Inertial Measures of Motion for Clinical Biomechanics: Comparative Assessment of Accuracy under Controlled Conditions - Effect of Velocity

Background

Inertial measurement of motion with Attitude and Heading Reference Systems (AHRS) is emerging as an alternative to 3D motion capture systems in biomechanics. The objectives of this study are: 1) to describe the absolute and relative accuracy of multiple units of commercially available AHRS under various types of motion; and 2) to evaluate the effect of motion velocity on the accuracy of these measurements.

Methods

The criterion validity of accuracy was established under controlled conditions using an instrumented Gimbal table. AHRS modules were carefully attached to the center plate of the Gimbal table and put through experimental static and dynamic conditions. Static and absolute accuracy was assessed by comparing the AHRS orientation measurement to those obtained using an optical gold standard. Relative accuracy was assessed by measuring the variation in relative orientation between modules during trials.

Findings

Evaluated AHRS systems demonstrated good absolute static accuracy (mean error < 0.5^o) and clinically acceptable absolute accuracy under condition of slow motions (mean error between 0.5^o and 3.1^o). In slow motions, relative accuracy varied from 2^o to 7^o depending on the type of AHRS and the type of rotation. Absolute and relative accuracy were significantly affected (p<0.05) by velocity during sustained motions. The extent of that effect varied across AHRS.

Interpretation

Absolute and relative accuracy of AHRS are affected by environmental magnetic perturbations and conditions of motions. Relative accuracy of AHRS is mostly affected by the ability of all modules to locate the same global reference coordinate system at all time.

Conclusions

Existing AHRS systems can be considered for use in clinical biomechanics under constrained conditions of use. While their individual capacity to track absolute motion is relatively consistent, the use of multiple AHRS modules to compute relative motion between rigid bodies needs to be optimized according to the conditions of operation.     

Body Structures and Physical Complaints in Upper Limb Reduction Deficiency: A 24-Year Follow-Up Study

Objective

To describe upper body structures associated with upper limb reduction deficiency and the development of these structures over time, to examine the presence of physical complaints in this population, and to compare body structures and complaints between groups based on prosthesis use.

Design

Prospective cohort study with a follow-up period of 24 years, with matched able-bodied controls.

Subjects

Twenty-eight patients with unilateral below-elbow reduction deficiency fitted with myoelectric prostheses, aged 8–18 years at inclusion.

Method

Measurements of upper arm, trunk and spine were performed and study-specific questionnaires were answered at baseline and follow-up; the Brief Pain Inventory and the Quick Disability of Arm, Shoulder, and Hand questionnaires were answered at follow-up.

Results

Both at baseline and follow-up, within-subjects differences in structures of the arm and trunk were shown in patients but not in controls. Spinal deviations, although small, were greater in patients compared to controls. Self-reported disability was higher in patients compared to controls. Differences in back pain and effect of prostheses use could not be shown.

Conclusions

Patients with unilateral below-elbow reduction deficiency have consistent differences in upper body structures. Deviations of the spine, probably of functional origin, do not progress to clinically relevant scoliosis.     

Novel Algorithm for Non-Invasive Assessment of Fibrosis in NAFLD

Introduction

Various conditions of liver disease and the downsides of liver biopsy call for a non-invasive option to assess liver fibrosis. A non-invasive score would be especially useful to identify patients with slow advancing fibrotic processes, as in Non-Alcoholic Fatty Liver Disease (NAFLD), which should undergo histological examination for fibrosis.

Patients/Methods

Classic liver serum parameters, hyaluronic acid (HA) and cell death markers of 126 patients undergoing bariatric surgery for morbid obesity were analyzed by machine learning techniques (logistic regression, k-nearest neighbors, linear support vector machines, rule-based systems, decision trees and random forest (RF)). Specificity, sensitivity and accuracy of the evaluated datasets to predict fibrosis were assessed.

Results

None of the single parameters (ALT, AST, M30, M60, HA) did differ significantly between patients with a fibrosis score 1 or 2. However, combining these parameters using RFs reached 79% accuracy in fibrosis prediction with a sensitivity of more than 60% and specificity of 77%. Moreover, RFs identified the cell death markers M30 and M65 as more important for the decision than the classic liver parameters.

Conclusion

On the basis of serum parameters the generation of a fibrosis scoring system seems feasible, even when only marginally fibrotic tissue is available. Prospective evaluation of novel markers, i.e. cell death parameters, should be performed to identify an optimal set of fibrosis predictors.     

