bluuebunny/crossref_metadata_2025_split huggingface dataset:
Site-Specific Contributions of Glutamine-Dependent Regulator GlnR and GlnR-Regulated Genes to Virulence of
Streptococcus pneumoniae
Authors: Hendriksen Wouter T. , Kloosterman Tomas G. , Bootsma Hester J. , Estevão Silvia , de Groot Ronald , Kuipers Oscar P. , Hermans Peter W. M. 
Published: January 2008

ABSTRACT

The transcriptional regulator GlnR of
Streptococcus pneumoniae
is involved in the regulation of glutamine and glutamate metabolism, controlling the expression of the
glnRA
and
glnPQ
-
zwf
operons, as well as the
gdhA
gene. To assess the contribution of the GlnR regulon to virulence, D39 wild-type and mutant strains lacking genes of this regulon were tested in an in vitro adherence assay and murine infection models. All of the mutants, except the Δ
glnR
mutant, were attenuated in adherence to human pharyngeal epithelial Detroit 562 cells, suggesting a contribution of these genes to adherence during the colonization of humans. During murine colonization, only the Δ
glnA
mutant and the
glnP
-
glnA
double mutant (Δ
glnAP
) were attenuated, in contrast to Δ
glnP
, indicating that the effect is caused by the lack of GlnA expression. In our pneumonia model, only Δ
glnP
and Δ
glnAP
showed a significantly reduced number of bacteria in the lungs and blood, indicating that GlnP is required for survival in the lungs and possibly for dissemination to the blood. In intravenously infected mice,
glnP
and
glnA
were individually dispensable for survival in the blood whereas the Δ
glnAP
mutant was avirulent. Finally, transcriptome analysis of the Δ
glnAP
mutant showed that many genes involved in amino acid metabolism were upregulated. This signifies the importance of glutamine/glutamate uptake and synthesis for full bacterial fitness and virulence. In conclusion, several genes of the GlnR regulon are required at different sites during pathogenesis, with
glnA
contributing to colonization and survival in the blood and
glnP
important for survival in the lungs and, possibly, efficient transition from the lungs to the blood.
Repression ofhlabyrotIs Dependent onsaeinStaphylococcus aureus
Authors: Li Dongmei , Cheung Ambrose 
Published: January 2008

ABSTRACTThe regulatory locussaeis a two-component system inStaphylococcus aureusthat regulates many important virulence factors, including alpha-toxin (encoded byhla) at the transcriptional level. The SarA homologs Rot and SarT were previously shown to be repressors ofhlain selectedS. aureusbackgrounds. To delineate the interaction ofrotandsaeand the contribution ofsarTtohlaexpression, an assortment ofrotandsaeisogenic single mutants, arot saedouble mutant, and arot sae sarTmarkerless triple mutant were constructed from wild-type strain COL. Using Northern blot analysis and transcriptional reporter gene green fluorescent protein, fusion, and phenotypic assays, we found that the repression ofhlabyrotis dependent onsae. Arot sae sarTtriple mutant was not able to rescue thehladefect of therot saedouble mutant. Among the threesaepromoters, the distalsaeP3 promoter is the strongest in vitro. Interestingly, thesaeP3 promoter activities correlate withhlaexpression inrot,rot sae, androt sae sarTmutants of COL. Transcriptional study has also shown thatrotrepressedsae, especially at thesaeP3 promoter. Collectively, our data implicated the importance ofsaein therot-mediated repression ofhlainS. aureus.
Clinical and Microbiological Aspects of Linezolid Resistance Mediated by the
cfr
Gene Encoding a 23S rRNA Methyltransferase
Authors: Arias Cesar A. , Vallejo Martha , Reyes Jinnethe , Panesso Diana , Moreno Jaime , Castañeda Elizabeth , Villegas Maria V. , Murray Barbara E. , Quinn John P. 
Published: January 2008

