bluuebunny/crossref_metadata_2025 huggingface dataset:
Genotyping for cytokine polymorphisms in a Northern Ivory Coast population reveals a high frequency of the heterozygote genotypes for the TNF‐α‐308G/A SNP
Authors: Santovito A. , Cervella P. , Schleicherova D. , Delpero M.
Published: February 2012

Cytokine polymorphisms influence the outcomes of parasitic diseases and vary among populations because of their different evolutionary histories and selective pressures imposed by host–pathogen interactions. In this frame, we investigated the frequencies of TNF‐α (‐308G/A), TGF‐β1 (codon 10C/T, codon 25C/G) and IL‐10 (‐1082A/G) SNPs in 133 individuals from Ouangolodougou, a rural village in Northern Ivory Coast, where malaria and other parasitic diseases are endemic. The SNPs alleles were determined by ARMS‐PCR methodology. Allele frequencies of the SNPs investigated were as follows: IL 10 ‐1082G = 0.741 and ‐1082A = 0.259; TGF‐β1 Codon 10 C = 0.835 and T = 0.165; TGF‐β1 Codon 25 G = 0.782 and C = 0.218. For the TNF‐α gene, we found high frequencies of the ‐308A allele (0.305) and heterozygote genotypes (0.594), with a consequent deviation from the Hardy–Weinberg equilibrium. The high heterozygosity at the TNF‐α locus suggests a possible selective advantage of the heterozygote genomes, associated with intermediate levels of TNF‐α expression, against the infectious agents endemic in Western Africa.
Water‐Soluble Binder System Based on Poly‐Methyl Methacrylate and Poly‐Ethylene Glycol for Injection Molding of Large‐Sized Ceramic Parts
Authors: Yang Xianfeng , Jia Cui , Xie Zhipeng , Liu Wei , Liu Qicheng
Published: February 2012

Water debinding technique was applied in preparing injection molded large‐sized parts. The results showed that the origin of cracking and blistering defects was the swelling from polyethylene glycols of folded chain crystal. The combination of polyethylene glycols with molecular weight 600 and 4000 could ensure both debinding quality and green body strength. It was shown that higher than 20% of insoluble backbone binder was sufficient to resist the stress from swelling. For the compact with length sale of 3.14 mm (the ratio of volume to surface area), approximately 65% of polyethylene glycols were leached after 22 h at 40°C.
Cardiovascular Protective Effects of On‐Line Hemodiafiltration: Comparison With Conventional Hemodialysis
Authors: Ohtake Takayasu , Oka Machiko , Ishioka Kunihiro , Honda Kenjiro , Mochida Yasuhiro , Maesato Kyoko , Moriya Hidekazu , Hidaka Sumi , Kobayashi Shuzo
Published: February 2012

Atherosclerotic complications have a significant effect on mortality in patients undergoing hemodialysis (HD) therapy. However, anti‐atherosclerotic and cardioprotective effects of on‐line hemodiafiltration (HDF) remain to be elucidated. We prospectively compared the anti‐atherosclerotic and cardioprotective effects in two randomly divided groups, i.e. on‐line HDF group (n = 13) and conventional HD group (n = 9) for 1 year. Surrogate markers were brachial‐ankle pulse wave velocity (baPWV), intima‐media thickness (IMT) of carotid artery as an atherosclerosis marker, and cardiac functional surrogate markers included left ventricular mass index (LVMI), ejection fraction (EF), and LV diastolic capacity represented as E/A and deceleration time (DT). LVMI in on‐line HDF patients showed significant regression after 1 year of treatment (131.9 ± 25.8 to 116.5 ± 24.7 g/m2, P = 0.03), while LVMI in HD patients did not show any significant change (148.0 ± 47.1 to 142.3 ± 35.5 g/m2). Levels of baPWV in HD patients showed a significant increase (11.4%) from basal levels, while on‐line HDF groups showed no significant increase. Furthermore, HD patients showed significant worsening of LV diastolic capacity (E/A: from 0.87 ± 0.12 to 0.79 ± 0.08, P = 0.03), while it was not shown in on‐line HDF patients. Ejection fraction and IMT did not show any significant change in both groups. Serum albumin, C‐reactive protein, β2 microglobulin, blood pressure, and anti‐hypertensive drug use did not change in both groups. On‐line HDF showed a significant improvement in LVMI and prevented a significant worsening of baPWV or LV diastolic capacity compared with patients on conventional HD therapy.
Left Ventricular End‐Diastolic Diameter Is an Independent Predictor of Mortality in Hemodialysis Patients
Authors: Inoue Tomoko , Ogawa Tetsuya , Iwabuchi Yuko , Otsuka Kuniaki , Nitta Kosaku
Published: February 2012

Left ventricular (LV) function is impaired in most hemodialysis (HD) patients. We conducted an observational cohort study to investigate whether LV end‐diastolic diameter (LVDd) could predict all‐cause mortality in a cohort of 166 HD patients. The LVDd values (5.06 ± 0.64 cm) of the non‐survivor group were significantly greater than in the survivor group (4.78 ± 0.71 cm). The area under the receiver operating characteristic curve for an LVDd cut‐off value of 5.01 cm was 0.6145 (P = 0.0234). The sensitivity and specificity of the LVDd threshold of 5.01 cm were 75.7% and 50.4%, respectively. The 4‐year survival rate was significantly lower in the group with LVDd ≥ 5.01 cm than in the group with LVDd < 5.01 cm (log‐rank test, P = 0.0047). Multivariate analysis with adjustments for clinical and echocardiographic parameters showed that increased LVDd was an independent predictor of all‐cause mortality (hazard ratio 2.363, 95% CI 1.320–4.228, P = 0.0013). The results of the present study showed that increased LVDd predicts the all‐cause mortality of chronic HD patients better than other echocardiographic parameters. Our findings suggest that LVDd measurements may be helpful for risk stratification and providing therapeutic direction for the management of HD patients.
Revealing Interaction Mode between HIV‐1 Protease and Mannitol Analog Inhibitor
Authors: Yan Guan‐Wen , Chen Yue , Li Yixue , Chen Hai‐Feng
Published: February 2012