Comparison of Modic Changes in the Lumbar and Cervical Spine,in 3167 Patients with and without Spinal Pain

Background Context

There are few comparisons of Modic changes (MCs) in the lumbar and cervical spine.

Purpose

Compare the prevalence of MCs in the lumbar and cervical spine, and determine how MC prevalence depends on spinal pain, age, disc degeneration, spinal level, and the presence or absence of kyphosis.

Study Design

Retrospective clinical survey.

Materials and Methods

Magnetic resonance images (MRIs) were compared from five patient groups: 1. 1223 patients with low-back pain/radiculopathy only; 2. 1023 patients with neck pain/radiculopathy only; 3. 497 patients with concurrent low-back and neck symptoms; 4. 304 asymptomatic subjects with lumbar MRIs; and 5. 120 asymptomatic subjects with cervical MRIs.

Results

The prevalence of MCs was higher in those with spinal pain than in those without, both in the lumbar spine (21.0% vs 10.5%) and cervical spine (8.8% vs 3.3%). Type II MCs were most common and Type III were least common in all groups. The prevalence of lumbar MCs in people with back pain was little affected by the presence of concurrent neck pain, and the same was true for the prevalence of cervical MCs in people with neck pain with or without concurrent back pain. When symptomatic patients were reclassified into two groups (back pain, neck pain), the prevalence of lumbar MCs in people with back pain was greater than that of cervical MCs in people with neck pain. The prevalence of lumbar and cervical MCs increased with age, disc degeneration, (descending) spinal level, and increased kyphosis.

Conclusions

There is a significantly higher prevalence of MCs in patients with back and neck pain. The reported association with increased kyphosis (flat back) is novel.     

Bone Mineral Density,Bone Turnover Markers and Fractures in Patients with Systemic Sclerosis: A Case Control Study

Objective

The aim of our study was to elucidate the pathophysiology of systemic sclerosis-related osteoporosis and the prevalence of vertebral fragility fracture in postmenopausal women with systemic sclerosis (SSc).

Methodology

Fifty-four postmenopausal women with scleroderma and 54 postmenopausal controls matched for age, BMI, and smoking habits were studied. BMD was measured by dual energy-x-ray absorptiometry at spine and femur, and by ultrasonography at calcaneus The markers of bone turnover included serum osteocalcin and urinary deoxypyridinoline. All subjects had a spine X-ray to ascertain the presence of vertebral fractures.

Results

bone mineral density at lumbar spine (BMD 0.78±0.08 vs 0.88±0.07; p<0,001), femoral neck (BMD: 0.56±0.04 vs 0.72±0.07; p<0,001) and total femur (BMD: 0.57±0.04 vs 0.71±0.06; p<0,001) and ultrasound parameter at calcaneus (SI: 80.10±5.10 vs 94.80±6.10 p<0,001) were significantly lower in scleroderma compared with controls; bone turnover markers and parathyroid hormone level were significantly higher in scleroderma compared with controls, while serum of 25(OH)D3 was significantly lower. In scleroderma group the serum levels of 25(OH)D3 significantly correlated with PTH levels, BMD, stiffness index and bone turnover markers. One or more moderate or severe vertebral fractures were found in 13 patients with scleroderma, wherease in control group only one patient had a mild vertebral fracture.

Conclusion

Our data shows, for the first time, that vertebral fractures are frequent in subjects with scleroderma, and suggest that lower levels of 25(OH)D3 may play a role in the risk of osteoporosis and vertebral fractures.     

Postural Abnormality as a Risk Marker for Leg Deep Venous Thrombosis in Parkinson’s Disease

Background

Pulmonary thromboembolism is a common cause of death in patients with autopsy-confirmed Parkinsonism. This study investigated the incidence of leg deep vein thrombosis in Parkinson’s disease and relationships between deep vein thrombosis and clinical/laboratory findings, including postural abnormalities as assessed by photographic measurements.

Methods

This cross-sectional study assessed the presence of deep vein thrombosis using bilateral leg Doppler ultrasonography in 114 asymptomatic outpatients with Parkinson’s disease.

