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Results for “Pathway analysis”

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PubMed2002

[Complications high frequency catheter destruction of heart conduction pathways].

An analysis of 490 operations in 442 patients with different variants of supraventricular and ventricular tachycardia was made. Complications developed in 23 cases (4.7%). The least (0.8%) risk of complications was noted in patients after destruction of the atrioventricular junction, the greatest (9.6%) in patients with abnormal junctions. Measures of treatment depended on the degree and severity of the complication and the character of concomitant disease. The division of complications into biogenic and technogenic allows the possible factors influencing their development to be differentiated. The frequency of complications is determined by complexity of the methods used and the necessary experience on the one hand, and by the severity of the patient's state and coexistent diseases on the other hand.

Adolescent↗

PubMed2005

[Effects of culture conditions on coenzyme Q10 production by Rhizobium radiobacter by metabolic flux analysis].

Metabolic pathway network of CoQ10 synthesis by R. radiobacter WSH2601 were instructed. The metabolic flux and its changes were determined under the conditions of changing DO concentration and addition of 1% CSL in the medium. The results illustrated that the Ru5P flux (r7) increased by 26.6 when increasing the DO concentration, r7 increased by 17.2 when addition of 1% CSL. The ratio of EMP and HMP flux as well as TCA flux decreased at these two conditions. DPP flux had a little change at these two conditions. Therefore, the CoQ10 accumulation is greatly determined by two key enzymes activities of condensation reaction between p-hydroxybenzoate acid (PHB) and decaprenyl diphosphate (DPP). The nodes of G6P, pyruvate and PEP are principal nodes in primary metabolism of CoQ10 fermentation. The flexibility of principal nodes was evaluated that the G6P node is elastic, while pyruvate node is weakly flexibility, at the condition of changing culture conditions. The increase of DCW is associated with the improvement of HMP pathway flux.

Agrobacterium tumefaciens↗

PubMed1999

Analysis of the p53/BAX pathway in colorectal cancer: low BAX is a negative prognostic factor in patients with resected liver metastases.

PURPOSE: To determine the prognostic value of the central downstream apoptosis effector BAX in relation to its upstream regulator p53 in R0-resected hepatic metastases of colorectal cancer. PATIENTS AND METHODS: Retrospective analysis of 41 patients who underwent potentially curative resection of liver metastases from colarectal cancer was performed. Tumor DNA was screened for p53 mutations by single-stranded conformational polymorphism polymerase chain reaction and for BAX frameshift mutations by fragment length analysis. Protein expression of BAX, p21, and p53 was investigated by immunohistochemistry. RESULTS: Overall median survival was 40.2 months. Tumors with BAX frameshift mutations were considered microsatellite mutator phenotype-positive and were excluded from further prognostic analyses. Patients with high BAX protein expression had a median survival of 53.6 months compared with 35.4 months for patients with low BAX expression (P < .05). The negative prognostic value of low BAX expression was more evident in those patients with wild-type p53 (median survival, 54.0 v 23.3 months for BAX-negative tumors; P < .01). Low BAX expression was an independent negative prognostic marker in multivariate regression analysis for all patients independent of the p53 status (relative risk, 3.03, P = .03), especially for p53 wild-type tumors (relative risk, 8.21; P = .0095). CONCLUSION: We conclude that low BAX expression is an independent negative prognostic marker in patients with hepatic metastases of colorectal cancer. The best survival was seen in patients with an intact p53-to-BAX pathway; ie, wild-type p53- and BAX-positive tumors. Thus, analysis of apoptosis signaling pathways (here, p53 in concert with its downstream death effector, BAX) might yield more prognostic power in future studies as compared with analysis of single genes such as p53 alone.

Adult↗

PubMed2004

Detection of somatic mosaicism and classification of Fanconi anemia patients by analysis of the FA/BRCA pathway.

