Muscle activity during multi-step descent.

Background: Previous step studies have shown mechanical variances across steps in descent; however, muscle activity differences have not been examined across steps in a staircase. The purpose of this study was to quantify differences in muscle activity during step descent between step strategies (step-over-step and step-match) and across steps.

Methods: Twenty-five individuals descended a seven-step staircase at self-selected pace (rise: 15.

Equine uveitis: Outcome and adverse effects after one or two intravitreal low-dose gentamicin injections.

Background: Uveitis is common in horses, potentially turning chronic (persistent or recurrent) resulting in impaired vision or blindness. All mainstay therapeutics aims at controlling inflammation, but long-term or lifelong treatment is often needed with possibly severe side effects. Therefore, intravitreal injections with low-dose gentamicin (IVGI) have been used in attempt to give a long-lasting result with potentially less side effects.

Fast and accurate genomic analyses using genome graphs.

The human reference genome serves as the foundation for genomics by providing a scaffold for alignment of sequencing reads, but currently only reflects a single consensus haplotype, thus impairing analysis accuracy. Here we present a graph reference genome implementation that enables read alignment across 2,800 diploid genomes encompassing 12.6 million SNPs and 4.

Strelka2: fast and accurate calling of germline and somatic variants.

We describe Strelka2 ( https://github.com/Illumina/strelka ), an open-source small-variant-calling method for research and clinical germline and somatic sequencing applications. Strelka2 introduces a novel mixture-model-based estimation of insertion/deletion error parameters from each sample, an efficient tiered haplotype-modeling strategy, and a normal sample contamination model to improve liquid tumor analysis.

Amniotic membrane transplantation for ligneous conjunctivitis in a doberman.

An approximately 2-year-old female Doberman Pinscher was referred for the evaluation of bilateral, chronic proliferative conjunctivitis. Ophthalmic examination revealed bilateral thick, opaque pseudomembranes originating from the conjunctivae that prevented visualization of the cornea and interior structures of the eye. Histopathological findings of biopsies of the pseudomembranes were consistent with ligneous conjunctivitis.

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.

Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of 17 individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased "Platinum" variant catalog of 4.

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.

Unlabelled: : We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50× genomic coverage is analyzed in less than 20 min. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs.

RaptorX server: a resource for template-based protein structure modeling.

Assigning functional properties to a newly discovered protein is a key challenge in modern biology. To this end, computational modeling of the three-dimensional atomic arrangement of the amino acid chain is often crucial in determining the role of the protein in biological processes. We present a community-wide web-based protocol, RaptorX server ( http://raptorx.

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms.

Summary: An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (Isaac Variant Caller) have been developed. We demonstrate that our combined pipeline (Isaac) is four to five times faster than BWA + GATK on equivalent hardware, with comparable accuracy as measured by trio conflict rates and sensitivity. We further show that Isaac is effective in the detection of disease-causing variants and can easily/economically be run on commodity hardware.

Cholesterol modulates cell signaling and protein networking by specifically interacting with PDZ domain-containing scaffold proteins.

Cholesterol is known to modulate the physical properties of cell membranes, but its direct involvement in cellular signaling has not been thoroughly investigated. Here we show that cholesterol specifically binds many PDZ domains found in scaffold proteins, including the N-terminal PDZ domain of NHERF1/EBP50. This modular domain has a cholesterol-binding site topologically distinct from its canonical protein-binding site and serves as a dual-specificity domain that bridges the membrane and juxta-membrane signaling complexes.

A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains.

Motivation: Peripheral membrane-targeting domain (MTD) families, such as C1-, C2- and PH domains, play a key role in signal transduction and membrane trafficking by dynamically translocating their parent proteins to specific plasma membranes when changes in lipid composition occur. It is, however, difficult to determine the subset of domains within families displaying this property, as sequence motifs signifying the membrane binding properties are not well defined. For this reason, procedures based on sequence similarity alone are often insufficient in computational identification of MTDs within families (yielding less than 65% accuracy even with a sequence identity of 70%).

Template-based protein structure modeling using the RaptorX web server.

A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.

Evaluation of cytologic findings in feline conjunctivitis.

Background: Cytologic examination of smears prepared from ocular swabs of conjunctiva from cats with conjunctivitis permits identification of the type of inflammation and possibly specific microorganisms. Results of studies of the diagnostic utility of cytology for detection of infectious causes of feline conjunctivitis have been inconsistent.

Objectives: The objectives of this study were to describe cytologic findings in cats with conjunctivitis and to compare those findings with results of PCR analysis for feline herpesvirus (FHV-1), Chlamydophila felis (C felis), and Mycoplasma felis (M felis).

Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions.

Emerging evidence indicates that membrane lipids regulate protein networking by directly interacting with protein-interaction domains (PIDs). As a pilot study to identify and functionally annodate lipid-binding PIDs on a genomic scale, we performed experimental and computational studies of PDZ domains. Characterization of 70 PDZ domains showed that ~40% had submicromolar membrane affinity.

An improved machine learning protocol for the identification of correct Sequest search results.

Background: Mass spectrometry has become a standard method by which the proteomic profile of cell or tissue samples is characterized. To fully take advantage of tandem mass spectrometry (MS/MS) techniques in large scale protein characterization studies robust and consistent data analysis procedures are crucial. In this work we present a machine learning based protocol for the identification of correct peptide-spectrum matches from Sequest database search results, improving on previously published protocols.

Structural feature extraction protocol for classifying reversible membrane binding protein domains.

Machine learning based classification protocols for automated function annotation of protein structures have in many instances proven superior to simpler sequence based procedures. Here we present an automated method for extracting features from protein structures by construction of surface patches to be used in such protocols. The utility of the developed patch-growing procedure is exemplified by its ability to identify reversible membrane binding domains from the C1, C2, and PH families.

The use of amniotic membrane transplantation for ocular surface reconstruction: a review and series of 58 equine clinical cases (2002-2008).

Amniotic membrane transplantation (AMT) is an effective clinical therapy for reconstruction of the ocular surface in human and veterinary patients. Amnion is avascular and strong, contains antiangiogenic and antiinflammatory properties and growth factors, and has properties that prevent or decrease fibrosis in healing tissue. Indications for its use are steadily growing and include grafting to replace diseased, missing or excised tissue, patching to support diseased tissue during the healing process and as a substrate for the expansion of epithelial cells for transplantation to the cornea.

Molecular basis of the potent membrane-remodeling activity of the epsin 1 N-terminal homology domain.

The mechanisms by which cytosolic proteins reversibly bind the membrane and induce the curvature for membrane trafficking and remodeling remain elusive. The epsin N-terminal homology (ENTH) domain has potent vesicle tubulation activity despite a lack of intrinsic molecular curvature. EPR revealed that the N-terminal alpha-helix penetrates the phosphatidylinositol 4,5-bisphosphate-containing membrane at a unique oblique angle and concomitantly interacts closely with helices from neighboring molecules in an antiparallel orientation.

Iris abscesses with and without intralenticular fungal invasion in the horse.

Objective: To describe clinical and histologic findings in horses with iris abscesses. Design Retrospective medical records study.

Animals Studied: Medical records of horses that had iris abscesses at the University of Florida Veterinary Medical Center, Peterson & Smith Equine Hospital, and Veterinary Eye Specialists of London, Ontario, from 2005 to 2008 were reviewed.

Mechanical signaling on the single protein level studied using steered molecular dynamics.

Efficient communication between the cell and its external environment is of the utmost importance to the function of multicellular organisms. While signaling events can be generally characterized as information exchange by means of controlled energy conversion, research efforts have hitherto mainly been concerned with mechanisms involving chemical and electrical energy transfer. Here, we review recent computational efforts addressing the function of mechanical force in signal transduction.

Deep lamellar endothelial keratoplasty in 10 horses.

Objective: To describe and evaluate a surgical technique utilized for the therapy of deep corneal stromal abscesses (DSA) in horses. The DSA is excised and replaced with a partial thickness corneal lamellar allograft.

Methods: A retrospective clinical study describing the indications for the surgical technique utilized and the outcomes of this procedure in 10 eyes of 10 horses.

Use of a biosynthetic material to repair the surgical defect following excision of an epibulbar melanoma in a cat.

A limbal melanoma was surgically excised from the OS of a 4-year-old castrated male Domestic Short-haired cat (DSH). The resultant scleral defect was repaired by placement of A-cell bio-scaffold material. The patient responded well in the postoperative period with no apparent discomfort, nor any observable complications.

Myocilin protein levels in the aqueous humor of the glaucomas in selected canine breeds.

Objective: To compare aqueous humor myocilin protein levels in dogs with the primary glaucomas to those with the secondary glaucomas, primary cataracts, and diabetic cataracts.

Materials And Methods: Four groups were selected, based on diagnosis by the attending veterinary ophthalmologists and included: primary glaucoma (primary open-angle glaucoma (POAG) and primary closed angle glaucoma (PCAG); n = 155); secondary glaucoma (n = 94); primary (presumed inherited) cataract (n = 142), and diabetic cataract (n = 83). A total of 474 samples (187 males, 263 females, 24 unreported) with average ages of 117 months for the males and 101 months for the females were analyzed.