Results

Deep vein thrombosis was detected in 23 patients (20%) with Parkinson’s disease. Deep vein thrombosis was located in the distal portion in 18 patients and in the proximal portion in 5 patients. No significant differences in age, sex, body mass index, disease duration, Hoehn-Yahr stage, anti-Parkinson’s drugs, or daily levodopa-equivalent dose were seen between deep vein thrombosis-positive and -negative groups. Univariate analysis for developing deep vein thrombosis in patients with Parkinson’s disease identified the following markers: long-term wheelchair use, bent knee, bent spine, and D-dimer elevation. Bending angles were significantly greater in the deep vein thrombosis-positive group at the knee and spine than in the deep vein thrombosis-negative group. Half of Parkinson’s disease patients with camptocormia had deep vein thrombosis. Among diabetes mellitus cases, long-term wheelchair use, bent knee over 15°, camptocormia, D-dimer elevation, the more risk markers were associated with a higher incidence of DVT. The presence of risk markers contributed to the development of deep vein thrombosis. On multivariate logistic regression analysis, a bent knee posture was strongly associated with an increased risk of deep vein thrombosis.

Conclusion

Presence of leg deep vein thrombosis correlated with postural abnormalities in Parkinson’s disease. We recommend non-invasive ultrasonographic screening for leg deep vein thrombosis in these high-risk patients with Parkinson’s disease.     

Interaction between Plate Make and Protein in Protein Crystallisation Screening

Background

Protein crystallisation screening involves the parallel testing of large numbers of candidate conditions with the aim of identifying conditions suitable as a starting point for the production of diffraction quality crystals. Generally, condition screening is performed in 96-well plates. While previous studies have examined the effects of protein construct, protein purity, or crystallisation condition ingredients on protein crystallisation, few have examined the effect of the crystallisation plate.

Methodology/Principal Findings

We performed a statistically rigorous examination of protein crystallisation, and evaluated interactions between crystallisation success and plate row/column, different plates of same make, different plate makes and different proteins. From our analysis of protein crystallisation, we found a significant interaction between plate make and the specific protein being crystallised.

Conclusions/Significance

Protein crystal structure determination is the principal method for determining protein structure but is limited by the need to produce crystals of the protein under study. Many important proteins are difficult to crystallise, so that identification of factors that assist crystallisation could open up the structure determination of these more challenging targets. Our findings suggest that protein crystallisation success may be improved by matching a protein with its optimal plate make.     

HIF1-Alpha Expression Predicts Survival of Patients with Squamous Cell Carcinoma of the Oral Cavity

Background

Oral squamous cell carcinoma is an important cause of death and morbidity wordwide and effective prognostic markers are still to be discovered. HIF1α protein is associated with hypoxia response and neovascularization, essential conditions for solid tumors survival. The relationship between HIF1α expression, tumor progression and treatment response in head and neck cancer is still poorly understood.

Patients and Methods

In this study, we investigated HIF1α expression by immunohistochemistry in tissue microarrays and its relationship with clinical findings, histopathological results and survival of 66 patients with squamous cell carcinoma of the lower mouth.

Results

Our results demonstrated that high HIF1α expression is associated with local disease-free survival, independently from the choice of treatment. Furthermore, high expression of HIF1α in patients treated with postoperative radiotherapy was associated with survival, therefore being a novel prognostic marker in squamous cell carcinoma of the mouth. Additionally, our results showed that MVD was associated with HIF1α expression and local disease relapse.

Conclusion

These findings suggest that HIF1α expression can be used as a prognostic marker and predictor of postoperative radiotherapy response, helping the oncologist choose the best treatment for each patient.     

The Nijmegen Decision Tool for Chronic Low Back Pain. Development of a Clinical Decision Tool for Secondary or Tertiary Spine Care Specialists

Background

In Western Europe, low back pain has the greatest burden of all diseases. When back pain persists, different medical specialists are involved and a lack of consensus exists among these specialists for medical decision-making in Chronic Low Back Pain (CLBP).

Objective

To develop a decision tool for secondary or tertiary spine care specialists to decide which patients with CLBP should be seen by a spine surgeon or by other non-surgical medical specialists.

Methods

A Delphi study was performed to identify indicators predicting the outcome of interventions. In the preparatory stage evidence from international guidelines and literature were summarized. Eligible studies were reviews and longitudinal studies. Inclusion criteria: surgical or non-surgical interventions and persistence of complaints, CLBP-patients aged 18–65 years, reported baseline measures of predictive indicators, and one or more reported outcomes had to assess functional status, quality of life, pain intensity, employment status or a composite score. Subsequently, a three-round Delphi procedure, to reach consensus on candidate indicators, was performed among a multidisciplinary panel of 29 CLBP-professionals (>five years CLBP-experience). The pre-set threshold for general agreement was ≥70%. The final indicator set was used to develop a clinical decision tool.