Fanconi anemia (FA) is characterized by congenital abnormalities, bone marrow failure, chromosome fragility, and cancer susceptibility. Eight FA-associated genes have been identified so far, the products of which function in the FA/BRCA pathway. A key event in the pathway is the monoubiquitination of the FANCD2 protein, which depends on a multiprotein FA core complex. In a number of patients, spontaneous genetic reversion can correct FA mutations, leading to somatic mosaicism. We analyzed the FA/BRCA pathway in 53 FA patients by FANCD2 immunoblots and chromosome breakage tests. Strikingly, FANCD2 monoubiquitination was detected in peripheral blood lymphocytes (PBLs) in 8 (15%) patients. FA reversion was further shown in these patients by comparison of primary fibro-blasts and PBLs. Reversion was associated with higher blood counts and clinical stability or improvement. Once constitutional FANCD2 patterns were determined, patients could be classified based on the level of FA/BRCA pathway disruption, as "FA core" (upstream inactivation; n = 47, 89%), FA-D2 (n = 4, 8%), and an unidentified downstream group (n = 2, 4%). FA-D2 and unidentified group patients were therefore relatively common, and they had more severe congenital phenotypes. These results show that specific analysis of the FA/BRCA pathway, combined with clinical and chromosome breakage data, allows a comprehensive characterization of FA patients.

Adolescent↗

PubMed2002

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.

MOTIVATION: We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway databases used by those algorithms, to the prediction accuracy. RESULTS: The comparisons we performed were as follows. (1) We compared two predictions of the pathway complements of Helicobacter pylori that were computed by an early version of our pathway-prediction algorithm: prediction A used the EcoCyc E. coli pathway DB as the reference database (DB) for prediction, and prediction B used the MetaCyc pathway DB (a superset of EcoCyc) as the reference pathway DB. The MetaCyc-based prediction contained 75% more pathway predictions, but we believe a significant number of those predictions were false positives. (2) We compared two predictions of the pathway complement of H. pylori that used MetaCyc as the reference pathway DB, but that used different algorithms: the original PathoLogic algorithm, and an enhanced version of the algorithm designed to eliminate false-positive pathway predictions. The improved algorithm predicted 30\% fewer metabolic pathways than the original algorithm; all of the eliminated pathways are believed to be false-positive predictions. (3) We compared the 98 pathways predicted by the enhanced algorithm with the results of a manual analysis of the pathways of H. pylori. Results: 40 of the computationally predicted pathways were consistent with the manual analysis, 13 pathways are considered false-positive predictions, and four pathways had partially overlapping topologies. Twenty-six predicted pathways were not mentioned in the manual analysis; we believe these are correct predictions by PathoLogic that were not found by the manual analysis. Five pathways from the manual analysis were not found computationally. Agreement between the computational and manual predictions was good overall, with the computational analysis inferring many pathways that the manual analysis did not identify. Ultimately the manual analysis is also partially speculative, and therefore is not an absolute measure of correctness. The algorithm is designed to err on the side of more false positives to bring more potential pathways to the user's attention. The resulting H. pylori pathway DB is freely available at http://ecocyc.org:1555/HPY/organism-summary?object=HPY. AVAILABILITY: The Pathway Tools software is freely available to academic users, and is available to commercial users for a fee. Contact pkarp@ai.sri.com for information on obtaining the software.

Algorithms↗

PubMed2026

Integrative post-GWAS analysis prioritizes immune regulatory pathways and candidate effector signals in systemic lupus erythematosus.

