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Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an ‘orphan crop legume’. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation’s Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an ‘orphan legume crop’ to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.

Breast cancer survival prediction can have an extreme effect on selection of best treatment protocols. Many approaches such as statistical or machine learning models have been employed to predict the survival prospects of patients, but newer algorithms such as deep learning can be tested with the aim of improving the models and prediction accuracy. In this study, we used machine learning and deep learning approaches to predict breast cancer survival in 4,902 patient records from the University of Malaya Medical Centre Breast Cancer Registry. The results indicated that the multilayer perceptron (MLP), random forest (RF) and decision tree (DT) classifiers could predict survivorship, respectively, with 88.2 %, 83.3 % and 82.5 % accuracy in the tested samples. Support vector machine (SVM) came out to be lower with 80.5 %. In this study, tumour size turned out to be the most important feature for breast cancer survivability prediction. Both deep learning and machine learning methods produce desirable prediction accuracy, but other factors such as parameter configurations and data transformations affect the accuracy of the predictive model. [ABSTRACT FROM AUTHOR]

Identification of taxonomy at a specific level is time consuming and reliant upon expert ecologists. Hence the demand for automated species identification incre-ased over the last two decades. Automation of data classification is primarily focussed on images while incorporating and analysing image data has recently become easier due to developments in computational technology. Research ef-forts on identification of species include specimens' image processing, extraction of identical features, followed by classifying them into correct categories. In this paper, we discuss recent automated species identification systems, mainly for categorising and evaluating their methods. We reviewed and compared different methods in step by step scheme of automated identification and classification systems of species images. The selection of methods is influenced by many variables such as level of classification, number of training data and complexity of images. The aim of writing this paper is to provide researchers and scientists an extensive background study on work related to automated species identification, focusing on pattern recognition techniques in building such systems for biodiversity studies. (Folia Morphol 2018; 77, 2: 179-193). [ABSTRACT FROM AUTHOR]

The mothers of 199 infants (mean age 36.7 days) were interviewed to determine how the infant was dressed and wrapped, and how the mother would deal with illness. These data were related to measures of the infant's toe and underarm temperatures and demographic information about the family. The data did not support the hypothesis that infants with particular types of clothing or bedding were at risk of overheating and shows that most mothers dress their infants appropriately. Mothers' ideas about management of illness were often inappropriate particularly in lower socioeducational groups. [ABSTRACT FROM AUTHOR]

The White Mountain magma series is the largest Mesozoic felsic igneous province on the eastern North American margin. Previous geochronology suggests that magmatism occurred over 50 m.y., with ages for the oldest units apparently coeval with the ca. 201 Ma Central Atlantic Magmatic Province, the flood basalt province associated with the end-Triassic mass extinction and the opening of the Atlantic Ocean. We use zircon U-Pb geochronology to show that emplacement of White Mountain magma series plutons was already underway at 207.5 Ma. The largest volcanic-plutonic complex, the White Mountain batholith, was emplaced episodically from ca. 198.5 Ma to ca. 180 Ma and is -25 m.y. older than published ages suggest, and all samples we dated from the Moat Volcanics are between ca. 185 Ma and 180 Ma. The Moat Volcanics and the White Mountain batholith are broadly comagmatic, which constrains the age of a key Jurassic paleomagnetic pole. Our data indicate that a regional mantle thermal anomaly in eastern North America developed at least 5 m.y. prior to the main stage of Central Atlantic Magmatic Province flood basalt volcanism and suggest a geodynamic link between the White Mountain magma series and the Central Atlantic Magmatic Province. [ABSTRACT FROM AUTHOR]

Abstract: We investigated the sexual reproductive mode of the two most important etiological agents of soybean sudden death syndrome, Fusarium tucumaniae and Fusarium virguliforme. F. tucumaniae sexual crosses often were highly fertile, making it possible to assign mating type and assess female fertility in 24 South American isolates. These crosses produced red perithecia and oblong-elliptical ascospores, as is typical for sexual members of the F. solani species complex. Genotyping of progeny from three F. tucumaniae crosses confirmed that sexual recombination had occurred. In contrast, pairings among 17 U.S. F. virguliforme isolates never produced perithecia. Inter-species crosses between F. tucumaniae and F. virguliforme, in which infertile perithecia were induced only in one of the two F. tucumaniae mating types, suggest that all U.S. F. virguliforme isolates are of a single mating type. We conclude that the F. tucumaniae life cycle in S. America includes a sexual reproductive mode, and thus this species has greater potential for rapid evolution than the F. virguliforme population in the U.S., which may be exclusively asexual. [Copyright &y& Elsevier]

