Quality control in resting-state fMRI: the benefits of visual inspection

Background: A variety of quality control (QC) approaches are employed in resting-state functional magnetic resonance imaging (rs-fMRI) to determine data quality and ultimately inclusion or exclusion of a fMRI data set in group analysis. Reliability of rs-fMRI data can be improved by censoring or “scrubbing” volumes affected by motion. While censoring preserves the integrity of participant-level data, including excessively censored data sets in group analyses may add noise. Quantitative motion-related metrics are frequently reported in the literature; however, qualitative visual inspection can sometimes catch errors or other issues that may be missed by quantitative metrics alone. In this paper, we describe our methods for performing QC of rs-fMRI data using software-generated quantitative and qualitative output and trained visual inspection. Results: The data provided for this QC paper had relatively low motion-censoring, thus quantitative QC resulted in no exclusions. Qualitative checks of the data resulted in limited exclusions due to potential incidental findings and failed pre-processing scripts. Conclusion: Visual inspection in addition to the review of quantitative QC metrics is an important component to ensure high quality and accuracy in rs-fMRI data analysis

White matter alterations in glaucoma and monocular blindness differ outside the visual system

The degree to which glaucoma has effects in the brain beyond the eye and the visual pathways is unclear. To clarify this, we investigated white matter microstructure (WMM) in 37 tracts of patients with glaucoma, monocular blindness, and controls. We used brainlife.io for reproducibility. White matter tracts were subdivided into seven categories ranging from those primarily involved in vision (the visual white matter) to those primarily involved in cognition and motor control. In the vision tracts, WMM was decreased as measured by fractional anisotropy in both glaucoma and monocular blind subjects compared to controls, suggesting neurodegeneration due to reduced sensory inputs. A test-retest approach was used to validate these results. The pattern of results was different in monocular blind subjects, where WMM properties increased outside the visual white matter as compared to controls. This pattern of results suggests that whereas in the monocular blind loss of visual input might promote white matter reorganization outside of the early visual system, such reorganization might be reduced or absent in glaucoma. The results provide indirect evidence that in glaucoma unknown factors might limit the reorganization as seen in other patient groups following visual loss

Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants.

A locus on human chromosome 11q23 tagged by marker rs3802842 was associated with colorectal cancer (CRC) in a genome-wide association study; this finding has been replicated in case-control studies worldwide. In order to identify biologic factors at this locus that are related to the etiopathology of CRC, we used microarray-based target selection methods, coupled to next-generation sequencing, to study 103 kb at the 11q23 locus. We genotyped 369 putative variants from 1,030 patients with CRC (cases) and 1,061 individuals without CRC (controls) from the Ontario Familial Colorectal Cancer Registry. Two previously uncharacterized genes, COLCA1 and COLCA2, were found to be co-regulated genes that are transcribed from opposite strands. Expression levels of COLCA1 and COLCA2 transcripts correlate with rs3802842 genotypes. In colon tissues, COLCA1 co-localizes with crystalloid granules of eosinophils and granular organelles of mast cells, neutrophils, macrophages, dendritic cells and differentiated myeloid-derived cell lines. COLCA2 is present in the cytoplasm of normal epithelial, immune and other cell lineages, as well as tumor cells. Tissue microarray analysis demonstrates the association of rs3802842 with lymphocyte density in the lamina propria (p = 0.014) and levels of COLCA1 in the lamina propria (p = 0.00016) and COLCA2 (tumor cells, p = 0.0041 and lamina propria, p = 6 × 10(-5)). In conclusion, genetic, expression and immunohistochemical data implicate COLCA1 and COLCA2 in the pathogenesis of colon cancer. Histologic analyses indicate the involvement of immune pathways

Real-time hit classification in a smart cajón

© 2018 Turchet, McPherson and Barthet. Smartmusical instruments are a class of IoT devices formusicmaking, which encompass embedded intelligence as well as wireless connectivity. In previous work, we established design requirements for a novel smart musical instrument, a smart cajón, following a user-centered approach. This paper describes the implementation and technical evaluation of the designed component of the smart cajón related to hit classification and repurposing. A conventional acoustic cajón was enhanced with sensors to classify position of the hit and the gesture that produced it. The instrument was equipped with five piezo pickups attached to the internal panels and a condenser microphone located inside. The developed sound engine leveraged digital signal processing, sensor fusion, and machine learning techniques to classify the position, dynamics, and timbre of each hit. The techniques were devised and implemented to achieve low latency between action and the electronically-generated sounds, as well as keep computational efficiency high. The system was tuned to classify two main cajón playing techniques at different locations and we conducted evaluations using over 2,000 hits performed by two professional players. We first assessed the classification performance when training and testing data related to recordings fromthe same player. In this configuration, classification accuracies of 100% were obtained for hit detection and location. Accuracies of over 90% were obtained when classifying timbres produced by the two playing techniques. We then assessed the classifier in a cross-player configuration (training and testing were performed using recordings from different players). Results indicated that while hit location scales relatively well across different players, gesture identification requires that the involved classifiers are trained specifically for each musician

