bluuebunny/crossref_metadata_2025 huggingface dataset:
Incorporating Traditional Culture Into Positive Youth Development Programs With American Indian/Alaska Native Youth
Authors: Kenyon DenYelle Baete , Hanson Jessica D.
Published: January 2012

Abstract— The majority of research and programs for American Indian/Alaska Native (AI/AN) youth focus on negative health behaviors and risks, ignoring the positive attributes that traditional AI/AN culture can provide. Therefore, it is critical to highlight the importance of incorporating traditional AI/AN worldviews and values into youth programming and health interventions. Accordingly, this article provides (a) a brief overview of AI/AN culture and historical policies and practices, (b) a description of the positive youth development (PYD) framework with a focus on research and programs that include AI/AN youth, (c) details on the strengths of AI/AN culture and how they can be incorporated into programming for AI/AN youth, and (d) examples of exemplary PYD programs for AI/AN youth.
The Need for a Broader Approach to Emotion Regulation Research in Autism
Authors: Mazefsky Carla A. , Pelphrey Kevin A. , Dahl Ronald E.
Published: January 2012

Abstract— Maladaptive emotional reactions are common among individuals diagnosed with an autism spectrum disorder (ASD) and often impair functioning. Most research on emotional processes in ASD has focused on the recognition of emotion in others. This article argues for a broader approach to affective research in ASD, one that includes investigations into emotional reactivity and regulation. For example, research has typically looked at perseveration in ASD from a cognitive or perceptual perspective, yet perseveration also appears to have emotional aspects. This article discusses examples of emotion regulation research in other populations to illustrate how this approach could inform understanding of perseveration in ASD, particularly related to affective interference with cognitive control. More broadly, it highlights the potential contributions of emotion regulation research in ASD in relation to improving treatment specificity, increasing understanding of individual differences and diagnostic conceptualizations, and, potentially, contributing to a deeper understanding the neurobehavioral underpinnings of ASD.
Genetic monitoring and complex population dynamics: insights from a 12‐year study of the Rio Grande silvery minnow
Authors: Osborne Megan J. , Carson Evan W. , Turner Thomas F.
Published: January 2012

The endangered Rio Grande silvery minnow persists as a remnant population in a highly fragmented and regulated arid‐land river system. The species is subject to dramatic annual fluctuations in density. Since 2003, the wild population has been supplemented by hatchery‐reared fish. We report on a 12‐year (1999–2010) monitoring study of genetic diversity and effective population size (Ne) of wild and hatchery stocks. Our goals were to evaluate how genetic metrics responded to changes in wild fish density and whether they corresponded to the number and levels of diversity of hatchery‐reared repatriates. Genetic diversity and all measures of Ne in the wild population did not correlate with wild fish density until hatchery supplementation began in earnest. Estimates of variance and inbreeding effective size were not correlated. Our results suggest source–sink dynamics where captive stocks form a genetically diverse source and the wild population behaves as a sink. Nevertheless, overall genetic diversity of silvery minnow has been maintained over the last decade, and we attribute this to a well‐designed and executed propagation management plan. When multiple factors like environmental fluctuation and hatchery supplementation act simultaneously on a population, interpretation of genetic monitoring data may be equally complex and require considerable ecological data.
Fault-Tolerant Control for Electric Ground Vehicles With Independently-Actuated In-Wheel Motors
Authors: Wang Rongrong , Wang Junmin
Published: January 2012

This paper presents an in-wheel motor fault diagnosis and fault-tolerant control method for four-wheel independently actuated (4WIA) electric vehicles. The 4WIA electric vehicle is one of the promising architectures for electric vehicles. While such a vehicle architecture greatly increases the flexibility for vehicle control, it also elevates the requirements on system reliability, safety, and fault tolerance due to the increased number of actuators. A fault diagnosis approach for finding the faulty in-wheel motor/motor driver pair is developed. The proposed diagnosis approach does not need an accurate knowledge on tire-road friction coefficient (TRFC) and is robust to tire force modeling inaccuracies. Based on the in-wheel motor/motor driver fault diagnosis mechanism, a control-allocation based vehicle fault-tolerant control system is designed to accommodate the in-wheel motor/motor driver fault by automatically allocating the control effort among other healthy wheels. Simulations using a high-fidelity, CarSim®, full-vehicle model show the effectiveness of the proposed in-wheel motor/motor driver fault diagnosis and fault-tolerant control approaches.
Better Research Needed on the Impact of Charter Schools
Authors: Betts Julian R. , Atkinson Richard C.
Published: January 2012

Randomized trials, although a promising approach, reflect impacts of only a limited subset of highly sought-after schools.
Composites Reinforced in Three Dimensions by Using Low Magnetic Fields
Authors: Erb Randall M. , Libanori Rafael , Rothfuchs Nuria , Studart André R.
Published: January 2012

Dispersal in 3D

The fabrication of composites containing small proportions of nanoparticles is limited by the ability to disperse the particles uniformly in all three dimensions.

Erb
et al.