BACKGROUND: Systemic lupus erythematosus (SLE) has a complex polygenic architecture, but translating genome-wide association signals into biologically interpretable candidates remains challenging. We applied an integrative post-GWAS framework to refine SLE-associated loci and prioritize candidate regulatory mechanisms. METHODS: European-ancestry SLE GWAS summary statistics from FinnGen and Bentham et al. were meta-analysed, comprising 8417 cases and 354,277 controls. After quality filtering, 6,782,131 SNPs were retained. Downstream analyses included LAVA regional prioritization, Bayesian colocalization with GTEx v8 whole-blood and spleen eQTLs, independent replication in the Julià et al. Spanish cohort, pathway enrichment, bivariate LAVA cross-trait local genetic correlation, and therapeutic annotation. RESULTS: The discovery meta-analysis identified 46 genome-wide significant SLE-associated loci, including putative novel signals requiring database/literature qualification. LAVA identified 14 candidate index variants across 12 high-confidence regions, of which nine index variants were retained as the primary prioritized set based on LAVA support and/or convergent regulatory evidence. The strongest association mapped to the chr6p21.3/MHC region (rs389884), where four genes showed colocalization support, including CLIC1 in whole blood and C4A in spleen. Because the chr6p21.3/MHC rs389884 region lead variant was unavailable for replication and no suitable proxy was identified, this signal was interpreted as an emerging candidate for functional validation rather than a replicated causal signal. Seven available variants replicated with concordant effects. An exploratory Roadmap immune chromatin-state overlap analysis placed 15 of 45 non-MHC lead variants (33.3%) directly, and 34 of 45 (75.6%) within ±10 kb, in active immune enhancer/promoter states. Pathway analyses highlighted type I interferon, JAK-STAT signaling, cytokine regulation, and antigen presentation, while bivariate LAVA analyses supported shared local genetic architecture with rheumatoid arthritis, systemic sclerosis, and Sjögren syndrome. CONCLUSIONS: This integrative post-GWAS analysis refines SLE association signals into biologically interpretable candidate regions and supports interferon and JAK-STAT signaling as central genetically supported pathways in SLE.

CLIC1↗

PubMed1999

Analysis of a catalytic pathway via a covalent adduct of D52E hen egg white mutant lysozyme by further mutation.

We previously demonstrated by X-ray crystallography and electrospray mass spectrometry that D52E mutant hen lysozyme formed a covalent enzyme-substrate adduct on reaction with N-acetylglucosamine oligomer. This observation indicates that D52E lysozyme may acquire a catalytic pathway via a covalent adduct. To explain this pathway, the formation and hydrolysis reactions of the covalent adduct were investigated. Kinetic analysis indicated that the hydrolysis step was the rate-limiting step, 60-fold slower than the formation reaction. In the formation reaction, the pH dependence was bell-shaped, which was plausibly explained by the functions of the two catalytic pKas of Glu35 and Glu52. On the other hand, the pH dependence in the hydrolysis was sigmoidal with a transition at pH 4. 5, which was identical with the experimentally determined pKa of Glu35 in the covalent adduct, indicating that Glu35 functions as a general base to hydrolyze the adduct. To improve the turnover rate of D52E lysozyme, the mutation of N46D was designed and introduced to D52E lysozyme. This mutation reduced the activation energy in the hydrolysis reaction of the covalent adduct by 1.8 kcal/mol at pH 5.0 and 40 degrees C but did not affect the formation reaction. Our data may provide a useful approach to understanding the precise mechanism of the function of natural glycosidases, which catalyze via a covalent adduct.

Animals↗

PubMed1999

Central mechanisms of temporal analysis in the knollenorgan pathway of mormyrid electric fish

Mormyrid electric fish communicate using pulse-type electric organ discharges (EODs). The fine temporal structure of the waveforms of EODs varies widely throughout the 200 or more species of mormyrids. These signals carry information about the species, the sex and even the individual identity of the signaller. Behavioral experiments have shown that some species of fish are capable of using this information. Of the four known types of electroreceptors in mormyrid fish, the knollenorgan electroreceptor is the one most likely to be involved in the detection of conspecific EOD signals. Here, we review some recent advances in understanding how the central knollenorgan pathway might be analyzing the temporal structure of the EOD waveform. Fine temporal analysis appears to take place in the nucleus exterolateralis pars anterior (ELa), where tightly phase-locked inputs from the hindbrain drive a direct, excitatory input through a long axonal delay line and also drive an indirect, inhibitory input with negligible delay through the ELa large cell. These two inputs converge on ELa small cells, where they are hypothesized to interact in a 'delay-line/blanking' model. This initial temporal analysis is further refined in the nucleus exterolateralis pars posterior, where units tuned to ranges of pulse durations have been identified physiologically.

Journal Article↗

PubMed1999

Analysis of a critical pathway in osteoplastic flap for frontal sinus obliteration.

