OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies

The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.

Misaligned foveal morphology and sector retinal dysfunction in AKT1-mosaic Proteus syndrome

PURPOSE

Proteus syndrome arises as a result of a post-zygotic mosaic activating mutation in the AKT1 oncogene, causing a disproportionate overgrowth of affected tissues. A small number of ocular complications have been reported. We present the unique findings in a patient who had molecular confirmation of AKT1 mosaicism alongside fulfilling the clinical criteria for Proteus syndrome.

METHODS

Pattern electroretinography, visual evoked potentials and multifocal electroretinography testing were performed alongside detailed retinal imaging and clinical examination to detail the ophthalmic characteristics.

RESULTS

Electrophysiological findings characterised unilateral macular dysfunction alongside sector retinal dysfunction of the right eye. This was demonstrated through optical coherence tomography and ultra-wide-field imaging to be associated with a misaligned foveal morphology and sector retinal dysfunction extending into the temporal retina.

CONCLUSION

We propose this patient has asymmetric foveal development and concomitant sector retinal dysfunction as the result of the mosaic AKT1 mutation, either through disruption in the retinal PI3K-AKT1 signalling pathway or through mechanical distortion of ocular growth, resulting in disproportionate inner retinal development. The findings expand the ocular phenotype of Proteus syndrome and encourage early assessment to identify any incipient ocular abnormalities.

Senescent human melanocytes drive skin ageing via paracrine telomere dysfunction

Cellular senescence has been shown to contribute to skin ageing. However, the role of melanocytes in the process is understudied. Our data show that melanocytes are the only epidermal cell type to express the senescence marker p16^INK4A during human skin ageing. Aged melanocytes also display additional markers of senescence such as reduced HMGB1 and dysfunctional telomeres, without detectable telomere shortening. Additionally, senescent melanocyte SASP induces telomere dysfunction in paracrine manner and limits proliferation of surrounding cells via activation of CXCR3-dependent mitochondrial ROS. Finally, senescent melanocytes impair basal keratinocyte proliferation and contribute to epidermal atrophy in vitro using 3D human epidermal equivalents. Crucially, clearance of senescent melanocytes using the senolytic drug ABT737 or treatment with mitochondria-targeted antioxidant MitoQ suppressed this effect. In conclusion, our study provides proof-of-concept evidence that senescent melanocytes affect keratinocyte function and act as drivers of human skin ageing.

Bringing Open Data to Whole Slide Imaging

Faced with the need to support a growing number of whole slide imaging (WSI) file formats, our team has extended a long-standing community file format (OME-TIFF) for use in digital pathology. The format makes use of the core TIFF specification to store multi-resolution (or "pyramidal") representations of a single slide in a flexible, performant manner. Here we describe the structure of this format, its performance characteristics, as well as an open-source library support for reading and writing pyramidal OME-TIFFs.

Identical and Nonidentical Twins: Risk and Factors Involved in Development of Islet Autoimmunity and Type 1 Diabetes

OBJECTIVE

There are variable reports of risk of concordance for progression to islet autoantibodies and type 1 diabetes in identical twins after one twin is diagnosed. We examined development of positive autoantibodies and type 1 diabetes and the effects of genetic factors and common environment on autoantibody positivity in identical twins, nonidentical twins, and full siblings.

RESEARCH DESIGN AND METHODS

Subjects from the TrialNet Pathway to Prevention Study (N = 48,026) were screened from 2004 to 2015 for islet autoantibodies (GAD antibody [GADA], insulinoma-associated antigen 2 [IA-2A], and autoantibodies against insulin [IAA]). Of these subjects, 17,226 (157 identical twins, 283 nonidentical twins, and 16,786 full siblings) were followed for autoantibody positivity or type 1 diabetes for a median of 2.1 years.

RESULTS

At screening, identical twins were more likely to have positive GADA, IA-2A, and IAA than nonidentical twins or full siblings (all P < 0.0001). Younger age, male sex, and genetic factors were significant factors for expression of IA-2A, IAA, one or more positive autoantibodies, and two or more positive autoantibodies (all P ≤ 0.03). Initially autoantibody-positive identical twins had a 69% risk of diabetes by 3 years compared with 1.5% for initially autoantibody-negative identical twins. In nonidentical twins, type 1 diabetes risk by 3 years was 72% for initially multiple autoantibody-positive, 13% for single autoantibody-positive, and 0% for initially autoantibody-negative nonidentical twins. Full siblings had a 3-year type 1 diabetes risk of 47% for multiple autoantibody-positive, 12% for single autoantibody-positive, and 0.5% for initially autoantibody-negative subjects.

