bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Mutations in theSGene of Hepatitis B Virus Strains in Patients with Chronic Infection by Online Bioinformatics Tools
Authors: Simon Benedikt , Kundi Michael , Puchhammer Elisabeth
Published: November 2012

Hepatitis B virus (HBV) genomes show a high rate of mutations. This can lead to a variety of amino acid changes in the surface and polymerase genes, causing changes in viral protein conformation that can result in diminished antibody binding or decreased secretion of surface antigen (HBsAg). HBV monitoring increasingly relies on HBsAg detection and quantification, and therefore epidemiological data on HBsAg mutations are needed. We therefore analyzed the frequency of HBsAg mutations possibly influencing the quantification of HBsAg (MUPIQHs) in an unselected patient collective. To this end, we determined the HBV surface and polymerase gene sequences of an unselected patient collective of 237 individuals chronically infected with HBV and analyzed the MUPIQHs in these sequences using three different online HBV sequence analysis tools. We found that 17 or 34% of the patients, depending on the online interpretation algorithm used, harbored MUPIQHs and that MUPIQHs were not significantly associated with the duration of disease, treatment, or HBV genotype. Thus, this study shows that a substantial amount of HBV sequences derived from unselected patients chronically infected with HBV carry MUPIQHs, and therefore the reliability of routine quantitative and qualitative HBsAg tests needs to be reevaluated.
Comparison of Sequencing (Barcode Region) and Sequence-Tagged-Site PCR for Blastocystis Subtyping
Authors: Stensvold Christen Rune
Published: November 2012

Blastocystis
is the most common nonfungal microeukaryote of the human intestinal tract and comprises numerous subtypes (STs), nine of which have been found in humans (ST1 to ST9). While efforts continue to explore the relationship between human health status and subtypes, no consensus regarding subtyping methodology exists. It has been speculated that differences detected in subtype distribution in various cohorts may to some extent reflect different approaches.
Blastocystis
subtypes have been determined primarily in one of two ways: (i) sequencing of small subunit rRNA gene (SSU-rDNA) PCR products and (ii) PCR with subtype-specific sequence-tagged-site (STS) diagnostic primers. Here, STS primers were evaluated against a panel of samples (
n
= 58) already subtyped by SSU-rDNA sequencing (barcode region), including subtypes for which STS primers are not available, and a small panel of DNAs from four other eukaryotes often present in feces (
n
= 18). Although the STS primers appeared to be highly specific, their sensitivity was only moderate, and the results indicated that some infections may go undetected when this method is used. False-negative STS results were not linked exclusively to certain subtypes or alleles, and evidence of substantial genetic variation in STS loci was obtained. Since the majority of DNAs included here were extracted from feces, it is possible that STS primers may generally work better with DNAs extracted from
Blastocystis
cultures. In conclusion, due to its higher applicability and sensitivity, and since sequence information is useful for other forms of research, SSU-rDNA barcoding is recommended as the method of choice for
Blastocystis
subtyping.
AMP-Activated Protein Kinase Is Required for the Macropinocytic Internalization of Ebolavirus
Authors: Kondratowicz Andrew S. , Hunt Catherine L. , Davey Robert A. , Cherry Sara , Maury Wendy J.
Published: November 2012

Identification of host factors that are needed for Zaire Ebolavirus (EBOV) entry provides insights into the mechanism(s) of filovirus uptake, and these factors may serve as potential antiviral targets. In order to identify novel host genes and pathways involved in EBOV entry, gene array findings in the National Cancer Institute's NCI-60 panel of human tumor cell lines were correlated with permissivity for EBOV glycoprotein (GP)-mediated entry. We found that the gene encoding the γ2 subunit of AMP-activated protein kinase (AMPK) strongly correlated with EBOV transduction in the tumor panel. The AMPK inhibitor compound C inhibited infectious EBOV replication in Vero cells and diminished EBOV GP-dependent, but not Lassa fever virus GPC-dependent, entry into a variety of cell lines in a dose-dependent manner. Compound C also prevented EBOV GP-mediated infection of primary human macrophages, a major target of filoviral replication
in vivo
. Consistent with a role for AMPK in filovirus entry, time-of-addition studies demonstrated that compound C abrogated infection when it was added at early time points but became progressively less effective when added later. Compound C prevented EBOV pseudovirion internalization at 37°C as cell-bound particles remained susceptible to trypsin digestion in the presence of the inhibitor but not in its absence. Mouse embryonic fibroblasts lacking the AMPKα1 and AMPKα2 catalytic subunits were significantly less permissive to EBOV GP-mediated infection than their wild-type counterparts, likely due to decreased macropinocytic uptake. In total, these findings implicate AMPK in macropinocytic events needed for EBOV GP-dependent entry and identify a novel cellular target for new filoviral antivirals.
The West Nile Virus Capsid Protein Blocks Apoptosis through a Phosphatidylinositol 3-Kinase-Dependent Mechanism
Authors: Urbanowski Matt D. , Hobman Tom C.
Published: November 2012

