bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Characteristic‐Hull Based Method for Home Range Estimation
Authors: Downs Joni A , Horner Mark W 
Published: December 2009

AbstractRecent literature has reported inaccuracies associated with some popular home range estimators such as kernel density estimation, especially when applied to point patterns of complex shapes. This study explores the use of characteristic hull polygons (CHPs) as a new method of home range estimation. CHPs are special bounding polygons created in GIS that can have concave edges, be composed of disjoint regions, and contain areas of unoccupied space within their interiors. CHPs are created by constructing the Delaunay triangulation of a set of points and then removing a subset of the resulting triangles. Here, CHPs consisting of 95% of the smallest triangles, measured in terms of perimeter, are applied for home range estimation. First, CHPs are applied to simulated animal locational data conforming to five point pattern shapes at three sample sizes. Then, the method is applied to black‐footed albatross (Phoebastria nigripes) locational data for illustration and comparison to other methods. For the simulated data, 95% CHPs produced unbiased home range estimates in terms of size for linear and disjoint point patterns and slight underestimates (8–20%) for perforated, concave, and convex ones. The estimated and known home ranges intersected one another by 72–96%, depending on shape and sample size, suggesting that the method has potential as a home range estimator. Additionally, the CHPs applied to estimate albatross home ranges illustrate how the method produces reasonable estimates for bird species that intensively forage in disjoint habitat patches.
Herpes simplex virus type‐2 in Egyptian patients with bladder cancer or cystitis
Authors: BADAWI HALA , AHMED HANEM , ABOUL FADL LAILA , HELMI AMIRA , FAM NEVINE , DIAB MANAL , ISMAIL AHMED , BADAWI AFKAR , SABER MOHAMED 
Published: December 2009

Badawi H, Ahmed H, Aboul Fadl L, Helmi A, Fam N, Diab M, Ismail A, Badawi A, Saber M. Herpes simplex virus type‐2 in Egyptian patients with bladder cancer or cystitis. APMIS 2010; 118: 37–44.The present study was designed to investigate the prevalence of herpes simplex virus type‐2 (HSV‐2) in Egyptian patients with bladder cancer or cystitis and to evaluate the performance of different diagnostic HSV‐2 assays. The study included 50 patients: 27 with bladder cancer (group I), 23 with cystitis (group II) and 20 subjects as controls (group III). HSV‐2 DNA was detected using polymerase chain reaction (PCR) on bladder tissue and buffy coat cells (BCC). Electron microscopic studies (EMS) on BCC and ELISAs for IgM, IgG and specific glycoprotein G‐2 (gG‐2) IgG were performed. HSV‐2 DNA was detected by PCR on bladder tissue biopsies in 29.6% and 21.7% of group I and II respectively and it was also detected by PCR on BCC in 22.2% and 21.7% of group I and II respectively. EMS revealed HSV like particles in 16.6% of cases. IgG, specific gG‐2 IgG and IgM were detected in 30%, 16% and 6% of cases respectively. The different assays were evaluated in relation to PCR on bladder tissue biopsies. The gG‐2‐based ELISA and EMS on BCC were found to be highly specific (97.3% and 100% respectively), with similar low sensitivity of ≈54%. PCR on BCC was the most sensitive assay. The association of HSV‐2 with bladder cancer is suggested especially in schistosomal patients.
P53 deletion may drive the clinical evolution and treatment response in multiple myeloma
Authors: López‐Anglada Lucía , Gutiérrez Norma C. , García Juan L. , Mateos María V. , Flores Teresa , San Miguel Jesús F. 
Published: December 2009

AbstractWe report a patient with multiple myeloma presenting with a paraspinal plasmacytoma with a marked dissociation between the response obtained in bone marrow (BM) infiltration and that achieved in soft tissue masses. While a complete remission was reached and maintained in BM, extramedullary plasmacytomas were refractory to every line of treatment. Genetic analysis identified the presence of t(4;14) and RB deletion in myeloma cells of both origins. However, a P53 deletion was only detected in plasma cells from extramedullary plasmacytomas. This finding suggests that P53 deletion has a role in the lack of treatment response of extramedullary plasmacytomas.
REAL‐TIME REVERSE TRANSCRIPTION PCR DETECTION OF VIABLE SHIGA TOXIN‐PRODUCING ESCHERICHIA COLI O157:H7 IN FOOD
Authors: DI R. , TUMER N.E. 
Published: December 2009

