Set-based particle swarm optimization applied to the multidimensional knapsack problem

Particle swarm optimization algorithms have been successfully applied to discrete/valued optimization problems. However, in many cases the algorithms have been tailored specifically for the problem at hand. This paper proposes a generic set-based particle swarm optimization algorithm for use in discrete-valued optimization problems that can be formulated as set-based problems. A detailed sensitivity analysis of the parameters of the algorithm is conducted. The performance of the proposed algorithm is then compared against three other discrete particle swarm optimization algorithms from literature using the multidimensional knapsack problem and is shown to statistically outperform the existing algorithms.     

Mucilage secretion: an adaptive mechanism to reduce seed removal by soil erosion?

Diaspores of many plant species inhabiting open vegetation in semi‐arid environments secrete mucilage after wetting (myxospermy) that glues the diaspores to the ground and prevents movement when the mucilage dries. In the present study, we test whether mucilage secretion can be considered as a selective response to soil erosion in plant species inhabiting semi‐arid environments. We relate the amount and type of mucilage secretion by seeds of Helianthemum violaceum and Fumana ericifolia (Cistaceae) to the number of raindrop impacts needed to remove these seeds after gluing them with their own mucilage to the ground and also the time that these seeds resist water run‐off without detaching. We also compare the amount of seed mucilage production by plants growing in habitats without erosion and plants affected by severe erosion by fitting mixed effect models. Our results show an important phenotypic variation in the amount of mucilage secretion in both species, although it is suggested that the effect of mucilage secretion in the rate of seed removal by erosion is species‐ and mechanism‐dependent. For F. ericifolia, the amount of mucilage secreted by the seeds is directly proportional to their resistance to raindrop impacts and is positively related to the intensity of the erosive processes that the plants experience. Nevertheless, all the seeds resist the force of run‐off during 60 min, irrespective of the amount of mucilage they produce. In H. violaceum, mucilage secretion per se, and not the amount of mucilage produced by the seeds, has an effect on the rate of seed removal by erosive processes. Furthermore, cellulosic fibrils were found only in the mucilage of F. ericifolia but not in H. violaceum. Overall, our results only partially support the hypothesis that a selective response to soil erosion exists. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 241–251.     

Tissue damage in organic rainbow trout muscle investigated by proteomics and bioinformatics

The response to tissue damage is a complex process, which involves the coordinated regulation of multiple proteins to ensure tissue repair. In order to investigate the effect of tissue damage in a lower vertebrate, samples were taken from rainbow trout (Oncorhynchus mykiss) at day 7 after damage and proteins were separated using 2DE. The experimental design included two groups of rainbow trout, which were fed organic feed either with or without astaxanthin. In total, 96 proteins were found to be affected by tissue damage, clearly demonstrating in this lower vertebrate the complexity and magnitude of the cellular response, in the context of a regenerative process. Using a bioinformatics approach, the main biological function of these proteins were assigned, showing the regulation of proteins involved in processes such as apoptosis, iron homeostasis, and regulation of muscular structure. Interestingly, it was established that exclusively within the astaxanthin feed group, three members of the annexin protein family (annexin IV, V, and VI) were regulated in response to tissue damage.     

Mitochondrial impairment observed in fibroblasts from South African Parkinson’s disease patients with parkin mutations

Parkinson’s disease (PD), defined as a neurodegenerative disorder, is characterized by the loss of dopaminergic neurons in the substantia nigra in the midbrain. Loss-of-function mutations in the parkin gene are a major cause of autosomal recessive, early-onset PD. Parkin has been implicated in the maintenance of healthy mitochondria, although previous studies show conflicting findings regarding mitochondrial abnormalities in fibroblasts from patients harboring parkin-null mutations. The aim of the present study was to determine whether South African PD patients with parkin mutations exhibit evidence for mitochondrial dysfunction. Fibroblasts were cultured from skin biopsies obtained from three patients with homozygous parkin-null mutations, two heterozygous mutation carriers and two wild-type controls. Muscle biopsies were obtained from two of the patients. The muscle fibers showed subtle abnormalities such as slightly swollen mitochondria in focal areas of the fibers and some folding of the sarcolemma. Although no differences in the degree of mitochondrial network branching were found in the fibroblasts, ultrastructural abnormalities were observed including the presence of electron-dense vacuoles. Moreover, decreased ATP levels which are consistent with mitochondrial dysfunction were observed in the patients’ fibroblasts compared to controls. Remarkably, these defects did not manifest in one patient, which may be due to possible compensatory mechanisms. These results suggest that parkin-null patients exhibit features of mitochondrial dysfunction. Involvement of mitochondria as a key role player in PD pathogenesis will have important implications for the design of new and more effective therapies.     

HLA-DRB1*04 and HLA-DQB1*03 association with the atrophic but not with the goitrous form of chronic autoimmune thyroiditis in a Brazilian population.

