Number Of Subpopulations Research Articles

<p><strong><em>Pouteria</em></strong><strong> <em>kossmanniae</em> (Sapotaceae): a new species from Central Amazonia, Brazil</strong></p>

Pouteria kossmanniae (Sapotaceae, Chrysophylloideae), a new species from Central Amazonia, is here described. It is known from the Manaus region, Amazonas, Brazil, and is found in non-flooded upland forests, known as terra firme. Illustrations are provided in addition to geographic distribution, with a comparison of the morphological and spectral (near-infrared) differences between P. kossmanniae and its very similar species Pouteria macrophylla, Pouteria manaosensis, and Pouteria rodriguesiana. The species is naturally common in some urban forest fragments, but since only a low number of subpopulations is known, we assign P. kossmanniae the preliminary conservation status of “Endangered”.

Половые различия морфофункциональных изменений иммунной системы у крыс Вистар разных возрастных групп при экспериментальной эндотоксинемии

Objective. The aim was revealing gender differences in morphological and functional changes of lymphoid organs (thymus and spleen), changes of cytokine production and subpopulation composition of peripheral blood lymphocytes in Wistar rats of three age groups with endotoxemia. Materials and methods. We used male and female Wistar rats of three age groups: newborns, prepubertal and sexually mature adult rats. A day after the injection of 15 mg/kg of O26:B6 E. coli lipopolysaccharide (LPS), the volume fraction of the functional zones of the thymus and spleen, the number of AnnexinV + apoptotically dying cells in the thymus, the relative and absolute number of lymphocyte subpopulations (CD3+CD4+, CD3+CD8a+, CD4+CD25+Foxp3+, CD3-CD45R+) in peripheral blood and ex vivo production of IL-2, IL-4, IFN-γ and TNF-α were estimated. Results. Sex differences in the response of the immune system after the LPS injection in different age periods are expressed differently: in the neonatal period, there is immunosuppression in females (decrease in the ex vivo production of IL-2, TNF-α and IFN-γ), and there is activation of pro-inflammatory reactions in males (increase in ex vivo production of IL-2 and TNF-α). As compared with other age periods at prepubertal age, LPS-induced immunological disorders are more pronounced, and gender differences are minimal and related only to the number of T-regulatory and B-lymphocytes. In the adults, the LPS-induced immunosuppression is most pronounced in males - they have a decrease in the production of all the cytokines studied and a decrease in the number of cytotoxic and regulatory T-lymphocytes and B-cells. Conclusion. Thus, in each of the studied age periods - newborn, prepubertal and adult, the sexual differences in the immune system reactions are expressed differently and, apparently, these differences are determined by the content of sex steroid hormones, the concentration of which varies with age.

Multi-population genetic algorithm with ER network for solving flexible job shop scheduling problems.

A genetic algorithm (GA) cannot always avoid premature convergence, and multi-population is usually used to overcome this limitation by dividing the population into several sub-populations (sub-population number) with the same number of individuals (sub-population size). In previous research, the questions of how a network structure composed of sub-populations affects the propagation rate of advantageous genes among sub-populations and how it affects the performance of GA have always been ignored. Therefore, we first propose a multi-population GA with an ER network (MPGA-ER). Then, by using the flexible job shop scheduling problem (FJSP) as an example and considering the total individual number (TIN), we study how the sub-population number and size and the propagation rate of advantageous genes affect the performance of MPGA-ER, wherein the performance is evaluated by the average optimal value and success rate based on TIN. The simulation results indicate the following regarding the performance of MPGA-ER: (i) performance shows considerable improvement compared with that of traditional GA; (ii) for an increase in the sub-population number for a certain TIN, the performance first increases slowly, and then decreases rapidly; (iii) for an increase in the sub-population size for a certain TIN, the performance of MPGA-ER first increases rapidly and then tends to remain stable; and (iv) with an increase in the propagation rate of advantageous genes, the performance first increases rapidly and then decreases slowly. Finally, we use a parameter-optimized MPGA-ER to solve for more FJSP instances and demonstrate its effectiveness by comparing it with that of other algorithms proposed in other studies.

