Pairing in two-dimensional boson-fermion mixtures

The possibilities of pairing in two-dimensional boson-fermion mixtures are carefully analyzed. It is shown that the boson-induced attraction between two identical fermions dominates the p wave pairing at low density. For a given fermion density, the pairing gap becomes maximal at a certain optimal boson concentration. The conditions for observing pairing in current experiments are discussed.

TwHistory : Sharing History Using Twitter

In light of the fact that several studies indicate that students can benefit from deeper understandings of the processes by which historical accounts are constructed, history educators have increasingly been focused on finding ways to teach students how to read and reason about events in the same manner as professional historians (Wineburg, 2001; Spoehr & Spoehr, 1994; Hynd, Holschuh, & Hubbard, 2004; Wiley & Voss, 1996). One possible resource for supporting this development may come out of emerging web-based technologies. New technologies and increased access to historical records and artifacts posted the Internet may be precisely the tools that can help students (Bass, Rosenzweig, & Mason, 1999). Given the right context, we believe it is possible to combine such resources and tools to create an environment for students that could strengthen their abilities to read and reason about historical events. Moreover, we believe that social media, specifically, microblogging (Nardi, Schiano, Gumbrecht, & Swartz, 2004) could play a key role.

Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.

GENCODE: producing a reference annotation for ENCODE

Background: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manualannotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.Results: The GENCODE gene features are divided into eight different categories of which onlythe first two (known and novel coding sequence) are confidently predicted to be protein-codinggenes. 5’ rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentallyverify the initial annotation. Of the 420 coding loci tested, 229 RACE products have beensequenced. They supported 5’ extensions of 30 loci and new splice variants in 50 loci. In addition,46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15putative transcripts. We assessed the comprehensiveness of the GENCODE annotation byattempting to validate all the predicted exon boundaries outside the GENCODE annotation. Outof 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only twoof them in intergenic regions.Conclusions: In total, 487 loci, of which 434 are coding, have been annotated as part of theGENCODE reference set available from the UCSC browser. Comparison of GENCODEannotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained withinthe two sets, which is a reflection of the high number of alternative splice forms with uniqueexons annotated. Over 50% of coding loci have been experimentally verified by 5’ RACE forEGASP and the GENCODE collaboration is continuing to refine its annotation of 1% humangenome with the aid of experimental validation.

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: We present the results of EGASP, a community experiment to assess the state-ofthe-art in genome annotation within the ENCODE regions, which span 1% of the human genomesequence. The experiment had two major goals: the assessment of the accuracy of computationalmethods to predict protein coding genes; and the overall assessment of the completeness of thecurrent human genome annotations as represented in the ENCODE regions. For thecomputational prediction assessment, eighteen groups contributed gene predictions. Weevaluated these submissions against each other based on a ‘reference set’ of annotationsgenerated as part of the GENCODE project. These annotations were not available to theprediction groups prior to the submission deadline, so that their predictions were blind and anexternal advisory committee could perform a fair assessment.Results: The best methods had at least one gene transcript correctly predicted for close to 70%of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into accountalternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotidelevel, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programsrelying on mRNA and protein sequences were the most accurate in reproducing the manuallycurated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could beverified.Conclusions: This is the first such experiment in human DNA, and we have followed thestandards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe theresults presented here contribute to the value of ongoing large-scale annotation projects and shouldguide further experimental methods when being scaled up to the entire human genome sequence.

K-Rb Fermi-Bose mixtures: Vortex states and sag

We study a confined mixture of bosons and fermions in the quantal degeneracy regime with attractive boson-fermion interaction. We discuss the effect that the presence of vortical states and the displacement of the trapping potentials may have on mixtures near collapse, and investigate the phase stability diagram of the K-Rb mixture in the mean-field approximation supposing in one case that the trapping potentials felt by bosons and fermions are shifted from each other, as it happens in the presence of a gravitational sag, and in another case, assuming that the Bose condensate sustains a vortex state. In both cases, we have obtained an analytical expression for the fermion effective potential when the Bose condensate is in the Thomas-Fermi regime, that can be used to determine the maxima of the Fermionic density. We have numerically checked that the values one obtains for the location of these maxima using the analytical formulas remain valid up to the critical boson and fermion numbers, above which the mixture collapses.