Autoimmune chronic lymphocytic thyroiditis appears in two forms, goitrous and atrophic. The evidence available is not enough to prove that the goitrous precedes the atrophic form, but immunogenetic analysis suggests that they may be distinct entities. The distribution of HLA class II alleles DRB1* and DQB1* was verified in patients from the region of Campinas, S?o Paulo, Brazil with both forms of thyroiditis. Ninety-one patients with primary hypothyroidism through autoimmune thyroiditis were classified as goitrous - 54 patients, 42.27 +/- 11.72 years old, having had hypothyroidism for 8.57 +/- 6.63 years - or atrophic - 37 patients, 42.72 +/- 12.01 years old, hypothyroidism for 6.73 +/- 4.07 years. The distribution of class II alleles was determined, DRB1* and DQB1* were genotyped after purifying DNA blood samples using the DNAzol technique, and the low-resolution PCR-SSP system was utilized for determination of generic alleles. Chi-square and Fisher's exact test were utilized to compare the distribution frequency of HLA alleles and the significant p-values were subjected to Bonferroni correction. We have demonstrated that the DRB1*04 allele is associated with autoimmune thyroiditis, and that there are genotypic differences regarding the presentation forms with a strong association between DRB1*04 and DQB1*03 and the atrophic form only.     

Viscoelastic dynamics of actin filaments coupled to rotary F-ATPase: angular torque profile of the enzyme

ATP synthase (F(O)F(1)) operates as two rotary motor/generators coupled by a common shaft. Both portions, F(1) and F(O), are rotary steppers. Their symmetries are mismatched (C(3) versus C(10-14)). We used the curvature of fluorescent actin filaments, attached to the rotating c-ring, as a spring balance (flexural rigidity of 8. 10(-26) Nm(2)) to gauge the angular profile of the output torque at F(O) during ATP hydrolysis by F(1) (see theoretical companion article (. Biophys. J. 81:1234-1244.)). The large average output torque (50 +/- 6 pN. nm) proved the absence of any slip. Variations of the torque were small, and the output free energy of the loaded enzyme decayed almost linearly over the angular reaction coordinate. Considering the threefold stepping and high activation barrier of the driving motor proper, the rather constant output torque implied a soft elastic power transmission between F(1) and F(O). It is considered as essential, not only for the robust operation of this ubiquitous enzyme under symmetry mismatch, but also for a high turnover rate of the two counteracting and stepping motor/generators.     

Growth inhibitory activity of extracts and compounds from Cimicifuga species on human breast cancer cells

The purpose of this report is to explore the growth inhibitory effect of extracts and compounds from black cohosh and related Cimicifuga species on human breast cancer cells and to determine the nature of the active components. Black cohosh fractions enriched for triterpene glycosides and purified components from black cohosh and related Asian species were tested for growth inhibition of the ER⁻ Her2 overexpressing human breast cancer cell line MDA-MB-453. Growth inhibitory activity was assayed using the Coulter Counter, MTT and colony formation assays.Results suggested that the growth inhibitory activity of black cohosh extracts appears to be related to their triterpene glycoside composition. The most potent Cimicifuga component tested was 25-acetyl-7,8-didehydrocimigenol 3-O-β-d-xylopyranoside, which has an acetyl group at position C-25. It had an IC₅₀ of 3.2 μg/ml (5 μM) compared to 7.2 μg/ml (12.1 μM) for the parent compound 7,8-didehydrocimigenol 3-O-β-d-xylopyranoside. Thus, the acetyl group at position C-25 enhances growth inhibitory activity.The purified triterpene glycoside actein (β-d-xylopyranoside), with an IC₅₀ equal to 5.7 μg/ml (8.4 μM), exhibited activity comparable to cimigenol 3-O-β-d-xyloside. MCF7 (ER⁺Her2 low) cells transfected for Her2 are more sensitive than the parental MCF7 cells to the growth inhibitory effects of actein from black cohosh, indicating that Her2 plays a role in the action of actein. The effect of actein on Her2 overexpressing MDA-MB-453 and MCF7 (ER⁺Her2 low) human breast cancer cells was examined by fluorescent microscopy. Treatment with actein altered the distribution of actin filaments and induced apoptosis in these cells.These findings, coupled with our previous evidence that treatment with the triterpene glycoside actein induced a stress response and apoptosis in human breast cancer cells, suggest that compounds from Cimicifuga species may be useful in the prevention and treatment of human breast cancer.     

Drought until death do us part: a case study of the desiccation-tolerance of a tropical moist forest seedling-tree,Licania platypus (Hemsl.) Fritsch

Studies of the desiccation tolerance of 15-month-old Licania platypus (Hemsl.) Fritsch seedlings were performed on potted plants. Pots were watered to field capacity and then dehydrated for 23-46 d to reach various visible wilting stages from slightly-wilted to dead. Root hydraulic conductance, k(r), was measured with a high-pressure flow meter and whole-stem hydraulic conductance, k(ws), was measured by a vacuum chamber method. Leaf punches were harvested for measurement of leaf water potential by a thermocouple psychrometer and for measurement of fresh- and dry-weight. L. platypus was surprisingly desiccation-tolerant, suggesting that most species of central Panama may be well adapted to the seasonality of rainfall in the region. The slightly-wilted stage corresponded to leaf water potentials and relative water contents of -2.7 MPa and 0.85, respectively, but plants did not die until these values fell to -7.5 MPa and 0.14, respectively. As desiccation proceeded k(r) and k(ws) declined relative to irrigated controls, but k(ws) was more sensitive to desiccation than k(r). Values of k(ws) declined by 70-85% in slightly-wilted to dead plants, respectively. By comparison, k(r) showed no significant change in slightly-wilted plants and fell by about 50% in plants having severely-wilted to dead shoots.