Computer Program For Prediction Research Articles

Primary Structure of Glycans by NMR Spectroscopy.

Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.

Комплексный подход к разработке и созданию компьютерной программы виртуального скрининга антиоксидантной активности

Патогенез многих распространенных заболеваний человека (в том числе патологии сердечнососудистой системы, дыхательных путей, злокачественные новообразования) имеет достаточно четко очерченную свободнорадикальную фазу. Поэтому важной задачей современной фармакологии является поиск и создание высокоэффективных антиоксидантов. Для предварительной оценки антиоксидантной активности (АОА) разрабатываются информационные технологии и компьютерные программы виртуального скрининга. Поэтому разработка подходов к созданию компьютерных программ прогноза АОА, а именно скавенджеров NO, является перспективным и актуальным направлением современной фундаментальной медицины. Цель исследования – на основании комплексного математико-теоретического подхода и результатов фармакологических исследований в ряду производных ксантина разработать высокоселективную программу виртуального скрининга АОА. В качестве объекта исследования было отобрано 122 соединения, производные ксантинил7-ацетатных и ксантинил-8-тиоацетатных кислот и 3-R-гидроксиметилксантинов. Для этих соединений были проведены квантово-химические расчеты энергетических дескрипторов молекулярных орбиталей, а также проведено исследование антиоксидантной активности in vitro по ингибированию NO в системе фотоиндуцированного окисления нитропруссида натрия. Проведен расчет корреляционной зависимости между квантово-химическими параметрами соединений и АОА по ингибированию NO. Показано использование электронно-топологического подхода, который позволяет производить поиск молекулярных фрагментов-признаков активности. Были рассчитаны квантово-химические параметры исследуемых молекул с помощью метода CNDO/2. Рассчитаны показатели энергии предельных орбиталей (НВМО, ВЗМО), показатели абсолютной жесткости молекулы, абсолютной электрической негативности молекулы. На основании этих данных рассчитаны показатели реактивного индекса. Кроме того, рассчитана зависимость антиоксидантного действия (по ингибированию NO) веществ от их квантово-химических дескрипторов и определена функция их зависимости. Определена корреляционная зависимость АОА от квантово-химических показателей. Для создания программного обеспечения с целью скрининга потенциальных скавенджеров NO были выбраны квантово-химические дескрипторы. При этом, исходя из химической природы и реакционной способности активных форм азота,особое внимание следует уделить энергиям высшей занятой и низшей вакантной молекулярных орбиталей, а также индексу реактивности Фукуи. Разработанная на основе комплексного подхода (совокупности теоретических концепций, математических методов и правил, и реализующих их алгоритмов) новая компьютерная программа прогноза является высокоэффективным инструментом виртуального скрининга скавенджеров NO в ряду вновь синтезированных структурно-сходных азагетекроциклов, что доказано вычислительным тестированием и подтверждено экспериментальными исследованиями. Так, применение новой компьютерной программы для прогноза АОА позволило выявить у вновь синтезированного соединения – гидразида 8-бензиламинотеофиллинил-7-уксусной кислоты (С-3) свойства скавенджера NO, что подтверждено в опытах in vitro.

Blast from the past: Perioperative use of the Maruyama computer program for prediction of lymph node involvement in the surgical treatment of gastric cancer following neoadjuvant chemotherapy

BackgroundSurgical quality assurance is a key element of gastric cancer treatment. The Maruyama Computer Program (MCP) allows to predict lymph node involvement in stations no. 1–16. The aim of the current study was to evaluate the accuracy of the MCP predictions in GC patients treated with neoadjuvant chemotherapy (nCTH) followed by gastrectomy with adequate lymphadenectomy. Methods101 patients who underwent preoperative nCTH followed by D2 gastrectomy with curative intent were analysed. The response to nCTH was measured using the tumour regression grade system. ResultsTest sensitivity, specificity, PPV, NPV and accuracy of the MCP were 92%, 33%, 41%, 89%, and 53%, respectively. In patients with response to nCTH, number of false positive (FP) results was significantly higher than in patients who did not respond to nCTH both in the N1 (56.3% vs 28.9%, p < 0.0001) and in the N2 (59% vs 41%, p < 0.0001) trier. The risk for FP results was 6 times higher in N1 (OR = 6.50, 95%CI: 3.91–10.82,; p < 0.0001) and N2 (OR = 5.84, 95%CI: 2.85–11.96; p < 0.0001) triers. In patients with intestinal type GC, the risk for FP results was 4 times higher than in other histologic types of GC in both N1 (OR = 4.23, 95%CI: 2.58–6.95; p < 0.0001) and N2 (OR = 4.23, 95%CI: 2.02–9.62; p = 0.0002) triers. ConclusionsMCP predictions in the GC patients treated with nCTH have low specificity due to significantly high number of FP results. Noticeably low accuracy level of predictions indicate a need for new prediction models, based on Laurén classification, since it may provide some information on expected regression grade.

