bluuebunny/crossref_metadata_2025 huggingface dataset:
Surgical regenerative treatment of peri‐implantitis lesions using a nanocrystalline hydroxyapatite or a natural bone mineral in combination with a collagen membrane: a four‐year clinical follow‐up report
Authors: Schwarz Frank , Sahm Narja , Bieling Katrin , Becker Jürgen
Published: July 2009

Objectives: The present case series aimed at investigating the 4‐year clinical outcomes following surgical regenerative therapy of peri‐implantitis lesions using either a nanocrystalline hydroxyapatite (NHA) or a natural bone mineral in combination with a collagen membrane (NBM+CM).

Materials and Methods: Twenty patients suffering from moderate peri‐implantitis (n=20 intrabony defects) were randomly treated with (1) access flap surgery (AFS) and the application of NHA (n=9), or with AFS and the application of NBM+CM (n=11). Clinical and radiographic (R) parameters were recorded at baseline (R) and after 36 and 48 (R) months of non‐submerged healing.

Results: One patient from the NBM+CM group was discontinued from the study due to severe pus formation at 36 months. Compared with NHA, the application of NBM+CM resulted in higher mean PD reductions (NBM+CM: 2.5 ± 0.9 mm versus NHA: 1.1 ± 0.3 mm) and clinical attachment‐level gains (NBM+CM: 2.0 ± 1.0 mm versus NHA: 0.6 ± 0.5 mm) at 48 months. A radiographic bone fill was observed for five sites in the NHA group, and eight sites in the NBM+CM group.

Conclusion: While the application of NBM+CM resulted in clinical improvements over a period of 4 years, the long‐term outcome obtained with NHA without barrier membrane must be considered as poor.
Extraction of high‐quality epidermal RNA after ammonium thiocyanate‐induced dermo‐epidermal separation of 4 mm human skin biopsies
Authors: Clemmensen Anders , Thomassen Mads , Clemmensen Ole , Tan Qihua , Kruse Torben A. , Petersen Thomas K. , Andersen Flemming , Andersen Klaus E.
Published: July 2009

Abstract:  To obtain a separation of the epidermal and dermal compartments to examine compartment specific biological mechanisms in the skin, we incubated 4 mm human skin punch biopsies in ammonium thiocyanate. We wanted to test (i) the histological quality of the dermo‐epidermal separation obtained by different incubation times; (ii) the amount and quality of extractable epidermal RNA and (iii) its impact on sample RNA expression profiles assessed by large‐scale gene expression microarray analysis in both normal and inflamed skin. At 30‐min incubation, the split between dermis and epidermis was not always histologically well‐defined (i.e. occurred partly intra‐epidermally), but also varied between subjects. Consequently, curettage along the dermal surface of the biopsy was added to the procedure. This modified method resulted in an almost perfect separation of the epidermal and dermal compartments, and satisfactory amounts of high‐quality RNA were obtained. Hybridization to Affymetrix HG_U133A 2.0 GeneChips showed that ammonium thiocyanate incubation had a minute effect on gene expression resulting in only one significantly downregulated gene (cystatin E/M). We conclude that epidermis can be reproducibly and almost completely separated from the dermis of 4 mm skin biopsies by 30 min incubation in 3.8% ammonium thiocyanate combined with curettage of the dermal surface, producing high‐quality RNA suitable for transcriptional analysis. Our refined method of dermo‐epidermal separation will undoubtedly prove valuable in the many different settings, where the epidermal and dermal compartments need to be evaluated separately.
Unusual transfer of CutA into the secretory pathway, evidenced by fusion proteins with acetylcholinesterase
Authors: Liang Dong , Carvalho Stéphanie , Bon Suzanne , Massoulié Jean
Published: July 2009

The mouse CutA protein exists as long and short components of 20 and 15 kDa, produced by the use of different in‐frame ATGs initiation codons, and by proteolytic cleavage. We recently showed that, surprisingly, the longer, uncleaved component resides mostly in the secretory pathway and is secreted, whereas the shorter component resides mostly in the cytoplasm. To confirm these subcellular localizations, we constructed fusion proteins in which the catalytic domain of rat acetylcholinesterase was placed downstream of the CutA variants. The acquisition of an active conformation and N‐glycosylation of the fusion proteins proved their transfer into the secretory pathway. We show that the CutA‐AChE fusion proteins produced and secreted active, N‐glycosylated molecules, while an AChE mutant lacking its secretory signal peptide did not produce any significant activity. Thus, an N‐terminal CutA domain actually drives AChE into the endoplasmic reticulum and allows its secretion. This was observed with full length CutA, starting at Met1, and at a much lower level with the shorter mutants starting at Met24 and Met44, although the latter is not predicted to possess any signal peptide. These experiments illustrate the value of using AChE as a reporter and reveals an unusual protein trafficking and secretory process.
Deviation of the neurosporaxanthin pathway towards β‐carotene biosynthesis in Fusarium fujikuroi by a point mutation in the phytoene desaturase gene
Authors: Prado‐Cabrero Alfonso , Schaub Patrick , Díaz‐Sánchez Violeta , Estrada Alejandro F. , Al‐Babili Salim , Avalos Javier
Published: July 2009

