Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

peer-reviewedBackground The trading of individual animal genotype information often involves only the exchange of the called genotypes and not necessarily the additional information required to effectively call structural variants. The main aim here was to determine if it is possible to impute copy number variants (CNVs) using the flanking single nucleotide polymorphism (SNP) haplotype structure in cattle. While this objective was achieved using high-density genotype panels (i.e., 713,162 SNPs), a secondary objective investigated the concordance of CNVs called with this high-density genotype panel compared to CNVs called from a medium-density panel (i.e., 45,677 SNPs in the present study). This is the first study to compare CNVs called from high-density and medium-density SNP genotypes from the same animals. High (and medium-density) genotypes were available on 991 Holstein-Friesian, 1015 Charolais, and 1394 Limousin bulls. The concordance between CNVs called from the medium-density and high-density genotypes were calculated separately for each animal. A subset of CNVs which were called from the high-density genotypes was selected for imputation. Imputation was carried out separately for each breed using a set of high-density SNPs flanking the midpoint of each CNV. A CNV was deemed to be imputed correctly when the called copy number matched the imputed copy number. Results For 97.0% of CNVs called from the high-density genotypes, the corresponding genomic position on the medium-density of the animal did not contain a called CNV. The average accuracy of imputation for CNV deletions was 0.281, with a standard deviation of 0.286. The average accuracy of imputation of the CNV normal state, i.e. the absence of a CNV, was 0.982 with a standard deviation of 0.022. Two CNV duplications were imputed in the Charolais, a single CNV duplication in the Limousins, and a single CNV duplication in the Holstein-Friesians; in all cases the CNV duplications were incorrectly imputed. Conclusion The vast majority of CNVs called from the high-density genotypes were not detected using the medium-density genotypes. Furthermore, CNVs cannot be accurately predicted from flanking SNP haplotypes, at least based on the imputation algorithms routinely used in cattle, and using the SNPs currently available on the high-density genotype panel

RNA-seq transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis

Bovine tuberculosis, caused by infection with Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including gene expression microarrays and RNA-sequencing (RNA-seq), has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix(®) GeneChip(®) Bovine Genome Array platform from the same PBL-extracted RNA. A total of 3,250 differentially expressed (DE) annotated genes were detected in the M. bovis-infected samples relative to the controls (adjusted P-value ≤0.05), with the number of genes displaying decreased relative expression (1,671) exceeding those with increased relative expression (1,579). Ingenuity(®) Systems Pathway Analysis (IPA) of all DE genes revealed enrichment for genes with immune function. Notably, transcriptional suppression was observed among several of the top-ranking canonical pathways including Leukocyte Extravasation Signaling. Comparative platform analysis demonstrated that RNA-seq detected a larger number of annotated DE genes (3,250) relative to the microarray (1,398), of which 917 genes were common to both technologies and displayed the same direction of expression. Finally, we show that RNA-seq had an increased dynamic range compared to the microarray for estimating differential gene expression

Flexural vibrations of conical shells with free edges

Resonant frequencies and mode shapes of truncated conical shells with free edges in transverse vibratio

Usefulness of mid-infrared spectroscopy as a tool to estimate body condition score change from milk samples in intensively-fed dairy cows.

