bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of Enterobacter cloacae subsp. cloacae Strain 08XA1, a Fecal Bacterium of Giant Pandas
Authors: Yan Yue , Zhao Chuan-Wu , Zhang Yi-Zheng , Zhang Zhi-He , Pan Guang-Lin , Liu Wen-Wang , Ma Qing-Yi , Hou Rong , Tan Xue-Mei 
Published: December 2012

ABSTRACT

Enterobacter cloacae
, a common pathogenic bacterium, is a Gram-negative bacillus. We analyzed the draft genome of
Enterobacter cloacae
subsp.
cloacae
strain 08XA1 from the feces of a giant panda in China. Genes encoding a β-lactamase and efflux pumps, as well as other factors, have been found in the genome.
Complete Sequence of the First Chimera Genome Constructed by Cloning the Whole Genome of Synechocystis Strain PCC6803 into the Bacillus subtilis 168 Genome
Authors: Watanabe Satoru , Shiwa Yuh , Itaya Mitsuhiro , Yoshikawa Hirofumi 
Published: December 2012

ABSTRACT

Genome synthesis of existing or designed genomes is made feasible by the first successful cloning of a cyanobacterium,
Synechocystis
PCC6803, in Gram-positive, endospore-forming
Bacillus subtilis
. Whole-genome sequence analysis of the isolate and parental
B. subtilis
strains provides clues for identifying single nucleotide polymorphisms (SNPs) in the 2 complete bacterial genomes in one cell.
Genome Sequence of the Alkane-Degrading Bacterium Alcanivorax hongdengensis Type Strain A-11-3
Authors: Lai Qiliang , Shao Zongze 
Published: December 2012

ABSTRACT

Alcanivorax hongdengensis
A-11-3
T
was isolated from an oil-enriched consortium enriched from the surface seawater of Hong-Deng dock in the Straits of Malacca and Singapore. Strain A-11-3
T
can degrade
n
-alkane and produce a lipopeptide biosurfactant. Here we report the genome of A-11-3
T
and the genes associated with alkane degradation.
Genome Sequence of Galbibacter marinum Type Strain ck-I2-15
Authors: Lai Qiliang , Li Chongping , Shao Zongze 
Published: December 2012

ABSTRACT

Galbibacter marinum
strain ck-I2-15
T
was isolated from an arsenite-resistant consortium enriched from the deep sea sediment of a hydrothermal vent field on the Southwest Indian Ocean Ridge. Here, we present the draft genome of strain ck-I2-15
T
, which contains 3,572,447 bp with a G+C content of 37.04% and contains 3,099 protein-coding genes and 38 tRNA genes.
Genome Sequence of Coxiella burnetii 109, a Doxycycline-Resistant Clinical Isolate
Authors: Rouli Laetitia , Rolain Jean-Marc , El Filali Adil , Robert Catherine , Raoult Didier 
Published: December 2012

ABSTRACT

Coxiella burnetii
109, with a 2.03-Mb genome, is a doxycycline-resistant human isolate that was isolated from the cardiac valve of a German male patient with Q fever endocarditis who died during the course of the treatment due to the bacterium's resistance to doxycycline. This new genome can be useful for future comparative genomic or Q fever studies.
Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, “Candidatus Nitrosopumilus koreensis” AR1, from Marine Sediment
Authors: Park Soo-Je , Kim Jong-Geol , Jung Man-Young , Kim So-Jeong , Cha In-Tae , Kwon KaeKyoung , Lee Jung-Hyun , Rhee Sung-Keun 
Published: December 2012