ABSTRACT Shiga toxin (Stx)‐producing Escherichia coli (STEC), particularly E. coli O157:H7, have been associated with food‐related outbreaks and have become a global health concern. Detection of low numbers of viable STEC in food is undoubtedly challenging. The present study demonstrated that 7 × 102 to 7 × 103 cfu E. coli O157:H7 cells in 50 mL of inoculated food samples including apple juice, lettuce and ground beef could be concentrated through a two‐step filtration technique. Bacterial RNA was effectively isolated from the concentrated E. coli O157:H7 cells with the combination of Trizol Max Bacterial RNA Isolation Enhancement Reagent and TriReagent®. Real‐time reverse transcription polymerase chain reaction with seven sets of primers targeting virulence and serotype genes of E. coli O157:H7 specifically detected the bacterial RNA representing 1 × 102 to 1 × 103 cfu viable bactersial cells. The total detection time from sampling to measurement was approximately 4 h. This study provides a rapid and specific detection method for viable STEC in food.PRACTICAL APPLICATIONSRapid detection of viable STEC including Escherichia coli O157:H7 cells in food has been difficult, especially when present in low numbers. This study has shown that 7 × 102 to 7 × 103 cfu E. coli O157:H7 in 50 mL of inoculated food samples, i.e., 14–140 cfu/mL bacterial cells, could be readily concentrated and the bacterial RNA could be detected by real‐time reverse transcription polymerase chain reaction (PCR) in a relatively short time. Use of seven primer sets makes this method very specific for real‐time PCR detection of E. coli O157:H7.
Flagellar Motions in Phototactic Steering in a Brown Algal Swarmer
Authors: Matsunaga Shigeru , Uchida Hiroko , Iseki Mineo , Watanabe Masakatsu , Murakami Akio 
Published: December 2009

AbstractUsing infrared high‐speed video microscopy, we observed light‐triggered transitory flagellar motions in flagellate reproductive cells (swarmers) of a brown alga, Scytosiphon lomentaria, under primary helical swimming conditions before and during negative phototactic orientation to unilateral actinic light. The posterior flagellum, which is autofluorescent and thought to be light‐sensing, was passively dragged in the dark and exhibited one to several rapid lateral beats during orientation changes for phototactic steering. Notably, a brief cessation of anterior flagellar beating was occasionally observed concomitantly with rapid beats of the posterior flagellum. This behavior caused a pause in helical body rotation, which may contribute to the accuracy of phototactic steering. Thus, coordinated regulation of the movement of the two flagella plays a crucial role in phototactic steering.
Issues in long‐term percutaneous endoscopic gastrostomy feeding in a nursing home: a case study
Authors: Adams John , Lewin David 
Published: December 2009

Aim.  To explore the experiences of care staff in managing long‐term percutaneous endoscopic gastrostomy (PEG) feeding regimes.Background.  Since its first description in 1980, PEG feeding has become a widely‐used technique to provide enteral nutritional support. Its initial use for short term feeding has subsequently been extended to encompass long‐term care.Methods.  A single institution case study, employing mixed methods, was conducted in one English nursing home. Data were collected from an unstructured interview, questionnaires and a focus group in 2004–2005.Results.  The two key concerns of care staff were found to relate to clinical issues, such as vomiting, and the ethical issues surrounding PEG insertion.Conclusions.  Care staff would value the creation of a safe forum in which their views could be shared.Relevance to clinical practice.  As PEG tube use becomes more common in long‐term care environments, care staff need to reflect upon the clinical and ethical issues that are raised.
Brain magnetic resonance imaging findings in patients with systemic sclerosis
Authors: MOHAMED Reem H. A. , NASSEF Amr A. 
Published: December 2009