(p.
199
; see the Perspective by

Fratzl

) describe a process for creating nanoparticle composites in which a magnetic field is used to align the nanoparticles. Surprisingly, the magnetic alignment of iron-oxide functionalized nanorods and discs was enabled using very small magnetic fields and low-volume fractions of magnetic nanoparticles, which allowed control of the orientation of the nanorods and discs three-dimensionally.
A DOC2 Protein Identified by Mutational Profiling Is Essential for Apicomplexan Parasite Exocytosis
Authors: Farrell Andrew , Thirugnanam Sivasakthivel , Lorestani Alexander , Dvorin Jeffrey D. , Eidell Keith P. , Ferguson David J.P. , Anderson-White Brooke R. , Duraisingh Manoj T. , Marth Gabor T. , Gubbels Marc-Jan
Published: January 2012

Parasite Invasion Strategy

Exocytosis is essential to the lytic cycle of apicomplexan parasites and is required for the pathogenesis of toxoplasmosis and malaria. DOC2 proteins recruit the membrane fusion machinery required for exocytosis in a Ca
2+
-dependent fashion.

Farrell
et al.

(p.
218
) describe the phenotype of a
Toxoplasma gondii
conditional mutant impaired in host cell invasion and egress. The phenotype was explained by a defect in secretion of the micronemes, an apicomplexan-specific organelle that contains adhesion proteins. A
T. gondii
Doc2 gene was identified, by whole-genome sequencing, to be involved in the secretion defect, and a conditional allele of the orthologous gene engineered into the malaria parasite,
Plasmodium falciparum
, also caused defects in microneme secretion.
Erasure of a Spinal Memory Trace of Pain by a Brief, High-Dose Opioid Administration
Authors: Drdla-Schutting Ruth , Benrath Justus , Wunderbaldinger Gabriele , Sandkühler Jürgen
Published: January 2012

Long-Lasting Pain Killers

Opioids are among the most widely used and extensively studied drugs in the world. A continuous application of relatively low opioid doses is thought to be necessary to maintain synaptic depression in pain pathways.

Drdla-Schutting
et al.

(p.
235
) found that a single opioid application could produce lasting reversal of synaptic long-term potentiation in pain pathways. Chronic pain is often associated with synaptic potentiation in nociceptive pathways. A brief, high-dose application of opioids depotentiated long-term potentiation in spinal pain pathways. The same dose also reversed hyperalgesia in behaving animals. Thus, opioids not only attenuate pain but also may eradicate a significant cause for chronic pain.
Universal Signatures of Fractionalized Quantum Critical Points
Authors: Isakov Sergei V. , Melko Roger G. , Hastings Matthew B.
Published: January 2012

Breaking Up the Indivisible

The famous Millikan oil drop experiment demonstrated that electric charge is quantized and cannot be divided into parts smaller than that of an electron. Decades later, the fractional quantum Hall effect was discovered that could only be explained through the existence of quasi-particles of fractional charge. Now,

Isakov
et al.

(p.
193
) numerically demonstrate the existence of an even more exotic object, a fractionalized quantum critical point (QCP), in the so-called Kagome lattice of bosons. Quantum Monte Carlo simulations were used to measure the critical exponents and revealed the fractionalization by comparison with a QCP of real bosons.
Direct Kinetic Measurements of Criegee Intermediate (CH
2
OO) Formed by Reaction of CH
2
I with O
2
Authors: Welz Oliver , Savee John D. , Osborn David L. , Vasu Subith S. , Percival Carl J. , Shallcross Dudley E. , Taatjes Craig A.
Published: January 2012

Criegee Sighting

Standard mechanistic models for the reaction of ozone with unsaturated hydrocarbons implicate a transient carbonyl oxide compound, termed the “Criegee intermediate,” which has largely eluded detection.

Welz
et al.

(p.
204
; see the Perspective by

Marston

) have now detected the compound by using mass spectrometry, following the low-pressure photolytic reaction of oxygen with diiodomethane, and measured its decay kinetics in the presence of nitric oxide, nitrogen dioxide, and sulfur dioxide. Reaction rates were higher than expected, suggesting that the intermediate may play a more prominent role in atmospheric chemistry than previously assumed.
iRhom2 Regulation of TACE Controls TNF-Mediated Protection Against
Listeria
and Responses to LPS
Authors: McIlwain David R. , Lang Philipp A. , Maretzky Thorsten , Hamada Koichi , Ohishi Kazuhito , Maney Sathish Kumar , Berger Thorsten , Murthy Aditya , Duncan Gordon , Xu Haifeng C. , Lang Karl S. , Häussinger Dieter , Wakeham Andrew , Itie-Youten Annick , Khokha Rama , Ohashi Pamela S. , Blobel Carl P. , Mak Tak W.
Published: January 2012

TACE Trafficking

The cytokine tumor necrosis factor (TNF) is a major driver of inflammation and contributes to the immune pathology seen in a variety of diseases, including inflammatory bowel disease, rheumatoid arthritis, and sepsis. Soluble TNF is produced by cleavage of its ectodomain by the ADAM family metalloprotease, TNFα-converting enzyme (TACE). However, the molecular regulation of TACE is not understood (see the Perspective by

Lichtenthaler

).

Adrain
et al.

(p.
225
) and

McIlwain
et al.

