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Comprehensive Genomic Analysis of Normal and Cancer Cells Elucidates the Elevated Mutation Burden in Cancer.

Self-renewing normal tissues generate several somatic mutations at each division. Previous studies have reported that cancer cells have more mutations than their normal counterparts. It is not obvious why dramatic differences in mutation burdens between normal tissues and cancers should exist. To fully understand human tumorigenesis, the increase of mutation burden in cancers will have to be understood. Here, we provided a systematic comparison of mutational burdens in normal and cancer cells from five different organs, revealing a four-fold increase of mutation burdens in cancerous vs. non-cancerous cells. Three proposed hypotheses that could account for the increased mutation burdens in cancer are: the classical hypothesis, where driver gene mutations explain the higher mutational burden; the catastrophic hypothesis, where extreme mutational events lead to large-scale genomic alterations; and the tail hypothesis, where differences in baseline mutation rates among individuals account for the differences. Testing through orthogonal observations showed that the observed medians and distributions of mutation burdens in cancers could be explained by the hypotheses to various degrees of significance, and only the tail hypothesis could easily explain the increase in median mutation burdens in the normal tissues of cancer patients compared to the normal tissues of non-cancer patients. Overall, this study characterizes an increased mutation burden across multiple types of cancer compared to normal tissue and provides insights into the contributing factors. A tenable hypothesis proposed in this study involving fundamental differences in baseline mutation rates among individuals could have implications for cancer prevention strategies.

Journal Article↗

Morphological predictors of acute complications after percutaneous excimer laser coronary angioplasty. Results of a comprehensive angiographic analysis: importance of the eccentricity index.

BACKGROUND: Percutaneous excimer laser coronary angioplasty (ELCA) is a new technique for recanalization of arteries obstructed by coronary atherosclerosis. This study was conducted to assess the complication rate and determine the influence of clinical and angiographic characteristics on complications after ELCA. METHODS AND RESULTS: A detailed, quantitative, angiographic core laboratory analysis of patients undergoing ELCA was performed by two experienced angiographers who were not the primary laser angioplasty operators. Two hundred patients underwent 203 separate procedures on 220 lesions at three medical centers. Laser success was achieved in 180 lesions (81.8%) and procedural success in 199 (90.5%). Emergency coronary artery bypass graft (CABG) was required in five patients (2.5%). One patient suffered a Q wave myocardial infarction; there were no deaths. Also, acute closure and perforation occurred in 10 (4.5%) and three (1.4%) vessels, respectively. Coronary dissections after laser treatment were seen in 36 vessels (16.4%). Multivariate analysis found two independent preprocedural factors related to complications: eccentricity index, which is the percent deviation of the lesion lumen from the center of the artery (p = 0.0007), and proximal vessel diameter (p = 0.033). In addition, an abrupt proximal face of the lesion was associated with angiographic complications by univariate analysis (p = 0.051). Multivariate analysis showed the eccentricity index (p = 0.032) to be the only independent predictor for the occurrence of any one or more of the important complications (emergency CABG, perforation, acute closure, or Q wave myocardial infarction), whereas lesion angle greater than 45 degrees was a significant univariate predictor (p = 0.029). Other predictors of complications with balloon percutaneous transluminal coronary angioplasty, such as increased lesion length, rough edges, calcification, ulceration, and branch point, were not predictive of complications with the excimer laser. CONCLUSIONS: The degree of lesion eccentricity is the most powerful predictor of complications after ELCA. This and other morphological predictors may be of benefit in the selection of patients for ELCA as well as directing future development of this new technology.

Aged↗

The costs of pursuing accreditation for methadone treatment sites: results from a national study.

The use of accreditation has been widespread among medical care providers, but accreditation is relatively new to the drug abuse treatment field. This study presents estimates of the costs of pursuing accreditation for methadone treatment sites. Data are from 102 methadone treatment sites that underwent accreditation as part of the Center for Substance Abuse Treatment's evaluation of the Opioid Treatment Program Accreditation Project. The analysis represents the most comprehensive analysis of the costs of pursuing accreditation by a health care provider. Importantly, it is the first analysis of the costs of pursuing accreditation by drug treatment providers. Policy makers and drug treatment providers can use this analysis to plan the labor requirements and costs of future accreditation initiatives.

