bluuebunny/crossref_metadata_2025 huggingface dataset:
Muscle Synergy Constraints Improve Prediction of Knee Contact Force During Gait
Authors: Fregly Benjamin J. , Walter Jonathan P. , Kinney Allison L. , Banks Scott A. , D’Lima Darryl D. , Besier Thor F. , Lloyd David G.
Published: January 2014

Knowledge of patient-specific muscle and joint contact forces during activities of daily living could improve the treatment of movement-related disorders (e.g., osteoarthritis, stroke, cerebral palsy, Parkinson’s disease). Unfortunately, it is currently impossible to measure these quantities directly under common clinical conditions, and calculation of these quantities using computer models is limited by the redundant nature of human neural control (i.e., more muscles than theoretically necessary to actuate the available degrees of freedom in the skeleton). Walking is a particularly important task to understand, since loss of mobility is associated with increased morbidity and decreased quality of life [1]. Though numerous musculoskeletal computer modeling studies have used optimization methods to resolve the neural control redundancy problem, these estimates remain unvalidated due to the lack of internal force measurements that can be used for validation purposes.
Hydration Effects on Tensile Properties of the Corneal Stroma
Authors: Rahimi Abdolrasol , Hatami-Marbini Hamed
Published: January 2014

The mechanical behavior of the cornea is mainly governed by the microstructure and composition of the stroma. The stroma is a highly ordered extracellular matrix and constitutes about 90% of the corneal thickness. From the mechanics point of view, the corneal stroma can be considered as a polyelectrolyte gel which is composed of collagen fibrils embedded in an aqueous matrix. The collagen fibrils compose about 70% of cornea’s dry mass and are arranged in a regular lattice structure [2]. Previous studies have shown that while the collagen fibrils are primarily located parallel to the surface, they are not distributed uniformly in all directions and their preferred orientation is not same in different species. For example, collagen fibrils are almost equally distributed in the nasal-temporal and inferior-superior directions in healthy human corneas [4] and they are mainly aligned in the inferior-superior direction in bovine corneas[2]. The differences in the orientations of the collagen fibrils have seen to have important implications on the mechanical properties of the cornea. In addition to this observation, the relative distance between the collagen fibrils is expected to play a role in defining the mechanics of the tissue. It is well-documented that the proteoglycans bind collagen fibrils at regular sites and control their relative position. The main proteoglycan in the corneal stroma is decorin. Decorin is the simplest small leucine-rich proteoglycan with a single glycosaminoglycan side chain. Chondroitin sulfate, dermatan sulfate, and keratan sulfate are among the prevalent glycosaminoglycans found in the cornea. Under physiological conditions, these linear carbohydrate polymers are ionized and carry negative charges. Therefore, a hydrated gel is formed in the empty space between collagen fibrils by attracting water. It is known that the interaction of these negatively charged glycosaminoglycans with themselves and with the free ions contribute to the corneal swelling pressure and subsequently to its compressive stiffness. Nevertheless, their possible influence on the corneal tensile properties is yet to be determined. In this work, we experimentally characterized the tensile properties of the bovine corneal stroma in different bathing solutions. Furthermore, a quasi-linear viscoelastic (QLV) model was used to examine the effect of bathing fluids and corneal hydration on mechanical parameter of the cornea.
Dynamic Simulation of Muscle Loading During ARED Squat Exercise on the International Space Station
Authors: Fregly Christopher D. , Kim Brandon T. , De Witt John K. , Fregly Benjamin J.
Published: January 2014

Loss of muscle mass due to reduced mechanical loading is a critical issue for long duration spaceflight on the International Space Station (ISS) [1]. To address this issue, NASA has developed the Advanced Resistive Exercise Device (ARED) that allows astronauts to perform resistance exercise on the ISS. To minimize force transmission to the ISS, the ARED is mounted to a vibration isolation system (VIS). During squat exercise, ARED rotates relative to the ISS, functioning like a nutcracker to compress the astronaut with a load provided by two vacuum cylinders. Though the ARED is an effective exercise countermeasure device, the extent to which squat exercise on the ISS achieves Earth-equivalent muscle moments remains unknown.
Analysis of the Active Response of Cells to Cyclic Loading Using a Modified AFM System
Authors: Weafer P. , Reynolds N. , Ronan W. , Dowling E. , Jarvis S. , McGarry P.
Published: January 2014

Dynamic mechanical loading is essential for cell function and tissue maintenance. In an effort to characterize the response of cells to cyclic deformation several in vitro studies have relied on the testing of large populations of cells seeded on 2D substrates or in 3D scaffolds and gels. However, such studies do not allow for the measurement of forces actively generated at a single cell level. In the present study deformation controlled cyclic loading experiments are performed on single osteoblasts at the whole cell level using a modified AFM system [1,2]. In addition to untreated cells, experiments are also performed on passive cells in which the actin cytoskeleton has been disrupted. A computational analysis of experimentally measured single cell forces reveals that passive cell behaviour is characterized by a non-linear visco-hyperelastic formulation and active forces generated by the actin cytoskeleton are accurately predicted by the a Hill-type contractility framework with tension dependent remodeling [3,4].
Development of Finite Element Rat Head Model to Study the Effect of Incident Pressure and Skull Rigidity Under Blast-Induced Biomechanical Loading
Authors: Sundaramurthy A. , Chandra N.
Published: January 2014

