bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance Enhancements and Validations of a Generic Ocean-Wave Energy Extractor
Authors: Tom Nathan , Yeung Ronald W.
Published: September 2013

This paper evaluates two aspects of enhancements made to a generic ocean-wave energy extraction device, developed recently at University of California (UC)-Berkeley with features reported in Yeung et al. (2010, “Design, Analysis, and Evaluation of the UC-Berkeley Wave-Energy Extractor,” ASME J. Offshore Mech. Arct. Eng., 134(2), p. 021902). First, the differences in hydrodynamic performance between flat- and hemispherical bottom floaters were investigated theoretically using the UC Berkeley 2D viscous-flow solver: FSRVM (Seah and Yeung, 2008, “Vortical-Flow Modeling for Ship Hulls in Forward and Lateral Motion,” Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea). The predicted enhancement was compared with experimental results, demonstrating that an increase in motion of over 50% was realizable. Second, important modifications to the design, fabrication, and material of the rotor and stator of the permanent magnet linear generator (PMLG) were made with the aim to increase both power output and mechanical-to-electrical conversion efficiency, ηel. Increased power extraction and efficiency were achieved, doubling what had been previously reported. The nonlinear relationship between the generator damping and the magnet-coil gap width was also investigated to verify that the conditions for optimal power extraction presented in Yeung et al. (2010, “Design, Analysis, and Evaluation of the UC-Berkeley Wave-Energy Extractor,” ASME J. Offshore Mech. Arct. Eng., 134(2), p. 021902) were achievable with the PMLG. Experimental results, obtained from testing the coupled floater and PMLG systems in a wave tank, revealed that realized capture widths were more than double those from the previous design. These results further confirmed that matching of the generator and floater damping significantly increased the global efficiency of the extraction process.
Optimizing a Class of Nonlinear Singularly Perturbed Systems Using SDRE Technique
Authors: Mostafa Ghadami Seyed , Amjadifard Roya , Khaloozadeh Hamid
Published: September 2013

In this paper, we address the finite-horizon optimization of a class of nonlinear singularly perturbed systems based on the state-dependent Riccati equation (SDRE) technique and singular perturbation theory. In such systems, both slow and fast variables are nonlinear. Moreover, the performance index for the system states is nonlinearly quadratic. In this study, unlike conventional methods, linearization does not occur around the equilibrium point, and it provides a description of the system as state-dependent coefficients (SDCs) in the form f(x) = A(x)x. One of the advantages of the state-dependent Riccati equation method is that no information about the Jacobian of the nonlinear system, just like the Hamilton–Jacobi–Belman (HJB) equation, is required. Thus, the state-dependent Riccati equation has simplicity of the linear quadratic method. On the other hand, one of the advantages of the singular perturbation theory is that it reduces high-order systems into two lower order subsystems due to the interaction between slow and fast variables. In the proposed method, the singularly perturbed state-dependent Riccati equations are first derived for the system under study. Using the singular perturbation theory, the singularly perturbed state and state-dependent Riccati equations are separated into outer layer, initial, and final layer correction equations. These equations are then solved to obtain the optimal control law. Simulation results in comparison with the previous methods indicate the desirable performance and efficiency of the proposed method. However, it should be noted that due to the dependence of the proposed method on the choice of state-dependent matrices and the presence of a nonlinear optimal control problem, the results are generally suboptimal.
Numerical Analysis and Scaled High Resolution Tank Testing of a Novel Wave Energy Converter
Authors: Rhinefrank Ken , Schacher Al , Prudell Joe , Cruz Joao , Stillinger Chad , Naviaux David , Brekken Ted , von Jouanne Annette , Newborn David , Yim Solomon , Cox Dan
Published: September 2013

This paper presents a novel point absorber wave energy converter (WEC), developed by Columbia Power Technologies (COLUMBIA POWER), in addition to the related numerical analysis and scaled wave tank testing. Three hydrodynamic modeling tools are employed to evaluate the performance of the WEC, including WAMIT, GL Garrad Hassan's GH WaveDyn, and OrcaFlex. GH WaveDyn is a specialized numerical code being developed specifically for the wave energy industry. Performance and mooring estimates at full scale are evaluated and optimized, followed by the development of a 1:33 scale physical model. The physical tests of the 1:33 scale model WEC were conducted at the multidirectional wave basin of Oregon State University's O.H. Hinsdale Wave Research Laboratory, in conjunction with the Northwest National Marine Renewable Energy Center (NNMREC). This paper concludes with an overview of the next steps for the modeling program and future experimental test plans.
Parametric Analysis of Turbulent Wall Jet in Still Air Over a Transitional Rough, With Asymptotes of Fully Rough and Fully Smooth Wall Jets
Authors: Afzal Noor , Seena Abu
Published: September 2013

The novel scalings for streamwise variations of the flow in a turbulent wall jet over a fully smooth, transitional, and fully rough surfaces have been analyzed. The universal scaling for arbitrary wall roughness is considered in terms of the roughness friction Reynolds number (that arises from the stream wise variations of roughness in the flow direction) and roughness Reynolds number at the nozzle jet exit. The transitional rough wall jet functional forms have been proposed, whose numerical constants power law index and prefactor are estimated from best fit to the data for several variables, like, maximum wall jet velocity, boundary layer thickness at maxima of wall jet velocity, the jet half width, the friction factor and momentum integral, which are supported by the experimental data. The data shows that the two asymptotes of fully rough and fully smooth surfaces are co-linear with transitional rough surface, predicting same constants for any variable of flow for full smooth, fully rough and transitional rough surfaces. There is no universality of scalings in terms of traditional variables as different expressions are needed for each stage of the transitional roughness. The experimental data provides very good support to our universal relations.
Penetration and Removal of the Mooring Dolphin Platform With Three Caisson Foundations
Authors: Zhang Puyang , Ding Hongyan , Le Conghuan
Published: September 2013