(p.
229
) now show that the rhomboid family member iRhom2 interacts with TACE in macrophages and is required for its proper intracellular trafficking and activation. In the absence of iRhom2, TACE was not released from the endoplasmic reticulum, and active protease did not reach the cell surface. Because of an inability to produce TNF, iRhom2-deficient mice were more resistant to lipopolysaccharide-induced septic shock but could not adequately control a
Listeria monocytogenes
infection.
An Elusive Intermediate Gets Caught
Authors: Marston George
Published: January 2012

Direct kinetic measurements elucidate the reactivity of an unstable atmospheric species that is central to atmospheric chemistry.
Tobacco Scientist's Election Tars Academy's Image
Authors: Hvistendahl Mara
Published: January 2012

The election of tobacco researcher Xie Jianping to the prestigious Chinese Academy of Engineering has become a touchstone for broad unease over the Chinese tobacco industry's encroachment in science.
Snapshots From the Meeting
Authors: Service Robert F.
Published: January 2012

Snapshots from the meeting include organic photovoltaics that break the 10% barrier, heat-stable stretchable electronics, a nanowire-based optical probe that can peer within individual cells, large-scale nanocarbons, and a light-sensitive protein that can turn a transistor on and off.
Evaluation of Biological Sample Preparation for Immunosignature-Based Diagnostics
Authors: Chase Brian Andrew , Johnston Stephen Albert , Legutki Joseph Barten
Published: January 2012

To address the need for a universal system to assess health status, we previously described a method termed “immunosignaturing” which splays the entire humoral antibody repertoire across a peptide microarray. Two important issues relative to the potential broad use of immunosignatures are sample preparation and stability. In the present study, we compared the immunosignatures developed from serum, plasma, saliva, and antibodies eluted from blood dried onto filter paper. We found that serum and plasma provide identical immunosignatures. Immunosignatures derived from dried blood also correlated well with those from nondried serum from the same individual. Immunosignatures derived from dried blood were capable of distinguishing naïve mice from those infected with influenza virus. Saliva was applied to the arrays, and the IgA immunosignature correlated strongly with that from dried blood. Finally, we demonstrate that dried blood retains immunosignature information even when exposed to high temperature. This work expands the potential diagnostic uses for immunosignatures. These features suggest that different forms of archival samples can be used for diagnosis development and that in prospective studies samples can be easily procured.
Genome Sequence of Lactobacillus rhamnosus ATCC 8530
Authors: Pittet Vanessa , Ewen Emily , Bushell Barry R. , Ziola Barry
Published: January 2012

Lactobacillus rhamnosus
is found in the human gastrointestinal tract and is important for probiotics. We became interested in
L. rhamnosus
isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available
L. rhamnosus
genome sequences.
Draft Genome Sequence of Pantoea ananatis B1-9, a Nonpathogenic Plant Growth-Promoting Bacterium
Authors: Kim Hyun Jung , Lee Jin Hee , Kang Beom Ryong , Rong Xiaoqing , McSpadden Gardener Brian B. , Ji Hyung Jin , Park Chang-Seuk , Kim Young Cheol
Published: January 2012

Pantoea ananatis
B1-9 is an endophytic Gram-negative rhizobacterium that was isolated for its ability to promote plant growth and improve crop yield in the field. Here we report the draft genome sequence of
P. ananatis
B1-9. Comparison of this sequence to the sequenced genome of a plant-pathogenic
P. ananatis
strain, LMG20103, indicated that the pathogenesis-related genes were absent, but a subset of gene functions that may be related to its plant growth promotion were present.
Complete Genome Sequence of Salmonella enterica Serovar Pullorum RKS5078
Authors: Feng Ye , Xu Hua-Feng , Li Qing-Hai , Zhang Si-Yao , Wang Chun-Xiao , Zhu Da-Ling , Cao Feng-Lin , Li Yong-Guo , Johnston Randal N. , Zhou Jin , Liu Gui-Rong , Liu Shu-Lin
Published: January 2012

Salmonella enterica
serovar Pullorum is a chicken-adapted pathogen, causing pullorum disease. Its strict host adaptation has been suspected to result in gene decay. To validate this hypothesis and identify the decayed genes, we sequenced the complete genome of
S.
Pullorum RKS5078. We found 263 pseudogenes in this strain and conducted functional analyses of the decayed genes.
First Comprehensive Evaluation of the M.I.C. Evaluator Device Compared to Etest and CLSI Broth Microdilution for MIC Testing of Aerobic Gram-Positive and Gram-Negative Bacterial Species
Authors: Rennie R. P. , Turnbull L. , Brosnikoff C. , Cloke J.
Published: January 2012

The M.I.C. Evaluator strip (Thermo Fisher Scientific, Basingstoke, United Kingdom) uses a methodology similar to that of Etest. In this first assessment of the M.I.C. Evaluator device, 409 strains of aerobic Gram-positive bacteria (staphylococci, streptococci, and enterococci) and 325 strains of
Enterobacteriaceae
,
Pseudomonas
species, and
Acinetobacter
species were tested by M.I.C. Evaluator strip, Etest, and broth microdilution as a reference standard. The Gram-positive bacteria included staphylococci (methicillin-resistant
Staphylococcus aureus
, methicillin-susceptible
S. aureus
, and coagulase-negative staphylococci),
Streptococcus pneumoniae
, beta-hemolytic streptococci and viridians group strains, vancomycin-resistant enterococci, and other enterococci. The Gram-negative bacteria included 250 strains of 60
Enterobacteriaceae
species plus 50
Pseudomonas
and 25
Acinetobacter
species. A total of 14 antimicrobial agents (depending on the species) were included. The same methodology and reading format were used for M.I.C. Evaluator strips and Etest. Broth microdilution methodology was performed according to CLSI document M07-A8. For the clinical strains, >95% of results were plus or minus one doubling dilution for all species. There were fewer than 5% minor errors, fewer than 3% major errors, and fewer than 1% very major errors. M.I.C. Evaluator strips and Etest often reported higher MICs than the reference broth microdilution method. The M.I.C. Evaluator strips provided results comparable to those of the predicate Etest device and are of value for the accurate testing of MICs for these important pathogens.
Comparison of Commercial Extraction Systems and PCR Assays for Quantification of Epstein-Barr Virus DNA Load in Whole Blood
Authors: Germi Raphaële , Lupo Julien , Semenova Touyana , Larrat Sylvie , Magnat Nelly , Grossi Laurence , Seigneurin Jean-Marie , Morand Patrice
Published: January 2012

