stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences.

The enzyme Dicer is a component of many small RNA (sRNA) pathways involved in RNA processing for post-transcriptional regulation, anti-viral response and control of transposable elements. Cleavage of double-stranded RNA by Dicer produces a signature overhanging sequence at the 3' end of the sRNA sequence relative to a complementary passenger strand in a RNA duplex. There is a need for reliable tools to computationally search for Dicer cleavage signatures to help characterise families of sRNAs.

piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode.

The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the C. elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway.

Colour plasticity in response to social context and parasitic infection in a self-fertilizing fish.

Many animal species rely on changes in body coloration to signal social dominance, mating readiness and health status to conspecifics, which can in turn influence reproductive success, social dynamics and pathogen avoidance in natural populations. Such colour changes are thought to be controlled by genetic and environmental conditions, but their relative importance is difficult to measure in natural populations, where individual genetic variability complicates data interpretation. Here, we studied shifts in melanin-related body coloration in response to social context and parasitic infection in two naturally inbred lines of a self-fertilizing fish to disentangle the relative roles of genetic background and individual variation.

Smell of Infection: A Novel, Noninvasive Method for Detection of Fish Excretory-Secretory Proteins.

Chemical signals are produced by aquatic organisms following predatory attacks or perturbations such as parasitic infection. Ectoparasites feeding on fish hosts are likely to cause release of similar alarm cues into the environment due to the stress, wounding, and immune response stimulated upon infection. Alarm cues are often released in the form of proteins, antimicrobial peptides, and immunoglobulins that provide important insights into bodily function and infection status.

Immune-Related Transcriptional Responses to Parasitic Infection in a Naturally Inbred Fish: Roles of Genotype and Individual Variation.

Parasites are strong drivers of evolutionary change and the genetic variation of both host and parasite populations can co-evolve as a function of parasite virulence and host resistance. The role of transcriptome variation in specific interactions between host and parasite genotypes has been less studied and can be confounded by differences in genetic variation. We employed two naturally inbred lines of a self-fertilizing fish to estimate the role of host genotype in the transcriptome response to parasite infection using RNA-seq.

Biomarkers of antioxidant status and lipid peroxidation in elderly patients with hypertension.

Objective: The objective of the present study was to examine selected parameters of the blood redox system in elderly patients with hypertension.examine selected parameters of the blood redox system in elderly patients with hypertension.

Methods: We analyzed differences in redox-associated molecules and enzymes among elderly hypertensive subjects (age above 65 years, n = 49) and two groups of normotensive subjects (<65 years old - Control group I; n = 27, and >65 - Control group II; n = 30).

Epigenetic regulation of sex ratios may explain natural variation in self-fertilization rates.

Self-fertilization (selfing) favours reproductive success when mate availability is low, but renders populations more vulnerable to environmental change by reducing genetic variability. A mixed-breeding strategy (alternating selfing and outcrossing) may allow species to balance these needs, but requires a system for regulating sexual identity. We explored the role of DNA methylation as a regulatory system for sex-ratio modulation in the mixed-mating fish Kryptolebias marmoratus.

Procurement of shared data instruments for Research Electronic Data Capture (REDCap).

REDCap (Research Electronic Data Capture) is a web-based software solution and tool set that allows biomedical researchers to create secure online forms for data capture, management and analysis with minimal effort and training. The Shared Data Instrument Library (SDIL) is a relatively new component of REDCap that allows sharing of commonly used data collection instruments for immediate study use by research teams. Objectives of the SDIL project include: (1) facilitating reuse of data dictionaries and reducing duplication of effort; (2) promoting the use of validated data collection instruments, data standards and best practices; and (3) promoting research collaboration and data sharing.

The inferior glenohumeral ligament: a correlative investigation.

The inferior glenohumeral ligament (IGHL) was investigated by correlating the biomechanical properties, biochemical composition, and histologic morphology of its 3 anatomic regions (superior band, anterior axillary pouch, and posterior axillary pouch) in 8 human cadaveric shoulders. The overall biochemical composition of the IGHL appeared similar to other ligaments, with average water content of 80.9 +/- 2.

Inhomogeneous mechanical behavior of the human supraspinatus tendon under uniaxial loading.

