Search

Previous studies demonstrate that self-reports of mammography screening for breast cancer and colonoscopy screening for colorectal cancer demonstrate concordance, based on adherence to screening guidelines, with electronic medical records (EMRs) in over 90% of those interviewed, as well as high sensitivity and specificity, and can be used for monitoring our Healthy People goals. However, for screening tests for cervical and lung cancers, and for various sub-populations, concordance between self-report and EMRs has been noticeably lower with poor sensitivity or specificity. This study aims to test the validity and reliability of lung, colorectal, cervical, and breast cancer screening questions from the 2021 and 2022 National Health Interview Survey (NHIS). We present the protocol for a study designed to measure the validity and reliability of the NHIS cancer screening questions compared to EMRs from four US-based healthcare systems. We planned a randomized trial of a phone- vs web-based survey with NHIS questions that were previously revised based on extensive cognitive interviewing. Our planned sample size will be 1576 validity interviews, and 1260 interviews randomly assigned at 1 or 3 months after the initial interview. We are enrolling people eligible for cancer screening based on age, sex, and smoking history per US Preventive Services Task Force recommendations. We will evaluate question validity using concordance, sensitivity, specificity, positive predictive value, negative predictive value, and report-to-records ratio. We further are randomizing participants to complete a second survey 1 vs 3 months later to assess question reliability. We suggest that typical measures of concordance may need to be reconsidered in evaluating cancer screening questions. [ABSTRACT FROM AUTHOR]

Genetic disease control is generally not given the importance it deserves. Information about what percentage of individuals carry a disorder-causing mutation is crucial for breeders to produce healthy offspring and maintain a healthy dog population of a particular breed. This study aims to provide information about the incidence of mutant alleles for the most frequently occurring hereditary diseases in the Australian Shepherd dog breed (AS). The samples were collected during a 10-years period (2012–2022) in the European population of the AS. Mutant alleles and incidence were calculated from all the obtained data for all the diseases, specifically: collie eye anomaly (9.71%), canine multifocal retinopathy type 1 (0.53%), hereditary cataract (11.64%), progressive rod-cone degeneration (1.58%), degenerative myelopathy (11.77%) and bob-tail/short-tail (31.74%). Our data provide more information to dog breeders to support their effort to limit the spread of hereditary diseases. [ABSTRACT FROM AUTHOR]

Bovine spongiform encephalopathy (BSE) is a prion disease of cattle that is caused by the misfolding of the cellular prion protein (PrPC) into an infectious conformation (PrPSc). PrPC is a predominantly α-helical membrane protein that misfolds into a β-sheet rich, infectious state, which has a high propensity to self-assemble into amyloid fibrils. Three strains of BSE prions can cause prion disease in cattle, including classical BSE (C-type) and two atypical strains, named L-type and H-type BSE. To date, there is no detailed information available about the structure of any of the infectious BSE prion strains. In this study, we purified L-type BSE prions from transgenic mouse brains and investigated their biochemical and ultrastructural characteristics using electron microscopy, image processing, and immunogold labeling techniques. By using phosphotungstate anions (PTA) to precipitate PrPSc combined with sucrose gradient centrifugation, a high yield of proteinase K-resistant BSE amyloid fibrils was obtained. A morphological examination using electron microscopy, two-dimensional class averages, and three-dimensional reconstructions revealed two structural classes of L-type BSE amyloid fibrils; fibrils that consisted of two protofilaments with a central gap and an average width of 22.5 nm and one-protofilament fibrils that were 10.6 nm wide. The one-protofilament fibrils were found to be more abundant compared to the thicker two-protofilament fibrils. Both fibrillar assemblies were successfully decorated with monoclonal antibodies against N- and C-terminal epitopes of PrP using immunogold-labeling techniques, confirming the presence of polypeptides that span residues 100–110 to 227–237. The fact that the one-protofilament fibrils contain both N- and C-terminal PrP epitopes constrains molecular models for the structure of the infectious conformer in favour of a compact four-rung β-solenoid fold. Author summary: Bovine spongiform encephalopathy (BSE), also called "mad cow disease," is a deadly neurodegenerative disease in cattle. BSE is caused by PrPSc, which is an aberrantly folded conformer of a normal protein in the host. PrPSc is an infectious protein and also referred to as a prion. BSE prions exist in three variants or strains: C-type BSE prions, which caused the epizootic "mad cow disease" outbreak, and two atypical forms L-type and H-type BSE prions, named according to their migration patterns during gel electrophoresis. For our investigations, we isolated L-type BSE prions from transgenic mouse brains and analyzed these samples using transmission electron microscopy and three-dimensional reconstruction techniques. Our study revealed that L-type BSE prions assemble into one- and two-protofilament containing amyloid fibrils and that the width of the two-protofilament fibrils is approximately twice that of one-protofilament fibrils. In addition, we labeled the L-type BSE fibrils at the ultrastructural level using specific anti-prion protein antibodies that recognize epitopes at both ends of the molecule. Our data agree with the previously proposed four-rung β-solenoid model for the structure of infectious PrPSc. [ABSTRACT FROM AUTHOR]

Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through time and the distribution of the sampling times depends on the effective population size, explicit statistical modeling of sampling times improves population size estimation. Previous work assumed that the genealogy relating sampled sequences is known and modeled sampling times as an inhomogeneous Poisson process with log-intensity equal to a linear function of the log-transformed effective population size. We improve this approach in two ways. First, we extend the method to allow for joint Bayesian estimation of the genealogy, effective population size trajectory, and other model parameters. Next, we improve the sampling time model by incorporating additional sources of information in the form of time-varying covariates. We validate our new modeling framework using a simulation study and apply our new methodology to analyses of population dynamics of seasonal influenza and to the recent Ebola virus outbreak in West Africa. Author summary: Estimating changes in the number of individuals in a given population is a challenging problem in some settings. For example, estimating population size trajectories of the number of people infected by a pathogen (e.g., Influenza virus) is a difficult problem, because many infections in a large population remain unobserved/hidden. One indirect way of assessing population size changes is to take a sample of individuals from the population of interest and analyze genetic sequences from these individuals (e.g., Influenza virus genomes). Intuitively, genetic data is informative about population size changes, because genetic diversity increases/decreases together with the population size. However, if we sample more individuals when the population size increases and less when it decreases, this strategy produces biased results. To avoid this bias, we propose a method that explicitly and flexibly models potential dependency of genetic sequence sampling on the population size. An added bonus of this new modeling framework is more precise estimation of population size changes. We demonstrate strengths of our new methodology on simulated data and on genetic sequences of Influenza and Ebola viruses. [ABSTRACT FROM AUTHOR]

The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally. [ABSTRACT FROM AUTHOR]

Background: Both people with autism spectrum conditions (ASC) and borderline personality disorder (BPD) are significantly challenged in terms of understanding and responding to emotions and in interpersonal functioning. Aims: To compare ASC, BPD, and comorbid patients in terms of autistic traits, empathy, and systemizing. Methods: 624 ASC, 23 BPD, and 16 comorbid (ASC+BPD) patients, and 2,081 neurotypical controls (NC) filled in the Autism Spectrum Quotient (AQ), the Empathy Quotient (EQ) and the Systemizing Quotient-Revised (SQ-R). Results: On the AQ, the ASC group scored higher than the BPD group, who in turn scored higher than the comorbid group, who scored higher than controls. On the EQ, we found the comorbid and ASC groups scored lower than the BPD group, who were not different from controls. Finally, on the SQ-R, we found the ASC and BPD group both scored higher than controls. Conclusions: Similar to ASC, BPD patients have elevated autistic traits and a strong drive to systemize, suggesting an overlap between BPD and ASC. [ABSTRACT FROM AUTHOR]

Chronic wasting disease (CWD) is a fatal prion disease of wild and captive cervids in North America. Prions are infectious agents composed of a misfolded version of a host-encoded protein, termed PrPSc. Infected cervids excrete and secrete prions, contributing to lateral transmission. Geographical distribution is expanding and case numbers in wild cervids are increasing. Recently, the first European cases of CWD have been reported in a wild reindeer and two moose from Norway. Therefore, methods to detect the infection early in the incubation time using easily available samples are desirable to facilitate effective disease management. We have adapted the real-time quaking induced conversion (RT-QuIC) assay, a sensitive in vitro prion amplification method, for pre-clinical detection of prion seeding activity in elk feces. Testing fecal samples from orally inoculated elk taken at various time points post infection revealed early shedding and detectable prion seeding activity throughout the disease course. Early shedding was also found in two elk encoding a PrP genotype associated with reduced susceptibility for CWD. In summary, we suggest that detection of CWD prions in feces by RT-QuIC may become a useful tool to support CWD surveillance in wild and captive cervids. The finding of early shedding independent of the elk’s prion protein genotype raises the question whether prolonged survival is beneficial, considering accumulation of environmental prions and its contribution to CWD transmission upon extended duration of shedding. [ABSTRACT FROM AUTHOR]