Blast waves generated by improvised explosive devices (IEDs) cause traumatic brain injury (TBI) in soldiers and civilians. Currently, in vivo animal models are extensively used to study blast TBI, to identify mechanisms of injury, and to develop injury thresholds. This work focuses on the study of the effect of Incident Pressure (IP), skull rigidity on the measured Intracranial Pressure (ICP) and maximum principle strain measured on the skull using a validated finite element model of the rat head. Our results indicate that the ICP has a negative correlation with the skull rigidity; i.e., with increase in the skull rigidity the ICP tends to decrease. Similarly, ICP linearly increases with an increase in the IP. Finally, the strain has a negative non linear relationship with the skull rigidity.
Characterization of Microscale Particles Using a Microfluidic Flow Cytometer Equipped With a Multi-Plex Photon Counter
Authors: Asrar Pouya , Hashemi Nastaran
Published: January 2014

We have shown the design and fabrication of a microfluidic flow cytometer. The microfluidic flow cytometer has been used to characterize microspheres of different sizes. The device is consisted of a microchannel, electronics, and integrated optics. The microchannel has three inlets. Two inlets are used to introduce sheath flows and one middle inlet is assigned as sample inlet. The sample flow is hydrodynamically focused at the center of the microchannel by two side streams (sheath flows). Also arrays of four chevron grooves compress the sample flow from the top and bottom of the microchannel. The core flow contains microspheres at a certain concentration. Detection of the microspheres at the interrogation region of the channel is performed by integrated optics and electronics. The scattered light emitted from the microspheres is collected by a multi-plex photo diode (MPPC). The results are recorded using data acquisition (DAQ) unit. The MPPCs employed in the setup is the new generation of photon counter devices with an excellent detection limit, a compact size, and capability of recording data at high gain compared to previous generation of photodetectors such as photomultipliers or avalanche photon diodes. The flow cytometer was sensitive enough to collect data from 3 μm microspheres using such mentioned sensitive photon counting unit. We have also used COMSOL Multiphysics software to investigate velocity and pressure distribution as well as concentration distribution along the microchannel. The average voltage collected by MPPC was 1.9 V for 10.2 μm and 1.6 V for 3.2 μm microsphere.
Implementation and Validation of Planar Soft Tissue Structural Constitutive Model
Authors: Fan Rong , Sacks Michael S.
Published: January 2014

Constitutive modeling is of fundamental important for numerical simulation and analysis of soft biological tissues. The mechanical behaviors of soft tissues are usually highly nonlinear and anisotropic. The complex behavior is the results from the interaction of tissue microstructure. By incorporating information of fiber orientation and distribution at tissue microscopic scale, the structural model avoids ambiguities in material characterization. Moreover, structural models produce much more information than just simple stress-strain results, but can provide much insight into how soft tissues internally reorganize to external loads by adjusting their internal microstructure. Moreover, it is only through simulation of an entire organ system can such information be derived and provide insight into physiological function. However, accurate implementation and rigorous validation of these models remains very limited. In the present study we implemented a structural constitutive model into a commercial finite element package. The structural model was verified against experiential test data for native bovine pericardium and fetal membrane. In addition to prediction of the mechanical response, we demonstrate how a structural model can provide deeper insights into fiber reorientation and fiber recruitment.
Developing Entrepreneurial Thinking in University of Kansas Bioengineering Students
Authors: Friis Elizabeth A. , Wilson Sara E.
Published: January 2014

Design and development of new biomedical products in an entrepreneurial environment requires technical expertise as well as an understanding of clinical applications, business considerations and regulatory aspects, and the ability to work across multidisciplinary boundaries. Advanced engineering skills must also interface with clinical needs and requirements.
A Multi-Modality Dataset for the Development of a Small Female Full Body Finite Element Model
Authors: Hayes Ashley R. , Gayzik F. Scott , Vavalle Nicholas A. , Moreno Daniel P. , Stitzel Joel D.
Published: January 2014

Motor vehicle fatalities and injuries remain a leading public health problem worldwide. In 2009, the World Health Organization reported more than 1.2 million people die each year worldwide as a result of motor vehicle crash [1]. Researchers are using a wide array of tools to mitigate the societal tool of this epidemic, and finite element (FE) computer models are one method gaining interest in the biomechanics field. Full body FE models are used to examine the potential for occupant injury in vehicle crash. Such models are often built to represent an average (50 th percentile) male occupant [2]. However computational models can be made to represent essentially any driving cohort.
Investigation of Child Neck Muscle Modeling Method in Frontal Impact
Authors: Dong Liqiang , Mao Haojie , Li Guangyao , Yang King H.
Published: January 2014

About 60 to 80% of motor vehicle related spinal injuries are in the cervical region [1]. Compared with adult, the pediatric spinal trauma induced higher mortality rate [2].
Cervical Assessment via Ultrasound Elastography: Calibrated Reference Material Development
Authors: Briggs Brandi N. , Donnelly Meghan , Ferguson Virginia L.
Published: January 2014