Aims: The aim of the present research was to synthesize glycoluril derivative 2,4-Bis(4- cyanobenzyl)glycoluril through a convergent scheme., Background: For this purpose, Sandmeyer reaction procedure was employed for the synthesis of said compound. The structure of the pure compound was confirmed by using different spectroscopic techniques, such as 1HNMR, 13C-NMR and (HR-MS) Mass spectrometry., Objective: Convergent synthesis of 2,4-BIS (4-CYANOBENZYL)GLYCOLURIL USING SANDMEYER REACTION and urease inhibition study., Methods: The structure of the pure compound was confirmed by using different spectroscopic techniques such as 1H-NMR, 13C-NMR and (HR-MS) Mass spectrometry. The electronic properties of the newly synthesized compound and thiourea were determined by using density functional theory., Results: Furthermore, the compound was evaluated against urease enzyme and was found to be potent inhibitors with an IC50 value of 11.5 ± 1.50 μM when compared with standard inhibitor thiourea (IC50 = 21.0 ± 1.90 μM). The compound may serve as a lead compound to synthesize new cyano-based bambusuril in the future with enhanced biological properties., Conclusion: We have synthesized a new glycoluril derivative 2,4-Bis(4-cyanobenzyl)glycoluril by the sandmeyer reaction. It has been obtained in the form of light yellowish powder in good yield (96%). Glycoluril based macrocycles have been used in various fields; starting from the 2,4-Bis(4-nitrobenzyl)glycoluril (already reported compound), which has undergone reduction (CH3OH,Pt/C) , diazotization (NaNO2/HCl), cyanation (CuCl/KCN), respectively in order to synthesize the desired new glycoluril derivative. The obtained product will be used as a building block for the synthesis of the cyano based bambusuril marcocycle in the future. The yield of the obtained product has been monitored by using different amounts of cyanating reagent, but the best results are shown by the use of 4 mmol of CuCl/KCN. KCN with CuCl assisted the conversion of diazo group into the cyano group with enhanced yield when used in excess amount. It acts as a catalyst. The solubility characteristic of 2,4-Bis(4-cyanobenzyl)glycoluril has also been determined in different organic solvents. 1H NMR technique proved to be very helpful for the structure determination of our desired product. Benzylic protons give signals at 7.5 ppm and 7.8 ppm, respectively. The downfield peaks confirm the presence of CN group near the benzylic protons. Methine protons show a signal at 5.2 ppm, which ensures the basic skeleton of glycoluril. Ureidyl protons also confirm the synthesis of the heterocyclic 2,4-Bis(4-cyanobenzyl)glycoluril compound. The negative and positive electrostatic potential sites, molecular descriptors, and charge density distribution of frontier molecular orbitals are revealing that 4a with promising sites for electrophilic and nucleophilic attacks would result to enhance the urease inhibition, which is in good agreement with the experimental data., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Acoustical geographic variation is common in widely distributed species and it is already described for several taxa, at various scales. In cetaceans, intraspecific variation in acoustic repertoires has been linked to ecological factors, geographical barriers, and social processes. For the common bottlenose dolphin (Tursiops truncatus), studies on acoustic variability are scarce, focus on a single signal type-whistles and on the influence of environmental variables. Here, we analyze the acoustic emissions of nine bottlenose dolphin populations across the Atlantic Ocean and the Mediterranean Sea, and identify common signal types and acoustic variants to assess repertoires' (dis)similarity. Overall, these dolphins present a rich acoustic repertoire, with 24 distinct signal sub-types including: whistles, burst-pulsed sounds, brays and bangs. Acoustic divergence was observed only in social signals, suggesting the relevance of cultural transmission in geographic variation. The repertoire dissimilarity values were remarkably low (from 0.08 to 0.4) and do not reflect the geographic distances among populations. Our findings suggest that acoustic ecology may play an important role in the occurrence of intraspecific variability, as proposed by the 'environmental adaptation hypothesis'. Further work may clarify the boundaries between neighboring populations, and shed light into vocal learning and cultural transmission in bottlenose dolphin societies.