Stability and Instability of Steady States for a Branching Random Walk

We consider the time evolution of a lattice branching random walk with local perturbations. Under certain conditions, we prove the Carleman type estimation for the moments of a particle subpopulation number and show the existence of a steady state.

Optimal Design in Hierarchical Random Effect Models for Individual Prediction with Application in Precision Medicine

Hierarchical random effect models are used for different purposes in clinical research and other areas. In general, the main focus is on population parameters related to the expected treatment effects or group differences among all units of an upper level (e.g. subjects in many settings). Optimal design for estimation of population parameters are well established for many models. However, optimal designs for the prediction for the individual units may be different. Several settings are identified in which individual prediction may be of interest. In this paper, we determine optimal designs for the individual predictions, e.g. in multi-cluster trials or in trials that investigate a new treatment in a number of different subpopulations, and compare them to a conventional balanced design with respect to treatment allocation. Our investigations show that in the case of uncorrelated cluster intercepts and cluster treatments the optimal allocations are far from being balanced if the treatment effects vary strongly as compared to the residual error and more subjects should be recruited to the active (new) treatment. Nevertheless, efficiency loss may be limited resulting in a moderate sample size increase when individual predictions are foreseen with a balanced allocation.

Is the USDA core collection of common bean representative of genetic diversity of the species, as assessed by SNP diversity?

AbstractCore collections are envisioned to be a representative subset of larger germplasm collections. They were introduced to facilitate the characterization and use of these germplasm collections. The common bean (Phaseolus vulgaris L.) core collection of the USDA Western Regional Plant Introduction Station was one of the first collections to be established in the early 1990s. Here, we evaluate the representativity of this common bean collection in light of the availability of a single nucleotide polymorphism (SNP) platform and new information about genetic diversity of the species, including phaseolin and seed type data. The SNP diversity was studied with a combination of STRUCTURE, principal coordinate analysis (PCoA), and neighbor‐joining analysis (NJA). STRUCTURE analyses were conducted for K (number of subpopulations) = 3 and K = 7, based on the ad hoc statistic ΔK. The K = 3 analysis recognized the split between Andean and Mesoamerican domesticates and the subdivision of the Mesoamerican domesticates into high‐ (Durango/Jalisco) and low‐altitude (Mesoamerica) ecogeographic races. The K = 7 analysis further subdivided the Andean group identified for K = 3, as well as the high‐altitude group from the Mesoamerican gene pool. It also identified smaller groups consisting of Mesoamerican wild beans. The PCoA and NJA confirmed the STRUCTURE results and highlighted the existence of presumed hybridization among groups. Our results suggest that this core collection should be updated by adding domesticated categories, developing a separate wild common bean core collection, and developing cores for specific purposes.

Research Note: Effect of age on the distribution of lymphocytes in the oviduct in Turkey breeder hens

Considering the lack of research on the local immunity of the reproductive tract in other poultry species than chickens, the aim of this study was to determine the contribution of T and B cell subpopulations in different parts of breeder turkey oviduct mucous membrane with the use of flow cytometry. In addition, the study aimed to establish an impact of bird age and different stages of the egg production cycle on the systemic and local oviduct-related immune system structure. Our study results demonstrated a lower percentage of T lymphocytes in 32-wk turkey hens followed by a successively increasing population of these cells up to the 38th week of bird's life. The results of our study have also shown a similar dependency between birds' age and number of B lymphocytes. In addition, we demonstrated a decrease in the number of immune system cells in the oviduct, blood, and spleen of turkey hens in the late and end laying period. The differences reported in the number of lymphocyte subpopulations in the reproductive system of laying turkey hens at various stages of the production cycle may, to some extent, explain the frequency and periods of increased predilection to the incidence of infectious diseases in birds under field conditions.

Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections.

Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America–Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date.

