bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of Mass Independent Oxygen Isotopic Compositions in Superscale Nitrate Mineral Deposits from Turpan‐Hami Basin, Xinjiang, China and Its Significance
Authors: Yanhe LI , Yan QIN , Feng LIU , Kejun HOU , Defang WAN 
Published: December 2010

Abstract:The Turpan‐Hami Basin in eastern Xinjiang is one of the driest regions on Earth and a premier environment to form and preserve nitrate. A large nitrate ore field in this basin was found recently. It is estimated there are about 2.5 billion tons of resources of nitrate, and the amount is as much as the Atacama Desert super‐scale nitrate deposit in Chile. Nitrate is one of a few minerals with mass‐independent fractionation (MIF), and the oxygen isotope MIF is an effective method to determine the source of nitrate. The δ17O, δ18O of nitrate were measured by fluorination and thermal decomposition method. The date indicated that this is the first time that oxygen isotope MIF has been located in inland nitrate minerals. The results obtained by two methods are similar, Δ17O=δ17O–0.52×δ18O=12‰–17‰. The experiment and observation data proved that oxygen isotope MIF of nitrate are the result of photochemical reactions in the troposphere and stratosphere. Thus, evidence from MIF oxygen isotopic compositions indicate that long term atmospheric deposition of nitrate aerosol particles produced by photochemical reactions is the source of the deposits.
Rapid Identification and Emergency Investigation of Surface Ruptures and Geohazards Induced by the Ms 7.1 Yushu Earthquake
Authors: Yongshuang ZHANG , Xin YAO , Tanyu XIONG , Yinsheng MA , Daogong HU , Nong YANG , Changbao GUO 
Published: December 2010

Abstract:The rapid identification based on InSAR technology was proved to be effective in our emergency investigation of surface ruptures and geohazards induced by the Yushu earthquake. The earthquake‐generating fault of the Yushu earthquake is the Yushu section of the Garzê‐Yushu faults zone. It strikes NWW‐NW, 23 km long near the Yushu County seat, dominated by left‐lateral strike slip, and appearing as a surface rupture zone. The macroscopic epicenter is positioned at Guo‐yang‐yan‐song‐duo of Gyegu Town (33°03′11″N, 96°51′26″E), where the co‐seismic horizontal offset measured is 1.75 m. Geohazards induced by the Yushu earthquake are mainly rockfalls, landslides, debris flows, and unstable slopes. They are controlled by the earthquake‐generating fault and are mostly distributed along it. There are several geohazard chains having been established, such as earthquake, canal damage, soil liquefying, landslide‐debris flow, earthquake, soil liquefying, roadbed deformation, etc. In order to prevent seismic hazards, generally, where there is a visible surface rupture induced by the Yushu earthquake, reconstruction should be at least beyond 20 m, on each side, from it. Sufficient attention should also be given to potential geohazards or geohazard chains induced by the earthquake.
Sediment‐hosted Pb‐Zn Deposits in Southwest Sanjiang Tethys and Kangdian Area on the Western Margin of Yangtze Craton
Authors: Changming WANG , Jun DENG , Shouting ZHANG , Chunji XUE , Liqiang YANG , Qingfei WANG , Xiang SUN 
Published: December 2010

Abstract:The western margin of Yangtze Craton is known as a significant sediment‐hosted base‐metal aggregate cluster, especially for Pb–Zn deposits in China, e.g. Jinding, Daliangzi, Tianbaoshan, Kuangshanchang and Qinlinchang deposits. In comparison with the classic MVT deposits in the world, based on the basic geology of the sediment‐hosted Pb‐Zn deposits, this paper focuses on temporalspatial distribution of this deposit to further discuss its large scale mineralization and tectonic evolution history. In the SW Sanjiang Thethys, Jinding deposit is typically thrust fault‐controlled and hosted mainly in the sandstones and breccia‐bearing sandstones, whereas MVT‐type deposits are controlled by lithology and faulting/fracturing with a strong preference for carbonate‐hosted rocks. Most importantly, Jinding Pb–Zn deposit differs from the other types of sediment‐hosted Pb–Zn deposits in which it was formed in a strongly deformed foreland basin within a continental collision zone. In the Kangdian area, the sediment‐hosted Pb–Zn deposits were formed in the extensional basin on the side of the continental orogenic belt along the Yangtze Craton. Compared with classic MVT deposits, the Pb–Zn deposits in the Kangdian area belong to MVT deposits. This paper is significant not only for interpretation of the genesis of sediment‐hosted Pb–Zn deposits but also for exploiting large base metal deposits in large sedimentary target areas.
Pool‐Forming Stages and Enrichment Models of Medium‐ to High‐Rank Coalbed Methane
Authors: Yan SONG , Mengjun ZHAO , Feng HONG , Shaobo LIU , Shengfei QIN , Hongyan WANG 
Published: December 2010