Translational control is a widespread mechanism that allows the cell to rapidly modulate gene expression in order to provide flexibility and adaptability to eukaryotic organisms. We applied translating ribosome affinity purification combined with RNA sequencing to characterize translational regulation of mRNAs at early stages of the nitrogen-fixing symbiosis established between Medicago truncatula and Sinorhizobium meliloti Our analysis revealed a poor correlation between transcriptional and translational changes and identified hundreds of regulated protein-coding and long noncoding RNAs (lncRNAs), some of which are regulated in specific cell types. We demonstrated that a short variant of the lncRNA Trans-acting small interference RNA3 ( TAS3 ) increased its association to the translational machinery in response to rhizobia. Functional analysis revealed that this short variant of TAS3 might act as a target mimic that captures microRNA390, contributing to reduce trans acting small interference Auxin Response Factor production and modulating nodule formation and rhizobial infection. The analysis of alternative transcript variants identified a translationally upregulated mRNA encoding subunit 3 of the SUPERKILLER complex (SKI3), which participates in mRNA decay. Knockdown of SKI3 decreased nodule initiation and development, as well as the survival of bacteria within nodules. Our results highlight the importance of translational control and mRNA decay pathways for the successful establishment of the nitrogen-fixing symbiosis., (© 2020 American Society of Plant Biologists. All rights reserved.)

Improvements in next-generation sequencing technologies have resulted in dramatically reduced sequencing costs. This has led to an explosion of '-seq'-based methods, of which RNA sequencing (RNA-seq) for generating transcriptomic data is the most popular. By analysing global patterns of gene expression in organs/tissues/cells of interest or in response to chemical or environmental perturbations, researchers can better understand an organism's biology. Tools designed to work with large RNA-seq data sets enable analyses and visualizations to help generate hypotheses about a gene's function. We present here a user-friendly RNA-seq data exploration tool, called the 'eFP-Seq Browser', that shows the read map coverage of a gene of interest in each of the samples along with 'electronic fluorescent pictographic' (eFP) images that serve as visual representations of expression levels. The tool also summarizes the details of each RNA-seq experiment, providing links to archival databases and publications. It automatically computes the reads per kilobase per million reads mapped expression-level summaries and point biserial correlation scores to sort the samples based on a gene's expression level or by how dissimilar the read map profile is from a gene splice variant, to quickly identify samples with the strongest expression level or where alternative splicing might be occurring. Links to the Integrated Genome Browser desktop visualization tool allow researchers to visualize and explore the details of RNA-seq alignments summarized in eFP-Seq Browser as coverage graphs. We present four cases of use of the eFP-Seq Browser for ABI3, SR34, SR45a and U2AF65B, where we examine expression levels and identify alternative splicing. The URL for the browser is https://bar.utoronto.ca/eFP-Seq_Browser/. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. Tool is at https://bar.utoronto.ca/eFP-Seq_Browser/; RNA-seq data at https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/ and https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/Klepikova/. Code is available at https://github.com/BioAnalyticResource/eFP-Seq-Browser., (© 2019 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Objective: To investigate the association of specific amino acid positions, residues, and haplotypes of HLA-DRB1 in black South Africans with autoantibody-positive rheumatoid arthritis (RA)., Methods: High-resolution HLA-DRB1 genotyping was performed in 266 black South Africans with autoantibody-positive RA and 362 ethnically and geographically matched controls. The alleles were converted to specific amino acid residues at polymorphic sites for downstream analyses. Logistic regression models were used to test whether variability at site, specific amino acid residues, and haplotypes (constructed from positions 11, 71, and 74) were associated with RA., Results: Of the 29 amino acid positions examined, positions 11, 13, and 33 (permutation p = 3.4 e-26 , 1.2 e-27 , and 2.1 e-28 , respectively) showed the strongest association with RA. Univariate analyses of individual amino acid residues showed valine at position 11 (OR 5.1, 95% CI 3.7-7.0) and histidine at position 13 (OR 6.1, 95% CI 4.2-8.6) conferred the highest risk. The valine containing haplotypes of position 11, 71, 74, V_K_A conferred the most risk (OR 4.52, 95% CI 2.68-7.61) and conversely the haplotype with serine at this position, S_K_R, conferred the most protection (OR 0.83, 95% CI 0.61-1.15)., Conclusion: Autoantibody-positive RA in black South Africans is associated with histidine at position 13 and valine at position 11 of HLA-DRB1, and haplotypes with valine at position 11 conferred the highest risk; conversely, serine at position 11 conveyed protection.

