bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and Characterization of a Novel Serine Protease, VvpS, That Contains Two Functional Domains and Is Essential for Autolysis of Vibrio vulnificus
Authors: Lim Moon Sub , Kim Jeong-A , Lim Jong Gyu , Kim Byoung Sik , Jeong Kwang Cheol , Lee Kyu-Ho , Choi Sang Ho
Published: June 2011

Little is known about the molecular mechanism for autolysis of Gram-negative bacteria. In the present study, we identified the
vvpS
gene encoding a serine protease, VvpS, from
Vibrio vulnificus
, a Gram-negative food-borne pathogen. The amino acid sequence predicted that VvpS consists of two functional domains, an N-terminal protease catalytic domain (PCD) and a C-terminal carbohydrate binding domain (CBD). A null mutation of
vvpS
significantly enhanced viability during stationary phase, as measured by enumerating CFU and differentially staining viable cells. The
vvpS
mutant reduced the release of cytoplasmic β-galactosidase and high-molecular-weight extracellular chromosomal DNA into the culture supernatants, indicating that VvpS contributes to the autolysis of
V. vulnificus
during stationary phase. VvpS is secreted via a type II secretion system (T2SS), and it exerts its effects on autolysis through intracellular accumulation during stationary phase. Consistent with this, a disruption of the T2SS accelerated intracellular accumulation of VvpS and thereby the autolysis of
V. vulnificus
. VvpS also showed peptidoglycan-hydrolyzing activity, indicating that the autolysis of
V. vulnificus
is attributed to the self-digestion of the cell wall by VvpS. The functions of the VvpS domains were assessed by C-terminal deletion analysis and demonstrated that the PCD indeed possesses a proteolytic activity and that the CBD is required for hydrolyzing peptidoglycan effectively. Finally, the
vvpS
mutant exhibited reduced virulence in the infection of mice. In conclusion, VvpS is a serine protease with a modular structure and plays an essential role in the autolysis and pathogenesis of
V. vulnificus
.
Regulation of Flagellum Number by FliA and FlgM and Role in Biofilm Formation by Rhodobacter sphaeroides
Authors: Wilkinson David A. , Chacko Sarah J. , Vénien-Bryan Catherine , Wadhams George H. , Armitage Judith P.
Published: June 2011

The FlgM secretion checkpoint plays a crucial role in coordinating bacterial flagellar assembly. Here we identify a new role for FlgM and FliA as part of a complex regulatory network which controls flagellum number and is essential for efficient swimming and biofilm formation in the monotrichous bacterium
Rhodobacter sphaeroides
.
Acinetobacter baumannii RecA Protein in Repair of DNA Damage, Antimicrobial Resistance, General Stress Response, and Virulence
Authors: Aranda Jesús , Bardina Carlota , Beceiro Alejandro , Rumbo Soraya , Cabral Maria P. , Barbé Jordi , Bou Germán
Published: June 2011

RecA is the major enzyme involved in homologous recombination and plays a central role in SOS mutagenesis. In
Acinetobacter
spp., including
Acinetobacter baumannii
, a multidrug-resistant bacterium responsible for nosocomial infections worldwide, DNA repair responses differ in many ways from those of other bacterial species. In this work, the function of
A. baumannii
RecA was examined by constructing a
recA
mutant. Alteration of this single gene had a pleiotropic effect, showing the involvement of RecA in DNA damage repair and consequently in cellular protection against stresses induced by DNA damaging agents, several classes of antibiotics, and oxidative agents. In addition, the absence of RecA decreased survival in response to both heat shock and desiccation. Virulence assays
in vitro
(with macrophages) and
in vivo
(using a mouse model) similarly implicated RecA in the pathogenicity of
A. baumannii
. Thus, the data strongly suggest a protective role for RecA in the bacterium and indicate that inactivation of the protein can contribute to a combined therapeutic approach to controlling
A. baumannii
infections.
Identification of an Anchor Residue for CheA-CheY Interactions in the Chemotaxis System of Escherichia coli
Authors: Thakor Hemang , Nicholas Sarah , Porter Ian M. , Hand Nicole , Stewart Richard C.
Published: June 2011

Transfer of a phosphoryl group from autophosphorylated CheA (P-CheA) to CheY is an important step in the bacterial chemotaxis signal transduction pathway. This reaction involves CheY (i) binding to the P2 domain of P-CheA and then (ii) acquiring the phosphoryl group from the P1 domain. Crystal structures indicated numerous side chain interactions at the CheY-P2 binding interface. To investigate the individual contributions of the P2 side chains involved in these contacts, we analyzed the effects of eight alanine substitution mutations on CheA-CheY binding interactions. An F214A substitution in P2 caused ∼1,000-fold reduction in CheA-CheY binding affinity, while Ala substitutions at other P2 positions had small effects (E171A, E178A, and I216A) or no detectable effects (H181A, D202A, D207A, and C213A) on binding affinity. These results are discussed in relation to previous
in silico
predictions of hot-spot and anchor positions at the CheA-CheY interface. We also investigated the consequences of these mutations for chemotaxis signal transduction in living cells. CheA(F214A) was defective in mediating localization of CheY-YFP to the large clusters of signaling proteins that form at the poles of
Escherichia coli
cells, while the other CheA variants did not differ from wild-type (wt) CheA (CheA
wt
) in this regard. In our set of mutants, only CheA(F214A) exhibited a markedly diminished ability to support chemotaxis in motility agar assays. Surprisingly, however, in FRET assays that monitored receptor-regulated production of phospho-CheY, CheA(F214A) (and each of the other Ala substitution mutants) performed just as well as CheA
wt
. Overall, our findings indicate that F214 serves as an anchor residue at the CheA-CheY interface and makes an important contribution to the binding energy
in vitro
and
in vivo
; however, loss of this contribution does not have a large negative effect on the overall ability of the signaling pathway to modulate P-CheY levels in response to chemoattractants.
Characterization of the Self-Cleaving Effector Protein NopE1 of Bradyrhizobium japonicum
Authors: Schirrmeister Jana , Friedrich Lars , Wenzel Mandy , Hoppe Markus , Wolf Christine , Göttfert Michael , Zehner Susanne
Published: June 2011

