bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recovery, Bioaccumulation, and Inactivation of Human Waterborne Pathogens by the Chesapeake Bay Nonnative Oyster,
Crassostrea ariakensis
Authors: Graczyk Thaddeus K. , Girouard Autumn S. , Tamang Leena , Nappier Sharon P. , Schwab Kellogg J. 
Published: May 2006

ABSTRACT

The introduction of nonnative oysters (i.e.,
Crassostrea ariakensis
) into the Chesapeake Bay has been proposed as necessary for the restoration of the oyster industry; however, nothing is known about the public health risks related to contamination of these oysters with human pathogens. Commercial market-size
C. ariakensis
triploids were maintained in large marine tanks with water of low (8-ppt), medium (12-ppt), and high (20-ppt) salinities spiked with 1.0 × 10
5
transmissive stages of the following human pathogens:
Cryptosporidium parvum
oocysts,
Giardia lamblia
cysts, and microsporidian spores (i.e.,
Encephalitozoon intestinalis
,
Encephalitozoon hellem
, and
Enterocytozoon bieneusi
). Viable oocysts and spores were still detected in oysters on day 33 post-water inoculation (pwi), and cysts were detected on day 14 pwi. The recovery, bioaccumulation, depuration, and inactivation rates of human waterborne pathogens by
C. ariakensis
triploids were driven by salinity and were optimal in medium- and high-salinity water. The concentration of human pathogens from ambient water by
C. ariakensis
and the retention of these pathogens without (or with minimal) inactivation and a very low depuration rate provide evidence that these oysters may present a public health threat upon entering the human food chain, if harvested from polluted water. This conclusion is reinforced by the concentration of waterborne pathogens used in the present study, which was representative of levels of infectious agents in surface waters, including the Chesapeake Bay. Aquacultures of nonnative oysters in the Chesapeake Bay will provide excellent ecological services in regard to efficient cleaning of human-infectious agents from the estuarine waters.
Rhizosphere Selection of Highly Motile Phenotypic Variants of
Pseudomonas fluorescens
with Enhanced Competitive Colonization Ability
Authors: Martínez-Granero Francisco , Rivilla Rafael , Martín Marta 
Published: May 2006

ABSTRACT

Phenotypic variants of
Pseudomonas fluorescens
F113 showing a translucent and diffuse colony morphology show enhanced colonization of the alfalfa rhizosphere. We have previously shown that in the biocontrol agent
P. fluorescens
F113, phenotypic variation is mediated by the activity of two site-specific recombinases, Sss and XerD. By overexpressing the genes encoding either of the recombinases, we have now generated a large number of variants (mutants) after selection either by prolonged laboratory cultivation or by rhizosphere passage. All the isolated variants were more motile than the wild-type strain and appear to contain mutations in the
gacA
and/or
gacS
gene. By disrupting these genes and complementation analysis, we have observed that the Gac system regulates swimming motility by a repression pathway. Variants isolated after selection by prolonged cultivation formed a single population with a swimming motility that was equal to the motility of
gac
mutants, being 150% more motile than the wild type. The motility phenotype of these variants was complemented by the cloned
gac
genes. Variants isolated after rhizosphere selection belonged to two different populations: one identical to the population isolated after prolonged cultivation and the other comprising variants that besides a
gac
mutation harbored additional mutations conferring higher motility. Our results show that
gac
mutations are selected both in the stationary phase and during rhizosphere colonization. The enhanced motility phenotype is in turn selected during rhizosphere colonization. Several of these highly motile variants were more competitive than the wild-type strain, displacing it from the root tip within 2 weeks.
Combination of Multiplex PCR and PCR-Denaturing Gradient Gel Electrophoresis for Monitoring Common Sourdough-Associated
Lactobacillus
Species
Authors: Settanni Luca , Valmorri Sara , van Sinderen Douwe , Suzzi Giovanna , Paparella Antonello , Corsetti Aldo 
Published: May 2006

