Robustly estimating the marginal likelihood for cognitive models via importance sampling.

Recent advances in Markov chain Monte Carlo (MCMC) extend the scope of Bayesian inference to models for which the likelihood function is intractable. Although these developments allow us to estimate model parameters, other basic problems such as estimating the marginal likelihood, a fundamental tool in Bayesian model selection, remain challenging. This is an important scientific limitation because testing psychological hypotheses with hierarchical models has proven difficult with current model selection methods. We propose an efficient method for estimating the marginal likelihood for models where the likelihood is intractable, but can be estimated unbiasedly. It is based on first running a sampling method such as MCMC to obtain samples for the model parameters, and then using these samples to construct the proposal density in an importance sampling (IS) framework with an unbiased estimate of the likelihood. Our method has several attractive properties: it generates an unbiased estimate of the marginal likelihood, it is robust to the quality and target of the sampling method used to form the IS proposals, and it is computationally cheap to estimate the variance of the marginal likelihood estimator. We also obtain the convergence properties of the method and provide guidelines on maximizing computational efficiency. The method is illustrated in two challenging cases involving hierarchical models: identifying the form of individual differences in an applied choice scenario, and evaluating the best parameterization of a cognitive model in a speeded decision making context. Freely available code to implement the methods is provided. Extensions to posterior moment estimation and parallelization are also discussed.

Incorporating blood-based liquid biopsy information into cancer staging: time for a TNMB system?

Tissue biopsy is the standard diagnostic procedure for cancer. Biopsy may also provide material for genotyping, which can assist in the diagnosis and selection of targeted therapies but may fall short in cases of inadequate sampling, particularly from highly heterogeneous tumors. Traditional tissue biopsy suffers greater limitations in its prognostic capability over the course of disease, most obviously as an invasive procedure with potential complications, but also with respect to probable tumor clonal evolution and metastasis over time from initial biopsy evaluation. Recent work highlights circulating tumor DNA (ctDNA) present in the blood as a supplemental, or perhaps an alternative, source of DNA to identify the clinically relevant cancer mutational landscape. Indeed, this noninvasive approach may facilitate repeated monitoring of disease progression and treatment response, serving as a means to guide targeted therapies based on detected actionable mutations in patients with advanced or metastatic solid tumors. Notably, ctDNA is heralding a revolution in the range of genomic profiling and molecular mechanisms to be utilized in the battle against cancer. This review will discuss the biology of ctDNA, current methods of detection and potential applications of this information in tumor diagnosis, treatment, and disease prognosis. Conventional classification of tumors to describe cancer stage follow the TNM notation system, heavily weighting local tumor extent (T), lymph node invasion (N), and detectable metastasis (M). With recent advancements in genomics and bioinformatics, it is conceivable that routine analysis of ctDNA from liquid biopsy (B) may make cancer diagnosis, treatment, and prognosis more accurate for individual patients. We put forward the futuristic concept of TNMB tumor classification, opening a new horizon for precision medicine with the hope of creating better outcomes for cancer patients.

Outbreak of Escherichia coli O157 Phage Type 32 linked to the consumption of venison products.

In September 2015, an outbreak of Escherichia coli Phage Type 32 with an indistinguishable multi locus variable number tandem repeat analysis profile was identified in Scotland. Twelve cases were identified; nine primary cases, two secondary and one asymptomatic case. Extensive food history investigations identified venison products containing wild venison produced by a single food business operator as the most likely source of the outbreak. Of the nine primary cases, eight had consumed venison products, and one case had not eaten venison themselves but had handled and cooked raw venison in the household. This was the first reported outbreak of Shiga toxin-producing Escherichia coli (STEC) linked to venison products in the UK, and was also notable due to the implicated products being commercially produced and widely distributed. In contrast, previous venison outbreaks reported from other countries have tended to be smaller and related to individually prepared carcases. The outbreak has highlighted some important knowledge gaps in relation to STEC in venison that are currently been investigated via a number of research studies.

