bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contrasting patterns of tree mortality in late‐successionalPicea abiesstands in two areas in northern Fennoscandia
Authors: Aakala Tuomas , Kuuluvainen Timo , Wallenius Tuomo , Kauhanen Heikki 
Published: August 2009

AbstractQuestion:What are tree mortality rates and how and why do they vary in late‐successionalPicea abies‐dominated forests? Do observed tree mortality patterns allow comparative assessment of models of long‐term stand development?Location:Northern boreal Fennoscandia.Methods:We measured stand structure in 10 stands in two different areas. We determined age distributions and constructed a chronology of tree deaths by cross‐dating the years of death of randomly sampled dead trees.Results:The stands in the two areas had contrasting tree age distributions, despite similar live tree structure. In one area, stands were relatively even‐aged and originated following a stand‐replacing fire 317 years earlier. The stands in the second area had an uneven age structure and virtually no signs of past fires, suggesting a very long period since the last major disturbance. The younger stands were characterized by a high mortality rate and inter‐annual variation, which we attributed to senescence of the relatively even‐aged stands approaching the maximum age ofP. abies. In contrast, the tree mortality rates in the older stands were low and relatively stable.Conclusions:Patterns of tree mortality were, to a large extent, dependent on the time since the last stand‐replacing disturbance, suggesting that northern borealP. abiesstands eventually reach a shifting mosaic state maintained through small‐scale dynamics, but the time needed to reach this state appears to be lengthy; even 300 years after a forest fire stands showed changes in patterns of tree mortality that were related to the developmental stage of the stands.
Geographical Gerontology: Mapping a Disciplinary Intersection
Authors: Andrews Gavin J. , Milligan Christine , Phillips David R. , Skinner Mark W. 
Published: August 2009

AbstractThe intersection between geography and gerontology arises structurally in institutions and intellectually both in academic debates surrounding disciplinary territoriality and substantive fields of empirical inquiry (population ageing and movement; services and policy; living environments; emplacement; emotions, images and the body). Although recent years have witnessed an increasing theoretical convergence between geography and gerontology – resulting in ever fertile ground for research – a range of contemporary social processes have yet to receive substantive attention. Arising as consumer niches and economic networks, these involve connectivity across geographical scales from the local to the global. Although they provide opportunities and enrich lives, they also contribute to the continued disadvantage of older people in the developing world. We argue that addressing these in research is not only morally justifiable, it potentially generates a distinct body of theoretical knowledge that might inform ongoing empirical work.
Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America
Authors: Pourbohloul Babak , Ahued Armando , Davoudi Bahman , Meza Rafael , Meyers Lauren A. , Skowronski Danuta M. , Villaseñor Ignacio , Galván Fernando , Cravioto Patricia , Earn David J. D. , Dushoff Jonathan , Fisman David , Edmunds W. John , Hupert Nathaniel , Scarpino Samuel V. , Trujillo Jesús , Lutzow Miguel , Morales Jorge , Contreras Ada , Chávez Carolina , Patrick David M. , Brunham Robert C. 
Published: August 2009

Background  Between 5 and 25 April 2009, pandemic (H1N1) 2009 caused a substantial, severe outbreak in Mexico, and subsequently developed into the first global pandemic in 41 years. We determined the reproduction number of pandemic (H1N1) 2009 by analyzing the dynamics of the complete case series in Mexico City during this early period.Methods  We analyzed three mutually exclusive datasets from Mexico City Distrito Federal which constituted all suspect cases from 15 March to 25 April: confirmed pandemic (H1N1) 2009 infections, non‐pandemic influenza A infections and patients who tested negative for influenza. We estimated the initial reproduction number from 497 suspect cases identified prior to 20 April, using a novel contact network methodology incorporating dates of symptom onset and hospitalization, variation in contact rates, extrinsic sociological factors, and uncertainties in underreporting and disease progression. We tested the robustness of this estimate using both the subset of laboratory‐confirmed pandemic (H1N1) 2009 infections and an extended case series through 25 April, adjusted for suspected ascertainment bias.Results  The initial reproduction number (95% confidence interval range) for this novel virus is 1·51 (1·32–1·71) based on suspected cases and 1·43 (1·29–1·57) based on confirmed cases before 20 April. The longer time series (through 25 April) yielded a higher estimate of 2·04 (1·84–2·25), which reduced to 1·44 (1·38–1·51) after correction for ascertainment bias.Conclusions  The estimated transmission characteristics of pandemic (H1N1) 2009 suggest that pharmaceutical and non‐pharmaceutical mitigation measures may appreciably limit its spread prior the development of an effective vaccine.
PCR‐ and Restriction Endonuclease‐Based Detection of IDH1 Mutations
Authors: Meyer Jochen , Pusch Stefan , Balss Jörg , Capper David , Mueller Wolf , Christians Arne , Hartmann Christian , Von Deimling Andreas 
Published: August 2009