ABSTRACT

The
cfr
(chloramphenicol-florfenicol resistance) gene encodes a 23S rRNA methyltransferase that confers resistance to linezolid. Detection of linezolid resistance was evaluated in the first
cfr
-carrying human hospital isolate of linezolid and methicillin-resistant
Staphylococcus aureus
(designated MRSA CM-05) by dilution and diffusion methods (including Etest). The presence of
cfr
was investigated in isolates of staphylococci colonizing the patient's household contacts and clinical isolates recovered from patients in the same unit where MRSA CM-05 was isolated. Additionally, 68 chloramphenicol-resistant Colombian MRSA isolates recovered from hospitals between 2001 and 2004 were screened for the presence of the
cfr
gene. In addition to
erm
(B), the
erm
(A) gene was also detected in CM-05. The isolate belonged to sequence type 5 and carried staphylococcal chromosomal cassette
mec
type I. We were unable to detect the
cfr
gene in any of the human staphylococci screened (either clinical or colonizing isolates). Agar and broth dilution methods detected linezolid resistance in CM-05. However, the Etest and disk diffusion methods failed to detect resistance after 24 h of incubation. Oxazolidinone resistance mediated by the
cfr
gene is rare, and acquisition by a human isolate appears to be a recent event in Colombia. The detection of
cfr
-mediated linezolid resistance might be compromised by the use of the disk diffusion or Etest method.
Molecular Characterization of
Mycobacterium massiliense
and
Mycobacterium bolletii
in Isolates Collected from Outbreaks of Infections after Laparoscopic Surgeries and Cosmetic Procedures
Authors: Viana-Niero Cristina , Lima Karla Valéria Batista , Lopes Maria Luiza , da Silva Rabello Michelle Christiane , Marsola Lourival Rodrigues , Brilhante Vânia Cristina Ribeiro , Durham Alan Mitchel , Leão Sylvia Cardoso 
Published: January 2008

ABSTRACT

An outbreak of infections affecting 311 patients who had undergone different invasive procedures occurred in 2004 and 2005 in the city of Belém, in the northern region of Brazil. Sixty-seven isolates were studied; 58 were from patients who had undergone laparoscopic surgeries, 1 was from a patient with a postinjection abscess, and 8 were from patients who had undergone mesotherapy. All isolates were rapidly growing nonpigmented mycobacteria and presented a pattern by PCR-restriction enzyme analysis of the
hsp65
gene with BstEII of bands of 235 and 210 bp and with HaeIII of bands of 200, 70, 60, and 50 bp, which is common to
Mycobacterium abscessus
type 2,
Mycobacterium bolletii
, and
Mycobacterium massiliense
.
hsp65
and
rpoB
gene sequencing of a subset of 20 isolates was used to discriminate between these three species.
hsp65
and
rpoB
sequences chosen at random from 11 of the 58 isolates from surgical patients and the postinjection abscess isolate presented the highest degrees of similarity with the corresponding sequences of
M. massiliense.
In the same way, the eight mesotherapy isolates were identified as
M. bolletii
. Molecular typing by pulsed-field gel electrophoresis (PFGE) grouped all 58 surgical isolates, while the mesotherapy isolates presented three different PFGE patterns and the postinjection abscess isolate showed a unique PFGE pattern. In conclusion, molecular techniques for identification and typing were essential for the discrimination of two concomitant outbreaks and one case, the postinjection abscess, not related to either outbreak, all of which were originally attributed to a single strain of
M. abscessus
.
Genetic Classification and Distinguishing of
Staphylococcus
Species Based on Different Partial
gap
, 16S rRNA,
hsp60
,
rpoB
,
sodA
, and
tuf
Gene Sequences
Authors: Ghebremedhin B. , Layer F. , König W. , König B. 
Published: January 2008

ABSTRACT

The analysis of 16S rRNA gene sequences has been the technique generally used to study the evolution and taxonomy of staphylococci. However, the results of this method do not correspond to the results of polyphasic taxonomy, and the related species cannot always be distinguished from each other. Thus, new phylogenetic markers for
Staphylococcus
spp. are needed. We partially sequenced the
gap
gene (∼931 bp), which encodes the glyceraldehyde-3-phosphate dehydrogenase, for 27
Staphylococcus
species. The partial sequences had 24.3 to 96% interspecies homology and were useful in the identification of staphylococcal species (F. Layer, B. Ghebremedhin, W. König, and B. König, J. Microbiol. Methods 70:542-549, 2007). The DNA sequence similarities of the partial staphylococcal
gap
sequences were found to be lower than those of 16S rRNA (∼97%),
rpoB
(∼86%),
hsp60
(∼82%), and
sodA
(∼78%). Phylogenetically derived trees revealed four statistically supported groups:
S. hyicus
/
S. intermedius
,
S. sciuri
,
S. haemolyticus
/
S. simulans
, and
S. aureus
/
epidermidis
. The branching of
S. auricularis
,
S. cohnii
subsp.
cohnii
, and the heterogeneous
S. saprophyticus
group, comprising
S. saprophyticus
subsp.
saprophyticus
and
S. equorum
subsp.
equorum
, was not reliable. Thus, the phylogenetic analysis based on the
gap
gene sequences revealed similarities between the dendrograms based on other gene sequences (e.g., the
S. hyicus
/
S. intermedius
and
S. sciuri
groups) as well as differences, e.g., the grouping of
S. arlettae
and
S. kloosii
in the
gap
-based tree. From our results, we propose the partial sequencing of the
gap
gene as an alternative molecular tool for the taxonomical analysis of
Staphylococcus
species and for decreasing the possibility of misidentification.
Reactivity: an issue for short-term pedometer studies?: Figure 1
Authors: Clemes S A , Matchett N , Wane S L 
Published: January 2008