Carotenoids are widespread terpenoid pigments with applications in the food and feed industries. Upon illumination, the gibberellin‐producing fungus Fusarium fujikuroi (Gibberella fujikuroi mating population C) develops an orange pigmentation caused by an accumulation of the carboxylic apocarotenoid neurosporaxanthin. The synthesis of this xanthophyll includes five desaturation steps presumed to be catalysed by the carB‐encoded phytoene desaturase. In this study, we identified a yellow mutant (SF21) by mutagenesis of a carotenoid‐overproducing strain. HPLC analyses indicated a specific impairment in the ability of SF21‐CarB to perform the fifth desaturation, as implied by the accumulation of γ‐carotene and β‐carotene, which arise through four‐step desaturation. Sequencing of the SF21 carB allele revealed a single mutation resulting in an exchange of a residue conserved in other five‐step desaturases. Targeted carB allele replacement proved that this single mutation is the cause of the SF21 carotenoid pattern. In support, expression of SF21 CarB in engineered carotene‐producing Escherichia coli strains demonstrated its reduced ability to catalyse the fifth desaturation step on both monocyclic and acyclic substrates. Further mutagenesis of SF21 led to the isolation of two mutants, SF73 and SF98, showing low desaturase activities, which mediated only two desaturation steps, resulting in accumulation of the intermediate ζ‐carotene at low levels. Both strains contained an additional mutation affecting a CarB domain tentatively associated with carotenoid binding. SF21 exhibited higher carotenoid amounts than its precursor strain or the SF73 and SF98 mutants, although carotenogenic mRNA levels were similar in the four strains.
RasGEF1A and RasGEF1B are guanine nucleotide exchange factors that discriminate between Rap GTP‐binding proteins and mediate Rap2‐specific nucleotide exchange
Authors: Yaman Elif , Gasper Raphael , Koerner Carolin , Wittinghofer Alfred , Tazebay Uygar H.
Published: July 2009

The highly conserved RasGEF1 family of proteins contain a C‐terminal CDC25‐Ras exchange motif domain and an N‐terminal RasGEF‐N domain, and are of unknown function and specificity. Using purified RasGEF1A and RasGEF1B proteins, as well as Ras family proteins, we established that RasGEF1A and RasGEF1B function as very specific exchange factors for Rap2, a member of the Rap subfamily of Ras‐like G‐proteins. They do not act on Rap1 or other members of the Ras subfamily. Although Rap2 was implicated in the regulation of cell adhesion, the establishment of cell morphology, and the modulation of synapses in neurons, no specific guanine nucleotide exchange factor for Rap2 was previously identified. Using reciprocal site‐directed mutagenesis, we analyzed residues that allow RasGEF1 proteins to discriminate between Rap1 and Rap2, and we were able to identify Phe39 in the switch I region of Rap2 as a specificity residue. Mutation of the corresponding Ser39 in Rap1 changed the specificity and allowed the nucleotide exchange of Rap1(S39F) to be stimulated by RasGEF1B.
Functional analysis of pyrimidine biosynthesis enzymes using the anticancer drug 5‐fluorouracil inCaenorhabditis elegans
Authors: Kim Seongseop , Park Dae‐Hun , Kim Tai Hoon , Hwang Moogak , Shim Jaegal
Published: July 2009

Pyrimidine biosynthesis enzymes function in many cellular processes and are closely associated with pyrimidine antagonists used in cancer chemotherapy. These enzymes are well characterized from bacteria to mammals, but not in a simple metazoan. To study the pyrimidine biosynthesis pathway inCaenorhabditis elegans, we screened for mutants exhibiting resistance to the anticancer drug 5‐fluorouracil (5‐FU). In several strains, mutations were identified in ZK783.2, the worm homolog of human uridine phosphorylase (UP). UP is a member of the pyrimidine biosynthesis family of enzymes and is a key regulator of uridine homeostasis.C. elegansUP homologous protein (UPP‐1) exhibited both uridine and thymidine phosphorylase activityin vitro. Knockdown of other pyrimidine biosynthesis enzyme homologs, such as uridine monophosphate kinase and uridine monophosphate synthetase, also resulted in 5‐FU resistance. Uridine monophosphate kinase and uridine monophosphate synthetase proteins are redundant, and show different, tissue‐specific expression patterns inC. elegans.Whereas pyrimidine biosynthesis pathways are highly conserved between worms and humans, no human thymidine phosphorylase homolog has been identified inC. elegans.UPP‐1 functions as a key regulator of the pyrimidine salvage pathway inC. elegans, as mutation ofupp‐1results in strong 5‐FU resistance.
Lowered albumin extravasation rate in heart but not in other organs in β3‐integrin‐deficient mice
Authors: Svendsen Ø. S. , Lidén Å. , Rubin K. , Reed R. K.
Published: July 2009

Aim:  The vascular protein permeability is dependent on the integrity of the vascular wall. The heart capillaries in male mice lacking β3 integrins have an immature phenotype. Previously, we have demonstrated a role for αvβ3 integrins in control of interstitial fluid pressure (Pif) and thereby in the fluid flux during inflammation. We wanted to explore a possible role for αvβ3 integrins in controlling capillary protein permeability during control situation and inflammation.

Methods:  We performed double‐tracer and microdialysis experiments on β3‐integrin‐deficient mice and wild type control mice. We also measured blood pressure and heart rate in the two mice strains.

Results:  We found reduced albumin extravasation (during 25 min) in the heart capillaries (0.053 ± 0.003 vs. 0.087 ± 0.009 mL g−1 dw, P < 0.05), and an increased cardiac mass/body weight (5.3 × 10−3 ± 0.3 × 10−3 vs. 3.8 × 10−3 ± 0.1 × 10−3, P < 0.01) in the β3‐integrin‐deficient mice (n = 6) compared with the controls (n = 6). Heart rate and blood pressure were the same in mice with and without β3‐integrins. No difference in permeability was found in other tissues studied, or under local inflammation.