ABSTRACT

A combination of denaturing gradient gel electrophoresis (DGGE) and a previously described multiplex PCR approach was employed to detect sourdough lactobacilli. Primers specific for certain groups of
Lactobacillus
spp. were used to amplify fragments, which were analyzed by DGGE. DGGE profiles obtained from
Lactobacillus
type strains acted as standards to analyze lactobacilli from four regional Abruzzo (central Italy) sourdoughs.
Spoligotyping of
Mycobacterium tuberculosis
Isolates from Pakistan Reveals Predominance of Central Asian Strain 1 and Beijing Isolates
Authors: Hasan Zahra , Tanveer Mahnaz , Kanji Akbar , Hasan Qaiser , Ghebremichael Solomon , Hasan Rumina 
Published: May 2006

ABSTRACT

The estimated incidence of tuberculosis in Pakistan is 181 per 100,000; however, there is limited information on
Mycobacterium tuberculosis
genotypes circulating in the country. We studied 314
M. tuberculosis
clinical isolates; of these, 197 (63%) isolates grouped into 22 different clusters, while 119 (37%) had unique spoligotypes. Eighty-nine percent of the isolates were pulmonary (Pul), and 11% were extrapulmonary (E-Pul). We identified Central Asian Strain (CAS), Beijing, T1, Latin American-Mediterranean, and East African-Indian genogroups. Beijing strains, reportedly the most prevalent spoligotype worldwide, constituted 6% of our strain population. The CAS1 strain comprised 121 (39%) of the study isolates. No difference was observed between clustered isolates from cases of Pul and E-Pul tuberculosis. However, E-Pul isolates included a greater number of unique spoligotypes than Pul isolates (
P
= 0.005). The overall percentage of drug resistance was 54%, and that of MDR strains was 40%. While CAS1 strains were not associated with drug resistance, the relative risk of MDR was significant in Beijing strains compared to the non-Beijing groups (95% confidence interval, 1.2 to 8.9). The fact that the predominant strain, CAS1, is not associated with drug resistance is encouraging and suggests that an effective tuberculosis control program should be able to limit the high incidence of disease in this region.
Prospective Study of the Value of Quantitative Culture of Organisms from Blood Collected through Central Venous Catheters in Differentiating between Contamination and Bloodstream Infection
Authors: Chatzinikolaou Ioannis , Hanna Hend , Darouiche Rabih , Samonis George , Tarrand Jeffrey , Raad Issam 
Published: May 2006

ABSTRACT
Collection of blood through a central venous catheter for the diagnosis of bacteremia is a debated topic. Quantitative cultures of organisms from blood collected through central venous catheters were found to be highly sensitive, specific, and predictive of bacteremia, especially when a cutoff point of 15 colonies of skin organisms was used.
Lack of Association between the Presence of the pVir Plasmid and Bloody Diarrhea in
Campylobacter jejuni
Enteritis
Authors: Louwen R. P. L. , van Belkum A. , Wagenaar J. A. , Doorduyn Y. , Achterberg R. , Endtz H. P. 
Published: May 2006

ABSTRACT

The main mechanisms by which
Campylobacter jejuni
causes diarrhea are unknown. In contrast to a recent communication, we report here the absence of an association with the plasmid pVir in patients infected with
C. jejuni
who developed bloody diarrhea in The Netherlands, and we suggest a role for other virulence determinants.
Multiplex PCR-Based Reverse Line Blot Hybridization Assay To Identify 23
Streptococcus pneumoniae
Polysaccharide Vaccine Serotypes
Authors: Kong Fanrong , Brown Mitchell , Sabananthan Archcna , Zeng Xianyu , Gilbert Gwendolyn L. 
Published: May 2006

