bluuebunny/crossref_metadata_2025 huggingface dataset:
Restaurant Organizational Forms and Community in the U.S. in 2005
Authors: Carroll Glenn R. , Torfason Magnus Thor
Published: February 2011

Recent sociological theory and research highlights food, drink, and restaurants as culturally meaningful and related to social identity. An implication of this view holds that the prevalence of corporate chain restaurants affects the sociological character of communities, as many activists, popular–based movements, and theorists contend. The analysis we report here seeks to identify the ecological niche properties of chain and independent restaurants—which kinds of communities support restaurant chains, and which kinds of communities tend to support independent local restaurants and food service providers instead. We analyze data from a 2005 sample of 49 counties across the United States with over 17,000 active restaurants. We argue that demographic stability affects the community composition of organizational forms, and we also investigate arguments about a community's income distribution, age distribution, population trends, geographic sprawl, and commuter population. We find that communities with less stable demographic make–ups support more chain restaurants, but that other factors, including suburban sprawl and public transit commuter, also have some impact.
Repealing Federal Oversight of State Health Policy: Lessons from the Boren Amendment
Authors: Miller Edward Alan
Published: February 2011

The Boren Amendment is frequently cited as an example where judicial involvement markedly shaped the implementation of federal legislation. Unlike other controversial health policies, Boren was eventually rescinded by Congress. Results indicate that the Amendment was repealed because changing socioeconomic, political, and programmatic conditions combined with policy‐oriented learning to facilitate a shift in policy venue away from the judiciary toward the President and Congress. This is because during the devolutionary climate of the mid‐to‐late 1990s, both the executive and legislature proved more conducive to the policy image promulgated by state officials that the Amendment unnecessarily restricted state discretion, than the policy image promulgated by providers that without the Amendment, low reimbursement levels would compromise access and quality. Data for this analysis derive from archival documents, secondary sources, and 101 interviews with state and federal experts.
Confronting the Governance Challenges of Developing Nigeria's Extractive Industry: Policy and Performance in the Oil and Gas Sector1
Authors: Okpanachi Eyene
Published: February 2011

The issue of economic growth and human development has been a central concern in the oil and gas sector of Nigeria's extractive industry, and this has featured prominently in the agitations and generalized restiveness in the Niger Delta, the oil‐producing region. While many studies have focused on these problems, policies aimed at confronting them have not received much broad attention. This article bridges this research gap by holistically focusing on the solution to the problem. In doing this, the article examines the policies during the Obasanjo administration from 1999 to 2007 in order to critically assess the efficacy or inefficiency of the policies in reversing the general problem now known as the “resource curse,” and to offer a better understanding of the deeper political, social, and economic issues that drive outcomes. The article finds that while significant efforts were made to avoid the boom and bust cycle of oil and lower volatility by de‐linking public expenditure from oil revenue through the “oil‐price‐based fiscal rule,” generally, progress in this area was not matched by improvement in the other areas examined by this study, notably peace and safety of lives and oil/gas installations, the development of the oil‐producing region, environmental security and sustainability, and the transparent and accountable use of oil/gas revenues.
Modelling recombinations during cosmological reionization
Authors: Raičević Milan , Theuns Tom
Published: February 2011

An ionization front expanding into a neutral medium can be slowed down significantly by recombinations. In cosmological numerical simulations the recombination rate is often computed using a ‘clumping factor’ that takes into account that not all scales in the simulated density field are resolved. Here we demonstrate that using a single value of the clumping factor significantly overestimates the recombination rate, and how a local estimate of the clumping factor is both easy to compute, and gives significantly better numerical convergence. We argue that this lower value of the recombination rate is more relevant during the reionization process and hence that the importance of recombinations during reionization has been overestimated.
EFFICACY OF SODIUM HYPOCHLORITE AND QUATERNARY AMMONIUM COMPOUNDS ON YEASTS ISOLATED FROM APPLE JUICE
Authors: BRUGNONI LORENA INÉS , LOZANO JORGE ENRIQUE , CUBITTO MARÍA AMELIA
Published: February 2011

In this work, we evaluated the effectiveness of sodium hypochlorite and a commercial quaternary ammonium compound against four wild yeast strains in their different growth forms: planktonic, sessile and forming microcolonies. These yeasts had been isolated from apple juice processing plant, and appropriate environmental conditions were employed throughout the work. For planktonic cells, 4 log reduction was obtained using the lowest concentration of sodium hypochlorite (200 ppm) on all tested strains. However, quaternary ammonium chloride was effective only on Zygosaccharomyces sp. in all in‐use concentrations tested, and only the stronger in‐use concentration (1:30) was effective on Rhodotorula mucilaginosa. Because of the above results, the disinfection on sessile yeast cells was performed only with sodium hypochlorite solutions. In cells attached in batch conditions, the highest concentration of sodium hypochlorite (500 ppm) was necessary to get 4 log reduction. In order to obtain a 3 log reduction on Zygosaccharomyces sp. microcolonies formed in laminar flow conditions, the combined action of 0.5% w/v NaOH and 500 ppm sodium hypochlorite was required. We concluded, thus, that cells forming microcolonies under laminar flow conditions were less susceptible to disinfectants than those suspended or attached in batch conditions. These results also indicated that attachment and colonization of autochthonous yeasts must be properly identified to evaluate the effectiveness of disinfectants used in apple juice processing plants.

