bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrophysiological Recordings from the Drosophila Giant Fiber System (GFS)
Authors: Allen Marcus J. , Godenschwege Tanja A.
Published: July 2010

INTRODUCTION

The giant fiber system (GFS) of Drosophila is a well-characterized neuronal circuit that mediates the escape response in the fly. It is one of the few adult neural circuits from which electrophysiological recordings can be made routinely. This protocol describes a simple procedure for stimulating the giant fiber neurons directly in the brain of the adult fly and obtaining recordings from the output muscles of the GFS: the tergotrochanteral “jump” muscle (TTM) and the large indirect flight muscles (dorsal longitudinal muscles, or DLMs). It is a relatively noninvasive method that allows the investigator to stimulate the giant fibers in the brain and assay the function of several central synapses within this neural circuit by recording from the thoracic musculature.
Enzymatic Method for Extracting Extracellular DNA in Biofilm Matrix
Authors: Wu Jianfeng , Xi Chuanwu
Published: July 2010

INTRODUCTION

Biofilm is an accumulation of bacterial cells encapsulated in a structurally assembled extracellular polymer matrix that adheres to surfaces. The extracellular polymer matrix is composed mainly of polysaccharides, proteins, and amphiphilic polymers, which are secreted by microorganisms into their environment. Extracellular DNA (eDNA) was recently identified as one of the major components of extracellular polymeric substances (EPSs) and plays an important role in the development of biofilm, especially the early stages, by facilitating initial bacterial attachment and maintaining biofilm structure. More research is needed to fully elucidate the role of eDNA in biofilm development, and such investigations require that extraction of eDNA from the complex biofilm matrix is achieved without any genomic DNA contamination. However, the physical and chemical association of eDNA with extracellular proteins, polysaccharides, and other polymers in the complex matrix of EPS may hinder the liberation of eDNA. Therefore, it is difficult to release eDNA and other materials from the biofilm matrix solely by vortexing or homogenizing, and degradation of certain components of EPSs in the biofilm matrix is necessary in order to release eDNAs that may bind to these compounds. In this protocol, N-glycanase (glycoprotein-degradation hydrolase), dispersin B (biofilm-dispersing glycoside hydrolase), and proteinase K (protein hydrolase) are used to break down biofilm matrix for more efficient and complete extraction of eDNA.
EdU (5-Ethynyl-2′-Deoxyuridine) Labeling of Drosophila Mitotic Neuroblasts: Figure 1.
Authors: Daul Aric L. , Komori Hideyuki , Lee Cheng-Yu
Published: July 2010

INTRODUCTION

When examining mutants that affect cell fate as a result of altered asymmetric division patterns, it is important to determine whether cells are mitotically active. Chemical labeling of newly synthesized DNA (during S-phase) by incorporation of BrdU (5-bromo-2′-deoxyuridine) is informative because this thymidine analog can be used to pulse-label dividing cells and then chased to identify the progeny of dividing cells. Such pulse-chase experiments can provide additional insight by distinguishing actively dividing cells from those that might be arrested at a mitotic checkpoint. EdU (5-ethynyl-2′-deoxyuridine) is another thymidine analog that provides a more sensitive and practical alternative to BrdU. Incorporation of EdU is detected through its reaction with an azide dye that is small enough to penetrate tissues efficiently. Visualization of EdU is rapid and does not interfere with subsequent antibody staining. The use of EdU in labeling Drosophila mitotic neuroblasts is described here.
Efficacy, tolerability and pharmacokinetics of a modified release formulation of ADX10059, a negative allosteric modulator of metabotropic glutamate receptor 5: an esophageal pH‐impedance study in healthy subjects
Authors: Zerbib F. , Keywood C. , Strabach G.
Published: July 2010

Background  Animal studies show metabotropic glutamate receptor 5 inhibition reduces transient lower esophageal sphincter relaxations and increases lower esophageal sphincter tone. A preliminary, single‐day study, demonstrated oral ADX10059 reduced 24‐h esophageal acid exposure and clinical symptoms in gastro‐esophageal reflux disease (GERD) patients, but had suboptimal tolerability, ascribable to the compound’s rapid absorption. This study evaluated ADX10059 modified‐release (MR) formulation pharmacokinetics, tolerability, and pharmacodynamics.

Methods  Randomized, double‐blind placebo‐controlled study. Three groups of eight healthy, male subjects received placebo (n = 2) or ADX10059 (n = 6) 50, 125 or 250 mg b.i.d. for 6 days. Esophageal pH‐impedance was performed on day 1 and day 6 of treatment, for 1‐h fasting and for 4 h post refluxogenic meal. Treatment effect was determined by Kruskall–Wallis test and placebo comparison by Wilcoxon rank sum.

Key Results  Following placebo, reflux episodes increased from day 1 to day 6. Significant treatment effect was seen for total esophageal acid exposure (P = 0.048) and postprandial number of weakly acidic reflux episodes (P = 0.041). Significant differences from placebo were seen for 125 mg b.i.d.; 250 mg b.i.d. was not more effective than 125 mg b.i.d. Twice daily ADX10059 MR gave satisfactory 24‐h exposure and good tolerability.

