The comparison of gene regulatory networks between diseased versus healthy individuals or between two different treatments is an important scientific problem. Here, we propose sc-compReg as a method for the comparative analysis of gene expression regulatory networks between two conditions using single cell gene expression (scRNA-seq) and single cell chromatin accessibility data (scATAC-seq). Our software, sc-compReg, can be used as a stand-alone package that provides joint clustering and embedding of the cells from both scRNA-seq and scATAC-seq, and the construction of differential regulatory networks across two conditions. We apply the method to compare the gene regulatory networks of an individual with chronic lymphocytic leukemia (CLL) versus a healthy control. The analysis reveals a tumor-specific B cell subpopulation in the CLL patient and identifies TOX2 as a potential regulator of this subpopulation.

Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.

Large-scale population analyses coupled with advances in technology have demonstrated that the human genome is more diverse than originally thought. To date, this diversity has largely been uncovered using short-read whole-genome sequencing. However, these short-read approaches fail to give a complete picture of a genome. They struggle to identify structural events, cannot access repetitive regions, and fail to resolve the human genome into haplotypes. Here, we describe an approach that retains long range information while maintaining the advantages of short reads. Starting from ∼1 ng of high molecular weight DNA, we produce barcoded short-read libraries. Novel informatic approaches allow for the barcoded short reads to be associated with their original long molecules producing a novel data type known as "Linked-Reads". This approach allows for simultaneous detection of small and large variants from a single library. In this manuscript, we show the advantages of Linked-Reads over standard short-read approaches for reference-based analysis. Linked-Reads allow mapping to 38 Mb of sequence not accessible to short reads, adding sequence in 423 difficult-to-sequence genes including disease-relevant genes STRC, SMN1, and SMN2 Both Linked-Read whole-genome and whole-exome sequencing identify complex structural variations, including balanced events and single exon deletions and duplications. Further, Linked-Reads extend the region of high-confidence calls by 68.9 Mb. The data presented here show that Linked-Reads provide a scalable approach for comprehensive genome analysis that is not possible using short reads alone.

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes, however, the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5-gigabase (Gb) diploid pepper ( Capsicum annuum ) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F 1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion. The Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Over 83% of the final assembly was anchored and oriented using four publicly available de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F 1 sample that represents pungent and nonpungent peppers, as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes. The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

In modern cancer treatment, there is significant interest in studying the use of drug molecules either directly injected into the bloodstream or delivered by nanoparticle (NP) carriers of various shapes and sizes. During treatment, these carriers may extravasate through pores in the tumor vasculature that form during angiogenesis. We provide an analytical, computational, and experimental examination of the extravasation of point particles (e.g., drug molecules) and finite-sized spheroidal particles. We study the advection-diffusion process in a model microvasculature, consisting of a shear flow over and a pressure-driven suction flow into a circular pore in a flat surface. For point particles, we provide an analytical formula S(kappa,P,Q) approximate to (1/kappa + pi/4(1 + 0.3959P(1/2))(2/3)))(-1) + 2PQ for the dimensionless Sherwood number S, i.e., the extravasation rate, in terms of the pore entry resistance (Damkohler number kappa), the shear rate (Peclet number P) , and the suction flow rate (suction strength Q) . Brownian dynamics (BD) simulations verify this result, and our simulations are then extended to include finite-sized NPs, in which no analytical solutions are available. BD simulations indicate that particles of different geometries have drastically different extravasation rates in different flow conditions. In general, extreme aspect ratio particles provide a greater flux through the pore because of favorable alignment with streamlines entering the pore and less hindered interaction with the pore. We validate the BD simulations by measuring the in vitro transport of both bacteriophage MS2 (a spherical NP) and free dye (a model drug molecule) across a porous membrane. Despite their vastly different sizes, BD predicts S = 8.53 E-4 and S = 27.6 E - 4, and our experiments agree favorably, with S-exp = 10.6 E-4 +/- 1.75 E-4 and S-exp = 16.3 E-4 +/- 3.09 E - 4, for MS2 and free dye, respectively, thus demonstrating the practical utility of our simulation framework.

The authors would like to correct errors in Figures 2, 4, and Supplemental Figure S3, which were inadvertently mislabeled in the initial publication of this article. In Figure 2C, the y-axis should read SEF (Log10). Similarly, in Figure 4, panels A, B, D, E, F, and H (both xand y-axes) and Supplemental Figure S3, Log2 should be corrected to Log10. This error underrepresents the differences in the data. Please note that the revised panels have now been published online with their respective figures and in the Revised Supplemental Material. The authors apologize for the inconvenience.