Conclusion:  These results show a function for the αvβ3 integrin in the regulation of protein permeability, selective for the heart capillaries.
Asymmetric sensorineural hearing thresholds in the non‐noise‐exposed UK population: a retrospective analysis
Authors: Lutman M.E. , Coles R.R.A.
Published: July 2009

Objectives:  To estimate the distribution of inter‐aural sensorineural hearing threshold level differences in the non‐noise‐exposed adult population of the UK.

Setting:  A two‐stage population study carried out in 1979–1986, initially by postal questionnaire, followed up in a proportion of participants by clinical and audiological examination.

Participants:  Volunteers (n = 48 313) initially selected at random from the electoral registers of four cities, subsequently selected at random from questionnaire respondents stratified by answers to questions about hearing.

Main outcomes measure:  Inter‐aural hearing threshold level differences measured audiometrically, as a function of age and gender.

Results:  Tables of inter‐aural threshold level differences provided as a resource with potential medicolegal, clinical and research applications. Based on the average of the frequencies 0.5, 1, 2 and 4 kHz, ≈ 1% of the general UK population aged 18–80 years have an asymmetry of 15 dB or more. The prevalence is greater in older than in younger people.

Conclusions:  Inter‐aural threshold differences greater than attributable to measurement error are not uncommon in the adult population, even after screening for conductive hearing loss and substantial noise exposure. They are typically of unknown origin.
Validation of the Clinical COPD Questionnaire as a psychophysical outcome measure in adult laryngotracheal stenosis
Authors: Nouraei S.A.R. , Randhawa P.S. , Koury E.F. , Abdelrahim A. , Butler C.R. , Venkataraman A. , Howard D.J. , Sandhu G.S.
Published: July 2009

Objectives:  To validate the Clinical Chronic Obstructive Pulmonary Disease Questionnaire (CCQ), a patient‐administered instrument developed for bronchopulmonary disease as a disease‐specific psychophysical outcome measure for adult laryngotracheal stenosis.

Design:  Prospective observational study.

Settings:  Tertiary/National referral airway reconstruction centre.

Participants:  Thirty‐three tracheostomy‐free patients undergoing endoscopic laryngotracheoplasty.

Main outcome measures:  CCQ and the Medical Research Council (MRC) Dyspnoea scale, a previously validated but more limited scale, were administered to patients 2 weeks before surgery, preoperatively, and 2 weeks after endoscopic laryngotracheoplasty. Pulmonary function was assessed preoperatively. Internal consistency was assessed with Cronbach α statistics and test–retest reliability was determined using intraclass correlation. Correlations between CCQ and MRC scale, and pulmonary function were used to assess convergent and divergent validity respectively. Instrument responsiveness was assessed by correlating total and domain‐specific CCQ scores with anatomical disease severity and post‐treatment effect size.

Results:  There were 12 males and 21 females. Mean age was 44 ± 15 years. Cronbach α coefficient and intraclass correlation coefficient were 0.88 and 0.95 respectively. Total and domain‐specific CCQ scores significantly correlated with the MRC scores (P < 0.001) and significant correlations between CCQ and peak expiratory flow rate and FEV1 were identified (P < 0.03). There were statistically significant changes in total and domain‐specific CCQ scores when different stenosis severities were compared. Clinical COPD Questionnaire scores also changed significantly and congruently following surgery (P < 0.05 in both cases).

Discussion:  Clinical COPD Questionnaire is a valid and sensitive instrument for assessing symptom severity and levels of function and well‐being in adult patients with laryngotracheal stenosis and can be used as a patient‐centred disease‐specific outcome measure for this condition.
A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic‐resistant Pseudomonas aeruginosa; a preliminary report of efficacy
Authors: Wright A. , Hawkins C.H. , Änggård E.E. , Harper D.R.
Published: July 2009

Objectives:  To evaluate the efficacy and safety of a therapeutic bacteriophage preparation (Biophage‐PA) targeting antibiotic‐resistant Pseudomonas aeruginosa in chronic otitis.

Design:  Randomised, double‐blind, placebo‐controlled Phase I/II clinical trial approved by UK Medicines and Healthcare products Regulatory Agency (MHRA) and the Central Office for Research Ethics Committees (COREC) ethical review process.

Setting:  A single specialist university hospital.

Participants:  24 patients with chronic otitis with a duration of several years (2–58). Each patient had, at the time of entry to the trial, an ear infection because of an antibiotic‐resistant P. aeruginosa strain sensitive to one or more of the six phages present in Biophage‐PA. Participants were randomised in two groups of 12 treated with either a single dose of Biophage‐PA or placebo and followed up at 7, 21 and 42 days after treatment by the same otologist. Ears were thoroughly cleaned on each occasion and clinical and microbiological indicators measured.

Main outcome measures:  Physician assessed erythema/inflammation, ulceration/granulation/polyps, discharge quantity, discharge type and odour using a Visual Analogue Scale (VAS). Patients reported discomfort, itchiness, wetness and smell also using a VAS. Bacterial levels of P. aeruginosa and phage counts from swabs were measured initially and at follow‐up. At each visit patients were asked about side effects using a structured form. Digital otoscopic images were obtained on days 0 and 42 for illustrative purposes only.

Results:  Relative to day 0, pooled patient‐ and physician‐reported clinical indicators improved for the phage treated group relative to the placebo group. Variation from baseline levels was statistically significant for combined data from all clinic days only for the phage treated group. Variation from baseline levels was statistically significant for the majority of the patient assessed clinical indicators only for the phage treated group. P. aeruginosa counts were significantly lower only in the phage treated group. No treatment related adverse event was reported.

