bluuebunny/crossref_metadata_2025_split huggingface dataset:
The nature of the ASCA/INTEGRAL source AX J183039-1002: A new Compton-thick AGN?
Authors: Bassani L. , Landi R. , Campana R. , McBride V. A. , Dean A. J. , Bird A. J. , Green D. A. , Ubertini P. , De Rosa A. 
Published: March 2009

Abstract
We report on the identification of the X/soft γ-ray source AX J183039–1002 detected with ASCA and INTEGRAL/IBIS. The source, which has an observed 20–100 keV flux of ∼8.6 × 10−11 erg cm−2 s−1, is inside a diffuse radio supernova remnant (SNR) and is spatially coincident with a compact radio source. We analysed archival Chandra and XMM–Newton observations in order to identify the ASCA/INTEGRAL source. A point-like Chandra X-ray object was found to be positionally coincident with the compact radio source and within the error circle of the ASCA and INTEGRAL sources. Although the association of a compact radio/X-ray source with a radio SNR could be indicative of a pulsar wind nebula (PWN), the XMM–Newton X-ray spectrum is compatible with an absorbed, Seyfert-2 like active galactic nucleus, since it provides evidence for an iron emission line of ∼1 keV equivalent width; furthermore the X-ray source spectrum is similar to that of other Compton thick AGN where the ≲2 keV data are associated to a warm reflector and the ≳10 keV one to a cold reflector.
Fast TeV variability in blazars: jets in a jet
Authors: Giannios Dimitrios , Uzdensky Dmitri A. , Begelman Mitchell C. 
Published: March 2009

Abstract
The fast TeV variability of the blazars Mrk 501 and PKS 2155−304 implies a compact emitting region that moves with a bulk Lorentz factor of Γem∼ 100 towards the observer. The Lorentz factor is clearly in excess of the jet Lorentz factors Γj≲ 10 measured on sub-pc scales in these sources. We propose that the TeV emission originates from compact emitting regions that move relativistically within a jet of bulk Γj∼ 10. This can be physically realized in a Poynting flux-dominated jet. We show that if a large fraction of the luminosity of the jet is prone to magnetic dissipation through reconnection, then material outflowing from the reconnection regions can efficiently power the observed TeV flares through synchrotron-self-Compton emission. The model predicts simultaneous far-ultraviolet/soft X-ray flares.
Protective effects of exercise preconditioning on hindlimb unloading‐induced atrophy of rat soleus muscle
Authors: Fujino H. , Ishihara A. , Murakami S. , Yasuhara T. , Kondo H. , Mohri S. , Takeda I. , Roy R. R. 
Published: March 2009

AbstractAim:  A chronic decrease in the activation and loading levels of skeletal muscles as occurs with hindlimb unloading (HU) results in a number of detrimental changes. Several proteolytic pathways are involved with an increase in myofibrillar protein degradation associated with HU. Exercise can be used to counter this increase in proteolytic activity and, thus, may be able to protect against some of the detrimental changes associated with chronic decreased use. The purpose of the present study was to determine the potential of a single bout of preconditioning endurance exercise in attenuating the effects of 2 weeks of HU on the mass, phenotype and force‐related properties of the soleus muscle in adult rats.Methods:  Male Wistar rats were subjected to HU for 2 weeks. One half of the rats performed a single bout of treadmill exercise for 25 min immediately prior to the 2 weeks of HU.Results:  Soleus mass, maximum tetanic tension, myofibrillar protein content, fatigue resistance and percentage of type I (slow) myosin heavy chain were decreased in HU rats. In addition, markers for the cathepsin, calpain, caspase and ATP‐ubiquitin‐proteasome proteolytic pathways were increased. The preconditioning endurance exercise bout attenuated all of the detrimental changes associated with HU, and increased HSP72 mRNA expression and protein levels.Conclusion:  These findings indicate that exercise preconditioning may be an effective countermeasure to the detrimental effects of chronic decreases in activation and loading levels on skeletal muscles and that an elevation in HSP72 may be one of the mechanisms associated with these responses.
Avian influenza A H5N1 infections in Bali province, Indonesia: a behavioral, virological and seroepidemiological study
Authors: Santhia Ketut , Ramy Ayu , Jayaningsih Putri , Samaan Gina , Putra Anak Agung Gde , Dibia Nyoman , Sulaimin Cynthia , Joni Gusti , Leung Connie Y. H. , Malik Peiris Joseph Sriyal , Wandra Toni , Kandun Nyoman 
Published: March 2009

