A simulated annealing-based maximum-margin clustering algorithm

© 2018 Wiley Periodicals, Inc. Maximum-margin clustering is an extension of the support vector machine (SVM) to clustering. It partitions a set of unlabeled data into multiple groups by finding hyperplanes with the largest margins. Although existing algorithms have shown promising results, there is no guarantee of convergence of these algorithms to global solutions due to the nonconvexity of the optimization problem. In this paper, we propose a simulated annealing-based algorithm that is able to mitigate the issue of local minima in the maximum-margin clustering problem. The novelty of our algorithm is twofold, ie, (i) it comprises a comprehensive cluster modification scheme based on simulated annealing, and (ii) it introduces a new approach based on the combination of k-means++ and SVM at each step of the annealing process. More precisely, k-means++ is initially applied to extract subsets of the data points. Then, an unsupervised SVM is applied to improve the clustering results. Experimental results on various benchmark data sets (of up to over a million points) give evidence that the proposed algorithm is more effective at solving the clustering problem than a number of popular clustering algorithms

Dynamics of the biodiversity of black and white cattle influenced by cross-breeding

The inter-breed crossing (crossbreeding) permits one to introduce new alleles, extend genetic diversity, and achieve desired phenotypic characteristics of initial breeds. On the other hand, crossbreeding may cause a decrease in genetic differentiation of indigenous breeds due to loss of the part of their unique allele pool. The objective of the present work was to investigate the effect of crossbreeding on the allele pool variability of Russian Black and White cattle by using 10 microsatellite loci (BM1818, BM2113, ETH10, ETH225, TGLA122, TGLA126, TGLA227, ILST005, ETH185, and ILST006). The study was performed with purebred pedigree bulls of the Russian Black and White breed (BW_PB, n = 14) and two groups of their crosses with Holsteins carrying 25,0–62,5 % (BW_KR1, n = 16) and less than 12,5 % of the Black and White gene pool (BW_KR2, n = 67). Purebred Holstein bulls (HOLST, n = 42) were used as a reference group. It was found that the increase in Holstein’s blood could lead to the observed decrease in genetic diversity evaluated by the average number of effective alleles per loci (from 4,59 ± 0,46 to 3,87 ± 0,53), by the value of the Shannon index (from 1,60 ± 0,13 to 1,46 ± 0,14) and by the observed heterozygosity degree (from 0,779 ± 0,053 to 0,687 ± 0,055). It is shown that crossbreeding with Holsteins increases the genetic similarity to HOLST: Fst = 0,058, 0,036, and 0,026; Rst = 0,088, 0,060, and 0,050; DNei = 0,306, 0,178, and 0,123 for BW_PB, BW_KR1, and BW_KR2, respectively. Decrease in the genetic difference between the Black and White breed and Holsteins due to crossbreeding is confirmed by cluster analysis. Thus, evaluation of the allele pool and the level of genetic variability in populations are necessary for the efficient management of farm animal genetic recourses

Single - particle correlations in events with the total disintegration of nuclei

New experimental data on the behaviour of the single-particle two-dimensional correlation functions R versus Q (Q is the number of nucleons emitted from nuc- lei) and Ap (Ap is the mass of projectile nuclei) are presented in this paper. The interactions of protons, d, 4He and 12C nuclei with carbon nuclei (at a momentum of 4.2 A GeV/c) are considered.The values of R are obtained separately for pi minus mesons and protons.In so doing,the values of R are normalized so that -1=<R=<1.The value of R=0 corresponds to the case of the absence of corre- lations.It has been found that the Q- and Ap-dependence of R takes place only for weak correlations (R< 0.3).In the main (90 %),these correlations are con- nected with the variable pt and have a nonlinear character, that is the regi- ons with different characters of the Q-dependence of R are separated: there is a change of regimes in the Q-dependences of R.The correlations weaken with increasing Ap, and the variable R gets the least values of all the considered ones in 12CC interactions.Simultaneously with weakening the correlations in the region of large Q, the character of the Q-dependence of R changes.Comment: 17 pages, submitted to Phys. Rew.

Chromosome synapsis, recombination and epigenetic modification in rams heterozygous for metacentric chromosome 3 of the domestic sheep Ovis aries and acrocentric homologs of the argali Ovis ammon

