bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental Study on the Effect of Deforming Material and Speed on Friction and Lubrication by Tip Test
Authors: Ajiboye Joseph S.
Published: April 2012

Choosing the proper metal forming lubricant for nonferrous metals such as aluminum, copper, and brass has become a difficult and complicated decision. The effects of deformation velocity and the influence of deforming material were determined in the two sets of experiments carried out using a single punch with a roughness magnitude Ra of 0.17 μm and four lubricants such as grease, corn oil, VG100, and VG32. In the first set, two different deformation speeds of 0.1 and 1 mm/s were used for cylindrical specimens made of aluminum alloys of 6061-O, 1050-O, and copper alloys tests using a counterpunch die of roughness magnitude Ra of 0.08 μm. In the second set of experiments, cylindrical specimens made of aluminum alloys of AA2024-O and AA6061-O and three deformation speeds of 0.1, 1, and 5 mm/s were used to evaluate the performance of each lubricant under increasing ram speed, but with a roughness magnitude Ra of 0.63 μm. All the lubricants show reduction in maximum load with increasing deformation speed except grease which shows a rise in the maximum load from zero to a maximum at a deformation speed of 1 mm/s and then descends gradually to a minimum load at a speed of 5 mm/s for AA2024-O and AA6061-O. This load reduction seen with grease as lubricant is probably due to thermal softening; therefore grease will not be considered a desirable lubricant under increasing deformation speed because of the adverse effects on the tooling. The present findings show that tip test can be utilized to select an appropriate lubricant for a particular alloy. It reveals that none of the tested lubricants can be used for copper alloy as all the lubricants show increasing measured load for increasing speed magnitude. However, of the liquid lubricants (corn oil, VG100, and VG32) considered, corn oil shows as the best lubricant for cold forging operations of aluminum 6061-O, 1050-O, and 2024-0 under increasing speed magnitude. Also, the tip test has been able to differentiate among materials.
Chemical Vapor Deposition Growth, Optical, and Thermal Characterization of Vertically Aligned Single-Walled Carbon Nanotubes
Authors: Maruyama Shigeo , Xiang Rong
Published: April 2012

Vertically aligned single-walled carbon nanotubes (VA-SWNTs) is expected to be an extra-ordinal material for various optical, electrical, energy, and thermal devices. The recent progress in growth control and characterization techniques will be discussed. The chemical vapor deposition (CVD) growth mechanism of VA-SWNTs is studied based on the in situ growth monitoring by laser absorption during CVD. The growth curves are characterized by an exponential decay of the growth rate from the initial rate determined by ethanol pressure. The initial growth rate and decay of it are discussed with carbon over-coat on metal catalysts and gas phase thermal decomposition of precursor ethanol. For the precisely patterned growth of SWNTs, we recently propose a surface-energy-difference driven selective deposition of catalyst for localized growth of SWNTs. For a self-assembled monolayer (SAM) patterned Si surface, catalyst particles deposit and SWNTs grow only on the hydrophilic regions. The proposed all-liquid-based approach possesses significant advantages in scalability and resolution over state-of-the-art techniques, which we believe can greatly advance the fabrication of nanodevices using high-quality as-grown SWNTs. The optical characterization of the VA-SWNT film using polarized absorption, polarized Raman, and photoluminescence spectroscopy will be discussed. Laser-excitation of a vertically aligned film from top means that each nanotube is excited perpendicular to its axis. Because of this predominant perpendicular excitation, interesting cross-polarized absorption and confusing and practically important Raman features are observed. The extremely high and peculiar thermal conductivity of single-walled carbon nanotubes has been explored by nonequilibrium molecular dynamics simulation approaches. The thermal properties of the vertically aligned film and composite materials are studied by several experimental techniques and Monte Carlo simulations based on molecular dynamics inputs of thermal conductivity and thermal boundary resistance. Current understanding of thermal properties of the film is discussed.
Synchronization Control for a Class of Underactuated Mechanical Systems via Energy Shaping
Authors: Zhu Dongfang , Zhou Di , Zhou Jingyang , Teo Kok Lay
Published: April 2012

A synchronization control strategy for a class of underactuated mechanical systems is proposed by using the energy shaping technique, aiming to achieve the required performance of the synchronization motion. A synchronization controller is designed based on the interconnection and damping assignment passivity-based control methodology. It will guarantee that the position tracking errors and the synchronization errors of the underactuated mechanical systems are to converge to zero asymptotically. Experiments on a synchronization control system with two single-inverted pendulums as well as simulations of a synchronization control system consisting of four ball-beam devices are presented to demonstrate the effectiveness of the proposed method.
On the Boundedness Property of the Inertia Matrix and Skew-Symmetric Property of the Coriolis Matrix for Vehicle-Manipulator Systems
Authors: Johan From Pål , Schjølberg Ingrid , Tommy Gravdahl Jan , Ytterstad Pettersen Kristin , Fossen Thor I.
Published: April 2012

