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Previously, we have introduced an improved version of jViz.RNA which enabled faster and more stable RNA visualization by employing compressed tree graphs. However, the new RNA representation and visualization method required a sophisticated mechanism of pseudoknot visualization. In this work, we present our novel pseudoknot classification and implementation of pseudoknot visualization in the context of the new RNA graph model. We then compare our approach with other RNA visualization software, and demonstrate jViz.RNA 4.0's benefits compared to other software. Additionally, we introduce interactive editing functionality into jViz.RNA and demonstrate its benefits in exploring and building RNA structures. The results presented highlight the new high degree of utility jViz.RNA 4.0 now offers. Users are now able to visualize pseudoknotted RNA, manipulate the resulting automatic layouts to suit their individual needs, and change both positioning and connectivity of the RNA molecules examined. Care was taken to limit overlap between structural elements, particularly in the case of pseudoknots to ensure an intuitive and informative layout of the final RNA structure. Availability: The software is freely available at: https://jviz.cs.sfu.ca/.

Certain Lathyrus species have recently been found suitable as multipurpose legume crops in the southern Australian dryland regions, with a potential growing area of 100,000–300,000 ha. However, their use is limited by the presence, mainly in seeds, of 3-(- N -oxalyl)- l -2,3-diamino propionic acid (ODAP), an agent which causes lathyrism. Researchers at the Centre for Legumes in Mediterranean Agriculture (CLIMA) have selected a high yielding variety of Lathyrus cicera (cv. Chalus) which contains consistently low levels of ODAP. The aim of the present study was to assess the nutritional value and animal health aspects of L. cicera cv. Chalus grain as a feed for sheep. Comparisons were made against lupin grain ( Lupinus angustifolius ). Eighty individually penned Merino wethers (35±0.3 kg) were allocated to four treatment groups of 20 sheep. Following a 4-week adjustment period, sheep were fed ad libitum the following treatment diets for up to 13 weeks: 35% lathyrus, 35% lupin, 70% lathyrus and 70% lupin. The remainder of the diet was oaten hay and minerals. After 10 weeks on treatments, 14 sheep per group were killed for carcass assessment. The remaining six sheep were fed to maintenance ME requirements for 1 week followed by a 10-day faecal and urinary collection period. Analysis of the grains showed that lathyrus contained less protein (28% versus 36%), fat (0.7 versus 4.1%) and fibre (25% versus 36% NDF), but more starch (42% versus 1%) and anti-nutritional compounds (ODAP, tannins, trypsin inhibitor) than lupin. Essential amino acid composition was similar for the two grains, as were in sacco degradabilities of dry matter (DM) (84% versus 81%) and protein (92% versus 94%). The feeding experiment showed that lathyrus had a higher nutritional value than lupin in terms of voluntary feed intake, liveweight gain ( P P P =0.05). Wool growth reflected ME intake, and there was no independent effect of grain type ( P >0.05). Results from the balance study showed that ME concentration was the same for both grains (14 MJ/kg DM). Microbial crude protein (CP) synthesis, estimated from urinary purine derivatives, was significantly lower for lathyrus than lupin, and was lower at 70% grain inclusion than at 35% ( P There were no visible or biochemical signs of ill health (in-appetence, lethargy, shaking or instability) in any sheep fed lathyrus. Several sheep fed the 70% lupin diet had mild diarrhoea, and two were eventually removed from the experiment due to anorexia. Meat from sheep fed lupin tended to be yellower than that from those fed lathyrus ( P =0.05). Apart from this, there were no differences in meat quality due to grain type (e.g. redness, pH, taste or tenderness). In conclusion, compared with lupin grain, low ODAP L. cicera grain appears to be of high nutritional value for sheep, with no evidence of adverse effects on sheep health.