West Nile virus (WNV) is a mosquito-transmitted pathogen that can cause serious disease in humans. Our laboratories are focused on understanding how interactions between WNV proteins and host cells contribute to virus replication and pathogenesis. WNV replication is relatively slow, and on the basis of earlier studies, the virus appears to activate survival pathways that delay host cell death during virus replication. The WNV capsid is the first viral protein produced in infected cells; however, its role in virus assembly is not required until after replication of the genomic RNA. Accordingly, from a temporal perspective, it is perfectly suited to block host cell apoptosis during virus replication. In the present study, we provide evidence that the WNV capsid protein blocks apoptosis through a phosphatidylinositol (PI) 3-kinase-dependent pathway. Specifically, expression of this protein in the absence of other viral proteins increases the levels of phosphorylated Akt, a prosurvival kinase that blocks apoptosis through multiple mechanisms. Treatment of cells with the PI 3-kinase inhibitor LY294002 abrogates the protective effects of the WNV capsid protein.
Cumulative Impact of Host and Viral Factors on HIV-1 Viral-Load Control during Early Infection
Authors: Yue Ling , Prentice Heather A. , Farmer Paul , Song Wei , He Dongning , Lakhi Shabir , Goepfert Paul , Gilmour Jill , Allen Susan , Tang Jianming , Kaslow Richard A. , Hunter Eric
Published: November 2012

In HIV-1 infection, the early set-point viral load strongly predicts both viral transmission and disease progression. The factors responsible for the wide spectrum of set-point viral loads are complex and likely reflect an interplay between the transmitted virus and genetically defined factors in both the transmitting source partner and the seroconverter. Indeed, analysis of 195 transmission pairs from Lusaka, Zambia, revealed that the viral loads in transmitting source partners contributed only ∼2% of the variance in early set-point viral loads of seroconverters (
P
= 0.046 by univariable analysis). In multivariable models, early set-point viral loads in seroconverting partners were a complex function of (i) the viral load in the source partner, (ii) the gender of the seroconverter, (iii) specific HLA class I alleles in the newly infected partner, and (iv) sharing of HLA-I alleles between partners in a transmission pair. Each of these factors significantly and independently contributed to the set-point viral load in the newly infected partner, accounting for up to 37% of the variance observed and suggesting that many factors operate in concert to define the early virological phenotype in HIV-1 infection.
Complete Nucleotide Sequence of Avian Paramyxovirus Type 6 Strain JL Isolated from Mallard Ducks in China
Authors: Tian Zhige , Chai Hongliang , Li Fengyong , Sun Jing , Chen Guang , Hu Xiaoliang , Hua Yuping , Xiang Wenhua
Published: November 2012

A new strain of avian paramyxovirus type 6 (APMV-6), JL, has been isolated from mallard ducks in China, and its complete genome has been sequenced and analyzed. This work is the first announced complete genome sequence of APMV-6 from mallards.
Complete Genome Sequence of a Velogenic Neurotropic Avian Paramyxovirus 1 Isolated from Peacocks (Pavo cristatus) in a Wildlife Park in Pakistan
Authors: Munir Muhammad , Shabbir Muhammad Z. , Yaqub Tahir , Shabbir Muhammad A. B. , Mukhtar Nadia , Khan Muhammad R. , Berg Mikael
Published: November 2012

Avian paramyxovirus serotype 1 (APMV-1) was isolated from an acute and highly contagious outbreak in peacocks (
Pavo cristatus
) in a wildlife park in Pakistan. A velogenic neurotropic form of APMV-1 caused a 100% case fatality rate and killed 190 peacocks within a week. Biological and serological characterizations showed features of a velogenic strain of APMV-1, and these results were further confirmed by sequence analysis of the cleavage site in the fusion protein. The complete genome of one of the isolates was sequenced, and phylogenetic analysis was conducted. The analysis showed that this isolate belonged to genotype VII, specifically, to subgenotype VIIa, and clustered closely with isolates characterized from Indonesia in the 1990s. Interestingly, the isolate showed significant differences from previously characterized APMV-1 isolates from commercial and rural chickens in Pakistan. The work presented here is the first complete genome sequence of any APMV-1 isolate from wild birds in the region and therefore highlights the need for increased awareness and surveillance in such bird species.
Full Genome Sequence of Bluetongue Virus Serotype 4 from China
Authors: Yang Heng , Zhu Jianbo , Li Huachun , Xiao Lei , Wang Jinpin , Li Nan , Zhang Nianzu , Kirkland Peter. D.
Published: November 2012

The complete genomic sequence of a bluetongue virus serotype 4 (BTV-4) strain (strain YTS-4), isolated from sentinel cattle in Yunnan Province, China, is reported here. This work is the first to document the complete genomic sequence of a BTV-4 strain from China. The sequence information will help determine the geographic origin of Chinese BTV-4 and provide data to facilitate future analyses of the genetic diversity and phylogenetic relationships of BTV strains.
Complete Genome Sequence of a Novel Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Variant
Authors: Wang Lianghai , Hou Jun , Zhang Hexiao , Feng Wen-hai
Published: November 2012

Highly pathogenic porcine reproductive and respiratory syndrome (HP-PRRS) emerged in China in 2006, and HP-PRRS virus (HP-PRRSV) has evolved continuously. Here, the complete genomic sequence of a novel HP-PRRSV field strain, JX, is reported. The present finding will contribute to further studies focusing on the evolutionary mechanism of PRRSV.
Complete Genome Sequence of Bacteriophage phiAC-1 Infecting Acinetobacter soli Strain KZ-1
Authors: Kim Ji Hyung , Oh Chulhong , Choresca Casiano H. , Shin Sang Phil , Han Jee Eun , Jun Jin Woo , Heo Soo-Jin , Kang Do-Hyung , Park Se Chang
Published: November 2012

To date, a number of bacteriophages (phages) infecting
Acinetobacter
species have been reported and characterized. However,
Acinetobacter
phages which infect
A. soli
have not been investigated yet. Here, we report the complete genome sequence of
Acinetobacter
phage phiAC-1, which belongs to the
Myoviridae
, infecting
Acinetobacter soli
strain KZ-1.
A Second CRM1-Dependent Nuclear Export Signal in the Influenza A Virus NS2 Protein Contributes to the Nuclear Export of Viral Ribonucleoproteins
Authors: Huang Shengping , Chen Jingjing , Chen Quanjiao , Wang Huadong , Yao Yanfeng , Chen Jianjun , Chen Ze
Published: November 2012