Hybridization of domestic animal breeds with their wild relatives is a promising method for increasing the genetic diversity of farm animals. Resource populations derived from the hybridization of various breeds of domestic sheep with mouflon and argali are an important source of breeding material. The karyotypes of argali and domestic sheep differ for a Robertsonian translocation, which occurred in the common ancestor of mouflon and domestic sheep (Ovis aries) due to the centric fusion of chromosomes 5 and 11 of the argali (O. ammon) into chromosome 3 of sheep. It is known that heterozygosity for translocation can lead to synapsis, recombination and chromosome segregation abnormalities in meiosis. Meiosis in the heterozygotes for translocation that distinguishes the karyotypes of sheep and argali has not yet been studied. We examined synapsis, recombination, and epigenetic modification of chromosomes involved in this rearrangement in heterozygous rams using immunolocalization of key proteins of meiosis. In the majority of cells, we observed complete synapsis between the sheep metacentric chromosome and two argali acrocentric chromosomes with the formation of a trivalent. In a small proportion of cells at the early pachytene stage we observed delayed synapsis in pericentromeric regions of the trivalent. Unpaired sites were subjected to epigenetic modification, namely histone H2A.X phosphorylation. However, by the end of the pachytene, these abnormalities had been completely eliminated. Asynapsis was replaced by a nonhomologous synapsis between the centromeric regions of the acrocentric chromosomes. By the end of the pachytene, the γH2A.X signal had been preserved only at the XY bivalent and was absent from the trivalent. The translocation trivalent did not differ from the normal bivalents of metacentric chromosomes for the number and distribution of recombination sites as well as for the degree of centromeric and crossover interference. Thus, we found that heterozygosity for the domestic sheep chromosome 3 and argali chromosomes 5 and 11 does not cause significant alterations in key processes of prophase I meiosis and, therefore, should not lead to a decrease in fertility of the offspring from interspecific sheep hybridization

Genomic assessment and phenotypic characteristics of F2 resource sheep population

The article presents the results of assessment of genetic diversity and Principal Component Analysis (PCA) in the re-source sheep population, originated from crossing of fast-growing (Katahdin) and slow growing (Romanov) breeds for QTL mapping and search for candidate genes associated with growth rate. The study was conducted on 88 sheep from the resource population, including two unrelated families that have been reared in the Moscow region since 2017. Each family consists of a Katahdin ram (founder), Romanov’s ewes (mothers), F1 hybrids, and two groups of backcrosses. All sheep were genotyped using a high-density DNA chip Illumina Ovine Infinium® HD SNP BeadChip (~ 600 thousand SNP markers). SNP markers were filtered in the PLINK v.1.90. PCA was performed in PLINK v.1.90 and visualized in R package ggplot2. The genetic diversity indices (Ho, uHe, Ar, FIS) were calculated in R package “diveRsity”. It was established that both crosses had higher level of genetic diversity in comparison with the mother breed. F1 hybrids were characterized by the highest level of observed heterozygosity (Ho = 0.409-0.407), while Ho ranged from 0.382 to 0.396 for the backcrosses, respectively. The expected heterozygosity ranged from 0.329 to 0.356 in the groups from the resource population. Allelic richness was high in all studied groups (more than 1.849). PCA showed that the mated parent breeds were highly differentiated, as it should be in successful establishment of the resource population. The phenotypic characteristic of the backcrosses on live weight and nine body measurements at 9, 42 and 90 days is given. The coefficients of variation were the highest by live weight (17.0-19.0%), body length (15.5-22.3%) and oblique body length (16.2% and 22.7%) at 90 days. The results are intermediate and create a geno-typic and phenotypic base to perform GWAS at the next stage of our study

ЭФФЕКТИВНОСТЬ ЭКСТРАПЛЕВРАЛЬНОЙ ПЛОМБИРОВКИ СИЛИКОНОВЫМ ИМПЛАНТОМ У БОЛЬНЫХ ДЕСТРУКТИВНЫМ ТУБЕРКУЛЕЗОМ ЛЕГКИХ И ЕЕ ВЛИЯНИЕ НА ФУНКЦИОНАЛЬНОЕ СОСТОЯНИЕ ЛЕГКИХ И ГАЗОВЫЙ СОСТАВ КРОВИ

