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Results for “systematic analysis”

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At least 91 records · Page 5Linked to original sources
PubMed2001

Systematic analysis of the TGF-beta-Smad signaling pathway in gastrointestinal cancer cells.

The transforming growth factor-beta (TGF-beta)-Smad signaling pathway has an important role in carcinogenesis. To study the frequency and mechanism of functional impairment of this pathway in human gastrointestinal cancers, we used a reporter assay to examine the response of 38 cell lines (11 colorectal, 9 pancreatic, 10 gastric, and 8 hepatic cancers) to TGF-beta. We then analyzed TGF-beta type II receptor (T beta RII) gene, immunoblots of Smad4, and restoration of the pathway by rescuing T beta R or Smad. We observed impaired signaling in 91% of colorectal, 67% of pancreatic, and 40% of gastric cancer cell lines, but in none of the hepatic cancer cells. We suggest that this pathway does not function as a tumor suppressor in hepatic carcinogenesis. The impairment is due to inactivation of T beta RII and Smad4 in colorectal and pancreatic cancers. However, because the signal was not recovered by rescuing T beta R or Smad genes in TGF-beta-response-defective gastric cancer cell lines, we suggest that novel molecules or mechanisms are involved in the impaired pathway in some gastric cancers.

Blotting, Western↗
PubMed1997

Sequence of the human immunoglobulin diversity (D) segment locus: a systematic analysis provides no evidence for the use of DIR segments, inverted D segments, "minor" D segments or D-D recombination.

We have determined the complete nucleotide sequence of the human immunoglobulin D segment locus on chromosome 14q32.3 and identified a total of 27 D segments, of which nine are new. Comparison with a database of rearranged heavy chain sequences indicates that the human antibody repertoire is created by VDJ recombination involving 25 of these 27 D segments, extensive processing at the V-D and D-J junctions and use of multiple reading frames. We could find no evidence for the proposed use of DIR segments, inverted D segments, "minor" D segments or D-D recombination. Conventional VDJ recombination, which obeys the 12/23 rule, is therefore sufficient to explain the wealth of lengths and sequences for the third hypervariable loop of human heavy chains.

Base Sequence↗
PubMed2027

Systematic Analysis of Tumor Microenvironment Using IOBR.

The Immuno-Oncology Biological Research (IOBR) package is an R-based analysis tool for exploring the tumor microenvironment (TME) and its influence on anti-tumor immunity. Built for high-throughput data-spanning both transcriptomic and genomic profiles-IOBR integrates six analytical modules, including transcriptomic data preprocessing, TME profiling, TME pattern identification, ligand-receptor interaction analysis, genome-TME interaction assessment, and visualization. In this chapter, we walk through a multi-omics workflow using example datasets, illustrating data preparation, distribution analyses, result interpretation, and graphical output. IOBR is open source and is available at https://github.com/IOBR/IOBR and a detailed GitBook ( https://iobr.github.io/book/ ) offers a complete manual and analysis guide for each function.

Tumor Microenvironment↗
PubMed1978

Systematic analysis of 95 reciprocal translocations of autosomes.

The statistical analysis of 95 cases of reciprocal translocations involving autosomes detected among about 10,000 patients studied with the R-banding technique gives the following information: 1. An excess of break points exists for chromosome arms 4p,9p, 10q, 21q, and 22q and a deficiency for 1p, 2p, and 6q. Furthermore, there are relatively more break points in the small arms than in the large arms, when the translocation is ascertained through an unbalanced translocation carrier. Except for chromosome 22, an ascertainment bias explain this non random distribution. 2. An excess of telomeric break points exists in all cases of translocations ascertained through unbalanced carriers, and an excess of centromeric break point exists in the case of 3:1 and 1:3 segregations only. These excesses are also explained by an ascertainment bias. 3. The break points are located usually at the junction of the bands (interfaces). 4. The size of the chromosomal imbalance varies in the ascertainment classes. It is very large in cases ascertained through balanced carriers (at least one break point is far from the telomere), large in cases ascertained through abortion, and relatively moderate in cases ascertained through unbalanced translocation carriers (at least one break point is juxta telomeric). 5. An excess of balanced reciprocal translocations exists in our sample of mentally retarded and malformed children (position effect?). 6. An excess of balanced reciprocal translocations (not involving chromosome 21) exists among the trisomics 21 and their parents (interchromosomal effect?). 7. A large excess of maternal transmission exists in cases of 3:1 segregation of reciprocal translocation.

Abnormalities, Multiple↗
PubMed1993

On the nature and ethics of health promotion. An attempt at a systematic analysis.

This paper attempts to analyse the notion of health promotion and related conceptual issues within an action-theoretical framework. The purpose is both theoretical and ethical. The paper provides a taxonomy as well as a system for classifying various types of health promotion. This system is inspired by Professor G H von Wright's theory of action explanation. The theoretical framework is used in the ethical part of the paper where some major ethical dilemmas in health promotion are analysed. Particular attention is paid to the use of manipulation and force in health promotion. An attempt is made to define when such measures are justified in various health enhancing contexts.

