DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources.

Circular Dichroism (CD) spectroscopy is a widely-used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally-related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format-compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.cryst.bbk.ac.uk/) resource, in which the CD spectral and associated metadata for each entry are linked to other structural and functional data bases including the Protein Data Bank (PDB), and the UniProt sequence data base, amongst others. These tools and resources thus provide the basis for a wide range of traceable structural characterizations of soluble, membrane and intrinsically-disordered proteins.

Automatic generation of pseudoknotted RNAs taxonomy.

BACKGROUND: The ability to compare RNA secondary structures is important in understanding their biological function and for grouping similar organisms into families by looking at evolutionarily conserved sequences such as 16S rRNA. Most comparison methods and benchmarks in the literature focus on pseudoknot-free structures due to the difficulty of mapping pseudoknots in classical tree representations. Some approaches exist that permit to cluster pseudoknotted RNAs but there is not a general framework for evaluating their performance. RESULTS: We introduce an evaluation framework based on a similarity/dissimilarity measure obtained by a comparison method and agglomerative clustering. Their combination automatically partition a set of molecules into groups. To illustrate the framework we define and make available a benchmark of pseudoknotted (16S and 23S) and pseudoknot-free (5S) rRNA secondary structures belonging to Archaea, Bacteria and Eukaryota. We also consider five different comparison methods from the literature that are able to manage pseudoknots. For each method we clusterize the molecules in the benchmark to obtain the taxa at the rank phylum according to the European Nucleotide Archive curated taxonomy. We compute appropriate metrics for each method and we compare their suitability to reconstruct the taxa.

Insights from analyses of low complexity regions with canonical methods for protein sequence comparison.

Low complexity regions are fragments of protein sequences composed of only a few types of amino acids. These regions frequently occur in proteins and can play an important role in their functions. However, scientists are mainly focused on regions characterized by high diversity of amino acid composition. Similarity between regions of protein sequences frequently reflect functional similarity between them. In this article, we discuss strengths and weaknesses of the similarity analysis of low complexity regions using BLAST, HHblits and CD-HIT. These methods are considered to be the gold standard in protein similarity analysis and were designed for comparison of high complexity regions. However, we lack specialized methods that could be used to compare the similarity of low complexity regions. Therefore, we investigated the existing methods in order to understand how they can be applied to compare such regions. Our results are supported by exploratory study, discussion of amino acid composition and biological roles of selected examples. We show that existing methods need improvements to efficiently search for similar low complexity regions. We suggest features that have to be re-designed specifically for comparing low complexity regions: scoring matrix, multiple sequence alignment, e-value, local alignment and clustering based on a set of representative sequences. Results of this analysis can either be used to improve existing methods or to create new methods for the similarity analysis of low complexity regions.

Comparative Evaluation of an Easy Laboratory Method for the Concentration of Oocysts and Commercial DNA Isolation Kits for the Molecular Detection of Cyclospora cayetanensis in Silt Loam Soil Samples.

Cyclospora cayetanensis is a protozoan parasite that causes foodborne outbreaks of diarrheal illness (cyclosporiasis) worldwide. Contact with soil may be an important mode of transmission for C. cayetanensis and could play a role in the contamination of foods. However, there is a scarcity of detection methods and studies for C. cayetanensis in soil. Traditional parasitology concentration methods can be useful for the detection of C. cayetanensis, as found for other protozoa parasites of similar size. The present study evaluated a concentration method using flotation in saturated sucrose solution, subsequent DNA template preparation and qPCR following the Bacteriological Analytical Manual (BAM) Chapter 19b method. The proposed flotation method was compared to three commercial DNA isolation kits (Fast DNATM 50 mL SPIN kit for soil (MP Biomedicals, Irvine, CA, USA), Quick-DNATM Fecal/Soil Microbe Midiprep kit (Zymo Research, Irvine, CA, USA) and DNeasy® PowerMax® Soil Kit (Qiagen, Hilden, Germany)) for the isolation and detection of DNA from experimentally seeded C. cayetanensis soil samples (5−10 g with 100 oocysts). Control unseeded samples were all negative in all methods. Significantly lower cycle threshold values (CT) were observed in the 100 oocyst C. cayetanensis samples processed via the flotation method than those processed with each of the commercial DNA isolation kits evaluated (p < 0.05), indicating higher recovery of the target DNA with flotation. All samples seeded with 100 oocysts (n = 5) were positive to the presence of the parasite by the flotation method, and no inhibition was observed in any of the processed samples. Linearity of detection of the flotation method was observed in samples seeded with different levels of oocysts, and the method was able to detect as few as 10 oocysts in 10 g of soil samples (limit of detection 1 oocyst/g). This comparative study showed that the concentration of oocysts in soil samples by flotation in high-density sucrose solutions is an easy, low-cost, and sensitive method that could be implemented for the detection of C. cayetanensis in environmental soil samples. The flotation method would be useful to identify environmental sources of C. cayetanensis contamination, persistence of the parasite in the soil and the role of soil in the transmission of C. cayetanensis.