Conclusion:  The first controlled clinical trial of a therapeutic bacteriophage preparation showed efficacy and safety in chronic otitis because of chemo‐resistant P. aeruginosa.
Long‐term RNA interference and its application to hepatitis B virus
Authors: PAN Jin Shui , WANG Xiao Zhong , REN Jian Lin
Published: July 2009

RNA interference (RNAi) is an ancient defensive mechanism in eukaryotes to control gene expressing and defend their genomes from foreign invaders. It refers to the phenomenon that double‐stranded RNA results in the sequence‐specific silencing of target gene expression. Although it was documented in a relatively short time ago, intensive research has facilitated making its mechanism clear. Researchers have found that it was a powerful tool for analyzing the functions of genes and treating tumors, infectious diseases and genetic abnormalities that are associated with a dominant gene defect. However, delivery in vivo, low blood stability and poor intracellular uptake present significant challenges for the development of RNAi reagents in clinical use. Thus, long‐term inducible RNAi was designed. There are hundreds of millions of hepatitis B virus (HBV) carriers in the world at present, a portion of whom will lose their lives after several years due to chronic complications such as cirrhosis, hepatocellular carcinomas or both. Although a preventive vaccine is now available, the present therapeutic options for chronically infected patients are limited and of low efficiency. Admittedly, to date most RNAi experiments have been done in vitro, but it is hoped that they may be developed into a therapeutic strategy for HBV in the near future. In this article the principles and construction of long‐term RNA are discussed. Its therapeutic potentiality and attention to the potential hazards will also outlined. We conclude that this ancient defensive mechanism can be recruited as a powerful weapon in the fight against HBV.
Post‐cholecystectomy cystic duct stump leak: a preventable morbidity
Authors: SHAIKH Irshad Ahammed A. , THOMAS Harun , JOGA Kishore , AMIN A. Ibrahim , DANIEL Thomas
Published: July 2009

OBJECTIVE:  While major bile duct injury is the most serious complication following laparoscopic cholecystectomy, bile leak from the cystic duct stump remains the commonest morbidity. This is a retrospective assessment of all patients who had a cholecystectomy over a 5‐year period from April 2003 to March 2008.

METHODS:  Data related to bile leakage were obtained from the Unisoft endoscopic retrograde cholangio‐pancreatography (ERCP) database.

RESULTS:  Overall 2011 cholecystectomies were performed, of which 488 were done as emergency procedures. Thirteen patients had significant bile leakage, three of which were from accessory ducts, in one the source could not be identified and nine had a cystic duct stump leak (CDSL), which formed the basis of this study. Eight of the nine CDSL patients had successful ERCP and stenting. One had a percutaneous trans‐hepatic cholangiography and stenting. CDSL following emergency laparoscopic cholecystectomy was up to threefold higher than after elective procedures.

CONCLUSION:  The CDSL of 0.44% was comparable to the reported incidence in the literature. Endoscopic management remains the treatment of choice. Emergency cholecystectomies seem to have a higher incidence of CDSL.
Baseline study of the leaf‐litter ant fauna in a French Guianese forest
Authors: GROC SARAH , ORIVEL JÉRÔME , DEJEAN ALAIN , MARTIN JEAN‐MICHEL , ETIENNE MARIE‐PIERRE , CORBARA BRUNO , DELABIE JACQUES H. C.
Published: July 2009

Abstract. 1. Leaf‐litter ants represent a major component of biodiversity and are excellent bioindicators reflecting the health of terrestrial ecosystems. This study, conducted in an unspoiled forest near the Nouragues Research Station, represents the first inventory of leaf‐litter ant diversity conducted in French Guiana, and so can be considered as the baseline dataset for ants in this country.

2. Ants were extracted from the leaf‐litter using the Ants of the Leaf Litter Protocol, along an altitudinal gradient at four forest sites, including an inselberg.

3. A total of 196 ant species representing 46 genera distributed over eight subfamilies were collected. Four distinct communities spread over a gradient of diversity were thus identified: the liana forest was the most species‐rich (140 species) followed by the forested plateau (102 species), the transition forest (87 species) and the forest at the top of the inselberg (71 species).

4. The discovery of species new to science plus several species recorded for the first time in French Guiana, coupled with the particular context of this area, suggests that the Nouragues Research Station might represent a centre of endemism. Once completed, this leaf‐litter ant dataset will contribute greatly to the knowledge of ant biodiversity in French Guiana, and has the potential to progressively become an indispensable tool for country‐wide conservation planning programmes.
Chiral Isotropic Liquids from Achiral Molecules
Authors: Hough L. E. , Spannuth M. , Nakata M. , Coleman D. A. , Jones C. D. , Dantlgraber G. , Tschierske C. , Watanabe J. , Körblova E. , Walba D. M. , Maclennan J. E. , Glaser M. A. , Clark N. A.
Published: July 2009

Packing Bananas and Boomerangs

Assembling achiral molecules typically generates achiral domains. However, odd things can happen when the molecules are banana-or boomerang-shaped—their cores can twist out of plain to form left- or right-handed helices, which can then pack into chiral domains that will polarize light (see the Perspective by
Amabilino
).

Hough
et al.

(p.
452
) show that if you make the situation even more complex by frustrating the packing of adjacent layers, you can create a material that appears to be macroscopically isotropic with only very local positional and orientational ordering of the molecules but still shows an overall chirality. In a second paper,

Hough
et al.