Mooring dolphin platforms (MDPs) with three caisson foundations were installed in the ice-drifting Bohai Sea of China. Before installation, prototype tests of penetration and removal processing were conducted near the design site. To determine the lateral soil pressure and skin friction of the caisson, soil pressure and strain gauge transducers were fixed along the external skirt of caisson B of MDP1. The shaft skin friction was calculated from the strain difference between any two points of the strain gauges. The transducer results indicated that when the soil property determined by unconsolidated and undrained (UU) triaxial tests was used to calculate the unit skin friction resistance, a value of the adhesion factor α of 1.5–2.0 is recommended. The factor α is 1–0.4 during the suction-assisted penetration phase. The lateral earth pressure coefficient K decreased with penetration depth, most likely due to seepage caused by underpressure. In addition, the difference between the measured values obtained from the soil pressure transducers represented the small tilt of MDP1 during the installation phase. The skin friction and lateral earth pressure significantly decreased in the removal phase, 12 h after the penetration phase, mainly due to the soil disturbance caused by suction penetration around the caisson.
Hedgehog Agonist Therapy Corrects Structural and Cognitive Deficits in a Down Syndrome Mouse Model
Authors: Das Ishita , Park Joo-Min , Shin Jung H. , Jeon Soo Kyeong , Lorenzi Hernan , Linden David J. , Worley Paul F. , Reeves Roger H.
Published: September 2013

In a mouse model of Down syndrome, treatment with a Sonic hedgehog agonist on the day of birth normalized cerebellar structure and improved learning and memory.
Blood Sugar—Food for Thought?
Authors: Tirosh Amir
Published: September 2013

Higher glucose concentrations may be a risk factor for dementia.
Sequester Cuts May Delay Drug Approvals—And More
Authors: Hudis Clifford A.
Published: September 2013

Clinical translation depends on an optimally functioning FDA, and sequestration may slow the drug approval process.
Efficacy of Ceftaroline Fosamil against Escherichia coli and Klebsiella pneumoniae Strains in a Rabbit Meningitis Model
Authors: Stucki A. , Acosta F. , Cottagnoud M. , Cottagnoud P.
Published: September 2013

In this study, the efficacy of ceftaroline fosamil was compared with that of cefepime in an experimental rabbit meningitis model against two Gram-negative strains (
Escherichia coli
QK-9 and
Klebsiella pneumoniae
1173687). The penetration of ceftaroline into inflamed and uninflamed meninges was also investigated. Both regimens were bactericidal, but ceftaroline fosamil was significantly superior to cefepime against
K. pneumoniae
and
E. coli
in this experimental rabbit meningitis model (
P
< 0.0007 against
K. pneumoniae
and
P
< 0.0016 against
E. coli
). The penetration of ceftaroline was approximately 15% into inflamed meninges and approximately 3% into uninflamed meninges.
In Vitro
Activities of Amoxicillin-Clavulanate, Doxycycline, Ceftazidime, Imipenem, and Trimethoprim-Sulfamethoxazole against Biofilm of Brazilian Strains of Burkholderia pseudomallei
Authors: Bandeira Tereza de Jesus Pinheiro Gomes , Moreira Camila Alencar , Brilhante Raimunda Sâmia Nogueira , Castelo-Branco Débora de Souza Collares Maia , Neto Manoel Paiva de Araújo , Cordeiro Rossana de Aguiar , Rodrigues Terezinha de Jesus Santos , Rocha Marcos Fábio Gadelha , Sidrim José Júlio Costa
Published: September 2013

This study aimed at investigating the
in vitro
activities of amoxicillin-clavulanate, doxycycline, ceftazidime, imipenem, and trimethoprim-sulfamethoxazole against
Burkholderia pseudomallei
in planktonic and biofilm forms, through broth microdilution and resazurin-based viability staining, respectively. In planktonic growth, the strains were susceptible to the drugs, while in biofilm growth, significantly higher antimicrobial concentrations were required, especially for ceftazidime and imipenem, surpassing the resistance breakpoints. These results highlight the importance of the routine evaluation of biofilm antimicrobial susceptibility.
Identification of Five Structurally Unrelated Quorum-Sensing Inhibitors of Pseudomonas aeruginosa from a Natural-Derivative Database
Authors: Tan Sean Yang-Yi , Chua Song-Lin , Chen Yicai , Rice Scott A. , Kjelleberg Staffan , Nielsen Thomas E. , Yang Liang , Givskov Michael
Published: September 2013