This paper addresses the boundedness property of the inertia matrix and the skew-symmetric property of the Coriolis matrix for vehicle-manipulator systems. These properties are widely used in control theory and Lyapunov-based stability proofs and thus important to identify. The skew-symmetric property does not depend on the system at hand but on the parameterization of the Coriolis matrix, which is not unique. It is the authors’ experience that many researchers take this assumption for granted without taking into account that several parameterizations exist. In fact, most researchers refer to references that do not show this property for vehicle-manipulator systems but for other systems such as single rigid bodies or fixed-base manipulators. As a result, the otherwise rigorous stability proofs fall apart. In this paper, we list some relevant references and give the correct proofs for some commonly used parameterizations for future reference. Depending on the choice of state variables, the boundedness of the inertia matrix will not necessarily hold. We show that deriving the dynamics in terms of quasi-velocities leads to an inertia matrix that is bounded in its variables. To the best of our knowledge, we derive for the first time the dynamic equations of vehicle-manipulator systems with non-Euclidean joints for which both properties are true.
Kinematics of Roller Migration in the Planetary Roller Screw Mechanism
Authors: Jones Matthew H. , Velinsky Steven A.
Published: April 2012

This paper develops a kinematic model to predict the axial migration of the rollers relative to the nut in the planetary roller screw mechanism (PRSM). This axial migration is an undesirable phenomenon that can cause binding and eventually lead to the destruction of the mechanism. It is shown that this migration is due to slip at the nut–roller interface, which is caused by a pitch mismatch between the spur-ring gear and the effective nut– roller helical gear pairs. This pitch circle mismatch can be due to manufacturing errors, deformations of the mechanism due to loading, and uncertainty in the radii of contact between the components. This paper derives the angle through which slip occurs and the subsequent axial migration of the roller. It is shown that this roller migration does not affect the overall lead of the PRSM. In addition, the general orbital mechanics, in-plane slip velocity at the nut–roller interface, and the axial slip velocities at the nut–roller and the screw–roller interfaces are also derived. Finally, an example problem is developed using a range of pitch mismatch values for the given roller screw dimensions, and the axial migration and slip velocities are determined.
Factors controlling the resistance of Ohmic contacts to n-InGaAs
Authors: Dormaier Robert , Mohney Suzanne E.
Published: April 2012

The authors report specific contact resistance (ρc) values for Mo-, Ti-, TiW-, Pd-, and Pt-based Ohmic contacts to n+-In0.86Ga0.14As that are deposited with either collimated sputter or electron-beam deposition. Palladium-based contacts with 5 nm of electron-beam evaporated Pd have a specific contact resistance of 7.6 ± 0.5 × 10−9 Ω cm2, while identical collimated sputter deposited contacts have a specific contact resistance of 4.1 ± 0.4 × 10−9 Ω cm2. Contacts with a very thin evaporated Pd layer (2 nm) or a sputtered Pd/Ti 1/1 nm × 4 multilayer have stable ρc values of 5.4 ± 0.5 × 10−9 and 5.0 ± 0.5 × 10−9 Ω cm2, respectively, after 2 h at 270 °C. The ρc of sputter deposited TiW-based contacts is an order of magnitude lower than for identical evaporated contacts (1.6 ± 0.3 × 10−8 vs 2.6 ± 0.3 × 10−7 Ω cm2) and is stable during annealing, while sputter deposition of Pt-based contacts yields rc values that are half an order of magnitude lower than similar evaporated contacts (4.5 ± 1.0 × 10−9 vs 1.7 ± 0.2 × 10−8 Ω cm2). However, the ρc values of the sputtered Pt contacts approach those of evaporated contacts after annealing. Surface preparations consisting of UV-ozone treatments followed by immersion in buffered oxide etch or ammonium hydroxide yield ρc values that are half an order of magnitude lower than values yielded by similar preparations in which HCl is used for oxide removal. The authors also discuss how to avoid over- and underestimation artifacts that may be encountered in measurements of very low specific contact resistances of Ohmic contacts to semiconductors that have low sheet resistances.
Large area patterning of single magnetic domains with assistance of ion irradiation in ion milling
Authors: Sun Zhenzhong , Li Dawen , Natarajarathinam Anusha , Su Hao , Gupta Subhadra
Published: April 2012

This study demonstrates a pronounced ion irradiation effect in ion milling of magnetic thin films. In fabrication of bit-patterned media, the ion irradiation could facilitate bit island isolation before complete removal of magnetic materials by ion milling. Combined with block copolymer lithography, sub-20 nm CoPt dots with uniaxial perpendicular anisotropy, resembling Stoner–Wohlfarth-like single domains, were achieved. X-ray diffraction demonstrates that the degradation of the magnetic film by ion irradiation is related to crystal structure damage.
Atomic layer deposited iridium oxide thin film as microelectrode coating in stem cell applications
Authors: Ryynänen Tomi , Ylä-Outinen Laura , Narkilahti Susanna , Tanskanen Jarno M. A. , Hyttinen Jari , Hämäläinen Jani , Leskelä Markku , Lekkala Jukka
Published: April 2012