Results

A draft list with 53 candidate indicators (38 with conclusive evidence and 15 with inconclusive evidence) was included for the Delphi study. Consensus was reached to include 47 indicators. A first version of the decision tool was developed, consisting of a web-based screening questionnaire and a provisional decision algorithm.

Conclusions

This is the first clinical decision tool based on current scientific evidence and formal multidisciplinary consensus that helps referring the patient for consultation to a spine surgeon or a non-surgical spine care specialist. We expect that this tool considerably helps in clinical decision-making spine care, thereby improving efficient use of scarce sources and the outcomes of spinal interventions.     

Differences between CusA and AcrB Crystallisation Highlighted by Protein Flexibility

Background

Until very recently, AcrB was the only Resistance Nodulation and cell Division transporter for which the structure has been elucidated. Towards a general understanding of this protein family, CusA and AcrB were compared.

Methodology/Principal Findings

In dodecylmaltoside, AcrB crystallised in many different conditions, while CusA does not. This could be due to the difference in dynamic between these proteins as judged from limited proteolysis assays. Addition of various compounds, in particular heavy metal cations, stabilises CusA.

Conclusion/Significance

This approach could constitute a first step towards CusA crystallisation.     

DLS 5.0 - The Biomechanical Effects of Dynamic Locking Screws

Introduction

Indirect reduction of dia-/metaphyseal fractures with minimally invasive implant application bridges the fracture zone in order to protect the soft-tissue and blood supply. The goal of this fixation strategy is to allow stable motion at the fracture site to achieve indirect bone healing with callus formation. However, concerns have arisen that the high axial stiffness and eccentric position of locked plating constructs may suppress interfragmentary motion and callus formation, particularly under the plate. The reason for this is an asymmetric fracture movement. The biological need for sufficient callus formation and secondary bone healing is three-dimensional micro movement in the fracture zone. The DLS was designed to allow for increased fracture site motion. The purpose of the current study was to determine the biomechanical effect of the DLS_5.0.

Methods

Twelve surrogate bone models were used for analyzing the characteristics of the DLS_5.0. The axial stiffness and the interfragmentary motion of locked plating constructs with DLS were compared to conventional constructs with Locking Head Screws (LS_5.0). A quasi-static axial load of 0 to 2.5 kN was applied. Relative motion was measured.

Results

The dynamic system showed a biphasic axial stiffness distribution and provided a significant reduction of the initial axial stiffness of 74.4%. Additionally, the interfragmentary motion at the near cortex increased significantly from 0.033 mm to 0.210 mm (at 200N).

Conclusions

The DLS may ultimately be an improvement over the angular stable plate osteosynthesis. The advantages of the angular stability are not only preserved but even supplemented by a dynamic element which leads to homogenous fracture movement and to a potentially uniform callus distribution.     

Intermittent hypoxia regulates stem-like characteristics and differentiation of neuroblastoma cells

Background

Neuroblastomas are the most common extracranial solid tumors in children. Neuroblastomas are derived from immature cells of the sympathetic nervous system and are characterized by clinical and biological heterogeneity. Hypoxia has been linked to tumor progression and increased malignancy. Intermittent hypoxia or repeated episodes of hypoxia followed by re-oxygenation is a common phenomenon in solid tumors including neuroblastoma and it has a significant influence on the outcome of therapies. The present study focuses on how intermittent hypoxia modulates the stem-like properties and differentiation in neuroblastoma cells.

Methods and Findings

Cell survival was assessed by clonogenic assay and cell differentiation was determined by morphological characterization. Hypoxia-inducible genes were analyzed by real-time PCR and Western blotting. Immunofluorescence, real-time PCR and Western blotting were utilized to study stem cell markers. Analysis of neural crest / sympathetic nervous system (SNS) markers and neuronal differentiation markers were done by real-time PCR and Western blotting, respectively. Intermittent hypoxia stimulated the levels of HIF-1α and HIF-2 α proteins and enhanced stem-like properties of neuroblastoma cells. In intermittent hypoxia-conditioned cells, downregulation of SNS marker genes and upregulation of genes expressed in the neural crest were observed. Intermittent hypoxia suppressed the retinoic acid-induced differentiation of neuroblastoma cells.