Background  Bali Province was affected by avian influenza H5N1 outbreaks in birds in October 2003. Despite ongoing circulation of the virus, no human infection had been identified by December 2005.Objectives  To assess behavioral patterns associated with poultry rearing in Bali, and to identify potential risk factors for H5N1 infection in humans and in household chickens, ducks and pigs.Methods  A behavioral, virological and seroepidemiologic survey in 38 villages and three live bird markets was completed in December 2005. A multi‐stage cluster design was used to select 291 households with 841 participants from all nine districts in Bali. Specimens were collected from participants as well as a maximum of three pigs, chickens and ducks from each household. Eighty‐seven market vendors participated, where specimens were collected from participants as well as chickens and ducks.Results  Twenty out of the 38 villages sampled had H5N1 outbreaks. Despite exposure to H5N1 outbreaks, none of the participants from villages or markets were seropositive for H5N1. None of the pigs tested were positive for H5N1. Virus isolation rate in ducks and chicken in markets was higher than in households. Transport of poultry in or out of villages was a risk factor for outbreaks in household chickens and ducks.Conclusions  The study highlighted that the market chain and associated behaviors may play a role in maintaining the virus in household flocks. The study adds evidence that transmission of H5N1 to humans remains a rare event despite high level handling of both healthy and sick birds.
Detecting methylation patterns of p16, MGMT, DAPK and E‐cadherin genes in multiple myeloma patients
Authors: YUREGIR O. OZALP , YURTCU E. , KIZILKILIC E. , KOCER N. E. , OZDOGU H. , SAHIN F. I. 
Published: March 2009

SummaryMultiple myeloma (MM) is a B‐cell neoplasia characterized by the clonal proliferation of plasma cells. Besides known genetic abnormalities, epigenetic changes are also known to effect MM pathogenesis. DNA methylation is an epigenetic mechanism that silences genes by adding methyl groups to cytosine‐guanine dinucleotides at the promoter regions. In this study, the methylation status of four genes; p16, O6‐methyl guanine DNA methyl transferase (MGMT), death‐associated protein kinase (DAPK) and E‐cadherin (ECAD); at the time of diagnosis was investigated using methylation‐specific polymerase chain reaction (MS‐PCR). In the 20 cases studied; methylation of the promoter regions of p16, MGMT, DAPK and ECAD genes was detected in 10%, 40%, 10% and 45% of the cases, respectively. In 65% (13/20) of cases, at least one of the genes studied had promoter methylation; while 35% of cases (7/20) had methylated promoters of more than one gene. There was a significant correlation between promoter hypermethylation of MGMT and the presence of extramedullary involvement; but for the other genes no correlation was found regarding disease properties like age, disease stage, clinical course and the presence of lytic bone lesions. Determining the methylation profiles of genes in MM, could lead to a new understanding of the disease pathogenesis and guide the assessment of treatment options.
Microsatellites from the charcoal rot fungus (Macrophomina phaseolina)
Authors: BAIRD RICHARD E. , WADL PHILLIP A. , WANG XINWANG , JOHNSON DENITA H. , RINEHART TIMOTHY A. , ABBAS HAMED K. , SHIER THOMAS , TRIGIANO ROBERT N. 
Published: March 2009