We study the problem of mass transport to surfaces with heterogeneous reaction rates in the presence of shear flow over these surfaces. The reactions are first order and the heterogeneity is due to the existence of inert regions on the surfaces. Such problems are ubiquitous in the field of heterogeneous catalysis, electrochemistry and even biological mass transport. In these problems, the microscale reaction rate is characterized by a Damköhler number $\unicode[STIX]{x1D705}$ , while the Péclet number $P$ is the dimensionless ratio of the bulk shear rate to the inverse diffusion time scale. The area fraction of the reactive region is denoted by $\unicode[STIX]{x1D719}$ . The objective is to calculate the yield of reaction, which is directly related to the mass flux to the reactive region, denoted by the dimensionless Sherwood number $S$ . Previously, we used boundary element simulations and examined the case of first-order reactive disks embedded in an inert surface (Shah & Shaqfeh J. Fluid Mech. , vol. 782, 2015, pp. 260–299). Various correlations for the Sherwood number as a function of $(\unicode[STIX]{x1D705},P,\unicode[STIX]{x1D719})$ were obtained. In particular, we demonstrated that the ‘method of additive resistances’ provides a good approximation for the Sherwood number for a wide range of values of $(\unicode[STIX]{x1D705},P)$ for $0<\unicode[STIX]{x1D719}<0.78$ . When $\unicode[STIX]{x1D719}\approx 0.78$ , the reactive disks are in a close packed configuration where the inert regions are essentially disconnected from each other. In this work, we develop an understanding of the physics when $\unicode[STIX]{x1D719}>0.78$ , by examining the inverse problem of inert disks on a reactive surface. We show that the method of resistances approach to obtain the Sherwood number fails in the limit as $\unicode[STIX]{x1D719}\rightarrow 1$ , i.e. in the dilute limit of periodic inert disks, due to the existence of a surface concentration boundary layer around each disk that scales with ( $1/\unicode[STIX]{x1D705}$ ). This boundary layer controls the screening length between inert disks and allows us to introduce a new theory, thus providing new correlations for the Sherwood number that are highly accurate in the limit of $\unicode[STIX]{x1D719}\rightarrow 1$ .

Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses, and in general, failing to capture sequences novel to a given genome. Some de novo assemblies have been constructed free of reference bias, but nearly all were constructed by merging homologous loci into single "consensus" sequences, generally absent from nature. These assemblies do not correctly represent the diploid biology of an individual. In exactly two cases, true diploid de novo assemblies have been made, at great expense. One was generated using Sanger sequencing, and one using thousands of clone pools. Here, we demonstrate a straightforward and low-cost method for creating true diploid de novo assemblies. We make a single library from ∼1 ng of high molecular weight DNA, using the 10x Genomics microfluidic platform to partition the genome. We applied this technique to seven human samples, generating low-cost HiSeq X data, then assembled these using a new "pushbutton" algorithm, Supernova. Each computation took 2 d on a single server. Each yielded contigs longer than 100 kb, phase blocks longer than 2.5 Mb, and scaffolds longer than 15 Mb. Our method provides a scalable capability for determining the actual diploid genome sequence in a sample, opening the door to new approaches in genomic biology and medicine.

Current short-read methods have come to dominate genome sequencing because they are cost-effective, rapid, and accurate. However, short reads are most applicable when data can be aligned to a known reference. Two new methods for de novo assembly are linked-reads and restriction-site labeled optical maps. We combined commercial applications of these technologies for genome assembly of an endangered mammal, the Hawaiian Monk seal.We show that the linked-reads produced with 10X Genomics Chromium chemistry and assembled with Supernova v1.1 software produced scaffolds with an N50 of 22.23 Mbp with the longest individual scaffold of 84.06 Mbp. When combined with Bionano Genomics optical maps using Bionano RefAligner, the scaffold N50 increased to 29.65 Mbp for a total of 170 hybrid scaffolds, the longest of which was 84.78 Mbp. These results were 161X and 215X, respectively, improved over DISCOVAR de novo assemblies. The quality of the scaffolds was assessed using conserved synteny analysis of both the DNA sequence and predicted seal proteins relative to the genomes of humans and other species. We found large blocks of conserved synteny suggesting that the hybrid scaffolds were high quality. An inversion in one scaffold complementary to human chromosome 6 was found and confirmed by optical maps.The complementarity of linked-reads and optical maps is likely to make the production of high quality genomes more routine and economical and, by doing so, significantly improve our understanding of comparative genome biology.

