Analysis of NVMe over fabrics with SCinet DTN-as-a-Service

Supporting transfers of science big data over Wide Area Networks (WANs) with Data Transfer Nodes (DTNs) requires optimizing multiple parameters within the underlying infrastructure. New solutions for such data movement require new paradigms and technologies, such as NVMe over Fabrics, which provides high-performance data movement with direct remote NVMe device access over traditional fabrics. However, recent NVMe over Fabrics studies have been limited to local storage fabrics. To support increasing demands for the large volume of science data movement during Supercomputing (SC) conferences, we proposed a SCinet DTN-as-a-Service framework orchestrating the desired optimization to meet users, applications, and providers’ requirements. Furthermore, we extend the SCinet DTN-as-a-Service framework to incorporate new techniques, solve optimization issues in data-intensive science and evaluate NVMe over Fabrics with multiple WAN testbeds to examine its performance and discover new opportunities for optimization.

     

Embryoid bodies from mouse stem cells express oxytocin receptor, Oct-4 and DAZL

Oxytocin is a nine amino acid peptide involved in a wide spectrum of physiological functions; predominantly those concerning reproduction and differentiation are of interest. Oxytocin receptors are expressed at early developmental stages of mammals, suggesting that oxytocin might be involved in the determination of the germ stem cell line, at the very early stages of mammalian development. In this respect, the proximate aim of the present study was to confirm and further analyze the existence of oxytocin receptors at a very early level of cell commitment, that is, the determination of germ cells derived from embryoid bodies. To achieve our purpose we have cultured mouse embryonic stem cells under conditions inducing formation of embryoid bodies. In this work, ES cells were allowed to aggregate in a novel medium, “Stefanidis medium” from day 0 to day 14 until formed EBs. RNA was isolated from EBs and using RT-PCR we showed that EBs expressed Oct-4, OTR, OT, and DAZL. To demonstrate simultaneous expression immunocytochemistry was preformed, in which EBs showed strong immunoreactivity for both, OTR and DAZL molecular markers. We found that 35% of the cells displayed OTR, using flow cytometry. In addition, this novel medium showed to increase OTR mRNA. We propose, that at least in murine induced embryoid bodies there is simultaneous expression of oxytocin receptors and germ cell markers (DAZL) in many cells (expressing Oct-4). We thus conclude that, the oxytocin might indeed be a molecule playing a leading role in germ cell determination.     

Effects of Fluctuating Temperatures and Different Host Plants on Development of Pasteuria penetrans in Meloidogyne javanica

Greenhouse and growth room experiments were conducted to investigate the effect of host plant in relation to different nematode inoculum levels, and temperature fluctuations on the development of Pasteuria penetrans. Host plant affected the development of P. penetrans indirectly through its effect on nematode development. Endospores collected from Meloidogyne javanica females reared on different hosts did not show any differences in subsequent attachment and infectivity. The numbers of endospores produced per infected female were reduced with increasing numbers of females parasitizing okra and tomato roots. Fluctuating temperatures retarded the development of P. penetrans. The life cycle of the parasite was completed faster at approximately constant temperatures close to 30 °C than when the temperature fluctuated away from 30 °C. The temperature of irrigation water did not affect the duration of life cycle of P. penetrans.     

Reproducibility of gastrocnemius medialis muscle architecture during treadmill running

The purpose of this study was to assess the reproducibility of fascicle length (FL) and pennation angle (PA) of gastrocnemius medialis (GM) muscle during running in vivo. Twelve male recreational long distance runners (mean ± SD; age: 24 ± 3 years, mass: 76 ± 7 kg) ran on a treadmill at a speed of 3.0 m/s, wearing their own running shoes, for two different 10 min sessions that were at least 2 days apart. For each test day 10 acceptable trials were recorded. Ankle and knee joint angle data were recorded by a Vicon 624 system with three cameras operating at 120 Hz. B-mode ultrasonography was used to examine fascicle length and pennation angle of gastrocnemius medialis muscle. The ultrasound probe was firmly secured on the muscle belly using a lightweight foam fixation. The results indicated that fascicle length and pennation angle demonstrated high reproducibility values during treadmill running both for within and between test days. The root mean square scores between the repeated waveforms of pennation angle and fascicle length were small (∼2° and ∼3.5 mm, respectively). However, ∼14 trials for pennation angle and ∼9 trials for fascicle length may be required in order to record accurate data from muscle architecture parameters. In conclusion, ultrasound measurements may be highly reproducible during dynamic movements such as treadmill running, provided that a proper fixation is used in order to assure the constant location and orientation of the ultrasound probe throughout the movement.     