Microelectrodes of microelectrode arrays (MEAs) used in cellular electrophysiology studies were coated with iridium oxide (IrOx) thin film using atomic layer deposition (ALD). This work was motivated by the need to find a practical alternative to commercially used titanium nitride (TiN) microelectrode coating. The advantages of ALD IrOx coating include decreased impedance and noise levels and improved stimulation capability of the microelectrodes compared to uncoated microelectrodes. The authors’ process also takes advantage of ALD’s exact process control and relatively low source material start costs compared to traditionally used sputtering and electrochemical methods. Biocompatibility and suitability of ALD IrOx microelectrodes for stem cell research applications were verified by culturing human embryonic stem cell derived neuronal cells for 28 days on ALD IrOx MEAs and successfully measuring electrical activity of the cell network. Electrode impedance of 450 kΩ at 1 kHz was achieved with ALD IrOx in the authors’ 30 μm microelectrodes. This is better than that reported for any uncoated microelectrodes with equal size, even equal to that of inactivated sputtered IrOx coating. Also, stimulation capability was demonstrated. However, further development, including, e.g., applying electrochemical activation, is needed to achieve the performance of commercial TiN-coated microelectrodes.
Characterization studies of aluminum oxide barrier coatings on polymeric substrates
Authors: Struller Carolin F. , Kelly Peter J. , Copeland Nick J. , Liauw Christopher M.
Published: April 2012

Aluminum coatings are widely used as oxygen and water barrier layers on food packaging materials to protect the product from contamination and to extend its shelf life. Thin layers of aluminum, of the order of a few tens of nanometers, are thermally evaporated onto polymeric web in high speed roll-to-roll vacuum metallizers. More recently, transparent barrier layers, based on silica or aluminum oxide, have been introduced to allow product visibility and provide retortable, sterilizable, or microwaveable packaging. In all cases, though, the barrier characteristics are critically dependent on both the structure and properties of the coating and the nature and surface properties of the polymer film substrate. This paper, therefore, reports on characterization trials of aluminum oxide (AlOx) coatings deposited onto polyethylene terephthalate (PET) and biaxially oriented polypropylene (BOPP) film substrates. Coating structures and properties have been investigated by scanning electron microscopy and atomic force microscopy; the influence of process parameters on barrier levels has been determined; surface energies have been determined through contact angle measurements; and coating-to-substrate adhesion has been assessed using “pull-off” tests. The main findings of this study are that the barrier performance of AlOx coated PET and BOPP films strongly depends on the surface properties of the plain film and the aluminum oxide film growth. While AlOx coated PET films deliver consistent barrier results, BOPP reveals considerable variations, depending on the individual substrate.
AID-Driven Deletion Causes Immunoglobulin Heavy Chain Locus Suicide Recombination in B Cells
Authors: Péron Sophie , Laffleur Brice , Denis-Lagache Nicolas , Cook-Moreau Jeanne , Tinguely Aurélien , Delpy Laurent , Denizot Yves , Pinaud Eric , Cogné Michel
Published: April 2012

Suicidal B cells

In response to an infection, immunological B cells undergo a maturation process that results in the production of immunoglobulin (Ig) that is better able to bind and clear the invading pathogen. This occurs through somatic cell hypermutation and class switch recombination of the Ig gene and requires activation-induced deaminase (AID).

Péron
et al.

(p.
931
, published online 26 April) observed that the 3' cis-regulatory region of the heavy-chain locus is transcribed and undergoes AID-mediated mutation and recombination. The resulting deletion of the Ig heavy gene cluster generates B cells that are no longer able to express Ig on the cell surface. Because cell-surface Ig expression is essential for B cell survival, this process is termed “locus suicide recombination” (LSR) and may be important in shaping the dynamics of B effector cell differentiation and homeostasis.
Driven by Basic Research
Authors: Gruss Peter
Published: April 2012

Are nations investing too little in basic research? In the context of the global debt crisis, several industrial countries have reduced their funding for this research. Even though the new understandings produced by this kind of science have long been the driving force behind an enormous number of key developments in society and the business world, many politicians seem to be entirely unaware of its importance beyond simply increasing the world's store of knowledge. Yet 400 years ago, a visionary political leader, the British statesman and philosopher Francis Bacon, emphasized that “Science discovery should be driven not just by the quest for intellectual enlightenment, but also for the relief of man's estate.”
Microbial Evolution in the Wild
Authors: DeLong Edward F.
Published: April 2012

A genetic study of microbes in an acid mine drainage site provide evolutionary rate estimates for wild microbe populations.
California Weighs Tobacco Tax Hike to Fund Research
Authors: Miller Greg
Published: April 2012

Thanks to the unhealthy habits of some of the state's residents, California voters have an opportunity on 5 June to make their home one of the world's biggest supporters of cancer research.
Ancient Migrants Brought Farming Way of Life to Europe
Authors: Balter Michael
Published: April 2012

In this week's issue of
Science
, researchers report using ancient DNA from two sets of Scandinavian burials to explore the long-running question of how farming spread across Europe.
Where Time Goes Up and Down
Authors: Normile Dennis
Published: April 2012

At the Tokyo Evolutionary Linguistics Forum, researchers presented an example of a different way of thinking—and gesturing—about time: topographically.
Expression and Immunogenicity of Recombinant Immunoreactive Surface Protein 2 of Anaplasma phagocytophilum
Authors: Yu Qiang , Chen Chuang-fu , Chen Qiang , Zhang Li-juan
Published: April 2012

