The effects of age and gender (bull vs steer) on the feeding behavior of young beef cattle fed grass silage

Natalia Puzio,Cezary Purwin,Zenon Nogalski,Ireneusz Bialobrzewski,Lukasz Tomczyk,Jacek P Michalski 아세아·태평양축산학회 2019 Animal Bioscience Vol.32 No.8

Objective: The objective of this study was to determine the effects of age and gender (bull vs steer) on feeding behavior parameters in young beef cattle fed grass silage. Methods: The study was conducted on 180 young beef cattle at 7 to 18 mo of age. The experimental materials comprised 90 bulls produced by commercial crossing of Polish Holstein-Friesian cows with Charolais, Limousin and Hereford bulls (30 animals of each breed) and 90 steers of the same genotypes. The animals had ad libitum access to grass silage; the concentrate was fed separately, in feed stations. They received 28 g dry matter of concentrate per kg of metabolic body weight per day. Bunk visit data and silage intake for all experimental animals were recorded individually using the Roughage Intake Control system (5 feed bunks per 15 animals). Results: Age and gender (bull vs steer) exerted significant effects on the feeding behavior of young beef cattle. The frequency of bunk visits and meal frequency decreased, whereas the feeding rate of silage, and the average duration and size of a single meal increased with age (p<0.01). Bunk attendance and meal frequency were higher (p<0.01) in steers than in bulls (49.1 vs 37.4 visits/d, and 8.63 vs 7.99 meals/d, respectively). Daily feeding time was longer in steers than in bulls (102.3 vs 100.3 min/d, respectively), but the feeding rate of silage was lower in steers, and their meals were smaller in size and shorter in duration (p<0.01). Daily silage dry matter intake was higher (p<0.01) in bulls than in steers (4.62 vs 4.47 kg/d, respectively). Conclusion: The results of this study indicate that age and gender (bull vs steer) exerted significant effects on the feeding behavior of young beef cattle.

An efficient molecular docking using conformational space annealing

Lee, Kyoungrim,Czaplewski, Cezary,Kim, Seung-Yeon,Lee, Jooyoung John Wiley Sons, Inc. 2005 Journal of computational chemistry Vol.26 No.1

<P>Molecular docking falls into the general category of global optimization problems because its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor–ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA, and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with the minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions, and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA, and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native-like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 78–87, 2005</P> <B>Graphic Abstract</B> <img src='wiley_img/01928651-2005-26-1-JCC20147-gra001.gif' alt='wiley_img/01928651-2005-26-1-JCC20147-gra001'>

Real Time Monitoring of Cars during European Rally Championships in Poland in 2005

Oszczak Bartlomiej,Specht Cezary,Oszczak Stanislaw,Eliza Sitnik 한국항해항만학회 2006 한국항해항만학회 학술대회논문집 Vol.1 No.-

The paper presents the preparations work and experiences gained from realtime GPS car monitoring during the European Rally Championships organized on 10-12 June 2005 in Poland. The developed system is based on GPS and GSM/GPRS technology. Distribution and teletransmission of data are possible using different GSM operators in Poland, which makes the system fully independent. The system's server collects data from rally cars, processing and send data through VPN connections to the SQL server located in main control room. Data can be collected in real time via Internet or GPRS. Some information on GSM/GPRS range during rally championships are also presented in the paper. The study covered many trials and tests of different software and various configurations of the GPRS modems before finally the system started to work. Information coming from 10 Rally Cars were collected to the SQL Server continuously in one second interval. In real time mode these all data were displayed simultaneously in the rally main control room and in the rally press conference room. Paper describes also adopted emergency procedures and remote reconfiguration of GPS/GPRS boxes inside rally cars made during championships. Some problems and method of practical solutions are presented to avoid active jamming dangerous for a driver and his pilot, having system of communication intercoms jammed by teletransmission of GPRS 900/1800 MHz. In cooperation with rally teams special GPS/GPRS safety boxes were designed and made. Monitoring of all 7 rally stages with GPS receivers and method of calibrations of the maps were presented. GSM signal coverage was also checked in all stages. All data transmitted from rally cars were recorded in the computer. Some of our GPS cars had accidents and dispite them information were continuously sent to server. There is possibility to show in post mission mode the position of chosen cars in our rally application. Some information of best rally cars are presented also in the paper.