CHIASM, the human brain albinism and achiasma MRI dataset

We describe a collection of T1-, diffusion- and functional T2*-weighted magnetic resonance imaging data from human individuals with albinism and achiasma. This repository can be used as a test-bed to develop and validate tractography methods like diffusion-signal modeling and fiber tracking as well as to investigate the properties of the human visual system in individuals with congenital abnormalities. The MRI data is provided together with tools and files allowing for its preprocessing and analysis, along with the data derivatives such as manually curated masks and regions of interest for performing tractography

brainlife.io: A decentralized and open source cloud platform to support neuroscience research

Neuroscience research has expanded dramatically over the past 30 years by advancing standardization and tool development to support rigor and transparency. Consequently, the complexity of the data pipeline has also increased, hindering access to FAIR data analysis to portions of the worldwide research community. brainlife.io was developed to reduce these burdens and democratize modern neuroscience research across institutions and career levels. Using community software and hardware infrastructure, the platform provides open-source data standardization, management, visualization, and processing and simplifies the data pipeline. brainlife.io automatically tracks the provenance history of thousands of data objects, supporting simplicity, efficiency, and transparency in neuroscience research. Here brainlife.io's technology and data services are described and evaluated for validity, reliability, reproducibility, replicability, and scientific utility. Using data from 4 modalities and 3,200 participants, we demonstrate that brainlife.io's services produce outputs that adhere to best practices in modern neuroscience research

The completion of the Mammalian Gene Collection (MGC)

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide

Self-care support for children and adolescents with long-term conditions : the REfOCUS evidence synthesis

Background: Self-care support (e.g. education, training, peer/professional support) is intended to enhance the self-care capacities of children and young people, while simultaneously reducing the financial burden facing health-care systems. Objectives: To determine which models of self-care support for long-term conditions (LTCs) are associated with significant reductions in health utilisation and costs without compromising outcomes for children and young people. Design: Systematic review with meta-analysis. Population: Children and young people aged 0–18 years with a long-term physical or mental health condition (e.g. asthma, depression). Intervention: Self-care support in health, social care, educational or community settings. Comparator: Usual care. Outcomes: Generic/health-related quality of life (QoL)/subjective health symptoms and health service utilisation/costs. Design: Randomised/non-randomised trials, controlled before-and-after studies, and interrupted time series designs. Data sources: MEDLINE, EMBASE, PsycINFO, Cumulative Index to Nursing and Allied Health Literature, ISI Web of Science, NHS Economic Evaluation Database, The Cochrane Library, Health Technology Assessment database, Paediatric Economic Database Evaluation, IDEAS, reference scanning, targeted author searches and forward citation searching. All databases were searched from inception to March 2015. Methods: We conducted meta-analyses, simultaneously plotting QoL and health utilisation effects. We conducted subgroup analyses for evidence quality, age, LTC and intervention (setting, target, delivery format, intensity). Results: Ninety-seven studies reporting 114 interventions were included. Thirty-seven studies reported adequate allocation concealment. Fourteen were UK studies. The vast majority of included studies recruited children and young people with asthma (n = 66, 68%). Four per cent of studies evaluated ‘pure’ self-care support (delivered through health technology without additional contact), 23% evaluated facilitated self-care support (≤ 2 hours’/four sessions’ contact), 65% were intensively facilitated (≥ 2 hours’/four sessions’ contact) and 8% were case management (≥ 2 hours’ support with multidisciplinary input). Self-care support was associated with statistically significant, minimal benefits for QoL [effect size (ES) –0.17, 95% confidence interval (CI) –0.23 to –0.11], but lacked clear benefit for hospital admissions (ES –0.05, 95% CI –0.12 to 0.03). This finding endured across intervention intensities and LTCs. Statistically significant, minimal reductions in emergency use were observed (ES –0.11, 95% CI –0.17 to –0.04). The total cost analysis was limited by the small number of data. Subgroup analyses revealed statistically significant, minimal reductions in emergency use for children aged ≤ 13 years (ES –0.10, 95% CI –0.17 to –0.04), children and young people with asthma (ES –0.12, 95% CI –0.18 to –0.06) and children and young people receiving ≥ 2 hours per four sessions of support (ES –0.10, 95% CI –0.17 to –0.03). Preliminary evidence suggested that interventions that include the child or young person, and deliver some content individually, may optimise QoL effects. Face-to-face delivery may help to maximise emergency department effects. Caution is required in interpreting these findings. Limitations: Identification of optimal models of self-care support is challenged by the size and nature of evidence available. The emphasis on meta-analysis meant that a minority of studies with incomplete but potentially relevant data were excluded. Conclusions: Self-care support is associated with positive but minimal effects on children and young people’s QoL, and minimal, but potentially important, reductions in emergency use. On current evidence, we cannot reliably conclude that self-care support significantly reduces health-care costs. Future work: Research is needed to explore the short- and longer-term effects of self-care support across a wider range of LTCs. Study registration: This study is registered as PROSPERO CRD42014015452. Funding: The National Institute for Health Research Health Services and Delivery Research programme

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead