bluuebunny/crossref_metadata_2025 huggingface dataset:
The Influence of Digital Surface Model Choice on Visibility‐based Mobile Geospatial Applications
Authors: Meek Sam , Goulding James , Priestnall Gary
Published: April 2013

In this work we investigate the effectiveness of different types of visibility models for use within location‐based services. This article outlines the methodology and results for our experiments, which were designed to understand the accuracy and effects of model choices for mobile visibility querying. Harnessing a novel mobile media consumption and authoring application called Zapp, the levels of accuracy of various digital surface representations used by a line of sight visibility algorithm are extensively examined by statistically assessing randomly sampled viewing sites across the 1 km2 study area, in relation to points of interest (POI) across the University of Nottingham campus. Testing was carried out on three different surface models derived from 0.5 m LiDAR data by visiting physical sites on each surface model with 14 random point of interest masks being viewed from between 10 and 16 different locations, totalling 190 data points. Each site was ground‐truthed by determining whether a given POI could be seen by the user and could also be identified by the mobile device. Our experiments in a semi‐urban area show that choice of surface model has important implications for mobile applications that utilize visibility in geospatial query operations.
Developments in Research on Mathematical Practice and Cognition
Authors: Pease Alison , Guhe Markus , Smaill Alan
Published: April 2013

We describe recent developments in research on mathematical practice and cognition and outline the nine contributions in this special issue of topiCS. We divide these contributions into those that address (a) mathematical reasoning: patterns, levels, and evaluation; (b) mathematical concepts: evolution and meaning; and (c) the number concept: representation and processing.
Perception of low red:far‐red ratio compromises both salicylic acid‐ and jasmonic acid‐dependent pathogen defences in Arabidopsis
Authors: de Wit Mieke , Spoel Steven H. , Sanchez‐Perez Gabino F. , Gommers Charlotte M. M. , Pieterse Corné M. J. , Voesenek Laurentius A. C. J. , Pierik Ronald
Published: April 2013

In dense stands of plants, such as agricultural monocultures, plants are exposed simultaneously to competition for light and other stresses such as pathogen infection. Here, we show that both salicylic acid (SA)‐dependent and jasmonic acid (JA)‐dependent disease resistance is inhibited by a simultaneously reduced red:far‐red light ratio (R:FR), the early warning signal for plant competition. Conversely, SA‐ and JA‐dependent induced defences did not affect shade‐avoidance responses to low R:FR. Reduced pathogen resistance by low R:FR was accompanied by a strong reduction in the regulation of JA‐ and SA‐responsive genes. The severe inhibition of SA‐responsive transcription in low R:FR appeared to be brought about by the repression of SA‐inducible kinases. Phosphorylation of the SA‐responsive transcription co‐activator NPR1, which is required for full induction of SA‐responsive transcription, was indeed reduced and may thus play a role in the suppression of SA‐mediated defences by low R:FR‐mediated phytochrome inactivation. Our results indicate that foraging for light through the shade‐avoidance response is prioritised over plant immune responses when plants are simultaneously challenged with competition and pathogen attack.
Self‐rescue of an EXTENSIN mutant reveals alternative gene expression programs and candidate proteins for new cell wall assembly in Arabidopsis
Authors: Saha Prasenjit , Ray Tui , Tang Yuhong , Dutta Indrajit , Evangelous Nicole R. , Kieliszewski Marcia J. , Chen Yuning , Cannon Maura C.
Published: April 2013

Plants encode a poorly understood superfamily of developmentally expressed cell wall hydroxyproline‐rich glycoproteins (HRGPs). One, EXTENSIN3 (EXT3) of the 168 putative HRGPs, is critical in the first steps of new wall assembly, demonstrated by broken and misplaced walls in its lethal homozygous mutant. Here we report the findings of phenotypic (not genotypic) revertants of the ext3 mutant and in‐depth analysis including microarray and qRT‐PCR (polymerase chain reaction). The aim was to identify EXT3 substitute(s), thus gaining a deeper understanding of new wall assembly. The data show differential expression in the ext3 mutant that included 61% (P ≤ 0.05) of the HRGP genes, and ability to self‐rescue by reprogramming expression. Independent revertants had reproducible expression networks, largely heritable over the four generations tested, with some genes displaying transgenerational drift towards wild‐type expression levels. Genes for nine candidate regulatory proteins as well as eight candidate HRGP building materials and/or facilitators of new wall assembly or maintenance, in the (near) absence of EXT3 expression, were identified. Seven of the HRGP fit the current model of EXT function. In conclusion, the data on phenotype comparisons and on differential expression of the genes‐of‐focus provide strong evidence that different combinations of HRGPs regulated by alternative gene expression networks, can make functioning cell walls, resulting in (apparently) normal plant growth and development. More broadly, this has implications for interpreting the cause of any mutant phenotype, assigning gene function, and genetically modifying plants for utilitarian purposes.
Spline representation of irregular and malformed stem profiles of broadleaved tree species in White Carpathian Mountains
Authors: Kuželka Karel , Marušák Róbert
Published: April 2013

