A novel numerical optimization algorithm inspired from weed colonization

This paper introduces a novel numerical stochastic optimization algorithm inspired from colonizing weeds. Weeds are plants whose vigorous, invasive habits of growth pose a serious threat to desirable, cultivated plants making them a threat for agriculture. Weeds have shown to be very robust and adaptive to change in environment. Thus, capturing their properties would lead to a powerful optimization algorithm. It is tried to mimic robustness, adaptation and randomness of colonizing weeds in a simple but effective optimizing algorithm designated as Invasive Weed Optimization (IWO). The feasibility, the efficiency and the effectiveness of IWO are tested in details through a set of benchmark multi-dimensional functions, of which global and local minima are known. The reported results are compared with other recent evolutionary-based algorithms: genetic algorithms, memetic algorithms, particle swarm optimization, and shuffled frog leaping. The results are also compared with different versions of simulated annealing — a generic probabilistic meta-algorithm for the global optimization problem — which are simplex simulated annealing, and direct search simulated annealing. Additionally, IWO is employed for finding a solution for an engineering problem, which is optimization and tuning of a robust controller. The experimental results suggest that results from IWO are better than results from other methods. In conclusion, the performance of IWO has a reasonable performance for all the test functions.     

A rapid algorithm for processing digital physiologic signals: Application to skeletal muscle contractions

Quantifying mechanical output is fundamental to understanding metabolism that fuels muscle contraction and more recent attempts to understand signal transduction and gene regulation. The latter requires long-term application of exercise protocols that result in large amounts of data on muscle performance. The purpose of this study was to develop software for automated quantification of skeletal muscle contractions. An in situ mouse sciatic nerve stimulation model was used to produce contractions over a broad range of frequencies and recorded as both digital and analog signals using a PC analog to digital converter board and chart recorder, respectively. Spectral analysis of the noise components formed the basis for designing a smoothing Chebyshev filter. Algorithms implemented in custom software identified twitches and estimated baseline levels from the smoothed signal. The time to peak force, peak force, tension-time integral, and half-relaxation time were determined for each twitch after baseline correction. The automated results were compared to those obtained from manual measurements of the analog signal. Bland–Altman analysis of the parameters computed from digital signals compared with the corresponding measurements by manual planometry demonstrates the agreement of the digital processing algorithm with planometry over a wide range of twitch characteristics. This program may also be used to study the mechanics of other preparations from isolated muscles, human proximal limb performance, and other digital physiologic signals. Adaptation of the filter function is required to apply the analysis to another experimental apparatus with differing noise characteristics. A full version of the program and instructions for its use are available for download at www.rad.msu.edu.     

Effects of high-relief structures on cold temperate fish assemblages: A field experiment

High-relief structures may influence the abundance and diversity of reef-associated fish. We conducted a field experiment to investigate whether the presence of vertical structures (PVC pipes) affects fish communities on artificial reefs. The effect of the height of the structures (1 and 3 m) was also tested. Furthermore, the effects on fish of placing artificial reefs on otherwise featureless bottoms were quantified. Algal and macro-invertebrate colonization of the reefs was also recorded. The experiment was carried out on the west coast of Sweden over a period of 1 year. The vertical structures had a positive effect on fish abundance but not on diversity. The height of the structures did not, however, influence the fish communities. Natural as well as urban vertical structures on the seafloor could have a positive effect on local fish abundance. The positive effects of artificial reefs on total fish abundance and diversity were immediate. Of the 10 species recorded, two, the black goby Gobius niger and the goldsinny wrasse Ctenolabrus rupestris, dominated over the whole survey period. There were significant temporal differences in fish abundance, and diversity increased with time.     

Deceleration time of systolic pulmonary venous flow: a new clinical marker of left atrial pressure and compliance.