The objective of the study: to analyze the efficacy of extrapleural plombage with silicone plug (EPSP) in those suffering from destructive pulmonary tuberculosis with multiple/extensive drug resistance (M/XDR) and to assess EPSP impact on pulmonary functions and blood gases. Subjects and methods. 34 patients with chronic persistent destructive pulmonary tuberculosis who underwent EPSP were enrolled in the study. 23 were men and 11 were women at the age from 18 to 54 years old (the median age made 36.29± 10.2 years). MDR was diagnosed in 31/34 (91.2%) patients, and of them, 22/31 (70.0%) had XDR. A high profile life long breast implants with texturized coating causing no rejection by the host were used for extrapleural plombage. Results. 18 patients who underwent EPSP as a single surgery had their cavities healed in the operated lung in 100% of cases (95% CI 96.3-100%). There were no lethal outcomes. 1/18 (5.6%) patient suffered from a late complication (empyema) related to EPSP. Postponed outcomes of tuberculosis treatment (effective course of treatment after EPSP) were favorable in 13/16 (81.3%; 95% CI 57.0-93.4%) patients. In 11 patients with disseminated destructive tuberculosis who had EPSP combined with resection or collapse surgery, 12/12 (100%; 95% CI 75.8-100%) had their cavities healed in the operated lung; 2/12 patients needed additional bronchial valve block. Surgeries for EPSP resulted in no lethal outcomes or complications. In 5 patients with destructive tuberculosis relapse in the only lung, EPSP was used to stop the progress of the disease due to poor efficacy of chemotherapy. The impact on cavities healing in the operated lung was achieved in 4/5 (80.0%; 95% CI (37.6-96.3%) patients. The complication after EPSP was observed in у 1/5 (20.0%) patient and resulted in the lethal outcome. 3/5 patients had favorable postponed outcomes. After EPSP, ventilation and gas exchange functions deteriorated in 32% of patients, while in 28% of patients, they improved. The intensity of change was moderate or significant. The most dynamic and informative indicators were the vital capacity of the lungs and the partial tension of oxygen in oxygenated blood (PaO2 ).Цель исследования: проанализировать эффективность операции экстраплевральной пломбировки силиконовым имплантом (ЭПСИ) у больных деструктивным туберкулезом легких с множественной/широкой лекарственной устойчивостью (МЛУ/ШЛУ), изучить влияние операции на функциональное состояние легких и газовый состав крови. Материалы и методы. В исследование включено 34 пациента с хронически текущим длительно леченным деструктивным туберкулезом легких, которым выполнена ЭПСИ. Мужчин было 23, женщин ‒ 11, их возраст от 18 до 54 лет (средний возраст ‒ 36,29 ± 10,2 года). МЛУ микобактерий туберкулеза (МБТ) диагностировали у 31/34 (91,2%) пациента, из них у 22/31 (70,0%) была ШЛУ МБТ. При экстраплевральной пломбировке использовали имплант молочной железы высокого профиля с текстурированной оболочкой, предназначенный для пожизненного нахождения в организме человека и не вызывающий реакцию отторжения. Результаты. У 18 пациентов, у которых ЭПСИ выполнялась как единственная операция, эффект по закрытию полостей распада в легком на стороне операции достигнут в 100% (95%-ный ДИ 96,3-100%) случаев. Летальных случаев не было. Позднее осложнение (эмпиема), связанное с операцией ЭПСИ, имело место у 1/18 (5,6%) пациента. Отдаленные результаты лечения туберкулеза (эффективный курс химиотерапии после ЭПСИ) были хорошими у 13/16 (81,3%; 95%-ный ДИ 57,0-93,4%). У 11 пациентов с распространенным деструктивным туберкулезом, у которых ЭПСИ проведена в сочетании с резекционными или КХО, эффект по закрытию полостей распада в легком на стороне операции достигнут в 12/12 случаях (100%; 95%-ный ДИ 75,8-100%), в 2/12 случаях понадобилось дополнительное воздействие клапанной бронхоблокации. Летальности в результате операции ЭПСИ не было, так же как и осложнений. У 5 пациентов с рецидивом деструктивного туберкулеза в единственном легком ЭПСИ применяли для ликвидации прогрессирования процесса при недостаточном эффекте химиотерапии. Эффект по закрытию полостей распада в легком на стороне операции достигнут у 4/5 (80,0%; 95%-ный ДИ (37,6-96,3%). Осложнение после ЭПСИ было у 1/5 (20,0%) пациента и закончилось летальным исходом. Отдаленные результаты оказались хорошими у 3/5 пациентов. После операции ЭПСИ ухудшение и улучшение вентиляционной и газообменной функции наблюдали у 32 и 28% пациентов соответственно. Выраженность сдвигов имела умеренную или значительную степень. Наиболее динамичными и информативными показателями являлись жизненная емкость легких и парциальное напряжение кислорода в артериализованной крови (PaO2 )

Suitability and managerial implications of a Master Surgical Scheduling approach

Abstract: Operating room (OR) planning and scheduling is a popular and challenging subject within the operational research applied to health services research (ORAHS). However, the impact in practice is very limited. The organization and culture of a hospital and the inherent characteristics of its processes impose specific implementation issues that affect the success of planning approaches. Current tactical OR planning approaches often fail to account for these issues.Master surgical scheduling (MSS) is a promising approach for hospitals to optimize resource utilization and patient flows. We discuss the pros and cons of MSS and compare MSS with centralized and decentralized planning approaches. Finally, we address various implementation issues of MSS and discuss its suitability for hospitals with different organizational foci and culture

AN INCREMENTAL NONSMOOTH OPTIMIZATION ALGORITHM FOR CLUSTERING USING L1 AND L? NORMS

2-s2.0-85096898399An algorithm is developed for solving clustering problems with the similarity measure defined using the L1and L? norms. It is based on an incremental approach and applies nonsmooth optimization methods to find cluster centers. Computational results on 12 data sets are reported and the proposed algorithm is compared with the X-means algorithm. © 2020, JOURNAL OF INDUSTRIAL AND JOURNAL OF INDUSTRIAL ANDChongqing Normal University, CNU Australian Government Australian Research Council, ARC: DP190100580The authors would like to thank two anonymous referees for their comments that helped to improve the quality of the paper. This research by Dr. A. Bagirov was funded by the Australian Government through the Australian Research Council?s Discovery Projects scheme (Project No.: DP190100580). The paper was completed when Dr. A. Bagirov visited Chongqing Normal University, China.Acknowledgements. The authors would like to thank two anonymous referees for their comments that helped to improve the quality of the paper. This research by Dr. A. Bagirov was funded by the Australian Government through the Australian Research Council’s Discovery Projects scheme (Project No.: DP190100580). The paper was completed when Dr. A. Bagirov visited Chongqing Normal University, China