AbstractHotspot mutations in codon 132 of the gene encoding isocitrate dehydrogenase 1 (IDH1) have emerged as the most frequent DNA alteration in astrocytomas, oligodendrogliomas and oligoastrocytomas. These mutations have been shown to be of significant diagnostic and prognostic value. So far, assessment of IDH1 mutation relied on DNA sequencing techniques.We generated a set of primers suitable for endonuclease‐based detection of hotspot mutations in codon 132 of IDH1. This primer set will allow determining these mutations without the need of DNA sequencing. One set of primer sets is designed to detect the presence or absence of IDH1 mutations in codon 132, while the other primer sets individually recognize the R132H, R132C, R132S, R132G and R132L mutations.
Microarray analysis yields candidate markers for rotation resistance in the western corn rootworm beetle, Diabrotica virgifera virgifera
Authors: Knolhoff Lisa M. , Walden Kimberly K. O. , Ratcliffe Susan T. , Onstad David W. , Robertson Hugh M. 
Published: August 2009

AbstractAs pest species may evolve resistance to chemical controls, they may also evolve resistance to cultural control methods. Yearly rotation of corn (Zea mays) with another crop interrupts the life cycle of the western corn rootworm beetle (Diabrotica virgifera virgifera, Coleoptera: Chrysomelidae), but behavioral resistance to crop rotation is now a major problem in the Midwest of the USA. Resistant adult females exhibit reduced fidelity to corn as a host and lay their eggs in the soil of both corn and soybean (Glycine max) fields. Behavioral assays suggest that the adaptation is related to increased locomotor activity, but finding molecular markers has been difficult. We used microarray analysis to search for gene expression differences between resistant and wild‐type beetles. Candidates validated with real‐time polymerase chain reaction exhibit predicted patterns from the microarray in independent samples across time and space. Many genes more highly expressed in the rotation‐resistant females have no matches to known proteins, and most genes that were more lowly expressed are involved in antimicrobial defense.
Quantification and reduction of bias from sampling larvae to infer population and landscape genetic structure
Authors: GOLDBERG CAREN S. , WAITS LISETTE P. 
Published: August 2009

AbstractA well‐designed sampling scheme is critical for obtaining accurate results from population genetic studies. Larval samples contain only the genetic material of successful breeders, often of a single year, and may be biased towards particular families. To quantify the bias of using larval samples to infer population and landscape genetic structure and explore how this bias may be reduced using sibship analysis, we analysed eight microsatellite loci from 484 tissue samples of larvae and adults of Columbia spotted frogs (Rana luteiventris) and long‐toed salamanders (Ambystoma macrodactylum) at nine breeding sites in north Idaho. Differences in allele frequencies between adult and larval samples were not detected after full‐siblings were removed from the larval data set for Columbia spotted frogs; for long‐toed salamanders, these differences remained at two out of four ponds. Data from Columbia spotted frog larvae indicated higher levels of differentiation among populations (median difference in FST = 0.020, P < 0.01), as predicted by population genetic theory, whereas data from larval samples of long‐toed salamanders showed some evidence of lower levels of differentiation among populations (median difference in FST = 0.012, P = 0.06). For both species, removing all but one individual from each full‐sibling family led to parameter estimates that were closer to those calculated from adult samples for both population and landscape genetic measures. Removal of full‐siblings is likely to improve estimates of population genetic parameters; however, knowledge of the species’ breeding system is essential for understanding additional sources of bias when inferring population genetic structure from larval samples.
A multiplex PCR assay to distinguish among three sympatric marsupial taxa from Huon Peninsula, Papua New Guinea, using the mitochondrial control region
Authors: McGREEVY T. J. , DABEK L. , HUSBAND T. P. 
Published: August 2009