HIV protease is a key enzyme to play a key role in the HIV‐1 replication cycle and control the maturation from HIV viruses to an infectious virion. HIV‐1 protease has become an important target for anti‐HIV‐1 drug development. Here, we used molecular dynamics simulation to study the binding mode between mannitol derivatives and HIV‐1 protease. The results suggest that the most active compound (M35) has more stable hydrogen bonds and stable native contacts than the less active one (M17). These mannitol derivatives might have similar interaction mode with HIV‐1 protease. Then, 3D‐QSAR was used to construct quantitative structure–activity models. The cross‐validated q2 values are found as 0.728 and 0.611 for CoMFA and CoMSIA, respectively. And the non‐cross‐validated r2 values are 0.973 and 0.950. Nine test set compounds validate the model. The results show that this model possesses better prediction ability than the previous work. This model can be used to design new chemical entities and make quantitative prediction of the bioactivities for HIV‐1 protease inhibitors before resorting to in vitro and in vivo experiment.
“The Value of Understanding”
Authors: Grimm Stephen
Published: February 2012

Over the last several years a number of leading philosophers – including Catherine Elgin, Linda Zagzebski, Jonathan Kvanvig, and Duncan Pritchard – have grown increasingly dissatisfied with the contemporary focus on knowledge in epistemology and have attempted to “recover” the notion of understanding. According to some of these philosophers, in fact, understanding deserves not just to be recovered, but to supplant knowledge as the focus of epistemological inquiry. This entry considers some of the main reasons why philosophers have taken understanding to be more valuable than knowledge, focusing on claims that it is more transparent, that it better reflects or mirrors the world, and that it is a greater intellectual achievement.
Epistemic Expressivism
Authors: Chrisman Matthew
Published: February 2012

Epistemic expressivism is the application of a nexus of ideas, which is prominent in ethical theory (more specifically, metaethics), to parallel issues in epistemological theory (more specifically, metaepistemology). Here, in order to help those new to the debate come to grips with epistemic expressivism and recent discussions of it, I first briefly present this nexus of ideas as it occurs in ethical expressivism. Then, I explain why and how some philosophers have sought to extend it to a version of epistemic expressivism. Finally, I consider a number of objections and replies with the aim of giving the reader the tools needed to begin to evaluate the promise and prospects of epistemic expressivism.
Bayesian Models of Cognition: What's Built in After All?
Authors: Perfors Amy
Published: February 2012

This article explores some of the philosophical implications of the Bayesian modeling paradigm. In particular, it focuses on the ramifications of the fact that Bayesian models pre‐specify an inbuilt hypothesis space. To what extent does this pre‐specification correspond to simply ‘‘building the solution in''? I argue that any learner (whether computer or human) must have a built‐in hypothesis space in precisely the same sense that Bayesian models have one. This has implications for the nature of learning, Fodor's puzzle of concept acquisition, and the role of modeling in cognitive science.
Network Theory in the Assessment of the Sustainability of Social–Ecological Systems
Authors: Gonzalès Rodolphe , Parrott Lael
Published: February 2012

As human activities increasingly threaten the ecosystems on which they depend, one of the main questions our societies are facing is related to the resilience – seen as a necessary element of sustainability – of social–ecological systems (SESs). SESs are composed of many heterogeneous elements including human actors such as institutions and resource users, and natural components such as land patches, animal species, etc. The numerous relationships between these different entities shape complex, dynamic networks of social–ecological interdependencies. Once described as networks, SESs can be analysed using a variety of network metrics, which may potentially help to better quantify and evaluate the resilience of SESs to external or internal perturbations. In this paper, we provide a broad overview of the latest progress in network theory as applied to SESs and discuss how network metrics may be used to assess the sustainability of an SES.
Geographies of the Performing Arts: Landscapes, Places and Cities
Authors: Rogers Amanda
Published: February 2012

The performing arts of dance, theatre, music and live art have become established means through which cultural geographers can examine how people experience and make sense of their everyday worlds. Simultaneously, performance theorists and practitioners increasingly seek geographical tools that help elucidate the broader processes or politics that underpin artistic genres of performance. This review article works at this interdisciplinary nexus, exploring the diverse areas of engagement between geography and the performing arts. It provides an overview of three spatialities around which interdisciplinary exchanges take place, and where there are interesting synergies in the conceptual approach to studying geographies of performance, namely: landscapes, places and cities. In so doing, the article outlines some avenues where geography and performance studies academics might further their mutual interests, and argues that geography is central to the constitution, meaning and form that performance works take.
Community Transitions to Low Carbon Futures in the Transition Towns Network (TTN)
Authors: Aiken Gerald
Published: February 2012

