SBML models and MathSBML

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

Mobile Thread Task Manager

The Mobile Thread Task Manager (MTTM) is being applied to parallelizing existing flight software to understand the benefits and to develop new techniques and architectural concepts for adapting software to multicore architectures. It allocates and load-balances tasks for a group of threads that migrate across processors to improve cache performance. In order to balance-load across threads, the MTTM augments a basic map-reduce strategy to draw jobs from a global queue. In a multicore processor, memory may be "homed" to the cache of a specific processor and must be accessed from that processor. The MTTB architecture wraps access to data with thread management to move threads to the home processor for that data so that the computation follows the data in an attempt to avoid L2 cache misses. Cache homing is also handled by a memory manager that translates identifiers to processor IDs where the data will be homed (according to rules defined by the user). The user can also specify the number of threads and processors separately, which is important for tuning performance for different patterns of computation and memory access. MTTM efficiently processes tasks in parallel on a multiprocessor computer. It also provides an interface to make it easier to adapt existing software to a multiprocessor environment

Injecting Artificial Memory Errors Into a Running Computer Program

Single-event upsets (SEUs) or bitflips are computer memory errors caused by radiation. BITFLIPS (Basic Instrumentation Tool for Fault Localized Injection of Probabilistic SEUs) is a computer program that deliberately injects SEUs into another computer program, while the latter is running, for the purpose of evaluating the fault tolerance of that program. BITFLIPS was written as a plug-in extension of the open-source Valgrind debugging and profiling software. BITFLIPS can inject SEUs into any program that can be run on the Linux operating system, without needing to modify the program s source code. Further, if access to the original program source code is available, BITFLIPS offers fine-grained control over exactly when and which areas of memory (as specified via program variables) will be subjected to SEUs. The rate of injection of SEUs is controlled by specifying either a fault probability or a fault rate based on memory size and radiation exposure time, in units of SEUs per byte per second. BITFLIPS can also log each SEU that it injects and, if program source code is available, report the magnitude of effect of the SEU on a floating-point value or other program variable

Major Constituents Analysis for the Vehicle Cabin Atmosphere Monitor

Vehicle Cabin Atmosphere Monitor (VCAM) can provide a means for monitoring the air within enclosed environments such as the International Space Station, the Crew Exploration Vehicle (CEV), a Lunar habitat, or another vehicle traveling to Mars. The software processes a sum total spectra (counts vs. mass channel) with the intention of computing abundance ratios for N2, O2, CO2, Ar2, and H2O. A brute-force powerset expansion compares a library of expected mass lines with those found within the data. Least squares error is combined with a penalty term for using small peaks

Histogrammatic Method for Determining Relative Abundance of Input Gas Pulse

To satisfy the Major Constituents Analysis (MCA) requirements for the Vehicle Cabin Atmosphere Monitor (VCAM), this software analyzes the relative abundance ratios for N2, O2, Ar, and CO2 as a function of time and constructs their best-estimate mean. A histogram is first built of all abundance ratios for each of the species vs time. The abundance peaks corresponding to the intended measurement and any obfuscating background are then separated via standard peak-finding techniques in histogram space. A voting scheme is then used to include/exclude this particular time sample in the final average based on its membership to the intended measurement or the background population. This results in a robust and reasonable estimate of the abundance of trace components such as CO2 and Ar even in the presence of obfuscating backgrounds internal to the VCAM device. VCAM can provide a means for monitoring the air within the enclosed environments, such as the ISS (International Space Station), Crew Exploration Vehicle (CEV), a Lunar Habitat, or another vehicle traveling to Mars. Its miniature pre-concentrator, gas chromatograph (GC), and mass spectrometer can provide unbiased detection of a large number of organic species as well as MCA analysis. VCAM s software can identify the concentration of trace chemicals and whether the chemicals are on a targeted list of hazardous compounds. This innovation s performance and reliability on orbit, along with the ground team s assessment of its raw data and analysis results, will validate its technology for future use and development

PickBlue: Seismic Phase Picking for Ocean Bottom Seismometers With Deep Learning

Detecting phase arrivals and pinpointing the arrival times of seismic phases in seismograms is crucial for many seismological analysis workflows. For land station data, machine learning methods have already found widespread adoption. However, deep learning approaches are not yet commonly applied to ocean bottom data due to a lack of appropriate training data and models. Here, we compiled an extensive and labeled ocean bottom seismometer (OBS) data set from 15 deployments in different tectonic settings, comprising ∼90,000 P and ∼63,000 S manual picks from 13,190 events and 355 stations. We propose PickBlue, an adaptation of the two popular deep learning networks EQTransformer and PhaseNet. PickBlue joint processes three seismometer recordings in conjunction with a hydrophone component and is trained with the waveforms in the new database. The performance is enhanced by employing transfer learning, where initial weights are derived from models trained with land earthquake data. PickBlue significantly outperforms neural networks trained with land stations and models trained without hydrophone data. The model achieves a mean absolute deviation of 0.05 s for P-waves and 0.12 s for S-waves, and we apply the picker on the Hikurangi Ocean Bottom Tremor and Slow Slip OBS deployment offshore New Zealand. We integrate our data set and trained models into SeisBench to enable an easy and direct application in future deployments

Call Me Caitlyn: Making and making over the 'authentic' transgender body in Anglo-American popular culture

A conception of transgender identity as an ‘authentic’ gendered core ‘trapped’ within a mismatched corporeality, and made tangible through corporeal transformations, has attained unprecedented legibility in contemporary Anglo-American media. Whilst pop-cultural articulations of this discourse have received some scholarly attention, the question of why this 'wrong body' paradigm has solidified as the normative explanation for gender transition within the popular media remains underexplored. This paper argues that this discourse has attained cultural pre-eminence through its convergence with a broader media and commercial zeitgeist, in which corporeal alteration and maintenance are perceived as means of accessing one’s ‘authentic’ self. I analyse the media representations of two transgender celebrities: Caitlyn Jenner and Nadia Almada, alongside the reality TV show TRANSform Me, exploring how these women’s gender transitions have been discursively aligned with a cultural imperative for all women, cisgender or trans, to display their authentic femininity through bodily work. This demonstrates how established tropes of authenticity-via-bodily transformation, have enabled transgender to become culturally legible through the wrong body trope. Problematically, I argue, this process has worked to demarcate ideals of ‘acceptable’ transgender subjectivity: self-sufficient, normatively feminine, and eager to embrace the possibilities for happiness and social integration provided by the commercial domain

A-FABP mediates adaptive thermogenesis by promoting intracellular activation of thyroid hormones in brown adipocytes

The adipokine adipocyte fatty acid-binding protein (A-FABP) has been implicated in obesity-related cardio-metabolic complications. Here we show that A-FABP increases thermogenesis by promoting the conversion of T4 to T3 in brown adipocytes. We find that A-FABP levels are increased in both white (WAT) and brown (BAT) adipose tissues and the bloodstream in response to thermogenic stimuli. A-FABP knockout mice have reduced thermogenesis and whole-body energy expenditure after cold stress or after feeding a high-fat diet, which can be reversed by infusion of recombinant A-FABP. Mechanistically, A-FABP induces the expression of type-II iodothyronine deiodinase in BAT via inhibition of the nuclear receptor liver X receptor α, thereby leading to the conversion of thyroid hormone from its inactive form T4 to active T3. The thermogenic responses to T4 are abrogated in A-FABP KO mice, but enhanced by A-FABP. Thus, A-FABP acts as a physiological stimulator of BAT-mediated adaptive thermogenesis.published_or_final_versio