Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA

For a long time biologists have used visual representations of biochemical networks to gain a quick overview of important structural properties. Recently SBGN, the Systems Biology Graphical Notation, has been developed to standardise the way in which such graphical maps are drawn in order to facilitate the exchange of information. Its qualitative Process Diagrams (SBGN-PD) are based on an implicit Process Flow Abstraction (PFA) that can also be used to construct quantitative representations, which can be used for automated analyses of the system. Here we explicitly describe the PFA that underpins SBGN-PD and define attributes for SBGN-PD glyphs that make it possible to capture the quantitative details of a biochemical reaction network. We implemented SBGNtext2BioPEPA, a tool that demonstrates how such quantitative details can be used to automatically generate working Bio-PEPA code from a textual representation of SBGN-PD that we developed. Bio-PEPA is a process algebra that was designed for implementing quantitative models of concurrent biochemical reaction systems. We use this approach to compute the expected delay between input and output using deterministic and stochastic simulations of the MAPK signal transduction cascade. The scheme developed here is general and can be easily adapted to other output formalisms

Collaborative Autonomy: Exploring the Professional Freedom of Three Science Teachers

Education reform efforts must support and protect professional autonomy for classroom teachers. When policymakers attempt to make systemic change in ways that reduce the professional autonomy of educators, student learning suffers. Teachers need the freedom to identify their professional goals, seek resources and collaboration opportunities in pursuit of those goals, and act on feedback regarding their progress in meeting those goals. We present three stories from teachers who share a department engaged in collaborative autonomy. These accounts provide guidance for how professional autonomy can be defended by those pursuing systemic change

The other side of the trading story: evidence from NYSE

We analyse the well-known TORQ dataset of trades on the NYSE over a 3-month period, breaking down transactions depending on whether the active or passive side was institutional or private. This allows us to compare the returns on the different trade categories. We find that, however we analyse the results, institutions are best informed, and earn highest returns when trading with individuals as counterparty. We also confirm the conclusions found elsewhere in the literature that informed traders often place limit orders, especially towards the end of the day (as predicted on the basis of laboratory experiments in Bloomfield, O�'Hara, and Saar (2005)). Finally, we find that trading between institutions accounts for the bulk of trading volume, but carries little information and seems to be largely liquidity-driven

Hot X-ray coronae around massive spiral galaxies: a unique probe of structure formation models

Luminous X-ray gas coronae in the dark matter halos of massive spiral galaxies are a fundamental prediction of structure formation models, yet only a few such coronae have been detected so far. In this paper, we study the hot X-ray coronae beyond the optical disks of two normal massive spirals, NGC1961 and NGC6753. Based on XMM-Newton X-ray observations, hot gaseous emission is detected to ~60 kpc - well beyond their optical radii. The hot gas has a best-fit temperature of kT~0.6 keV and an abundance of ~0.1 Solar, and exhibits a fairly uniform distribution, suggesting that the quasi-static gas resides in hydrostatic equilibrium in the potential well of the galaxies. The bolometric luminosity of the gas in the (0.05-0.15)r_200 region (r_200 is the virial radius) is ~6e40 erg/s for both galaxies. The baryon mass fractions of NGC1961 and NGC6753 are f_b~0.1, which fall short of the cosmic baryon fraction. The hot coronae around NGC1961 and NGC6753 offer an excellent basis to probe structure formation simulations. To this end, the observations are confronted with the moving mesh code Arepo and the smoothed particle hydrodynamics code Gadget. Although neither model gives a perfect description, the observed luminosities, gas masses, and abundances favor the Arepo code. Moreover, the shape and the normalization of the observed density profiles are better reproduced by Arepo within ~0.5r_200. However, neither model incorporates efficient feedback from supermassive black holes or supernovae, which could alter the simulated properties of the X-ray coronae. With the further advance of numerical models, the present observations will be essential in constraining the feedback effects in structure formation simulations.Comment: 19 pages, 13 figures, 6 tables, accepted for publication in Ap

