bluuebunny/crossref_metadata_2025 huggingface dataset:
Neutrophil activity in chronic venous leg ulcers—A target for therapy?
Authors: McDaniel Jodi C. , Roy Sashwati , Wilgus Traci A.
Published: March 2013

Chronic venous leg ulcers (CVLUs) affect approximately 600,000 people annually in the United States and accrue yearly treatment costs of US$2.5–5 billion. As the population ages, demands on health care resources for CVLU treatments are predicted to drastically increase because the incidence of CVLUs is highest in those ≥65 years of age. Furthermore, regardless of current standards of care, healing complications and high recurrence rates prevail. Thus, it is critical that factors leading to or exacerbating CVLUs be discerned and more effective, adjuvant, evidence‐based treatment strategies be utilized. Previous studies have suggested that CVLUs' pathogenesis is related to the prolonged presence of high numbers of activated neutrophils secreting proteases in the wound bed that destroy growth factors, receptors, and the extracellular matrix that are essential for healing. These events are believed to contribute to a chronically inflamed wound that fails to heal. Therefore, the purpose of this project was to review studies from the past 15 years (1996–2011) that characterized neutrophil activity in the microenvironment of human CVLUs for new evidence that could explicate the proposed relationship between excessive, sustained neutrophil activity and CVLUs. We also appraised the strength of evidence for current and potential therapeutics that target excessive neutrophil activity.
An Approach to Determine Important Attributes for Engineering Change Evaluation
Authors: Mehta Chandresh , Patil Lalit , Dutta Debasish
Published: March 2013

Enterprises plan detailed evaluation of only those engineering change (EC) effects that might have a significant impact. Using past EC knowledge can prove effective in determining whether a proposed EC effect has significant impact. In order to utilize past EC knowledge, it is essential to identify important attributes that should be compared to compute similarity between ECs. This paper presents a knowledge-based approach for determining important EC attributes that should be compared to retrieve similar past ECs so that the impact of proposed EC effect can be evaluated. The problem of determining important EC attributes is formulated as the multi-objective optimization problem. Measures are defined to quantify importance of an attribute set. The knowledge in change database and the domain rules among attribute values are combined for computing the measures. An ant colony optimization (ACO)-based search approach is used for efficiently locating the set of important attributes. An example EC knowledge-base is created and used for evaluating the measures and the overall approach. The evaluation results show that our measures perform better than state-of-the-art evaluation criteria. Our overall approach is evaluated based on manual observations. The results show that our approach correctly evaluates the value of proposed change impact with a success rate of 83.33%.
A Comprehensive Elliptic Integral Solution to the Large Deflection Problems of Thin Beams in Compliant Mechanisms
Authors: Zhang Aimei , Chen Guimin
Published: March 2013

The elliptic integral solution is often considered to be the most accurate method for analyzing large deflections of thin beams in compliant mechanisms. In this paper, a comprehensive solution based on the elliptic integrals is proposed for solving large deflection problems. By explicitly incorporating the number of inflection points and the sign of the end-moment load in the derivation, the comprehensive solution is capable of solving large deflections of thin beams with multiple inflection points and subject to any kinds of load cases. The comprehensive solution also extends the elliptic integral solutions to be suitable for any beam end angle. Deflected configurations of complex modes solved by the comprehensive solution are presented and discussed. The use of the comprehensive solution in analyzing compliant mechanisms is also demonstrated by examples.
Experimental and Numerical Study of a Loaded Cylindrical PA66 Gear
Authors: Cathelin Julien , Letzelter Eric , Guingand Michele , de Vaujany Jean-Pierre , Chazeau Laurent
Published: March 2013

Polymer gears replace metal ones in many motion and light power transmission applications. This paper presents a numerical method to predict the mechanical behavior of plastic cylindrical gears and its experimental validation. The numerical method uses a viscoelastic model in its linear domain depending on temperature, humidity, and rotational speed. This numerical simulation computes the load sharing between instantaneously engaged gears and provides results such as contact pressure, tooth root stress, or transmission error. The numerical results are then compared to experimental measures on a test bench developed at the LaMCoS laboratory. This comparison allows the validation of the load sharing model.
Model Validation of an Octopus Inspired Continuum Robotic Arm for Use in Underwater Environments
Authors: Zheng Tianjiang , Branson David T. , Guglielmino Emanuele , Kang Rongjie , Medrano Cerda Gustavo A. , Cianchetti Matteo , Follador Maurizio , Godage Isuru S. , Caldwell Darwin G.
Published: March 2013

Octopuses are an example of dexterous animals found in nature. Their arms are flexible, can vary in stiffness, grasp objects, apply high forces with respect to their relatively light weight, and bend in all directions. Robotic structures inspired by octopus arms have to undertake the challenges of a high number of degrees of freedom (DOF), coupled with highly flexible continuum structure. This paper presents a kinematic and dynamic model for underwater continuum robots inspired by Octopus vulgaris. Mass, damping, stiffness, and external forces such as gravity, buoyancy, and hydrodynamic forces are considered in the dynamic model. A continuum arm prototype was built utilizing longitudinal and radial actuators, and comparisons between the simulated and experimental results show good agreement.
Effect of Joint Size on Microstructure and Growth Kinetics of Intermetallic Compounds in Solid-Liquid Interdiffusion Sn3.5Ag/Cu-Substrate Solder Joints
Authors: Abdelhadi Ousama M. , Ladani Leila
Published: March 2013