PRACTICAL APPLICATIONS

Biofilm formation is a serious hygienic problem in food industry. In fruit processing plants, the microbial attachment causes serious engineering problems such as decreases in permeate flow in membrane processes, greatly reducing operating efficiency of ultrafiltration process. Moreover, the presence of microorganisms attached to food contact surfaces could increase the fluid frictional resistance of surfaces, increases the corrosion rate of surfaces leading to energy and production losses and compromises the hygienic quality of the final product causing significant economic losses. Our results show that the evaluation of the effectiveness of a disinfectant on biofilms should be performed using a method where the adhesion and colonization of cells was carried out in flow conditions similar to those of the environment where the disinfectant is applied. We observed that even when using new surfaces, and performing both cleaning and sanitizing under optimal conditions, the risk that the number of viable cells remaining on the surface can generate a new biofilm subsists.
MICROENCAPSULATED LYCOPENE FOR PRE‐EXTRUSION COLORING OF FOODS
Authors: CHOUDHARI SHEETAL , BAJAJ ISHWAR , SINGHAL REKHA , KARWE MUKUND
Published: February 2011

The effect of extrusion conditions on the retention of lycopene during extrusion of rice flour, chosen as a model, was evaluated as a function of moisture content, screw speed and die temperature by response surface methodology using central composite rotatable design (CCRD). Experiments were carried out by extrusion of rice flour containing 1% lycopene microcapsules and free lycopene equivalent to that present in the microcapsules, using a single‐screw extruder at a constant feed rate of 55 g/min. At all conditions of extrusion, the microencapsulated lycopene gave better retention of color in the extrudates than the free lycopene. The quadratic model developed by CCRD showed a good agreement between the experimental and predicted values of color. The storage stability of microencapsulated lycopene increased twofold as compared to free lycopene over a period of 96 h.

PRACTICAL APPLICATIONS

This work evaluates the potential of free lycopene in comparison with microencapsulated lycopene in a 1:3 blend of gum Arabic and a modified starch (n‐octenyl succinic anhydride or n‐OSA), as pre‐extrusion coloring of rice flour extrudate.
INFLUENCE OF DRYING METHOD ON THE REHYDRATION PROPERTIES OF APRICOT AND APPLE
Authors: CONTRERAS CAROLINA , MARTÍN‐ESPARZA MARÍA EUGENIA , MARTÍNEZ‐NAVARRETE NURIA
Published: February 2011

This study aims to determine the influence of microwave drying coupled with air drying of apricot and apple in terms of the rehydration rate and capacity of dried samples. The microwave power level was 0.4 W/g for apricot and 0.5 W/g for apple samples. The effect of air temperature (50 and 30C) and vacuum impregnation pretreatment (with a commercial isotonic juice) was examined. The sample mass change, water gain and soluble solids loss, were obtained before sample rehydration (in distilled water at 20C for 8 h). Peleg's model was used to assess the effect of process conditions on rehydration kinetics, with a good fit of the experimental data. Taking into account the lower values for Peleg's constants of k1(i) and k2(i), the vacuum impregnation pretreatment and microwave application to air drying allow us to obtain a dried product with a better rehydration capacity, promoting the rate and capacity of water gain and solute loss, although the structure of product remains with a lower liquid phase retention capacity. A less relevant influence of air temperature on water gain kinetics was observed, improving the rehydration ratio only for nonvacuum‐impregnated samples.

PRACTICAL APPLICATIONS

Dehydration is widely applied to food preservation in stable and safe conditions. Dried and rehydrated fruits are key ingredients in dairy products, breakfast cereals, dietetic foods formulated for people suffering from physiological disorders or for healthy people with additional needs and traditional foods such as puddings, desserts, cakes, biscuits. Rehydration product behavior must be known when a total or partial reconstitution is required. This work provides information on the influence of microwave‐assisted air drying method and vacuum impregnation pretreatment on the rehydration capacity and kinetic analysis of dried apricot and apple, in order to obtain rehydrated foods in accordance with the requirements in further processing and consumer expectations.
A Case Study on the Evaluation and Implementation of Green and Sustainable Remediation Principles and Practices During a RCRA Corrective Action Cleanup
Authors: Petruzzi Nick M.
Published: February 2011

Green and Sustainable Remediation (GSR) principles and practices were incorporated into various phases of the remediation life cycle during a Resource Conservation and Recovery Act (RCRA) Corrective Action cleanup. GSR best management practices (BMPs) were identified and employed to the extent possible during the investigation, remedy evaluation, and remedy implementation phases of the cleanup. As part of the remedy evaluation phase, potential remedial alternatives were evaluated against GSR principles and practices to support the selection of a preferred remedial alternative. This included the identification of inherent GSR similarities within the five existing RCRA balancing criteria and the development of a sixth new balancing criterion. The sixth criterion consisted of five relevant GSR categories, including consumption of resources and materials, CO2 emissions, waste minimization and reuse, community benefit, and corporate image and corporate sustainability. Because of the lack of consensus, the constantly evolving nature, and limited guidance associated with GSR, various GSR‐related uncertainties and barriers were encountered. These uncertainties and barriers primarily related to the development of a GSR evaluation approach; contractual mechanisms; worker routines; regulatory agency support; and facility benefits, incentives, and recognition. In an effort to overcome some of these uncertainties and barriers, professional judgment was used to support various decision‐making processes. The GSR evaluation and implementation approaches considered are discussed in this case study as well as the various uncertainties and barriers encountered. In general, this case study provides a successful demonstration of GSR, given guidance limitations, facility permit constraints, complexities associated with site‐specific conditions, and a situation where the most feasible options were not considered the most green and sustainable (primarily because of their energy‐intensive nature, resource consumption, or waste generation).
Evaluating fluorescence and ultraviolet photometry to assess dissolved organic matter removal during coagulation–flocculation
Authors: Droh Lanciné Gone , Bamory Kamagate , Raymond Ligban , Issiaka Savane , Jean Biemi
Published: February 2011