基于门控递归单元神经网络的高速公路行程时间预测

To efficiently predict the travel time on the expressway, the travel time was studied with the gated recurrent neural network through collection of the swiping data of vehicles at toll gates on the expressway. By means of the developed prediction computer program, the effects of the proposed method were then tested with the charging data of the Guangzhou Airport south expressway. The results show that the prediction effects are satisfying. Comparison with the LSTM neural network and the BP neural network indicates that, the gated recurrent neural network is better in prediction accuracy.

部位別特性を考慮した生体内温度予測プログラムの開発 : 第3報-被験者実験の深部温,皮膚温の測定値と計算値の比較

部位別特性を考慮した生体内温度予測プログラムの開発 : 第3報-被験者実験の深部温,皮膚温の測定値と計算値の比較

部位別特性を考慮した生体内温度予測プログラムの開発 : 第2報-皮膚血流量調節の数理モデルの検討

部位別特性を考慮した生体内温度予測プログラムの開発 : 第2報-皮膚血流量調節の数理モデルの検討

部位別特性を考慮した生体内温度予測プログラムの開発 : 第1報-生体内熱移動方程式とその解法

部位別特性を考慮した生体内温度予測プログラムの開発 : 第1報-生体内熱移動方程式とその解法

The effect of biguanide derivatives on antioxidant status during the development of oxidative stress

The intensity of free radical processes, activity of antioxidant enzymes (superoxide dismutase, catalase), and the content of low molecular weight antioxidants (reduced glutathione, citrate) in skeletal muscle and liver from rats with experimental rheumatoid arthritis administered with biguanide synthetic derivatives (2,4-dicarbomethoxyphenyl-biguanide and 4-methyl-phenyl biguanide) selected by Prediction of Activity Spectra for Substances (PASS), a computer program for the prediction of biological activity, were studied. The observed changes in the studied parameters toward the reference values under the effect of tested compounds can be explained by their antioxidant and protective properties during pathology, which are accompanied by oxidative stress. The results can be used for the development of new methods for the prevention and treatment of rheumatoid arthritis.

Preparatory work for the pest categorisation of three bacteria listed in the annexes of the Council directive 2000/29/EC Erwinia amylovora Winslow et al. Xylophilus ampelinus (Panagopoulos) Willems et al. Clavibacter michiganensis subsp. insidiosus(McCulloch) Davis et al

Preparatory work for the pest categorisation of three bacteria listed in the annexes of the Council directive 2000/29/EC Erwinia amylovora Winslow et al. Xylophilus ampelinus (Panagopoulos) Willems et al. Clavibacter michiganensis subsp. insidiosus(McCulloch) Davis et al

RETRACTED: A simple predictive tool for monitoring steam loss in traps

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).This article has been retracted at the request of the Editor-in-Chief.The article duplicates significant parts of the following papers:1. Alireza Bahadori, Hari B. Vuthaluru, A method for estimation of recoverable heat from blowdown systems during steam generation, Energy, Volume 35, Issue 8, August 2010, Pages 3501-3507, ISSN 0360-5442, (http://dx.doi.org/10.1016/j.energy.2010.04.054)2. Alireza Bahadori, Estimation of combustion flue gas acid dew point during heat recovery and efficiency gain, Applied Thermal Engineering, Volume 31, Issues 8-9, June 2011, Pages 1457-1462, ISSN 1359-4311, (http://dx.doi.org/10.1016/j.applthermaleng.2011.01.020)3. Alireza Bahadori, Hari B. Vuthaluru, Prediction of methanol loss in vapor phase during gas hydrate inhibition using Arrhenius-type functions, Journal of Loss Prevention in the Process Industries, Volume 23, Issue 3, May 2010, Pages 379-384, ISSN 0950-4230, (http://dx.doi.org/10.1016/j.jlp.2010.01.002)4. Alireza Bahadori, Mansour Al-Haddabi, Hari Vuthaluru, & Bahadori, M. (2011, January 1). A Simple-to-Use Matlab-based Computer Program for Prediction of Formation Water Properties. Society of Petroleum Engineers.(http://dx.doi.org/10.2118/140644-MS)One of the conditions of submission of a paper for publication is that authors declare explicitly that the paper is not under consideration for publication elsewhere. Re-use of any data should be appropriately cited. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