Conclusions & Inferences  ADX10059 decreased reflux episodes in healthy subjects. The MR formulation is suitable for longer‐term treatment to evaluate symptom control in GERD patients.
Limb blastema cell: A stem cell for morphological regeneration
Authors: Tamura Koji , Ohgo Shiro , Yokoyama Hitoshi
Published: July 2010

The limb blastema cell, which is a major source of mesenchymal components in the limb regenerate, serves as a stem cell that possesses an undifferentiated state and multipotency. A remarkable property of the limb blastema cell can be seen in its capability for morphogenesis. Elucidation of the molecular basis for morphological regeneration is essential for success in organ regeneration in humans, and characterization of limb blastema cells will provide many insights into how to create three‐dimensional morphology during the regeneration process. In this review, we deal with positional memory, a key trait of the limb blastema cell in regard to morphological regeneration, making reference to classic surgical experiments, comparative descriptions of limb and fin blastemas, and genetic/epigenetic regulation of gene transcription. Urodele amphibians, anuran amphibians, and teleosts are likely to share fundamental mechanisms for morphological regeneration, but there are several differences in the process of regeneration, including the epigenetic conditions. Accumulation of knowledge of the molecular mechanisms and epigenetic modifications of gene activation in morphological regeneration of the model organisms for which an overview is provided in this review will lead to successful stimulation of regenerative capacity in amniotes, which only have a limited capability for morphological regeneration.
Oxidative‐inflammatory damage in cirrhosis: Effect of vitamin E and a fermented papaya preparation
Authors: Marotta Francesco , Yoshida Chisato , Barreto Rafael , Naito Yasuhiro , Packer Lester
Published: July 2010

Background and Aim:  Oxidative DNA damage occurs as an early event in hepatitis C virus (HCV) infection and is an indication of the potential for carcinogenesis. The aim of this study was to test a novel antioxidant/immunomodulator in patients with HCV‐related cirrhosis.

Methods:  The study group consisted of 50 patients with HCV‐related cirrhosis with transaminase values less than twofold increased (alanine aminotransferase [ALT] < 80 IU/L). Patients underwent a standardized food‐vitamin composition assessment and were assessed for dietary intake, nutritional status and iron level. Patients were randomly allocated into two groups and then given either α‐tocopherol 900 IU/day or 9 g/day of a fermented papaya preparation (FPP, Immun‐Age, Osato Research Institute, Gifu, Japan) at bedtime for 6 months. Ten healthy subjects served as controls. Patients were checked monthly for: routine tests, redox status (reduced glutathione, glutathione peroxidase, oxidized glutathione, malondialdehyde), plasma α‐tocopherol, 8‐hydroxy‐deoxy‐guanidine (8‐OHdG) level in circulating leukocyte DNA and serum levels of cytokines.

Results:  Patients with cirrhosis showed a significant imbalance of redox status (low antioxidants/high oxidative stress markers) (P < 0.005 vs controls). Neither treatment regimen affected transaminases as a whole. However, vitamin E supplementation almost normalized ALT only in the limited vitamin‐E‐deficient subgroup. A significant improvement of redox status was obtained by both regimens. However, only FPP significantly decreased 8‐OHdG and the improvement of cytokine balance with FPP was significantly better than with vitamin E treatment (P < 0.05).

Conclusions:  Although the present data seem to suggest a potential supportive role of antioxidants/immunomodulators as FPP in HCV patients, more studies are needed to substantiate their effect on the natural history of the disease.
MICROSTRUCTURAL EFFECTS ON THE SMALL FATIGUE CRACK BEHAVIOUR OF AN ALUMINUM ALLOY PLATE
Authors: Zabett A. , Plumtree A.
Published: July 2010

Abstract A study has been conducted on the initiation and growth of fatigue cracks in the three principal directions of an aluminium alloy 2024‐T351 plate tested under stress control (R, minimum to maximum stress =– 1). Early and multiple fatigue crack nucleation from broken Al7Cu2Fe second phase particles resulted in shorter lives for the longitudinal direction specimens in the medium to long life regime. Although fatigue cracks nucleated in large surface grains, rather than at broken particles, the lives of the short‐transverse direction specimens were marginally longer. Cracks also nucleated in large surface grains in the transverse direction specimens, yet the average fatigue lives were about twice as long. This was the consequence of wider slip bands and fewer initial micro‐cracks.
Australian evidence on student expectations and perceptions of introductory business finance
Authors: Balachandran Balasingham , Skully Michael , Tant Kevin , Watson John
Published: July 2010

This study examines the differences in perceptions and expectations between students at the Caulfield and Peninsula campuses of Monash University with different entrance criteria and degree availability to determine whether two different introductory finance subjects should be offered rather than one. Results reported in this study suggest that students at the Caulfield campus are interested in studying a challenging introductory finance subject, whereas students at the Peninsula campus perceived that introductory finance is ‘difficult’. Capital structure and cost of capital topics are statistically significantly ranked higher by Caulfield students than Peninsula students. The results reported in this study revealed that two different introductory finance subjects would be more effective. The core subject at the finance major campus (Caulfield) follows a traditional structure with more emphasis on finance theory, whereas the new subject at the non‐finance campus (Peninsula) places greater emphasis on applications.
Changed cortical activity after anterior cruciate ligament reconstruction in a joint position paradigm: an EEG study
Authors: Baumeister J. , Reinecke K. , Weiss M.
Published: July 2010