AbstractBackground:  Systemic sclerosis is a multisystem disease where functional and structural abnormalities of small blood vessels prevail. Recently, transient ischemic attacks, ischemic stroke, and hemorrhages have been reported as primary consequence of vascular central nervous system affection in systemic sclerosis. Magnetic resonance imaging (MRI) is considered to be the most sensitive diagnostic technique for detecting symptomatic and asymptomatic lesions in the brain in cases of multifocal diseases.Objective:  Evaluate brain changes in patients with systemic sclerosis using MRI.Patients and methods:  Thirty female patients with systemic sclerosis aged 27–61 years, with disease duration of 1–9 years and with no history of other systemic disease or cerebrovascular accidents, were enrolled. An age‐matched female control group of 30 clinically normal subjects, underwent brain MR examination.Results:  Central nervous system involvement in the form of white matter hyperintense foci of variable sizes were found in significantly abundant forms in systemic sclerosis patients on MR evaluation than in the age‐related control group, signifying a form of central nervous system vasculopathy. Such foci showed no definite correlation with disease duration, yet they showed significant correlation to severity of peripheral vascular disease, headaches, fainting attacks and depression in the group under study.Conclusion:  Asymptomatic as well as symptomatic central nervous system ischemic vasculopathy is not uncommon in systemic sclerosis patients and MRI is considered a sensitive noninvasive screening tool for early detection of CNS involvement in patients with systemic sclerosis.
Direct Link between Toluene Degradation in Contaminated-Site Microcosms and a
Polaromonas
Strain
Authors: Sun Weimin , Xie Shuguang , Luo Chunling , Cupples Alison M. 
Published: December 2009

ABSTRACT

Stable isotope probing (SIP) was used to identify the aerobic toluene-degrading microorganism in soil microcosms. Several approaches (terminal restriction fragment length polymorphism, 16S rRNA gene sequencing, and quantitative PCR) provided evidence that the microorganism responsible was a member of the genus
Polaromonas
and could grow on toluene. This microorganism also transformed benzene, but not
m
-xylene or
cis
-dichloroethene.
Correlation of
Dehalococcoides
16S rRNA and Chloroethene-Reductive Dehalogenase Genes with Geochemical Conditions in Chloroethene-Contaminated Groundwater
Authors: van der Zaan Bas , Hannes Fredericke , Hoekstra Nanne , Rijnaarts Huub , de Vos Willem M. , Smidt Hauke , Gerritse Jan 
Published: December 2009

ABSTRACT

Quantitative analysis of genes that code for
Dehalococcoides
16S rRNA and chloroethene-reductive dehalogenases TceA, VcrA, and BvcA was done on groundwater sampled from 150 monitoring wells spread over 11 chlorinated ethene polluted European locations. Redundancy analysis was used to relate molecular data to geochemical conditions.
Dehalococcoides
16S rRNA- and vinyl chloride (VC)-reductase genes were present at all tested locations in concentrations up to 10
6
gene copies per ml of groundwater. However, differences between and also within locations were observed. Variation in
Dehalococcoides
16S rRNA gene copy numbers were most strongly correlated to dissolved organic carbon concentration in groundwater and to conditions appropriate for biodegradation of chlorinated ethenes (U.S. Environmental Protection Agency score). In contrast,
vcrA
gene copy numbers correlated most significantly to VC and chlorinated ethene concentrations. Interestingly,
bvcA
and especially
tce
A were more correlated with oxidizing conditions. In groundwater microcosms, dechlorination of 1 mM VC was correlated to an increase of
vcrA
and/or
bvcA
gene copies by 2 to 4 orders of magnitude. Interestingly, in 34% of the monitoring wells and in 40% of the active microcosms, the amount of individual VC-reductase gene copies exceeded that of
Dehalococcoides
16S rRNA gene copies. It is concluded that the geographical distribution of the genes was not homogeneous, depending on the geochemical conditions, whereby
tceA
and
bvcA
correlated to more oxidized conditions than
Dehalococcoides
16S rRNA and
vcrA
. Because the variation in VC-reductase gene numbers was not directly correlated to variation in
Dehalococcoides
spp., VC-reductase genes are better monitoring parameters for VC dechlorination capacity than
Dehalococcoides
spp.
Bacteria Associated with Immunoregulatory Cells in Mice
Authors: Presley Laura L. , Wei Bo , Braun Jonathan , Borneman James 
Published: December 2009

ABSTRACTThis study examined bacteria-immune interactions in a mouse model possessing microbiota-dependent immune regulatory features similar to those occurring in human atopy, colitis, and immune regulation. Associations between the abundance of several bacterial phylotypes and immunoregulatory target cell types were identified, suggesting that they may play a role in these phenotypes.
Reductive Debromination of Polybrominated Diphenyl Ethers by Anaerobic Bacteria from Soils and Sediments
Authors: Lee Lip Kim , He Jianzhong 
Published: December 2009

