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PubMed2004

Angiographic and hemodynamic predictors for successful outcome of transcatheter occlusion of patent ductus arteriosus in infants less than 8 kilograms.

Transcatheter occlusion of patent ductus arteriosus (PDA) using Gianturco coils (GCs) has been performed for the past decade. However, little has been written regarding anatomical and hemodynamic predictors for successful occlusion of the PDA in infants. This report is to evaluate the outcome of transcatheter occlusion of PDA in symptomatic infants less than 8 kg and to assess predictors of successful occlusion. Retrospective review of catheterization charts and cineangiograms of 42 symptomatic infants who underwent cardiac catheterization for attempted transcatheter occlusion of their PDA was conducted. The hemodynamic and angiographic data evaluated included the length/diameter (L/D) ratio, defined as the length divided by the narrowest diameter of the ductus arteriosus, and preocclusion pulmonary artery pressures. Thirty-one out of 42 patients (74%) had successful occlusion. Twenty-nine out of 42 infants had an L/D ratio > 3. Of these, 26 (90%) had successful occlusion of their PDA. Thirteen out of 42 patients had an L/D ratio < or = 3. Of these, 8 (62%) had unsuccessful occlusion. Complications encountered were transient loss of femoral arterial pulse (n = 6), coil embolization (n = 5), hemolysis (n = 2), and mild left pulmonary artery obstruction (n = 2). No permanent loss of femoral arterial pulse was noted. These complications resulted in no mortality and minimal morbidity. The L/D ratio was the strongest predictor of successful outcome, with an L/D ratio greater than 3.0 being more amenable to transcatheter occlusion (odds ratio of 4.6). Other predictors for success included lower preocclusion systolic, diastolic, and mean pulmonary artery pressure and smaller ductal diameter. Our conclusion was that infants less than 8 kg with an L/D ratio > 3.0 can safely and successfully undergo transcatheter occlusion of their PDA using transcatheter coils.

Body Weight↗

PubMed2007

Incidence and predictors of recurrent restenosis following implantation of drug-eluting stents for in-stent restenosis.

OBJECTIVES: We investigated the incidence and predictors of recurrent restenosis after drug-eluting stent (DES) implantation for in-stent restenosis (ISR) in routine clinical practice. BACKGROUND: Although DESs have been increasingly used for treatment of ISR, little is known about the predictors of DES failure. METHODS: We determined the incidence of recurrent restenosis and major adverse cardiac events (MACE) in 224 consecutive patients with 239 lesions treated with sirolimus-eluting (n=217 lesions) or paclitaxel-eluting (n=22 lesions) stents for the first episode of ISR. RESULTS: The procedural success rate was 99.2%, and in-hospital complications did not occur in any patient. Follow-up angiography at 6 months was obtained in 73.7% of patients. Angiographic re-restenosis rate was 12.6%, and target lesion revascularization was required in 7.6% of patients. Of the 22 incidents of re-restenosis, 15 were focal (68.2%), 5 were diffuse (22.7%), and 2 were total (9.1%) restenosis. Univariate analysis showed that lesion length, use of paclitaxel-eluting stent, and number of stents per lesion were significant predictors of re-restenosis. In multivariate analysis, however, lesion length and use of paclitaxel-eluting stent were independent predictors of re-restenosis. During the follow-up (mean, 18.3+/-8.1 months), there were 4 deaths (1 cardiac, 3 noncardiac), but no nonfatal myocardial infarctions (MIs). MACE occurred in 18 patients. The cumulative probability of MACE-free survival was 92.9+/-1.8% at 1 year and 90.5+/-2.4% at 2 years. CONCLUSIONS: DESs are highly effective for treatment of ISR, with recurrent restenosis related to lesion length and type of DES.

Chi-Square Distribution↗

PubMed2002

Investigation of the predictors of transition to persistent atrial fibrillation in patients with paroxysmal atrial fibrillation.