The effect of joint size on the interfacial reaction in the Sn3.5Ag/Cu-substrate soldering system was examined. An experiment was conducted in which parameters such as bonding time, temperature, and pressure were varied at multiple levels. The morphology and thickness of all intermetallic compounds (IMC) were analyzed using the scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX) techniques. An examination of the microstructures of solder joints of different sizes revealed that the size of the solder joint has no effect on the type of IMCs formed during the process. It was found that the joint size significantly affected the thickness of the intermetallic layers. The Cu3Sn intermetallic layers formed in the smaller sized solder joints were found to be thicker than those in the larger sized solder joints. In all specimen sizes, the increase in the thickness of Cu3Sn intermetallic layers with soldering time was found to obey a parabolic relationship. Additionally, for the cases when eutectic solder is available in the joints, a similar soldering time and temperature dependency were found for the Cu6Sn5 IMC phase. The intermetallic growth of the Cu3Sn phase was under a volume-diffusion controlled mechanism. The growth rate constants and activation energies of intermetallic layers were also reported for different joint thicknesses. Furthermore, the growth rate constants of the Cu3Sn intermetallic layer were found to depend upon the size of the joints.
Quasi-Static Motion Simulation and Slip Prediction of Articulated Planetary Rovers Using a Kinematic Approach
Authors: Benamar Faiz , Grand Christophe
Published: March 2013

Wheel slips are unavoidable when moving on a 3D rough surface. They are mainly due to geometrical features of contact surfaces. In this paper, we propose a model for predicting rover motion and contact slips by using a kineto-static model coupled with a linear contact model derived from semiempirical tire/terramechanics approaches. The paper also introduces a coherent approach for motion simulation of uneven articulated rovers which is computationally efficient and can then be used for autonomous on-line path planning. Model results are compared to another numerical model based on a multibody dynamic model including frictional contacts. The well-known rocker-bogie chassis, a highly articulated structure, is chosen to illustrate results and their comparison. Results demonstrate that for a slow motion, the proposed model approximates with a good accuracy the general behavior of the robot with a minimal time computation.
Electrothermomechanical Modeling and Analyses of Carbon Nanotube Polymer Composites
Authors: Xu S. , Rezvanian O. , Zikry M. A.
Published: March 2013

A new finite element (FE) modeling method has been developed to investigate how the electrical-mechanical-thermal behavior of carbon nanotube (CNT)–reinforced polymer composites is affected by electron tunneling distances, volume fraction, and physically realistic tube aspect ratios. A representative CNT polymer composite conductive path was chosen from a percolation analysis to establish the three-dimensional (3D) computational finite-element (FE) approach. A specialized Maxwell FE formulation with a Fermi-based tunneling resistance was then used to obtain current density evolution for different CNT/polymer dispersions and tunneling distances. Analyses based on thermoelectrical and electrothermomechanical FE approaches were used to understand how CNT-epoxy composites behave under electrothermomechanical loading conditions.
Direct Observations of the Evolution of Polar Cap Ionization Patches
Authors: Zhang Qing-He , Zhang Bei-Chen , Lockwood Michael , Hu Hong-Qiao , Moen Jøran , Ruohoniemi J. Michael , Thomas Evan G. , Zhang Shun-Rong , Yang Hui-Gen , Liu Rui-Yuan , McWilliams Kathryn A. , Baker Joseph B. H.
Published: March 2013

Patchy Polar Cap

Patches of enhanced density plasma in the polar ionosphere (or polar cap patches) disturb radio communications and satellite positioning at high latitudes during magnetospheric storms. Using data from Global Positioning System satellites and a high-frequency radar network,

Q.-H. Zhang
et al.

(p.
1597
) analyzed a magnetospheric storm driven by a strong coronal mass ejection from the Sun and followed the evolution and motion of a patch of ionization throughout the polar cap. The localized dayside flow response to the solar disturbance allowed a patch to be stored and grow in the dayside polar cap, and the gaps between patches were controlled by the onset of magnetic reconnection in the magnetosphere's tail.
The Structural Basis of ZMPSTE24-Dependent Laminopathies
Authors: Quigley Andrew , Dong Yin Yao , Pike Ashley C. W. , Dong Liang , Shrestha Leela , Berridge Georgina , Stansfeld Phillip J. , Sansom Mark S. P. , Edwards Aled M. , Bountra Chas , von Delft Frank , Bullock Alex N. , Burgess-Brown Nicola A. , Carpenter Elisabeth P.
Published: March 2013

Lamin Loppers

The nuclear lamina provides mechanical stability to the nuclear envelope and is involved in regulation of cellular processes such as DNA replication. Defects in the nuclear lamina lead to diseases such as progeria and metabolic disorders. One of the components of the nuclear lamina, lamin A, undergoes a complex maturation process. A key player is an inner nuclear membrane zinc metalloprotease (ZMP) that is responsible for two proteolysis steps (see the Perspective by

Michaelis and Hrycyna

).

Quigley
et al.

(p.
1604
) report the crystal structure of human ZMPSTE24 and

Pryor
et al.

(p.
1600
) that of the yeast homolog Ste24p. The structures provide insight into the mechanism of catalysis and into why mutations in ZMPSTE24 lead to laminopathies.
Tuning Selectivity in Propylene Epoxidation by Plasmon Mediated Photo-Switching of Cu Oxidation State
Authors: Marimuthu Andiappan , Zhang Jianwen , Linic Suljo
Published: March 2013

Copper in the Spotlight

Elemental copper should, in principle, be a productive catalyst for the commercial preparation of propylene oxide; however, in practice, surface oxidation under industrial conditions quickly diminishes selectivity below a useful threshold.