After reconstruction of the anterior cruciate ligament (ACL) afferent proprioceptive information from the knee joint may be altered. In order to examine changes in central activation patterns, spectral features of the electroencephalography (EEG) were measured. Patients after ACL reconstruction and healthy controls carried out an knee‐angle reproduction task in a groups × limbs × trials design. Cortical activity was recorded using international standards. FFT were conducted to determine power at Theta, Alpha‐1, Alpha‐2 and Beta‐1. Statistics show significantly larger aberrations in the reconstructed limbs compared with the controls whereas there are no differences between the uninvolved land controls. Brain activity demonstrates significantly higher frontal Theta‐power (F3, F4, F8) in both limbs of the ACL group vs the controls and a significantly higher Alpha‐2 power was shown in the ACL‐reconstructed limb compared with controls at parietal positions (P3, P4). No such differences were found between the uninvolved side and the controls. The EEG was able to measure a change in joint position sense at the cortical level after the reconstruction of the ACL. The results of these findings might indicate differences in focused attention with involvement of the anterior cingulate cortex (frontal Theta) and sensory processing in the parietal somatosensory cortex (Alpha‐2).
Studying the costs of crime across offender trajectories
Authors: Cohen Mark A. , Piquero Alex R. , Jennings Wesley G.
Published: July 2010

Research Summary

Longitudinal studies of delinquency and crime have generated an important source of descriptive information regarding patterns of offending across the life course, and have helped inform and spur theoretical and methodological contributions. One particular method that has received considerable attention is based on offending trajectories, but applications of this method have not extended much beyond descriptive accounts of offending. This study links offender trajectories to monetary costs associated with criminal offending by members of the Second Philadelphia Birth Cohort. Results indicate that chronic offenders who frequently commit crimes when they are young turn to more serious crimes when they are adults and impose far greater costs than low‐frequency chronic offenders and those whose offending peaks during adolescence.

Policy Implications

Preventing individuals from becoming high‐rate chronic offenders would yield significant cost savings of more than $200 million. In terms of overall costs, offending frequency accounts for the bulk of costs in the juvenile years, whereas the seriousness of individual crimes drives total costs in the adult years. Moreover, because some trajectory groups impose higher costs in their juvenile years, whereas others impose higher costs in their adult years, policies that target particular (high‐rate chronic) trajectory groups as opposed to all at‐risk youth, for example, have the potential to provide significantly greater benefits at lower costs. These findings suggest that the allocation of prevention and intervention efforts should be targeted differentially across the offender population, with those individuals exhibiting early, frequent, and chronic offending deserving the most attention. Promising programs aimed at such individuals include early childhood prevention programs, such as those based on family–parent training, self‐control improvement, and cognitive therapies.
Field emission behavior study of multiwalled carbon nanotube yarn under the influence of adsorbents
Authors: Liu Peng , Jiang Kaili , Wei Yang , Liu Kai , Liu Liang , Fan Shoushan
Published: July 2010

The authors have studied the field emission (FE) behavior of multiwalled carbon nanotube (MWCNT) yarn at different temperatures. By analyzing how the FE characteristics change with temperature and the residual gas spectra of the vacuum chamber, it was concluded that the intrinsic FE of MWCNTs follows the Fowler–Nordheim theory fairly well, and the deviation from the theory at low temperature (below ∼700 K) is caused by the influence of adsorption. Water is deduced to be the dominant species that influences the FE. It was found that the adsorbents can be desorbed at high voltage due to the Joule heating of the FE current. The adsorption was deduced to be physical from the value of the desorption temperature. The FE current recovery time at different pressures shows that monolayer adsorption is enough to cause obvious FE current changes.
Newly developed electron beam stepper for nanoimprint mold fabrication
Authors: Okada Makoto , Kishiro Takashi , Yanagihara Kaori , Ataka Masashi , Anazawa Norimichi , Matsui Shinji
Published: July 2010

The nanoimprint molds are usually fabricated by electron beam (EB) lithography. In recent years, a large-area mold fabrication with a high throughput is required to use nanoimprint lithography to produce devices in mass production. Using a conventional EB system to fabricate a large-area mold requires a very long exposure. To shorten the time, the authors have newly developed an EB stepper. The hole pattern (300 nm hole and 600 nm pitch) was exposed on a whole 4 in. SiO2/Si substrate with ZEP-520A (ZEON Co.) positive resist by the stepper. The exposure time was only 15 min. After this exposure, the authors did reactive ion etching and thermal nanoimprinting by using the 4 in. SiO2/Si mold. The whole patterns on the 4 in. SiO2/Si mold were imprinted on a 4 in. Si substrate coated with ZEP-520A.
The Unconscious Will: How the Pursuit of Goals Operates Outside of Conscious Awareness
Authors: Custers Ruud , Aarts Henk
Published: July 2010

Blissful Ignorance?

Although recent research has established the remarkable ways in which cognitive processing can occur without our being aware of it—for instance, casual exposure to retiree-related words, such as “elderly,” induces us to walk more slowly—behavior that is directed toward goals still seems to be the product of conscious thought.
Custers and Aarts
(p.
47
) review a set of findings that point toward the possibility that goals may, in fact, also be vulnerable to manipulation via avenues of which we remain blissfully unaware. They place these results within a framework that reveals how thoroughly unconscious processes permeate our everyday activities.
Science Attachés in Embassies
Authors: El-Baz Farouk
Published: July 2010

