bluuebunny/crossref_metadata_2025_split huggingface dataset:
Germination responses of Reaumuria vermiculata to salinity and temperature
Authors: Gorai M. , Neffati M. 
Published: June 2007

Abstract Reaumuria vermiculata is a xerohalophytic perennial dwarf shrub distributed in many gypseous and saline areas in southern Tunisia. A laboratory experiment was carried out to assess the effects of temperature and salinity on germination. The germination responses of the seeds in darkness were determined under a range of salinity and temperature regimes. Temperatures between 10°C and 30°C seem to be favourable for the germination of this species. Germination was inhibited by either an increase or a decrease in temperature from the optimal temperature (15°C). Highest germination percentages were obtained under non‐saline conditions and increases in salinity inhibited seed germination. Salt stress decreased both the germination percentage and the germination speed (increase of the mean time to germinate). Seed germination decreased with an increase in NaCl concentrations at all temperatures. An interaction between salinity and temperature yielded no germination at salinity of 300 mM, whereas some seeds germinated under the optimal temperature.
Determining the specific DNA sequences of the Gastrodia tuber and their potential importance
Authors: Tao J. , Luo Z.‐Y. , Liu S.‐P. , Tang Y.‐H. , Shu X.‐S. , Wen L. , Luo S.‐Q. , Wang Z.‐C. , Hu W.‐X. 
Published: June 2007

AbstractThe Gastrodia tuber, as well as the gastrodine extract derived from it, has been found to have many pharmacological effects. The gastrodine content of different tuber populations was determined, and their genomic DNA fingerprints were investigated. Through recovery, cloning, sequencing and bioinformatics analyses of DNA fragments, five DNA sequences were proved to be new discoveries. Using the PCR technique, we further studied the distribution of the sequences in eight Gastrodia populations, as well as their correlation with gastrodine content. The distribution of the five DNA sequences varied greatly among the populations. DNA sequences 1 and 5 were found in all the populations studied and determined to be specific DNA molecular markers that differentiate Gastrodia from other species. DNA sequence 2 was found only in the populations showing the highest gastrodine content. Hence, these sequences can be applied to identify genuine Gastrodia tubers and to optimise the selection of better populations.
Architecture and Climate: The Environmental Continuum
Authors: Pearlmutter David 
Published: June 2007

AbstractArchitecture and climate have always been linked in a pattern of mutual influence. In its role as a provider of shelter, architecture intentionally modifies the climate of an immediate area – and traditionally, its design has been shaped by the stresses and opportunities inherent in the regional climate. In modern times, this cycle of influence has been obscured, because technology and cheap fuel have allowed architects the option of ignoring climatic cues. In the process, buildings and cities have produced unintentional modifications to climate at different scales, from the local to the global. In tandem with these trends, efforts have been made to better understand the dynamic interactions between the built and natural environments, and to pursue paths for bringing them into balance. This essay traces some of the milestones in these cross‐disciplinary efforts, and examines the directions in which leading‐edge research is headed. Finally, some thoughts are offered on sustainable architecture in an age of dwindling resources and questionable climatic stability.
Rethinking Economic Geographies of Knowledge
Authors: Vallance Paul 
Published: June 2007

AbstractThis article reviews recent research on knowledge and learning in economic geography that moves away from established regional development approaches. This conventional position is briefly outlined, focusing on the fixity of tacit knowledge in local inter‐firm relations and institutions, within settings such as clusters and learning regions. The literature that I focus on here explores a range of alternative ways to conceptualise learning processes and the movement of knowledge in the global economy. In this article, I identify and discuss two cross‐theoretical themes within this literature. The first theme examines the diversity of learning processes in different types of organisational and spatial setting. The second theme considers the circulation of mobile forms of knowledge across geographical space. Together these trends suggest the emergence of multiple economic geographies of knowledge.
Methods for Generating Longitudinally Correlated Binary Data
Authors: Farrell Patrick J. , Rogers‐Stewart Katrina 
Published: June 2007

Summary The analysis of longitudinally correlated binary data has attracted considerable attention of late. Since the estimation of parameters in models for such data is based on asymptotic theory, it is necessary to investigate the small‐sample properties of estimators by simulation. In this paper, we review the mechanisms that have been proposed for generating longitudinally correlated binary data. We compare and contrast these models with regard to various features, including computational efficiency, flexibility and the range restrictions that they impose on the longitudinal association parameters. Some extensions to the data generation mechanism originally suggested by Kanter (1975) are proposed.
Development and Preliminary Evaluation of a Loop-Mediated Isothermal Amplification Procedure for Sensitive Detection of
Cryptosporidium
Oocysts in Fecal and Water Samples
Authors: Karanis Panagiotis , Thekisoe Oriel , Kiouptsi Klytaimnistra , Ongerth Jerry , Igarashi Ikuo , Inoue Noborou 
Published: July 2007