Abstract:The pool‐forming mechanism of coalbed methane has its own characteristics. In this paper, based on studies on the typical coal‐bearing basins in China, it is pointed out that the reservoir formation of medium‐ to high‐rank coalbed methane has experienced three critical stages: the coalbed methane generation and adsorption stage, the coalbed adsorption capacity enhancement stage, and the coalbed methane desorption‐diffusion and preservation stage. The regional tectonic evolution, hydrodynamic conditions and sealing conditions play important roles in the stage of coalbed methane desorption‐diffusion and preservation. Medium‐ to high‐rank coalbed methane has three types of enrichment models, that is, the most favorable, the relatively favorable, and the unfavorable enrichment models.
Features of the Excess Adsorption Isotherms of High‐Pressure Methane Adsorption on Coal and Simulation Model
Authors: Yongjun CUI , Dengfeng ZHANG , Qun ZHANG , Weigang LIN , Wenli SONG , Yuhui LI , Wenping JIANG 
Published: December 2010

Abstract:Four coal samples of different ranks are selected to perform the adsorption measurement of high‐pressure methane (CH4). The highest equilibrium pressure of the measurement exceeds 20 MPa. Combined with the measuring results and theoretical analyses, the reasons for the peak or the maximum adsorption capacity appearing in the excess adsorption isotherms are explained. The rules of the peak occurrence are summarized. And then, based on the features of coal pore structure, the adsorption features of high‐pressure gas, the microcosmic interaction relationship of coal surface and CH4 molecule, and the coalbed methane reservoir conditions, three theoretical assumptions on the coal adsorption high‐pressure CH4 are suggested. Thereafter, on the basis of these theoretical assumptions, the Ono‐Kondo lattice model is processed for simplification and deformation. Subsequently, the equations modeling the excess adsorption isotherm of high‐pressure CH4 adsorption on coal are obtained. Through the verification on the measurement data, the fitting results indicate that it is feasible to use the Ono‐Kondo lattice mode to model the excess adsorption isotherm of high‐pressure CH4 adsorption on coal.
Accessing the Soil Metagenome for Studies of Microbial Diversity
Authors: Delmont Tom O. , Robe Patrick , Cecillon Sébastien , Clark Ian M. , Constancias Florentin , Simonet Pascal , Hirsch Penny R. , Vogel Timothy M. 
Published: December 2010

ABSTRACT
Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome.
Target Genes, Consensus Binding Site, and Role of Phosphorylation for the Response Regulator MtrA ofCorynebacterium glutamicum
Authors: Brocker Melanie , Mack Christina , Bott Michael 
Published: December 2010

ABSTRACTThe two-component signal transduction system consisting of the sensor kinase MtrB and the response regulator MtrA is highly conserved in corynebacteria and mycobacteria. WhereasmtrAofMycobacterium tuberculosiswas reported to be essential, we recently succeeded in creating ΔmtrABand ΔmtrAdeletion mutants ofCorynebacterium glutamicumand provided evidence thatmepAandnlpC, both encoding putative cell wall peptidases, are directly repressed by MtrA, whereasproPandbetP, both encoding carriers for compatible solutes, are directly activated by MtrA. In the present study, novel MtrA target genes were identified, includingmepB, encoding another putative cell wall peptidase. The repressor or activator functions of MtrA correlate with the distance between the MtrA binding site and the transcriptional start site. From the identified binding sites within 20 target promoters, a 19-bp MtrA consensus motif was derived which represents a direct repeat of 8 base pairs separated by 3 base pairs. Gene expression of a strain containing MtrA with a D53N mutation instead of wild-type MtrA resembled that of a ΔmtrAmutant, indicating that MtrA is active in its phosphorylated form. This result was confirmed by electrophoretic mobility shift assays with phosphorylated MtrA which showed an increased binding affinity.
Genome Sequence of the Emerging Pathogen
Aeromonas caviae
Authors: Beatson Scott A. , das Graças de Luna Maria , Bachmann Nathan L. , Alikhan Nabil-Fareed , Hanks Kirstin R. , Sullivan Mitchell J. , Wee Bryan A. , Freitas-Almeida Angela C. , dos Santos Paula A. , de Melo Janyne T. B. , Squire Derrick J. P. , Cunningham Adam F. , Fitzgerald J. Ross , Henderson Ian R. 
Published: December 2010

