A guide to interpreting a study of patient-reported outcomes

Outcomes measured from the patient perspective are particularly important in plastic surgery, where many of the treatments are aimed at improving physical function, psychosocial function, and quality of life. Understanding the measurement of patient-reported outcomes is critical to determine the value of the interventions performed, to better inform clinical decision-making, and to guide policy debates. It is critical that physicians understand their patients' individual values when making treatment and policy recommendations based on evidence. This guide outlines the questions that readers should ask when appraising literature using patient-reported outcomes.     

JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles

The JEOL Automated Data Acquisition System (JADAS) is a software system built for the latest generation of the JEOL Transmission Electron Microscopes. It is designed to partially or fully automate image acquisition for ice-embedded single particles under low dose conditions. Its built-in flexibility permits users to customize the order of various imaging operations. In this paper, we describe how JADAS is used to accurately locate and image suitable specimen areas on a grid of ice-embedded particles. We also demonstrate the utility of JADAS by imaging the epsilon 15 bacteriophage with the JEM3200FSC electron cryo-microscope, showing that sufficient images can be collected in a single 8h session to yield a subnanometer resolution structure which agrees with the previously determined structure.     

Estimating viability of plant protoplasts using double and single staining

Summary The utility of numerous dyes for determining the viability of barley (Hordeum vulgare L. cv. Himalaya) aleurone protoplasts was studied. Protoplasts isolated from the barley aleurone layer synthesize and secrete -amylase isozymes in response to treatment with gibberellic acid (GA) and Ca²⁺. These cells also undergo dramatic morphological changes which eventually result in cell death. To monitor the viability of protoplasts during incubation in GA and Ca²⁺, several types of fluorescent and nonfluorescent dyes were tested. Evans blue and methylene blue were selected as nonfluorescent dyes. Living cells exclude Evans blue, but dead cells and cell debris stain blue. Both living and dead cells take up methylene blue, but living cells reduce the dye to its colorless form whereas dead cells and cell debris stain blue. The relatively low extinction coefficient of these dyes sometimes makes it difficult to distinguish blue-stained cells against a background of blue dye. Several types of fluorescent dyes were tested for their ability to differentially stain dead or living cells. Tinopal CBS-X, for example, stains only dead cells, and its high extinction coefficient allows its ultraviolet fluorescence to be recorded even when preparations are simultaneously illuminated with visible light. To double-stain protoplasts, the most effective stain was a combination of fluorescein diacetate (FDA) and propidium iodide (PI). By employing a double-exposure method to record the fluorescence from cells stained with both FDA and PI, dead and living cells could be distinguished on the basis of fluorochromasia.     

Cancelling of Fresnel reflections in in situ,double beam laser,fluorimetry using a single optical fibre

This paper describes several techniques used to cancel Fresnel reflection on the extremities of the optical fibre in in situ double beam laser fluorimetry when the single optical fibre is adopted. The reasons for the technical choices are exposed and the results on several media are presented (water, air, finger pad, rat heart).     

Quantitative trait prediction based on genetic marker-array data, a simulation study

MOTIVATION: Using simulation studies for quantitative trait loci (QTL), we evaluate the prediction quality of regression models that include as covariates single-nucleotide polymorphism (SNP) genetic markers which did not achieve genome-wide significance in the original genome-wide association study, but were among the SNPs with the smallest P-value for the selected association test. We compare the results of such regression models to the standard approach which is to include only SNPs that achieve genome-wide significance. Using mean square prediction error as the model metric, our simulation results suggest that by using the coefficient of determination (R(2)) value as a guideline to increase or reduce the number of SNPs included in the regression model, we can achieve better prediction quality than the standard approach. However, important parameters such as trait heritability, the approximate number of QTLs, etc. have to be determined from previous studies or have to be estimated accurately.     

Generation of double gene disruptions in Dictyostelium discoideum using a single antibiotic marker selection

Gene targeting is a powerful molecular genetic technique that has been widely used to understand specific gene function in vivo. This technique allows the ablation of an endogenous gene by recombination between an introduced DNA fragment and the homologous target gene. However, when multiple gene disruptions are needed, the availability of only a limited number of marker genes becomes a complication. Here we describe a new approach to perform double gene disruptions in Dictyostelium discoideum by simultaneous transfection of two gene targeting cassettes followed by performing clonal selection against only one marker gene. The subsequent PCR-based screens of blasticidin-resistant clones revealed the integration of both the selected and the nonselected targeting cassettes at their original respective loci creating complete gene disruptions. For the genes we have tested in these studies (myosin heavy chain kinases B and C), the efficiency of the double gene targeting event is found in the range of 2%-5% of all blasticidin-resistant colonies following the transfection step. This approach for the simultaneous disruptions of multiple genes should prove to be a valuable tool for other laboratories interested in creating multiple gene disruptants in Dictyostelium or other organisms where a limited number of selectable markers are available.     

