Tag Datasets Research Articles

English

Genus cotton has total 50 species, diploid species fall into 8 genomic groups (A–G, and K). To the extent of our knowledge, frequency of single nucleotide polymorphisms (SNPs) has not been calculated in genes of multiple genomes of the genus Gossypium. Here we present the frequency of SNPs in the transcribed regions of the multiple genes, and their utility in resolving phylogenies among 11 diploid species representing five of the eight diploid genomes of the genus Gossypium. We explored the expressed sequence tags (ESTs) data set of G. arboreum showing homology with genes encoding for mitochondrial small heat shock protein (MT-sHSP), histone H2B1, S-adenosyl methionine synthetase, cytochrome p450, actin-depolymerizing factor 2, C-terminal domain of helicases and histone H2B3 for designing primers. The resultant PCR products amplifying partial gene sequences were sequenced. In total, 61 SNPs were detected in cotton genomes which include 53 substitutions and 8 Indels in the total 1920 bp genome length. Phylogenetic analysis using this data revealed grouping of genomes comparable with previous studies. A1 and A2 genomes were most similar (98.0%) while D9 and Oryza genomes were least similar (31.2%). Oryza was most distantly related with other genomes. In conclusion SNPs are potent markers to delineate cotton genomes according to their evolutionary positions.

Structure, evolution, and expression of antimicrobial silk proteins, seroins in Lepidoptera

The silks of silkworm and waxworm contain abundant antimicrobial proteins, including protease inhibitors and seroins. Protease inhibitors have antifungal activities, whereas seroins have antiviral and antibacterial activities. In order to obtain insights into the structure, evolution, and expression of seroins, we performed an extensive survey based on the available genome, transcriptome, and expressed sequence tags datasets. Sixty-four seroins were identified in 32 lepidopteran species. The phylogenetic and structural analyses revealed that seroins can be classified into five subfamilies: seroin 1, seroin 2, seroin 3, seroin 2 + 1, and seroin 3 + 3. It is interesting that seroin 2 + 1 contains two tandem seroin domains, seroin 2 and seroin 1, whereas seroin 3 + 3 has two tandem seroin 3 domains. Each seroin domain contains a proline-rich N-terminal motif and a conserved C-terminal motif. The transcriptome and EST data indicated that seroin 1 and seroin 2 genes were expressed in the silk gland but seroin 3 genes were not. Semi-quantitative RT–PCR and western blot analyses suggested that seroin 1 and seroin 2 were constantly accumulated in the silk gland of silkworm during the fifth instar, and then secreted into cocoon silk during spinning. Immunofluorescence analyses indicated that seroin 1 was secreted into the fibroin and sericin layers, whereas seroin 2 protein was only secreted into the sericin layer. However, the antimicrobial activity of seroin 2 was more effective than that of seroin 1. The presence of seroin 1 in the fibroin layer suggested that this protein not only acts as an antimicrobial protein, but might also play a role in the assembly and secretion of fibroins. Seroin 3, which was first identified here, might be related to pheromone synthesis or recognition, as it was highly expressed in male antennae and in the pheromone gland.

Combining User Reputation and Provenance Analysis for Trust Assessment

Trust is a broad concept that in many systems is often reduced to user reputation alone. However, user reputation is just one way to determine trust. The estimation of trust can be tackled from other perspectives as well, including by looking at provenance. Here, we present a complete pipeline for estimating the trustworthiness of artifacts given their provenance and a set of sample evaluations. The pipeline is composed of a series of algorithms for (1) extracting relevant provenance features, (2) generating stereotypes of user behavior from provenance features, (3) estimating the reputation of both stereotypes and users, (4) using a combination of user and stereotype reputations to estimate the trustworthiness of artifacts, and (5) selecting sets of artifacts to trust. These algorithms rely on the W3C PROV recommendations for provenance and on evidential reasoning by means of subjective logic. We evaluate the pipeline over two tagging datasets: tags and evaluations from the Netherlands Institute for Sound and Vision’s Waisda? video tagging platform, as well as crowdsourced annotations from the Steve.Museum project. The approach achieves up to 85% precision when predicting tag trustworthiness. Perhaps more importantly, the pipeline provides satisfactory results using relatively little evidence through the use of provenance.

