Image resonance in the many-body density of states at a metal surface

The electronic properties of a semi-infinite metal surface without a bulk gap are studied by a formalism that is able to account for the continuous spectrum of the system. The density of states at the surface is calculated within the GW approximation of many-body perturbation theory. We demonstrate the presence of an unoccupied surface resonance peaked at the position of the first image state. The resonance encompasses the whole Rydberg series of image states and cannot be resolved into individual peaks. Its origin is the shift in spectral weight when many-body correlation effects are taken into account

The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish

The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). It serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. Subsections of the database are tightly related, allowing a user with a sequence or search string of interest to navigate seamlessly from one area to another. As catfish genome sequencing proceeds and ongoing quantitative trait loci (QTL) projects bear fruit, cBARBEL will allow rapid data integration and dissemination within the catfish research community and to interested stakeholders. cBARBEL can be accessed at http://catfishgenome.org

Interactive handwriting recognition with limited user effort

The final publication is available at Springer via http://dx.doi.org/10.1007/s10032-013-0204-5[EN] Transcription of handwritten text in (old) documents is an important, time-consuming task for digital libraries. Although post-editing automatic recognition of handwritten text is feasible, it is not clearly better than simply ignoring it and transcribing the document from scratch. A more effective approach is to follow an interactive approach in which both the system is guided by the user, and the user is assisted by the system to complete the transcription task as efficiently as possible. Nevertheless, in some applications, the user effort available to transcribe documents is limited and fully supervision of the system output is not realistic. To circumvent these problems, we propose a novel interactive approach which efficiently employs user effort to transcribe a document by improving three different aspects. Firstly, the system employs a limited amount of effort to solely supervise recognised words that are likely to be incorrect. Thus, user effort is efficiently focused on the supervision of words for which the system is not confident enough. Secondly, it refines the initial transcription provided to the user by recomputing it constrained to user supervisions. In this way, incorrect words in unsupervised parts can be automatically amended without user supervision. Finally, it improves the underlying system models by retraining the system from partially supervised transcriptions. In order to prove these statements, empirical results are presented on two real databases showing that the proposed approach can notably reduce user effort in the transcription of handwritten text in (old) documents.The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under Grant Agreement No 287755 (transLectures). Also supported by the Spanish Government (MICINN, MITyC, "Plan E", under Grants MIPRCV "Consolider Ingenio 2010", MITTRAL (TIN2009-14633-C03-01), erudito.com (TSI-020110-2009-439), iTrans2 (TIN2009-14511), and FPU (AP2007-02867), and the Generalitat Valenciana (Grants Prometeo/2009/014 and GV/2010/067).Serrano Martinez Santos, N.; Giménez Pastor, A.; Civera Saiz, J.; Sanchis Navarro, JA.; Juan Císcar, A. (2014). Interactive handwriting recognition with limited user effort. International Journal on Document Analysis and Recognition. 17(1):47-59. https://doi.org/10.1007/s10032-013-0204-5S4759171Agua, M., Serrano, N., Civera, J., Juan, A.: Character-based handwritten text recognition of multilingual documents. In: Proceedings of Advances in Speech and Language Technologies for Iberian Languages (IBERSPEECH 2012), Madrid (Spain), pp. 187–196 (2012)Ahn, L.V., Maurer, B., Mcmillen, C., Abraham, D., Blum, M.: reCAPTCHA: human-based character recognition via web security measures. 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In: Proceedings of the 10th International Conference on Document Analysis and Recognition, Barcelona (Spain), pp. 301–305 (2009)Plötz, T., Fink, G.A.: Markov models for offline handwriting recognition: a survey. Int. J. Doc. Anal. Recognit. 12(4), 269–298 (2009)Quiniou, S., Cheriet, M., Anquetil, E.: Error handling approach using characterization and correction steps for handwritten document analysis. Int. J. Doc. Anal. Recognit. 15(2), 125–141 (2012)Rodríguez, L., García-Varea, I., Vidal, E.: Multi-modal computer assisted speech transcription. In: International Conference on Multimodal Interfaces and the Workshop on Machine Learning for Multimodal Interaction, ACM, New York, NY, USA, pp. 30:1–30:7 (2010)Serrano, N., Pérez, D., Sanchis, A., Juan, A.: Adaptation from partially supervised handwritten text transcriptions. In: Proceedings of the 11th International Conference on Multimodal Interfaces and the 6th Workshop on Machine Learning for Multimodal Interaction, Cambridge, MA (USA), pp. 289–292 (2009)Serrano, N., Castro, F., Juan, A.: The RODRIGO database. In: Proceedings of the 7th International Conference on Language Resources and Evaluation, Valleta (Malta), pp. 2709–2712 (2010)Serrano, N., Giménez, A., Sanchis, A., Juan, A.: Active learning strategies for handwritten text transcription. In: Proceedings of the 12th International Conference on Multimodal Interfaces and the 7th Workshop on Machine Learning for Multimodal, Interaction, Beijing (China) (2010)Serrano, N., Sanchis, A., Juan, A.: Balancing error and supervision effort in interactive-predictive handwriting recognition. In: Proceedings of the 15th International Conference on Intelligent User Interfaces, Hong Kong (China), pp. 373–376 (2010)Serrano, N., Tarazón, L., Pérez, D., Ramos-Terrades, O., Juan, A.: The GIDOC prototype. 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A pilot study for channel catfish whole genome sequencing and de novo assembly