ABSTRACT

Ammonia-oxidizing archaea (AOA) are ubiquitous in various marine environments and play important roles in the global nitrogen and carbon cycles. We here present a high-quality draft genome sequence of an ammonia-oxidizing archaeon, “
Candidatus
Nitrosopumilus koreensis” AR1, which was found to dominate an ammonia-oxidizing enrichment culture in marine sediment off Svalbard, the Arctic Circle. Despite a significant number of nonoverlapping genes (ca. 30%), similarities of this strain to “
Candidatus
Nitrosopumilus maritimus” were revealed by core genes for archaeal ammonia oxidation and carbon fixation, G+C content, and extensive synteny conservation.
Genome Sequence of Acinetobacter baumannii TYTH-1
Authors: Liou Ming-Li , Liu Chih-Chin , Lu Chia-Wei , Hsieh Ming-Feng , Chang Kai-Chih , Kuo Han-Yueh , Lee Chi-Ching , Chang Chun-Tien , Yang Cheng-Yao , Tang Chuan Yi 
Published: December 2012

ABSTRACT

Acinetobacter baumannii
has emerged recently as a major cause of health care-associated infections due to the extent of its antimicrobial resistance and its propensity to cause large nosocomial outbreaks. Here we report the genome sequence of
Acinetobacter baumannii
TYTH-1 isolated in Taiwan during 2008.
Complete Genome Sequence of Brucella abortus Strain BCB034, a Strain of Biovar 2 Isolated from Human
Authors: Zhong Zhijun , Wang Lulu , Chen Yanfen , Wang Zhoujia , Wang Yufei , Cui Mingquan , Li Tiefeng , Ke Yuehua , Yuan Xitong , Wang Dali , Chen Zeliang , Peng Guangneng 
Published: December 2012

ABSTRACT

Brucella abortus
is divided into eight biovars, of which biovars 1 to 3 are the most frequently represented biovars in strains isolated from humans. Here, we report the genome sequence of
B. abortus
strain BCB034, a strain isolated from a human patient and that belongs to biovar 2.
Genome Sequence of “Candidatus Methanomethylophilus alvus” Mx1201, a Methanogenic Archaeon from the Human Gut Belonging to a Seventh Order of Methanogens
Authors: Borrel Guillaume , Harris Hugh M. B. , Tottey William , Mihajlovski Agnès , Parisot Nicolas , Peyretaillade Eric , Peyret Pierre , Gribaldo Simonetta , O'Toole Paul W. , Brugère Jean-François 
Published: December 2012

ABSTRACT

We report the draft genome sequence of “
Candidatus
Methanomethylophilus alvus” Mx1201, a methanogen present in the human gut. It was enriched from human feces under anaerobic conditions with methanol as the substrate. Its circular genome, of around 1.7 Mb, contains genes needed for methylotrophic methanogenesis from methanol and tri-, di-, and monomethylamine.
Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, “Candidatus Nitrosopumilus sediminis” AR2, from Svalbard in the Arctic Circle
Authors: Park Soo-Je , Kim Jong-Geol , Jung Man-Young , Kim So-Jeong , Cha In-Tae , Ghai Rohit , Martín-Cuadrado Ana-Belén , Rodríguez-Valera Francisco , Rhee Sung-Keun 
Published: December 2012

ABSTRACT

Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in marine sediments. We herein present the draft genome sequence of an ammonia-oxidizing archaeon, “
Candidatus
Nitrosopumilus sediminis” AR2, which was enriched in culture from a marine sediment obtained off Svalbard, within the Arctic Circle. The typical genes involved in archaeal ammonia oxidation and carbon fixation necessary for chemolithoautotrophic growth were observed. Interestingly, the AR2 genome sequence was revealed to possess, uniquely among cultivated AOA from marine environments, a capability for urea utilization.
Genome Sequence of Thalassospira xiamenensis Type Strain M-5
Authors: Lai Qiliang , Shao Zongze 
Published: December 2012

ABSTRACT

Thalassospira xiamenensis
M-5
T
was isolated from the surface water of a waste oil pool at the oil storage dock in the city of Xiamen, Fujian Province, China. Here, we present the draft genome of strain M-5
T
, which contains 4,705,237 bp with a G+C content of 54.65% and contains 4,343 protein-coding genes and 46 tRNA genes.
Draft Genome Sequence of Staphylococcus massiliensis Strain 5402776
T
Authors: Roux Véronique , Robert Catherine , Gimenez Grégory , Raoult Didier 
Published: December 2012