This paper examines the use of ‘community’ rhetoric in the Transition Town Network (TTN). This is seen in both its external and internal context. Externally, TTN has emerged against the backdrop of an increasing use of ‘community’ rhetoric in environmental governance, for example, in renewable energy projects. Internally, the use of ‘community’ language and ‘community’ ways of operating are crucial for understanding this movement, in how it sees itself and the lineage it builds upon. Particularly, TTN builds upon the polysemic, subjective nature of the word, fused with their unique permaculture inspired meaning. TTN have emerged as an important response to climate change and peak oil (Bailey et al. 2010; Mason and Whitehead 2011). This paper attempts to address their crucial, if neglected, focus on ‘community’. In the wide sweep of writing on ‘community’, what distinctive, if anything, can TTN add to current understandings and practices of ‘community’?
Health Reform and Child Health: Progress, Cautions, and Future Directions
Authors: Morrissey Taryn W.
Published: February 2012

Abstract— The Affordable Care Act (ACA) represents a historic legislative advance in social policy that will dramatically change Americans’ access to health insurance and health‐care services. Although nonelderly adults stand to reap the greatest benefits in coverage and access to health care, children will also benefit from improvements in health insurance and health‐care quality. The move to eliminate individual provisions or “repeal and replace” the ACA threatens this progress. Rather, this article argues that the benefits provided by the ACA lay the foundation for addressing the major issues facing children’s health: uninsurance, underinsurance, subpar health‐care quality, and growing rates of obesity and chronic disease. It describes the major provisions in the ACA that will address these issues and highlights concerns for the law’s implementation and directions for future child health research and policy.
Evaluation of Diethyl‐3‐3′‐(9,10‐anthracenediyl)bis Acrylate as a Probe for Singlet Oxygen Formation during Photodynamic Therapy
Authors: Kessel David , Price Michael
Published: February 2012

The cell‐permeable anthracene analog diethyl‐3‐3′‐(9,10‐anthracenediyl)bis acrylate (DADB) was recently identified as a highly selective probe for singlet oxygen (1O2). Now, we show that DADB can be used to monitor 1O2 formation in cell culture during photodynamic therapy. An atypical property of DADB is that fluorescence emission is decreased upon oxidation. Using photosensitizers that target specific organelles, we determined that DADB could detect 1O2 whether formed in ER, mitochondria or lysosomes. DADB fluorescence was not, however, significantly altered when the photosensitizing agent was the palladium bacteriopheophorbide termed WST11, an agent reported to produce mainly oxygen radicals upon irradiation in an aqueous environment, whereas singlet oxygen was formed in organic solvents.
Effect of substrate availability on nitrous oxide production by deammonification processes under anoxic conditions
Authors: Schneider Yvonne , Beier Maike , Rosenwinkel Karl‐Heinz
Published: February 2012

Due to its high global warming potential, nitrous oxide (N2O) emissions from wastewater treatment processes have recently received a high degree of attention. Nevertheless, there is still a lack of information regarding the microbiological processes leading to N2O production. In this study, two lab‐scale sequencing batch reactors were operated with deammonification biomass to investigate the role of denitrification and the influence of substrate availability regarding N2O formation during the anoxic phase of deammonification. Three different operational phases were established: within the first phase conversion by anammox was favoured and after a transition phase, denitrification activity was promoted. Low nitrous oxide production was observed during stable operation aiming for anammox conversion. Pulsed inflow of the wastewater containing ammonium (NH4+) and nitrite (NO2‐) led to increased N2O production rates. Within the period of denitrification as dominating nitrogen conversion process, the nitrous oxide concentration level was higher during continuous inflow conditions, but the reaction to pulsed inflow was less pronounced. The results indicated that denitrification was responsible for N2O formation from the deammonification biomass. Operational settings to achieve suppression of denitrification processes to a large extend were deducted from the results of the experiments.
Short‐Term Hydroscheduling with Discrepant Objectives Using Multi‐Step Progressive Optimality Algorithm1
Authors: Cheng Chuntian , Shen Jianjian , Wu Xinyu , Chau Kwok‐wing
Published: February 2012

Cheng, Chuntian, Jianjian Shen, Xinyu Wu, and Kwok‐wing Chau, 2012. Short‐Term Hydroscheduling with Discrepant Objectives Using Multi‐step Progressive Optimality Algorithm. Journal of the American Water Resources Association (JAWRA) 48(3): 464‐479. DOI: 10.1111/j.1752‐1688.2011.00628.x

Abstract:  With increase in the number and total capacity of hydropower plants in power systems, optimality algorithms with a single objective are not suitable for optimizing the operation of complex hydropower systems to meet complex demands. Hydropower plants should prioritize discrepant objectives, such as peak regulation and maximizing generation during solving of optimal operation problems of hydropower systems. In this article, we present a multi‐step progressive optimality algorithm (MSPOA) for the short‐term hydroscheduling (STHS) problem to improve the quality of optimal solutions and enhance the convergence speed of progressive optimality algorithm (POA). In MSPOA, the original problem is first decomposed into a sequence of problems with the longer time steps. Next, the problem with the longest time step is solved, and the optimal solution is used as the initial solution for the problem with the second longest time step. This process proceeds until the original problem with the shortest time step is solved. The proposed discrepant‐objective method and solution technique are tested for two types of hydroelectric systems. The results show that MSPOA can give better solutions and cost less time than POA due to enlarging feasible range of decision variables and reducing the number of computational stages. Discrepant objectives among hydropower plants can express the operation characteristics of complex hydropower systems more accurately than unique objective or multiple objectives.
Spatial Variability of Pool‐Tail Fines in Mountain Gravel‐Bed Stream Affects Grid‐Count Results1
Authors: Bunte Kristin , Potyondy John P. , Swingle Kurt W. , Abt Steven R.
Published: February 2012