Under-reporting giardiasis: time to consider the public health implications.

Giardiasis is a treatable disease, caused by the flagellated protozoan parasite, Giardia duodenalis (G. duodenalis). It is one of the most common enteric parasites found globally to cause gastrointestinal disturbances, and infections may result in long-term irritable bowel syndrome-like symptoms. It is a common misconception that giardiasis is associated with foreign travel, which results in locally acquired cases in the UK being underdiagnosed. This report highlights the findings from one large Scottish Health Board, arising from a change in testing methodology, which resulted in the screening of all stools submitted for enteric investigations for G. duodenalis. Previous selection criteria were restricted to patients with a travel history to specific regions of the world, or on the basis of certain clinical details. In this report, clinical details were recorded from samples shown to be positive using two methods: an ELISA-based antigen detection assay and microscopy. Clinical details were assessed for a total of 28 laboratory-confirmed positive cases against the original selection criteria. Twenty-six cases (93%) would have been excluded from Giardia testing if the previous selection criteria had been applied. Although nine cases stated foreign travel, only two had been to regions deemed to be 'high risk'. Therefore, those seven cases that travelled to perceived 'low-risk' regions would have been excluded from testing for this reason. This summary highlights the need for significant improvements to the selection criteria for Giardia testing. Laboratories should be encouraged towards the testing of all routinely submitted stools for this neglected pathogen to ensure cases that are acquired locally are properly identified and treated effectively.

Randomised crossover trial of telemonitoring in chronic respiratory patients (TeleCRAFT trial).

DESIGN: Randomised crossover trial with 6 months of standard best practice clinical care (control group) and 6 months with the addition of telemonitoring. PARTICIPANTS: 68 patients with chronic lung disease (38 with COPD; 30 with chronic respiratory failure due to other causes), who had a hospital admission for an exacerbation within 6 months of randomisation and either used long-term oxygen therapy or had an arterial oxygen saturation (SpO2) of <90% on air during the previous admission. Individuals received telemonitoring (second-generation system) via broadband link to a hospital-based care team. OUTCOME MEASURES: Primary outcome measure was time to first hospital admission for an acute exacerbation. Secondary outcome measures were hospital admissions, general practitioner (GP) consultations and home visits by nurses, quality of life measured by EuroQol-5D and hospital anxiety and depression (HAD) scale, and self-efficacy score (Stanford). RESULTS: Median (IQR) number of days to first admission showed no difference between the two groups­77 (114) telemonitoring, 77.5 (61) control ( p=0.189). Hospital admission rate at 6 months increased (0.63 telemonitoring vs 0.32 control p=0.026). Home visits increased during telemonitoring; GP consultations were unchanged. Self-efficacy fell, while HAD depression score improved marginally during telemonitoring. CONCLUSIONS: Telemonitoring added to standard care did not alter time to next acute hospital admission, increased hospital admissions and home visits overall, and did not improve quality of life in chronic respiratory patients. TRIAL REGISTRATION NUMBER: NCT02180919 (ClinicalTrials.gov).

eQTL of bronchial epithelial cells and bronchial alveolar lavage deciphers GWAS-identified asthma genes.