(p.
456
) also show that if you change the chemistry of the molecules to allow for better overall packing, you can create a situation where helical filaments form that also tend to pack in layered structures. However, the frustration between the two types of packing leads to macroscopically chiral and mesoporous structures.
Observational and Model Evidence for Positive Low-Level Cloud Feedback
Authors: Clement Amy C. , Burgman Robert , Norris Joel R.
Published: July 2009

Positve Feedback

The uncertain effect of feedback between climate and clouds is one of the largest obstacles to producing more confident projections of global climate.

Clement
et al.

(p.
460
) examined how clouds, sea surface temperature, and large-scale atmospheric circulation vary in the Northeast Pacific region. Change in cloud coverage was the primary cause of sea surface temperature variations, and clouds provided a positive feedback to temperature variations. Furthermore, regional atmospheric circulation patterns were linked to patterns of cloudiness. One model produced realistic covariability between cloud cover, sea surface temperatures, and atmospheric circulation for the 20th century.
Predicting the Behavior of Techno-Social Systems
Authors: Vespignani Alessandro
Published: July 2009

We live in an increasingly interconnected world of techno-social systems, in which infrastructures composed of different technological layers are interoperating within the social component that drives their use and development. Examples are provided by the Internet, the World Wide Web, WiFi communication technologies, and transportation and mobility infrastructures. The multiscale nature and complexity of these networks are crucial features in understanding and managing the networks. The accessibility of new data and the advances in the theory and modeling of complex networks are providing an integrated framework that brings us closer to achieving true predictive power of the behavior of techno-social systems.
Synchronous and Stochastic Patterns of Gene Activation in the
Drosophila
Embryo
Authors: Boettiger Alistair N. , Levine Michael
Published: July 2009

Stalled Development?

Most developmental control genes that pattern the
Drosophila
embryo appear to have stalled RNA polymerase II (Pol II) bound to them prior to their activation. Classical studies on the
Drosophila
heat shock genes have shown that stalled Pol II renders these genes “poised” for rapid induction by stress.
Boettiger and Levine
(p.
471
) now provide evidence for another potential function of stalled Pol II: Stalled genes exhibit synchronous patterns of gene activation in the early
Drosophila
embryo so that most or all cells in an embryonic tissue display nascent transcripts at the onset of expression. This synchrony might promote transcriptional precision during development.
A Flare for Acceleration
Authors: Begelman Mitchell
Published: July 2009

Radio and gamma-ray observations show that particles are accelerated to extremely high energies very close to a black hole.
How Deformation Can Lend a Hand to Molecular Ordering
Authors: Amabilino David B.
Published: July 2009

Liquid crystal phases of molecules with no inherent handedness undergo subtle deformations that create unusual chiral fluids and nanostructures.
Research Data in the Digital Age
Authors: Kleppner Daniel , Sharp Phillip A.
Published: July 2009

This week, the U.S. National Academies released an overview report
*
on the challenges of maintaining the integrity of scientific research data in an age of revolutionary digital technologies. The report,
Ensuring the Integrity, Accessibility, and Stewardship of Research Data in the Digital Age
, provides a framework for dealing with the challenges to the community generated by the onrush of digital technology. As chairs of the report committee, we hope that it moves the research community forward, collectively, to consider the integrity of data in ways that best support the advancement of scientific, engineering, and medical knowledge, as well as the maintenance of public trust.
Forensic Finds Add Substance to Claims of War Atrocities
Authors: Stone Richard
Published: July 2009

Last week, South Korea's Truth and Reconciliation Commission revealed evidence from an ongoing excavation confirming the February 1951 Bulgap massacre as one of the Korean War's darker chapters.
DOE Puts Up $85 Million for Grants to Young Scientists
Authors: Mervis Jeffrey
Published: July 2009

The U.S. Department of Energy (DOE) has committed $85 million next year for a new program to help 50 young scientists establish their research careers. It is the latest federal agency to try to lend a hand to this vulnerable population.
Clouds Appear to Be Big, Bad Player in Global Warming
Authors: Kerr Richard A.
Published: July 2009

On page 460 of this week's issue of
Science
, the first reliable analysis of cloud behavior over past decades suggests—but falls short of proving—that clouds are strongly amplifying global warming. If that's true, then almost all climate models have got it wrong.
ExxonMobil Fuels Venter's Efforts To Run Vehicles on Algae-Based Oil
Authors: Service Robert F.
Published: July 2009

Last week, in one of the biggest biofuel bets so far, ExxonMobil announced that it will spend up to $600 million over 5 to 6 years to produce biofuels from algae.
Test Ban Monitoring: No Place to Hide
Authors: Clery Daniel
Published: July 2009

A nearly complete global network can reliably spot secret nuclear explosions, researchers say. Will holdout nations now ratify the test ban?
Phytoplasma Research Begins to Bloom
Authors: Strauss Evelyn
Published: July 2009

Spread by insects, bacteria called phytoplasmas co-opt plant development, sometimes creating beauty but more often bringing devastation.
Investigating Networks: The Dark Side
Authors: Bohannon John
Published: July 2009

A few months ago, Lawrence Wilkerson, a former U.S. State Department official and Army colonel, painted a nightmare scenario of how social network science can be applied in a battle zone, outlining something he called "the mosaic philosophy."
A Live AttenuatedBordetella pertussisCandidate Vaccine Does Not Cause Disseminating Infection in Gamma Interferon Receptor Knockout Mice
Authors: Skerry Ciaran M. , Cassidy Joseph P. , English Karen , Feunou-Feunou Pascal , Locht Camille , Mahon Bernard P.
Published: July 2009