Bunte, Kristin, John P. Potyondy, Kurt W. Swingle, and Steven R. Abt, 2012. Spatial Variability of Pool‐Tail Fines in Mountain Gravel‐Bed Stream Affects Grid‐Count Results. Journal of the American Water Resources Association (JAWRA) 48(3): 530‐545. DOI: 10.1111/j.1752‐1688.2011.00629.x

Abstract:  Fine sediment (<2 and <6 mm) particles underlying a 49‐intersection grid placed on a streambed at 25, 50, and 75% of the wetted pool‐tail width are commonly counted to assess the status and trend of aquatic ecosystems or to monitor changes in the supply of fines in mountain gravel‐bed streams. However, results vary even when crews perform nearly identical procedures. This study hypothesized that spatial variability of pool‐tail fines affects grid‐count results and that a sampling scheme can be optimized for precision and accuracy. Grid counts taken at seven evenly spaced locations across the wetted width of 10 pool tails in a pool‐riffle study stream indicated a bankward fining trend with secondary peaks of fines within the stream center. Sampling locations close to the waterlines harbored more than twice as many fines as central locations. Most of the five grid‐count schemes derived from the seven sampled locations produced significantly different results. Compared with sampling at all seven locations, schemes that focus near waterlines overpredicted fines, while those that focus on the center underpredicted them. Variability of fines among pool tails was the highest within a broad band along the waterlines; hence, focusing sampling there yielded the most variable results. The scheme sampling at 25, 50, and 75% of the wetted width had the lowest precision and moderate accuracy. Accuracy and precision of grid‐count results can be greatly improved by sampling at seven even‐spaced locations across the pool tail.
Large trees are keystone structures in urban parks
Authors: Stagoll Karen , Lindenmayer David B. , Knight Emma , Fischer Joern , Manning Adrian D.
Published: February 2012

Large trees are considered keystone structures in agricultural and forestry production landscapes, but research demonstrating this in urban landscapes is urgently needed. If large trees are keystone structures in urban parks, it is imperative that this is recognized in policy to ensure their ongoing existence. We studied the role of large native trees for birds in urban parks in Canberra, Australia. We found that (1) large trees had a consistent, strong, and positive relationship with five measures of bird diversity, and (2) as trees became larger in size, their positive effect on bird diversity increased. Large urban trees are therefore keystone structures that provide crucial habitat resources for wildlife. Hence, it is vital that they are managed appropriately. With evidence‐based tree preservation policies that recognize biodiversity values, and proactive planning for future large trees, the protection and perpetuation of these important keystone structures can be achieved.
Activation of c‐Jun N‐terminal kinase in non‐cancerous liver tissue predicts a high risk of recurrence after hepatic resection for hepatocellular carcinoma
Authors: Hagiwara Satoru , Kudo Masatoshi , Chung Hobyung , Ueshima Kazuomi , Inoue Tatsuo , Haji Seiji , Watanabe Tomohiro , Park Ah‐Mee , Munakata Hiroshi , Sakurai Toshiharu
Published: February 2012

Aim:  Hepatocellular carcinoma (HCC) ranks as the third leading cause of cancer deaths worldwide. Hepatic resection is the mainstay of curative treatment for early stage HCC. Although c‐Jun N‐terminal kinase (JNK) activation contributes to hepatocyte proliferation and HCC development in mice, the extent of involvement of JNK in human HCC development is unknown. The aim of this study is to assess the predictive value of JNK for postoperative recurrence in HCC.

Methods:  From April 2005 to March 2008, 159 patients underwent curative resection for HCC. From the 159 patients, 20 patients each matched for age, gender and etiology were registered as three groups: (i) without recurrence (no recurrence group), (ii) with recurrence within one year after surgery (early recurrence group), and (iii) with recurrence at one year or more after surgery (late recurrence group) (a cross‐sectional control study). We investigated factors contributing to postoperative early and late phase recurrence.

Results:  Multivariate analysis using a Logistic regression model showed that JNK activity in non‐cancerous liver tissue was correlated with postoperative late recurrence. (P = 0.02, odds ratio; 5.79, 95% confidence interval [CI]; 1.33–25.36).

Conclusions:  JNK activity in non‐cancerous liver tissue is considered as a reliable predictive biomarker for post‐operative recurrence in HCC.
Congenital abnormalities of the cervix in mares
Authors: Card C
Published: February 2012

The case report in this issue by Witte et al. (2012) is a description of an uncommon case of a short (3 cm) congenitally incompetent cervix associated with a pneumouterus in a 5‐year‐old maiden Quarter Horse mare with a normal 64 XX karyotype. Serial ultrasonographic examinations showed active ovaries of normal size with regular follicular activity.

The causes of congenital cervical abnormalities may be multifold. Congenital abnormalities of the cervix may be related to sporadic accidents of development, chromosomal factors, genetic abnormalities and environmental effects on phenotype. The clinician is presented with the equid's phenotype and must be familiar with the usefulness of determining the gonadal sex, sex hormone levels, cytogenetic sex and pedigree analysis.
Fatigue of Tubular Joints: Hot Spot Stress Method Revisited
Authors: Dong Pingsha , Hong Jeong K.
Published: February 2012