Bacteria communicate by means of small signal molecules in a process termed quorum sensing (QS). QS enables bacteria to organize their activities at the population level, including the coordinated secretion of virulence factors. Certain small-molecule compounds, known as quorum-sensing inhibitors (QSIs), have been shown to effectively block QS and subsequently attenuate the virulence of
Pseudomonas aeruginosa
, as well as increasing its susceptibility to both antibiotics and the immune system. In this study, a structure-based virtual screening (SB-VS) approach was used for the discovery of novel QSI candidates. Three-dimensional structures of 3,040 natural compounds and their derivatives were obtained, after which molecular docking was performed using the QS receptor LasR as a target. Based on docking scores and molecular masses, 22 compounds were purchased to determine their efficacies as quorum-sensing inhibitors. Using a live reporter assay for quorum sensing, 5 compounds were found to be able to inhibit QS-regulated gene expression in
P. aeruginosa
in a dose-dependent manner. The most promising compound, G1, was evaluated by isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis, and it was found to significantly affect the abundance of 46 proteins (19 were upregulated; 27 were downregulated) in
P. aeruginosa
PAO1. It specifically reduced the expression of several quorum-sensing-regulated virulence factors, such as protease IV, chitinase, and pyoverdine synthetases. G1 was also able to reduce extracellular DNA release and inhibited the secretion of the virulence factor, elastase, whose expression is regulated by LasR. These results demonstrate the utility of SB-VS for the discovery of target-specific QSIs.
Isavuconazole Pharmacodynamic Target Determination for Candida Species in an
In Vivo
Murine Disseminated Candidiasis Model
Authors: Lepak Alexander J. , Marchillo Karen , VanHecker Jamie , Diekema Daniel , Andes David R.
Published: September 2013

Pharmacodynamic (PD) studies with triazoles in the neutropenic murine disseminated candidiasis model have been performed extensively for
Candida albicans
. They have consistently shown that the pharmacodynamic index most closely correlated with efficacy is the ratio of the 24-h area under the concentration-time curve (AUC) to the MIC, and a target 24-h free-drug AUC/MIC ratio near 25 is associated with 50% of maximal microbiologic efficacy. We utilized this model to investigate the pharmacodynamics of isavuconazole. Isavuconazole pharmacokinetics were linear over the dose range studied. Oral-gastric doses of 640, 160, 40, and 10 mg of prodrug/kg of body weight produced peak levels of 0.51 to 25.4 mg/liter, an elimination half-life of 1 to 5 h, and an AUC from 0 h to infinity (AUC
0-∞
) of 0.9 to 287 mg · h/liter. The AUC/MIC ratio was the pharmacodynamic index that correlated best with efficacy (
R
2
, 0.84). Pharmacodynamic target studies were performed using 4
C. albicans
isolates with both a 24-h and a 96-h treatment duration. The strains were chosen to include previously characterized fluconazole-resistant strains. The mean 50% effective doses (ED
50
) (expressed in mg/kg of body weight/12 h) and associated 24-h free-drug AUC/MIC ratios were 89.3 ± 46.7 and 67.7 ± 35 for the 24-h treatment and 59.6 ± 22 and 33.3 ± 25.5 for the 96-h treatment. These differences were not statistically significant. Pharmacodynamic targets for two non-
albicans Candida
species were also explored. The mean ED
50
(expressed in mg/kg/12 h) and associated 24-h free-drug AUC/MIC ratios were 31.2 and 6.2 for
Candida tropicalis
(
n
= 1) and 50.5 and 1.6 for
Candida glabrata
(
n
= 2). These PD targets were significantly different from
C. albicans
targets (
P
, 0.04). Isavuconazole PD targets for
C. albicans
are similar to those observed in this model with other triazoles. However, the PD targets for non-
albicans Candida
species were more than 10-fold lower than those for
C. albicans
(
P
, 0.04). This difference is similar to the species-specific PD relationships for the echinocandins. The lower PD targets for these species in this model will be important to consider in the analysis of clinical trial data and during the development of susceptibility breakpoints.
Deciphering the Contribution of Human Meningothelial Cells to the Inflammatory and Antimicrobial Response at the Meninges
Authors: Royer Pierre-Joseph , Rogers Andrew J. , Wooldridge Karl G. , Tighe Patrick , Mahdavi Jafar , Rittig Michael G. , Ala'Aldeen Dlawer
Published: September 2013

We have investigated the response of primary human meningothelial cells to
Neisseria meningitidis
. Through a transcriptome analysis, we provide a comprehensive examination of the response of meningothelial cells to bacterial infection. A wide range of chemokines are elicited which act to attract and activate the main players of innate and adaptive immunity. We showed that meningothelial cells expressed a high level of Toll-like receptor 4 (TLR4), and, using a gene silencing strategy, we demonstrated the contribution of this pathogen recognition receptor in meningothelial cell activation. Secretion of interleukin-6 (IL-6), CXCL10, and CCL5 was almost exclusively TLR4 dependent and relied on MyD88 and TRIF adaptor cooperation. In contrast, IL-8 induction was independent of the presence of TLR4, MyD88, and TRIF. Transcription factors NF-κB p65, p38 mitogen-activated protein kinase (MAPK), Jun N-terminal protein kinase (JNK1), IRF3, and IRF7 were activated after contact with bacteria. Interestingly, the protein kinase IRAK4 was found to play a minor role in the meningothelial cell response to
Neisseria
infection. Our work highlights the role of meningothelial cells in the development of an immune response and inflammation in the central nervous system (CNS) in response to meningococcal infection. It also sheds light on the complexity of intracellular signaling after TLR triggering.
Mutation of the Conserved Calcium-Binding Motif in Neisseria gonorrhoeae PilC1 Impacts Adhesion but Not Piliation
Authors: Cheng Yuan , Johnson Michael D. L. , Burillo-Kirch Christine , Mocny Jeffrey C. , Anderson James E. , Garrett Christopher K. , Redinbo Matthew R. , Thomas Christopher E.
Published: September 2013

