pROC: an open-source package for R and S+ to analyze and compare ROC curves

Background  

Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface.     

WaveletQuant,an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis

Background  

Quantitative proteomics technologies have been developed to comprehensively identify and quantify proteins in two or more complex samples. Quantitative proteomics based on differential stable isotope labeling is one of the proteomics quantification technologies. Mass spectrometric data generated for peptide quantification are often noisy, and peak detection and definition require various smoothing filters to remove noise in order to achieve accurate peptide quantification. Many traditional smoothing filters, such as the moving average filter, Savitzky-Golay filter and Gaussian filter, have been used to reduce noise in MS peaks. However, limitations of these filtering approaches often result in inaccurate peptide quantification. Here we present the WaveletQuant program, based on wavelet theory, for better or alternative MS-based proteomic quantification.     

Anisotropic Smoothing Improves DT-MRI-Based Muscle Fiber Tractography

Purpose

To assess the effect of anisotropic smoothing on fiber tracking measures, including pennation angle, fiber tract length, and fiber tract number in the medial gastrocnemius (MG) muscle in healthy subjects using diffusion-weighted magnetic resonance imaging (DW-MRI).

Materials and Methods

3T DW-MRI data were used for muscle fiber tractography in the MG of healthy subjects. Anisotropic smoothing was applied at three levels (5%, 10%, 15%), and pennation angle, tract length, fiber tract number, fractional anisotropy, and principal eigenvector orientation were quantified for each smoothing level.

Results

Fiber tract length increased with pre-fiber tracking smoothing, and local heterogeneities in fiber direction were reduced. However, pennation angle was not affected by smoothing.

Conclusion

Modest anisotropic smoothing (10%) improved fiber-tracking results, while preserving structural features.     

Relationship of compartment-specific structural knee status at baseline with change in cartilage morphology: a prospective observational study using data from the osteoarthritis initiative

Introduction  

The aim was to investigate the relationship of cartilage loss (change in medial femorotibial cartilage thickness measured with magnetic resonance imaging (MRI)) with compartment-specific baseline radiographic findings and MRI cartilage morphometry features, and to identify which baseline features can be used for stratification of fast progressors.     

Optimized LOWESS normalization parameter selection for DNA microarray data

Background  

Microarray data normalization is an important step for obtaining data that are reliable and usable for subsequent analysis. One of the most commonly utilized normalization techniques is the locally weighted scatterplot smoothing (LOWESS) algorithm. However, a much overlooked concern with the LOWESS normalization strategy deals with choosing the appropriate parameters. Parameters are usually chosen arbitrarily, which may reduce the efficiency of the normalization and result in non-optimally normalized data. Thus, there is a need to explore LOWESS parameter selection in greater detail.     

Comparing transformation methods for DNA microarray data

Background  

When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order to improve comparability and signal/noise ratio. These steps may include subtraction of an estimated background signal, subtracting the reference signal, smoothing (to account for nonlinear measurement effects), and more. Different authors use different approaches, and it is generally not clear to users which method they should prefer.     

Levels of anti-citrullinated protein antibodies and IgM rheumatoid factor are not associated with outcome in early arthritis patients: a cohort study

Introduction  

To investigate whether baseline levels of anti-citrullinated protein antibody (ACPA) or IgM rheumatoid factor (IgM-RF) and changes in the year thereafter are associated with disease activity, functional and radiographic outcome in early arthritis patients, and provide additional information over baseline autoantibody status.     

Impact of female age and male infertility on ovarian reserve markers to predict outcome of assisted reproduction technology cycles

Background  

This study was designed to assess the capability of ovarian reserve markers, including baseline FSH levels, baseline anti-Müllerian hormone (AMH) levels, and antral follicle count (AFC), as predictors of live births during IVF cycles, especially for infertile couples with advanced maternal age and/or male factors.     

Effect of duloxetine in patients with fibromyalgia: tiredness subgroups

Introduction  

This study tested the hypothesis that baseline ratings of fatigue/tiredness would be negatively associated with the efficacy of duloxetine on measures of pain and functional ability in patients with fibromyalgia.     

SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

Background  

General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets.     

Baseline serum MMP-3 levels in patients with Rheumatoid Arthritis are still independently predictive of radiographic progression in a longitudinal observational cohort at 8 years follow up

Introduction  

At present, there is no reliable tool for predicting disease outcome in patients with rheumatoid arthritis (RA). We previously demonstrated an association between specific baseline biomarkers/clinical measures including matrix metalloproteinase-3 (MMP-3) and 2-year radiographic progression in patients with RA. This study further evaluates the predictive capability of these baseline variables with outcome extended over 8-years.     

Association between Intraoperative Blood Pressure and Postoperative Delirium in Elderly Hip Fracture Patients

Background

One possible area of intervention to prevent postoperative delirium (PD) is intraoperative blood pressure management. However, the relationship between intraoperative blood pressure and PD is unclear. A secondary analysis of a RCT study examining the PD risk over the range of absolute intraoperative mean arterial blood pressure (MAP) readings and the corresponding relative changes from preoperative baseline level was performed to determine the role of MAP on PD.

Methods

Nonparametric locally weighted quadratic polynomial smoothing (LOESS) regression explored the pattern of PD risk at postoperative day 2 as a function of mean surgery MAP (msMAP) and percent change of msMAP from baseline in 103 elderly hip fracture patients. Segment-linear logistic regression models were then constructed to determine the odds ratios (OR) of PD over the observed range of these msMAP measures, adjusting for potential confounds.

Results

Twenty-three patients (22%) developed PD on day 2. LOESS regression revealed a j-shaped association between absolute levels of msMAP and PD risk. When msMAP was ≥80 mmHg, higher msMAP imparted greater PD risk (OR = 2.28 per 10 mmHg msMAP increase; 95% CI: 1.11–4.70), while higher msMAP was associated with lower PD risk (OR = 0.19 per 10 mmHg increase; CI: 0.05–0.76) if msMAP was <80 mmHg. There was no statistically significant relationship between PD risk and average percent change from baseline in these msMAP measures.

Conclusion

In elderly hip fracture patients, both very high and very low levels of msMAP were associated with significantly increased risk of PD.     

Detection of early Alzheimer's disease in MCI patients by the combination of MMSE and an episodic memory test

Background  

Mild cognitive impairment (MCI) is a heterogeneous clinical entity that comprises the prodromal phase of Alzheimer's disease (Pr-AD). New biomarkers are useful in detecting Pr-AD, but they are not universally available. We aimed to investigate baseline clinical and neuropsychological variables that might predict progression from MCI to AD dementia.     

Perception of stroke and knowledge of potential risk factors among Omani patients at increased risk for stroke

Background  

Previous studies have demonstrated poor knowledge of stroke among patients with established risk factors. This study aims to assess the baseline knowledge, among patients with increased risk for stroke in Oman, of warning symptoms of stroke, impending risk factors, treatment, and sources of information.     

Life cycle analysis of algae biodiesel

Background, aim, and scope  

Algae biomass has great promise as a sustainable alternative to conventional transportation fuels. In this study, a well-to-pump life cycle assessment (LCA) was performed to investigate the overall sustainability and net energy balance of an algal biodiesel process. The goal of this LCA was to provide baseline information for the algae biodiesel process.     

caBIG™ VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data

Background

We sketch our species identification tool for palm sized computers that helps knowledgeable observers with census activities. An algorithm turns an identification matrix into a minimal length series of questions that guide the operator towards identification. Historic observation data from the census geographic area helps minimize question volume. We explore how much historic data is required to boost performance, and whether the use of history negatively impacts identification of rare species. We also explore how characteristics of the matrix interact with the algorithm, and how best to predict the probability of observing a previously unseen species.

Results

Point counts of birds taken at Stanford University's Jasper Ridge Biological Preserve between 2000 and 2005 were used to examine the algorithm. A computer identified species by correctly answering, and counting the algorithm's questions. We also explored how the character density of the key matrix and the theoretical minimum number of questions for each bird in the matrix influenced the algorithm. Our investigation of the required probability smoothing determined whether Laplace smoothing of observation probabilities was sufficient, or whether the more complex Good-Turing technique is required.

