An intracardiac electrogram model to bridge virtual hearts and implantable cardiac devices

Virtual heart models have been proposed to enhance the safety of implantable cardiac devices through closed loop validation. To communicate with a virtual heart, devices have been driven by cardiac signals at specific sites. As a result, only the action potentials of these sites are sensed. However, the real device implanted in the heart will sense a complex combination of near and far-field extracellular potential signals. Therefore many device functions, such as blanking periods and refractory periods, are designed to handle these unexpected signals. To represent these signals, we develop an intracardiac electrogram (IEGM) model as an interface between the virtual heart and the device. The model can capture not only the local excitation but also far-field signals and pacing afterpotentials. Moreover, the sensing controller can specify unipolar or bipolar electrogram (EGM) sensing configurations and introduce various oversensing and undersensing modes. The simulation results show that the model is able to reproduce clinically observed sensing problems, which significantly extends the capabilities of the virtual heart model in the context of device validation

Ground state search, hysteretic behaviour, and reversal mechanism of skyrmionic textures in confined helimagnetic nanostructures

Magnetic skyrmions have the potential to provide solutions for low-power, high-density data storage and processing. One of the major challenges in developing skyrmion-based devices is the skyrmions' magnetic stability in confined helimagnetic nanostructures. Through a systematic study of equilibrium states, using a full three-dimensional micromagnetic model including demagnetisation effects, we demonstrate that skyrmionic textures are the lowest energy states in helimagnetic thin film nanostructures at zero external magnetic field and in absence of magnetocrystalline anisotropy. We also report the regions of metastability for non-ground state equilibrium configurations. We show that bistable skyrmionic textures undergo hysteretic behaviour between two energetically equivalent skyrmionic states with different core orientation, even in absence of both magnetocrystalline and demagnetisation-based shape anisotropies, suggesting the existence of Dzyaloshinskii-Moriya-based shape anisotropy. Finally, we show that the skyrmionic texture core reversal dynamics is facilitated by the Bloch point occurrence and propagation.Comment: manuscript: 14 pages, 7 figures; supplementary information: 8 pages, 7 figure

Observation of a mesoscopic magnetic modulation in chiral Mn1/3NbS2

We have investigated the structural, magnetic, thermodynamic, and charge transport properties of Mn1/3NbS2 single crystals through x-ray and neutron diffraction, magnetization, specific heat, magnetoresistance, and Hall effect measurements. Mn1/3NbS2 displays a magnetic transition at TC ~ 45 K with highly anisotropic behavior expected for a hexagonal structured material. Below TC, neutron diffraction reveals increased scattering near the structural Bragg peaks having a wider Q-dependence along the c-axis than the nuclear Bragg peaks. This indicates helimagnetism with a long pitch length of ~250 nm (or a wavevector q~0.0025 {\AA}-1) along the c-axis. This q is substantially smaller than that found for the helimagnetic state in isostructural Cr1/3NbS2 (0.015 {\AA}-1). Specific heat capacity measurements confirm a second-order magnetic phase transition with a substantial magnetic contribution that persists to low temperature. The large low-temperature specific heat capacity is consistent with a large density of low-lying magnetic excitations that are likely associated with topologically interesting magnetic modes. Changes to the magnetoresistance, the magnetization, and the magnetic neutron diffraction, which become more apparent below 20 K, imply a modification in the character of the magnetic ordering corresponding to the magnetic contribution to the specific heat capacity. These observations signify a more complex magnetic structure both at zero and finite fields for Mn1/3NbS2 than for the well-investigated Cr1/3NbS2.Comment: 22 pages, 7 figure

Osteoarthritis: toward a comprehensive understanding of pathological mechanism

Osteoarthritis (OA) is the most common degenerative joint disease and a major cause of pain and disability in adult individuals. The etiology of OA includes joint injury, obesity, aging, and heredity. However, the detailed molecular mechanisms of OA initiation and progression remain poorly understood and, currently, there are no interventions available to restore degraded cartilage or decelerate disease progression. The diathrodial joint is a complicated organ and its function is to bear weight, perform physical activity and exhibit a joint-specific range of motion during movement. During OA development, the entire joint organ is affected, including articular cartilage, subchondral bone, synovial tissue and meniscus. A full understanding of the pathological mechanism of OA development relies on the discovery of the interplaying mechanisms among different OA symptoms, including articular cartilage degradation, osteophyte formation, subchondral sclerosis and synovial hyperplasia, and the signaling pathway(s) controlling these pathological processes

Differences in transcription between free-living and CO_2-activated third-stage larvae of Haemonchus contortus

