Detection of Thermal Emission from a Super-Earth

We report on the detection of infrared light from the super-Earth 55 Cnc e, based on four occultations obtained with Warm Spitzer at 4.5 microns. Our data analysis consists of a two-part process. In a first step, we perform individual analyses of each dataset and compare several baseline models to optimally account for the systematics affecting each lightcurve. We apply independent photometric correction techniques, including polynomial detrending and pixel-mapping, that yield consistent results at the 1-sigma level. In a second step, we perform a global MCMC analysis including all four datasets, that yields an occultation depth of 131+-28ppm, translating to a brightness temperature of 2360+-300 K in the IRAC-4.5 micron channel. This occultation depth suggests a low Bond albedo coupled to an inefficient heat transport from the planetary dayside to the nightside, or else possibly that the 4.5-micron observations probe atmospheric layers that are hotter than the maximum equilibrium temperature (i.e., a thermal inversion layer or a deep hot layer). The measured occultation phase and duration are consistent with a circular orbit and improves the 3-sigma upper limit on 55 Cnc e's orbital eccentricity from 0.25 to 0.06.Comment: Accepted to ApJL on April, 6th 201

Fast and Correct Load-Link/Store-Conditional Instruction Handling in DBT Systems

Dynamic Binary Translation (DBT) requires the implementation of load-link/store-conditional (LL/SC) primitives for guest systems that rely on this form of synchronization. When targeting e.g. x86 host systems, LL/SC guest instructions are typically emulated using atomic Compare-and-Swap (CAS) instructions on the host. Whilst this direct mapping is efficient, this approach is problematic due to subtle differences between LL/SC and CAS semantics. In this paper, we demonstrate that this is a real problem, and we provide code examples that fail to execute correctly on QEMU and a commercial DBT system, which both use the CAS approach to LL/SC emulation. We then develop two novel and provably correct LL/SC emulation schemes: (1) A purely software based scheme, which uses the DBT system’s page translation cache for correctly selecting between fast, but unsynchronized, and slow, but fully synchronized memory accesses, and (2) a hardware accelerated scheme that leverages hardware transactional memory (HTM) provided by the host. We have implemented these two schemes in the Synopsys DesignWare® ARC® nSIM DBT system, and we evaluate our implementations against full applications, and targeted micro-benchmarks. We demonstrate that our novel schemes are not only correct, but also deliver competitive performance on-par or better than the widely used, but broken CAS scheme.Postprin

Granger causal time-dependent source connectivity in the somatosensory network

Peer reviewedPublisher PD

VO: Vaccine Ontology

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO, "http://www.violinet.org/vaccineontology":http://www.violinet.org/vaccineontology) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented.
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VO: Vaccine Ontology

The collaborative, community-based Vaccine Ontology (VO) was developed to promote vaccine data standardization, integration, and computer-assisted reasoning. Currently VO covers a variety of aspects of the vaccine domain, with an emphasis on classification of vaccines and vaccine components, and on host immune response to vaccines. VO can be used for a number of applications, e.g., ontology-based vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI)

CLO: The cell line ontology

Abstract Background Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. Construction and content Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms. Utility and discussion The CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO’s utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development.http://deepblue.lib.umich.edu/bitstream/2027.42/109554/1/13326_2013_Article_185.pd

A stress-induced source of phonon bursts and quasiparticle poisoning.

The performance of superconducting qubits is degraded by a poorly characterized set of energy sources breaking the Cooper pairs responsible for superconductivity, creating a condition often called quasiparticle poisoning. Both superconducting qubits and low threshold dark matter calorimeters have observed excess bursts of quasiparticles or phonons that decrease in rate with time. Here, we show that a silicon crystal glued to its holder exhibits a rate of low-energy phonon events that is more than two orders of magnitude larger than in a functionally identical crystal suspended from its holder in a low-stress state. The excess phonon event rate in the glued crystal decreases with time since cooldown, consistent with a source of phonon bursts which contributes to quasiparticle poisoning in quantum circuits and the low-energy events observed in cryogenic calorimeters. We argue that relaxation of thermally induced stress between the glue and crystal is the source of these events

Mobilise-D Insights To Estimate Real-World Walking Speed in Multiple Conditions With a Wearable Device

This study aimed to validate a wearable device\u27s walking speed estimation pipeline, considering complexity, speed, and walking bout duration. The goal was to provide recommendations on the use of wearable devices for real-world mobility analysis. Participants with Parkinson\u27s Disease, Multiple Sclerosis, Proximal Femoral Fracture, Chronic Obstructive Pulmonary Disease, Congestive Heart Failure, and healthy older adults (n = 97) were monitored in the laboratory and the real-world (2.5 h), using a lower back wearable device. Two walking speed estimation pipelines were validated across 4408/1298 (2.5 h/laboratory) detected walking bouts, compared to 4620/1365 bouts detected by a multi-sensor reference system. In the laboratory, the mean absolute error (MAE) and mean relative error (MRE) for walking speed estimation ranged from 0.06 to 0.12 m/s and - 2.1 to 14.4%, with ICCs (Intraclass correlation coefficients) between good (0.79) and excellent (0.91). Real-world MAE ranged from 0.09 to 0.13, MARE from 1.3 to 22.7%, with ICCs indicating moderate (0.57) to good (0.88) agreement. Lower errors were observed for cohorts without major gait impairments, less complex tasks, and longer walking bouts. The analytical pipelines demonstrated moderate to good accuracy in estimating walking speed. Accuracy depended on confounding factors, emphasizing the need for robust technical validation before clinical application.Trial registration: ISRCTN - 12246987

A Stress Induced Source of Phonon Bursts and Quasiparticle Poisoning

The performance of superconducting qubits is degraded by a poorly characterized set of energy sources breaking the Cooper pairs responsible for superconductivity, creating a condition often called "quasiparticle poisoning." Recently, a superconductor with one of the lowest average quasiparticle densities ever measured exhibited quasiparticles primarily produced in bursts which decreased in rate with time after cooldown. Similarly, several cryogenic calorimeters used to search for dark matter have also observed an unknown source of low-energy phonon bursts that decrease in rate with time after cooldown. Here, we show that a silicon crystal glued to its holder exhibits a rate of low-energy phonon events that is more than two orders of magnitude larger than in a functionally identical crystal suspended from its holder in a low-stress state. The excess phonon event rate in the glued crystal decreases with time since cooldown, consistent with a source of phonon bursts which contributes to quasiparticle poisoning in quantum circuits and the low-energy events observed in cryogenic calorimeters. We argue that relaxation of thermally induced stress between the glue and crystal is the source of these events, and conclude that stress relaxation contributes to quasiparticle poisoning in superconducting qubits and the athermal phonon background in a broad class of rare-event searches.Comment: 13 pages, 6 figures. W. A. Page and R. K. Romani contributed equally to this work. Correspondence should be addressed to R. K. Roman