AbstractMicrosatellite loci were identified from the charcoal rot fungus (Macrophomina phaseolina). Primer pairs for 46 loci were developed, and of these, 13 were optimized and screened using genomic DNA from 55 fungal isolates collected predominantly from two soybean fields in Mississippi. Twelve of the optimized loci were polymorphic and the number of alleles per locus ranged from 6 to 22. These microsatellites will be useful in population and pathogenicity studies to correspond with development of potential disease‐resistant soybean and other susceptible crops.
Isolation and characterization of microsatellite loci in Symbiodinium B1/B184, the dinoflagellate symbiont of the Caribbean sea fan coral, Gorgonia ventalina
Authors: ANDRAS JASON P. , KIRK NATHAN L. , COFFROTH MARY ALICE , HARVELL C. DREW 
Published: March 2009

AbstractHere we report primers targeting 10 microsatellite loci of dinoflagellates in the genus Symbiodinium (clade B1/B184) symbiotic with the Caribbean sea fan coral, Gorgonia ventalina. Primers were tested on 12 Symbiodinium B1/B184 cultures, as well as 40 genomic DNA extracts of G. ventalina tissue samples. All loci were polymorphic with allelic richness ranging from 4–16. Gene diversity ranged from 0.15 to 0.91. These primers provide powerful tools for examining the fine‐scale population structure and dynamics of Symbiodinium within a single host species.
Isolation and characterization of eight microsatellite loci from the longheaded eagle ray, Aetobatus flagellum (Elasmobranchii, Myliobatidae)
Authors: YAGISHITA N. , YAMAGUCHI A. 
Published: March 2009

AbstractThe longheaded eagle ray, Aetobatus flagellum feeds mainly on bivalves, and there have been some indications that the current reduction in the bivalve population in southern Japan may be due to an increase in the number of longheaded eagle rays. Consequently, the ‘predator control programme’ for reducing the longheaded eagle ray population was established in 2001 in Japan. For studying the population genetics of the longheaded eagle ray, we isolated eight polymorphic microsatellite loci (two to six alleles per locus; expected heterozygosity, 0.172–0.700) from this species.
New Holland honeyeater (Phylidonyris novaehollandiae) microsatellites: isolation and characterization of 15 novel markers using an enrichment method
Authors: MYERS STEVEN A. , GARDNER MICHAEL G. , DONNELLAN STEPHEN , KLEINDORFER SONIA 
Published: March 2009

AbstractThe New Holland honeyeater (Phylidonyris novaehollandiae) plays a significant role in the pollination and sustainability of Australia's endemic flora, and hence fauna. Despite this key ecosystem function, knowledge of P. novaehollandiae life‐history traits and population dynamics remain poorly understood. We describe the development of primers amplifying 22 P. novaehollandiae microsatellite loci. Fifteen of the loci were found to be polymorphic, with observed heterozygosity between 0.500 and 1.000, and from four to 17 alleles per locus in adult birds from the study site.
Highly polymorphic microsatellite markers for Radix balthica (Linnaeus 1758)
Authors: SALINGER M. , PFENNINGER M. 
Published: March 2009

AbstractWe present data for eight polymorphic microsatellite markers isolated from a microsatellite‐enriched DNA library for the freshwater snail Radix balthica. Three of them were specific for R. balthica while five also amplified polymorphic products in two congeneric species. Test application on populations from all over the species range has shown that these loci are highly informative for analysing population structure and estimating migration rates. Observed deviations from Hardy–Weinberg equilibrium are attributed to a mixed mating system.
New polymorphic microsatellite markers and development of mitotyping primers for West Mediterranean green toad species (Bufo viridis subgroup)
Authors: COLLIARD CAROLINE , SICILIA ALESSANDRA , MORITZ CRAIG , PERRIN NICOLAS , STÖCK MATTHIAS 
Published: March 2009