Aluminium nitride films are deposited by reactive rf sputtering, and a wide variation of deposition parameters is examined. Optical and structural properties dependent on these parameters are studied, and e.g. the optical band gap, the degree of crystallinity, and the effects of hydrogen incorporation are determined. Electronic properties of the films are measured by applying X-ray photoelectron spectroscopy and electron energy loss spectroscopy. From these data an AlN energy level scheme was derived. Depth profiles of AlN on Si are measured mainly by secondary ion mass spectroscopy and photoelectron spectroscopy. They lead to the conclusion that the interfaces are relatively sharp (5 to 10 nm) if the film is deposited at moderate temperatures (

Splice junctions are important regions in genes, which have been studied in many studies in Genetics. Recently some attempts in computer science have been made to use computer power in distinguishing the different splice junctions and non-junctions regions in genes. Ambiguity in the measurements of nucleotides is an important issue in dealing with these regions. In this paper a novel method is proposed along with an encoding schema which take ambiguities into account using probabilistic intuitions. The method is based on Decision Trees, using K-Nearest Negihbours and Support Vector Machines. The results have shown the significance of using the proposed encoding schema and classification method.

Ribonucleic acid, a single stranded linear molecule, is essential to all biological systems. Different regions of the same RNA strand will fold together via base pair interactions to make intricate secondary and tertiary structures that guide crucial homeostatic processes in living organisms. Since the structure of RNA molecules is key to their function, algorithms for the prediction of RNA structure are of great value. This paper discusses significant improvements made to SARNA-Predict, an RNA secondary structure prediction algorithm based on Simulated Annealing (SA). One major improvement is the incorporation of a sophisticated thermodynamic model (efn2). This model is used by mfold to rank sub-optimal structures, but cannot be used directly by mfold during the structure prediction. Experiments on eight individual known structures from four RNA classes (5S rRNA, Group I intron 23S rRNA, Group I intron 16S rRNA and 16S rRNA) were performed. The data demonstrate the robustness and the effectiveness of our improved prediction algorithm. The new algorithm shows results which surpass the dynamic programming algorithm mfold in terms of prediction accuracy on all tested structures.

This paper presents a comparison of two types of algorithms for RNA secondary structure prediction: an implementation of Nussinov's dynamic programming algorithm (DPA), and P-RnaPredict, a parallel evolutionary algorithm (EA). The research presented here builds on previous work and examines the results from tests of three RNA sequences that are 118, 543, and 784 nucleotides in length. A variety of EA parameter settings were employed based on previous experimentation. Predicted structures were compared to those generated by the Nussinov DPA and to known structures to determine relative accuracy. Results indicate that the EA demonstrated high prediction accuracy and outperformed the Nussinov DPA on all tested sequences

This paper presents a new coarse-grained distributed genetic algorithm (GA) for the prediction of the secondary structure of RNA molecules, based largely on a serial permutation-based GA. The benefits of the distributed GA over our existing serial GA are analyzed and demonstrated. We also analyze the impact of the keep-best reproduction (KBR) and roulette wheel selection (STDS) GA replacement techniques. Finally, we verify the increase in convergence speed of our distributed GA. Tests was performed on 241 and 785 nucleotide sequences. Overall, the distributed GA is found to improve upon the serial GA performances, with a much more pronounced impact on the STDS selection strategy. There is also a notable acceleration in convergence speed.

RNA is an important molecule as it serves a key role in the translation from the genetic information encoded in DNA in protein synthesis. Computational techniques for RNA folding suffer from combinatorial explosion. In this paper, a genetic algorithm (GA) will be used to attempt to solve the secondary structure prediction of RNA molecules.

The basic function of a biomolecule is determined by its 3 dimensional shape, otherwise known as the tertiary structure. However, existing empirical methods to determine this shape are too costly and lengthy to be practical. RNA is of interest as a biomolecule because it is central in several stages of protein synthesis. Also, its secondary structure dominates its tertiary structure. In our model, RNA secondary structure develops as a consequence of bonds which form between specific pairs of nucleotides known as the canonical base pairs. Searching a sequence of nucleotides for all possible base pairs is rapid and straightforward; the challenge comes from attempting to predict which specific canonical base pairs will form bonds in the real structure. Various algorithms have been used for RNA structure prediction such as dynamic programming, and comparative methods [1] and stochastic methods such as genetic algorithms (GA).

