The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.

The Crux tandem mass spectrometry data analysis toolkit provides a collection of algorithms for analyzing bottom-up proteomics tandem mass spectrometry data. Many publications have described various individual components of Crux, but a comprehensive summary has not been published since 2014. The goal of this work is to summarize the functionality of Crux, focusing on developments since 2014. We begin with empirical results demonstrating our recently implemented speedups to the Tide search engine. Other new features include a new score function in Tide, two new confidence estimation procedures, as well as three new tools: Param-medic for estimating search parameters directly from mass spectrometry data, Kojak for searching cross-linked mass spectra, and DIAmeter for searching data independent acquisition data against a sequence database.

Atmospheric dispersion modeling for an accidental release from a SLOWPOKE-2 research reactor: a case study.

Atmospheric dispersion modeling was performed for a postulated design basis accident at a SLOWPOKE research reactor. The MCNP-5 computer code was used to estimate the neutron flux spectrum which was then used in the ORIGEN-S code to perform core depletion calculations and determine the radiological source term. The HotSpot health physics code was then used to model the atmospheric transport of the radioactive material released to estimate the resulting doses to the population downwind of the reactor. The highest total effective dose (TED) for a release from the reactor's exhaust stack in predominant meteorological conditions, stability class C, was 0.37 mSv, while a maximum TED of 4.29 mSv was estimated for a release at ground level. Ground deposition was estimated to be 3900 kBq/m2. It was shown that any hypothetical release of radioactive material resulting from such an accident would have no significant adverse effect on the municipal water reservoir close to the reactor.

T-Gene: improved target gene prediction.

MOTIVATION: Identifying the genes regulated by a given transcription factor (TF) (its 'target genes') is a key step in developing a comprehensive understanding of gene regulation. Previously, we developed a method (CisMapper) for predicting the target genes of a TF based solely on the correlation between a histone modification at the TF's binding site and the expression of the gene across a set of tissues or cell lines. That approach is limited to organisms for which extensive histone and expression data are available, and does not explicitly incorporate the genomic distance between the TF and the gene. RESULTS: We present the T-Gene algorithm, which overcomes these limitations. It can be used to predict which genes are most likely to be regulated by a TF, and which of the TF's binding sites are most likely involved in regulating particular genes. T-Gene calculates a novel score that combines distance and histone/expression correlation, and we show that this score accurately predicts when a regulatory element bound by a TF is in contact with a gene's promoter, achieving median precision above 60%. T-Gene is easy to use via its web server or as a command-line tool, and can also make accurate predictions (median precision above 40%) based on distance alone when extensive histone/expression data is not available for the organism. T-Gene provides an estimate of the statistical significance of each of its predictions. AVAILABILITY AND IMPLEMENTATION: The T-Gene web server, source code, histone/expression data and genome annotation files are provided at http://meme-suite.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MoMo: discovery of statistically significant post-translational modification motifs.

MOTIVATION: Post-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence patterns called 'motifs' that help localize the modifying enzyme. Accordingly, many algorithms have been designed to identify these motifs from mass spectrometry data. Accurate statistical confidence estimates for discovered motifs are critically important for proper interpretation and in the design of downstream experimental validation. RESULTS: We describe a method for assigning statistical confidence estimates to PTM motifs, and we demonstrate that this method provides accurate P-values on both simulated and real data. Our methods are implemented in MoMo, a software tool for discovering motifs among sets of PTMs that we make available as a web server and as downloadable source code. MoMo re-implements the two most widely used PTM motif discovery algorithms-motif-x and MoDL-while offering many enhancements. Relative to motif-x, MoMo offers improved statistical confidence estimates and more accurate calculation of motif scores. The MoMo web server offers more proteome databases, more input formats, larger inputs and longer running times than the motif-x web server. Finally, our study demonstrates that the confidence estimates produced by motif-x are inaccurate. This inaccuracy stems in part from the common practice of drawing 'background' peptides from an unshuffled proteome database. Our results thus suggest that many of the papers that use motif-x to find motifs may be reporting results that lack statistical support. AVAILABILITY AND IMPLEMENTATION: The MoMo web server and source code are provided at http://meme-suite.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Carotid Ultrasound to Predict Fluid Responsiveness: A Systematic Review.