The automation of DNA extraction and the use of commercial quantitative real-time PCR assays could help obtain more reliable results for the quantification of Epstein-Barr virus DNA loads (EBV VL). This study compared two automated extraction platforms and two commercial PCRs for measurement of EBV VL in 10 EBV specimens from Quality Control for Molecular Diagnostics (QCMD) and in 200 whole-blood (WB) specimens from transplant (
n
= 137) and nontransplant (
n
= 63) patients. The WB specimens were extracted using the QIAcube or MagNA Pure instrument; VL were quantified with the EBV R-gene quantification kit (Argene) or the artus EBV RG PCR kit (Qiagen) on the Rotor-Gene 6000 real-time analyzer; and the results were compared with those of a laboratory-developed PCR. DNA was extracted from the QCMD specimens by use of the QIAamp DNA minikit and was quantified by the three PCR assays. The extraction platforms and the PCR assays showed good correlation (
R
, >0.9;
P
, <0.0001), but as many as 10% discordant results were observed, mostly for low viral loads (<3 log
10
copies/ml), and standard deviations reached as high as 0.49 log
10
copy/ml. In WB but not in QCMD samples, Argene PCR tended to give higher VL values than artus PCR or the laboratory-developed PCR (mean difference for the 200 WB VL, −0.42 or −0.36, respectively). In conclusion, the two automated extraction platforms and the two PCRs provided reliable and comparable VL results, but differences greater than 0.5 log
10
copy/ml remained between the two commercial PCRs after common DNA extraction.
Genotype MTBDRplus for Direct Detection of Mycobacterium tuberculosis and Drug Resistance in Strains from Gold Miners in South Africa
Authors: Dorman Susan E. , Chihota Violet N. , Lewis James J. , van der Meulen Minty , Mathema Barun , Beylis Natalie , Fielding Katherine L. , Grant Alison D. , Churchyard Gavin J.
Published: January 2012

GenoType MTBDRplus is a molecular assay for detection of
Mycobacterium tuberculosis
and drug resistance. Assay performance as applied directly to consecutive unselected sputum samples has not been established. The objective of this study was to determine the accuracy of the MTBDRplus test for direct detection of
M. tuberculosis
(in sputum) and for drug resistance in consecutively submitted sputum samples. In this cross-sectional study in South Africa, one sputum specimen from each person suspected of having pulmonary tuberculosis was tested by smear microscopy, direct MTBDRplus, and Mycobacterial Growth Indicator Tube (MGIT) culture with MGIT drug susceptibility testing. MGIT results were the reference standard. We tested 2,510 sputum samples, and 529 (21.1%) were positive for
M. tuberculosis
by MGIT. Direct MTBDRplus identified
M. tuberculosis
in 256 of 529 specimens (sensitivity, 48.4%; 95% confidence interval [CI], 44.1, 52.7). The sensitivity of MTBDRplus for
M. tuberculosis
detection by sputum smear status was as follows: smear negative, 13.7% (95% CI, 9.8, 18.4); smear scanty, 46.2% (95% CI, 19.2, 74.9); smear 1+, 69.1% (95% CI, 55.2, 80.9); smear 2+, 86.3% (95% CI, 73.7, 94.3); smear 3+, 89.8% (95% CI, 83.7, 94.2). Direct MTBDRplus testing was negative for 1,594/1,612 sputum samples that were culture negative for
M. tuberculosis
(specificity, 98.9%; 95% CI, 98.2, 99.3). For specimens positive for
M. tuberculosis
by MTBDRplus, this assay's sensitivity and specificity for rifampin resistance were 85.7% (95% CI, 57.2, 98.2) and 96.6% (95% CI, 93.2, 98.6) and for isoniazid resistance they were 62.1% (95% CI, 42.3, 79.3) and 97.9% (95% CI, 94.8, 99.4). For sputum testing, the sensitivity of MTBDRplus is directly related to the specimen's bacillary burden. Our results support recommendations that the MTBDRplus test not be used for direct testing of smear-negative or paucibacillary sputum samples.
Bacteriuria Screening by Automated Whole-Field-Image-Based Microscopy Reduces the Number of Necessary Urine Cultures
Authors: Falbo Rosanna , Sala M. Roberta , Signorelli Silvia , Venturi Natascia , Signorini Stefano , Brambilla Paolo
Published: January 2012

We evaluated a new automated urine sediment analyzer that provides whole-field images for the screening of urine samples prior to bacterial culture. Sterile urine samples from 1,011 male and female outpatients and inpatients (mean age 54.7) with a urinary tract infection prevalence of 18.3% were studied. Screening rapidly provides negative results.
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
Authors: Larsen Mette V. , Cosentino Salvatore , Rasmussen Simon , Friis Carsten , Hasman Henrik , Marvig Rasmus Lykke , Jelsbak Lars , Sicheritz-Pontén Thomas , Ussery David W. , Aarestrup Frank M. , Lund Ole
Published: January 2012

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the “gold standard” of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at
www.cbs.dtu.dk/services/MLST
.
A Simple, Semiselective Medium for Anaerobic Isolation of Anginosus Group Streptococci from Patients with Chronic Lung Disease
Authors: Waite Richard D. , Wareham David W. , Gardiner Samuel , Whiley Robert A.
Published: January 2012