Human granulocytic anaplasmosis (HGA), caused by
Anaplasma phagocytophilum
, is an emerging tick-borne zoonotic disease throughout the world. The first HGA cases in China were documented in 2008, and the greatest challenge posed by the disease is rapid and accurate diagnosis during the acute phage of illness. In this study, we successfully cloned and expressed an
A. phagocytophilum
immunoreactive surface protein (major surface protein 2 [MSP2]) and demonstrated that this recombinant protein has natural immunogenicity by Western blotting and enzyme-linked immunosorbent assay (ELISA) using human HGA-positive sera and reference rabbit HGA-positive sera. The rabbit antisera against the recombinant protein also reacted actively with the natural antigen of
A. phagocytophilum
by immunofluorescence assay (IFA). No cross-reaction was observed between the recombinant protein and rabbit antisera against 10 common members of the order
Rickettsiales
by ELISA when the sera were diluted more than 1:100. We concluded that the recombinant MSP2 protein exhibited excellent antigenicity and specificity, results that should lay the foundation for the development of a simple and rapid diagnostic reagent and a vaccination for anaplasmosis.
Sequencing of Cladosporium sphaerospermum, a Dematiaceous Fungus Isolated from Blood Culture
Authors: Ng Kee Peng , Yew Su Mei , Chan Chai Ling , Soo-Hoo Tuck Soon , Na Shiang Ling , Hassan Hamimah , Ngeow Yun Fong , Hoh Chee-Choong , Lee Kok-Wei , Yee Wai-Yan
Published: April 2012

Cladosporium sphaerospermumis one of the most widely distributed allergens causing serious problems in patients with respiratory tract disease. We report the 26,644,473-bp draft genome sequence and gene annotation ofC. sphaerospermumUM843. Analysis of the genome sequence led to the finding of genes associated withC. sphaerospermum'smelanin biosynthesis, allergens, and antifungal drug resistance.
Rapid, High-Throughput Detection of Rifampin Resistance and Heteroresistance in Mycobacterium tuberculosis by Use of Sloppy Molecular Beacon Melting Temperature Coding
Authors: Chakravorty Soumitesh , Kothari Harsheel , Aladegbami Bola , Cho Eun Jin , Lee Jong Seok , Roh Sandy S. , Kim Hyunchul , Kwak Hyungkyung , Lee Eun Gae , Hwang Soo Hee , Banada Padmapriya P. , Safi Hassan , Via Laura E. , Cho Sang-Nae , Barry Clifton E. , Alland David
Published: April 2012

Rifampin resistance in
Mycobacterium tuberculosis
is largely determined by mutations in an 80-bp rifampin resistance determining region (RRDR) of the
rpoB
gene. We developed a rapid single-well PCR assay to identify RRDR mutations. The assay uses sloppy molecular beacons to probe an asymmetric PCR of the
M. tuberculosis
RRDR by melting temperature (

T
m

) analysis. A three-point

T
m

code is generated which distinguishes wild-type from mutant RRDR DNA sequences in approximately 2 h. The assay was validated on synthetic oligonucleotide targets containing the 44 most common RRDR mutations. It was then tested on a panel of DNA extracted from 589 geographically diverse clinical
M. tuberculosis
cultures, including isolates with wild-type RRDR sequences and 25 different RRDR mutations. The assay detected 236/236 RRDR mutant sequences as mutant (sensitivity, 100%; 95% confidence interval [CI], 98 to 100%) and 353/353 RRDR wild-type sequences as wild type (specificity, 100%; 95% CI, 98.7 to 100%). The assay identified 222/225 rifampin-resistant isolates as rifampin resistant (sensitivity, 98.7%; 95% CI, 95.8 to 99.6%) and 335/336 rifampin-susceptible isolates as rifampin susceptible (specificity, 99.7%; 95% CI, 95.8 to 99.6%). All mutations were either individually identified or clustered into small mutation groups using the triple

T
m

code. The assay accurately identified mixed (heteroresistant) samples and was shown analytically to detect RRDR mutations when present in at least 40% of the total
M. tuberculosis
DNA. This was at least as accurate as Sanger DNA sequencing. The assay was easy to use and well suited for high-throughput applications. This new sloppy molecular beacon assay should greatly simplify rifampin resistance testing in clinical laboratories.
The 2010 Global Proficiency Study of Human Papillomavirus Genotyping in Vaccinology
Authors: Eklund Carina , Forslund Ola , Wallin Keng-Ling , Zhou Tiequn , Dillner Joakim
Published: April 2012