Accreditation↗

Comprehensive functional analysis of shoulders following complete acromioclavicular separation.

The purpose of this study was to examine the results of the two major methods of treatment of complete acromioclavicular separation: surgery and nonsurgical techniques. Twenty male patients with complete acromioclavicular separation within the preceding 13 months were retrospectively examined and tested for recovery of shoulder strength and function. Comparisons were conducted between 10 of the patients who had been treated nonsurgically (Group 1), and 10 who had been treated surgically (Group 2). An additional group of 10 uninjured male subjects as controls was also tested for comparison of strength between dominant and nondominant limbs (Group 3). All of the patients were tested for strength of both shoulders using the Kin-Com isokinetic dynamometer, for shoulder flexibility using the Leighton flexometer, and for grip strength using a standard grip dynamometer. A questionnaire concerning patient evaluation of the injury was also administered to all of the subjects. The majority of strength and flexibility tests showed no significant differences between the nonsurgical and surgical groups. The nonsurgical group was statistically superior to the surgical group in the following test scores: eccentric abduction (fast speeds), concentric external rotation (slow speeds), eccentric external rotation (fast), eccentric abduction (slow), and flexibility in external rotation. These findings generally indicated that the nonsurgical treatment of a third-degree acromioclavicular separation is superior in restoring normal shoulder function in the 1st year following injury.

Acromioclavicular Joint↗

Identification of potential biomarkers and mechanisms for keloid disorder based on comprehensive bioinformatics analysis and machine learning algorithms.

BACKGROUND: Keloid disorder (KD) encompasses a spectrum of fibroproliferative dermal conditions, the pathogenesis remains complex and incompletely understood. This study sought to identify biomarkers and potential therapeutic targets for KD through an integrative bioinformatics approach and machine learning analysis of RNA sequencing data. METHODS: RNA sequencing was performed on skin tissue samples from 13 patients with KD and 14 healthy controls. Using weighted gene co-expression network analysis and differential expression analysis revealed differentially expressed key module genes, and the CytoHubba plugin identified candidate genes. Subsequently analyzed using least absolute shrinkage and selection operator (LASSO) and support vector machine recursive feature elimination (SVM-RFE) methods to pinpoint feature genes associated with KD. Following this, biomarkers were determined through expression level validation, enrichment analysis, and immune infiltration analysis. RESULTS: A total of 420 differentially expressed key module genes were identified, and the top 10 genes with DMNC values were selected as candidate genes. Five feature genes were selected through LASSO and SVM-RFE, with NID2, MFAP2, COL8A1, and P4HA3 showing significant expression differences between KD and control samples, along with consistent expression patterns across datasets, identified as potential biomarkers. These four biomarkers were proved to possess high diagnostic potential, and they were found to exhibit significant positive correlations with one another. Functional enrichment analysis indicated that the primary KEGG pathways associated with these biomarkers included "steroid hormone biosynthesis" and "cytokine-cytokine receptor interaction." Moreover, immune infiltration analysis revealed that the four biomarkers were negatively correlated with type 17 T helper cells and positively correlated with 15 immune cell types, including activated B cells and central memory CD4 T cells. CONCLUSION: In conclusion, NID2, MFAP2, COL8A1, and P4HA3 were identified as key biomarkers for KD, offering new avenues for more targeted and effective diagnostic and therapeutic strategies for managing this condition.

Humans↗

A comprehensive statewide analysis of seatbelt non-use with injury and hospital admissions: new data, old problem.

OBJECTIVES: To investigate the association of seatbelt nonuse with injury patterns, injury severity, and in-patient hospital admission among adults presenting to emergency departments (EDs) in a statewide, population-based, sample of motor vehicle crashes. METHODS: Using data from the 2002 Crash Outcome Data Evaluation System (CODES) for Wisconsin, 23,920 occupants of motor vehicle crashes, aged 16 years or older, who were treated in an ED, were analyzed. Logistic regression was used to compare the odds ratio of having sustained an injury to specific body regions and of being admitted to an inpatient unit in unbelted individuals compared with those who were belted. RESULTS: Compared with belted occupants presenting to an ED, their unbelted counterparts were more likely to be male (56% vs. 40%) and to have used alcohol (17% vs. 4%). Unbelted occupants were younger (31 years vs. 38 years) and incurred higher ED charges ($681 vs. $509) than belted occupants. Additionally, unbelted occupants have a higher proportion of single-vehicle crashes, such as rollovers (44% vs. 22%), and rural crashes (56% vs. 44%). Unbelted occupants comprised 20% of study patients treated in the ED and discharged, 44% of patients treated in the ED and admitted, and 68% of patients dying in the ED. Unbelted occupants were more likely to be admitted (odds ratio [OR] = 2.6) than belted individuals and were more likely to suffer severe injuries to the head, face, thorax, abdomen, spine, upper and lower extremities (OR ranging from 1.6 to 3.9). CONCLUSIONS: Among patients presenting to an ED after a motor vehicle crash, unbelted occupants are more likely to require inpatient admission and to have sustained a severe injury to numerous body regions than are belted occupants.