ABSTRACT

Aeromonas caviae
is a Gram-negative, motile and rod-shaped facultative anaerobe that is increasingly being recognized as a cause of diarrhea in children. Here we present the first genome sequence of an
A. caviae
strain that was isolated as the sole pathogen from a child with profuse diarrhea.
Complete Genome Sequence of
Algoriphagus
sp. PR1, Bacterial Prey of a Colony-Forming Choanoflagellate
Authors: Alegado Rosanna A. , Ferriera Steven , Nusbaum Chad , Young Sarah K. , Zeng Qian , Imamovic Alma , Fairclough Stephen R. , King Nicole 
Published: December 2010

ABSTRACT

Bacteria are the primary food source of choanoflagellates, the closest known relatives of animals. Studying signaling interactions between the Gram-negative
Bacteroidetes
bacterium
Algoriphagus
sp. PR1 and its predator, the choanoflagellate
Salpingoeca rosetta
, provides a promising avenue for testing hypotheses regarding the involvement of bacteria in animal evolution. Here we announce the complete genome sequence of
Algoriphagus
sp. PR1 and initial findings from its annotation.
Brain Abscess Caused by Phaeoacremonium parasiticum in an Immunocompromised Patient
Authors: McNeil Candice J. , Luo Robert F. , Vogel Hannes , Banaei Niaz , Ho Dora Y. 
Published: December 2010

ABSTRACT

Phaeoacremonium parasiticum
is an environmental fungus usually associated with subcutaneous infections. We report the first documented case of central nervous system involvement with brain abscess formation in a patient with chronic granulomatous disease and review the literature on
Phaeoacremonium parasiticum
infections.
Molecular Epidemiology of Hepatitis D Virus Infection among Injecting Drug Users with and without Human Immunodeficiency Virus Infection in Taiwan
Authors: Chang Sui-Yuan , Yang Chia-Ling , Ko Wei-Shin , Liu Wen-Chun , Lin Chi-Ying , Wu Cheng-Hsin , Su Yi-Chin , Chang Shu-Fang , Chen Mao-Yuan , Sheng Wang-Huei , Hung Chien-Ching , Chang Shan-Chwen 
Published: December 2010

ABSTRACT

An outbreak of human immunodeficiency virus (HIV) infection occurred among injecting drug users (IDU) in Taiwan between 2003 and 2006, when an extremely high prevalence of hepatitis C virus (HCV) infection was also detected. To determine whether clusters of hepatitis D virus (HDV) infection occurred in this outbreak, 4 groups of subjects were studied: group 1, HIV-infected IDU (
n
= 904); group 2, HIV-infected non-IDU (
n
= 880); group 3, HIV-uninfected IDU (
n
= 211); and group 4, HIV-uninfected non-IDU (
n
= 1,928). The seroprevalence of hepatitis B virus (HBV) was 19.8%, 18.4%, 17.1%, and 6.7%, and HDV seroprevalence among HBV carriers was 75.4%, 9.3%, 66.7%, and 2.3%, for groups 1, 2, 3, and 4, respectively. Ninety-nine of 151 (65.6%) HDV-seropositive IDU had HDV viremia: 5 were infected with HDV genotype I, 41 with genotype II, 51 with genotype IV, and 2 with genotypes II and IV. In the phylogenetic analysis, only one cluster of 4 strains within the HDV genotype II was identified. Among patients with HCV viremia, a unique cluster within genotype 1a was observed; yet, patients within this cluster did not overlap with those observed in the HDV phylogenetic analysis. In summary, although IDU had a significantly higher HDV seroprevalence, molecular epidemiologic investigations did not support that HDV was introduced at the same time as HCV among IDU.
Simultaneous Identification of Mycobacterial Isolates to the Species Level and Determination of Tuberculosis Drug Resistance by PCR Followed by Electrospray Ionization Mass Spectrometry
Authors: Massire Christian , Ivy Cristina Agasino , Lovari Robert , Kurepina Natalia , Li Haijing , Blyn Lawrence B. , Hofstadler Steven A. , Khechinashvili George , Stratton Charles W. , Sampath Rangarajan , Tang Yi-Wei , Ecker David J. , Kreiswirth Barry N. 
Published: December 2010