The anaerobic isolation of anginosus group streptococci (AGS) from respiratory specimens containing diverse microbiota using a semiselective blood agar medium incorporating nalidixic acid and sulfamethazine (NAS) is described. AGS were detected in 60% of tested sputa from patients with cystic fibrosis, chronic obstructive pulmonary disease, and bronchiectasis. This demonstrates NAS to be a diagnostic tool for detecting AGS within the complex microbial communities associated with chronic lung disorders.
Biological and Phylogenetic Characterization of a Genotype VII Newcastle Disease Virus from Venezuela: Efficacy of Field Vaccination
Authors: Perozo Francisco , Marcano Rosmar , Afonso Claudio L.
Published: January 2012

Here we report the biological and molecular characterization of a virulent genotype VII Newcastle disease virus (NDV) circulating in Venezuela and the assessment of the vaccination efficacy under field conditions compared to controlled rearing conditions. Biological pathotyping showed a mean embryo dead time of 50 h and an intracerebral pathogenicity index of 1.86. Sequence-based phylogenetic analysis demonstrated that the virus belongs to genotype VII in class II (a genotype often found in Asia and Africa), representing the first report of the presence of this genotype in the continent of South America. A vaccine-challenge trial in commercial broilers reared in fields or in a experimental setting included dual (live/killed) priming of 1-day-old chicks plus two live NDV and infectious bursal disease virus (IBDV) field vaccinations at days 7 and 17, followed by a very stringent genotype VII NDV challenge at day 28. Serology for NDV and IBDV, bursal integrity, and protection against NDV lethal challenge were assessed. At 28 days, field vaccinates showed significantly lower NDV (1,356 versus 2,384) and higher IBD (7,295 versus 1,489) enzyme-linked immunosorbent assay (ELISA) antibody titers than the experimentally reared birds. A lower bursal size and bursa-body weight ratio (
P
< 0.05) and higher bursa lesion score were also detected in the field set. Only 57.1% of field vaccinates survived the lethal challenge, differing (
P
< 0.05) from 90.5% survival in the experimental farm. Overall, results confirmed the presence of the genotype VII viruses in South America and suggest that field-associated factors such as immunosuppression compromise the efficacy of the vaccination protocols implemented.
Mast Cell-Induced Lung Injury in Mice Infected with H5N1 Influenza Virus
Authors: Hu Yanxin , Jin Yi , Han Deping , Zhang Guozhong , Cao Shanping , Xie Jingjing , Xue Jia , Li Yi , Meng Di , Fan Xiaoxu , Sun Lun-Quan , Wang Ming
Published: January 2012

Although an important role for mast cells in several viral infections has been demonstrated, its role in the invasion of highly pathogenic H5N1 influenza virus is unknown. In the present study, we demonstrate that mast cells were activated significantly by H5N1 virus (A/chicken/Henan/1/2004) infection bothin vivoandin vitro. Mast cells could possibly intensify the lung injury that results from H5N1 infection by releasing proinflammatory mediators, including histamine, tryptase, and gamma interferon (IFN-γ). Lung lesions and apoptosis induced by H5N1 infection were reduced dramatically by treatment with ketotifen, which is a mast cell degranulation inhibitor. A combination of ketotifen and the neuraminidase inhibitor oseltamivir protected 100% of the mice from death postinfection. In conclusion, our data suggest that mast cells play a crucial role in the early stages of H5N1 influenza virus infection and provide a new approach to combat highly pathogenic influenza virus infection.
Simian Virus 40 Strains with Novel Properties Generated by Replacing the Viral Enhancer with Synthetic Oligonucleotides
Authors: Günther Viola , Strassen Till , Lindert Uschi , Dagani Patrizia , Waldvogel Dominique , Georgiev Oleg , Schaffner Walter , Bethge Tobias
Published: January 2012

Typical enhancers of viral or cellular genes are approximately 100 to 400 bp long and contain several transcription factor binding sites. Previously, we have shown that simian virus 40 (SV40) genomic DNA that lacks its own enhancer can be used as an “enhancer trap” since it reacquires infectivity upon incorporation of heterologous enhancers. Here, we show that SV40 infectivity can be restored with synthetic enhancers that are assembled by the host cell. We found that several oligonucleotides, cotransfected with enhancerless SV40 DNA into host cells, were incorporated into the viral genome via cellular DNA end joining. The oligonucleotides tested included metal response elements (MREs), the binding sites for the transcription factor MTF-1, which induces gene activity in response to heavy metals. These recombinant SV40 strains showed preferential growth on cells overloaded with zinc or cadmium. We also cotransfected enhancerless SV40 DNA with oligonucleotides corresponding to enhancer motifs of human and mouse cytomegalovirus (HCMV and MCMV, respectively). In contrast to SV40 wild type, the viruses with cytomegalovirus-derived patchwork enhancers strongly expressed T-antigen in human HEK293 cells, accompanied by viral DNA replication. Occasionally, we also observed the assembly of functional viral genomes by incorporation of fragments of bovine DNA, an ingredient of the fetal calf serum in the medium. These fragments contained, among other sites, binding sites for AP-1 and CREB transcription factors. Taken together, our studies show that viruses with novel properties can be generated by intracellular incorporation of synthetic enhancer DNA motifs.
Filoviruses Require Endosomal Cysteine Proteases for Entry but Exhibit Distinct Protease Preferences
Authors: Misasi John , Chandran Kartik , Yang Jin-Yi , Considine Bryden , Filone Claire Marie , Côté Marceline , Sullivan Nancy , Fabozzi Giulia , Hensley Lisa , Cunningham James
Published: January 2012