Accidents, Traffic↗

Hodgkin's lymphoma in elderly patients: a comprehensive retrospective analysis from the German Hodgkin's Study Group.

PURPOSE: With improved prognosis for patients with Hodgkin's lymphoma (HL), interest increasingly focuses on high-risk groups such as elderly patients. We thus performed a retrospective analysis using the German Hodgkin's Study Group (GHSG) database to determine clinical risk factors, course of treatment, and outcome in elderly HL patients in comparison with younger adults. PATIENTS AND METHODS: A total of 4,251 patients included in the GHSG studies HD5 to HD9 were analyzed, of whom 372 (8.8%) were 60 years or older and 3,879 (91.2%) were younger than 60 years. Patient characteristics, treatment results, toxicity, freedom from treatment failure (FFTF), and overall survival (OS) were compared. RESULTS: Elderly patients more often had mixed cellularity subtype, "B" symptoms, elevated erythrocyte sedimentation rate, and poorer performance status. Less frequently observed were nodular sclerosis subtype, large mediastinal mass, and bulky disease. Acute toxicity during chemotherapy was generally higher in elderly patients. This was most obvious for severe infections (grade 3 or 4; 15% v 6%) correlating with more severe leukopenia in elderly patients (grade 4; 38% v 23%). As a result, significantly fewer elderly patients received the intended full chemotherapy dose (75% v 91%). The survival analysis showed a significantly poorer treatment outcome for elderly patients in terms of 5-year OS (65% v 90%), FFTF (60% v 80%), and HL-specific FFTF (73% v 82%). CONCLUSION: Elderly patients have a poorer risk profile compared with younger HL patients and experience more severe treatment-associated toxicity. Higher mortality during treatment as well as lower dose-intensity are the major factors explaining the poorer overall outcome of elderly HL patients.

Age Factors↗

A comprehensive policy analysis of and recommendations for senior center gambling trips.

Gambling is one of the fastest growing industries in America. Public support is high for legalized gambling among all age groups. Because gambling is growing in popularity as an activity among those 65 and over, many senior centers are beginning to offer group trips to casinos and other gambling attractions such as dog tracks. This paper analyzes senior center casino gambling trips, with particular attention to the number of trips offered, how trips are funded, the policy implications of offering trips, and policy alternatives for state and local policymakers. Data for the study come from personal interviews with activity directors of 16 senior centers across Massachusetts and a formal survey of 30 additional senior centers in Central Massachusetts. Benefits of a new policy option, a public education strategy, are also reviewed.

Aged↗

Comprehensive microarray analysis of bone morphogenetic protein 2-induced osteoblast differentiation resulting in the identification of novel markers for bone development.

Osteoblasts are cells responsible for matrix deposition during bone development and although temporal expression of many genes has been related to osteoblast differentiation, a complete description of osteoblast-specific gene regulation will lead to a better understanding of osteoblast function. In this study, microarray technology was used to analyze gene expression on a broad scale during osteoblast differentiation. Expression analysis of 9596 sequences revealed 342 genes and expressed sequence tags (ESTs) to be modulated differentially during a time course experiment in which murine C2C12 mesenchymal progenitor cells were induced to differentiate into mature osteoblasts by treatment with bone morphogenetic protein 2 (BMP-2). By means of hierarchical clustering, these genes were grouped by similarities in their expression profiles, resulting in subsets of early, intermediate, and late response genes, which are representative of the distinct stages of osteoblast differentiation. To identify new bone markers, the bone specificity of the late response genes was determined by comparing BMP-induced expression in C2C12 and MC3T3 osteoblasts with that in NIH3T3 fibroblasts. This resulted in the identification of nine novel genes and ESTs that were induced specifically in osteoblasts, in addition to the well-known markers ALP and osteocalcin. For at least one of these novel genes, Wnt inhibitory factor 1, and two of the ESTs, expression in developing bone was verified in vivo by in situ hybridization of E16.5 mouse embryos. In conclusion, by a combination of in vitro and in vivo screening approaches, a set of new genes related to osteoblast differentiation and skeletal development has been identified.