ABSTRACT

A loop-mediated isothermal amplification (LAMP) procedure for the detection of
Cryptosporidium
in environmental and fecal samples was developed and evaluated. This is the first demonstration of LAMP applied to detection of
Cryptosporidium
. Due to its specificity and simplicity, the method could become a useful diagnostic tool for epidemiologic studies of
Cryptosporidium
presence.
Detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
Infections in North American Women by Testing SurePath Liquid-Based Pap Specimens in APTIMA Assays
Authors: Chernesky Max , Freund Gregory G. , Hook Edward , Leone Peter , D'Ascoli Peter , Martens Mark 
Published: June 2007

ABSTRACT

The APTIMA COMBO 2 assay, which detects and amplifies rRNA from
Chlamydia trachomatis
and/or
Neisseria gonorrhoeae
, is approved for use on ThinPrep liquid-based Pap test specimens. The objective was to determine the clinical utility of the APTIMA assays (APTIMA COMBO 2 assay, APTIMA CT assay for
Chlamydia trachomatis
, and APTIMA GC assay for
Neisseria gonorrhoeae
) for screening women during their annual Pap exam, using SurePath liquid-based Pap test specimens. Two cervical samples were collected from 1,615 females attending six clinical sites in North America. A cervical broom sample was processed for cytology, with the residuum aliquoted into an APTIMA specimen transfer kit tube. The second cervical swab sample was put into APTIMA specimen transport medium, and both samples were tested with each APTIMA assay on a direct sampling system. Using a subject-infected status that utilized cervical-swab specimen results from two APTIMA assays, the prevalence was 7.9% for
Chlamydia trachomatis
and 2.5% for
N. gonorrhoeae
. For the liquid-based Pap samples, the sensitivities, specificities, positive predictive values, and negative predictive values for
Chlamydia trachomatis
detection were 85.2%, 99.5%, 93.2%, and 98.7%, respectively, for the APTIMA COMBO 2 assay and 89.1%, 98.7%, 85.7%, and 99.1%, respectively, for the APTIMA CT assay. For
N. gonorrhoeae
detection, the values were 92.5%, 100%, 100%, and 99.8%, respectively, for the APTIMA COMBO 2 assay and 92.5%, 99.9%, 97.4%, and 99.8%, respectively, for the APTIMA GC assay. The high predictive values support the use of the assays with SurePath liquid-based Pap specimens processed with the APTIMA specimen transfer kit.
Evaluation of Methods To Identify the
Klebsiella pneumoniae
Carbapenemase in
Enterobacteriaceae
Authors: Anderson K. F. , Lonsway D. R. , Rasheed J. K. , Biddle J. , Jensen B. , McDougal L. K. , Carey R. B. , Thompson A. , Stocker S. , Limbago B. , Patel J. B. 
Published: June 2007

ABSTRACT

The
Klebsiella pneumoniae
carbapenem (KPC) β-lactamase occurs in
Enterobacteriaceae
and can confer resistance to all β-lactam agents including carbapenems. The enzyme may confer low-level carbapenem resistance, and the failure of susceptibility methods to identify this resistance has been reported. Automated and nonautomated methods for carbapenem susceptibility were evaluated for identification of KPC-mediated resistance. Ertapenem was a more sensitive indicator of KPC resistance than meropenem and imipenem independently of the method used. Carbapenemase production could be confirmed with the modified Hodge test.
Relevance of Routine Use of the Anaerobic Blood Culture Bottle
Authors: Grohs Patrick , Mainardi Jean-Luc , Podglajen Isabelle , Hanras Xavier , Eckert C. , Buu-Hoï A. , Varon E. , Gutmann Laurent 
Published: June 2007