This paper presents a genetic algorithm (GA) to predict the secondary structure of RNA molecules, where the secondary structure is encoded as a permutation. More specifically the proposed algorithm predicts which specific canonical base pairs will form hydrogen bonds and build helices, also known as stem loops. Since RNA is involved in both transcription and translation and also has catalytic and structural roles in the cell, knowing its structure is of fundamental importance since it will determine the function of the RNA molecule. We discuss results on RNA sequences of lengths 76, 681, and 785 nucleotides and present several improvements to our algorithm. We show that the Keep-Best Reproduction operator has similar benefits as in the TSP domain. In addition, a comparison of several crossover operators is provided, demonstrating that CX, an operator that is marginal in the TSP domain, performs very well in the RNA folding domain.

We measured methylmalonic acid (MMA) in plasma and succinate in the rumen during the depletion of sheep to a state of severe cobalt deficiency and repletion by various forms of supplementation. Groups of 10, cobalt-deficient weaners were allocated to one of 4 treatments: no supplement, 0.1 or 4.0 mg/day of cobalt as a solution of CoSO4.7H2O per os, or intramuscular vitamin B12. Plasma concentrations of MMA were elevated above the normal range (5 µmol/L) after 35 days on the cobalt-deficient diet, before a reduction in feed intake and while liveweights were still increasing. In all 3 supplemented groups of sheep, plasma vitamin B12 concentrations increased to normal levels within 10 days of supplementation (P

This study investigated the effect of 5 levels of rumen-protected methionine (0, 1, 2, 3, or 5 g/head.day) on growth rate, feed conversion efficiency, carcass composition, and wool growth in lambs fed a production diet ad libitum. Merino and Poll Dorset × Merino (crossbred) wether lambs (120 of each genotype) were housed in group pens each of 6 sheep. After a 1-week adjustment period, all lambs were fed a pelleted diet of lupins, cereal grain, and hay ad libitum. Rumen-protected methionine was added to the diets in the form of Smartamine™-M. The crossbred lambs were slaughtered after 28 days on the treatment diet and the Merino lambs after 42 days.Increasing the level of methionine supplementation did not lead to an increase in growth rate, daily feed intake, feed conversion efficiency, wool growth, skin thickness, or final liveweight and condition score. The Merino lambs had a lower growth rate, thinner skin, faster rate of wool growth, and were less efficient at converting feed into liveweight gain than the crossbred lambs (P < 0.05). There was no interaction between breed and methionine treatment.Increasing the level of methionine treatment also did not improve hot carcass weight, dressing percentage, tissue depth over the rib, longissimus dorsi (LD) cross-sectional area, meat pH, or meat colour. The only beneficial effect of methionine supplementation on carcass attributes was a decline in fat depth over the deepest part of the LD as methionine level increased (P < 0.05).There were no differences in tenderness, juiciness, or flavour intensity between the breeds or as a main effect with methionine supplementation. However, there was an interaction between breed and methionine for flavour intensity, such that methionine supplementation reduced the flavour intensity of Merino meat but not that of the crossbred meat (P < 0.05).This work suggests that there are unlikely to be production gains in terms of liveweight gain, feed conversion efficiency, or wool growth in supplementing lambs with protected methionine if they are being fed a high performance diet ad libitum. However, there were 2 benefits that may have scope for further investigation. The first was a reduction in fat cover over the loin as the level of methionine supplementation increased. The second was a reduction in the intensity of flavour found in Merino lamb when the lambs were supplemented with methionine. The study also provided some useful guidelines for the differences in growth and carcass characteristics between Merino and crossbred lambs when they are finished under identical conditions to an even fat cover, and demonstrated that Merino lambs can produce carcasses of very acceptable eating quality when well finished.