Neisseria gonorrhoeae
PilC1 is a member of the PilC family of type IV pilus-associated adhesins found in
Neisseria
species and other type IV pilus-producing genera. Previously, a calcium-binding domain was described in the C-terminal domains of PilY1 of
Pseudomonas aeruginosa
and in PilC1 and PilC2 of
Kingella kingae
. Genetic analysis of
N. gonorrhoeae
revealed a similar calcium-binding motif in PilC1. To evaluate the potential significance of this calcium-binding region in
N. gonorrhoeae
, we produced recombinant full-length PilC1 and a PilC1 C-terminal domain fragment. We show that, while alterations of the calcium-binding motif disrupted the ability of PilC1 to bind calcium, they did not grossly affect the secondary structure of the protein. Furthermore, we demonstrate that both full-length wild-type PilC1 and full-length calcium-binding-deficient PilC1 inhibited gonococcal adherence to cultured human cervical epithelial cells, unlike the truncated PilC1 C-terminal domain. Similar to PilC1 in
K. kingae
, but in contrast to the calcium-binding mutant of
P. aeruginosa
PilY1, an equivalent mutation in
N. gonorrhoeae
PilC1 produced normal amounts of pili. However, the
N. gonorrhoeae
PilC1 calcium-binding mutant still had partial defects in gonococcal adhesion to ME180 cells and genetic transformation, which are both essential virulence factors in this human pathogen. Thus, we conclude that calcium binding to PilC1 plays a critical role in pilus function in
N. gonorrhoeae
.
Control of Bacterial Virulence by the RalR Regulator of the Rabbit-Specific Enteropathogenic Escherichia coli Strain E22
Authors: Srikhanta Yogitha N. , Hocking Dianna M. , Wakefield Matthew J. , Higginson Ellen , Robins-Browne Roy M. , Yang Ji , Tauschek Marija
Published: September 2013

Atypical enteropathogenic
Escherichia coli
(aEPEC) causes endemic diarrhea, diarrheal outbreaks, and persistent diarrhea in humans, but the mechanism by which aEPEC causes disease is incompletely understood. Virulence regulators and their associated regulons, which often include adhesins, play key roles in the expression of virulence factors in enteric pathogenic bacteria. In this study we identified a transcriptional regulator, RalR, in the rabbit-specific aEPEC strain, E22 (O103:H2) and examined its involvement in the regulation of virulence. Microarray analysis and quantitative real-time reverse transcription-PCR demonstrated that RalR enhances the expression of a number of genes encoding virulence-associated factors, including the Ral fimbria, the Aap dispersin, and its associated transport system, and downregulates several housekeeping genes, including
fliC
. These observations were confirmed by proteomic analysis of secreted and heat-extracted surface-associated proteins and by adherence and motility assays. To investigate the mechanism of RalR-mediated activation, we focused on its most highly upregulated target operons,
ralCDEFGHI
and
aap
. By using primer extension, electrophoretic mobility shift assay, and mutational analysis, we identified the promoter and operator sequences for these two operons. By employing promoter-
lacZ
reporter systems, we demonstrated that RalR activates the expression of its target genes by binding to one or more 8-bp palindromic sequences (with the consensus of TGTGCACA) located immediately upstream of the promoter core regions. Importantly, we also demonstrated that RalR is essential for virulence since infection of rabbits with E22 carrying a knockout mutation in the
ralR
gene completely abolished its ability to cause disease.
B Cell Production of Tumor Necrosis Factor in Response to Pneumocystis murina Infection in Mice
Authors: Opata Michael M. , Ye Zhan , Hollifield Melissa , Garvy Beth A.
Published: September 2013

Pneumocystisspecies are opportunistic fungal pathogens that induce tumor necrosis factor (TNF) production by alveolar macrophages. Here we report that B cells from the draining lymph nodes as well as lung CD4+T cells are important producers of TNF uponPneumocystis murinainfection. To determine the importance of B cell-derived TNF in the primary response toP. murina, we generated bone marrow chimeras whose B cells were unable to produce TNF. The lungP. murinaburden at 10 days postinfection in TNF knockout (TNFKO) chimeras was significantly higher than that in wild-type (WT) chimeras, which corresponded to reduced numbers of activated CD4+T cells in the lungs at this early time point. Furthermore, CD4+T cells isolated fromP. murina-infected TNFKO chimeras were unable to stimulate clearance ofP. murinaupon adoptive transfer to recombinase-deficient (RAG1KO) hosts. Together, these data indicate that B cell-derived TNF plays an important function in promoting CD4+T cell expansion and production of TNF and facilitating protection againstP. murinainfection.
YaxAB, a Yersinia enterocolitica Pore-Forming Toxin Regulated by RovA
Authors: Wagner Nikki J. , Lin Carolina P. , Borst Luke B. , Miller Virginia L.
Published: September 2013

