bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrical and microstructural properties of N+ ion-implanted ZnO and ZnO:Ag thin films
Authors: Myers Michelle A. , Myers Michael T. , Tsai Chen-Fong , Lee Joon Hwan , Lu Tianlin , Shao Lin , Wang Haiyan
Published: February 2011

ZnO and Ag-doped ZnO films were grown on sapphire (0001) substrates by pulsed-laser deposition in vacuum both with and without oxygen at 700 °C. N+ ions were implanted in these films at room temperature and at 300 °C to a dose of 1×1014 cm−2 at 50 keV. Hall measurements indicate that ZnO films deposited in vacuum without oxygen and implanted with N+ at elevated temperatures are p-type with a hole-carrier concentration of 6×1016 cm−3, a mobility of 2.1 cm2 V−1 s−1, and a resistivity of 50 Ω cm. Both scanning-electron microscopy and transmission-electron microscopy studies on the implanted films reveal microstructural differences in grain size, surface roughness, and the nature of defects, which may impact the activation of N atoms as p-type carriers. Low-energy ion implantation at elevated temperatures is shown to be an effective method to introduce p-type N dopants into ZnO, which minimizes defect clustering and promotes defect annihilation during implantation.
The dynamic behavior of squash balls
Authors: Lewis Gareth J. , Arnold J. Cris , Griffiths Iwan W.
Published: February 2011

The behavior of a squash ball constitutes an excellent case study of the dynamic behavior of rubbery materials. It is shown that the complex viscoelastic behavior of rubber can be investigated using simple drop bounce tests and compression tests. The drop tests show that the coefficient of restitution increases as the ball temperature increases. The compression tests show that as the speed of compression increases or as the ball temperature decreases, the compressive force and the energy loss both increase. These effects are due to the viscoelastic nature of the rubber and are an excellent example of the time-temperature equivalence of polymers. Compression tests were performed on balls with small holes at the base to separate the effects of the internal air pressure from the material deformation. It was found that the internal air pressure contributed about one-third to the compressive force, but contributed little to energy loss. This behavior shows that the rubber material dominates the rebound behavior and that the normal warming up process at the start of a squash game is important to raise the temperature of the rubber rather than to increase the internal air pressure.
Studio optics: Adapting interactive engagement pedagogy to upper-division physics
Authors: Sorensen Christopher M. , McBride Dyan L. , Rebello N. Sanjay
Published: February 2011

The use of interactive engagement strategies to improve learning in introductory physics is not new, but have not been used as often for upper-division physics courses. We describe the development and implementation of a Studio Optics course for upper-division physics majors at Kansas State University. The course adapts a three-stage Karplus learning cycle and other elements to foster an environment that promotes learning through an integration of lecture, laboratories, and problem solving. Some of the instructional materials are described. We discuss the evaluation of the course using data collected from student interviews, a conceptual survey, an attitudinal survey, and the instructor’s reflections. Overall, students responded positively to the new format and showed modest gains in learning. The instructor’s experiences compared favorably with the traditional course that he had taught in the past.
A Hand to Support the Implantation Window
Authors: Hewitt Sylvia C. , Korach Kenneth S.
Published: February 2011

A signaling pathway connects ovarian hormones to preparation of the mammalian uterus for pregnancy.
Gene Patents: The Shadow of Uncertainty
Authors: Cook-Deegan Robert
Published: February 2011

Uncertainty regarding gene patents will affect what genomic technologies get developed in the real world.
Formulation Development of Retrocyclin 1 Analog RC-101 as an Anti-HIV Vaginal Microbicide Product
Authors: Sassi A. B. , Cost M. R. , Cole A. L. , Cole A. M. , Patton D. L. , Gupta P. , Rohan L. C.
Published: February 2011

RC-101 is a synthetic microbicide analog of retrocyclin, which has shown
in vitro
activity against X4 and R5 HIV-1. In an effort to develop a safe and effective RC-101 vaginal microbicide product, we assessed safety in
ex vivo
macaque and human models and efficacy using
in vitro
and
ex vivo
models. A polyvinyl-alcohol vaginal film containing RC-101 (100 μg/film) was developed. Formulation assessment was conducted by evaluating disintegration, drug content, mechanical properties, and stability. Efficacy was evaluated by
in vitro
peripheral blood mononuclear cells (PBMC) assay and
ex vivo
human ectocervical tissue explant model.
Ex vivo
safety studies were conducted by exposing RC-101 to an excised monkey reproductive tract and excised human ectocervical tissue. RC-101 100 μg films were shown to be safe to human and monkey tissue and effective against HIV-1
in vitro
and
ex vivo
in human ectocervical tissue. The 90% inhibitory concentration (IC
90
) for RC-101 films at 2,000 μg (IC
90
= 57.5 μM) using an
ex vivo
model was 10-fold higher than the IC
90
observed using an
in vitro
model (IC
90
= 5.0 μM). RC-101 films were stable for 1 month at 25°C, with
in vitro
bioactivity maintained for up to 6 months. RC-101 was developed in a quick-dissolve film formulation that was shown to be safe in an
ex vivo
model and effective in
in vitro
and
ex vivo
models. RC-101 film formulations were shown to maintain bioactivity for a period of 6 months. Findings from the present study contribute to the development of a safe and effective topical microbicide product.
In Vitro
Susceptibility of Burkholderia vietnamiensis to Aminoglycosides
Authors: Jassem Agatha N. , Zlosnik James E. A. , Henry Deborah A. , Hancock Robert E. W. , Ernst Robert K. , Speert David P.
Published: February 2011