POLYAR, a new computer program for prediction of poly(A) sites in human sequences

BackgroundmRNA polyadenylation is an essential step of pre-mRNA processing in eukaryotes. Accurate prediction of the pre-mRNA 3'-end cleavage/polyadenylation sites is important for defining the gene boundaries and understanding gene expression mechanisms.Results28761 human mapped poly(A) sites have been classified into three classes containing different known forms of polyadenylation signal (PAS) or none of them (PAS-strong, PAS-weak and PAS-less, respectively) and a new computer program POLYAR for the prediction of poly(A) sites of each class was developed. In comparison with polya_svm (till date the most accurate computer program for prediction of poly(A) sites) while searching for PAS-strong poly(A) sites in human sequences, POLYAR had a significantly higher prediction sensitivity (80.8% versus 65.7%) and specificity (66.4% versus 51.7%) However, when a similar sort of search was conducted for PAS-weak and PAS-less poly(A) sites, both programs had a very low prediction accuracy, which indicates that our knowledge about factors involved in the determination of the poly(A) sites is not sufficient to identify such polyadenylation regions.ConclusionsWe present a new classification of polyadenylation sites into three classes and a novel computer program POLYAR for prediction of poly(A) sites/regions of each of the class. In tests, POLYAR shows high accuracy of prediction of the PAS-strong poly(A) sites, though this program's efficiency in searching for PAS-weak and PAS-less poly(A) sites is not very high but is comparable to other available programs. These findings suggest that additional characteristics of such poly(A) sites remain to be elucidated. POLYAR program with a stand-alone version for downloading is available at http://cub.comsats.edu.pk/polyapredict.htm.

A Computer Program for Automatic Watering Based on Potential Evapotranspiration by Penman Method and Predicted Leaf Area in Miniature Pot Rose Production

In this study, we developed a computer program for automatic prediction of watering time point by considering the environmental factors such as solar radiation, air temperature and relative humidity based on the multiple linear regression equation of leaf area and Penman Method. The experiments were carried out for a year in two watering experimental plots, one of which was controlled by pF value, and the other by the computer program. After comparing the results of the two plots, the following findings were obtained. In the computer program plot, the observed and predicted values of both leaf area and evapotranspiration indicated significant correlation at the 1% level, which suggested that the computer program had high prediction accuracy. In addition, no significant difference was observed between the two experimental plots with respects to the plant height, plant diameter, leaf area, leaf number, fresh weight, and dry weight, which demonstrated that the plants in the computer program plot had normal growth. On the other hand, although the number of flower buds and flowering shoots showed higher values at the end of certain cultivations in the computer program plot than those in pF value plot, we proposed that it was due to the effect of cumulative daily solar radiation in the greenhouse, rather than the watering. Thus, we have reached the conclusion that the computer program for automatic prediction of watering time point developed by this study has high applicability in miniature pot rose production.

Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs

The cell cycle-dependent nucleocytoplasmic transport of proteins is predominantly regulated by CDK kinase activities; however, it is currently difficult to predict the proteins thus regulated, largely because of the low prediction efficiency of the motifs involved. Here, we report the successful prediction of CDK1-regulated nucleocytoplasmic shuttling proteins using a prediction system for nuclear localization signals (NLSs). By systematic amino acid replacement analyses in budding yeast, we created activity-based profiles for different classes of importin-alpha-dependent NLSs that represent the functional contributions of different amino acids at each position within an NLS class. We then developed a computer program for prediction of the classical importin-alpha/beta pathway-specific NLSs (cNLS Mapper, available at http//nls-mapper.iab.keio.ac.jp/) that calculates NLS activities by using these profiles and an additivity-based motif scoring algorithm. This calculation method achieved significantly higher prediction accuracy in terms of both sensitivity and specificity than did current methods. The search for NLSs that overlap the consensus CDK1 phosphorylation site by using cNLS Mapper identified all previously reported and 5 previously uncharacterized yeast proteins (Yen1, Psy4, Pds1, Msa1, and Dna2) displaying CDK1- and cell cycle-regulated nuclear transport. CDK1 activated or repressed their nuclear import activity, depending on the position of CDK1-phosphorylation sites within NLSs. The application of this strategy to other functional linear motifs should be useful in systematic studies of protein-protein networks.