Aims and Objectives: Acute renal failure is a severe complication of lower extremity major arterial reconstructions, which could even be fatal. Levosimendan is a dual-acting positive inotropic and vasodilatory agent, which is suspected to have protective effects against cardiac ischemia. However, there is no data available on lower limb or remote organ ischemic injuries therefore the aim of the study was to investigate the effect of levosimendan on lower limb ischemia-reperfusion injury and the corollary renal dysfunction. Methods: Male Wistar rats underwent 180 min bilateral lower limb ischemia followed by 4 or 24 hours of reperfusion. Intravenous Levosimendan was administered continuously (0.2μg/bwkg/min) throughout the whole course of ischemia and the first 3h of reperfusion. Results were compared with sham-operated and ischemia-reperfusion groups. Hemodynamic monitoring was performed by invasive arterial blood pressure measurement. Kidney and lower limb muscle microcirculation was registered by a laser Doppler flowmeter. After 4h and 24h of reperfusion, serum, urine and histological samples were collected. Results: Systemic hemodynamic parameters and microcirculation of kidney and the lower limb significantly improved in the Levosimendan treated group. Muscle viability was significantly preserved 4 and 24 hours after reperfusion. At the same time, renal functional laboratory tests and kidney histology demonstrated significantly less expressive kidney injury in Levosimendan groups. TNF-α levels were significantly less elevated in the Levosimendan group 4 hours after reperfusion. Conclusion: The results claim a protective role for Levosimendan administration during major vascular surgeries to prevent renal complications. [ABSTRACT FROM AUTHOR]

Background: The Cub and Sushi Multiple Domains 1 (CSMD1) gene, located on the short arm of chromosome 8, codes for a type I transmembrane protein whose function is currently unknown. CSMD1 expression is frequently lost in many epithelial cancers. Our goal was to characterize the relationships between CSMD1 somatic mutations, allele imbalance, DNA methylation, and the clinical characteristics in colorectal cancer patients. Methods: We sequenced the CSMD1 coding regions in 54 colorectal tumors using the 454FLX pyrosequencing platform to interrogate 72 amplicons covering the entire coding sequence. We used heterozygous SNP allele ratios at multiple CSMD1 loci to determine allelic balance and infer loss of heterozygosity. Finally, we performed methylation-specific PCR on 76 colorectal tumors to determine DNA methylation status for CSMD1 and known methylation targets ALX4, RUNX3, NEUROG1, and CDKN2A. Results: Using 454FLX sequencing and confirming with Sanger sequencing, 16 CSMD1 somatic mutations were identified in 6 of the 54 colorectal tumors (11%). The nonsynonymous to synonymous mutation ratio of the 16 somatic mutations was 15∶1, a ratio significantly higher than the expected 2∶1 ratio (p = 0.014). This ratio indicates a presence of positive selection for mutations in the CSMD1 protein sequence. CSMD1 allelic imbalance was present in 19 of 37 informative cases (56%). Patients with allelic imbalance and CSMD1 mutations were significantly younger (average age, 41 years) than those without somatic mutations (average age, 68 years). The majority of tumors were methylated at one or more CpG loci within the CSMD1 coding sequence, and CSMD1 methylation significantly correlated with two known methylation targets ALX4 and RUNX3. C:G>T:A substitutions were significantly overrepresented (47%), suggesting extensive cytosine methylation predisposing to somatic mutations. Conclusions: Deep amplicon sequencing and methylation-specific PCR reveal that CSMD1 alterations can correlate with earlier clinical presentation in colorectal tumors, thus further implicating CSMD1 as a tumor suppressor gene. [ABSTRACT FROM AUTHOR]

