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.

     

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.     

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.     

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.     

Anaerobic bacteria in clinical infections

The findings of 275 cultures from routine clinical specimens obtained from lesions in different sites of body, during a period of 11 months, are presented. The clinical specimens were obtained from surgical wounds, abdominal infections, orthopaedic operations, biliary tract infections and pleuropulmonary infections. The total number of positive cultures including both aerobes and anaerobes was 203 out of 275 (73.8%). Of the 38 cultures positive for anaerobes, 29 (76.3%) grew both aerobic and anaerobic bacteria, while in nine (23.7%) cultures only anaerobes were found. A total of 42 strains of anaerobic bacteria were isolated. The majority of them were found in clinical specimens obtained from abdominal infections (62%), while a low percentage (3.6%) was found in specimens from orthopaedic operations. Strains belonging to the genus Bacteroides were the most frequently isolated anaerobes, accounting for 35.7% of the total, followed by Clostridia 28.5%, Peptostreptococci 23.8% and Prevotella 12%.