AbstractMatschie’s tree kangaroo (Dendrolagus matschiei) is an endangered arboreal macropodid marsupial that is difficult to locate in the wild. The Tree Kangaroo Conservation Program noninvasively collected D. matschiei faecal samples, but a high percentage of samples were misidentified and belonged to two terrestrial macropods, New Guinea pademelon (Thylogale browni) and small dorcopsis (Dorcopsulus vanheurni). We developed species‐specific primers that produced a unique sized mitochondrial DNA control region gene product for each taxon and achieved an 89% correct assignment rate. The species‐specific primers can increase the accuracy of D. matschiei density estimates and facilitate additional genetic analyses of wild D. matschiei.
Flow Characteristics in a Curved Rectangular Channel With Variable Cross-Sectional Area
Authors: Bhunia Avijit , Chen C. L. 
Published: August 2009

Abstract
Laminar air flow through a curved rectangular channel with a variable cross-sectional (c/s) area (diverging-converging channel) is computationally investigated. Such a flow passage is formed between the two fin walls of a 90 deg bend curved fin heat sink, used in avionics cooling. Simulations are carried out for two different configurations: (a) a curved channel with long, straight, constant c/s area inlet and outlet sections (entry and exit lengths); and (b) a short, curved channel with no entry and exit lengths. Formation of a complex 3D flow pattern and its evolution in space is studied through numerical flow visualization. Results show that a secondary motion sets in the radial direction of the curved section, which in combination with the axial (bulk) flow leads to the formation of a base vortex. In addition, under certain circumstances the axial and secondary flow separate from multiple locations on the channel walls, creating Dean vortices and separation bubbles. Velocity above which the Dean vortices appear is cast in dimensionless form as the critical Dean number, which is calculated to be 129. Investigation of the friction factor reveals that pressure drop in the channel is governed by both the curvature effect as well as the area expansion effect. For a short curved channel where area expansion effect dominates, pressure drop for developing flow can be even less than that of a straight channel. A comparison with the flow in a constant c/s area, curved channel shows that the variable c/s area channel geometry leads to a lower critical Dean number and friction factor.
Fluoroquinolone Resistance in
Mycobacterium tuberculosis
and Mutations in
gyrA
and
gyrB
Authors: Von Groll Andrea , Martin Anandi , Jureen Pontus , Hoffner Sven , Vandamme Peter , Portaels Françoise , Palomino Juan Carlos , da Silva Pedro Almeida 
Published: August 2009

ABSTRACT

This study evaluated cross-resistance of
Mycobacterium tuberculosis
strains to ofloxacin, moxifloxacin, and gatifloxacin and investigated the presence of mutations in
gyrA
and
gyrB
. Fluoroquinolone susceptibilities were determined for 41
M. tuberculosis
strains by the proportion method on 7H11, and MICs were determined by the resazurin microtiter assay. Forty strains shared the same resistance results for the three fluoroquinolones. However, one strain, with an Asn-533 → Thr mutation in
gyrB
, was susceptible to ofloxacin but resistant to moxifloxacin and gatifloxacin.
Influence of Antidrug Antibodies on Plectasin Efficacy and Pharmacokinetics
Authors: Brinch Karoline Sidelmann , Frimodt-Møller Niels , Høiby Niels , Kristensen Hans-Henrik 
Published: August 2009

ABSTRACT

Plectasin is a 4.4-kDa antimicrobial peptide with the potential to be a treatment of infections caused by gram-positive bacteria. Since plectasin is a large molecule compared to conventional antibiotics, the development of antidrug antibodies (ADAs) could be anticipated. The immunogenic properties of plectasin were assessed through immunization studies. In mice treated for 5 days with one to two daily subcutaneous doses of plectasin, no antibody response was observed. If the animals were immunized again, after a rest period, low levels of antibodies developed in approximately half the animals. Additionally, mice were immunized with plectasin in Freund's incomplete adjuvant (FIA). Ninety-two percent of these mice developed ADAs after repeated immunizations, with two-thirds having high levels of antibodies. An agar diffusion bioassay showed that sera from animals immunized with plectasin did not inhibit the efficacy of the drug, while hyperimmune sera from animals in which an immune response was provoked by immunization with plectasin in FIA reduced the efficacy of plectasin at the lowest concentration tested. Studies in the murine peritonitis model showed an excellent efficacy of plectasin for the treatment of
Streptococcus pneumoniae
infections both in naïve animals and in animals with ADAs. No difference in bacterial counts was seen when the animals were treated with plectasin at 2.5 mg/kg of body weight, a dose below the expected therapeutic level. When animals were treated with plectasin at 0.625 mg/kg, the effect was reduced but not neutralized in animals with high levels of ADAs. No animals showed signs of hypersensitivity or injection site reactions toward plectasin, and the half-life of the compound did not vary between animals with and without antibodies.
Horizontal Transfer of Tetracycline Resistance among
Chlamydia
spp. In Vitro
Authors: Suchland R. J. , Sandoz K. M. , Jeffrey B. M. , Stamm W. E. , Rockey D. D. 
Published: August 2009

