Search

Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing. We validate the performance with 80 pairs of deep and shallow-coverage whole-genome sequencing and whole-genome bisulfite sequencing data., (© 2024. The Author(s).)

Contagious respiratory diseases, such as COVID-19, depend on sufficiently prolonged exposures for the successful transmission of the underlying pathogen. It is important that organizations evaluate the efficacy of non-pharmaceutical interventions aimed at mitigating viral transmission among their personnel. We have developed a operational risk assessment simulation framework that couples a spatial agent-based model of movement with an agent-based SIR model to assess the relative risks of different intervention strategies. By applying our model on MIT's Stata center, we assess the impacts of three possible dimensions of intervention: one-way vs unrestricted movement, population size allowed onsite, and frequency of leaving designated work location for breaks. We find that there is no significant impact made by one-way movement restrictions over unrestricted movement. Instead, we find that reducing the frequency at which individuals leave their workstations combined with lowering the number of individuals admitted below the current recommendations lowers the likelihood of highly connected individuals within the contact networks that emerge, which in turn lowers the overall risk of infection. We discover three classes of possible interventions based on their epidemiological effects. By assuming a direct relationship between data on secondary attack rates and transmissibility in the agent-based SIR model, we compare relative infection risk of four respiratory illnesses, MERS, SARS, COVID-19, and Measles, within the simulated area, and recommend appropriate intervention guidelines., (© 2022. The Author(s).)

Aim: Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at a late, incurable stage. We sought to determine whether individuals at high risk of developing PDAC could be identified early using routinely collected data., Methods: Electronic health record (EHR) databases from two independent hospitals in Boston, Massachusetts, providing inpatient, outpatient, and emergency care, from 1979 through 2017, were used with case-control matching. PDAC cases were selected using International Classification of Diseases 9/10 codes and validated with tumour registries. A data-driven feature selection approach was used to develop neural networks and L2-regularised logistic regression (LR) models on training data (594 cases, 100,787 controls) and compared with a published model based on hand-selected diagnoses ('baseline'). Model performance was validated on an external database (408 cases, 160,185 controls). Three prediction lead times (180, 270 and 365 days) were considered., Results: The LR model had the best performance, with an area under the curve (AUC) of 0.71 (confidence interval [CI]: 0.67-0.76) for the training set, and AUC 0.68 (CI: 0.65-0.71) for the validation set, 365 days before diagnosis. Data-driven feature selection improved results over 'baseline' (AUC = 0.55; CI: 0.52-0.58). The LR model flags 2692 (CI 2592-2791) of 156,485 as high risk, 365 days in advance, identifying 25 (CI: 16-36) cancer patients. Risk stratification showed that the high-risk group presented a cancer rate 3 to 5 times the prevalence in our data set., Conclusion: A simple EHR model, based on diagnoses, can identify high-risk individuals for PDAC up to one year in advance. This inexpensive, systematic approach may serve as the first sieve for selection of individuals for PDAC screening programs., Competing Interests: Conflict of interest statement The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

A new optical microscopy technique, termed high spatial and temporal resolution synthetic aperture phase microscopy (HISTR-SAPM), is proposed to improve the lateral resolution of wide-field coherent imaging. Under plane wave illumination, the resolution is increased by twofold to around 260 nm, while achieving millisecond-level temporal resolution. In HISTR-SAPM, digital micromirror devices are used to actively change the sample illumination beam angle at high speed with high stability. An off-axis interferometer is used to measure the sample scattered complex fields, which are then processed to reconstruct high-resolution phase images. Using HISTR-SAPM, we are able to map the height profiles of subwavelength photonic structures and resolve the period structures that have 198 nm linewidth and 132 nm gap (i.e., a full pitch of 330 nm). As the reconstruction averages out laser speckle noise while maintaining high temporal resolution, HISTR-SAPM further enables imaging and quantification of nanoscale dynamics of live cells, such as red blood cell membrane fluctuations and subcellular structure dynamics within nucleated cells. We envision that HISTR-SAPM will broadly benefit research in material science and biology.

We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the nucleus, and delineates heterogeneity of both the chromatin architecture and DNA methylome in a mixed population. It enables simultaneous characterization of cell-type-specific chromatin organization and epigenome in complex tissues.

Background: Predictive gene expression modelling is an important tool in computational biology due to the volume of high-throughput sequencing data generated by recent consortia. However, the scope of previous studies has been restricted to a small set of cell-lines or experimental conditions due an inability to leverage distributed processing architectures for large, sharded data-sets., Results: We present a distributed implementation of gene expression modelling using the MapReduce paradigm and prove that performance improves as a linear function of available processor cores. We then leverage the computational efficiency of this framework to explore the variability of epigenetic function across fifty histone modification data-sets from variety of cancerous and non-cancerous cell-lines., Conclusions: We demonstrate that the genome-wide relationships between histone modifications and mRNA transcription are lineage, tissue and karyotype-invariant, and that models trained on matched -omics data from non-cancerous cell-lines are able to predict cancerous expression with equivalent genome-wide fidelity.

Background: Characterising programs of gene regulation by studying individual protein-DNA and protein-protein interactions would require a large volume of high-resolution proteomics data, and such data are not yet available. Instead, many gene regulatory network (GRN) techniques have been developed, which leverage the wealth of transcriptomic data generated by recent consortia to study indirect, gene-level relationships between transcriptional regulators. Despite the popularity of such methods, previous methods of GRN inference exhibit limitations that we highlight and address through the lens of information theory., Results: We introduce new model-free and non-linear information theoretic measures for the inference of GRNs and other biological networks from continuous-valued data. Although previous tools have implemented mutual information as a means of inferring pairwise associations, they either introduce statistical bias through discretisation or are limited to modelling undirected relationships. Our approach overcomes both of these limitations, as demonstrated by a substantial improvement in empirical performance for a set of 160 GRNs of varying size and topology., Conclusions: The information theoretic measures described in this study yield substantial improvements over previous approaches (e.g. ARACNE) and have been implemented in the latest release of NAIL (Network Analysis and Inference Library). However, despite the theoretical and empirical advantages of these new measures, they do not circumvent the fundamental limitation of indeterminacy exhibited across this class of biological networks. These methods have presently found value in computational neurobiology, and will likely gain traction for GRN analysis as the volume and quality of temporal transcriptomics data continues to improve.