Development of an instrument for assessing the quality of forensic evidence and expert testimony from three feature-comparison methods: DNA, voice, and fingerprint analysis.

In a context of rising violence and long-lasting impunity, in 2008, Mexico's criminal justice system underwent a radical change from an inquisitorial model to an adversarial one, to make it more effective, transparent, and expeditious. The new system tasked judges with publicly determining the admissibility of forensic evidence, as well as assessing its technical quality and probative value-tasks for which they currently receive little to no training. With the aim of contributing to the consolidation of the adversarial model, a comparative framework-in the form of a checklist-of the analysis of fingerprints, DNA samples, and voice recordings was created. To do so, a review of the academic literature, published reports, and guidelines was performed. The collected data were synthesized and submitted to a panel of Mexican judges, who provided feedback on its adequacy. The framework focuses on the steps on which quality assurance of forensic evidence depends, organized in five discrete stages that span from the collection of samples at the scene of a crime to the presentation of evidence at trial, specifying the main technical criteria experts should state to allow a decision maker to examine its accuracy and reliability. Differences and commonalities among the three methods were identified, particularly in terms of how qualitative and quantitative analyses are performed in each. Besides its potential usefulness as an aid for judicial decision-making, the checklist could be a valuable resource for training programs aimed at judges, as well as quality assurance programs.

Bland-Altman methods for comparing methods of measurement and response to criticisms.

Introduced in 1983, Bland-Altman methods is now considered the standard approach for assessment of agreement between two methods of measurement. The method is widely used by researchers in various disciplines so that the Bland-Altman 1986 Lancet paper has been named as the 29th mostly highly cited paper ever, over all fields. However, two papers by Hopkins (2004) and Krouwer (2007) questioned the validity of the Bland-Altman analysis. We review the points of critical papers and provide responses to them. The discussions in the critical papers of the Bland-Altman method are scientifically delusive. Hopkins misused the Bland-Altman methodology for research question of model validation and also incorrectly used least-square regression when there is measurement error in the predictor. The problem with Krouwers' paper is making sweeping generalisation of a very narrow and somewhat unrealistic situation. The method proposed by Bland and Altman should be used when the research question is method comparison.

Methods to adjust for multiple comparisons in the analysis and sample size calculation of randomised controlled trials with multiple primary outcomes.

BACKGROUND: Multiple primary outcomes may be specified in randomised controlled trials (RCTs). When analysing multiple outcomes it's important to control the family wise error rate (FWER). A popular approach to do this is to adjust the p-values corresponding to each statistical test used to investigate the intervention effects by using the Bonferroni correction. It's also important to consider the power of the trial to detect true intervention effects. In the context of multiple outcomes, depending on the clinical objective, the power can be defined as: 'disjunctive power', the probability of detecting at least one true intervention effect across all the outcomes or 'marginal power' the probability of finding a true intervention effect on a nominated outcome. We provide practical recommendations on which method may be used to adjust for multiple comparisons in the sample size calculation and the analysis of RCTs with multiple primary outcomes. We also discuss the implications on the sample size for obtaining 90% disjunctive power and 90% marginal power. METHODS: We use simulation studies to investigate the disjunctive power, marginal power and FWER obtained after applying Bonferroni, Holm, Hochberg, Dubey/Armitage-Parmar and Stepdown-minP adjustment methods. Different simulation scenarios were constructed by varying the number of outcomes, degree of correlation between the outcomes, intervention effect sizes and proportion of missing data. RESULTS: The Bonferroni and Holm methods provide the same disjunctive power. The Hochberg and Hommel methods provide power gains for the analysis, albeit small, in comparison to the Bonferroni method. The Stepdown-minP procedure performs well for complete data. However, it removes participants with missing values prior to the analysis resulting in a loss of power when there are missing data. The sample size requirement to achieve the desired disjunctive power may be smaller than that required to achieve the desired marginal power. The choice between whether to specify a disjunctive or marginal power should depend on the clincial objective.