Accurate and internationally comparable human papillomavirus (HPV) DNA genotyping is essential both for evaluation of HPV vaccines and for effective monitoring and implementation of vaccination programs. The World Health Organization (WHO) HPV Laboratory Network (LabNet) regularly issues international proficiency studies. The 2010 HPV genotyping proficiency panel for HPV vaccinology contained 43 coded samples composed of purified plasmids of 16 HPV types (HPV types 6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68a and 68b) and 3 coded extraction controls. Proficient typing was defined as detection in both single and multiple infections of 50 international units (IU) of HPV type 16 (HPV-16) and HPV-18 DNA and 500 genome equivalents (GE) for the other 14 HPV types. Ninety-eight laboratories worldwide submitted a total of 132 data sets. Twenty-four different HPV genotyping assay methods were used, with Linear Array being the most commonly used. Other major assays used were a line blot assay (Inno-LiPa), CLART, type-specific real-time PCR, PCR Luminex, and different microarray assays. Altogether, 72 data sets were proficient for detection of more than 1 type, and only 26 data sets proficiently detected all 16 HPV types. The major oncogenic HPV types, 16 and 18, were proficiently detected in 95.0% (114/120) and 87.0% (94/108) of data sets, respectively. Forty-six data sets reported multiple false-positive results and were considered nonproficient. A trend toward increased sensitivity of assays was seen for the 41 laboratories that participated in both 2008 and 2010. In conclusion, continued global proficiency studies will be required for establishing comparable and reliable HPV genotyping services for vaccinology worldwide.
Survival of Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococcus spp. for an Extended Period of Transport
Authors: Robinson Gwen L. , Harris Anthony D. , Morgan Daniel J. , Pineles Lisa , Belton Beverly M. , Johnson J. Kristie ,   the Benefits of Universal Gloving and Gowning (BUGG) Study Group
Published: April 2012

This study determined the survivability of methicillin-resistant
Staphylococcus aureus
(MRSA) and vancomycin-resistant enterococci (VRE) for extended periods of time and temperatures using a standard swab for assessment. Our study showed that transportation in Liquid Amies medium could be performed at room temperature or 4°C for up to 14 days without a decrease in recovery of MRSA or VRE.
Replication of Herpes Simplex Virus: Egress of Progeny Virus at Specialized Cell Membrane Sites
Authors: Mingo Rebecca M. , Han Jun , Newcomb William W. , Brown Jay C.
Published: April 2012

In the final stages of the herpes simplex virus 1 (HSV-1) life cycle, a viral nucleocapsid buds into a vesicle of
trans
-Golgi network (TGN)/endosome origin, acquiring an envelope and an outer vesicular membrane. The virus-containing vesicle then traffics to the plasma membrane where it fuses, exposing a mature virion. Although the process of directed egress has been studied in polarized epithelial cell lines, less work has been done in nonpolarized cell types. In this report, we describe a study of HSV-1 egress as it occurs in nonpolarized cells. The examination of infected Vero cells by electron, confocal, and total internal reflection fluorescence (TIRF) microscopy revealed that HSV-1 was released at specific pocket-like areas of the plasma membrane that were found along the substrate-adherent surface and cell-cell-adherent contacts. Both the membrane composition and cytoskeletal structure of egress sites were found to be modified by infection. The plasma membrane at virion release sites was heavily enriched in viral glycoproteins. Small glycoprotein patches formed early in infection, and virus became associated with these areas as they expanded. Glycoprotein-rich areas formed independently from virion trafficking as confirmed by the use of a UL25 mutant with a defect in capsid nuclear egress. The depolymerization of the cytoskeleton indicated that microtubules were important for the trafficking of virions and glycoproteins to release sites. In addition, the actin cytoskeleton was found to be necessary for maintaining the integrity of egress sites. When actin was depolymerized, the glycoprotein concentrations dispersed across the membrane, as did the surface-associated virus. Lastly, viral glycoprotein E appeared to function in a different manner in nonpolarized cells compared to previous studies of egress in polarized epithelial cells; the total amount of virus released at egress sites was slightly increased in infected Vero cells when gE was absent. However, gE was important for egress site formation, as Vero cells infected with gE deletion mutants formed glycoprotein patches that were significantly reduced in size. The results of this study are interpreted to indicate that the egress of HSV-1 in Vero cells is directed to virally induced, specialized egress sites that form along specific areas of the cell membrane.
Implication of Inflammatory Macrophages, Nuclear Receptors, and Interferon Regulatory Factors in Increased Virulence of Pandemic 2009 H1N1 Influenza A Virus after Host Adaptation
Authors: Josset Laurence , Belser Jessica A. , Pantin-Jackwood Mary J. , Chang Jean H. , Chang Stewart T. , Belisle Sarah E. , Tumpey Terrence M. , Katze Michael G.
Published: April 2012

While pandemic 2009 H1N1 influenza A viruses were responsible for numerous severe infections in humans, these viruses do not typically cause corresponding severe disease in mammalian models. However, the generation of a virulent 2009 H1N1 virus following serial lung passage in mice has allowed for the modeling of human lung pathology in this species. Genetic determinants of mouse-adapted 2009 H1N1 viral pathogenicity have been identified, but the molecular and signaling characteristics of the host response following infection with this adapted virus have not been described. Here we compared the gene expression response following infection of mice with A/CA/04/2009 (CA/04) or the virulent mouse-adapted strain (MA-CA/04). Microarray analysis revealed that increased pathogenicity of MA-CA/04 was associated with the following: (i) an early and sustained inflammatory and interferon response that could be driven in part by interferon regulatory factors (IRFs) and increased NF-κB activation, as well as inhibition of the negative regulator TRIM24, (ii) early and persistent infiltration of immune cells, including inflammatory macrophages, and (iii) the absence of activation of lipid metabolism later in infection, which may be mediated by inhibition of nuclear receptors, including PPARG and HNF1A and -4A, with proinflammatory consequences. Further investigation of these signatures in the host response to other H1N1 viruses of various pathogenicities confirmed their general relevance for virulence of influenza virus and suggested that lung response to MA-CA/04 virus was similar to that following infection with lethal H1N1 r1918 influenza virus. This study links differential activation of IRFs, nuclear receptors, and macrophage infiltration with influenza virulence
in vivo
.
Kaposi's Sarcoma-Associated Herpesvirus Inhibits Expression and Function of Endothelial Cell Major Histocompatibility Complex Class II via Suppressor of Cytokine Signaling 3
Authors: Butler L. M. , Jeffery H. C. , Wheat R. L. , Long H. M. , Rae P. C. , Nash G. B. , Blackbourn D. J.
Published: April 2012