The United States' intention to increase International Cooperation in Science and technology (S&T) is welcome news. Such efforts would be particularly effective in the Muslim world, where countries are in need of the economic development that would result from improvements in their S&T sectors. Last year, President Obama appointed three Science Envoys to Muslim-majority countries: Bruce Alberts, former president of the U.S. National Academy of Sciences (and current Editor-in-Chief of
Science
); Ahmed Zewail, Nobel Laureate and professor at the California Institute of Technology; and Elias Zerhouni, former director of the U.S. National Institutes of Health. The appointment of several more Science Envoys is expected soon. However, this promising new initiative will require committed institutional support, which can best be provided by the appointment of Science (and Technology) Attachés in the relevant U.S. embassies.
Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
Authors: Yi Xin , Liang Yu , Huerta-Sanchez Emilia , Jin Xin , Cuo Zha Xi Ping , Pool John E. , Xu Xun , Jiang Hui , Vinckenbosch Nicolas , Korneliussen Thorfinn Sand , Zheng Hancheng , Liu Tao , He Weiming , Li Kui , Luo Ruibang , Nie Xifang , Wu Honglong , Zhao Meiru , Cao Hongzhi , Zou Jing , Shan Ying , Li Shuzheng , Yang Qi , Asan  , Ni Peixiang , Tian Geng , Xu Junming , Liu Xiao , Jiang Tao , Wu Renhua , Zhou Guangyu , Tang Meifang , Qin Junjie , Wang Tong , Feng Shuijian , Li Guohong , Huasang  , Luosang Jiangbai , Wang Wei , Chen Fang , Wang Yading , Zheng Xiaoguang , Li Zhuo , Bianba Zhuoma , Yang Ge , Wang Xinping , Tang Shuhui , Gao Guoyi , Chen Yong , Luo Zhen , Gusang Lamu , Cao Zheng , Zhang Qinghui , Ouyang Weihan , Ren Xiaoli , Liang Huiqing , Zheng Huisong , Huang Yebo , Li Jingxiang , Bolund Lars , Kristiansen Karsten , Li Yingrui , Zhang Yong , Zhang Xiuqing , Li Ruiqiang , Li Songgang , Yang Huanming , Nielsen Rasmus , Wang Jun , Wang Jian
Published: July 2010

No Genetic Vertigo

Peoples living in high altitudes have adapted to their situation (see the Perspective by

Storz

). To identify gene regions that might have contributed to high-altitude adaptation in Tibetans,

Simonson
et al.

(p.
72
, published online 13 May) conducted a genome scan of nucleotide polymorphism comparing Tibetans, Han Chinese, and Japanese, while

Yi
et al.

(p.
75
) performed comparable analyses on the coding regions of all genes—their exomes. Both studies converged on a gene,
endothelial Per-Arnt-Sim domain protein 1
(also known as
hypoxia-inducible factor 2
α), which has been linked to the regulation of red blood cell production. Other genes identified that were potentially under selection included adult and fetal hemoglobin and two functional candidate loci that were correlated with low hemoglobin concentration in Tibetans. Future detailed functional studies will now be required to examine the mechanistic underpinnings of physiological adaptation to high altitudes.
Tropical Arthropod Species, More or Less?
Authors: May Robert M.
Published: July 2010

New research on tropical beetles could help narrow estimates of how many species live on Earth.
Increased Mutagenesis and Unique Mutation Signature Associated with Mitotic Gene Conversion
Authors: Hicks Wade M. , Kim Minlee , Haber James E.
Published: July 2010

Dodgy Repair

A double-strand break (DSB) in genomic DNA poses a serious threat to genome stability, and yet vertebrate cells may suffer 10 or more DSBs every time the genome is replicated. Pathways have thus evolved that can recognize and repair DSBs before they reek havoc in the cell.

Hicks
et al.

(p.
82
) show that this repair can come at a price. DSBs were induced in the budding yeast genome. Repair of a break was accompanied by a massive increase in the rate of mutation in the vicinity of the break. The mutations generated displayed a specific “signature” that included the copying of divergent sequences from other chromosomes.
A Guardian of T Cell Fate
Authors: Di Santo James P.
Published: July 2010

The repressive activity of a transcription factor allows thymocytes to shed alternative cell fates and become T cells.
Evidence for Free-Flowing Supersolid Slipping Away?
Authors: Cho Adrian
Published: July 2010

An experiment has called into question the first, best evidence for supersolidity. What physicists took as a sign of resistance-free flow at very low temperatures is in fact a manifestation of an odd softening of the solid at slightly higher temperatures, says the author of the work.
A Role for Epigenetics in Cognition
Authors: Miller Greg
Published: July 2010

The push to show that epigenetics can translate early life experiences into lasting changes in behavior has been accompanied by a parallel surge of interest in how chemical modifications to DNA can affect cognition.
In Archaeobotanist's Hands, Tiny Fossils Yield Big Answers
Authors: Balter Michael
Published: July 2010

Dolores Piperno's microscopic techniques overcame skeptics and revolutionized views of early agriculture in the Americas.
Righting a 65-Year-Old Wrong
Authors: Stone Richard
Published: July 2010

The head of Indonesia's best known science institute was accused of contaminating vaccines and executed by Japanese forces in 1945; new evidence suggests he was innocent.
Candidemia Surveillance in Brazil: Evidence for a Geographical Boundary Defining an Area Exhibiting an Abatement of Infections by
Candida albicans
Group 2 Strains
Authors: Da Matta Daniel A. , Melo Analy S. , Colombo Arnaldo L. , Frade Joao P. , Nucci Marcio , Lott Timothy J.
Published: July 2010