Conclusions

Our results suggest that intermittent hypoxia enhances stem-like characteristics and suppresses differentiation propensities in neuroblastoma cells.     

Dissociation of Neural Substrates of Response Inhibition to Negative Information between Implicit and Explicit Facial Go/Nogo Tasks: Evidence from an Electrophysiological Study

Background

Although ample evidence suggests that emotion and response inhibition are interrelated at the behavioral and neural levels, neural substrates of response inhibition to negative facial information remain unclear. Thus we used event-related potential (ERP) methods to explore the effects of explicit and implicit facial expression processing in response inhibition.

Methods

We used implicit (gender categorization) and explicit emotional Go/Nogo tasks (emotion categorization) in which neutral and sad faces were presented. Electrophysiological markers at the scalp and the voxel level were analyzed during the two tasks.

Results

We detected a task, emotion and trial type interaction effect in the Nogo-P3 stage. Larger Nogo-P3 amplitudes during sad conditions versus neutral conditions were detected with explicit tasks. However, the amplitude differences between the two conditions were not significant for implicit tasks. Source analyses on P3 component revealed that right inferior frontal junction (rIFJ) was involved during this stage. The current source density (CSD) of rIFJ was higher with sad conditions compared to neutral conditions for explicit tasks, rather than for implicit tasks.

Conclusions

The findings indicated that response inhibition was modulated by sad facial information at the action inhibition stage when facial expressions were processed explicitly rather than implicitly. The rIFJ may be a key brain region in emotion regulation.     

A role for thrombospondin-1 deficits in astrocyte-mediated spine and synaptic pathology in Down's syndrome

Background

Down''s syndrome (DS) is the most common genetic cause of mental retardation. Reduced number and aberrant architecture of dendritic spines are common features of DS neuropathology. However, the mechanisms involved in DS spine alterations are not known. In addition to a relevant role in synapse formation and maintenance, astrocytes can regulate spine dynamics by releasing soluble factors or by physical contact with neurons. We have previously shown impaired mitochondrial function in DS astrocytes leading to metabolic alterations in protein processing and secretion. In this study, we investigated whether deficits in astrocyte function contribute to DS spine pathology.

Methodology/Principal Findings

Using a human astrocyte/rat hippocampal neuron coculture, we found that DS astrocytes are directly involved in the development of spine malformations and reduced synaptic density. We also show that thrombospondin 1 (TSP-1), an astrocyte-secreted protein, possesses a potent modulatory effect on spine number and morphology, and that both DS brains and DS astrocytes exhibit marked deficits in TSP-1 protein expression. Depletion of TSP-1 from normal astrocytes resulted in dramatic changes in spine morphology, while restoration of TSP-1 levels prevented DS astrocyte-mediated spine and synaptic alterations. Astrocyte cultures derived from TSP-1 KO mice exhibited similar deficits to support spine formation and structure than DS astrocytes.

Conclusions/Significance

These results indicate that human astrocytes promote spine and synapse formation, identify astrocyte dysfunction as a significant factor of spine and synaptic pathology in the DS brain, and provide a mechanistic rationale for the exploration of TSP-1-based therapies to treat spine and synaptic pathology in DS and other neurological conditions.     

Dynamic Status of REST in the Mouse ESC Pluripotency Network

Background

REST is abundantly expressed in mouse embryonic stem cells (ESCs). Many genome-wide analyses have found REST to be an integral part of the ESC pluripotency network. However, experimental systems have produced contradictory findings: (1) REST is required for the maintenance of ESC pluripotency and loss of REST causes increased expression of differentiation markers, (2) REST is not required for the maintenance of ESC pluripotency and loss of REST does not change expression of differentiation markers, and (3) REST is not required for the maintenance of ESC pluripotency but loss of REST causes decreased expression of differentiation markers. These reports highlight gaps in our knowledge of the ESC network.

Methods

Employing biochemical and genome-wide analyses of various culture conditions and ESC lines, we have attempted to resolve some of the discrepancies in the literature.