Influenza A virus NS2 protein, also called nuclear export protein (NEP), is crucial for the nuclear export of viral ribonucleoproteins. However, the molecular mechanisms of NEP mediation in this process remain incompletely understood. A leucine-rich nuclear export signal (NES2) in NEP, located at the predicted N2 helix of the N-terminal domain, was identified in the present study. NES2 was demonstrated to be a transferable NES, with its nuclear export activity depending on the nuclear export receptor chromosome region maintenance 1 (CRM1)-mediated pathway. The interaction between NEP and CRM1 is coordinately regulated by both the previously reported NES (NES1) and now the new NES2. Deletion of the NES1 enhances the interaction between NEP and CRM1, and deletion of the NES1 and NES2 motifs completely abolishes this interaction. Moreover, NES2 interacts with CRM1 in the mammalian two-hybrid system. Mutant viruses containing NES2 alterations generated by reversed genetics exhibit reduced viral growth and delay in the nuclear export of viral ribonucleoproteins (vRNPs). The NES2 motif is highly conserved in the influenza A and B viruses. The results demonstrate that leucine-rich NES2 is involved in the nuclear export of vRNPs and contributes to the understanding of nucleocytoplasmic transport of influenza virus vRNPs.
Clinical benefits of alpharadin in castrate-chemotherapy-resistant prostate cancer: case report and literature review
Authors: Croke Jennifer , Leung Eugene , Segal Roanne , Malone Shawn
Published: November 2012

Prostate cancer has the second-highest mortality worldwide in men. The most common site of metastasis is bone. Bone metastases and their resulting complications represent a significant source of morbidity. Radioisotopes have been used for treatment of painful bony metastases. Although shown to decrease pain and analgesia use, this has not improved outcomes. The following case report describes a patient with castrate-resistant prostate cancer who was treated with the radioisotope radium-223 as part of the phase III clinical trial Alpharadin in Patients with Symptomatic Hormone Refractory Prostate Cancer with Skeletal Metastases (ALSYMPCA). He responded to radium-223 with pain relief, bone scan response, stabilisation of prostate specific antigen (PSA) and normalisation of alkaline phosphatase. Interim analysis of this trial has shown that radium-223 significantly prolongs overall survival, time to first skeletal-related event and is well tolerated. Alpharadin is a new treatment option for men with castrate-resistant prostate cancer and symptomatic bone metastases.
Acute pyelonephritis and secondary bacteraemia caused byVeillonelladuring pregnancy
Authors: Yagihashi Yusuke , Arakaki Yoshitaka
Published: November 2012

We report a case of pyelonephritis and secondary bacteraemia caused byVeillonellaspecies during pregnancy.Veillonellais part of the normal flora from the oral cavity, gut and vagina. However, becauseVeillonellais usually isolated from cultures of clinical specimens as part of commensal flora, it is frequently regarded as a contaminant. In the present case,Veillonellawas isolated from the patient's urine and blood samples that showed evidence of pyelonephritis and secondary bacteraemia. We found that ureteral stenting is an extremely effective therapeutic option for pregnant woman with hydronephrosis and clear signs and symptoms of urosepsis.
Sudden cardiac death screening in adolescent athletes: an evaluation of compliance with national guidelines
Authors: Madsen Nicolas L , Drezner Jonathan A , Salerno Jack C
Published: November 2012

Objective

In the USA, the preparticipation physical evaluation (PPE) is the standard of care for screening eight million high-school athletes for their risk of sudden cardiac death (SCD). Our aim was to evaluate both physician and school compliance with national guidelines for SCD screening.

Methods

We conducted a confidential survey of the Washington Chapter of the American Academy of Pediatrics (AAP), the Washington Academy of Family Physicians (WAFP) and Washington State high-school athletic directors. Responses were evaluated for compliance with the American Heart Association (AHA) guidelines for SCD screening.

Results

We received a response rate of 72% (559/776) from the AAP, 56% (554/990) from the WAFP and 78% (317/409) from the athletic directors. Only 6% of all providers and 0% of schools were in compliance with AHA guidelines. In addition, 47% of the physicians and 6% of athletic directors reported awareness of the guidelines. There was no difference in compliance between physician specialties (p=0.20). Physician location, years of experience and exposure to SCD were not significantly associated with compliance. Provider knowledge of the guidelines, number of PPE/month and frequency of referrals to cardiology were all positively associated with improved overall compliance (p<0.05).

Conclusions

Despite the unaltered presence of the AHA SCD screening guidelines for the past 15 years, compliance with the recommendations is poor. Lack of compliance does not reflect clinical experience, but rather lack of knowledge of the guidelines themselves. New directions for provider education and policy requirements are needed to improve this implementation gap.
Reported medication events in a paediatric emergency research network: sharing to improve patient safety
Authors: Shaw Kathy N , Lillis Kathleen A , Ruddy Richard M , Mahajan Prashant V , Lichenstein Richard , Olsen Cody S , Chamberlain James M ,   for the Pediatric Emergency Care Applied Research Network
Published: November 2012

Objective

Medication errors are an important cause of preventable morbidity, especially in children in emergency department (ED) settings. Internal use of voluntary incident reporting (IR) is common within hospitals, with little external reporting or sharing of this information across institutions. We describe the analysis of paediatric medication events (ME) reported in 18 EDs in a paediatric research network in 2007–2008.