Optimal control on the mathematical models of dengue epidemic by giving vaccination and repellent strategies

Dengue is a very dangerous disease in the tropic and subtropic areas. This disease is transmitted through the bite of an infected female Aedes Aegypti. In this study, optimal control of the dengue model will be discussed by applying 3 strategies, there are vaccination, repellent, and both of them. A dengue epidemic model was built without control with assumptions given by facts obtained by researchers. Then from the model, the equilibrium point is formulated and the equilibrium point stability of the model is evaluated. The next discussion is to determine the optimal control of the dengue epidemic model and minimize the costs of implementing controls. Numerical simulation results showed that 3rd strategy, which is vaccination and repellent, can reduce the subpopulations number of humans infected by dengue with the minimum cost of implementing control.

Island-based Crow Search Algorithm for solving optimal control problems

Crow Search Algorithm (CROW) is one of the members of recently developed swarm-based metaheuristic algorithms. Literature includes different applications of this algorithm on engineering design problems. However, this optimization method suffers from some drawbacks such as premature convergence and trapping into local optima at the early phase of iterations. In order to conquer this algorithm specific inabilities, many research studies have been conducted in the literature dealing with the improvements and enhancements on the search mechanism of CROW. Structured population mechanism plays a vital role in preserving and controlling diversity, and thus increases the solution efficiency in evolutionary algorithms. Among the different types of methods used in structured algorithms, the island model is one of the widely applied solution strategies, in which the population individuals are subdivided into a predefined number of subpopulations. Migration mechanism is the key factor increasing population diversity, which takes place between independently running subpopulations during iterations to exchange valuable and useful solution information. This study embeds the fundamentals of the island model concepts into the Crow Search Algorithm to improve its probing capabilities of the search domain, by means of the periodically interacting subpopulations on the course of iterations. In addition, four different hierarchical migration topologies have been proposed, and their search effectiveness have been evaluated and compared over 45 optimization test functions. The optimization function test set includes classic benchmark optimization problems and CEC 2015 benchmark functions. Furthermore, each hierarchical island model is applied for solving six different optimal control problems in order to investigate their efficiencies on multi-dimensional real world optimization problems. The investigated optimal control problems are parallel reaction, continuous stirred tank reactor, batch reactor consecutive reaction, nonlinear constrained mathematical system, nonlinear continuous stirred tank reactor and nonlinear crane container problems. It is found out that the island model concepts improved the optimization performance of CROW. The proposed island models outperformed or showed similar performance compared to the six selected literature optimizers for 27–29 classic benchmark optimization problems. Moreover, incorporating the master sub-population to the island model improved the optimization capability of the algorithm further in most cases. The island models that employ the master sub-population came up with more favorable results compared to their non-master sub-population peers in all optimal control problems. The island model that includes the master sub-population and has the migration topology entitled “82” found the most desirable solutions for 4–6 optimal control problems.

Subpopulation initialization driven by linkage learning for dealing with the Long-Way-To-Stuck effect

The maintenance of many subpopulations is an important technique employed in evolutionary methods. However, the use of a multi-population approach has its drawbacks. Among all, it requires spending high amounts of available resources. Therefore, the methods that dynamically manage the number of subpopulations gain an increasing interest due to their capability of adjusting the subpopulation number to their current state. They are shown to be capable of reaching excellent results. In this paper, we identify the Long-Way-To-Stuck effect and show it on the base of the practical, NP-complete problem. Such a phenomenon occurs when a randomly initialized population of an evolutionary method must be processed through many iterations before it is incapable of improving the best-found solution. If so, then a large amount of computational resources must be spent on subpopulation initialization, which may turn multi-population methods ineffective. Therefore, in this paper, we propose the Linkage Learning-Driven Subpopulation Initialization (LLDSI) that limits the costs of subpopulation initialization and significantly improves the effectiveness methods dynamically managing the subpopulation number.