Burkholderia cepacia
complex (BCC) bacteria are opportunistic pathogens that can cause severe disease in cystic fibrosis (CF) patients and other immunocompromised individuals and are typically multidrug resistant. Here we observed that unlike other BCC species, most environmental and clinical
Burkholderia vietnamiensis
isolates were intrinsically susceptible to aminoglycosides but not to cationic antimicrobial peptides or polymyxin B. Furthermore, strains acquired aminoglycoside resistance during chronic CF infection, a phenomenon that could be induced under tobramycin or azithromycin pressure
in vitro
. In comparing susceptible and resistant
B. vietnamiensis
isolates, no gross differences in lipopolysaccharide structure were observed, all had lipid A-associated 4-amino-4-
deoxy
-
l
-arabinose residues, and all were resistant to the permeabilizing effects of aminoglycosides, a measure of drug entry via self-promoted uptake. However, susceptible isolates accumulated 5 to 6 times more gentamicin than a resistant isolate, and aminoglycoside susceptibility increased in the presence of an efflux pump inhibitor.
B. vietnamiensis
is therefore unusual among BCC bacteria in its susceptibility to aminoglycosides and capacity to acquire resistance. Aminoglycoside resistance appears to be due to decreased cellular accumulation as a result of active efflux.
Impact of a Low-Oxygen Environment on the Efficacy of Antimicrobials against Intracellular Chlamydia trachomatis
Authors: Shima Kensuke , Szaszák Márta , Solbach Werner , Gieffers Jens , Rupp Jan
Published: February 2011

Emergence of chronic inflammation in the urogenital tract induced by
Chlamydia trachomatis
infection in females is a long-standing concern. To avoid the severe sequelae of
C. trachomatis
infection, such as pelvic inflammatory diseases (PID), ectopic pregnancies, and tubal infertility, antibiotic strategies aim to eradicate the pathogen even in asymptomatic and uncomplicated infections. Although first-line antimicrobials have proven successful for the treatment of
C. trachomatis
infection, treatment failures have been observed in a notable number of cases. Due to the obligate intracellular growth of
C. trachomatis
, reliable antimicrobial susceptibility assays have to consider environmental conditions and host cell-specific factors. Oxygen concentrations in the female urogenital tract are physiologically low and decrease further during an inflammatory process. We compared MIC testing and time-kill curves (TKC) for doxycycline, azithromycin, rifampin, and moxifloxacin under hypoxia (2% O
2
) and normoxia (20% O
2
). While low oxygen availability only moderately decreased the antichlamydial activity of azithromycin in conventional MIC testing (0.08 μg/ml versus 0.04 μg/ml;
P
< 0.05), TKC analyses revealed profound divergences for antibiotic efficacies between the two conditions. Thus,
C. trachomatis
was significantly less rapidly killed by doxycycline and azithromycin under hypoxia, whereas the efficacies of moxifloxacin and rifampin remained unaffected using concentrations at therapeutic serum levels. Chemical inhibition of multidrug resistance protein 1 (MDR-1), but not multidrug resistance-associated protein 1 (MRP-1), restored doxycycline activity against intracellular
C. trachomatis
under hypoxia. We suggest careful consideration of tissue-specific characteristics, including oxygen availability, when testing antimicrobial activities of antibiotics against intracellular bacteria.
Antimicrobial Activity of CXA-101, a Novel Cephalosporin Tested in Combination with Tazobactam against Enterobacteriaceae, Pseudomonas aeruginosa, and Bacteroides fragilis Strains Having Various Resistance Phenotypes
Authors: Sader Helio S. , Rhomberg Paul R. , Farrell David J. , Jones Ronald N.
Published: February 2011

CXA-101, a novel oxyimino-aminothiazolyl cephalosporin, CXA-201 (CXA-101 combined with tazobactam), and various comparators were susceptibility tested by broth microdilution methods against 1,301 well-characterized clinical strains collected worldwide, including ceftazidime-resistant members of the family
Enterobacteriaceae
and
Klebsiella pneumoniae
carbapenemase (KPC)- and extended-spectrum β-lactamase (ESBL)-producing strains of
Pseudomonas aeruginosa
and
Bacteroides fragilis
. CXA-201 was 2- to 32-fold more active than ceftazidime and piperacillin-tazobactam against ceftazidime-resistant
Enterobacteriaceae
species but less active than cefepime for some species. CXA-101 and CXA-201 were very active against
P. aeruginosa
(MIC
50
, 1 μg/ml for both compounds), including imipenem-resistant strains.
Antibiotic Treatment Alters the Colonic Mucus Layer and Predisposes the Host to Exacerbated
Citrobacter rodentium
-Induced Colitis
Authors: Wlodarska M. , Willing B. , Keeney K. M. , Menendez A. , Bergstrom K. S. , Gill N. , Russell S. L. , Vallance B. A. , Finlay B. B.
Published: February 2011

Antibiotics are often used in the clinic to treat bacterial infections, but the effects of these drugs on microbiota composition and on intestinal immunity are poorly understood.
Citrobacter rodentium
was used as a model enteric pathogen to investigate the effect of microbial perturbation on intestinal barriers and susceptibility to colitis. Streptomycin and metronidazole were used to induce alterations in the composition of the microbiota prior to infection with
C. rodentium
. Metronidazole pretreatment increased susceptibility to
C. rodentium
-induced colitis over that of untreated and streptomycin-pretreated mice, 6 days postinfection. Both antibiotic treatments altered microbial composition, without affecting total numbers, but metronidazole treatment resulted in a more dramatic change, including a reduced population of
Porphyromonadaceae
and increased numbers of lactobacilli. Disruption of the microbiota with metronidazole, but not streptomycin treatment, resulted in an increased inflammatory tone of the intestine characterized by increased bacterial stimulation of the epithelium, altered goblet cell function, and thinning of the inner mucus layer, suggesting a weakened mucosal barrier. This reduction in mucus thickness correlates with increased attachment of
C. rodentium
to the intestinal epithelium, contributing to the exacerbated severity of
C. rodentium
-induced colitis in metronidazole-pretreated mice. These results suggest that antibiotic perturbation of the microbiota can disrupt intestinal homeostasis and the integrity of intestinal defenses, which protect against invading pathogens and intestinal inflammation.
Induction of Experimental Endocarditis by Continuous Low-Grade Bacteremia Mimicking Spontaneous Bacteremia in Humans
Authors: Veloso T. R. , Amiguet M. , Rousson V. , Giddey M. , Vouillamoz J. , Moreillon P. , Entenza J. M.
Published: February 2011