ABSTRACT

A draft genome sequence of
Staphylococcus massiliensis
, Gram-positive cocci isolated from a human brain abscess sample, is described here. One clustered regularly interspaced short palindromic repeat, three transposases, six putative transposases, and one potential provirus were characterized.
Draft Genome Sequence of Agrobacterium albertimagni Strain AOL15
Authors: Trimble William L. , Phung Le T. , Meyer Folker , Gilbert Jack A. , Silver Simon 
Published: December 2012

ABSTRACT

Agrobacterium albertimagni
strain AOL15 is an alphaproteobacterium isolated from arsenite-oxidizing biofilms whose draft genome contains 5.1 Mb in 55 contigs with 61.2% GC content and includes a 21-gene arsenic gene island. This is the first available genome for this species and the second
Agrobacterium
arsenic gene island.
Genome Sequence of Afipia birgiae, a Rare Bacterium Associated with Amoebae
Authors: Pagnier Isabelle , Croce Olivier , Robert Catherine , Raoult Didier , La Scola Bernard 
Published: December 2012

ABSTRACT

Afipia birgiae
is an alphaproteobacterium from the family
Bradyrhizobiaceae
, growing in amoebae, and a potential human pathogen. We sequenced the genome of type strain 34632
T
. It is composed of 5,325,467 bp and contains 5,160 protein-coding genes and 53 RNA genes, including 3 rRNA genes.
Genome Sequence of Bartonella rattimassiliensis, a Bacterium Isolated from European Rattus norvegicus
Authors: Merhej Vicky , Croce Olivier , Robert Catherine , Rolain Jean-Marc , Raoult Didier 
Published: December 2012

ABSTRACT

Bartonella rattimassiliensis
is a facultative intracellular bacterium isolated from the blood of
Rattus norvegicus
in Marseille. The present study reports the draft genome of
B. rattimassiliensis
strain 15908 (CIP 107705
T
).
Genome Sequence of the Pathogenic Herbaspirillum seropedicae Strain Os45, Isolated from Rice Roots
Authors: Zhu Bo , Ye Shuting , Chang Siping , Chen Mingyue , Sun Li , An Qianli 
Published: December 2012

ABSTRACT

Most
Herbaspirillum seropedicae
strains are beneficial to plants. In contrast,
H. seropedicae
strain Os45, isolated from rice roots, is pathogenic. The draft genome sequence of strain Os45 presented here allows an in-depth comparative genome analysis to understand the subtle mechanisms of beneficial and pathogenic
Herbaspirillum
-plant interactions.
Draft Genome Sequencing of Bacillus sp. Strain M2-6, Isolated from the Roots of Korean Ginseng, Panax ginseng C. A. Meyer, after High-Hydrostatic-Pressure Processing
Authors: Kim Chong-Tai , Kim Bong-Soo , Kim Min-Ji , Park Bang Heon , Kwon Sujin , Maeng Hack Young , Kwak Jangyul , Chun Jongsik , Cho Yong-Jin , Kim Namsoo , Kim Chul-Jin , Maeng Jin-Soo 
Published: December 2012

ABSTRACT

A bacterium, designated M2-6, was isolated from Korean ginseng,
Panax ginseng
C. A. Meyer, roots after high-hydrostatic-pressure processing. On the basis of 16 rRNA gene phylogeny, the isolate was presumptively identified as a
Bacillus
sp. Here we report the draft genome sequence of
Bacillus
sp. strain M2-6 (= KACC 16563).
Genome Sequence of the Immunomodulatory Strain Bifidobacterium bifidum LMG 13195
Authors: Gueimonde Miguel , Ventura Marco , Margolles Abelardo , Sánchez Borja 
Published: December 2012

ABSTRACT

In this work, we report the genome sequences of
Bifidobacterium bifidum
strain LMG13195. Results from our research group show that this strain is able to interact with human immune cells, generating functional regulatory T cells.
A Sault-outlet-referenced mid- to late-Holocene paleohydrograph for Lake Superior constructed from strandplains of beach ridges
Authors: Johnston John W. , Argyilan Erin P. , Thompson Todd A. , Baedke Steve J. , Lepper Kenneth , Wilcox Douglas A. , Forman Steven L. 
Published: December 2012