Objectives:To investigate the influence of wearing a pedometer and recording daily step counts on ambulatory activity.Methods:During the first visit to the laboratory, 50 healthy volunteers, blinded to the study aim, were provided with a sealed pedometer (New-Lifestyles NL-2000) and informed that it was a “body posture monitor” (sealed condition). Participants wore the pedometer throughout waking hours for one week. Upon returning to the laboratory step counts were downloaded and participants were informed that the device was actually a pedometer. They were requested to wear it unsealed for a second one-week period, and to record their step counts in an activity log (unsealed condition).Results:Mean (SD) daily step counts reported in the sealed condition (9541 (3186) steps/day) were significantly lower than step counts reported in the unsealed condition (11385 (3763) steps/day) (p<0.001).Conclusions:Step counts increased significantly in the unsealed condition. Possible mechanisms for this include the knowledge of wearing a pedometer, the visible step count display and the completion of the activity log. This has validity implications for short-term studies (duration ⩽1 week) investigating habitual pedometer-determined activity levels.
Multiple Oscillatory Modes of the Argentine Basin. Part I: Statistical Analysis
Authors: Weijer Wilbert , Vivier Frédéric , Gille Sarah T. , Dijkstra Henk A. 
Published: January 2008

Abstract
Observations of the sea surface height in the Argentine Basin indicate that strong variability occurs on a time scale of 20−30 days. The aim of this study is to determine the physical processes responsible for this variability. First, results are presented from two statistical techniques applied to a decade of altimetric data. A complex empirical orthogonal function (CEOF) analysis identifies the recently discovered dipole mode as the dominant mode of variability. A principal oscillation pattern (POP) analysis confirms the existence of this mode, which has a period of 25 days. The second CEOF displays a propagating pattern in the northern Argentine Basin, plus a rotating dipole in the southwest corner. The POP analysis identifies both patterns as individual modes, with periods of 30 and 20 days, respectively. Second, the barotropic normal modes of the Argentine Basin are studied, using a shallow-water model capturing the full bathymetry of the basin. Coherences between the spatial patterns of these modes and altimeter data suggest that several of the basin modes are involved in the observed variability. This analysis implies that the 20-day mode detected by recent bottom-pressure measurements is a true barotropic mode. However, the 25-day variability, as found in altimeter data, cannot be directly attributed to the excitation of a free Rossby basin mode. This study indicates that the results of several apparently conflicting observations of the flow variability in the Argentine Basin can be reconciled by assuming that multiple basin modes are involved.
Observational Evidence of Winter Spice Injection
Authors: Yeager Stephen G. , Large William G. 
Published: January 2008

Abstract
Temperature and salinity (T–S) profiles from the global array of Argo floats support the existence of spice-formation regions in the subtropics of each ocean basin where large, destabilizing vertical salinity gradients coincide with weak stratification in winter. In these characteristic regions, convective boundary layer mixing generates a strongly density-compensated (SDC) layer at the base of the well-mixed layer. The degree of density compensation of the T–S gradients of an upper-ocean water column is quantified using a bulk vertical Turner angle (Tub) between the surface and upper pycnocline. The winter generation of the SDC layer in spice-formation zones is clearly seen in Argo data as a large-amplitude seasonal cycle of Tub in regions of the subtropical oceans characterized by high mean Tub. In formation regions, Argo floats provide ample evidence of large, abrupt spice injection (T–S increase on subducted isopycnals due to vertical mixing) associated with the winter increase in Tub. A simple conceptual model of the spice-injection mechanism is presented that is based on known behavior of convective boundary layers and supported by numerical model results. It suggests that penetrative convective mixing of a partially density-compensated water column will enhance the Turner angle within a transition layer between the mixed layer and the upper pycnocline, generating seasonal T–S increases on density surfaces below the mixed layer. Observations are consistent with this hypothesis. In OGCMs, regions showing high Tub mean and seasonal amplitude are also the sources of significant interannual spice variability in the permanent pycnocline. Decadal changes in the North Pacific of a model hindcast simulation show qualitative resemblance to the observed multiyear time series from the Hawaii Ocean Time series (HOT) station ALOHA. Modeled pycnocline variations near Hawaii can be linked to high Tub seasonality and winter spice injection within a formation region upstream of ALOHA, suggesting that spice injection may explain the origins of observed large, interannual variations on isopycnals in the ocean interior.
Optimal Surface Salinity Perturbations Influencing the Thermohaline Circulation
Authors: Sévellec Florian , Ben Jelloul Mahdi , Huck Thierry 
Published: January 2008