Automatic Electronic Cleansing in Computed Tomography Colonography Images using Domain Knowledge.

Electronic cleansing is an image post processing technique in which the tagged colonic content is subtracted from colon using CTC images. There are post processing artefacts, like: 1) soft tissue degradation; 2) incomplete cleansing; 3) misclassification of polyp due to pseudo enhanced voxels; and 4) pseudo soft tissue structures. The objective of the study was to subtract the tagged colonic content without losing the soft tissue structures. This paper proposes a novel adaptive method to solve the first three problems using a multi-step algorithm. It uses a new edge model-based method which involves colon segmentation, priori information of Hounsfield units (HU) of different colonic contents at specific tube voltages, subtracting the tagging materials, restoring the soft tissue structures based on selective HU, removing boundary between air-contrast, and applying a filter to clean minute particles due to improperly tagged endoluminal fluids which appear as noise. The main finding of the study was submerged soft tissue structures were absolutely preserved and the pseudo enhanced intensities were corrected without any artifact. The method was implemented with multithreading for parallel processing in a high performance computer. The technique was applied on a fecal tagged dataset (30 patients) where the tagging agent was not completely removed from colon. The results were then qualitatively validated by radiologists for any image processing artifacts.

Development of EST-SSR markers in the relict tree Davidia involucrata (Davidiaceae) using transcriptome sequencing.

Davidia involucrata, reputed to be a "living fossil" in the plant kingdom, is a relict tree endemic to China. Extant natural populations are diminishing due to anthropogenic disturbance. In order to understand its ability to survive in a range of climatic conditions and to design conservation strategies for this endangered species, we developed genic simple sequence repeats (SSRs) from mRNA transcripts. In total, 142,950 contigs were assembled. Of these, 30,411 genic SSR loci were discovered and 12,208 primer pairs were designed. Dinucleotides were the most common (77.31%) followed by trinucleotides (16.44%). Thirteen randomly selected primers were synthesized and validated using 24 individuals of D. involucrata. The markers displayed high polymorphism with the number of alleles per locus ranging from 3 to 12 and the observed and expected heterozygosities ranging from 0.083 to 1.0 and 0.102 to 0.69, respectively. This large expressed sequence tag dataset and the novel SSR markers will be key tools in comparative studies that may reveal the adaptive evolution, population structure, and resolve the genetic diversity in this endangered species.

Privacy preserving data release for tagging recommender systems

Tagging recommender systems allow Internet users to annotate resources with personalized tags. The connection among users, resources and these annotations, often called a folksonomy, permits users the freedom to explore tags, and to obtain recommendations. Releasing these tagging datasets accelerates both commercial and research work on recommender systems. However, tagging recommender systems has been confronted with serious privacy concerns because adversaries may re-identify a user and her/his sensitive information from the tagging dataset using a little background information. Recently, several private techniques have been proposed to address the problem, but most of them lack a strict privacy notion, and can hardly resist the number of possible attacks. This paper proposes an private releasing algorithm to perturb users' profile in a strict privacy notion, differential privacy, with the goal of preserving a user's identity in a tagging dataset. The algorithm includes three privacy-preserving operations: Private Tag Clustering is used to shrink the randomized domain and Private Tag Selection is then applied to find the most suitable replacement tags for the original tags. To hide the numbers of tags, the third operation, Weight Perturbation, finally adds Laplace noise to the weight of tags. We present extensive experimental results on two real world datasets, De.licio.us and Bibsonomy. While the personalization algorithm is successful in both cases, our results further suggest the private releasing algorithm can successfully retain the utility of the datasets while preserving users' identity.