A series of well-known tubular joints tested in UKSORP II have been re-evaluated using the mesh-insensitive structural stress method as a part of the on-going Battelle Structural Stress JIP efforts. In this report, the structural stress based analysis procedure is first presented for applications in tubular joints varying from simple T joints, double T Joints, YT joints with overlap, and K joints with various internal stiffening configurations. The structural stress based SCFs are then compared with those obtained using traditional surface extrapolation based hot spot stress methods. Their abilities in effectively correlating the fatigue data collected from these tubular joints are demonstrated. These tests are also compared with the T curve typically used for fatigue design of tubular joints as well as the structural stress based master S-N curve adopted by ASME Section VIII Div 2. Finally, some of the implications on fracture mechanics based remaining life assessment for tubular joints are discussed in light of the results obtained in this investigation.
Preliminary Design of Bottom-Fixed Lattice Offshore Wind Turbine Towers in the Fatigue Limit State by the Frequency Domain Method
Authors: Long Haiyan , Moe Geir
Published: February 2012

The fatigue assessment of support structures is one of the most significant challenges in the design of offshore wind turbines (OWT). Fatigue analysis can be conducted in either the time-domain or the frequency-domain. The advantage of frequency-domain analysis is its time efficiency. This paper shows how the frequency domain method can be used to dimension lattice-type OWT towers such that they meet the fatigue criteria in the preliminary design stage. Two types of lattice towers, a three-legged and four-legged version, were redesigned in the fatigue limit state for the NREL 5 MW baseline wind turbine sited at a water depth of 35 m. The wall thickness of the members was chosen as the only variable and varied during the design process until the towers could survive for at least 20 years. In comparison with designs based upon ultimate strength, the mass of both types of towers increased no more than 30% when the fatigue limit state was considered. It is concluded that the lattice type structure requires only half as much material as its tubular counterpart. The three-legged tower is promising because of its simple geometry, even though it displayed a lower torsional stiffness than the four-legged tower. All the analyses in this paper were performed by an in-house FE code, intended for the early design stage of lattice towers. Once the optimum configuration is found in the early design stage, integrated time-domain analyses for the entire OWT system might be required to refine the design, taking all the nonlinear parameters into account.
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota
Authors: Iverson Vaughn , Morris Robert M. , Frazar Christian D. , Berthiaume Chris T. , Morales Rhonda L. , Armbrust E. Virginia
Published: February 2012

Mystery of an Unextreme Microbe

Metagenomics has given us glimpses into the huge diversity of microorganisms that are the engines of Earth's elemental cycling. These kinds of surveys can supply a good idea of the dominant organisms in ecosystems, but, because the majority of environmental microbes are difficult to culture and the most abundant organisms swamp metagenomes, it is difficult to discern the functional significance of other contributors.

Iverson
et al.

(p.
587
) sampled the Puget Sound and developed methods to reconstruct individual genomes from metagenomes, which allowed closure of a genome from the enigmatic marine group II
Euryarchaeota
. This Archaean is evidently motile, shows signs of extensive gene-swapping with bacteria, and offers some hints to the origin of proteorhodopsin—a molecule that some marine bacteria use to harvest energy from sunlight.
Iron Catalysts for Selective Anti-Markovnikov Alkene Hydrosilylation Using Tertiary Silanes
Authors: Tondreau Aaron M. , Atienza Crisita Carmen Hojilla , Weller Keith J. , Nye Susan A. , Lewis Kenrick M. , Delis Johannes G. P. , Chirik Paul J.
Published: February 2012

An Iron Hand for Silicon

Carbon-silicon bonds are integral to the structure of the silicone materials widely used in adhesives, cosmetics, and numerous other industrial and consumer products. Generally, platinum-based catalysts have performed best in the hydrosilylation reactions that form these bonds, but the expense of the precious metal and, in some cases, by-product formation have motivated a search for alternatives.

Tondreau
et al.

(p.
567
) now show that a class of iron compounds readily catalyzes hydrosilylation of certain commercially important substrates with rates and selectivities comparable to, or even exceeding, those associated with platinum.
When Do Incentives Corrupt?
Strings Attached
Untangling the Ethics of Incentives

by Ruth W. Grant

Russell Sage Foundation, New York, and Princeton University Press, Princeton, NJ, 2012. 220 pp. $24.95, £16.95. ISBN 9780691151601.
Authors: Cowen Tyler
Published: February 2012

Analyzing incentives in terms of power rather than as trades, Grant concludes that their use to further desired social and political goals raises some ethical concerns.
Seeing the Superfluid Transition of a Gas
Authors: Zwerger Wilhelm
Published: February 2012

The universal thermodynamic functions of a superfluid formed from a fermion gas of strongly interacting lithium atoms have been measured precisely.
Surviving in a Toxic World
Authors: Wolstenholme Adrian J.
Published: February 2012

Natural variations in a single gene of wild
C. elegans
populations confer resistance to the bacterial toxin avermectin.
Marching in Near Lock-Step
Authors: Rodbell Donald T.
Published: February 2012

A cave record from Peru closely matches climate patterns seen in cores from Greenland and the North Atlantic Ocean.
The Limits of Avian Flu Studies in Ferrets
Authors: Cohen Jon
Published: February 2012

How concerned should people be that what happened in the controversial experiments that exposed ferrets to H5N1 avian influenza viruses engineered to be more transmissible will apply to humans?
Donation Spurs a Cell Observatory—And Bigger Plans
Authors: Kaiser Jocelyn
Published: February 2012

The Broad Institute received a $32.5 million gift last week to take on one of the biggest challenges in biology: mapping the molecular "circuitry" inside several kinds of mammalian cells.
Rebuilding Wetlands by Managing the Muddy Mississippi
Authors: Gramling Carolyn
Published: February 2012