ABSTRACT

Using the BacT/Alert automated system, we conducted a 1-year retrospective study on blood cultures, focusing on the relevance of routine use of the anaerobic bottle. The rate of patients with positive blood cultures was 19.7%. Among these, 13.5% had a positive anaerobic bottle in the absence of any aerobic bottle, and 2/3 of these grew with nonobligate anaerobes. These patients were hospitalized in 20 out of 26 wards of the hospital group. For 65.4% of the monomicrobial-positive blood cultures growing
Enterobacteriaceae
, the anaerobic bottle detected growth earlier than the corresponding aerobic bottle. These data suggest that, in our institution, the use of an anaerobic bottle is still relevant.
The Emergence and Importation of Diverse Genotypes of Methicillin-Resistant
Staphylococcus aureus
(MRSA) Harboring the Panton-Valentine Leukocidin Gene (
pvl
) Reveal that
pvl
Is a Poor Marker for Community-Acquired MRSA Strains in Ireland
Authors: Rossney Angela S. , Shore Anna C. , Morgan Pamela M. , Fitzgibbon Margaret M. , O'Connell Brian , Coleman David C. 
Published: June 2007

ABSTRACT

Community-acquired methicillin-resistant
Staphylococcus aureus
(CA-MRSA) carrying
pvl
is an emerging problem worldwide. CA-MRSA tends to harbor staphylococcal cassette chromosome
mec
type IV (SCC
mec
IV), to be non-multiantibiotic resistant, and to have different genotypes from the local hospital-acquired MRSA (HA-MRSA). However, in Ireland, 80% of HA-MRSA isolates have the non-multiantibiotic-resistant genotype ST22-MRSA-IV. This study investigated MRSA isolates from Ireland (CA-MRSA, health care-associated MRSA, and HA-MRSA) for the carriage of
pvl
and determined the genotypic characteristics of all
pvl
-positive isolates identified. All 1,389 MRSA isolates were investigated by antibiogram-resistogram typing and SmaI DNA macrorestriction analysis.
pvl
-positive isolates were further characterized by multilocus sequence typing and SCC
mec
,
agr
, and toxin gene typing. Twenty-five (1.8%) MRSA isolates belonging to six genotypes (ST30, ST8, ST22, ST80, ST5, and ST154) harbored
pvl
. Nineteen of these (76%) were CA-MRSA isolates, but a prospective study of MRSA isolates from 401 patients showed that only 6.7% (2/30) of patients with CA-MRSA yielded
pvl
-positive isolates. Thus,
pvl
cannot be used as a sole marker for CA-MRSA. Fifty-two percent of
pvl
-positive MRSA isolates were recovered from patients with skin and soft tissue infections; thirty-six percent were from patients of non-Irish ethnic origin, reflecting the increasing heterogeneity of the Irish population due to immigration. All 25
pvl
-positive isolates carried SCC
mec
IV; 14 (56%) harbored SCC
mec
IV.1 or IV.3, and the remaining 11 isolates could not be subtyped. This study demonstrates that
pvl
is not a reliable marker for CA-MRSA in Ireland and reveals the emergence and importation of diverse genotypes of
pvl
-positive MRSA in Ireland.
Changes in Karyotype and Azole Susceptibility of Sequential Bloodstream Isolates from Patients with
Candida glabrata
Candidemia
Authors: Shin Jong Hee , Chae Myung Jong , Song Jeong Won , Jung Sook-In , Cho Duck , Kee Seung Jung , Kim Soo Hyun , Shin Myung Geun , Suh Soon Pal , Ryang Dong Wook 
Published: June 2007

ABSTRACT

We examined the changes in genotypes and azole susceptibilities among sequential bloodstream isolates of
Candida glabrata
during the course of fungemia and the relationship of these changes to antifungal therapy. Forty-one isolates were obtained from 15 patients (9 patients who received antifungal therapy and 6 patients who did not) over periods of up to 36 days. The isolates were analyzed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) and tested for antifungal susceptibility to fluconazole, itraconazole, and voriconazole. PFGE typing consisted of electrophoretic karyotyping and restriction endonuclease analysis of genomic DNA by use of NotI (REAG-N). The 41 isolates yielded 23 different karyotypes and 11 different REAG-N patterns but only 3 MLST types. The sequential strains from each patient had identical or similar REAG-N patterns. However, they had two or three different karyotypes in 6 (40%) of 15 patients. The isolates from these six patients exhibited the same or similar azole susceptibilities, and five patients did not receive antifungal therapy. Development of acquired azole resistance in sequential isolates was detected for only one patient. For this patient, an isolate of the same genotype obtained after azole therapy showed three- or fourfold increases in the MICs of all three azole antifungals and exhibited increased expression of the
CgCDR1
efflux pump. This study shows that karyotypic changes can develop rapidly among sequential bloodstream strains of
C. glabrata
from the same patient without antifungal therapy. In addition, we confirmed that
C. glabrata
could acquire azole resistance during the course of fungemia in association with azole therapy.
Evaluation of Gen-Probe APTIMA-Based
Neisseria gonorrhoeae
and
Chlamydia trachomatis
Confirmatory Testing in a Metropolitan Setting of High Disease Prevalence
Authors: Munson Erik , Boyd Vivian , Czarnecka Jolanta , Griep Judy , Lund Brian , Schaal Nancy , Hryciuk Jeanne E. 
Published: June 2007

