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Identification of macromolecular complexes in cryoelectron tomograms of phantom cells.

Electron tomograms of intact frozen-hydrated cells are essentially three-dimensional images of the entire proteome of the cell, and they depict the whole network of macromolecular interactions. However, this information is not easily accessible because of the poor signal-to-noise ratio of the tomograms and the crowded nature of the cytoplasm. Here, we describe a template matching algorithm that is capable of detecting and identifying macromolecules in tomographic volumes in a fully automated manner. The algorithm is based on nonlinear cross correlation and incorporates elements of multivariate statistical analysis. Phantom cells, i.e., lipid vesicles filled with macromolecules, provide a realistic experimental scenario for an assessment of the fidelity of this approach. At the current resolution of approximately 4 nm, macromolecules in the size range of 0.5-1 MDa can be identified with good fidelity.

Algorithms↗

Effect of fetal brainsparing on the early neonatal cerebral circulation.

The effect of antenatal brainsparing on subsequent neonatal cerebral blood flow velocity (CBFV) was studied in very preterm infants. CBFV was determined, using a pulsed Doppler technique, both in the fetal and neonatal period. Neonatally, blood pressure and transcutaneous carbon dioxide tension (TcPCO2) was monitored simultaneously; daily cranial ultrasound examinations were performed. In infants with evidence of brainsparing a higher mean value of CBFV and a different pattern of changes of CBFV during the first week of life was demonstrated compared with infants with normal fetal cerebral haemodynamics. No differences were found in blood pressure and TcPCO2. The incidence of intracranial haemorrhages and of ischaemic echo-dense lesions was also the same for both groups. In a multivariate statistical model gestational age, antepartum brainsparing, and TcPCO2 all contributed significantly in explanation of variation in CBFV. It is speculated that a different setting of cerebral autoregulation related to differences in gestational age or to brainsparing might explain the difference in changes found in neonatal CBFV.

Blood Flow Velocity↗

Hepatitis C virus genotypes and risk of hepatocellular carcinoma in cirrhosis: a prospective study.

A prospective study was performed to establish whether infection with specific hepatitis C virus (HCV) genotypes was associated with an increased risk of development of hepatocellular carcinoma (HCC) in cirrhosis. A cohort of 163 consecutive hepatitis C virus antibody (anti-HCV)-positive cirrhotic patients was prospectively evaluated for the development of HCC at 6-month intervals by ultrasound (US) scan and alpha-fetoprotein (AFP) concentration. HCV genotypes were determined according to Okamoto. Risk factors associated with cancer development were analyzed by univariate and multivariate statistics. At enrollment, 101 patients (62%) were infected with type 1b, 48 (29.5%) were infected with type 2a/c, 2 (1.2%) were infected with type 3a, 1 (0.6%) was infected with type 1a, 3 (1.8%) had a mixed-type infection, and, in 8 patients (4.9%), genotype could not be assigned. After a 5- to 7-year follow-up (median, 68 months), HCC developed in 22 of the patients, 19 infected with type 1b and 3 with type 2a/c (P < .005). Moreover, HCC developed more frequently in males (P < .01), patients with excessive alcohol intake (P < .01), those over 60 years of age (P < .02), and in patients who did not receive interferon treatment (P < .02). Multivariate analysis showed that type 1b was the most important risk factor associated with tumor development (odds ratio 6.14, 1.77-21.37 95% confidence interval). Other independent risk factors were older age and male sex. Cirrhotic patients infected with HCV type 1b carry a significantly higher risk of developing HCC than patients infected by other HCV types. The latter may require a less intensive clinical surveillance for the early detection of neoplasia.

Adult↗

Inflammatory biomarkers for persistent fatigue in breast cancer survivors.