The transcriptional regulator RovA positively regulates transcription of the
Yersinia enterocolitica
virulence gene
inv
. Invasin, encoded by
inv
, is important for establishment of
Y. enterocolitica
infection. However, a
rovA
mutant is more attenuated for virulence than an
inv
mutant, implying that RovA regulates additional virulence genes. When the
Y. enterocolitica
RovA regulon was defined by microarray analysis, YE1984 and YE1985 were among the genes identified as being upregulated by RovA. Since these genes are homologous to
Xenorhabdus nematophila
cytotoxin genes
xaxA
and
xaxB
, we named them
yaxA
and
yaxB
, respectively. In this work, we demonstrate the effects of YaxAB on the course of infection in the murine model. While a
yaxAB
mutant (Δ
yaxAB
) is capable of colonizing mice at the same level as the wild type, it slightly delays the course of infection and results in differing pathology in the spleen. Further, we found that
yaxAB
encode a probable cytotoxin capable of lysing mammalian cells, that both YaxA and YaxB are required for cytotoxic activity, and that the two proteins associate. YaxAB-mediated cell death occurs via osmotic lysis through the formation of distinct membrane pores.
In silico
tertiary structural analysis identified predicted structural homology between YaxA and proteins in pore-forming toxin complexes from
Bacillus cereus
(HBL-B) and
Escherichia coli
(HlyE). Thus, it appears that YaxAB function as virulence factors by inducing cell lysis through the formation of pores in the host cell membrane. This characterization of YaxAB supports the hypothesis that RovA regulates expression of multiple virulence factors in
Y. enterocolitica
.
LtpD Is a Novel Legionella pneumophila Effector That Binds Phosphatidylinositol 3-Phosphate and Inositol Monophosphatase IMPA1
Authors: Harding Clare R. , Mattheis Corinna , Mousnier Aurélie , Oates Clare V. , Hartland Elizabeth L. , Frankel Gad , Schroeder Gunnar N.
Published: September 2013

The Dot/Icm type IV secretion system (T4SS) of
Legionella pneumophila
is crucial for the pathogen to survive in protozoa and cause human disease. Although more than 275 effector proteins are delivered into the host cell by the T4SS, the function of the majority is unknown. Here we have characterized the Dot/Icm effector LtpD. During infection, LtpD localized to the cytoplasmic face of the membrane of the
Legionella
-containing vacuole (LCV). In A549 lung epithelial cells, ectopically expressed LtpD localized to large vesicular structures that contained markers of endosomal compartments. Systematic analysis of LtpD fragments identified an internal 17-kDa fragment, LtpD
471-626
, which was essential for targeting ectopically expressed LtpD to vesicular structures and for the association of translocated LtpD with the LCV. LtpD
471-626
bound directly to phosphatidylinositol 3-phosphate [PtdIns(3)P]
in vitro
and colocalized with the PtdIns(3)P markers FYVE and SetA in cotransfected cells. LtpD was also found to bind the host cell enzyme inositol (
myo
)-1 (or 4)-monophosphatase 1, an important phosphatase involved in phosphoinositide production. Analysis of the role of LtpD in infection showed that LtpD is involved in bacterial replication in THP-1 macrophages, the larvae of
Galleria mellonella
, and mouse lungs. Together, these data suggest that LtpD is a novel phosphoinositide-binding
L. pneumophila
effector that has a role in intracellular bacterial replication.
Evidence for a Structural Role for Acid-Fast Lipids in Oocyst Walls of
Cryptosporidium
,
Toxoplasma
, and
Eimeria
Authors: Bushkin G. Guy , Motari Edwin , Carpentieri Andrea , Dubey Jitender P. , Costello Catherine E. , Robbins Phillips W. , Samuelson John
Published: September 2013

Coccidia are protozoan parasites that cause significant human disease and are of major agricultural importance.
Cryptosporidium
spp. cause diarrhea in humans and animals, while
Toxoplasma
causes disseminated infections in fetuses and untreated AIDS patients.
Eimeria
is a major pathogen of commercial chickens. Oocysts, which are the infectious form of
Cryptosporidium
and
Eimeria
and one of two infectious forms of
Toxoplasma
(the other is tissue cysts in undercooked meat), have a multilayered wall. Recently we showed that the inner layer of the oocyst walls of
Toxoplasma
and
Eimeria
is a porous scaffold of fibers of β-1,3-glucan, which are also present in fungal walls but are absent from
Cryptosporidium
oocyst walls. Here we present evidence for a structural role for lipids in the oocyst walls of
Cryptosporidium
,
Toxoplasma
, and
Eimeria
. Briefly, oocyst walls of each organism label with acid-fast stains that bind to lipids in the walls of mycobacteria. Polyketide synthases similar to those that make mycobacterial wall lipids are abundant in oocysts of
Toxoplasma
and
Eimeria
and are predicted in
Cryptosporidium
. The outer layer of oocyst wall of
Eimeria
and the entire oocyst wall of
Cryptosporidium
are dissolved by organic solvents. Oocyst wall lipids are complex mixtures of triglycerides, some of which contain polyhydroxy fatty acyl chains like those present in plant cutin or elongated fatty acyl chains like mycolic acids. We propose a two-layered model of the oocyst wall (glucan and acid-fast lipids) that resembles the two-layered walls of mycobacteria (peptidoglycan and acid-fast lipids) and plants (cellulose and cutin).