Fast Algorithms for Computing Floating-Point Reciprocal Cube Root Functions

Leonid Moroz,Volodymyr Samotyy,Cezary Walczyk International Journal of Computer ScienceNetwork S 2023 International journal of computer science and netw Vol.23 No.6

In this article the problem of computing floating-point reciprocal cube root functions is considered. Our new algorithms for this task decrease the number of arithmetic operations used for computing $1/{\sqrt[3]{x}}$. A new approach for selection of magic constants is presented in order to minimize the computation time for reciprocal cube roots of arguments with movable decimal point. The underlying theory enables partitioning of the base argument range x∈[1,8) into 3 segments, what in turn increases accuracy of initial function approximation and decreases the number of iterations to one. Three best algorithms were implemented and carefully tested on 32-bit microcontroller with ARM core. Their custom C implementations were favourable compared with the algorithm based on cbrtf(x) function taken from C ＜math.h＞ library on three different hardware platforms. As a result, the new fast approximation algorithm for the function $1/{\sqrt[3]{x}}$ was determined that outperforms all other algorithms in terms of computation time and cycle count.

The Prevalence of Founder Mutations among Individuals from Families with Familial Pancreatic Cancer Syndrome

Marcin R. Lener,Aniruddh Kashyap,Wojciech Kluzniak,Cezary Cybulski,Agnieszka Soluch,Sandra Pietrzak,Tomasz Huzarski,Jacek Gronwald,Jan Lubinski 대한암학회 2017 Cancer Research and Treatment Vol.49 No.2

Purpose Familial pancreatic cancer describes families with at least two first-degree relatives with pancreatic cancer that do not fulfil the criteria of other inherited tumor syndromes with increased risks of pancreatic cancer. Although much has been learned regarding the aggregation of pancreatic cancer in some families, the genetic basis for this familial aggregation is poorly understood. This study evaluated the prevalence of 10 Polish founder mutations in four genes among individuals from families with diagnosed familial pancreatic cancer syndrome and assessed their possible association with the familial pancreatic cancer (FPC) risk in Poland. Materials and Methods In this study, 400 FPC individuals and 4,000 control subjects were genotyped for founder mutations in BRCA1 (5382insC, 4153delA, C61G), CHEK2 (1100delC, IVS2+1G>A, del5395, I157T), NBS1 (657del5), and PALB2 (509_510delGA, 172_175delTTGT) genes. Results A statistically significant association was observed between the 172_175delTTGT mutation of the PALB2 gene and an increased risk of FPC syndrome (odds ratio [OR], 10.05; p=0.048). In addition, an increased risk of cancer was observed in the FPC family members with a BRCA1 mutation (OR, 6.72; p=0.006). Novel associations were found between the FPC family members with cancer and CHEK2mutations (OR, 2.26; p=0.008) with a noticeable contribution of the missense variant, I157T of CHEK2 (OR, 2.17; p=0.026). Conclusion The founder mutations in the genes, BRCA1, PALB2, and CHEK2, cause a small percentage of familial pancreatic cancer syndrome in the Polish population. Following confirmation in larger studies, these mutations can be added to the panel of genes to be tested in families with a diagnosis of FPC syndrome.

Incorporating Neutrophil-to-Lymphocyte Ratio and Platelet-to-Lymphocyte Ratio in Place of Neutrophil Count and Platelet Count Improves Prognostic Accuracy of the International Metastatic Renal Cell Carcinoma Database Consortium Model

Pawel Chrom,Rafal Stec,Lubomir Bodnar,Cezary Szczylik 대한암학회 2018 Cancer Research and Treatment Vol.50 No.1