ABSTRACT

Mycobacterium tuberculosis
that is resistant to both isoniazid (INH) and rifampin (RIF) is spreading. It has become a public health problem in part because the standard culture methods used to determine the appropriate treatment regimen for patients often take months following the presumptive diagnosis of tuberculosis. Furthermore, the misidentification of nontuberculosis mycobacteria (NTM) in patients presumably suffering from tuberculosis results in additional human and health care costs. The mechanisms of resistance for several drugs used to treat
Mycobacterium tuberculosis
are well understood and therefore should be amenable to determination by rapid molecular methods. We describe here the use of PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) in an assay that simultaneously determines INH and RIF resistance in
Mycobacterium tuberculosis
and identifies and determines the species of NTMs. The assay panel included 16 primer pairs in eight multiplexed reactions and was validated using a collection of 1,340 DNA samples from cultured specimens collected in the New York City area, the Republic of Georgia, and South Africa. Compared with phenotypic data, the PCR/ESI-MS assay had 89.3% sensitivity and 95.8% specificity in the determination of INH resistance and 96.3% sensitivity and 98.6% specificity in the determination of RIF resistance. Based on a set of 264 previously characterized liquid culture specimens, the PCR/ESI-MS method had 97.0% sensitivity and 99.9% specificity for determination of NTM identity. The assay also provides information on ethambutol, fluoroquinolone, and diarylquinoline resistance and lineage-specific polymorphisms, to yield highly discriminative digital signatures potentially suitable for epidemiology tracking.
Pathogen-Specific DNA Enrichment Does Not Increase Sensitivity of PCR for Diagnosis of Invasive Aspergillosis in Neutropenic Patients
Authors: Springer Jan , Loeffler Juergen , Heinz Werner , Schloßnagel Hannes , Lehmann Marc , Morton Oliver , Rogers Thomas R. , Schmitt Corinna , Frosch Matthias , Einsele Hermann , Kurzai Oliver 
Published: December 2010

ABSTRACT
PCR assays designed for the diagnosis of invasive aspergillosis (IA) in high-risk patients have to detect minute amounts of target DNA to reach sufficient analytical sensitivity to be of clinical use. This prospective study assessed the use of a novel strategy for selective pathogen DNA enrichment for enhancing the performance of diagnostic PCR in a direct comparison with a highly sensitive in-house quantitative PCR (qPCR) assay and the galactomannan enzyme-linked immunosorbent assay (ELISA). Surprisingly, and in contrast to experience with other patient groups, the novel protocol for selective pathogen DNA enrichment did not enhance but instead significantly impaired sensitivity. This could be explained by the small amounts of host DNA in the specimens, which were derived mostly from severely neutropenic patients. In the qPCR assay, positive samples required an average of 43.5 amplification cycles (range, 39.2 to 50) for detection in the in-house PCR. Repetitive testing of selected samples showed test positivity to be variable, most likely due to the small amounts of target DNA. Despite this, the in-house protocol proved helpful in the diagnosis of IA, detecting 2 out of 3 patients with probable IA and 10 out of 19 patients with possible IA. Our results underline the necessity for diagnostic PCR protocols that help diagnose IA to be highly sensitive and show that selective pathogen DNA enrichment using affinity purification may not be useful in severely neutropenic patients.
Evaluation of the Rapid MGIT TBc Identification Test for Culture Confirmation of Mycobacterium tuberculosis Complex Strain Detection
Authors: Yu Ming-Chih , Chen Huang-Yao , Wu Mei-Hua , Huang Wei-Lun , Kuo Yuh-Min , Yu Fang-Lan , Jou Ruwen 
Published: December 2010