3T3 Cells↗

Toward a comprehensive genetic analysis of male fertility in Drosophila melanogaster.

Drosophila melanogaster is a widely used model organism for genetic dissection of developmental processes. To exploit its full potential for studying the genetic basis of male fertility, we performed a large-scale screen for male-sterile (ms) mutations. From a collection of 12,326 strains carrying ethyl-methanesulfonate-treated, homozygous viable second or third chromosomes, 2216 ms lines were identified, constituting the largest collection of ms mutations described to date for any organism. Over 2000 lines were cytologically characterized and, of these, 81% failed during spermatogenesis while 19% manifested postspermatogenic processes. Of the phenotypic categories used to classify the mutants, the largest groups were those that showed visible defects in meiotic chromosome segregation or cytokinesis and those that failed in sperm individualization. We also identified 62 fertile or subfertile lines that showed high levels of chromosome loss due to abnormal mitotic or meiotic chromosome transmission in the male germ line or due to paternal chromosome loss in the early embryo. We argue that the majority of autosomal genes that function in male fertility in Drosophila are represented by one or more alleles in the ms collection. Given the conservation of molecular mechanisms underlying important cellular processes, analysis of these mutations should provide insight into the genetic networks that control male fertility in Drosophila and other organisms, including humans.

Animals↗

Tetraphyllidean plerocercoids from Western Mediterranean cetaceans and other marine mammals around the world: a comprehensive morphological analysis.

Tetraphyllidean plerocercoids have occasionally been reported in marine mammals, but they have rarely been described in detail, and the ecological significance of these infections is unclear. We described plerocercoids collected from the mucosa of the terminal colon and rectum, the anal crypts, and the hepatopancreatic ducts of 7 striped dolphins Stenella coeruleoalba, 1 Cuvier's beaked whale Ziphius cavirostris, and 3 Risso's dolphins Grampus griseus from the Spanish Mediterranean. We also examined undescribed plerocercoids from 3 cetacean species from the Atlantic and the Pacific. All plerocercoids had a lanceolate body, and a scolex with an apical sucker and 4 sessile monolocular bothridia. The bothridia had free posterior edges and an accessory sucker at their anterior end. Under light microscopy, the bothridia of some Mediterranean specimens looked bilocular without accessory suckers, but a true accessory sucker was observed in histological sections. A principal component analysis revealed 2 stable clusters of specimens along the first principal component regardless of host species. These "large" and "small" morphotypes are thought to represent early migratory stages of Phyllobothrium delphini and Monorygma grimaldii. The similarity in scolex morphology, the observation of plerocercoids buried in intestinal regions close to the sites where M. grimaldii and P. delphini occur, and the coexistence of all larval forms in the same individual hosts would support this hypothesis. Future molecular analysis may confirm it.

Anal Canal↗

A comprehensive evolutionary analysis based on nucleotide and amino acid sequences of the alpha- and beta-subunits of glycoprotein hormone gene family.

On the basis of nucleotide sequences of the coding region and their predicted amino acid sequences, 58 glycoprotein hormone subunit genes were compared, aligned and used to construct phylogenetic trees for this family. The analysis included 17 alpha-subunits, eight TSH beta-, six FSH beta-, 17 LH beta/CG beta-, four fish gonadotropin (GTH)-I beta-, five fish GTH-II beta- and one additional fish GTH beta-subunit. The reliability of the phylogenetic trees was probed with the bootstrapping test. Our results indicated that: both the alpha- and beta-subunits of the family diverged from a common ancestral gene about 927 million years ago, the initial precursor of the beta-subunit duplicated to give rise to the LH beta and a second hormone, the latter then duplicating to FSH beta and TSH beta, so that FSH beta is related more to TSH beta than to LH beta; and bony fish GTH-I beta is highly related to mammalian FSH beta, whereas the bony fish GTH-II beta is more related to mammalian LH beta. For scientific consistency and convenience, we propose that the following nomenclature be adopted, all fish gonadotropins of type I be classified as FSH and all type II be classified as LH hormones. In addition, on the basis of results from this and other studies, we propose an evolutionary history for this glycoprotein hormone family. Reconstruction of the evolutionary history of this family would not only provide clues to understanding thyrotropin and gonadotropin functions, but would also allow further revision of the present nomenclature of the gonadotropins in fish.