Bordetella pertussisis the cause of whooping cough and responsible for 300,000 infant deaths per annum. Current vaccines require 6 months to confer optimal immunity on infants, the population at highest risk. Recently, an attenuated strain ofB. pertussis(BPZE1) has been developed to be used as a low-cost, live, intranasal, single-dose vaccine for newborns. Preclinical proof of concept has been established; however, it is necessary to evaluate the safety of BPZE1, especially in immunodeficient models, prior to human clinical trials. Here, the preclinical safety of BPZE1 was examined in well-characterized murine models. Immunocompetent and gamma interferon (IFN-γ) receptor knockout mice were challenged by aerosol with either virulentB. pertussisor BPZE1. The two strains colonized the lung at equal levels, but inflammation was associated with carriage of only virulent bacteria. Virulent bacteria disseminated to the liver of IFN-γ receptor-deficient mice, resulting in atypical pathology. In contrast, attenuated BPZE1 did not disseminate in either immunocompetent or immunodeficient mice and did not induce atypical pathology. In neonatal challenge models, virulentB. pertussisinfection resulted in significant mortality of both immunodeficient and immunocompetent mice, whereas no mortality was observed for any neonatal mice challenged with BPZE1. BPZE1 was shown to elicit strong IFN-γ responses in mice, equivalent to those elicited by the virulent streptomycin-resistantB. pertussisTohama I derivative BPSM, also inducing immunoglobulin G2a, a process requiring TH1 cytokines in mice. These data indicate that a live attenuated whooping cough vaccine candidate shows no signs of disseminating infection in preclinical models but rather evokes an immunological profile associated with optimal protection against disease.
Prevalence and Clinical Characterization of a Newly Identified Human Rhinovirus C Species in Children with Acute Respiratory Tract Infections
Authors: Jin Yu , Yuan Xin-Hui , Xie Zhi-Ping , Gao Han-Chun , Song Jing-Rong , Zhang Rong-Fang , Xu Zi-Qian , Zheng Li-Shu , Hou Yun-De , Duan Zhao-Jun
Published: July 2009

Human rhinovirus C (HRV-C) is a newly identified genotype of HRV found in patients with respiratory tract infections (RTIs); however, its epidemiological profile and clinical characteristics are not well understood. In this study, Chinese children with RTIs were screened for HRV-C and their epidemiological and clinical characteristics were analyzed. From December 2006 to November 2007, 406 nasopharyngeal aspirates from children younger than 14 years of age with RTIs were screened for HRV and other common respiratory viruses by PCR or reverse transcription-PCR. Two-hundred twenty-four (55.2%) of the specimens were infected with at least one virus, including 53 patients with HRV (13%). HRV-A, HRV-B, and HRV-C were detected in 22, 12, and 19 specimens, respectively. HRV-C was detected mainly from December 2006 to April 2007 and from October to November 2007, with peaks in December and April (10/19). Acute upper respiratory infection and bronchopneumonia were observed in 53 and 37% of the cases, respectively. The most common symptoms were cough (82%), runny nose (53%), and fever (37%). Wheezing and bronchiolitis were less common in patients infected with HRV-C than in those infected with respiratory syncytial virus (RSV). Partial sequencing of the genes coding for VP4 and VP2 revealed that the HRV-C strains were 56 to 62% identical at the amino acid level to HRV-B and HRV-A reference strains and 80 to 99% identical to HRV-C reference strains. In conclusion, HRV-C is an important cause of RTIs in children, and highly diversified strains of HRV-C are prevalent in China. HRV-C may produce different epidemiological features, and patients infected with HRV-C may exhibit different clinical features from patients infected with RSV or HRV-A/B.
Strain Typing and Antimicrobial Resistance of Fluoroquinolone-ResistantNeisseria gonorrhoeaeCausing a California Infection Outbreak
Authors: Morris Sheldon R. , Moore Douglas F. , Hannah Paul B. , Wang Susan A. , Wolfe Julia , Trees David L. , Bolan Gail , Bauer Heidi M.
Published: July 2009

Antimicrobial-resistantNeisseria gonorrhoeaeis an emerging public health problem as a result of the alarming limitation in treatment options. We examined an outbreak in California of fluoroquinolone-resistantNeisseria gonorrhoeae(QRNG) by evaluation of a combination of routine isolates from the Gonococcal Isolate Surveillance Project and isolates collected by expanded surveillance performed between April 2000 and June 2002. QRNG isolates were characterized by two methods: (i) determination of a combination of antibiogram, auxotype, serovar, Lip type, and patterns of amino acid alteration in the quinolone resistance-determining region of GyrA and ParC (ASLGP) and (ii) pulsed-field gel electrophoresis (PFGE). Strain typing was used to describe the QRNG outbreak strains and the associated antimicrobial resistance profiles. Among 79 isolates that were completely characterized, we identified 20 different ASLGP strain types, and 2 of the types were considered to belong to outbreak strains that comprised 65% (51/79) of the isolates. By PFGE typing, there were 24 different strain types, and 4 of these were considered outbreak types and comprised 66% (52/79) of the isolates. The overall agreement between the typing methods in distinguishing outbreak strains and non-outbreak strains was 84% (66/79). The most common QRNG ASLGP strain type had chromosomally mediated resistance to penicillin and tetracycline and an azithromycin MIC of 0.5 μg/ml. The occurrence of an outbreak caused by QRNG strains that could fail to be eradicated by most antibiotic classes reinforces the serious problem with antimicrobial resistance inNeisseria gonorrhoeaethat the public health system faces. Adherence to a regimen with the recommended antibiotics at the appropriate dose is critical, and monitoring for antimicrobial susceptibility needs to be actively maintained to adapt treatment guidelines appropriately.
Evaluation of the Abbott Investigational Use Only RealTi
m
e Hepatitis C Virus (HCV) Assay and Comparison to the Roche TaqMan HCV Analyte-Specific Reagent Assay
Authors: Pyne Michael T. , Konnick Eric Q. , Phansalkar Amit , Hillyard David R.
Published: July 2009