Hardenability Testing and Simulation of Gas-Quenched Steel

The aim of a joint project between the Stiftung Institut für Werkstofftechnik, Bremen (IWT), the company Ipsen International, and the Faculty of Mechanical Engineering and Naval Architecture (FMENA), the University of Zagreb is to develop a computer program for prediction of hardness on the axial section of axially-symmetrical workpieces of any complex shape, thereupon high pressure gas quenching. The hardenability for the specimens made of tool steel grade EN-90MnCrV8 and the cooling dynamics under two gas pressures are measured using the unique facility at IWT. With developed computer simulation model, the cooling curves at different positions (J) along the end-quenched specimen are determined. Based on them, the cooling time from 800 to 500°C (t 8/5) is determined, and the curves J = f(t 8/5) are derived for different quenching conditions. This curves together with curves of hardness distributions along the end-quenched specimens can serve for the prediction of hardness distribution on the cross-sections of a batch of workpieces cooled in vacuum furnace.

SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling

SCWRL and MolIDE are software applications for prediction of protein structures. SCWRL is designed specifically for the task of prediction of side-chain conformations given a fixed backbone usually obtained from an experimental structure determined by X-ray crystallography or NMR. SCWRL is a command-line program that typically runs in a few seconds. MolIDE provides a graphical interface for basic comparative (homology) modeling using SCWRL and other programs. MolIDE takes an input target sequence and uses PSI-BLAST to identify and align templates for comparative modeling of the target. The sequence alignment to any template can be manually modified within a graphical window of the target-template alignment and visualization of the alignment on the template structure. MolIDE builds the model of the target structure on the basis of the template backbone, predicted side-chain conformations with SCWRL and a loop-modeling program for insertion-deletion regions with user-selected sequence segments. SCWRL and MolIDE can be obtained at (http://dunbrack.fccc.edu/Software.php).

The use of artificial neural networks in adiabatic curves modeling

Adiabatic hydration curves are the most suitable data for temperature calculations in concrete hardening structures. However, it is very difficult to predict the adiabatic hydration curve of an arbitrary concrete mixture. The idea of modeling adiabatic temperature rise during concrete hydration with the use of artificial neural networks was introduced in order to describe the adiabatic hydration of an arbitrary concrete mixture, depending on factors which influence the hydration process of cement in concrete. The influence of these factors was determined by our own experiments. A comparison between experimentally determined adiabatic curves and adiabatic curves, evaluated by proposed numerical model shows that artificial neural networks can be used to predict adiabatic hydration curves effectively. This model can be easily incorporated in the computer programs for prediction of the thermal fields in young concrete structures, implemented in the finite element or finite difference codes. New adiabatic hydration curves with some other initial parameters of the concrete mixture can be easily included in this model in order to expand the range of suitability of artificial neural networks to predict the adiabatic hydration curves.

Prediction Computer Program for Whole Body Temperatures and its Application under Various Working Level and Thermal Environmental Condition Combinations

We introduced a computer program developed for the numerical analysis of thermal conditions of all segments and blood circulatory systems in the human body to precisely evaluate human thermal physiological responses. In this program, a cylindrical model consisting of internal multi-layers is adapted for the segment of the human body. For the multi-layered concentric cylindrical model we adopted a new numerical solution method. By using this computer program the internal tissue temperatures, heat fluxes and blood temperatures of all segments in the human body could be calculated simultaneously. This program also included a subroutine for calculation of thermoregulatory response. This paper describes the improvements made to this computer program for simulating individual physical differences and its application to various working levels. The main points for improvement were the assigning procedures of physical characteristics of individuals and local muscle heat production. The improved computer program was used to simulate the whole body temperatures of the subjects during exercise described in Gagge, Stolwijk and Saltin (1969) were simulated. The calculated results were agreed with the measured results under the combination of the three kinds of exercise and the three types of environmental condition.