The most detailed Lake Superior paleohydrograph relative to the current outlet near Sault Ste. Marie, Ontario–Michigan, was constructed from four strandplains of beach ridges. This provides a history of water-level, glacial isostatic adjustment (GIA), and the active outlet prior to monitoring and regulation. Four relative paleohydrographs that are offset and subparallel owing to differences in GIA were produced from 321 basal foreshore elevations and 56 optically stimulated luminescence ages. Subtracting modeled elevations in defined millennial lake phases between relative paleohydrographs and similarity between an inferred Sault Ste. Marie (hereinafter, Sault) paleohydrograph and data near the zero isobase corroborates rates of GIA derived from water-level gauges. A change in trend in the Sault paleohydrograph is related to the final separation of Lake Superior from Lakes Michigan and Huron and is the youngest age reported at 1060 ± 100 years. A near-horizontal trend in the Sault paleohydrograph for the past millennium has an intercept that is close to the historical average for Lake Superior. A consistently linear trend from about 2 to 1 ka suggests a relatively stable outlet similar to the past millennium, but a decreasing trend from 3 to 1 ka suggests an outlet other than the Sault. Although intercept data beyond the last millennium are similar in elevation to the reported bedrock sill near Chicago (Hansel et al. 1985), we argue that the Port–Huron outlet was the active outlet during this time and the inferred paleohydrograph of Baedke and Thompson (2000) requires reevaluation.
WORST-OF OPTIONS AND CORRELATION SKEW UNDER A STOCHASTIC CORRELATION FRAMEWORK
Authors: MARABEL ROMO JACINTO 
Published: December 2012

This article considers a multi-asset model based on Wishart processes that accounts for stochastic volatility and for stochastic correlations between the underlying assets, as well as between their volatilities. The model accounts for the existence of correlation term structure and correlation skew. The article shows that the Wishart specification can generate different patterns corresponding to the correlation skew for a wide range of correlation term structures. Another advantage of the model is that it is analytically tractable and, hence, it is possible to obtain semi-closed-form solutions for the prices of plain vanilla options, as well as for the price of exotic derivatives. In this sense, this article develops semi-closed-form formulas for the price of European worst-of options with barriers and/or forward-start features. To motivate the introduction of the Wishart volatility model, the article compares the prices obtained under this model and under a multi-asset stochastic volatility model with constant instantaneous correlations. The results reveal the existence of a stochastic correlation premium and show that the consideration of stochastic correlation is a key element for the valuation of these structures.
Emergency Medicine Pharmacists and Sepsis Management
Authors: Weant Kyle A. , Baker Stephanie N. 
Published: December 2012

Purpose: To describe the role that an emergency medicine (EM) clinical pharmacist has on the management of patients presenting to the emergency department (ED) with sepsis, severe sepsis, or septic shock. Methods: The clinical consultations documented by the EM pharmacists at an academic, teaching hospital over a 2-year period were retrospectively reviewed. Results: During the study period, a total of 585 consultations were provided by the EM pharmacists to 130 patients who presented to the ED with a diagnosis of sepsis, severe sepsis, or septic shock. Dosing recommendations were the most frequent consultations provided (n = 309, 53%), followed by the addition of appropriate empiric antibiotics (n = 131, 22%) and medication preparation (n = 108, 19%). Antibiotics (n = 307, 83%) and vasopressors (n = 31, 8%) were the medication classes regularly involved in EM pharmacist consultations. Vancomycin (n = 90, 28%) and norepinephrine (n = 15, 48%) were the most common agents involved in these consultations. Conclusion: A clinical EM pharmacist has multiple roles in the early management of patients presenting with sepsis, severe sepsis, or septic shock in the ED. Most commonly, they have a role in optimizing empiric antibiotic selection and dosing; thereby ensuring adequate antimicrobial coverage in this complex patient population.
The hybrid steepest descent method for solving variational inequality over triple hierarchical problems
Authors: Wairojjana Nopparat , Jitpeera Thanyarat , Kumam Poom 
Published: December 2012