CONCLUSIONS

Risk of type 1 diabetes at 3 years is high for initially multiple and single autoantibody-positive identical twins and multiple autoantibody-positive nonidentical twins. Genetic predisposition, age, and male sex are significant risk factors for development of positive autoantibodies in twins.

Low-Dose Anti-Thymocyte Globulin (ATG) Preserves β-Cell Function and Improves HbA1c in New-Onset Type 1 Diabetes

OBJECTIVE

A pilot study suggested that combination therapy with low-dose anti-thymocyte globulin (ATG) and pegylated granulocyte colony-stimulating factor (GCSF) preserves C-peptide in established type 1 diabetes (T1D) (duration 4 months to 2 years). We hypothesized that 1) low-dose ATG/GCSF or 2) low-dose ATG alone would slow the decline of β-cell function in patients with new-onset T1D (duration <100 days).

RESEARCH DESIGN AND METHODS

A three-arm, randomized, double-masked, placebo-controlled trial was performed by the Type 1 Diabetes TrialNet Study Group in 89 subjects: 29 subjects randomized to ATG (2.5 mg/kg intravenously) followed by pegylated GCSF (6 mg subcutaneously every 2 weeks for 6 doses), 29 to ATG alone (2.5 mg/kg), and 31 to placebo. The primary end point was mean area under the curve (AUC) C-peptide during a 2-h mixed-meal tolerance test 1 year after initiation of therapy. Significance was defined as one-sided P value < 0.025.

RESULTS

The 1-year mean AUC C-peptide was significantly higher in subjects treated with ATG (0.646 nmol/L) versus placebo (0.406 nmol/L) (P = 0.0003) but not in those treated with ATG/GCSF (0.528 nmol/L) versus placebo (P = 0.031). HbA_1c was significantly reduced at 1 year in subjects treated with ATG and ATG/GCSF, P = 0.002 and 0.011, respectively.

CONCLUSIONS

Low-dose ATG slowed decline of C-peptide and reduced HbA_1c in new-onset T1D. Addition of GCSF did not enhance C-peptide preservation afforded by low-dose ATG. Future studies should be considered to determine whether low-dose ATG alone or in combination with other agents may prevent or delay the onset of the disease.

A Type 1 Diabetes Genetic Risk Score Predicts Progression of Islet Autoimmunity and Development of Type 1 Diabetes in Individuals at Risk

OBJECTIVE

We tested the ability of a type 1 diabetes (T1D) genetic risk score (GRS) to predict progression of islet autoimmunity and T1D in at-risk individuals.

RESEARCH DESIGN AND METHODS

We studied the 1,244 TrialNet Pathway to Prevention study participants (T1D patients' relatives without diabetes and with one or more positive autoantibodies) who were genotyped with Illumina ImmunoChip (median [range] age at initial autoantibody determination 11.1 years [1.2-51.8], 48% male, 80.5% non-Hispanic white, median follow-up 5.4 years). Of 291 participants with a single positive autoantibody at screening, 157 converted to multiple autoantibody positivity and 55 developed diabetes. Of 953 participants with multiple positive autoantibodies at screening, 419 developed diabetes. We calculated the T1D GRS from 30 T1D-associated single nucleotide polymorphisms. We used multivariable Cox regression models, time-dependent receiver operating characteristic curves, and area under the curve (AUC) measures to evaluate prognostic utility of T1D GRS, age, sex, Diabetes Prevention Trial-Type 1 (DPT-1) Risk Score, positive autoantibody number or type, HLA DR3/DR4-DQ8 status, and race/ethnicity. We used recursive partitioning analyses to identify cut points in continuous variables.