Conclusion

Historic data improved identification speed, but only impacted the top 25% most frequently observed birds. For rare birds the history based algorithms did not impose a noticeable penalty in the number of questions required for identification. For our dataset neither age of the historic data, nor the number of observation years impacted the algorithm. Density of characters for different taxa in the identification matrix did not impact the algorithms. Intrinsic differences in identifying different birds did affect the algorithm, but the differences affected the baseline method of not using historic data to exactly the same degree. We found that Laplace smoothing performed better for rare species than Simple Good-Turing, and that, contrary to expectation, the technique did not then adversely affect identification performance for frequently observed birds.     

Changes in the Perceptions of Self‐weighing Across Time in a Behavioral Weight Loss Intervention

Objective

Changes in beliefs about self‐weighing were examined across time in a behavioral weight loss intervention.

Methods

Active duty military personnel (n = 248) enrolled in a 12‐month counselor‐initiated or self‐paced intervention based on the Look AHEAD (Action for Health in Diabetes) Intensive Lifestyle Intervention. Using an electronic scale, participants were asked to self‐weigh daily. Self‐weighing perceptions were compared from baseline to 4 months (weight loss phase), from 4 months to 12 months (weight maintenance phase), and from baseline to 12 months (full intervention), as well as across time by behavioral and demographic characteristics.

Results

Overall, participants perceived self‐weighing as more helpful and positive, less frustrating, and making them less self‐conscious after the weight loss phase. After weight maintenance, individuals believed self‐weighing was less helpful and positive, more frustrating and anxiety provoking, and making them more self‐conscious. However, after the intervention, participants still viewed self‐weighing as more helpful and positive and less frustrating than at baseline. Weight change, self‐weighing behavior prior to the intervention, and intervention condition were associated with perception change. Controlling for these influencing factors, differences in gender, BMI, age, ethnicity, and race were observed in how beliefs changed across time.

Conclusions

Results suggest engaging in a weight loss intervention promoting daily self‐weighing increases positive and decreases negative beliefs about self‐weighing.     

The role of patient expectations in predicting outcome after total knee arthroplasty

Introduction  

Patient's expectations are variably reported to influence self-rated outcome and satisfaction after medical treatment; this prospective study examined which of the following was the most important unique determinant of global outcome/satisfaction after total knee arthroplasty (TKA): baseline expectations; fulfilment of expectations; or current symptoms and function.     

Total cholesterol and triglycerides are associated with the development of new bone marrow lesions in asymptomatic middle-aged women - a prospective cohort study

Introduction  

Given the emerging evidence that osteoarthritis (OA) may have a vascular basis, the aim of this study was to determine whether serum lipids were associated with change in knee cartilage, presence of bone marrow lesions (BMLs) at baseline and the development of new BMLs over a 2-year period in a population of pain-free women in mid-life.     

Effect of menstrual cycle phase and hormonal treatments on evaluation of tubal patency in baboons

Background

We evaluated whether menstrual cycle phase influences the assessment of tubal patency by hysterosalpingography (HSG) in baboons.

Methods

Retrospective analysis of baseline tubal patency studies and serum estradiol (E₂) and progesterone (P4) values obtained from female baboons used as models for development of non‐surgical permanent contraception in women. The main outcome measure was bilateral tubal patency (BTP) in relationship with estradiol level.

Results

Female baboons (n = 110) underwent a single (n = 81), two (n = 26), or three (n = 3) HSG examinations. In 33/142 (23%) HSG examinations, one or both tubes showed functional occlusion (FO). The median E₂ in studies with BTP (49 pg/mL) was significantly higher than in those studies with FO (32 pg/mL, P = .005). Among 18 animals with repeat examinations where serum E₂ changed from <60 to ≥ 60 pg/mL, 13 results changed from FO to BTP (P = .0001). No sets showed a change from BTP to FO with an increase in estradiol.

Conclusion

In baboons, functional occlusion of the fallopian tube is associated with low estradiol levels, supporting a role for estrogen‐mediated relaxation of the utero‐tubal junction.