Abstract
An explicit algorithm is introduced to solve the monotone variational inequality over a triple hierarchical problem. The strong convergence for the proposed algorithm to the solution is guaranteed under some assumptions. Our results extend those of Iiduka (Nonlinear Anal. 71:e1292-e1297, 2009), Marino and Xu (J. Optim. Theory Appl. 149(1):61-78, 2011), Yao et al. (Fixed Point Theory Appl. 2011:794203, 2011) and other authors.

MSC:46C05, 47H06, 47H09, 47H10, 47J20, 47J25, 65J15.
The serum vaspin levels are reduced in Japanese chronic hemodialysis patients
Authors: Inoue Junko , Wada Jun , Teshigawara Sanae , Hida Kazuyuki , Nakatsuka Atsuko , Takatori Yuji , Kojo Shoichirou , Akagi Shigeru , Nakao Kazushi , Miyatake Nobuyuki , McDonald John F , Makino Hirofumi 
Published: December 2012

AbstractBackgroundVisceral adipose tissue-derived serine proteinase inhibitor (vaspin) is an adipokine identified in genetically obese rats that correlates with insulin resistance and obesity in humans. Recently, we found that 7% of the Japanese population with the minor allele sequence (A) of rs77060950 exhibit higher levels of serum vaspin. We therefore evaluated the serum vaspin levels in Japanese chronic hemodialysis patients.MethodsHealthy Japanese control volunteers (control; n = 95, 49.9±6.91 years) and Japanese patients undergoing hemodialysis therapy (HD; n = 138, 51.4±10.5 years) were enrolled in this study, and serum samples were subjected to the human vaspin RIA system.ResultsThe measurement of the serum vaspin levels demonstrated that a fraction of control subjects (n = 5) and HD patients (n = 11) exhibited much higher levels (> 10 ng/ml; VaspinHighgroup), while the rest of the population exhibited lower levels (< 3 ng/ml; VaspinLowgroup). By comparing the patients in the VaspinLowgroup, the serum vaspin levels were found to be significantly higher in the control subjects (0.87±0.24 ng/ml) than in the HD patients (0.32±0.15 ng/ml) (p < 0.0001). In the stepwise regression analyses, the serum creatinine and triglyceride levels were found to be independently and significantly associated with the vaspin concentrations in all subjects.ConclusionsThe creatinine levels are negatively correlated with the serum vaspin levels and were significantly reduced in the Japanese HD patients in the VaspinLowgroup.
Efficacy of once-daily indacaterol 75 μg relative to alternative bronchodilators in COPD: A study level and a patient level network meta-analysis
Authors: Cope Shannon , Zhang Jie , Williams James , Jansen Jeroen P 
Published: December 2012

