A layout algorithm for signaling pathways

Cataloged from PDF version of article.Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user's comprehension of the underlying biological phenomenon. We present a new, elegant algorithm for layout of biological signaling pathways. Our algorithm uses a force-directed layout scheme, taking into account directional and rectangular regional constraints enforced by different molecular interaction types and subcellular locations in a cell. The algorithm has been successfully implemented as part of a pathway visualization and analysis toolkit named PATIKA, and results with respect to computational complexity and quality of the layout have been found satisfactory. The algorithm may be easily adapted to be used in other applications with similar conventions and constraints as well. PATIKA version 1.0 beta is available upon request at http://www.patika.org. (C) 2004 Elsevier Inc. All rights reserved

Estimating mine planning software utilization for decision-making strategies in the South African gold mining sector.

The work presented in this paper is part of a PhD research study in the School of Mining Engineering at the University of the Witwatersrand.This paper discusses a new methodology for defining and measuring mine planning software utilization in the South African gold mining sector within an evolving data-set framework. An initial data-set showing the mine planning software providers, their corresponding software solutions, as well as the software capabilities and information on the number of licences was collected and compiled in 2012 in an online database for software utilized in the South African mining industry. Details of the database development and implementation were published in the Journal of the Southern African Institute of Mining and Metallurgy in 2013. In 2014 the data-set was updated with additional and new information. Using the 2012 and 2014 timestamps, a methodology for estimating the software utilization was developed. In this methodology, the three variables of commodity, functionality, and time factor were used to define and measure the software utilization in order to ultimately inform decision-making strategies for optimal software utilization. Using six different functionalities, namely Geological Data Management, Geological Modelling and Resource Estimation, Design and Layout, Scheduling, Financial Valuation, and Optimization, utilization in the gold sector was measured. This paper presents the methodology employed for measuring the mine planning software utilization. The methodology is useful for stakeholders reviewing existing software combinations or intending to purchase new software in the near future and who want to estimate the comparative attractiveness of a certain software package. These stakeholders include mining companies, consulting companies, educational institutions, and software providers. The work presented in this paper is part of a PhD research study in the School of Mining Engineering at the University of the Witwatersrand.MvdH2017http://www.saimm.co.za/publications/journal-paper

Effects of various inulin levels on in vitro digestibility of corn silage, perennial ryegrass (Lolium perenne L.) and common vetch (Vicia sativa L.)/oat (Avena sativa L.) hay

The aim of this study was to investigate the effects of various inulin levels on in vitro true dry matter digestibility (IVTDDM) and in vitro neutral detergent fibre digestibility (IVTDNDF) of corn silage (CS), perennial ryegrass (PR), and common vetch/oat hay (VO). Inulin was added to the fermenter at concentrations of 0 (CSC, PRC, VOC), 100 (CS100, PR100, VO100), 200 (CS200, PR200, VO200), and 300 (CS300, PR300, VO300) mg/litre of total culture fluid using an in vitro DaisyII incubator. Each fermenter contained 1600 ml buffer solution and 400 ml rumen fluid. The IVTDDM and IVTDNDF were determined with a DaisyII incubator and rumen fluid obtained from three cannulated Karayaka rams. The IVTDDM values (%) for PRC, PR100, PR200, and PR300 were 70.06 ± 1.133, 73.21 ± 4.153, 70.36 ± 0.506, and 66.69 ± 1.317, respectively. The effects of various inulin levels on IVTDDM and IVTDNDF values of PR were significant (P <0.05). The IVTDDM and IVTDNDF values for CS and VO were not significantly (P >0.05) different. Among the treatments, supplementation of inulin to CS and VO did not have a significant (P >0.05) effect on IVTDDM and IVTDNDF values. The high dose of inulin (PR300) reduced IVTDDM and IVTDNDF, whereas PR100 showed a statistically significant (P <0.05) increase on IVTDDM and IVTDNDF. However, in vivo studies with PR may be required to show the effects of various levels of inulin supplementation to support the IVTD findings of the current study.Keywords: Inulin, in vitro true digestibility, hay, silag

Effects of standard diets from different sources on growth and some organ parameters of rats