NopE1 is a type III-secreted protein of the symbiont
Bradyrhizobium japonicum
which is expressed in nodules.
In vitro
it exhibits self-cleavage in a duplicated domain of unknown function (DUF1521) but only in the presence of calcium. Here we show that either domain is self-sufficient for cleavage. An exchange of the aspartic acid residue at the cleavage site with asparagine prevented cleavage; however, cleavage was still observed with glutamic acid at the same position, indicating that a negative charge at the cleavage site is sufficient. Close to each cleavage site, an EF-hand-like motif is present. A replacement of one of the conserved aspartic acid residues with alanine prevented cleavage at the neighboring site. Except for EDTA, none of several protease inhibitors blocked cleavage, suggesting that a known protease-like mechanism is not involved in the reaction. In line with this, the reaction takes place within a broad pH and temperature range. Interestingly, magnesium, manganese, and several other divalent cations did not induce cleavage, indicating a highly specific calcium-binding site. Based on results obtained by blue-native gel electrophoresis, it is likely that the uncleaved protein forms a dimer and that the fragments of the cleaved protein oligomerize. A database search reveals that the DUF1521 domain is present in proteins encoded by
Burkholderia phytofirmans
PsNJ (a plant growth-promoting betaproteobacterium) and
Vibrio coralliilyticus
ATCC BAA450 (a pathogenic gammaproteobacterium). Obviously, this domain is more widespread in proteobacteria, and it might contribute to the interaction with hosts.
Wall Teichoic Acid-Dependent Adsorption of Staphylococcal Siphovirus and Myovirus
Authors: Xia Guoqing , Corrigan Rebecca M. , Winstel Volker , Goerke Christiane , Gründling Angelika , Peschel Andreas
Published: June 2011

The molecular interactions between staphylococcal phages and host cell surfaces are poorly understood. Employing
Staphylococcus aureus
teichoic acid mutants, we demonstrate that wall teichoic acid (WTA), but not lipoteichoic acid, serves as a receptor for staphylococcal siphovirus and myovirus, while only the siphovirus requires glycosylated WTA.
Structure of the Flagellar Motor Protein Complex PomAB: Implications for the Torque-Generating Conformation
Authors: Yonekura Koji , Maki-Yonekura Saori , Homma Michio
Published: June 2011

The bacterial flagellar motor is driven by an ion flux through a channel called MotAB in
Escherichia coli
or
Salmonella
and PomAB in
Vibrio alginolyticus
. PomAB is composed of two transmembrane (TM) components, PomA and PomB, and converts a sodium ion flux to rotation of the flagellum. Its homolog, MotAB, utilizes protons instead of sodium ions. PomB/MotB has a peptidoglycan (PG)-binding motif in the periplasmic domain, allowing it to function as the stator by being anchored to the PG layer. To generate torque, PomAB/MotAB is thought to undergo a conformational change triggered by the ion flux and to interact directly with FliG, a component of the rotor. Here, we present the first three-dimensional structure of this torque-generating stator unit analyzed by electron microscopy. The structure of PomAB revealed two arm domains, which contain the PG-binding site, connected to a large base made of the TM and cytoplasmic domains. The arms lean downward to the membrane surface, likely representing a “plugged” conformation, which would prevent ions leaking through the channel. We propose a model for how PomAB units are placed around the flagellar basal body to function as torque generators.
Residues in a Conserved α-Helical Segment Are Required for Cleavage but Not Secretion of an Escherichia coli Serine Protease Autotransporter Passenger Domain
Authors: Dautin Nathalie , Bernstein Harris D.
Published: June 2011

Autotransporters are a superfamily of virulence factors produced by Gram-negative bacteria that are comprised of an N-terminal extracellular domain (passenger domain) and a C-terminal β barrel domain (β domain) that resides in the outer membrane (OM). The β domain promotes the translocation of the passenger domain across the OM by an unknown mechanism. Available evidence indicates that an α-helical segment that spans the passenger domain-β domain junction is embedded inside the β domain at an early stage of assembly. Following its secretion, the passenger domain of the
s
erine
p
rotease
a
uto
t
ransporters of the

