Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

Studying the causes and correlates of natural variation in gene expression in healthy populations assumes that individual differences in gene expression can be reliably and stably assessed across time. However, this is yet to be established. We examined 4-hour test-retest reliability and 10 month test-retest stability of individual differences in gene expression in ten 12-year-old children. Blood was collected on four occasions: 10 a.m. and 2 p.m. on Day 1 and 10 months later at 10 a.m. and 2 p.m. Total RNA was hybridized to Affymetrix-U133 plus 2.0 arrays. For each probeset, the correlation across individuals between 10 a.m. and 2 p.m. on Day 1 estimates test-retest reliability. We identified 3,414 variable and abundantly expressed probesets whose 4-hour test-retest reliability exceeded .70, a conventionally accepted level of reliability, which we had 80% power to detect. Of the 3,414 reliable probesets, 1,752 were also significantly reliable 10 months later. We assessed the long-term stability of individual differences in gene expression by correlating the average expression level for each probe-set across the two 4-hour assessments on Day 1 with the average level of each probe-set across the two 4-hour assessments 10 months later. 1,291 (73.7%) of the 1,752 probe-sets that reliably detected individual differences across 4 hours on two occasions, 10 months apart, also stably detected individual differences across 10 months. Heritability, as estimated from the MZ twin intraclass correlations, is twice as high for the 1,752 reliable probesets versus all present probesets on the array (0.68 vs 0.34), and is even higher (0.76) for the 1,291 reliable probesets that are also stable across 10 months. The 1,291 probesets that reliably detect individual differences from a single peripheral blood collection and stably detect individual differences over 10 months are promising targets for research on the causes (e.g., eQTLs) and correlates (e.g., psychopathology) of individual differences in gene expression

Decreased occurrence of ketoacidosis and preservation of beta cell function in relatives screened and monitored for type 1 diabetes in Australia and New Zealand

Published December 2022Aims: Islet autoantibody screening of infants and young children in the Northern Hemisphere, together with semi-annual metabolic monitoring, is associated with a lower risk of ketoacidosis (DKA) and improved glucose control after diagnosis of clinical (stage 3) type 1 diabetes (T1D). We aimed to determine if similar benefits applied to older Australians and New Zealanders monitored less rigorously. Methods: DKA occurrence and metabolic control were compared between T1D relatives screened and monitored for T1D and unscreened individuals diagnosed in the general population, ascertained from the Australasian Diabetes Data Network. Results: Between 2005 and 2019, 17,105 relatives (mean (SD) age 15.7 (10.8) years; 52% female) were screened for autoantibodies against insulin, glutamic acid decarboxylase, and insulinoma-associated protein 2. Of these, 652 screened positive to a single and 306 to multiple autoantibody specificities, of whom 201 and 215, respectively, underwent metabolic monitoring. Of 178 relatives diagnosed with stage 3 T1D, 9 (5%) had DKA, 7 of whom had not undertaken metabolic monitoring. The frequency of DKA in the general population was 31%. After correction for age, sex and T1D family history, the frequency of DKA in screened relatives was >80% lower than in the general population. HbA1c and insulin requirements following diagnosis were also lower in screened relatives, consistent with greater beta cell reserve. Conclusions: T1D autoantibody screening and metabolic monitoring of older children and young adults in Australia and New Zealand, by enabling pre-clinical diagnosis when beta cell reserve is greater, confers protection from DKA. These clinical benefits support ongoing efforts to increase screening activity in the region and should facilitate the application of emerging immunotherapies.John M. Wentworth, Helena Oakey, Maria E. Craig, Jennifer J. Couper, Fergus J. Cameron, Elizabeth A. Davis, Antony R. Lafferty, Mark Harris, Benjamin J. Wheeler, Craig Jefferies, Peter G. Colman, Leonard C. Harriso

Protocol for a nested case-control study design for omics investigations in the Environmental Determinants of Islet Autoimmunity cohort

Background: The Environmental Determinants of Islet Autoimmunity (ENDIA) pregnancy-birth cohort investigates the developmental origins of type 1 diabetes (T1D), with recruitment between 2013 and 2019. ENDIA is the first study in the world with comprehensive data and biospecimen collection during pregnancy, at birth and through childhood from at-risk children who have a first-degree relative with T1D. Environmental exposures are thought to drive the progression to clinical T1D, with pancreatic islet autoimmunity (IA) developing in genetically susceptible individuals. The exposures and key molecular mechanisms driving this progression are unknown. Persistent IA is the primary outcome of ENDIA; defined as a positive antibody for at least one of IAA, GAD, ZnT8 or IA2 on two consecutive occasions and signifies high risk of clinical T1D.Method: A nested case-control (NCC) study design with 54 cases and 161 matched controls aims to investigate associations between persistent IA and longitudinal omics exposures in ENDIA. The NCC study will analyse samples obtained from ENDIA children who have either developed persistent IA or progressed to clinical T1D (cases) and matched control children at risk of developing persistent IA. Control children were matched on sex and age, with all four autoantibodies absent within a defined window of the case's onset date. Cases seroconverted at a median of 1.37 years (IQR 0.95, 2.56). Longitudinal omics data generated from approximately 16,000 samples of different biospecimen types, will enable evaluation of changes from pregnancy through childhood.Conclusions: This paper describes the ENDIA NCC study, omics platform design considerations and planned univariate and multivariate analyses for its longitudinal data. Methodologies for multivariate omics analysis with longitudinal data are discovery-focused and data driven. There is currently no single multivariate method tailored specifically for the longitudinal omics data that the ENDIA NCC study will generate and therefore omics analysis results will require either cross validation or independent validation.KEY MESSAGESThe ENDIA nested case-control study will utilize longitudinal omics data on approximately 16,000 samples from 190 unique children at risk of type 1 diabetes (T1D), including 54 who have developed islet autoimmunity (IA), followed during pregnancy, at birth and during early childhood, enabling the developmental origins of T1D to be explored.Helena Oakey ... Lynne C. Giles ... Rebecca L. Thomson ... Pat Ashwood ... Emma J. Knight ... Simon C. Barry ... Kelly McGorm ... Jennifer J. Couper ... Megan A. S. Penno ... the ENDIA Study Group ... et al