BACKGROUND: Genome-wide association studies (GWASs) have identified various genes associated with asthma, yet, causal genes or single nucleotide polymorphisms (SNPs) remain elusive. We sought to dissect functional genes/SNPs for asthma by combining expression quantitative trait loci (eQTLs) and GWASs. METHODS: Cis-eQTL analyses of 34 asthma genes were performed in cells from human bronchial epithelial biopsy (BEC, n = 107) and from bronchial alveolar lavage (BAL, n = 94). RESULTS: For TSLP-WDR36 region, rs3806932 (G allele protective against eosinophilic esophagitis) and rs2416257 (A allele associated with lower eosinophil counts and protective against asthma) were correlated with decreased expression of TSLP in BAL (P = 7.9 × 10(-11) and 5.4 × 10(-4) , respectively) and BEC, but not WDR36. Surprisingly, rs1837253 (consistently associated with asthma) showed no correlation with TSLP expression levels. For ORMDL3-GSDMB region, rs8067378 (G allele protective against asthma) was correlated with decreased expression of GSDMB in BEC and BAL (P = 1.3 × 10(-4) and 0.04) but not ORMDL3. rs992969 in the promoter region of IL33 (A allele associated with higher eosinophil counts and risk for asthma) was correlated with increased expression of IL33 in BEC (P = 1.3 × 10(-6) ) but not in BAL. CONCLUSIONS: Our study illustrates cell-type-specific regulation of the expression of asthma-related genes documenting SNPs in TSLP, GSDMB, IL33, HLA-DQB1, C11orf30, DEXI, CDHR3, and ZBTB10 affect asthma risk through cis-regulation of its gene expression. Whenever possible, disease-relevant tissues should be used for transcription analysis. SNPs in TSLP may affect asthma risk through up-regulating TSLP mRNA expression or protein secretion. Further functional studies are warranted.

Hepatitis B prevention, diagnosis, treatment and care: a review.

Hepatitis B virus (HBV) infection is a major cause of morbidity and mortality worldwide. Chronic hepatitis B (CHB) infection is associated with an increased risk of cirrhosis, hepatic decompensation and hepatocellular carcinoma (HCC). The likelihood of developing CHB is related to the age at which infection is acquired; the risk being lowest in adults and >90% in neonates whose mothers are hepatitis B e antigen positive. Treatment of CHB infection aims to clear HBV DNA and prevent the development of complications. There are currently seven drugs available for the treatment of CHB: five nucleos(t)ide analogues and two interferon-based therapies. Long-term treatment is often required, and the decision to treat is based on clinical assessment including the phase of CHB infection and the presence and extent of liver damage. A safe and effective HBV vaccine has been available since the early 1980s. Vaccination plays a central role in HBV prevention strategies worldwide, and a decline in the incidence and prevalence of HBV infection following the introduction of universal HBV vaccination programmes has been observed in many countries including the USA and parts of South East Asia and Europe. Post-exposure prophylaxis (PEP) with HBV vaccine +/- hepatitis B immunoglobulin is highly effective in preventing mother to child transmission and in preventing transmission following sharps injuries, sexual contact and other exposures to infected blood and body fluids. Transmission of HBV in the health care setting has become an increasingly rare event in developed nations. However, it remains a significant risk in developing countries reflecting the higher prevalence of CHB, limited access to HBV vaccination and PEP and a lack of adherence to standard infection control precautions.

Clinicopathologic characterization of naturally occurring diabetes mellitus in vervet monkeys.

Diabetes mellitus (DM) is a group of chronic metabolic diseases characterized by persistent fasting hyperglycemia, and it can be of either polygenic or monogenic origin. Animal models have played an important role in elucidating the pathophysiology of the polygenic Type 1 and type 2 DM forms; however, useful animal models of the monogenic forms do not exist. The authors describe 4 cases of naturally occurring DM in vervet monkeys (Chlorocebus aethiops sabaeus), 1 of which has clinicopathologic findings consistent with type 2 DM, including persistent hyperglycemia, hypertriglyceridemia, islet amyloidosis, and reduced islet insulin immunostaining. In contrast, the 3 remaining animals have clinicopathologic similarities to a monogenic form of the disease, including a lack of islet amyloidosis and hypertriglyceridemia, as well as normal islet insulin immunostaining. In addition, pedigree analysis conducted on one of these animals is consistent with either an autosomal dominant or mitochondrial inheritance pattern, which supports a monogenic form of DM. The authors thus hypothesize that a naturally occurring monogenic form of diabetes may occur in vervet monkeys, making them a potential animal model for future studies.

