Do commonly used indices of β‐diversity measure species turnover?

Abstract. Indices of β‐diversity are of two major types, (1) those that measure among‐plot variability in species composition independently of the position of individual plots on spatial or environmental gradients, and (2) those that measure the extent of change in species composition along predefined gradients, i.e. species turnover. Failure to recognize this distinction can lead to the inappropriate use of some β‐diversity indices to measure species turnover. Several commonly‐used indices of β‐diversity are based on Whittaker's β_W (β_W = γ/α, where γ is the number of species in an entire study area and α is the number of species per plot within the study area). It is demonstrated that these indices do not take into account the distribution of species on spatial or environmental gradients, and should therefore not be used to measure species turnover. The terms ‘β‐diversity’ and ‘species turnover’ should not be used interchangeably. Species turnover can be measured using matrices of compositional similarity and physical or environmental distances among pairs of study plots. The use of indices of β‐diversity and similarity‐distance curves is demonstrated using simulated data sets.     

Antagonistic effect of enterocin CCM 4231 from Enterococcus faecium on “bryndza”, a traditional Slovak dairy product from sheep milk

“Bryndza” is a traditional Slovak dairy product (type of soft cheese) made from sheep cheese which was ripened for 14 days. Because its manufacture, transporting and/or storing represent conditions which facilitate contamination, the effect of enterocin CCM4231 in “bryndza” was investigated with the aim to reduce the contaminant agents. “Bryndza” was divided into equal portions (50 g). The experimental sample (ES) as well as the control sample one (C1) were inoculated with Listeria innocua Li1 strain. The other control samples C2 and C3 were without Li1 strain. C3 control was selected as a reference control. ES and C2 portions were treated with purified enterocin CCM4231 in a concentration of 6400 AU/ml. Before the experimental inoculation, “bryndza” was checked for the presence of contaminant agents. The experiment lasted 1 week and the samples were stored in the refrigerator at 4 °C. Sampling was performed on day 1, on day 4 and on day 7. The control samples C2 and C3 were checked only on day 1 and then after 1 week. The following contaminant agents were detected in “bryndza” before its experimental inoculation with L. innocua Li1 strain: Escherichia coli in the amount 10³ cfu/ml/g, Staphylococcus aureus (10² cfu/ml/g) and enterococci (10⁴ cfu/ml/g). In the control sample C2, the number of E. coli was reduced to 10² cfu/ml/g. Enterococci and staphylococci were totally eliminated there. Concerning C3 control, natural decrease of bacteria was found and/or their unchanged counts. The value of pH (5) was stable during the whole experiment. In the experimental sample inoculated with Li1 strain, its counts were decreased immediately after enterocin CCM4231 addition approximately by one order of magnitude. This inhibitory effect was also detectable on day 4 by the difference of one order of magnitude between ES and C1. On day 7, 10³ cfu/ml/g of Li1 strain were detected in both samples (ES, C1). The difference by one order of magnitude indicated, an inhibitory effect of enterocin CCM4231 in “bryndza”. However, bacteriocin activity was not determined by laboratory analyses.     

Challenges in calculation of the gamma index in radiotherapy – Towards good practice

The gamma index (γ) is one of the most commonly used metrics for the verification of complex modulated radiotherapy. The mathematical definition of the γ is computationally expensive and various techniques have been reported to speed up the calculation either by mathematically refining the γ or employing various computational techniques. These techniques can cause variation in output with different software implementations. The γ has traditionally been used to compare a 2D measured plane against a 2D or 3D dose distribution. Recently, software algorithm and hardware improvements have led to the possibility of using measured 2D data from commercial detector arrays to reconstruct a 3D-dose distribution and perform a volumetric comparison against the treatment planning system (TPS). A limitation in this approach is that commercial detector arrays have so far been limited by their spatial resolution which may affect the accuracy of the reconstructed 3D volume and subsequently the γ calculation. Additionally, 3D versus 3D γ comparison adds a layer of complication in the calculation of the γ given the increase in the number of calculation points and the result cannot be as easily interpreted in the same way as 2D comparison. This review summarises and highlights the computational challenges of the γ calculation and sheds light on some of these issues by means of a bespoke MATLAB software to demonstrate the impact of interpolation, γ search distance, resolution and 2D and 3D calculations. Finally, a recommendation is made on the minimum information that should be reported when publishing γ results.     

Correspondence between Scientific and Traditional Ecological Knowledge: Rain Forest Classification by the Non-Indigenous Ribereños in Peruvian Amazonia

Traditional ecological knowledge (TEK) is a potential source of ecological information. Typically TEK has been documented at the species level, but habitat data would be equally valuable for conservation applications. We compared the TEK forest type classification of ribereños, the non-indigenous rural peasantry of Peruvian Amazonia, to a floristic classification produced using systematically collected botanical data. Indicator species analysis of pteridophytes in 300 plots detected two forest types on non-flooded tierra firme, each associated with distinct soil texture and fertility, and one forest type in areas subject to flooding. Nine TEK forest types were represented in the same set of plots. Each TEK forest type was consistently (>82%) associated with one of the three floristic classes and there were also clear parallels in the ecological characterizations of the forest types. Ribereños demonstrated clear preferences for certain forest types when selecting sites for slash-and-burn agriculture and hunting. Our results indicate that the non-tribal inhabitants of Amazonia possess valuable TEK that could be used in biodiversity inventories and wildlife management and conservation for characterizing primary rain forest habitats in Amazonia.     