A New Computer Program for Pile Capacity Prediction using CPT Data

An interactive computer program “GLAMCPT” is developed for application in soil profiling and prediction of pile load capacity using cone penetration test (CPT) and laboratory soil test results. GLAMCPT calculates pile capacity according to 10 selected methods from European design codes, refereed international publications and recommendations of professional institutions. To demonstrate the capabilities of the program, a database of comprehensive ground investigation and full-scale pile tests in sand, at a Belgian site, is analysed using GLAMCPT. The database comprises 11 static tests and 12 dynamic tests on piles of different construction techniques, including driven pre-cast concrete piles and screwed cast in-situ piles, installed using 5 different procedures. Prior to pile installation, CPTs were carried out at each proposed pile location. Comparison of GLAMCPT predictions with the observed pile capacities reveals that the most accurate of the existing methods yields an average, μ, of predicted to observed pile head capacity [P uh(p)/P uh(m)] equal to 0.94. The most consistent method produces a coeffcient of variation (COV) of [P uh(p)/P uh(m)] equal to 0.1 and ranking index (RI) of 0.08. Parametric studies have been carried out using GLAMCPT to formulate an improved predictive method, which yielded: μ = 0.99, COV = 0.07 and RI = 0.04.

Analysis and computer program for rupture-risk prediction of abdominal aortic aneurysms

BackgroundRuptured abdominal aortic aneurysms (AAAs) are the 13th leading cause of death in the United States. While AAA rupture may occur without significant warning, its risk assessment is generally based on critical values of the maximum AAA diameter (>5 cm) and AAA-growth rate (>0.5 cm/year). These criteria may be insufficient for reliable AAA-rupture risk assessment especially when predicting possible rupture of smaller AAAs.MethodsBased on clinical evidence, eight biomechanical factors with associated weighting coefficients were determined and summed up in terms of a dimensionless, time-dependent severity parameter, SP(t). The most important factor is the maximum wall stress for which a semi-empirical correlation has been developed.ResultsThe patient-specific SP(t) indicates the risk level of AAA rupture and provides a threshold value when surgical intervention becomes necessary. The severity parameter was validated with four clinical cases and its application is demonstrated for two AAA cases.ConclusionAs part of computational AAA-risk assessment and medical management, a patient-specific severity parameter 0 < SP(t) < 1.0 has been developed. The time-dependent, normalized SP(t) depends on eight biomechanical factors, to be obtained via a patient's pressure and AAA-geometry measurements. The resulting program is an easy-to-use tool which allows medical practitioners to make scientific diagnoses, which may save lives and should lead to an improved quality of life.

CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS)

Palmitoylation is an important post-translational lipid modification of proteins. Unlike prenylation and myristoylation, palmitoylation is a reversible covalent modification, allowing for dynamic regulation of multiple complex cellular systems. However, in vivo or in vitro identification of palmitoylation sites is usually time-consuming and labor-intensive. So in silico predictions could help to narrow down the possible palmitoylation sites, which can be used to guide further experimental design. Previous studies suggested that there is no unique canonical motif for palmitoylation sites, so we hypothesize that the bona fide pattern might be compromised by heterogeneity of multiple structural determinants with different features. Based on this hypothesis, we partition the known palmitoylation sites into three clusters and score the similarity between the query peptide and the training ones based on BLOSUM62 matrix. We have implemented a computer program for palmitoylation site prediction, Clustering and Scoring Strategy for Palmitoylation Sites Prediction (CSS-Palm) system, and found that the program's prediction performance is encouraging with highly positive Jack-Knife validation results (sensitivity 82.16% and specificity 83.17% for cut-off score 2.6). Our analyses indicate that CSS-Palm could provide a powerful and effective tool to studies of palmitoylation sites. CSS-Palm is implemented in PHP/PERL+MySQL and can be freely accessed at http://bioinformatics.lcd-ustc.org/css_palm/ yaoxb@ustc.edu.cn; xuyn@bmb.uga.edu Supplementary data are available at Bionformatics online.