Background: The disease caused by Haemonchus contortus, a blood-feeding nematode of small ruminants, is of major economic importance worldwide. The infective third-stage larva (L3) of this gastric nematode is enclosed in a cuticle (sheath) and, once ingested with herbage by the host, undergoes an exsheathment process that marks the transition from the free-living (L3) to the parasitic (xL3) stage. This study explored changes in gene transcription associated with this transition and predicted, based on comparative analysis, functional roles for key transcripts in the metabolic pathways linked to larval development. Results: Totals of 101,305 (L3) and 105,553 (xL3) expressed sequence tags (ESTs) were determined using 454 sequencing technology, and then assembled and annotated; the most abundant transcripts encoded transthyretin-like, calcium-binding EF-hand, NAD(P)-binding and nucleotide-binding proteins as well as homologues of Ancylostoma-secreted proteins (ASPs). Using an in silico-subtractive analysis, 560 and 685 sequences were shown to be uniquely represented in the L3 and xL3 stages, respectively; the transcripts encoded ribosomal proteins, collagens and elongation factors (in L3), and mainly peptidases and other enzymes of amino acid catabolism (in xL3). Caenorhabditis elegans orthologues of transcripts that were uniquely transcribed in each L3 and xL3 were predicted to interact with a total of 535 other genes, all of which were involved in embryonic development. Conclusion: The present study indicated that some key transcriptional alterations taking place during the transition from the L3 to the xL3 stage of H. contortus involve genes predicted to be linked to the development of neuronal tissue (L3 and xL3), formation of the cuticle (L3) and digestion of host haemoglobin (xL3). Future efforts using next-generation sequencing and bioinformatic technologies should provide the efficiency and depth of coverage required for the determination of the complete transcriptomes of different developmental stages and/or tissues of H. contortus as well as the genome of this important parasitic nematode. Such advances should lead to a significantly improved understanding of the molecular biology of H. contortus and, from an applied perspective, to novel methods of intervention

Automatic unpaired shape deformation transfer

Transferring deformation from a source shape to a target shape is a very useful technique in computer graphics. State-of-the-art deformation transfer methods require either point-wise correspondences between source and target shapes, or pairs of deformed source and target shapes with corresponding deformations. However, in most cases, such correspondences are not available and cannot be reliably established using an automatic algorithm. Therefore, substantial user effort is needed to label the correspondences or to obtain and specify such shape sets. In this work, we propose a novel approach to automatic deformation transfer between two unpaired shape sets without correspondences. 3D deformation is represented in a high-dimensional space. To obtain a more compact and effective representation, two convolutional variational autoencoders are learned to encode source and target shapes to their latent spaces. We exploit a Generative Adversarial Network (GAN) to map deformed source shapes to deformed target shapes, both in the latent spaces, which ensures the obtained shapes from the mapping are indistinguishable from the target shapes. This is still an under-constrained problem, so we further utilize a reverse mapping from target shapes to source shapes and incorporate cycle consistency loss, i.e. applying both mappings should reverse to the input shape. This VAE-Cycle GAN (VC-GAN) architecture is used to build a reliable mapping between shape spaces. Finally, a similarity constraint is employed to ensure the mapping is consistent with visual similarity, achieved by learning a similarity neural network that takes the embedding vectors from the source and target latent spaces and predicts the light field distance between the corresponding shapes. Experimental results show that our fully automatic method is able to obtain high-quality deformation transfer results with unpaired data sets, comparable or better than existing methods where strict correspondences are required

Multi-Messenger Gravitational Wave Searches with Pulsar Timing Arrays: Application to 3C66B Using the NANOGrav 11-year Data Set

When galaxies merge, the supermassive black holes in their centers may form binaries and, during the process of merger, emit low-frequency gravitational radiation in the process. In this paper we consider the galaxy 3C66B, which was used as the target of the first multi-messenger search for gravitational waves. Due to the observed periodicities present in the photometric and astrometric data of the source of the source, it has been theorized to contain a supermassive black hole binary. Its apparent 1.05-year orbital period would place the gravitational wave emission directly in the pulsar timing band. Since the first pulsar timing array study of 3C66B, revised models of the source have been published, and timing array sensitivities and techniques have improved dramatically. With these advances, we further constrain the chirp mass of the potential supermassive black hole binary in 3C66B to less than $(1.65\pm0.02) \times 10^9~{M_\odot}$ using data from the NANOGrav 11-year data set. This upper limit provides a factor of 1.6 improvement over previous limits, and a factor of 4.3 over the first search done. Nevertheless, the most recent orbital model for the source is still consistent with our limit from pulsar timing array data. In addition, we are able to quantify the improvement made by the inclusion of source properties gleaned from electromagnetic data to `blind' pulsar timing array searches. With these methods, it is apparent that it is not necessary to obtain exact a priori knowledge of the period of a binary to gain meaningful astrophysical inferences.Comment: 14 pages, 6 figures. Accepted by Ap

Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum

Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3) of A. suum was constructed by suppressive-subtractive hybridization (SSH), and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498) shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer). Using gene ontology (GO), 235 of these molecules were assigned to ‘biological process’ (n = 68), ‘cellular component’ (n = 50), or ‘molecular function’ (n = 117). Of the 91 clusters assembled, 56 molecules (61.5%) had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5%) had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors), and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein–protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50) to be involved in apoptosis and insulin signaling (2%), ATP synthesis (2%), carbon metabolism (6%), fatty acid biosynthesis (2%), gap junction (2%), glucose metabolism (6%), or porphyrin metabolism (2%), although 34 (68%) of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%), anchored (2%), and/or transmembrane (12%) proteins. Functionally, 17 (34%) of them were predicted to be associated with (non-wild-type) RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb) (13 types; 58.8%), larval arrest (Lva) (23.5%) and larval lethality (Lvl) (47%). A genetic interaction network was predicted for these 17 C. elegans orthologues, revealing highly significant interactions for nine molecules associated with embryonic and larval development (66.9%), information storage and processing (5.1%), cellular processing and signaling (15.2%), metabolism (6.1%), and unknown function (6.7%). The potential roles of these molecules in development are discussed in relation to the known roles of their homologues/orthologues in C. elegans and some other nematodes. The results of the present study provide a basis for future functional genomic studies to elucidate molecular aspects governing larval developmental processes in A. suum and/or the transition to parasitism