Research on the performance of multi-population genetic algorithms with different complex network structures

Genetic algorithm is a frequently used evolutionary algorithm that cannot avoid premature convergence. Multi-population is usually used to overcome this disadvantage, obtaining multi-population genetic algorithm (MGA). If sub-populations and communications among them are considered as nodes and edges, respectively, an MGA can be represented as a complex network. After reviewing previous researches, we find that the network structures used to design MGAs are limited and some parameters (SPS, sub-population size, and SPN, sub-population number) under a certain total individual number (TIN) are always ignored. Using seven network structures (BAnet, BDnet, CTnet, ERnet, HAnet, LCnet, and SWnet) to design MGAs that are used to solve some flexible job shop scheduling problems, how the network structures and parameters affect the performances of MGAs is addressed. The simulation results indicate that: (i) the MGA with ERnet rather than the famous BAnet often performs well although their performances are problem-dependent; (ii) the Hamming distance index proposed here can properly capture the phenomenon that the smaller the average path length, the higher the propagation rate; and (iii) under a certain TIN, their performances first increase and then decrease gradually as SPN increases, and their performances first increase rapidly and then remain almost unchanged as SPS increases.

Effects of gene–environment and gene–gene interactions in case-control studies: A novel Bayesian semiparametric approach

Present day bio-medical research is pointing towards the fact that cognizance of gene–environment interactions along with genetic interactions may help prevent or detain the onset of many complex diseases like cardiovascular disease, cancer, type2 diabetes, autism or asthma by adjustments to lifestyle. In this regard, we propose a Bayesian semiparametric model to detect not only the roles of genes and their interactions, but also the possible influence of environmental variables on the genes in case-control studies. Our model also accounts for the unknown number of genetic sub-populations via finite mixtures composed of Dirichlet processes. An effective parallel computing methodology, developed by us harnesses the power of parallel processing technology to increase the efficiencies of our conditionally independent Gibbs sampling and Transformation based MCMC (TMCMC) methods. Applications of our model and methods to simulation studies with biologically realistic genotype datasets and a real, case-control based genotype dataset on early onset of myocardial infarction (MI) have yielded quite interesting results beside providing some insights into the differential effect of gender on MI.

Dynamic changes in peripheral type II innate lymphoid cell (ILC2) subpopulation and its clinical significance in children with hay fever during the pollen season

Objective To analyze the dynamic changes in the expression and function of peripheral type Ⅱ innate lymphoid cell (ILC2) subpopulation and the activity of signal transducers and activators of transcription (STAT6) in children with hay fever during pollen season. Methods A total of 10 patients with hay fever, 10 patients with house dust mite (HDM)-sensitized asthma and 12 healthy controls (HC) were enrolled in this study. Changes in peripheral ILC2 and the intracellular expression of Th2-related cytokines were detected by flow cytometry during and outside the pollen season. Peripheral Lin- cell population was isolated from each group and cultured with the presence of IL-25 or IL-33 for 7 d. The concentrations of IL-5 and IL-13 in culture supernatants were measured by ELISA. Expression of phospho-STAT6 at protein level was quantified by Western blot. Results Within the pollen season, the percentage of peripheral ILC2 cells was significantly higher in children with hay fever [(23.09±7.86)%] than in children with HDM-sensitized asthma [(6.84±3.85)%, P<0.05] and healthy children[(1.69±0.87)%, P<0.05]. In the non-pollen season, the peripheral ILC2 cells in children with hay fever presented a decreasing trend [(11.30±2.45)%], but was still higher than that in HDM-sensitized asthmatics [(3.76±1.96)%, P<0.05] and HC [(1.32±0.91)%, P<0.05] at the same time point. Moreover, peripheral IL-13+ ILC2 cells in children with hay fever [(6.94±3.16)% vs(4.17±1.98)%, P<0.05] and in HDM-sensitized asthmatics [(1.89±0.70)% vs(1.44±0.55)%, P<0.05] during the pollen season were significantly higher than those in the non-pollen season. After the in vitro stimulation with IL25 or IL-33, the levels of IL-5 and IL-13 in culture supernatants were both increased in children with hay fever and HDM-sensitized asthmatics, and a synergistic action was observed when IL25 and IL-33 were used in combination. Meanwhile, the protein level of phospho-STAT4 in Lin- cells was significantly up-regulated in the hay fever group after stimulation with IL25 and IL-33. Conclusions During the pollen season, the abnormal number and function of ILC2 subpopulation in children with hay fever might be another cause of the occurrence of clinical symptoms in a short period of time or acute exacerbation. Key words: Hay fever; House dust mite; Artemisia; Signal transducer and activator of transcription 6; Type Ⅱ innate lymphocyte cells