Ultraviolet absorption at 254 nm (UV254) and peaks (A, C and T) fluorescence intensities were evaluated to assess dissolved organic carbon (DOC) removal during coagulation–flocculation. The consistency of fluorescence data was checked to ensure that no inner filter effect, quenching or enhanced intensities affected the data. The decreases in UV254 and peak intensities were calculated in percentage terms between raw and clarified water and compared with measured DOC removal. The results indicate that peak A, peak C, peak T and UV254 exhibit strong linear relationships (R2: 0.91, 0.89, 0.92 and 0.99, respectively) with DOC removal, implying that these parameters are useful indicators of DOC removal.
What Gets Measured, Gets Changed: Evaluating Law and Policy for Maximum Impact
Authors: Chriqui Jamie F. , O'Connor Jean C. , Chaloupka Frank J.
Published: February 2011

Does law matter regarding public health outcomes? Regardless of what one may think about the answer to this age-old question, in recent years the public health community has increasingly demonstrated and recognized the roles that public health laws and policies play in effectuating long-lasting and broad-based population-wide changes. Public health laws and policies have been instrumental in the following ways: reducing smoking prevalence; reducing underage alcohol-related drinking, driving, crashes, and fatalities; reducing exposure to second-hand smoke; eliminating vaccine–associated paralytic poliomyelitis (VAPP); increasing seat-belt use and reducing traffic fatalities; reducing dental carries; and reducing access to and consumption of unhealthy foods and beverages sold in schools and to reductions in caloric intake and overweight. In fact, in a review of the ten greatest public health achievements in the 20th century, all were influenced by policy change.
Global Public Health Legal Responses to H1N1
Authors: Gable Lance , Courtney Brooke , Gatter Robert , Kinney Eleanor D.
Published: February 2011

Pandemics challenge the law and often highlight its strengths or expose its limits. The novel strain of influenza A (H1N1) virus that emerged in the spring of 2009 and rapidly spread around the globe was no exception. The H1N1 pandemic prompted the first significant application of a number of international legal and policy mechanisms that have been developed in the last decade to respond to this kind of event. Furthermore, it presented a considerable test for public health systems at all levels, from global to local.

Although initial predictions forecasting high morbidity and mortality from this virus overestimated its eventual impact, the human toll of the pandemic was nevertheless significant. The World Health Organization (WHO) reported approximately 1.5 million people were infected worldwide in 214 countries, resulting in over 25,000 confirmed deaths, but the actual health impact of the outbreak was certainly much higher.
Protecting the Mental Health of First Responders: Legal and Ethical Considerations
Authors: Rutkow Lainie , Gable Lance , Links Jonathan M.
Published: February 2011

The public safety, human services, health, and relief workers who comprise the first wave of a response to natural or man-made disasters play a critical role in emergency preparedness. These first responders provide care and services in the immediate aftermath of emergencies and may remain in affected communities for weeks or months. They often work long hours under stressful conditions, witnessing the human harms, physical destruction, and psychological devastation that can accompany disasters.
Right to Health Litigation and HIV/AIDS Policy
Authors: Meier Benjamin Mason , Yamin Alicia Ely
Published: February 2011

Domestic litigation has become a principal strategy for realizing international treaty obligations for the human right to health, providing causes of action for the public’s health and empowering individuals to raise human rights claims for HIV prevention, treatment, and care. In the past 15 years, advocates have laid the groundwork on which a rapidly expanding enforcement paradigm has arisen at the intersection of human rights litigation and HIV/AIDS policy. As this enforcement develops across multiple countries, human rights are translated from principle to practice in the global response to HIV/AIDS, transforming aspirational declarations into justiciable obligations and implementing human rights through national policies and programs.
Diagnostic test of rifampicin resistance in mycobacterium tuberculosis: a meta‐analysis
Authors: MA Bin , Qi Guo‐qin , Li Hai‐ming , ZHU Bing‐dong , YANG Ke‐hu
Published: February 2011

Objective To evaluate available evidence on the diagnostic value of radioactivity‐free cultivation and detection technologies for rapid detection of rifampicin resistance in Mycobacterium tuberculosis.

Methods A fully recursive literature search was conducted in PubMed, EMBASE, Biosis, Web of Science (all 1990–2010), CBMWeb (1978–2010), and Google Scholar. QUADAS items were used to evaluate the quality of included studies. Sensitivity, specificity, Summary receiver‐operating curve SEN, SPE, SROC, and related techniques were used to assess the diagnostic value of radioactivity‐free Mycobacterium tuberculosis cultivation and detection technologies.

Results Six studies were included in the final analysis. The MB/BacT, BACTEC MGIT 960, and Manual MGIT systems were highly sensitive and specific for detecting rifampicin‐resistant TB. The summary SEN and summary SPE of the MB/BacT and BACTEC MGIT 960 systems were 100%, 99%, 100%, and 96%, respectively. The SROC of the BACTEC MGIT 960 system was 0.9943.