Methods

Confidential, deidentified incident reports (IRs) were collected, and MEs were independently categorised by two investigators. Discordant responses were resolved by consensus.

Results

MEs (597) accounted for 19% of all IRs, with reporting rates varying 25-fold across sites. Anti-infective agents were the most commonly reported, followed by analgesics, intravenous fluids and respiratory medicines. Of the 597 MEs, 94% were medication errors and 6% adverse reactions; further analyses are reported for medication errors. Incorrect medication doses were related to incorrect weight (20%), duplicate doses (21%), and miscalculation (22%). Look-alike/sound-alike MEs were 36% of incorrect medications. Human factors contributed in 85% of reports: failure to follow established procedures (41%), calculation (13%) or judgment (12%) errors, and communication failures (20%). Outcomes were: no deaths or permanent disability, 13% patient harm, 47% reached patient (no harm), 30% near miss or unsafe conditions, and 9% unknown.

Conclusions

ME reporting by the system revealed valuable data across sites on medication categories and potential human factors. Harm was infrequently reported. Our analyses identify trends and latent systems issues, suggesting areas for future interventions to reduce paediatric ED medication errors.
Guttural pouch mycosis in horses: a retrospective study of 28 cases
Authors: Dobesova O. , Schwarz B. , Velde K. , Jahn P. , Zert Z. , Bezdekova B.
Published: November 2012

The medical records of 28 horses with guttural pouch mycosis were reviewed. The most commonly observed clinical signs were nasal discharge, epistaxis, dysphagia and/or cough. All 28 horses had the disease unilaterally, however, in five of them, it had spread into the contralateral pouch via the mesial septum. Three horses were treated medically, 11 horses underwent surgery and seven horses were treated both medically and surgically. Fifty percent of horses (14/28) were euthanased or died, fifty percent of horses (14/28) survived. There was no significant correlation between treatment method (medical, surgical, combination) and survival rate. The most common reason for euthanasia was dysphagia due to pharyngeal dysfunction. There was a highly significant correlation between the presence of dysphagia and non‐survival (p=0.008).
Increased blood cholesterol after a high saturated fat diet is prevented by aerobic exercise training
Authors: Ortega Juan Fernando , Fernández-Elías Valentín Emilio , Hamouti Nassim , Mora-Rodriguez Ricardo
Published: November 2012

A high saturated fatty acids diet (HSFAD) deteriorates metabolic and cardiovascular health while aerobic training improves them. The aim of this study was to investigate in physically inactive and overweight people if 2 weeks of HSFAD leads to hyperlipemia or insulin resistance and if concurrent aerobic exercise training counteracts those effects. Fourteen overweight (body mass index, 27.5 ± 0.6 kg·m−2), healthy, young individuals (aged 24.8 ± 1.8 years) were randomly assigned to a diet (D) or a diet plus exercise (D + E) group. During 14 consecutive days both groups increased dietary saturated fatty acids from 31 ± 10 to 52 ± 14 g·day−1(p < 0.001) while maintaining total fat intake. Concurrent to the diet, the D + E group underwent 11 cycle-ergometer sessions of 55 min at 60% peak oxygen uptake (V˙O2peak). Before and after intervention, insulin sensitivity and body composition were estimated, and blood lipids, resting blood pressure, and V̇O2peakwere measured. Body weight and composition, plasma free fatty acids composition and concentration, and insulin sensitivity remained unchanged in both groups. However, post-intervention total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) increased above pre-intervention values in the D group (147 ± 8 to 161 ± 9 mg·dL−1, p = 0.018 and 71 ± 10 to 82 ± 10 mg·dL−1, p = 0.034, respectively). In contrast, in the D + E group, TCand LDL-C remained unchanged (153 ± 20 to 157 ± 24 mg·dL−1and 71 ± 21 to 70 ± 25 mg·dL−1). Additionally, the D + E group lowered systolic blood pressure (6 ± 2 mm Hg, p = 0.029) and increased V̇O2peak(6 ± 2 mL·kg−1·min−1, p = 0.020). Increases in TCand LDL-C concentration induced by 14 days of HSFAD can be prevented by concurrent aerobic exercise training, which, in addition, improves cardiorespiratory fitness.
Effect of recovery mode on postexercise vagal reactivation in elite synchronized swimmers
Authors: Schaal Karine , Le Meur Yann , Bieuzen François , Petit Odile , Hellard Philippe , Toussaint Jean-François , Hausswirth Christophe
Published: November 2012

This study investigated the effect of whole-body cryostimulation (WBC), contrast-water therapy (CWT), active recovery (ACT), and passive condition (PAS) protocols on the parasympathetic reactivation and metabolic parameters of recovery in elite synchronized swimmers who performed 2 simulated competition ballets (B1 and B2) separated by 70 min. After determining maximal oxygen consumption (V̇O2max400) and blood lactate concentrations ([La−]b400) during a 400-m swim trial, 11 swimmers performed 1 protocol per week in randomized order. Heart rate variability (HRV) was measured at rest (PreB1), 5 min after B1 (PostB1), before B2 (PreB2), and 5 min after B2 (PostB2). V̇O2peakwas measured at PostB1 and PostB2, and [La−]bwas measured at PostB1, PreB2, and PostB2. PostB1 V̇O2peakand V̇O2max400were similar, but PostB1 [La−]bwas higher than [La−]b400(p = 0.004). Each ballet caused significant decreases in HRV indices. At PreB2, all HRV indices had returned to PreB1 levels in the CWT, PAS, and ACT protocols, whereas the WBC protocol yielded a 2- to 4-fold increase in vagal-related HRV indices, compared with PreB1. WBC and ACT both increased [La−]brecovery, compared with PAS (p = 0.06 and p = 0.04, respectively), and yielded an increased V̇O2peakfrom B1 to B2; however, it decreased after PAS (+5.4%, +3.4%, and −3.6%; p < 0.01). This study describes the physiological response to repeated maximal work bouts that are highly specific to elite synchronized swimming. In the context of short-term recovery, WBC yields a strong parasympathetic reactivation, and shows similar effectiveness to ACT on the metabolic parameters of recovery and subsequent exercise capacity.
Relative importance of overstory canopy openness and seedling density on crown morphology and growth ofAcer nipponicumseedlings
Authors: Saito Waka , Kawamura Koji , Takeda Hiroshi
Published: November 2012