Dual control of fault intersections on stop-start rupture in the 2016 Central Italy seismic sequence

Large continental earthquakes necessarily involve failure of multiple faults or segments. But these same critically-stressed systems sometimes fail in drawn-out sequences of smaller earthquakes over days or years instead. These two modes of failure have vastly different implications for seismic hazard and it is not known why fault systems sometimes fail in one mode or the other, or what controls the termination and reinitiation of slip in protracted seismic sequences. A paucity of modern observations of seismic sequences has hampered our understanding to-date, but a series of three Mw>6 earthquakes from August to November 2016 in Central Italy represents a uniquely well-observed example. Here we exploit a wealth of geodetic, seismological and field data to understand the spatio-temporal evolution of the sequence. Our results suggest that pre-existing fault structures controlled the extent and termination of rupture in each event in the sequence, and that fluid diffusion, channelled along these same structures, may have also determined the timing of rupture reinitiation. This dual control of subsurface structure on the stop-start rupture in seismic sequences may be common; future efforts should focus on investigating its prevalence

Agreement between diagnoses of otitis media by audiologists and otolaryngologists in Aboriginal Australian children

Objectives: To determine the degree of agreement of diagnoses by audiologists and otolaryngologists of otitis media (OM) in Aboriginal children. Design: Cross-sectional study of agreement between diagnoses. Setting: Study of Environment on Aboriginal Resilience and Child Health (SEARCH), a prospective cohort study of Aboriginal children attending four Aboriginal Community Controlled Health Services in New South Wales (three metropolitan, one regional) during 2008–2012. Participants: 1310 of 1669 SEARCH participants (78.5%; mean age, 7.0 years; SD, 4.4 years) were assessed and received a diagnosis from one of five experienced audiologists. Test results (but not case histories) were forwarded to one of three otolaryngologists for blinded independent assessment. Main outcome measures: Agreement of OM diagnoses by audiologists and otolaryngologists at ear and child levels; correctness of audiologist diagnoses (otolaryngologist diagnosis as reference). Results: Paired diagnoses by audiologists and otolaryngologists were available for 863 children at the child level and 1775 ears (989 children) at the ear level. Otolaryngologists diagnosed OM in 251 children (29.1%), including 11 (1.3%) with tympanic membrane perforation, and in 396 ears (22.3%), including 12 (0.7%) with perforation. Agreement between audiologists and otolaryngologists for OM at the ear level was 92.2% (κ = 0.78; 95% CI, 0.74–0.82), and at the child level 91.7% (κ = 0.81; 95% CI, 0.77–0.85). No otolaryngologist-diagnosed perforation was missed by audiologists. Among 1000 children triaged by an audiologist, there would be 45 false positives and 30 false negatives when compared with assessments by an otolaryngologist, with no missed perforations. Conclusions: There was substantial agreement between audiologists’ and otolaryngologists’ diagnoses of OM in a high prevalence population of Aboriginal children. In settings with limited access to otolaryngologists, audiologists may appropriately triage children and select those requiring specialist review.SEARCH was funded by Australian National Health and Medical Research Council (NHMRC) grants (358457, 512685, 1023998, 1035378), the NSW Ministry of Health, the Australian Primary Care Research Institute, beyondblue, and the Rio Tinto Aboriginal Fund. Kathleen Falster was supported by an NHMRC Early Career Fellowship (1016475) and an NHMRC Capacity Building Grant (573122). Emily Banks was supported by an NHMRC Senior Research Fellowship (1042717)

When Is a Preannounced New Product Likely to Be Delayed?

Consider that a firm announces a deadline for a new product introduction. Conditional on such a preannouncement, how must an external observer evaluate whether the product will be delayed beyond that deadline? Using data collected from managers in the computer hardware, software, and telecommunications industries, the authors present an analysis that demonstrates that delays in new product introductions beyond preannounced deadlines can be jointly explained by factors related to (1) the firm's motivations to delay the product, (2) the presence of constraints that prevent delay (or the availability of opportunities to delay the product), and (3) the firm's abilities pertaining to product development

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo