Identifiability of parameters and behaviour of MCMC chains: a case study using the reaction norm model.

Markov chain Monte Carlo (MCMC) enables fitting complex hierarchical models that may adequately reflect the process of data generation. Some of these models may contain more parameters than can be uniquely inferred from the distribution of the data, causing non-identifiability. The reaction norm model with unknown covariates (RNUC) is a model in which unknown environmental effects can be inferred jointly with the remaining parameters.

Nasoseptal chondrosarcoma resection requiring anterior fossa floor repair: a case report.

We present a case in which a 23-year-old male patient diagnosed with nasoseptal chondrosarcoma with anterior cranial fossa extension underwent combined surgical approaches to optimize complete resection of the tumor. Surgery was followed by a 6-month course of proton-beam radiation therapy. Extensive tumors of this type with significant intracranial extension require surgical repair of the anterior fossa floor.

The ground state correlation energy of the random phase approximation from a ring coupled cluster doubles approach.

We present an analytic proof demonstrating the equivalence between the random phase approximation (RPA) to the ground state correlation energy and a ring-diagram simplification of the coupled cluster doubles (CCD) equations. In the CCD framework, the RPA equations can be solved in O(N(4)) computational effort, where N is proportional to the number of basis functions.

Selection for environmental variation: a statistical analysis and power calculations to detect response.

Data from uterine capacity in rabbits (litter size) were analyzed to determine whether the environmental variance was partly genetically determined. The fit of a classical homogeneous variance mixed linear (HOM) model and that of a genetically structured heterogeneous variance mixed linear (HET) model were compared. Various methods to assess the quality of fit favor the HET model.

Nuclear interleukin-33 is generally expressed in resting endothelium but rapidly lost upon angiogenic or proinflammatory activation.

Interleukin (IL)-33 is a novel member of the IL-1 family of cytokines that promotes Th2 responses in lymphocytes as well as the activation of both mast cells and eosinophils via the ST2 receptor. Additionally, IL-33 has been proposed to act as a chromatin-associated transcriptional regulator in both endothelial cells of high endothelial venules and chronically inflamed vessels. Here we show that nuclear IL-33 is expressed in blood vessels of healthy tissues but down-regulated at the earliest onset of angiogenesis during wound healing; in addition, it is almost undetectable in human tumor vessels.

Pyrene fate affected by humic acid amendment in soil slurry systems.

Background: Humic acid (HA) has been found to affect the solubility, mineralization, and bound residue formation of polycyclic aromatic hydrocarbons (PAHs). However, most of the studies on the interaction between HA and PAH concentrated on one or two of the three phases. Few studies have provided a simple protocol to demonstrate the overall effects of HA on PAH distribution in soil systems for all three phases.

Developments in statistical analysis in quantitative genetics.

A remarkable research impetus has taken place in statistical genetics since the last World Conference. This has been stimulated by breakthroughs in molecular genetics, automated data-recording devices and computer-intensive statistical methods. The latter were revolutionized by the bootstrap and by Markov chain Monte Carlo (McMC).

An unusual case of adult airway obstruction from a lymphovenous malformation.

Lymphatic, venous, and mixed lymphovenous malformations are low-flow lesions that are present at birth and grow proportionately with the patient. We describe an unusual presentation of a lymphovenous malformation in an adult. A 19-year-old man presented to the emergency department with complaints of recent upper respiratory tract symptoms, increasing left-sided sore throat, voice change, odynophagia, dysphagia, and occasional subjective fevers and blood-tinged sputum.

Reference data for distal blood pressure in healthy elderly and middle-aged individuals measured with the strain gauge technique. Part II: Distal blood pressure after exercise.

Objective: Distal blood pressure (DBP) determination after an exercise test is used on suspicion of arterial peripheral vascular disease (apvd). In our department. the average age of these patients is about 60 years.

Efficiency of alternative MCMC strategies illustrated using the reaction norm model.