OBJECTIVES: A critical pathway was applied to patients undergoing osteoplastic flap (OPF) for frontal sinus obliteration to determine whether efficiency could be improved. STUDY DESIGN: A retrospective review of consecutive OPF procedures (n = 51) performed between 1992 and July 1997 was conducted. METHODS: The patient groups were subdivided into those who underwent OPF alone and those who had endoscopic sinus procedures performed in addition to OPF. Comparisons were made between the precritical pathway and post-critical pathway groups, specifically noting operative time, total operating room (OR) time, estimated blood loss (EBL), length of hospital stay, and costs. We used a critical pathway that was developed for endoscopic sinus procedures at our institution through a multidisciplinary team approach. Preoperative evaluation and testing, intraoperative equipment and medications, and postoperative care including follow-up clinic visits were all standardized. An unpaired, two-tailed Student t test was used to evaluate the data. RESULTS: Statistically significant (P<.05) reductions in operative times, total OR time, EBL, and length of hospital stay were observed in the post-critical pathway group who underwent endoscopic sinus procedures as well as OPF. Costs to the OR were reduced 29% and 15% for OPF and for OPF with endoscopic surgery, respectively. Patient costs were reduced 5% and 4% in these groups, respectively. CONCLUSIONS: With implementation of effective critical pathways, significant decreases in length of stay are seen, and cost reductions can be realized through the improved efficiency, shortened OR times, and decreases in redundancy of ordering materials.

Bone Transplantation↗

PubMed1993

Molecular cloning of the yeast OPI3 gene as a high copy number suppressor of the cho2 mutation.

By functional complementation of the auxotrophic requirements for choline of a cdg1, cho2 double-mutant, by transformation with a genomic DNA library in a high copy number plasmid, two different types of complementing DNA inserts were identified. One type of insert was earlier shown to represent the CHO2 structural gene. In this report we describe the molecular and biochemical chemical characterization of the second type of complementing activity. The transcript encoded by the cloned gene was about 1000-nt in length and was regulated in response to the soluble phospholipid precursors, inositol and choline. A gene disruption resulted in no obvious growth phenotype at 23 degrees C or 30 degrees C, but in a lack of growth at 37 degrees C in the presence of monomethylethanolamine. Null-mutants exhibited an inositol-secretion phenotype, indicative of mutations in the lipid biosynthetic pathway. Complementation analysis, biochemical analysis of the phospholipid methylation pathway in vivo, and comparison of the restriction pattern of the cloned gene to published sequences, unequivocally identified the cloned gene as the OPI3 gene, encoding phospholipid-N-methyltransferase in yeast. When present in multiple copies the OPI3 gene efficiently suppresses the phospholipid methylation defect of a cho2 mutation. As a result of impaired synthesis of phosphatidylcholine, the INO1-deregulation phenotype is abolished in cho2 mutants transformed with the OPI3 gene on a high copy number plasmid.(ABSTRACT TRUNCATED AT 250 WORDS)

Cloning, Molecular↗

PubMed2026

[Study on mechanism of Wendan Decoction in intervening in nonalcoholic fatty liver disease based on proteomics and network pharmacology].