BACKGROUND: Until now, no clinically useful indicators have existed that predict the transition from paroxysmal to persistent atrial fibrillation (AF). HYPOTHESIS: The current prospective study was conducted for identifying predictors of progression to persistent AF over the long term. METHODS: We studied 102 consecutive patients (mean age: 55 +/- 10 years: 75 men and 27 women) diagnosed with paroxysmal AF. Standard 12-lead electrocardiography, echocardiography, and P-wave-triggered signal-averaged electrocardiography (P-SAECG) were performed on all patients at the time of their entry into the study. RESULTS: The mean follow-up period was 61 +/- 13 months. Group 1 (n = 66) comprised patients in whom paroxysmal AF did not progress to persistent AF, and Group 2 (n = 36) comprised those who developed persistent AF. In Group 2 the patients were significantly older, and P-wave dispersion, filtered P-wave duration (FPD), and left atrial dimension were significantly higher than in Group 1 (p < 0.05). The root mean square voltage for the last 30 ms of the filtered P-wave was also significantly lower in Group 2 (p < 0.05). Multivariate logistic regression analysis using these five factors identified left atrial dimension (odds ratio [OR] 2.29; 95% confidence interval [CI] 1.16-4.54; p = 0.02) and FPD (OR 2.71; 95% CI 1.78-4.13; p < 0.01) as independent predictors of transition to persistent AF. Left atrial dimension > or = 40 mm predicted progression to persistent AF with a sensitivity of 64%, specificity of 76%, positive predictive value of 59%, negative predictive value of 79%, and an accuracy of 71%. An FPD > or = 150 ms predicted persistent AF with a sensitivity of 81%, specificity of 91%, positive predictive value of 88%, negative predictive value of 90%, and an accuracy of 87%. Filtered P-wave duration was a significantly more sensitive and specific predictor than left atrial dimension (p < 0.05). CONCLUSION: We conclude that FPD is a clinically useful predictor of progression from paroxysmal to persistent AF over the long term.

Aged↗

PubMed2000

Intravascular ultrasound predictors of major adverse cardiac events in patients with unstable angina.

BACKGROUND: Intravascular ultrasound (IVUS) predictors of native culprit lesion morphology for occurrence of major adverse cardiac events (MACE) have not been reported. Moreover, the published data on IVUS predictors of restenosis include patients with stable and unstable angina, although the development and progression of atherosclerosis related to unstable coronary syndrome is different from that of stable angina. HYPOTHESIS: This study investigated whether IVUS-derived qualitative and quantitative parameters of native (preangioplastic) plaque morphologic features can predict major adverse cardiac events in patients with unstable angina. METHODS: Clinical (age, gender, coronary risk factors), qualitative and quantitative angiographic (lesion localization, morphology, pre- and postangioplastic minimal lumen diameter, reference diameter, and percent diameter stenosis), and IVUS variables (soft/fibrocalcific plaque, calcification, presence of thrombus or plaque disruption, different types of arterial remodeling, pre- or postangioplastic minimal lumen, external elastic membrane and plaque cross-sectional area, and plaque burden of the target lesion and reference segments) were analyzed by regression analyses using the Cox model, assuming proportional hazards. RESULTS: Of 60 consecutively enrolled patients, 21 suffered from MACE, while 39 remained event-free during the followup period. Multivariate regression analyses revealed that the presence of adaptive remodeling [p = 0.0177, risk ratio (RR) = 3.108, with 95% confidence interval (CI) = 1.371-8.289] and the preangioplastic lumen cross-sectional area (p = 0.0130, RR = 0.869, with 95% CI = 0.667-0.913) are independent predictors of MACE during follow-up, as is postangioplastic angiographic minimal lumen diameter (p = 0.0330, RR = 0.715 with 95% CI = 0.678-0.812). CONCLUSIONS: Adaptive remodeling and preangioplastic lumen cross-sectional area determined by IVUS and postangioplastic minimal lumen diameter calculated by quantitative angiography are significant independent predictors of time-dependent MACE in patients with unstable angina.

Angina, Unstable↗

PubMed2002

Lipoprotein(a) was an independent predictor for major coronary events in treated hypertensive men.