Marimuthu
et al.

(p.
1590
) now show that irradiating the copper with visible light during the reaction excites surface plasmon resonances that lead to reduction of the oxide coating and restore selectivity.
Cancer Pharmacogenomics: Early Promise, But Concerted Effort Needed
Authors: McLeod Howard L.
Published: March 2013

The past decade has brought together substantial advances in human genome analysis and a maturation of understanding of tumor biology. Although there is much progress still to be made, there are now several prominent examples in which tumor-associated somatic mutations have been used to identify cellular signaling pathways in tumors. This in turn has led to the development of targeted therapies, with somatic mutations serving as genomic predictors of tumor response and providing new leads for drug development. There is also a realization that germline DNA variants can help optimize cancer drug dosing and predict the susceptibility of patients to the adverse side effects of these drugs—knowledge that ultimately can be used to improve the benefit:risk ratio of cancer treatment for individual patients.
Cancer Genome Landscapes
Authors: Vogelstein Bert , Papadopoulos Nickolas , Velculescu Victor E. , Zhou Shibin , Diaz Luis A. , Kinzler Kenneth W.
Published: March 2013

Over the past decade, comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer. For most cancer types, this landscape consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of “hills” (genes altered infrequently). To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance. A better understanding of these pathways is one of the most pressing needs in basic cancer research. Even now, however, our knowledge of cancer genomes is sufficient to guide the development of more effective approaches for reducing cancer morbidity and mortality.
Fungal Carbon Sequestration
Authors: Treseder Kathleen K. , Holden Sandra R.
Published: March 2013

Mycorrhizal fungi associated with plant roots may contribute to carbon sequestration in soils.

[Also see Report by

Clemmensen
et al.

]
A Protease for the Ages
Authors: Michaelis Susan , Hrycyna Christine A.
Published: March 2013

Structures of membrane metalloproteases provide the basis for understanding mutations associated with premature aging.

[Also see Reports by

Pryor
et al.

and

Quigley
et al.

]
U.S. Science Agencies Finally Have (Reduced) Budgets for This Year
Authors: Mervis Jeffrey
Published: March 2013

The final 2013 budget gives all but one research agency less money than in 2012, although it softens the impact of an earlier version passed by the House of Representatives.
As Threats to Corals Grow, Hints of Resilience Emerge
Authors: Schmidt Charles
Published: March 2013

Some reefs are showing a surprising ability to resist or bounce back from damage. Could such resilience help corals survive in a rapidly changing ocean?
The Downside of Diversity
Authors: Kaiser Jocelyn
Published: March 2013

Increasing genetic evidence that tumors contain a heterogeneous mix of cells may explain why cancer treatments often fail.
Lactobacillus rhamnosus Ingestion Promotes Innate Host Defense in an Enteric Parasitic Infection
Authors: McClemens Jessica , Kim Janice J. , Wang Huaqing , Mao Yu-Kang , Collins Matthew , Kunze Wolfgang , Bienenstock John , Forsythe Paul , Khan Waliul I.
Published: March 2013

Enteric parasite infections around the world are a huge economic burden and decrease the quality of life for many people. The use of beneficial bacteria has attracted attention for their potential therapeutic applications in various diseases. However, the effects of beneficial bacteria in enteric parasitic infections remain largely unexplored. We investigated the effects of ingestion of
Lactobacillus rhamnosus
(JB-1) in a model of enteric nematode (
Trichuris muris
) infection. C57BL/6 (resistant to infection), AKR (susceptible to infection), interleukin 10 (IL-10) knockout (KO), and mucin Muc2 KO mice were infected with
T. muris
and treated orally with probiotic JB-1 or medium. The mice were sacrificed on various days postinfection to examine goblet cells, epithelial cell proliferation, cytokines, and worm burdens. Treatment with JB-1 significantly enhanced worm expulsion in resistant C57BL/6 mice, and this was associated with increases in IL-10 levels, goblet cell numbers, and epithelial cell proliferation. Beneficial effects of JB-1 were absent in IL-10 KO and resistant mice treated with γ-irradiated bacteria. Live JB-1 treatment also expedited worm expulsion in Muc2 KO mice and, more importantly, in AKR mice (susceptible to infection). Injection of IL-10 directly into the colonic tissue of uninfected mice induced goblet cell hyperplasia. These findings demonstrate that JB-1 modulates goblet cell biology and promotes parasite expulsion via an IL-10-mediated pathway and provide novel insights into probiotic effects on innate defense in nematode infection.
Transgenic Parasites Stably Expressing Full-Length Plasmodium falciparum Circumsporozoite Protein as a Model for Vaccine Down-Selection in Mice Using Sterile Protection as an Endpoint
Authors: Porter Michael D. , Nicki Jennifer , Pool Christopher D. , DeBot Margot , Illam Ratish M. , Brando Clara , Bozick Brooke , De La Vega Patricia , Angra Divya , Spaccapelo Roberta , Crisanti Andrea , Murphy Jittawadee R. , Bennett Jason W. , Schwenk Robert J. , Ockenhouse Christian F. , Dutta Sheetij
Published: March 2013