This study systematically explored the molecular mechanism of Wendan Decoction(WDD) in treating nonalcoholic fatty liver disease(NAFLD) by integrating network pharmacology, proteomics, and experimental validation. A mouse NAFLD model was established using a high-fat diet, and the mice were randomly divided into a blank control group, a model group, a positive drug group(simvastatin, 3.03 mg·kg~(-1)), and low-(3.035 g·kg~(-1)), medium-(6.07 g·kg~(-1)), and high-dose(12.14 g·kg~(-1)) WDD groups, with intervention lasting for 6 weeks. After the intervention, the serum levels of alanine aminotransferase(ALT), aspartate aminotransferase(AST), triglycerides(TG), total cholesterol(TC), low-density lipoprotein cholesterol(LDL-C), and high-density lipoprotein cholesterol(HDL-C) were measured using an automatic biochemical analyzer. The serum levels of interleukin-1β(IL-1β), interleukin-6(IL-6), and tumor necrosis factor-α(TNF-α) were detected by ELISA. Liver histopathology was observed via hematoxylin-eosin(HE) staining and oil red O staining. Network pharmacology was used to predict potential targets and pathways, and proteomics was applied to identify differentially expressed proteins and related pathways. RT-qPCR and Western blot were performed to detect mRNA and protein expression of relevant genes. Animal experiments demonstrated that WDD dose-dependently ameliorated hepatic steatosis, inflammation, and lipid deposition, significantly reducing serum levels of ALT, AST, TG, TC, LDL-C, and pro-inflammatory cytokines(IL-1β, IL-6, and TNF-α), while significantly increasing serum HDL-C levels. Network pharmacology screening identified naringenin, baicalein, and other key active components, which were involved in pathways such as the peroxisome proliferator-activated receptor(PPAR), lipid, and atherosclerosis pathways. Proteomics further revealed differentially expressed pathways including the PPAR and advanced glycation end product-receptor(AGE-RAGE) signaling pathways. Integrated analysis highlighted the PPAR signaling pathway as the core mechanism. Molecular biology validation showed that WDD significantly regulated the mRNA expression of sterol regulatory element-binding protein-1c(SREBP-1c), fatty acid synthase(FASN), carnitine palmitoyl transferase 1A(CPT1A), acyl-CoA oxidase 1(ACOX1), and PPARα, as well as protein expression of PPARα, CPT1A, and PPARγ in mouse liver tissue. These results suggested that WDD might exert a multi-component, multi-target, and multi-pathway synergistic effect to improve lipid metabolism disorders and inflammatory responses with the PPAR signaling pathway as the central hub, thereby alleviating NAFLD progression.

Animals↗

PubMed2025

Comparative genomic analysis of key oncogenic pathways in hepatocellular carcinoma among diverse populations.

BACKGROUND/OBJECTIVES: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality, with significant racial and ethnic disparities in incidence, tumor biology, and clinical outcomes. Hispanic/Latino (H/L) patients tend to be diagnosed at younger ages and more advanced stages than Non-Hispanic White (NHW) patients, yet the molecular mechanisms underlying these disparities remain poorly understood. Key oncogenic pathways, including RTK/RAS, TGF-Beta, WNT, PI3K, and TP53, play pivotal roles in tumor progression, treatment resistance, and response to targeted therapies. However, ethnicity-specific alterations within these pathways remain largely unexplored. This study aims to compare pathway-specific mutations in HCC between H/L and NHW patients, assess tumor mutation burden, and identify ethnicity-associated oncogenic drivers using publicly available datasets. Findings from this analysis may inform precision medicine strategies for improving early detection and targeted therapies in underrepresented populations. METHODS: We conducted a bioinformatics analysis using publicly available HCC datasets to assess mutation frequencies in RTK/RAS, TGF-Beta, WNT, PI3K, and TP53 pathway genes. The study included 547 patients, consisting of 69 H/L patients and 478 NHW patients. Patients were stratified by ethnicity (H/L vs. NHW) to evaluate differences in mutation prevalence. Chi-squared tests were used to compare mutation frequencies, while Kaplan-Meier survival analysis assessed overall survival differences associated with pathway-specific alterations in both populations. RESULTS: Significant differences were observed in the RTK/RAS pathway related genes, particularly in FGFR4 mutations, which were more prevalent in H/L patients compared to NHW patients (4.3% vs. 0.6%, p = 0.02). Additionally, IGF1R mutations exhibited borderline significance (7.2% vs. 2.9%, p = 0.07). In the PI3K pathway, INPP4B alterations were more frequent in H/L patients than in NHW patients (4.3% vs. 1%, p = 0.06), while in the TGF-Beta pathway, TGFBR2 mutations were more common in H/L patients (2.9% vs. 0.4%, p = 0.07), suggesting potential ethnicity-specific variations. Survival analysis revealed no significant differences in overall survival between H/L and NHW patients, indicating that molecular alterations alone may not fully explain survival disparities and suggesting a role for additional factors such as immune response, environmental exposures, or access to targeted therapies. CONCLUSIONS: This study provides one of the first ethnicity-focused analyses of key oncogenic pathway alterations in HCC, revealing distinct molecular differences between H/L and NHW patients. The findings suggest that RTK/RAS (FGFR4, IGF1R), PI3K (INPP4B), and TGF-Beta (TGFBR2) pathway alterations may play a distinct role in HCC among H/L patients, while their prognostic significance in NHW patients remains unclear. These insights emphasize the importance of incorporating ethnicity-specific molecular profiling into precision medicine approaches to improve early detection, targeted therapies, and clinical outcomes in HCC, particularly for underrepresented populations.

