Hello ADIOS: the challenges and lessons of developing leadership class I/O frameworks

Applications running on leadership platforms are more and more bottlenecked by storage input/output (I/O). In an effort to combat the increasing disparity between I/O throughput and compute capability, we created Adaptable IO System (ADIOS) in 2005. Focusing on putting users first with a service oriented architecture, we combined cutting edge research into new I/O techniques with a design effort to create near optimal I/O methods. As a result, ADIOS provides the highest level of synchronous I/O performance for a number of mission critical applications at various Department of Energy Leadership Computing Facilities. Meanwhile ADIOS is leading the push for next generation techniques including staging and data processing pipelines. In this paper, we describe the startling observations we have made in the last half decade of I/O research and development, and elaborate the lessons we have learned along this journey. We also detail some of the challenges that remain as we look toward the coming Exascale era. Copyright © 2013 John Wiley & Sons, Ltd.     

Gene Variant of Barrier to Autointegration Factor 2 (Banf2w) Is Concordant with Female Determination in Cichlids

Oreochromis fishes exhibit variability of sex-determination (SD) genes whose characterization contributes to understanding of the sex differentiation network, and to effective tilapia farming, which requires all-male culture. However, O. niloticus (On) amh is the only master-key regulator (MKR) of SD that has been mapped (XY/XX SD-system on LG23). In O. aureus (Oa), LG3 controls a WZ/ZZ SD-system that has recently been delimited to 9.2 Mbp, with an embedded interval rich with female-specific variation, harboring two paics genes and banf2. Developing genetic markers within this interval and using a hybrid Oa stock that demonstrates no recombination repression in LG3, we mapped the critical SD region to 235 Kbp on the orthologous On physical map (p < 1.5 × 10⁻²⁶). DNA-seq assembly and peak-proportion analysis of variation based on Sanger chromatograms allowed the characterization of copy-number variation (CNV) of banf2. Oa males had three exons capable of encoding 90-amino-acid polypeptides, yet in Oa females, we found an extra copy with an 89-amino-acid polypeptide and three non-conservative amino acid substitutions, designated as banf2w. CNV analysis suggested the existence of two to five copies of banf2 in diploidic Cichlidae. Disrupting the Hardy–Weinberg equilibrium (p < 4.2 × 10⁻³), banf2w was concordant with female determination in Oa and in three cichlids with LG3 WZ/ZZ SD-systems (O. tanganicae, O. hornorum and Pelmatolapia mariae). Furthermore, exclusive RNA-seq expression in Oa females strengthened the candidacy of banf2w as the long-sought LG3 SD MKR. As banf genes mediate nuclear assembly, chromatin organization, gene expression and gonad development, banf2w may play a fundamental role inducing female nucleus formation that is essential for WZ/ZZ SD.     

Influence of the structure of the nanotube on the mechanical properties of binder-free multi-walled carbon nanotube solids

We prepared and characterized multi-walled carbon nanotube (MWCNT) solids by de-fluorination of fluorinated MWCNTs using spark plasma sintering. In order to investigate the influence of the structure of MWCNT on the mechanical strength of the resulting solids, MWCNTs used in this experiment were as-defected MWCNTs modified by nitric acid and as-purified ones as non-defected nanotubes by comparison. The bend strength and modulus of the resulting solids were lower than those of de-fluorinated MWCNT solids derived from as-purified MWCNTs. The mechanical properties of the resulting MWCNT solids were found to be strongly dependent on the structure of the MWCNT.     

Pacemaker Activity of the Human Sinoatrial Node: An Update on the Effects of Mutations in HCN4 on the Hyperpolarization-Activated Current

Since 2003, several loss-of-function mutations in the HCN4 gene, which encodes the HCN4 protein, have been associated with sinus node dysfunction. In human sinoatrial node (SAN), HCN4 is the most abundant of the four isoforms of the HCN family. Tetramers of HCN subunits constitute the ion channels that conduct the hyperpolarization-activated “funny” current (I_f), which plays an important modulating role in SAN pacemaker activity. Voltage-clamp experiments on HCN4 channels expressed in COS-7, CHO and HEK-293 cells, as well as in Xenopus oocytes have revealed changes in the expression and kinetics of mutant channels, but the extent to which especially the kinetic changes would affect I_f flowing during a human SAN action potential often remains unresolved. In our contribution to the Topical Collection on Human Single Nucleotide Polymorphisms and Disease Diagnostics, we provide an updated review of the mutation-induced changes in the expression and kinetics of HCN4 channels and provide an overview of their effects on I_f during the time course of a human SAN action potential, as assessed in simulated action potential clamp experiments. Future research may solve apparent inconsistencies between data from clinical studies and data from in vitro and in silico experiments.     