The paper deals with representation of individual stem profiles of beech and oak in White Carpathian Mountains, Czech Republic. Due to complicacy and irregularity of stem profiles of most trees common taper functions are not applicable for individual stem profile description. Selected spline functions were used to model the irregular stem profiles. To fit complicated stem profiles with a spline more input points are needed than for regular stems. The splines were computed using four fixed input points representing diameters in four conventional heights (base diameter, stump diameter, DBH and the height) and another two input points interactively added to describe the location of the most significant malformation. More input points were added in respect of the malformation position. To evaluate the accuracy of each spline a number of stems have been measured. For each stem diameters with interspaces of 0.2 m have been measured from the base to the top. At each measurement position predicted diameters with the real value were compared. Five different statistical indicators were used to evaluate the accuracy of the spline models. The profiles were the best represented by Catmull-Rom spline with tangent vector length corrections. Previously frequently used natural cubic spline is not suitable for irregular stems. When interpolating complicated stem profiles it suffers from oscillation considerably more than for regular stems of coniferous species.
Diversity of small mammals synusias of the open forest sites of the Beskydy and Jeseníky Mts.
Authors: Čepelka L. , Suchomel J. , Purchart L. , Heroldová M.
Published: April 2013

Small mammal communities were studies in tree plantations in 2007-2011. The monitoring was conducted at 18 plots in the Jeseníky Mts. and 18 plots in the Beskydy Mts. using snap traps placed in lines. A total of 588 individuals of 10 species were captured in the Jeseníky Mts. and 577 individuals of 13 species in the Beskydy Mts. The Beskydy lot encompassed 5 insectivorous species and 8 rodent species, 4 of them eudominant (Apodemus flavicollis, D=43.33 %; Clethrionomys glareolus, D=21.49 %; Microtus agrestis, D=18.54 %; and Sorex araneus, D=10.05 %), one subdominant (Apodemus sylvaticus, D=2.77 %), two recedent (Microtus arvalis, D=1.39 %; Muscardinus avellanarius, D=1.04 %) and six sub-recedent (Microtus subterraneus and Sorex minutus: D=0.35 % and Apodemus agrarius, Neomys anomalus, Sorex alpinus and Talpa europea: D=0.17 %). The occurrence of 3 insectivorous species and 7 rodent species was confirmed in the Jeseníky Mts. Four species were eudominant (A. flavicollis, D=30.1 %; Clethrionomys glareolus, D=27.04 %; Microtus agrestis, D=24.49 %; and S. araneus, D=12.59 %), one species subdominant (Microtus arvalis; D=3.57 %), five species sub-recedent (A. sylvaticus, D=0.68 %; Crocidura suaveolens and Microtus subterraneus: D=0.34 %, Muscardinus avellanarius and S. minutus: D=0.17 %). According to the employed indexes, the total biodiversity was slightly higher in the Jeseníky Mts. (H=1.53; d=0.76; E=0.66) than in the Beskydy Mts. (H=1.52; d=0.72; E=0.59). The structure of the small mammal communities was strongly affected by the herb layer composition.
Differences in acid phosphomonoesterase activity in forest soils of the Smrk Massive in the Moravskoslezské Beskydy Mts. (Czech Republic)
Authors: Bajer A. , Samec P. , Žárník M.
Published: April 2013

The purpose of this paper is to determine the individual relations between APEA and specific soils and environmental factors. To disclose these relations, analysis of component vectors and principal component analysis (PCA) were performed. Vectors of soil characteristics with participation of APEA (aAKFE) and vectors of pedochemical variables (aCHEM) were also calculated. Their ratio (ia) indicated the relative size of the APEA impact on the relations between pedochemical characteristics. Based on the statistical analyses, different role of APEA in Norway spruce and in European beech stands was detected. While APEA in spruce stands did not show significant correlations with the other examined soil chemical properties, soils under beech stands displayed strong correlations with some of the pedochemical variables. The idea of this research is to find out whether APEA could be used as an indicator of forest vegetation status and of the anthropogenic load on a site.
Biomass of dwarf pine in the Orlické hory Mountains
Authors: Dušek D. , Novák J. , Kacálek D. , Slodičák M.
Published: April 2013

In order to evaluate weight and nutrients content in dwarf pine biomass, sample trees were taken for destructive analysis in the formerly air-polluted Orlické Hory Mountains. Investigated stand of dwarf pine was planted in 1988–1989 within clear-cut at elevation 1060–1110 m (NW aspect, Sorbeto - Piceetum). Totally 29,000 kg.ha-1 of dry biomass was accumulated in the stand. Above-ground biomass accounts for 27,000 kg (needles 8,000 kg and wood 19,000 kg) and main root biomass represents ca 2,000 kg.ha-1. The biomass of dwarf pine stand contained following amounts of nutrients per hectare: 153 kg of Nitrogen (from this 64 % in needles, 27 % in wood and 8 % in roots), 14.5 kg of Phosphorus (52 % in needles), 46 kg of Potassium (52 % in needles), 22 kg of Calcium (45 % in needles) and 15 kg of Magnesium (40 % in needles and 44 % in wood).
Laminar Flow Forced Convection Heat Transfer Behavior of a Phase Change Material Fluid in Microchannels
Authors: Kondle Satyanarayana , Alvarado Jorge L. , Marsh Charles
Published: April 2013

In this paper, a phase change material (PCM) fluid (N-eicosane) is compared with pure water as heat transfer fluid. The heat transfer behavior of PCM fluid under laminar flow conditions (Reynolds number of 700) in circular and rectangular microchannels was studied numerically. In the numerical study, an effective specific heat model was used to take into account the phase change process. Heat transfer results for circular and rectangular microchannels with PCM fluid were obtained under hydrodynamically and thermally fully developed conditions. A PCM fluid in microchannels with aspect ratios of 1 to 2, 1 to 4, and 1 to 8 was found to enhance the thermal behavior of microchannels which can be beneficial in a host of cooling applications. The flow was assumed to be hydrodynamically fully developed at the inlet and thermally developing inside the microchannel. Heat transfer characteristics of PCM slurry flow in microchannels have been studied under three types of wall boundary conditions including constant axial heat flux with constant peripheral temperature (H1), constant heat flux with variable peripheral temperature (H2), and constant wall temperature (T) boundary condition. The fully developed Nusselt number was found to be higher for H1 than for H2 and T boundary conditions for all the geometries. Moreover, Nusselt number also increased with aspect ratio and was sensitive to the variations in effective specific heat.
Dissimilarity of Turbulent Fluxes of Momentum and Heat in Perturbed Turbulent Flows
Authors: Pasinato H. D.
Published: April 2013

