Balanced ROC analysis (BAROC) protocol for the evaluation of protein similarities

Identification of problematic protein classes (domain types, protein families) that are difficult to predict from sequence is a key issue in genome annotation. ROC (Receiver Operating Characteristic) analysis is routinely used for the evaluation of protein similarities, however its results – the area under curve (AUC) values – are differentially biased for the various protein classes that are highly different in size. We show the bias can be compensated for by adjusting the length of the top list in a class-dependent fashion, so that the number of negatives within the top list will be equal to (or proportional with) the size of the positive class. Using this balanced protocol the problematic classes can be identified by their AUC values, or by a scatter diagram in which the AUC values are plotted against positive/negative ratio of the top list. The use of likelihood-ratio scoring (Kaján et al, Bioinformatics, 22, 2865–2869, 2007) the bias caused by class imbalance can be further decreased.     

Conservation categories of siluroid fishes in North-East Sundarbans,India

In stock fishery of North-East Sundarbans, siluroid fishes hold a remarkable position owing to the culture potentiality of many of them. Scales in fishes play significant role in protection and resistance against environmental stresses and the lack of scalation in case of siluroid fishes is supposed to be one of the reasons for their decline in eco-degraded aquatic habitats. 11 species of fishes belonging to 9 genera, 8 families under the order Siluriformes have been recorded from different water bodies of North-East Sundarbans, India. Fish Magnitude Value (FMV) of those catfishes were recorded especially by information harvested from local fishermen community and stakeholders as well as from market survey on fish landing. The extensive damage to the population of catfishes in the area has placed the fishes under threat categories. Following the IUCN guidelines and also through Participatory Rural Appraisal (PRA) methods, an attempt has been made to assess the status of such fishes. Trend analysis, Fish Magnitude Value (FMV) and Rank Based Quotient (RBQ) revealed 1 catfish as Endangered, 5 as Vulnerable and 5 as Near Threatened species. The situation warrants immediate attention of ecologists, administrators, managers and entrepreneurs to propose remedial measures for revival of the fishes. The study also delineates distribution, present status and conservation measures for revival of the fishes in North-East Sundarbans wet-land environment of West Bengal, India.     

On Fisher's Method of Combining p-Values

The problem of combining p-values from independent experiments is discussed. It is shown that Fisher's solution to the problem can be derived from a “weight-free” method that has been suggested for the purpose of ranking vector observations (Biometrics 19: 85–97, 1963). The method implies that the value p = 0.37 is a critical one: p-values below 0.37 suggest that the null hypothesis is more likely to be false, whereas p-values above 0.37 suggest that it is more likely to be true.     

Blinded predictions of binding modes and energies of HSP90-α ligands for the 2015 D3R grand challenge

In the framework of the 2015 D3R inaugural grand challenge, blind binding pose and affinity predictions were performed for a set of 180 ligands of the Heat Shock Protein HSP90-α protein, a relevant cancer target. Spectral clustering was used to rapidly identify alternative binding site conformations in publicly available crystallographic HSP90-α structures. Subsequently, multiple docking and scoring protocols employing the software Autodock Vina and rDock were applied to predict binding modes and rank order ligands. Alchemical free energy calculations were performed with the software FESetup and Sire/OpenMM to predict binding affinities for three congeneric series subsets. Some of the protocols used here were ranked among the top submissions according to most of the evaluation metrics. Docking performance was excellent, but the scoring results were disappointing. A critical assessment of the results is reported, as well as suggestions for future similar competitions.     

Ranked set sampling: cost and optimal set size

McIntyre (1952, Australian Journal of Agricultural Research 3, 385-390) introduced ranked set sampling (RSS) as a method for improving estimation of a population mean in settings where sampling and ranking of units from the population are inexpensive when compared with actual measurement of the units. Two of the major factors in the usefulness of RSS are the set size and the relative costs of the various operations of sampling, ranking, and measurement. In this article, we consider ranking error models and cost models that enable us to assess the effect of different cost structures on the optimal set size for RSS. For reasonable cost structures, we find that the optimal RSS set sizes are generally larger than had been anticipated previously. These results will provide a useful tool for determining whether RSS is likely to lead to an improvement over simple random sampling in a given setting and, if so, what RSS set size is best to use in this case.     

Ranking introduced into phenological recording

Generally, phenological recording is based on the recognition of separate phases of development in the organism of interest. In the present study samples were ranked with respect to the stage of bud or leaf development reached at the time of sampling. In April 1982 budding and leaf development of all species of trees and shrubs were recorded over 2 km² of the northeastern slope of Nävlingeåsen, a horst in southernmost Sweden. During 3 days, of which the first two were consecutive, the author walked a stretch of 12 km, divided into 107 sections. In each of these the first living twig at about 1.5 m above ground was sampled for each species. At the end of the day all twigs from the same species were ranked by two persons independently. The ranks were normalized, and a mean calculated for each section. To reduce the impact of natural variation within a species, and also the influence of microclimate where species cluster, the ranks of the sections were smoothed by weighted moving averages. Using three localities which were investigated twice as fixed points, the ranking lists of separate days were integrated into a single system. A time lag of 4 or 5 days in the onset of spring was established between different localities.     

Application of fuzzy theory and PROMETHEE technique to evaluate suitable ecotechnology method: A case study in Shihmen Reservoir Watershed, Taiwan

With the increase in industrial development and improper land uses, Taiwan has faced the extinction crisis and is seeing the signs of nature, revenge in the forms of frequent landslides, floods, and debris flows in recent years. The government has strongly promoted the concept of ecotechnology in the hope of maintaining the ecosystem and its integrity. However, the application of ecotechnology is still in its infancy, so there is currently no objective evaluation standard to assess its effectiveness. Deficiencies in the scientific approach to quantify the results are due to current disputes and bottlenecks in its implementation. In order to seek reasonable and feasible methods to overcome the deficiencies in the implementation of the scientific approach, this study collected domestic and international ecological evaluation models to develop innovative processes that utilize ecological, safety, and cost indices. First, the commonly used ecotechnology methods for river embankment were acquired from the governmental departments. Second, the ecological, safety and cost indices for the acquired ecotechnology methods and construction sites were analyzed and quantified using fuzzy theory. Third, indices of ecotechnology methods were linked with those of construction sites for the PROMETHEE technique evaluation for suitable ecotechnology method selection. A practical construction case located in Shihmen reservoir watershed was chosen for evaluation and verification. The results show that the developed model can provide useful information for decision making while performing ecotechnology engineering.