bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Analysis Reveals
Mycoplasma pneumoniae
Repetitive Element 1-Mediated Recombination in a Clinical Isolate
Authors: Musatovova Oxana , Kannan T. R. , Baseman Joel B. 
Published: January 2008

ABSTRACT

Mycoplasmas are cell wall-less bacteria that evolved by drastic reduction of the genome size. Complete genome analysis of
Mycoplasma pneumoniae
revealed the presence of numerous copies of four distinct large
M. pneumoniae
repetitive elements (RepMPs). One copy each of RepMP2/3, RepMP4, and RepMP5 are localized within the P1 operon (MPN140 to MPN142 loci), and their involvement in sequence variation in adhesin P1 and adherence-related protein B/C has been documented. Here we analyzed a clinical strain of
M. pneumoniae
designated S1 isolated from a 1993 outbreak of respiratory infections in San Antonio, TX. Based on the type of RepMPs within the P1 operon, we classified clinical isolate S1 as type 2 with unique minor sequence variations. Hybridization with oligonucleotide arrays revealed sequence divergence in two previously unsuspected hypothetical genes (MPN137 and MPN138 loci). Closer inspection of this region revealed that the MPN137 and MPN138 loci harbored previously unrecognized unique RepMP1 sequences found only in
M. pneumoniae
. PCR and sequence analyses revealed a recombination event involving three RepMP1-containing genes that resulted in fusion of MPN137 and MPN138 reading frames and loss of all but a short fragment of another RepMP1-containing locus, MPN130. The multiple copies of unique RepMP1 elements spread throughout the chromosome could allow vast numbers of sequence variations in clinical strains. Comparisons of amino acid sequences showed the presence of leucine zipper motifs in MPN130 and MPN138 proteins in reference strain M129 and the absence of these motifs in the fused protein of S1. The presence of tandem leucine and other repeats points to possible regulatory functions of proteins encoded by RepMP1-containing genes.
Molecular Evidence of Nosocomial
Pneumocystis jirovecii
Transmission among 16 Patients after Kidney Transplantation
Authors: Schmoldt Sabine , Schuhegger Regina , Wendler Thorsten , Huber Ingrid , Söllner Heidelore , Hogardt Michael , Arbogast Helmut , Heesemann Jürgen , Bader Lutz , Sing Andreas 
Published: January 2008

ABSTRACT

In recent years, clusters of
Pneumocystis jirovecii
(formerly
Pneumocystis carinii
) pneumonia (PCP) among immunocompromised individuals have been reported. Mostly, the source of infections was suspected to be within the clinical settings when transplant recipients and PCP patients shared hospital facilities. We report on a cluster of 16 renal transplant recipients positive for
P. jirovecii
. None of them received anti-
Pneumocystis
prophylaxis prior to
P. jirovecii
detection. Epidemiological studies revealed that 15 of them had received kidney transplants at a German university hospital and attended the same inpatient and outpatient clinic from January through September 2006. Multilocus sequence typing (MLST) was performed on the following genes:
ITS1
, β-
tub, 26S
, and
mt26S. P. jirovecii
DNA was available from 14 patients and showed identical MLST types among these renal transplant recipients. Surprisingly, one patient who was treated at a different nephrological center and reported no personal contact with patients from the renal transplantation cluster harbored an identical
P. jirovecii
MLST type. Three HIV-positive patients and one bone-marrow-transplanted hematologic malignancy patient—treated at different medical centers—were used as controls, and different MLST types were revealed. Interestingly, in three of the four previously described regions, new alleles were detected, and one new polymorphism was observed in the
mt26S
region. The epidemiological data and the genotyping results strongly suggest a nosocomial patient-to-patient transmission of
P. jirovecii
as the predominant transmission route. Therefore, strict segregation and isolation of
P. jirovecii
-positive/suspected patients in clinical settings seems warranted.
E4Orf6-E1B-55k-Dependent Degradation of De Novo-Generated Adeno-Associated Virus Type 5 Rep52 and Capsid Proteins Employs a Cullin 5-Containing E3 Ligase Complex
Authors: Nayak Ramnath , Farris K. David , Pintel David J. 
Published: January 2008