ABSTRACT

There are no examples of stable tetracycline resistance in clinical strains of
Chlamydia trachomatis
. However, the swine pathogen
Chlamydia suis
is commonly tetracycline resistant, both in America and in Europe. In tested U.S. strains, this resistance is mediated by a genomic island carrying a
tet
(C) allele. In the present study, the ability of
C. suis
to mobilize
tet
(C) into other chlamydial species was examined. Differently antibiotic resistant strains of
C. suis
,
C. trachomatis
, and
Chlamydia muridarum
were used in coculture experiments to select for multiply antibiotic resistant progeny. Coinfection of mammalian cells with a naturally occurring tetracycline-resistant strain of
C. suis
and a
C. muridarum
or
C. trachomatis
strain containing selected mutations encoding rifampin (rifampicin) or ofloxacin resistance readily produced doubly resistant recombinant clones that demonstrated the acquisition of tetracycline resistance. The resistance phenotype in the progeny from a
C. trachomatis
L2/ofl
R
-
C. suis
R19/tet
R
cross resulted from integration of a 40-kb fragment into a single ribosomal operon of a recipient, leading to a merodiploid structure containing three rRNA operons. In contrast, a cross between
C. suis
R19/tet
R
and
C. muridarum
MoPn/ofl
R
led to a classical double-crossover event transferring 99 kb of DNA from
C. suis
R19/tet
R
into
C. muridarum
MoPn/ofl
R
. Tetracycline resistance was also transferred to recent clinical strains of
C. trachomatis
. Successful crosses were not obtained when a rifampin-resistant
Chlamydophila caviae
strain was used as a recipient for crosses with
C. suis
or
C. trachomatis
. These findings provide a platform for further exploration of the biology of horizontal gene transfer in
Chlamydia
while bringing to light potential public health concerns generated by the possibility of acquisition of tetracycline resistance by human chlamydial pathogens.
Complete Nucleotide Sequences of Plasmids pEK204, pEK499, and pEK516, Encoding CTX-M Enzymes in Three Major
Escherichia coli
Lineages from the United Kingdom, All Belonging to the International O25:H4-ST131 Clone
Authors: Woodford Neil , Carattoli Alessandra , Karisik Edi , Underwood Anthony , Ellington Matthew J. , Livermore David M. 
Published: August 2009