BACKGROUND AND HYPOTHESIS: Lipoprotein(a) may play a part in the development of coronary heart disease. The purpose of this prospective study was to evaluate lipoprotein(a) as a predictor of major coronary events (fatal and nonfatal myocardial infarction and sudden death). METHODS: This was a prospective study of 118 men, aged 56 to 77 years, with treated hypertension and at least one additional cardiovascular risk factor (hypercholesterolemia, diabetes mellitus, or smoking) were included in the study. Lipoprotein(a) was measured at entry and major coronary events were followed during follow-up. RESULTS: The mean observation time was 3.0 years. Fourteen patients had a major coronary event during the follow-up period. Subjects with coronary heart disease (previous myocardial infarction, angina pectoris, or major electrocardiographic changes) at entry (n = 27) had significantly higher lipoprotein(a) levels than subjects without (n = 91) known coronary heart disease (p < 0.05). Lipoprotein(a) was a significant predictor for major coronary events (p = 0.033). Furthermore, when coronary disease at entry was included into the Cox regression analysis, lipoprotein(a) was an independent predictor for major coronary events (p = 0.044). CONCLUSIONS: Among treated hypertensive men, lipoprotein(a) was an independent predictor of major coronary events.

Aged↗

PubMed2005

Predictors of systemic recurrence and disease-specific survival after ipsilateral breast tumor recurrence.

BACKGROUND: In patients with breast carcinoma, ipsilateral breast tumor recurrence (IBTR) after breast-conserving therapy (BCT) is an independent predictor of systemic recurrence and disease-specific survival (DSS). However, only a subgroup of patients with IBTR develop systemic recurrences. Therefore, the management of isolated IBTR remains controversial. The objective of the current study was to identify determinants of systemic recurrence and DSS after IBTR. METHODS: The medical records of 120 women who underwent BCT for Stage 0-III breast carcinoma between 1971 and 1996 and who subsequently developed isolated IBTR were reviewed. Clinicopathologic factors were studied using univariate and multivariate analyses for their association with DSS and the development of systemic recurrence after IBTR. RESULTS: The median time to IBTR was 59 months. At a median follow-up of 80 months after IBTR, 45 patients (37.5%) had a systemic recurrence. Initial lymph node status was the strongest predictor of systemic recurrence according to the a univariate analysis (P = 0.001). Other significant factors included lymphovascular invasion (LVI) in the primary tumor, time to IBTR < or = 48 months, clinical and pathologic IBTR tumor size > 1 cm, LVI in the recurrent tumor, and skin involvement at IBTR. In a multivariate logistic regression analysis, initially positive lymph node status (relative risk [RR], 5.3; 95% confidence interval [95% CI], 1.4-20.1; P = 0.015) and skin involvement at IBTR (RR, 15.1; 95% CI, 1.5-153.8; P = 0.022) remained independent predictors of systemic recurrence. The 5-year and 10-year DSS rates after IBTR were 78% and 68%, respectively. In a multivariate Cox proportional hazards model analysis, only LVI in the recurrent tumor was found to be an independent predictor of DSS (RR, 4.6; 95% CI, 1.5-14.1; P = 0.008). CONCLUSIONS: Patients who initially had lymph node-positive disease or skin involvement or LVI at IBTR represented especially high-risk groups that warranted consideration for aggressive, systemic treatment and novel, targeted therapies after IBTR. Determinants of prognosis after IBTR should be taken into account when evaluating the need for further systemic therapy and designing risk-stratified clinical trials.

Adult↗

PubMed2007

Cognitive and psychiatric predictors of medical treatment adherence among older adults in primary care clinics.

OBJECTIVES: Medical treatment non-adherence among older adults is common and represents a significant public health care concern. Treatment non-adherence has been associated with a number of factors in older adults; however few studies have delineated the role of cognition and psychiatric status. PARTICIPANTS: Data were collected from 212 ethnically diverse older primary care patients as part of a larger study. MEASUREMENTS: Cognitive status was evaluated with the Mattis Dementia Rating scale (DRS). Psychiatric status was evaluated using the Geriatric Depression Scale (GDS) and the Beck Anxiety Inventory (BAI). Treatment adherence was assessed by the total number of missed healthcare appointments and by physician and patient ratings. Physician ratings of patients' understanding of medical instructions were also obtained. DESIGN: A series of multiple regression analyses were conducted to determine cognitive and psychiatric predictors for each measure of treatment adherence. RESULTS: GDS and DRS memory scores were both independent predictors of the total number of missed medical appointments, F(7,55) = 2.34, p = 0.038. GDS score was also shown to be a significant predictor of physician ratings of patients' understanding of medical instructions, F(7,33) = 0.89, p = 0.031. Neither cognitive performance nor psychiatric status was associated with patient or physician ratings of treatment adherence. CONCLUSIONS: Measures of cognitive functioning and depression severity were supported as predictors of objective measures of treatment adherence but they were not associated with physician or patient ratings of adherence. Patient depression may influence physician ratings of patients' comprehension of medical instructions.

