Compressed Genotyping

Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in applying this knowledge routinely in the clinic, largely due to the relatively tedious and expensive process of DNA sequencing. Since the genetic polymorphisms that underlie these disorders are relatively rare in the human population, the presence or absence of a disease-linked polymorphism can be thought of as a sparse signal. Using methods and ideas from compressed sensing and group testing, we have developed a cost-effective genotyping protocol. In particular, we have adapted our scheme to a recently developed class of high throughput DNA sequencing technologies, and assembled a mathematical framework that has some important distinctions from 'traditional' compressed sensing ideas in order to address different biological and technical constraints.Comment: Submitted to IEEE Transaction on Information Theory - Special Issue on Molecular Biology and Neuroscienc

Expanding connectomics to the laminar level: A perspective

AbstractDespite great progress in uncovering the complex connectivity patterns of the human brain over the last two decades, the field of connectomics still experiences a bias in its viewpoint of the cerebral cortex. Due to a lack of information regarding exact end points of fiber tracts inside cortical gray matter, the cortex is commonly reduced to a single homogenous unit. Concurrently, substantial developments have been made over the past decade in the use of relaxometry and particularly inversion recovery imaging for exploring the laminar microstructure of cortical gray matter. In recent years, these developments have culminated in an automated framework for cortical laminar composition analysis and visualization, followed by studies of cortical dyslamination in epilepsy patients and age-related differences in laminar composition in healthy subjects. This perspective summarizes the developments and remaining challenges of multi-T1 weighted imaging of cortical laminar substructure, the current limitations in structural connectomics, and the recent progress in integrating these fields into a new model-based subfield termed ‘laminar connectomics’. In the coming years, we predict an increased use of similar generalizable, data-driven models in connectomics with the purpose of integrating multimodal MRI datasets and providing a more nuanced and detailed characterization of brain connectivity

T1 relaxometry of crossing fibres in the human brain

A comprehensive tract-based characterisation of white matter should include the ability to quantify myelin and axonal attributes irrespective of the complexity of fibre organisation within the voxel. Recently, a new experimental framework that combines inversion recovery and diffusion MRI, called inversion recovery diffusion tensor imaging (IR-DTI), was introduced and applied in an animal study. IR-DTI provides the ability to assign to each unique fibre population within a voxel a specific value of the longitudinal relaxation time, T1, which is a proxy for myelin content. Here, we apply the IR-DTI approach to the human brain in vivo on 7 healthy subjects for the first time. We demonstrate that the approach is able to measure differential tract properties in crossing fibre areas, reflecting the different myelination of tracts. We also show that tract-specific T1 has less inter-subject variability compared to conventional T1 in areas of crossing fibres, suggesting increased specificity to distinct fibre populations. Finally we show in simulations that changes in myelination selectively affecting one fibre bundle in crossing fibre areas can potentially be detected earlier using IR-DTI

Why diffusion tensor MRI does well only some of the time: Variance and covariance of white matter tissue microstructure attributes in the living human brain

Fundamental to increasing our understanding of the role of white matter microstructure in normal/abnormal function in the living human is the development of MR-based metrics that provide increased specificity to distinct attributes of the white matter (e.g., local fibre architecture, axon morphology, and myelin content). In recent years, different approaches have been developed to enhance this specificity, and the Tractometry framework was introduced to combine the resulting multi-parametric data for a comprehensive assessment of white matter properties. The present work exploits that framework to characterise the statistical properties, specifically the variance and covariance, of these advanced microstructural indices across the major white matter pathways, with the aim of giving clear indications on the preferred metric(s) given the specific research question. A cohort of healthy subjects was scanned with a protocol that combined multi-component relaxometry with conventional and advanced diffusion MRI acquisitions to build the first comprehensive MRI atlas of white matter microstructure. The mean and standard deviation of the different metrics were analysed in order to understand how they vary across different brain regions/individuals and the correlation between them. Characterising the fibre architectural complexity (in terms of number of fibre populations in a voxel) provides clear insights into correlation/lack of correlation between the different metrics and explains why DT-MRI is a good model for white matter only some of the time. The study also identifies the metrics that account for the largest inter-subject variability and reports the minimal sample size required to detect differences in means, showing that, on the other hand, conventional DT-MRI indices might still be the safest choice in many contexts