Endothelial cells (EC) can present antigen to either CD8+T lymphocytes through constitutively expressed major histocompatibility complex class I (MHC-I) or CD4+T lymphocytes through gamma interferon (IFN-γ)-induced MHC-II. Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma (KS), an EC neoplasm characterized by dysregulated angiogenesis and a substantial inflammatory infiltrate. KSHV is understood to have evolved strategies to inhibit MHC-I expression on EC and MHC-II expression on primary effusion lymphoma cells, but its effects on EC MHC-II expression are unknown. Here, we report that the KSHV infection of human primary EC inhibits IFN-γ-induced expression of the MHC-II molecule HLA-DR at the transcriptional level. The effect is functionally significant, since recognition by an HLA-DR-restricted CD4+T-cell clone in response to cognate antigen presented by KSHV-infected EC was attenuated. Inhibition of HLA-DR expression was also achieved by exposing EC to supernatant from KSHV-inoculated EC before IFN-γ treatment, revealing a role for soluble mediators. IFN-γ-induced phosphorylation of STAT-1 and transcription ofCIITAwere suppressed in KSHV-inoculated EC via a mechanism involving SOCS3 (suppressor of cytokine signaling 3). Thus, KSHV infection resulted in transcriptional upregulation of SOCS3, and treatment with RNA interference against SOCS3 relieved virus-induced inhibition of IFN-γ-induced STAT-1 phosphorylation. Since cell surface MHC-II molecules present peptide antigens to CD4+T lymphocytes that can function either as direct cytolytic effectors or to initiate and regulate adaptive immune responses, inhibition of this antigen-presenting pathway would provide a survival advantage to the virus.
Social and geographical factors affecting access to treatment of colorectal cancer: a cancer registry study
Authors: Crawford S Michael , Sauerzapf Violet , Haynes Robin , Forman David , Jones Andrew P
Published: April 2012

Objective

Cancer outcomes vary between and within countries with patients from deprived backgrounds known to have inferior survival. The authors set out to explore the effect of deprivation in relation to the accessibility of hospitals offering diagnostic and therapeutic services on stage at presentation and receipt of treatment.

Design

Analysis of a Cancer Registry Database. Data included stage and treatment details from the first 6 months. The socioeconomic status of the immediate area of residence and the travel time from home to hospital was derived from the postcode.

Setting

Population-based study of patients resident in a large area in the north of England.

Participants

39 619 patients with colorectal cancer diagnosed between 1994 and 2002.

Outcomes measured

Stage of diagnosis and receipt of treatment in relation to deprivation and distance from hospital.

Results

Patients in the most deprived quartile were significantly more likely to be diagnosed at stage 4 for rectal cancer (OR 1.516, p<0.05) but less so for colonic cancer. There was a trend for both sites for patients in the most deprived quartile to be less likely to receive chemotherapy for stage 4 disease. Patients with colonic cancer were very significantly less likely to receive any treatment if they came from any but the most affluent area (ORs 0.639, 0.603 and 0.544 in increasingly deprived quartiles), this may have been exacerbated if the hospital was distant from their residence (OR for forth quartile for both travel and deprivation 0.731, not significant). The effect was less for rectal cancer and no effect of distance was seen.

Conclusions

Residing in a deprived area is associated with tendencies to higher stage at diagnosis and especially in the case of colonic cancer to reduced receipt of treatment. These observations are consistent with other findings and indicate that access to diagnosis requires further investigation.
Evaluation of single reactor bovine tuberculosis breakdowns based on analysis of reactors slaughtered at an Irish export meat plant
Authors: Murray D. , Clegg T. A. , More S. J.
Published: April 2012

The ‘Singleton Protocol’ was adopted by the Irish Department of Agriculture Fisheries and Food (DAFF) in 1996 to address the incomplete specificity of the single intra‐dermal comparative tuberculin test (SICTT) used in Ireland for the detection of animals infected with bovine tuberculosis (bTB). The protocol allows the early restoration of disease‐free status to herds with a single reactor breakdown, where the herd was not confirmed as infected with Mycobacterium bovis by epidemiological investigation, by postmortem examination or by further test. The current study examines the ability of the Singleton Protocol to identify false‐positive reactors. It investigates the subsequent herd‐reactor rate following single reactor removal and analyses the factors leading to a positive postmortem lesion outcome and a positive reactor retest result. Postmortem lesion results were obtained for 371 reactor animals from single reactor breakdowns that were killed at an export meat plant over a 19‐month period. Epidemiological and test data for these animals and their herds were obtained from DAFF databases and analysed by univariate and multivariate statistical analysis. Singleton candidates had an 18.7 per cent lower lesion rate than single animal breakdowns not meeting the singleton criteria. No significant difference was found between Singletons and non singletons in the subsequent reactor retest results. Skin thickness at the SICTT is the most significant determinant of a positive lesion result. The area bTB history was shown to be a significant variable in producing a positive reactor retest result.
Resonance classification of mixed assemblages of fish with swimbladders using a modified commercial broadband acoustic echosounder at 1–6 kHz
Authors: Stanton Timothy K. , Sellers Cynthia J. , Jech J. Michael
Published: April 2012