When spillways were opened to divert the flooding Mississippi last spring, scientists studying the waters sought data that might help restore the river's eroding delta.
Improved Skin Test for Differential Diagnosis of Bovine Tuberculosis by the Addition of Rv3020c-Derived Peptides
Authors: Jones Gareth J. , Whelan Adam , Clifford Derek , Coad Mick , Vordermeier H. Martin
Published: February 2012

A peptide cocktail derived from the mycobacterial antigens ESAT-6, CFP-10, and Rv3615c allowed differentiation betweenMycobacterium bovis-infected and M. bovis bacillus Calmette-Guérin (BCG)-vaccinated cattle when used as a skin test reagent for a “DIVA” test (i.e., a test capable ofdifferentiatinginfected and uninfectedvaccinatedanimals). Addition of the antigen Rv3020c improves the diagnostic sensitivity without compromising specificity in the face of BCG or Johne's disease vaccination.
β-Galactomannan and Saccharomyces cerevisiae var. boulardii Modulate the Immune Response against Salmonella enterica Serovar Typhimurium in Porcine Intestinal Epithelial and Dendritic Cells
Authors: Badia Roger , Brufau M. Teresa , Guerrero-Zamora Ana Maria , Lizardo Rosil , Dobrescu Irina , Martin-Venegas Raquel , Ferrer Ruth , Salmon Henri , Martínez Paz , Brufau Joaquim
Published: February 2012

Salmonella entericaserovar Typhimurium is a facultative intracellular pathogen that causes inflammation, necrosis, and diarrhea in pigs, as well as being an important source of food-borne diseases in humans. Probiotics and prebiotics are promising alternatives to antibiotics to control and prevent intestinal infections. The present work investigated a recently developed β-galactomannan (βGM) prebiotic compared to the proven probioticSaccharomyces cerevisiaevar.boulardiion porcine ileum intestinal epithelial cells (IECs) of the IPI-2I line and monocyte-derived dendritic cells (DCs) coculturedin vitrowithSalmonella. We observed that bothS. cerevisiaevar.boulardiiand βGM inhibited the association ofSalmonellawith IECsin vitro. Our data indicated that βGM has a higher ability thanS. cerevisiaevar.boulardiito inhibitSalmonella-induced proinflammatory mRNA (cytokines tumor necrosis factor alpha [TNF-α], interleukin-1α [IL-1α], IL-6, and granulocyte-macrophage colony-stimulating factor [GM-CSF] and chemokines CCL2, CCL20, and CXCL8) and at protein levels (IL-6 and CXCL8). Additionally, βGM andS. cerevisiaevar.boulardiiinduced some effects on DCs that were not observed on IECs: βGM andS. cerevisiaevar.boulardiishowed slight upregulation of mRNA for TNF-α, GM-CSF, and CCR7 receptor on porcine monocyte-derived dendritic cells (DCs). Indeed, the addition of βGM orS. cerevisiaevar.boulardiion DCs cocultured withSalmonellashowed higher gene expression (mRNA) for TNF-α, GM-CSF, and CXCL8 compared to that of the control withSalmonella. In conclusion, the addition of βGM inhibitsSalmonella-induced proinflammatory profiles in IECs but may promote DC activation, although associated molecular mechanisms remain to be elucidated.
Serological Diagnosis of Paracoccidioidomycosis through a Western Blot Technique
Authors: Perenha-Viana M. C. Z. , Gonzales I. A. A. , Brockelt S. R. , Machado L. N. C. , Svidzinski T. I. E.
Published: February 2012

Paracoccidioidomycosis (PCM) is a serious infectious disease that progresses toward death if untreated. Its confirmatory diagnosis is made by the detection of the fungusParacoccidioides brasiliensisin a direct mycological examination or by histopathology. However, these techniques are of low sensitivity. Serological tests seem to be more promising. The objective of this study was to test Western blot (WB) analysis using sera from patients suspected of PCM to determine whether it represents a safe and sensitive serological technique for a rapid and effective diagnosis for this disease. Sera from 517 patients were analyzed through WB analysis and double-immunodiffusion (DID) techniques using a crude exoantigen ofP. brasiliensis339. DID gave positive reactions for 140 sera (27%) and WB for 250 sera (48.4%). All sera that had a positive reaction by DID also had a positive result with a 43-kDa glycoprotein by WB analysis. Among the 377 samples that were negative by DID, 29.1% were reactive in WB analysis. For the cutoff dilution used (1:400), a positive reaction was not observed with any of the 102 sera from patients with other diseases in regions where such diseases are endemic and 30 healthy individuals tested as negative controls. These results prove WB analysis to be a sensitive technique and suggest its inclusion among routine laboratory assays as a safe method for PCM diagnosis.
Genome Sequence of the Fungus Glarea lozoyensis: the First Genome Sequence of a Species from the Helotiaceae Family
Authors: Youssar Loubna , Grüning Björn Andreas , Erxleben Anika , Günther Stefan , Hüttel Wolfgang
Published: February 2012

The anamorphic fungus
Glarea lozoyensis
mutant strain 74030 is an overproducer of pneumocandin B
0
, which is chemically converted into Cancidas, a potent antibiotic against clinically important fungal pathogens. Pneumocandins are acylated, cyclic hexapeptides with unusual hydroxylated amino acids. With the
Glarea lozoyensis
genome, the first species from the large polyphyletic family
Helotiaceae
has been sequenced.
Identification of Hepatitis C Virus Transmission Using a Next-Generation Sequencing Approach
Authors: Escobar-Gutiérrez Alejandro , Vazquez-Pichardo Mauricio , Cruz-Rivera Mayra , Rivera-Osorio Pilar , Carpio-Pedroza Juan Carlos , Ruíz-Pacheco Juan Alberto , Ruiz-Tovar Karina , Vaughan Gilberto
Published: February 2012