The Markov chain Monte Carlo (MCMC) strategy provides remarkable flexibility for fitting complex hierarchical models. However, when parameters are highly correlated in their posterior distributions and their number is large, a particular MCMC algorithm may perform poorly and the resulting inferences may be affected. The objective of this study was to compare the efficiency (in terms of the asymptotic variance of features of posterior distributions of chosen parameters, and in terms of computing cost) of six MCMC strategies to sample parameters using simulated data generated with a reaction norm model with unknown covariates as an example.

Complications after the surgical treatment of malignant thyroid disease.

Objectives: Our objectives were to document the complication rates after total thyroidectomy or lobectomy for malignant thyroid disease and to compare these rates with previously documented complication rates after operations for benign thyroid disease.

Methods: This is a retrospective chart review of patients diagnosed with thyroid carcinoma at a tertiary military medical center from 1996 to 2000.

Results: Eighty-two patients were identified with thyroid carcinoma, of which 81 underwent surgical treatment.

Reference data for distal blood pressure in healthy elderly and middle-aged individuals measured with the strain gauge technique. Part I: resting distal blood pressure.

Objective: Most patients referred to our department for distal blood pressure (DBP) determination on suspicion of arterial peripheral vascular disease (apvd) are more than 60 years of age, whereas the only available reference data for resting pressure are based on data from healthy individuals aged between 43 and 57 years. Our aim was to investigate whether newly collected reference data for DBP measured using the strain-gauge technique in healthy subjects older than 60 years and in others between 45 and 58 years were significantly different from the old reference data used in daily practice.

Material And Methods: .

Aggression in cataract-bearing alpha-1,3-galactosyltransferase knockout mice.

The Galalpha1-3Galbeta1-4GlcNAc epitope is the key antigen in the hyperacute rejection of pig-to-man xenotransplantation. In the alpha-1,3-galactosyltransferase knockout (alpha-1,3GT-KO) mouse - a model for xenograft donor pigs - a targeted mutation of the alpha-1,3 galactosyltransferase gene (Ggta1) has been constructed. These mice are depleted of the carbohydrate antigen and besides the mice are also known to develop cortical cataracts.

A comparison of strategies for Markov chain Monte Carlo computation in quantitative genetics.

In quantitative genetics, Markov chain Monte Carlo (MCMC) methods are indispensable for statistical inference in non-standard models like generalized linear models with genetic random effects or models with genetically structured variance heterogeneity. A particular challenge for MCMC applications in quantitative genetics is to obtain efficient updates of the high-dimensional vectors of genetic random effects and the associated covariance parameters. We discuss various strategies to approach this problem including reparameterization, Langevin-Hastings updates, and updates based on normal approximations.

Selective isolation of in vitro phase II conjugates using a lipophilic anionic exchange solid phase extraction method.

Identification, characterization and structure elucidation of human metabolites of drug candidates is crucial for the pharmaceutical industry to assess their activity against the therapeutic target of interest and potential toxicological effects. It often requires in vitro synthesis of microgram quantities of metabolites of interest with enzymatic preparations, pre-concentration of the reaction mixture by solid phase extraction (SPE), metabolite isolation using HPLC systems coupled to fraction collectors prior to nuclear magnetic resonance characterization. The method reported herein is a rapid and simple technique using solely off-line mixed phase anionic exchange lipophilic SPE cartridges to selectively isolate glucuronide and sulfate metabolites from their parent compound.

Variance and covariance components for liability of piglet survival during different periods.

Variance and covariance components for piglet survival in different periods were estimated from individual records of 133 004 Danish Landrace piglets and 89 928 Danish Yorkshire piglets, using a liability threshold model including both direct and maternal additive genetic effects. At the individual piglet level, the estimates of direct heritability in Landrace were 0.035, 0.

A study of heterogeneity of environmental variance for slaughter weight in pigs.

This work presents an analysis of heterogeneity of environmental variance for slaughter weight (175 days) in pigs. This heterogeneity is associated with systematic and additive genetic effects. The model also postulates the presence of additive genetic effects affecting the mean and environmental variance.