Methyl-CpG binding domain protein sequencing (MBD-seq) is widely used to survey DNA methylation patterns. However, the optimal experimental parameters for MBD-seq remain unclear and the data analysis remains challenging. In this study, we generated high depth MBD-seq data in MCF-7 cell and developed a bi-asymmetric-Laplace model (BALM) to perform data analysis. We found that optimal efficiency of MBD-seq experiments was achieved by sequencing 100 million unique mapped tags from a combination of 500 mM and 1000 mM salt concentration elution in MCF-7 cells. Clonal bisulfite sequencing results showed that the methylation status of each CpG dinucleotides in the tested regions was accurately detected with high resolution using the proposed model. These results demonstrated the combination of MBD-seq and BALM could serve as a useful tool to investigate DNA methylome due to its low cost, high specificity, efficiency and resolution. [ABSTRACT FROM AUTHOR]

GWAS of prostate cancer have been remarkably successful in revealing common genetic variants and novel biological pathways that are linked with its etiology. A more complete understanding of inherited susceptibility to prostate cancer in the general population will come from continuing such discovery efforts and from testing known risk alleles in diverse racial and ethnic groups. In this large study of prostate cancer in African American men (3,425 prostate cancer cases and 3,290 controls), we tested 49 risk variants located in 28 genomic regions identified through GWAS in men of European and Asian descent, and we replicated associations (at p≤0.05) with roughly half of these markers. Through fine-mapping, we identified nearby markers in many regions that better define associations in African Americans. At 8q24, we found 9 variants (p≤6x10-4 ) that best capture risk of prostate cancer in African Americans, many of which are more common in men of African than European descent. The markers found to be associated with risk at each locus improved risk modeling in African Americans (per allele OR = 1.17) over the alleles reported in the original GWAS (OR = 1.08). In summary, in this detailed analysis of the prostate cancer risk loci reported from GWAS, we have validated and improved upon markers of risk in some regions that better define the association with prostate cancer in African Americans. Our findings with variants at 8q24 also reinforce the importance of this region as a major risk locus for prostate cancer in men of African ancestry. [ABSTRACT FROM AUTHOR]

Bovine spongiform encephalopathy (BSE) surveillance programs have been employed in numerous countries to monitor BSE prevalence and to protect animal and human health. Since 1999, the European Commission (EC) authorized the evaluation and approval of 20 molecular based tests for the rapid detection of the pathological prion protein (PrPsc) in BSE infection. The diagnostic sensitivity, convenience, and speed of these tests have made molecular diagnostics the preferred method for BSE surveillance. The aim of this study was to determine the analytical sensitivity of 4 commercially available BSE rapid-test kits, including the Prionics®-Check WESTERN, the Prionics® Check-PrioSTRIP™, the BioRad® TeSeE™ ELISA, and the IDEXX® HerdChek™ EIA. Performances of these tests were then compared to 2 confirmatory tests, including the BioRad® TeSeE™ Western Blot and the modified Scrapie Associated Fibrils (SAF)/OIE Immunoblot. One 50% w/v homogenate was made from experimentally generated C-type BSE brain tissues in ddH2O. Homogenates were diluted through a background of BSE-negative brainstem homogenate. Masses of both positive and negative tissues in each dilution were calculated to maintain the appropriate tissue amounts for each test platform. Specific concentrated homogenization buffer was added accordingly to maintain the correct buffer condition for each test. ELISA-based tests were evaluated using their respective software/detection platforms. Blot-protocols were evaluated by manual measurements of blot signal density. Detection limitations were determined by fitted curves intersecting the manufacturers' positive/negative criteria. The confirmatory SAF Immunoblot displayed the highest analytical sensitivity, followed by the IDEXX® HerdChek™ EIA, Bio-Rad® TeSeE™ Western Blot, the Bio-Rad® TeSeE™ ELISA, Prionics®-Check PrioSTRIP™, and Prionics®-Check WESTERN™, respectively. Although the tests performed at different levels of sensitivity, the most sensitive and least sensitive of the rapid tests were separated by 2 logs in analytical sensitivity, meeting European performance requirements. All rapid tests appear suitable for targeted BSE surveillance programs, as implemented in Canada. [ABSTRACT FROM AUTHOR]