AbstractWe report new polymorphic microsatellites for three species of Palearctic green toads (Bufo viridis subgroup): 10 in B. balearicus and seven each in B. siculus and B. boulengeri. Diversity at these loci, measured for 27 B. balearicus, 23 B. siculus and 11 B. boulengeri, ranged from low to high (two to 10 alleles). Mitotyping primers, specific to the control region, which allow fast screening of parapatric Sicilian endemic B. siculus and Italian mainland‐origin B. balearicus, were developed.
Geraniol Restores Antibiotic Activities against Multidrug-Resistant Isolates from Gram-Negative Species
Authors: Lorenzi Vannina , Muselli Alain , Bernardini Antoine François , Berti Liliane , Pagès Jean-Marie , Amaral Leonard , Bolla Jean-Michel 
Published: March 2009

ABSTRACT

The essential oil of
Helichrysum italicum
significantly reduces the multidrug resistance of
Enterobacter aerogenes
,
Escherichia coli
,
Pseudomonas aeruginosa
, and
Acinetobacter baumannii
. Combinations of the two most active fractions of the essential oil with each other or with phenylalanine arginine β-naphthylamide yield synergistic activity. Geraniol, a component of one fraction, significantly increased the efficacy of β-lactams, quinolones, and chloramphenicol.
Characterization of Macrolide Efflux Pump
mef
Subclasses Detected in Clinical Isolates of
Streptococcus pyogenes
Isolated between 1999 and 2005
Authors: Blackman Northwood J. , Del Grosso M. , Cossins L. R. , Coley M. D. , Creti R. , Pantosti A. , Farrell D. J. 
Published: March 2009

ABSTRACT

The macrolide efflux mechanism of resistance,
mef
, was characterized in community-acquired respiratory tract infections with
Streptococcus pyogenes.
Fifty-four (4.6%) M phenotype isolates were screen tested as negative for
mef
(A). Of these 54 isolates, 5 (0.4%), 27 (2.3%), and 1 (0.1%) were considered to be
mef
(I) positive, a novel mosaic variant of
mef
, or a novel subclass of
mef
, respectively. This study shows (i) the definitive presence of
mef
(E) in
S. pyogenes
and its global distribution, (ii) the presence of a mosaic variant of
mef
composed of
mef
(A) and
mef
(E), (iii) the previously undescribed presence of
mef
(I) in
S. pyogenes
, and (iv) the presence of a novel subclass of
mef
in
S. pyogenes
.
Reverse Transcriptase Inhibitors as Potential Colorectal Microbicides
Authors: Herrera Carolina , Cranage Martin , McGowan Ian , Anton Peter , Shattock Robin J. 
Published: March 2009

ABSTRACTWe investigated whether reverse transcriptase (RT) inhibitors (RTI) can be combined to inhibit human immunodeficiency virus type 1 (HIV-1) infection of colorectal tissue ex vivo as part of a strategy to develop an effective rectal microbicide. The nucleotide RTI (NRTI) PMPA (tenofovir) and two nonnucleoside RTI (NNRTI), UC-781 and TMC120 (dapivirine), were evaluated. Each compound inhibited the replication of the HIV isolates tested in TZM-bl cells, peripheral blood mononuclear cells, and colorectal explants. Dual combinations of the three compounds, either NRTI-NNRTI or NNRTI-NNRTI combinations, were more active than any of the individual compounds in both cellular and tissue models. Combinations were key to inhibiting infection by NRTI- and NNRTI-resistant isolates in all models tested. Moreover, we found that the replication capacities of HIV-1 isolates in colorectal explants were affected by single point mutations in RT that confer resistance to RTI. These data demonstrate that colorectal explants can be used to screen compounds for potential efficacy as part of a combination microbicide and to determine the mucosal fitness of RTI-resistant isolates. These findings may have important implications for the rational design of effective rectal microbicides.
New Combinations of Mutations in VanD-Type Vancomycin-Resistant
Enterococcus faecium
,
Enterococcus faecalis
, and
Enterococcus avium
Strains
Authors: Depardieu F. , Foucault M.-L. , Bell J. , Dubouix A. , Guibert M. , Lavigne J.-P. , Levast M. , Courvalin P. 
Published: March 2009