The human cervix serves a dual structural function throughout pregnancy. Prior to term, the cervix remains closed and firm to support the increasing weight of the fetus. At term, it must soften ( i.e., ripen) and dilate to permit birth. Timing of cervical ripening is critical for pregnancy outcome. Cervical insufficiency, or preterm ripening, is diagnosed if a cervix is not stiff enough to support the pregnancy to term and may cause miscarriage or preterm labor. This is sometimes observed mid-pregnancy when funneling at the internal os or shortening of the cervix is observed during a routine ultrasound. Women with a shorter cervix are at a higher risk for spontaneous preterm delivery. 1,2 While cervical length is not a definitive predictor of preterm delivery, a short cervix increases the risk. Moreover, the exact length at which the cervix is considered to be ‘short’ is poorly defined. While transvaginal B-mode ultrasound can identify a short cervix, this procedure is performed when clinically indicated. Cervical ripening and effacement is asymptomatic and thus is often missed until after a patient has suffered a second or third trimester miscarriage.
A Feature-Based Morphing Methodology for In-Vivo Strain Assessment in Biological Structures
Authors: Satriano Alessandro , Rivolo Simone , Di Martino Elena S.
Published: January 2014

It is often important, for diagnostic purposes, to evaluate quantitatively the motion undergone by a biological structure, starting from a viable tomographic imaging technique, such as Computed Tomography (CT) or Magnetic Resonance (MR). This is often associated with the need of the clinical personnel to perform an evaluation of a risk factor associated with pathology, e.g. ventricle performance [1]. As of today, the problem has been approached by using the magnetic resonance (MR) tagging technique [2] or experimentally by determining the location of a series of surgically implanted markers in each temporal phase [3]. The latter procedure is naturally very invasive, while MR tagging requires the use of sophisticated MR sequences that are rarely employed in standard care. Multi-detector row computer tomography (CT) scanners (routinely used in cardiac pathology diagnosis) as well as routine cine-MR sequences, on the other hand, allow dynamic imaging of the heart and large vessels with cardiac gating. In order to exploit these dynamic sequences, we have developed a tag-less method to estimate local strains from dynamic tomography gated images.
Analytical Anisotropic Multi-Shell Model of a Simplified Intervertebral Disc Subjected to Axial Compression
Authors: Demers Sébastien , Nadeau Sylvie , Bouzid Abdel-Hakim
Published: January 2014

The nucleus pulposus (NP) and the anulus fibrosus (AF) are the two main components of the intervertebral discs. At low deformation rates, in young and healthy adults, the NP reacts like an inviscid and incompressible fluid. Its internal pressure varies depending on the external forces acting on it. The AF surrounds the NP and, together with the vertebral endplates, they form a pressurized vessel.
Identifying the Presence of Dyskinesia in Patients With Parkinson’s Disease From Accelerometer Data
Authors: Darnall Nathan D. , Krishnan Narayanan C. , Carlson Jonathan D. , Greeley David R. , Mark Jamie , Schmitter-Edgecombe Maureen , Lin David C.
Published: January 2014

Movement disorders associated with Parkinson’s Disease include tremor, slowness of movement, lack of movement, and involuntary movement. During the clinicial assessment of Parkinson’s disease, patients typically self-report their daily clinical states, which includes the amount of time they experienced dyskinesia (i.e., involuntary twisting or writhing movements). The clinician then uses the self-reported information to adjust treatments in the form of medication or deep brain stimulation. Because the accuracy of the self-report is often very low, the treatment modification may not be optimal. The overall objective of this study is to develop computational algorithms that automatically identify periods of dyskinesia in patients of Parkinson’s disease from body-worn accelerometer data during activities of daily living (ADL). Specifically, unlike previous studies which used supervised learning algorithms (i.e., knowledge of prior events is used to “train” the algorithm to identify future events), our goal is to classify the periods of dyskinesia solely by identifying key features from the accelerometer data. Our desired long-term outcome is to provide clinicians a timeline showing the presence of dyskinesia over an extended time period without the clinician having to train the computational algorithm by examining video for each patient.
Sensitivity of Neck Musculoskeletal Model Predictions to Variation in Intervertebral Kinematics
Authors: Nevins Derek D. , Zheng Liying , Vasavada Anita N.
Published: January 2014

In-vivo measurement of loads and displacements in the head and neck is very difficult. Musculoskeletal biomechanical models are useful tools for investigating biomechanical phenomena in this system, but they require several assumptions and simplifications regarding tissue mechanical properties and intervertebral kinematics (IVK). In particular, IVK show considerable variation among subjects [1], and quantifying the influence of this variation on model estimates is important for the application of models toward understanding neck biomechanical function. Variation in IVK parameters may affect model estimates of neck strength (neck muscle moment, the product of muscle force and muscle moment arm), as well as the location of the head center of mass, which influences the gravitational load on the neck due to the weight of the head. The magnitude of gravitational load relative to neck extension strength, referred to here as fatiguability, is an estimate of demand on neck muscles and may be related to chronic neck pain induced by forward head postures [2]. The goal of this study was to quantify variation in model estimates of flexion strength, extension strength and fatigability over sagittal plane postures, due to variation in IVK.
Patient-Specific Hemodynamic Simulations in a Group of Patients With Coronary Artery Aneurysms Caused by Kawasaki Disease
Authors: Sengupta Dibyendu , Burns Jane C. , Kahn Andrew , Marsden Alison L.
Published: January 2014