Filoviruses are enveloped viruses that cause sporadic outbreaks of severe hemorrhagic fever [CDC, MMWR Morb. Mortal. Wkly. Rep. 50:73–77, 2001; Colebunders and Borchert, J. Infect. 40:16–20, 2000; Colebunders et al., J. Infect. Dis. 196(Suppl. 2):S148–S153, 2007; Geisbert and Jahrling, Nat. Med. 10:S110-S121, 2004]. Previous studies revealed that endosomal cysteine proteases are host factors for ebolavirus Zaire (Chandran et al., Science 308:1643–1645, 2005; Schornberg et al., J. Virol. 80:4174–4178, 2006). In this report, we show that infection mediated by glycoproteins from other phylogenetically diverse filoviruses are also dependent on these proteases and provide additional evidence indicating that they cleave GP1 and expose the binding domain for the critical host factor Niemann-Pick C1. Using selective inhibitors and knockout-derived cell lines, we show that the ebolaviruses Zaire and Cote d'Ivoire are strongly dependent on cathepsin B, while the ebolaviruses Sudan and Reston and Marburg virus are not. Taking advantage of previous studies of cathepsin B inhibitor-resistant viruses (Wong et al., J. Virol. 84:163–175, 2010), we found that virus-specific differences in the requirement for cathepsin B are correlated with sequence polymorphisms at residues 47 in GP1 and 584 in GP2. We applied these findings to the analysis of additional ebolavirus isolates and correctly predicted that the newly identified ebolavirus species Bundibugyo, containing D47 and I584, is cathepsin B dependent and that ebolavirus Zaire-1995, the single known isolate of ebolavirus Zaire that lacks D47, is not. We also obtained evidence for virus-specific differences in the role of cathepsin L, including cooperation with cathepsin B. These studies strongly suggest that the use of endosomal cysteine proteases as host factors for entry is a general property of members of the family
Filoviridae
.
Deep Sequencing Identifies Viral and Wasp Genes with Potential Roles in Replication of Microplitis demolitor Bracovirus
Authors: Burke Gaelen R. , Strand Michael R.
Published: January 2012

Viruses in the genus
Bracovirus
(BV) (
Polydnaviridae
) are symbionts of parasitoid wasps that specifically replicate in the ovaries of females. Recent analysis of expressed sequence tags from two wasp species,
Cotesia congregata
and
Chelonus inanitus
, identified transcripts related to 24 different nudivirus genes. These results together with other data strongly indicate that BVs evolved from a nudivirus ancestor. However, it remains unclear whether BV-carrying wasps contain other nudivirus-like genes and what types of wasp genes may also be required for BV replication.
Microplitis demolitor
carries
Microplitis demolitor
bracovirus (
Md
BV). Here we characterized
Md
BV replication and performed massively parallel sequencing of
M. demolitor
ovary transcripts. Our results indicated that
Md
BV replication begins in stage 2 pupae and continues in adults. Analysis of prereplication- and active-replication-stage ovary RNAs yielded 22 Gb of sequence that assembled into 66,425 transcripts. This breadth of sampling indicated that a large percentage of genes in the
M. demolitor
genome were sequenced. A total of 41 nudivirus-like transcripts were identified, of which a majority were highly expressed during
Md
BV replication. Our results also identified a suite of wasp genes that were highly expressed during
Md
BV replication. Among these products were several transcripts with conserved roles in regulating locus-specific DNA amplification by eukaryotes. Overall, our data set together with prior results likely identify the majority of nudivirus-related genes that are transcriptionally functional during BV replication. Our results also suggest that amplification of proviral DNAs for packaging into BV virions may depend upon the replication machinery of wasps.
The E1 Protein of Human Papillomavirus Type 16 Is Dispensable for Maintenance Replication of the Viral Genome
Authors: Egawa Nagayasu , Nakahara Tomomi , Ohno Shin-ichi , Narisawa-Saito Mako , Yugawa Takashi , Fujita Masatoshi , Yamato Kenji , Natori Yukikazu , Kiyono Tohru
Published: January 2012

Papillomavirus genomes are thought to be amplified to about 100 copies per cell soon after infection, maintained constant at this level in basal cells, and amplified for viral production upon keratinocyte differentiation. To determine the requirement for E1 in viral DNA replication at different stages, an E1-defective mutant of the human papillomavirus 16 (HPV16) genome featuring a translation termination mutation in the E1 gene was used. The ability of the mutant HPV16 genome to replicate as nuclear episomes was monitored with or without exogenous expression of E1. Unlike the wild-type genome, the E1-defective HPV16 genome became established in human keratinocytes only as episomes in the presence of exogenous E1 expression. Once established, it could replicate with the same efficiency as the wild-type genome, even after the exogenous E1 was removed. However, upon calcium-induced keratinocyte differentiation, once again amplification was dependent on exogenous E1. These results demonstrate that the E1 protein is dispensable for maintenance replication but not for initial and productive replication of HPV16.
Mutating Conserved Cysteines in the Alphavirus E2 Glycoprotein Causes Virus-Specific Assembly Defects
Authors: Snyder Anthony J. , Sokoloski Kevin J. , Mukhopadhyay Suchetana
Published: January 2012