Amino Acid Sequence↗

Shared Genetic Basis, Biological Function and Causal Relationship Between Sleep Traits and Hypothyroidism: Evidence from a Comprehensive Genetic Analysis.

BACKGROUND: This research attempts to clarify whether there are any genetic similarities between sleep traits and hypothyroidism based on publicly accessible large-scale genomewide association studies. METHODS: The methodology included colocalization analysis, cross-phenotype association analysis, and linkage disequilibrium score regression analysis to find common genetic overlap. Through tissue function specificity and functional mapping, we were able to identify the shared genetic level. Genetic instrumental factors were used for causal inference in two-sample univariate and multivariable Mendelian randomization analyses. RESULTS: A hereditary correlation between hypothyroidism and napping during the day and getting up in the morning (rg= -0.0982, P= 0.0007; rg= -0.101, P= 0.0001). MAGI3, and HLA-DRB1 BX296568.1 may be potential targets for shared treatments. Colocalization and tissue-specific analysis demonstrated that the common genes and SNPs were identified in the thyroid, lung, brain, and lymphatic tissues. Functional analysis emphasized the importance of these common genes in processes like as protein transport, inflammatory response, and MHC class II protein synthesis. Furthermore, an association has been established between hypothyroidism and sleep duration (IVW, OR 1.5208; 95% CI 1.1142-2.0758, P=0.0082) and getting up in the morning (IVW, OR 1.8375; 95%CI: 1.4502-2.3284, P=4.73E-07). Furthermore, the reverse MR analysis revealed no causal connection between aberrant sleep traits and hypothyroidism. The enduring impact of insomnia on hypothyroidism persists despite controlling for alcohol consumption and smoking habits. CONCLUSION: Certain genetic correlations between sleep traits and hypothyroidism have been emphasized. These findings may elucidate the origin of comorbidity and have implications for future clinical trials.

Humans↗

Comprehensive genotypic analysis of human prostate cancer cell lines and sublines derived from metastases after orthotopic implantation in nude mice.

We recently reported on a prostate cancer progression model which was based on repeated orthotopic implantation of human prostate cancer cell lines into athymic nude mice leading to an increase of tumor cell aggressiveness. To assess progression-associated clonal evolution of genotypic changes, we now performed comparative cytogenetic characterization of the original cell lines DU145 and PC3 with derived sublines DU145MN1 and PC3-N. Cell line PC3-125-1L, isolated from a lung metastasis after subcutaneous inoculation of PC3 into nude mice, was included in the study. Whole-genome analysis was performed using spectral karyotyping and comparative genomic hybridization. Fluorescence in situ hybridization was used to assess amplification of selected genes, which are supposed to play a role in prostate cancer progression. Differences in the genetic constitution between parental cell lines and sublines involved gains of genetic material at 2q, 5q, 12p/q, and 18p as well as losses at 6p, 7q, 17p, 18q, and 22q. Loss of 17p in DU145MN1 and high-level amplification of MYC in PC3-125-1L resulted in loss of p53 expression and upregulation of Myc expression, respectively, as was assessed by Western blotting. Thus, the nude mice model is very useful to follow clonal evolution of genetic changes during increase of prostate cancer aggressiveness and possibly to clone genes associated with the progression of prostate cancer.

Animals↗

[Theoretical analysis on comprehensive national power for sustainable development].

The connotation of comprehensive national power (CNP) was studied, the relationships between CNP and other related notions were comparatively analyzed, and the process for the study of CNP was reviewed. Based on the principles of sustainable development and the idea of ecosystem services, the concept of comprehensive national power for sustainable development (CNPSD) was proposed, and the main significance of CNQSD was discussed.

China↗