We investigated the effects of overstory canopy openness and seedling density on seedling morphology and growth in the mid-successional species Acer nipponicum Hara in a cool-temperate forest. Studied seedlings were 46 seedlings of 30–160 cm height, and their overstory canopy openness ranged between 7.2% and 17.0%. Seedling density, measured as the number of conspecific neighboring seedlings within a 50 cm radius of the target seedling, ranged between 0 and 19. There were no significant correlations between seedling height, canopy openness, and seedling density. Multiple regression analysis showed that crown depth, leaf mass fraction, and leaf area index decreased with decreasing canopy openness and increasing seedling density, while the ratio of trunk-lateral branches mass increased. Overstory canopy openness did not affect crown area, leaf size, or petiole length, all of which decreased with increasing seedling density. Standardized regression coefficients indicated that seedling density affected morphology and growth more than canopy openness did. The morphological responses to canopy openness cannot be considered as adaptive plasticity, as total leaf area and leaf mass fraction decreased with decreasing light levels. In contrast, responses to seedling density indicate adaptive responses to neighborhood competition. The results highlight the importance of seedling density that influenced seedling growth and morphology independently of overstory canopy openness.
Limited divergence in the spatially subdivided population of the Hawaiian mushroomRhodocollybia laulaha
Authors: Keirle M.R. , Avis P.G. , Hemmes D.E. , Mueller G.M.
Published: November 2012

Here we report the first population genetic examination of a fungus in Hawaii and, to our knowledge, the only investigation of a saprotrophic fungal population distributed across an oceanic archipelago. Rhodocollybia laulaha fruits abundantly in the native rain forests of Hawaii from June through December. Its range includes the geographic extent of the Hawaiian Archipelago; however, this range is highly fragmented because of the discontinuous distribution of the native forest habitat where R. laulaha occurs. We hypothesized that significant patterns of population structure would be recovered within the geographic range of the Hawaiian mushroom R. laulaha resulting from divergence between isolated subpopulations. We tested for population structure and related inferred patterns of restricted gene flow to geographic distance, major geographic features such as mountain peaks and oceans, elevation zones, and spore morphology. We included 120 R. laulaha collections using data from the rRNA IGS1 region, two microsatellite loci, and 184 AFLP loci. Analyses of these genetic data suggest limited genetic structure among R. laulaha subpopulations in Hawaii correlated mostly with geographic distance. Patterns associated with specialization to elevation or spore morphology were not recovered. The limited geographic structure observed in R. laulaha is consistent with relatively recent population fragmentation.
Ethyl acrylate conjugated polystyryl-diphenylphosphine — An extremely efficient catalyst for Henry reaction under solvent-free conditions (SolFC)
Authors: Rokhum Lalthazuala , Bez Ghanashyam
Published: November 2012

Over the last few decades, the fast-growing development of polymer supported reagents has led to the synthesis of a variety of reagents on solid support. Some of the major advantages of using such reagents are that they are less hygroscopic, easy to recover, and can be recycled. Here, we have demonstrated that in situ generated ethyl acrylate conjugated polystyryl-diphenylphosphine (PDPP–EA) derived from the reaction of a mixture of polystyryl-diphenylphosphine and ethyl acrylate in a stoichiometric ratio can efficiently catalyze the synthesis of β-nitroalcohols from the reaction of aldehydes and nitroalkanes under solvent-free conditions (SolFC).
Relationships between fatty acid composition and bile tolerance in lactobacillus isolates from plants and from non-plant materials
Authors: Kimoto-Nira Hiromi , Suzuki Shigenori , Yakabe Takafumi , Suzuki Chise
Published: November 2012

Twenty plant-derived and 18 non-plant-derived strains of Lactobacillus casei were compared for their growth in tryptone – yeast extract – glucose broth containing 0.3% bile by measuring absorbance at a wavelength of 620 nm after 24 h of incubation at 37 °C. Bile tolerance — a fundamental probiotic property — was calculated by dividing the experimental data by control values (growth without bile). We found that bile tolerance was strain specific but that the average bile tolerance of the plant-derived strains was significantly (P < 0.05) lower than that of the non-plant-derived strains tested. All tested strains could not deconjugate sodium taurocholate, indicating that the difference in bile tolerance was not due to the ability to deconjugate bile. The fatty acid compositions of the test strains with and without exposure to 0.3% bile were investigated, and a statistical correlation analysis between these compositions and their bile tolerance was conducted. The fatty acids correlated with bile tolerance differed between plant and non-plant lactobacilli. This is the first report to show that the origin (i.e., growth environment) of lactobacilli affects their fatty acid composition, which in turn, appears to be related to their bile tolerance.
Phylogenetic relationships and selective pressure on gene families related to iron homeostasis in land plants
Authors: Victoria Filipe de Carvalho , Bervald Clauber Mateus Priebe , da Maia Luciano Carlos , de Sousa Rogerio Oliveira , Panaud Olivier , de Oliveira Antônio Costa
Published: November 2012

