Use of information on disease diagnoses from databases for animal health economic, welfare and food safety purposes: strengths and limitations of recordings

Many animal health, welfare and food safety databases include data on clinical and test-based disease diagnoses. However, the circumstances and constraints for establishing the diagnoses vary considerably among databases. Therefore results based on different databases are difficult to compare and compilation of data in order to perform meta-analysis is almost impossible. Nevertheless, diagnostic information collected either routinely or in research projects is valuable in cross comparisons between databases, but there is a need for improved transparency and documentation of the data and the performance characteristics of tests used to establish diagnoses. The objective of this paper is to outline the circumstances and constraints for recording of disease diagnoses in different types of databases, and to discuss these in the context of disease diagnoses when using them for additional purposes, including research. Finally some limitations and recommendations for use of data and for recording of diagnostic information in the future are given. It is concluded that many research questions have such a specific objective that investigators need to collect their own data. However, there are also examples, where a minimal amount of extra information or continued validation could make sufficient improvement of secondary data to be used for other purposes. Regardless, researchers should always carefully evaluate the opportunities and constraints when they decide to use secondary data. If the data in the existing databases are not sufficiently valid, researchers may have to collect their own data, but improved recording of diagnostic data may improve the usefulness of secondary diagnostic data in the future

Development and evaluation of a gentamicin pharmacokinetic model that facilitates opportunistic gentamicin therapeutic drug monitoring in neonates and infants.

Trough gentamicin therapeutic drug monitoring (TDM) is time-consuming, disruptive to neonatal clinical care and a patient safety issue. Bayesian models could allow TDM to be performed opportunistically at the time of routine blood tests. This study aimed to develop and prospectively evaluate a new gentamicin model and a novel Bayesian computer tool (neoGent) for TDM use in neonatal intensive care. We also evaluated model performance for predicting peak concentrations and AUC(0-t). A pharmacokinetic meta-analysis was performed on pooled data from three studies (1325 concentrations from 205 patients). A 3-compartment model was used with covariates being: allometric weight scaling, postmenstrual and postnatal age, and serum creatinine. Final parameter estimates (standard error) were: clearance: 6.2 (0.3) L/h/70kg; central volume (V) 26.5 (0.6) L/70kg; inter-compartmental disposition: Q=2.2 (0.3) L/h/70kg, V2=21.2 (1.5) L/70kg, Q2=0.3 (0.05) L/h/70kg, V3=148 (52.0) L/70kg. The model's ability to predict trough concentrations from an opportunistic sample was evaluated in a prospective observational cohort study that included data from 163 patients with 483 concentrations collected in five hospitals. Unbiased trough predictions were obtained: median (95% confidence interval (CI)) prediction error was 0.0004 (-1.07, 0.84) mg/L. Results also showed peaks and AUC(0-t) could be predicted (from one randomly selected sample) with little bias but relative imprecision with median (95% CI) prediction error being 0.16 (-4.76, 5.01) mg/L and 10.8 (-24.9, 62.2) mg h/L, respectively. NeoGent was implemented in R/NONMEM, and in the freely available TDMx software

A comparison of user testing and heuristic evaluation methods for identifying website usability problems

This study compared the effectiveness and efficiency of two usability testing methods, user testing and heuristic evaluation. Thirty two participants took part in the study, sixteen for each of the two methods. Four measures were used to compare their performance: number of problems identified, severity of problems, type of problems and time taken to find problems. It was found that heuristic evaluation found nearly 5 times more individual problems than user testing, so could be seen as more effective. However, user testing found on average slightly more severe problems and took less time to complete than heuristic evaluation. Heuristic evaluation had a faster problem identification rate (number of seconds per problem found), so could also be seen as more efficient. While each method had advantages in the test both methods are seen as complementary to each other in practice

Cost-utility analysis of genetic screening in families of patients with germline MUTYH mutations

<p>Abstract</p> <p>Background</p> <p>MUTYH associated polyposis (MAP) is an autosomal recessive inherited disorder. Carriers of bi-allelic <it>MUTYH </it>germline mutations have a risk of approximately 60% to develop colorectal carcinoma (CRC). In the general population about 1.5% is a heterozygous <it>MUTYH </it>mutation carrier. Children of MAP patients have an increased risk of inheriting two <it>MUTYH </it>mutations compared to the general population, implicating an increased risk for developing CRC.</p> <p>Methods</p> <p>Using data from the literature and Dutch MAP patients (n = 40), we constructed a Markov model to perform a societal cost-utility analysis of genetic screening in MAP families. Genetic screening was done by testing the spouse first and, in case of a heterozygous spouse, also testing of the children.</p> <p>Results</p> <p>The cost of genetic screening of families of MAP patients, when compared to no genetic screening, was estimated at €25,000 per quality-adjusted life year (QALY). The presence of Fecal Occult Blood testing (FOBT) population screening only slightly increased this cost-utility ratio to €25,500 per QALY. For a MUTYH heterozygote index-patient, the ratio was €51,500 per QALY. The results of our analysis were sensitive to several of the parameters in the model, including the cost assumed for molecular genetic testing.</p> <p>Conclusion</p> <p>The costs per QALY of genetic screening in families of MAP patients are acceptable according to international standards. Therefore, genetic testing of spouses and/or children should be discussed with and offered to counselees.</p

Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

<p>Abstract</p> <p>Background</p> <p>The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches. Metabolic engineering is often complimented by directed evolution, where selective pressure is applied to a partially genetically engineered strain to confer a desirable phenotype. The exact genetic modification or resulting genotype that leads to the improved phenotype is often not identified or understood to enable further metabolic engineering.</p> <p>Results</p> <p>In this work we performed whole genome high-throughput sequencing and annotation can be used to identify single nucleotide polymorphisms (SNPs) between <it>Saccharomyces cerevisiae </it>strains S288c and CEN.PK113-7D. The yeast strain S288c was the first eukaryote sequenced, serving as the reference genome for the <it>Saccharomyces </it>Genome Database, while CEN.PK113-7D is a preferred laboratory strain for industrial biotechnology research. A total of 13,787 high-quality SNPs were detected between both strains (reference strain: S288c). Considering only metabolic genes (782 of 5,596 annotated genes), a total of 219 metabolism specific SNPs are distributed across 158 metabolic genes, with 85 of the SNPs being nonsynonymous (e.g., encoding amino acid modifications). Amongst metabolic SNPs detected, there was pathway enrichment in the galactose uptake pathway (<it>GAL1</it>, <it>GAL10</it>) and ergosterol biosynthetic pathway (<it>ERG8</it>, <it>ERG9</it>). Physiological characterization confirmed a strong deficiency in galactose uptake and metabolism in S288c compared to CEN.PK113-7D, and similarly, ergosterol content in CEN.PK113-7D was significantly higher in both glucose and galactose supplemented cultivations compared to S288c. Furthermore, DNA microarray profiling of S288c and CEN.PK113-7D in both glucose and galactose batch cultures did not provide a clear hypothesis for major phenotypes observed, suggesting that genotype to phenotype correlations are manifested post-transcriptionally or post-translationally either through protein concentration and/or function.</p> <p>Conclusions</p> <p>With an intensifying need for microbial cell factories that produce a wide array of target compounds, whole genome high-throughput sequencing and annotation for SNP detection can aid in better reducing and defining the metabolic landscape. This work demonstrates direct correlations between genotype and phenotype that provides clear and high-probability of success metabolic engineering targets. The genome sequence, annotation, and a SNP viewer of CEN.PK113-7D are deposited at <url>http://www.sysbio.se/cenpk</url>.</p

An increased response to experimental muscle pain is related to psychological status in women with chronic non-traumatic neck-shoulder pain

<p>Abstract</p> <p>Background</p> <p>Neck-shoulder pain conditions, e.g., chronic trapezius myalgia, have been associated with sensory disturbances such as increased sensitivity to experimentally induced pain. This study investigated pain sensitivity in terms of bilateral pressure pain thresholds over the trapezius and tibialis anterior muscles and pain responses after a unilateral hypertonic saline infusion into the right legs tibialis anterior muscle and related those parameters to intensity and area size of the clinical pain and to psychological factors (sleeping problems, depression, anxiety, catastrophizing and fear-avoidance).</p> <p>Methods</p> <p>Nineteen women with chronic non-traumatic neck-shoulder pain but without simultaneous anatomically widespread clinical pain (NSP) and 30 age-matched pain-free female control subjects (CON) participated in the study.</p> <p>Results</p> <p>NSP had lower pressure pain thresholds over the trapezius and over the tibialis anterior muscles and experienced hypertonic saline-evoked pain in the tibialis anterior muscle to be significantly more intense and locally more widespread than CON. More intense symptoms of anxiety and depression together with a higher disability level were associated with increased pain responses to experimental pain induction and a larger area size of the clinical neck-shoulder pain at its worst.</p> <p>Conclusion</p> <p>These results indicate that central mechanisms e.g., central sensitization and altered descending control, are involved in chronic neck-shoulder pain since sensory hypersensitivity was found in areas distant to the site of clinical pain. Psychological status was found to interact with the perception, intensity, duration and distribution of induced pain (hypertonic saline) together with the spreading of clinical pain. The duration and intensity of pain correlated negatively with pressure pain thresholds.</p

Overdiagnosis and overtreatment of breast cancer: Progression of ductal carcinoma in situ: the pathological perspective

Ductal carcinoma in situ (DCIS) is encountered much more frequently in the screening population compared to the symptomatic setting. The behaviour of DCIS is highly variable and this presents difficulties in choosing appropriate treatment strategies for individual cases. This review discusses the current data on the frequency and rate of progression of DCIS, the value and limitations of clinicopathological and biological variables in predicting disease behaviour and suggests strategies to develop more robust means of predicting progression of DCIS

Urine/Plasma Neutrophil Gelatinase Associated Lipocalin Ratio Is a Sensitive and Specific Marker of Subclinical Acute Kidney Injury in Mice

Background Detection of acute kidney injury (AKI) is still a challenge if conventional markers of kidney function are within reference range. We studied the sensitivity and specificity of NGAL as an AKI marker at different degrees of renal ischemia. Methods Male C57BL/6J mice were subjected to 10-, 20- or 30-min unilateral renal ischemia, to control operation or no operation, and AKI was evaluated 1 day later by histology, immunohistochemistry, BUN, creatinine, NGAL (plasma and urine) and renal NGAL mRNA expression. Results A short (10-min) ischemia did not alter BUN or kidney histology, but elevated plasma and urinary NGAL level and renal NGAL mRNA expression although to a much smaller extent than longer ischemia. Surprisingly, control operation elevated plasma NGAL and renal NGAL mRNA expression to a similar extent as 10-min ischemia. Further, the ratio of urine to plasma NGAL was the best parameter to differentiate a 10-min ischemic injury from control operation, while it was similar in the non and control-operated groups. Conclusions These results suggest that urinary NGAL excretion and especially ratio of urine to plasma NGAL are sensitive and specific markers of subclinical acute kidney injury in mice