The dissimilarity between the Reynolds stresses and the heat fluxes in perturbed turbulent channel and plane Couette flows was studied using direct numerical simulation. The results demonstrate that the majority of the dissimilarity was due to the difference between the wall-normal fluxes, while the difference between the streamwise fluxes was lower. The main causes for the dissimilarity were the production terms, followed by the velocity-pressure interaction terms. Further insights into the importance of the velocity-pressure interaction in the origin of the dissimilarity are provided using two-point correlation. Furthermore, an octant conditional averaged dataset reveals that not only the wall-normal heat flux but also the streamwise heat flux is strongly related to the wall-normal gradient of the mean temperature. A simple Reynolds-averaged Navier–Stokes (RANS) heat flux model is proposed as a function of the Reynolds stresses. A comparison of the direct numerical simulation data with an “a priori” prediction suggests that this simple model performs reasonably well.
Note on a New Blackbody Fraction Function Used for Surfaces With a Linear Emissivity in a Wavelength Interval
Authors: Jing Wei , Fang Tiegang
Published: April 2013

In this note, a new blackbody radiation fraction function is proposed for calculating the emissive power or total emissivity of a surface that has an emissivity depending linearly on wavelength in a wavelength interval. This new fraction function is expressed as a function of the product of wavelength and temperature and the numerical values are tabulated. Based on the new defined fraction function, the emissive power in a given wavelength interval can be calculated very conveniently combined with the traditional blackbody radiation fraction function. This new function can be used in many practical applications with good accuracy without numerical integration.
Magnetohydrodynamics Thermocapillary Marangoni Convection Heat Transfer of Power-Law Fluids Driven by Temperature Gradient
Authors: Lin Yanhai , Zheng Liancun , Zhang Xinxin
Published: April 2013

This paper presents an investigation for magnetohydrodynamics (MHD) thermocapillary Marangoni convection heat transfer of an electrically conducting power-law fluid driven by temperature gradient. The surface tension is assumed to vary linearly with temperature and the effects of power-law viscosity on temperature fields are taken into account by modified Fourier law for power-law fluids (proposed by Pop). The governing partial differential equations are converted into ordinary differential equations and numerical solutions are presented. The effects of the Hartmann number, the power-law index and the Marangoni number on the velocity and temperature fields are discussed and analyzed in detail.
On the Anomalous Convective Heat Transfer Enhancement in Nanofluids: A Theoretical Answer to the Nanofluids Controversy
Authors: Yang C. , Li W. , Sano Y. , Mochizuki M. , Nakayama A.
Published: April 2013

A theoretical answer to the controversial issue on the anomalous convective heat transfer in nanofluids has been provided, exploiting the Buongiorno model for convective heat transfer in nanofluids with modifications to fully account for the effects of nanoparticle volume fraction distributions on the continuity, momentum, and energy equations. A set of exact solutions have been obtained for hydrodynamically and thermally fully developed laminar nanofluid flows in channels and tubes, subject to constant heat flux. From the solutions, it has been concluded that the anomalous heat transfer rate, exceeding the rate expected from the increase in thermal conductivity, is possible in such cases as titania–water nanofluids in a channel, alumina–water nanofluids in a tube and also titania–water nanofluids in a tube. Moreover, the maximum Nusselt number based on the bulk mean nanofluid thermal conductivity is captured when the ratio of Brownian and thermophoretic diffusivities is around 0.5, which can be exploited for designing nanoparticles for high-energy carriers.
Critical Invalidation of Temperature Dependence of Nanofluid Thermal Conductivity Enhancement
Authors: Han Kisoo , Lee Wook-Hyun , Kleinstreuer Clement , Koo Junemo
Published: April 2013

Of interest is the accurate measurement of the enhanced thermal conductivity of certain nanofluids free from the impact of natural convection. Owing to its simplicity, wide range of applicability and short response time, the transient hot-wire method (THWM) is frequently used to measure the thermal conductivity of fluids. In order to gain a sufficiently high accuracy, special care should be taken to assure that each measurement is not affected by initial heat supply delay, natural convection, and signal noise. In this study, it was found that there is a temperature limit when using THWM due to the incipience of natural convection. The results imply that the temperature-dependence of the thermal conductivity enhancement observed by other researchers might be misleading when ignoring the impact of natural convection; hence, it could not be used as supporting evidence of the effectiveness of micromixing due to Brownian motion. Thus, it is recommended that researchers report how they keep the impact of the natural convection negligible and check the integrity of their measurements in the future researches.
Frequency Response of Laminated Glass Elements: Analytical Modeling and Effective Thickness
Authors: Aenlle M. L. , Pelayo F.
Published: April 2013

Laminated glass elements are sandwich structures where the glass presents linear-elastic behavior, whereas the polymer interlayer is, in general, a linear-viscoelastic material. Several analytical models have been proposed since the 1950s to determine the response of laminated glass elements to both frequency and thermal conditions. In this paper, it is proved that Ross, Kerwin, and Ungar's model can be considered as a particular case of the Mead and Markus model when the exponential decay rate per unit length is neglected. The predictions of these models are compared with those obtained from operational modal tests carried out on a laminated glass beam at different temperatures. Finally, a new effective thickness for the dynamic behavior of laminated glass beams, which allows the determination of the dynamic response using a simple monolithic elastic model, is proposed.
GammaPod—A new device dedicated for stereotactic radiotherapy of breast cancer
Authors: Yu Cedric X. , Shao Xinyu , Zhang Jin , Regine William , Zheng Mike , Yu Ying S. , Deng Jianchun , Duan Zhengcheng
Published: April 2013

Purpose:

This paper introduces a new external beam radiotherapy device named GammaPod that is dedicated for stereotactic radiotherapy of breast cancer.