Tracking the fidelity of Atlantic bluefin tuna released in Canadian waters to the Gulf of Mexico spawning grounds

The objective of this study was to advance the use of pop-up satellite archival tags to track the migrations of Atlantic bluefin tuna (Thunnus thynnus) to their spawning grounds. Deployment of tags occurred in the Gulf of St. Lawrence, Canada, during fall months from 2007 to 2013. Pop-up satellite archival tags (n = 135) were attached to 125 Atlantic bluefin tuna (curved fork length (CFL) = 268 ± 20 cm (mean ± SD)) with the objective of keeping tags on until visitation to a spawning area or longer. A dataset of 18 800 days was acquired, which included 5800 days of time-series data from 19 recovered satellite tags. Many Atlantic bluefin tuna visited the Gulf of Mexico spawning grounds (74%), the mean size of which was 275 ± 14 cm (CFL ± SD, n = 49), with a measured CFL of 243 to 302 cm. These fish had a mean entry date into the Gulf of Mexico of 14 January ± 42 days (SD). The mean residency period for fish that had tracks with entrance and exit from the Gulf of Mexico was 123 ± 49 days (SD) (n = 22). Atlantic bluefin tuna that moved into the Gulf of Mexico during the spawning season remained west of the 45°W meridian for the duration of the track. Electronic tagging datasets from two fish were obtained before, during, and after the Deepwater Horizon oil spill. Both fish utilized habitat in the vicinity of the Macondo Well on 20 April 2010 when the Deepwater Horizon oil drilling rig accident occurred. Spawning hotspots are identified in the Gulf of Mexico using kernel density analyses and compared with the newly established closed areas.

MitoMiner v3.1, an update on the mitochondrial proteomics database.

Mitochondrial proteins remain the subject of intense research interest due to their implication in an increasing number of different conditions including mitochondrial and metabolic disease, cancer, and neuromuscular degenerative and age-related disorders. However, the mitochondrial proteome has yet to be accurately and comprehensively defined, despite many studies. To support mitochondrial research, we developed MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk), a freely accessible mitochondrial proteomics database. MitoMiner integrates different types of subcellular localisation evidence with protein information from public resources, and so provides a comprehensive central resource for data on mitochondrial protein localisation. Here we report important updates to the database including the addition of subcellular immunofluorescent staining results from the Human Protein Atlas, computational predictions of mitochondrial targeting sequences, and additional large-scale mass-spectrometry and GFP tagging data sets. This evidence is shared across the 12 species in MitoMiner (now including Schizosaccharomyces pombe) by homology mapping. MitoMiner provides multiple ways of querying the data including simple text searches, predefined queries and custom queries created using the interactive QueryBuilder. For remote programmatic access, API's are available for several programming languages. This combination of data and flexible querying makes MitoMiner a unique platform to investigate mitochondrial proteins, with application in mitochondrial research and prioritising candidate mitochondrial disease genes.

Music Annotation and Retrieval using Unlabeled Exemplars: Correlation and Sparse Codes

Tagging music signals with semantic labels such as genres, moods and instruments is important for content-based music retrieval and recommendation. While considerable effort has been made, automatic music annotation is still considered challenging due to the difficulty of extracting good audio features that capture the characteristics of different tags. To address this issue, we present in this letter two exemplar-based approaches that represent the content of a music clip by referring to a large set of unlabeled audio exemplars. The first approach represents a music clip by the set of audio exemplars that is highly correlated with the short-time feature vectors of the clip, whereas the second approach represents a music clip as sparse linear combinations of its short-time feature vectors over the audio exemplars. Music annotation is then performed by learning the relevance of the audio examples to different tags using labeled data. These two approaches effectively capitalize the availability of unlabeled data to explore the commonality of music signals to find out tag-specific acoustic patterns, without domain knowledge and feature design. Evaluation on the CAL10k music genre tagging dataset for tag-based music retrieval shows that, with thousands of unlabeled audio examples randomly drawn from the Million Song Dataset, the proposed approaches lead to remarkably higher precision rates than existing approaches.

