Authors:A. Jiménez-Valverde, J. Lobo, and J. Hortal
Prevalence (the presence/absence ratio in the training data) is commonly thought to influence the reliability of the predictions of species distribution models. However, little is known about its precise impact. We studied its effects using a virtual species, avoiding the presence of unaccounted-for effects in the modeling process (false absences, non-explanatory predictors, etc.). We sampled the distribution of the virtual species to obtain several data subsets of varying sample size and prevalence, and then modeled these data subsets using logistic regressions. Our results show that model predictions can be highly accurate over a wide range of sample sizes and prevalence scores, provided that the predictors are truly related to the distribution of the species and the training data are reliable. The effect of sample size becomes apparent for datasets of less than 70 data points, and the effect of prevalence is significant only for datasets with extremely unbalanced samples (<0.01 and >0.99). There is also a strong interaction between sample size and prevalence, indicating that the most negative factor is the sample size of each event (absence and/or presence), and not biased prevalence, as previously thought. We suggest that, in the real world, an interaction must exist between the sample size of each event and the quality of the training data. We discuss that biased prevalences can be a desirable property of the data, instead of a problem to be avoided, also pointing out the importance of using the best absence data possible when modeling the distribution of species of narrow geographic range.
Authors:Sonja Obersteller, Heinrich Neubauer, Ralf Matthias Hagen, and Hagen Frickmann
, Tenner-Racz K , Eggert P , Schwarz NG , Poppert S , Tannich E , Hagen RM : Influence of parasite density and sample storage time on the reliability of Entamoeba histolytica -specific PCR from formalin-fixed and paraffinembedded tissues . Diagn Mol
Nilsson, C. 1992. Increasing the reliability of vegetation analyses by using a team of two investigators. J. Veg. Sci. 3:565.
Increasing the reliability of vegetation analyses by using a team of two investigators
Methicillin-resistant Staphylococcus aureus (MRSA) poses an infection risk for international military deployments. In the presented mini-review, the history of MRSA in the medical service and modern warfare is highlighted. To allow rapid diagnosis, various molecular diagnostic point-of-care solutions are available. Most evaluation studies, however, are focused on screening swabs rather than clinical materials and evaluation data from harsh environments are widely lacking. Accordingly, studies with complex sample materials under difficult environmental conditions, e.g., in the desert or in the tropics, are desirable to close this gap of knowledge regarding the diagnostic reliability of such modern molecular point-of-care devices.
A method is presented and discussed that minimises uncertainties in change analysis of sequential vegetation maps due tot subjectivity in boundary interpretation. This previous boundary method is based upon the concept of „map changes”, which implies that sequential maps are not made independently but are based upon a previous map: only changes in the old maps boundaries (both in space and vegetation typology) are interpreted. It was shown that the map changes concept increased the reliability of change analysis results in a coastal salt marsh in the Netherlands. The method may be applied easily in other studies in which photo-interpretation is used for monitoring purposes. The method is especially recommended in low dynamic areas, where slow changes in vegetation patterns take place and the effects of photo-interpretation uncertainty are relatively high.
Authors:S. Popovski, K. Kos, B. Jakovac Strajn, and F.A. Celar
The genus Fusarium consists of multiple diverse species, which, as a result of their frequency in nature and pathogenicity, are significant in agriculture, as well as in human and veterinary medicine. In the course of field trials, by using standard phytopathological methods, and performing analyses of 19 different varieties of wheat and a portion of infected grains gathered from two distinct locations in Slovenia, we have determined the presence of various phytopathogenic species of the genus Fusarium. Because of the reliability, the experiment was performed in two consecutive years, 2012 and 2013. A laboratory analysis was conducted with an ELISA test on all grain samples for the determination of deoxynivalenol (DON) concentration. The results show that the main differences in the infection levels (F. culmorum + F. graminearum; FC + FG) of wheat samples were found in Jable (humid area), at the same time showing higher levels of DON content than Rakičan (dry area). Such a statement is supported by correlation test, where correlation is evident between FC + FG and DON in every variation. The data for both wheat types (awned and awnless) together showed that the grain in Jable is statistically significant more infected by FC + FG when compared to that in Rakičan. Moreover, our descriptive analysis confirms that the infection rate of grain with FC and FG shows a strong correlation with the emergence of DON.
Authors:Carola Edler, Henri Derschum, Mirko Köhler, Heinrich Neubauer, Hagen Frickmann, and Ralf Matthias Hagen
Reliable identification of pathogenic Burkholderia spp. like Burkholderia mallei and Burkholderia pseudomallei in clinical samples is desirable. Three different selective media were assessed for reliability and selectivity with various Burkholderia spp. and nontarget organisms.
Mast Burkholderia cepacia agar, Ashdown + gentamicin agar, and B. pseudomallei selective agar were compared. A panel of 116 reference strains and well-characterized clinical isolates, comprising 30 B. pseudomallei, 20 B. mallei, 18 other Burkholderia spp., and 48 nontarget organisms, was used for this assessment.
While all B. pseudomallei strains grew on all three tested selective agars, the other Burkholderia spp. showed a diverse growth pattern. Nontarget organisms, i.e., nonfermentative rod-shaped bacteria, other species, and yeasts, grew on all selective agars. Colony morphology did not allow unambiguous discrimination.
While the assessed selective media reliably allowed the growth of a wide range of B. pseudomallei strains, growth of other Burkholderia spp. is only partially ensured. Growth of various nontarget organisms has to be considered. Therefore, the assessed media can only be used in combination with other confirmative tests in the diagnostic procedure for the screening for melioidosis or glanders.
Authors:S. Esfandani-Bozchaloyi, M. Sheidai, and M. Hassanzadeh Kalalegh
The genus Geranium (Geraniaceae); with about 320 species throughout the temperate regions, is chemically characterised by the presence of tannins, flavonoids, anthocyanins and essential oils which interfere with the extraction of pure genomic DNA. It is necessary to optimise the extraction protocols to reduce the effects of the presence of these compounds to the lowest level.
The present study compares the plant genomic DNA extraction Kit (DNP™ Kit), CTAB DNA extraction method by Murray and Thompson and Sahu et al., from the extracting DNA point of view Geranium species. The results showed significant differences in DNA contents between the three methods. Quantity and quality of extracted genomic DNAs were compared by employing the spectrophotometer, Nano-Drop, agarose gel electrophoresis, and polymerase chain reaction (PCR) methods and molecular marker such as (ITS and trnL-F) and ISSR. The method of Sahu et al., provided the best results (200 ng/µL) in terms of quantity and quality of DNA, therefore, this method was taken and optimised for DNA extraction. Our results proposed that this method could be effective for plants with same polysaccharides, proteins and polyphenols components. The advantage of this method is that it omits the use of liquid nitrogen and toxic phenols which are expensive. The success of this method in obtaining high-quality genomic DNA has been demonstrated in the Geranium species group and the reliability of this method has been discussed.