OBJECTIVES: To perform a systematic review of the accuracy of carotid ultrasound measures in determining volume responsiveness in adults. METHODS: We conducted a systematic review of Ovid MEDLINE and Scopus from conception until January 1, 2019. Two independent reviewers used an iterative process to identify relevant articles and abstract information from them. The quality and risk of bias were assessed with the Quality Assessment of Diagnostic Accuracy Studies version 2 tool. RESULTS: We identified 17 relevant articles with 956 patients. The 2 most frequently cited carotid measures of fluid responsiveness were corrected flow time and peak velocity or change in peak velocity with respiration (ΔCDPV). Accordingly, the diagnostic characteristics of corrected flow time in these studies varied widely, with sensitivities from 60% to 73%, specificities from 82% to 92%, and areas under the receiver operating characteristic curves from 0.75 to 0.88. Optimal cutoff values for ΔCDPV ranged from 9.1% to 14%, with areas under the receiver operating characteristic curves from 0.81 to 0.91, sensitivities from 73% to 86%, and specificities from 78% to 86%. Other measures, such as carotid blood flow and carotid diameter, had limited data to support their use. Heterogeneity of the studies prohibited a meta-analysis. Most studies had a moderate risk of bias and high applicability. CONCLUSIONS: Preliminary research suggests that carotid ultrasound measures may be useful adjunct measures of fluid status; however, they should not be interpreted as absolute and should be placed in a clinical context. The most well-defined and supported measure currently is ΔCDPV, with cutoffs from 9% to 14%. Corrected flow time shows promise, because of heterogeneity of how this value is measured, an optimal cutoff has not been established.

MCAST: scanning for cis-regulatory motif clusters.

UNLABELLED: Precise regulatory control of genes, particularly in eukaryotes, frequently requires the joint action of multiple sequence-specific transcription factors. A cis-regulatory module (CRM) is a genomic locus that is responsible for gene regulation and that contains multiple transcription factor binding sites in close proximity. Given a collection of known transcription factor binding motifs, many bioinformatics methods have been proposed over the past 15 years for identifying within a genomic sequence candidate CRMs consisting of clusters of those motifs. RESULTS: The MCAST algorithm uses a hidden Markov model with a P-value-based scoring scheme to identify candidate CRMs. Here, we introduce a new version of MCAST that offers improved graphical output, a dynamic background model, statistical confidence estimates based on false discovery rate estimation and, most significantly, the ability to predict CRMs while taking into account epigenomic data such as DNase I sensitivity or histone modification data. We demonstrate the validity of MCAST's statistical confidence estimates and the utility of epigenomic priors in identifying CRMs. AVAILABILITY AND IMPLEMENTATION: MCAST is part of the MEME Suite software toolkit. A web server and source code are available at http://meme-suite.org and http://alternate.meme-suite.org CONTACT: t.bailey@imb.uq.edu.au or william-noble@uw.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The MEME Suite.

The MEME Suite is a powerful, integrated set of web-based tools for studying sequence motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their detection and characterization is important in the study of molecular interactions in the cell, including the regulation of gene expression. Since the previous description of the MEME Suite in the 2009 Nucleic Acids Research Web Server Issue, we have added six new tools. Here we describe the capabilities of all the tools within the suite, give advice on their best use and provide several case studies to illustrate how to combine the results of various MEME Suite tools for successful motif-based analyses. The MEME Suite is freely available for academic use at http://meme-suite.org, and source code is also available for download and local installation.

Crux: rapid open source protein tandem mass spectrometry analysis.

Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit ( http://cruxtoolkit.sourceforge.net ) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data.

Assessment of the bioavailability of cadmium in Jamaican soils.

Extraordinary geogenic concentrations of cadmium (Cd) have been reported for some Jamaican soils. However, the bioavailability of the metal in these soils remains unknown. Here, the bioavailability of Cd in selected Jamaican soils was investigated through the determination of total and sequentially extractable concentrations in paired soil-plant (yam; Dioscorea sp.) samples (n = 24), using neutron activation analysis and atomic absorption spectroscopy as primary analytical techniques. Our results indicate that total soil Cd varied widely (2.2-148.7 mg kg(-1)), and on average, total extractable Cd accounted for ~55 % of the total soil Cd. The exchangeable and oxidizable species averaged 1.5 and 6.4 % of the total Cd, respectively, and, based on Spearman analysis, are the best predictors of yam Cd. There is also good evidence to suggest that variation in the bioavailability of the metal is in part controlled by the geochemical characteristics of the soils analyzed and is best explained by pH, cation exchange capacity (CEC) and organic matter content (% LOI).