Transient high-grade bacteremia following invasive procedures carries a risk of infective endocarditis (IE). This is supported by experimental endocarditis. On the other hand, case-control studies showed that IE could be caused by cumulative exposure to low-grade bacteremia occurring during daily activities. However, no experimental demonstration of this latter possibility exists. This study investigated the infectivity in animals of continuous low-grade bacteremia compared to that of brief high-grade bacteremia. Rats with aortic vegetations were inoculated with
Streptococcus intermedius
,
Streptococcus gordonii
or
Staphylococcus aureus
(strains Newman and P8). Animals were challenged with 10
3
to 10
6
CFU. Identical bacterial numbers were given by bolus (1 ml in 1 min) or continuous infusion (0.0017 ml/min over 10 h). Bacteremia was 50 to 1,000 times greater after bolus than during continuous inoculation. Streptococcal bolus inoculation of 10
5
CFU infected 63 to 100% vegetations compared to 30 to 71% infection after continuous infusion (
P
> 0.05). When increasing the inoculum to 10
6
CFU, bolus inoculation infected 100% vegetations and continuous infusion 70 to 100% (
P
> 0.05).
S. aureus
bolus injection of 10
3
CFU infected 46 to 57% valves. This was similar to the 53 to 57% infection rates produced by continuous infusion (
P
> 0.05). Inoculation of 10
4
CFU of
S. aureus
infected 80 to 100% vegetations after bolus and 60 to 75% after continuous infusion (
P
> 0.05). These results show that high-level bacteremia is not required to induce experimental endocarditis and support the hypothesis that cumulative exposure to low-grade bacteremia represents a genuine risk of IE in humans.
Reductionistic and Holistic Science
Authors: Fang Ferric C. , Casadevall Arturo
Published: February 2011

A reductionistic approach to science, epitomized by molecular biology, is often contrasted with the holistic approach of systems biology. However, molecular biology and systems biology are actually interdependent and complementary ways in which to study and make sense of complex phenomena.
Impact of
Salmonella
Infection on Host Hormone Metabolism Revealed by Metabolomics
Authors: Antunes L. Caetano M. , Arena Ellen T. , Menendez Alfredo , Han Jun , Ferreira Rosana B. R. , Buckner Michelle M. C. , Lolić Petra , Madilao Lufiani L. , Bohlmann Jörg , Borchers Christoph H. , Finlay B. Brett
Published: February 2011

The interplay between pathogens and their hosts has been studied for decades using targeted approaches, such as the analysis of mutants and host immunological responses. Although much has been learned from such studies, they focus on individual pathways and fail to reveal the global effects of infection on the host. To alleviate this issue, high-throughput methods, such as transcriptomics and proteomics, have been used to study host-pathogen interactions. Recently, metabolomics was established as a new method to study changes in the biochemical composition of host tissues. We report a metabolomic study of
Salmonella enterica
serovar Typhimurium infection. Our results revealed that dozens of host metabolic pathways are affected by
Salmonella
in a murine infection model. In particular, multiple host hormone pathways are disrupted. Our results identify unappreciated effects of infection on host metabolism and shed light on mechanisms used by
Salmonella
to cause disease and by the host to counter infection.
Development of a Real-Time PCR Assay for Detecting and Quantifying Human Bocavirus 2
Authors: Xu Zi-qian , Cheng Wei-xia , Li Bo-wen , Li Jie , Lan Bei , Duan Zhao-jun
Published: February 2011

Human bocavirus 2 (HBoV2) is a parvovirus that has been recently identified in stool samples from children. Any association between the virus and clinical disease is unclear. A rapid, reliable diagnostic method is necessary to address this issue. In this study, we developed a sensitive and specific HBoV2 quantitative real-time PCR assay that targets the HBoV2
NP-1
gene, based on the TaqMan method. The assay could reproducibly detect 10 copies of a recombinant DNA plasmid containing a partial region of the HBoV2 genome, with a dynamic range of 8 log units (10
1
to 10
8
copies). A clinical evaluation detected HBoV2 in 85 (24.6%) of 345 children with gastroenteritis, with viral loads ranging from 1.67 × 10
2
to 4.27 × 10
9
copies per ml of stool specimen.
Genotypes and Characteristics of Clustering and Drug Susceptibility of Mycobacterium tuberculosis Isolates Collected in Heilongjiang Province, China
Authors: Wang Juan , Liu Yan , Zhang Chun-Lei , Ji Bin-Ying , Zhang Liu-Zhuo , Shao Yong-Zhen , Jiang Shui-Lian , Suzuki Yasuhiko , Nakajima Chie , Fan Chang-Long , Ma Yuan-Ping , Tian Geng-Wen , Hattori Toshio , Ling Hong
Published: February 2011