Iron is involved in many metabolic processes, such as respiration and photosynthesis, and therefore an essential element for plant development. Comparative analysis of gene copies between crops and lower plant groups can shed light on the evolution of genes important to iron homeostasis. A phylogenetic analysis of five metal homeostasis gene families (NAS, NRAMP, YSL, FRO, and IRT) selected in monocots, dicots, gymnosperms, and bryophytes was performed. The homologous genes were found using known iron homeostasis gene sequences of Oryza sativa, Arabidopsis thaliana, and Physcomitrella patens as queries. The phylogeny was constructed using bioinfomatics tools. A total of 243 gene sequences for 30 plant species were found. The evolutionary fingerprint analysis suggested a purifying selective pressure of iron homeostasis genes for most of the plant gene homologues. The NAS and YSL genes appear to accumulate more negative selection sites, suggesting a strong selective pressure on these two gene families. The divergence time analysis indicates IRT as the most ancient gene family and FRO as the most recent. NRAMP and YSL genes appear to share a close relationship in the evolution of iron homeostasis gene families.
Identification of novel QTL for resistance to Fusarium head blight in a tetraploid wheat population
Authors: Ruan Yuefeng , Comeau André , Langevin François , Hucl Pierre , Clarke John M. , Brule-Babel Anita , Pozniak Curtis J.
Published: November 2012

Most tetraploid durum wheat (Triticum turgidum L var. durum) cultivars are susceptible to Fusarium head blight (FHB). This study reports novel quantitative trait loci (QTL) associated with FHB resistance. A backcross recombinant inbred line (BCRIL) population was developed from the cross BGRC3487/2*DT735, and 160 lines were evaluated for resistance to Fusarium graminearum Schwabe (teleomorph Gibberella zeae (Schwein. Petch) in field trials over 3 years (2008–2010) and to a F. graminearum 3-acetyl-deoxynivalenol (3-ADON) chemotype in greenhouse trials. The population was genotyped with 948 polymorphic loci using DArT and microsatellite markers. Eleven QTL were associated with FHB resistance under field conditions on chromosomes 2A, 3B, 5A, 5B, 7A, and 7B. Two of these, QFhb.usw-3B from BGRC3487 and QFhb.usw-7A2, were consistently detected over environments. The QFhb.usw-3B QTL was in a similar position to a resistance QTL in hexaploid wheat. The combination of the two QTL reduced field index by 53.5%–86.2%. Two QTL for resistance to the 3-ADON chemotype were detected on chromosomes 1B and 4B. Both BGRC3487 and DT735 could provide new sources of FHB resistance and the combination of QTL reported here could be valuable tools in breeding FHB-resistant durum wheat.
FOURIER TRANSFORM AND RIGIDITY OF CERTAIN DISTRIBUTIONS
Authors: SUN BINYONG , ZHU CHEN-BO
Published: November 2012

Let E be a finite-dimensional vector space over a local field, and F be its dual. For a closed subset X of E, and Y of F, consider the space D-ξ(E; X, Y) of tempered distributions on E whose support are contained in X and support of whose Fourier transform are contained in Y. We show that D-ξ(E; X, Y) possesses a certain rigidity property, for X, Y which are some finite unions of affine subspaces.
ARE QUANTUM CORRELATIONS GENUINELY QUANTUM?
Authors: DI LORENZO ANTONIO
Published: November 2012

It is shown that the probabilities for the spin singlet can be reproduced through classical resources, with no communication between the distant parties, by using merely shared (pseudo-)randomness. If the parties are conscious beings aware of both the hidden-variables and the random mechanism, then one has a conspiracy. If the parties are aware of only the random variables, they may be induced to believe that they are able to send instantaneous information to one another. It is also possible to reproduce the correlations at the price of reducing the detection efficiency. It is further demonstrated that the same probability decomposition could be realized through action-at-a-distance, provided it existed.
FALLING RIGHT WHILE MOVING SLOW: TRUE TESTS OF THE WEAK EQUIVALENCE PRINCIPLE FOR ANTIPARTICLES
Authors: UNNIKRISHNAN C. S. , GILLIES G. T.
Published: November 2012

A significant question in experimental gravity is the nature of free fall of antiparticles under gravity and elaborate preparations are underway to directly test this with cold antihydrogen. Earlier, the Shapiro delay of supernova 1987A neutrinos was interpreted as testing the weak equivalence principle (WEP). We establish the surprising result that the Shapiro delay of relativistic particles does not test WEP for intrinsic properties or quantum numbers of particles or antiparticles. This is because essentially the entire gravitational mass of the relativistic neutrinos is contributed by kinetic energy, diluting to insignificance any EP violating contribution from intrinsic properties, by the relativistic factor. The crucial message here is that a true test of the WEP involving intrinsic properties of matter or antimatter — the foundation of relativistic gravity — necessarily requires nonrelativistic "cold" matter and antimatter.
DIFFERENCES IN CYTOCOMPATIBILITY BETWEEN MWCNTs AND CARBOXYLIC FUNCTIONALIZED MWCNTs
Authors: ZHANG YITENG , LI DEJUN , ZHAO MENGLI , GUO MEIXIAN , DENG XIANGYUN , GU HANQING , WAN RONGXIN
Published: November 2012

