unified framework for comparative analysis or that the appropriate field of application for single tools should be better understood. The goals of this article are to create a better foundation for the understanding of the nature and coverage of available tools and to identify the remaining gaps. None of the tools is designed to deal with all 10 types of risk. Provided data suggest that, of the 10 types of identified risks, those associated with changes in disposable income may be particularly significant when decision alternatives differ with respect to their effects on disposable income. Finally, the present analysis was limited to analytical questions and did not capture the important role of the decision-making process itself.

Cost-Benefit Analysis↗
PubMed1999

Combined spectral karyotyping and DAPI banding analysis of chromosome abnormalities in myelodysplastic syndrome.

Spectral karyotyping (SKY) is a new molecular cytogenetic technique that allows simultaneous visualization of each chromosome in a different color. We have used SKY for comprehensive analysis of 20 myelodysplastic syndromes (MDSs) (13 primary MDSs, 3 therapy-related MDSs, and 4 acute leukemias developed from MDS, including 1 cell line established from a secondary leukemia), previously analyzed by G-banding. To locate the chromosomal breakpoints, DAPI-counterstained band images from all metaphases were transformed to G-band-like patterns. By using SKY, it was possible to identify the origin and organization of all clonal marker chromosomes (mar), as well as the origin of all abnormalities defined as additional material of unknown origin (add) or homogeneously staining regions (hsr) by G-banding. In total, SKY identified the chromosomal basis of 38 mar, add, and hsr, corrected 8 abnormalities misidentified by G-banding, and revealed 6 cryptic translocations in 5 cases. Total or partial chromosomal loss (mainly of -5/5q- and -7/7q-) is the most frequent cytogenetic abnormality in MDS. In 3 of 11 cases with -5/5q- and in 4 of 8 with -7/7q-, lost material was detected by SKY in unbalanced translocations. A total of 60 chromosomal losses were identified by G-banding in 16 cases with multiple chromosome abnormalities involving at least 3 chromosomes. For 26 of these losses (43%), SKY analysis suggested that the losses were not complete, but had been translocated to a variety of partner chromosomes. Moreover, SKY analysis revealed that a ring chromosome in a case of acute leukemia developed from MDS contained three to six segments that originated from chromosome 21 material. Fluorescence in situ hybridization showed the amplification of the AML1 gene on regions derived from chromosome 21, providing the first evidence of amplification involving this gene in MDS. Genes Chromosomes Cancer 26:336-345, 1999.

Adult↗