PI3K pathway↗

PubMedDate not supplied

Analysis of apoptosis signaling pathway in human cancer cells by codeinone, a synthetic derivative of codeine.

We have recently found that codeinone, an oxidation metabolite of codeine, induced apoptosis, characterized by internucleosomal DNA fragmentation and mitochondrial cytochrome c release in HL-60 human promyelocytic leukemic cell lines, most effectively among 10 opioids. These findings prompted us to investigate whether codeinone induces apoptosis in other human cancer cells and possible changes in mitochondrial enzyme. FACS analysis demonstrated that codeinone induced the production of ANNEXIN-positive apoptotic cells in three different human cancer cells (HL-60, MCF7, A549). The apoptotic cells were visualized by microscopical observation after staining with Hoechst (H)-33342. Fluorometric assay showed that codeinone time-dependently activated caspase 3 and caspase 9, but not caspase 8, suggesting the activation of intrinsic apoptotic signaling pathway via mitochondria. Western blot analysis demonstrated that codeinone enhanced the Pro-apoptotic Bax protein expression, but reduced the anti-apoptotic Bcl-2 protein expression. Codeinone did not significantly change the manganese superoxide dismutase (MnSOD) activity nor its mRNA expression. This apoptosis-inducing activity, in conjunction with antinociceptive activity, further substantiated the antitumor potential of codeinone.

Apoptosis↗

PubMedDate not supplied

Metabolic control analysis of the penicillin biosynthetic pathway in a high-yielding strain of Penicillium chrysogenum.

Metabolic control analysis is used to identify the rate-limiting step in the penicillin biosynthetic pathway in Penicillium chrysogenum. The analysis is carried out using a kinetic model for the first two steps in the pathway, i.e., the ACV synthetase (ACVS) and the isopenicillin N synthetase (IPNS). The kinetic model is based on Michaelis-Menten type kinetics, with noncompetitive inhibition of the ACVS by ACV and competitive inhibition of the IPNS by glutathione. From measurements of the enzyme activities and intracellular metabolites during a fed-batch cultivation, the kinetic model is used to predict the flux through the pathway. The model prediction corresponds well with the measured rate of penicillin biosynthesis. From measurement of the activity of the acyl-CoA:isopenicillin acyltransferase, which catalyzes the third and last reaction in the pathway, it is concluded that the rate-limiting step is either at the ACVS or at the IPNS. From the kinetic model, the elasticity coefficients and the flux control coefficients are calculated throughout the fed-batch cultivations, and it is found that there is a shift in the flux control from the ACVS to the IPNS during the cultivation.

Anti-Bacterial Agents↗

PubMed2005

Pharmacoeconomic analysis of sequential treatment pathways in the treatment of onychomycosis.

This study examines the budgetary effect of using ciclopirox, itraconazole (pulse treatment), terbinafine, or itraconazole (continuous treatment) as first-, second-, or third-line therapy in the treatment of toenail onychomycosis by determining which therapeutic sequence is most cost effective. Using a disease treatment pathway model, alternative agents were compared based on cost per clinical response. The results from this sequential treatment analysis demonstrated that ciclopirox followed by itraconazole pulse and then terbinafine provides the lowest-cost approach to the treatment of onychomycosis (dollar 757.89 per clinical response), followed by the sequence of ciclopirox, terbinafine, and itraconazole pulse (dollar 796.13 per clinical response). This study provides a framework for formulary decision makers to evaluate a sequential treatment pathway that resembles actual practice.