The curvilinearity of the atrial pressure-volume curve implies that atrial compliance decreases progressively with increasing left atrial (LA) pressure (LAP). We predicted that reduced LA compliance leads to more rapid deceleration of systolic pulmonary venous (PV) flow. With this rationale, we investigated whether the deceleration time (t dec) of PV systolic flow velocity reflects mean LAP. In eight patients during coronary surgery, before extracorporeal circulation, PV flow by ultrasonic transit time and invasive LAP were recorded during stepwise volume loading. The t dec was calculated using two methods: by drawing a tangent through peak deceleration and by drawing a line from peak systolic flow through the nadir between the systolic and early diastolic flow waves. LA compliance was calculated as the systolic PV flow integral divided by LAP increment. Volume loading increased mean LAP from 11 +/- 3 to 20 +/- 5 mmHg (P < 0.001) (n = 40), reduced LA compliance from 1.16 +/- 0.42 to 0.72 +/- 0.40 ml/mmHg (P < 0.004) (n = 40), and reduced t dec from 320 +/- 50 to 170 +/- 40 ms (P < 0.0005) (n = 40). Mean LAP correlated well with t dec (r = 0.84, P < 0.0005) (n = 40) and LA compliance (r = 0.79, P < 0.0005) (n = 40). Elevated LAP caused a decrease in LA compliance and therefore more rapid deceleration of systolic PV flow. The t dec has potential to become a semiquantitative marker of LAP and an index of LA passive elastic properties.     

Quantitative characterization of airspace enlargement in emphysema.

The mean linear intercept (L(m)) can be used to estimate the surface area for gas exchange in the lung. However, in recent years, it is most commonly used as an index for characterizing the enlargement of airspaces in emphysema and the associated severity of structural destruction in the lung. Specifically, an increase in L(m) is thought to result from an increase in airspace sizes. In this paper, we examined how accurately L(m) measures the linear dimensions of airspaces from histological sections and a variety of computer-generated test images. To this end, we developed an automated method for measuring linear intercepts from digitized images of tissue sections and calculate L(m) as their mean. We examined how the shape of airspaces and the variability of their sizes influence L(m) as well as the distribution of linear intercepts. We found that, for a relatively homogeneous enlargement of airspaces, L(m) was a reliable index for detecting emphysema. However, in the presence of spatial heterogeneities with a large variability of airspace sizes, L(m) did not significantly increase and sometimes even decreased compared with its value in normal tissue. We also developed an automated method for measuring the area and computed an equivalent diameter of each individual airspace that is independent of shape. Finally, we introduced new indexes based on the moments of diameter that we found to be more reliable than L(m) to characterize airspace enlargement in the presence of heterogeneities.     

Enhanced mitochondrial sensitivity to creatine in rats bred for high aerobic capacity.

Qualitative and quantitative measures of mitochondrial function were performed in rats selectively bred 15 generations for intrinsic aerobic high running capacity (HCR; n = 8) or low running capacity (LCR; n=8). As estimated from a speed-ramped treadmill exercise test to exhaustion (15 degrees slope; initial velocity of 10 m/min, increased 1 m/min every 2 min), HCR rats ran 10 times further (2,375+/-80 m) compared with LCR rats (238+/-12 m). Fiber bundles were obtained from the soleus and chemically permeabilized. Respiration was measured 1) in the absence of ADP, 2) in the presence of a submaximally stimulating concentration of ADP (0.1 mM ADP, with and without 20 mM creatine), and 3) in the presence of a maximally stimulating concentration of ADP (2 mM). Although non-ADP-stimulated and maximally ADP-stimulated rates of respiration were 13% higher in HCR compared with LCR, the difference was not statistically significant (P>0.05). Despite a similar rate of respiration in the presence of 0.1 mM ADP, HCR rats demonstrated a higher rate of respiration in the presence of 0.1 mM ADP+20 mM creatine (HCR 33% higher vs. LCR, P<0.05). Thus mitochondria from HCR rats exhibit enhanced mitochondrial sensitivity to creatine (i.e., the ability of creatine to decrease the Km for ADP). We propose that increased respiratory sensitivity to ADP in the presence of creatine can effectively increase muscle sensitivity to ADP during exercise (when creatine is increased) and may be, in part, a contributing factor for the increased running capacity in HCR rats.     

Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene,toluene and ethylbenzene under microaerobic conditions

In the present study, the bacterial community structure of enrichment cultures degrading benzene under microaerobic conditions was investigated through culturing and 16S rRNA gene Illumina amplicon sequencing. Enrichments were dominated by members of the genus Rhodoferax followed by Pseudomonas and Acidovorax. Additionally, a pale amber-coloured, motile, Gram-stain-negative bacterium, designated B7^T was isolated from the microaerobic benzene-degrading enrichment cultures and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene and whole genome-based phylogenetic analyses revealed that strain B7^T formed a lineage within the family Comamonadaceae, clustered as a member of the genus Ideonella and most closely related to Ideonella dechloratans CCUG 30977^T. The sole respiratory quinone is ubiquinone-8. The major fatty acids are C_16:0 and summed feature 3 (C_16:1 ω7c/iso-C_15:0 2-OH). The DNA G?+?C content of the type strain is 68.8?mol%. The orthologous average nucleotide identity (OrthoANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain B7^T and closest relatives were below the threshold values for species demarcation. The genome of strain B7^T, which is approximately 4.5?Mb, contains a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete meta-cleavage pathway including a I.2.C-type catechol 2,3-dioxygenase (C23O) gene. As predicted by the genome, the type strain is involved in aromatic hydrocarbon-degradation: benzene, toluene and ethylbenzene are degraded aerobically and also microaerobically as sole source of carbon and energy. Based on phenotypic characteristics and phylogenetic analysis, strain B7^T is a member of the genus Ideonella and represents a novel species for which the name Ideonella benzenivorans sp. nov. is proposed. The type strain of the species is strain B7^T (=?LMG 32,345^T?=?NCAIM B.02664^T).

     

Evidence that dams promote biotic differentiation of zooplankton communities in two Brazilian reservoirs

Hydrobiologia - Human activities may change beta diversity—the spatial variation in species composition—in different ways. Positive and negative trends in beta diversity are referred as...     

Impacts of climate change on stream benthic diatoms—a nation-wide perspective of reference conditions

Hydrobiologia - Consequences of anthropogenic climate change directly affect freshwater ecosystems and their aquatic biological communities. Diatoms are amongst the most sensitive organisms to...     

Hierarchical Bayesian integrated model for estimating migratory bird harvest in Canada

The Canadian Wildlife Service (CWS) requires reliable estimates of the harvest of migratory game birds, including waterfowl, to effectively manage populations of these hunted species. The National Harvest Survey is an annual survey of hunters who purchase Canada's mandatory migratory game bird hunting permit, integrating information from a survey of hunting activity with information from a separate survey of species composition in the harvest. We used these survey data to estimate the number of birds harvested for each species and hunting activity metrics (e.g., number of active hunters, days spent hunting). The analytical methods used to generate these estimates have not changed since the survey was first designed in the early 1970s. We describe a new hierarchical Bayesian integrated model, which replaces the series of ratio estimators that comprised the old model. We are using this new model to generate estimates for migratory bird harvests as of the 2019–2020 hunting season, and to generate updated estimates for all earlier years. The hierarchical Bayesian model uses over-dispersed Poisson distributions to model mean hunter activity and harvest (zero-inflated Poisson and zero-truncated Poisson, respectively). It also includes multinomial distributions to model some key components (e.g., variation in harvest across periods of the hunting season, the species composition of the harvest within each of those periods, the age and sex composition in the harvests of a given species). We estimated the parameters of the Poisson and the multinomial distributions for each year as random effects using first-difference time-series. This time-series component allows the model to share information across years and reduces the sensitivity of the estimates to annual sampling noise. The new model estimates are generally very similar to those from the old model, particularly for the species that occur most commonly in the harvest, so the results do not suggest any major changes to harvest management decisions and regulations. Estimates for all species from the new model are more precise and less susceptible to annual sampling error, particularly for species that occur less commonly in the harvest (e.g., sea ducks, other species of conservation concern). This new model, with its hierarchical Bayesian framework, will also facilitate future improvements and elaborations, allowing the incorporation of prior information from the rich literature and knowledge in game bird management and biology.