The accurate and sensitive measurement of hepatitis C virus (HCV) RNA is essential for the clinical management and treatment of infected patients and as a research tool for studying the biology of HCV infection. We evaluated the linearity, reproducibility, precision, limit of detection, and concordance of viral genotype quantitation of the Abbott investigational use only RealTi
m
e HCV (RealTi
m
e) assay using the Abbott
m
2000 platform and compared the results to those of the Roche TaqMan Analyte-Specific Reagent (TaqMan) and Bayer Versant HCV bDNA 3.0 assay. Comparison of 216 samples analyzed by RealTi
m
e and TaqMan assays produced the following Deming regression equation: RealTi
m
e = 0.940 (TaqMan) + 0.175 log
10
HCV RNA IU/ml. The average difference between the assays was 0.143 log
10
RNA IU/ml and was consistent across RealTi
m
e's dynamic range of nearly 7 log
10
HCV RNA IU/ml. There was no significant difference between genotypes among these samples. The limit of detection using eight replicates of the World Health Organization HCV standard was determined to be 7.74 HCV RNA IU/ml by probit analysis. Replicate measurements of commercial genotype panels were significantly higher than TaqMan measurements for most samples and showed that the RealTi
m
e assay is able to detect all genotypes with no bias. Additionally, we showed that the amplicon generated by the widely used Roche COBAS Amplicor Hepatitis C Virus Test, version 2.0, can act as a template in the RealTi
m
e assay, but potential cross-contamination could be mitigated by treatment with uracil-
N
-glycosylase. In conclusion, the RealTi
m
e assay accurately measured HCV viral loads over a broad dynamic range, with no significant genotype bias.
Respiratory Syncytial Virus Nonstructural Proteins Decrease Levels of Multiple Members of the Cellular Interferon Pathways
Authors: Swedan Samer , Musiyenko Alla , Barik Sailen
Published: July 2009

Viruses of the
Paramyxoviridae
family, such as the respiratory syncytial virus (RSV), suppress cellular innate immunity represented by type I interferon (IFN) for optimal growth in their hosts. The two unique
n
on
s
tructural (NS) proteins, NS1 and NS2, of RSV suppress IFN synthesis, as well as IFN function, but their exact targets are still uncharacterized. Here, we investigate if either or both of the NS proteins affect the steady-state levels of key members of the IFN pathway. We found that both NS1 and NS2 decreased the levels of TRAF3, a strategic integrator of multiple IFN-inducing signals, although NS1 was more efficient. Only NS1 reduced IKKε, a key protein kinase that specifically phosphorylates and activates IFN regulatory factor 3. Loss of the TRAF3 and IKKε proteins appeared to involve a nonproteasomal mechanism. Interestingly, NS2 modestly increased IKKε levels. In the IFN response pathway, NS2 decreased the levels of STAT2, the essential transcription factor for IFN-inducible antiviral genes. Preliminary mapping revealed that the C-terminal 10 residues of NS1 were essential for reducing IKKε levels and the C-terminal 10 residues of NS2 were essential for increasing and reducing IKKε and STAT2, respectively. In contrast, deletion of up to 20 residues of the C termini of NS1 and NS2 did not diminish their TRAF3-reducing activity. Coimmunoprecipitation studies revealed that NS1 and NS2 form a heterodimer. Clearly, the NS proteins of RSV, working individually and together, regulate key signaling molecules of both the IFN activation and response pathways.
Assembly of Arenavirus Envelope Glycoprotein GPC in Detergent-Soluble Membrane Microdomains
Authors: Agnihothram Sudhakar S. , Dancho Brooke , Grant Kenneth W. , Grimes Mark L. , Lyles Douglas S. , Nunberg Jack H.
Published: July 2009

The family
Arenaviridae
includes a number of highly pathogenic viruses that are responsible for acute hemorrhagic fevers in humans. Genetic diversity among arenavirus species in their respective rodent hosts supports the continued emergence of new pathogens. In the absence of available vaccines or therapeutic agents, the hemorrhagic fever arenaviruses remain a serious public health and biodefense concern. Arenaviruses are enveloped virions that assemble and bud from the plasma membrane. In this study, we have characterized the microdomain organization of the virus envelope glycoprotein (GPC) on the cell surface by using immunogold electron microscopy. We find that Junín virus (JUNV) GPC clusters into discrete microdomains of 120 to 160 nm in diameter and that this property of GPC is independent of its myristoylation and of coexpression with the virus matrix protein Z. In cells infected with the Candid#1 strain of JUNV, and in purified Candid#1 virions, these GPC microdomains are soluble in cold Triton X-100 detergent and are thus distinct from conventional lipid rafts, which are utilized by numerous other viruses for assembly. Virion morphogenesis ultimately requires colocalization of viral components, yet our dual-label immunogold staining studies failed to reveal a spatial association of Z with GPC microdomains. This observation may reflect either rapid Z-dependent budding of virus-like particles upon coassociation or a requirement for additional viral components in the assembly process. Together, these results provide new insight into the molecular basis for arenavirus morphogenesis.
The Size of the Viral Inoculum Contributes to the Outcome of Hepatitis B Virus Infection
Authors: Asabe Shinichi , Wieland Stefan F. , Chattopadhyay Pratip K. , Roederer Mario , Engle Ronald E. , Purcell Robert H. , Chisari Francis V.
Published: July 2009