ABSTRACT

Prompted by reports challenging the validity of the low-positive
Neisseria gonorrhoeae
and
Chlamydia trachomatis
results generated by the APTIMA Combo 2 assay (Gen-Probe, Incorporated) and by a Centers for Disease Control and Prevention recommendation to confirm
N. gonorrhoeae
- or
C. trachomatis
-positive screens by using an alternative amplification target, we report on a comparison of this means of confirmation with an in-house algorithm of repeat testing. Primary clinical specimens yielding
N. gonorrhoeae
- or
C. trachomatis
-specific luminescent values between 100,000 and 1,000,000 were repeat tested in duplicate. A subset of specimens was forwarded for confirmatory assays (Gen-Probe) individualized for alternative
N. gonorrhoeae
or
C. trachomatis
targets. An 18-month audit revealed that 230 of 29,977
C. trachomatis
screens (0.8%) and 41 of 29,064
N. gonorrhoeae
assays (0.1%) yielded low-positive data. When a subset of 40 low-positive
N. gonorrhoeae
screens was repeat tested, 20 (50.0%) remained positive; 22 (55.0%) of the screens remained positive following performance of the confirmatory assay. In contrast, repeat testing of 153 low-positive
C. trachomatis
screens yielded a positive result for fewer specimens (
n
= 97; 63.4%) than when commercial confirmatory testing was used (
n
= 124; 81.0%). However, confirmation of the results for additional
C. trachomatis
screens by use of an alternative target did not translate into significant differences in the calculated overall
C. trachomatis
-positive screen rates (7.39% by repeat testing versus 7.52% by the confirmatory assay;
P
= 0.53). Furthermore, use of the confirmatory assay raised the positive predictive value only 1.8% over that of repeat testing. Molecular confirmatory testing did not significantly enhance the reliability of
C. trachomatis
- or
N. gonorrhoeae
-specific nucleic acid amplification testing in this metropolitan setting compared to the reliability of repeat testing.
Development of a Sensitive and Specific Multiplex PCR Method Combined with DNA Microarray Primer Extension To Detect Betapapillomavirus Types
Authors: Gheit Tarik , Billoud Gaëlle , de Koning Maurits N. C. , Gemignani Federica , Forslund Ola , Sylla Bakary S. , Vaccarella Salvatore , Franceschi Silvia , Landi Stefano , Quint Wim G. V. , Canzian Federico , Tommasino Massimo 
Published: June 2007

ABSTRACT

Emerging lines of evidence indicate that the cutaneous human papillomavirus (HPV) types that belong to the genus
Betapapillomavirus
(beta HPV) are involved in the development of nonmelanoma skin cancer. Unlike the situation for mucosal HPV types, highly sensitive and reliable methods to identify characterized cutaneous HPV types in a single assay are limited. Here, we describe a novel one-shot method for the detection of all characterized beta HPV types, namely, HPV type 5 (HPV5), 8, 9, 12, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 47, 49, 75, 76, 80, 92, 93, and 96. This assay combines two different techniques: multiplex PCR using HPV type-specific primers for amplification of each E7 gene and array primer extension (APEX) for typing. This method has been validated using clinical samples which were analyzed simultaneously for the presence of cutaneous HPV types by two additional methods, i.e., the FAP59/64 PCR protocol and a commercially available PCR-reverse hybridization assay (PM-PCR RHA). Our data show good agreement between the results obtained with the multiplex PCR/APEX assay and the PM-PCR RHA method (overall HPV positivity of 92.2% for multiplex PCR/APEX assay versus 90.6% with the PM-PCR RHA) (kappa value, 50; 95% confidence interval, 13 to 88). In addition, the multiplex PCR/APEX assay showed higher sensitivity than the PM-PCR RHA did. This favorable feature and the high-throughput potential make this assay ideal for large-scale clinical and epidemiological studies aimed at determining the spectrum of cutaneous types in skin cancer.
Characterization of a Catalase-Negative Methicillin-Resistant
Staphylococcus aureus
Strain
Authors: Grüner B. M. , Han S.-R. , Meyer H.-G. , Wulf U. , Bhakdi S. , Siegel E. K. 
Published: June 2007