Aged↗

PubMed2002

Predictors of institutionalization in patients with dementia in Korea.

BACKGROUND: Many studies have sought to determine the predictors of institutionalization of patients with dementia. Such studies, performed in developed western societies, have come to various conclusions which may not be supported in an East Asian culture such as that found in Korea. OBJECTIVES: This study aimed to determine the factors that predict institutionalization of patients in Korea diagnosed with dementia. METHODS: Seventy-nine cases (37 institutionalized, 42 community-dwelling) in the Kwangju area were evaluated for patient characteristics, severity of dementia symptoms, caregiver characteristics, burden and distress. Logistic regression was performed to determine predictors of actual institutionalization. RESULTS: Six predictors of institutionalization were identified. Of these, three were patient-related factors: higher score on the Clinical Dementia Rating, higher score on the Brief Psychiatric Rating Scale, and shorter duration of dementia. The other three were caregiver-related factors: younger age, higher education (formal schooling), and higher cost of home care. CONCLUSIONS: As seen in previous western studies, institutionalization of dementia sufferers was influenced by both patient and caregiver factors. But, the specific predictors and their relative influences might be explained best by the particular social, cultural and economic situation in Korea. This study was the first of its kind in Korea and, as such, could serve as a reference for future intra-cultural and cross-cultural comparisons.

Aged↗

PubMed2002

Course of minimal dementia and predictors of outcome.

BACKGROUND: Previous studies have indicated that not all subjects who meet the CAMDEX criteria of 'minimal dementia' progress to dementia. In the present study, predictors of outcome in minimally demented subjects were tested. METHODS: Forty-five subjects with minimal dementia who were participating in a population-based study were followed-up for on average 2.3 years. Variables tested as predictors of outcome were age, the apolipoprotein E (APOE) genotype, and the baseline scores on the MMSE, CAMCOG memory subscale, and fluency. Depression at baseline was tested as a predictor of reversible minimal dementia. RESULTS: At follow-up, minimal dementia turned out to be reversible in 11 subjects (24%), and persistent in ten subjects (22%). Twenty-four subjects (53%) had become demented. Predictors of outcome in multivariate analyses were age, score on the CAMCOG memory subscale, and the APOE genotype. Depression was not associated with reversible minimal dementia. CONCLUSIONS: Subjects who meet the CAMDEX criteria of minimal dementia form a heterogenous group with respect to clinical outcome. Age, the score on the CAMCOG memory subscale, and the APOE genotype can improve predictive accuracy in these subjects.

Aged↗

PubMed2003

Possible predictors of response to fluvoxamine for depression.

INTRODUCTION: An investigation of the characteristics of patients being treated with antidepressants would seem to be useful in determining which patients would be most likely benefit from antidepressant medication. AIMS: The purpose of this preliminary study was to examine the possible predictors of response to fluvoxamine for depression. METHOD: A retrospective cohort analysis was carried out among depression patients treated in the Department of Psychiatry, Kawasaki Medical School Hospital, Kurashiki, Japan, in 2000. Seventy two patients were identified who were receiving fluvoxamine to treat depression. RESULTS: A variety of clinical factors including age, gender, type of depression, frequency of episodes, family history and daily dose of fluvoxamine were examined as possible predictors of the response to fluvoxamine. A Weibull regression analysis showed age, frequency of episodes and daily dose to be the independent predictive factors of improvement in fluvoxamine treatment. The most influential factor was age (ecoef = 2.109), followed by daily dose (ecoef = 0.648) and frequency of episode (ecoef = 0.512). An age of 49 years or younger (chi(2) = 6.767, df = 1, p = 0.0093), a first episode (chi(2) = 9.079, df = 1, p = 0.0026) and a daily dose of 100-150 mg (chi(2) = 5.353, df = 1, p = 0.02) were significantly better predictors of improvement. CONCLUSIONS: Age, the frequency of episodes and the daily dose of fluvoxamine may be considered as predictors of the response to fluvoxamine treatment for depression. This result should be examined in future prospective study.