Conclusion We recommended that the BACTEC 460 system be replaced by MB/BacT or BACTEC MGIT 960 as the final diagnostic test for rifampicin resistance in Mycobacterium tuberculosis. More studies are needed on the diagnostic value of other radioactivity‐free cultivation and detection technologies to reliably determine their sensitivity and specificity for this bacterium.
Promise of Urinary Nerve Growth Factor for Assessment of Overactive Bladder Syndrome
Authors: KUO Hann‐Chorng , LIU Hsin‐Tzu , GUAN Zhonghong , TYAGI Pradeep , CHANCELLOR Michael B.
Published: February 2011

Overactive bladder syndrome (OAB) is highly prevalent bladder disorder in men and women. About 10–15% of the population suffers from urgency frequency with or without urgency urinary incontinence. It is estimated that 50–75% of patients with OAB may have urodynamic detrusor overactivity (DO). Urodynamic study invasive and most of the OAB patients might not accept it as a routine assessment. Therefore, a more objective and non‐invasive test for diagnosis and assessing DO from OAB patients is needed. Recently, urinary nerve growth factor (NGF) has gained great interest in detecting DO in patients with OAB. Urinary NGF level was found to increase in OAB and urodynamic DO. Urinary NGF levels correlated with severity of OAB symptoms. Patients with either idiopathic or neurogenic DO may have increased urinary NGF levels. Urinary NGF levels have been shown to decrease in patients with patients with OAB and DO who have been well treated with antimuscarinics or botulinum toxin injection, but not in those with persistent OAB after treatment. Not all patients with OAB can have an elevated urinary NGF level; it may also be increased in patients with interstitial cystitis/painful bladder syndrome and other lower urinary tract diseases, suggesting urinary NGF expression could be a product of bladder inflammation and a limited specificity of urinary NGF for diagnosing DO. The source of urinary NGF has not yet been fully explored yet. Nevertheless, urinary NGF level is likely to be a promising biomarker for diagnosis of DO from OAB patients, to monitor therapeutic outcome and predict disease progression.
Thunder Bay Transportation: A Case of Business Valuation and Negotiation*
Authors: Lento Camillo
Published: February 2011

Thunder Bay Transportation (TBT) is a very versatile case that can be used in several milieus and at various levels of difficulty. The case describes the process involved in the purchase and sale of a private business. Mr. Getzko, owner/manager of TBT, is attempting to sell his business to pursue retirement. Sudbury Systems (SS) is pursuing an acquisition of TBT. Students are required to assume the role of either Mr. Getzko’s accountants (seller) or Sudbury Systems’ accountants (buyer) to: (1) develop a preliminary business value, (2) negotiate adjustments, and (3) arrive at an agreed‐upon business value to finalize the sale. Students will explore both business valuation approaches (earnings based and asset based) and various business valuation concepts (e.g., normalized earnings, sustaining capital reinvestment, earnings multiple, redundant assets, etc.).
Deciphering the nebular and asteroidal record of silicates and organic material in the matrix of the reduced CV3 chondrite Vigarano
Authors: ABREU Neyda M. , BREARLEY Adrian J.
Published: February 2011

Abstract–

We have conducted scanning electron microscope (SEM) and transmission electron microscope (TEM) studies of a variety of occurrences of matrix in the reduced CV3 chondrite breccia Vigarano. Matrix, which occurs as clastic interchondrule material and finer‐grained rims, is dominated by morphologically variable olivines that host submicron, hercynitic spinel, and carbonaceous inclusions. Clastic matrix and fine‐grained rims show significant differences in their olivine morphologies, abundance, and composition of olivine inclusions, and characteristics of the carbonaceous matter. We suggest that these differences are the result of different degrees of alteration of clastic matrix and rims and are not due to variability in their precursor materials. Textural and compositional characteristics of olivine in the matrix are consistent with formation by growth, possibly from an amorphous precursor material during asteroidal metamorphism, in the presence of limited quantities of aqueous fluids. Spinel inclusions in olivine may be nebular condensates that acted as seeds for nucleation of olivine or may have formed during metamorphism and were subsequently overgrown by olivine. Carbonaceous material occurs as nanometer‐sized inclusions within olivine in both fine‐grained rims and clastic matrix, but is most abundant as 100–200 nm grains, interstitial to matrix olivines. Most carbonaceous material is amorphous, but poorly graphitized carbon (PGC) also occurs as a minor component in both olivine inclusions and interstitial C. The widespread occurrence of fine‐grained amorphous carbon grains in the interstitial regions between olivine grains may preserve the distribution and grain size of nebular organic material. No clear textural relationships exist between carbonaceous grains and the other mineralogical components of Vigarano matrix that could help constrain the origin of the organic grains (i.e., evidence for Fischer‐Tropsch‐type reactions). Finally, there are considerable differences between matrix olivines in Vigarano in comparison with those in oxidized CV3 chondrites. In particular, the mineralogy and morphology of the matrix olivines and the nature, composition, and distribution of inclusions in the olivine grains are distinct. Based on these differences, we conclude that matrix in the oxidized CV3 chondrites could not have formed by thermal processing of Vigarano‐like material.
Meteorites from the United Arab Emirates: Description, weathering, and terrestrial ages
Authors: HEZEL Dominik C. , SCHLÜTER Jochen , KALLWEIT Heiko , JULL A. J. Timothy , AL FAKEER Osama Y. , AL SHAMSI Mubarak , STREKOPYTOV S.
Published: February 2011