Methods:

The design goal of the GammaPod as a dedicated system for treating breast cancer is the ability to deliver ablative doses with sharp gradients under stereotactic image guidance. Stereotactic localization of the breast is achieved by a vacuum‐assisted breast immobilization cup with built‐in stereotactic frame. Highly focused radiation is achieved at the isocenter due to the cross‐firing from 36 radiation arcs generated by rotating 36 individual Cobalt‐60 beams. The dedicated treatment planning system optimizes an optimal path of the focal spot using an optimization algorithm borrowed from computational geometry such that the target can be covered by 90%–95% of the prescription dose and the doses to surrounding tissues are minimized. The treatment plan is intended to be delivered with continuous motion of the treatment couch. In this paper the authors described in detail the gamma radiation unit, stereotactic localization of the breast, and the treatment planning system of the GammaPod system.

Results:

A prototype GammaPod system was installed at University of Maryland Medical Center and has gone through a thorough functional, geometric, and dosimetric testing. The mechanical and functional performances of the system all meet the functional specifications.

Conclusions:

An image‐guided breast stereotactic radiotherapy device, named GammaPod, has been developed to deliver highly focused and localized doses to a target in the breast under stereotactic image guidance. It is envisioned that the GammaPod technology has the potential to significantly shorten radiation treatments and even eliminate surgery by ablating the tumor and sterilizing the tumor bed simultaneously.
Injectable, Cellular-Scale Optoelectronics with Applications for Wireless Optogenetics
Authors: Kim Tae-il , McCall Jordan G. , Jung Yei Hwan , Huang Xian , Siuda Edward R. , Li Yuhang , Song Jizhou , Song Young Min , Pao Hsuan An , Kim Rak-Hwan , Lu Chaofeng , Lee Sung Dan , Song Il-Sun , Shin GunChul , Al-Hasani Ream , Kim Stanley , Tan Meng Peun , Huang Yonggang , Omenetto Fiorenzo G. , Rogers John A. , Bruchas Michael R.
Published: April 2013

The Smaller, the Better

New semiconductor device technology enables injection of light-emitting diodes, silicon devices, actuators, and sensors at precisely controlled locations within biological tissues, such as the brain.

Kim
et al.

(p.
211
) show how wireless control of animal models using these technologies and the techniques of optogenetics provide new insights into basic behavioral neuroscience.
Mandibular Remains Support Taxonomic Validity of
Australopithecus sediba
Authors: de Ruiter Darryl J. , DeWitt Thomas J. , Carlson Keely B. , Brophy Juliet K. , Schroeder Lauren , Ackermann Rebecca R. , Churchill Steven E. , Berger Lee R.
Published: April 2013

Since the announcement of the species
Australopithecus sediba
, questions have been raised over whether the Malapa fossils represent a valid taxon or whether inadequate allowance was made for intraspecific variation, in particular with reference to the temporally and geographically proximate species
Au
.
africanus
. The morphology of mandibular remains of
Au. sediba
, including newly recovered material discussed here, shows that it is not merely a late-surviving morph of
Au. africanus
. Rather—as is seen elsewhere in the cranium, dentition, and postcranial skeleton—these mandibular remains share similarities with other australopiths but can be differentiated from the hypodigm of
Au. africanus
in both size and shape as well as in their ontogenetic growth trajectory.
The Upper Limb of
Australopithecus sediba
Authors: Churchill Steven E. , Holliday Trenton W. , Carlson Kristian J. , Jashashvili Tea , Macias Marisa E. , Mathews Sandra , Sparling Tawnee L. , Schmid Peter , de Ruiter Darryl J. , Berger Lee R.
Published: April 2013

The evolution of the human upper limb involved a change in function from its use for both locomotion and prehension (as in apes) to a predominantly prehensile and manipulative role. Well-preserved forelimb remains of 1.98-million-year-old
Australopithecus sediba
from Malapa, South Africa, contribute to our understanding of this evolutionary transition. Whereas other aspects of their postcranial anatomy evince mosaic combinations of primitive (australopith-like) and derived (
Homo
-like) features, the upper limbs (excluding the hand and wrist) of the Malapa hominins are predominantly primitive and suggest the retention of substantial climbing and suspensory ability. The use of the forelimb primarily for prehension and manipulation appears to arise later, likely with the emergence of
Homo erectus
.
Comment on “Apatite
4
He/
3
He and (U-Th)/He Evidence for an Ancient Grand Canyon”
Authors: Karlstrom Karl E. , Lee John , Kelley Shari , Crow Ryan , Young Richard A. , Lucchitta Ivo , Beard L. Sue , Dorsey Rebecca , Ricketts Jason W. , Dickinson William R. , Crossey Laura
Published: April 2013

Flowers and Farley (Reports, 21 December 2012, p. 1616; published online 29 November 2012) propose that the Grand Canyon is 70 million years old. Starkly contrasting models for the age of the Grand Canyon—70 versus 6 million years—can be reconciled by a shallow paleocanyon that was carved in the eastern Grand Canyon 25 to 15 million years ago (Ma), negating the proposed 70 Ma and 55 Ma paleocanyons. Cooling models and geologic data are most consistent with a 5 to 6 Ma age for western Grand Canyon and Marble Canyon.
Enantioselective Synthesis of Pactamycin, a Complex Antitumor Antibiotic
Authors: Malinowski Justin T. , Sharpe Robert J. , Johnson Jeffrey S.
Published: April 2013

Preparing Pactamycin

Microbially derived organic compounds often have remarkably intricate structures that confer striking bioactivity, but such complexity may become an impediment to drug development. Pactamycin is one such case—a potent antibiotic used to probe ribosome structure and function that in its native form is too cytotoxic for therapeutic application.