Prospective population surveillance has been conducted for candidemia in Brazil (A. L. Colombo, M. Nucci, B. J. Park, et al., J. Clin. Microbiol. 44:2816-2823, 2006). In the present study, a total of 63 isolates from 61 patients, representing 11 medical centers from nine geographic regions, were characterized by multilocus sequence typing (MLST). A total of 48 unique profiles or diploid sequence types (DSTs) were observed, with nine new sequence types (STs) and 32 new DSTs. There were no apparent correlations between center/region and DST patterns. Subtypes were compared to those in a known characterized reference set, including a large database of strains obtained worldwide. Significantly, only one
C. albicans
group 2 isolate was found in our collection, although isolates from this particular group are commonly found worldwide. These data, combined with information from other previously reported studies, establish a statistically significant diminishment of group 2 strains in Central and South America, including Mexico and portions of the Southwestern United States.
Multiplex PCR for Differential Identification of Broad Tapeworms (Cestoda:Diphyllobothrium) Infecting Humans
Authors: Wicht Barbara , Yanagida Tetsuya , Scholz Tomáš , Ito Akira , Jiménez Juan A. , Brabec Jan
Published: July 2010

The specific identification of broad tapeworms (genusDiphyllobothrium) infecting humans is very difficult to perform by morphological observation. Molecular analysis by PCR and sequencing represents the only reliable tool to date to identify these parasites to the species level. Due to the recent spread of human diphyllobothriosis in several countries, a correct diagnosis has become crucial to better understand the distribution and the life cycle of human-infecting species as well as to prevent the introduction of parasites to disease-free water systems. Nevertheless, PCR and sequencing, although highly precise, are too complicated, long, and expensive to be employed in medical laboratories for routine diagnostics. In the present study we optimized a cheap and rapid molecular test for the differential identification of the most commonDiphyllobothriumspecies infecting humans (D. latum,D. dendriticum,D. nihonkaiense, andD. pacificum), based on a multiplex PCR with the cytochromecoxidase subunit 1 gene of mitochondrial DNA.
Real-Time PCR Assay Provides Reliable Assessment of Intrapartum Carriage of Group B
Streptococcus
Authors: Alfa Michelle J. , Sepehri Shadi , De Gagne Pat , Helawa Michael , Sandhu Gunwat , Harding Godfrey K. M.
Published: July 2010

The objective of this study was to determine the reliability of the real-time PCR assay for determining the group B
Streptococcus
(GBS) status of women in labor. In this prospective study we compared the results of culture and PCR testing of vaginal and rectal samples collected by nursing staff when women were in labor. Patients' charts were also reviewed to obtain relevant information about pregnancy risk factors. Our results demonstrated a sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 90.5%, 96.1%, 86.4%, and 97.4%, respectively, for rapid PCR. Of the 196 women evaluated, 29 (14.8%) presented with unknown GBS status, 11 (37.9%) of whom received unnecessary intrapartum antibiotics. The rapid real-time PCR test was robust and was able to reliably detect the presence of GBS in women in labor within 1 h of specimen submission to the laboratory. We recommend that the rapid PCR test be targeted to women who present in labor with unknown GBS status. In cases where the laboratory does not offer 24-h availability of testing, sample collection followed by PCR testing the next morning is still valuable and provides reliable results 24 to 48 h faster than culture and will aid appropriate decision-making regarding continuing or stopping antibiotics for neonates of women with unknown GBS status.
Chlamydophila psittaci
Zoonotic Risk Assessment in a Chicken and Turkey Slaughterhouse
Authors: Dickx V. , Geens T. , Deschuyffeleer T. , Tyberghien L. , Harkinezhad T. , Beeckman D. S. A. , Braeckman L. , Vanrompay D.
Published: July 2010

Chlamydophila psittaci
causes respiratory disease in poultry and can be transmitted to humans. We conducted a
C. psittaci
zoonotic risk assessment study of a chicken and turkey slaughterhouse. Eighty-five percent of the slaughtered chicken flocks tested positive by PCR and culture. Genotype D was discovered. Fifty-seven percent of the slaughtered turkey flocks tested positive by PCR and culture. Genotype D was present. For the chicken slaughterhouse employees, 7.5% and 6% tested positive for
C. psittaci
by PCR and culture, respectively. In the turkey slaughterhouse, 87% and 61% of the employees tested positive by PCR and culture, respectively. All genotyped human samples contained genotype D. Using stationary bioaerosol monitoring by means of an MAS-100 ecosampler and ChlamyTrap collection medium, chlamydial DNA, and viable organisms were detected in both the chicken and turkey slaughterhouses. Positive air samples were most frequently found in the animal reception area and evisceration room. Zoonotic transmissions were very common, especially from processed turkeys. Accurate diagnostic monitoring and reporting of
C. psittaci
infections should be promoted in poultry workers.
Coxiella burnetii
Infection of a Steller Sea Lion (
Eumetopias jubatus
) Found in Washington State
Authors: Kersh Gilbert J. , Lambourn Dyanna M. , Self Joshua S. , Akmajian Adrianne M. , Stanton James B. , Baszler Timothy V. , Raverty Stephen A. , Massung Robert F.
Published: July 2010

A pregnant sea lion stranded in the State of Washington was found to have placentitis caused by a unique strain of
Coxiella burnetii
. This is the first description of coxiellosis in a sea lion and suggests that exposure to sea lions may be a risk factor for contracting Q fever.
Frequency of Detection of Upper Respiratory Tract Viruses in Patients Tested for Pandemic H1N1/09 Viral Infection
Authors: Nisii Carla , Meschi Silvia , Selleri Marina , Bordi Licia , Castilletti Concetta , Valli Maria Beatrice , Lalle Eleonora , Lauria Francesco Nicola , Piselli Pierluca , Lanini Simone , Ippolito Giuseppe , Di Caro Antonino , Capobianchi Maria Rosaria
Published: July 2010