Circumsporozoite protein (CSP) ofPlasmodium falciparumis a protective human malaria vaccine candidate. There is an urgent need for models that can rapidly down-select novel CSP-based vaccine candidates. In the present study, the mouse-mosquito transmission cycle of a transgenicPlasmodium bergheimalaria parasite stably expressing a functional full-lengthP. falciparumCSP was optimized to consistently produce infective sporozoites for protection studies. A minimal sporozoite challenge dose was established, and protection was defined as the absence of blood-stage parasites 14 days after intravenous challenge. The specificity of protection was confirmed by vaccinating mice with multiple CSP constructs of differing lengths and compositions. Constructs that induced high NANP repeat-specific antibody titers in enzyme-linked immunosorbent assays were protective, and the degree of protection was dependent on the antigen dose. There was a positive correlation between antibody avidity and protection. The antibodies in the protected mice recognized the native CSP on the parasites and showed sporozoite invasion inhibitory activity. Passive transfer of anti-CSP antibodies into naive mice also induced protection. Thus, we have demonstrated the utility of a mouse efficacy model to down-select human CSP-based vaccine formulations.
Development of a Singleplex PCR Assay for Rapid Identification and Differentiation of Cryptococcus neoformans var.grubii, Cryptococcus neoformans var. neoformans, Cryptococcus gattii, and Hybrids
Authors: Feng Xiaobo , Fu Xiaohua , Ling Bo , Wang Lei , Liao Wanqing , Yao Zhirong
Published: March 2013

A singleplex PCR assay using a single primer pair targeting the putative sugar transporter gene was developed here to distinguishCryptococcus neoformansvar.grubii,Cryptococcus neoformansvar.neoformans, andCryptococcus gattiiaccording to the distinct size of the amplicon. The interspecies and intravarietal hybrids were also characterized on the basis of distinct combined profiles of amplicons. This PCR assay is a rapid, simple, and reliable approach suitable for laboratory diagnoses and large-scale epidemiologic studies.
Does Neutralization of Gastric Aspirates from Children with Suspected Intrathoracic Tuberculosis Affect Mycobacterial Yields on MGIT Culture?
Authors: Parashar Deepak , Kabra Sushil K. , Lodha Rakesh , Singh Varinder , Mukherjee Aparna , Arya Tina , Grewal Harleen M. S. , Singh Sarman ,   Delhi Pediatric TB Study Group
Published: March 2013

The microbiological confirmation of pulmonary tuberculosis in children relies on cultures of gastric aspirate (GA) specimens. Conventionally, GAs are neutralized to improve culture yields of mycobacteria. However, there are limited data to support this practice. To study the utility of neutralization of GAs with sodium bicarbonate in children with intrathoracic tuberculosis, a total of 116 children of either sex, aged 6 months to 14 years (median age, 120 months; interquartile range [IQR], 7 to 192 months), underwent gastric aspiration on 2 consecutive days. Gastric aspirates were divided into two aliquots, and only one aliquot was neutralized with 1% sodium bicarbonate. Both aliquots were processed for smear and culture examinations. Out of the 232 gastric aspirates, 12 (5.17%) were acid-fast bacilli (AFB) smear positive. There were no differences in smear positivity rates from samples with or without neutralization. The yield of
Mycobacterium tuberculosis
on a Bactec MGIT 960 culture system was significantly lower in the neutralized samples (16.3% [38/232]) than in the nonneutralized samples (21.5% [50/232]) (
P
= 0.023). There was no significant difference between the neutralized and the nonneutralized samples in time to detection using the MGIT 960 system (average, 24.6 days; IQR, 12 to 37 days) (
P
= 0.9). The contamination rates were significantly higher in the neutralized samples than in the nonneutralized samples (17.2% [40/232] versus 3.9% [9/232]) (
P
= 0.001). The agreement for positive mycobacterial culture between the two approaches was 66.5% (
P
= 0.001). Hence, we recommend that gastric aspirate samples not be neutralized with sodium bicarbonate prior to culture for
M. tuberculosis
.
Detection of IMP Metallo-β-Lactamase in Carbapenem-Nonsusceptible Enterobacteriaceae and Non-Glucose-Fermenting Gram-Negative Rods by Immunochromatography Assay
Authors: Notake Shigeyuki , Matsuda Mari , Tamai Kiyoko , Yanagisawa Hideji , Hiramatsu Keiichi , Kikuchi Ken
Published: March 2013

Metallo-β-lactamases (MBLs) are transmissible carbapenemases of increasing prevalence in Gram-negative bacteria among health care facilities worldwide. Control of the further spread of these carbapenem-resistant bacteria relies on clinical microbiological laboratories correctly identifying and classifying the MBLs. In this study, we evaluated a simple and rapid method for detecting IMP, the most prevalent MBL in Japan. We used an immunochromatography (IC) assay for 181 carbapenem-nonsusceptible (CNS) (nonsusceptible to imipenem or meropenem) strains comprising 74 IMP-producing and 33 non-IMP-producing strains of non-glucose-fermenting Gram-negative rods (NFGNR), as well as 64 IMP-producing and 10 non-IMP-producingEnterobacteriaceaestrains. The IC assay results were compared to those from the double-disk synergy test (DDST), the MBL Etest, and the modified Hodge test (MHT) (only forEnterobacteriaceae). The IMP type was confirmed by specific PCR and direct sequencing. The IC assay detected all of the IMP-type MBLs, including IMP-1, -2, -6, -7, -10, -11, -19, -20, and -22 and IMP-40, -41, and -42 (new types), with 100% specificity and sensitivity against all strains tested. Although the sensitivity and specificity values for the DDST and MHT were equivalent to those for the IC assay, the MBL Etest was positive for only 87% of NFGNR and 31% ofEnterobacteriaceaedue to the low MIC of imipenem, causing an indeterminate evaluation. These results indicated that the IC assay might be a useful alternative to PCR for IMP MBL detection screening.
HIV-1 Gag Associates with Specific Uropod-Directed Microdomains in a Manner Dependent on Its MA Highly Basic Region
Authors: Llewellyn G. Nicholas , Grover Jonathan R. , Olety Balaji , Ono Akira
Published: March 2013