Coronary Progenitor Cells and Soluble Biomarkers in Cardiovascular Prognosis after Coronary Angioplasty

Major adverse cardiovascular events (MACEs) negatively impact the cardiovascular prognosis of patients undergoing coronary angioplasty due to coronary ischemic injury. The extent of coronary damage and the mechanisms of vascular repair are factors influencing the future development of MACEs. Intrinsic vascular features like the plaque characteristics and coronary artery complexity have demonstrated prognostic information for MACEs. However, the use of intracoronary circulating biomarkers has been postulated as a convenient method for the early identification and prognosis of MACEs, as they more closely reflect dynamic mechanisms involving coronary damage and repair. Determination of coronary circulating biomarkers during angioplasty, such as the number of subpopulations of mononuclear progenitor cells (MPCs) as well as the concentration of soluble molecules reflecting inflammation, cell adhesion, and repair, allows for assessment of future developments and the prognosis of MACEs 6 months post coronary angioplasty. This method is highlighted by its translational nature and better performance than peripheral blood circulating biomarkers regarding prediction of MACEs and its effect on the cardiovascular prognosis, which may be applied for risk stratification of patients with coronary artery disease undergoing angioplasty.

Self-adaptive Multi-population Rao Algorithms for Engineering Design Optimization

ABSTRACTThe performance of various population-based advanced optimization algorithms has been significantly improved by using the multi-population search scheme. The multi-population search process improves the diversity of solutions by dividing the total population into a number of sub-populations groups to search for the best solution in different areas of a search space. This paper proposes improved optimization algorithms based on self-adaptive multi-population for solving engineering design optimization problems. These proposed algorithms are based on Rao algorithms which are recently proposed simple and algorithm-specific parameter-less advanced optimization algorithms. In this work, Rao algorithms are upgraded with the multi-population search process to enhance the diversity of search. The number of sub-populations is changed adaptively considering the strength of solutions to control the exploration and exploitation of the search process. The performance of proposed algorithms is investigated on 25 unconstrained benchmark functions and 14 complex constrained engineering design optimization problems. The results obtained using proposed algorithms are compared with the various advanced optimization algorithms. The comparison of results shows the effectiveness of proposed algorithms for solving engineering design optimization problems. The significance of the proposed methods has proved using a well-known statistical test known as “Friedman test.” Furthermore, the convergence plots are illustrated to show the convergence speed of the proposed algorithms.

Characterizing Magnetic Reconnection Regions Using Gaussian Mixture Models on Particle Velocity Distributions

Abstract We present a method based on unsupervised machine learning to identify and characterize regions of interest using particle velocity distributions as a signature pattern. An automatic density estimation technique is applied to particle distributions provided by particle-in-cell simulations to study magnetic reconnection regions. Its application to magnetic reconnection is new. The key components of the method involve (i) a Gaussian mixture model determining the presence of a given number of subpopulations within an overall population, and (ii) a model selection technique with a Bayesian information criterion to estimate the appropriate number of subpopulations. Thus, this method automatically identifies the presence of complex distributions, such as beams or other non-Maxwellian features, and can be used as a detection algorithm able to identify reconnection regions. The approach is demonstrated for a specific double Harris sheet simulation, but it can in principle be applied to any other type of simulation data on the particle distribution function.

Unveiling the pathophysiology of gestational diabetes: Studies on local and peripheral immune cells.