Abstract–

We report on the first meteorite search campaign in the United Arab Emirates (UAE). The geology and proximity of our search region suggest that it is the north‐western extension of the Oman meteorite fields. We found 26 ordinary chondrites, bringing the total number of official meteorites from the UAE to 28. The campaign was organized and conducted in close cooperation with the UAE government and the main masses of the meteorites remained in the country where they will become part of an exhibition. The bulk composition of five meteorite and three soil samples indicates an uptake of U, Mo, Sr, Ba, Li, and Pb from the soil into the meteorites during terrestrial weathering. Terrestrial ages determined from14C decay of 21 meteorites range from recent falls to 24.4 ka, with two meteorites having >37 ka and approximately 39 ka, respectively. Weak correlations between weathering degree, meteorite bulk chemical composition, and terrestrial age suggest highly localized weathering conditions, possibly related to abundant occurrences of sabkhas in the search region.
A Mixed‐Method Study: Assessing the BAR Model's Impact on Preservice Teachers' Efficacy Beliefs
Authors: Rethlefsen Ann Lyle , Park Hyesung
Published: February 2011

This study took place at a mid‐sized, Midwestern university located in a mid‐sized town. The researchers developed the BAR model to teach mathematics methods both in the classroom and in the field. The preservice teachers took Enochs, Smith, and Huinker's Mathematics Teaching Efficacy Beliefs Instrument (MTEBI) on the first and last day of class. A total of 297 responses were collected from the pre‐ and posttests, with 280 matching responses, which were then used for data analysis. Mixed methods were used to analyze qualitative and quantitative data. The researchers sought to determine if the specific teaching methods from the BAR model led to positive changes in preservice teacher efficacy beliefs. They also explored if efficacy beliefs changed as a result of field experiences. Preservice teachers' efficacy scores changed positively on every item on the MTEBI. The researchers also determined that there was an increase in preservice teachers' outputs as a result of their field experiences.
Public Perceptions of International Development and Support for Aid in the UK: Results of a Qualitative Enquiry
Authors: Henson Spencer , Lindstrom Johanna , Haddad Lawrence , Mulmi Rajendra
Published: February 2011

Aid budgets face immense pressure – despite overseas aid being critical for poverty alleviation in developing countries and the explicit commitments of the world's industrialised countries to the Millennium Development Goals (MDGs). Public support for international development and aid will play a key role. Will the public become unsure about the UK's aid budget when they begin to feel cuts in government expenditure at home? How well equipped are we to ‘sell’ the UK's aid programme to a sceptical public in times of economic austerity? This working paper presents the results of a qualitative enquiry into public perceptions of international development and aid in the UK. Using data from the Mass Observation Project (MOP) at the University of Sussex, the authors investigate the views of 185 members of the general public.

The study finds that, while people can conjure up ideas of why poverty exists, they know very little about the confluence of factors that actually drive poverty and/or the daily lives of the poor. Thus, poverty is seen as caused primarily by bad governments and natural disasters, almost as a stereotype. People have major doubts about the effectiveness of aid, perhaps reflecting the fact that they tend to be much better at picturing aid ‘failure’ than aid ‘success’. Nonetheless, there is support for aid in principle; people think that the UK has a responsibility to help the poor in developing countries, primarily on ethical grounds.

This research has clear implications for the way in which the UK communicates with the British public about aid and development and the authors suggest a more considered approach that recognises the complexities of aid and is honest about what works and what doesn't. The paper concludes with a call for further research to fill the knowledge gaps that still exist about the drivers of public support for development and how those drivers can be influenced.
An Approach for Acceleration Analysis of Lower Mobility Parallel Manipulators
Authors: Liu Haitao , Huang Tian , Chetwynd Derek G.
Published: February 2011

This paper presents a new approach to the velocity and acceleration analyses of lower mobility parallel manipulators. Building on the definition of the “acceleration motor,” the forward and inverse velocity and acceleration equations are formulated such that the relevant analyses can be integrated under a unified framework that is based on the generalized Jacobian. A new Hessian matrix of serial kinematic chains (or limbs) is developed in an explicit and compact form using Lie brackets. This idea is then extended to cover parallel manipulators by considering the loop closure constraints. A 3-PRS parallel manipulator with coupled translational and rotational motion capabilities is analyzed to illustrate the generality and effectiveness of this approach.
Climate Data Challenges in the 21st Century
Authors: Overpeck Jonathan T. , Meehl Gerald A. , Bony Sandrine , Easterling David R.
Published: February 2011

Climate data are dramatically increasing in volume and complexity, just as the users of these data in the scientific community and the public are rapidly increasing in number. A new paradigm of more open, user-friendly data access is needed to ensure that society can reduce vulnerability to climate variability and change, while at the same time exploiting opportunities that will occur.
Embryological Evidence Identifies Wing Digits in Birds as Digits 1, 2, and 3
Authors: Tamura Koji , Nomura Naoki , Seki Ryohei , Yonei-Tamura Sayuri , Yokoyama Hitoshi
Published: February 2011