Ussing chamber results for amino acid absorption of protein hydrolysates in porcine jejunum must be corrected for endogenous protein

BACKGROUND: Ussing chambers have been used extensively as an ex vivo model to investigate intestinal nutrient absorption. In this study Ussing chambers were used to investigate the absorption of amino acids and peptides in pig jejunal tissue using a highly hydrolysed casein hydrolysate (PeptoPro®), casein and whey protein isolate after they had been digested with pepsin and pancreatin to simulate digestion products in the jejunum. Jejunal tissue was collected from three pigs and mounted into Ussing chambers, equilibrated, and the luminal chamber loaded with one of three test nitrogen sources. Luminal solution samples were taken every 10 min over a 90 min incubation period and the amino acid concentration determined. To determine the endogenous amino acid contribution of the tissue to the luminal solution, Ussing chambers containing no test N source (blanks) were prepared and treated similarly to the Ussing chambers containing the test N sources. RESULTS: The endogenous amino acid contribution was 0.5 mg in the luminal solution at time 0 and increased to 1 mg after 90 min. The mean amino acid absorption after 10 min incubation for the pre‐digested highly hydrolysed casein hydrolysate (16.6%) was significantly (P < 0.05) higher than for the pre‐digested casein (7.6%) and whey protein isolate (6.7%). CONCLUSION: Endogenous amino acids were a quantitatively significant portion of the luminal solution amino acids present in the Ussing chambers containing the test N sources. Ussing chambers may be a suitable tool for studying amino acid absorption of protein hydrolysates but correction for the endogenous amino acid contribution from the intestinal tissue must be made. Copyright © 2009 Society of Chemical Industry     

Deep learning for location prediction on noisy trajectories

Pattern Analysis and Applications - Precise tracking of a point-target on a nonlinear trajectory is challenging and has applications ranging from traffic analysis to microscopic particle tracking....     

Dicarboxy-Starch by Sodium Hypochlorite/Bromide Oxidation and Its Calcium Binding Properties

Various aspects of the glycolic oxidation of the glucose units of starch with stoichiometric amounts of sodium hypochlorite applying sodium bromide as the catalyst have been investigated. The main objective of the study was to optimize the reaction conditions for the preparation of dicarboxy-starch and to establish the calcium sequestering capacity of the material. The products, polycarboxylates, are obtained in high yields (90-95%) and they have a sequestering capacity up to 1.4 mmole Ca/g, which is somewhat higher than that of the materials obtained in a non-catalyzed oxidation. This result is attributed to the facts that the reaction with sodium bromide may be carried out at higher pH (>9) than the non-catalyzed reaction and that a relatively low concentration of hypochlorite throughout the process could be maintained. In this way the decomposition of hypochlorous acid/hypochlorite, especially occurring at high concentration of hypochlorous acid at lower pH (6-8) is prevented. Other advantages of this procedure are the colourless appearance of the materials and the higher reaction rate. The feasibility for largescale preparation follows from the results of a few exploratory experiments, including an electrochemical preparation.     

Assessing migratory bottlenecks and escapement of silver eel (Anguilla anguilla) in the highly urbanized North Sea Canal basin,the Netherlands

Habitat fragmentation and migration barriers have attributed to the decline of European eel (Anguilla anguilla). The migration of silver eels through pumping stations, ship locks, and migration facilities within the North Sea Canal basin using acoustic telemetry and overall escapement by mark–recapture was studied. A network of 61 acoustic receivers and three PIT-tag stations was built, and 305 silver eels were tagged with acoustic transmitters and 3923 with PIT-tags. Of all the silver eels that were detected, 55% passed barriers between the polders and the canal and 46% also passed the barrier complex at IJmuiden to sea, mainly via the ship locks. Overall, silver eel escapement to the North Sea per year averaged 81,629 silver eels and 14.3% suffered mortality in the pumping station at IJmuiden. Migration speed was lower for silver eels that initiated their migration upstream compared with silver eels further downstream, higher for silver eels passing barriers later in the migration period, and highest at sea. This study of silver eel movement and escapement in the North Sea canal basin indicated several bottlenecks. Passage success along barriers varied strongly between sites and types of barriers. While at two smaller locations, silver eels migrated through the pedal valves in the ship lock gates, a small passage facility and the pedal valves in a ship lock at complex IJmuiden did not enhance silver eel migration. The barriers and unnatural canal system caused additional delay during silver eel migrations. Mitigation measures for management could include installing fish-friendly pumps, using pumping stations only during the day, and in addition opening ship locks and pedal valves at the beginning of the night.