PURPOSE: This study seeks to define immunologic and inflammatory variables associated with persistent post-treatment fatigue in breast cancer survivors. EXPERIMENTAL DESIGN: Leukocyte subsets, plasma inflammatory markers, and ex vivo proinflammatory cytokine production were assessed in 50 fatigued and nonfatigued breast cancer survivors recruited > or = 2 years after successful primary therapy. Multivariate statistical analyses were used to define a composite immunologic biomarker of fatigue risk. RESULTS: Fatigued breast cancer survivors were distinguished from nonfatigued survivors by increased ex vivo monocyte production of interleukin (IL)-6 and tumor necrosis factor-alpha following lipopolysaccharide stimulation, elevated plasma IL-1ra and soluble IL-6 receptor (sIL-6R/CD126), decreased monocyte cell-surface IL-6R, and decreased frequencies of activated T lymphocytes and myeloid dendritic cells in peripheral blood (all P < 0.05). An inverse correlation between sIL-6R and cell-surface IL-6R was consistent with inflammation-mediated shedding of IL-6R, and in vitro studies confirmed that proinflammatory cytokines induced such shedding. Multivariate linear discriminant function analysis identified two immunologic markers, the ratio of sIL-6R to monocyte-associated IL-6R and decreased circulating CD69+ T lymphocytes, as highly diagnostic of fatigue (P = 0.0005), with cross-validation estimates indicating 87% classification accuracy (sensitivity = 0.83; specificity = 0.83). CONCLUSION: These results extend links between fatigue and inflammatory markers to show a functional alteration in proinflammatory cytokine response to lipopolysaccharide and define a prognostic biomarker of behavioral fatigue.

Biomarkers↗

Variation in cuticular hydrocarbons among strains of the Anopheles gambiae sensu stricto by analysis of cuticular hydrocarbons using gas liquid chromatography of larvae.

Cuticular hydrocarbons of larvae of individual strains of the Anopheles gambiae sensu stricto were investigated using gas liquid chromatography. Biomedical discriminant analysis involving multivariate statistics suggests that there was clear hydrocarbon difference between the Gambian(G3), the Nigerian (16CSS and, its malathion resistant substrain, REFMA) and the Tanzanian (KWA) strains. The high degree of segregation (95%) in hydrocarbons among the four strains investigated indicates that further analysis is needed to enable understanding of hydrocarbon variation in samples of An. gambiae especially from areas where these populations co-exist.

Animals↗

[A mathematical analysis of the flow-velocity curves in the femoral arteries].

In order to improve the early diagnosis of the aortoiliac injuries, 98 arteries from several supposedly health patients (different ages) and 41 femoral arteries from patients with occlusion at this level (demonstrated by arteriography) were studied. The analysis from the Fourier's series showed highly significant differences between both groups, and so did the comparison of some indexes automatically measured by the Vasoscan VL equip. By multivariant statistics methods was selected the main group of parameters that allows the differentiation between the ill patients and the healthy ones. This procedure can be useful for the physiopathological study and it may be used as a non-invasive method of diagnosis.

Adult↗

Clinical course and risk factors of hepatitis C virus related liver disease in the general population: report from the Dionysos study.

BACKGROUND: The severity, clinical course, and risk of hepatitis C virus (HCV) related chronic liver disease are still rather poorly defined. AIMS: To investigate the prevalence, risk factors, and severity of HCV related liver disease in the general population, and investigate whether infection with a specific genotype is associated with an increased risk of cirrhosis or hepatocellular carcinoma. METHODS: HCV RNA determination by polymerase chain reaction (PCR) and HCV genotyping were performed in all anti-HCV positive subjects belonging to the Dionysos study (6917 subjects). Diagnosis of cirrhosis and hepatocellular carcinoma was established by liver biopsy in all cases. All the data were analysed by univariate and multivariate statistics in all the cohort. To investigate the natural history of HCV infection, anti-HCV positive subjects were followed up every six months for three years with liver function tests and ultrasonograms. RESULTS: The overall prevalence of HCV RNA positivity was 2.3%. Positivity increased progressively with age, and was higher in women (ratio of men to women = 0.7). Genotypes 1b and 2a were the most frequent (42 and 24% of HCV RNA positive patients), with a prevalence of 1 and 0.6% respectively. Intravenous drug use, blood transfusions received before 1990, history of previous hepatitis among the cohabiting, and history of animal (mainly dogs) bites were significantly (p<0.05) associated with HCV infection, independently of age and sex. Multivariate analysis showed that, independently of age, sex, and alcohol intake, genotype 1b infection, with or without coinfection with other genotypes, is the major risk factor associated with the presence of cirrhosis and/or hepatocellular carcinoma. During the three years of follow up, 57 (35%) of the HCV RNA positive subjects had consistently normal alanine aminotransferase and gamma-glutamyltransferase values. Two of the 22 HCV RNA positive cirrhotic patients, all drinking more than 90 g of alcohol a day, developed hepatocellular carcinoma (incidence rate = 3.0% per year). CONCLUSIONS: In the general population of Northern Italy, HCV infection is widespread, but only less than 50% of the anti-HCV positive subjects, particularly those infected with genotype 1b, are associated with a more severe liver disease. Alcohol consumption greater that 30 g a day significantly aggravates the natural course of the disease.