Choosing haplotype-tagging SNPS based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the Multiethnic Cohort Study

We describe an approach for picking haplotype-tagging single nucleotide polymorphisms (htSNPs) that is presently being taken in two large nested case-control studies within a multiethnic cohort (MEC), which are engaged in a search for associations between risk of prostate and breast cancer and common genetic variations in candidate genes. Based on a preliminary sample of 70 control subjects chosen at random from each of the 5 ethnic groups in the MEC we estimate haplotype frequencies using a variant of the Excoffier-Slatkin E-M algorithm after genotyping a high density of SNPs selected every 3-5 kb in and surrounding a candidate gene. In order to evaluate the performance of a candidate set of htSNPS (which will be genotyped in the much larger case-control sample) we treat the haplotype frequencies estimate above as known, and carry out a formal calculation of the uncertainty of the number of copies of common haplotypes carried by an individual, summarizing this calculation as a coefficient of determination, R2h. A candidate set of htSNPS of a given size is chosen so as to maximize the minimum value of R2h over the common haplotypes, h.     

A computer method for analysis of radioactivity data from single and double labeled experiments

A generally applicable program has been devised for the machine processing and plotting of radioactivity data. The program can be used with single or double labeled experiments; it includes numerous options which increase its flexibility and facilitate optimization of data presentation.     

Effects of VDT monitor placement and single versus bifocal glasses on somatic discomfort and postural profiles in data entry tasks

A study was conducted to determine the effects of VDT monitor positions and the use of single vision versus bifocal glasses on somatic elements in the data entry task. Eight male subjects performed data entry using a word processor in eight half-hour sessions with the four different monitor placements, i.e. "eye-level", "shoulder-level-front", "shoulder-level-side", and "sunken-level", wearing the two types of glasses. A subjective discomfort rating questionnaire covering 12 somatic elements was completed by the subject after each session. The head inclination and angle of gaze to the monitor were measured with a goniometer. The results revealed that the somatic elements which were affected significantly by the placement of the VDT monitor and the type of glasses were discomfort in the neck and back regions and eyestrain, respectively. The neck-back discomfort scores were highest at the "eye-level", lowest at the "sunken-level", and intermediate at the "shoulder-level-side" position. The "shoulder-level-front" position was not significantly different in the discomfort from other three positions. The eyestrain was significantly greater with the bifocal than with the single vision glasses. The lower the monitor was placed, the more forward was the head and gaze inclined. The head was inclined less forward, or even more backward, and the gaze was inclined more forward, with the bifocal than with the single vision glasses. As a conclusion, the VDT operators were advised to avoid the "eye-level" and "shoulder-level-side" positions and to prefer the "sunken-level" and "shoulder-level-front" positions as the first and second best choices, respectively. The preference becomes more critical for the wearers of bifocal glasses that suffer from postural constraints in viewing.     

Obesity and revision surgery,mortality, and patient-reported outcomes after primary knee replacement surgery in the National Joint Registry: A UK cohort study