Lupin grain typically provides the main source of protein in most lamb finisher diets in Western Australia. The aim of this work was to determine whether alternative sources of nitrogen could provide a less expensive means of achieving the desired rate of liveweight gain and carcass characteristics. Fifty-one crossbred lambs were finished using 3 different sources of crude protein. These sources were either: (i) a control diet consisting of lupins, oats, barley and cereal chaff in which lupins provided 49% of the nitrogen (lupin diet); (ii) a diet consisting of a combination of cereal grain and urea (urea diet); or (iii) a diet in which lupins were partially replaced with expeller canola meal (canola diet). Diets were isonitrogenous (14.4% crude protein) and isoenergetic (10.5 MJ ME/kg DM). Lambs were gradually introduced to the diets over 2 weeks before being fed the diets ad�libitum for 5 weeks.Lambs fed the canola diet performed the best in terms of feed intake and liveweight gain while those fed the urea diet performed the worst. Respective growth rates for sheep fed the canola, lupin and urea diets were 272, 233 and 180 g/day, respectively, with significant (P

Etude de la reaction des hypobromite et hypochorite de methyle avec l'hexene-1, cyclohexene, styrene, butadiene-1,3, butene-3one-2, acrylate de methyle en presence de BF 3 . Formation de fluorohalogenures vicinaux et d'ethers d'halohydrines correspondants

Fluoro chlorides are major products in the reaction of methyl hypochlorite with certain olefins in the presence of boron trifluoride.

SEVERAL investigators have shown that a chick’s viability and its storage of the vitamins at hatching time are influenced by the intake of these specific essential nutrients by the parent stock. It is well established that some other as yet unidentified factor (or factors) is transmitted from the hen to the egg and subsequently to the newly hatched chick. When placed on a diet deficient in this constituent, the chick’s ability to grow at a normal rate is dependent upon an adequate storage of this unknown. Bird and associates (1946) found that the viability of chicks was low when hens were fed a soybean oil meal supplemented diet, adequate in all known factors. Mortality of chicks from hens receiving a soybean oil meal diet was 38.0 percent, whereas, hens receiving this diet plus 5.0 percent cow manure or sardine meal produced chicks with a mortality rate of 12.0 and 11.0 . . .

PEROSIS, an anatomical deformity of the leg bones of young chicks, was first described by Hunter and Funk (1930). The condition is associated with a high intake of calcium and phosphorus, and a low intake of manganese (Hunter et al., 1931; Milby, 1934; Wilgus et al., 1936–1937; Clifcorn et al., 1938). Later, the work of Wiese et al. (1939) showed that the blood and bone phosphatase activity of perotic birds was lower than that of chicks receiving an adequate amount of manganese in their diet. As the leg bones of chicks with perosis are bent and twisted from their normal shape it was thought that there might be an abnormal distribution of the enzyme phosphatase in the bones of these chicks. In this paper we wish to report the results we have observed on the distribution of this enzyme in the leg bones of perotic and normal chicks. EXPERIMENTAL

VITAMIN B12 is recognized as an essential dietary nutrient for hatchability. Limited data is now available concerning animal protein factor supplements as a source of this vitamin and other factors. Carver and McGinnis (1950a) found that a fermentation APF supplement was effective at levels of 0.5, 0.25, and 0.125 percent in improving hatchability from a low level or maintaining high hatchability in a nine-week experiment with hens on litter or wire. Another APF supplement with a content of 12.5 mg. of vitamin B12 per pound was reported by Hill et al. (1950) to be as effective in maintaining hatchability as 6 percent fish meal. These experimental birds were reared from day-old to 10 months on wire floors and fed the same supplements during the entire period. This product, when used at 0.11 percent, apparently contained adequate B12 to support good hatchability and permitted even greater transfer to the chick than . . .

SEVERAL investigators have reported that vitamin B12 is essential for hatchability, and that it can successfully replace animal proteins as a source of vitamin B12. A.P.F. supplements containing this vitamin improved hatchability with an all-vegetable diet as reported by Lindstrom et al. (1949a), Carver and McGinnis (1950a), and Hill et al. (1950). Crystalline vitamin B12 has also been shown to support good hatchability by Petersen et al. 1950), Carver and McGinnis (1950b), and Milligan and Combs (1950). This paper reports the results obtained when hens, which had received various levels of vitamin B12 for an 8-week experimental period, were returned to the all-vegetable basal ration. The value of feeding antibiotics on hatchability with or without vitamin B12 has been investigated and the results are presented. EXPERIMENTAL Ninety-six White Leghorn hens were placed in individual raised wire-bottom laying cages at approximately 5 months of age. A ration low in vitamin B12, . . .