IMPORTANCE
Oocysts, which are essential for the fecal-oral spread of coccidia, have a wall that is thought responsible for their survival in the environment and for their transit through the stomach and small intestine. While oocyst walls of
Toxoplasma
and
Eimeria
are strengthened by a porous scaffold of fibrils of β-1,3-glucan and by proteins cross-linked by dityrosines, both are absent from walls of
Cryptosporidium
. We show here that all oocyst walls are acid fast, have a rigid bilayer, dissolve in organic solvents, and contain a complex set of triglycerides rich in polyhydroxy and long fatty acyl chains that might be synthesized by an abundant polyketide synthase. These results suggest the possibility that coccidia build a waxy coat of acid-fast lipids in the oocyst wall that makes them resistant to environmental stress.
A Strategy To Estimate Unknown Viral Diversity in Mammals
Authors: Anthony Simon J. , Epstein Jonathan H. , Murray Kris A. , Navarrete-Macias Isamara , Zambrana-Torrelio Carlos M. , Solovyov Alexander , Ojeda-Flores Rafael , Arrigo Nicole C. , Islam Ariful , Ali Khan Shahneaz , Hosseini Parviez , Bogich Tiffany L. , Olival Kevin J. , Sanchez-Leon Maria D. , Karesh William B. , Goldstein Tracey , Luby Stephen P. , Morse Stephen S. , Mazet Jonna A. K. , Daszak Peter , Lipkin W. Ian
Published: September 2013

The majority of emerging zoonoses originate in wildlife, and many are caused by viruses. However, there are no rigorous estimates of total viral diversity (here termed “virodiversity”) for any wildlife species, despite the utility of this to future surveillance and control of emerging zoonoses. In this case study, we repeatedly sampled a mammalian wildlife host known to harbor emerging zoonotic pathogens (the Indian Flying Fox,Pteropus giganteus) and used PCR with degenerate viral family-level primers to discover and analyze the occurrence patterns of 55 viruses from nine viral families. We then adapted statistical techniques used to estimate biodiversity in vertebrates and plants and estimated the total viral richness of these nine families inP. giganteusto be 58 viruses. Our analyses demonstrate proof-of-concept of a strategy for estimating viral richness and provide the first statistically supported estimate of the number of undiscovered viruses in a mammalian host. We used a simple extrapolation to estimate that there are a minimum of 320,000 mammalian viruses awaiting discovery within these nine families, assuming all species harbor a similar number of viruses, with minimal turnover between host species. We estimate the cost of discovering these viruses to be ~$6.3 billion (or ~$1.4 billion for 85% of the total diversity), which if annualized over a 10-year study time frame would represent a small fraction of the cost of many pandemic zoonoses.

IMPORTANCERecent years have seen a dramatic increase in viral discovery efforts. However, most lack rigorous systematic design, which limits our ability to understand viral diversity and its ecological drivers and reduces their value to public health intervention. Here, we present a new framework for the discovery of novel viruses in wildlife and use it to make the first-ever estimate of the number of viruses that exist in a mammalian host. As pathogens continue to emerge from wildlife, this estimate allows us to put preliminary bounds around the potential size of the total zoonotic pool and facilitates a better understanding of where best to allocate resources for the subsequent discovery of global viral diversity.
Imaging Mass Spectrometry Reveals Highly Specific Interactions between Actinomycetes To Activate Specialized Metabolic Gene Clusters
Authors: Hopwood David A.
Published: September 2013

The genomes of actinomycetes contain numerous gene clusters potentially able to encode the production of many antibiotics and other specialized metabolites that are not expressed during growth under typical laboratory conditions. Undoubtedly, this reflects the soil habitat of these organisms, which is highly complex physically, chemically, and biotically; the majority of the compounds that make up the specialized metabolome are therefore adaptive only under specific conditions. While there have been numerous previous reports of “waking up” the “sleeping” gene clusters, many involving genetic interventions or nutritional challenges, the role of competing microorganisms has been comparatively little studied. Now, Traxler et al. [M. F. Traxler, J. D. Watrous, T. Alexandrov, P. C. Dorrestein, and R. Kolter, mBio 4(4):e00459-13, 2013, doi:10.1128/mBio.00459-13] have used the recently described technique of microscale imaging mass spectrometry to analyze in detail the stimulation of specialized metabolite production by the model actinomyceteStreptomyces coelicolorA3(2) by growth in proximity to other actinomycetes. The striking finding from these experiments was that growth ofS. coelicolorclose to each of the five other actinomycetes studied caused it to produce many specialized metabolites that were not made when it was grown in isolation and that the majority of the compounds were interaction specific, i.e., they occurred only in one of the five pairwise combinations, emphasizing the highly specific nature of the interactions. These observations contribute substantially to the increasing awareness of communication between microorganisms in complex natural communities, as well as auguring well for the discovery of useful specialized metabolites based on microbial interactions.
Patterns and Processes of Microbial Community Assembly
Authors: Nemergut Diana R. , Schmidt Steven K. , Fukami Tadashi , O'Neill Sean P. , Bilinski Teresa M. , Stanish Lee F. , Knelman Joseph E. , Darcy John L. , Lynch Ryan C. , Wickey Phillip , Ferrenberg Scott
Published: September 2013

Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol.
85
:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.
Type IV Pili in Gram-Positive Bacteria
Authors: Melville Stephen , Craig Lisa
Published: September 2013

Type IV pili (T4P) are surface-exposed fibers that mediate many functions in bacteria, including locomotion, adherence to host cells, DNA uptake (competence), and protein secretion and that can act as nanowires carrying electric current. T4P are composed of a polymerized protein, pilin, and their assembly apparatuses share protein homologs with type II secretion systems in eubacteria and the flagella of archaea. T4P are found throughout Gram-negative bacterial families and have been studied most extensively in certain model Gram-negative species. Recently, it was discovered that T4P systems are also widespread among Gram-positive species, in particular the clostridia. Since Gram-positive and Gram-negative bacteria have many differences in cell wall architecture and other features, it is remarkable how similar the T4P core proteins are between these organisms, yet there are many key and interesting differences to be found as well. In this review, we compare the two T4P systems and identify and discuss the features they have in common and where they differ to provide a very broad-based view of T4P systems across all eubacterial species.
Pathogenesis of Human Enterovirulent Bacteria: Lessons from Cultured, Fully Differentiated Human Colon Cancer Cell Lines
Authors: Liévin-Le Moal Vanessa , Servin Alain L.
Published: September 2013