Adolescent↗

PubMed2002

P53 is the strongest predictor of survival in high-risk primary breast cancer patients undergoing high-dose chemotherapy with autologous blood stem cell support.

Our purpose was to determine the predictive value of tumor biologic parameters in patients with HRPBC who received HDCT with ASCT as first-line treatment. From September 1992 to May 2000, 149 stage II or III HRPBC patients were enrolled in a single-arm trial using a tandem HDCT regimen followed by ASCT. Her2/neu, p53, Ki67 and bcl-2 protein expression was studied using immunohistochemic staining on formalin-fixed, paraffin-embedded primary tumor sections. DNA content of tumor cells (DNA index) and tumor cell proliferation (SPF) were measured by DNA flow cytometry. The relationship between these tumor biologic parameters, on the one hand, and DFS, DDFS and OS, on the other, was analyzed. With a median follow-up of 43 months (range 7-106), p53 protein accumulation (p = 0.000004), negative combined hormone receptor status (p = 0.003) and Her2/neu overexpression (p = 0.02) were significant negative predictors of OS in univariate analysis. A poorer DFS was associated with p53 positivity (p = 0.04) and nodal ratio > or = 0.8 (p = 0.008). Poorer DDFS was associated with p53 positivity (p = 0.03). In multivariate analysis, Her2/neu overexpression (RR = 3.86, 95% CI 1.48-10.1, p = 0.006) and p53 overexpression (RR = 6.06, 95% CI 2.22-16.52, p < 0.001) proved to be independent predictors of adverse OS. p53 overexpression was the only independent predictor of DFS (RR = 2.21, 95% CI 1.07-4.57, p = 0.03). p53 overexpression and Her2/neu overexpression are independent negative predictors of survival in HRPBC treated with HDCT. The adverse impact of these biologic features was probably not altered by HDCT. For HRPBC patients with tumors not overexpressing Her2/neu or p53, HDCT may be an appropriate approach to achieve long-term survival and tumor control.

Adult↗

PubMed1999

Racial differences in metabolic predictors of obesity among postmenopausal women.

OBJECTIVE: This study determined whether there are racial differences in resting metabolic rate (RMR), fat oxidation, and maximal oxygen consumption (VO2max) in obese [body mass index (BMI = 34+/-2 kg/m2)], postmenopausal (58+/-2 years) women. RESEARCH METHODS AND PROCEDURES: Twenty black and 20 white women were matched for fat mass and lean mass (LM), as determined by dual energy X-ray absorptiometry. RMR and fat oxidation were measured by indirect calorimetry in the early morning after a 12-hour fast using the ventilated hood technique. VO2max was measured on a treadmill during a progressive exercise test to voluntary exhaustion. RESULTS: RMR, adjusted for differences in LM, was 5% higher in white than black women (1566+/-27 and 1490+/-26 kcal/day, respectively; p<0.05); and fat oxidation rate was 17% higher in white than black women (87+/-4 and 72+/-3 g/day, respectively; p<0.01). VO2max (L/minute) was 150 mL per minute (8%) higher (p<0.05) in white than black women. VO2max correlated with LM in black (r=0.44, p=0.05) and white (r=0.53, p<0.05) women, but the intercept of the regression line was higher in white than black women (p<0.05), with no significant difference in slopes. In a multiple regression model including race, body weight, LM, and age, LM was the only independent predictor of RMR (r2 = 0.46, p<0.0001), whereas race was the only independent predictor of fat oxidation (r2 = 0.18, p<0.05). The best predictors of VO2max were LM (r2 = 0.22, p<0.05) and race (cumulative r2 = 0.30, p<0.05). DISCUSSION: These results show there are racial differences in metabolic predictors of obesity. Determination of whether these ethnic differences lead to, or are an effect of, obesity status or other lifestyle factors requires further study.

Basal Metabolism↗

PubMed2003

Surgeon volume compared to hospital volume as a predictor of outcome following primary colon cancer resection.