Molecular testing of 270 consecutive nasopharyngeal swab samples taken in May and June 2009 and 274 samples from patients hospitalized between July and December 2009 showed similar findings of respiratory viruses, with influenza A pandemic virus H1N1/09 being the most represented, followed by human parainfluenza virus type 3 and rhinoviruses. Statistical analyses suggested virus cocirculation in the absence of viral interference.
False-Positive Transcription-Mediated Amplification Assay Detection of West Nile Virus in Blood from a Patient with Viremia Caused by an Usutu Virus Infection
Authors: Gaibani Paolo , Pierro Anna Maria , Cavrini Francesca , Rossini Giada , Landini Maria Paola , Sambri Vittorio
Published: July 2010

Detection of West Nile virus (WNV) by nucleic acid amplification technology (NAAT) is used widely to screen blood and organ donations in areas where WNV is endemic. We report a false-positive result of a WNV transcription-mediated amplification assay (TMA) in a patient with viremia that was caused by Usutu virus, a mosquito-borne flavivirus.
Adaptation of Pandemic H1N1 Influenza Viruses in Mice
Authors: Ilyushina Natalia A. , Khalenkov Alexey M. , Seiler Jon P. , Forrest Heather L. , Bovin Nicolai V. , Marjuki Henju , Barman Subrata , Webster Robert G. , Webby Richard J.
Published: July 2010

The molecular mechanism by which pandemic 2009 influenza A viruses were able to sufficiently adapt to humans is largely unknown. Subsequent human infections with novel H1N1 influenza viruses prompted an investigation of the molecular determinants of the host range and pathogenicity of pandemic influenza viruses in mammals. To address this problem, we assessed the genetic basis for increased virulence of A/CA/04/09 (H1N1) and A/TN/1-560/09 (H1N1) isolates, which are not lethal for mice, in a new mammalian host by promoting their mouse adaptation. The resulting mouse lung-adapted variants showed significantly enhanced growth characteristics in eggs, extended extrapulmonary tissue tropism, and pathogenicity in mice. All mouse-adapted viruses except A/TN/1-560/09-MA2 grew faster and to higher titers in cells than the original strains. We found that 10 amino acid changes in the ribonucleoprotein (RNP) complex (PB2 E158G/A, PA L295P, NP D101G, and NP H289Y) and hemagglutinin (HA) glycoprotein (K119N, G155E, S183P, R221K, and D222G) controlled enhanced mouse virulence of pandemic isolates. HA mutations acquired during adaptation affected viral receptor specificity by enhancing binding to α2,3 together with decreasing binding to α2,6 sialyl receptors. PB2 E158G/A and PA L295P amino acid substitutions were responsible for the significant enhancement of transcription and replication activity of the mouse-adapted H1N1 variants. Taken together, our findings suggest that changes optimizing receptor specificity and interaction of viral polymerase components with host cellular factors are the major mechanisms that contribute to the optimal competitive advantage of pandemic influenza viruses in mice. These modulators of virulence, therefore, may have been the driving components of early evolution, which paved the way for novel 2009 viruses in mammals.
Gene Expression Differences in Lungs of Mice during Secondary Immune Responses to Respiratory Syncytial Virus Infection
Authors: Schuurhof Annemieke , Bont Louis , Pennings Jeroen L. A. , Hodemaekers Hennie M. , Wester Piet W. , Buisman Annemarie , de Rond Lia C. G. H. , Widjojoatmodjo Myra N. , Luytjes Willem , Kimpen Jan L. L. , Janssen Riny
Published: July 2010

Vaccine-induced immunity has been shown to alter the course of a respiratory syncytial virus (RSV) infection both in murine models and in humans. To elucidate which mechanisms underlie the effect of vaccine-induced immunity on the course of RSV infection, transcription profiles in the lungs of RSV-infected mice were examined by microarray analysis. Three models were used: RSV reinfection as a model for natural immunity, RSV challenge after formalin-inactivated RSV vaccination as a model for vaccine-enhanced disease, and RSV challenge following vaccination with recombinant RSV virus lacking the G gene (ΔG-RSV) as a model for vaccine-induced immunity. Gene transcription profiles, histopathology, and viral loads were analyzed at 1, 2, and 5 days after RSV challenge. On the first 2 days after challenge, all mice displayed an expression pattern in the lung similar of that found in primary infection, showing a strong innate immune response. On day 5 after RSV reinfection or after challenge following ΔG-RSV vaccination, the innate immune response was waning. In contrast, in mice with vaccine-enhanced disease, the innate immune response 5 days after RSV challenge was still present even though viral replication was diminished. In addition, only in this group was Th2 gene expression induced. These findings support a hypothesis that vaccine-enhanced disease is mediated by prolonged innate immune responses and Th2 polarization in the absence of viral replication.
Nonintegrating Foamy Virus Vectors
Authors: Deyle David R. , Li Yi , Olson Erik M. , Russell David W.
Published: July 2010

Foamy viruses (FVs), or spumaviruses, are integrating retroviruses that have been developed as vectors. Here we generated nonintegrating foamy virus (NIFV) vectors by introducing point mutations into the highly conserved DD35E catalytic core motif of the foamy virus integrase sequence. NIFV vectors produced high-titer stocks, transduced dividing cells, and did not integrate. Cells infected with NIFV vectors contained episomal vector genomes that consisted of linear, 1-long-terminal-repeat (1-LTR), and 2-LTR circular DNAs. These episomes expressed transgenes, were stable, and became progressively diluted in the dividing cell population. 1-LTR circles but not 2-LTR circles were found in all vector stocks prior to infection. Residual integration of NIFV vectors occurred at a frequency 4 logs lower than that of integrase-proficient FV vectors. Cre recombinase expressed from a NIFV vector mediated excision of both an integrated, floxed FV vector and a gene-targeted
neo
expression cassette, demonstrating the utility of these episomal vectors. The broad host range and large packaging capacity of NIFV vectors should make them useful for a variety of applications requiring transient gene expression.
Reduced Fitness in Cell Culture of HIV-1 with Nonnucleoside Reverse Transcriptase Inhibitor-Resistant Mutations Correlates with Relative Levels of Reverse Transcriptase Content and RNase H Activity in Virions
Authors: Wang Jiong , Bambara Robert A. , Demeter Lisa M. , Dykes Carrie
Published: July 2010

Nonnucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are important components of multidrug therapy for HIV-1. Understanding the effect of NNRTI-resistant mutants on virus replication and reverse transcriptase (RT) function is valuable for the development of extended-spectrum NNRTIs. We measured the fitness of six NNRTI-resistant mutants, the K103N, V106A, Y181C, G190A, G190S, and P236L viruses, using a flow cytometry-based cell culture assay. K103N and Y181C viruses had fitness similar to that of the wild type while V106A, G190A, G190S, and P236L viruses had reduced fitness. We also determined the biochemical correlates of fitness by measuring the RNase H and polymerization activities of recombinant mutant RTs and virion-associated RTs. The RNase H activities of recombinant and virion-associated RTs correlated with the relative fitness for each mutant. K103N and Y181C mutants had normal RNase H activity; V106A, G190A, and G190S mutants had moderate reductions in activity; and the P236L mutant had substantially reduced activity. With the exception of the P236L mutant, reduced fitness correlates with low virion-associated polymerization efficiency and reduced RT content. Reduced polymerase function in virions derived from low RT content rather than an intrinsic polymerization defect in each RT protein. In conclusion, severe defects in RNase H activity alone, exemplified by the P236L mutant, appear sufficient to cause a substantial reduction in fitness. For the other NNRTI mutants, reductions in RT content decreased both polymerization and RNase H activity in virions. RNase H reduction was compounded by intrinsic RNase H defects in the mutant RTs.
Human Enterovirus 109: a Novel Interspecies Recombinant Enterovirus Isolated from a Case of Acute Pediatric Respiratory Illness in Nicaragua
Authors: Yozwiak Nathan L. , Skewes-Cox Peter , Gordon Aubree , Saborio Saira , Kuan Guillermina , Balmaseda Angel , Ganem Don , Harris Eva , DeRisi Joseph L.
Published: July 2010

Enteroviruses (
Picornaviridae
family) are a common cause of human illness worldwide and are associated with diverse clinical syndromes, including asymptomatic infection, respiratory illness, gastroenteritis, and meningitis. In this study, we report the identification and complete genome sequence of a novel enterovirus isolated from a case of acute respiratory illness in a Nicaraguan child. Unbiased deep sequencing of nucleic acids from a nose and throat swab sample enabled rapid recovery of the full-genome sequence. Phylogenetic analysis revealed that human enterovirus 109 (EV109) is most closely related to serotypes of human enterovirus species C (HEV-C) in all genomic regions except the 5′ untranslated region (5′ UTR). Bootstrap analysis indicates that the 5′ UTR of EV109 is likely the product of an interspecies recombination event between ancestral members of the HEV-A and HEV-C groups. Overall, the EV109 coding region shares 67 to 72% nucleotide sequence identity with its nearest relatives. EV109 isolates were detected in 5/310 (1.6%) of nose and throat swab samples collected from children in a pediatric cohort study of influenza-like illness in Managua, Nicaragua, between June 2007 and June 2008. Further experimentation is required to more fully characterize the pathogenic role, disease associations, and global distribution of EV109.
A Short N-Terminal Peptide Motif on Flavivirus Nonstructural Protein NS1 Modulates Cellular Targeting and Immune Recognition
Authors: Youn Soonjeon , Cho Hyelim , Fremont Daved H. , Diamond Michael S.
Published: July 2010

Flavivirus NS1 is a versatile nonstructural glycoprotein, with intracellular NS1 functioning as an essential cofactor for viral replication and cell surface and secreted NS1 antagonizing complement activation. Even though NS1 has multiple functions that contribute to virulence, the genetic determinants that regulate the spatial distribution of NS1 in cells among different flaviviruses remain uncharacterized. Here, by creating a panel of West Nile virus-dengue virus (WNV-DENV) NS1 chimeras and site-specific mutants, we identified a novel, short peptide motif immediately C-terminal to the signal sequence cleavage position that regulates its transit time through the endoplasmic reticulum and differentially directs NS1 for secretion or plasma membrane expression. Exchange of two amino acids within this motif reciprocally changed the cellular targeting pattern of DENV or WNV NS1. For WNV, this substitution also modulated infectivity and antibody-induced phagocytosis of infected cells. Analysis of a mutant lacking all three conserved N-linked glycosylation sites revealed an independent requirement of N-linked glycans for secretion but not for plasma membrane expression of WNV NS1. Collectively, our experiments define the requirements for cellular targeting of NS1, with implications for the protective host responses, immune antagonism, and association with the host cell sorting machinery. These studies also suggest a link between the effects of NS1 on viral replication and the levels of secreted or cell surface NS1.
Identification of a Critical T(Q/D/E)x
5
ADx
2
(I/L) Motif from Primate Lentivirus Vif Proteins That Regulate APOBEC3G and APOBEC3F Neutralizing Activity
Authors: Dang Ying , Wang Xiaojun , York Ian A. , Zheng Yong-Hui
Published: July 2010