An outbreak of infection with Bacillus anthracis in injecting drug users in Scotland.

An investigation is currently underway to explore and control an outbreak of Bacillus anthracis among drug users (mainly injecting) in Scotland. Contaminated heroin or a contaminated cutting agent mixed with the heroin is considered to be the most likely source and vehicle of infection. Heroin users have been advised of the risk. The risk to the general public is regarded as very low.

A large-scale hole in the ionosphere caused by the launch of skylab.

A dramatic ionospheric phenomenon, unique in magnitude and in spatial and temporal extent, occurred along the Atlantic Coast of North America after the launch of the NASA Skylab Workshop on 14 May 1973. The effect was a large and rapid decrease in the total number of ionospheric electrons within a distance of 1000 kilometers of the burning engines of the Saturn V launch vehicle. The observations are interpreted in terms of exceptionally enhanced chemical loss rates due to the molecular hydrogen and water vapor contained in the Saturn second-stage exhaust plume.

Transcutaneous oximetry in clinical practice: consensus statements from an expert panel based on evidence.

Transcutaneous oximetry (PtcO2) is finding increasing application as a diagnostic tool to assess the peri-wound oxygen tension of wounds, ulcers, and skin flaps. It must be remembered that PtcO2 measures the oxygen partial pressure in adjacent areas of a wound and does not represent the actual partial pressure of oxygen within the wound, which is extremely difficult to perform. To provide clinical practice guidelines, an expert panel was convened with participants drawn from the transcutaneous oximetry workshop held on June 13, 2007, in Maui, Hawaii. Important consensus statements were (a) tissue hypoxia is defined as a PtcO2 <40 mm Hg; (b) in patients without vascular disease, PtcO2 values on the extremity increase to a value >100 mm Hg when breathing 100% oxygen under normobaric pressures; (c) patients with critical limb ischemia (ankle systolic pressure of < or =50 mm Hg or toe systolic pressure of < or =30 mm Hg) breathing air will usually have a PtcO2 <30 mm Hg; (d) low PtcO2 values obtained while breathing normobaric air can be caused by a diffusion barrier; (e) a PtcO2 <40 mm Hg obtained while breathing normobaric air is associated with a reduced likelihood of amputation healing; (f) if the baseline PtcO2 increases <10 mm Hg while breathing 100% normobaric oxygen, this is at least 68% accurate in predicting failure of healing post-amputation; (g) an increase in PtcO2 to >40 mm Hg during normobaric air breathing after revascularization is usually associated with subsequent healing, although the increase in PtcO2 may be delayed; (h) PtcO2 obtained while breathing normobaric air can assist in identifying which patients will not heal spontaneously.

Delivery of radionuclides to pretargeted monoclonal antibodies using dihydrofolate reductase and methotrexate in an affinity system.

A novel affinity system for a two-phase delivery of radionuclides to tumor cells has been developed. In the first phase, a nontoxic bivalent monoclonal antibody conjugated to an enzyme is targeted to the tumor cells. In the second phase, a radionuclide-derivatized enzyme inhibitor, specific for the enzyme conjugated to the antibody, is administered. The model system selected for this study is the recombinant human enzyme dihydrofolate reductase (rhDHFR) and its high-affinity competitive inhibitor methotrexate (MTX). MTX was labeled with a radionuclide by covalent attachment of diethylenetriaminepentaacetic acid (DTPA) complexed with 111In. Using the gamma-carboxyl residue of MTX for the attachment of DTPA, binding of the inhibitor to rhDHFR was not affected. The inhibitory activities of nonderivatized MTX and DTPA-MTX were indistinguishable. Human K562 erythroleukemia cells were used to evaluate under in vitro conditions the DHFR-MTX affinity system for the delivery of 111In-labeled DTPA-MTX to pretargeted alpha-transferrin receptor antibody-rhDHFR conjugates (alpha-TFR-DHFR). The data demonstrate that the delivery of 111In is dose dependent and highly specific. Under saturating conditions, binding of 111In-DTPA-MTX to alpha-TFR-DHFR-treated cells was 14-fold higher than to cells treated with nonconjugated alpha-TFR antibody. Further experiments indicated that the low level of nonspecific binding of 111In-DTPA-MTX was comparable to that of 111In-DTPA, known for its complete extracellular distribution and rapid clearance through the kidneys. Based on the data of this study, antibody-conjugated rhDHFR and radionuclide-labeled DTPA-MTX complexes provide components for an alternative radioimmunotherapeutic approach that can be expected to result in improved tumor tissue ratios of both the targeting moiety and the radionuclide-labeled derivative as compared to current approaches.