ABSTRACT

We studied the clinical isolates
Enterococcus faecium
NEF1, resistant to high levels of vancomycin (MIC, 512 μg/ml) and teicoplanin (MIC, 64 μg/ml);
Enterococcus faecium
BM4653 and BM4656 and
Enterococcus avium
BM4655, resistant to moderate levels of vancomycin (MIC, 32 μg/ml) and to low levels of teicoplanin (MIC, 4 μg/ml); and
Enterococcus faecalis
BM4654, moderately resistant to vancomycin (MIC, 16 μg/ml) but susceptible to teicoplanin (MIC, 0.5 μg/ml). The strains were distinct, were constitutively resistant via the synthesis of peptidoglycan precursors ending in
d
-alanyl-
d
-lactate, and harbored a chromosomal
vanD
gene cluster that was not transferable. New mutations were found in conserved domains of VanS
D
: at T
170
I near the phosphorylation site in NEF1, at V
67
A at the membrane surface in BM4653, at G
340
S in the G2 ATP-binding domain in BM4655, in the F domain in BM4656 (a 6-bp insertion), and in the G1 and G2 domains of BM4654 (three mutations). The mutations resulted in constitutivity, presumably through the loss of the phosphatase activity of the sensor. The chromosomal Ddl
d
-Ala:
d
-Ala ligase had an IS
19
copy in NEF1, a mutation in the serine (S
185
F) or near the arginine (T
289
P) involved in
d
-Ala1 binding in BM4653 or BM4655, respectively, and a mutation next to the lysine (P
180
S) involved in
d
-Ala2 binding in BM4654, leading to the production of an impaired enzyme. In BM4653

vanY
D

, a new insertion sequence, IS
Efa9
, belonging to the IS
3
family, resulted in the absence of
d
,
d
-carboxypeptidase activity. Strain BM4656 had a functional
d
-Ala:
d
-Ala ligase, associated with high levels of both VanX
D
and VanY
D
activities, and is the first example of a VanD-type strain with a functional Ddl enzyme. Study of these five clinical isolates, displaying various assortments of mutations, confirms that all VanD-type strains isolated so far have undergone mutations in the

vanS
D

or

vanR
D

gene, leading to constitutive resistance, but that the Ddl host ligase is not always impaired. Based on sequence differences, the
vanD
gene clusters could be assigned to two subtypes:
vanD-1
and
vanD-4
.
Genetic Organization of Transposase Regions Surrounding
bla
KPC
Carbapenemase Genes on Plasmids from
Klebsiella
Strains Isolated in a New York City Hospital
Authors: Gootz Thomas D. , Lescoe Mary Kay , Dib-Hajj Fadia , Dougherty Brian A. , He Wen , Della-Latta Phyllis , Huard Richard C. 
Published: March 2009

ABSTRACT

Carbapenem-resistant
Klebsiella
strains carrying
Klebsiella pneumoniae
carbapenemases (KPC) are endemic to New York City and are spreading across the United States and internationally. Recent studies have indicated that the KPC structural gene is located on a 10-kb plasmid-borne element designated Tn
4401
. Fourteen
Klebsiella pneumoniae
strains and one
Klebsiella oxytoca
strain isolated at a New York City hospital in 2005 carrying either
bla
KPC-2
or
bla
KPC-3
were examined for isoforms of Tn
4401
. Ten of the
Klebsiella
strains contained a 100-bp deletion in Tn
4401
, corresponding to the Tn
4401
a isoform. The presence of this deletion adjacent to the upstream promoter region of
bla
KPC
in Tn
4401
a resulted in a different −35 promoter sequence of TGGAGA than that of CTGATT present in isoform Tn
4401
b. Complete sequencing of one plasmid carrying
bla
KPC
from each of three nonclonal isolates indicated the presence of genes encoding other types of antibiotic resistance determinants. The 70.6-kb plasmid from
K. pneumoniae
strain S9 carrying
bla
KPC-2
revealed two identical copies of Tn
4401
b inserted in an inverse fashion, but in this case, one of the elements disrupted a group II self-splicing intron. In
K. pneumoniae
strain S15, the Tn
4401
a element carrying
bla
KPC-2
was found on both a large 120-kb plasmid and a smaller 24-kb plasmid. Pulsed-field gel electrophoresis results indicate that the isolates studied represent a heterogeneous group composed of unrelated as well as closely related
Klebsiella
strains. Our results suggest that endemic KPC-positive
Klebsiella
strains constitute a generally nonclonal population comprised of various alleles of
bla
KPC
on several distinct plasmid genetic backgrounds. This study increases our understanding of the genetic composition of the evolving and expanding role of KPC-producing, healthcare-associated, gram-negative pathogens.
New Plasmid-Mediated Quinolone Resistance Gene,
qnrC
, Found in a Clinical Isolate of
Proteus mirabilis
Authors: Wang Minghua , Guo Qinglan , Xu Xiaogang , Wang Xiaoying , Ye Xinyu , Wu Shi , Hooper David C. , Wang Minggui 
Published: March 2009