Kawasaki disease (KD) is an acute febrile illness that can result in life threatening coronary artery aneurysms in up to 25% of untreated patients. These aneurysms put patients at risk for thrombus formation, myocardial infarction and sudden death. Currently, clinical decisions are made based on anatomy alone, with aneurysm diameter > 8mm as the arbitrary cutoff for anticoagulation therapy, despite a lack of evidence for this choice. We postulate that patient specific hemodynamics may be a better predictor for the risk of thrombosis than maximum diameter alone. To quantify hemodynamics, we performed computational fluid dynamics (CFD) simulations using patient specific models with custom coronary boundary conditions.
Phenomenology of Hemolysis in Turbulent Flows
Authors: Dasi Lakshmi Prasad , Morshed Khandakar Niaz , Forleo Marcio
Published: January 2014

Shear induced hemolysis (SIH) refers to the rupture of red blood cells in shear flows resulting in the release of hemoglobin into plasma. Hemolysis in turn triggers a chain of bio-chemical events involving all the components of blood leading to the formation of thrombosis (blood clots). While SIH is negligible in a healthy circulatory system, it is widespread in life saving blood contacting devices such as heart valves, ventricular assist devices, and blood pumps. Thus an accurate physical understanding of the process of hemolysis is critical towards developing better predictive models of SIH, particularly in the context of engineering future blood contacting devices that are significantly more blood cell friendly.
A Public Repository of Image-Based Computational Models and Patient-Specific Blood Flow Simulation Results
Authors: Wilson Nathan M. , Ortiz Ana K. , Johnson Allison B. , Feinstein Jeffrey A. , LaDisa John F. , Marsden Alison
Published: January 2014

To significantly increase publicly available clinical data for blood flow simulation research, the NHLBI sponsored Open Source Medical Software Corporation (Contracts No: HHSN268200800008C & HHSN268201100035C) and its university collaborators to build a public repository to include realistic, image-based anatomic models and related hemodynamic simulation results. The ultimate goal of this effort is to include over 100 medical image data sets, anatomic models, and hemodynamic simulation results in a public repository.
Test Chamber Design for Remotely Deployed Migratory Tracking Tags Used on Large Whales
Authors: Summers Michael P. , Oliver Peter J. , Parmigiani John P.
Published: January 2014

Knowing the location of whales as they migrate, eat, and breed is of significant interest to those concerned with the conservation of endangered whale species. This information can be used to adjust human activities, such as naval traffic, commercial fishing, and the exploration for oil and gas, to manage the recovery of these species. When tracking large whales over long distances and periods of time, satellite-monitored radio tags are used to communicate where the whales are located. These tags are remotely deployed as either dorsal body tags or dorsal fin tags. A dorsal body tag, is a radio transmitter that anchors subdermally in a region near the dorsal fin so that it can transmit whenever the whale surfaces. Dorsal fin tags are a similar form of radio transmitter that anchors directly to the dorsal fin. Tag trials on stranded whale carcasses are commonly used to test both dorsal body tag and dorsal fin tag designs [1,2]. However, there is a need to develop a more readily available testing method for dorsal body tags.
The Complex Shear Modulus of Humpback Whale Blubber
Authors: Summers Michael P. , Holst Jonathan A. , Parmigiani John P.
Published: January 2014

Further investigations of the mechanical properties of whale blubber will benefit its morphology and those who use it. Located below the dermas, blubber is an insular tissue constructed of a lipid matrix cross-weaved with strong, structural collagen and elastic fiber bundles. The blubber transitions into the superficial fascia layer, a loose connective tissue, which sheaths the muscle surrounding the whale. [1] Blubber should behave viscoelastically because it is a soft tissue. [2] The complex shear modulus G* = G′+iG″ is a viscoelastic property commonly used in defining soft tissues. It is comprised of both an elastic energy storage term (G′) and a viscous energy dissipation term (G″). Apart from adding to the morphology of whale blubber, these properties can currently be used for the improvement of certain whale tracking tag designs. The tags that would gain from these measurements deploy remotely and anchor subdermally in the body of the whale, near the dorsal fin. Once attached, they transmit a radio signal to a monitoring satellite. Knowing the migratory and behavioral patterns of whales allows for the adjustment of human activities to help in the recovery of endangered species.
Static and Dynamic Properties of a 6-DOF Robotic System for Knee Joint Biomechanics Study
Authors: Fujie Hiromichi , Kimura Kei , Yamakawa Satoshi
Published: January 2014

The application of robotic technology to the field of joint biomechaics has started more than 20 years ago 1). Since then, a variety of studies have employed commercially available articulated manipulators for the joint biomechanical studies 1–5). However, such articulated manipulators are generally poor at stiffness and precision although they were basically designed to achieve high speeds of motion while performing tasks in a large work space. To solve the problem, we have previously developed a robotic system consisting of a custom-made 6-degree of freedom (6-DOF) manipulator and a universal force-moment sensor (UFS) 6). The present study was aimed to evaluate the static and dynamic properties of the system.
Sonar Class Adaptive Sailing Jib Transfer Bench
Authors: Walsh Michael , Kowalyshyn Charles , Koch Zeb , Davis Nicholas , Leipold Kate , DeBartolo Elizabeth
Published: January 2014