RESULTS

Higher T1D GRS significantly increased the rate of progression to T1D adjusting for DPT-1 Risk Score, age, number of positive autoantibodies, sex, and ethnicity (hazard ratio [HR] 1.29 for a 0.05 increase, 95% CI 1.06-1.6; P = 0.011). Progression to T1D was best predicted by a combined model with GRS, number of positive autoantibodies, DPT-1 Risk Score, and age (7-year time-integrated AUC = 0.79, 5-year AUC = 0.73). Higher GRS was significantly associated with increased progression rate from single to multiple positive autoantibodies after adjusting for age, autoantibody type, ethnicity, and sex (HR 2.27 for GRS >0.295, 95% CI 1.47-3.51; P = 0.0002).

CONCLUSIONS

The T1D GRS independently predicts progression to T1D and improves prediction along T1D stages in autoantibody-positive relatives.

Cyberbullying prevention: Insight and recommendations from youths, parents, and paediatricians

BACKGROUND

The purpose of this study was to identify injunctive norms for cyberbullying prevention among youths, parents, and primary care providers, as well as barriers to preventive behaviours.

METHODS

Semi-structured interviews on the topic of cyberbullying were conducted with 29 adolescents, 13 paediatricians, and 15 parents recruited from 3 primary care sites. Transcripts were coded for themes related to various stakeholders' perceived roles in cyberbullying prevention and barriers to preventive behaviours.

RESULTS

Participants reported perceptions that youths should intervene in the moment and get outside help for others. Fear of repercussions emerged as a significant barrier to these behaviours. Participants believed that parents should communicate with their children and monitor and supervise youths' online activities. Barriers included perception of priority and low parental efficacy or naiveté. Participants believed that providers should provide education and resources and ask screening questions; the most frequently identified barrier to those behaviours was the perception of providers' role.

CONCLUSIONS

Youths and providers may not be aware of their potential to prevent cyberbullying before it occurs. Educating youths, parents, and providers about cyberbullying prevention is warranted.

Pleomorphic xanthoastrocytoma of childhood: MR imaging and diffusion MR imaging features

BACKGROUND AND PURPOSE

Pleomorphic xanthoastrocytomas are rare astrocytic neoplasms of childhood and young adulthood. The purpose of this retrospective review was to evaluate MR imaging features of pediatric pleomorphic xanthoastrocytomas with an emphasis on diffusion MR imaging.

MATERIALS AND METHODS

Review of the neuro-oncology data base revealed 11 pediatric patients (range, 4.7-16.1 years) with pleomorphic xanthoastroacytomas with 9 of these patients having preoperative MR imaging available. Six patients had preoperative diffusion MR imaging. Demographics, histopathology slides, conventional imaging characteristics (location, cystic component, hemorrhage, enhancement, vasogenic edema, inner table scalloping), and ADC metrics (mean tumor ADC and tumor to normal brain ADC ratio) were evaluated.

RESULTS

Three pleomorphic xanthoastrocytomas had anaplastic features. Ten tumors were supratentorial. Two-thirds (6 of 9) of all tumors were either predominantly cystic or had cystic components, and three-fourths (6 of 8) of the supratentorial tumors had associated inner table scalloping. Seven of the 9 tumors had marked vasogenic edema (>10 mm). Mean tumoral ADC (n = 7) was 912 ± 219 × 10(-6) mm(2)/s (min-max: 617-1189). The tumor to normal brain ADC ratio was 1.14 ± 0.26 (min-max: 0.75-1.47).

CONCLUSIONS

Pleomorphic xanthoastrocytoma should be entertained in the differential diagnosis of peripheral supratentorial tumors that appear during childhood. Cysts, inner table scalloping, and marked vasogenic edema are relatively frequent features. Relatively low ADC values and ADC ratios are not uncommon in pleomorphic xanthoastrocytoma.

Diffusion MRI improves the accuracy of preoperative diagnosis of common pediatric cerebellar tumors among reviewers with different experience levels

BACKGROUND AND PURPOSE

Although utility of diffusion MR imaging in the preoperative diagnosis of common pediatric cerebellar tumors is generally recognized, its added value has not been systematically studied previously. The purpose of this study was to evaluate the impact of diffusion MR imaging on the accuracy of preoperative diagnosis of common pediatric cerebellar tumors among reviewers with different experience levels.