Rapid re-identification of human samples using portable DNA sequencing

DNA re-identification is used for a broad suite of applications, ranging from cell line authentication to forensics. However, current re-identification schemes suffer from high latency and limited access. Here, we describe a rapid, inexpensive, and portable strategy to robustly re-identify human DNA called 'MinION sketching'. MinION sketching requires as few as 3 min of sequencing and 60-300 random SNPs to re-identify a sample enabling near real-time applications of DNA re-identification. Our method capitalizes on the rapidly growing availability of genomic reference data for cell lines, tissues in biobanks, and individuals. This empowers the application of MinION sketching in research and clinical settings for periodic cell line and tissue authentication. Importantly, our method enables considerably faster and more robust cell line authentication relative to current practices and could help to minimize the amount of irreproducible research caused by mix-ups and contamination in human cell and tissue cultures

Lightsolver challenges a leading deep learning solver for Max-2-SAT problems

Maximum 2-satisfiability (MAX-2-SAT) is a type of combinatorial decision problem that is known to be NP-hard. In this paper, we compare LightSolver's quantum-inspired algorithm to a leading deep-learning solver for the MAX-2-SAT problem. Experiments on benchmark data sets show that LightSolver achieves significantly smaller time-to-optimal-solution compared to a state-of-the-art deep-learning algorithm, where the gain in performance tends to increase with the problem size

Hot Electron-Based Solid State TiO2|Ag Solar Cells

The present work reports a simple and direct sputtering deposition to form solid state TiO2|Ag independent plasmonic solar cells. The independent plasmonic solar cells are based on a Schottky barrier between two materials, TiO2 and Ag. The Ag functions as the absorber generating “hot” electrons, as well as the contact for the solar cell. The Ag sputtering is performed for different durations, to form Ag nanoparticles with a wide size distribution on the surface of rough spray pyrolysis deposited TiO2. Incident photon to current efficiency (IPCE) measurements show photovoltaic activity below the TiO2 bandgap, which is caused by the silver nanoparticles that have a wide plasmonic band, leading to the generation of “hot” electrons. X-ray photoelectron spectroscopy analysis supports the “hot” electron injection mechanism by following the Ag plasmon band and detecting local photovoltages. The measurements show that electrons are formed in the Ag upon illumination and are injected into the TiO2, producing photovoltaic activity. J–V measurements show photocurrents up to 1.18 mA cm−2 and photovoltages up to 430 mV are achieved, with overall efficiencies of 0.2%. This is, to our knowledge, the highest performance reported for such independent plasmonic solar cells

Environmental Stresses Disrupt Telomere Length Homeostasis

Telomeres protect the chromosome ends from degradation and play crucial roles in cellular aging and disease. Recent studies have additionally found a correlation between psychological stress, telomere length, and health outcome in humans. However, studies have not yet explored the causal relationship between stress and telomere length, or the molecular mechanisms underlying that relationship. Using yeast as a model organism, we show that stresses may have very different outcomes: alcohol and acetic acid elongate telomeres, whereas caffeine and high temperatures shorten telomeres. Additional treatments, such as oxidative stress, show no effect. By combining genome-wide expression measurements with a systematic genetic screen, we identify the Rap1/Rif1 pathway as the central mediator of the telomeric response to environmental signals. These results demonstrate that telomere length can be manipulated, and that a carefully regulated homeostasis may become markedly deregulated in opposing directions in response to different environmental cues

In-Vivo Estimates of Axonal Characteristics Using Optimized Diffusion MRI Protocols for Single Fibre Orientation

This work presents diffusion MR protocols that allow estimation of axonal parameters like diameter and density in the live human brain. Previous approaches demand very high field experimental systems or suffer from long acquisition times and are therefore impractical for use in clinical studies. We propose a method that significantly reduces scan time by making use of the a-priori known fibre orientation in structures with well defined single fibre (SF) organisation like the corpus callosum (CC) and produces protocols that can be performed in under 25 minutes on a standard clinical system. Results from a computer simulation experiment show that our SF protocols can generate parameter estimates with similar precision to previously proposed orientation invariant (OI) protocols. Furthermore, we acquire the 20 minute long SF protocol and the 1 hour long OI protocol in a scan/rescan study on two healthy subjects and compare the axonal parameter maps from both protocols. © 2010 Springer-Verlag