BACKGROUND AND OBJECTIVES: A strong association between high hospital procedure volume and survival following colon cancer resection has been demonstrated. However, the importance of surgeon case volume as a determinant of outcome has been less well studied, and it is unclear whether hospital or surgeon volume is the more powerful predictor of outcomes. METHODS: A retrospective population-based cohort study utilizing the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked database identified 24,166 colon cancer patients aged 65 years and older who had surgery for a primary tumor diagnosed in 1991-1996 in a SEER area. Hospital and surgeon-specific procedure volume was ascertained based on the number of claims submitted over the 6-year study period. Outcome measures were mortality at 30 days and 2 years, overall survival, and the frequency of operations requiring an intestinal stoma. Age, sex, race, comorbid illness, cancer stage, socioeconomic status, emergent hospitalization, and the presence of obstruction/perforation were used to adjust for differences in case-mix. RESULTS: After adjusting for surgeon procedure volume, high hospital procedure volume remained a strong predictor of low post-operative mortality rates (P < 0.001 for each outcome with and without adjustment for surgeon procedure volume). Surgeon-specific procedure volume was also an important predictor of surgical outcomes (P = 0.002 for 30-day mortality, P = 0.001 for 2-year mortality), although this effect was attenuated after adjusting for hospital volume (P = 0.03 for 30-day mortality, P = 0.02 for 2-year mortality). Hospital volume and surgeon volume were each an important predictor of the ostomy rate. Among high volume institutions and surgeons, individual providers with unusually high ostomy rates could be identified. CONCLUSIONS: Both hospital and surgeon-specific procedure volume predict outcomes following colon cancer resection; but hospital volume may exert a stronger effect. Therefore, efforts to optimize the quality of colon cancer surgery should focus on multidisciplinary aspects of hospital care rather than solely on intraoperative technique.

Aged↗

PubMed2004

Predictors of long-term survival in pN3 gastric cancer patients.

BACKGROUND AND OBJECTIVES: Patients with pN3 gastric cancer are classified as having a stage IV disease just by virtue of having more than 15 metastatic lymph nodes according to the 5th UICC cancer staging criteria. We tried to verify whether the pN3 gastric cancer patients truly constitute a homogeneous group with the same poor prognosis by looking for predictors of long-term survival within the group. METHODS: Medical records of 347 patients who had gastrectomy with D2/D3 lymph node dissection for gastric cancer and diagnosed with pN3 disease by pathology, between January 1987 and December 1997 were reviewed. Clinicopathologic prognostic variables were evaluated as predictors of long-term survival by univariate and multivariate analysis. RESULTS: The overall 5-year survival rate was 13.0% (95% CI, 9.3-16.6%). The extent of gastric resection and metastatic lymph node ratio were significant independent predictors of long-term survival on multivariate analysis. The 5-year survival rates for the subtotal and total gastrectomy groups were 18.2 and 8.8%, respectively. The 5-year survival rate according to the metastatic lymph node ratio was 20.2, 8.9, and 1.9% when the ratio was <0.33, 0.33-0.67, and > 0.67, respectively. CONCLUSIONS: Patients with pN3 gastric cancer appear to be a heterogeneous group with clinicopathologic predictors that identify subgroups with significantly different long-term prognoses. The metastatic lymph node ratio may serve as a valuable tool to predict the long-term prognosis of these patients.

Adult↗

PubMed2003

3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor.

To gain a better understanding of the biological role of proteins encoded in genome sequences, knowledge of their three-dimensional (3D) structure and function is required. The computational assignment of folds is becoming an increasingly important complement to experimental structure determination. In particular, fold-recognition methods aim to predict approximate 3D models for proteins bearing no sequence similarity to any protein of known structure. However, fully automated structure-prediction methods can currently produce reliable models for only a fraction of these sequences. Using a number of semiautomated procedures, human expert predictors are often able to produce more and better predictions than automated methods. We describe a novel, fully automatic, fold-recognition meta-predictor, named 3D-SHOTGUN, which incorporates some of the strategies human predictors have successfully applied. This new method is reminiscent of the so-called cooperative algorithms of Computer Vision. The input to 3D-SHOTGUN are the top models predicted by a number of independent fold-recognition servers. The meta-predictor consists of three steps: (i) assembly of hybrid models, (ii) confidence assignment, and (iii) selection. We have applied 3D-SHOTGUN to an unbiased test set of 77 newly released protein structures sharing no sequence similarity to proteins previously released. Forty-six correct rank-1 predictions were obtained, 30 of which had scores higher than that of the first incorrect prediction-a significant improvement over the performance of all individual servers. Furthermore, the predicted hybrid models were, on average, more similar to their corresponding native structures than those produced by the individual servers. This opens the possibility of generating more accurate, full-atom homology models for proteins with no sequence similarity to proteins of known structure. These improvements represent a step forward toward the wider applicability of fully automated structure-prediction methods at genome scales.