ABSTRACT

A culture confirmation test for the detection of
Mycobacterium tuberculosis
complex strains that uses a lateral-flow immunochromatographic assay to detect the MPB64 antigen, the MGIT TBc identification (TBc ID) test, has been developed. We evaluated the performance of the TBc ID test in the detection of the
M. tuberculosis
complex in 222 primary-positive liquid cultures. We compared these results to those of nucleic acid-based identification and conventional biochemical tests. The validity of the TBc ID test was determined, and all of the nontuberculous mycobacteria (NTM) and
Nocardia
species tested were found to be negative. The detection limit of the TBc ID test was 5 × 10
5
CFU/ml, and for IS
6110
real-time PCR it was 5 CFU/ml. All of the
M. tuberculosis
and
M. africanum
cultures were found to be positive, while
M. bovis
and
M. bovis
BCG cultures were negative. With the exception of 1 contaminated culture, the 221 culture-positive isolates contained 171 (77.5%)
M. tuberculosis
isolates, 39 (17.6%) NTM species, and 11 (5.0%) unidentified species. Two culture-positive isolates harbored a 63-bp deletion at position 196 of the
mpb64
gene. The sensitivity, specificity, positive predictive values, and negative predictive values of the TBc ID test were 98.8, 100, 100, and 95.1%, respectively. Furthermore, the approximate turnaround time for real-time PCR was 4 h (including buffer and sample preparation), while for the TBc ID test it was less than 1 h. We suggest an algorithm for the primary identification of
M. tuberculosis
in liquid culture using the TBc ID test as an alternative to conventional subculture followed by identification using biochemical methods.
Adjuvant-Free Immunization with Hemagglutinin-Fc Fusion Proteins as an Approach to Influenza Vaccines
Authors: Loureiro Silvia , Ren Junyuan , Phapugrangkul Pongsathon , Colaco Camilo A. , Bailey Christopher R. , Shelton Holly , Molesti Eleonora , Temperton Nigel J. , Barclay Wendy S. , Jones Ian M. 
Published: December 2010

ABSTRACT
The hemagglutinins (HAs) of human H1 and H3 influenza viruses and avian H5 influenza virus were produced as recombinant fusion proteins with the human immunoglobulin Fc domain. Recombinant HA-human immunoglobulin Fc domain (HA-HuFc) proteins were secreted from baculovirus-infected insect cells as glycosylated oligomer HAs of the anticipated molecular mass, agglutinated red blood cells, were purified on protein A, and were used to immunize mice in the absence of adjuvant. Immunogenicity was demonstrated for all subtypes, with the serum samples demonstrating subtype-specific hemagglutination inhibition, epitope specificity similar to that seen with virus infection, and neutralization. HuFc-tagged HAs are potential candidates for gene-to-vaccine approaches to influenza vaccination.
North American Porcine Reproductive and Respiratory Syndrome Viruses Inhibit Type I Interferon Production by Plasmacytoid Dendritic Cells
Authors: Calzada-Nova Gabriela , Schnitzlein William M. , Husmann Robert J. , Zuckermann Federico A. 
Published: December 2010

ABSTRACTAlthough enveloped viruses typically trigger the prodigious secretion of alpha interferon (IFN-α) by plasmacytoid dendritic cells (pDC), porcine pDC remain quiescent when exposed to porcine reproductive and respiratory syndrome virus (PRRSV). This inactivity is likely due to virus-mediated interference since the typical IFN-α response by either purified or nonsorted porcine pDC to transmissible gastroenteritis virus (TGEV) or the Toll-like receptor 9 agonist, oligodeoxynucleotide (ODN) D19, was markedly reduced in the presence of PRRSV. Suppression occurred independently of virus viability and acidification of pDC early endosomes but correlated with diminished levels of IFN-α mRNA. This change was attributed to an abrogation of transcription resulting from a decrease in the otherwise enhanced amounts of the requisite interferon regulatory factor 7 (IRF-7), whose gene expression in turn was limited as a consequence of a lessened availability of nuclear-localized signal transducer and activator of transcription 1 (STAT1). While PRRSV also inhibited tumor necrosis factor alpha (TNF-α) synthesis by pDC responding to either agent, only the interleukin-2 (IL-2) and IL-6 production instigated by ODN D19 exposure was blocked. Likewise, PRRSV did not impact a specific TGEV-associated enhancement of IL-8 expression. Moreover, an augmented phosphorylation of NF-κB seen in activated pDC was not only unaffected by PRRSV but actually occurred in its presence. Thus, as supported by a demonstrated resilience of pDC to PRRSV infection, this pathogen may interact with a cell surface protein(s) to selectively impede the completion of cascades involved in cytokine production by stimulated pDC.