Adolescent↗

The ECOMAN project: A novel approach to defining sustainable ecosystem function.

The ECOMAN was initiated in 2001 by the University of Plymouth, UK, Plymouth Marine Laboratory and the Department of the Environment, Fisheries and Rural Affairs (DEFRA) to address the need for more pragmatic assessment techniques linking environmental degradation with its causes. The primary aim of the project was to develop an evidence-based approach in which suites of easy-to-use, cost-effective and environmentally valid biological responses (biomarkers) could be used together to assess the health of coastal systems through the general condition of individuals. A range of sub-lethal endpoints, chosen to reflect successive levels of biological organisation (molecular, cellular, physiological), was evaluated in common coastal organisms showing different feeding types (filter feeding, grazing, predation) and habitat requirements (estuary, rocky shore). Initially, the suite of biomarkers was used in laboratory studies to determine the relative sensitivities of key species within different functional groups to common contaminants. These results were then validated in field studies performed in a range of ecosystems exhibiting different degrees/signatures of contamination. Here, an example is provided of a field study in the Humber Estuary, UK, which illustrates how multivariate statistical analysis can be used to identify patterns of response to discriminate between contaminated and clean sites. The use of a holistic, integrated approach of this kind is advocated as a practical means of assessing the impact of chemical contamination on organismal health and of ranking the status of marine ecosystems.

Animals↗

Analysis of autoantibody repertoires in sera of patients with glaucoma.

PURPOSE: Glaucoma is the second cause of blindness worldwide. It is usually considered a neurodegenerative disease. There is evidence that an autoimmune mechanism is involved in the development of glaucoma in some patients. The aim of this study was to analyze the IgG autoantibody repertoires in sera of glaucoma patients and healthy subjects. METHODS: A total of 82 patients were divided into four groups: healthy volunteers without any ocular disorders (CO, n = 30), patients with primary open-angle glaucoma (POAG, n = 19), ocular hypertension (OHT, n = 16), and normal tension glaucoma (NTG, n = 17). All groups were matched for age and gender. The sera of these patients were tested against Western blots of retinal antigens. Immunodetection was done using 4-chloro-1-naphthol staining. The autoantibody patterns were digitized and subsequently analyzed by multivariate statistical techniques. RESULTS: All patients showed different, complex staining patterns of autoantibodies against retinal antigens. There was an increase in the number of peaks in sera of patients with primary open-angle glaucoma (POAG) compared to healthy subjects (CO). Including all peaks the analysis of discriminance revealed a statistically significant difference between the patterns of POAG compared to all other groups (p < 0.01). Sera of normal tension glaucoma (NTG) had no statistically different autoantibody pattern compared to those of control subjects. CONCLUSIONS: In this study, we demonstrated a difference in the IgG autoantibody patterns of primary open-angle glaucoma patients compared to healthy subjects. However, the patterns were not significantly different in normal tension glaucoma compared to control subjects.

Aged↗

Factors associated with tumor volume and primary metastases in Ewing tumors: results from the (EI)CESS studies.