E

nterobacteriaceae
(SPATEs) and the pertactin family of
Bordetella pertussis
autotransporters is released from the β domain through an intrabarrel autoproteolytic cleavage of the α-helical segment. Although the mutation of conserved residues that surround the cleavage site has been reported to impair both the translocation and cleavage of the passenger domain of a SPATE called Tsh, we show here that the mutation of the same residues in another SPATE (EspP) affects only passenger domain cleavage. Our results strongly suggest that the conserved residues are required to position the α-helical segment for the cleavage reaction and are not required to promote passenger domain secretion.
Complete Genome Sequence of the Anaerobic, Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LF
Authors: Zhao Baisuo , Mesbah Noha M. , Dalin Eileen , Goodwin Lynne , Nolan Matt , Pitluck Sam , Chertkov Olga , Brettin Thomas S. , Han James , Larimer Frank W. , Land Miriam L. , Hauser Loren , Kyrpides Nikolaos , Wiegel Juergen
Published: June 2011

The genome of the anaerobic halophilic alkalithermophile
Natranaerobius thermophilus
consists of one 3,165,557-bp chromosome and two plasmids (17,207 bp and 8,689 bp). The present study is the first to report the completely sequenced genome of an anaerobic polyextremophile and genes associated with roles in regulation of intracellular osmotic pressure, pH homeostasis, and growth at elevated temperatures.
Genome Sequence of the Mercury-Methylating and Pleomorphic Desulfovibrio africanus Strain Walvis Bay
Authors: Brown Steven D. , Wall Judy D. , Kucken Amy M. , Gilmour Cynthia C. , Podar Mircea , Brandt Craig C. , Teshima Hazuki , Detter John C. , Han Cliff S. , Land Miriam L. , Lucas Susan , Han James , Pennacchio Len , Nolan Matt , Pitluck Sam , Woyke Tanja , Goodwin Lynne , Palumbo Anthony V. , Elias Dwayne A.
Published: June 2011

Desulfovibrio africanus
strain Walvis Bay is an anaerobic sulfate-reducing bacterium capable of producing methylmercury (MeHg), a potent human neurotoxin. The mechanism of methylation by this and other organisms is unknown. We present the 4.2-Mb genome sequence to provide further insight into microbial mercury methylation and sulfate-reducing bacteria.
Genome Sequence of the Repetitive-Sequence-Rich Mycoplasma fermentans Strain M64
Authors: Shu Hung-Wei , Liu Tze-Tze , Chan Huang-I , Liu Yen-Ming , Wu Keh-Ming , Shu Hung-Yu , Tsai Shih-Feng , Hsiao Kwang-Jen , Hu Wensi S. , Ng Wailap Victor
Published: June 2011

Mycoplasma fermentans
is a microorganism commonly found in the genitourinary and respiratory tracts of healthy individuals and AIDS patients. The complete genome of the repetitive-sequence-rich
M. fermentans
strain M64 is reported here. Comparative genomics analysis revealed dramatic differences in genome size between this strain and the recently completely sequenced JER strain.
Microbial Ecology of the Dark Ocean above, at, and below the Seafloor
Authors: Orcutt Beth N. , Sylvan Jason B. , Knab Nina J. , Edwards Katrina J.
Published: June 2011

The majority of life on Earth—notably, microbial life—occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean—the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.—has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.
Does hormone replacement therapy cause breast cancer? An application of causal principles to three studies: Table 1
Authors: Shapiro Samuel , Farmer Richard D T , Mueck Alfred O , Seaman Helen , Stevenson John C
Published: June 2011

Background

Based principally on findings in three studies, the Collaborative Reanalysis (CR), the Women's Health Initiative (WHI), and the Million Women Study (MWS), it is claimed that combined hormone replacement therapy (HRT) with estrogen plus progestogen is now an established cause of breast cancer. For unopposed estrogen therapy the evidence in the three studies is conflicting: the CR and MWS have reported increased risks in estrogen users, while the WHI has not. The authors have previously reviewed the findings in the CR (Part 1).

Objective

To evaluate the evidence for causality in the WHI studies.

Methods

Using generally accepted causal criteria, in this paper (Part 2) the authors evaluate the findings in the WHI for estrogen plus progestogen; in a related paper (Part 3) the authors evaluate the findings for unopposed estrogen. An evaluation of the MWS (Part 4), and of trends in breast cancer incidence following publication of the WHI findings in 2002 (Part 5) will follow.

Results

For estrogen plus progestogen the findings did not adequately satisfy the criteria of bias, confounding, statistical stability and strength of association, duration-response, internal consistency, external consistency or biological plausibility.

Conclusion

HRT with estrogen plus progestogen may or may not increase the risk of breast cancer, but the WHI did not establish that it does.
Does hormone replacement therapy cause breast cancer? An application of causal principles to three studies
Authors: Shapiro Samuel , Farmer Richard D T , Mueck Alfred O , Seaman Helen , Stevenson John C
Published: June 2011

Background

Studies from the Women's Health Initiative have reported an increased risk of breast cancer in users of estrogen plus progestogen. Among users of estrogen alone an increased risk was not observed.

Objective To evaluate the evidence for unopposed estrogen.

Methods

In a related article (Part 2) the authors apply generally accepted causal criteria to the findings for estrogen plus progestogen. Here (Part 3) the authors apply the criteria to the findings for unopposed estrogen, as reported in a clinical trial, and in combined data from the trial and an observational study.