The bottlenose dolphin, genus Tursiops is one of the best studied of all the Cetacea with a minimum of two species widely recognised. Common bottlenose dolphins (T. truncatus), are the cetacean species most frequently held in captivity and are known to hybridize with species from at least 6 different genera. In this study, we document several intra-generic hybridization events between T. truncatus and T. aduncus held in captivity. We demonstrate that the F1 hybrids are fertile and can backcross producing apparently healthy offspring, thereby showing introgressive inter-specific hybridization within the genus. We document that female F1 hybrids can reach sexual maturity at 4 yr and 3 mo of age, and can become pregnant and give birth before being fully weaned. The information presented has implications for understanding hybrid reticulation among cetacean species and practical implications for captive facilities housing either Tursiops species or hybrids thereof., Competing Interests: GH and FL are employees of uShaka Sea World. The authors TG and SE have declared that no competing interests exist. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

The costs of predation may exert significant pressure on the mode of communication used by an animal, and many species balance the benefits of communication (e.g. mate attraction) against the potential risk of predation. Four groups of toothed whales have independently evolved narrowband high-frequency (NBHF) echolocation signals. These signals help NBHF species avoid predation through acoustic crypsis by echolocating and communicating at frequencies inaudible to predators such as mammal-eating killer whales. Heaviside's dolphins ( Cephalorhynchus heavisidii ) are thought to exclusively produce NBHF echolocation clicks with a centroid frequency around 125 kHz and little to no energy below 100 kHz. To test this, we recorded wild Heaviside's dolphins in a sheltered bay in Namibia. We demonstrate that Heaviside's dolphins produce a second type of click with lower frequency and broader bandwidth in a frequency range that is audible to killer whales. These clicks are used in burst-pulses and occasional click series but not foraging buzzes. We evaluate three different hypotheses and conclude that the most likely benefit of these clicks is to decrease transmission directivity and increase conspecific communication range. The expected increase in active space depends on background noise but ranges from 2.5 (Wenz Sea State 6) to 5 times (Wenz Sea State 1) the active space of NBHF signals. This dual click strategy therefore allows these social dolphins to maintain acoustic crypsis during navigation and foraging, and to selectively relax their crypsis to facilitate communication with conspecifics., (© 2018 The Author(s).)

Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.

Identification of taxonomy at a specific level is time consuming and reliant upon expert ecologists. Hence the demand for automated species identification incre-ased over the last two decades. Automation of data classification is primarily focussed on images while incorporating and analysing image data has recently become easier due to developments in computational technology. Research ef-forts on identification of species include specimens' image processing, extraction of identical features, followed by classifying them into correct categories. In this paper, we discuss recent automated species identification systems, mainly for categorising and evaluating their methods. We reviewed and compared different methods in step by step scheme of automated identification and classification systems of species images. The selection of methods is influenced by many variables such as level of classification, number of training data and complexity of images. The aim of writing this paper is to provide researchers and scientists an extensive background study on work related to automated species identification, focusing on pattern recognition techniques in building such systems for biodiversity studies. (Folia Morphol 2018; 77, 2: 179-193).

A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an "app" on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research., (© 2017 American Society of Plant Biologists. All rights reserved.)

Background: Monogeneans are flatworms (Platyhelminthes) that are primarily found on gills and skin of fishes. Monogenean parasites have attachment appendages at their haptoral regions that help them to move about the body surface and feed on skin and gill debris. Haptoral attachment organs consist of sclerotized hard parts such as hooks, anchors and marginal hooks. Monogenean species are differentiated based on their haptoral bars, anchors, marginal hooks, reproductive parts' (male and female copulatory organs) morphological characters and soft anatomical parts. The complex structure of these diagnostic organs and also their overlapping in microscopic digital images are impediments for developing fully automated identification system for monogeneans (LNCS 7666:256-263, 2012), (ISDA; 457-462, 2011), (J Zoolog Syst Evol Res 52(2): 95-99. 2013;). In this study images of hard parts of the haptoral organs such as bars and anchors are used to develop a fully automated identification technique for monogenean species identification by implementing image processing techniques and machine learning methods., Result: Images of four monogenean species namely Sinodiplectanotrema malayanus, Trianchoratus pahangensis, Metahaliotrema mizellei and Metahaliotrema sp. (undescribed) were used to develop an automated technique for identification. K-nearest neighbour (KNN) was applied to classify the monogenean specimens based on the extracted features. 50% of the dataset was used for training and the other 50% was used as testing for system evaluation. Our approach demonstrated overall classification accuracy of 90%. In this study Leave One Out (LOO) cross validation is used for validation of our system and the accuracy is 91.25%., Conclusions: The methods presented in this study facilitate fast and accurate fully automated classification of monogeneans at the species level. In future studies more classes will be included in the model, the time to capture the monogenean images will be reduced and improvements in extraction and selection of features will be implemented.