Ultrafast processing of pixel detector data with machine learning frameworks

Modern photon science performed at high repetition rate free-electron laser (FEL) facilities and beyond relies on 2D pixel detectors operating at increasing frequencies (towards 100 kHz at LCLS-II) and producing rapidly increasing amounts of data (towards TB/s). This data must be rapidly stored for offline analysis and summarized in real time. While at LCLS all raw data has been stored, at LCLS-II this would lead to a prohibitive cost; instead, enabling real time processing of pixel detector raw data allows reducing the size and cost of online processing, offline processing and storage by orders of magnitude while preserving full photon information, by taking advantage of the compressibility of sparse data typical for LCLS-II applications. We investigated if recent developments in machine learning are useful in data processing for high speed pixel detectors and found that typical deep learning models and autoencoder architectures failed to yield useful noise reduction while preserving full photon information, presumably because of the very different statistics and feature sets between computer vision and radiation imaging. However, we redesigned in Tensorflow mathematically equivalent versions of the state-of-the-art, "classical" algorithms used at LCLS. The novel Tensorflow models resulted in elegant, compact and hardware agnostic code, gaining 1 to 2 orders of magnitude faster processing on an inexpensive consumer GPU, reducing by 3 orders of magnitude the projected cost of online analysis at LCLS-II. Computer vision a decade ago was dominated by hand-crafted filters; their structure inspired the deep learning revolution resulting in modern deep convolutional networks; similarly, our novel Tensorflow filters provide inspiration for designing future deep learning architectures for ultrafast and efficient processing and classification of pixel detector images at FEL facilities.Comment: 9 pages, 9 figure

Nox2 redox signaling maintains essential cell populations in the brain.

Reactive oxygen species (ROS) are conventionally classified as toxic consequences of aerobic life, and the brain is particularly susceptible to ROS-induced oxidative stress and damage owing to its high energy and oxygen demands. NADPH oxidases (Nox) are a widespread source of brain ROS implicated in seizures, stroke and neurodegeneration. A physiological role for ROS generation in normal brain function has not been established, despite the fact that mice and humans lacking functional Nox proteins have cognitive deficits. Using molecular imaging with Peroxyfluor-6 (PF6), a new selective fluorescent indicator for hydrogen peroxide (H(2)O(2)), we show that adult hippocampal stem/progenitor cells (AHPs) generate H(2)O(2) through Nox2 to regulate intracellular growth signaling pathways, which in turn maintains their normal proliferation in vitro and in vivo. Our results challenge the traditional view that brain ROS are solely deleterious by demonstrating that controlled ROS chemistry is needed for maintaining specific cell populations

The intrinsic stiffness of human trabecular meshwork cells increases with senescence.

Dysfunction of the human trabecular meshwork (HTM) plays a central role in the age-associated disease glaucoma, a leading cause of irreversible blindness. The etiology remains poorly understood but cellular senescence, increased stiffness of the tissue, and the expression of Wnt antagonists such as secreted frizzled related protein-1 (SFRP1) have been implicated. However, it is not known if senescence is causally linked to either stiffness or SFRP1 expression. In this study, we utilized in vitro HTM senescence to determine the effect on cellular stiffening and SFRP1 expression. Stiffness of cultured cells was measured using atomic force microscopy and the morphology of the cytoskeleton was determined using immunofluorescent analysis. SFRP1 expression was measured using qPCR and immunofluorescent analysis. Senescent cell stiffness increased 1.88±0.14 or 2.57±0.14 fold in the presence or absence of serum, respectively. This was accompanied by increased vimentin expression, stress fiber formation, and SFRP1 expression. In aggregate, these data demonstrate that senescence may be a causal factor in HTM stiffening and elevated SFRP1 expression, and contribute towards disease progression. These findings provide insight into the etiology of glaucoma and, more broadly, suggest a causal link between senescence and altered tissue biomechanics in aging-associated diseases

Carbon Free Boston: Transportation Technical Report

Part of a series of reports that includes: Carbon Free Boston: Summary Report; Carbon Free Boston: Social Equity Report; Carbon Free Boston: Technical Summary; Carbon Free Boston: Buildings Technical Report; Carbon Free Boston: Waste Technical Report; Carbon Free Boston: Energy Technical Report; Carbon Free Boston: Offsets Technical ReportOVERVIEW: Transportation connects Boston’s workers, residents and tourists to their livelihoods, health care, education, recreation, culture, and other aspects of life quality. In cities, transit access is a critical factor determining upward mobility. Yet many urban transportation systems, including Boston’s, underserve some populations along one or more of those dimensions. Boston has the opportunity and means to expand mobility access to all residents, and at the same time reduce GHG emissions from transportation. This requires the transformation of the automobile-centric system that is fueled predominantly by gasoline and diesel fuel. The near elimination of fossil fuels—combined with more transit, walking, and biking—will curtail air pollution and crashes, and dramatically reduce the public health impact of transportation. The City embarks on this transition from a position of strength. Boston is consistently ranked as one of the most walkable and bikeable cities in the nation, and one in three commuters already take public transportation. There are three general strategies to reaching a carbon-neutral transportation system: • Shift trips out of automobiles to transit, biking, and walking;1 • Reduce automobile trips via land use planning that encourages denser development and affordable housing in transit-rich neighborhoods; • Shift most automobiles, trucks, buses, and trains to zero-GHG electricity. Even with Boston’s strong transit foundation, a carbon-neutral transportation system requires a wholesale change in Boston’s transportation culture. Success depends on the intelligent adoption of new technologies, influencing behavior with strong, equitable, and clearly articulated planning and investment, and effective collaboration with state and regional partners.Published versio

The Demand for Beef in Indonesia: Implications for Australian Agribusiness

Meat consumption and socio-demographic data from the 1990, 1993 and 1996 SUSENAS Household Food Expenditure and Consumption Surveys were employed to estimate the demand for meats in Indonesia. The focus was on the Provinces of DKI Jakarta and West Java where about one-fourth of the Indonesian population reside. Statistical and econometric procedures were used to aggregate the 16 meat types recorded in the SUSENAS into four Meat Groups. They were then used to estimate the Linear Approximation of the Almost Ideal Demand System (LA/AIDS) model, taking into account zero observations and the restrictions on budget shares. The demand for Meat Group 1 (with the dominant meat, beef) is income-inelastic, whereas for Meat Group 2 (with the dominant meat, commercial and native chicken) it is income-elastic. These two groups comprise nearly 95 per cent of all meat purchases. The estimated own-price elasticity of the beef group is -0.92, while that for the chicken group is -1.09. The cross-price elasticities indicate that all the meat groups are substitute goods, as expected. The results suggest that the current focus of the Indonesian government on strengthening the domestic poultry industry is well placed, as the demand for chicken is likely to respond more quickly to income growth than the demand for beef. Further, consumers seem more likely to adapt their chicken consumption patterns to price changes than they do for beef. However, these differences are relatively minor and there is still a major opportunity for Australian agribusiness firms in the cattle and beef sectors to take advantage of the projected rapid growth in Indonesian beef demand.beef demand, almost ideal demand system, commodity aggregation, Demand and Price Analysis, Food Consumption/Nutrition/Food Safety, Livestock Production/Industries,

Second-generation PLINK: rising to the challenge of larger and richer datasets

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information. The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.Comment: 2 figures, 1 additional fil

Aerobic Epoxidation of Olefins Catalyzed by Electronegative Vanadyl Salen Complexes

Vanadyl salen complexes bearing electron-withdrawing substituents have been prepared and characterized. Systematic substitutions on the ancillary ligand have allowed V^(5+)/V^(4+) reduction potentials to be tuned over a range of approximately 500 mV. The complexes are catalysts for the aerobic epoxidation of cyclohexene; catalytic activity roughly increases with increasing V^(5+)/V^(4+) reduction potential. The mechanism likely involves oxygen transfer from intermediate hydroperoxides that are formed by radical-chain autoxidation

Magneto-optic Kerr effect in a spin-polarized zero-moment ferrimagnet

The magneto-optical Kerr effect (MOKE) is often assumed to be proportional to the magnetisation of a magnetically ordered metallic sample; in metallic ferrimagnets with chemically distinct sublattices, such as rare-earth transition-metal alloys, it depends on the difference between the sublattice contributions. Here we show that in a highly spin polarized, fully compensated ferrimagnet, where the sublattices are chemically similar, MOKE is observed even when the net moment is strictly zero. We analyse the spectral ellipsometry and MOKE of Mn 2 Ru x Ga, and show that this behaviour is due to a highly spin-polarized conduction band dominated by one of the two manganese sublattices which creates helicity-dependent reflectivity determined by a broad Drude tail. Our findings open new prospects for studying spin dynamics in the infra-red.Comment: 7 pages, 7 figure

RhoJ/TCL Regulates Endothelial Motility and Tube Formation and Modulates Actomyosin Contractility and Focal Adhesion Numbers

Objective—RhoJ/TCL was identified by our group as an endothelial-expressed Rho GTPase. The aim of this study was to determine its tissue distribution, subcellular localization, and function in endothelial migration and tube formation. Methods and Results—Using in situ hybridization, RhoJ was localized to endothelial cells in a set of normal and cancerous tissues and in the vasculature of mouse embryos; endogenous RhoJ was localized to focal adhesions by immunofluorescence. The proangiogenic factor vascular endothelial growth factor activated RhoJ in endothelial cells. Using either small interfering (si)RNA-mediated knockdown of RhoJ expression or overexpression of constitutively active RhoJ (daRhoJ), RhoJ was found to positively regulate endothelial motility and tubule formation. Downregulating RhoJ expression increased focal adhesions and stress fibers in migrating cells, whereas daRhoJ overexpression resulted in the converse. RhoJ downregulation resulted in increased contraction of a collagen gel and increased phospho–myosin light chain, indicative of increased actomyosin contractility. Pharmacological inhibition of Rho-kinase (which phosphorylates myosin light chain) or nonmuscle myosin II reversed the defective tube formation and migration of RhoJ knockdown cells. Conclusion—RhoJ is endothelial-expressed in vivo, activated by vascular endothelial growth factor, localizes to focal adhesions, regulates endothelial cell migration and tube formation, and modulates actomyosin contractility and focal adhesion numbers