Results

In the clinical trial, after 7.1 years of follow-up the relative risk (RR) of invasive breast cancer for women assigned to estrogen was 0.77 in an ‘intention-to-treat’ analysis (95% CI 0.59–1.01) and 0.67 (95% CI 0.47–0.97) in an ‘as treated’ analysis; after 10.7 years the risk reduction persisted. Time order was correctly specified; detection bias was minimal; in the ‘as treated’ analysis confounding was unlikely; duration-response and internal consistency could be evaluated only to a limited extent because of scanty data; the findings were discordant with increased risks observed in the Collaborative Reanalysis and the Million Women Study; biological plausibility could not be assessed.

In the combined analysis, among women who had previously used estrogen soon after the menopause there was no clear evidence of either a reduction or an increase in the risk of breast cancer among women assigned to estrogen during the trial, or among women who were using estrogen in the observational study when follow-up commenced. The combined analysis did not satisfy the criteria of time order, bias, confounding, statistical stability and strength of association, duration-response, and internal consistency; biological plausibility could not be assessed.

Conclusions

The evidence from the clinical trial suggests that unopposed estrogen does not increase the risk of breast cancer, and may even reduce it. The latter possibility, however, is based on statistically borderline evidence.
Optimising surgical training: use of feedback to reduce errors during a simulated surgical procedure
Authors: Boyle Emily , Al-Akash Musallam , Gallagher Anthony G , Traynor Oscar , Hill Arnold D K , Neary Paul C
Published: June 2011

Objective

To assess the effect of proximate or immediate feedback during an intensive training session. The authors hypothesised that provision of feedback during a training session would improve performance and learning curves.

Methods

Twenty-eight trainee surgeons participated in the study between September and December 2008. They were consecutively assigned to group 1 (n=16, no feedback) or group 2 (n=12, feedback) All the participants performed five hand-assisted laparoscopic colectomy procedures on the ProMIS surgical simulator. Efficiency of instrument use (instrument path length and smoothness) and predefined intraoperative error scores were assessed. Facilitators assisted their performance and answered questions when asked. Group 1 participants were given no extra assistance, but group 2 participants received standardised feedback and the chance to review errors after every procedure. Data were analysed using SPSS V.15. Mann–Whitney U tests were used to compare mean performance results, and analysis of variance was used to calculate within-subject improvement.

Results

Group 1 achieved better results for instrument path length (23 874 mm vs 39 086 mm, p=0.001) and instrument smoothness (2015 vs 2567, p=0.045) However, group 2 (feedback) performed significantly better with regard to error scores (14 vs 4.42, p=0.000). In addition, they demonstrated a smoother learning curve. Inter-rater reliability for the error scores was 0.97.

Conclusion

The provision of standardised proximate feedback was associated with significantly fewer errors and an improved learning curve. Reducing errors in the skills lab environment should lead to safer clinical performance. This may help to make training more efficient and improve patient safety.
Assessment of potential toxicity of a smokeless tobacco product (naswar) available on the Pakistani market
Authors: Zakiullah  , Saeed Muhammad , Muhammad Naveed , Khan Saeed Ahmad , Gul Farah , Khuda Fazli , Humayun Muhammad , Khan Hamayun
Published: June 2011

Background

‘Naswar’ is a smokeless tobacco product (STP) widely used in Pakistan. It has been correlated with oral and oesophageal cancer in recent clinical studies. The toxic effects associated with STPs have been associated with trace level contaminants present in these products. The toxin levels of Pakistani naswar are reported for the first time in this study.

Methods

A total of 30 Pakistani brands of naswar were tested for a variety of toxic constituents and carcinogens such as cadmium, arsenic, lead and other carcinogenic metals, nitrite and nitrate, and nicotine and pH.

Results

The average values of all the toxins studied were well above their allowable limits, making the product a health risk for consumers. Calculated lifetime cancer risk from cadmium and lead was 1 lac (100000) to 10 lac (1000000) times higher than the minimum 10E_4 (0.00001) to 10E_6 (0.000001), which is the ‘target range’ for potentially hazardous substances, according to the US Environmental Protection Agency. Similarly, the level of arsenic was in the range of 0.15 to 14.04 μg/g, the average being 1.25 μg/g. The estimated average bioavailable concentration of arsenic is 0.125–0.25 μg/g, which is higher than the allowable standard of 0.01 μg/g. Similarly, the average minimum daily intake of chromium and nickel was 126.97 μg and 122.01 μg, as compared to allowable 30–35 μg and 35 μg, respectively; a 4–5 times higher exposure. However, beryllium was not detected in any of the brands studied. The pH was highly basic, averaging 8.56, which favours the formation of tobacco specific amines thus making the product potentially toxic. This study validates clinical studies correlating incidence of cancer with naswar use in Pakistan.

Conclusions

This study shows that the production, packaging, sale and consumption of naswar should be regulated so as to protect the public from the health hazards associated with its consumption.
Long‐term efficacy and safety of firocoxib in the treatment of dogs with osteoarthritis
Authors: Autefage A. , Palissier F. M. , Asimus E. , Pepin‐Richard C.
Published: June 2011

Thirty‐nine client‐owned dogs with osteoarthritis were treated with 5 mg/kg firocoxib administered orally, once a day for 52 weeks. Veterinary examinations were performed on approximately days 0, 15, 90, 180, 270 and 360. Twenty‐five dogs completed the study. The withdrawal rate associated with gastrointestinal side effects was low (5.1 per cent of dogs). Based on the owners' assessment, 82 per cent of the dogs had improved at day 15, 84 per cent of the 32 remaining dogs had improved at day 90, and 96 per cent of the 25 dogs that completed the trial had improved at day 360. During this trial, 12 (48 per cent) of the 25 remaining dogs showed an improvement in their lameness from day 90 to day 360 (P<0.05).
Quantitative trait loci influencing endosperm texture, dough-mixing strength, and bread-making properties of the hard red spring wheat breeding lines
Authors: Tsilo Toi J. , Simsek Senay , Ohm Jae-Bom , Hareland Gary A. , Chao Shiaoman , Anderson James A.
Published: June 2011