Influence of carboxylic functionalization on the cytocompatibility of multiwalled carbon nanotubes (MWCNTs) was investigated in this work. Water contact angle assay showed that the surface of MWCNTs-containing carboxyl (MWCNTs-COOH) became much more hydrophilic compared with pure MWCNTs. In cell-adhesion assays, two cell lines, mouse fibroblast cells (L929) and human umbilical vein endothelial cells (EAHY926) were used to assess the cytocompatibility of materials. The MWCNTs-COOH displayed the improved cell proliferation, viability and adhesion due to the enhanced wettability, indicating their superior cytocompatibility over MWCNTs. The existence of carboxyl groups should be benefit to the adhesion and growth of both cells, which implied that MWCNTs-COOH were helpful for seeding both cells and could be used as the functional surface for the adhesion and growth of cells.
Solvent Effects on the Transient Characteristics of Liquid-Gate Field Effect Transistors with Silicon Substrate
Authors: Yanase Takashi , Hasegawa Tetsuya , Nagahama Taro , Shimada Toshihiro
Published: November 2012

The transient characteristics of electric double layer (EDL) gated field-effect transistors with Si as an active semiconductor were studied using various electrolyte solutions of LiBF4 by applying a step-function voltage to determine the optimum electrolyte for semiconductor circuits using EDLs. The t
R, determined by EDL dynamics in the present experiment, was minimum as a function of the kind of solvent used owing to the competing effects of the EDL thickness and viscosity. The responses of the electrolyte solutions with various solvents at the same concentration were classified into three categories on the basis of t
R: slow response of a complex-forming solvent, intermediate response of protic solvents, and fast response of nonprotic solvents. The best response time was 55 µs when a 1.0 M acetonitrile solution was used as the liquid-gate insulator.
Characterizations of High Stability of Field Emission of ZnO Nanorods Synthesized by Thermal-Vapor Growth
Authors: Yang Su-Hua , Syu Jia-Huei , Hsu Yi-Ming , Chuang Wen-Min
Published: November 2012

In this paper, we present the synthesis and characteristics of high stability of field emission of ZnO nanorods grown on a ZnO seed-deposited Si substrate by thermal-vapor growth. ZnO and graphite powders were used as sources and O2 and N2 as process gases. It was found that the growth of nanorods was poor when they were synthesized under one of the following conditions: 1) synthesis temperature ≤800 °C; 2) ZnO/graphite weight ratio ≤3/7; 3) O2/N2 flow ratio ≥9/7. Nevertheless, nanoleaves developed when the synthesis temperature was higher than 1200 °C, and nanoneedles grew when the synthesis time was longer than 1.5 h. Homogeneous nanorods were grown at 1000 °C for 1 h with an O2/N2 flow ratio of 5/7 and a ZnO/graphite weight ratio of 7/3. Improving the crystalline property of nanorods increased their UV emission intensity and field-emission current. Nanorods with a high aspect ratio possessed a high field enhancement factor and low turn-on electric field, whereas the photoluminescence intensity of nanorods was less dependent on their aspect ratios. The emission current variation was less than 20% when the nanorods were examined under an electric field of 7.3 MV/m for 5 h.
Charge and Mobility Enhancements in In-Polar InAl(Ga)N/Al(Ga)N/GaN Heterojunctions Grown by Metal–Organic Chemical Vapor Deposition Using a Graded Growth Strategy
Authors: Lu Jing , Hu Yan-Ling , Brown David F. , Wu Feng , Keller Stacia , Speck James S. , DenBaars Steven P. , Mishra Umesh K.
Published: November 2012

In this paper, we investigated the Ga incorporation effect in InAl(Ga)N/Al(Ga)N/GaN heterojunctions grown by a close coupled showerhead metal–organic chemical vapor reactor and proposed a grading growth strategy, where the indium composition was graded from Al(Ga)N to InAl(Ga)N, to mitigate the deleterious effect of Ga carry-over on the transport properties of two dimensional electron gas (2DEG). In contrast to non-graded samples grown by conventional growth strategy without grading, hall measurements revealed significant charge and mobility enhancements for the graded samples, with an electron mobility of 1300 cm2 V-1 s-1, a sheet charge density of 2.35 ×1013 cm-2 and a resultant low sheet resistance of 205 Ω/□ compared to the non-graded sample with an low sheet charge density of 1.4 ×1013 cm-2 and mobility of 1100 ±50 cm2 V-1 s-1. The reason of the enhancements were then analyzed by transmission electron microscopy (TEM) and atom probe techniques, which revealed that grading strategy led to a higher average Al composition in the barrier layer.
Properties of Indium–Zinc-Oxide Films Synthesized by Radio Frequency Magnetron Sputtering Based on Gas Phase Monitoring Using Multi-Micro Hollow Cathode Lamp
Authors: Inoue Mari , Ohta Takayuki , Takota Naoki , Tsuchitani Shigeki , Takashima Seigo , Yamakawa Koji , Kano Hiroyuki , Takeda Keigo , Hori Masaru , Ito Masafumi
Published: November 2012

Indium–zinc-oxide (IZO) films were synthesized by radio frequency magnetron sputtering. In order to clarify the mechanisms of IZO film formation, the absolute densities of In and Zn atoms were measured simultaneously by absorption spectroscopy employing the multi-micro hollow cathode lamp. Their densities were measured to be 109 to 1011 cm-3 and increased with pressure from 1 to 10 Pa. The density ratios of In to Zn in the gas phase corresponded to the ratios of film composition, and the relative amount of Zn atom increased with decreasing pressure. Carrier density increased with decreasing density ratio of In to Zn owing to the increase in the number of oxygen vacancies, which was clarified from the O 1s spectra obtained by X-ray photoelectron spectroscopy. A low resistivity of 10-6 Ω m and an optical transmission of over 80% in the visible region were achieved at a pressure of 1 Pa.
Stochastic Effect of Acid Catalytic Chain Reaction in Chemically Amplified Extreme Ultraviolet Resists
Authors: Kozawa Takahiro
Published: November 2012