MATERIALS AND METHODS

Review of the neuro-oncology data base yielded 96 patients whose preoperative brain MR imaging included both diffusion MR imaging (b = 1000 s/mm(2)) and ADC maps. There were 38 pilocytic astrocytomas, 33 medulloblastomas, 17 ependymomas, and 8 atypical teratoid/rhabdoid tumors. Six reviewers (4 residents, 2 neuroradiologists) evaluated the examinations. Two sessions were conducted with each reviewer, without and with diffusion MR imaging data on 2 separate days. The impact of diffusion MR imaging on accuracy of diagnoses was assessed.

RESULTS

In choosing the correct diagnosis of the 4 alternatives, performances of 5 of the 6 reviewers improved significantly with inclusion of the diffusion MR imaging data, from 63%-77% (P = .0003-.0233). The performance of 1 reviewer also improved, but the difference did not attain statistical significance (P = .1944). Inclusion of diffusion MR imaging data improved the likelihood of rendering a correct diagnosis (odds ratio = 3.16, 95% confidence interval = 2.07-4.00) over all tumor types. When embryonal tumors were regarded as a single group, the rate of correct diagnosis increased from 66%-83% with diffusion MR imaging data, and performances of all of the reviewers improved significantly (P = .0001-.05). The improvement in performances resulted from increased correct diagnoses of pilocytic astrocytomas, medulloblastomas, and atypical teratoid/rhabdoid tumors. There was no improvement in the correct diagnoses of ependymomas with inclusion of the diffusion MR imaging data.

CONCLUSIONS

Diffusion MR imaging improves accuracy of preoperative diagnosis of common pediatric cerebellar tumors significantly among reviewers with differing experience levels.

The biochemical, physiological and psychological consequences of a "1,000 miles in 1,000 hours" walking challenge

The combined effects of 42 days of chronic sleep disruption and repeated hourly bouts of physical exertion have not been described. This case study reports the physiological and psychological demands placed on one individual who walked 1 mile in each consecutive hour for a period of 1,000 h (42 days), covering a total distance of 1,000 miles. The participant walked at a mean speed of 1.75 m/s completing each mile in approximately 15 min. Over the course of the challenge, the individual lost 1.6 kg in body weight. Markers of skeletal muscle damage, increased gradually whilst free testosterone levels decreased over the course of the challenge. Stress hormones increased whilst inflammatory markers (CRP) initially rose but then returned towards baseline over the course of the study. Cognitive motor performance measured via reaction time was maintained throughout the 42 days. The participant also displayed mood states typical of an elite athlete at baseline and throughout the challenge. Participation in this novel '1,000 mile 1,000 h' walking challenge evoked considerable physiological stress in a fit, healthy middle-aged participant but did not markedly alter cognitive performance or mood over the 42-day period.

The putative AKH receptor of the tobacco hornworm, Manduca sexta, and its expression

Adipokinetic hormones are peptide hormones that mobilize lipids and/or carbohydrates for flight in adult insects and activate glycogen Phosphorylase in larvae during starvation and during molt. We previously examined the functional roles of adipokinetic hormone in Manduca sexta L. (Lepidoptera: Sphingidae). Here we report the cloning of the full-length cDNA encoding the putative adipokinetic hormone receptor from the fat body of M. sexta. The sequence analysis shows that the deduced amino acid sequence shares common motifs of G protein-coupled receptors, by having seven hydrophobic transmembrane segments. We examined the mRNA expression pattern of the adipokinetic hormone receptor by quantitative Real-Time PCR in fat body during development and in different tissues and found the strongest expression in fat body of larvae two days after molt to the fifth instar. We discuss these results in relation to some of our earlier results. We also compare the M. sexta adipokinetic hormone receptor with the known adipokinetic hormone receptors of other insects and with gonadotropin releasing hormone-like receptors of invertebrates.

Metadata matters: access to image data in the real world

Data sharing is important in the biological sciences to prevent duplication of effort, to promote scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires centralized repositories, and submission to and utility of these resources require common data formats. This is particularly challenging for multidimensional microscopy image data, which are acquired from a variety of platforms with a myriad of proprietary file formats (PFFs). In this paper, we describe an open standard format that we have developed for microscopy image data. We call on the community to use open image data standards and to insist that all imaging platforms support these file formats. This will build the foundation for an open image data repository.