Green and hawksbill turtles in the Lesser Antilles demonstrate behavioural plasticity in inter-nesting behaviour and post-nesting migration

Satellite transmitters were deployed on three green turtles, Chelonia mydas, and two hawksbill turtles, Eretmochelys imbricata, nesting in the Lesser Antilles islands, Caribbean, between 2005 and 2007 to obtain preliminary information about the inter-nesting, migratory and foraging habitats in the region. Despite the extremely small dataset, both year-round residents and migrants were identified; specifically, (1) two green turtles used local shallow coastal sites within 50 km of the nesting beach during all of their inter-nesting periods and then settled at these sites on completion of their breeding seasons, (2) one hawksbill turtle travelled 200 km westward before reversing direction and settling within 50 km of the original nesting beach and (3) one green and one hawksbill turtle initially nested at the proximate site, before permanently relocating to an alternative nesting site over 190 km distant. A lack of nesting beach fidelity was supported by flipper tag datasets for the region. Tagging datasets from 2002 to 2012 supported that some green and hawksbill individuals exhibit low fidelity to nesting beaches, whereas other females exhibited a high degree of fidelity (26 turtles tagged, 40.0 km maximum distance recorded from original nesting beach). Individual turtles nesting on St Eustatius and St Maarten appear to exhibit behavioural plasticity in their inter-nesting behaviour and post-nesting migration routes in the eastern Caribbean. The tracking and tagging data combined indicate that some of the green and hawksbill females that nest in the Lesser Antilles islands are year-round residents, whilst others may nest and forage at alternative sites. Thus, continued year-round protection of these islands and implementation of protection programmes in nearby islands could contribute towards safeguarding the green and hawksbill populations of the region.

Comparative Transcriptome Analysis of Two Species of Curcuma Contrasting in a High-Value Compound Curcumin: Insights into Genetic Basis and Regulation of Biosynthesis

Turmeric (Curcuma longa L), one of the widely used spices and herbal medicines, is rich in biologically active compound curcumin. Efficacy of curcumin in treating various diseases has been established through over 1000 published in vivo and in vitro studies. Curcumin content is reported to vary between accessions and subject to agro-climatic conditions, and the reasons are unexplored. Gaining an understanding on the molecular mechanism underlying curcumin biosynthesis will help in improving its content and maintaining stability under all conditions of cultivation. To investigate the genes involved in curcuminoid biosynthesis, we used Illumina sequencing platform and generated a substantial amount of expressed sequence tag (EST) dataset from two species viz., C. longa and its wild relative Curcuma aromatica Salisb. contrasting in curcumin content. The data reads of Illumina sequencing have been deposited in the National Center for Biotechnology Information Sequence Read Archive under BioProject ID PRJNA270561 and PRJNA277549 for C. longa and C. aromatica, respectively. De novo assembly produced a total of 99,482 and 104,514 contigs with an average length of 367 and 359 bp for C. longa and C. aromatica, respectively. The transcripts were assembled by BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology identifiers. Bioinformatics analysis using BLASTX revealed that both the transcriptomes contained all the ten genes putatively involved in curcuminoid biosynthesis. Two novel polyketide synthase genes showing similarity to that of Musa accuminata (clpks1 and clpks2) were found to be upregulated in C. longa in comparison with C. aromatica. Transcription factors with putative roles in phenylpropanoid biosynthetic pathway were also reported for the first time in Curcuma spp. We also identified 5488 and 5620 putative simple sequence repeats (SSRs) for C. longa and C. aromatica, respectively. By using the assemblies as reference, 190 single-nucleotide polymorphisms (SNPs) for C. longa and 108 SNPs for C. aromatica in the candidate genes of curcuminoid biosynthetic pathway were identified. We could also detect 68 and 64 transcripts as microRNA (miRNA) targets from C. longa and C. aromatica, respectively. This study generated an extensive transcriptome data of C. longa and C. aromatica using deep sequencing. The candidate genes for enzymes involved in curcuminoid biosynthesis were identified from both the species. Differentially expressed genes, novel polyketide synthases, transcription factors, SSRs, SNPs and miRNA targets were identified from the transcriptomes. These EST sequences are a valuable public information platform for functional studies in turmeric and form a rich resource for studies on marker development and turmeric breeding.