Purpose The study investigated whether a replacement of neutrophil count and platelet count by neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) within the International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) model would improve its prognostic accuracy. Materials and Methods This retrospective analysis included consecutive patients with metastatic renal cell carcinoma treated with first-line tyrosine kinase inhibitors. The IMDC and modified-IMDC models were compared using: concordance index (CI), bias-corrected concordance index (BCCI), calibration plots, the Grønnesby and Borgan test, Bayesian Information Criterion (BIC), generalized R2, Integrated Discrimination Improvement (IDI), and continuous Net Reclassification Index (cNRI) for individual risk factors and the three risk groups. Results Three hundred and twenty-one patients were eligible for analyses. The modified-IMDC model with NLR value of 3.6 and PLR value of 157 was selected for comparison with the IMDC model. Both models were well calibrated. All other measures favoured the modified-IMDC model over the IMDC model (CI, 0.706 vs. 0.677; BCCI, 0.699 vs. 0.671; BIC, 2,176.2 vs. 2,190.7; generalized R2, 0.238 vs. 0.202; IDI, 0.044; cNRI, 0.279 for individual risk factors; and CI, 0.669 vs. 0.641; BCCI, 0.669 vs. 0.641; BIC, 2,183.2 vs. 2,198.1; generalized R2, 0.163 vs. 0.123; IDI, 0.045; cNRI, 0.165 for the three risk groups). Conclusion Incorporation of NLR and PLR in place of neutrophil count and platelet count improved prognostic accuracy of the IMDC model. These findings require external validation before introducing into clinical practice.

<i>Metschnikowia</i> cf. <i>typographi</i> and other pathogens from the bark beetle <i>Ips sexdentatus</i> – Prevalence, histological and ultrastructural evidence, and molecular characterization

Kleespies, Regina G.,Lim, Young Woon,Tkaczuk, Cezary,Wrzosek, Marta,Steinwender, Bernhardt M.,Wegensteiner, Rudolf Elsevier 2017 Journal of invertebrate pathology Vol.143 No.-

<P><B>Abstract</B></P> <P> <I>Ips sexdentatus</I> (six-spined engraver beetle) from Austria and Poland were dissected and examined for the presence of pathogens. Specimens collected in Austria were found to contain the ascomycetous fungus <I>Metschnikowia</I> cf. <I>typographi</I>. Infection rates ranged from 3.6% to 26.8% at different collection sites. <I>M.</I> cf. <I>typographi</I> infected midguts were investigated by histological, ultrastructural and molecular techniques. Extraordinary ultrastructural details are shown, such as ascospores with bilateral flattened flanks resembling alar rims at both sides of their attenuating tube-like ends. These have not yet been described in other yeast species. Molecular investigations showed a close phylogenetic relationship to the fungi <I>Metschnikowia agaves</I> and <I>Candida wancherniae</I>. Presence of the entomopathogenic fungus <I>Beauveria bassiana</I> found in Austria was confirmed both morphologically and molecularly. The eugregarine <I>Gregarina typographi</I> was diagnosed most frequently. Infection rates of all <I>I. sexdentatus</I> specimens ranged from 21.4% to 71.9% in Austria and 54.1% to 68.8% in Poland. Other entomopathogenic protists, bacteria, or viruses were not detected.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Prevalence of <I>Metschnikowia</I> cf. <I>typographi</I> in <I>Ips sexdentatus</I> is described. </LI> <LI> Extraordinary ultrastructural details of <I>M.</I> cf. <I>typographi</I> are shown first with TEM. </LI> <LI> Phylogenetic relationship of <I>M.</I> cf. <I>typographi</I> is presented. </LI> <LI> Close relationship to <I>Metschnikowia agaves</I> and <I>Candida wancherniae</I> is shown. </LI> <LI> <I>Gregarina typographi</I> was diagnosed most frequently in Austria and Poland. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

A Maximum-Likelihood Approach to Force-Field Calibration

Zaborowski, Bartłomiej,Jagieła, Dawid,Czaplewski, Cezary,Hałabis, Anna,Lewandowska, Agnieszka,Ż,mudziń,ska, Wioletta,Ołdziej, Stanisław,Karczyń,ska, Agnieszka,Omieczynski, Christian American Chemical Society 2015 JOURNAL OF CHEMICAL INFORMATION AND MODELING Vol.55 No.9

