Establishment of an Innovative Telehealth Speech and Language Therapy Placement as a Rapid Response to COVID-19: Sharing the Learning

The aim of this evaluation was to explore practice educators’ and speech and language therapy (SLT) students’ experiences of a rapid response telehealth placement in response to the COVID-19 pandemic in order to inform quality improvement. In March 2020, public health restrictions were imposed across Ireland in efforts to ‘flatten the curve’ in response to the COVID-19 pandemic. All placements were cancelled. According to an Irish Association of Speech and Language Therapists survey in April 2020, 47% of SLTs were redeployed to swabbing and contact tracing roles, and many remain redeployed seven months later. This redeployment, along with strict public health measures in clinical sites, significantly reduced the availability of clinical placements. A rapid response was required to enable students to develop clinical competencies. Although telehealth has been used to deliver speech and language therapy in other countries, it had not been used routinely in service provision in Ireland. In this article, we outline how we built on existing partnerships with practice educators, both on- and off-site, to design a much-needed telehealth placement. We explored educators’ and students’ experiences using an online focus group and online survey respectively. The evaluations of practice educators were positive in that despite their initial apprehension, they reported that this placement provided valuable learning opportunities for students while also providing benefits for clients. They also reported some technological and sustainability challenges. The students also evaluated this placement positively with 83.3% of respondents rating the placement as ‘excellent ‘and 16.7% rating it as ‘good’. All stakeholders valued this learning experience

A survey of best practices for RNA-seq data analysis.

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.This is the final published version. It first appeared at http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8

Higher Protein Density Diets Are Associated With Greater Diet Quality and Micronutrient Intake in Healthy Young Adults

Objective: This study characterized habitual dietary protein intake in healthy young adults entering military service and explored whether diet protein density is associated with diet quality and micronutrient intake.Methods: An FFQ was used to estimate habitual dietary intake and calculate HEI scores in 276 males [mean(SD), age:21.1y(3.8)] and 254 females [age:21.2y(3.7)]. Multivariate-adjusted MANCOVA and ANCOVA models were used to identify associations between protein density quartiles and HEI scores and micronutrient intake. Higher HEI components scores for sodium, refined grains, and empty calories indicate lower intake; higher scores for all other components indicate higher intakes.Results: Mean(SD) energy-adjusted protein intakes were 29.3(3.2), 36.0(1.4), 40.8(1.3), and 47.9(3.9) g/1,000 kcal for protein density quartiles 1–4, respectively. For males, empty calorie scores as well as dark green and orange vegetable scores were higher in quartiles 3 and 4 than 1 and 2 (all, p < 0.05). Scores for total vegetable, dairy, and total protein foods were lower in quartile 1 vs. quartiles 2, 3, and 4 (all, p < 0.05). Sodium scores decreased as quartiles increased (p < 0.001). Total HEI, fruit, whole grains, seafood and plant protein, fatty acids, and refined grain scores did not differ. For females, total HEI, vegetable, and total protein foods scores were higher in quartiles 3 and 4 than 1 and 2 (all, p < 0.05). Empty calorie scores increased as quartile increased (p < 0.05). Dairy scores were higher in quartiles 2, 3, and 4 than 1 (p < 0.05). Whole fruit scores were lowest in quartile 1 (p < 0.05). Whole grain as well as seafood and plant protein scores were higher in quartile 4 vs. 1 (both, p < 0.05). Sodium scores decreased as quartile increased (p < 0.001). Fatty acids scores did not differ. For males and females, micronutrient intakes progressively increased across quartiles with the exception of calcium and vitamin C, (all, p < 0.05). Intakes remained nearly the same when controlled for fruit and vegetable intake.Conclusion: These cross-sectional data suggest that habitually consuming a higher protein density diet is associated with better scores for some, but not all, diet quality components in males, better overall diet quality scores in females, and greater intakes of micronutrients in both male and female healthy, young adults entering military service

Teagasc submission made in response to the Discussion document for the preparation of a National Policy Statement on the Bioeconomy

Teagasc SubmissionThis document is Teagasc’s response to the “Discussion Document for the Preparation of a National Policy Statement on the Bioeconomy” issued by the Department of the Taoiseach’s Economic Division in July 2017. It recognises the potential significance of the bioeconomy to Ireland, offers some policy and strategic insights from other countries, and identifies Teagasc’s role in supporting the development of the bioeconomy in Ireland