Abstract
Optimal surface salinity perturbations influencing the meridional overturning circulation maximum are exhibited and interpreted on a stable steady state of a 2D latitude–depth ocean thermohaline circulation model. Despite the stability of the steady state, the nonnormality of the dynamics is able to create some transient growth and variability through stimulation by optimal perturbations. Two different measures are compared to obtain the optimum—one associated with the departure from steady state in terms of density, and the other with the overturning circulation intensity. It is found that such optimal analysis is measure dependent; hence, the latter measure is chosen for studying the following physical mechanisms. The response to the optimal initial sea surface salinity perturbation involves a transient growth mechanism leading to a maximum modification of the circulation intensity after 67 yr; the amplification is linked to the most weakly damped linear eigenmode, oscillating on a 150-yr period. Optimal constant surface salinity flux perturbations are also obtained, and confirm that a decrease in the freshwater flux amplitude enhances the circulation intensity. At last, looking for the optimal stochastic surface salinity flux perturbation, it is established that the variance of the circulation intensity is controlled by the weakly damped 150-yr oscillation. Two approaches are tested to consider extending such studies in more realistic 3D models. Explicit solutions (versus eigenvalue problems) are found for the overturning circulation measure (except for the stochastic optimal); a truncation method on a few leading eigenmodes usually provides the optimal perturbations for analyses on long time scales.
Multiple Oscillatory Modes of the Argentine Basin. Part II: The Spectral Origin of Basin Modes
Authors: Weijer Wilbert , Vivier Frédéric , Gille Sarah T. , Dijkstra Henk A. 
Published: January 2008

Abstract
In this paper the spectrum of barotropic basin modes of the Argentine Basin is shown to be connected to the classical Rossby basin modes of a flat-bottom (constant depth), rectangular basin. First, the spectrum of basin modes is calculated for the Argentine Basin, by performing a normal-mode analysis of the barotropic shallow-water equations. Then a homotopy transformation is performed that gradually morphs the full-bathymetry geometry through a flat-bottom configuration into a rectangular basin. Following the eigenmodes through this transition establishes a connection between most of the basin modes and the classical Rossby basin modes of a rectangular geometry. In particular, the 20-day mode of the Argentine Basin is identified with the lowest-order mode of classical theory. Sensitivity studies show that the decay rate of each mode is controlled by bottom friction, but that it is insensitive to lateral friction; lateral friction strongly impacts the oscillation frequency. In addition, the modes are found to be only slightly sensitive to the presence of a background flow.
The Convective Storm Initiation Project
Authors: Browning Keith A. , Blyth Alan M. , Clark Peter A. , Corsmeier Ulrich , Morcrette Cyril J. , Agnew Judith L. , Ballard Sue P. , Bamber Dave , Barthlott Christian , Bennett Lindsay J. , Beswick Karl M. , Bitter Mark , Bozier Karen E. , Brooks Barbara J. , Collier Chris G. , Davies Fay , Deny Bernhard , Dixon Mark A. , Feuerle Thomas , Forbes Richard M. , Gaffard Catherine , Gray Malcolm D. , Hankers Rolf , Hewison Tim J. , Kalthoff Norbert , Khodayar Samiro , Kohler Martin , Kottmeier Christoph , Kraut Stephan , Kunz Michael , Ladd Darcy N. , Lean Humphrey W. , Lenfant Jürgen , Li Zhihong , Marsham John , McGregor James , Mobbs Stephan D. , Nicol John , Norton Emily , Parker Douglas J. , Perry Felicity , Ramatschi Markus , Ricketts Hugo M. A. , Roberts Nigel M. , Russell Andrew , Schulz Helmut , Slack Elizabeth C. , Vaughan Geraint , Waight Joe , Wareing David P. , Watson Robert J. , Webb Ann R. , Wieser Andreas 
Published: January 2008