<P>A new approach to the calibration of the force fields is proposed, in which the force-field parameters are obtained by maximum-likelihood fitting of the calculated conformational ensembles to the experimental ensembles of training system(s). The maximum-likelihood function is composed of logarithms of the Boltzmann probabilities of the experimental conformations, calculated with the current energy function. Because the theoretical distribution is given in the form of the simulated conformations only, the contributions from all of the simulated conformations, with Gaussian weights in the distances from a given experimental conformation, are added to give the contribution to the target function from this conformation. In contrast to earlier methods for force-field calibration, the approach does not suffer from the arbitrariness of dividing the decoy set into native-like and non-native structures; however, if such a division is made instead of using Gaussian weights, application of the maximum-likelihood method results in the well-known energy-gap maximization. The computational procedure consists of cycles of decoy generation and maximum-likelihood-function optimization, which are iterated until convergence is reached. The method was tested with Gaussian distributions and then applied to the physics-based coarse-grained UNRES force field for proteins. The NMR structures of the tryptophan cage, a small α-helical protein, determined at three temperatures (<I>T</I> = 280, 305, and 313 K) by Hałabis et al. (J. Phys. Chem. B<x> </x>2012<x>, </x>116<x>, </x>6898−<lpage>6907</lpage>), were used. Multiplexed replica-exchange molecular dynamics was used to generate the decoys. The iterative procedure exhibited steady convergence. Three variants of optimization were tried: optimization of the energy-term weights alone and use of the experimental ensemble of the folded protein only at <I>T</I> = 280 K (run 1); optimization of the energy-term weights and use of experimental ensembles at all three temperatures (run 2); and optimization of the energy-term weights and the coefficients of the torsional and multibody energy terms and use of experimental ensembles at all three temperatures (run 3). The force fields were subsequently tested with a set of 14 α-helical and two α + β proteins. Optimization run 1 resulted in better agreement with the experimental ensemble at <I>T</I> = 280 K compared with optimization run 2 and in comparable performance on the test set but poorer agreement of the calculated folding temperature with the experimental folding temperature. Optimization run 3 resulted in the best fit of the calculated ensembles to the experimental ones for the tryptophan cage but in much poorer performance on the training set, suggesting that use of a small α-helical protein for extensive force-field calibration resulted in overfitting of the data for this protein at the expense of transferability. The optimized force field resulting from run 2 was found to fold 13 of the 14 tested α-helical proteins and one small α + β protein with the correct topologies; the average structures of 10 of them were predicted with accuracies of about 5 Å C<SUP>α</SUP> root-mean-square deviation or better. Test simulations with an additional set of 12 α-helical proteins demonstrated that this force field performed better on α-helical proteins than the previous parametrizations of UNRES. The proposed approach is applicable to any problem of maximum-likelihood parameter estimation when the contributions to the maximum-likelihood function cannot be evaluated at the experimental points and the dimension of the configurational space is too high to construct histograms of the experimental distributions.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jcisd8/2015/jcisd8.2015.55.issue-9/acs.jcim.5b00395/production/images/me

Ischemia-Driven Computed Tomography-Guided Revascularization of Chronic Total Occlusion Missed by Conventional Angiography

Maksymilian P. Opolski,Krzysztof Kotlinski,Jacek Wnuk,Cezary Kepka,Adam Witkowski 대한심장학회 2013 Korean Circulation Journal Vol.43 No.2

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field

Krupa, Paweł,Mozolewska, Magdalena A.,Joo, Keehyoung,Lee, Jooyoung,Czaplewski, Cezary,Liwo, Adam American Chemical Society 2015 Journal of chemical information and modeling Vol.55 No.6

<P>A new approach to the prediction of protein structures that uses distance and backbone virtual-bond dihedral angle restraints derived from template-based models and simulations with the united residue (UNRES) force field is proposed. The approach combines the accuracy and reliability of template-based methods for the segments of the target sequence with high similarity to those having known structures with the ability of UNRES to pack the domains correctly. Multiplexed replica-exchange molecular dynamics with restraints derived from template-based models of a given target, in which each restraint is weighted according to the accuracy of the prediction of the corresponding section of the molecule, is used to search the conformational space, and the weighted histogram analysis method and cluster analysis are applied to determine the families of the most probable conformations, from which candidate predictions are selected. To test the capability of the method to recover template-based models from restraints, five single-domain proteins with structures that have been well-predicted by template-based methods were used; it was found that the resulting structures were of the same quality as the best of the original models. To assess whether the new approach can improve template-based predictions with incorrectly predicted domain packing, four such targets were selected from the CASP10 targets; for three of them the new approach resulted in significantly better predictions compared with the original template-based models. The new approach can be used to predict the structures of proteins for which good templates can be found for sections of the sequence or an overall good template can be found for the entire sequence but the prediction quality is remarkably weaker in putative domain-linker regions.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jcisd8/2015/jcisd8.2015.55.issue-6/acs.jcim.5b00117/production/images/medium/ci-2015-00117f_0010.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ci5b00117'>ACS Electronic Supporting Info</A></P>