Gestational diabetes mellitus (GDM) has been associated with impaired maternal immune response. Our aim was to review the available literature linking immune cells profile to GDM, in order to comprehend the role that different subpopulations play in the development of this pathology. We searched in PubMed for studies published in the last decade on circulating levels and placenta expression of immune cells on GDM. We identified 18 studies with several differences regarding the study design, clinical characteristics, number of participants, cell subpopulation and type of sample. Most studies assessed only one subpopulation either in peripheral blood or placenta and did not analyse functional properties of the cells. The most frequently evaluated immune cells were T lymphocytes, especially regulatory T (Tregs), and natural killer (NK) cells in the peripheral blood, and placental macrophages. No studies analysing B cells were identified, and only one study each evaluating γδT cells, dendritic cell (DC) and monocytes was found. Although there are controversies, at least one study reported positive association between GDM and CD4+ (activated), Tregs, Th17 and γδT cells; neutrophil/lymphocyte; NK cell (cytotoxic); macrophages; and monocytes. The number of studies is still small, so caution should be exercised in interpreting the data, and further research is required to validate these findings and establish the role of adaptive and innate immune cells in GDM pathophysiology.

Myeloid-derived suppressor cells in secondary sepsis: Is there an association with lethal outcome?

Background/Aim. Role of myeloid-derived suppressor cells (MDSCs) in human host response to sepsis still needs to be clarified. The aim of our study was to determine whether frequency and/or absolute numbers of the MDSCs were associated with outcome in critically ill patients with secondary sepsis and/or septic shock. Methods. Total of 40 critically ill patients with secondary sepsis were enrolled in a prospective study. We detected and enumerated both main subsets of MDSCs: granulocytic (G)-MDSCs and monocytic (M)- MDSCs on the Day 1 (the day of hospital admission) and the Day 5 after the. The primary end-point was hospital mortality. Results. Increased frequencies and absolute numbers of subpopulations corresponding to MDSCs were associated with poor outcome. As far as relative kinetics was concerned, in both survivors and non-survivors, sepsis duration from 1th to 5th day was accompanied by an increase in MDSCs values of both investigated subpopulations. In contrast to findings of stepwise multivariate logistic regression analysis of the variables on the Day 1, on the Day 5 it was determined that the Sequential Organ Failure Assessment (SOFA) score (OR 2.350; p &lt; 0.05) and G-MDSCs frequencies (OR 3.575; p &lt; 0.05) were independent predictors of lethal outcome. Conclusion. These findings suggest harmful role of MDSCs in secondary sepsis.

Subsets of T regulatory cells in patients with IgE-mediated allergy

Background. It is presently known that several subsets of T-regulatory (Treg) cells, both natural and inducible maintain tolerance to environmental allergens. But the relative importance of distinct phenotypically defined Treg subsets for the clinical manifestations of IgE-mediated allergy has not been elucidated yet.The aim of the study was to investigate the phenotype and number of different Treg subpopulations from patients with IgE-mediated allergy compared with healthy non-allergic individuals.Materials and methods. A group of 20 patients with clinically manifested IgE allergy and a group of 10 healthy no allergic controls were included in the study. Peripheral blood samples were taken after informed consent. Percentage and absolute count (AC) of the following regulatory subsets: naive (CD45RO-FoxP3lo), memory (RO+FoxP3+), effector (Treg eff, RO+FoxP3hi), induced (CD39+CD134+), Thl7/Treg (CD196+FoxP3+CD4Treg); Tr1 (IL-10+FoxP3-), were determined using standard 8-parameter flow cytometry (BD FACSCanto II).Results and discussion. The share and AC of FoxP3+CD4 Treg was significantly decreased in sensitized patients as compared to controls (mean 0,6% vs. 3,3%, p0.05 and 8,7 vs. 55 cells/μl p0.001). In addition, a significantly decreased level of Tr1 cells was observed in the patients with allergy, 0,4% vs. 2,1 % in healthy controls (p0,05) as well for subset of Thl7/Treg (mean 7,7% vs. 28,4% in healthy persons, p0.01).Conclusion. The significantly decreased number of FoxP3+CD4 Treg as well as periphery induced Tr1 and Thl7/Treg cells in patients with respiratory allergy lead to dysregulation and loss of peripheral immune tolerance, which is the pathophysiological basis for development of widely spread allergic diseases like allergic rhinitis and bronchial asthma.