Hosts are protected from attack by potentially harmful enteric microorganisms, viruses, and parasites by the polarized fully differentiated epithelial cells that make up the epithelium, providing a physical and functional barrier. Enterovirulent bacteria interact with the epithelial polarized cells lining the intestinal barrier, and some invade the cells. A better understanding of the cross talk between enterovirulent bacteria and the polarized intestinal cells has resulted in the identification of essential enterovirulent bacterial structures and virulence gene products playing pivotal roles in pathogenesis. Cultured animal cell lines and cultured human nonintestinal, undifferentiated epithelial cells have been extensively used for understanding the mechanisms by which some human enterovirulent bacteria induce intestinal disorders. Human colon carcinoma cell lines which are able to express in culture the functional and structural characteristics of mature enterocytes and goblet cells have been established, mimicking structurally and functionally an intestinal epithelial barrier. Moreover, Caco-2-derived M-like cells have been established, mimicking the bacterial capture property of M cells of Peyer's patches. This review intends to analyze the cellular and molecular mechanisms of pathogenesis of human enterovirulent bacteria observed in infected cultured human colon carcinoma enterocyte-like HT-29 subpopulations, enterocyte-like Caco-2 and clone cells, the colonic T84 cell line, HT-29 mucus-secreting cell subpopulations, and Caco-2-derived M-like cells, including cell association, cell entry, intracellular lifestyle, structural lesions at the brush border, functional lesions in enterocytes and goblet cells, functional and structural lesions at the junctional domain, and host cellular defense responses.
Acute pancreatitis and severe hypertriglyceridaemia masking unsuspected underlying diabetic ketoacidosis
Authors: Aboulhosn Kewan , Arnason Terra
Published: September 2013

A healthy 18-year-old girl presented to a local emergency room with 48 h of abdominal pain and vomiting. A radiological and biochemical diagnosis of moderate acute pancreatitis was made. Bloodwork demonstrated prominent hypertriglyceridaemia (HTG) of 19.5 mmol/L (severe HTG: 11.2–22.4), detectable urine ketones and a random blood glucose of 13 mmol/L dropping to 10.5 mmol/L on repeat (normal random <11). Ketone levels were deemed consistent with fasting ketosis after 48 h of vomiting. There was no known history of diabetes in the patient. Management included aggressive rehydration and pain control, yet the patient rapidly decompensated into shock requiring intensive care unit support. Blood gases revealed severe metabolic acidosis (pH 6.99) and unsuspected underlying diabetic ketoacidosis was diagnosed. The HTG gradually resolved following intravenous fluids and insulin infusion with slower correction of the metabolic acidosis. Importantly, her glycated haemoglobin was 12%, indicating the silent presence of chronic glucose elevations.
Long-term benefit of hepatitis C therapy in a safety net hospital system: a cross-sectional study with median 5-year follow-up
Authors: Singal Amit G , Dharia Tushar D , Malet Peter F , Alqahtani Saleh , Zhang Song , Cuthbert Jennifer A
Published: September 2013

Objectives

To demonstrate the survival benefit from sustained virological response (SVR) in a safety net hospital population with limited resources for hepatitis C virus (HCV) therapy.

Design and setting

We conducted a retrospective study at an urban safety net hospital in the USA.

Participants and intervention

242 patients receiving standard HCV therapy between 2001 and 2006.

Primary and secondary outcome measures

Response rates, including SVR, were recorded for each patient. Univariate and multivariate analyses were performed to identify predictors of SVR and 5-year survival.

Results

A total of 242 eligible patients were treated. Treatment was completed in 197 (81%) patients, with 43 patients discontinuing therapy early—32 due to adverse events and 11 due to non-compliance. Complications on treatment were frequent, including three deaths. SVR was achieved in 83 patients (34%). On multivariate analysis, independent predictors of adecreasedlikelihood of achieving SVR included African–American race (OR 0.20, 95% CI 0.07 to 0.54), genotype 1 HCV infection (OR 0.25, 95% CI 0.13 to 0.50) and the presence of cirrhosis (OR 0.26, 95% CI 0.12 to 0.58). Survival was 98% in those achieving SVR (median follow-up 72 months) and 71% in non-responders and those discontinuing therapy (n=91, median known follow-up 65 and 36 months, respectively). On multivariate analysis, the only independent predictor of improved survival was SVR (HR 0.12, 95% CI 0.03 to 0.52). Both cirrhosis and hypoalbuminaemia were independent predictors of increased mortality.

Conclusions

Treatment before histological cirrhosis develops, in combination with careful selection, may improve long-term outcomes without compromising other healthcare endeavours in safety net hospitals and areas with financial limitations.
Outcomes of transplantation of livers from donation after circulatory death donors in the UK: a cohort study
Authors: Callaghan Christopher J , Charman Susan C , Muiesan Paolo , Powell James J , Gimson Alexander E , van der Meulen Jan H P ,   on behalf of the UK Liver Transplant Audit
Published: September 2013

Objectives

Outcomes of liver transplantations from donation after circulatory death (DCD) donors may be inferior to those achieved with donation after brain death (DBD) donors. The impact of using DCD donors is likely to depend on specific national practices. We compared risk-adjusted graft loss and recipient mortality after transplantation of DCD and DBD livers in the UK.