Wheat end product quality is determined by a complex group of traits including dough viscoelastic characteristics and bread-making properties. Quantitative trait loci (QTL) mapping and analysis were conducted for endosperm texture, dough-mixing strength, and bread-making properties in a population of 139 (MN99394 × MN98550) recombinant inbred lines that were evaluated at three environments in 2006. Based on the genetic map of 534 loci, six QTL were identified for endosperm texture, with the main QTL on chromosomes 1A (R2= 6.6%–17.3%), 5A (R2= 6.1%–17.1%), and 5D (R2= 15.8%–22%). Thirty-four QTL were identified for eight dough-mixing strength and bread-making properties. Major QTL clusters were associated with the low-molecular weight glutenin gene Glu-A3, the two high-molecular weight glutenin genes Glu-B1 and Glu-D1, and two regions on chromosome 6D. Alleles at these QTL clusters have previously been proven useful for wheat quality, except one of the QTL clusters on chromosome 6D. A QTL cluster on chromosome 6D is one of the novel chromosome regions influencing dough-mixing strength and bread-making properties. The QTL for endosperm texture on chromosomes 1A, 5A, and 5B also influenced flour ash content (12.4%–23.3%), flour protein content (10.5%–12.5%), and flour colour (7.7%–13.5%), respectively.
Haplotype combination of SREBP-1c gene sequence variants is associated with growth traits in cattle
Authors: Huang Yong-Zhen , He Hua , Sun Jia-Jie , Wang Jing , Li Zhuan-Jian , Lan Xian-Yong , Lei Chu-Zhao , Zhang Chun-Lei , Zhang En-Ping , Wang Ju-Qiang , Chen Hong
Published: June 2011

The aim of this study was to examine the association of the SREBP-1c polymorphism with growth traits in cattle breeds. Five sequence variants (SVs) were identified within the bovine sterol regulatory element-binding protein-1c gene (SREBP-1c), using DNA sequencing, PCR, PCR–RFLP, and forced PCR–RFLP methods. These polymorphisms include three missense mutations (SV1, SV4, and SV5) in exons 7, 9, and 12, a silent mutation (SV3) in exon 9, and a large deletion (SV2) in intron 7. Overall, we report the validation of polymorphisms within the bovine SREBP-1c gene, and the haplotype variability and extent of linkage disequilibrium (LD) in 1061 individuals representing the five main cattle breeds from China. We also investigated haplotype frequencies and LD coefficients for five SVs in all study populations. LD and haplotype structure of SREBP-1c were different between breeds. The result of haplotype analysis of five SVs showed that 27 different haplotypes were identified by all breeds. Two haplotypes (Hap1 and Hap2) shared by all five populations accounted for 42.75%, 35.68%, 36.44%, 25.43%, and 96.26% of all haplotypes observed in the cattle breeds Nanyang, Qinchuan, Jiaxian, Jinnan, and Chinese Holstein, respectively. The statistical analyses indicated that one single SV and 38 combined haplotypes were significantly associated with growth traits in the Nanyang cattle population (P < 0.05 or P < 0.01). The results of this study suggest that the SREBP-1c gene possibly is a strong candidate gene that affects growth traits in the Chinese beef cattle breeding program.
Variation in wood density components within and between Quercus faginea trees
Authors: Knapic Sofia , Louzada José L. , Pereira Helena
Published: June 2011

The wood of Quercus faginea Lam. was studied regarding its density variation within and between trees using microdensitometry techniques in 10 trees growing in northern Portugal. The observations were made in mature trees at several height levels (stem base and 1.3, 3.4, 5.5, 7.6, and 9.7 m). Variance analysis was done considering the core cylinder (first 15 rings) and the sheath (last 10 rings) in relation to tree, height level, and ring effects and their interactions. The wood revealed a high mean density of 0.848 g·cm–3 with small differences between earlywood and latewood (0.717 and 0.908 g·cm–3, respectively). Latewood corresponded on average to 66% of the total ring width, which averaged 2.4 mm. Wood density decreased with height and radially from pith to cambium. However, within-tree variation was of very moderate magnitude although higher for juvenile wood. Variation between trees was also small (6% coefficient of variation of the mean) and higher for the mature wood. Quercus faginea wood compares favourably with other oak species with regard to density characteristics and may be considered for production of quality solid wood products.
Utilization of family genetic variability to improve the rooting ability of white spruce (Picea glauca) cuttings
Authors: Gravel-Grenier J. , Lamhamedi M.S. , Beaulieu J. , Carles S. , Margolis H.A. , Rioux M. , Stowe D.C. , Lapointe L.
Published: June 2011

