Vegetative and reproductive growth behaviour of Xanthostemon chrysanthus (F. Muell.) benth. – an ornamental tree in Malaysia

A study was conducted to investigate the duration of growth stages and flowering behaviour of a landscape tree, Xanthostemon chrysanthus (F. Muell.) Benth. This species is known as golden penda and locally known as jambu kuning. It is widely planted for urban beautification due to its distinctive coloured flowers. Under local climate condition, this species flowers throughout the year. However, the flowering of this species has not been studied extensively. In the present study, the growth of selected trees aged approximately six years after planting was monitored for a year. The growth duration was determined using the extended Biologishe Bundesanstalt, Bundessortenamt and Chemical Industry (BBCH) scale. Percentages of flower and fruit and new leaf abundances were expressed as estimated percentage of each stage as compared to total surface area of the tree crown. The vegetative and reproductive stages of the species required 198 and 176 days, respectively. The flowering period took about 40 days from inflorescence bud swelling to drying and senescence of stamens and petals. Unsynchronized flowering was observed among the trees. The occurrence of flowers was also influenced by the development of new leaves or fruits. The information on the duration of each growth stage and the flowering behaviour of the species may enhance a more detailed study related to flowering of urban trees in Malaysia

MANAGEMENT PRE-START REVIEW FINAL REPORT FOR THE BIOSAFETY LEVEL 3 (BSL-3) FACILITY (B368) LAWRENCE LIVERMORE NATIONAL LABORATORY

A Lawrence Livermore National Laboratory (LLNL) Management Pre-Start Review (MPR) Team was formed to independently verify the operational readiness of Building 368 (B368) Biosafety Level III (BSL-3) Facility to conduct research with biological pathogens and toxins including those considered Select Agents. Review objectives and criteria were developed from the DOE/NNSA and LLNL requirements. These were provided in the Implementation Plan for the Biosafety Level III (BSL-3) Facility Management Pre-Start Review (BSL-3 MPR) at Lawrence Livermore National Laboratory that was reviewed and approved by DOE/NNSA-LSO. The formal part of the LLNL MPR for the BSL-3 Facility was begun in August of 2005 but work on the MPR was stopped in October of 2005 due to the need for LLNL to reassess organizational and operational controls and respond to Centers for Disease Control and Prevention inquiries related to a shipping incident involving select agents. The MPR was restarted in mid-June of 2006. Preliminary facility tours and familiarization with project documents took place in June of 2005. The Independent Management Review Team consists of seven members led by a Team Leader with expertise in management, operations, and safety basis experience with biosafety laboratories. Other team members have expertise in electrical engineering, security, environmental/waste management/regulatory compliance, biosafety/industrial hygiene/medical, structural engineering, and mechanical engineering. The MPR Team reviewed various documents, including authorization basis, safety, emergency preparedness, and various operations, configuration, and management plans. They also reviewed building plans, equipment repair/maintenance documents, training records, and many standard operating procedures. The MPR resulted in three Pre-Start Findings, one Post-Start/Critical Finding, and four observations which are shown on Tables 1, 2, and 3, respectively. Based upon this review the Team feels that the B368 Facility can be operated safely provided the Pre-Start Findings are satisfactorily closed. The Team therefore seen no reason not to expeditiously proceed towards the startup of this facility in accordance with the processes defined in DOE Order 425.1C, and the LLNL ES&H Manual. Details of the MPR Team evaluations of the various Subject (functional) Areas of the review are contained in the completed MPR Assessment Forms in Appendix A. Findings are described in completed MPR Deficiency Forms in Appendix B. The format of these forms is consistent with DOE-STD-3006

Expression of Regulatory Platelet MicroRNAs in Patients with Sickle Cell Disease

Background: Increased platelet activation in sickle cell disease (SCD) contributes to a state of hypercoagulability and confers a risk of thromboembolic complications. The role for post-transcriptional regulation of the platelet transcriptome by microRNAs (miRNAs) in SCD has not been previously explored. This is the first study to determine whether platelets from SCD exhibit an altered miRNA expression profile. Methods and Findings: We analyzed the expression of miRNAs isolated from platelets from a primary cohort (SCD = 19, controls = 10) and a validation cohort (SCD = 7, controls = 7) by hybridizing to the Agilent miRNA microarrays. A dramatic difference in miRNA expression profiles between patients and controls was noted in both cohorts separately. A total of 40 differentially expressed platelet miRNAs were identified as common in both cohorts (p-value 0.05, fold change>2) with 24 miRNAs downregulated. Interestingly, 14 of the 24 downregulated miRNAs were members of three families - miR-329, miR-376 and miR-154 - which localized to the epigenetically regulated, maternally imprinted chromosome 14q32 region. We validated the downregulated miRNAs, miR-376a and miR-409-3p, and an upregulated miR-1225-3p using qRT-PCR. Over-expression of the miR-1225-3p in the Meg01 cells was followed by mRNA expression profiling to identify mRNA targets. This resulted in significant transcriptional repression of 1605 transcripts. A combinatorial approach using Meg01 mRNA expression profiles following miR-1225-3p overexpression, a computational prediction analysis of miRNA target sequences and a previously published set of differentially expressed platelet transcripts from SCD patients, identified three novel platelet mRNA targets: PBXIP1, PLAGL2 and PHF20L1. Conclusions: We have identified significant differences in functionally active platelet miRNAs in patients with SCD as compared to controls. These data provide an important inventory of differentially expressed miRNAs in SCD patients and an experimental framework for future studies of miRNAs as regulators of biological pathways in platelets. © 2013 Jain et al