BackgroundOne in 10 people in the United Kingdom will need a total knee replacement (TKR) during their lifetime. Access to this life-changing operation has recently been restricted based on body mass index (BMI) due to belief that high BMI may lead to poorer outcomes. We investigated the associations between BMI and revision surgery, mortality, and pain/function using what we believe to be the world’s largest joint replacement registry.Methods and findingsWe analysed 493,710 TKRs in the National Joint Registry (NJR) for England, Wales, Northern Ireland, and the Isle of Man from 2005 to 2016 to investigate 90-day mortality and 10-year cumulative revision. Hospital Episodes Statistics (HES) and Patient Reported Outcome Measures (PROMs) databases were linked to the NJR to investigate change in Oxford Knee Score (OKS) 6 months postoperatively.After adjustment for age, sex, American Society of Anaesthesiologists (ASA) grade, indication for operation, year of primary TKR, and fixation type, patients with high BMI were more likely to undergo revision surgery within 10 years compared to those with “normal” BMI (obese class II hazard ratio (HR) 1.21, 95% CI: 1.10, 1.32 (p < 0.001) and obese class III HR 1.13, 95% CI: 1.02, 1.26 (p = 0.026)). All BMI classes had revision estimates within the recognised 10-year benchmark of 5%. Overweight and obese class I patients had lower mortality than patients with “normal” BMI (HR 0.76, 95% CI: 0.65, 0.90 (p = 0.001) and HR 0.69, 95% CI: 0.58, 0.82 (p < 0.001)). All BMI categories saw absolute increases in OKS after 6 months (range 18–20 points). The relative improvement in OKS was lower in overweight and obese patients than those with “normal” BMI, but the difference was below the minimal detectable change (MDC; 4 points). The main limitations were missing BMI particularly in the early years of data collection and a potential selection bias effect of surgeons selecting the fitter patients with raised BMI for surgery.ConclusionsGiven revision estimates in all BMI groups below the recognised threshold, no evidence of increased mortality, and difference in change in OKS below the MDC, this large national registry shows no evidence of poorer outcomes in patients with high BMI. This study does not support rationing of TKR based on increased BMI.

Jonathan Evans and co-workers study associations between patients’ weight and outcomes of total knee replacement in the UK.     

Classification of drugs based on properties of sodium channel inhibition: a comparative automated patch-clamp study

Background

There is only one established drug binding site on sodium channels. However, drug binding of sodium channels shows extreme promiscuity: ∼25% of investigated drugs have been found to potently inhibit sodium channels. The structural diversity of these molecules suggests that they may not share the binding site, and/or the mode of action. Our goal was to attempt classification of sodium channel inhibitors by measuring multiple properties of inhibition in electrophysiology experiments. We also aimed to investigate if different properties of inhibition correlate with specific chemical properties of the compounds.

Methodology/Principal Findings

A comparative electrophysiological study of 35 compounds, including classic sodium channel inhibitors (anticonvulsants, antiarrhythmics and local anesthetics), as well as antidepressants, antipsychotics and neuroprotective agents, was carried out using rNav1.2 expressing HEK-293 cells and the QPatch automatic patch-clamp instrument. In the multi-dimensional space defined by the eight properties of inhibition (resting and inactivated affinity, potency, reversibility, time constants of onset and offset, use-dependence and state-dependence), at least three distinct types of inhibition could be identified; these probably reflect distinct modes of action. The compounds were clustered similarly in the multi-dimensional space defined by relevant chemical properties, including measures of lipophilicity, aromaticity, molecular size, polarity and electric charge. Drugs of the same therapeutic indication typically belonged to the same type. We identified chemical properties, which were important in determining specific properties of inhibition. State-dependence correlated with lipophilicity, the ratio of the neutral form of molecules, and aromaticity: We noticed that the highly state dependent inhibitors had at least two aromatic rings, logP>4.0, and pKa<8.0.

Conclusions/Significance

The correlations of inhibition properties both with chemical properties and therapeutic profiles would not have been evident through the sole determination of IC₅₀; therefore, recording multiple properties of inhibition may allow improved prediction of therapeutic usefulness.     

A machine learning approach for automated recognition of movement patterns using basic, kinetic and kinematic gait data

This paper investigated application of a machine learning approach (Support vector machine, SVM) for the automatic recognition of gait changes due to ageing using three types of gait measures: basic temporal/spatial, kinetic and kinematic. The gaits of 12 young and 12 elderly participants were recorded and analysed using a synchronized PEAK motion analysis system and a force platform during normal walking. Altogether, 24 gait features describing the three types of gait characteristics were extracted for developing gait recognition models and later testing of generalization performance. Test results indicated an overall accuracy of 91.7% by the SVM in its capacity to distinguish the two gait patterns. The classification ability of the SVM was found to be unaffected across six kernel functions (linear, polynomial, radial basis, exponential radial basis, multi-layer perceptron and spline). Gait recognition rate improved when features were selected from different gait data type. A feature selection algorithm demonstrated that as little as three gait features, one selected from each data type, could effectively distinguish the age groups with 100% accuracy. These results demonstrate considerable potential in applying SVMs in gait classification for many applications.     

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

Background  

DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2–5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study.     