A genetic linkage map for cattle.

We report the most extensive physically anchored linkage map for cattle produced to date. Three-hundred thirteen genetic markers ordered in 30 linkage groups, anchored to 24 autosomal chromosomes (n = 29), the X and Y chromosomes, four unanchored syntenic groups and two unassigned linkage groups spanning 2464 cM of the bovine genome are summarized. The map also assigns 19 type I loci to specific chromosomes and/or syntenic groups and four cosmid clones containing informative microsatellites to chromosomes 13, 25 and 29 anchoring syntenic groups U11, U7 and U8, respectively. This map provides the skeletal framework prerequisite to development of a comprehensive genetic map for cattle and analysis of economic trait loci (ETL).

Toward a model-based cognitive neuroscience of mind wandering.

People often "mind wander" during everyday tasks, temporarily losing track of time, place, or current task goals. In laboratory-based tasks, mind wandering is often associated with performance decrements in behavioral variables and changes in neural recordings. Such empirical associations provide descriptive accounts of mind wandering - how it affects ongoing task performance - but fail to provide true explanatory accounts - why it affects task performance. In this perspectives paper, we consider mind wandering as a neural state or process that affects the parameters of quantitative cognitive process models, which in turn affect observed behavioral performance. Our approach thus uses cognitive process models to bridge the explanatory divide between neural and behavioral data. We provide an overview of two general frameworks for developing a model-based cognitive neuroscience of mind wandering. The first approach uses neural data to segment observed performance into a discrete mixture of latent task-related and task-unrelated states, and the second regresses single-trial measures of neural activity onto structured trial-by-trial variation in the parameters of cognitive process models. We discuss the relative merits of the two approaches, and the research questions they can answer, and highlight that both approaches allow neural data to provide additional constraint on the parameters of cognitive models, which will lead to a more precise account of the effect of mind wandering on brain and behavior. We conclude by summarizing prospects for mind wandering as conceived within a model-based cognitive neuroscience framework, highlighting the opportunities for its continued study and the benefits that arise from using well-developed quantitative techniques to study abstract theoretical constructs.

Pathogenesis of human poliovirus infection in mice. I. Clinical and pathological studies.

Human poliovirus infection in mice was studied to determine the similarities to human poliomyelitis, the selective vulnerability of neurons to infection, the role of the immune response in age-dependent susceptibility, and possible viral persistence. Mice inoculated intracerebrally (ic) with the Lansing type 2 poliovirus developed a disease with clinical, pathological, and age-dependent features resembling human poliomyelitis. Adult mice had a shorter incubation period (50% paralysis, Day 8 vs. Day 13) and a higher incidence of paralysis (97% vs. 79%) than newborns. Only paralyzed animals had pathologic changes in the spinal cord, and these corresponded to the degree of paralysis. Fluorescent antibody staining showed that selective infection of neurons was most intense in the anterior horn motor neurons of the spinal cord. There was no extraneural virus replication and no systemic neutralizing antibody response. Cyclophosphamide immunosuppression enhanced rather than diminished disease, indicating that maturation of immune responses did not explain the relative resistance of newborns to paralysis.