Malinowski
et al.

(p.
180
; see the Perspective by

Codelli and Reisman

) present a 15-step laboratory-scale synthesis of this molecule that offers prospects for the generation of structural analogs that could facilitate further exploratory medicinal research.
Persistent LCMV Infection Is Controlled by Blockade of Type I Interferon Signaling
Authors: Teijaro John R. , Ng Cherie , Lee Andrew M. , Sullivan Brian M. , Sheehan Kathleen C. F. , Welch Megan , Schreiber Robert D. , Carlos de la Torre Juan , Oldstone Michael B. A.
Published: April 2013

INTERFER(ON)ing Persistence

During persistent viral infections, a dysregulated immune response fails to control the infection.

Wilson
et al.

(p.
202
) and

Teijaro
et al.

(p.
207
; see the Perspective by

Odorizzi and Wherry

) show this occurs because type I interferons (IFN I), critical for early responses to viral infection, contribute to the altered immunity seen during persistent infection. Antibody blockade of IFN I signaling during chronic lymphocytic choriomeningitis virus (LCMV) in mice resulted in reduced viral titers at later stages of infection, reduced expression of inhibitory immune molecules and prevented the disruptions to secondary lymphoid organs typically observed during persistent infection with LCMV. Whether type I IFNs are also detrimental to persistent viral infection humans, such as HIV and hepatitis C virus, remains to be determined.
Self-Medication in Animals
Authors: de Roode Jacobus C. , Lefèvre Thierry , Hunter Mark D.
Published: April 2013

Animal self-medication against parasites is more widespread than previously thought, with profound implications for host-parasite biology.
Nature's True Self
Nature's Oracle
The Life and Work of W. D. Hamilton

by Ullica Segerstrale

Oxford University Press, Oxford, 2013. 459 pp. S35, £25. ISBN 9780198607274.
Authors: Boomsma Jacobus J.
Published: April 2013

In this biography of the often controversial evolutionary biologist W. D. Hamilton, Segerstrale argues for the importance of his version of Darwinism.
An Important Anniversary
Authors: Cicerone Ralph J.
Published: April 2013

One hundred fifty years ago, on 22 April 1863, the U.S. National Academy of Sciences (NAS) held its first meeting. The founding of the academy was but one of an impressive array of federal actions that would prepare the United States of America for a bright future. During the dark days of 1862 and 1863, mired in a bloody and intense Civil War, Congress passed, and President Lincoln signed, the Morrill Act, creating a system of Land Grant Colleges. The Act greatly enhanced access to higher education for Americans and promoted scientific and technical research in the coming generations. In the same period, Congress authorized the completion of the Transcontinental Railroad, and President Lincoln issued the Emancipation Proclamation. Only a few months later, President Lincoln and Congress took another major step to advance the young nation by creating NAS, a bold way to elevate American science and to incorporate science into the U.S. future. This was a remarkable set of government actions during very tough times.
A Decade After SARS, China's Flu Response Wins Cautious Praise
Authors: Hvistendahl Mara
Published: April 2013

Coming at the 10-year anniversary of the SARS outbreak, the Chinese government's announcement that a new influenza virus is killing people elicited suspicion from many Chinese, but scientists are praising the country this time around.
A Human Smile and Funny Walk for
Australopithecus sediba
Authors: Gibbons Ann
Published: April 2013

New analyses
detail many traits shared with our genus
Homo
, in the spine, vertebral column, knee, teeth, and jaws.
Pesky Perchlorates All Over Mars
Authors: Kerr Richard A.
Published: April 2013

Curiosity rover has discovered perchlorates in equatorial Gale crater, implying that they carpet the martian surface and explaining why the rover stumbled in its first search for organic traces of ancient martian life.
More Support for an Ocean in Enceladus
Authors: Kerr Richard A.
Published: April 2013

Researchers argued that the latest Cassini observations make sense if liquid water is escaping from a deep ocean through cracks in Enceladus's outer ice shell.
The Alveolar Microenvironment of Patients Infected with Human Immunodeficiency Virus Does Not Modify Alveolar Macrophage Interactions with Streptococcus pneumoniae
Authors: Gordon Stephen B. , Jagoe R. Thomas , Jarman Elizabeth R. , North James C. , Pridmore Alison , Musaya Janelisa , French Neil , Zijlstra Eduard E. , Molyneux Malcolm E. , Read Robert C.
Published: April 2013