ABSTRACT

Polybrominated diphenyl ethers (PBDEs) have attracted attention recently due to their proven adverse effects on animals and their increasing concentrations in various environmental media and biota. To gain insight into the fate of PBDEs, microcosms established with soils and sediments from 28 locations were investigated to determine their debromination potential with an octa-brominated diphenyl ether (octa-BDE) mixture consisting of hexa- to nona-BDEs. Debromination occurred in microcosms containing samples from 20 of the 28 locations when they were spiked with octa-BDE dissolved in the solvent trichloroethene (TCE), which is a potential cosubstrate for stimulating PBDE debromination, and in microcosms containing samples from 11 of the 28 locations when they were spiked with octa-BDE dissolved in nonane. Debromination products ranging from hexa- to mono-BDEs were generated within 2 months. Notably, the toxic tetra-BDEs accounted for 50% of the total product. In sediment-free culture C-N-7* amended with the octa-BDE mixture and nonane (containing 45 nM nona-BDE, 181 nM octa-BDEs, 294 nM hepta-BDE, and 19 nM hexa-BDE) there was extensive debromination of the parent compounds, which produced hexa-BDE (56 nM), penta-BDEs (124 nM), and tetra-BDEs (150 nM) within 42 days, possibly by a metabolic process. A 16S rRNA gene-based analysis revealed that
Dehalococcoides
species were present in 11 of 14 active microcosms. However, unknown debrominating species in some of the microcosms debrominated the octa-BDE mixture in the absence of other added halogenated electron acceptors (such as TCE). These findings provide information that is useful for assessing microbial reductive debromination of higher brominated PBDEs to less-brominated congeners, a possible source of the more toxic congeners (e.g., penta- and tetra-BDEs) detected in the environment.
Diversity and Evolution of the Phenazine Biosynthesis Pathway
Authors: Mavrodi Dmitri V. , Peever Tobin L. , Mavrodi Olga V. , Parejko James A. , Raaijmakers Jos M. , Lemanceau Philippe , Mazurier Sylvie , Heide Lutz , Blankenfeldt Wulf , Weller David M. , Thomashow Linda S. 
Published: December 2009

ABSTRACT

Phenazines are versatile secondary metabolites of bacterial origin that function in biological control of plant pathogens and contribute to the ecological fitness and pathogenicity of the producing strains. In this study, we employed a collection of 94 strains having various geographic, environmental, and clinical origins to study the distribution and evolution of phenazine genes in members of the genera
Pseudomonas
,
Burkholderia
,
Pectobacterium
,
Brevibacterium
, and
Streptomyces
. Our results confirmed the diversity of phenazine producers and revealed that most of them appear to be soil-dwelling and/or plant-associated species. Genome analyses and comparisons of phylogenies inferred from sequences of the key phenazine biosynthesis (
phzF
) and housekeeping (
rrs
,
recA
,
rpoB
,
atpD
, and
gyrB
) genes revealed that the evolution and dispersal of phenazine genes are driven by mechanisms ranging from conservation in
Pseudomonas
spp. to horizontal gene transfer in
Burkholderia
spp. and
Pectobacterium
spp. DNA extracted from cereal crop rhizospheres and screened for the presence of
phzF
contained sequences consistent with the presence of a diverse population of phenazine producers in commercial farm fields located in central Washington state, which provided the first evidence of United States soils enriched in indigenous phenazine-producing bacteria.
Key Process Conditions for Production of C
4
Dicarboxylic Acids in Bioreactor Batch Cultures of an Engineered
Saccharomyces cerevisiae
Strain
Authors: Zelle Rintze M. , de Hulster Erik , Kloezen Wendy , Pronk Jack T. , van Maris Antonius J. A. 
Published: December 2009