Transcriptome analyses to investigate symbiotic relationships between marine protists.

Rhizaria are an important component of oceanic plankton communities worldwide. A number of species harbor eukaryotic microalgal symbionts, which are horizontally acquired in the environment at each generation. Although these photosymbioses are determinant for Rhizaria ability to thrive in oceanic ecosystems, the mechanisms for symbiotic interactions are unclear. Using high-throughput sequencing technology (i.e., 454), we generated large Expressed Sequence Tag (EST) datasets from four uncultured Rhizaria, an acantharian (Amphilonche elongata), two polycystines (Collozoum sp. and Spongosphaera streptacantha), and one phaeodarian (Aulacantha scolymantha). We assessed the main genetic features of the host/symbionts consortium (i.e., the holobiont) transcriptomes and found rRNA sequences affiliated to a wide range of bacteria and protists in all samples, suggesting that diverse microbial communities are associated with the holobionts. A particular focus was then carried out to search for genes potentially involved in symbiotic processes such as the presence of c-type lectins-coding genes, which are proteins that play a role in cell recognition among eukaryotes. Unigenes coding putative c-type lectin domains (CTLD) were found in the species bearing photosynthetic symbionts (A. elongata, Collozoum sp., and S. streptacantha) but not in the non-symbiotic one (A. scolymantha). More particularly, phylogenetic analyses group CTLDs from A. elongata and Collozoum sp. on a distinct branch from S. streptacantha CTLDs, which contained carbohydrate-binding motifs typically observed in other marine photosymbiosis. Our data suggest that similarly to other well-known marine photosymbiosis involving metazoans, the interactions of glycans with c-type lectins is likely involved in modulation of the host/symbiont specific recognition in Radiolaria.

Estimating survival of rock lobsters from long-term tagging programmes: how survey number and interval influence estimates

Abstract A long-term tagging dataset on southern rock lobster (Jasus edwardsii) conducted at the Crayfish Point Scientific Reserve near Hobart, Tasmania, Australia, was used to determine how survey number and survey duration affected the precision of survival estimates of male and female lobsters to ensure sustainable exploitation of the population. Tagging surveys were undertaken twice yearly during 2000–2003 with unequal time-intervals between surveys and then once a year with equal time-intervals during 2004–2012 during the January–February period. The most parsimonious Cormack–Jolly–Seber model for estimating survival of lobsters was dependent on (i) timing of the tagging and recapture surveys, (ii) time between consecutive recapture surveys, and (iii) gender. The number of surveys required to provide a precise survival probability varied with gender and time between recapture surveys. For surveys where there was unequal time between recapture surveys, seven and five surveys were required for female and male lobsters, respectively, whereas only five surveys were required when annual surveys were undertaken. Thus, lobster tagging projects using annual surveys should ideally extend to at least 5 years, which is beyond the 3-year project duration common in marine science.

Ectopic overexpression of a novel Glycine soja stress-induced plasma membrane intrinsic protein increases sensitivity to salt and dehydration in transgenic Arabidopsis thaliana plants.