Estimation of the economic loss due to irrigation water use inefficiency in Tunisia.

The main objective of this study is to estimate the total economic loss due to inefficient use of irrigation water in Tunisia. Several approaches have been used for this purpose. The optimal level of water application for different crops is calculated using the actual crop evapotranspiration which is based on FAO-56 method. The residual imputation and yield comparison methods have been used to estimate the economic value of irrigation water for different irrigated crops in different bioclimatic areas. For the empirical analysis, primary data were obtained from a series of surveys that covered 78% of the total irrigated areas and were collected within the framework of the "Virtual Water and Food Security in Tunisia project" (2013-2015). Secondary data about land distribution of crops in Tunisia were taken from the Ministry of Agriculture (2016). Around 724 farms were randomly sampled considering their bioclimatic area, farm type, and production system. The survey included the main 20 crops produced in Tunisia. Results show that most of farmers are either under or over utilizing irrigation water. The value of total direct economic losses, at the country level, of both types of water inefficiencies, was estimated to around 470 million Tunisian Dinars. Therefore, an improvement of water use efficiency at field level through dissemination of information/knowledge on irrigation scheduling and crop water requirements by extension services to farmers is needed to reduce this huge economic loss, reach higher sustainability in water use and improve food security.

Finding the way forward for forensic science in the US-A commentary on the PCAST report.

A recent report by the US President's Council of Advisors on Science and Technology (PCAST), (2016) has made a number of recommendations for the future development of forensic science. Whereas we all agree that there is much need for change, we find that the PCAST report recommendations are founded on serious misunderstandings. We explain the traditional forensic paradigms of match and identification and the more recent foundation of the logical approach to evidence evaluation. This forms the groundwork for exposing many sources of confusion in the PCAST report. We explain how the notion of treating the scientist as a black box and the assignment of evidential weight through error rates is overly restrictive and misconceived. Our own view sees inferential logic, the development of calibrated knowledge and understanding of scientists as the core of the advance of the profession.

Comparison of diagnostic potential of serological, molecular and cell culture methods for detection of Q fever in ruminants.

Q fever is an infectious disease caused by Coxiella burnetii. Diagnosis of Q fever based on clinical symptoms is unattainable; thus, different laboratory techniques are used to detect the infection. The aim of the study was to compare the diagnostic potential of ELISA, CFT, conventional PCR, real-time PCR and cell culture. The tests were carried out on 2251 serum samples from ruminants. Moreover, 668 placentas, 1277 vaginal swabs and 306 specimens of the internal organs of aborted foetuses were examined by PCR and cell culture. Pearson's chi-square test was used to compare the results obtained by ELISA, CFT, PCR, real-time PCR and isolation in cell culture. The χ(2) test confirmed that in most cases the results obtained by means of the different methods were correlated with each other (P<0.05). The highest correlation coefficients (r=0.76-0.87) were observed in the case of real-time PCR and conventional PCR. ELISA and CFT were moderately correlated (r=0.43-0.45). When the comparison was made between the results of tests run on samples from swabs and aborted foetuses, the r values between ELISA and CFT were lower than those between ELISA and PCRs. A negligible, or weak to moderate relationship was mostly observed when the method of cell culture isolation was compared with all the other analytical techniques investigated. The use of a combination of different laboratory methods, preferably ELISA for serology and polymerase chain reactions for the agent detection, is suggested to achieve the correct diagnosis of Q fever.

A survey strategy for human respiratory syncytial virus detection among haematopoietic stem cell transplant patients: epidemiological and methodological analysis

Human respiratory syncytial virus (HRSV) causes severe infections among children and immunocompromised patients. We compared HRSV infections among Haematopoietic Stem Cell Transplant program (HSCT) patients and children using direct immunofluorescence (DFA), point-of-care RSV Bio Easy® and a polymerase chain reaction (PCR) assay. Overall, 102 samples from HSCT patients and 128 from children obtained positivity rate of 18.6% and 14.1% respectively. PCR sensitivity was highest mainly on samples collected after five days of symptoms onset. A combination of both DFA and reverse transcriptase-PCR methods for HSCT high-risk patients is the best diagnostic flow for HRSV diagnosis among these patients.