In polarized T cells, HIV-1 Gag localizes to a rear-end protrusion known as the uropod in a multimerization-dependent manner. Gag-laden uropods participate in formation of virological synapses, intercellular contact structures that play a key role in cell-to-cell HIV-1 transmission. Our previous observations suggest that Gag associates with uropod-directed microdomains (UDMs) that eventually comigrate with Gag to the uropod over the cell surface. However, the nature of Gag multimerization required for this movement, the composition of the UDMs, and the molecular determinants for Gag association with these microdomains remain unknown. In this study, we found that Gag multimerization prior to budding but beyond dimerization is necessary for Gag localization to the uropods, indicating that uropod localization occurs early in the assembly process. We also found that prior to membrane curvature, Gag multimers associate with a specific subset of UDMs containing PSGL-1, CD43, and CD44 but not ICAM-1, ICAM-3, or CD59. Notably, upon association, Gag excludes ICAM-3 from this subset of UDMs, revealing an active and selective reorganization of these microdomains by Gag. This specific association between Gag and UDMs is dependent on the highly basic region (HBR) in the Gag matrix (MA) domain. The overall positive charge of the HBR was needed for the interaction with the specific UDM subset, while the exact HBR sequence was not, unlike that seen for MA binding to the plasma membrane phospholipid phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P
2
]. Taken totogether, these findings revealed that HIV-1 Gag associates with specific microdomains present in polarized T cells in an MA-dependent manner, which results in modification of the microdomain constituents.
Differential Recognition of Old World and New World Arenavirus Envelope Glycoproteins by Subtilisin Kexin Isozyme 1 (SKI-1)/Site 1 Protease (S1P)
Authors: Burri Dominique J. , Ramos da Palma Joel , Seidah Nabil G. , Zanotti Giuseppe , Cendron Laura , Pasquato Antonella , Kunz Stefan
Published: March 2013

The arenaviruses are an important family of emerging viruses that includes several causative agents of severe hemorrhagic fevers in humans that represent serious public health problems. A crucial step of the arenavirus life cycle is maturation of the envelope glycoprotein precursor (GPC) by the cellular subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P). Comparison of the currently known sequences of arenavirus GPCs revealed the presence of a highly conserved aromatic residue at position P7 relative to the SKI-1/S1P cleavage side in Old World and clade C New World arenaviruses but not in New World viruses of clades A and B or cellular substrates of SKI-1/S1P. Using a combination of molecular modeling and structure-function analysis, we found that residueY285 of SKI-1/S1P, distal from the catalytic triad, is implicated in the molecular recognition of the aromatic “signature residue” at P7 in the GPC of Old World Lassa virus. Using a quantitative biochemical approach, we show that Y285 of SKI-1/S1P is crucial for the efficient processing of peptides derived from Old World and clade C New World arenavirus GPCs but not of those from clade A and B New World arenavirus GPCs. The data suggest that during coevolution with their mammalian hosts, GPCs of Old World and clade C New World viruses expanded the molecular contacts with SKI-1/S1P beyond the classical four-amino-acid recognition sequences and currently occupy an extended binding pocket.
Human Cytomegalovirus Induces a Biphasic Inflammatory Response in Primary Endothelial Cells
Authors: Jeffery H. C. , Söderberg-Naucler C. , Butler L. M.
Published: March 2013

Contradictory studies report either pro- or anti-inflammatory endothelial cell (EC) responses to human cytomegalovirus (hCMV) infection, hindering the validation of a potential link between this virus and associated inflammatory pathologies. Clarifying this issue, we report that hCMV induces a biphasic response. Early after inoculation, hCMV promoted lymphocyte and, to a lesser extent, neutrophil capture under
in vivo
relevant shear stresses. In contrast, later stages of infection rendered EC refractory to basal, or cytokine-induced, leukocyte recruitment.
Role of E1B55K in E4orf6/E1B55K E3 Ligase Complexes Formed by Different Human Adenovirus Serotypes
Authors: Cheng Chi Ying , Gilson Timra , Wimmer Peter , Schreiner Sabrina , Ketner Gary , Dobner Thomas , Branton Philip E. , Blanchette Paola
Published: March 2013

The E4orf6 protein of serotypes representing all human adenovirus species forms Cullin-based E3 ubiquitin ligase complexes that facilitate virus infection by inducing degradation of cellular proteins that impede efficient viral replication. This complex also includes the viral E1B55K product believed to bind and introduce substrates for ubiquitination. Heterogeneity in the composition of these ligases exists, as some serotypes form Cul5-based complexes whereas others utilize Cul2. Significant variations in substrate specificities also exist among serotypes, as some degrade certain substrates very efficiently whereas others induce more modest or little degradation. As E1B55K is believed to function as the substrate acquisition component of the ligase, we undertook studies to compare the ability of representative E1B55K proteins to bind substrates with the efficacy of degradation by their respective E4orf6-based ligases. Interestingly, although efficient degradation in some cases corresponded to the ability of E1B55K to bind to or relocalize substrates, there were several examples of substrates that bound efficiently to E1B55K but were not degraded and others in which substrates were degraded even though binding to E1B55K was low or undetectable. These results suggest that transient interactions with E1B55K may be sufficient for efficient substrate degradation and that binding alone is not sufficient, implying that the orientation of the substrate in the ligase complex is probably crucial. Nevertheless, we found that the substrate specificity of certain E4orf6-based ligases could be altered through the formation of hybrid complexes containing E1B55K from another serotype, thus confirming identification of E1B55K as the substrate acquisition component of the complex.
Deep Sequencing Reveals Mutagenic Effects of Ribavirin during Monotherapy of Hepatitis C Virus Genotype 1-Infected Patients
Authors: Dietz Julia , Schelhorn Sven-Eric , Fitting Daniel , Mihm Ulrike , Susser Simone , Welker Martin-Walter , Füller Caterina , Däumer Martin , Teuber Gerlinde , Wedemeyer Heiner , Berg Thomas , Lengauer Thomas , Zeuzem Stefan , Herrmann Eva , Sarrazin Christoph
Published: March 2013

