SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.

SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto the human reference genome and is at least 7.

Reaction of an osmium(VI) nitrido complex with cyanide: formation and reactivity of an osmium(III) hydrogen cyanamide complex.

Reaction of [Os(VI)(N)(L(1))(Cl)(OH(2))] (1) with CN(-) under various conditions affords (PPh(4))[Os(VI)(N)(L(1))(CN)(Cl)] (2), (PPh(4))(2)[Os(VI)(N)(L(2))(CN)(2)] (3), and a novel hydrogen cyanamido complex, (PPh(4))(2)[Os(III){N(H)CN}(L(3))(CN)(3)] (4). Compound 4 reacts readily with both electrophiles and nucleophiles. Protonation and methylation of 4 produce (PPh(4))[Os(III)(NCNH(2))(L(3))(CN)(3)] (5) and (PPh(4))[Os(III)(NCNMe(2))(L(3))(CN)(3)] (6), respectively.

Metallo-macrocycles with labile coordination sites through self assembly: binuclear phenyl bridged bisbipyridine manganese complexes.

Self assembly of phenyl bridged bisbipyridines with manganese perchlorate gave structurally different metallo-macrocycles having cis-labile coordination sites which can catalyse olefin epoxidation with peracetic acid in good yield.

Luminescent rhenium(I) complexes with acetylamino- and trifluoroacetylamino-containing phenanthroline ligands: anion-sensing study.

A series of rhenium complexes with acetylamino- and trifluoroacetylamino-containing 1,10-phenanthroline ligands have been synthesized, characterized and their photophysical and electrochemical properties studied. These complexes were found to show significant UV-vis and emission changes on addition of CN(-), F(-) and AcO(-) anions. Their reactivity towards CN(-), F(-) and AcO(-) anions, was also investigated by UV-vis, emission and (1)H NMR spectroscopy.

Patterns and predictors of short-term death after emergency department discharge.

Study Objective: The emergency department (ED) is an inherently high-risk setting. Early death after an ED evaluation is a rare and devastating outcome; understanding it can potentially help improve patient care and outcomes. Using administrative data from an integrated health system, we describe characteristics and predictors of patients who experienced 7-day death after ED discharge.

Serial measurement of tear meniscus by FD-OCT after instillation of artificial tears in patients with dry eyes.

Background And Objective: To use Fourier-domain optical coherence tomography (FD-OCT) to study the effect of artificial tears on the tear meniscus in patients with dry eyes.

Patients And Methods: The lower tear meniscus of 16 consecutive patients with dry eyes was imaged by an FD-OCT system (RTVue; Optovue, Inc., Fremont, CA).

Novel heterobimetallic ruthenium(III)-cobalt(II) compounds constructed from trans-[Ru(III)(Q)2(CN)2](-) (Q = 8-quinolinolato): synthesis, structures and magnetic properties.

Reaction of [Ru(II)(PPh(3))(3)Cl(2)] with HQ and KCN produces a new dicyanoruthenium(III) building block, [Ru(III)(Q)(2)(CN)(2)](-). It reacts with hydrated CoCl(2) in MeOH or DMF to produce a trinuclear compound 2 or a 1-D zigzag chain 3.

Management of Corneal Graft Rejection - A Case Series Report and Review of the Literature.

PURPOSE: To report long-term results in a case series of patients treated with systemic immune suppression for prevention of penetrating keratoplasty (PKP) graft rejection. DESIGN: Retrospective noncomparative chart review. PARTICIPANTS: Three patients presented with PKP graft failure.

Meta-IDBA: a de Novo assembler for metagenomic data.

Motivation: Next-generation sequencing techniques allow us to generate reads from a microbial environment in order to analyze the microbial community. However, assembling of a set of mixed reads from different species to form contigs is a bottleneck of metagenomic research. Although there are many assemblers for assembling reads from a single genome, there are no assemblers for assembling reads in metagenomic data without reference genome sequences.

RNASAlign: RNA structural alignment system.

Motivation: Structural alignment of RNA is found to be a useful computational technique for idenitfying non-coding RNAs (ncRNAs). However, existing tools do not handle structures with pseudoknots. Although algorithms exist that can handle structural alignment for different types of pseudoknots, no software tools are available and users have to determine the type of pseudoknots to select the appropriate algoirthm to use which limits the usage of structural alignment in identifying novel ncRNAs.

Local structural alignment of RNA with affine gap model.

Background: Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps.

Results: In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model.

Synthesis, functionalization, characterization, and photophysical study of carbonyl-containing isocyano rhenium(I) diimine complexes.