For the last decade China has occupied second place, after India, among the top five countries with high burdens of tuberculosis (TB). Heilongjiang Province is located in northeastern China. The prevalence of drug-resistant TB in Heilongjiang Province is higher than the average level in China. To determine the transmission characteristics of
Mycobacterium tuberculosis
strains isolated in this area and their genetic relationships, especially among the Beijing family strains, we investigated their genotypes. From May 2007 to October 2008, 200
M. tuberculosis
isolates from patients presenting pulmonary TB were analyzed by molecular typing using PCR-based methods: spacer-oligonucleotide typing (spoligotyping), Beijing family-specific PCR (detection of the deletion of region of difference 105 [RD105]), and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) analysis. Different combinations of MIRU-VNTR loci were evaluated to define the genotypes and clustering characteristics of the local strains. We found that Beijing family strains represented 89.5% of the isolates studied. However, the rates of multidrug-resistant (MDR)
M. tuberculosis
among Beijing and non-Beijing family strains were not statistically different. The 15-locus set is considered the optimal MIRU-VNTR locus combination for analyzing the
M. tuberculosis
strains epidemic in this area, while the 10-locus set is an ideal set for first-line molecular typing. We found that the clustering rate of all the
M. tuberculosis
isolates analyzed was 10.0% using the 15-locus set typing. We conclude that the Beijing family genotype is predominant and that highly epidemic TB and MDR TB are less likely associated with the active transmission of
M. tuberculosis
in the study area.
Evidence that TMPRSS2 Activates the Severe Acute Respiratory Syndrome Coronavirus Spike Protein for Membrane Fusion and Reduces Viral Control by the Humoral Immune Response
Authors: Glowacka Ilona , Bertram Stephanie , Müller Marcel A. , Allen Paul , Soilleux Elizabeth , Pfefferle Susanne , Steffen Imke , Tsegaye Theodros Solomon , He Yuxian , Gnirss Kerstin , Niemeyer Daniela , Schneider Heike , Drosten Christian , Pöhlmann Stefan
Published: February 2011

The spike (S) protein of the severe acute respiratory syndrome coronavirus (SARS-CoV) can be proteolytically activated by cathepsins B and L upon viral uptake into target cell endosomes. In contrast, it is largely unknown whether host cell proteases located in the secretory pathway of infected cells and/or on the surface of target cells can cleave SARS S. We along with others could previously show that the type II transmembrane protease TMPRSS2 activates the influenza virus hemagglutinin and the human metapneumovirus F protein by cleavage. Here, we assessed whether SARS S is proteolytically processed by TMPRSS2. Western blot analysis revealed that SARS S was cleaved into several fragments upon coexpression of TMPRSS2 (cis-cleavage) and upon contact between SARS S-expressing cells and TMPRSS2-positive cells (trans-cleavage).cis-cleavage resulted in release of SARS S fragments into the cellular supernatant and in inhibition of antibody-mediated neutralization, most likely because SARS S fragments function as antibody decoys.trans-cleavage activated SARS S on effector cells for fusion with target cells and allowed efficient SARS S-driven viral entry into targets treated with a lysosomotropic agent or a cathepsin inhibitor. Finally, ACE2, the cellular receptor for SARS-CoV, and TMPRSS2 were found to be coexpressed by type II pneumocytes, which represent important viral target cells, suggesting that SARS S is cleaved by TMPRSS2 in the lung of SARS-CoV-infected individuals. In summary, we show that TMPRSS2 might promote viral spread and pathogenesis by diminishing viral recognition by neutralizing antibodies and by activating SARS S for cell-cell and virus-cell fusion.
Internal Initiation Is Responsible for Synthesis of Wuhan Nodavirus Subgenomic RNA
Authors: Qiu Yang , Cai Dawei , Qi Nan , Wang Zhaowei , Zhou Xi , Zhang Jiamin , Hu Yuanyang
Published: February 2011

Nodaviruses are small nonenveloped spherical viruses with a bipartite genome of RNAs. In nodaviruses, subgenomic RNA3 (sgRNA3) plays a critical role in viral replication and survival, as it coordinates the replication of two viral genomic RNAs (RNA1 and RNA2) and encodes protein B2, which is a potent RNA-silencing inhibitor. Despite its importance, the molecular mechanism of nodaviral sgRNA3 synthesis is still poorly understood. Here, we propose that sgRNA3 of Wuhan nodavirus (WhNV) is internally initiated from a promoter on the negative template of genomic RNA1. Serial deletion and mutation analyses further revealed that the core promoter of WhNV sgRNA3 is between nucleotide positions −22 and +6 of its transcription start site. Besides, a stem-loop structure of WhNV sgRNA3 was computationally predicted upstream of sgRNA3's transcription start site. Both the secondary structure and the primary sequence were determined to be required for promoter activity. Furthermore, our results show that the synthesis of WhNV sgRNA3 is counterregulated by the replication of WhNV genomic RNA2, which encodes a viral capsid precursor protein. And this sgRNA3 synthesis is also able to
trans
-activate the replication of RNA2. Altogether, findings in this study indicate that there is a newly discovered internal initiation model for the synthesis of nodaviral sgRNA.
Early Induction of Autophagy in Human Fibroblasts after Infection with Human Cytomegalovirus or Herpes Simplex Virus 1
Authors: McFarlane Steven , Aitken James , Sutherland Jane S. , Nicholl Mary Jane , Preston Valerie G. , Preston Chris M.
Published: February 2011

