XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services

Background  

Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use.     

Rotationally oscillating drill (Ros-Drill) for mouse ICSI without using mercury

Intracytoplasmic sperm injection (ICSI) is an important assisted reproductive technology (ART). Due to deployment difficulties and low efficiency of the earlier (conventional) version of ICSI, especially in the mouse, a piezo-assisted ICSI technique had evolved as a popular ART methodology in recent years. An important and remaining problem with this technique, however, is that it requires small amounts of mercury to stabilize the pipette tip when piezoelectric force pulses are applied. To eliminate this problem we developed and tested a completely different and mercury-free technology, called the "Ros-Drill" (rotationally oscillating drill). The technique uses microprocessor-controlled rotational oscillations on a spiked micropipette without mercury or piezo. Preliminary experimental results show that this new microinjection technology gives high survival rate (>70% of the injected oocytes) and fertilization rate (>80% of the survived oocytes), and blastocyst formation rates in early trials (approximately 50% of the survived oocytes). Blastocysts created by Ros-Drill ICSI were transferred into the uteruses of pseudopregnant surrogate mothers and healthy pups were born and weaned. The Ros-Drill ICSI technique is automated and therefore; it requires a very short preliminary training for the specialists, as evidenced in many successful biological trials. These advantages of Ros-Drill ICSI over conventional and piezo-assisted ICSI are clearly demonstrated and it appears to have resolved an important problem in reproductive biology.     

Effect of Collagen Gel Configuration on the Cytoskeleton in Cultured Rat Hepatocytes

The cytoskeleton is important in the maintenance of cellular morphology and differentiated function in a number of cell types, including hepatocytes. In this study, adult rat hepatocytes sandwiched between two layers of collagen gel were compared to cells cultured on a single collagen gel for differences in the organization and expression of the cytoskeletal proteins actin and tubulin. Hepatocytes cultured between two layers of hydrated rat tail tendon collagen (sandwich gel) morphologically resembled cells in intact liver for several weeks. Actin filaments (F-actin) in these hepatocytes were concentrated under the plasma membrane in regions of cell-cell contact. In contrast, hepatocytes cultured on a single collagen gel were flattened and motile and had F-actin containing stress fibers. This was accompanied by a severalfold increase in actin mRNA. Microtubules formed an interwoven network in hepatocytes cultured in a sandwich gel, but in single gel cultures they formed long parallel arrays extending out to the cell periphery. Tubulin mRNA was severalfold greater in hepatocytes cultured on a single gel. Fibronectin and laminin staining were greater in single gel cultures, and these proteins were concentrated in fibrils radiating from the cell periphery. Overlaying a second collagen gel onto hepatocytes that had been cultured on a single gel (double gel rescue) reversed cell spreading and reduced stress fibers. Double gel rescue also resulted in a decrease in actin and tubulin mRNA to levels present in sandwich gel cultures and freshly isolated hepatocytes. These results show that the configuration of the external matrix has a dynamic effect on cytoskeletal proteins in cultured rat hepatocytes.     

Determination of maximal aerobic power during upper-body exercise

The purpose of this investigation was to evaluate four protocols for their effectiveness in eliciting maximal aerobic power (peak VO2) during arm-crank exercise. Comparisons were made 1) between a continuous (CON) and an intermittent (INT) protocol (both employed a crank rate of 50 rpm) and 2) among the CON protocols employing crank rates of 30, 50, or 70 rpm. For the first group of experiments no significant (P greater than 0.05) differences were found between the CON and INT protocols for peak VO2, maximal pulmonary ventilation (VEmax), maximal heart rate (HRmax), or maximal blood lactate (LAmax) responses. For the second group of experiments, the CON-50 was compared with the CON-30 and CON-70 protocols. In comparison to the CON-50, significantly higher peak VO2 (+10%) and VEmax (+14%) responses were elicited by the CON-70 protocol, whereas significantly lower peak VO2 (-11%), VEmax (-23%), HRmax (-8%), and LAmax (-29%) responses were elicited by the CON-30 protocol. Of the arm-crank protocols examined the combination of a continuous design and a crank rate of 70 rpm provided the most effective protocol to elicit peak VO2 values.     

Summer distribution of Red-legged Partridges Alectoris rufa in relation to water availability on Mediterranean farmland

The suggestion that the summer distribution of Red-legged Partridges Alectoris rufa in the Mediterranean region is determined by the availability of surface water was examined on the agricultural farm, Alto Alentejo, southern Portugal. Partridge coveys were surveyed between 15 July and 15 August in 1993 and 1994. Using a vector-based Geographic Information System, we assessed, for each covey location and for the locations of a double number of random points, the distance to the nearest water point, distance to field boundaries, distance to water lines and land use classes. Univariate comparisons were made between the two groups of locations, and three multivariate logistic models were fitted through forward stepwise selection to the 1993, 1994 and pooled data sets to estimate the probability of sighting partridge coveys in the study area. Distance to water was significantly lower for partridge locations than for random points in both years and was the only variable selected for all logistic models. Apart from water availability, Red-legged Partridge locations were also affected by land use and distance to field boundaries.     

Oxygen uptake rates in cultured rat hepatocytes

One potential treatment of acute liver failure involves the use of an extracorporeal device composed of functional hepatocytes. A major issue in the design of such a large-scale device is providing the hepatocytes with a sufficient supply of oxygen and other nutrients. In this study, we have designed and characterized a simple perfusion system hepatocytes using this system. The OUR of hepatocytes was determined during the first day after seeding on a single collagen gel and during the long-term stable culture after the addition of a top layer of collagen. The OUR increased to 20.7 +/- 0.57 pmol/sec/mug DNA during the first 13 hours of culture on a single collagen gel, while during the next 11 hours, the OUR declined to 10.6 +/- 1.5 pmol/sec/mug DNA. In parallel with the increase in OUR during the first 10 hours, we observed significant cell spreading, suggesting that the oxygen supply to the cells may be critical for the spreading and adaptation of the anchorage-dependent hepatocytes following isolation. Addition of a top layer of collagen to hepatocyte cultures for 24 hours of culture on a single collagen layer resulted in a stable OUR for 15 days. These results indicate that OUR of hepatocytes in culture may vary depending on the phase of culture (i.e., early vs. late) and on the extracellular environment. (c) 1992 John Wiley & Sons, Inc.     

The role of uterine luminal fluid in uterine contractions, sperm transport and fertility of rats

The role of accumulated intrauterine fluid in rats at oestrus was investigated by experimentally altering the fluid volume in 106 rats. Complete evacuation of uterine fluid or low natural fluid volume did not significantly reduce the number of embryos on Day 10 of pregnancy overall. Transuterine (but not transcervical) sperm transport was reduced by uterine fluid removal, but did not vary significantly with naturally occurring variations in fluid content. Irrespective of fluid content, transuterine sperm transport was, on average, greater in right than left horns. Distensible balloons inserted into the uterus indicated that increasing and decreasing volume increased and decreased respectively myometrial activity at oestrus and dioestrus. Left horns contracted less frequently than did right horns at low volumes. While uterine fluid volume clearly affected uterine contractility and transuterine sperm transport, we were unable to demonstrate a major role of fluid for fertility.