ABSTRACT

We determined the complete nucleotide sequences of three plasmids that encode CTX-M extended-spectrum β-lactamases (ESBLs) in pulsed-field gel electrophoresis-defined United Kingdom variants (strains A, C, and D) of the internationally prevalent
Escherichia coli
O25:H4-ST131 clone. Plasmid pEK499 (strain A; 117,536 bp) was a fusion of type FII and FIA replicons and harbored the following 10 antibiotic resistance genes conferring resistance to eight antibiotic classes:
bla
CTX-M-15
,
bla
OXA-1
,
bla
TEM-1,
aac6′-Ib-cr
,
mph
(A),
catB4
,
tet
(A), and the integron-borne
dfrA7
,
aadA5
, and
sulI
genes. pEK516 (strain D; 64,471 bp) belonged to incompatibility group IncFII and carried seven antibiotic resistance genes:
bla
CTX-M-15
,
bla
OXA-1
,
bla
TEM-1
,
aac6′-Ib-cr
,
catB4
, and
tet
(A), all as in pEK499. It also carried
aac3-IIa
, conferring gentamicin resistance, and was highly related to pC15-1a, a plasmid encoding the CTX-M-15 enzyme in Canada. By contrast, pEK204 (strain C; 93,732 bp) belonged to incompatibility group IncI1 and carried only two resistance genes,
bla
CTX-M-3
and
bla
TEM-1
. It probably arose by the transposition of Tn
3
and IS
Ecp1
-
bla
CTX-M-3
elements into a pCOLIb-P9-like plasmid. We conclude that (i) United Kingdom variants of the successful
E. coli
ST131 clone have acquired different plasmids encoding CTX-M ESBLs on separate occasions, (ii) the
bla
CTX-M-3
and
bla
CTX-M-15
genes on pEK204 and pEK499/pEK516 represent separate escape events, and (iii) IncFII plasmids harboring
bla
CTX-M-15
have played a crucial role in the global spread of CTX-M-15 ESBLs in
E. coli
.
CS-8958, a Prodrug of the Novel Neuraminidase Inhibitor R-125489, Demonstrates a Favorable Long-Retention Profile in the Mouse Respiratory Tract
Authors: Koyama Kumiko , Takahashi Makoto , Oitate Masataka , Nakai Naoko , Takakusa Hideo , Miura Shin-ichi , Okazaki Osamu 
Published: August 2009

ABSTRACT

CS-8958 is a prodrug of the pharmacologically active form R-125489, a selective neuraminidase inhibitor, and has long-acting anti-influenza virus activity in vivo. In this study, the tissue distribution profiles after a single intranasal administration of CS-8958 (0.5 μmol/kg of body weight) to mice were investigated, focusing especially on the retention of CS-8958 in the respiratory tract by comparing it with R-125489 and a marketed drug, zanamivir. After administration of [
14
C]CS-8958, radioactivity was retained in the respiratory tract over long periods. At 24 h postdose, the radioactivity concentrations after administration of [
14
C]CS-8958 were approximately 10-fold higher in both the trachea and the lung than those of [
14
C]R-125489 and [
14
C]zanamivir. The [
14
C]CS-8958-derived radioactivity present in these two tissues consisted both of unchanged CS-8958 and of R-125489 at 1 h postdose, while only R-125489, and no other metabolites, was detected at 24 h postdose. After administration of unlabeled CS-8958, CS-8958 was rapidly eliminated from the lungs, whereas the lung R-125489 concentration reached a maximum at 3 h postdose and gradually declined, with an elimination half-life of 41.4 h. The conversion of CS-8958 to R-125489 was observed in mouse trachea and lung S9 fractions and was inhibited by esterase inhibitors, such as diisopropylfluorophosphate and bis-
p
-nitrophenylphosphate. These results demonstrated that CS-8958 administered intranasally to mice was efficiently converted to R-125489 by a hydrolase(s) such as carboxylesterase, and then R-125489 was slowly eliminated from the respiratory tract. These data support the finding that CS-8958 has potential as a long-acting neuraminidase inhibitor, leading to significant efficacy as an anti-influenza drug by a single treatment.
Two Distinct Major Facilitator Superfamily Drug Efflux Pumps Mediate Chloramphenicol Resistance in
Streptomyces coelicolor
Authors: Vecchione James J. , Alexander Blair , Sello Jason K. 
Published: August 2009

ABSTRACT

Chloramphenicol, florfenicol, and thiamphenicol are used as antibacterial drugs in clinical and veterinary medicine. Two efflux pumps of the major facilitator superfamily encoded by the
cmlR1
and
cmlR2
genes mediate resistance to these antibiotics in
Streptomyces coelicolor
, a close relative of
Mycobacterium tuberculosis
. The transcription of both genes was observed by reverse transcription-PCR. Disruption of
cmlR1
decreased the chloramphenicol MIC 1.6-fold, while disruption of
cmlR2
lowered the MIC 16-fold. The chloramphenicol MIC of wild-type
S. coelicolor
decreased fourfold and eightfold in the presence of reserpine and Phe-Arg-β-naphthylamide, respectively. These compounds are known to potentiate the activity of some antibacterial drugs via efflux pump inhibition. While reserpine is known to potentiate drug activity against gram-positive bacteria, this is the first time that Phe-Arg-β-naphthylamide has been shown to potentiate drug activity against a gram-positive bacterium.