Algorithms↗

PubMed2003

3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3.

The performance of the 3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3 is reported. The 3D-SHOTGUN meta-predictors are fully automatic fold recognition servers that attempt to incorporate into the prediction process a number of successful strategies that human predictors often apply. Namely, the input to 3D-SHOTGUN are the top five models predicted by a number of independent fold recognition servers and its output are hybrid models, assembled by using the recurrent structural information from the input models. The resulting hybrid models are, on average, more accurate and more complete than the input models. When evaluated on a large set of prediction targets, the 3D-SHOTGUN servers show increased sensitivities and significantly better specificities. For CAFASP3, the 3DS3 and 3DS3 and 3DS5 used a preliminary implementation of the 3D-SHOTGUN method, which lacked a refinement step. Although this did not have a significant effect on the easier targets, for the hardest prediction targets, where the input models had significant structural conflicts, the 3D-SHOTGUN models contained a number of non-native-like features such as fragmentation and overlaps. The CAFASP3 evaluation identified the 3D-SHOTGUN meta-predictors within the top three most sensitive and most specific servers. A fully automated refinement step to the 3D-SHOTGUN method is currently being implemented, and preliminary results indicate that in addition to "cleaning up" such undesirable features, it is able to further increase the accuracy of the resulting models.

Computational Biology↗

PubMed1993

Quadratic minimization of predictors for protein secondary structure. Application to transmembrane alpha-helices.

Sliding-window averaging of amino acid properties is often used for predicting protein secondary structure. Such a scheme (linear convolutional recognizer, LCR) assigns a number (weight) to each type of monomer, and then convolutes a window function with the sequence of weights to yield a decision function. Features, regions having the property of interest, are predicted to occur where the decision function exceeds some threshold. A general method for approximating the best possible window and weights is presented. The needed data are the sequences of some chains and the locations of their features. The method is applied to transmembrane helices (TMH) of membrane proteins. Optimal weights and windows are calculated, using bacteriorhodopsin and photosynthetic reaction centers as the reference chains. The predictor is then tested on other proteins. No TMH are predicted in porin, whose transmembrane segments are beta-sheets. This shows that the predictor is specific for helical segments. Few segments are predicted for non-membrane globular proteins. The predictor thus correctly rejects their hydrophobic helices. Finally, the predictor is tested with some membrane proteins whose transmembrane topology is partially known. Among their TMH, the LCR is unable to resolve 6% which are closely spaced. Taking 17 as the minimum allowed length of a predicted TMH, 4% of the known ones are missed and 6% of the predicted ones are false. For a minimum length of 10, 0.5% are missed and 14% are false. The mean magnitude of the endpoint error is about four residues. Alternative prediction methods make more errors.

Algorithms↗

PubMedDate not supplied

Predictors of state legislators' intentions to vote for cigarette tax increases.

BACKGROUND: This study analyzed influences on state legislators' decisions about cigarette tax increase votes using a research strategy based on political science and social-psychological models. METHODS: Legislators from three states representing a spectrum of tobacco interests participated in personal interviews concerned with tobacco control legislation (n = 444). Measures of potential predictors of voting intention were based on the consensus model of legislative decision-making and the theory of planned behavior. Multiple logistic regression methods were used to identify social-psychological and other predictors of intention to vote for cigarette tax increases. RESULTS: General attitudes and norms concerning cigarette tax increases predicted legislators' intention to vote for cigarette tax increases. More specific predictors included perceptions of public health impact and retail sales impact of cigarette tax increases. Constituent pressure was the strongest perceived social influence. Political party and state also were strong predictors of intention. Results were consistent with related research based on political science models. CONCLUSIONS: Legislators' votes on cigarette tax increases may be influenced by their perceptions of positive and negative outcomes of a cigarette tax increase and by perceived constituent pressures. This research model provides useful insights for theory and practice and should be refined in future tobacco control research.

Female↗