BACKGROUND: Tumor volumes of more than 100 ml and the presence of primary metastases have been identified as determinants of poor prognosis in patients with Ewing tumors. We sought to assess the prevalence of critical tumor size and primary metastases in a large national sample of patients at the time of first diagnosis and to identify factors that are associated with their occurrence. PATIENTS: The present report is based on data of 945 German patients who were enrolled into the (EI)CESS therapy studies between 1980 and 1997. It is assumed that registration of German patients with Ewing tumors under the age of 15 years was almost complete since around 1985. Diagnoses of primary tumors were ascertained exclusively by biopsies. Analyses were restricted to patients with Ewing tumors of bone due to the few occurrences in soft tissues. METHODS: Tumor volume data as assessed by radiography, computed tomography or nuclear magnetic imaging were available for 821 patients. The diagnosis of primary metastases was based on thoracic computed tomography or on whole body bone scans in 936 patients. Suspicious lesions had to be confirmed by bone marrow biopsies. We explored how year of first diagnosis, age at first diagnosis, sex, histological subtype and site of the primary tumor related to tumor size and presence of metastases by univariate and multivariate statistical techniques. RESULTS: Sixty-eight percent of the patients (n = 559) had a volume above 100 ml with smaller tumors being more common in childhood than in late adolescence and early adulthood. Extensive volumes were observed in almost 90% of the tumors located in femur and pelvis while they were less common in other sites (P < 0.001). On average, 26% of all patients presented with clinically apparent primary metastases. The detection rate of metastases was markedly higher in patients diagnosed after 1991 (P < 0.001). Primary metastases were also significantly more common for tumors originating in the pelvis and for peripheral neuroectodermal tumors (PNET; P < 0.01). Tumors greater than 100 ml were positively associated with metastatic disease (P < 0.001). Multivariate analyses, which included simultaneously all univariate predictors in a logistic regression model, indicated that most of the observed associations were essentially unconfounded. The adjusted odds ratios (OR) for the presence of tumor volumes > or = 100 ml were OR = 1.5 per age rise of 10 years, and OR = 5.8 for pelvis and OR = 7.1 for femur as primary tumor site (all P < 0.001). The presence of metastases was significantly associated with the year of diagnosis (OR = 1.9, after 1991 vs. before 1986), pelvis as site of the primary tumor (OR = 1.8), a PNET (OR = 1.5), and tumor size > or = 100 ml (OR = 1.6). CONCLUSIONS: In conclusion, we find that the prevalence of established factors for an unfavorable prognosis is disturbingly high among patients diagnosed with Ewing tumors. Recent progress in imaging techniques seems to account for much of the rise in the detection rate of metastases after 1991. We identify age and, in particular pelvic and femoral site as the major determinants of local tumor extension. Occurrence of primary metastases is independently related to tumor size, pelvic site, and PNET.

Adolescent↗

Nationwide survey of the role of travel medicine in primary care in Germany.

BACKGROUND: With more persons traveling to (sub)tropical destinations, travel medicine is an increasing challenge for the health care system in many countries. This study investigated the role and scope of travel medicine provided by general practitioners (GPs) in primary health care, assessed the determinants of specific prophylactic recommendations, and identified the needs of GPs regarding training and cooperation in travel medicine. METHODS: A national survey was conducted among randomly selected GPs in Germany. Information on the type and extent of activities in travel medicine, the number and characteristics of patients, the use of specific information systems, and training and cooperation, was obtained with a standardized postal questionnaire. Representativeness was assessed by a computer-assisted telephone survey among nonrespondents. Univariate and multivariate statistical analysis was performed. RESULTS: Of all GPs (n=1,320), 95% provided medical pretravel advice or post-travel counseling (13.2 patients/month). The most common topics in pretravel consultation were immunizations (95%), malaria chemoprophylaxis (94%), advice on exposure prophylaxis (41%), and advice on protection from sexually transmitted infections (STIs) (43%). GPs frequently advised certain patient groups (e.g., cardiovascular patients 68%, pregnant women 20%). Travelers' diarrhea was the most common topic in post-travel consultation (89%), followed by fever (38%). Of the GPs, 25% cooperated regularly with institutions with special expertise in travel medicine or tropical diseases. Sixty-four percent had received some training in travel medicine, and 86% stated a need for additional training. In the multivariate analysis, independent determinants for advice on exposure prophylaxis and STI risks included special training in travel medicine, use of country-specific information sources, and location of the practice in the former West Germany and urban areas. CONCLUSIONS: Travel medicine is of importance in primary health care in Germany. There is a need for improved counseling on exposure and STI prophylaxis. GPs' training in travel medicine and cooperation with institutions such as institutes, clinics and laboratories for tropical medicine should be improved.

Adult↗

Direct continuous supercritical fluid extraction as a novel method of wine analysis. Comparison with conventional indirect extraction and implications for wine variety identification.