Directly measuring individual cow energy balance is not trivial. Other traits, like body condition score (BCS) and BCS change (ΔBCS) can, however, be used as an indicator of cow energy status. Body condition score is a metric used world-wide to estimate cow body reserves and the estimation of ΔBCS was, until now, conditional on the availability of multiple BCS assessments. The aim of the present study was to estimate ΔBCS from milk mid-infrared (MIR) spectra and days in milk (DIM) in intensively-fed dairy cows using statistical prediction methods. Daily BCS was interpolated from cubic splines fitted through the BCS records and daily ΔBCS was calculated from these splines. Body condition score change records were merged with milk MIR spectra recorded on the same week. The data set comprised 37,077 ΔBCS phenotypes across 9,403 lactations from 6,988 cows in 151 herds based in Quebec (Canada). Partial least squares regression (PLSR) and a neural network (NN) were then used to estimate ΔBCS from 1) MIR spectra only, 2) DIM only, or 3) MIR spectra and DIM together. ΔBCS data in both the first 120 DIM and 305 DIM of lactation were used to develop the estimates. Daily ΔBCS had a standard deviation of 4.40*10-3 BCS units in the 120-d data set and of 3.63*10-3 BCS units in the 305-d data set. 4-fold cross-validation was used to calibrate and test the prediction equations. External validation was also conducted using more recent years of data. Irrespective of whether based on the first 120 or 305 DIM, or when MIR spectra only, DIM only or MIR spectra and DIM were jointly used as prediction variables, NN produced the lowest root mean square error (RMSE) of cross-validation (1.81*10-3 BCS units and 1.51*10-3 BCS units, respectively, using the 120-d and 305-d data set). Relative to predictions for the entire 305 DIM, the RMSE of cross-validation was 15.4% and 1.5% lower in the first 120 DIM when using PLSR and NN, respectively. Predictions from DIM only were more accurate than those using just MIR spectra data but, irrespective of the data set and of the prediction model used, the combining DIM information with MIR spectral data as prediction variables reduced the RMSE compared with inclusion of DIM alone, albeit the benefit was small (the RMSE from cross-validation was reduced up to 5.5% when DIM and spectral data were jointly used as model features instead of DIM only). However, when predicting extreme ΔBCS records, the MIR spectral data was more informative than DIM. Model performance when predicting ΔBCS records in future years was similar to that from cross-validation demonstrating the ability of MIR spectra of milk and DIM combined to estimate ΔBCS, particularly in early lactation. This can be used to routinely generate estimates of ΔBCS to aid in day-to-day individual cow management

Improving adherence to multiple medications in older people in primary care: Selecting intervention components to address patient-reported barriers and facilitators

Background: Medication adherence is vital to ensuring optimal patient outcomes, particularly amongst multimorbid older people prescribed multiple medications. Interventions targeting adherence often lack a theoretical underpinning and this may impact on effectiveness. The theoretical domains framework (TDF) of behaviour can aid intervention development by systematically identifying key determinants of medication adherence. Objectives: This study aimed to (i) identify determinants (barriers, facilitators) of adherence to multiple medications from older people's perspectives; (ii) identify key domains to target for behaviour change; and (iii) map key domains to intervention components [behaviour change techniques (BCTs)] that could be delivered in an intervention by community pharmacists. Method Focus groups were conducted with older people (>65 years) receiving ≥4 medications. Questions explored the 12 domains of the TDF (eg “Knowledge,” “Emotion”). Data were analysed using the framework method and content analysis. Identification of key domains and mapping to intervention components (BCTs) followed established methods. Results: Seven focus groups were convened (50 participants). A wide range of determinants were identified as barriers (eg forgetfulness, prioritization of medications) and facilitators (eg social support, personalized routines) of adherence to multiple medications. Eight domains were identified as key targets for behaviour change (eg “Social influences,” “Memory, attention and decision processes,” “Motivation and goals”) and mapped to 11 intervention components (BCTs) to include in an intervention [eg “Social support or encouragement (general),” “Self-monitoring of the behaviour,” “Goal-setting (behaviour)”]. Conclusion: This study used a theoretical underpinning to identify potential intervention components (BCTs). Future work will incorporate the selected BCTs into an intervention that will undergo feasibility testing in community pharmacies