Unmanned weapons systems and just wars:the psychological dimensions

This chapter explores the psychological impact of unmanned weapons systems on military decision making. Just war theory is used as a normative framework to evaluate whether decision making is morally acceptable before, during, and after conflict. We discuss the psychology of decision making at the strategic, operational, and tactical levels, and question whether the novelty of unmanned weapons systems can bias the consideration of ethics during conflict. We provide theoretical hypotheses that describe how the possession of unmanned weapons systems may influence military decisions. We query whether military decision makers have an appropriate level of understanding and expertise in using these systems; importantly when considering the trade-off between short-term tactical advantage and long-term strategic goals, and offer recommendations for research

Bladder Metastasis of Gastric Adenocarcinoma

Teaching point: Metastatic involvement has to be considered in the differential diagnosis for diffuse bladder wall thickenin

Unraveling the Mysteries of Galaxy Clusters: Recurrent Inference Deconvolution of X-ray Spectra

In the realm of X-ray spectral analysis, the true nature of spectra has remained elusive, as observed spectra have long been the outcome of convolution between instrumental response functions and intrinsic spectra. In this study, we employ a recurrent neural network framework, the Recurrent Inference Machine (RIM), to achieve the high-precision deconvolution of intrinsic spectra from instrumental response functions. Our RIM model is meticulously trained on cutting-edge thermodynamic models and authentic response matrices sourced from the Chandra X-ray Observatory archive. Demonstrating remarkable accuracy, our model successfully reconstructs intrinsic spectra well below the 1-sigma error level. We showcase the practical application of this novel approach through real Chandra observations of the galaxy cluster Abell 1550 - a vital calibration target for the recently launched X-ray telescope, XRISM. This work marks a significant stride in the domain of X-ray spectral analysis, offering a promising avenue for unlocking hitherto concealed insights into spectra.Comment: NeurIPS 2023 ML4PS accepted conference abstrac

Prospective Evaluation of Patient Satisfaction, and Surgeon and Patient Trainer Assessment of the Coloplast Titan One Touch Release Three‐Piece Inflatable Penile Prosthesis

Introduction.  A single‐armed, prospective, multicenter international study evaluated the redesigned Coloplast Titan One Touch Release (OTR) pump inflatable penile prosthesis. The OTR pump has a unique release valve that permits deflation of the implant with one squeeze of opposing touch pads. Aims.  To assess the impact of a new penile prosthesis design, the Titan OTR, on patient ease of operation. Furthermore, to assess patient satisfaction, surgeon acceptance, and the ease with which patients were trained in device operation in the clinic setting. Methods.  A total of 113 eligible patients from eight centers were recruited from men presenting with erectile dysfunction without prior prosthetic implantation. The subjects had a mean age of 61 years, and had a number of comorbidities, including diabetes (31.9%), hypertension (34.5%), and Peyronie's disease (23.9%). All underwent implantation of the study device. Main Outcome Measures.  Questionnaires were used to capture patient satisfaction as well as physician feedback on ease of implantation and patient education. A paired analysis was completed for patient satisfaction at 6 (N = 96) and 12 (N = 90) months. Results.  Overall satisfaction with the device was 90.6% and 90.0% at 6 and 12 months, respectively. The primary end point, ease of deflation, was seen in 70.8% and 73.3% at these two time points, with the 12‐month value statistically better than historical controls. Physicians overwhelmingly reported straightforward/simple intraoperative product preparation (97.3%) and equivalent or easier training compared with their previous pump of choice (96.4%). Adverse events for all subjects (N = 113) included removal of the device in four cases (3.5%) for infection and one case for chronic pain (0.8%). Conclusions.  The Titan OTR represents an advance in penile prosthetic technology that is well accepted by patients and physicians. The study design allowed for realistic evaluation of the new technology aimed at enhancing clinical outcomes. Ohl DA, Brock G, Ralph D, Bogache W, Jones L, Munarriz R, Levine L, and Ritenour C. Prospective evaluation of patient satisfaction, and surgeon and patient trainer assessment of the Coloplast Titan One Touch Release three‐piece inflatable penile prosthesis. J Sex Med 2012;9:2467–2474.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/93661/1/j.1743-6109.2012.02819.x.pd