Results

We show that Rest+/− and Rest−/− AB-1 mutant ESCs, which did not exhibit a role of REST in ESC pluripotency when cultured in the presence of feeder cells, did show impaired self-renewal when compared with the parental cells under feeder-free culture conditions, but only in early passage cells. In late passage cells, both Rest+/− and Rest−/− AB-1 ESCs restored pluripotency, suggesting a passage and culture condition-dependent response. Genome-wide analysis followed by biochemical validation supported this response and further indicated that the restoration of pluripotency was associated by increased expression of the ESC pluripotency factors. E14Tg2a.4 ESCs with REST-knockdown, which earlier showed a REST-dependent pluripotency when cultured under feeder-free conditions, as well as Rest−/− AB-1 ESCs, showed no REST-dependent pluripotency when cultured in the presence of either feeder cells or laminin, indicating that extracellular matrix components can rescue REST''s role in ESC pluripotency.

Conclusions

REST regulates ESC pluripotency in culture condition- and ESC line-dependent fashion and ESC pluripotency needs to be evaluated in a context dependent manner.     

Vibration influences haptic perception of surface compliance during walking

Background

The haptic perception of ground compliance is used for stable regulation of dynamic posture and the control of locomotion in diverse natural environments. Although rarely investigated in relation to walking, vibrotactile sensory channels are known to be active in the discrimination of material properties of objects and surfaces through touch. This study investigated how the perception of ground surface compliance is altered by plantar vibration feedback.

Methodology/Principal Findings

Subjects walked in shoes over a rigid floor plate that provided plantar vibration feedback, and responded indicating how compliant it felt, either in subjective magnitude or via pairwise comparisons. In one experiment, the compliance of the floor plate was also varied. Results showed that perceived compliance of the plate increased monotonically with vibration feedback intensity, and depended to a lesser extent on the temporal or frequency distribution of the feedback. When both plate stiffness (inverse compliance) and vibration amplitude were manipulated, the effect persisted, with both factors contributing to compliance perception. A significant influence of vibration was observed even for amplitudes close to psychophysical detection thresholds.

Conclusions/Significance

These findings reveal that vibrotactile sensory channels are highly salient to the perception of surface compliance, and suggest that correlations between vibrotactile sensory information and motor activity may be of broader significance for the control of human locomotion than has been previously acknowledged.     

ApoE receptor 2 regulates synapse and dendritic spine formation

Background

Apolipoprotein E receptor 2 (ApoEr2) is a postsynaptic protein involved in long-term potentiation (LTP), learning, and memory through unknown mechanisms. We examined the biological effects of ApoEr2 on synapse and dendritic spine formation—processes critical for learning and memory.

Methodology/Principal Findings

In a heterologous co-culture synapse assay, overexpression of ApoEr2 in COS7 cells significantly increased colocalization with synaptophysin in primary hippocampal neurons, suggesting that ApoEr2 promotes interaction with presynaptic structures. In primary neuronal cultures, overexpression of ApoEr2 increased dendritic spine density. Consistent with our in vitro findings, ApoEr2 knockout mice had decreased dendritic spine density in cortical layers II/III at 1 month of age. We also tested whether the interaction between ApoEr2 and its cytoplasmic adaptor proteins, specifically X11α and PSD-95, affected synapse and dendritic spine formation. X11α decreased cell surface levels of ApoEr2 along with synapse and dendritic spine density. In contrast, PSD-95 increased cell surface levels of ApoEr2 as well as synapse and dendritic spine density.

Conclusions/Significance

These results suggest that ApoEr2 plays important roles in structure and function of CNS synapses and dendritic spines, and that these roles are modulated by cytoplasmic adaptor proteins X11α and PSD-95.     

DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis

Background

Dynamic Flux Balance Analysis (DFBA) is a dynamic simulation framework for biochemical processes. DFBA can be performed using different approaches such as static optimization (SOA), dynamic optimization (DOA), and direct approaches (DA). Few existing simulators address the theoretical and practical challenges of nonunique exchange fluxes or infeasible linear programs (LPs). Both are common sources of failure and inefficiencies for these simulators.

Results

DFBAlab, a MATLAB-based simulator that uses the LP feasibility problem to obtain an extended system and lexicographic optimization to yield unique exchange fluxes, is presented. DFBAlab is able to simulate complex dynamic cultures with multiple species rapidly and reliably, including differential-algebraic equation (DAE) systems. In addition, DFBAlab’s running time scales linearly with the number of species models. Three examples are presented where the performance of COBRA, DyMMM and DFBAlab are compared.