The impact of virus dose on the outcome of infection is poorly understood. In this study we show that, for hepatitis B virus (HBV), the size of the inoculum contributes to the kinetics of viral spread and immunological priming, which then determine the outcome of infection. Adult chimpanzees were infected with a serially diluted monoclonal HBV inoculum. Unexpectedly, despite vastly different viral kinetics, both high-dose inocula (10
10
genome equivalents [GE] per animal) and low-dose inocula (10° GE per animal) primed the CD4 T-cell response after logarithmic spread was detectable, allowing infection of 100% of hepatocytes and requiring prolonged immunopathology before clearance occurred. In contrast, intermediate (10
7
and 10
4
GE) inocula primed the T-cell response before detectable logarithmic spread and were abruptly terminated with minimal immunopathology before 0.1% of hepatocytes were infected. Surprisingly, a dosage of 10
1
GE primed the T-cell response after all hepatocytes were infected and caused either prolonged or persistent infection with severe immunopathology. Finally, CD4 T-cell depletion before inoculation of a normally rapidly controlled inoculum precluded T-cell priming and caused persistent infection with minimal immunopathology. These results suggest that the relationship between the kinetics of viral spread and CD4 T-cell priming determines the outcome of HBV infection.
Systematic Study of the Genetic Response of a Variable Virus to the Introduction of Deleterious Mutations in a Functional Capsid Region
Authors: Luna Eva , Rodríguez-Huete Alicia , Rincón Verónica , Mateo Roberto , Mateu Mauricio G.
Published: July 2009

We have targeted the intersubunit interfaces in the capsid of foot-and-mouth disease virus to investigate the genetic response of a variable virus when individual deleterious mutations are systematically introduced along a functionally defined region of its genome. We had previously found that the individual truncation (by mutation to alanine) of 28 of the 42 amino acid side chains per protomer involved in interactions between capsid pentameric subunits severely impaired infectivity. We have now used viral RNAs individually containing each of those 28 deleterious mutations (or a few others) to carry out a total of 96 transfections of susceptible cells, generally followed by passage(s) of the viral progeny in cell culture. The results revealed a very high frequency of fixation in the capsid of second-site, stereochemically diverse substitutions that compensated for the detrimental effect of primary substitutions at many different positions. Most second-site substitutions occurred at or near the capsid interpentamer interfaces and involved residues that are spatially very close to the originally substituted residue. However, others occurred far from the primary substitution, and even from the interpentamer interfaces. Remarkably, most second-site substitutions involved only a few capsid residues, which acted as “second-site hot spots.” Substitutions at these hot spots compensated for the deleterious effects of many different replacements at diverse positions. The remarkable capacity of the virus to respond to the introduction of deleterious mutations in the capsid with the frequent fixation of diverse second-site mutations, and the existence of second-site hot spots, may have important implications for virus evolution.
Micro-RNAs in thyroid neoplasms: molecular, diagnostic and therapeutic implications
Authors: Menon M P , Khan A
Published: July 2009

Micro-RNAs (miRNAs) belong to a class of small non-coding messenger RNA species that have emerged as potent regulators of a variety of biological processes including oncogenesis. They serve as master regulators with a single miRNA capable of regulating as many as 100 different target genes. Thyroid carcinomas encompass a wide spectrum ranging from well-differentiated thyroid carcinomas to poorly differentiated and anaplastic carcinoma. Currently, a considerable degree of interobserver variability exists in the morphological diagnosis of certain types of thyroid carcinomas especially the follicular pattern neoplasm. The prediction of progression of these differentiated carcinoma to more aggressive forms like poorly differentiated and anaplastic types is of considerable interest to physicians and pathologists for determining prognosis and making therapeutic decisions. Several investigators have proposed a more cohesive approach to thyroid cancer diagnosis incorporating molecular and proteomics based tools in addition to the conventional morphological diagnosis. In this context, miRNAs serve as an important diagnostic tool, and several studies have demonstrated their utility as class identifiers especially in the context of follicular thyroid carcinoma, papillary thyroid carcinoma and anaplastic thyroid carcinoma. Larger studies and/or meta-analyses could further delineate their role in predicting cancer progression and prognosis. In the same vein, miRNAs and their target genes could be targeted for novel therapeutics in the future.
A PEAK ENERGY CRITERION (P. E.) FOR THE SELECTION OF RESONANCE BANDS IN COMPLEX SHIFTED MORLET WAVELET (CSMW) BASED DEMODULATION OF DEFECTIVE ROLLING ELEMENT BEARINGS VIBRATION RESPONSE
Authors: GRYLLIAS KONSTANTINOS C. , ANTONIADIS IOANNIS
Published: July 2009

Complex Shifted Morlet Wavelets (CSMW) present a number of advantages when used for the demodulation of the vibration response of defective rolling element bearings: (A) They present the optimally located window simultaneously in the time and in the frequency domains; (B) They allow for the maximal time-frequency resolution; (C) The magnitudes of the complex wavelet coefficients in the time domain lead directly to the required envelope; (D) They allow for the optimal selection of both the center frequency and the bandwidth of the requested filter. A Peak Energy criterion (P. E.) is proposed in this paper for the simultaneous automatic selection of both the center frequency and the bandwidth of the relevant wavelet window to be used. As shown in a number of application cases, this criterion presents a more effective behavior than other criteria used (Crest Factor, Kurtosis, Smoothness Index, Number of Peaks), since it combines the advantages of energy based criteria, with criteria characterizing the spikiness of the response.