Here, we describe a transmission event of hepatitis C virus (HCV) among injection drug users. Next-generation sequencing (NGS) was used to assess the intrahost viral genetic variation. Deep amplicon sequencing of HCV hypervariable region 1 allowed for a detailed analysis of the structure of the viral population. Establishment of the genetic relatedness between cases was accomplished by phylogenetic analysis. NGS is a powerful tool with applications in molecular epidemiology studies and outbreak investigations.
Molecular Markers for Detection and Differentiation of Plasmodium falciparum and Plasmodium vivax in Human Blood Samples by Pyrosequencing
Authors: Lulitanond Viraphong , Intapan Pewpan M. , Tantrawatpan Chairat , Sankuntaw Nipaporn , Sanpool Oranuch , Janwan Penchom , Maleewong Wanchai
Published: February 2012

PCR amplification coupled with pyrosequencing was used to measure molecular markers that could be used to detect and differentiate
Plasmodium falciparum
and
Plasmodium vivax
in human blood samples. The detection rates were in agreement with the results of Giemsa-stained film microscopy, which is the current gold standard for detection. This method provides an exciting alternative for malaria diagnosis.
Performance of Tuberculosis Drug Susceptibility Testing in U.S. Laboratories from 1994 to 2008
Authors: Angra Pawan K. , Taylor Thomas H. , Iademarco Michael F. , Metchock Beverly , Astles J. Rex , Ridderhof John C.
Published: February 2012

We present a statistical summary of results from the Model Performance Evaluation Program (MPEP) for
Mycobacterium tuberculosis
Drug Susceptibility Testing, 1994 to 2008, implemented by the U.S. Centers for Disease Control and Prevention (CDC). During that period, a total of 57,733 test results for culture isolates were reported by 216 participating laboratories for the first-line antituberculosis drugs used in the United States—isoniazid (INH), rifampin (RMP), ethambutol (EMB), and pyrazinamide (PZA). Using Clinical Laboratory and Standards Institute (CLSI)-recommended concentrations for one or more of three methods, agar proportion (AP), BACTEC460 (Bactec), and MGIT-960 (MGIT), yielded overall agreement of 97.0% for first-line drugs. For susceptible strains, agreement was 98.4%; for resistant strains, agreement was 91.0%, with significantly lower accuracy (chi-square test,
P
< 0.0001). For resistant strains, overall agreement by methods was 91.3% for AP, 93.0% for Bactec, and 82.6% for MGIT and by drugs was 92.2% for INH, 91.5% for RMP, 79.0% for EMB, and 97.5% for PZA. For some strains, performance by method varied significantly. Use of duplicate strains in the same shipment and repeat strains over time revealed consistent performance even for strains with higher levels of interlaboratory discordance. No overall differences in performance between laboratories were observed based on volume of testing or type of facility (e.g., health department, hospital, independent). By all methods, decreased performance was observed for strains with low-level INH resistance, RMP resistance, and EMB-resistant strains. These results demonstrate a high level of performance in detection of drug-resistant
M. tuberculosis
in U.S. laboratories.
A Noncanonical mu-1A-Binding Motif in the N Terminus of HIV-1 Nef Determines Its Ability To Downregulate Major Histocompatibility Complex Class I in T Lymphocytes
Authors: Iijima Sayuki , Lee Young-Jung , Ode Hirotaka , Arold Stefan T. , Kimura Nobuyuki , Yokoyama Masaru , Sato Hironori , Tanaka Yasuhito , Strebel Klaus , Akari Hirofumi
Published: February 2012

Downregulation of major histocompatibility complex class I (MHC-I) by HIV-1 Nef protein is indispensable for evasion of protective immunity by HIV-1. Though it has been suggested that the N-terminal region of Nef contributes to the function by associating with a mu-1A subunit of adaptor protein 1, the structural basis of the interaction between Nef and mu-1A remains elusive. We found that a tripartite hydrophobic motif (Trp13/Val16/Met20) in the N terminus of Nef was required for the MHC-I downregulation. Importantly, the motif functioned as a noncanonical mu-1A-binding motif for the interaction with the tyrosine motif-binding site of the mu-1A subunit. Our findings will help understanding of how HIV-1 evades the antiviral immune response by selectively redirecting the cellular protein trafficking system.
Induced Pluripotent Stem Cell Clones Reprogrammed via Recombinant Adeno-Associated Virus-Mediated Transduction Contain Integrated Vector Sequences
Authors: Weltner J. , Anisimov A. , Alitalo K. , Otonkoski T. , Trokovic R.
Published: February 2012

Fibroblasts can be reprogrammed into induced pluripotent stem cells (iPSC) by ectopic expression of key transcription factors. Current methods for the generation of integration-free iPSC are limited by the low efficiency of iPSC generation and by challenges in reprogramming methodology. Recombinant adeno-associated virus (rAAV) is a potent gene delivery vehicle capable of efficient transduction of transgenic DNA into cells. rAAV stays mainly as an episome in nondividing cells, and the extent of integration is still poorly defined for various replicating cells. In this study, we aimed to induce iPSC from mouse and human fibroblasts by using rAAV vector-mediated transient delivery of reprogramming factors. We succeeded in deriving induced pluripotent stem cells from mouse but not human fibroblasts. Unexpectedly, the rAAV vector-mediated reprogramming led to frequent genomic integration of vector sequences during the reprogramming process, independent of the amount of virus used, and to persistent expression of reprogramming factors in generated iPSC clones. It thus appears that rAAV vectors are not compatible with the derivation of integration-free iPSC.
Characterization of the 55-Residue Protein Encoded by the 9S E1A mRNA of Species C Adenovirus
Authors: Miller Matthew S. , Pelka Peter , Fonseca Gregory J. , Cohen Michael J. , Kelly Jenna N. , Barr Stephen D. , Grand Roger J. A. , Turnell Andrew S. , Whyte Peter , Mymryk Joe S.
Published: February 2012