ΔΕΝ ΔΙΑΤΙΘΕΤΑΙ ΠΕΡΙΛΗΨΗThis study aims to determine the effects of open and closed formulated standard diets supplied from different sources on growth performance and internal organ development of laboratory rats. Five-week-old 32 Wistar rats were used. A special control group diet was produced in accordance with the criteria determined by the National Research Council (NRC) (1995). Three different most preferred commercial open and closed-formula diets produced by international and local companies were used as trial groups’ diets. The experiment was carried out for 12 weeks. Weekly feed consumption, body weight change, internal organ weight, intestinal organ weigths and lengths, intestinal villi heigth and crypt depth were measured in groups. The body weight values of the control group and the first group fed with open-formula diet were found at the highest level (P <0.05). The control group diet had a positive effect on small intestine villi heigth and crypt depth (P <0.05). The nutrient contents and energy values of the diets of experimental groups were determined as different from the commercial firm notifications. As a result of the research, it is concluded that the diets prepared with open-formula give more reliable results in the growth performance and development of internal organs of Wistar rats

Apparent stress-strain relationships in experimental equipment where magnetorheological fluids operate under compression mode

Abstract: This paper presents an experimental investigation of two different magnetorheological ( MR) fluids, namely, water-based and hydrocarbon-based MR fluids in compression mode under various applied currents. Finite element method magnetics was used to predict the magnetic field distribution inside the MR fluids generated by a coil. A test rig was constructed where the MR fluid was sandwiched between two flat surfaces. During the compression, the upper surface was moved towards the lower surface in a vertical direction. Stress-strain relationships were obtained for arrangements of equipment where each type of fluid was involved, using compression test equipment. The apparent compressive stress was found to be increased with the increase in magnetic field strength. In addition, the apparent compressive stress of the water-based MR fluid showed a response to the compressive strain of greater magnitude. However, during the compression process, the hydrocarbon-based MR fluid appeared to show a unique behaviour where an abrupt pressure drop was discovered in a region where the apparent compressive stress would be expected to increase steadily. The conclusion is drawn that the apparent compressive stress of MR fluids is influenced strongly by the nature of the carrier fluid and by the magnitude of the applied current

The utility of multidetector computed tomography for evaluation of congenital heart disease

Background: Congenital heart diseases (CHD) are the leading cause of birthdefect-related deaths. Multidedector computed tomography (MDCT) plays animportant role for imaging CHD in addition to echocardiography and providesa comprehensive evaluation of complex heart malformations for the referringcardiologist. The aim of the study was to evaluate the utility of MDCT in theassessment of CHD.Materials and methods: A 102 patients with CHD were investigated after initialassessment by echocardiography. The information obtained by MDCT and findingsof echocardiography were reviewed together by paediatric cardiologistsand cardiac radiologists. Perioperative anatomic descriptions, wherever available(n = 34) formed the gold standard for the comparison.Results: The clinical consensus diagnosis defined 154 cardiovascular lesions inthe patients. The results were classified in groups. We present the appearanceof various congenital cardiac lesions seen in clinical practice.Conclusions: MDCT provides important information about anatomic details ofCHD for the referring cardiologist. The evaluation of different anatomic structuressuch as heart, great vessels, lungs and abdomen is possible in one acquisitionwith this technique

The effects of seasonal variation on the microbial-n flow to the small intestine and prediction of feed intake in grazing karayaka sheep

The objectives of the present study were to estimate the microbial-N flow to the small intestine and to predict the digestible organic matter intake (DOMI) in grazing Karayaka sheep based on urinary excretion of purine derivatives (xanthine, hypoxanthine, uric acid and allantoin) by the use of spot urine sampling under field conditions. In the trial, 10 Karayaka sheep from 2 to 3 years of age were used. The animals were grazed in a pasture for ten months and fed with concentrate and vetch plus oat hay for the other two months (January and February) indoors. Highly significant linear and cubic relationships (P<0.001) were found among months for purine derivatives index, purine derivatives excretion, purine derivatives absorption, microbial-N and DOMI. Through urine sampling and the determination of levels of excreted urinary PD and the Purine Derivatives:Creatinine ratio (PDC index), microbial-N values were estimated and they indicated that the protein nutrition of the sheep was insufficient. In conclusion, the prediction of protein nutrition of sheep under the field conditions may be possible with the use of spot urine sampling, urinary excreted PD and PDC index. The mean purine derivative levels in spot urine samples from sheep were highest in June, July and October. Protein nutrition of pastured sheep may be affected by weather changes, including rainfall. Spot urine sampling may useful in modeling the feed consumption of pasturing sheep. However, further studies are required under different field conditions with different breeds of sheep to develop spot urine sampling as a model