Antifungal Agents↗

PubMed2005

Metabolomic identification of novel biomarkers of myocardial ischemia.

BACKGROUND: Recognition of myocardial ischemia is critical both for the diagnosis of coronary artery disease and the selection and evaluation of therapy. Recent advances in proteomic and metabolic profiling technologies may offer the possibility of identifying novel biomarkers and pathways activated in myocardial ischemia. METHODS AND RESULTS: Blood samples were obtained before and after exercise stress testing from 36 patients, 18 of whom demonstrated inducible ischemia (cases) and 18 of whom did not (controls). Plasma was fractionated by liquid chromatography, and profiling of analytes was performed with a high-sensitivity electrospray triple-quadrupole mass spectrometer under selected reaction monitoring conditions. Lactic acid and metabolites involved in skeletal muscle AMP catabolism increased after exercise in both cases and controls. In contrast, there was significant discordant regulation of multiple metabolites that either increased or decreased in cases but remained unchanged in controls. Functional pathway trend analysis with the use of novel software revealed that 6 members of the citric acid pathway were among the 23 most changed metabolites in cases (adjusted P=0.04). Furthermore, changes in 6 metabolites, including citric acid, differentiated cases from controls with a high degree of accuracy (P<0.0001; cross-validated c-statistic=0.83). CONCLUSIONS: We report the novel application of metabolomics to acute myocardial ischemia, in which we identified novel biomarkers of ischemia, and from pathway trend analysis, coordinate changes in groups of functionally related metabolites.

Adenosine Monophosphate↗

PubMed1991

An analysis of protein folding pathways.

We have developed a model of the protein folding process based on three primary assumptions: that burying of hydrophobic area is the dominant contribution to the relative free energy of a conformation, that a record of the folding process is largely preserved in the final structure, and that the denatured state is a random coil. Detailed folding pathways are identified for 19 protein structures. The picture of the folding process that emerges from this analysis is one of nucleation by regions of 8-16 residues. Nucleation sites then lead to larger structures by two mechanisms: propagation and diffusion/collision. A Monte Carlo simulation is used to follow the folding pathway when propagation is the dominant mechanism. Because detailed pathways are derived for each protein, the models are susceptible to experimental verification.

Amino Acid Sequence↗

PubMed2005

Critical pathway effectiveness: assessing the impact of patient, hospital care, and pathway characteristics using qualitative comparative analysis.

OBJECTIVE: To qualitatively describe patient, hospital care, and critical pathway characteristics that may be associated with pathway effectiveness in reducing length of stay. DATA SOURCES/STUDY SETTING: Administrative data and review of pathway documentation and a sample of medical records for each of 26 surgical critical pathways in a tertiary care center's department of surgery, 1988-1998. STUDY DESIGN: Retrospective qualitative study. DATA COLLECTION/ABSTRACTION METHODS: Using information from a literature review and consultation with experts, we developed a list of characteristics that might impact critical pathway effectiveness. We used hypothesis-driven qualitative comparative analysis to describe key primary and secondary characteristics that might differentiate effective from ineffective critical pathways. PRINCIPAL FINDINGS: " All 7 of the 26 pathways associated with a reduced length of stay had at least one of the following characteristics: (1) no preexisting trend toward lower length of stay for the procedure (71 percent), and/or (2) it was the first pathway implemented in its surgical service (71 percent). In addition, pathways effective in reducing length of stay tended to be for procedures with lower patient severity of illness, as indicated by fewer intensive care days and lower mortality. Effective pathways tended to be used more frequently than ineffective pathways (77 versus 59 percent of medical records with pathway documents present), but high rates of documented pathway use were not necessary for pathway effectiveness. CONCLUSIONS: Critical pathway programs may have limited effectiveness, and may be effective only in certain situations. Because pathway utilization was not a strong predictor of pathway effectiveness, the mechanism by which critical pathways may reduce length of stay is unclear.

Baltimore↗