Early region 1A (E1A) of human adenovirus (HAdV) has been the focus of over 30 years of investigation and is required for the oncogenic capacity of HAdV in rodents. Alternative splicing of the E1A transcript generates mRNAs encoding multiple E1A proteins. The 55-residue (55R) E1A protein, which is encoded by the 9S mRNA, is particularly interesting due to the unique properties it displays relative to all other E1A isoforms. 55R E1A does not contain any of the conserved regions (CRs) present in the other E1A isoforms. The C-terminal region of the 55R E1A protein contains a unique sequence compared to all other E1A isoforms, which results from a frameshift generated by alternative splicing. The 55R E1A protein is thought to be produced preferentially at the late stages of infection. Here we report the first study to directly investigate the function of the species C HAdV 55R E1A protein during infection. Polyclonal rabbit antibodies (Abs) have been generated that are capable of immunoprecipitating HAdV-2 55R E1A. These Abs can also detect HAdV-2 55R E1A by immunoblotting and indirect immunofluorescence assay. These studies indicate that 55R E1A is expressed late and is localized to the cytoplasm and to the nucleus. 55R E1A was able to activate the expression of viral genes during infection and could also promote productive replication of species C HAdV. 55R E1A was also found to interact with the S8 component of the proteasome, and knockdown of S8 was detrimental to viral replication dependent on 55R E1A.
Paramyxovirus V Proteins Interact with the RNA Helicase LGP2 To Inhibit RIG-I-Dependent Interferon Induction
Authors: Childs Kay , Randall Richard , Goodbourn Stephen
Published: February 2012

RIG-I and mda-5 are activated by viral RNA and stimulate type I interferon production. Laboratory of genetics and physiology 2 (LGP2) shares homology with RIG-I and mda-5 but lacks the CARD domains required for signaling. The V proteins of paramyxoviruses limit interferon induction by binding mda-5 and preventing its activation; however, they do not bind RIG-I and have not been considered inhibitors of RIG-I signaling. Here we uncover a novel mechanism of RIG-I inhibition in which the V protein of parainfluenzavirus type 5 (PIV5; formerly known as simian virus type 5 [SV5]) interacts with LGP2 and cooperatively inhibits induction by RIG-I ligands. A complex between RIG-I and LGP2 is observed in the presence of PIV5-V, and we propose that this complex is refractory to activation by RIG-I ligands. The V proteins from other paramyxoviruses also bind LGP2 and demonstrate LGP2-dependent inhibition of RIG-I signaling. This is significant, because it demonstrates a general mechanism for the targeting of the RIG-I pathway by paramyxoviruses.
Transmission of Influenza B Viruses in the Guinea Pig
Authors: Pica Natalie , Chou Yi-Ying , Bouvier Nicole M. , Palese Peter
Published: February 2012

Epidemic influenza is typically caused by infection with viruses of the A and B types and can result in substantial morbidity and mortality during a given season. Here we demonstrate that influenza B viruses can replicate in the upper respiratory tract of the guinea pig and that viruses of the two main lineages can be transmitted with 100% efficiency between inoculated and naïve animals in both contact and noncontact models. Our results also indicate that, like in the case for influenza A virus, transmission of influenza B viruses is enhanced at colder temperatures, providing an explanation for the seasonality of influenza epidemics in temperate climates. We therefore present, for the first time, a small animal model with which to study the underlying mechanisms of influenza B virus transmission.
Disulfide Linkages Mediating Nucleocapsid Protein Dimerization Are Not Required for Porcine Arterivirus Infectivity
Authors: Zhang Rong , Chen Chunyan , Sun Zhi , Tan Feifei , Zhuang Jinshan , Tian Debin , Tong Guangzhi , Yuan Shishan
Published: February 2012

The nucleocapsid (N) proteins of the North American (type II) and European (type I) genotypes of porcine reproductive and respiratory syndrome virus (PRRSV) share only approximately 60% genetic identity, and the functionality of N in both genotypes, especially its role in virion assembly, is still poorly understood. In this study, we demonstrated that the ORF7 3′ untranslated region or ORF7 of type I is functional in the type II PRRSV background. Based on these results, we postulated that the cysteine at position 90 (Cys90) of the type II N protein, which corresponds to an alanine in the type I protein, is nonessential for virus infectivity. The replacement of Cys90 with alanine confirmed this hypothesis. We then hypothesized that all of the cysteines in the N protein could be replaced by alanines. Mutational analysis revealed that, in contradiction to previously reported findings, the replacement of all of the cysteines, either singly or in combination, did not impair the growth of either type II or type I PRRSV. Treatment with the alkylating agent
N
-ethylmaleimide inhibited cysteine-mediated N dimerization in living cells but not in released virions. Additionally, bimolecular fluorescence complementation assays revealed noncovalent interactions in living cells among the N and C termini and between the N-terminal and C-terminal regions of the N proteins of both genotypes of PRRSV. These results demonstrate that the disulfide linkages mediating the N dimerization are not required for PRRSV viability and help to promote our understanding of the mechanism underlying arterivirus particle assembly.