Cyclin D1-mediated microRNA expression signature predicts breast cancer outcome

Background: Genetic classification of breast cancer based on the coding mRNA suggests the evolution of distinct subtypes. Whether the non-coding genome is altered concordantly with the coding genome and the mechanism by which the cell cycle directly controls the non-coding genome is poorly understood. Methods: Herein, the miRNA signature maintained by endogenous cyclin D1 in human breast cancer cells was defined. In order to determine the clinical significance of the cyclin D1-mediated miRNA signature, we defined a miRNA expression superset from 459 breast cancer samples. We compared the coding and non-coding genome of breast cancer subtypes. Results: Hierarchical clustering of human breast cancers defined four distinct miRNA clusters (G1-G4) associated with distinguishable relapse-free survival by Kaplan-Meier analysis. The cyclin D1-regulated miRNA signature included several oncomirs, was conserved in multiple breast cancer cell lines, was associated with the G2 tumor miRNA cluster, ERα+ status, better outcome and activation of the Wnt pathway. The coding and non-coding genome were discordant within breast cancer subtypes. Seed elements for cyclin D1-regulated miRNA were identified in 63 genes of the Wnt signaling pathway including DKK. Cyclin D1 restrained DKK1 via the 3\u27UTR. In vivo studies using inducible transgenics confirmed cyclin D1 induces Wnt-dependent gene expression. Conclusion: The non-coding genome defines breast cancer subtypes that are discordant with their coding genome subtype suggesting distinct evolutionary drivers within the tumors. Cyclin D1 orchestrates expression of a miRNA signature that induces Wnt/β-catenin signaling, therefore cyclin D1 serves both upstream and downstream of Wnt/β-catenin signaling

New graduate doctors' preparedness for practice: A multistakeholder, multicentre narrative study

This is the final version. Available on open access from BMJ Publishing Group via the link in this recordData sharing statement The raw data for this research consist of audio-recordings of narrative interviews and audio diaries. The principal investigator (Professor Lynn V Monrouxe) has access to this specific data set, including audio-recordings of interviews and interview transcripts, in addition to participant contact details and signed consent forms. All authors have access to anonymised data from this set. All data are stored securely on password-protected and encrypted computers. Participants have not given their permission for data sharing outside the research group. Thus, no additional data are available.Objective While previous studies have begun to explore newly graduated junior doctors' preparedness for practice, findings are largely based on simplistic survey data or perceptions of newly graduated junior doctors and their clinical supervisors alone. This study explores, in a deeper manner, multiple stakeholders' conceptualisations of what it means to be prepared for practice and their perceptions about newly graduated junior doctors' preparedness (or unpreparedness) using innovative qualitative methods. Design A multistakeholder, multicentre qualitative study including narrative interviews and longitudinal audio diaries. Setting Four UK settings: England, Northern Ireland, Scotland and Wales. Participants Eight stakeholder groups comprising n=185 participants engaged in 101 narrative interviews (27 group and 84 individual). Twenty-six junior doctors in their first year postgraduation also provided audio diaries over a 3-month period. Results We identified 2186 narratives across all participants (506 classified as 'prepared', 663 as 'unprepared', 951 as 'general'). Seven themes were identified; this paper focuses on two themes pertinent to our research questions: (1) explicit conceptualisations of preparedness for practice; and (2) newly graduated junior doctors' preparedness for the General Medical Council's (GMC) outcomes for graduates. Stakeholders' conceptualisations of preparedness for practice included short-term (hitting the ground running) and long-term preparedness, alongside being prepared for practical and emotional aspects. Stakeholders' perceptions of medical graduates' preparedness for practice varied across different GMC outcomes for graduates (eg, Doctor as Scholar and Scientist, as Practitioner, as Professional) and across stakeholders (eg, newly graduated doctors sometimes perceived themselves as prepared but others did not). Conclusion Our narrative findings highlight the complexities and nuances surrounding new medical graduates' preparedness for practice. We encourage stakeholders to develop a shared understanding (and realistic expectations) of new medical graduates' preparedness. We invite medical school leaders to increase the proportion of time that medical students spend participating meaningfully in multiprofessional teams during workplace learning.General Medical Counci