The epidemiology and possibly the etiology of bovine spongiform encephalopathy (BSE) have recently been recognized to be heterogeneous. In particular, three types [classical (C) and two atypical (H, L)] have been identified, largely on the basis of characteristics of the proteinase K (PK)-resistant core of the misfolded prion protein associated with the disease (PrPres). The present study was conducted to characterize the 17 Canadian BSE cases which occurred prior to November 2009 based on the molecular and biochemical properties of their PrPres, including immunoreactivity, molecular weight, glycoform profile and relative PK sensitivity. Two cases exhibited molecular weight and glycoform profiles similar to those of previously reported atypical cases, one corresponding to H-type BSE (case 6) and the other to L-type BSE (case 11). All other cases were classified as C-type. PK digestion under mild and stringent conditions revealed a reduced protease resistance in both of these cases compared to the C-type cases. With Western immunoblotting, N-terminal-specific antibodies bound to PrPres from case 6 but not to that from case 11 or C-type cases. C-terminal-specific antibodies revealed a shift in the glycoform profile and detected a fourth protein fragment in case 6, indicative of two PrPres subpopulations in H-type BSE. No mutations suggesting a genetic etiology were found in any of the 17 animals by sequencing the full PrP-coding sequence in exon 3 of the PRNP gene. Thus, each of the three known BSE types have been confirmed in Canadian cattle and show molecular characteristics highly similar to those of classical and atypical BSE cases described from Europe, Japan and the USA. The occurrence of atypical cases of BSE in countries such as Canada with low BSE prevalence and transmission risk argues for the occurrence of sporadic forms of BSE worldwide. [ABSTRACT FROM AUTHOR]

Bone morphogenic protein (BMP)-7 is a member of the BMP family which are structurally and functionally related, and part of the TGFb super family of growth factors. BMP-7 has been reported to inhibit renal fibrosis and TGFβ1-induced epithelialmesenchymal transition (EMT), in part through negative interactions with TGFb1 induced Smad 2/3 activation. We utilized in vivo bleomycin-induced fibrosis models in the skin and lung to determine the potential therapeutic effect of BMP-7. We then determined the effect of BMP-7 on TGFβ1-induced EMT in lung epithelial cells and collagen production by human lung fibroblasts. We show that BMP-7 did not affect bleomycin-induced fibrosis in either the lung or skin in vivo; had no effect on expression of pro-fibrotic genes by human lung fibroblasts, either at rest or following exposure to TGFβ1; and did not modulate TGFβ1 -induced EMT in human lung epithelial cells. Taken together our data indicates that BMP-7 has no antifibrotic effect in lung or skin fibrosis either in vivo or in vitro. This suggests that the therapeutic options for BMP-7 may be confined to the renal compartment. [ABSTRACT FROM AUTHOR]

Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44.7% (se: 3.7%) for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1) whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2) whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported) height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the variability of height, and by implication other complex phenotypes. Our overall conclusions are that when study sizes are quite large (5,000 or so) the additive heritability estimate for height is not apparently biased upwards using the linear mixed model; however there is evidence in our simulation that a very large number of causal variants (many thousands) each with very small effect on phenotypic variance will need to be discovered to fill the gap between the heritability explained by known versus unknown causal variants. We conclude that today's GWAS data will remain useful in the future for causal variant prediction, but that finding the causal variants that need to be predicted may be extremely laborious.

Background:Impairments in mismatch negativity (MMN) generation have been consistently reported in patients with schizophrenia. However, underlying oscillatory activity of MMN deficits in schizophrenia and the relationship with cognitive impairments have not been investigated in detail. Time-frequency power and phase analyses can provide more detailed measures of brain dynamics of MMN deficits in schizophrenia. Method:21 patients with schizophrenia and 21 healthy controls were tested with a roving frequency paradigm to generate MMN. Time-frequency domain power and phase-locking (PL) analysis was performed on all trials using short-time Fourier transforms with Hanning window tapering. A comprehensive battery (CANTAB) was used to assess neurocognitive functioning. Results:Mean MMN amplitude was significantly lower in patients with schizophrenia (95% CI 0.18 - 0.77). Patients showed significantly lower EEG power (95% CI -1.02 - -0.014) in the ~4-7 Hz frequency range (theta band) between 170 and 210 ms. Patients with schizophrenia showed cognitive impairment in multiple domains of CANTAB. However, MMN impairments in amplitude and power were not correlated with clinical measures, medication dose, social functioning or neurocognitive performance. Conclusion:The findings from this study suggested that while MMN may be a useful marker to probe NMDA receptor mediated mechanisms and associated impairments in gain control and perceptual changes, it may not be a useful marker in association with clinical or cognitive changes. Trial-by-trial EEG power analysis can be used as a measure of brain dynamics underlying MMN deficits which also can have implications for the use of MMN as a biomarker for drug discovery. [ABSTRACT FROM AUTHOR]