Evolution of Neuronal and Endothelial Transcriptomes in Primates

The study of gene expression evolution in vertebrates has hitherto focused on the analysis of transcriptomes in tissues of different species. However, because a tissue is made up of different cell types, and cell types differ with respect to their transcriptomes, the analysis of tissues offers a composite picture of transcriptome evolution. The isolation of individual cells from tissue sections opens up the opportunity to study gene expression evolution at the cell type level. We have stained neurons and endothelial cells in human brains by antibodies against cell type-specific marker proteins, isolated the cells using laser capture microdissection, and identified genes preferentially expressed in the two cell types. We analyze these two classes of genes with respect to their expression in 62 different human tissues, with respect to their expression in 44 human “postmortem” brains from different developmental stages and with respect to between-species brain expression differences. We find that genes preferentially expressed in neurons differ less across tissues and developmental stages than genes preferentially expressed in endothelial cells. We also observe less expression differences within primate species for neuronal transcriptomes. In stark contrast, we see more gene expression differences between humans, chimpanzees, and rhesus macaques relative to within-species differences in genes expressed preferentially in neurons than in genes expressed in endothelial cells. This suggests that neuronal and endothelial transcriptomes evolve at different rates within brain tissue

Mapping interactions between the RNA chaperone FinO and its RNA targets

Bacterial conjugation is regulated by two-component repression comprising the antisense RNA FinP, and its protein co-factor FinO. FinO mediates base-pairing of FinP to the 5′-untranslated region (UTR) of traJ mRNA, which leads to translational inhibition of the transcriptional activator TraJ and subsequent down regulation of conjugation genes. Yet, little is known about how FinO binds to its RNA targets or how this interaction facilitates FinP and traJ mRNA pairing. Here, we use solution methods to determine how FinO binds specifically to its minimal high affinity target, FinP stem–loop II (SLII), and its complement SLIIc from traJ mRNA. Ribonuclease footprinting reveals that FinO contacts the base of the stem and the 3′ single-stranded tails of these RNAs. The phosphorylation or oxidation of the 3′-nucleotide blocks FinO binding, suggesting FinO binds the 3′-hydroxyl of its RNA targets. The collective results allow the generation of an energy-minimized model of the FinO–SLII complex, consistent with small-angle X-ray scattering data. The repression complex model was constrained using previously reported cross-linking data and newly developed footprinting results. Together, these data lead us to propose a model of how FinO mediates FinP/traJ mRNA pairing to down regulate bacterial conjugation

Common genetic variation drives molecular heterogeneity in human iPSCs.

Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells

Spondylarthropathies (including psoriatic arthritis): 244. Validity of Colour Doppler and Spectral Doppler Ultrasound of Sacroilicac Joints Againts Physical Examination as Gold Standard

Background: Sacroiliac joints (SJ) involvement is a distinctive and charasteristic feature of Spondyloarthritis (SpA) and x-ray is the test routinely used to make a diagnosis. However, x-ray reveals late structural damage but cannot detect active inflammation. The objective of this study was to assess the validity of Doppler ultrasound in SJ. Methods: Prospective blinded and controlled study of SJ, in which three populations were compared. We studied 106 consecutive cases, who were divided into three groups: a) 53 patients diagnosed with SpA who had inflammatory lumbar and gluteal pain assessed by a rheumatologist; b) 26 patients diagnosed with SpA who didn't have SJ tenderness and had normal physical examination; c) control group of 27 subjects (healthy subjetcs or with mechanical lumbar pain). All patients included that were diagnosed with SpA met almost the European Spondyloarthropathy Study Group (ESSG) classification criteria. Physical examination of the SJ included: sacral sulcus tenderness, iliac gapping, iliac compression, midline sacral thrust test, Gaenslen's test, and Patrick s test were used as gold standard. Both SJ were examined with Doppler ultrasound (General Electric Logiq 9, Wauwatosa WI, USA) fitted with a 9-14 Mhz lineal probe. The ultrasonographer was blinded to clinical data. Doppler in SJ was assessed as positive when both Doppler colour and resistance index (RI) < 0.75 within the SJ area were present. Statistical analysis was performed estimating sensitivity and specificity against gold standard. The Kappa correlation coefficient was used for reliability study. Results: 106 cases (53 female, 55 male; mean age 36 10 years) were studied. There were no statistical differences between groups related to age or sex. Physical examination of SJ was positive in 38 patients (59 sacroiliac joints). US detected Doppler signal within SJ in 37 patients (58 SJ): 33 of them were symptomatic SpA (52 SJ), one of them were asymptomatic SpA (1 SJ) and one was a healthy control (1 SJ). The accuracy of US when compared to clinical data as gold standard at subject level in the overall group was: sensitivity of 68.6% and specificity of 85.7%, positive predictive value of 70.5% and negative predictive value of 84.5%. A positive likelihood ratio of 4.8, a negative likelihood ratio of 0.36 and a kappa coefficient of 0.55 were achieved. Conclusions: Doppler US of SJ seems to be a valid method to detect active SJ inflammation. Disclosure statement: The authors have declared no conflicts of interes