Mucosal vaccination with phage-displayed tumour antigens identified through proteomics-based strategy inhibits the growth and metastasis of 4T1 breast adenocarcinoma.

Cancer immunotherapy relies on the identification and characterization of tumour antigens that can be recognized by effector T cells. Here, we used a proteomics-based approach to identify tumour antigens recognized by serum antibodies from patients with breast cancer. Specific reactivity against a set of spots was identified and their identity was revealed by MALDI-TOF peptide mass fingerprinting.

Analysis of milk production traits in early lactation using a reaction norm model with unknown covariates.

The reaction norm model is becoming a popular approach to study genotype x environment interaction (GxE), especially when there is a continuum of environmental effects. These effects are typically unknown, and an approximation that is used in the literature is to replace them by the phenotypic means of each environment. It has been shown that this method results in poor inferences and that a more satisfactory alternative is to infer environmental effects jointly with the other parameters of the model.

Analysis of litter size and average litter weight in pigs using a recursive model.

An analysis of litter size and average piglet weight at birth in Landrace and Yorkshire using a standard two-trait mixed model (SMM) and a recursive mixed model (RMM) is presented. The RMM establishes a one-way link from litter size to average piglet weight. It is shown that there is a one-to-one correspondence between the parameters of SMM and RMM and that they generate equivalent likelihoods.

Selection for litter size at day five to improve litter size at weaning and piglet survival rate.

Selection for total number of piglets born (TNB) since 1992 has led to a significant increase in this trait in Danish Landrace and Danish Yorkshire but has also been accompanied by an increase in piglet mortality. The objective of this study was to estimate the genetic and phenotypic parameters for litter size and survival to find alternative selection criteria to improve litter size at weaning. Data from Landrace (9,300 litters) and Yorkshire (6,861 litters) were analyzed using REML based on a linear model including genetic effects of sow and service-sire.

The application of random regression models in the genetic analysis of monthly egg production in turkeys and a comparison with alternative longitudinal models.

Random regression models (RR) have become a popular methodology for the genetic study of longitudinal data since the last decade. The first objective of the current study was to investigate the application of RR models for the genetic analysis of egg production in turkeys. Data collected from a heavy dam line were used to estimate genetic parameters with 2 RR models, one having second-order Legendre polynomials as regression over time (RR2) and another with third-order polynomials (RR3).

Isolation and structure elucidation by LC-MS-SPE/NMR: PR toxin- and cuspidatol-related eremophilane sesquiterpenes from Penicillium roqueforti.

Three eremophilane sesquiterpenes (1, 2, and 3) were isolated from Penicillium roqueforti DAOM 232127, and their structures were established. The new (3S)-3-acetoxyeremophil-1(2),7(11),9(10)-trien-8-one (3) is a likely biosynthetic precursor of PR toxin. 1-Hydroxyeremophil-7(11),9(10)-dien-8-one (1) is related to the immunosuppressant cuspidatol.

The impact of tail tip amputation and ink tattoo on C57BL/6JBomTac mice.

Genetic material for polymerase chain reaction (PCR) and Southern blot analysis on transgenic mice is normally obtained by tail biopsy. Additionally, it may be necessary to tattoo the mice, as it is essential to have a good and permanent identification. The aim of this study was to evaluate the effects of amputating the tip of the tail to obtain a biopsy for genetic analysis and of ink tattooing on welfare in C57BL/6J mice, a strain often used as genetic background for transgenes.

Humic acid effect on pyrene degradation: finding an optimal range for pyrene solubility and mineralization enhancement.

The addition of humic acid (HA) to polycyclic aromatic hydrocarbon (PAH) contaminated systems has been shown to enhance, inhibit, or have no effect on the biodegradation of these PAHs. In this study, the surfactant effects of Elliott soil HA (ESHA) at two pH values were tested. At pH 7.