A novel hybrid random forest linear model approach for forecasting groundwater fluoride contamination.

Groundwater quality in the Datong basin is threatened by high fluoride contamination. Laboratory analysis is a standard method for estimating groundwater quality parameters, which is expensive and time-consuming. Therefore, this paper proposes a hybrid random forest linear model (HRFLM) as a novel approach for estimating groundwater fluoride contamination. Light gradient boosting (LightGBM), random forest (RF), and extreme gradient boosting (Xgboost) were also employed in comparison with HRFLM for predicting fluoride contamination in groundwater. 202 groundwater samples were collected to draw up the performance capability of several models in forecasting subsurface water fluoride contamination. The performance of the models was assessed utilizing the receiver operating characteristic (ROC) area under the curve (AUC) and the confusion matrix (CM). The CM results reveal that with nine predictor variables, the hybrid HRFLM achieved an accuracy of 95%, outperforming the Xgboost, LightGBM, and RF models, which attained 88%, 88%, and 85%, respectively. Likewise, the AUC results of the hybrid HRFLM show high performance with an AUC of 0.98 compared to Xgboost, LightGBM, and RF, which achieved an AUC of 0.95, 0.90, and 0.88, respectively. The study demonstrates that the HRFLM can be applied as an advanced approach for groundwater fluoride contamination prediction in the Datong basin and could be adopted in various areas facing a similar challenge.

Overexpression of the UDP-glycosyltransferase UGT34A23 confers resistance to the diamide insecticide chlorantraniliprole in the tomato leafminer, Tuta absoluta.

The tomato leafminer, Tuta absoluta, is an invasive crop pest that has evolved resistance to many of the insecticides used for its control. To facilitate the investigation of the underpinning mechanisms of resistance in this species we generated a contiguous genome assembly using long-read sequencing data. We leveraged this genomic resource to investigate the genetic basis of resistance to the diamide insecticide chlorantraniliprole in Spanish strains of T. absoluta that exhibit high levels of resistance to this insecticide. Transcriptomic analyses revealed that, in these strains, resistance is not associated with previously reported target-site mutations in the diamide target-site, the ryanodine receptor, but rather is associated with the marked overexpression (20- to >100-fold) of a gene encoding a UDP-glycosyltransferase (UGT). Functional expression of this UGT, UGT34A23, via ectopic expression in Drosophila melanogaster demonstrated that it confers strong and significant resistance in vivo. The genomic resources generated in this study provide a powerful resource for further research on T. absoluta. Our findings on the mechanisms underpinning resistance to chlorantraniliprole will inform the development of sustainable management strategies for this important pest.

Results and analysis of an intercomparisons study for individual monitoring services of Latin American and Caribbean regions.

The aim of this paper is to present the results obtained by the Latin-American and Caribbean personal dosimetry services that participated, with the support of IAEA, in the 2020-Eurados whole-body dosemeter intercomparison for photon radiation. All participant services in this study use thermoluminescent dosimetry (TLD) systems except one that uses optically stimulated luminescence (OSL) dosemeters. Data analysis shows that 93.4% of the results are within the acceptance range, according to International ISO Standard ISO 14146: 2018. The evaluation of the trumpet curves shows that only three laboratories presented a few dosemeters results outside the limits of acceptability. Participation in this Eurados intercomparison exercise gave the Latin American and Caribbean laboratories the opportunity to show compliance with their own quality management system, to compare results with other participants and to develop plans for improving their dosimetry systems. It also gave the assurance that occupational doses are being measured properly and following the international standards in the regions.

FIMO: scanning for occurrences of a given motif.