There are 80 trimeric, glycoprotein spikes that cover the surface of an alphavirus particle. The spikes, which are composed of three E2 and E1 glycoprotein heterodimers, are responsible for receptor binding and mediating fusion between the viral and host-cell membranes during entry. In addition, the cytoplasmic domain of E2 interacts with the nucleocapsid core during the last stages of particle assembly, possibly to aid in particle stability. During assembly, the spikes are nonfusogenic until the E3 glycoprotein is cleaved from E2 in the
trans
-Golgi network. Thus, a mutation in E2 potentially has effects on virus entry, spike assembly, or spike maturation. E2 is a highly conserved, cysteine-rich transmembrane glycoprotein. We made single cysteine-to-serine mutations within two distinct regions of the E2 ectodomain in both Sindbis virus and Ross River virus. Each of the E2 Cys mutants produced fewer infectious particles than wild-type virus. Further characterization of the mutant viruses revealed differences in particle morphology, fusion activity, and polyprotein cleavage between Sindbis and Ross River virus mutants, despite the mutations being made at corresponding positions in E2. The nonconserved assembly defects suggest that E2 folding and function is species dependent, possibly due to interactions with a virus-specific chaperone.
Endogenous Lentiviruses in the Ferret Genome
Authors: Cui Jie , Holmes Edward C.
Published: January 2012

By screening 74 chordate genomes for endogenous lentiviruses using Pol sequences of exogenous lentiviruses as a reference, we identified a novel endogenous lentivirus in the genome of the ferret (
Mustela putorius furo
). Phylogenetic analysis suggested that the ferret endogenous lentivirus, denoted ELVmpf, diverged early in the evolution of the mammalian lentiviruses, although with a lack of resolution at key nodes. These data support the notion that lentiviruses have evolved on timescales of millions of years.
Postexposure Treatment with the Live-Attenuated Rabies Virus (RV) Vaccine TriGAS Triggers the Clearance of Wild-Type RV from the Central Nervous System (CNS) through the Rapid Induction of Genes Relevant to Adaptive Immunity in CNS Tissues
Authors: Li Jianwei , Ertel Adam , Portocarrero Carla , Barkhouse Darryll A. , Dietzschold Bernhard , Hooper D. Craig , Faber Milosz
Published: January 2012

Postexposure treatment (PET) of wild-type rabies virus (RV)-infected mice with a live-attenuated triple-glycoprotein RV variant (TriGAS) promotes survival but does not prevent the pathogenic RV from invading and replicating in the brain. Successful PET is associated with the induction of a robust virus-neutralizing antibody response and clearance of the wild-type RV from brain tissues. Comparison of the transcriptomes of normal mouse brain with those of wild-type-RV-infected mice that had received either mock or TriGAS PET treatment revealed that many of the host genes activated in the mock-treated mice represent type I interferon (IFN) response genes. This indicates that RV infection induces an early type I IFN response that is unable to control the infection. In contrast, most of the activated genes in the brain of the RV-infected, TriGAS-treated mouse play a role in adaptive immunity, including the regulation of T cell activation, T cell differentiation, and the regulation of lymphocyte and mononuclear cell proliferation. These findings were confirmed by quantitative PCR (qPCR) array studies, which showed that 3 genes in particular, encoding chemokine ligand 3 (Ccl3), natural killer cell activator 2 (interleukin 12B [IL-12B]), and granzyme A (GzmA), were activated earlier and to a greater extent in the brains of RV-infected mice treated with TriGAS than in the brains of mock-treated mice. The activation of these genes, known to play key roles in the regulation of lymphocyte and mononuclear cell proliferation, is likely an important part of the mechanism by which TriGAS mediates its PET activity.
Varicella-Zoster Virus Infects Human Embryonic Stem Cell-Derived Neurons and Neurospheres but Not Pluripotent Embryonic Stem Cells or Early Progenitors
Authors: Dukhovny Anna , Sloutskin Anna , Markus Amos , Yee Michael B. , Kinchington Paul R. , Goldstein Ronald S.
Published: January 2012

Pluripotent human stem cells are a powerful tool for the generation of differentiated cells that can be used for the study of human disease. We recently demonstrated that neurons derived from pluripotent human embryonic stem cells (hESC) can be infected by the highly host-restricted human alphaherpesvirus varicella-zoster virus (VZV), permitting the interaction of VZV with neurons to be readily evaluated in culture. In the present study, we examine whether pluripotent hESC and neural progenitors at intermediate stages of differentiation are permissive for VZV infection. We demonstrate here that VZV infection is blocked in naïve hESC. A block to VZV replication is also seen when a bacterial artificial chromosome (BAC) containing the VZV genome is transfected into hESC. In contrast, related alphaherpesviruses herpes simplex virus 1 (HSV-1) and pseudorabies virus (PrV) productively infect naïve hESC in a cell-free manner, and PrV replicates from a BAC transfected into hESC. Neurons differentiate from hESC via neural progenitor intermediates, as is the case in the embryo. The first
in vitro
stage at which permissiveness of hESC-derived neural precursors to VZV replication is observed is upon formation of “neurospheres,” immediately after detachment from the inductive stromal feeder layer. These findings suggest that hESC may be useful in deciphering the yet enigmatic mechanisms of specificity of VZV infection and replication.
Genome-Wide Networks of Amino Acid Covariances Are Common among Viruses
Authors: Donlin Maureen J. , Szeto Brandon , Gohara David W. , Aurora Rajeev , Tavis John E.
Published: January 2012