Plasma membrane intrinsic proteins (PIPs) belong to the aquaporin family and facilitate water movement across plasma membranes. Existing data indicate that PIP genes are associated with the abilities of plants to tolerate certain stress conditions. A review of our Glycine soja expressed sequence tag (EST) dataset revealed that abiotic stress stimulated expression of a PIP, herein designated as GsPIP2;1 (GenBank_Accn: FJ825766). To understand the roles of this PIP in stress tolerance, we generated a coding sequence for GsPIP2;1 by in silico elongation and cloned the cDNA by 5'-RACE. Semiquantitative RT-PCR showed that GsPIP2;1 expression was stimulated in G. soja leaves by cold, salt, or dehydration stress, whereas the same stresses suppressed GsPIP2;1 expression in the roots. Transgenic Arabidopsis thaliana plants overexpressing GsPIP2;1 grew normally under unstressed and cold conditions, but exhibited depressed tolerance to salt and dehydration stresses. Moreover, greater changes in water potential were detected in the transgenic A. thaliana shoots, implying that GsPIP2;1 may negatively impact stress tolerance by regulating water potential. These results, deviating from those obtained in previous reports, provide new insights into the relationship between PIPs and abiotic stress tolerance in plants.

Ranking on heterogeneous manifolds for tag recommendation in social tagging services

Abstract Nowadays, most social Websites allow users to annotate resources (such as Web pages and images) with keywords, i.e. tags. Collaborative tagging data reflects the semantic perception of users, thus providing valuable information for the related recommendation problems, e.g. tag recommendation, resource recommendation. In this paper, we tackle the problem of personalized tag recommendation in social tagging services by generalizing the traditional manifold ranking idea. Specifically, we model the complex relationships in tagging data as a heterogeneous graph and propose a novel ranking algorithmic framework for heterogeneous manifolds, named GRoMO (Graph-based Ranking of Multi-type interrelated Objects). In our system both the resource to be tagged (accounting for relevance) and the user׳s historical tags (accounting for personalization) are treated as query inputs. Then tags are ranked according to the output of GRoMO and the top tags are recommended to that user. We also explore adapting GRoMO for resource recommendation. For experiments we crawled a tagging dataset from the well-known tagging service, Del.icio.us. Experimental results indicate (1) the proposed method is effective and significantly outperforms baseline methods; (2) the iterative form solutions of GRoMO converge very fast and can be used when the dataset is large; (3) GRoMO can also be used for resource recommendation.

High-throughput analysis and characterization of Astragalus membranaceus transcriptome using 454 GS FLX.

Astragalus membranaceus (Fisch.) Bge (AR), one of the most important medicinal plants in Asia, was found to exhibit various bioactivities. Due to limited genomic and transcriptomic data, the biosynthetic pathway of the major bioactive compound in AR, is currently unclear. In this study, 454 GS FLX technology was employed to produce a substantial expressed sequence tag (EST) dataset from the AR. In all, 742721 high-quality reads from the AR were produced using Roche GS FLX Titanium. A total of 9893 unique sequences were obtained and annotated by a similarity search against the public databases, and involved in the secondary metabolic pathway, which would facilitate deciphering the molecular mechanism of secondary metabolism in AR. The assembled sequences were annotated with gene names and Gene Ontology (GO) terms. GO revealed the unique sequences that could be assigned to 34 vocabularies. In the KEGG mapping, unique sequences were established as associated with 46 biochemical pathways. These results provided the largest EST collections in AR and will contribute to biosynthetic and biochemical studies that lead to drug improvement. With respect to the genes related to metabolism and biosynthesis pathway were also found. Our work demonstrated the utility of 454 GS FLX as a method for the rapid and cost-effective identification of AR transcriptome, and this EST dataset will be a powerful resource for further studies such as taxonomy, molecular breeding, and secondary metabolism in AR.

A novel cohort of cancer-testis biomarker genes revealed through meta-analysis of clinical data sets.

The identification of cancer-specific biomolecules is of fundamental importance to the development of diagnostic and/or prognostic markers, which may also serve as therapeutic targets. Some antigenic proteins are only normally present in male gametogenic tissues in the testis and not in normal somatic cells. When these proteins are aberrantly produced in cancer they are referred to as cancer/testis (CT) antigens (CTAs). Some CTA genes have been proven to encode immunogenic proteins that have been used as successful immunotherapy targets for various forms of cancer and have been implicated as drug targets. Here, a targeted in silico analysis of cancer expressed sequence tag (EST) data sets resulted in the identification of a significant number of novel CT genes. The expression profiles of these genes were validated in a range of normal and cancerous cell types. Subsequent meta-analysis of gene expression microarray data sets demonstrates that these genes are clinically relevant as cancer-specific biomarkers, which could pave the way for the discovery of new therapies and/or diagnostic/prognostic monitoring technologies.