The infection of human fetal foreskin fibroblasts (HFFF2) with human cytomegalovirus (HCMV) resulted in the induction of autophagy. This was demonstrated by the increased lipidation of microtubule-associated protein 1 light chain 3 (LC3), a hallmark of autophagy, and by the visualization of characteristic vesicles within infected cells. The response was detected first at 2 h postinfection and persisted for at least 3 days.
De novo
protein synthesis was not required for the effect, since HCMV that was irradiated with UV light also elicited the response, and furthermore the continuous presence of cycloheximide did not prevent induction. Infection with herpes simplex virus type 1 (HSV-1) under conditions that inhibited viral gene expression provoked autophagy, whereas UV-irradiated respiratory syncytial virus did not. The induction of autophagy occurred when cells were infected with HCMV or HSV-1 that was gradient purified, but HCMV dense bodies and HSV-1 light particles, each of which lack nucleocapsids and genomes, were inactive. The depletion of regulatory proteins Atg5 and Atg7, which are required for autophagy, reduced LC3 modification in response to infection but did not result in any detectable difference in viral or cellular gene expression at early times after infection. The electroporation of DNA into HFFF2 cultures induced the lipidation of LC3 but double-stranded RNA did not, even though both agents stimulated an innate immune response. The results show a novel, early cellular response to the presence of the incoming virion and additionally demonstrate that autophagy can be induced by the presence of foreign DNA within cells.
Dehydrocoupling of SiMe2H substituents in permethylated zirconocene complexes
Authors: Pinkas Jiří , Gyepes Róbert , Císařová Ivana , Kubišta Jiří , Mach Karel , Horáček Michal
Published: February 2011

Complex [Zr{η5-C5Me4(SiMe2H)}2Cl2] (1) was prepared by the reaction of lithium salt of 2,3,4,5-tetramethyl-1-(dimethylsilyl)cyclopenta-2,4-diene with [ZrCl4] in boiling THF. The reduction of 1 with excess magnesium in THF in the presence of excess bis(trimethylsilyl)acetylene (btmsa) afforded the bivalent metal ansa-disilylene complex with π-coordinated btmsa [Zr(η2-btmsa){η5-C5Me4(SiMe2)}2] (2). The dehydrocoupling of SiMe2H groups was accompanied by a hydrogen transfer to releasing btmsa to give a mixture of cis- and trans-1,2-bis(trimethylsilyl)ethene. Chlorination of 2 with PbCl2 afforded ansa-[Zr{η5-C5Me4(SiMe2)}2Cl2] (3) and liberated btmsa. The crystal structures of complexes, 1, 2 and 3 have been determined by X-ray crystallography.
High-density fluorescence in situ hybridization signal detection on barley (Hordeum vulgare L.) chromosomes with improved probe screening and reprobing procedures
Authors: Kato Akio
Published: February 2011

The barley ( Hordeum vulgare L.) genome was screened to identify sequences that could be used for fluorescence in situ hybridization (FISH). From 2000 transformed bacterium colonies carrying barley clones, 56 colonies were selected on the basis of the patterns that their PCR products produced when subjected to agarose gel electrophoresis. Among them, 42 (75%) exhibited fluorescent signals on barley chromosomes after in situ hybridization using the directly labeled PCR products. Sequencing revealed seven clones, pHv-365, pHv-177, pHv-1112, pHv-689, pHv-1476, pHv-1889, and pHv-1972, to be newly identified FISH-positive sequences. The remainder possess previously described sequences such as 5S, GAA microsatellite, centromere repeats, HVT01, and pHvMWG2315 (324 bp repeat). It is shown here that a combination of five probes, which produce strong signals on barley chromosomes, pHv-38 (5S), pHv-365, pHv-961 (HVT01), GAA, and TAG microsatellites, offer unequivocal recognition of each chromosome. The combination of three probes, i.e., pHv-1123 (barley 324 bp repeat), GAA, and TAG, decorated entire chromosomes with fine dotted signals and was useful for detecting the break points of aberrant chromosomes. The signals’ distributions of pHv-177, pHv-1112, and TAG were highly polymorphic. An improved reprobing procedure and its usefulness are also discussed.
Comparative transcriptome analysis of yeast strains carryingslt2,rlm1,andpop2deletions
Authors: Becerra M. , Lombardía L. J. , Lamas-Maceiras M. , Canto E. , Rodríguez-Belmonte E. , Cerdán M. E.
Published: February 2011

The function of the genes SLT2 (encoding the Mpk1 protein), RLM1, and POP2 have previously been related to several stress responses in yeasts. DNA arrays have been used to identify differences among the transcriptomes of a Saccharomyces cerevisiae wild type strain and its derivative Δslt2, Δrlm1, and Δpop2 mutants. Correspondence analyses indicate that the vast majority of genes that show lower expression in Δrlm1 also show lower expression in Δslt2. In contrast, there is little overlap between the results of the transcriptome analyses of the Δpop2 strain and the Δslt2 or Δrlm1 strains. The DNA array data were validated by reverse Northern blotting and chromatin immunoprecipitation (ChIp). ChIp assays demonstrate Rlm1p binding to specific regions of the promoters of two genes that show expression differences between the Δrlm1 mutant and wild type strains. Interestingly, RLM1 deletion decreases the transcription of SLT2, encoding the Mpk1p kinase that phosphorylates Rlm1p, suggesting a feedback control in the signal transduction pathway. Also, deletion of RLM1 causes a decrease in the mRNA level of KDX1, which is paralogous to SLT2. In contrast, deletion of POP2 is accompanied by an increase of both SLT2 and KDX1 levels. We show that SLT2 mRNA increase in the Δpop2 strain is due to a decrease in RNA turnover, consistent with the expected loss of RNA-deadenylase activity in this strain.
Time to move beyond a brainless exercise physiology: the evidence for complex regulation of human exercise performance
Authors: Noakes Timothy David
Published: February 2011