Behavior Control↗
PubMed1993

Systematic analysis of glycosphingolipids in the human gastrointestinal tract: enrichment of sulfatides with hydroxylated longer-chain fatty acids in the gastric and duodenal mucosa.

The composition of the glycosphingolipids of the human gastrointestinal tract was studied. The major neutral glycosphingolipids were ceramide monohexosides (e.g., GalCer, GlcCer), LacCer, Gb3Cer, Gb4Cer and more polar ones with more than four sugars, whereas neither Gg3Cer nor Gg4Cer were present. The acidic glycosphingolipids consisted of sulfatides and gangliosides such as GM3, GM1, GD3 and GD1a. Also a large amount of sulfatides was found in the gastric mucosa and duodenum. The concentrations of sulfatides in the fundic mucosa, antral mucosa and duodenum amounted to 416.0, 933.8 and 682.9 nmol/g of dry weight, respectively, exceeding those in the gastric mucosa and kidney of other mammals. The major molecular species of the sulfatides were identified as I3SO3-GalCer with hydroxylated longer-chain fatty acids based on the analyses by gas-liquid chromatography and negative ion fast-atom bombardment mass spectrometry. In contrast, gangliosides in these regions showed a tendency to be lower than sulfatides, and the molar ratios of sulfatides to gangliosides were about 2.0, whereas those in other parts were less than 0.5. A high content of sulfatides in the gastric and duodenal mucosa, where mucosa is easily insulted by acid, pepsin and bile salts, may be closely related to their roles in mucosal protection.

Carbohydrates↗
PubMed1999

[The value of CT in classification and decision making in acetabulum fractures. A systematic analysis].

UNLABELLED: The classification of acetabular fractures and especially the diagnosis of additional lesions can be misleading, when the personal experience is limited and the decisions are based only on conventional radiographs. The introduction of Spiral-CT with multiplanar reformations and 3-D views has improved the quality of visualization. Due to their higher costs, the need of these additional diagnostic tools is frequently questioned. This paper discusses the relevance of plain radiographs, 2-D-CTs, 3-D-CTs and Femursubtraction-CTs (FsCT) for the classification of acetabular fractures, based on a controlled study. METHODS: Thirty physicians with different levels of experience in acetabular surgery were divided in three groups of 10 each: group I comprised residents without operative experience in acetabular surgery, group II was physicians with 3-10 years of operative experience, and group III was experts in acetabular surgery. A total of 10 complete radiographic cases of high quality providing all levels of preoperative diagnostics (plain radiographs, 2-D-CT, CT with multiplanar reformation, 3-D-CT, Fs-CT) of different acetabular fracture types were prepared. The task for each candidate was to classify the fracture according to Letournel and to identify all additional injuries within the hip joint (e.g. marginal impaction, head fractures, etc.). The different diagnostic "levels" could be ordered stepwise according to personal need and no time limit was given. The case was finished when the candidate presented his final diagnosis. The use of the different radiographs, the preliminary diagnosis, the changes in diagnosis, and the final decisions were recorded. These findings were correlated with the different levels of experience and against a "consensus classification" which was generated by thorough discussion, and the use of intraoperative information and postoperative radiographs not accessible to the candidates. RESULTS: The "correct" fracture classification based on plain radiographs was: group I, 11%; group II, 32%; group III, 61%. Based on 2-D-CT a "correct" diagnosis was reached by 30% in group I, by 55% in group II, and by 76% in group III. With consideration of the "transient forms" in acetabular fractures based on Letournel and the 3-D-CT used mainly by group I, the rate of "correct" classifications rose to 65% in group I, 64% in group II and 83% in group III. The modifiers were diagnosed "correctly" in group I by 37%, in group II by 56%, and in group III by 73%. The use of the 3-D-CT and especially the Fs-CT by group I resulted in an improvement in the rate of correct classifications to 61%, whereas in group II the Fs-Ct was used only exceptionally. The 2-D-CT was the basis for the diagnosis of the additional lesions in acetabular fractures within all groups resulting in 73% complete diagnoses in group III. This study showed the importance of CT for the exact analysis and classification of acetabular fractures. In particular, the secondary reformations in CT and the 3-D-views dramatically improved the rate of "correct" classifications in the group of surgeons with limited personal experience in acetabular surgery. This allows the less experienced an acceptable level of "correct" diagnoses, so that the treatment options can be weighed correctly. Among the "experts" a rate of divergent classifications of approximately 20% was observed, especially in "transient" forms of acetabular fractures.

Acetabulum↗
PubMed1983

Systematic analysis of contrast echocardiograms.