AbstractBackgroundThe objective of this study was to evaluate the comparative efficacy of indacaterol 75 μg once daily (OD), tiotropium 18 μg OD, salmeterol 50 μg twice daily (BID), formoterol 12 μg BID, and placebo for the treatment of chronic obstructive pulmonary disease (COPD) based on individual patient data (IPD) from randomized controlled trials (RCTs) from the indacaterol trial program and aggregate data (AD) identified from a systematic review of RCTs.Methods22 RCTs were included in the AD analysis that evaluated: indacaterol 75 μg (n = 2 studies), indacaterol 150 μg n = 5 (i.e. salmeterol 50 μg) (n = 5), indacaterol 300 μg (n = 2), tiotropium 18 μg (n = 10), salmeterol 50 μg (n = 7), and formoterol 12 μg (n = 4). All of the studies except for one head-to-head comparison (tiotropium vs. salmeterol) were placebo controlled. Outcomes of interest were trough forced expiratory volume in 1 second (FEV1) and St. George’s Respiratory Questionnaire (SGRQ) total score at week 12. The AD from all trials was analysed simultaneously using a Bayesian network meta-analysis (NMA) and relative treatment effects between all regimens were obtained. In a separate analysis, the IPD available from the 6 indacaterol RCTs was analysed in a NMA. Treatment-by-covariate interactions were included in both analyses to improve similarity of the trials.ResultsAll interventions compared were more efficacious than placebo regarding FEV1at 12 weeks. Indacaterol 75 μg is expected to result in a comparable FEV1at 12 weeks to tiotropium and salmeterol based on both IPD and AD analyses. In comparison to formoterol, the IPD and AD results indicate indacaterol 75 μg is more efficacious (IPD = 0.07 L difference; 95%Credible Interval (CrI) 0.02 to 0.11; AD = 0.05 L difference; 95%CrI 0.01; 0.09). In terms of SGRQ total score at 12 weeks, indacaterol 75 μg and formoterol were more efficacious than placebo, whereas for tiotropium and salmeterol the credible intervals included zero for the AD results only (tiotropium: -2.99 points improvement versus placebo; 95%CrI −6.48 to 0.43; salmeterol:-2.52; 95%CrI: -5.34; 0.44). Both IPD and AD results suggest that indacaterol 75 μg is expected to be comparable to all active treatments.ConclusionsBased on a synthesis of currently available AD RCT evidence as well as an IPD network meta-analysis of six RCTs, indacaterol 75 μg is expected to be at least as efficacious as formoterol and comparable to tiotropium and salmeterol regarding FEV1. Furthermore, indacaterol 75 μg shows comparable level of improvement in health-related quality of life to tiotropium, salmeterol, and formoterol, as measured by the SGRQ.
Artificial biosynthesis of phenylpropanoic acids in a tyrosine overproducing Escherichia coli strain
Authors: Kang Sun-Young , Choi Oksik , Lee Jae Kyung , Hwang Bang Yeon , Uhm Tai-Boong , Hong Young-Soo 
Published: December 2012

Abstract

Background
The phenylpropanoid metabolites are an extremely diverse group of natural products biosynthesized by plants, fungi, and bacteria. Although these compounds are widely used in human health care and nutrition services, their availability is limited by regional variations, and isolation of single compounds from plants is often difficult. Recent advances in synthetic biology and metabolic engineering have enabled artificial production of plant secondary metabolites in microorganisms.

Results
We develop an Escherichia coli system containing an artificial biosynthetic pathway that yields phenylpropanoic acids, such as 4-coumaric acid, caffeic acid, and ferulic acid, from simple carbon sources. These artificial biosynthetic pathways contained a codon-optimized tal gene that improved the productivity of 4-coumaric acid and ferulic acid, but not caffeic acid in a minimal salt medium. These heterologous pathways extended in E. coli that had biosynthesis machinery overproducing tyrosine. Finally, the titers of 4-coumaric acid, caffeic acid, and ferulic acid reached 974 mg/L, 150 mg/L, and 196 mg/L, respectively, in shake flasks after 36-hour cultivation.

Conclusions
We achieved one gram per liter scale production of 4-coumaric acid. In addition, maximum titers of 150 mg/L of caffeic acid and 196 mg/L of ferulic acid were achieved. Phenylpropanoic acids, such as 4-coumaric acid, caffeic acid, and ferulic acid, have a great potential for pharmaceutical applications and food ingredients. This work forms a basis for further improvement in production and opens the possibility of microbial synthesis of more complex plant secondary metabolites derived from phenylpropanoic acids.
Junction investigation of graphene/silicon Schottky diodes
Authors: Mohammed Muatez , Li Zhongrui , Cui Jingbiao , Chen Tar-pin 
Published: December 2012

Abstract
Here we present a facile technique for the large-scale production of few-layer graphene flakes. The as-sonicated, supernatant, and sediment of the graphene product were respectively sprayed onto different types of silicon wafers. It was found that all devices exhibited current rectification properties, and the supernatant graphene devices have the best performance. Schottky junctions formed between graphene flakes and silicon n-type substrates exhibit good photovoltaic conversion efficiency while graphene/p-Si devices have poor light harvesting capability.