In 1923, Nobel Laureate A.V. Hill proposed that maximal exercise performance is limited by the development of anaerobiosis in the exercising skeletal muscles. Variants of this theory have dominated teaching in the exercise sciences ever since, but 90 years later there is little biological evidence to support Hill’s belief, and much that disproves it. The cardinal weakness of the Hill model is that it allows no role for the brain in the regulation of exercise performance. As a result, it is unable to explain at least 6 common phenomena, including (i) differential pacing strategies for different exercise durations; (ii) the end spurt; (iii) the presence of fatigue even though homeostasis is maintained; (iv) fewer than 100% of the muscle fibers have been recruited in the exercising limbs; (v) the evidence that a range of interventions that act exclusively on the brain can modify exercise performance; and (vi) the finding that the rating of perceived exertion is a function of the relative exercise duration rather than the exercise intensity. Here I argue that the central governor model (CGM) is better able to explain these phenomena. In the CGM, exercise is seen as a behaviour that is regulated by complex systems in the central nervous system specifically to ensure that exercise terminates before there is a catastrophic biological failure. The complexity of this regulation cannot be appreciated if the body is studied as a collection of disconnected components, as is the usual approach in the modern exercise sciences.
A comprehensive evaluation of motion sensor step-counting error
Authors: Abel Mark G. , Peritore Nicole , Shapiro Robert , Mullineaux David R. , Rodriguez Kelly , Hannon James C.
Published: February 2011

The purpose of this study was to conduct a comprehensive evaluation of the effect that walking speed, gender, leg length, motion sensor tilt angle, brand, and placement have on motion sensor step-counting error. Fifty-nine participants performed treadmill walking trials at 6 speeds while wearing 5 motion sensor brands placed on the anterior (Digiwalker, DW; Walk4Life, WFL; New Lifestyles, NL; Omron, OM), midaxillary (DW; WFL; NL; ActiGraph, AG), and posterior (DW, WFL, NL) aspects of the waistline. The anterior-placed NL and midaxillary-placed AG were the most accurate motion sensors. Motion sensor step-count error tended to decrease at faster walking speeds, with lesser tilt angles, and with an anterior waistline placement. Gender and leg length had no effect on motion sensor step-count error. We conclude that the NL and AG yielded the most accurate step counts at a range of walking speeds in individuals with different physical characteristics.
Directives canadiennes en matière de comportement sédentaire à l’intention des enfants et des jeunes
Authors: Tremblay Mark S. , LeBlanc Allana G. , Janssen Ian , Kho Michelle E. , Hicks Audrey , Murumets Kelly , Colley Rachel C. , Duggan Mary
Published: February 2011

La Société canadienne de physiologie de l’exercice (SCPE) en collaboration avec le groupe de recherche Healthy Active Living and Obesity Research Group (HALO) de l’Institut de recherche du Centre hospitalier pour enfants de l’est de l’Ontario, de ParticipACTION et d’autres organismes a élaboré les Directives canadiennes en matière de comportement sédentaire à l’intention des enfants âgés de 5 à 11 ans et des jeunes âgés de 12 à 17 ans. Les directives comprennent un préambule situant le contexte et des recommandations spécifiques en matière de comportement sédentaire. L’élaboration complète des directives a respecté la Grille II d’évaluation de la qualité des recommandations pour la pratique clinique (AGREE), un outil reconnu internationalement pour l’élaboration des lignes directrices en pratique clinique. L’élaboration des directives est donc le résultat d’un processus rigoureux et transparent, et les recommandations présentées dans cet article sont basées sur l’interprétation des données probantes relevées dans une analyse documentaire systématique. Les directives finales sont le fruit d’une vaste consultation en ligne auprès de 230 intervenants concernés et de sources de premier plan sur la scène nationale et internationale. Les directives finales énoncent ce qui suit : Afin de profiter des bienfaits pour leur santé, les enfants âgés de 5 à 11 ans et les jeunes âgés de 12 à 17 ans doivent diminuer chaque jour le temps consacré à des activités sédentaires. Ceci peut être accompli (i) en limitant le temps de loisir passé devant l’écran à moins de 2 h par jour; moins de temps passé devant l’écran est associé à des bienfaits supplémentaires pour la santé; (ii) en diminuant les déplacements en véhicule motorisé et en réduisant le temps passé assis à l’intérieur pendant la journée. Ces directives sont les premières Directives canadiennes en matière de comportement sédentaire à l’intention des enfants et des jeunes; elles résultent de la synthèse, de l’interprétation et de l’application des données probantes les plus récentes à ce jour et comportent des recommandations importantes qui arrivent à un moment opportun dans la promotion de la santé publique.
MeCP2: structure and functionThis paper is one of a selection of papers published in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.
Authors: Adkins Nicholas L. , Georgel Philippe T.
Published: February 2011

Despite a vast body of literature linking chromatin structure to regulation of gene expression, the role of architectural proteins in higher order chromatin transitions required for transcription activation and repression has remained an under-studied field. To demonstrate the current knowledge of the role of such proteins, we have focused our attention on the methylated DNA binding and chromatin-associated protein MeCP2. Structural studies using chromatin assembled in vitro have revealed that MeCP2 can associate with nucleosomes in an N-terminus dependent manner and efficiently condense nucleosome arrays. The present review attempts to match MeCP2 structural domains, or lack thereof, and specific chromatin features needed for the proper recruitment of MeCP2 to its multiple functions as either activator or repressor. We specifically focused on MeCP2’s role in Rett syndrome, a neurological disorder associated with specific MeCP2 mutations.
Comparative evaluation of a chromogenic agar medium – PCR protocol with a conventional method for isolation of Vibrio parahaemolyticus strains from environmental and clinical samples
Authors: Canizalez-Roman Adrian , Flores-Villaseñor Héctor , Zazueta-Beltran Jorge , Muro-Amador Secundino , León-Sicairos Nidia
Published: February 2011