Digit identities in living birds are the same as in three-fingered dinosaurs, in agreement with paleontological evidence.
K
+
Channel Mutations in Adrenal Aldosterone-Producing Adenomas and Hereditary Hypertension
Authors: Choi Murim , Scholl Ute I. , Yue Peng , Björklund Peyman , Zhao Bixiao , Nelson-Williams Carol , Ji Weizhen , Cho Yoonsang , Patel Aniruddh , Men Clara J. , Lolis Elias , Wisgerhof Max V. , Geller David S. , Mane Shrikant , Hellman Per , Westin Gunnar , Åkerström Göran , Wang Wenhui , Carling Tobias , Lifton Richard P.
Published: February 2011

Potassium channel mutations drive both cell growth and hormone production in an adrenal tumor that causes severe hypertension.
Leishmania
RNA Virus Controls the Severity of Mucocutaneous Leishmaniasis
Authors: Ives Annette , Ronet Catherine , Prevel Florence , Ruzzante Giulia , Fuertes-Marraco Silvia , Schutz Frederic , Zangger Haroun , Revaz-Breton Melanie , Lye Lon-Fye , Hickerson Suzanne M. , Beverley Stephen M. , Acha-Orbea Hans , Launois Pascal , Fasel Nicolas , Masina Slavica
Published: February 2011

An RNA virus of a parasite binds to human Toll-like receptor 3 and modulates host immune responses to the parasite.
Metaknowledge
Authors: Evans James A. , Foster Jacob G.
Published: February 2011

The growth of electronic publication and informatics archives makes it possible to harvest vast quantities of knowledge about knowledge, or “metaknowledge.” We review the expanding scope of metaknowledge research, which uncovers regularities in scientific claims and infers the beliefs, preferences, research tools, and strategies behind those regularities. Metaknowledge research also investigates the effect of knowledge context on content. Teams and collaboration networks, institutional prestige, and new technologies all shape the substance and direction of research. We argue that as metaknowledge grows in breadth and quality, it will enable researchers to reshape science—to identify areas in need of reexamination, reweight former certainties, and point out new paths that cut across revealed assumptions, heuristics, and disciplinary boundaries.
The Eukaryotic Ribosome
Authors: Ramakrishnan V.
Published: February 2011

New crystal structures break impasse, offer insight into how eukaryotes synthesize proteins.
What Will Drive Genomics Over the Next 10 Years?
Authors: Caplan Arthur
Published: February 2011

Most thought that the ability to predict an individual’s risk of developing diseases would drive the use of genomic information. That did not turn out to be so.
Personal Genomes: For One and for All
Authors: Wang Jun
Published: February 2011

A personal genome benefits not only one individual, but all humanity.
The Disappearing Third Dimension
Authors: Rowe Timothy , Frank Lawrence R.
Published: February 2011

Three-dimensional computing is driving what many would call a revolution in scientific visualization. However, its power and advancement are held back by the absence of sustainable archives for raw data and derivative visualizations. Funding agencies, professional societies, and publishers each have unfulfilled roles in archive design and data management policy.
Coming Soon to a Lab Near You: Drag-and-Drop Virtual Worlds
Authors: Service Robert F.
Published: February 2011

Researchers at Microsoft hope to convince scientists that transparent, easy-to-tweak numerical simulations are as straightforward as clicking a mouse.
Rescue of Old Data Offers Lesson for Particle Physicists
Authors: Curry Andrew
Published: February 2011

Old data tends to get forgotten as physicists move on to new and better machines. The tale of the JADE experiment suggests that they should be more careful.
Detection of Group 1 Trypanosoma brucei gambiense by Loop-Mediated Isothermal Amplification
Authors: Njiru Z. K. , Traub R. , Ouma J. O. , Enyaru J. C. , Matovu E.
Published: February 2011

Trypanosoma brucei gambiense
group 1 is the major causative agent of the Gambian human African trypanosomiasis (HAT). Accurate diagnosis of Gambian HAT is still challenged by lack of precise diagnostic methods, low and fluctuating parasitemia, and generally poor services in the areas of endemicity. In this study, we designed a rapid loop-mediated isothermal amplification (LAMP) test for
T. b. gambiense
based on the 3′ end of the
T. b. gambiense
-specific glycoprotein (TgsGP) gene. The test is specific and amplifies DNA from
T. b. gambiense
isolates and clinical samples at 62°C within 40 min using a normal water bath. The analytical sensitivity of the TgsGP LAMP was equivalent to 10 trypanosomes/ml using purified DNA and ∼1 trypanosome/ml using supernatant prepared from boiled blood, while those of classical PCR tests ranged from 10 to 10
3
trypanosomes/ml. There was 100% agreement in the detection of the LAMP product by real-time gel electrophoresis and the DNA-intercalating dye SYBR green I. The LAMP amplicons were unequivocally confirmed through sequencing and analysis of melting curves. The assay was able to amplify parasite DNA from native cerebrospinal fluid (CSF) and double-centrifuged supernatant prepared from boiled buffy coat and bone marrow aspirate. The robustness, superior sensitivity, and ability to inspect results visually through color change indicate the potential of TgsGP LAMP as a future point-of-care test.
Standardization of Hepatitis E Virus (HEV) Nucleic Acid Amplification Technique-Based Assays: an Initial Study To Evaluate a Panel of HEV Strains and Investigate Laboratory Performance
Authors: Baylis Sally A. , Hanschmann Kay-Martin , Blümel Johannes , Nübling C. Micha
Published: February 2011