The Simons Observatory: Cryogenic Half Wave Plate Rotation Mechanism for the Small Aperture Telescopes

We present the requirements, design and evaluation of the cryogenic continuously rotating half-wave plate (CHWP) for the Simons Observatory (SO). SO is a cosmic microwave background (CMB) polarization experiment at Parque Astron\'{o}mico Atacama in northern Chile that covers a wide range of angular scales using both small (0.42 m) and large (6 m) aperture telescopes. In particular, the small aperture telescopes (SATs) focus on large angular scales for primordial B-mode polarization. To this end, the SATs employ a CHWP to modulate the polarization of the incident light at 8~Hz, suppressing atmospheric $1/f$ noise and mitigating systematic uncertainties that would otherwise arise due to the differential response of detectors sensitive to orthogonal polarizations. The CHWP consists of a 505 mm diameter achromatic sapphire HWP and a cryogenic rotation mechanism, both of which are cooled down to $\sim$50 K to reduce detector thermal loading. Under normal operation the HWP is suspended by a superconducting magnetic bearing and rotates with a constant 2 Hz frequency, controlled by an electromagnetic synchronous motor. The rotation angle is detected through an angular encoder with a noise level of 0.07$\mu\mathrm{rad}\sqrt{\mathrm{s}}$. During a cooldown, the rotor is held in place by a grip-and-release mechanism that serves as both an alignment device and a thermal path. In this paper we provide an overview of the SO SAT CHWP: its requirements, hardware design, and laboratory performance.Comment: 19 pages, 21 figures, submitted to RS

Exploring the Design Space of Static and Incremental Graph Connectivity Algorithms on GPUs

Connected components and spanning forest are fundamental graph algorithms due to their use in many important applications, such as graph clustering and image segmentation. GPUs are an ideal platform for graph algorithms due to their high peak performance and memory bandwidth. While there exist several GPU connectivity algorithms in the literature, many design choices have not yet been explored. In this paper, we explore various design choices in GPU connectivity algorithms, including sampling, linking, and tree compression, for both the static as well as the incremental setting. Our various design choices lead to over 300 new GPU implementations of connectivity, many of which outperform state-of-the-art. We present an experimental evaluation, and show that we achieve an average speedup of 2.47x speedup over existing static algorithms. In the incremental setting, we achieve a throughput of up to 48.23 billion edges per second. Compared to state-of-the-art CPU implementations on a 72-core machine, we achieve a speedup of 8.26--14.51x for static connectivity and 1.85--13.36x for incremental connectivity using a Tesla V100 GPU

The Simons Observatory: Beam characterization for the Small Aperture Telescopes

We use time-domain simulations of Jupiter observations to test and develop a beam reconstruction pipeline for the Simons Observatory Small Aperture Telescopes. The method relies on a map maker that estimates and subtracts correlated atmospheric noise and a beam fitting code designed to compensate for the bias caused by the map maker. We test our reconstruction performance for four different frequency bands against various algorithmic parameters, atmospheric conditions and input beams. We additionally show the reconstruction quality as function of the number of available observations and investigate how different calibration strategies affect the beam uncertainty. For all of the cases considered, we find good agreement between the fitted results and the input beam model within a ~1.5% error for a multipole range l = 30 - 700.Comment: 22 pages, 21 figures, to be submitted to Ap

Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces

The key to obtaining the model-free description of the dynamics of a macromolecule is the optimisation of the model-free and Brownian rotational diffusion parameters using the collected R1, R2 and steady-state NOE relaxation data. The problem of optimising the chi-squared value is often assumed to be trivial, however, the long chain of dependencies required for its calculation complicates the model-free chi-squared space. Convolutions are induced by the Lorentzian form of the spectral density functions, the linear recombinations of certain spectral density values to obtain the relaxation rates, the calculation of the NOE using the ratio of two of these rates, and finally the quadratic form of the chi-squared equation itself. Two major topological features of the model-free space complicate optimisation. The first is a long, shallow valley which commences at infinite correlation times and gradually approaches the minimum. The most severe convolution occurs for motions on two timescales in which the minimum is often located at the end of a long, deep, curved tunnel or multidimensional valley through the space. A large number of optimisation algorithms will be investigated and their performance compared to determine which techniques are suitable for use in model-free analysis. Local optimisation algorithms will be shown to be sufficient for minimisation not only within the model-free space but also for the minimisation of the Brownian rotational diffusion tensor. In addition the performance of the programs Modelfree and Dasha are investigated. A number of model-free optimisation failures were identified: the inability to slide along the limits, the singular matrix failure of the Levenberg–Marquardt minimisation algorithm, the low precision of both programs, and a bug in Modelfree. Significantly, the singular matrix failure of the Levenberg–Marquardt algorithm occurs when internal correlation times are undefined and is greatly amplified in model-free analysis by both the grid search and constraint algorithms. The program relax (http://www.nmr-relax.com) is also presented as a new software package designed for the analysis of macromolecular dynamics through the use of NMR relaxation data and which alleviates all of the problems inherent within model-free analysis