Contrast echocardiography was first described in 1968. Since then, many reports have described clinical and experimental uses for the technique. Contrast echocardiography is performed at least occasionally in most echocardiography laboratories, but most physicians use this technique merely to determine the presence of a shunt or, more rarely, for structure identification. Contrast echocardiography can provide much more information. Some different types of information available from contrast echocardiographic records are discussed, including timing of contrast appearance within the cardiac cycle, relative timing of appearance in different cardiac structures, relative intensity of contrast opacification, cyclical changes in contrast opacification, negative contrast effect, slope of contrast trajectories on M-mode contrast echocardiography, and clearance times.

Contrast Media↗
PubMed1983

A reinterpretation of schedule-induced behaviors based on a systematic analysis of behavior.

Confusion exists regarding the criteria to be used in determining whether or not particular behaviors are schedule-induced. Four critical characteristics of schedule-induced behaviors are suggested and a comparison made of the complete range of behaviors exhibited by body weight-reduced rats drinking in response to one of three stimuli. These were (1) a fixed-time food reinforcement schedule, (2) a meal of dry food, and (3) 24 hour water deprivation. Drinking, locomotion, rearing and oral and perioral behaviors occurred in accordance with the defining characteristics of schedule-induced behaviors. Rats in the fixed-time reinforcement condition also deposited significantly greater numbers of fecal boli. Sniffing and food bowl related behaviors occurred as terminal responses for this group. It is concluded that animals which receive reinforcers intermittently maintain high levels of arousal for extended periods, and that the presence of the schedule may mimic conditions experienced by wild rats in non-laboratory settings. In such conditions ambulatory behaviors may be particularly adaptive. In contrast, reinforcing sensory feedback and a stress reducing role may be particularly important in the mediation of oral behaviors (such as drinking) which occur during intermittent reinforcement.

Animals↗
PubMed1990

Lanosterol 14 alpha-demethylase-encoding gene: systematic analysis of homologous overexpression in Saccharomyces cerevisiae using strong yeast promoters.

The Saccharomyces cerevisiae 14DM gene, encoding cytochrome P450 lanosterol 14 alpha-demethylase (14DM), was overexpressed in various S. cerevisiae strains under the control of three strong heterologous yeast transcription promoters (pADC1, pGPD, pPHO5) and under the control of its own promoter. Striking, strain-specific differences in 14DM transcription and in 14DM contents have been observed. The relative abundances of 14DM-specific mRNA and protein derived from a series of different expression plasmids were compared. It was found that the inducible PHO5 promoter in combination with the JL745 host led to the highest expression levels. 14DM-specific RNA reached up to 2% of the total cellular mRNA in this strain and approx. 3% of the total soluble yeast-cell protein was determined to be 14DM by quantitative Western blotting. By comparing the abundances of the different fusion transcripts with the transcript originating from the corresponding endogenous gene from which the promoter was derived, it could be concluded that the expression levels of the different 14DM fusion genes were far below the theoretically attainable values.

Base Sequence↗
PubMed1993

Identification of new genes by systematic analysis of cDNAs and database construction.

The large-scale collection of partial cDNA sequences is becoming a powerful tool in biology. Similarity or motif searches in DNA databases using these partial cDNA sequences have facilitated the discovery of new genes of interest. By collecting and registering large numbers of partial sequences with a well designed non-biased cDNA library, an expression profile of active genes in a particular tissue can be obtained. Tissue-specific or stage-specific genes can be discovered by comparing the profiles from different tissues or from a tissue at different stages of development, respectively. The compilation of such expression profiles enables genes to be mapped to the tissue(s) where they are actively transcribed. The large-scale collation of gene sequences actively expressed in the body into databases complements efforts directed towards the structural analysis of the genome, with the ultimate aim of decoding all the genetic information carried in the human genome. This cDNA strategy is also being widely applied to organisms other than man.

Animals↗
PubMed1999

Molecular systematic analysis of the order Proteocephalidea (Eucestoda) based on mitochondrial and nuclear rDNA sequences.

Two ribosomal DNA sequences were used to infer phylogenetic relationships among the Eucestoda order Proteocephalidea. A 437 bp portion of the 16S mitochondrial and a 1149 bp 5' portion of the nuclear large sub-unit rRNA molecule were sequenced for 53 proteocephalidean cestodes (representing nine subfamilies and 22 genera) and for one outgroup species. Parsimony and distance-based analyses of the two databases, alone and combined, failed to support the monophyly of the two traditionally accepted families, of numerous subfamilies (with the exception of the Rudolphielliinae and Othinoscolescinae which were validated in our analysis) and of various genera, including the genus Nomimoscolex (Woodland), Ophiotaenia (La Rue) as well as the type genus Proteocephalus (Weinland). Palaearctic Proteocephalus species nevertheless constituted a well-defined clade. The two genes globally yielded compatible results; however, the nuclear ribosomal gene provided a better resolution of relations among Proteocephalidea.

Animals↗