Recently developed broadband acoustic methods were used to study mixed assemblages of fish spanning a wide range of lengths and species. Through a combination of resonance classification and pulse-compression signal processing, which provides for high-range resolution, a modified commercial broadband echosounder was demonstrated to provide quantitative information on the spatial distribution of the individual size classes within an assemblage. In essence, this system spectrally resolves the different size classes of fish that are otherwise not resolved spatially. This method reveals new insights into biological processes, such as predator–prey interactions, that are not obtainable through the use of a conventional narrowband high-frequency echosounder or previous broadband systems. A recent study at sea with this system revealed aggregations containing bladdered fish 15–30 cm in length (Atlantic herring ( Clupea harengus ) and silver hake ( Merluccius bilinearis )) and a variety of species of smaller fish 2–5 cm in length. These observations infer that the smaller 2–5 cm fish can be colocated in the same aggregations as their predator, the larger silver hake, as well as pre-spawning herring. While this technological advancement provides more information, there remain challenges in interpreting the echo spectra in terms of meaningful biological quantities such as size distribution and species composition.
Using electronic tag data to improve mortality and movement estimates in a tag-based spatial fisheries assessment model
Authors: Eveson J. Paige , Basson Marinelle , Hobday Alistair J.
Published: April 2012

Despite increased deployment of archival tags on exploited fish species, analytical methods for including archival tag data in fishery assessment models are lacking. We present a method for integrating archival tag data into a spatial tag–recapture model for estimating natural mortality, fishing mortality, abundance, and movement. Archival tags provide important information on fish movement not available from conventional tags that facilitates separation of movement from mortality estimates. Using simulations, we evaluate the benefit of including archival tag data in the model using two model formulations: one with a general spatial structure and one with movement and fishery dynamics based on juvenile southern bluefin tuna (SBT; Thunnus maccoyii ). If fish are not tagged in all regions and time periods, then including archival tag data can substantially improve the precision of the fishing mortality and movement estimates. For example, with the general spatial structure and specific scenario presented, standard errors of the fishing mortality estimates decreased by an average of 34% (21%) when 25 archival tags were released in addition to 500 (2500) conventional tags in each region and period of tagging, respectively. Furthermore, with the SBT spatial structure, archival tag data were necessary for all parameters to be estimable.
Environmental factors correlate with hybridization in stocked brook charr (Salvelinus fontinalis)
Authors: Marie Amandine D. , Bernatchez Louis , Garant Dany
Published: April 2012

Stocking is a common practice throughout the world that may increase hybridization between wild and domesticated populations. Stocking intensity alone does not always fully explain the observed patterns of hybridization, suggesting that the intensity of hybridization may be modulated by environmental factors. Using brook charr (i.e., brook trout, Salvelinus fontinalis ) as a model, the objective of this study was to assess the relative effect of environmental factors and stocking intensity on the level of hybridization observed within brook charr from 15 lacustrine populations of two wildlife reserves in Quebec, Canada. The level of hybridization significantly increased with (i) the number of stocking events, (ii) a reduction in both surface area and maximum depth of lakes, and (iii) a reduction in dissolved oxygen and an increase in temperature and pH. These results suggest that levels of hybridization were affected by the availability and quality of lacustrine habitats as well as by the extent of propagule pressure. Our study provides the first demonstration that knowledge of environmental features may help predict the effects of stocking on the genetic integrity of wild populations.
Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka)
Authors: Gomez-Uchida Daniel , Seeb James E. , Habicht Christopher , Seeb Lisa W.
Published: April 2012

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and contemporary collections of Alaskan sockeye salmon ( Oncorhynchus nerka ) to evaluate the stability of allele frequencies over 25–42 years (4.9–8.4 generations). First, our results show that temporal changes were dramatically (between 40- and 250-fold) smaller than spatial differences in allele frequencies when based on nuclear SNPs. Second, the magnitude of temporal change was consistent with a model of genetic drift: (i) SNPs with high levels of differentiation (large θ) and candidates for diversifying selection were not more likely to show significant temporal changes than small-θ SNPs; and (ii) the fraction of single-locus significant tests was consistent with theoretical predictions relating sample size and the annual number of breeders (Nb). Third, estimates of Nbwere bound by infinitely large upper 95% confidence intervals, except for one paired collection with unique life-history attributes of both a smoltification phase and generation time shorter than the other paired collections. Use of multigenerational SNP data sets seems a safe practice in management of Alaska sockeye salmon that could be extended to other large, wild aquatic populations.
Estimating westslope cutthroat trout (Oncorhynchus clarkii lewisi) movements in a river network using strontium isoscapes
Authors: Muhlfeld Clint C. , Thorrold Simon R. , McMahon Thomas E. , Marotz Brian
Published: April 2012