Surfaces that include heterogeneous mass transfer at the microscale are ubiquitous in nature and engineering. Many such media are modelled via an effective surface reaction rate or mass transfer coefficient employing the conventional ansatz of kinetically limited transport at the microscale. However, this assumption is not always valid, particularly when there is strong flow. We are interested in modelling reactive and/or porous surfaces that occur in systems where the effective Damköhler number at the microscale can be $O(1)$ and the local Péclet number may be large. In order to expand the range of the effective mass transfer surface coefficient, we study transport from a uniform bath of species in an unbounded shear flow over a flat surface. This surface has a heterogeneous distribution of first-order surface-reactive circular patches (or pores). To understand the physics at the length scale of the patch size, we first analyse the flux to a single reactive patch. We use both analytic and boundary element simulations for this purpose. The shear flow induces a 3-D concentration wake structure downstream of the patch. When two patches are aligned in the shear direction, the wakes interact to reduce the per patch flux compared with the single-patch case. Having determined the length scale of the interaction between two patches, we study the transport to a periodic and disordered distribution of patches again using analytic and boundary integral techniques. We obtain, up to non-dilute patch area fraction, an effective boundary condition for the transport to the patches that depends on the local mass transfer coefficient (or reaction rate) and shear rate. We demonstrate that this boundary condition replaces the details of the heterogeneous surfaces at a wall-normal effective slip distance also determined for non-dilute patch area fractions. The slip distance again depends on the shear rate, and weakly on the reaction rate, and scales with the patch size. These effective boundary conditions can be used directly in large-scale physics simulations as long as the local shear rate, reaction rate and patch area fraction are known.

Motivated by recent studies on tumor treatments using the drug delivery of nanoparticles, we provide a singular perturbation theory and perform Brownian dynamics simulations to quantify the extravasation rate of Brownian particles in a shear flow over a circular pore with a lumped mass transfer resistance. The analytic theory we present is an expansion in the limit of a vanishing Péclet number (\(P\)), which is the ratio of convective fluxes to diffusive fluxes on the length scale of the pore. We state the concentration of particles near the pore and the extravasation rate (Sherwood number) to \(O(P^{1/2})\). This model improves upon previous studies because the results are valid for all values of the particle mass transfer coefficient across the pore, as modeled by the Damköhler number (\(\kappa \)), which is the ratio of the reaction rate to the diffusive mass transfer rate at the boundary. Previous studies focused on the adsorption-dominated regime (i.e., \(\kappa \rightarrow \infty \)). Specifically, our work provides a theoretical basis and an interpolation-based approximate method for calculating the Sherwood number (a measure of the extravasation rate) for the case of finite resistance [\(\kappa \sim O(1)\)] at small Péclet numbers, which are physiologically important in the extravasation of nanoparticles. We compare the predictions of our theory and an approximate method to Brownian dynamics simulations with reflection–reaction boundary conditions as modeled by \(\kappa \). They are found to agree well at small \(P\) and for the \(\kappa \ll 1\) and \(\kappa \gg 1\) asymptotic limits representing the diffusion-dominated and adsorption-dominated regimes, respectively. Although this model neglects the finite size effects of the particles, it provides an important first step toward understanding the physics of extravasation in the tumor vasculature.

There exist many web based news provider applications (e.g. Pulse News reader application for iPhone/iPad and Android platforms) that gather news articles from the myriad ‘feeds’ the user is subscribed to and displays them with-in each feed category. A feed refers to a stream of news articles that may represent a news category (e.g. Gadgets, Technology, Sports, etc.) or may be very general (e.g. RSS feed provided by some newspaper for top articles, etc.). In this project, we analyze and develop machine learning techniques for personalized feed based news prediction and recommendation.

A new generation of robots is being designed for human occupied workspaces where safety is of great concern. This research demonstrates the use of a capacitive skin sensor for collision detection. Tests demonstrate that the sensor reduces impact forces and can detect and characterize collision events, providing information that may be used in the future for force reduction behaviors. Various parameters that affect collision severity, including interface friction, interface stiffness, end tip velocity and joint stiffness irrespective of controller bandwidth are also explored using the sensor to provide information about the contact force at the site of impact. Joint stiffness is made independent of controller bandwidth limitations using passive torsional springs of various stiffnesses. Results indicate a positive correlation between peak impact force and joint stiffness, skin friction and interface stiffness, with implications for future skin and robot link designs and post-collision behaviors.

capacitive skin sensor for collision detection. Tests demonstrate that the sensor reduces impact forces and can detect and characterize collision events, providing information that may be used in the future for force reduction behaviors. Various parameters that affect collision severity, including interface friction, interface stiffness, end tip velocity and joint stiffness irrespective of controller bandwidth are also explored using the sensor to provide information about the contact force at the site of impact. Joint stiffness is made independent of controller bandwidth limitations using passive torsional springs of various stiffnesses. Results indicate a positive correlation between peak impact force and joint stiffness, skin friction and interface stiffness, with implications for future skin and robot link designs and post-collision behaviors.

Spontaneous rupture of hepatocellular carcinomas are uncommon but constitute a critical and life threatening condition. Diagnosis is important so that either surgery or emergency arterial embolisation can be considered for hepatic haemostasis. We describe active extravasation of intravenous contrast medium on CT in a patient who presented with intraperitoneal haemorrhage secondary to spontaneous rupture of hepatocellular carcinoma.