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

A comparison of the dental status and treatment needs of older adults with and without chronic mental illness in Sevilla, Spain

Objectives: To study the dental status and treatment needs of institutionalized older adults with chronic mental illness compared to a non-psychiatric control sample. Study Design: The sample size was 100, in which 50 were psychogeriatric patients (study group; SG) classified according to DSM-IV, with a mean age of 69.6 ± 6.7 years, and 50 non-psychiatric patients (control group; CG), with a mean age of 68.3 ± 6.9 years. Clinical oral health examinations were conducted and caries were recorded clinically using the Decayed, Missing and Filled Teeth Index (DMFT). Results were analyzed statistically using the Student"s t-test or analysis of variance. Results: Caries prevalence was 58% and 62% in SG and CG, respectively. DMFT index was 28.3 ± 6.6 in SG and 21.4 ± 6.07 in CG (p < 0.01). Mean number of decayed teeth was higher in SG (3.1) compared to CG (1.8) (p=0.047). Mean number of missing teeth were 25.2 and 16.4 in SG and CG respectively (p<0.05). DMFT scores were higher in SG in all the age groups (p < 0.01). Mean number of teeth per person needing treatment was 3.4 in SG and 1.9 in CG (p= 0.037). The need for restorative dental care was significantly lower in the SG (0.8 teeth per person) than in the CG (1.7 teeth per person) (p = 0.043). Conclusions: Institutionalized psychiatric patients have significantly worse dental status and more dental treatment needs than non-psychiatric patients.

Study of the effect of oral health on physical condition of professional soccer players of the Football Club Barcelona

Objectives: The objective of this study was to evaluate the oral health status of professional soccer players of F.C. Barcelona and its relation to the incidence of sport lesions. Methods: Thirty professional soccer players were consecutively evaluated in the seasons 2003/4, 2004/5 and 2005/6. A research protocol to assess their oral health was developed. DMFT, Quigley & Hein plaque index (PI), Löe & Silness gingival index (GI), World Health Organization malocclusion index, Ramfjord teeth probing pocket depth (PPD), TMJ examination and history of dental trauma were recorded. All physical injuries sustained by players during the season were documented from F.C. Barcelona medical services. Results: Mean DMFT score was 5.7 (SD 4.1), Quigley & Hein plaque index score was 2.3 (SD 1.1), Löe & Silness gingival index was 1.1 (SD 0.8), and periodontal pocket depth was 1.9 mm (SD 0.3). Pearson"s analysis showed a significant correlation between PI and GI (p<0.01). Nine players (30%) presented bruxism - the same proportion of those with severe malocclusion. Seven (23.3%) players had suffered uncomplicated crown fractures. The mean incidence of physical injuries was 8 (SD 3.4) per player. PI and PPD showed a statistically significant correlation to muscle injuries (p<0.05). Conclusions: Soccer players, despite intensive medical follow-up, have significant oral health problems such as untreated caries, gingivitis or malocclusion, and suffer dental trauma as a result of sports activities. Their physical condition could also be associated to oral health

Bose-Fermi mixtures in optical lattices

Using mean field theory, we have studied Bose-Fermi mixtures in a one-dimensional optical lattice in the case of an attractive boson-fermion interaction. We consider that the fermions are in the degenerate regime and that the laser intensities are such that quantum coherence across the condensate is ensured. We discuss the effect of the optical lattice on the critical rotational frequency for vortex line creation in the Bose-Einstein condensate, as well as how it affects the stability of the boson-fermion mixture. A reduction of the critical frequency for nucleating a vortex is observed as the strength of the applied laser is increased. The onset of instability of the mixture occurs for a sizably lower number of fermions in the presence of a deep optical lattice.

Fast generation of spin-squeezed states in bosonic Josephson junctions

We describe methods for the fast production of highly coherent-spin-squeezed many-body states in bosonic Josephson junctions. We start from the known mapping of the two-site Bose-Hubbard (BH) Hamiltonian to that of a single effective particle evolving according to a Schrödinger-like equation in Fock space. Since, for repulsive interactions, the effective potential in Fock space is nearly parabolic, we extend recently derived protocols for shortcuts to adiabatic evolution in harmonic potentials to the many-body BH Hamiltonian. A comparison with current experiments shows that our methods allow for an important reduction in the preparation times of highly squeezed spin states.

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrodinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge.net/