The stochastic effect of incident photons is a significant concern in nanometer-scale fabrication using highly sensitive resists because the fluctuation of the line edges of resist patterns should be suppressed to guarantee normal operation of fabricated devices. However, what matters the most in the line edge roughness (LER) formation is not photon fluctuation but protected unit fluctuation. In this study, the changes in the stochastic effect of acid catalytic chain reaction were investigated using the Monte Carlo method. It was theoretically confirmed that the reason why LER decreases with the increase in exposure dose and/or acid generator concentration is not the reduction of the fluctuations of concentrations of photons (shot noise), acids, or protected units but the increase in chemical gradient.
Synkinematic emplacement of Lassiter Coast Intrusive Suite plutons during the Palmer Land Event: evidence for mid-Cretaceous sinistral transpression at the Beaumont Glacier in eastern Palmer Land
Authors: Vaughan Alan P. M. , Storey Craig , Kelley Simon P. , Barry Tiffany L. , Curtis Michael L.
Published: November 2012

New structural and geochronological data from the Eastern Palmer Land Shear Zone, in the vicinity of Beaumont Glacier, provide the first evidence of dated structural control on emplacement of the 119–95 Ma, >13000 km
2
Cretaceous Lassiter Coast Intrusive Suite, during the accretionary mid-Cretaceous Palmer Land Event orogeny. A previously undated >100 m thick dyke-like quartz tonalite intrusion was emplaced at 116.5 ± 1.5 Ma (Ar–Ar biotite cooling age) along a NW–SE axis, coeval with NW–SE compressional deformation, and possibly controlled by sinistral transpression along the Beaumont Glacier shear zone. The quartz tonalite preserves two styles of deformation and was probably progressively deformed by normal-sinistral shearing during magmatic cooling with initial deformation of mafic enclaves in the dyke interior and final formation of proto-mylonite to mylonite on the dyke margin. The quartz tonalite cuts folding associated with Phase 1 of the Palmer Land Event, indicating that this folding is older than 116 Ma, extending the onset of Phase 1 back in time. Mylonite on the quartz tonalite sheet margin was subsequently thermally reset at
c
. 107 Ma (Ar–Ar biotite method), during a peak in Lassiter Coast Intrusive Suite magmatism.

Supplementary material:

Country rock lithological data, petrographic description of tonalite and Ar–Ar geochronology data are available at
www.geolsoc.org.uk/SUP18552
.
Large-scale magmatic pulses drive plant ecosystem dynamics
Authors: Jolley David W. , Passey Simon R. , Hole Malcolm , Millett John
Published: November 2012

The 6.6 km gross thickness of the Palaeogene lava field of the Faroe Islands Basalt Group was erupted in the initial phases of North Atlantic rifting. Thin interlava sedimentary rocks yield palynofloras that vary in composition and diversity with the duration of the interlava period. Long-term trends in plant ecological succession occur within the record, each reflecting initially rapid and subsequently slowing eruption tempo. TiO
2
and MgO plots derived from the basalt lava flows show corresponding fractionation trends. These link melt column processes to vegetation ecosystem dynamics via controls on eruption tempo, thermal support and substrate disturbance.

Supplementary material:

Further data are available at
www.geolsoc.org.uk/SUP18538
.
Cretaceous sequence of deformation in the SE Zagros fold–thrust belt
Authors: Farahpour Mohammad M. , Hessami Khaled
Published: November 2012

Several major zones across the Zagros fold–thrust belt have been interpreted as indicating that orogeny took place progressively from NE to SW through discrete orogenic episodes during Tertiary time. This paper uses field evidence of growth onlaps and angular unconformities within the Cretaceous stratigraphic column as well as existing geological maps and cross-sections to indicate that deformation started as early as the Late Aptian and folded the whole width of the Zagros belt simultaneously. Later events are indicated by folding at the end of the Cenomanian, and in the Late Turonian and Santonian. Following the Late Cretaceous deformation phases, the SE Zagros basin was divided into several longitudinal intra-shelf basins, which were separated by NW–SE-trending Cretaceous anticlines. However, with reference to our previous work, it can be suggested that each of the sub-basins was folded serially from NE to SW through a series of tectonic phases during the next episode of Zagros orogeny in Tertiary time. The change of deformation style from concomitant to serial folding, during the Cretaceous and Tertiary respectively, is attributed to the existence of the Hormuz Salt and shearing at the base of the former basin and its absence at the base of the Tertiary intra-shelf basins.
Imaging new opportunities and play concepts in the Adriatic Sea and Levantine Basin
Authors: Peace David G. , Stieglitz Theodore , Spoors Richard
Published: November 2012

There is significant opportunity in re-working older data with modern geophysical technology to develop new plays and concepts in the northern and eastern Mediterranean. New exploration success and higher commodity prices have encouraged both majors and independents to reconsider the Mediterranean as a viable entry point to North African and Southern European energy markets. Two case studies in the Adriatic Sea and Levantine Basin are examined for play concepts and leads using vintage seismic data re-imaged with modern imaging techniques integrated together with a geologically driven workflow. The Adriatic was selected based upon maturity of hydrocarbon discovery; in comparison the Levantine Basin ranks as a region of new territory which we are only just beginning to understand.