Within the disabled community, there are many that enjoy the sport of sailing. To a disabled person, the experience of sailing on the open water can feel liberating, while providing meaningful and entertaining recreation. However, certain disabilities restrict one’s capacity to function as a member of a sailing crew.
Artificial Swimmer Powered by Cardiomyocytes
Authors: Williams Brian , Anand Sandeep , Rajagopalan Jagannathan , Saif Taher
Published: January 2014

We present, for the first time, a micro scale 1D swimmer powered by cardiamyocytes. It consists of a PDMS “flagella” with a head. Cardiomyocytes are plated near the head. Synchronized contraction of a small number of cells generates an elastic deformation wave in the flagella, which interacts with the fluid. Solid-fluid interaction results in a net propulsive force on the swimmer, which drives it through the fluid overcoming the drag.
IGRT/ART phantom with programmable independent rib cage and tumor motion
Authors: Haas Olivier C. L. , Mills John A. , Land Imke , Mulholl Pete , Menary Paul , Crichton Robert , Wilson Adrian , Sage John , Anna Morenc , Depuydt Tom
Published: January 2014

Purpose:

This paper describes the design and experimental evaluation of the Methods and Advanced Equipment for Simulation and Treatment in Radiation Oncology (MAESTRO) thorax phantom, a new anthropomorphic moving ribcage combined with a 3D tumor positioning system to move target inserts within static lungs.

Methods:

The new rib cage design is described and its motion is evaluated using Vicon Nexus, a commercial 3D motion tracking system. CT studies at inhale and exhale position are used to study the effect of rib motion and tissue equivalence.

Results:

The 3D target positioning system and the rib cage have millimetre accuracy. Each axis of motion can reproduce given trajectories from files or individually programmed sinusoidal motion in terms of amplitude, period, and phase shift. The maximum rib motion ranges from 7 to 20 mm SI and from 0.3 to 3.7 mm AP with LR motion less than 1 mm. The repeatability between cycles is within 0.16 mm root mean square error. The agreement between CT electron and mass density for skin, ribcage, spine hard and inner bone as well as cartilage is within 3%.

Conclusions:

The MAESTRO phantom is a useful research tool that produces programmable 3D rib motions which can be synchronized with 3D internal target motion. The easily accessible static lungs enable the use of a wide range of inserts or can be filled with lung tissue equivalent and deformed using the target motion system.
Ultrasonic Nakagami‐parameter characterization of parotid‐gland injury following head‐and‐neck radiotherapy: A feasibility study of late toxicity
Authors: Yang Xiaofeng , Tridandapani Srini , Beitler Jonathan J. , Yu David S. , Wu Ning , Wang Yuefeng , Bruner Deborah W. , Curran Walter J. , Liu Tian
Published: January 2014

Purpose:

The study aims to investigate whether Nakagami parameters—estimated from the statistical distribution of the backscattered ultrasound radio‐frequency (RF) signals—could provide a means for quantitative characterization of parotid‐gland injury resulting from head‐and‐neck radiotherapy.

Methods:

A preliminary clinical study was conducted with 12 postradiotherapy patients and 12 healthy volunteers. Each participant underwent one ultrasound study in which ultrasound scans were performed in the longitudinal, i.e., vertical orientation on the bilateral parotids. For the 12 patients, the mean radiation dose to the parotid glands was 37.7 ± 9.5 Gy, and the mean follow‐up time was 16.3 ± 4.8 months. All enrolled patients experienced grade 1 or 2 late salivary‐gland toxicity (RTOG/EORTC morbidity scale). The normal parotid glands served as the control group. The Nakagami‐scaling and Nakagami‐shape parameters were computed from the RF data to quantify radiation‐induced parotid‐gland changes.

Results:

Significant differences in Nakagami parameters were observed between the normal and postradiotherapy parotid glands. Compared with the control group, the Nakagami‐scaling parameter of the postradiotherapy group decreased by 25.8% (p < 0.001), and the Nakagami‐shape parameter decreased by 31.3% (p < 0.001). The area under the receiver operating characteristic curve was 0.85 for the Nakagami‐scaling parameter and was 0.95 for the Nakagami‐shape parameter, which further demonstrated the diagnostic efficiency of the Nakagami parameters.

Conclusions:

Nakagami parameters could be used to quantitatively measure parotid‐gland injury following head‐and‐neck radiotherapy. Moreover, the clinical feasibility was demonstrated and this study provides meaningful preliminary data for future clinical investigation.
Bioengineering Dermo-Epidermal Skin Grafts with Blood and Lymphatic Capillaries
Authors: Marino Daniela , Luginbühl Joachim , Scola Simonetta , Meuli Martin , Reichmann Ernst
Published: January 2014

Human lymphatic capillaries were engineered in a 3D hydrogel system to improve dermo-epidermal skin grafting.
Turning the Titanic
Authors: Zerhouni Elias A.
Published: January 2014