The preeminent mode of action of the broad-spectrum antiviral nucleoside ribavirin in the therapy of chronic hepatitis C is currently unresolved. Particularly under contest are possible mutagenic effects of ribavirin that may lead to viral extinction by lethal mutagenesis of the hepatitis C virus (HCV) genome. We applied ultradeep sequencing to determine ribavirin-induced sequence changes in the HCV coding region (nucleotides [nt] 330 to 9351) of patients treated with 6-week ribavirin monotherapy (n= 6) in comparison to placebo (n= 6). Baseline HCV RNA levels maximally declined on average by −0.8 or −0.1 log10IU/ml in ribavirin- versus placebo-treated patients. No general increase in rates of nucleotide substitutions in ribavirin-treated patients was observed. However, more HCV genome positions with high G-to-A and C-to-U transition rates were detected between baseline and treatment week 6 in ribavirin-treated patients in comparison to placebo-treated patients (rate of 0.0041 transitions per base pair versus rate of 0.0022 transitions per base pair;P= 0.049). Similarly, the sensitive detection of low-frequency minority variants by statistical filtering indicated significantly more positions with G-to-A and C-to-U transitions in ribavirin-treated patients than in placebo-treated patients (rate of 0.0331 transitions versus rate of 0.0186 transitions per G/C-containing position at baseline;P= 0.018). In contrast, non-ribavirin-associated A-to-G and U-to-C transitions were not enriched in the ribavirin group (P= 0.152). We conclude that ribavirin exerts a mutagenic effect on the virus in patients with chronic hepatitis C by facilitating G-to-A and C-to-U nucleotide transitions.
MDA5 Localizes to Stress Granules, but This Localization Is Not Required for the Induction of Type I Interferon
Authors: Langereis Martijn A. , Feng Qian , van Kuppeveld Frank J.
Published: March 2013

Virus infection can initiate a type I interferon (IFN-α/β) response via activation of the cytosolic RNA sensors retinoic acid-inducible gene-I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5). Furthermore, it can activate kinases that phosphorylate eukaryotic translation initiation factor 2α (eIF2α), which leads to inhibition of (viral) protein translation and formation of stress granules (SG). Most viruses have evolved mechanisms to suppress these cellular responses. Here, we show that a mutant mengovirus expressing an inactive leader (L) protein, which we have previously shown to be unable to suppress IFN-α/β, triggered SG formation in a protein kinase R (PKR)-dependent manner. Furthermore, we show that infection of cells that are defective in SG formation yielded higher viral RNA levels, suggesting that SG formation acts as an antiviral defense mechanism. Since the induction of both IFN-α/β and SG is suppressed by mengovirus L, we set out to investigate a potential link between these pathways. We observed that MDA5, the intracellular RNA sensor that recognizes picornaviruses, localized to SG. However, activation of the MDA5 signaling pathway did not trigger and was not required for SG formation. Moreover, cells that were unable to form SG—by protein kinase R (PKR) depletion, using cells expressing a nonphosphorylatable eIF2α protein, or by drug treatment that inhibits SG formation—displayed a normal IFN-α/β response. Thus, although MDA5 localizes to SG, this localization seems to be dispensable for induction of the IFN-α/β pathway.
The Receptor Attachment Function of Measles Virus Hemagglutinin Can Be Replaced with an Autonomous Protein That Binds Her2/
neu
While Maintaining Its Fusion-Helper Function
Authors: Rasbach Anke , Abel Tobias , Münch Robert C. , Boller Klaus , Schneider-Schaulies Jürgen , Buchholz Christian J.
Published: March 2013

Cell entry of enveloped viruses is initiated by attachment to the virus receptor followed by fusion between the virus and host cell membranes. Measles virus (MV) attachment to its receptor is mediated by the hemagglutinin (H), which is thought to produce conformational changes in the membrane fusion protein (F) that trigger insertion of its fusion peptide into the target cell membrane. Here, we uncoupled receptor attachment and the fusion-helper function of H by introducing Y481A, R533A, S548L, and F549S mutations into the viral attachment protein that made it blind to its normal receptors. An artificial receptor attachment protein specific for Her2/
neu
was incorporated into the membranes of pseudotyped lentivirus particles as a separate transmembrane protein along with the F protein. Surprisingly, these particles entered efficiently into Her2/
neu
-positive SK-OV-3 as well as CHO-Her2 cells. Cell entry was independent of endocytosis but strictly dependent on the presence of H. H-specific monoclonal antibodies, as well as a mutation in H interfering with H/F cooperation, blocked cell entry. The particles mediated stable and specific transfer of reporter genes into Her2/
neu
-positive human tumor cells also
in vivo
, while exhibiting improved infectivity and higher titers than Her2/
neu
-targeted vectors displaying the targeting domain on H. Extending the current model of MV cell entry, the data suggest that receptor binding of H is not required for its fusion-helper function but that particle-cell contact in general may be sufficient to induce the conformational changes in the H/F complex and activate membrane fusion.
TMPRSS2 Activates the Human Coronavirus 229E for Cathepsin-Independent Host Cell Entry and Is Expressed in Viral Target Cells in the Respiratory Epithelium
Authors: Bertram Stephanie , Dijkman Ronald , Habjan Matthias , Heurich Adeline , Gierer Stefanie , Glowacka Ilona , Welsch Kathrin , Winkler Michael , Schneider Heike , Hofmann-Winkler Heike , Thiel Volker , Pöhlmann Stefan
Published: March 2013