Screening for pathogenic Vibrio parahaemolyticus has become routine in certain areas associated with food-borne outbreaks. This study is an evaluation of the CHROMagar Vibrio (CV) medium – PCR protocol and the conventional method (TCBS (thiosulfate – citrate – bile salts – sucrose) agar plus biochemical and Wagatsuma agar tests) for detection of V. parahaemolyticus in shrimp, water, sediment, and stool samples collected for biosurveillance in an endemic area of northwestern Mexico. A total of 131 environmental and clinical samples were evaluated. The CV medium – PCR protocol showed a significantly improved ability (P < 0.05) to isolate and detect V. parahaemolyticus, identifying isolates of this bacteria missed by the conventional method. Although some other bacteria, distinct from pathogenic V. parahaemolyticus, produced violet colonies similar to that of V. parahaemolyticus on CV medium, we were able to detect a superior number of samples of V. parahaemolyticus with the CV medium – PCR protocol than with the conventional method. The Kanagawa phenomenon is routinely determined on Wagatsuma agar for the diagnosis of V. parahaemolyticus (pathogenic) positive for thermostable direct hemolysin (TDH) in developing countries. In our results, Wagatsuma agar showed low sensitivity (65.4% at 24 h and 75.6% at 48 h) and specificity (52.4% at 48 h) for identifying V. parahaemolyticus positive for TDH. Overall, our data support the use of the CV medium – PCR protocol in place of the conventional method (TCBS – biochemical tests – Wagatsuma agar) for detection of pathogenic V. parahaemolyticus, both in terms of effectiveness and cost efficiency.
Lactobacillus caseias a probiotic in malnourishedGiardia lamblia-infected mice: a biochemical and histopathological study
Authors: Shukla Geeta , Sidhu Ramandeep Kaur
Published: February 2011

The study describes the in vivo activity of Lactobacillus casei in malnourished Giardia lamblia -infected BALB/c mice. By experimentation, it was found that daily administration of the probiotic 7 days before inoculation with Giardia trophozoites in malnourished mice efficiently reduced both the severity and duration of giardiasis. More specifically, excretion of Giardia cysts and trophozoites counts were reduced, while faecal lactobacilli counts increased significantly in probiotic-fed malnourished mice, compared with control mice. Interestingly, it was also observed that oral feeding of the probiotic to malnourished mice abrogated all the anthropometric and biochemical anomalies. Histologically, morphological and cellular alteration of microvillus membrane integrity revealed that probiotic administration ameliorated the mucosal damage in malnourished, probiotic-inoculated, Giardia-infected mice compared with the severe microvillus atrophy, œdematous and vacuolated epithelial cells, and ileitis in malnourished Giardia-infected mice. The results clearly show the antigiardial effect of the probiotic in vivo by modulating the gut cells to inhibit the colonization and multiplication of Giardia trophozoites, thus reducing the severity and duration of murine giardiasis.
Multiscale population genetic analysis of mule deer (Odocoileus hemionus hemionus) in western Canada sheds new light on the spread of chronic wasting disease
Authors: Cullingham C. I. , Nakada S. M. , Merrill E. H. , Bollinger T. K. , Pybus M. J. , Coltman D. W.
Published: February 2011

To successfully manage wildlife diseases, it is necessary to understand factors that influence spread. One approach is to analyze host movement and social structure, as these behaviors can be associated with the probability of transmission. Some populations of mule deer ( Odocoileus hemionus hemionus (Rafinesque, 1817)) in western Canada are infected with chronic wasting disease (CWD), a transmissible and fatal neurodegenerative disease. We used population analysis of spatial genetic structure of mule deer at broad and local scales to understand factors that influence spread. We genotyped 2535 mule deer sampled from Alberta, Saskatchewan, and portions of British Columbia using 16 microsatellite loci. We found weak genetic structure at broad spatial scales (overall FST = 0.008) that was well defined by geographic distance, indicating the risk of CWD spread from the focus of infection will decline gradually with increasing distance, but there are no barriers to the spread over time. At the local scale of approximately 2 km, elevated relatedness among CWD-infected individuals suggests transmission rates within social groups. Sex-biased spatial autocorrelation in genetic relatedness also indicates that female philopatry underlies the social structure, and therefore transmission among relatives is potentially driving local disease persistence.
IMPORTANCE OF STRANGE QUARKS IN HADRONS, NUCLEI AND DENSE MATTER
Authors: Thomas A. W.
Published: February 2011

We review recent progress in our understanding of the role of strange quarks in the structure of the nucleon. For the contribution to its mass the result is remarkably small, an order of magnitude smaller than commonly assumed. This has profound consequences for the searches for dark matter which are currently underway. There has also been remarkable progress in the understanding of hypernuclei. In particular, there is a very natural explanation at the quark level of why Λ-hypernuclei are bound whereas Σ-hypernuclei are not. The consequences for dense matter, for example in neutron stars, are not yet fully understood but we know they are significant.
PROGRESS AND ISSUES IN THE ELECTROMAGNETIC PRODUCTION OF KAON ON THE NUCLEON
Authors: Mart T.
Published: February 2011

The present status of kaon photo- and electroproduction on the nucleon is briefly reviewed. Some current important issues in this field are discussed.
THE FINUDA EXPERIMENT AT DAɸNE
Authors: Lucherini V.
Published: February 2011

The FINUDA (FIsica NUcleare a DAɸNE) experiment was built in order to study the interactions of stopped K - on nuclei, with emphasis on Hypernuclear spectroscopy and Hypernuclei decays. Due to the nice performances of the spectrometer, it proved also suited to study, more generally, final states with several particles and able to recostruct secondary vertices, hence greatly enlarging the physical topics that could be addressed.
PRODUCTION OF NEUTRON-RICH LAMBDA HYPERNUCLEI AT J-PARC
Authors: Sakaguchi A. , Ajimura S. , Bhang H. , Busso L. , Endo M. , Faso D. , Fukuda T. , Kishimoto T. , Matsuda K. , Matsuoka K. , Mizoi Y. , Morra O. , Noumi H. , Saha P. K. , Samanta C. , Shimizu Y. , Takahashi T. , Takahashi T. N. , Yoshida K.
Published: February 2011