ABSTRACT

We describe an unusual clinical strain of catalase-negative methicillin-resistant
Staphylococcus aureus
sensu stricto. Sequence analysis of its catalase gene showed 99.60% identities to the catalase genes of the reference strains. A 5-base deletion, however, led to a shift of the nucleotide reading frame and a loss of the enzymatic activity.
Nosocomial Outbreak Due to Extended-Spectrum-Beta-Lactamase- Producing
Enterobacter cloacae
in a Cardiothoracic Intensive Care Unit
Authors: Manzur Adriana , Tubau Fe , Pujol Miquel , Calatayud Laura , Dominguez Maria Angeles , Peña Carmen , Sora Mercedes , Gudiol Francesc , Ariza Javier 
Published: June 2007

ABSTRACT

Enterobacter cloacae
has been associated with several outbreaks, usually involving strains that overproduce chromosomal β-lactamase or, uncommonly, strains expressing extended-spectrum β-lactamases (ESBL). Only sporadic cases of ESBL-producing
E. cloacae
have been identified in our hospital in recent years. We describe the epidemiology and clinical and microbiological characteristics of an outbreak caused by ESBL-producing
E. cloacae
in a cardiothoracic intensive care unit (CT-ICU). Prospective surveillance of patients with infection or colonization by ESBL-producing
E. cloacae
among patients admitted to the CT-ICU was performed during the outbreak. Production of ESBL was determined by decreased susceptibility to expanded-spectrum cephalosporins and a positive double-disk test result. Clone relatedness was determined by pulsed-field gel electrophoresis (PFGE). From July to September 2005, seven patients in the CT-ICU with ESBL-producing
E. cloacae
were identified (four males; median age, 73 years; range, 45 to 76 years); six patients had cardiac surgery. Four patients developed infections; three had primary bacteremia, one had ventilator-associated pneumonia, and one had tracheobronchitis. ESBL-producing
E. cloacae
showed resistance to quinolones and aminoglycosides. PFGE revealed two patterns. Five isolates belonged to clone A; two carried a single ESBL (pI 8.2 and a positive PCR result for the SHV type), and three carried two ESBLs (pIs 8.1 and 8.2 and positive PCR results for the SHV and CTX-M-9 types). Isolates belonging to clone B carried a single ESBL (pI 5.4 and a positive PCR result for the TEM type). Review of antibiotic consumption showed increased use of cefepime and quinolones during June and July 2005. The outbreak was stopped by the implementation of barrier measures and cephalosporin restriction. ESBL production could be increasingly common in nosocomial pathogens other than
Escherichia coli
or
Klebsiella pneumoniae
.
A Membrane Leucine Heptad Contributes to Trafficking, Signaling, and Transformation by Latent Membrane Protein 1
Authors: Lee Jisook , Sugden Bill 
Published: June 2007

ABSTRACT
Latent membrane protein 1 (LMP1) of Epstein Barr virus (EBV) is important for maintaining proliferation of EBV-infected B cells. LMP1, unlike its cellular counterpart, CD40, signals without a ligand and is largely internal to the plasma membrane. In order to understand how LMP1 initiates its ligand-independent signaling, we focused on a leucine heptad in LMP1's first membrane-spanning domain that was shown to be necessary for LMP1's signaling through NF-κB. LZ1EBV, a recombinant EBV genetically altered to express LZ1, a derivative of LMP1 in which a leucine heptad was replaced with alanines, transformed B cells with 56% of wild-type (wt) EBV's efficiency, demonstrating the importance of this heptad. To elucidate the mechanism by which this domain contributes to the functions of LMP1, the properties of the wt and LZ1 were compared in transfected cells. LZ1 failed to home to lipid rafts as efficiently as did wt LMP1. The distribution of tagged derivatives of LZ1 also differed from that of wt LMP1 in transfected cells. LZ1's defect in homing to lipid rafts and altered trafficking likely underlie the defect in transformation of LZ1EBV. While the third and fourth membrane-spanning domains of LMP1 foster its trafficking to the Golgi, the leucine heptad within the first membrane-spanning domain contributes to its trafficking, particularly to internal rafts. B cells that are successfully transformed by LZ1EBV have the same average number of viral genomes and the same fraction of cells with capped LZ1 at the cell surface but express 50% more of the LZ1 allele than wt infected cells.