Infection with human coronavirus 229E (HCoV-229E) is associated with the common cold and may result in pneumonia in immunocompromised patients. The viral spike (S) protein is incorporated into the viral envelope and mediates infectious entry of HCoV-229E into host cells, a process that depends on the activation of the S-protein by host cell proteases. However, the proteases responsible for HCoV-229E activation are incompletely defined. Here we show that the type II transmembrane serine proteases TMPRSS2 and HAT cleave the HCoV-229E S-protein (229E-S) and augment 229E-S-driven cell-cell fusion, suggesting that TMPRSS2 and HAT can activate 229E-S. Indeed, engineered expression of TMPRSS2 and HAT rendered 229E-S-driven virus-cell fusion insensitive to an inhibitor of cathepsin L, a protease previously shown to facilitate HCoV-229E infection. Inhibition of endogenous cathepsin L or TMPRSS2 demonstrated that both proteases can activate 229E-S for entry into cells that are naturally susceptible to infection. In addition, evidence was obtained that activation by TMPRSS2 rescues 229E-S-dependent cell entry from inhibition by IFITM proteins. Finally, immunohistochemistry revealed that TMPRSS2 is coexpressed with CD13, the HCoV-229E receptor, in human airway epithelial (HAE) cells, and that CD13
+
TMPRSS2
+
cells are preferentially targeted by HCoV-229E, suggesting that TMPRSS2 can activate HCoV-229E in infected humans. In sum, our results indicate that HCoV-229E can employ redundant proteolytic pathways to ensure its activation in host cells. In addition, our observations and previous work suggest that diverse human respiratory viruses are activated by TMPRSS2, which may constitute a target for antiviral intervention.
Patients who call emergency ambulances for primary care problems: a qualitative study of the decision-making process
Authors: Booker Matthew J , Simmonds Rosemary L , Purdy Sarah
Published: March 2013

Background

Telephone calls for emergency ambulances are rising annually, increasing the pressure on ambulance resources for clinical problems that could often be appropriately managed in primary care.

Objective

To explore and understand patient and carer decision making around calling an ambulance for primary care-appropriate health problems.

Methods

Semistructured interviews were conducted with patients and carers who had called an ambulance for a primary care-appropriate problem. Participants were identified using a purposive sampling method by a non-participating research clinician attending ‘999’ ambulance calls. A thematic analysis of interview transcripts was undertaken.

Results

A superordinate theme, patient and carer anxiety in urgent-care decision making, and four subthemes were explored: perceptions of ambulance-based urgent care; contrasting perceptions of community-based urgent care; influence of previous urgent care experiences in decision making; and interpersonal factors in lay assessment and management of medical risk and subsequent decision making.

Conclusions

Many calls are based on fundamental misconceptions about the types of treatment other urgent-care avenues can provide, which may be amenable to educational intervention. This is particularly relevant for patients with chronic conditions with frequent exacerbations. Callers who have care responsibilities often default to the most immediate response available, with decision making driven by a lower tolerance of perceived risk. There may be a greater role for more detailed triage in these cases, and closer working between ambulance responses and urgent primary care, as a perceived or actual distance between these two service sectors may be influencing patient decision making on urgent care.
Teaching medical students to recognise their strengths and limitations in leadership, teamwork and communication by military led tutorials
Authors: Clark James , Hall T Falconer , O'Mahony K
Published: March 2013

Objectives

The General Medical Council has stipulated that greater importance must be placed on undergraduate students developing their ability to lead and work effectively as part of a team. Wales Universities’ Officer Training Corps have attempted to meet this requirement through a third year interactive tutorial which aims to encourage students to recognise their strengths and limitations in the six outcomes of leadership, teamwork, accountability, management, feedback and communication.

Methods

16 tutorial groups of 10–15 students were each led by one officer who divided the tutorial group into three teams. The teams worked on complex planning exercises with an intrateam constructive feedback discussion to raise students’ awareness of their strengths and limitations as individuals during the task, as perceived by others.

Results

The student perception was that all six learning outcomes were achieved by the session. 163 students returned feedback questionnaires and learning outcomes 1–4 were felt to have been addressed effectively or very effectively by 90%, 91%, 90% and 86% respondents, respectively. The fifth and sixth outcomes were less well achieved with only 66% and 64% respondents agreeing that the outcomes were achieved effectively or very effectively.