ABSTRACT
Degradation of de novo-generated adeno-associated virus type 5 (AAV5) Rep52 and capsid proteins is part of the limited target specificity displayed by adenovirus type 5 E4Orf6-E1B-55k as part of a cullin 5-containing E3 ligase complex. Both Rep and capsid proteins can be found in the ligase complex, and their presence is dependent on interaction between E4Orf6 and elongins B and C. Degradation of AAV5 proteins can be inhibited by a dominant-negative ubiquitin that prevents chain elongation or by small interfering RNA directed against cullin 5.
Levels and correlates of awareness of tobacco promotional activities among adult smokers in Malaysia and Thailand: findings from the International Tobacco Control Southeast Asia (ITC-SEA) Survey
Authors: Yong H-H , Borland R , Hammond D , Sirirassamee B , Ritthiphakdee B , Awang R , Omar M , Kin F , Zain Z bt M , Lee W B , Siahpush M , Fong G T 
Published: January 2008

Aim:To examine the impact of tobacco advertising policy on adult smokers’ awareness of tobacco promotion in two developing countries—Malaysia and Thailand.Methods:Data from 2004 Malaysian and 2000 Thai adult smokers who participated in the baseline wave of the International Tobacco Control Southeast Asia survey (ITC-SEA). Respondents were asked in a face-to-face interview conducted between January and March 2005 to indicate their levels of awareness of tobacco advertising and promotional activities in the last six months.Results:Unprompted awareness of any tobacco marketing activities was very low in Thailand (20%) but significantly higher in Malaysia (53%; OR = 5.6, 95% CI: 3.5 to 8.9, p<0.001). When prompted about specific locations, Thai adult smokers reported very low recall of tobacco advertising where it was banned, being highest around point of sale, particularly street vendors (7.5%). In contrast, Malaysian adult smokers reported significantly higher levels of awareness of tobacco advertising in all locations (range = 17.7% noticing in disco lounges to 59.3% on posters) including where they are notionally banned (for example, billboards).Conclusions:These findings demonstrate that comprehensive tobacco advertising legislation when well implemented can lead to dramatic decline in awareness of tobacco promotion, thus supporting strong implementation of Article 13 of the Framework Convention on Tobacco Control.
The role of tobacco control policies in reducing smoking and deaths in a middle income nation: results from the Thailand SimSmoke simulation model
Authors: Levy D T , Benjakul S , Ross H , Ritthiphakdee B 
Published: January 2008

Objectives:With the male smoking prevalence near 60% in 1991, Thailand was one of the first Asian nations to implement strict tobacco control policies. However, the success of their efforts has not been well documented.Methods:The role of tobacco control policies are examined using the “SimSmoke” tobacco control model. We first validated the model against survey data on smoking prevalence. We then distinguished the effect of policies implemented between 1991 and 2006 from long-term trends in smoking rates. We also estimated smoking attributable deaths and lives saved as a result of the policies.Results:The model validates well against survey data. The model shows that by the year 2006, policies implemented between 1991 and 2006 had already decreased smoking prevalence by 25% compared to what it would have been in the absence of the policies. Tax increases on cigarettes and advertising bans had the largest impact, followed by media anti-smoking campaigns, clean air laws and health warnings. The model estimates that the policies saved 31 867 lives by 2006 and will have saved 319 456 lives by 2026.Conclusions:The results document the success of Thailand in reducing smoking prevalence and reducing the number of lives lost to smoking, thereby showing the potential of tobacco control policies specifically in a middle-income country. Additional improvements can be realised through higher taxes, stronger clean air policies, comprehensive cessation treatment policies, and targeted media campaigns.
Comparative study of 7 fluorescent pseudomonad clinical isolates
Authors: Chapalain A. , Rossignol G. , Lesouhaitier O. , Merieau A. , Gruffaz C. , Guerillon J. , Meyer J.-M. , Orange N. , Feuilloley M.G.J. 
Published: January 2008