THE requirements for a number of the known vitamins have been determined for the laying hen. These requirements are for vitamin A and D, riboflavin, pantothenic acid, folacin, and pyridoxine and have been compiled by the National Research Council (1954) as averages of results of several comparable experiments. Using high energy rations, Thayer (1953) reported that levels of niacin, riboflavin, pantothenic acid, and folic acid above recommended requirements were necessary for maximum egg production and feed efficiency. However, Berg and Bearse (1956), using high energy rations, did not obtain improved egg production and feed efficiency with an additional B-complex vitamin supplement. These workers did report significant differences in body weight gain in favor of the birds fed the vitamin-supplemented rations. This concurred with the results of Thayer. The increased feed efficiency obtained when high energy rations are fed to growing chickens has prompted considerable study of the effect of high . . .

Our interest in the effects of cosmic radiation is directed towards understanding the behavior of cells in vitro rather than towards its possible consequences on man. The human cell line K-562 can be induced in culture to express erythroid-specific markers by addition of hemin. Growth, metabolism and differentiation of K-562 cells were measured. The most striking result was that hemoglobin biosynthesis was markedly depressed in flight. However, cell growth was not significantly altered while glucose consumption was increased in the flight samples. Although the results presented here are derived from one single experiment, it appears that there is a marked effect of cosmic radiation on K-562 cells in vitro.

BLOOD spots in eggs represent a serious loss to the poultry industry and the loss may become greater with more general use of electronic blood spot detection in the future. Numerous workers have investigated the effects of nutrients on the incidence of blood spots. Nalbandov and Card (1944) observed that blood spots were due to hemorrhaging within the follicular membrane and reported that vitamins A, C, D, E, K, and P had no effect on the incidence of blood spots, but that there was a definite seasonal increase from December through the following July. However, these same workers (1947) reported the feeding of cerograss reduced the incidence of blood spots materially in one of 2 years’ studied. Bearse et al. (1960) found that vitamin A was essential in reducing blood spots and that low levels of vitamin A increased blood spot incidence. The level of vitamin A recommended by the…

Animal protein supplements including liver meal, condensed fish solubles, fish meal, meat meals, and milk products have been shown to contain an unknown factor (or factors) required by chickens for reproduction and early growth. Rubin and Bird (1946) and Whitson, Titus and Bird (1946) found dried cow manure to contain similar factors. An animal protein factor supplement, available following the isolation of vitamin B12, was found by Lindstrom et al. (1949a) to contain factors essential for hatchability when hens received an all-plant ration. Lillie, Olsen and Bird (1949) have reported that crystalline vitamin B12 injected into eggs improved hatchability when the breeder hens were fed a diet deficient in this vitamin. Subsequent chick studies also showed improved livability and feathering following the B12 injections into the eggs. Their data is not completely in agreement or conclusive, primarily because of fairly high hatchability of eggs from the basal diet without vitamin . . .

Crystalline vitamin B12, isolated from liver by Rickes et al. (1948) was shown by Ott et al. (1948) to give response similar to the animal protein factor (APF ) required for chick growth. Preparations of a microbiologically produced material by Stokstad et al. (1948) have also been shown to be highly active as a source of APF, when measured by chick assay. A vitamin B12 ** concentrate (4.4 ug. of B12 per gram) was fed at a 1% level to APF depleted chicks to determine its effect upon chick growth and to APF depleted laying hens to determine the effect upon hatchability. The concentrate was used to supplement both a synthetic and a natural type chick diet. The synthetic diet contained alpha soybean protein, cerelose, soybean oil, salts, amino acids, and vitamins A, D, and B-complex supplements. The natural type diet contained wheat bran, ground corn, oats and wheat, soybean oil . . .