Conclusions

Students commended the instructor's demonstration of leadership and the novel teaching method but improvements could be made in reinforcing why these skills are important.
Aspergillus galactose metabolism is more complex than that of Saccharomyces: the story of GalDGAL7 and GalEGAL1
Authors: Alam Md. Kausar , Kaminskyj Susan G.W.
Published: March 2013

Saccharomyces cerevisiae Hansen GAL1 (galactokinase) generates galactose-1-phosphate; GAL7 (galactose-1-phosphate uridylyltransferase) transfers UDP between galactose or glucose and their respective sugar-1-phosphate conjugates, and both are essential on galactose. Aspergillus nidulans ANID_04957 has 41% amino acid sequence identity with GAL1; ANID_06182 has 50% sequence identity with GAL7. The names Aspergillus nidulans GalE (galactokinase) and GalD (galactose-1-phosphate uridylyltransferase) are consistent with prior studies. Complemented galDΔ:ScGAL7 and galEΔ:ScGAL1 strains had wild-type phenotype, demonstrating functional homology. The galD5 and galE9 alleles were truncated. Strains galDΔ and galD5 were impaired on minimal medium containing 1% galactose (MM-Gal) at pH 7.5 and did not grow on MM-Gal pH 4.5. Strains galEΔ and galE9 grew on MM-Gal at both pH levels. Strains galDΔ and galEΔ produced wild-type conidiophores on minimal medium containing 1% glucose (MM-Glu) but few spores; for both, sporulation was lower on MM-Gal pH 7.5. GalD-GFP (green fluorescent protein) and GalE-GFP were cytosolic and upregulated on MM-Gal, consistent with quantitative real-time polymerase chain reaction. Galactofuranose immunolocalization in galDΔ resembled wild type on MM-Glu but was reduced on MM-Gal. The galEΔ strains had immunolocalizable Galf on all these media. Strains galDΔ and galEΔ were more sensitive to calcofluor, caspofungin, and itraconazole on MM-Gal. Neither galD nor galE is essential on galactose at high pH, implying additional routes for galactose metabolism in Aspergillus. Aspergillus galactose metabolism is more complex than that of S. cerevisiae.
Including independent estimates and uncertainty to quantify total abundance of fish migrating in a large river system: walleye (Sander vitreus) in the Maumee River, Ohio
Authors: Pritt Jeremy J. , DuFour Mark R. , Mayer Christine M. , Kocovsky Patrick M. , Tyson Jeffrey T. , Weimer Eric J. , Vandergoot Christopher S.
Published: March 2013

Walleye (Sander vitreus) in Lake Erie is a valuable and migratory species that spawns in tributaries. We used hydroacoustic sampling, gill net sampling, and Bayesian state-space modeling to estimate the spawning stock abundance, characterize size and sex structure, and explore environmental factors cuing migration of walleye in the Maumee River for 2011 and 2012. We estimated the spawning stock abundance to be between 431 000 and 1 446 000 individuals in 2011 and between 386 400 and 857 200 individuals in 2012 (95% Bayesian credible intervals). A back-calculation from a concurrent larval fish study produced an estimate of 78 000 to 237 000 spawners for 2011. The sex ratio was skewed towards males early in the spawning season but approached 1:1 later, and larger individuals entered the river earlier in the season than smaller individuals. Walleye migration was greater during low river discharge and intermediate temperatures. Our approach to estimating absolute abundance and uncertainty as well as characterization of the spawning stock could improve assessment and management of this species, and our methodology is applicable to other diadromous populations.
Decrease in fungal biodiversity along an available phosphorous gradient in arable Andosol soils in Japan
Authors: Bao Zhihua , Matsushita Yuko , Morimoto Sho , Hoshino Yuko Takada , Suzuki Chika , Nagaoka Kazunari , Takenaka Makoto , Murakami Hiroharu , Kuroyanagi Yukiko , Urashima Yasufumi , Sekiguchi Hiroyuki , Kushida Atsuhiko , Toyota Koki , Saito Masanori , Tsushima Seiya
Published: March 2013

Andosols comprise one of the most important soil groups for agricultural activities in Japan because they cover about 46.5% of arable upland fields. In this soil group, available phosphorus (P) is accumulated by application of excessive fertilizer, but little is known about the influence of increasing P availability on microbial community diversity at large scales. We collected soil samples from 9 agro-geographical sites with Andosol soils across an available P gradient (2048.1–59.1 mg P2O5·kg−1) to examine the influence of P availability on the fungal community diversity. We used polymerase chain reaction – denaturing gradient gel electrophoresis to analyze the fungal communities based on 18S rRNA genes. Statistical analyses revealed a high negative correlation between available P and fungal diversity (H′). Fungal diversity across all sites exhibited a significant hump-shaped relationship with available P (R2 = 0.38, P < 0.001). In addition, the composition of the fungal community was strongly correlated with the available P gradient. The ribotype F6, which was positively correlated with available P, was closely related to Mortierella. The results show that both the diversity and the composition of the fungal community were influenced by available P concentrations in Andosols, at a large scale. This represents an important step toward understanding the processes responsible for the maintenance of fungal diversity in Andosolic soils.
Finding of IFNγ gene enhancers and their core sequences
Authors: Lv Zhanjun , Cheng Jianjun , Xie Ying , Jing Xiangyang , Zhang Yuan , Wang Xiufang
Published: March 2013

DNA segmentation methods were used to study which fragments of the human IFNγ gene possess enhancer activity. The human IFNγ gene was divided into 240-bp fragments, which were inserted between the GFP gene and the Alu tandem sequence to determine whether the inserted sequences eliminate the inhibition induced by the Alu tandem sequence. We found that five different 240-bp fragments (FUIFN3F3R, IFN4F4R, IFN6F6R, IFN21F21R, and IFN22F22R) and two 60-bp core sequences (IFN6-2F2R and IFN21-3-4F3-4R) derived from the IFNγ gene contain enhancers that can activate the GFP reporter gene. These enhancers may be targets of IFNγ gene expression regulation.