We discuss the usefulness of the double charge-exchange reactions (DCX) for the production of the neutron-rich Λ-hypernuclei. We believe the (π-, K+) reaction is one of the most promising DCX reactions, and propose to produce the neutron-rich Λ-hypernuclei, [Formula: see text] and [Formula: see text], at the J-PARC 50 GeV PS by the reaction (J-PARC E10 experiment). The design of the experiment is presented.
SURFACE STRUCTURAL DESIGN OF SELECTIVE EMITTER FOR METHANE STEAM REFORMING
Authors: MAEGAMI Y. , IGUCHI F. , YUGAMI H.
Published: February 2011

We performed structural optimization of a selective emitter with two-dimensional silicon based gratings coated by platinum as a thermal radiator to promote methane steam reforming reaction. The structural parameters were optimized by numerical calculation to radiate high thermal power in a vibrational absorption band of methane molecule at 3.3 μm. Optical property of the fabricated optimum selective emitter with periodicity Λ = 2.6 μm found that the emission peak was resonant with this absorption band. The amount of hydrogen produced by the methane steam reforming process using the optimized selective emitter became four times greater than that obtained by the flat emitter.
LONG-RANGE SURFACE PLASMONS ON HIGHLY ANISOTROPIC DIELECTRIC SUBSTRATES
Authors: GUMEN L. , NAGARAJ  , NEOGI A. , KROKHIN A.
Published: February 2011

We calculate the propagation length of surface plasmons in metal-dielectric structures with anisotropic substrates. We show that the Joule losses can be minimized by appropriate orientation of the optical axis of a birefringent substrate and that the favorable orientation of the axis depends on ω. A simple Kronig-Penney model for anisotropic plasmonic crystal is also proposed.
LIGHT TRAPPING TECHNIQUE FOR DYE SENSITIZED SOLAR CELL
Authors: CHEN LINDA , ALKAISI MAAN M. , LIAO MEI-YI
Published: February 2011

Dye Sensitized Solar Cells (DSSC) possess huge potential in solar energy utilisation. Immense research has been carried out in order to improve its performance. This paper suggests an alternative way of employing Light Trapping technique on DSSC by dry etching substrates before depositing the transparent conductive oxide (TCO) layer on one of the electrodes. The result demonstrated a decrease in reflectance before depositing the TCO, but an increase in reflectance after depositing the TCO. Texturing might also help to increase the effective surface area at the interface between various cell layers, providing a shorter path for the electron transport layer and improving collection efficiencies.
NONLINEAR OPTICAL PROPERTIES OF ZINC DOPED GERMANO-SILICATE GLASS OPTICAL FIBER
Authors: JU SEONGMIN , WATEKAR PRAMOD R. , JEONG SEONGMOOK , KIM YOUNGWOONG , HAN WON-TAEK
Published: February 2011

Zinc doped germano-silicate glass optical fiber was developed by using the modified chemical vapor deposition and the drawing tower process. Absorption peaks of the germano-silicate glass optical fiber preform appeared at 240 nm and 330 nm were due to the incorporated Zn metal nano-particles (MNPs) and ZnO semiconductor nano-particles (SNPs), respectively and the average diameter of nano-particles (NPs) was estimated to be about 2 nm by transmission electron microscopy. However, the absorption peak of the zinc doped optical fiber due to ZnO SNPs was found to appear at 490 nm red-shifted from 330 nm can be explained by the increase in average size of ZnO SNPs in the fiber core due to growth or recrystallization of ZnO SNPs during the fiber drawing process about 2150°C. The nonlinear refractive index coefficient, n2, of the fiber was estimated to be 5.62 × 10-20 m2/W due to the stable dispersion of ZnO SNPs using the continuous-wave self-phase modulation method.
GIGO or not GIGO
Authors: Askira Gelman Irit
Published: February 2011

The relationship between data accuracy and the resulting information accuracy is of great interest in numerous problem domains. An understanding of this relationship can improve the efficiency of data management and increase the accuracy and utility of information in problem-solving settings. Nonetheless, our understanding of that relationship is still partial. In fact, even the sign of the relationship is not well understood. Nearly all researchers have embraced the popular belief in GIGO (Garbage In, Garbage Out), which indicates a strong positive link between input accuracy and output accuracy. However, there is evidence that hints to a more complex association. This article addresses the relationship between input accuracy and output accuracy, particularly the sign of that relationship, in satisficing decisions that apply a conjunctive or disjunctive rule for combining selected criteria. Analysis of a simple scenario shows a surprising result: the sign of that relationship varies; higher input accuracy can lead to lower output accuracy. This article derives criteria that determine the sign of the relationship and explains and illustrates conditions in which the sign is negative. The findings of this research imply certain rules for guiding data quality management resource allocation and design decisions in similar scenarios.
Passive online wireless LAN health monitoring from a single measurement point
Authors: Chen Xian , Wang Bing , Suh Kyoungwon , Wei Wei
Published: February 2011

Wireless LANs that are deployed in corporations and university campuses can contain a large number of access points and wireless hosts. In this paper, we develop a scalable approach that relies on measurements collected by a single monitor for WLAN health monitoring. We propose two metrics, local RTT and local loss rate, that indicate whether a wireless host experiences performance degradations inside a WLAN, and both can be obtained from measurements at the single monitor. Preliminary evaluation through data collected by a monitor at a university gateway router demonstrates the effectiveness of these two metrics.