We used natural variation in the strontium concentration (Sr:Ca) and isotope composition (87Sr:86Sr) of stream waters and corresponding values recorded in otoliths of westslope cutthroat trout ( Oncorhynchus clarkii lewisi ) to examine movements during their life history in a large river network. We found significant spatial differences in Sr:Ca and 87Sr:86Sr values (strontium isoscapes) within and among numerous spawning and rearing streams that remained relatively constant seasonally. Both Sr:Ca and 87Sr:86Sr values in the otoliths of juveniles collected from nine natal streams were highly correlated with those values in the ambient water. Strontium isoscapes measured along the axis of otolith growth revealed that almost half of the juveniles had moved at least some distance from their natal streams. Finally, otolith Sr profiles from three spawning adults confirmed homing to natal streams and use of nonoverlapping habitats over their migratory lifetimes. Our study demonstrates that otolith geochemistry records movements of cutthroat trout through Sr isoscapes and therefore provides a method that complements and extends the utility of conventional tagging techniques in understanding life history strategies and conservation needs of freshwater fishes in river networks.
A Bayesian hierarchical model of size-at-age in ocean-harvested stocks — quantifying effects of climate and temporal variability
Authors: Satterthwaite William Hallowell , Mohr Michael Steven , O’Farrell Michael Robert , Wells Brian Kenneth
Published: April 2012

Quantifying size-at-age in harvested marine fish populations is a challenge with implications for both conservation and management. We describe a Bayesian hierarchical modeling approach for estimating mean and variation in size-at-age, incorporating environmental covariates. We apply the approach to two runs of Sacramento River Chinook salmon ( Oncorhynchus tshawytscha ): one data-rich (fall) and one data-poor (winter). We combine information on the size of recreationally harvested tagged fish and fishery size limits to reconstruct time-dependent marine size distributions. Our framework allows informed modeling of environmental effects on size-at-age, estimation of annual variability without overfitting, estimating size in years with limited data, and projecting sizes in future years. We found that fall run fish are anomalously small in years following Novembers with low values of the Northern Oscillation Index (NOI). Winter run data did not include anomalously low NOI years, but typical annual variability could be quantified. Importantly, our results suggest that it is possible to predict small size and slow growth during the upcoming fishery season on the basis of an environmental index available months in advance.
Predicting the interactions between “ecologically equivalent” indigenous and nonindigenous brachyurans
Authors: Breen Erin , Metaxas Anna
Published: April 2012

Predictive models used to determine the impacts of nonindigenous brachyurans on their “ecological equivalents” in marine ecosystems are sorely lacking. Determining the spatial and temporal extent and magnitude of such impacts by nonindigenous species is difficult because of the broad range of qualitative and quantitative criteria currently used to describe their effects. Forecasting potential impacts requires the development of predictive models that incorporate the effects of interspecific interactions and the mechanisms that give rise to these interactions. Successful validation of such models requires improved techniques for measuring and estimating the functional responses on bioenergetic processes across species compositions, abundances, and environmental conditions. Species-specific information used to support predictive modeling of nonindigenous brachyurans is currently heavily biased towards (i) estimating per capita consumption and growth rates in laboratory conditions and (ii) incorporating the effects of abiotic and biotic factors on these measures. Robust predictive models require repetitive experimentation that advances the understanding of species’ interactions (beyond consumption alone) across variable densities and considers their effects across different spatial and temporal scales.
A detrimental soil disturbance prediction model for ground-based timber harvesting
Authors: Reeves Derrick A. , Reeves Matthew C. , Abbott Ann M. , Page-Dumroese Deborah S. , Coleman Mark D.
Published: April 2012

Soil properties and forest productivity can be affected during ground-based harvest operations and site preparation. The degree of impact varies widely depending on topographic features and soil properties. Forest managers who understand site-specific limits to ground-based harvesting can alter harvest method or season to limit soil disturbance. To determine the potential areal extent of detrimental (potentially plant growth limiting) soil disturbance based on site characteristics and season of harvest, we developed a predictive model based on soil monitoring data collected from 167 ground-based harvest units. Data collected included dominant site parameters (e.g., slope, aspect, soil texture, and landtype), harvest season, harvest type (intermediate or regeneration), and the machine(s) used during ground-based harvest operations. Aspect (p = 0.0217), slope (p = 0.0738), landtype (p = 0.0002), and the interaction of harvest season × landtype (p = 0.0002) were the key variables controlling the areal extent and magnitude of detrimental soil disturbance. For example, harvesting during non-winter months on gently rolling topography resulted in greater soil disturbance than similar harvest operations on landscapes that are highly dissected. This is likely due to the ease with which equipment can move off designated trails. A geospatially explicit predictive model was developed using general linear model variables found to significantly influence the areal extent of detrimental soil disturbance on nine defined landtypes. This tool provides a framework that, with local calibration, can be used on other forest lands as a decision support tool to geospatially depict landtypes susceptible to detrimental soil disturbance during ground-based harvest operations.