We tested the hypothesis that HIV infection results in activation of alveolar macrophages and that this might be associated with impaired defense against pneumococcus. We compared alveolar macrophages and lymphocytes in 131 bronchoalveolar lavage samples from HIV-infected and healthy controls using inflammatory gene microarrays, flow cytometry, real-time PCR, and enzyme-linked immunosorbent assay (ELISA) to determine the pattern of macrophage activation associated with HIV infection and the effect of this activation on defense against pneumococcus. We used gamma interferon (IFN-γ) priming to mimic the cellular milieu in HIV-infected lungs. InnateDB and BioLayout 3D were used to analyze the interactions of the upregulated genes. Alveolar macrophages from HIV-infected adults showed increased gene expression and cytokine production in a classical pattern. Bronchoalveolar lavage from HIV-infected subjects showed excess CD8+lymphocytes with activated phenotype. Toll-like receptor 4 (TLR4) expression was increased in macrophages from HIV-infected subjects, but function was similar between the groups; lung lavage fluid did not inhibit TLR function in transfected HeLa cells. Alveolar macrophages from HIV-infected subjects showed normal binding and internalization of opsonized pneumococci, with or without IFN-γ priming. Alveolar macrophages from HIV-infected subjects showed classical activation compared to that of healthy controls, but this does not alter macrophage interactions with pneumococci.
A Novel High-Resolution Melt PCR Assay Discriminates Anaplasma phagocytophilum and “Candidatus Neoehrlichia mikurensis”
Authors: Krücken Jürgen , Schreiber Cécile , Maaz Denny , Kohn Mareen , Demeler Janina , Beck Stefanie , Schein Eberhard , Olias Philipp , Richter Dania , Matuschka Franz-Rainer , Pachnicke Stefan , Krieger Klemens , Kohn Barbara , von Samson-Himmelstjerna Georg
Published: April 2013

“
Candidatus
Neoehrlichia mikurensis” (
Anaplasmataceae
) is an emerging pathogen transmitted by
Ixodes
ticks. Conventional PCR and the newly developed high-resolution melt PCR were used to detect and discriminate “
Candidatus
Neoehrlichia mikurensis” and
Anaplasma phagocytophilum
. Both bacterial species were frequently found in
Ixodes ricinus
and
Ixodes hexagonus
but virtually absent from
Dermacentor reticulatus
. In rodents, “
Candidatus
N. mikurensis” was significantly more prevalent than
A. phagocytophilum
, whereas in cats, only
A. phagocytophilum
was found.
Visualizing the Beta Interferon Response in Mice during Infection with Influenza A Viruses Expressing or Lacking Nonstructural Protein 1
Authors: Kallfass Carsten , Lienenklaus Stefan , Weiss Siegfried , Staeheli Peter
Published: April 2013

The innate host defense against influenza virus is largely dependent on the type I interferon (IFN) system. However, surprisingly little is known about the cellular source of IFN in the infected lung. To clarify this question, we employed a reporter mouse that contains the firefly luciferase gene in place of the IFN-β-coding region. IFN-β-producing cells were identified either by simultaneous immunostaining of lungs for luciferase and cellular markers or by generating conditional reporter mice that express luciferase exclusively in defined cell types. Two different strains of influenza A virus were employed that either do or do not code for nonstructural protein 1 (NS1), which strongly suppresses innate immune responses of infected cells. We found that epithelial cells and lung macrophages, which represent the prime host cells for influenza viruses, showed vigorous IFN-β responses which, however, were severely reduced and delayed if the infecting virus was able to produce NS1. Interestingly, CD11c
+
cell populations that were either expressing or lacking macrophage markers produced the bulk of IFN-β at 48 h after infection with wild-type influenza A virus. Our results demonstrate that the virus-encoded IFN-antagonistic factor NS1 disarms specifically epithelial cells and lung macrophages, which otherwise would serve as main mediators of the early response against infection by influenza virus.
New Model for the Genesis and Maturation of Viroplasms Induced by Fijiviruses in Insect Vector Cells
Authors: Mao Qianzhuo , Zheng Shenglan , Han Qingmei , Chen Hongyan , Ma Yuanyuan , Jia Dongsheng , Chen Qian , Wei Taiyun
Published: April 2013

Plant reoviruses are thought to replicate and assemble within cytoplasmic, nonmembranous structures called viroplasms. Here, we established continuous cell cultures of the white-backed planthopper (
Sogatella furcifera
Horváth) to investigate the mechanisms for the genesis and maturation of the viroplasm induced by Southern rice black-streaked dwarf virus (SRBSDV), a fijivirus in the family
Reoviridae
, during infection of its insect vector. Electron and confocal microscopy revealed that the viroplasm consisted of a granular region, where viral RNAs and nonstructural proteins P6 and P9-1 accumulated, and a filamentous region, where viral RNAs, progeny cores, viral particles, as well as nonstructural proteins P5 and P6 accumulated. Our results suggested that the filamentous viroplasm matrix was the site for the assembly of progeny virions. Because viral RNAs were produced by assembled core particles within the filamentous viroplasm matrix, we propose that these viral RNAs might be transported to the granular viroplasm matrix. P5 formed filamentous inclusions and P9-1 formed granular inclusions in the absence of viral infection, suggesting that the filamentous and granular viroplasm matrices were formed primarily by P5 and P9-1, respectively. P6 was apparently recruited in the whole viroplasm matrix by direct interaction with P9-1 and P5. Thus, the present results suggested that P5, P6, and P9-1 are collectively required for the genesis and maturation of the filamentous and granular viroplasm matrix induced by SRBSDV infection. Based on these results, we propose a new model to explain the genesis and maturation of the viroplasms induced by fijiviruses in insect vector cells.
Foot-and-Mouth Disease Virus Modulates Cellular Vimentin for Virus Survival
Authors: Gladue D. P. , O'Donnell V. , Baker-Branstetter R. , Holinka L. G. , Pacheco J. M. , Fernández Sainz I. , Lu Z. , Ambroggio X. , Rodriguez L. , Borca M. V.
Published: April 2013