The R&D engine must be redirected toward deciphering the natural histories of human diseases and using this knowledge to select therapeutic targets.
Efficacy of an Abbreviated Induction Regimen of Amphotericin B Deoxycholate for Cryptococcal Meningoencephalitis: 3 Days of Therapy Is Equivalent to 14 Days
Authors: Livermore Joanne , Howard Susan J. , Sharp Andrew D. , Goodwin Joanne , Gregson Lea , Felton Timothy , Schwartz Julie A. , Walker Catherine , Moser Bill , Müller Werner , Harrison Thomas S. , Perfect John R. , Hope William W.
Published: January 2014

Cryptococcal meningoencephalitis is an urgent global health problem. Induction regimens using 14 days of amphotericin B deoxycholate (dAmB) are considered the standard of care but may not be suitable for resource-poor settings. We investigated the efficacy of conventional and abbreviated regimens of dAmB for cryptococcal meningoencephalitis in both murine and rabbit models of cryptococcal meningoencephalitis. We examined the extent to which immunological effectors contribute to the antifungal effect. We bridged the results to humans as a first critical step to define regimens suitable for further study in clinical trials. There were significant differences in the murine plasma-versus-cerebrum dAmB concentration-time profiles. dAmB was detectable in the cerebrum throughout the experimental period, even following the administration of only three doses of 3 mg/kg. dAmB induced a fungistatic effect in the cerebrum with a 2- to 3-log10CFU/g reduction compared with controls. The effect of 3 days of therapy was the same as that of daily therapy for 14 days. There was no evidence of increased numbers of CD3+CD4+or CD3+CD8+cells in treated mice to account for the persistent antifungal effect of an abbreviated regimen. The administration of dAmB at 1 mg/kg/day for 3 days was the same as daily therapy in rabbits. The bridging studies suggested that a human regimen of 0.7 mg/kg/day for 3 days resulted in nearly maximal antifungal activity in both the cerebrum and cerebrospinal fluid. An abbreviated regimen (3 days of therapy) of dAmB appears to be just as effective as conventional induction therapy for cryptococcal meningoencephalitis.

IMPORTANCECryptococcal meningitis is a significant and neglected infection that is associated with excessive morbidity and mortality. In well-resourced health care settings, induction therapy with at least 2 weeks of amphotericin B deoxycholate (dAmB) is advocated. Multiple clinical studies suggest that dAmB is the drug of choice for cryptococcal meningitis. In many parts of the world where the burden of cryptococcal meningitis is highest, it is infeasible to administer dAmB for prolonged periods. This paper provides the experimental basis for the efficacy of abbreviated regimens of dAmB for cryptococcal meningitis. The concept was explored in two well-validated laboratory animal models of cryptococcal meningitis, and the results were bridged to humans by using a range of mathematical modeling techniques. A 3-day regimen is as effective as the standard 14-day course. An abbreviated regimen is significantly more feasible and may enable better antifungal therapy to be administered to many patients with this frequently lethal disease.
Live-Cell Imaging of Phosphoinositide Dynamics and Membrane Architecture during
Legionella
Infection
Authors: Weber Stephen , Wagner Maria , Hilbi Hubert
Published: January 2014

The causative agent of Legionnaires’ disease,
Legionella pneumophila
, replicates in amoebae and macrophages in a distinct membrane-bound compartment, the
Legionella
-containing vacuole (LCV). LCV formation is governed by the bacterial Icm/Dot type IV secretion system that translocates ~300 different “effector” proteins into host cells. Some of the translocated effectors anchor to the LCV membrane via phosphoinositide (PI) lipids. Here, we use the soil amoeba
Dictyostelium discoideum
, producing fluorescent PI probes, to analyze the LCV PI dynamics by live-cell imaging. Upon uptake of wild-type or Icm/Dot-deficient
L. pneumophila
, PtdIns(3,4,5)
P
3
transiently accumulated for an average of 40 s on early phagosomes, which acquired PtdIns(3)
P
within 1 min after uptake. Whereas phagosomes containing Δ
icmT
mutant bacteria remained decorated with PtdIns(3)
P
, more than 80% of wild-type LCVs gradually lost this PI within 2 h. The process was accompanied by a major rearrangement of PtdIns(3)
P
-positive membranes condensing to the cell center. PtdIns(4)
P
transiently localized to early phagosomes harboring wild-type or Δ
icmT L. pneumophila
and was cleared within minutes after uptake. During the following 2 h, PtdIns(4)
P
steadily accumulated only on wild-type LCVs, which maintained a discrete PtdIns(4)
P
identity spatially separated from calnexin-positive endoplasmic reticulum (ER) for at least 8 h. The separation of PtdIns(4)
P
-positive and ER membranes was even more pronounced for LCVs harboring Δ
sidC
-
sdcA
mutant bacteria defective for ER recruitment, without affecting initial bacterial replication in the pathogen vacuole. These findings elucidate the temporal and spatial dynamics of PI lipids implicated in LCV formation and provide insight into host cell membrane and effector protein interactions.