Direct supercritical fluid extraction (SFE) of wines with carbon dioxide was compared to SFE of the sorbent used for solid-phase extraction of the same wine samples (SPE-SFE). Compared to SPE-SFE, the direct SFE results in amore specific and representative gas chromatographic fingerprint of the wine sample. The multivariate statistical processing of the direct SFE-GC data provides a clear-cut and sharp discrimination among the individual wine varieties while the discrimination based on the SPE-SFE-GC data is relatively poor. This finding reflects the adverse effects of additional analyte-sorbent interactions and sorption/desorption steps involved in SPE-SFE.

Chromatography, Supercritical Fluid↗

Mass spectrometry-based metabolic profiling reveals different metabolite patterns in invasive ovarian carcinomas and ovarian borderline tumors.

Metabolites are the end products of cellular regulatory processes, and their levels can be regarded as the ultimate response of biological systems to genetic or environmental changes. We have used a metabolite profiling approach to test the hypothesis that quantitative signatures of primary metabolites can be used to characterize molecular changes in ovarian tumor tissues. Sixty-six invasive ovarian carcinomas and nine borderline tumors of the ovary were analyzed by gas chromatography/time-of-flight mass spectrometry (GC-TOF MS) using a novel contamination-free injector system. After automated mass spectral deconvolution, 291 metabolites were detected, of which 114 (39.1%) were annotated as known compounds. By t test statistics with P < 0.01, 51 metabolites were significantly different between borderline tumors and carcinomas, with a false discovery rate of 7.8%, estimated with repeated permutation analysis. Principal component analysis (PCA) revealed four principal components that were significantly different between both groups, with the highest significance found for the second component (P = 0.00000009). PCA as well as additional supervised predictive models allowed a separation of 88% of the borderline tumors from the carcinomas. Our study shows for the first time that large-scale metabolic profiling using GC-TOF MS is suitable for analysis of fresh frozen human tumor samples, and that there is a consistent and significant change in primary metabolism of ovarian tumors, which can be detected using multivariate statistical approaches. We conclude that metabolomics is a promising high-throughput, automated approach in addition to functional genomics and proteomics for analyses of molecular changes in malignant tumors.

Cluster Analysis↗

The relationship between self-efficacy and student physician assistant clinical performance.

The purpose of this study was to investigate the predictive relationship between student self-efficacy beliefs, achievement expectations, perceived outcome values, and subsequent clinical performance. The study investigated whether measures of self-efficacy, measures of achievement expectancy, or measures of perceived task value (relevance) correlated significantly with physician assistant clinical performance; also, it investigated whether utilizing both noncognitive criteria and cognitive criteria will improve upon the predictability of physician assistant clinical performance. The independent variables include grade point average, previous health care experience, self-efficacy, values, and outcome expectations. The research population comprised a group of approximately 300 students attending the 14 accredited programs within Pennsylvania who, at the time of the surveys, were beginning the clinical year of their professional education. Data collection methods included surveys and quantitative data sources. The data were subjected to multivariate statistical methods including multiple regression and discriminate analysis. The analysis included both correlation and regression to predict clinical performance from the noncognitive and cognitive variables. The results reveal that self-efficacy, and not just academic performance, is a significant predictor of a student's clinical performance. Utilizing both noncognitive and cognitive variables can improve upon the predictability of the student physician assistant's clinical performance.

Achievement↗

Risk factors for congestive heart failure after aortic valve replacement with a Carpentier-Edwards pericardial prosthesis in the elderly.

BACKGROUND AND AIM OF THE STUDY: Congestive heart failure (CHF) after aortic valve replacement (AVR) is an important cause of morbidity. The study aim was to identify preoperative risk factors for CHF. METHODS: A total of 500 consecutive patients (271 males, 229 females; median age 73 years; range: 71-77 years) was investigated retrospectively. The AVR was performed using a Carpentier-Edwards pericardial valve, and a total of 348 additional procedures (313 coronary artery bypass grafts; CABG) was carried out. The outcome studied was CHF, during both hospital stay and long-term follow up. Univariate and multivariate statistical analyses were used to investigate 15 risk factors. RESULTS: During the hospital stay, 13 patients developed CHF, with four fatalities. Significant risk factors for CHF included urgent operation (p = 0.031), preoperative atrial fibrillation (AF) (p = 0.031) and NYHA functional class IV (p = 0.05). A logistic regression analysis revealed need for urgent operation (p = 0.034) as the sole factor. During long-term follow up, 43 patients developed CHF, with seven fatalities. Univariate analysis identified seven risk factors with significant effect: valve size <19 mm (p = 0.004), preoperative conduction defects (p = 0.007), chronic postoperative AF (p = 0.013), cross-clamp time >75 min (p = 0.032), NYHA class IV (p = 0.041), coronary artery disease (CAD) (p = 0.043) and additional CABG (p = 0.050). Multivariate analysis identified three risk factors: preoperative conduction defects (p = 0.004), postoperative AF (p = 0.005) and CAD (p = 0.037) CONCLUSION: Morbidity due to CHF after AVR could be minimized with correct treatment of AF and of conduction defects. Patient age, valve size, cross-clamp time and preoperative severity or symptoms were not independent risk factors. Moreover, small native aortic valve rings should not necessarily be enlarged, the cross-clamp time should be kept to a minimum, and surgery should not be delayed when symptoms have developed.