Defining cut-off values for disease activity states and improvement scores for patient-reported outcomes: the example of the Rheumatoid Arthritis Impact of Disease (RAID)

Introduction

The Rheumatoid Arthritis Impact of Disease (RAID) is a patient-reported outcome measure evaluating the impact of rheumatoid arthritis (RA) on patient quality of life. It comprises 7 domains that are evaluated as continuous variables from 0 (best) to 10 (worst). The objective was to define and identify cut-off values for disease activity states as well as improvement scores in order to present results at the individual level (for example, patient in acceptable state, improved patient).

Methods

Patients with definite active RA requiring anti-tumour necrosis factor (anti-TNF) therapy were seen at screening, baseline and after 4 and 12 weeks of etanercept therapy. Answers to "Gold standard" questions on improvement (MCII: Minimum Clinically Important Improvement) and an acceptable status (PASS: Patient Acceptable Symptom State) were collected as well as the RAID score and Disease Activity Score 28- erythrocyte sedimentation rate (DAS28-ESR). Cut-offs were defined by different techniques including empirical, measurement error and gold standard anchors. The external validity of these cut-offs was evaluated using the positive likelihood ratio (LR) based on the patient's perspective (for example, patient's global) and on low disease activity status (such as DAS28-ESR).

Results

Ninety-seven (97) of the 108 recruited patients (age: 54 ± 13 years old, female gender: 75%, rheumatoid factor positive: 81%, disease duration: 8 ± 7 years, CRP: 18 ± 30 mg/l, DAS28-ESR: 5.4 ± 0.8) completed the 12 weeks of the study. The different techniques suggested thresholds ranging from 0.2 to 3 (absolute change) and from 6 to 50% (relative change) for defining MCII and thresholds from less than 1 to less than 4.2 for defining PASS. The evaluation of external validity (LR+) showed the highest LR+ was obtained with thresholds of 3 for absolute change; 50% for relative change and less than 2 for an acceptable status.

Conclusions

This study showed that thresholds defined for continuous variables are closely related to the methodological technique, justifying a systematic evaluation of their validity. Our results suggested that a change of at least 3 points (absolute) or 50% (relative) in the RAID score should be used to define a MCII and that a maximal value of 2 defines an acceptable status.

Trial Registration

Clinicaltrial.gov: NCT004768053     

Qualitative measurements of the entry of L-lactate into single surface fibres of frog skeletal muscle using a lactate-sensitive microelectrode

The present results demonstrate the sensitivity of the Corning chloride liquid ion exchanger 477913 to L-lactate. Microelectrodes filled with this exchanger showed responses to changes in L-lactate concentration in chloride-free solutions. In these experiments L-lactate replaced gluconate in equimolar amounts. Microelectrodes filled with this exchanger were used to qualitatively detect changes in intracellular anion in chloride-depleted frog sartorius muscle fibres during exposure to extracellular concentrations of L-lactate. The increase in intracellular anion concentration is consistent with the movement of L-lactate into the cell. This microelectrode enables one to qualitatively monitor changes in intracellular L-lactate in chloride-free experiments without incorporating selectivity coefficients.     

Contrasting insights provided by single and multispecies data in a regional comparative phylogeographic study

Many single‐species freshwater phylogeographic studies have been carried out in south‐east Queensland; however comparative phylogeography requires multiple lines of evidence to infer deep, significant relationships between landscape and biota. The present study aimed to test conclusions resulting from single taxon studies in a multispecies comparative framework: (1) how influential are river basins in the genetic structure of freshwater species; (2) are there biogeographic frontiers between groups of basins; and (3) could deep intraspecific lineages be explained by a single event? New and existing data from 33 freshwater species (23 fishes and 10 crustaceans) were combined, and both standard single‐species analyses (haplotype networks, genetic distances, Φ_ST) and multispecies methods (hierarchical ABC) were carried out for 1814 sequences from eight basins. More than half of the species displayed a high phylogeographic structure and contained at least two distinct lineages. Almost all of the lineage divergences displayed an element of north/south geographic breaks, with the most influential boundary being between the Mary and Brisbane rivers. Of the 11 basin‐pair multispecies coalescent analyses, four implied a single divergence as being most likely. A regional analysis of deep lineages within 16 taxon‐pairs resulted in a strongly supported inference of a single divergence, probably dating to the Pleistocene. Basin boundaries are a key determinant of phylogeographic patterns for most of these freshwater species, although the specific biogeographic relationship between basins often varies depending on the species. There are a number of influential biogeographic frontiers, with the Brisbane‐Mary being the most important. The finding that a single event may be responsible for multiple deep lineages across the region implies that a highly influential climate change event may have been detected. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 554–569.