Disorders of the rotator cuff, particularly tears of the rotator cuff tendons, cause significant shoulder disability. Among numerous factors thought to be responsible for the initiation and progression of supraspinatus tears are those related to the tendon's biomechanical properties. We hypothesized that in supraspinatus tendons subjected to tensile loading a strain gradient (difference) exists between the articular and bursal tendon surfaces, that regional strain differences exist on each of these two tendon surfaces, and that tendon surface strains vary with glenohumeral abduction.

Comparison of glenohumeral mechanics following a capsular shift and anterior tightening.

Background: Numerous surgical techniques have been developed to treat glenohumeral instability. Anterior tightening procedures have been associated with secondary glenohumeral osteoarthritis, unlike the anterior-inferior capsular shift procedure, which has been widely advocated as a more anatomical repair. The objective of the present study was to quantify glenohumeral joint translations, articular contact, and resultant forces in cadaveric specimens in order to compare the effects of unidirectional anterior tightening with those of the anterior-inferior capsular shift.

Glenohumeral mechanics: a study of articular geometry, contact, and kinematics.

Stereophotogrammetry was used to investigate the functional relations between the articular surface geometry, contact patterns, and kinematics of the glenohumeral joint. Nine normal shoulder specimens were elevated in the scapular plane by using simulated muscle forces in neutral rotation (NR) and starting rotation (SR). Motion was quantified by analyzing the translations of the geometric centers of the humeral head cartilage and bone surfaces relative to the glenoid surface.

Effects of repetitive subfailure strains on the mechanical behavior of the inferior glenohumeral ligament.

The mechanical response of the inferior glenohumeral ligament to varying subfailure cyclic strains was studied in 33 fresh frozen human cadaver shoulders. The specimens were tested as bone-ligament-bone preparations representing the 3 regions of the inferior glenohumeral ligament (superior band and anterior and posterior axillary pouches) through use of uniaxial tensile cycles. After mechanical preconditioning, each specimen was subjected to 7 test segments, consisting of a baseline strain level L1 (400 cycles) alternating with either 1 (group A, 10 shoulders), 10 (group B, 13 shoulders), or 100 (group C, 10 shoulders) cycles at increasing levels (L2, L3, L4) of subfailure strain.

Osteoarthritic changes in the biochemical composition of thumb carpometacarpal joint cartilage and correlation with biomechanical properties.

The biochemical composition and biomechanical properties of articular cartilage from 53 human thumb carpometacarpal (CMC) joints from cadavers aged 20 to 79 years were measured and studied in normal, mildly fibrillated, and advanced osteoarthritic (OA) joints. Statistical analyses were performed to determine the correlations between the compositional measures and biomechanical properties. For these CMC joint tissues we found that water content increased, proteoglycan content decreased, and collagen content per dry weight remained unaltered with progression of OA degeneration.

A prospective assessment of breath-hold fast spin echo and inversion recovery fast spin echo techniques for detection and characterization of focal hepatic lesions.

The purpose of this study was to prospectively assess two breath-hold T(2)-weighted fast spin-echo sequences and two breath-hold inversion recovery fast spin-echo sequences to determine their relative ability to detect and characterize focal hepatic lesions. Fourteen patients with a total of nineteen proven focal hepatic lesions were imaged with two breath-hold T(2)-weighted (T2W) fast spin echo sequences (HASTE TE = 66 and HASTE TE = 120), two breath-hold inversion recovery fast spin echo sequences (IRFSE TE = 64 and IRFSE TE = 95), and a nonbreath-hold T(2)-weighted fast-spin echo sequence (FSE TE = 96-120). Contrast-to-noise ratios (CNRs) were measured for all proven lesions on all sequences.

Thenar insertion of abductor pollicis longus accessory tendons and thumb carpometacarpal osteoarthritis.

Although the etiology of osteoarthritis of the thumb carpometacarpal (CMC) joint remains unclear, some theories have focused on variations in the local anatomy of the abductor pollicis longus tendon insertion. This cadaver study of 68 specimens analyzed the relationship between a thenar insertion of an accessory abductor pollicis longus tendon and the presence and severity of thumb CMC osteoarthritis. The joint cartilage surfaces were visually graded for degenerative changes.

A retrospective analysis of the accuracy of T2-weighted images and dynamic gadolinium-enhanced sequences in the detection and characterization of focal hepatic lesions.