ABSTRACT
We developed a multiplex PCR-based reverse line blot assay to identify 23 pneumococcal serotypes represented in the polysaccharide vaccine, using 334 well-characterized isolates, representing all 90 serotypes, and 268 “unknowns.” The assay identified all target serotypes, but 11, which cross-react with 1 to 4 nonvaccine serotypes, could be distinguished using serotype-specific antisera.
Early Diagnosis of
Acanthamoeba
Infection during Routine Cytological Examination of Cerebrospinal Fluid
Authors: Petry Franz , Torzewski Michael , Bohl Jürgen , Wilhelm-Schwenkmezger Thomas , Scheid Patrick , Walochnik Julia , Michel Rolf , Zöller Lothar , Werhahn Konrad J. , Bhakdi Sucharit , Lackner Karl J. 
Published: May 2006

ABSTRACT

Early identification of
Acanthamoeba
in cerebrospinal fluid is mandatory to prevent fatal granulomatous amebic encephalitis. In the case presented here amebic trophozoites were detected in a routine cerebrospinal fluid sample. The antibiotic treatment and the apparently low virulence of this isolate were responsible for the benign progression of the infection.
Minimal Residual Disease in Hairy Cell Leukemia Patients Assessed by Clone-Specific Polymerase Chain Reaction
Authors: Arons Evgeny , Margulies Inger , Sorbara Lynn , Raffeld Mark , Stetler-Stevenson Maryalice , Pastan Ira , Kreitman Robert J. 
Published: May 2006

Abstract
Cladribine induces long-term complete remission in hairy cell leukemia (HCL) patients but does not clear minimal residual disease (MRD) according to high-sensitivity PCR assays. To quantify MRD in patients after anti-CD22 recombinant immunotoxin BL22 and other agents, we used a relative quantitative PCR (RQ-PCR) assay using a primer and probe, both patient specific for the immunoglobulin heavy chain rearrangement. Using this method, we were able to detect one Bonna 12 HCL cell in either 106 Jurkat cells or in 106 normal mononuclear cells. We studied 84 samples from 10 patients, taken before or after treatment with BL22 and other agents. Patient-specific RQ-PCR was much more sensitive than flow cytometry, which in turn was (as recently reported) more sensitive than PCR using consensus primers. RQ-PCR was positive in 62 of 62 (100%) flow-positive samples in 10 patients and in 20 of 22 (91%) flow-negative samples in six patients. The relative level of MRD as quantified by RQ-PCR correlated with disease status and remission. Thus, patient-specific RQ-PCR is the most sensitive test for MRD in HCL patients and could be used to determine maximal response in patients obtaining multiple cycles of nonmyelotoxic biological treatment for this disease.
Chk2 Molecular Interaction Map and Rationale for Chk2 Inhibitors
Authors: Pommier Yves , Weinstein John N. , Aladjem Mirit I. , Kohn Kurt W. 
Published: May 2006

Abstract
To organize the rapidly accumulating information on bioregulatory networks related to the histone γ-H2AX-ATM-Chk2-p53-Mdm2 pathways in concise and unambiguous diagrams, we used the molecular interaction map notation (http://discover.nci.nih.gov/min). Molecular interaction maps are particularly useful for networks that include protein-protein binding and posttranslational modifications (e.g., phosphorylation). Both are important for nearly all of the proteins involved in DNA double-strand break signaling. Visualizing the regulatory circuits underlying cellular signaling may help identify key regulatory reactions and defects that can serve as targets for anticancer drugs.
Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package
Authors: Kumar Yadhu , Westram Ralf , Kipfer Peter , Meier Harald , Ludwig Wolfgang 
Published: May 2006

Abstract

Background
Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment.

Results
Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA.

Conclusion
Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via http://www.arb-home.de.
Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines
Authors: Liu Ying , Shin Soojung , Zeng Xianmin , Zhan Ming , Gonzalez Rodolfo , Mueller Franz-Josef , Schwartz Catherine M , Xue Haipeng , Li Huai , Baker Shawn C , Chudin Eugene , Barker David L , McDaniel Timothy K , Oeser Steffen , Loring Jeanne F , Mattson Mark P , Rao Mahendra S 
Published: May 2006

Abstract

Background
In order to compare the gene expression profiles of human embryonic stem cell (hESC) lines and their differentiated progeny and to monitor feeder contaminations, we have examined gene expression in seven hESC lines and human fibroblast feeder cells using Illumina® bead arrays that contain probes for 24,131 transcript probes.