<p>Abstract</p> <p>Background</p> <p>Recent advances in next-generation sequencing technologies have drastically increased throughput and significantly reduced sequencing costs. However, the average read lengths in next-generation sequencing technologies are short as compared with that of traditional Sanger sequencing. The short sequence reads pose great challenges for <it>de novo </it>sequence assembly. As a pilot project for whole genome sequencing of the catfish genome, here we attempt to determine the proper sequence coverage, the proper software for assembly, and various parameters used for the assembly of a BAC physical map contig spanning approximately a million of base pairs.</p> <p>Results</p> <p>A combination of low sequence coverage of 454 and Illumina sequencing appeared to provide effective assembly as reflected by a high N50 value. Using 454 sequencing alone, a sequencing depth of 18 X was sufficient to obtain the good quality assembly, whereas a 70 X Illumina appeared to be sufficient for a good quality assembly. Additional sequencing coverage after 18 X of 454 or after 70 X of Illumina sequencing does not provide significant improvement of the assembly. Considering the cost of sequencing, a 2 X 454 sequencing, when coupled to 70 X Illumina sequencing, provided an assembly of reasonably good quality. With several software tested, Newbler with a seed length of 16 and ABySS with a K-value of 60 appear to be appropriate for the assembly of 454 reads alone and Illumina paired-end reads alone, respectively. Using both 454 and Illumina paired-end reads, a hybrid assembly strategy using Newbler for initial 454 sequence assembly, Velvet for initial Illumina sequence assembly, followed by a second step assembly using MIRA provided the best assembly of the physical map contig, resulting in 193 contigs with a N50 value of 13,123 bp.</p> <p>Conclusions</p> <p>A hybrid sequencing strategy using low sequencing depth of 454 and high sequencing depth of Illumina provided the good quality assembly with high N50 value and relatively low cost. A combination of Newbler, Velvet, and MIRA can be used to assemble the 454 sequence reads and the Illumina reads effectively. The assembled sequence can serve as a resource for comparative genome analysis. Additional long reads using the third generation sequencing platforms are needed to sequence through repetitive genome regions that should further enhance the sequence assembly.</p

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor β (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter

Deep Lenses of Circumpolar Water in the Argentine Basin

Three deep anticyclonic eddies of a species only reported once before [ Gordon and Greengrove, 1986 ] were intersected by hydrographic lines of the World Ocean Circulation Experiment (WOCE) and South Atlantic Ventilation Experiment (SAVE) programs in the Argentine Basin. The vortices are centered near 3500 m depth at the interface between North Atlantic Deep Water and Bottom Water. They have ∼1500-m-thick cores containing Lower Circumpolar Deep Water and a dynamic influence that may span up to two thirds of the water column. As one eddy was observed just downstream of the western termination of the Falkland Escarpment, a destabilization of the deep boundary current by the sudden slope relaxation is suggested as a potential cause of eddy formation. Besides isopycnal interleaving at the eddy perimeters, strongly eroded core properties in the upper parts of the lenses, associated with low density ratios, hint at double diffusion at the top of the structures as another major decay mechanism. The presence of an eddy in the northern Argentine Basin shows the possibility for a northward drift of the vortices, in this basin at least. Deep events in recent current measurements from the Vema Channel are presented that raise the question of further equatorward motion to the Brazil Basin

A novel family of diversified immunoregulatory receptors in teleosts is homologous to both mammalian Fc receptors and molecules encoded within the leukocyte receptor complex

Three novel and closely related leukocyte immune-type receptors (IpLITR) have been identified in channel catfish (Ictalurus punctatus). These receptors belong to a large polymorphic and polygenic subset of the Ig superfamily with members located on at least three independently segregating loci. Like mammalian and avian innate immune regulatory receptors, IpLITRs have both putative inhibitory and stimulatory forms, with multiple types coexpressed in various lymphoid tissues and clonal leukocyte cell lines. IpLITRs have an unusual and novel relationship to mammalian and avian innate immune receptors: the membrane distal Ig domains of an individual IpLITR are related to fragment crystallizable receptors (FcRs) and FcR-like proteins, whereas the membrane proximal Ig domains are related to several leukocyte receptor complex encoded receptors. This unique composition of Ig domains within individual receptors supports the hypothesis that functionally and genomically distinct immune receptor families found in tetrapods may have evolved from such ancestral genes by duplication and recombination events. Furthermore, the discovery of a large heterogeneous family of immunoregulatory receptors in teleosts, reminiscent of amphibian, avian, and mammalian Ig-like receptors, suggests that complex innate immune receptor networks have been conserved during vertebrate evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available for this article at http://dx.doi.org/10.1007/s00251-006-0134-1 and is accessible for authorized users

Generation of the first BAC-based physical map of the common carp genome

<p>Abstract</p> <p>Background</p> <p>Common carp (<it>Cyprinus carpio</it>), a member of Cyprinidae, is the third most important aquaculture species in the world with an annual global production of 3.4 million metric tons, accounting for nearly 14% of the all freshwater aquaculture production in the world. Apparently genomic resources are needed for this species in order to study its performance and production traits. In spite of much progress, no physical maps have been available for common carp. The objective of this project was to generate a BAC-based physical map using fluorescent restriction fingerprinting.</p> <p>Result</p> <p>The first generation of common carp physical map was constructed using four- color High Information Content Fingerprinting (HICF). A total of 72,158 BAC clones were analyzed that generated 67,493 valid fingerprints (5.5 × genome coverage). These BAC clones were assembled into 3,696 contigs with the average length of 476 kb and a N50 length of 688 kb, representing approximately 1.76 Gb of the common carp genome. The largest contig contained 171 BAC clones with the physical length of 3.12 Mb. There are 761 contigs longer than the N50, and these contigs should be the most useful resource for future integrations with linkage map and whole genome sequence assembly. The common carp physical map is available at <url>http://genomics.cafs.ac.cn/fpc/WebAGCoL/Carp/WebFPC/</url>.</p> <p>Conclusion</p> <p>The reported common carp physical map is the first physical map of the common carp genome. It should be a valuable genome resource facilitating whole genome sequence assembly and characterization of position-based genes important for aquaculture traits.</p