ABSTRACT

Since the discovery of
qnrA
in 1998, two additional
qnr
genes,
qnrB
and
qnrS
, have been described. These three plasmid-mediated genes contribute to quinolone resistance in gram-negative pathogens worldwide. A clinical strain of
Proteus mirabilis
was isolated from an outpatient with a urinary tract infection and was susceptible to most antimicrobials but resistant to ampicillin, sulfamethoxazole, and trimethoprim. Plasmid pHS10, harbored by this strain, was transferred to azide-resistant
Escherichia coli
J53 by conjugation. A transconjugant with pHS10 had low-level quinolone resistance but was negative by PCR for the known
qnr
genes,
aac(6′)-Ib-cr
and
qepA
. The ciprofloxacin MIC for the clinical strain and a J53/pHS10 transconjugant was 0.25 μg/ml, representing an increase of 32-fold relative to that for the recipient, J53. The plasmid was digested with HindIII, and a 4.4-kb DNA fragment containing the new gene was cloned into pUC18 and transformed into
E. coli
TOP10. Sequencing showed that the responsible 666-bp gene, designated
qnrC
, encoded a 221-amino-acid protein, QnrC, which shared 64%, 42%, 59%, and 43% amino acid identity with QnrA1, QnrB1, QnrS1, and QnrD, respectively. Upstream of
qnrC
there existed a new IS
3
family insertion sequence, IS
Pmi1
, which encoded a frameshifted transposase.
qnrC
could not be detected by PCR, however, in 2,020 strains of
Enterobacteriaceae
. A new quinolone resistance gene,
qnrC
, was thus characterized from plasmid pHS10 carried by a clinical isolate of
P
.
mirabilis
.
Statins as Potential Antimalarial Drugs: Low Relative Potency and Lack of Synergy with Conventional Antimalarial Drugs
Authors: Wong Rina P. M. , Davis Timothy M. E. 
Published: March 2009

ABSTRACT

The in vitro sensitivity of
Plasmodium falciparum
to atorvastatin and rosuvastatin was assessed using chloroquine-sensitive and chloroquine-resistant strains. Although atorvastatin was more potent, it had weak activity (mean 50% inhibitory concentration of ≥17 μM) and an indifferent interaction with chloroquine and dihydroartemisinin. Bioassay of plasma from an atorvastatin-treated subject showed similar results.
Avian
Aspergillus fumigatus
Strains Resistant to both Itraconazole and Voriconazole
Authors: Beernaert L. A. , Pasmans F. , Van Waeyenberghe L. , Dorrestein G. M. , Verstappen F. , Vercammen F. , Haesebrouck F. , Martel A. 
Published: March 2009

ABSTRACT

The in vitro susceptibilities of 59 avian
Aspergillus fumigatus
strains to amphotericin B, itraconazole, and voriconazole were determined using the standard microdilution broth method (CLSI M38-A2). Four isolates showed acquired resistance to itraconazole and voriconazole, harboring implications for the treatment of aspergillosis in both birds and humans.