Results
A total of 48 different samples (including duplicates) grown in multiple laboratories under different conditions were analyzed and pairwise comparisons were performed in all groups. Hierarchical clustering showed that blinded duplicates were correctly identified as the closest related samples. hESC lines clustered together irrespective of the laboratory in which they were maintained. hESCs could be readily distinguished from embryoid bodies (EB) differentiated from them and the karyotypically abnormal hESC line BG01V. The embryonal carcinoma (EC) line NTera2 is a useful model for evaluating characteristics of hESCs. Expression of subsets of individual genes was validated by comparing with published databases, MPSS (Massively Parallel Signature Sequencing) libraries, and parallel analysis by microarray and RT-PCR.

Conclusion
we show that Illumina's bead array platform is a reliable, reproducible and robust method for developing base global profiles of cells and identifying similarities and differences in large number of samples.
Prolonged labour associated with lower expression of syndecan 3 and connexin 43 in human uterine tissue
Authors: Cluff Ann Hjelm , Byström Birgitta , Klimaviciute Aurelija , Dahlqvist Camilla , Cebers Gvido , Malmström Anders , Ekman-Ordeberg Gunvor 
Published: May 2006

Abstract

Background
Prolonged labour is associated with greater morbidity and mortality for mother and child. Connexin 43 is a major myometrial gap junction protein found in human myometrium. Syndecan 3 seems to prevail in the human uterus among heparan sulphate proteoglycans, showing the most significant increase during labour. The aims of the present study were to investigate syndecan 3 and connexin 43 mRNA expressions and protein distributions in human uterine tissue during normal and prolonged labour.

Methods
Uterine isthmic biopsies were collected from non-pregnant (n = 7), term pregnant women not in labour (n = 14), in normal labour (n = 7) and in prolonged labour (n = 7). mRNA levels of syndecan 3 and connexin 43 were determined by real time RT-PCR. The localization and expression were demonstrated by immunohistochemistry and confocal microscopy.

Results
In women with prolonged labour, the mRNA expressions of syndecan 3 and Connexin 43 were considerably lower than the expression level at normal labour (p < 0.05). In term-pregnant tissue, the expression of syndecan 3 and connexin 43 did not differ significantly compared to non-pregnant and normal labour. The immunoreactivity of syndecan 3 was strong at normal labour, in contrast to prolonged labour, where both a weaker expression and an irregular distribution were detected. The immunoreactivity of connexin 43 increased until term and further stronger staining occurred at normal labour. At prolonged labour, the immunoreactivity was weaker and more unevenly distributed. At labour, a co-localization of syndecan 3 and connexin 43 could be demonstrated in the smooth muscle by confocal microscopy.

Conclusion
The high expression of syndecan 3 and connexin 43 and their co-localization to the smooth muscle bundles during normal labour, together with the significant reduction in prolonged labour, may indicate a role for these proteins in the co-ordination of myometrial contractility.
The effects of rumination and distraction on over‐general autobiographical memory retrieval during social problem solving
Authors: Kao Chih‐Mei , Dritschel Barbara H. , Astell Arlene 
Published: May 2006

Objectives .  We examined the effects of rumination and distraction on over‐general autobiographical memory (AM) retrieval during social problem solving (SPS), as well as SPS performance in terms of means and effectiveness.Design and Methods .  After undergoing a rumination or distraction manipulation, dysphoric and non‐dysphoric participants performed a SPS task and reported the memories retrieved during SPS.Results .  The dysphoric ruminators performed significantly less effectively on the SPS task than the other groups. However, the dysphoric ruminators did not differ from the dysphoric distracters on the numbers of categoric memories retrieved during SPS although they retrieved significantly more categoric memories than the non‐dysphoric distracters and non‐dysphoric ruminators. For all groups, the effectiveness score was significantly negatively correlated with categoric memories retrieved during SPS.Conclusion .  The results demonstrated that in a dysphoric sample, rumination impaired SPS performance but did not influence categoric AM retrieval during SPS. The results suggested that in a dysphoric sample, rumination might affect SPS performance by affecting processes like initiation and motivation rather than AM retrieval during SPS.
Characteristics of NAEM salt-catalyzed alcohol organosolv pulping as a biorefinery
Authors: Yawalata Dominggus , Paszner Laszlo 
Published: May 2006