Primate lentiviruses are unique in that they produce several accessory proteins to help in the establishment of productive viral infection. The major function of these proteins is to clear host resistance factors that inhibit viral replication. Vif is one of these proteins. It functions as an adaptor that binds to the cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) and bridges them to a cullin 5 (Cul5) and elongin (Elo) B/C E3 ubiquitin ligase complex for proteasomal degradation. So far, 11 discontinuous domains in Vif have been identified that regulate this degradation process. Here we report another domain, T(Q/D/E)x
5
ADx
2
(I/L), which is located at residues 96 to 107 in the human immunodeficiency virus type 1 (HIV-1) Vif protein. This domain is conserved not only in all HIV-1 subtypes but also in other primate lentiviruses, including HIV-2 and simian immunodeficiency virus (SIV), which infects rhesus macaques (SIVmac) and African green monkeys (SIVagm). Mutations of the critical residues in this motif seriously disrupted Vif's neutralizing activity toward both A3G and A3F. This motif regulates Vif interaction not only with A3G and A3F but also with Cul5. When this motif was inactivated in the HIV-1 genome, Vif failed to exclude A3G and A3F from virions, resulting in abortive HIV replication in nonpermissive human T cells. Thus, T(Q/D/E)x
5
ADx
2
(I/L) is a critical functional motif that directly supports the adaptor function of Vif and is an attractive target for inhibition of Vif function.
Mutational and Metal Binding Analysis of the Endonuclease Domain of the Influenza Virus Polymerase PA Subunit
Authors: Crépin Thibaut , Dias Alexandre , Palencia Andrés , Swale Christopher , Cusack Stephen , Ruigrok Rob W. H.
Published: July 2010

Influenza virus polymerase initiates the biosynthesis of its own mRNAs with capped 10- to 13-nucleotide fragments cleaved from cellular (pre-)mRNAs. Two activities are required for this cap-snatching activity: specific binding of the cap structure and an endonuclease activity. Recent work has shown that the cap-binding site is situated in the central part of the PB2 subunit and that the endonuclease activity is situated in the N-terminal domain of the PA subunit (PA-Nter). The influenza endonuclease is a member of the PD-(D/E)XK family of nucleases that use divalent metal ions for nucleic acid cleavage. Here we analyze the metal binding and endonuclease activities of eight PA-Nter single-point mutants. We show by calorimetry that the wild-type active site binds two Mn
2+
ions and has a 500-fold higher affinity for manganese than for magnesium ions. The endonuclease activity of the isolated mutant domains are compared with the cap-dependent transcription activities of identical mutations in trimeric recombinant polymerases previously described by other groups. Mutations that inactivate the endonuclease activity in the isolated PA-Nter knock out the transcription but not replication activity in the recombinant polymerase. We confirm the importance of a number of active-site residues and identify some residues that may be involved in the positioning of the RNA substrate in the active site. Our results validate the use of the isolated endonuclease domain in a drug-design process for new anti-influenza virus compounds.
GRID VERTEX-UNFOLDING ORTHOSTACKS
Authors: DEMAINE ERIK D. , IACONO JOHN , LANGERMAN STEFAN
Published: July 2010

Biedl et al.1 presented an algorithm for unfolding orthostacks into one piece without overlap by using arbitrary cuts along the surface. They conjectured that orthostacks could be unfolded using cuts that lie in a plane orthogonal to a coordinate axis and containing a vertex of the orthostack. We prove the existence of a vertex unfolding using only such cuts.
A METHOD FOR THE REGISTRATION OF A KNOWN CAD MODEL INTO THE WORKSPACE FRAME OF A ROBOT
Authors: ARISTOS DIMITRIS , TZAFESTAS SPYROS
Published: July 2010

In many robotic applications it is required to manipulate a specific rigid object whose CAD model is known a priori, but its position and orientation in space are unknown. This category of tasks includes piercing, painting or iron welding on some specific points of the rigid object's surface. For this kind of tasks to become feasible the CAD data of the rigid object should be registered into the robot's workspace frame, so that the robot arm becomes aware of the position and orientation of the rigid body with reference to its own flange or base coordinate frame. In order to achieve this goal several techniques from the fields of image processing, 3D modeling and robot kinematics should be combined. This paper provides a convenient combination of such methods that can be used for the successful on-line registration of a rigid object's CAD data to the robot's workspace frame.
NEW APPROACH TO MULTI-LEVEL PROCESSOR SCHEDULING
Authors: SEMNANI SAMANEH HOSSEINI , ZAMANIFAR KAMRAN
Published: July 2010

The problem of finding the best quantum time in multi-level processor scheduling is addressed in this paper. Processor scheduling is one of the most important issues in operating systems design. Different schedulers are introduced to solve this problem. In one scheduling approach, processes are placed in different queues according to their properties, and the processor allocates time to each queue iteratively. One of the most important parameters of a processor's efficiency in this approach is the amount of time slices associated to each processor queue. In this paper, an ant colony optimization (ACO) algorithm is presented to solve the problem of finding appropriate time slices to assign to each processor queue. In this technique, each ant tries to find an appropriate scheduling. Ant algorithm searches the problem space to find the best scheduling. The quality of each ant's solution is evaluated using a new fitness function. This fitness function is designed according to the evaluation parameters of each processor queue and also according to the queue theory's relations. Also a heuristic function is presented which prompts ant to select better solutions. Computational tests are presented and the comparisons made with genetic algorithm (GA) and particle swarm optimization (PSO) algorithms which try to solve same problem. The results show the efficiency of this algorithm.