The Uses of Chiral Anomaly for Determination of the Number of Colors

The $N_c$-dependence of the vertices $PPP\gamma$, where $P$ is a pseudoscalar meson and $N_c$ is the number of colors, is analyzed with regard for the $N_c$-dependence of the quark charges. It is shown that the best processes for the determination of $N_c$ are the reactions $K\gamma \to K\pi$ and $\pi^pm\gamma\to\pi^\pm\eta$ as well as the decay \eta\ra\pi^+\pi^-\gamma. The measurement of the cross section \sigma(\pi^-\gamma\ra\pi^-\eta) at the VES facility at the IHEP agrees with the value $N_c=3$.Comment: 7 pages, 1 figure; accepted to Phys. Atom. Nucl., references adde

Effects of the Pre-K Program of Kalamazoo County Ready 4s on Kindergarten Entry Test Scores: Estimates Based on Data from the Fall of 2011 and the Fall of 2012

This paper uses a regression discontinuity model to examine the effects on kindergarten entrance assessments of the Kalamazoo County Ready 4s (KC Ready 4s) program, a half-day pre-K program for four-year-olds in Kalamazoo County, Michigan. The results are based on test scores and other characteristics of up to 220 children participating in KC Ready 4s, with data coming from both 2011–2012 and 2012–2013 participants in the program. The estimates find consistently statistically significant effects of this pre-K program on improving entering kindergartners’ math test scores. Some estimates also suggest marginally statistically significant effects of KC Ready 4s on vocabulary test scores. No statistically significant effects are found on letter-word identification test scores, due in part to the small available sample size, but some of the point estimates are large. The program does not appear to have large or statistically significant effects in improving children’s behavioral assessments. The overall average effects of KC Ready 4s on the three academic test scores are large, at an effect size of at least 0.52. This is toward the high end of effects found in previous studies of short-term effects of pre-K programs. These estimates also are consistent with program benefits exceeding program costs

A novel DLX3-PKC integrated signaling network drives keratinocyte differentiation

Epidermal homeostasis relies on a well-defined transcriptional control of keratinocyte proliferation and differentiation, which is critical to prevent skin diseases such as atopic dermatitis, psoriasis or cancer. We have recently shown that the homeobox transcription factor DLX3 and the tumor suppressor p53 co-regulate cell cycle-related signaling and that this mechanism is functionally involved in cutaneous squamous cell carcinoma development. Here we show that DLX3 expression and its downstream signaling depend on protein kinase C alpha (PKC alpha) activity in skin. We found that following 12-O-tetradecanoyl-phorbol-13-acetate (TPA) topical treatment, DLX3 expression is significantly upregulated in the epidermis and keratinocytes from mice overexpressing PKC alpha by transgenic targeting (K5-PKC alpha), resulting in cell cycle block and terminal differentiation. Epidermis lacking DLX3 (DLX3cKO), which is linked to the development of a DLX3-dependent epidermal hyperplasia with hyperkeratosis and dermal leukocyte recruitment, displays enhanced PKC alpha activation, suggesting a feedback regulation of DLX3 and PKC alpha. Of particular significance, transcriptional activation of epidermal barrier, antimicrobial peptide and cytokine genes is significantly increased in DLX3cKO skin and further increased by TPA-dependent PKC activation. Furthermore, when inhibiting PKC activity, we show that epidermal thickness, keratinocyte proliferation and inflammatory cell infiltration are reduced and the PKC-DLX3-dependent gene expression signature is normalized. Independently of PKC, DLX3 expression specifically modulates regulatory networks such as Wnt signaling, phosphatase activity and cell adhesion. Chromatin immunoprecipitation sequencing analysis of primary suprabasal keratinocytes showed binding of DLX3 to the proximal promoter regions of genes associated with cell cycle regulation, and of structural proteins and transcription factors involved in epidermal differentiation. These results indicate that Dlx3 potentially regulates a set of crucial genes necessary during the epidermal differentiation process. Altogether, we demonstrate the existence of a robust DLX3-PKC alpha signaling pathway in keratinocytes that is crucial to epidermal differentiation control and cutaneous homeostasis