The performance of hepatitis E virus (HEV) RNA nucleic acid amplification (NAT)-based assays has been investigated using a panel of HEV-containing plasma samples. The panel comprised 22 HEV-positive plasma samples representing 10-fold serial dilutions of HEV genotypes 3a, 3b, 3f, and 4c obtained from blood donors. Two negative-control plasma samples were included. All samples were blinded. The plasma samples were prepared as liquid/frozen materials and distributed to participants on dry ice. Laboratories were requested to test the panel using their routine HEV assays and to score samples as either positive or negative and could optionally return data in copies/ml for HEV RNA. Twenty laboratories from 10 different countries participated in the study. Data were returned by all participating laboratories; 10 laboratories returned quantitative data. All assays except one were developed in-house using conventional or real-time reverse transcriptase PCR (RT-PCR) methodologies. There was a 100- to 1,000-fold difference in sensitivity between the majority of assays, independent of the virus strain. Although the quantitative data were limited, for the samples in the range of ∼6 to 4 log
10
copies/ml, the standard deviations of the geometric means of the samples ranged between 0.38 and 1.09. Except for one equivocal result, HEV RNA was not detected in the negative samples. The variability of assay sensitivity highlights the need for the standardization of HEV RNA NAT assays.
Assembly of Helper-Dependent Adenovirus DNA into Chromatin Promotes Efficient Gene Expression
Authors: Ross P. Joel , Kennedy Michael A. , Christou Carin , Risco Quiroz Milagros , Poulin Kathy L. , Parks Robin J.
Published: February 2011

Helper-dependent adenovirus (hdAd) vectors have shown tremendous potential in animal models of human disease in numerous preclinical studies. Expression of a therapeutic transgene can be maintained for several years after a single administration of the hdAd vector. However, despite the long-term persistence of hdAd DNA in the transduced cell, little is known of the fate and structure of hdAd DNA within the host nucleus. In this study, we have characterized the assembly of hdAd DNA into chromatin in tissue culture. Eviction of the Ad DNA-packaging protein VII, histone deposition, and vector-associated gene expression all began within 2 to 6 h of host cell transduction. Inhibition of transcription elongation through the vector DNA template had no effect on the loss of VII, suggesting that transcription was not necessary for removal of the majority of protein VII. Vector DNA assembled into physiologically spaced nucleosomes within 6 h. hdAd vectors incorporated the histone H3 variant H3.3, which was dependent on the histone chaperone HIRA. Knockdown of HIRA reduced hdAd association with histones and reduced expression of the vector-carried transgene by 2- to 3-fold. Our study elucidates an essential role for hdAd DNA chromatinization for optimal vector gene expression.
Soluble Respiratory Syncytial Virus Fusion Protein in the Fully Cleaved, Pretriggered State Is Triggered by Exposure to Low-Molarity Buffer
Authors: Chaiwatpongsakorn Supranee , Epand Raquel F. , Collins Peter L. , Epand Richard M. , Peeples Mark E.
Published: February 2011

The paramyxovirus fusion (F) glycoprotein is anchored in the virion membrane in a metastable, pretriggered form. Once triggered, the F protein undergoes a dramatic conformational extension that inserts its hydrophobic fusion peptide into the target cell membrane, then folds back on itself to bring the membranes together and initiate fusion. Unlike most other paramyxoviruses, the respiratory syncytial virus (RSV) F protein alone is sufficient to mediate membrane fusion and virus infection. To study the triggering mechanism of the RSV F protein, we have generated a soluble F (sF) protein by replacing the transmembrane and cytoplasmic tail domains with a 6His tag. The sF protein is secreted efficiently from 293T cells in a fully cleaved form. It is recognized by neutralizing monoclonal antibodies, appears spherical by electron microscopic analysis, and is not aggregated, all consistent with a native, pretriggered trimer. The sF protein was purified on a Ni
+2
column and eluted with 50 mM phosphate buffer containing 500 mM NaCl and 250 mM imidazole. Dialysis against 10 mM buffer caused the sF protein to trigger, forming “hat pin”-shaped molecules that aggregated as rosettes, characteristic of the posttriggered form. Further dialysis experiments indicated that the efficiency of triggering correlated well with the reduction of buffer molarity. Reduction of buffer molarity by dilution also resulted in exposure of the fusion peptide, as detected by liposome association, confirming sF protein triggering. Mutation of the furin cleavage site adjacent to the fusion peptide prevented liposome association, further confirming that association is via the fusion peptide.
Oligonucleotide Motifs That Disappear during the Evolution of Influenza Virus in Humans Increase Alpha Interferon Secretion by Plasmacytoid Dendritic Cells
Authors: Jimenez-Baranda Sonia , Greenbaum Benjamin , Manches Olivier , Handler Jesse , Rabadán Raúl , Levine Arnold , Bhardwaj Nina
Published: February 2011