Design

Prospective cohort study. Multivariable Cox regression and propensity score matching were used to estimate risk-adjusted HR.

Setting

7 liver transplant centres in the National Health Service (NHS) hospitals in England and Scotland.

Participants

Adults who received a first elective liver transplant between January 2005 and December 2010 who were identified in the UK Liver Transplant Audit.

Interventions

Transplantation of DCD and DBD livers.

Outcomes

Graft loss and recipient mortality.

Results

In total, 2572 liver transplants were identified with 352 (14%) from DCD donors. 3-year graft loss (95% CI) was higher with DCD livers (27.3%, 21.8% to 33.9%) than with DBD livers (18.2%, 16.4% to 20.2%). After adjustment with regression, HR for graft loss was 2.3 (1.7 to 3.0). Similarly, 3-year mortality was higher with DCD livers (19.4%, 14.5% to 25.6%) than with DBD livers (14.1%, 12.5% to 16.0%) with an adjusted HR of 2.0 (1.4 to 2.8). Propensity score matching gave similar results. Centre-specific adjusted HRs for graft loss and recipient mortality seemed to differ among transplant centres, although statistical evidence is weak (p value for interaction 0.08 and 0.24, respectively).

Conclusions

Graft loss and recipient mortality were about twice as high with DCD livers as with DBD livers in the UK. Outcomes after DCD liver transplantation may vary between centres. These results should inform policies for the use of DCD livers.
The mortality and cancer experience of New Zealand Vietnam war veterans: a cohort study
Authors: McBride David , Cox Brian , Broughton John , Tong Darryl
Published: September 2013

Objectives

The aim was to observe the patterns of mortality and cancer incidence in New Zealand Vietnam veterans. The objectives were to assess whether the patterns of disease observed were consistent with those associated with military service in Vietnam, and similar to the patterns identified in other groups of Vietnam veterans.

Design

A historical cohort study.

Setting

Veterans, identified from service records, with Vietnam service between 1964 and 1972.

Participants

Of the 3322 survivors of Vietnam service, we followed up 2783 (84%).

Outcome measures

Standardised mortality and incidence ratios (SMRs and SIRs, respectively) were calculated based on the number of deaths and cancer registrations observed, those expected being based on New Zealand national rates.

Results

All cause mortality was significantly reduced (SMR 0.85, 95% CI 0.77 to 0.94) and cancer incidence non-significantly increased (SIR 1.06, 95% CI 0.97 to 1.16). The risk of mortality from cancers of the head and neck (SMR 2.20, 95% CI 1.09 to 3.93); oral cavity pharynx and larynx (SMR 2.13, 95% CI 1.06 to 3.81) and the incidence of chronic lymphatic leukaemia (CLL) (SIR 1.91, 95% CI 1.04 to 3.20) were, however, significantly increased. Other lymphohaematopoietic disorders, specifically multiple myeloma and Hodgkin disease, showed non-significant mortality excesses, reflected by a similar increase in incidence.

Conclusions

Service in the Vietnam war was associated with defoliant herbicide exposure, including 2,4,5-trichlorophenoxyacetic acid, 2,4-dichlorophenoxyacetic acid, picloram and cacodylic acid. Subsequent reviews of mechanistic, animal and epidemiological evidence led to certain conditions being deemed compensable. The pattern of mortality and cancer incidence is not at odds with the list of compensable conditions and consistent with that found in Australian veterans serving in the same area of Vietnam, but also consistent with smoking and the healthy soldier effect. In common with the Australian experience, this is the only veterans group to show a significant excess of CLL.
Improving outcomes for patients with type 2 diabetes using general practice networks: a quality improvement project in east London
Authors: Hull Sally , Chowdhury Tahseen A , Mathur Rohini , Robson John
Published: September 2013

Background

Structured diabetes care can improve outcomes and reduce risk of complications, but improving care in a deprived, ethnically diverse area can prove challenging. This report evaluates a system change to enhance diabetes care delivery in a primary care setting.

Methods

All 35 practices in one inner London Primary Care Trust were geographically grouped into eight networks of four to five practices, each supported by a network manager, clerical staff and an educational budget. A multidisciplinary team developed a ‘care package’ for type 2 diabetes management, with financial incentives based on network achievement of targets. Monthly electronic performance dashboards enabled networks to track and improve performance. Network multidisciplinary team meetings including the diabetic specialist team supported case management and education. Key measures for improvement included the number of diabetes care plans completed, proportion of patients attending for digital retinal screen and proportions of patients achieving a number of biomedical indices (blood pressure, cholesterol, glycated haemoglobin).

Results

Between 2009 and 2012, completed care plans rose from 10% to 88%. The proportion of patients attending for digital retinal screen rose from 72% to 82.8%. The proportion of patients achieving a combination of blood pressure ≤140/80 mm Hg and cholesterol ≤4 mmol/L rose from 35.3% to 46.1%. Mean glycated haemoglobin dropped from 7.80% to 7.66% (62–60 mmol/mol).

Conclusions

Investment of financial, organisational and education resources into primary care practice networks can achieve clinically important improvements in diabetes care in deprived, ethnically diverse communities. This success is predicated on collaborative working between practices, purposively designed high-quality information on network performance and engagement between primary and secondary care clinicians.