UNLABELLED: A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides. Over the past several decades, many computational methods have been described for identifying, characterizing and searching with sequence motifs. Critical to nearly any motif-based sequence analysis pipeline is the ability to scan a sequence database for occurrences of a given motif described by a position-specific frequency matrix. RESULTS: We describe Find Individual Motif Occurrences (FIMO), a software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. The program computes a log-likelihood ratio score for each position in a given sequence database, uses established dynamic programming methods to convert this score to a P-value and then applies false discovery rate analysis to estimate a q-value for each position in the given sequence. FIMO provides output in a variety of formats, including HTML, XML and several Santa Cruz Genome Browser formats. The program is efficient, allowing for the scanning of DNA sequences at a rate of 3.5 Mb/s on a single CPU. AVAILABILITY AND IMPLEMENTATION: FIMO is part of the MEME Suite software toolkit. A web server and source code are available at http://meme.sdsc.edu.

Improved similarity scores for comparing motifs.

MOTIVATION: A question that often comes up after applying a motif finder to a set of co-regulated DNA sequences is whether the reported putative motif is similar to any known motif. While several tools have been designed for this task, Habib et al. pointed out that the scores that are commonly used for measuring similarity between motifs do not distinguish between a good alignment of two informative columns (say, all-A) and one of two uninformative columns. This observation explains why tools such as Tomtom occasionally return an alignment of uninformative columns which is clearly spurious. To address this problem, Habib et al. suggested a new score [Bayesian Likelihood 2-Component (BLiC)] which uses a Bayesian information criterion to penalize matches that are also similar to the background distribution. RESULTS: We show that the BLiC score exhibits other, highly undesirable properties, and we offer instead a general approach to adjust any motif similarity score so as to reduce the number of reported spurious alignments of uninformative columns. We implement our method in Tomtom and show that, without significantly compromising Tomtom's retrieval accuracy or its runtime, we can drastically reduce the number of uninformative alignments. AVAILABILITY AND IMPLEMENTATION: The modified Tomtom is available as part of the MEME Suite at http://meme.nbcr.net.

A pilot study on the use of neutron activation analysis and multivariate statistics for the provenance of Jamaican Cannabis sativa L (Marijuana).

The aim of this study was to use instrumental neutron activation analysis and multivariate analysis to determine the provenance of Jamaican Cannabis sativa L. Sixty-three samples were collected from various areas in Jamaica, with no other data but their known or self-reported growing regions. The samples were analysed for Al, As, Br, Ca, Cd, Co, Cs, Fe, K, La, Mg, Mn, Na, Rb, Sb, Sc, Sm, Sr, V, and Zn. The resulting elemental data were statistically evaluated using agglomerative hierarchical cluster analysis and principal component analysis. Cluster analysis was able to group the samples into their known or reported growing regions with a high degree of accuracy. Principal component analysis was also able to elucidate some of the underlying geochemical factors that could explain the clustering. These included the underlying bauxitic geochemistry and the influence of fertilizer inputs. Of the analysed elements, Al, As, Cd, Co, Fe, K, La, Mg, Mn, Sc, Sm, V, and Zn appear to be most significant in identifying the growing regions of the cannabis samples. Results indicate the promise of this methodology with an increased dataset and potentially further refinement of the identifying elements.

MEME SUITE: tools for motif discovery and searching.

The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms--MAST, FIMO and GLAM2SCAN--allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm TOMTOM. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and TOMTOM), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters. All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net.

Parthenogenesis in UK field populations of the tomato leaf miner, Tuta absoluta, exposed to the mating disruptor Isonet T.

BACKGROUND: The tomato leafminer, Tuta absoluta is a damaging pest of tomato crops worldwide. In the UK T. absoluta is controlled using an integrated pest management (IPM) strategy that includes pheromone-based mating disruption. However, some growers have reported a loss of efficacy of this technology, and there are concerns that T. absoluta may evolve resistance via changes in its capacity to reproduce asexually. In this study we investigated the reproductive capacity of virgin populations of T. absoluta collected from a UK glasshouse before (EVH2016) and after (EVH2019) the introduction of the mating disrupter Isonet T. RESULTS: In line with earlier reports, we demonstrate that UK populations of T. absoluta can reproduce parthenogenetically, and observed a small but significant increase in the rate of parthenogenesis associated with the use of Isonet T. Marked differences in several other life history traits associated with reproduction were also observed between the two virgin populations, with the EVH2019 strain producing fewer eggs, a delayed onset of egg laying and increased lifespan. CONCLUSION: The low rate of parthenogenetic reproduction seen in this study is unlikely to result in loss of efficacy of mating disruption. However, the observed changes in longevity and egg laying may allow T. absoluta to persist for longer within the crop, and, together with the increased rate of parthenogenesis, may reflect selection from the use of Isonet T. Thus, regular monitoring of the reproductive capacity of UK populations should be conducted, and mating disruption used only as part of IPM to avoid the emergence of resistance. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Challenges in the control of neglected insect vector diseases of human importance in the Anglo-Caribbean.

INTRODUCTION: Neglected tropical diseases (NTDs) in developing countries like the Caribbean, negatively affect multiple income-generating sectors, including the tourism industry upon which island states are highly dependent. Insect-transmitted NTDs include, but are not limited to, malaria, dengue and lymphatic filariasis. Control measures for these disease, are often ignored because of the associated cost. Many of the developing country members are thus retained in a financially crippling cycle, balancing the cost of prophylactic measures with that of controlling an outbreak.The purpose of the paper is to bring awareness to NTDs transmitted by insects of importance to humans, and to assess factors affecting such control, in the English-speaking Caribbean. METHOD: Comprehensive literature review on reports pertaining to NTDs transmitted by insects in the Caribbean and Latin America was conducted. Data search was carried out on PubMed, and WHO and PAHO websites. RESULTS AND CONCLUSION: Potential risk factors for NTDs transmitted by arthropods in the English-speaking Caribbean are summarised. The mosquito appears to be the main insect-vector of human importance within the region of concern. Arthropod-vectors of diseases of veterinary importance are also relevant because they affect the livelihood of farmers, in highly agriculture based economies. Other NTDs may also be in circulation gauged by the presence of antibodies in Caribbean individuals. However, routine diagnostic tests for specific diseases are expensive and tests may not be conducted when diseases are not prevalent in the population. It appears that only a few English-speaking Caribbean countries have examined secondary reservoirs of pathogens or assessed the effectivity of their insect control methods. As such, disease risk assessment appears incomplete. Although continuous control is financially demanding, an integrated and multisectoral approach might help to deflect the cost. Such interventions are now being promoted by health agencies within the region and various countries are creating and exploring the use of novel tools to be incorporated in their insect-vector control programmes.

Assessing phylogenetic motif models for predicting transcription factor binding sites.

MOTIVATION: A variety of algorithms have been developed to predict transcription factor binding sites (TFBSs) within the genome by exploiting the evolutionary information implicit in multiple alignments of the genomes of related species. One such approach uses an extension of the standard position-specific motif model that incorporates phylogenetic information via a phylogenetic tree and a model of evolution. However, these phylogenetic motif models (PMMs) have never been rigorously benchmarked in order to determine whether they lead to better prediction of TFBSs than obtained using simple position weight matrix scanning. RESULTS: We evaluate three PMM-based prediction algorithms, each of which uses a different treatment of gapped alignments, and we compare their prediction accuracy with that of a non-phylogenetic motif scanning approach. Surprisingly, all of these algorithms appear to be inferior to simple motif scanning, when accuracy is measured using a gold standard of validated yeast TFBSs. However, the PMM scanners perform much better than simple motif scanning when we abandon the gold standard and consider the number of statistically significant sites predicted, using column-shuffled 'random' motifs to measure significance. These results suggest that the common practice of measuring the accuracy of binding site predictors using collections of known sites may be dangerously misleading since such collections may be missing 'weak' sites, which are exactly the type of sites needed to discriminate among predictors. We then extend our previous theoretical model of the statistical power of PMM-based prediction algorithms to allow for loss of binding sites during evolution, and show that it gives a more accurate upper bound on scanner accuracy. Finally, utilizing our theoretical model, we introduce a new method for predicting the number of real binding sites in a genome. The results suggest that the number of true sites for a yeast TF is in general several times greater than the number of known sites listed in the Saccharomyces cerevisiae Database (SCPD). Among the three scanning algorithms that we test, the MONKEY algorithm has the highest accuracy for predicting yeast TFBSs.