The Convective Storm Initiation Project (CSIP) is an international project to understand precisely where, when, and how convective clouds form and develop into showers in the mainly maritime environment of southern England. A major aim of CSIP is to compare the results of the very high resolution Met Office weather forecasting model with detailed observations of the early stages of convective clouds and to use the newly gained understanding to improve the predictions of the model.
A large array of ground-based instruments plus two instrumented aircraft, from the U.K. National Centre for Atmospheric Science (NCAS) and the German Institute for Meteorology and Climate Research (IMK), Karlsruhe, were deployed in southern England, over an area centered on the meteorological radars at Chilbolton, during the summers of 2004 and 2005. In addition to a variety of ground-based remote-sensing instruments, numerous rawinsondes were released at one- to two-hourly intervals from six closely spaced sites. The Met Office weather radar network and Meteosat satellite imagery were used to provide context for the observations made by the instruments deployed during CSIP.
This article presents an overview of the CSIP field campaign and examples from CSIP of the types of convective initiation phenomena that are typical in the United Kingdom. It shows the way in which certain kinds of observational data are able to reveal these phenomena and gives an explanation of how the analyses of data from the field campaign will be used in the development of an improved very high resolution NWP model for operational use.
Detecting Depressive Disorder With a 19-Item Local Instrument in Tanzania
Authors: Kaaya Sylvia F. , Lee Bandy , Mbwambo Jessie K. , Smith-Fawzi Mary C. , Leshabari Melkizedek T. 
Published: January 2008

Background: Based on experience with the Hopkins Symptom Checklist-25 (HSCL-25) in a Tanzanian population, this study attempted to develop a locally specific screen that employs indigenous expressions. Aim and method: Thirty ethnographically derived local idioms were added and the final 47-item questionnaire administered to 787 randomly selected antenatal clinic attendees. Results: Logistic regression identified 19 items for the Dar-es-Salaam Symptom Questionnaire (DSQ), which demonstrated good internal consistency (Cronbach's α = 0.84), interrater reliability (intraclass r = 0.89), and test-retest reliability (intraclass r = 0.82). Positive endorsement overall increased only slightly, but the report of mild symptoms was more frequent with the DSQ (15.0%) than the HSCL-25 (10.8%). Content and discriminant validation of the local scale conformed to expectation, but depressed affect failed to emerge as an important feature. Conclusion: Locally derived expressions may aid in the reporting of illness and illness severity. Further studies are recommended to uncover universal aspects and culturally specific manifestations of illness expression. Declaration of interest: None to report.
Ethnicity, Gender and Mental Health: Social Worker Perspectives
Authors: Barn Ravinder 
Published: January 2008

Background: This paper draws on a two-year Department of Health research study on social worker conceptualisations of ethnicity, gender and mental health. The findings and discussion are placed within the `culturalist' and an `integrative' perspective on the mental health needs of Asian women. It is argued that the culturalist perspective has led to an overemphasis of individual and group differences in theoretical and practice debates, and by design or default has resulted in an under-emphasis of the interconnections between `race', ethnicity, gender and social class, as well as an underemphasis on the adequacy and appropriateness of existing service provision. The importance of the latter is highlighted in its integrative nature in pointing to the interconnections between race, ethnicity, gender and social class. Aims: To study professional perspectives to enhance understanding of the interconnections of ethnicity, gender, social class and mental health, to promote improved policy, provision and practice. Methods: Semi-structured interviews with social work professionals to obtain their perceptions of Bangladeshi women's mental illness, well-being, sources of stress and service provision. Results: In understanding the mental health situation of Bangladeshi women, a thematic analysis identified a multiplicity of factors including poverty, poor and overcrowded housing, racism, language, culture, religion, and gender and patriarchy. Low use of social services by Bangladeshi women, combined with fear and mistrust and lack of familiarity, raised important concerns about unmet need. Conclusions: Social worker perceptions demonstrate an understanding that suggests that the experience of ethnicity is gendered and that gender relations are ethnically distinct and impacted by social class. The paper highlights the importance of understanding patriarchy and gender relations, as well as the wider context of race and ethnicity and the interconnections between ethnicity, gender and social class.