Nonlinear coupling of nano mechanical resonators to Josephson quantum circuits

We propose a technique to couple the position operator of a nano mechanical resonator to a SQUID device by modulating its magnetic flux bias. By tuning the magnetic field properly, either linear or quadratic couplings can be realized, with a discretely adjustable coupling strength. This provides a way to realize coherent nonlinear effects in a nano mechanical resonator by coupling it to a Josephson quantum circuit. As an example, we show how squeezing of the nano mechanical resonator state can be realized with this technique. We also propose a simple method to measure the uncertainty in the position of the nano mechanical resonator without quantum state tomography

Kinetic-inductance-limited reset time of superconducting nanowire photon counters

We investigate the recovery of superconducting NbN-nanowire photon counters after detection of an optical pulse at a wavelength of 1550 nm, and present a model that quantitatively accounts for our observations. The reset time is found to be limited by the large kinetic inductance of these nanowires, which forces a tradeoff between counting rate and either detection efficiency or active area. Devices of usable size and high detection efficiency are found to have reset times orders of magnitude longer than their intrinsic photoresponse time.Comment: Submitted to Applied Physics Letter

Dissipative phase-fluctuations in superconducting wires capacitively coupled to diffusive metals

We study the screening of the Coulomb interaction in a quasi one-dimensional superconductor given by the presence of either a one- or a two-dimensional non-interacting electron gas. To that end, we derive an effective low-energy phase-only action, which amounts to treating the Coulomb and superconducting correlations in the random-phase approximation. We concentrate on the study of dissipation effects in the superconductor, induced by the effect of Coulomb coupling to the diffusive density-modes in the metal, and study its consequences on the static and dynamic conductivity. Our results point towards the importance of the dimensionality of the screening metal in the behavior of the superconducting plasma mode of the wire at low energies. In absence of topological defects, and when the screening is given by a one-dimensional electron gas, the superconducting plasma mode is completely damped in the limit $q\to 0$, and consequently superconductivity is lost in the wire. In contrast, we recover a Drude-response in the conductivity when the screening is provided by a two-dimensional electron gas.Comment: 16 pages, 8 figures, 1 table, 2 appendice

Integrating image caption information into biomedical document classification in support of biocuration.

Gathering information from the scientific literature is essential for biomedical research, as much knowledge is conveyed through publications. However, the large and rapidly increasing publication rate makes it impractical for researchers to quickly identify all and only those documents related to their interest. As such, automated biomedical document classification attracts much interest. Such classification is critical in the curation of biological databases, because biocurators must scan through a vast number of articles to identify pertinent information within documents most relevant to the database. This is a slow, labor-intensive process that can benefit from effective automation. We present a document classification scheme aiming to identify papers containing information relevant to a specific topic, among a large collection of articles, for supporting the biocuration classification task. Our framework is based on a meta-classification scheme we have introduced before; here we incorporate into it features gathered from figure captions, in addition to those obtained from titles and abstracts. We trained and tested our classifier over a large imbalanced dataset, originally curated by the Gene Expression Database (GXD). GXD collects all the gene expression information in the Mouse Genome Informatics (MGI) resource. As part of the MGI literature classification pipeline, GXD curators identify MGI-selected papers that are relevant for GXD. The dataset consists of ~60 000 documents (5469 labeled as relevant; 52 866 as irrelevant), gathered throughout 2012-2016, in which each document is represented by the text of its title, abstract and figure captions. Our classifier attains precision 0.698, recall 0.784, f-measure 0.738 and Matthews correlation coefficient 0.711, demonstrating that the proposed framework effectively addresses the high imbalance in the GXD classification task. Moreover, our classifier\u27s performance is significantly improved by utilizing information from image captions compared to using titles and abstracts alone; this observation clearly demonstrates that image captions provide substantial information for supporting biomedical document classification and curation. Database URL