Family genetic variability of the rooting characteristics of white spruce ( Picea glauca (Moench) Voss) cuttings harvested from 3-year-old stock plants was evaluated for 75 half-sib families. Growth, root system architecture, and gas exchange of the cuttings during the rooting phase (B+0) and the two subsequent growing seasons (B+1 and B+2) were evaluated. The root initiation phase (B+0) and the root development phases (B+1 and B+2) were found to be under strong genetic control. The weak correlations found between B+0 and the B+1 and B+2 phases may indicate that gene expression during B+0 is not related to root growth and development during B+1 and B+2. Strong positive correlations were observed between plant root and aboveground characteristics at the end of the B+1 and B+2 phases. This suggests that an indirect and efficient selection for white spruce families producing cuttings with heavier root dry masses could be based on the measures of aboveground morphological characteristics. Finally, the strong genetic control of morphological characteristics found in this study indicates that the selection of superior genotypes at a clonal level is possible for intensive forest management.
Intra-annual patterns of tracheid size in the Mediterranean tree Juniperus thurifera as an indicator of seasonal water stress
Authors: DeSoto Lucía , De la Cruz Marcelino , Fonti Patrick
Published: June 2011

Because climate can affect xylem cell anatomy, series of intra-annual cell anatomical features have the potential to retrospectively supply seasonal climatic information. In this study, we explored the ability to extract information about water stress conditions from tracheid features of the Mediterranean conifer Juniperus thurifera L. Tracheidograms of four climatic years from two drought-sensitive sites in Spain were compared to evaluate whether it is possible to link intra-annual cell size patterns to seasonal climatic conditions. Results indicated site-specific anatomical adjustment such as smaller and thicker tracheids at the dryer site but also showed a strong climatic imprint on the intra-annual pattern of tracheid size. Site differences in cell size reflected expected structural adjustments against cavitation failures. Differences between intra-annual patterns, however, indicated a response to seasonal changes in water availability whereby cells formed under drought conditions were smaller and thicker, and vice versa. This relationship was more manifest and stable at the dryer site.
Orchid abundance in hemiboreal forests: stand-scale effects of clear-cutting, green-tree retention, and artificial drainage
Authors: Lõhmus Asko , Kull Tiiu
Published: June 2011

The current knowledge on the impact of forest management on plant species of conservation concern is poor. We asked how three basic silvicultural techniques (clear-cutting, green-tree retention, and artificial drainage) affect the abundance of terrestrial orchid species and their communities in Estonia, hemiboreal Europe. Fixed-area, fixed-effort surveys (4 h per 2 ha plot) were used in 29 plot clusters representing five site types, with each cluster including plots of four treatments (old growth, mature managed forest, and cutover with and without live retention trees). Altogether 11 species of orchids were recorded in those 116 plots, with the most complete sets of species in artificially drained plots and mature stands. Five species were widely distributed among treatments and site types, but most site types also hosted shade-tolerant orchids (six species) that characteristically disappeared after timber harvesting. Cutover areas (3–7 years after harvest) hosted no species absent from uncut forest stands, and retention of solitary trees had no effect on orchid abundance over clear-cuts. Modern Estonian forest landscapes appear to support viable populations of many orchids, with rotation ages sufficient for population development of the majority of shade-tolerant species.
Long-term impact of liming on growth and vigor of northern hardwoods
Authors: Long Robert P. , Horsley Stephen B. , Hall Thomas J.
Published: June 2011

Sugar maple (Acer saccharum Marsh.) is a keystone species in the northern hardwood forest, and decline episodes have negatively affected the growth and health of sugar maple in portions of its range over the past 50+ years. Crown health, growth, survival, and flower and seed production of sugar maple were negatively affected by a widespread decline event in the mid-1980s on the unglaciated Allegheny Plateau in northern Pennsylvania. A long-term liming study was initiated in 1985 to evaluate responses to a one-time application of 22.4 Mg·ha–1 of dolomitic limestone in four northern hardwood stands. Over the 23-year period ending in 2008, sugar maple basal area increment (BAINC) increased significantly (P ≤ 0.05) in limed plots from 1995 through 2008, whereas American beech (Fagus grandifolia Ehrh.) BAINC was unaffected. For black cherry (Prunus serotina Ehrh.), the third principal overstory species, BAINC and survival were reduced in limed plots compared with unlimed plots. Foliar Ca and Mg remained significantly higher in sugar maple foliage sampled 21 years after lime application, showing persistence of the lime effect. These results show long-term species-specific responses to lime application.
A methodological analysis of canopy disturbance reconstructions using Quercus alba
Authors: Buchanan Megan L. , Hart Justin L.
Published: June 2011

Forest disturbance history reconstructions in the eastern US commonly rely on the analysis of a single tree-ring series per individual. However, this method can result in an underrepresentation of radial growth releases and canopy disturbance events. We analyzed paired tree-ring series from 884 Quercus alba L. individuals to quantify discrepant patterns of intratree release frequency, magnitude, and initiation years. We also developed a model for Q. alba that accounts for this underrepresentation of releases. Of the 884 trees analyzed, 216 exhibited radial growth releases. Only 13 of these 216 trees recorded the same canopy disturbance events in both series. Through analysis of a single growth-ring series per tree, a minimum of 39 and a maximum of 241 releases could be detected from the trees in the data set. Of the total number of release events, 238 (85%) occurred only in one of the paired tree-ring series. For stand development studies requiring the frequency of canopy disturbance alone, a multiplicative factor of 1.72 can provide the information necessary without deviating from the standard practice in the eastern US of collecting and analyzing a single increment core per tree. Studies requiring spatially and temporally explicit information regarding disturbance should extract and analyze two or more tree-ring series per individual.
TILT ANGLE AND THE TEMPERATURE SHIFTS CALCULATED AS A FUNCTION OF CONCENTRATION FOR THE AC* PHASE TRANSITION IN A BINARY MIXTURE OF LIQUID CRYSTALS
Authors: YURTSEVEN H. , KURT M.
Published: June 2011