IMPORTANCE
The environmental bacterium
Legionella pneumophila
is the causative agent of Legionnaires’ pneumonia. The bacteria form in free-living amoebae and mammalian immune cells a replication-permissive compartment, the
Legionella
-containing vacuole (LCV). To subvert host cell processes, the bacteria secrete the amazing number of ~300 different proteins into host cells. Some of these proteins bind phosphoinositide (PI) lipids to decorate the LCV. PI lipids are crucial factors involved in host cell membrane dynamics and LCV formation. Using
Dictyostelium
amoebae producing one or two distinct fluorescent probes, we elucidated the dynamic LCV PI pattern in high temporal and spatial resolution. Notably, the endocytic PI lipid PtdIns(3)
P
was slowly cleared from LCVs, thus incapacitating the host cell’s digestive machinery, while PtdIns(4)
P
gradually accumulated on the LCV, enabling critical interactions with host organelles. The LCV PI pattern underlies the spatiotemporal configuration of bacterial effector proteins and therefore represents a crucial aspect of LCV formation.
Comprehensive Functional Analysis of N-Linked Glycans on Ebola Virus GP1
Authors: Lennemann Nicholas J. , Rhein Bethany A. , Ndungo Esther , Chandran Kartik , Qiu Xiangguo , Maury Wendy
Published: January 2014

Ebola virus (EBOV) entry requires the virion surface-associated glycoprotein (GP) that is composed of a trimer of heterodimers (GP1/GP2). The GP1 subunit contains two heavily glycosylated domains, the glycan cap and the mucin-like domain (MLD). The glycan cap contains only N-linked glycans, whereas the MLD contains both N- and O-linked glycans. Site-directed mutagenesis was performed on EBOV GP1 to systematically disrupt N-linked glycan sites to gain an understanding of their role in GP structure and function. All 15 N-glycosylation sites of EBOV GP1 could be removed without compromising the expression of GP. The loss of these 15 glycosylation sites significantly enhanced pseudovirion transduction in Vero cells, which correlated with an increase in protease sensitivity. Interestingly, exposing the receptor-binding domain (RBD) by removing the glycan shield did not allow interaction with the endosomal receptor, NPC1, indicating that the glycan cap/MLD domains mask RBD residues required for binding. The effects of the loss of GP1 N-linked glycans on Ca
2+
-dependent (C-type) lectin (CLEC)-dependent transduction were complex, and the effect was unique for each of the CLECs tested. Surprisingly, EBOV entry into murine peritoneal macrophages was independent of GP1 N-glycans, suggesting that CLEC-GP1 N-glycan interactions are not required for entry into this important primary cell. Finally, the removal of all GP1 N-glycans outside the MLD enhanced antiserum and antibody sensitivity. In total, our results provide evidence that the conserved N-linked glycans on the EBOV GP1 core protect GP from antibody neutralization despite the negative impact the glycans have on viral entry efficiency.

IMPORTANCE
Filovirus outbreaks occur sporadically throughout central Africa, causing high fatality rates among the general public and health care workers. These unpredictable hemorrhagic fever outbreaks are caused by multiple species of Ebola viruses, as well as Marburg virus. While filovirus vaccines and therapeutics are being developed, there are no licensed products. The sole viral envelope glycoprotein, which is a principal immunogenic target, contains a heavy shield of glycans surrounding the conserved receptor-binding domain. We find that disruption of this shield through targeted mutagenesis leads to an increase in cell entry, protease sensitivity, and antiserum/antibody sensitivity but is not sufficient to allow virion binding to the intracellular receptor NPC1. Therefore, our studies provide evidence that filoviruses maintain glycoprotein glycosylation to protect against proteases and antibody neutralization at the expense of efficient entry. Our results unveil interesting insights into the unique entry process of filoviruses and potential immune evasion tactics of the virus.
Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems
Authors: Gomaa Ahmed A. , Klumpe Heidi E. , Luo Michelle L. , Selle Kurt , Barrangou Rodolphe , Beisel Chase L.
Published: January 2014

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems in bacteria and archaea employ CRISPR RNAs to specifically recognize the complementary DNA of foreign invaders, leading to sequence-specific cleavage or degradation of the target DNA. Recent work has shown that the accidental or intentional targeting of the bacterial genome is cytotoxic and can lead to cell death. Here, we have demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species. Using the type I-E CRISPR-Cas system in
Escherichia coli
as a model, we found that this effect could be elicited using native or imported systems and was similarly potent regardless of the genomic location, strand, or transcriptional activity of the target sequence. Furthermore, the specificity of targeting with CRISPR RNAs could readily distinguish between even highly similar strains in pure or mixed cultures. Finally, varying the collection of delivered CRISPR RNAs could quantitatively control the relative number of individual strains within a mixed culture. Critically, the observed selectivity and programmability of bacterial removal would be virtually impossible with traditional antibiotics, bacteriophages, selectable markers, or tailored growth conditions. Once delivery challenges are addressed, we envision that this approach could offer a novel means to quantitatively control the composition of environmental and industrial microbial consortia and may open new avenues for the development of “smart” antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms.

IMPORTANCE
Controlling the composition of microbial populations is a critical aspect in medicine, biotechnology, and environmental cycles. While different antimicrobial strategies, such as antibiotics, antimicrobial peptides, and lytic bacteriophages, offer partial solutions, what remains elusive is a generalized and programmable strategy that can distinguish between even closely related microorganisms and that allows for fine control over the composition of a microbial population. This study demonstrates that RNA-directed immune systems in bacteria and archaea called CRISPR-Cas systems can provide such a strategy. These systems can be employed to selectively and quantitatively remove individual bacterial strains based purely on sequence information, creating opportunities in the treatment of multidrug-resistant infections, the control of industrial fermentations, and the study of microbial consortia.
Postinduction serum infliximab trough level and decrease of C-reactive protein level are associated with durable sustained response to infliximab: a retrospective analysis of the ACCENT I trial
Authors: Cornillie Freddy , Hanauer Stephen B , Diamond Robert H , Wang Jianping , Tang Kezhen L , Xu Zhenhua , Rutgeerts Paul , Vermeire Séverine
Published: January 2014

Background

Serum infliximab trough levels correlate with efficacy; dose escalation is often beneficial in patients with Crohn's disease who stop responding to infliximab treatment.