ABSTRACT

A recent effort to improve malic acid production by
Saccharomyces cerevisiae
by means of metabolic engineering resulted in a strain that produced up to 59 g liter
−1
of malate at a yield of 0.42 mol (mol glucose)
−1
in calcium carbonate-buffered shake flask cultures. With shake flasks, process parameters that are important for scaling up this process cannot be controlled independently. In this study, growth and product formation by the engineered strain were studied in bioreactors in order to separately analyze the effects of pH, calcium, and carbon dioxide and oxygen availability. A near-neutral pH, which in shake flasks was achieved by adding CaCO
3
, was required for efficient C
4
dicarboxylic acid production. Increased calcium concentrations, a side effect of CaCO
3
dissolution, had a small positive effect on malate formation. Carbon dioxide enrichment of the sparging gas (up to 15% [vol/vol]) improved production of both malate and succinate. At higher concentrations, succinate titers further increased, reaching 0.29 mol (mol glucose)
−1
, whereas malate formation strongly decreased. Although fully aerobic conditions could be achieved, it was found that moderate oxygen limitation benefitted malate production. In conclusion, malic acid production with the engineered
S. cerevisiae
strain could be successfully transferred from shake flasks to 1-liter batch bioreactors by simultaneous optimization of four process parameters (pH and concentrations of CO
2
, calcium, and O
2
). Under optimized conditions, a malate yield of 0.48 ± 0.01 mol (mol glucose)
−1
was obtained in bioreactors, a 19% increase over yields in shake flask experiments.
PrhG, a Transcriptional Regulator Responding to Growth Conditions, Is Involved in the Control of the Type III Secretion System Regulon in
Ralstonia solanacearum
Authors: Plener Laure , Manfredi Pablo , Valls Marc , Genin Stéphane 
Published: December 2009

ABSTRACT

The ability of
Ralstonia solanacearum
to cause disease in plants depends on its type III secretion system (T3SS). The expression of the T3SS and its effector substrates is coordinately controlled by a regulatory cascade, at the bottom of which is HrpB. Transcription of the
hrpB
gene is activated by a plant-responsive regulator named HrpG, which is a master regulator of a wide array of pathogenicity functions in
R
.
solanacearum
. We have identified in the genome of strain GMI1000 a close paralog of
hrpG
(83% overall similarity at the protein level) that we have named
prhG
. Despite this high similarity, the expression pattern of
prhG
is remarkably different from that of
hrpG
:
prhG
expression is activated after growth of bacteria in minimal medium but not in the presence of host cells, while
hrpG
expression is specifically induced in response to plant cell signals. We provide genetic evidence that
prhG
is a transcriptional regulator that, like
hrpG
, controls the expression of
hrpB
and the
hrpB
-regulated genes under minimal medium conditions. However, the regulatory functions of
prhG
and
hrpG
are distinct:
prhG
has no influence on
hrpB
expression when the bacteria are in the presence of plant cells, and transcriptomic profiling analysis of a
prhG
mutant revealed that the PrhG and HrpG regulons have only one pathogenicity target in common,
hrpB
. Functional complementation experiments indicated that PrhG and HrpG are individually sufficient to activate
hrpB
expression in minimal medium. Rather surprisingly, a
prhG
disruption mutant had little impact on pathogenicity, which may indicate that
prhG
has a minor role in the activation of T3SS genes when
R
.
solanacearum
grows parasitically inside the plant. The cross talk between pathogenicity regulatory proteins and environmental signals described here denotes that an intricate network is at the basis of the bacterial disease program.
Identification of Conserved Amino Acid Residues of the
Salmonella
σ
S
Chaperone Crl Involved in Crl-σ
S
Interactions
Authors: Monteil Véronique , Kolb Annie , D'Alayer Jacques , Beguin Pierre , Norel Françoise 
Published: December 2009

ABSTRACT

Proteins that bind σ factors typically attenuate the function of the σ factor by restricting its access to the RNA polymerase (RNAP) core enzyme. An exception to this general rule is the Crl protein that binds the stationary-phase sigma factor σ
S
(RpoS) and enhances its affinity for the RNAP core enzyme, thereby increasing expression of σ
S
-dependent genes. Analyses of sequenced bacterial genomes revealed that
crl
is less widespread and less conserved at the sequence level than
rpoS.
Seventeen residues are conserved in all members of the Crl family. Site-directed mutagenesis of the
crl
gene from
Salmonella enterica
serovar Typhimurium and complementation of a Δ
crl
mutant of
Salmonella
indicated that substitution of the conserved residues Y22, F53, W56, and W82 decreased Crl activity. This conclusion was further confirmed by promoter binding and abortive transcription assays. We also used a bacterial two-hybrid system (BACTH) to show that the four substitutions in Crl abolish Crl-σ
S
interaction and that residues 1 to 71 in σ
S
are dispensable for Crl binding. In
Escherichia coli
, it has been reported that Crl also interacts with the ferric uptake regulator Fur and that Fur represses
crl
transcription. However, the
Salmonella
Crl and Fur proteins did not interact in the BACTH system. In addition, a
fur
mutation did not have any significant effect on the expression level of Crl in
Salmonella.
These results suggest that the relationship between Crl and Fur is different in
Salmonella
and
E. coli
.