A pilot study of assertive community treatment for patients with chronic psychotic disorders.

This study measured hospital utilization and residential status of 51 patients with chronic psychoses before and after a 1-year program of assertive community treatment. Time hospitalized was reduced by 94%, and 82% of the patients previously living in hospitals or group homes attained independent living status, suggesting that this form of clinical management may reduce institutional care and costs to mental health care systems.

Synergistic influence of polypeptide growth factors on cultured human muscle.

In two- to five-week tissue cultures of biopsied adult human skeletal muscle, combined addition to the culture medium of insulin, fibroblast growth factor, and epidermal growth factor synergistically increased creatine kinase activity 17-fold, increased acetylcholine receptors tenfold, and accelerated muscle differentiation. This study provides the first demonstration of the beneficial influence of these peptides on human muscle. It also establishes a new culture medium, resulting in the following: (1) much better long-term growth and differentiation of biopsied adult human muscle; and (2) by allowing elimination of embryo extract and reduction of serum, an important step toward developing a fully defined medium for culturing biopsied adult human normal and pathologic muscle tissue.

Plasma polymerase chain reaction for cytomegalovirus DNA after allogeneic marrow transplantation: comparison with polymerase chain reaction using peripheral blood leukocytes, pp65 antigenemia, and viral culture.

In a prospective longitudinal study, detection of cytomegalovirus (CMV) DNA in plasma (plasma polymerase chain reaction [PCR]) was compared with PCR of CMV DNA in peripheral blood leukocytes (PBL PCR), the CMV pp65 antigenemia assay, and viral cultures from blood, urine, and throat of 29 patients, 14 of whom received pp65 antigenemia-guided early ganciclovir treatment and 15 of whom received ganciclovir at engraftment. Among 328 blood samples tested by all methods, PBL PCR was the most sensitive test, followed by the pp65 antigenemia assay, plasma PCR, and viremia. In the 14 patients who received pp65 antigenemia-guided early treatment, the incidence of PBL PCR, pp65 antigenemia, plasma PCR, and viremia before day 100 was 79%, 79%, 71%, and 27%, respectively, with a median day of onset of day 32, 42, 45, and 51, respectively. Nine patients (64%) became positive by PBL PCR, pp65 antigenemia, and plasma PCR. Of 15 patients who were treated with ganciclovir at engraftment, 12 (80%) became positive by PBL PCR, plasma PCR, and/or pp65 antigenemia while receiving ganciclovir; 3 (20%) had breakthrough infection with all three methods, including 2 with high-grade antigenemia (more than three positive cells in duplicate staining); none of these patients subsequently developed positive CMV cultures or disease. In 49 specimens, PBL PCR and/or pp65 antigenemia assay could not be performed because of insufficient neutrophil counts. In conclusion, the sensitivity of plasma PCR is significantly lower than that of PBL PCR but similar to that of the pp65 antigenemia assay. Plasma PCR may be particularly useful in clinical situations in which a less sensitive and possibly more specific assay is warranted or in which leukocyte counts are inadequate to perform cell-based assays.

Fibroblast growth factor, epidermal growth factor and insulin exert a neuronal-like influence on acetylcholine receptors in aneurally cultured human muscle.

Fibroblast growth factor (FGF), epidermal growth factor (EGF) and insulin added in combination to the culture medium in which normal human muscle was cultured caused a 4.0-fold (P less than 0.005) increase of the total number of nicotinic acetylcholine receptors (AChRs) and a 4.5-fold (P less than 0.001) increase in AChR aggregation. Individually, only FGF caused a 3.0-fold increase (P less than 0.005) in AChR aggregation, without influencing the total number of AChRs. To the contrary, insulin alone caused a 2.0-fold increase (P less than 0.05) in the total number of AChRs without influencing AChR aggregation. These findings show that these three polypeptide growth factors exert a neuronal-like influence on cultured human muscle in regard to AChRs.