Foot-and-mouth disease virus (FMDV), the causative agent of foot-and-mouth disease, is an Aphthovirus within the
Picornaviridae
family. During infection with FMDV, several host cell membrane rearrangements occur to form sites of viral replication. FMDV protein 2C is part of the replication complex and thought to have multiple roles during virus replication. To better understand the role of 2C in the process of virus replication, we have been using a yeast two-hybrid approach to identify host proteins that interact with 2C. We recently reported that cellular Beclin1 is a natural ligand of 2C and that it is involved in the autophagy pathway, which was shown to be important for FMDV replication. Here, we report that cellular vimentin is also a specific host binding partner for 2C. The 2C-vimentin interaction was further confirmed by coimmunoprecipitation and immunofluorescence staining to occur in FMDV-infected cells. It was shown that upon infection a vimentin structure forms around 2C and that this structure is later resolved or disappears. Interestingly, overexpression of vimentin had no effect on virus replication; however, overexpression of a truncated dominant-negative form of vimentin resulted in a significant decrease in viral yield. Acrylamide, which causes disruption of vimentin filaments, also inhibited viral yield. Alanine scanning mutagenesis was used to map the specific amino acid residues in 2C critical for vimentin binding. Using reverse genetics, we identified 2C residues that are necessary for virus growth, suggesting that the interaction between FMDV 2C and cellular vimentin is essential for virus replication.
Rotavirus-Encoded Nonstructural Protein 1 Modulates Cellular Apoptotic Machinery by Targeting Tumor Suppressor Protein p53
Authors: Bhowmick Rahul , Halder Umesh Chandra , Chattopadhyay Shiladitya , Nayak Mukti Kant , Chawla-Sarkar Mamta
Published: April 2013

p53, a member of the innate immune system, is triggered under stress to induce cell growth arrest and apoptosis. Thus, p53 is an important target for viruses, as efficient infection depends on modulation of the host apoptotic machinery. This study focuses on how rotaviruses manipulate intricate p53 signaling for their advantage. Analysis of p53 expression revealed degradation of p53 during initial stages of rotavirus infection. However, in nonstructural protein-1 (NSP1) mutant strain A5-16, p53 degradation was not observed, suggesting a role of NSP1 in this process. This function of NSP1 was independent of its interferon or phosphatidylinositol 3-kinase (PI3K)/AKT modulation activity since p53 degradation was observed in Vero cells as well as in the presence of PI3K inhibitor. p53 transcript levels remained the same in SA11-infected cells (at 2 to 14 h postinfection), but p53 protein was stabilized only in the presence of MG132, suggesting a posttranslational process. NSP1 interacted with the DNA binding domain of p53, resulting in ubiquitination and proteasomal degradation of p53. Degradation of p53 during initial stages of infection inhibited apoptosis, as the proapoptotic genes PUMA and Bax were downregulated. During late viral infection, when progeny dissemination is the main objective, the NSP1-p53 interaction was diminished, resulting in restoration of the p53 level, with initiation of proapoptotic signaling ensuing. Overall results highlight the multiple strategies evolved by NSP1 to combat the host immune response.
Sustained Hyperresponsiveness of Dendritic Cells Is Associated with Spontaneous Resolution of Acute Hepatitis C
Authors: Pelletier Sandy , Bédard Nathalie , Said Elias , Ancuta Petronela , Bruneau Julie , Shoukry Naglaa H.
Published: April 2013

Some studies have reported that dendritic cells (DCs) may be dysfunctional in a subset of patients with chronic hepatitis C virus (HCV) infection. However, the function of DCs during acute HCV infection and their role in determining infectious outcome remain elusive. Here, we examined the phenotype and function of myeloid DCs (mDCs) and plasmacytoid DCs (pDCs) during acute HCV infection. Three groups of injection drug users (IDUs) at high risk of HCV infection were studied: an uninfected group, a group with acute HCV infection with spontaneous resolution, and a group with acute infection with chronic evolution. We examined the frequency, maturation status, and cytokine production capacity of DCs in response to the Toll-like receptor 4 (TLR4) and TLR7/8 ligands lipopolysaccharide (LPS) and single-stranded RNA (ssRNA), respectively. Several observations could distinguish HCV-negative IDUs and acute HCV resolvers from patients with acute infection with chronic evolution. First, we observed a decrease in the frequency of mature CD86
+
, programmed death-1 receptor ligand-positive (PDL1
+
), and PDL2
+
pDCs. This phenotype was associated with the increased sensitivity of pDCs from resolvers and HCV-negative IDUs versus the group with acute infection with chronic evolution to ssRNA stimulation
in vitro
. Second, LPS-stimulated mDCs from resolvers and HCV-negative IDUs produced higher levels of cytokines than mDCs from the group with acute infection with chronic evolution. Third, mDCs from all patients with acute HCV infection, irrespective of their outcomes, produced higher levels of cytokines during the early acute phase in response to ssRNA than mDCs from healthy controls. However, this hyperresponsiveness was sustained only in spontaneous resolvers. Altogether, our results suggest that the immature pDC phenotype and sustained pDC and mDC hyperresponsiveness are associated with spontaneous resolution of acute HCV infection.
Molecular Evolution of the HIV-1 Thai Epidemic between the Time of RV144 Immunogen Selection to the Execution of the Vaccine Efficacy Trial
Authors: Kijak Gustavo H. , Tovanabutra Sodsai , Rerks-Ngarm Supachai , Nitayaphan Sorachai , Eamsila Chirapa , Kunasol Prayura , Khamboonruang Chirasak , Thongcharoen Prasert , Namwat Chawetsan , Premsri Nakorn , Benenson Michael , Morgan Patricia , Bose Meera , Sanders-Buell Eric , Paris Robert , Robb Merlin L. , Birx Deborah L. , De Souza Mark S. , McCutchan Francine E. , Michael Nelson L. , Kim Jerome H.
Published: April 2013