New classes of tunable rhenium(I) diimine luminophores with formula of [Re(CO)(CNR)(3)(N-N)]PF(6) and [Re(CO)(L(x))(CNC(6)H(4)Cl-4)(2)(1,10-phenanthroline)]PF(6), (R = C(6)H(5), 4-BrC(6)H(4), 4-ClC(6)H(4), 4-MeOC(6)H(4), 2,6-(i)Pr(2)C(6)H(3); N-N = 1,10-phenanthroline, 5,6-dibromo-1,10-phenanthroline, 4,4'-di-tert-butyl-2,2'-bipyridine; L(x) = MeCN, pyridine and PPh(3)) have been synthesized. Different synthetic routes including photo-ligand substitution and thermal carbonyl ligand substitution through the oxidative decarbonylation with trimethyl amine N-oxide, for the facial and meridional isomeric forms of [Re(CO)(CNR)(3)(N-N)]PF(6) were investigated. On the basis of these synthetic strategies, different ligand modification and functionalization of the rhenium(I) diimine luminophores with tailored excited state properties could be readily achieved.

A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio.

Motivation: With the rapid development of next-generation sequencing techniques, metagenomics, also known as environmental genomics, has emerged as an exciting research area that enables us to analyze the microbial environment in which we live. An important step for metagenomic data analysis is the identification and taxonomic characterization of DNA fragments (reads or contigs) resulting from sequencing a sample of mixed species. This step is referred to as 'binning'.

Memory efficient algorithms for structural alignment of RNAs with pseudoknots.

In this paper, we consider the problem of structural alignment of a target RNA sequence of length n and a query RNA sequence of length m with known secondary structure that may contain simple pseudoknots or embedded simple pseudoknots. The best known algorithm for solving this problem runs in O(mn3) time for simple pseudoknot or O(mn4) time for embedded simple pseudoknot with space complexity of O(mn3) for both structures, which require too much memory making it infeasible for comparing noncoding RNAs (ncRNAs) with length several hundreds or more. We propose memory efficient algorithms to solve the same problem.

Investigation of femtosecond laser--enabled keratoplasty wound geometry using optical coherence tomography.

Purpose: To measure the wound geometry after femtosecond laser-enabled keratoplasty (FLEK) using optical coherence tomography (OCT).

Design: Prospective nonrandomized clinical study and laboratory study.

Participants: Patients who were candidates for penetrating keratoplasty at an academic referral center.

Oxygen evolution from BF3/MnO4-.

MnO(4)(-) is activated by BF(3) to undergo intramolecular coupling of two oxo ligands to generate O(2). DFT calculations suggest that there should be a spin intercrossing between the singlet and triplet potential energy surfaces on going from the active intermediate [MnO(2)(OBF(3))(2)](-) to the O···O coupling transition state.

Improving the accuracy of signal transduction pathway construction using Level-2 neighbours.

In this paper, we consider the problem of reconstructing a pathway for a given set of proteins based on available genomics and proteomics information such as gene expression data. In all previous approaches, the scoring function for a candidate pathway usually only depends on adjacent proteins in the pathway. We propose to also consider proteins that are of distance two in the pathway (we call them Level-2 neighbours).

Amniotic membrane transplantation for restrictive strabismus.

Purpose: To report the use of amniotic membrane transplant in patients with restrictive strabismus.

Design: Retrospective, interventional case series.

Participants: Patients with restrictive strabismus treated with amniotic membrane transplantation.

Binuclear (salen)osmium phosphinidine and phosphiniminato complexes.

The preparation of a number of binuclear (salen)osmium phosphinidine and phosphiniminato complexes using various strategies are described. Treatment of [Os(VI)(N)(L(1))(sol)](X) (sol = H(2)O or MeOH) with PPh(3) affords an osmium(IV) phosphinidine complex [Os(IV){N(H)PPh(3)}(L(1))(OMe)](X) (X = PF(6)1a, ClO(4)1b). If the reaction is carried out in CH(2)Cl(2) in the presence of excess pyrazine the osmium(III) phosphinidine species [Os(III){N(H)PPh(3)}(L(1))(pz)](PF(6)) 2 can be generated.

Structural alignment of RNA with complex pseudoknot structure.

The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature.

Refining orthologue groups at the transcript level.

Background: Orthologues are genes in different species that are related through divergent evolution from a common ancestor and are expected to have similar functions. Many databases have been created to describe orthologous genes based on existing sequence data. However, alternative splicing (in eukaryotes) is usually disregarded in the determination of orthologue groups and the functional consequences of alternative splicing have not been considered.

A data-mining approach for multiple structural alignment of proteins.

Comparing the 3D structures of proteins is an important but computationally hard problem in bioinformatics. In this paper, we propose studying the problem when much less information or assumptions are available. We model the structural alignment of proteins as a combinatorial problem.

Formation of μ-dinitrogen (salen)osmium complexes via ligand-induced N···N coupling of (salen)osmium(VI) nitrides.

Treatment of [N(n)Bu(4)][Os(VI)(N)Cl(4)] with a stoichiometric amount of H(2)L (L = N,N'-bis(salicylidene)-o-cyclohexylenediamine dianion) in the presence of PF(6)(-) or ClO(4)(-) in MeOH affords [Os(VI)(N)(L)(OH(2))](PF(6)) 1a and [Os(VI)(N)(L)(CH(3)OH)](ClO(4)) 1b, respectively. The structure of 1b has been determined by X-ray crystallography and the Os≡N bond distance is 1.627(3) Å.