We study here the tilt angle and the temperature shifts as a function of concentration for the AC* phase transition in a binary mixture, using our mean field model with the biquadratic P2θ2 coupling — and also with the bilinear Pθ and P2θ2 couplings. By expanding the free energy in terms of the tilt angle and polarization, the tilt angle and the temperature shift are evaluated by using the coefficients given in the free energy expansion. By employing a concentration-dependent coefficient, the tilt angle and the temperature shift are calculated as a function of concentration of 10.O.4 for the SmAC* transition in a binary mixture of C7 and 10.O.4.

Our calculated values of the tilt angle and the temperature shifts decrease as the concentration of 10.O.4 increases, as confirmed experimentally for the AC* transition in this binary mixture. This indicates that our mean field models studied here are satisfactory to explain the observed behavior of the AC* transition of the binary mixture of C7 and 10.O.4.
A NEW CHAOTIC ENCRYPTION ALGORITHM BASED ON THE ERGODICITY OF CHAOS
Authors: WANG XING-YUAN , WANG XIAO-JUAN
Published: June 2011

This paper proposes a new symmetric key encryption algorithm based on one-dimensional chaotic map. This algorithm uses the random-like property and ergodicity of chaotic systems. In the process of encryption or decryption, this algorithm generates a chaotic pseudo-random sequence, changes the initial iterative times and the increment to encrypt the plaintext, and realizes fast encryption and decryption of all kinds of files. When analyzing the algorithm's performance and security, the result shows that, compared with the method of Baptista, the proposed method is safer, faster and more powerful.
APPEARANCE OF A ZERO-n AND A ZERO-ϕeff GAP IN DIFFERENT FREQUENCY RANGES IN A SINGLE 1D PHOTONIC BAND GAP STRUCTURE
Authors: ALI MUNAZZA ZULFIQAR , ABDULLAH TARIQ
Published: June 2011

We present a scheme to realize both the zero-n and the zero-ϕ eff gap in a one-dimensional photonic band gap structure containing metamaterials. The frequency dispersion of the effective electric permittivity and magnetic permeability of the metamaterials in the adjacent layers in one period are represented by the Drude model and the resonant model. The chosen structure is composed of alternate double-negative and double-positive layers which exhibit a zero-n gap in a certain frequency range whereas in a higher frequency range it behaves as alternate permittivity negative and permeability negative layers to exhibit a zero-ϕ eff gap. Some properties and benefits of having the zero-n and the zero-ϕ eff gap in the same physical system are discussed.
Flexible Ferroelectric Liquid Crystal Cell Stabilized by Column Spacer and Polymer Wall: Influence of Bending and Pressing on the Mechanical Stability
Authors: Lee Ji-Hoon , Choi Min-Ki , Lim Tong-Kun , Yoon Tae-Hoon
Published: June 2011

We prepared a flexible ferroelectric liquid crystal cell stabilized by column spacers and polymer walls. The column-shaped spacers were built on a plastic substrate and a liquid crystal-reactive monomer mixture was printed on it. The polymer walls were formed perpendicular to the column spacers by a polymerization-induced phase-separation technique, and the polymer networks were formed in the pixel area by an additional UV curing. The change of the liquid crystal orientation was examined vs the bending and pressing of the plastic substrates.
Extremely High Purcell Factor of Plasmonic Modes in Thin Nano-Metallic Cylinders
Authors: Yang Jin-Kyu
Published: June 2011

We numerically study the ultrahigh Purcell factor (>104) of plasmonic modes in thin metallic nanodisk and nanoring structures by fully three-dimensional (3D) finite-difference time-domain (FDTD) simulation. Because of their extremely small mode volume (∼10-5 λ0
3, λ0 is the resonant wavelength in vacuum), plasmonic modes with a large radiative loss can have a high decay rate. Because of a uniform field enhancement inside their rings, nano-metallic ring structures show high potential for controlling high-extraction efficiency and single molecular sensing utilized in surface-enhanced Raman scattering.
Color Reproduction of Multi-Wavelength Digital Holography Using a Color Correction Algorithm
Authors: Tu Han-Yen , Lai Xin-Ji , Cheng Chau-Jern , Lin Li-Chien
Published: June 2011

This work describes color reproduction of multi-wavelength digital holographic recording and reconstruction of real objects based on color correction procedures. Color correction primarily consists of tone correction and chromaticity correction for reconstructed images from a multi-wavelength digital hologram. With recording and reconstruction knowledge from a standard ColorChecker chart, a color profile can be generated to characterize the color properties of the multi-wavelength digital holography system and then use this profile for color reproduction of different target images. The color accuracy of reconstructed images via the proposed method is demonstrated experimentally.
Fabrication of Epitaxial Interface between Transition Metal Cyanides
Authors: Kurihara Yutaro , Moritomo Yutaka
Published: June 2011

