Neuroconductor: an R platform for medical imaging analysis

Neuroconductor (https://neuroconductor.org) is an open-source platform for rapid testing and dissemination of reproducible computational imaging software. The goals of the project are to: (i) provide a centralized repository of R software dedicated to image analysis, (ii) disseminate software updates quickly, (iii) train a large, diverse community of scientists using detailed tutorials and short courses, (iv) increase software quality via automatic and manual quality controls, and (v) promote reproducibility of image data analysis. Based on the programming language R (https://www.r-project.org/), Neuroconductor starts with 51 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing. We provide a description of the purpose of Neuroconductor and the user and developer experience

XUV Frequency Combs via Femtosecond Enhancement Cavities

We review the current state of tabletop extreme ultraviolet (XUV) sources based on high harmonic generation (HHG) in femtosecond enhancement cavities (fsEC). Recent developments have enabled generation of high photon flux (1014 photons/sec) in the XUV, at high repetition rates (>50 MHz) and spanning the spectral region from 40 nm - 120 nm. This level of performance has enabled precision spectroscopy with XUV frequency combs and promises further applications in XUV spectroscopic and photoemission studies. We discuss the theory of operation and experimental details of the fsEC and XUV generation based on HHG, including current technical challenges to increasing the photon flux and maximum photon energy produced by this type of system. Current and future applications for these sources are also discussed.Comment: invited review article, 38 page

Implementing an integrated standards-based management system to ensure compliance at Los Alamos National Laboratory

Los Alamos National Laboratory (LANL or the Laboratory) is developing and implementing a comprehensive, Integrated Standards-Based Management System (ISBMS) to enhance environmental, safety, and health (ESH) compliance efforts and streamline management of ESH throughout the Laboratory. The Laboratory recognizes that to be competitive in today`s business environment and attractive to potential Partnerships, Laboratory operations must be efficient and cost-effective. The Laboratory also realizes potential growth opportunities for developing ESH as a strength in providing new or improved services to its customers. Overall, the Laboratory desires to establish and build upon an ESH management system which ensures continuous improvement in protecting public health and safety and the environment and which fosters a working relationship with stakeholders. A team of process experts from the LANL Environmental Management (EM) Program Office, worked with management system consultants, and the Department of Energy (DOE) to develop an ESH management systems process to compare current LANL ESH management Systems and programs against leading industry standards. The process enabled the Laboratory to gauge its performance in each of the following areas: Planning and Policy Setting; Systems and Procedures; Implementation and Education; and Monitoring and Reporting. The information gathered on ESH management systems enabled LANL to pinpoint and prioritize opportunities for improvement in the provision of ESH services throughout the Laboratory and ultimately overall ESH compliance

Neuroconductor: an R platform for medical imaging analysis

Neuroconductor (https://neuroconductor.org) is an open-source platform for rapid testing and dissemination of reproducible computational imaging software. The goals of the project are to: (i) provide a centralized repository of R software dedicated to image analysis, (ii) disseminate software updates quickly, (iii) train a large, diverse community of scientists using detailed tutorials and short courses, (iv) increase software quality via automatic and manual quality controls, and (v) promote reproducibility of image data analysis. Based on the programming language R (https://www.r-project.org/), Neuroconductor starts with 51 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing. We provide a description of the purpose of Neuroconductor and the user and developer experience

Productive performance and carcass characteristics of lambs fed diets containing different levels of palm kernel cake

ABSTRACT Objective. The objective of this study was to determine the effect on productiveperformance and carcass characteristics in lambs fed with different amounts of palmkernel cake. Material and methods. Thirty-two Santa Inês lambs, with an initial livebody weight of 24.8 ± 3.59 kg were used. Treatments consisted of four levels (0; 6.5;13.0 and 19.5%) of palm kernel cake added to the dry matter diet. Lambs were fed for80 days, and then slaughtered to be evaluated for the quantitative characteristics of thecarcass. Results. Intake of dry matter and non-structural carbohydrates decreased withincreasing levels of palm kernel cake. The intake of neutral detergent fiber showed a linearincrease. Crude protein and total digestive nutrient intake were not affected. Weight gain,and the feed:gain ratio of dry matter, organic matter, crude protein and total digestivenutrients were similar among the four treatments. There was an increase on the feed:gainratio of neutral detergent fiber and a decrease of nonstructural carbohydrates. The weightgain at slaughter and biometric measures were not affected by treatment. The carcasscompactness index showed a linear decrease. The indexes of leg muscularity, compactnessof the leg and rib eye area were similar among treatments. There was a linear decrease inthe cold carcass weight and commercial yield of the carcass. Conclusions. The diet madeof up to 19.5% palm kernel cake reduced DM intake, the carcass compactness index andcarcass commercial yield, but did not alter weight gain, or feed dry matter intake

Structure functions for the three nucleon system

The spectral functions and light-cone momentum distributions of protons and neutrons in 3He and 3H are given in terms of the three-nucleon wave function for realistic nucleon-nucleon interactions. To reduce computational complexity, separable expansions are employed for the nucleon-nucleon potentials. The results for the light-cone momentum distributions suggest that they are not very sensitive to the details of the two-body interaction, as long as it has reasonable short-range repulsion. The unpolarised and polarised structure functions are examined for both 3He and 3H in order to test the usefulness of 3He as a neutron target. It is found that the measurement of the spin structure function of polarised 3H would provide a very clear test of the predicted change in the polarised parton distributions of a bound proton.Comment: 30 pages, REVTeX, 11 figure

Gene Expression Changes Associated with the Airway Wall Response to Injury

Understanding the way in which the airway heals in response to injury is fundamental to dissecting the mechanisms underlying airway disease pathology. As only limited data is available in relation to the in vivo characterisation of the molecular features of repair in the airway we sought to characterise the dynamic changes in gene expression that are associated with the early response to physical injury in the airway wall.We profiled gene expression changes in the airway wall using a large animal model of physical injury comprising bronchial brush biopsy in anaesthetised sheep. The experimental design featured sequential studies in the same animals over the course of a week and yielded data relating to the response at 6 hours, and 1, 3 and 7 days after injury. Notable features of the transcriptional response included the early and sustained preponderance of down-regulated genes associated with angiogenesis and immune cell activation, selection and differentiation. Later features of the response included the up-regulation of cell cycle genes at d1 and d3, and the latter pronounced up-regulation of extracellular matrix-related genes at d3 and d7.It is possible to follow the airway wall response to physical injury in the same animal over the course of time. Transcriptional changes featured coordinate expression of functionally related genes in a reproducible manner both within and between animals. This characterisation will provide a foundation against which to assess the perturbations that accompany airway disease pathologies of comparative relevance