Doxorubicin-induced alterations in kidney functioning,oxidative stress,DNA damage,and renal tissue morphology; Improvement by Acacia hydaspica tannin-rich ethyl acetate fraction

Doxorubicin (DOX) is an anthracycline drug used for cancer treatment. However, its treatment is contiguous with toxic effects. We examined the nephroprotective potential of A. hydaspica polyphenol-rich ethyl acetate extract (AHE) against DOX persuaded nephrotoxicity. 36 male Sprague Dawley rats were randomly assorted into 6 groups. Control group received saline; DOX group: 3 mg/kg b.w. dosage of DOX intraperitoneally for 6 weeks (single dose/week). In co-treatment groups, 200 and 400 mg/kg b.w AHE was given orally for 6 weeks in concomitant with DOX (3 mg/kg b.w, i.p. injection per week) respectively. Standard group received silymarin 400 mg/kg b.w daily + DOX (single dose/week). Biochemical kidney function tests, oxidative stress markers, genotoxicity, antioxidant enzyme status, and histopathological changes were examined. DOX caused significant body weight loss and decrease kidney weight. DOX-induced marked deterioration in renal function indicators in both urine and serum, i.e., PH, specific gravity, total protein, albumin, urea, creatinine, uric acid, globulin, blood urea nitrogen, etc. Also, DOX treatment increases renal tissue oxidative stress markers, while lower antioxidant enzymes in tissue along with degenerative alterations in the renal tissue compared to control rats. AHE co-treatment ameliorates DOX-prompted changes in serum and urine chemistry. Likewise, AHE treatment decreases sensitive markers of oxidative stress and prevented DNA damages by enhancing antioxidant enzyme levels. DOX induction in rats also caused DNA fragmentation which was restored by AHE co-treatment. Moreover, the histological observations evidenced that AHE effectively rescued the kidney tissue from DOX interceded oxidative damage. Our results suggest that co-treatment of AHE markedly improve DOX-induced deleterious effects in a dose-dependent manner. The potency of AHE co-treatment at 400 mg/kg dose is similar to silymarin. These outcomes revealed that A. hydaspica AHE extract might serve as a potential adjuvant that avoids DOX-induced nephrotoxicity.     

Factors affecting growth and nodulation ofHippophaë rhamnoides L. ssp.Rhamnoides in soils from two successional stages of dune formation

Summary To explain the decline of Hippopha? scrub in the vegetation succession in the dunes of The Netherlands, the growth and nodulation of Hippopha? plants grown in pots, using soil from an early stage (site AH) and a post-optimum stage (site HP), were investigated. In HP-soil nodulation, yield, and the nitrogen and phosphorus content of test plants were always lower and the number of necrotic nodules and the dry matter content were always higher than in AH-soil, even after inoculation with crushed nodules and the addition of a nutrient solution. Plants in HP-soil also had darker roots, less root hairs, a higher number of short lateral roots and a higher percentage of dead roots than those in AH-soil. These characteristics of adverse growth conditions disappeared upon ignition or gamma-irradiation of HP-soil. Possible explanations of these results are discussed. The degeneration of Hippopha? scrub cannot be ascribed to the age of the plants, the absence of sufficient infective endophyte particles or to abiotic factors such as unfavourable physical (particle size) or chemical soil conditions but is caused by biotic factors. No indications were obtained that plant-pathogenic fungi and bacteria are involved. HP-soil in contrast to AH-soil, however, contained large numbers of the nematodeLongidorus sp., a species known to cause root deformations. The conclusion was that this nematode is one of the biotic factors involved in the degeneration of the Hippopha? scrub. This degeneration is due to a restriction of the root system resulting in a low phosphate uptake, a low nodulation capacity and, as a consequence, a low nitrogen content. The results demonstrate that biotic soil factors are important in influencing succession in higher plant communities.     

中药联合微生态制剂防治呼吸、消化系统病毒病

本文阐述了中药防治病毒病的历史及其应用概况,中药联合微生态制剂防治呼吸、消化系统病毒病的理论依据、临床应用和发展前景。     

The feasibility of an approximate irregular field dose distribution simulation program applied to a respiratory motion compensation system

PurposeThis study optimized our previously proposed simulation program for the approximate irregular field dose distribution (SPAD) and applied it to a respiratory motion compensation system (RMCS) and respiratory motion simulation system (RMSS). The main purpose was to rapidly analyze the two-dimensional dose distribution and evaluate the compensation effect of the RMCS during radiotherapy.MethodsThis study modified the SPAD to improve the rapid analysis of the dose distribution. In the experimental setup, four different respiratory signal patterns were input to the RMSS for actuation, and an ultrasound image tracking algorithm was used to capture the real-time respiratory displacement, which was input to the RMCS for actuation. A linear accelerator simultaneously irradiated the EBT3 film. The gamma passing rate was used to verify the dose similarity between the EBT3 film and the SPAD, and conformity index (CI) and compensation rate (CR) were used to quantify the compensation effect.ResultsThe Gamma passing rates were 70.48–81.39% (2%/2mm) and 88.23–96.23% (5%/3mm) for various collimator opening patterns. However, the passing rates of the SPAD and EBT3 film ranged from 61.85% to 99.85% at each treatment time point. Under the four different respiratory signal patterns, CR ranged between 21% and 75%. After compensation, the CI for 85%, 90%, and 95% isodose constraints were 0.78, 0.57, and 0.12, respectively.ConclusionsThis study has demonstrated that the dose change during each stage of the treatment process can be analyzed rapidly using the improved SPAD. After compensation, applying the RMCS can reduce the treatment errors caused by respiratory movements.