Coordinated variation among positions in amino acid sequence alignments can reveal genetic dependencies at noncontiguous positions, but methods to assess these interactions are incompletely developed. Previously, we found genome-wide networks of covarying residue positions in the hepatitis C virus genome (R. Aurora, M. J. Donlin, N. A. Cannon, and J. E. Tavis, J. Clin. Invest.
119:
225–236, 2009). Here, we asked whether such networks are present in a diverse set of viruses and, if so, what they may imply about viral biology. Viral sequences were obtained for 16 viruses in 13 species from 9 families. The entire viral coding potential for each virus was aligned, all possible amino acid covariances were identified using the observed-minus-expected-squared algorithm at a false-discovery rate of ≤1%, and networks of covariances were assessed using standard methods. Covariances that spanned the viral coding potential were common in all viruses. In all cases, the covariances formed a single network that contained essentially all of the covariances. The hepatitis C virus networks had hub-and-spoke topologies, but all other networks had random topologies with an unusually large number of highly connected nodes. These results indicate that genome-wide networks of genetic associations and the coordinated evolution they imply are very common in viral genomes, that the networks rarely have the hub-and-spoke topology that dominates other biological networks, and that network topologies can vary substantially even within a given viral group. Five examples with hepatitis B virus and poliovirus are presented to illustrate how covariance network analysis can lead to inferences about viral biology.
Acupuncture in practice: mapping the providers, the patients and the settings in a national cross-sectional survey
Authors: Hopton A K , Curnoe S , Kanaan M , MacPherson H
Published: January 2012

Background

There is relatively limited knowledge about the practitioners who provide acupuncture treatment within the UK, what conditions patients consult for and the treatment provided.

Objectives

To characterise the conditions treated and by whom, to examine characteristics of the treatment and to explore trends over time.

Method

A cross-sectional survey of the UK acupuncture practitioners was conducted; 800 practitioners were selected by computer-generated randomisation sequences from the four major UK-based professional associations. Data collected on the practitioners included demographic details, association membership, statutorily regulated status, practice setting, style of acupuncture, diagnostic methods and needle response sought. Practitioners recorded details of their 10 most recent patients, including demographic details, primary reason for consulting and lifestyle advice provided.

Results

330 practitioners responded comprising doctors (29%) physiotherapists (29%), nurses (15%) and independent acupuncturists (27%): 62% were women with median age of 48 years. The majority (68%) practiced in independent settings and 42% practiced within the National Health Service. Patients most commonly consulted for low back, neck, shoulder and knee pain, as well as headaches and migraine. Treatment for infertility by independent acupuncturists was found to have increased fivefold in 10 years.

Conclusion

Acupuncture provides a substantial contribution to the healthcare of the UK, with an estimated 4 million sessions provided annually. The primary complaints for which patients consult reflect the growing evidence base on acupuncture for these conditions. These data provide a basis for decision-making regarding policy and practice.
Risk and protective factors associated with gang affiliation among high-risk youth: a public health approach
Authors: McDaniel Dawn Delfin
Published: January 2012

Background

Gang violence accounted for 20% of homicides in large cities from 2002 to 2006. Preventing gang affiliation (ie, youth who either desire or have gang membership) might reduce subsequent gang activity. Previous research has focused on identifying risk factors for gang affiliation; however, little information is available on protective factors.

Aim

To identify risk and protective factors to provide more direction for gang violence prevention strategies.

Methods

The author analysed cross-sectional survey data from 4131 youths in grades 7, 9, 11 and 12. Data were collected in 2004 from students in a high-risk, urban public school district. Regression analyses were conducted to assess the association between gang affiliation and alcohol and drug use, delinquency, depressed mood, suicidal ideation, peer victimisation, parental monitoring and positive reinforcement, adult, family and peer support, coping skills, and school connectedness. Analyses were controlled for sex, race/ethnicity and age.

Results

An estimated 7% of youths were gang affiliated. Adjusting for all factors, gang affiliation was positively associated with engaging in any delinquent behaviours (prevalence OR: 2.07; 95% CI 1.18 to 3.64), frequent alcohol use (OR: 2.62; 95% CI 1.85 to 3.72) and frequent drug use (OR: 1.95; 95% CI 1.15 to 3.29). Gang affiliation was negatively associated with moderate levels of parental monitoring (OR: 0.67; 95% CI 0.54 to 0.85) and coping skills (OR: 0.54; 95% CI 0.42 to 0.71).

Conclusions

The findings suggest the potential benefit of increasing parental monitoring and coping skills and reducing delinquency, alcohol use and drug use to prevent gang affiliation.
Economic analysis of outbreaks of porcine reproductive and respiratory syndrome virus in nine sow herds
Authors: Nieuwenhuis N. , Duinhof T. F. , van Nes A.
Published: January 2012

The economic losses due to porcine reproductive and respiratory syndrome virus (PRRSv) outbreaks are reported in the literature to be substantially high, but recent figures are not available. The aim of this study was to quantify the economic effects of epidemic PRRSv outbreaks in Dutch sow herds. Nine sow herds were selected based on a confirmed PRRSv outbreak within those populations. The economic impact during the first 18 weeks after the outbreak was estimated by comparing the overall costs between pre‐ and postoutbreak periods, using different factors (production data, medication, diagnostics, labour, etc.). An outbreak of PRRSv resulted in a reduced number of sold pigs per sow of 1.7. The economic loss varied between €59 and €379 for one sow per 18‐week period outbreak. The mean loss per sow per outbreak was €126. The costs after the outbreak varied significantly from €3 to 160 per sow, due to the different methods used by farmers to tackle PRRSv outbreaks. The calculated costs in this study correlate with the costs of the initial outbreak in The Netherlands of 98 per sow.