Tissue-Point Motion Tracking in the Tongue From Cine MRI and Tagged MRI

PURPOSE Accurate tissue motion tracking within the tongue can help professionals diagnose and treat vocal tract-related disorders, evaluate speech quality before and after surgery, and conduct various scientific studies. The authors compared tissue tracking results from 4 widely used deformable registration (DR) methods applied to cine magnetic resonance imaging (MRI) with harmonic phase (HARP)-based tracking applied to tagged MRI. METHOD Ten subjects repeated the phrase "a geese" multiple times while sagittal images of the head were collected at 26 Hz, first in a tagged MRI data set and then in a cine MRI data set. HARP tracked the motion of 8 specified tissue points in the tagged data set. Four DR methods including diffeomorphic demons and free-form deformations based on cubic B-spline with 3 different similarity measures were used to track the same 8 points in the cine MRI data set. Individual points were tracked and length changes of several muscles were calculated using the DR- and HARP-based tracking methods. RESULTS The results showed that the DR tracking errors were nonsystematic and varied in direction, amount, and timing across speakers and within speakers. Comparison of HARP and DR tracking with manual tracking showed better tracking results for HARP except at the tongue surface, where mistracking caused greater errors in HARP than DR. CONCLUSIONS Tissue point tracking using DR tracking methods contains nonsystematic tracking errors within and across subjects, making it less successful than tagged MRI tracking within the tongue. However, HARP sometimes mistracks points at the tongue surface of tagged MRI because of its limited bandpass filter and tag pattern fading, so that DR has better success measuring surface tissue points on cine MRI than HARP does. Therefore, a hybrid method is being explored.

Survival and remigration probabilities for loggerhead turtles (Caretta caretta) nesting in the eastern Gulf of Mexico

Few long-term mark-recapture tagging datasets exist to estimate population parameters for loggerhead sea turtle (Caretta caretta) recovery units. Using a two-state open robust design model, we analyzed a 20-year (1990–2009) mark-recapture dataset from the Keewaydin Island loggerhead nesting assemblage off the southwest coast of Florida (USA) in the eastern Gulf of Mexico. For this analysis, 2,292 turtle encounters were evaluated, representing 841 individual nesting turtles. Survival was estimated at 0.73 (95 % CI 0.69–0.76). This estimate is comparable with survival estimates elsewhere in the Peninsular Florida subpopulation and is among the lowest estimates for the Northwest Atlantic loggerhead population. We documented no changes in remigration rates or clutch frequency over time. These are the first survival and remigration probabilities estimated for a loggerhead nesting assemblage in the eastern Gulf of Mexico.

Dealing with the long tail: Providing uniformity to compound tags

In using social tags, it has been a challenge to deal with the long tail of the tag distribution. A good portion of tag distribution includes compound tags. Based on the observation that the various forms of compound tags exist in a tag data set, this study tests a way to process various compound tag forms into a uniformed form. The tag uniformity process is introduced with the decomposition algorithm by identifying forms of compound tags. With the tag uniformity process, this study explores the potential of better use of social tags by reducing tag noise and shortening the long tail of the tag distribution. In addition, it is expected that the uniformity process will enhance the effectiveness of the measurements for tag use such as tag frequency. The results demonstrate that the tag uniformity process can successfully shorten the long tail and make the tag frequency precise as a measurement. Although the uniformity process may not solve all the issues related to the long tail, it can be implicated for improving tag analysis and services using tags. The benefits and limitations as well as potential implications of the tag uniformity process for tag analysis and use are discussed.