Aged↗

Prognostic factors of nosocomial pneumonia in general wards: a prospective multivariate analysis in Japan.

To determine prognostic factors of nosocomial pneumonia in general wards, we performed prospective clinical study using multivariate statistical analysis. Eighty patients with nosocomial pneumonia in our units were enrolled in the study between December, 1996 and January 1998. Clinical setting and severity of pneumonia were evaluated, and laboratory data were collected at the occurrence of nosocomial pneumonia. Death due to nosocomial pneumonia occurred in 29 of 80 patients (mortality rate 36%). Univariate analysis showed the following factors associated with mortality: the presence of an ultimately or rapidly fatal underlying condition, prior antibiotics use, use of antacids, presence of 'high-risk' micro-organisms, sepsis, respiratory failure, multiple organ failure, bilateral chest X-ray infiltrates, a Simplified Acute Physiology Score (SAPS) index > or = 11, albumin < 3.0 g dl(-1), and lactate dehydrogenase (LDH) > or = 796 IUI(-1). Furthermore, multivariate analysis identified three factors significantly associated with mortality: the presence of an ultimately or rapidly fatal underlying condition [odds ratio (OR)=7.0; 95% confidence interval (CI)=1.2-41.1; P=0.03]; SAPS index > or = 11 (OR=7.6; 95% CI=1.1-51.9, P=0.04); LDH > or = 796 IUI(-1) (OR=28.2; 95% CI=2.0-406, P=0.01). Our study indicates that host factors and disease severity factors are important prognostic factors of nosocomial pneumonia in general wards.

Aged↗

Married women's dissatisfaction with tubal sterilization and vasectomy at first-year follow-up: effects of perceived spousal dominance.

Examination of first-year follow-up data obtained from 234 tubal ligation women and 154 vasectomy wives indicated a very low incidence of actual regret in both groups. However, use of a broader measure of satisfaction/dissatisfaction indicated that tubal ligation women had significantly more positive feelings about the sterilization decision than did vasectomy wives. Results of a series of multivariate statistical analyses demonstrated that group differences in satisfaction were related to (1) the disproportionate prevalence of perceived male control (particularly extensive control) over reproductive decisions among vasectomy wives and the negative effect it had upon subjects in both groups and (2) the disproportionate prevalence of female control over reproductive decision-making among tubal ligation women and the positive effect it had among subjects in this group. Study results point to the importance of couple counseling and exercising control over one's own body.

Adult↗

137Cs in freshwater fish in Finland since 1986--a statistical analysis with multivariate linear regression models.

The accident at the Chernobyl nuclear power plant in 1986 significantly elevated the 137Cs levels of fish in Finnish lakes. About 6200 fish samples from 390 lakes comprising 20 species have been analysed for 137Cs since 1986. The sizes of the lakes varied from a few hectares to about 1000 km2. Activity concentrations of 137Cs in fish still varied widely in 2003, from 16 to 6400 Bq/kg fresh weight. This paper presents the results of statistical analyses with multivariate linear regression models carried out on the empirical data collected since 1986. The statistical analysis resulted in separate models for two time periods describing temporal changes of 137Cs in fish. The explanatory variables were fish species with various feeding habits, the size class of the lake, municipal division, drainage area, time since the deposition and deposition level of the municipality. The calculated values for 137Cs in fish did not differ statistically significantly from the observed values in the validation data. The explanatory variables explained 58% (the first time period) and 72% (the second time period) of the total variability of 137Cs in fish.

Animal Feed↗