Conclusions

Lexicographic optimization is used to determine unique exchange fluxes which are necessary for a well-defined dynamic system. DFBAlab does not fail during numerical integration due to infeasible LPs. The extended system obtained through the LP feasibility problem in DFBAlab provides a penalty function that can be used in optimization algorithms.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0409-8) contains supplementary material, which is available to authorized users.     

Bronchoabsorption; a novel bronchoscopic technique to improve biomarker sampling of the airway

Background

Current techniques used to obtain lung samples have significant limitations and do not provide reproducible biomarkers of inflammation. We have developed a novel technique that allows multiple sampling methods from the same area (or multiple areas) of the lung under direct bronchoscopic vision. It allows collection of mucosal lining fluid and bronchial brushing from the same site; biopsy samples may also be taken. The novel technique takes the same time as standard procedures and can be conducted safely.

Methods

Eight healthy smokers aged 40–65 years were included in this study. An absorptive filter paper was applied to the bronchial mucosa under direct vision using standard bronchoscopic techniques. Further samples were obtained from the same site using bronchial brushings. Bronchoalveolar lavage (BAL) was obtained using standard techniques. Chemokine (C-C Motif) Ligand 20 (CCL20), CCL4, CCL5, Chemokine (C-X-C Motif) Ligand 1 (CXCL1), CXCL8, CXCL9, CXCL10, CXCL11, Interleukin 1 beta (IL-1β), IL-6, Vascular endothelial growth factor (VEGF), Matrix metalloproteinase 8 (MMP-8) and MMP-9 were measured in exudate and BAL. mRNA was collected from the bronchial brushings for gene expression analysis.

Results

A greater than 10 fold concentration of all the biomarkers was detected in lung exudate in comparison to BAL. High yield of good quality RNA with RNA integrity numbers (RIN) between 7.6 and 9.3 were extracted from the bronchial brushings. The subset of genes measured were reproducible across the samples and corresponded to the inflammatory markers measured in exudate and BAL.

Conclusions

The bronchoabsorption technique as described offers the ability to sample lung fluid direct from the site of interest without the dilution effects caused by BAL. Using this method we were able to successfully measure the concentrations of biomarkers present in the lungs as well as collect high yield mRNA samples for gene expression analysis from the same site. This technique demonstrates superior sensitivity to standard BAL for the measurement of biomarkers of inflammation. It could replace BAL as the method of choice for these measurements. This method provides a systems biology approach to studying the inflammatory markers of respiratory disease progression.

Trial registration

NHS Health Research Authority (13/LO/0256).     

Validation of a Laboratory Method for Evaluating Dynamic Properties of Reconstructed Equine Racetrack Surfaces

Background

Racetrack surface is a risk factor for racehorse injuries and fatalities. Current research indicates that race surface mechanical properties may be influenced by material composition, moisture content, temperature, and maintenance. Race surface mechanical testing in a controlled laboratory setting would allow for objective evaluation of dynamic properties of surface and factors that affect surface behavior.

Objective

To develop a method for reconstruction of race surfaces in the laboratory and validate the method by comparison with racetrack measurements of dynamic surface properties.

Methods

Track-testing device (TTD) impact tests were conducted to simulate equine hoof impact on dirt and synthetic race surfaces; tests were performed both in situ (racetrack) and using laboratory reconstructions of harvested surface materials. Clegg Hammer in situ measurements were used to guide surface reconstruction in the laboratory. Dynamic surface properties were compared between in situ and laboratory settings. Relationships between racetrack TTD and Clegg Hammer measurements were analyzed using stepwise multiple linear regression.

Results

Most dynamic surface property setting differences (racetrack-laboratory) were small relative to surface material type differences (dirt-synthetic). Clegg Hammer measurements were more strongly correlated with TTD measurements on the synthetic surface than the dirt surface. On the dirt surface, Clegg Hammer decelerations were negatively correlated with TTD forces.

Conclusions

Laboratory reconstruction of racetrack surfaces guided by Clegg Hammer measurements yielded TTD impact measurements similar to in situ values. The negative correlation between TTD and Clegg Hammer measurements confirms the importance of instrument mass when drawing conclusions from testing results. Lighter impact devices may be less appropriate for assessing dynamic surface properties compared to testing equipment designed to simulate hoof impact (TTD).

Potential Relevance

Dynamic impact properties of race surfaces can be evaluated in a laboratory setting, allowing for further study of factors affecting surface behavior under controlled conditions.