Nanoporous materials are currently attracting the interest of materials scientists, because nanopores can transfer and accommodate guest cations. We may realize a rapid cation transfer from one material to another through an epitaxial interface. In this study, we fabricated bilayer films of nanoporous transition metal cyanides by an electrochemical deposition technique. Scanning electron microscopy (SEM) images as well as X-ray diffraction patterns strongly suggest that the cyanide layers are epitaxially connected to each other. We compared the current–voltage (I–V) properties of the epitaxial bilayer films with those of the monolayer films.
Detecting and resolving policy misconfigurations in access-control systems
Authors: Bauer Lujo , Garriss Scott , Reiter Michael K.
Published: June 2011

Access-control policy misconfigurations that cause requests to be erroneously denied can result in wasted time, user frustration, and, in the context of particular applications (e.g., health care), very severe consequences. In this article we apply association rule mining to the history of accesses to predict changes to access-control policies that are likely to be consistent with users' intentions, so that these changes can be instituted in advance of misconfigurations interfering with legitimate accesses. Instituting these changes requires the consent of the appropriate administrator, of course, and so a primary contribution of our work is how to automatically determine from whom to seek consent and how to minimize the costs of doing so. We show using data from a deployed access-control system that our methods can reduce the number of accesses that would have incurred costly time-of-access delays by 43%, and can correctly predict 58% of the intended policy. These gains are achieved without impacting the total amount of time users spend interacting with the system.
Access controls for oblivious and anonymous systems
Authors: Coull Scott E. , Green Matthew , Hohenberger Susan
Published: June 2011

The use of privacy-enhancing cryptographic protocols, such as anonymous credentials and oblivious transfer, could have a detrimental effect on the ability of providers to effectively implement access controls on their content. In this article, we propose a
stateful anonymous credential
system that allows the provider to implement nontrivial, real-world access controls on oblivious protocols conducted with anonymous users. Our system models the behavior of users as a state machine and embeds that state within an anonymous credential to restrict access to resources based on the state information. The use of state machine models of user behavior allows the provider to restrict the users' actions according to a wide variety of access control models without learning anything about the users' identities or actions. Our system is secure in the standard model under basic assumptions and, after an initial setup phase, each transaction requires only constant time. As a concrete example, we show how to implement the Brewer--Nash (Chinese Wall) and Bell-La Padula (Multilevel Security) access control models within our credential system. Furthermore, we combine our credential system with an adaptive oblivious transfer scheme to create a privacy-friendly oblivious database with strong access controls.
10 rules for scalable performance in 'simple operation' datastores
Authors: Stonebraker Michael , Cattell Rick
Published: June 2011

Partition data and operations, keep administration simple, do not assume one size fits all.
Specification and verification
Authors: Barnett Mike , Fähndrich Manuel , Leino K. Rustan M. , Müller Peter , Schulte Wolfram , Venter Herman
Published: June 2011

Can a programming language really help programmers write better programs?
Dremel
Authors: Melnik Sergey , Gubarev Andrey , Long Jing Jing , Romer Geoffrey , Shivakumar Shiva , Tolton Matt , Vassilakis Theo
Published: June 2011

Dremel is a scalable, interactive ad hoc query system for analysis of read-only nested data. By combining multilevel execution trees and columnar data layout, it is capable of running aggregation queries over trillion-row tables in seconds. The system scales to thousands of CPUs and petabytes of data, and has thousands of users at Google. In this paper, we describe the architecture and implementation of Dremel, and explain how it complements MapReduce-based computing. We present a novel columnar storage representation for nested records and discuss experiments on few-thousand node instances of the system.
Sample-efficient batch reinforcement learning for dialogue management optimization
Authors: Pietquin Olivier , Geist Matthieu , Chandramohan Senthilkumar , Frezza-Buet Hervé
Published: June 2011

Spoken Dialogue Systems (SDS) are systems which have the ability to interact with human beings using natural language as the medium of interaction. A dialogue policy plays a crucial role in determining the functioning of the dialogue management module. Handcrafting the dialogue policy is not always an option, considering the complexity of the dialogue task and the stochastic behavior of users. In recent years approaches based on Reinforcement Learning (RL) for policy optimization in dialogue management have been proved to be an efficient approach for dialogue policy optimization. Yet most of the conventional RL algorithms are data intensive and demand techniques such as user simulation. Doing so, additional modeling errors are likely to occur. This paper explores the possibility of using a set of approximate dynamic programming algorithms for policy optimization in SDS. Moreover, these algorithms are combined to a method for learning a sparse representation of the value function. Experimental results show that these algorithms when applied to dialogue management optimization are particularly
sample efficient
, since they learn from few hundreds of dialogue examples. These algorithms learn in an
off-policy
manner, meaning that they can learn optimal policies with dialogue examples generated with a quite simple strategy. Thus they can learn good dialogue policies directly
from data
, avoiding user modeling errors.
Comparing user simulations for dialogue strategy learning
Authors: Ai Hua , Litman Diane
Published: June 2011

Recent studies show that user simulations can be used to generate training corpora for learning dialogue strategies automatically. However, it is unclear what type of simulation is most suitable in a particular task setting. We observe that a simulation which generates random behaviors in a restricted way outperforms simulations that mimic human user behaviors in a statistical way. Our finding suggests that we do not always need to construct a realistic user simulation. Since constructing realistic user simulations is not a trivial task, we can save engineering cost by wisely choosing simulation models that are appropriate for our task.