The mouse genome database (MGD): new features facilitating a model system

The mouse genome database (MGD, ), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGD's primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and expert human curation. MGD collaborates with the bioinformatics community on the development of data and semantic standards, and it incorporates key ontologies into the MGD annotation system, including the Gene Ontology (GO), the Mammalian Phenotype Ontology, and the Anatomical Dictionary for Mouse Development and the Adult Anatomy. MGD is the authoritative source for mouse nomenclature for genes, alleles, and mouse strains, and for GO annotations to mouse genes. MGD provides a unique platform for data mining and hypothesis generation where one can express complex queries simultaneously addressing phenotypic effects, biochemical function and process, sub-cellular location, expression, sequence, polymorphism and mapping data. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the incorporation of single nucleotide polymorphism data and search tools, the addition of PIR gene superfamily classifications, phenotype data for NIH-acquired knockout mice, images for mouse phenotypic genotypes, new functional graph displays of GO annotations, and new orthology displays including sequence information and graphic displays

The Mouse Genome Database (MGD): from genes to mice—a community resource for mouse biology

The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics

The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data

We have developed an ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse. The Adult Mouse Anatomical Dictionary is structured as a directed acyclic graph, and is organized hierarchically both spatially and functionally. The ontology will be used to annotate and integrate different types of data pertinent to anatomy, such as gene expression patterns and phenotype information, which will contribute to an integrated description of biological phenomena in the mouse

Resistivity scaling and critical dynamics of fully frustrated Josephson-junction arrays with on-site dissipation

We study the scaling behavior and critical dynamics of the resistive transition in Josephson-junction arrays, at f=1/2 flux quantum per plaquette, by numerical simulation of an on-site dissipation model for the dynamics. The results are compared with recent simulations using the resistively-shunted-junction model. For both models, we find that the resistivity scaling and critical dynamics of the phases are well described by the same critical temperature as for the chiral (vortex-lattice) transition, with a power-law divergent correlation length. The behavior is consistent with the single transition scenario, where phase and chiral variables order at the same temperature, but with different dynamic exponents z for phase coherence and chiral order.Comment: 17 pages, 13 figures, to appear in Phys. Rev.

Mouse Genome Database (MGD) 2019.

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism genetic and genome resource for the laboratory mouse. MGD is the authoritative source for biological reference data sets related to mouse genes, gene functions, phenotypes, and mouse models of human disease. MGD is the primary outlet for official gene, allele and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. In this report we describe significant enhancements to MGD, including two new graphical user interfaces: (i) the Multi Genome Viewer for exploring the genomes of multiple mouse strains and (ii) the Phenotype-Gene Expression matrix which was developed in collaboration with the Gene Expression Database (GXD) and allows researchers to compare gene expression and phenotype annotations for mouse genes. Other recent improvements include enhanced efficiency of our literature curation processes and the incorporation of Transcriptional Start Site (TSS) annotations from RIKEN\u27s FANTOM 5 initiative

Mouse Genome Informatics (MGI): latest news from MGD and GXD.

The Mouse Genome Informatics (MGI) database system combines multiple expertly curated community data resources into a shared knowledge management ecosystem united by common metadata annotation standards. MGI\u27s mission is to facilitate the use of the mouse as an experimental model for understanding the genetic and genomic basis of human health and disease. MGI is the authoritative source for mouse gene, allele, and strain nomenclature and is the primary source of mouse phenotype annotations, functional annotations, developmental gene expression information, and annotations of mouse models with human diseases. MGI maintains mouse anatomy and phenotype ontologies and contributes to the development of the Gene Ontology and Disease Ontology and uses these ontologies as standard terminologies for annotation. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are MGI\u27s two major knowledgebases. Here, we highlight some of the recent changes and enhancements to MGD and GXD that have been implemented in response to changing needs of the biomedical research community and to improve the efficiency of expert curation. MGI can be accessed freely at http://www.informatics.jax.org