The aim of this study was to determine the relative ability of T2-weighted and dynamic gadolinium-enhanced T1-weighted gradient-echo sequences to detect and characterize focal hepatic lesions. We retrospectively studied 37 patients with proven focal hepatic lesions using the following sequences: a T1-weighted spin-echo sequence (T1), a T2-weighted sequence (T2), and a series of breath-hold dynamic gadolinium-enhanced T1-weighted gradient-echo sequences (Gd). Two observers were asked to determine retrospectively the number and type of focal hepatic lesions present using images from three combinations of sequences (T1+T2, T1+Gd, T1+T2+Gd).

Topography of the osteoarthritic thumb carpometacarpal joint and its variations with regard to gender, age, site, and osteoarthritic stage.

The articular topography of 46 osteoarthritic thumb carpometacarpal joints was quantitatively analyzed, as well as variations with regard to gender, age, site, and anatomic osteoarthritic stage. It was found that for osteoarthritic thumb carpometacarpal joints, (1) the opposing articular surfaces of elder and severely degenerated joints are more congruent than those of middle-aged and minimally or moderately degenerated joints, although the articular contact area is not significantly different when accounting for thinning of the cartilage layer with age or disease; (2) significant changes in joint topography due to osteoarthritis only occur in severely degenerated joints; (3) joints in women are less congruent, have smaller contact areas, and are likely to experience higher contact stresses than joints in men for similar activities of daily living that involve similar joint loads; and (4) osteoarthritic changes are less severe on the dorsoulnar aspect of the trapezium and the dorsal aspect of the metacarpal, which are known to be low load-bearing regions.

Inferior glenohumeral ligament: geometric and strain-rate dependent properties.

The inferior glenohumeral ligament (IGHL) is an important structure for maintaining shoulder stability. This study was aimed at determining the geometric and anatomic characteristics of the IGHL and its tensile properties at a higher strain rate than previously tested. Eight fresh-frozen human cadaver shoulders (average age 69 years, age range 62 to 73 years) from four female and four male cadavers were used to harvest bone-ligament-bone specimens from the three regions of the IGHL (superior band, anterior axillary pouch, and posterior axillary pouch).

Contact areas in the thumb carpometacarpal joint.

The thumb carpometacarpal joint is a common site of osteoarthritis. It has been hypothesized that peaks of localized stress on the dorsoradial or volar-ulnar regions, or both, of the articular surfaces of the trapezium and metacarpal lead to erosion of cartilage and may be responsible for the progression of the disease. The objective of this study was to determine the contact areas in this joint under the functional position of lateral (key) pinch and in the extremes of range of motion of the joint.

Excursion of the rotator cuff under the acromion. Patterns of subacromial contact.

Nine fresh-frozen, human cadaveric shoulders were elevated in the scapular plane in two different humeral rotations by applying forces along action lines of rotator cuff and deltoid muscles. Stereophotogrammetry determined possible regions of subacromial contact using a proximity criterion; radiographs measured acromiohumeral interval and position of greater tuberosity. Contact starts at the anterolateral edge of the acromion at 0 degrees of elevation; it shifts medially with arm elevation.

Computer simulation of glenohumeral and patellofemoral subluxation. Estimating pathological articular contact.

Analytic stereophotogrammetry and an interactive computer graphics program were used to obtain first order assessments of joint contact patterns in patellofemoral and glenohumeral joints, simulating normal and abnormal articulations. Precise (90 microns accuracy) computer graphic representations of the humeral head, glenoid, patella, and femoral articular surfaces were obtained from cadaver knees and shoulders. These surface representations were then manipulated into an articulated position, and joint contact areas computed by a proximity criterion.

Quantitation of in situ contact areas at the glenohumeral joint: a biomechanical study.

Glenohumeral arthritis may result from abnormal articular mechanics, and shoulder reconstructive procedures often rely implicitly on the belief that the restoration of normal articular mechanics is required to obtain satisfactory clinical results. Despite this, limited knowledge of normal or pathologic glenohumeral joint articular mechanics and contact is available. This study uses a stereophotogrammetry technique to determine contact areas in normal cadaver glenohumeral joints with intact ligaments and capsule through a large range of motion using simulated forces of the four rotator cuff muscles and three deltoid heads.

Tensile properties of the inferior glenohumeral ligament.

The tensile properties of the inferior glenohumeral ligament have been determined in 16 freshly frozen cadaver shoulders. The inferior glenohumeral ligament was divided into three anatomical regions: a superior band, an anterior axillary pouch, and a posterior axillary pouch. This yielded 48 bone-ligament-bone specimens, which were tested to failure in uniaxial tension.