Objective

To carry out a post hoc analysis of A Crohn's Disease Clinical Trial Evaluating Infliximab in a New Long-term Treatment Regimen I (ACCENT I) to evaluate the association between serum infliximab trough levels and C-reactive protein (CRP) after 14 weeks of induction treatment with durable sustained long-term response (Crohn's Disease Activity Index decrease ≥70 points and reduction ≥25% from baseline).

Design

ACCENT I was a multicentre, randomised, placebo-controlled study. Week 14 trough levels and CRP percentage decrease from baseline to week 14 were compared between patients with and without durable sustained response through week 54. Sensitivity and specificity were determined to predict durable sustained response. Receiver operating characteristic (ROC) curves identified optimal cut-off points; logistic regression determined ORs.

Results

After induction with 5 mg/kg infliximab, 25% (37/147) and 33% (47/144) of patients sustained week 14 response to infliximab 5 or 10 mg/kg, respectively, administered every 8 weeks without dose escalation, through week 54. Median week 14 trough levels of patients with and without durable sustained response to infliximab 5 mg/kg were 4.0 and 1.9 μg/mL, respectively (p=0.0331). Optimal predictors of durable sustained response to maintenance infliximab 5 mg/kg were week 14 trough level ≥3.5 µg/mL and ≥60% CRP decrease (ORs (95% CI), 3.5 (1.1 to 11.4) and 7.3 (1.4 to 36.7)), respectively, in patients with raised baseline CRP (>8.0 mg/L); area under the ROC curve was 0.75 for both predictors. A ≥3.5 µg/mL week 14 infliximab serum level did not predict durable sustained response to 10 mg/kg maintenance infliximab.

Conclusions

Patients with durable sustained response to maintenance infliximab 5 mg/kg had higher postinduction trough levels than patients without durable sustained response. Serum infliximab trough levels ≥3.5 µg/mL and ≥60% CRP decrease were significantly associated with durable sustained response.
The implications of the relative risk for road mortality on road safety programmes in Qatar
Authors: Consunji Rafael J , Peralta Ruben R , Al-Thani Hassan , Latifi Rifat
Published: January 2014

The epidemiology of road deaths and in particular the relative risk for road mortality (RRRM) in Qatar has not been fully defined. This study will analyse and compare the proportionate mortality and age-specific death rates from road traffic injuries (RTIs) and make recommendations for targeted injury prevention programmes for road safety in Qatar. Data from the Qatar Statistics Authority (QSA), for the year 2010, was collected and analysed. All deaths classified as ‘ICD-10 (V89) Motor- or Nonmotor-Vehicle, Accident Type of Vehicle Unspecified’ were included. There were 247 RTI related deaths in Qatar in 2010. An overall death rate was computed at 14.4 deaths per 100 000 population. The RRRM varied over 10 times among different populations with Qatari males (QM) having an increased RRRM from 10 years of age, those aged 20–29 years had the highest RRRM of 10.2. The lowest RRRM was for Qatari females who did not have a single reported road fatality in 2010. Populations with a significantly elevated RRRM (ie, RRRM>1.0) were non-Qatari men older than 50 years and Qatari males from the age of 10 onward. Proven and definite programmes must be implemented to reduce these unnecessary deaths among the populations at the highest risk. Multidisciplinary approaches must be implemented and their efficacy evaluated.
‘Workshops in healing’ for senior medical students: a 5-year overview and appraisal
Authors: Kearsley John H , Lobb Elizabeth A
Published: January 2014

We report upon the design, content and feedback from an interactive, experiential series of Workshops in Healing for senior medical students. Fifty-six final year medical students enrolled in 2×3 h workshops designed around the core themes of ‘physician know thyself’ (Workshop 1) and ‘confronting suffering’ (Workshop 2). Of the 56 students who initially enrolled, 48 students completed both workshops and provided a written open-ended reflection of their learning experience. The study, undertaken over a consecutive 5-year period (2008–2012), employed an emergent, qualitative design using thematic analysis of the reflective comments. We found that the design and content of both workshops promoted transformative learning for these final year medical students. Students identified the following benefits: (1) the opportunity to reaffirm their commitment to their chosen career path; (2) the value of listening to other students share their stories; (3) the importance of the timing of the workshops to occur after exams; (4) the use of various mediums such as art, poetry, music and contemporary/classic literature to present concepts of suffering and healing; and (5) the creation of a safe and confidential space. Students reported that these innovative workshops gave them a renewed sense of drive and enthusiasm for their chosen career. They highlighted the importance of addressing an aspect of medicine (healing) not covered in the traditional medical curriculum. Workshops in Healing helped them to rediscover a deeper meaning to medicine and their roles as future healthcare professionals.