CpG motifs in an A/U context have been preferentially eliminated from classical H1N1 influenza virus genomes during virus evolution in humans. The hypothesis of the current work is that CpG motifs in a uracil context represent sequence patterns with the capacity to induce an immune response, and the avoidance of this immunostimulatory signal is the reason for the observed preferential decline. To analyze the immunogenicity of these domains, we used plasmacytoid dendritic cells (pDCs). pDCs express pattern recognition receptors, including Toll-like receptor 7 (TLR7), which recognizes guanosine- and uridine-rich viral single-stranded RNA (ssRNA), including influenza virus ssRNA. The signaling through TLR7 results in the induction of inflammatory cytokines and type I interferon (IFN-I), an essential process for the induction of specific adaptive immune responses and for mounting a robust antiviral response mediated by IFN-α. Secretion of IFN-α is also linked to the activation of other immune cells, potentially amplifying the effect of an initial IFN-α secretion. We therefore also examined the role of IFN-α-driven activation of NK cells as another source of selective pressure on the viral genome. We found direct evidence that CpG RNA motifs in a U-rich context control pDC activation and IFN-α-driven activation of NK cells, likely through TLR7. These data provide a potential explanation for the loss of CpG motifs from avian influenza viruses as they adapt to mammalian hosts. The selective decrease of CpG motifs surrounded by U/A may be a viral strategy to avoid immune recognition, a strategy likely shared by highly expressed human immune genes.
The Changing Role of mTOR Kinase in the Maintenance of Protein Synthesis during Human Cytomegalovirus Infection
Authors: Clippinger Amy J. , Maguire Tobi G. , Alwine James C.
Published: February 2011

The mammalian target of rapamycin (mTOR) kinase occurs in mTOR complex 1 (mTORC1) and complex 2 (mTORC2), primarily differing by the substrate specificity factors raptor (in mTORC1) and rictor (in mTORC2). Both complexes are activated during human cytomegalovirus (HCMV) infection. mTORC1 phosphorylates eukaryotic initiation factor 4E (eIF4E)-binding protein (4E-BP1) and p70S6 kinase (S6K) in uninfected cells, and this activity is lost upon raptor depletion. In infected cells, 4E-BP1 and S6K phosphorylation is maintained when raptor or rictor is depleted, suggesting that either mTOR complex can phosphorylate 4E-BP1 and S6K. Studies using the mTOR inhibitor Torin1 show that phosphorylation of 4E-BP1 and S6K in infected cells depends on mTOR kinase. The total levels of 4E-BP1 and viral proteins representative of all temporal classes were lowered by Torin1 treatment and by raptor, but not rictor, depletion, suggesting that mTORC1 is involved in the production of all classes of HCMV proteins. We also show that Torin1 inhibition of mTOR kinase is rapid and most deleterious at early times of infection. While Torin1 treatment from the beginning of infection significantly inhibited translation of viral proteins, its addition at later time points had far less effect. Thus, with respect to mTOR's role in translational control, HCMV depends on it early in infection but can bypass it at later times of infection. Depletion of 4E-BP1 by use of short hairpin RNAs (shRNAs) did not rescue HCMV growth in Torin1-treated human fibroblasts as it has been shown to in murine cytomegalovirus (MCMV)-infected 4E-BP1
−/−
mouse embryo fibroblasts (MEFs), suggesting that during HCMV infection mTOR kinase has additional roles other than phosphorylating and inactivating 4E-BP1. Overall, our data suggest a dynamic relationship between HCMV and mTOR kinase which changes during the course of infection.
Kaposi's Sarcoma-Associated Herpesvirus Bacterial Artificial Chromosome Contains a Duplication of a Long Unique-Region Fragment within the Terminal Repeat Region
Authors: Yakushko Yuri , Hackmann Christian , Günther Thomas , Rückert Jessica , Henke Marc , Koste Lars , Alkharsah Khaled , Bohne Jens , Grundhoff Adam , Schulz Thomas F. , Henke-Gendo Cornelia
Published: February 2011

Use of the Kaposi's sarcoma-associated herpesvirus (KSHV) bacterial artificial chromosome 36 (KSHV-BAC36) genome permits reverse genetics approaches to study KSHV biology. While sequencing the complete KSHV-BAC36 genome, we noted a duplication of a 9-kb fragment of the long unique region in the terminal repeat region. This duplication covers a part of open reading frame (ORF) 19, the complete ORFs 18, 17, 16, K7, K6, and K5, and the putative ORF in the left origin of lytic replication, and it contains the BAC cassette. This observation needs to be kept in mind if viral genes located within the duplicated region are to be mutated in KSHV-BAC36.
The IRF-3/Bax-Mediated Apoptotic Pathway, Activated by Viral Cytoplasmic RNA and DNA, Inhibits Virus Replication
Authors: Chattopadhyay Saurabh , Yamashita Michifumi , Zhang Ying , Sen Ganes C.
Published: February 2011

Induction of apoptosis in cells infected by Sendai virus (SeV), which triggers the cytosolic RIG-I pathway, requires the presence of interferon regulatory factor 3 (IRF-3). Independent of IRF-3's transcriptional role, a novel IRF-3 activation pathway causes its interaction with the proapoptotic protein Bax and its mitochondrial translocation to induce apoptosis. Here we report that two other RNA viruses, vesicular stomatitis virus (VSV) and encephalomyocarditis virus (EMCV), may also activate the same pathway. Moreover, cytosolic DNA, produced by adenovirus or introduced by transfection, activated the pathway in an RNA polymerase III-dependent fashion. To evaluate the contribution of this newly discovered apoptotic pathway to the host's overall antiviral response, we measured the efficiencies of replication of various viruses
in vitro
and viral pathogenesis
in vivo
, using cells and mice that are selectively deficient in components required for the apoptotic pathway of IRF-3. Our results clearly demonstrate that the IRF-3/Bax-mediated apoptotic signaling branch contributes significantly to the host's protection from viral infection and consequent pathogenesis.