This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2015 and co-published as a series in Critical Care. Other articles in the series can be found online at http://ccforum.com/series/annualupdate2015. Further information about the Annual Update in Intensive Care and Emergency Medicine is available from http://www.springer.com/series/8901.

Imaging biomarkers derived from magnetic resonance imaging (MRI) data are used to quantify normal development, disease, and the effects of disease-modifying therapies. However, motion during image acquisition introduces image artifacts that, in turn, affect derived markers. A systematic effect can be problematic since factors of interest like age, disease, and treatment are often correlated with both a structural change and the amount of head motion in the scanner, confounding the ability to distinguish biology from artifact. Here we evaluate the effect of head motion during image acquisition on morphometric estimates of structures in the human brain using several popular image analysis software packages (FreeSurfer 5.3, VBM8 SPM, and FSL Siena 5.0.7). Within-session repeated T1-weighted MRIs were collected on 12 healthy volunteers while performing different motion tasks, including two still scans. We show that volume and thickness estimates of the cortical gray matter are biased by head motion with an average apparent volume loss of roughly 0.7%/mm/min of subject motion. Effects vary across regions and remain significant after excluding scans that fail a rigorous quality check. In view of these results, the interpretation of reported morphometric effects of movement disorders or other conditions with increased motion tendency may need to be revisited: effects may be overestimated when not controlling for head motion. Furthermore, drug studies with hypnotic, sedative, tranquilizing, or neuromuscular-blocking substances may contain spurious "effects" of reduced atrophy or brain growth simply because they affect motion distinct from true effects of the disease or therapeutic process., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Johnson-Lindenstrauss (JL) matrices implemented by sparse random synaptic connections are thought to be a prime candidate for how convergent pathways in the brain compress information. However, to date, there is no complete mathematical support for such implementations given the constraints of real neural tissue. The fact that neurons are either excitatory or inhibitory implies that every so implementable JL matrix must be sign consistent (i.e., all entries in a single column must be either all nonnegative or all nonpositive), and the fact that any given neuron connects to a relatively small subset of other neurons implies that the JL matrix should be sparse. We construct sparse JL matrices that are sign consistent and prove that our construction is essentially optimal. Our work answers a mathematical question that was triggered by earlier work and is necessary to justify the existence of JL compression in the brain and emphasizes that inhibition is crucial if neurons are to perform efficient, correlation-preserving compression.

Optical tweezers have emerged as a promising technique for manipulating biological objects. Instead of direct laser exposure, more often than not, optically-trapped beads are attached to the ends or boundaries of the objects for translation, rotation, and stretching. This is referred to as indirect optical manipulation. In this paper, we utilize the concept of robotic gripping to explain the different experimental setups which are commonly used for indirect manipulation of cells, nucleic acids, and motor proteins. We also give an overview of the kind of biological insights provided by this technique. We conclude by highlighting the trends across the experimental studies, and discuss challenges and promising directions in this domain of active current research.

Monitoring vital signs and locations of certain classes of ambulatory patients can be useful in overcrowded emergency departments and at disaster scenes, both on-site and during transportation. To be useful, such monitoring needs to be portable and low cost, and have minimal adverse impact on emergency personnel, e.g., by not raising an excessive number of alarms. The SMART (Scalable Medical Alert Response Technology) system integrates wireless patient monitoring (ECG, SpO(2)), geo-positioning, signal processing, targeted alerting, and a wireless interface for caregivers. A prototype implementation of SMART was piloted in the waiting area of an emergency department and evaluated with 145 post-triage patients. System deployment aspects were also evaluated during a small-scale disaster-drill exercise.

Motivation: Gene expression profiling is a powerful approach to identify genes that may be involved in a specific biological process on a global scale. For example, gene expression profiling of mutant animals that lack or contain an excess of certain cell types is a common way to identify genes that are important for the development and maintenance of given cell types. However, it is difficult for traditional computational methods, including unsupervised and supervised learning methods, to detect relevant genes from a large collection of expression profiles with high sensitivity and specificity. Unsupervised methods group similar gene expressions together while ignoring important prior biological knowledge. Supervised methods utilize training data from prior biological knowledge to classify gene expression. However, for many biological problems, little prior knowledge is available, which limits the prediction performance of most supervised methods., Results: We present a Bayesian semi-supervised learning method, called BGEN, that improves upon supervised and unsupervised methods by both capturing relevant expression profiles and using prior biological knowledge from literature and experimental validation. Unlike currently available semi-supervised learning methods, this new method trains a kernel classifier based on labeled and unlabeled gene expression examples. The semi-supervised trained classifier can then be used to efficiently classify the remaining genes in the dataset. Moreover, we model the confidence of microarray probes and probabilistically combine multiple probe predictions into gene predictions. We apply BGEN to identify genes involved in the development of a specific cell lineage in the C. elegans embryo, and to further identify the tissues in which these genes are enriched. Compared to K-means clustering and SVM classification, BGEN achieves higher sensitivity and specificity. We confirm certain predictions by biological experiments., Availability: The results are available at http://www.csail.mit.edu/~alanqi/projects/BGEN.html.