External air pollution costs of telework

Background, Aims and Scope  Telework is associated with a number of costs and benefits, including reduced company overhead costs, need for office and parking space, office energy consumption, increased productivity, reduced absenteeism, retention of specialized employees, reduction in transportation-related fuel consumption and air pollution, and many others. This paper applies a systems model to telework and nontelework scenarios to quantify direct energy and fuel costs and external costs related to air emissions from transportation, heating, cooling, lighting, and electronic and electrical equipment use both at the company and the home office, including rebound effects. Methods  E-COMMUTair, a scalable web-based tool created by the authors and designed to assess the air pollution effects of individual or company telework programs versus nontelework is employed along with Monte Carlo simulation and sensitivity analysis. E-COMMUTair is using the latest available U.S. energy use and air emission factors. The external costs of air emissions are estimated. The role of telecommuting frequency is emphasized, and differences between various states are explored. The paper identifies the drivers of external costs, and presents an example breakeven analysis focused on CO₂ and key model parameters. Results and Discussion  Nontelework’s external costs are equal to or higher than telework’s costs for every model component, demonstrating that telework programs could provide benefits, including monetary benefits, to society. Transportation is the major contributor to the total costs, with home heating and cooling, and office cooling following. Most of the monetary costs associated with transportation are borne by individuals rather than society. Teleworking employees increase their home-related expenses but reduce their travel-related expenses, ending up with smaller total costs. Energy and fuel costs get reduced in the office space when telework programs are applied, resulting in benefits to companies. Energy and external costs decrease as telework frequency increases. When compared to not teleworking, 5-day telework scenarios on cooling days in California can have about 50–70% lower total costs. The probabilistic analysis confirms the results of the deterministic analysis. The sensitivity analysis reveals that for the nontelework scenario, transportation-related variables such as commuting distance and average number of passengers affect CO₂, CO, and NO_x emissions, while for the telework part, frequency and the number of roundtrips are the most relevant. Conclusions  Both analyses show that telework programs have the potential to lower both energy and external costs creating a favorable bottom line for society, employees, and companies by decreasing tailpipe emissions, lowering transportation costs, and decreasing energy costs at the company office. However, important parameters such as telecommuting frequency, characteristics of the office and home space, climate patterns, and rebound effects that determine external costs along with the price of gasoline, electricity and natural gas in the state where the program is implemented can greatly influence the final results, and should be carefully examined. Recommendations and Perspectives  The effects of telework programs on people’s daily lives are complex and difficult to predict and quantify. The current analysis showed that significant financial benefits can be expected from telework programs, but as seen often in environmental policy-making, the details of implementation will make or break the success of a program. formerly Postdoctoral Researcher, University of California, Berkeley ESS-Submission Editor: Dr. Gerald Rebitzer (Gerald.Rebitzer@alcan.com)     

GRASP55, a second mammalian GRASP protein involved in the stacking of Golgi cisternae in a cell-free system.

We have identified a 55 kDa protein, named GRASP55 (Golgi reassembly stacking protein of 55 kDa), as a component of the Golgi stacking machinery. GRASP55 is homologous to GRASP65, an N-ethylmaleimide-sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. GRASP65 exists in a complex with the vesicle docking protein receptor GM130 to which it binds directly, and the membrane tethering protein p115, which also functions in the stacking of Golgi cisternae. GRASP55 binding to GM130, could not be detected using biochemical methods, although a weak interaction was detected with the yeast two-hybrid system. Cryo-electron microscopy revealed that GRASP65, like GM130, is present on the cis-Golgi, while GRASP55 is on the medial-Golgi. Recombinant GRASP55 and antibodies to the protein block the stacking of Golgi cisternae, which is similar to the observations made for GRASP65. These results demonstrate that GRASP55 and GRASP65 function in the stacking of Golgi cisternae.     

Transient receptor potential-like channels are essential for calcium signaling and fluid transport in a Drosophila epithelium

Calcium signaling is an important mediator of neuropeptide-stimulated fluid transport by Drosophila Malpighian (renal) tubules. We demonstrate the first epithelial role, in vivo, for members of the TRP family of calcium channels. RT-PCR revealed expression of trp, trpl, and trpγ in tubules. Use of antipeptide polyclonal antibodies for TRP, TRPL, and TRPγ showed expression of all three channels in type 1 (principal) cells in the tubule main segment. Neuropeptide (CAP_2b)-stimulated fluid transport rates were significantly reduced in tubules from the trpl³⁰² mutant and the trpl;trp double mutant, trpl³⁰²;trp³⁴³. However, a trp null, trp³⁴³, had no impact on stimulated fluid transport. Measurement of cytosolic calcium concentrations ([Ca²⁺]_i) in tubule principal cells using an aequorin transgene in trp and trpl mutants showed a reduction in calcium responses in trpl³⁰². Western blotting of tubule preparations from trp and trpl mutants revealed a correlation between TRPL levels and CAP_2b-stimulated fluid transport and calcium signaling. Rescue of trpl³⁰² with a trpl transgene under heat-shock control resulted in a stimulated fluid transport phenotype that was indistinguishable from wild-type tubules. Furthermore, restoration of normal stimulated rates of fluid transport by rescue of trpl³⁰² was not compromised by introduction of the trp null, trp³⁴³. Thus, in an epithelial context, TRPL is sufficient for wild-type responses. Finally, a scaffolding component of the TRPL/TRP-signaling complex, INAD, is not expressed in tubules, suggesting that inaD is not essential for TRPL/TRP function in Drosophila tubules.