The RV144 HIV-1 vaccine trial (Thailand, 2003 to 2009), using immunogens genetically matched to the regional epidemic, demonstrated the first evidence of efficacy for an HIV-1 vaccine. Here we studied the molecular evolution of the HIV-1 epidemic from the time of immunogen selection to the execution of the efficacy trial. We studied HIV-1 genetic diversity among 390 volunteers who were deferred from enrollment in RV144 due to preexisting HIV-1 infection using a multiregion hybridization assay, full-genome sequencing, and phylogenetic analyses. The subtype distribution was 91.7% CRF01_AE, 3.5% subtype B, 4.3% B/CRF01_AE recombinants, and 0.5% dual infections. CRF01_AE strains were 31% more diverse than the ones from the 1990s Thai epidemic. Sixty-nine percent of subtype B strains clustered with the cosmopolitan Western B strains. Ninety-three percent of B/CRF01_AE recombinants were unique; recombination breakpoint analysis showed that these strains were highly embedded within the larger network that integrates recombinants from East/Southeast Asia. Compared to Thai sequences from the early 1990s, the distance to the RV144 immunogens increased 52% to 68% for CRF01_AE Env immunogens and 12% to 29% for subtype B immunogens. Forty-three percent to 48% of CRF01_AE sequences differed from the sequence of the vaccine insert in Env variable region 2 positions 169 and 181, which were implicated in vaccine sieve effects in RV144. In conclusion, compared to the molecular picture at the early stages of vaccine development, our results show an overall increase in the genetic complexity of viruses in the Thai epidemic and in the distance to vaccine immunogens, which should be considered at the time of the analysis of the trial results.
CD27-CD70 Costimulation Controls T Cell Immunity during Acute and Persistent Cytomegalovirus Infection
Authors: Welten Suzanne P. M. , Redeker Anke , Franken Kees L. , Benedict Chris A. , Yagita Hideo , Wensveen Felix M. , Borst Jannie , Melief Cornelis J. M. , van Lier René A. W. , van Gisbergen Klaas P. J. M. , Arens Ramon
Published: April 2013

Cytomegaloviruses (CMVs) establish lifelong infections that are controlled in part by CD4+and CD8+T cells. To promote persistence, CMVs utilize multiple strategies to evade host immunity, including modulation of costimulatory molecules on infected antigen-presenting cells. In humans, CMV-specific memory T cells are characterized by the loss of CD27 expression, which suggests a critical role of the costimulatory receptor-ligand pair CD27-CD70 for the development of CMV-specific T cell immunity. In this study, thein vivorole of CD27-CD70 costimulation during mouse CMV infection was examined. During the acute phase of infection, the magnitudes of CMV-specific CD4+and CD8+T cell responses were decreased in mice with abrogated CD27-CD70 costimulation. Moreover, the accumulation of inflationary memory T cells during the persistent phase of infection and the ability to undergo secondary expansion required CD27-CD70 interactions. The downmodulation of CD27 expression, however, which occurs gradually and exclusively on inflationary memory T cells, is ligand independent. Furthermore, the IL-2 production in both noninflationary and inflationary CMV-specific T cells was dependent on CD27-CD70 costimulation. Collectively, these results highlight the importance of the CD27-CD70 costimulation pathway for the development of CMV-specific T cell immunity during acute and persistent infection.
APOBEC3G Impairs the Multimerization of the HIV-1 Vif Protein in Living Cells
Authors: Batisse Julien , Guerrero Santiago Xavier , Bernacchi Serena , Richert Ludovic , Godet Julien , Goldschmidt Valérie , Mély Yves , Marquet Roland , de Rocquigny Hugues , Paillart Jean-Christophe
Published: April 2013

The HIV-1 viral infectivity factor (Vif) is a small basic protein essential for viral fitness and pathogenicity. Vif allows productive infection in nonpermissive cells, including most natural HIV-1 target cells, by counteracting the cellular cytosine deaminases APOBEC3G (
apo
lipoprotein
B
mRNA-editing
e
nzyme
c
atalytic polypeptide-like
3G
[A3G]) and A3F. Vif is also associated with the viral assembly complex and packaged into viral particles through interactions with the viral genomic RNA and the nucleocapsid domain of Pr55
Gag
. Recently, we showed that oligomerization of Vif into high-molecular-mass complexes induces Vif folding and influences its binding to high-affinity RNA binding sites present in the HIV genomic RNA. To get further insight into the role of Vif multimerization in viral assembly and A3G repression, we used fluorescence lifetime imaging microscopy (FLIM)- and fluorescence resonance energy transfer (FRET)-based assays to investigate Vif-Vif interactions in living cells. By using two N-terminally tagged Vif proteins, we show that Vif-Vif interactions occur in living cells. This oligomerization is strongly reduced when the putative Vif multimerization domain (
161
PPLP
164
) is mutated, indicating that this domain is crucial, but that regions outside this motif also participate in Vif oligomerization. When coexpressed together with Pr55
Gag
, Vif is largely relocated to the cell membrane, where Vif oligomerization also occurs. Interestingly, wild-type A3G strongly interferes with Vif multimerization, contrary to an A3G mutant that does not bind to Vif. These findings confirm that Vif oligomerization occurs in living cells partly through its C-terminal motif and suggest that A3G may target and perturb the Vif oligomerization state to limit its functions in the cell.