AbstractCharacteristics of the NAEM [neutral alkali-earth metal; CaCl2and Mg(NO3)2in this study] salt-catalyzed alcohol organosolv pulping of softwood were investigated and compared to AlCl3-catalyzed kraft pulping. The catalysts control the acidity of the cooking liquor, which is the key factor for pulping selectivity and fiber separation. The crucial role of catalysts in alcohol organosolv pulping is demonstrated. The pulp yield and quality were satisfactory. The dissolved wood components in the spent liquor have high potential to be converted into value-added co-products.
The creep of wood destabilized by change in moisture content. Part 3: The influence of changing moisture history on creep behavior
Authors: Takahashi Chika , Ishimaru Yutaka , Iida Ikuho , Furuta Yuzo 
Published: May 2006

AbstractThe creep of wood increases remarkably during moisture changes, a phenomenon called mechano-sorptive creep. The microstructure in cell walls of wood is destabilized by changes in temperature and/or moisture content. The mechanical properties of destabilized wood change over long periods of time. In the present study, the influence of moisture conditioning history on bending creep was examined. During changes in moisture, greater creep occurred in wood subjected to the first moisture change after long-term moisture conditioning than immediately after desorption or adsorption. This result indicates a kind of memory effect immediately after moisture change. During desorption processes, greater creep occurred immediately after slow adsorption than immediately after rapid adsorption. In the course of adsorption, the reverse was observed: the creep was greater immediately after rapid desorption than immediately after slow desorption. Accordingly, greater instability immediately after a change in moisture does not always cause greater creep during the next moisture change. The size of the moisture change and the load level affect the recovery of creep during adsorption processes.
The Relationship of Transforming Growth Factor‐β1 Gene Polymorphism, Its Plasma Level, and Gingival Overgrowth in Renal Transplant Recipients Receiving Different Immunosuppressive Regimens
Authors: Radwan‐Oczko Małgorzata , Boratyńska Maria , Ziętek Marek , Zołędziewska Magdalena , Jonkisz Anna 
Published: May 2006

Background: Cyclosporin A (CsA) induces gingival overgrowth (GO) in patients who seem to be prone to this disorder. It is still impossible to determine which patients will develop GO. Patients treated with the new immunosuppressive drug tacrolimus seem not to have GO. The aims of this study were to investigate transforming growth factor‐β1 (TGF‐β1) gene polymorphisms in renal transplant recipients treated with CsA or tacrolimus and to establish an association between these polymorphisms and TGF‐β1 plasma concentration and the incidence of GO.Methods: The examined group consisted of 134 renal transplant recipients. Ninety‐two underwent CsA treatment (50 with and 42 without GO), and 42 underwent tacrolimus treatment. Age, gender, time after transplantation, calcineurin inhibitor total dosage, number of teeth, and sulcus bleeding index were analyzed. TGF‐β1 plasma levels were estimated in 60 CsA‐ and 30 tacrolimus‐treated patients. Two biallelic polymorphisms of the TGF‐β1 gene were studied at codon 10 (at position +869) and at codon 25 (at position +915) in patients from the examined group and in 108 healthy volunteers (the control group).Results: The distribution of the high, intermediate, and low TGF‐β1 producer phenotypes was comparable in all the studied groups and in the healthy controls. The high producer phenotype was more frequent in patients with GO. TGF‐β1 levels in the CsA group showed correlation with the phenotypes. The lowest incidence of GO was observed in the 10C/C genotype, whereas the highest was observed in the 10T/C genotype.Conclusion: High and intermediate TGF‐β1 producer phenotypes and heterozygous genotype 10T/C might be considered risk factors for GO in patients treated with CsA.