There is some debate about the potential survival of Pseudomonas fluorescens at temperatures above 37 °C and its consequences for infectious potential, owing to the heterogeneity of clinical strains. Seven clinical strains growing at 37 °C or more were submitted for polyphasic identification; 2 were identified as Pseudomonas mosselii and 4 were precisely characterized as P. fluorescens bv. I or II. The binding indexes on glial cells of the strains identified as P. fluorescens bv. I and P. mosselii were compared with that of a reference psychrotrophic strain, P. fluorescens MF37 (bv. V). Clinical P. fluorescens had a similar adherence potential range than strain MF37. Conversely, the binding indexes for P. mosselii strains were 3 times greater than that for strain MF37. These data, and those obtained by comparing the cytotoxic activities of P. fluorescens clinical strains, suggest the existence of different virulence mechanisms, leading either to a low infectious form or to a microorganism with cytotoxic activity in the same range as that of P. mosselii or even Pseudomonas aeruginosa .
Generalized Nonlinear Variational Inclusions Involving "Equation missing" -Monotone Mappings in Hilbert Spaces
Authors: Cho Yeol Je , Qin Xiaolong , Shang Meijuan , Su Yongfu 
Published: January 2008

AbstractA new class of generalized nonlinear variational inclusions involving "Equation missing"-monotone mappings in the framework of Hilbert spaces is introduced and then based on the generalized resolvent operator technique associated with "Equation missing"-monotonicity, the approximation solvability of solutions using an iterative algorithm is investigated. Since "Equation missing"-monotonicity generalizes "Equation missing"-monotonicity and "Equation missing"-monotonicity, results obtained in this paper improve and extend many others.
The Sensitivity of the Isentropic Slope in a Primitive Equation Dry Model
Authors: Zurita-Gotor Pablo 
Published: January 2008

Abstract
This paper discusses the sensitivity of the isentropic slope in a primitive equation dry model forced with Newtonian cooling when the heating is varied. This is done in two different ways, changing either the radiative equilibrium baroclinicity or the diabatic time scale for the zonal-mean flow. When the radiative equilibrium baroclinicity is changed, the isentropic slope remains insensitive against changes in the forcing, in agreement with previous results. However, the isentropic slope steepens when the diabatic heating rate is accelerated for the zonal-mean flow. Changes in the ratio between the interior and the boundary diffusivities as the diabatic heating rate is varied appear to be responsible for the violation of the constant criticality constraint in this model. Theoretical arguments are used to relate the sensitivity of the isentropic slope to that of the isentropic mass flux, which also remains constant when the radiative-equilibrium baroclinicity is changed. The sensitivity of the isentropic mass flux on the heating depends on how the gross stability changes. Bulk stabilities calculated from isobaric averages and gross stabilities estimated from isentropic diagnostics are not necessarily equivalent because a significant part of the return flow occurs at potential temperatures colder than the mean surface temperature.
Predictability in Wet and Dry Convective Turbulence
Authors: Spyksma K. , Bartello P. 
Published: January 2008

Abstract
There is a growing interest in understanding the role that moisture plays in atmospheric dynamics, particularly in its effect on predictability. Current research indicates that when moisture effects are added to an atmospheric model, the error growth produced by the new moist dynamics reduces the predictability times, especially at the scales of moist convection.
The issue of moist convection’s effect on predictability is addressed herein. By performing high-resolution large-ensemble runs, it is shown that although nonprecipitating moist convection is less predictable than dry convection resulting from the same forcing, this effect can be explained by the energy injected into the system through the latent heating and cooling arising from the convective motion. This extra energy is spread evenly over most scales of the convective dynamics. When the predictability times are scaled to account for the extra kinetic energy, and the resulting earlier growth of error energy, wet and dry convection have very similar error growth characteristics.
Sensitivity tests are performed to ensure that the results from the large ensembles have converged and that they are consistent with either changing resolution, diffusion levels, initial error energy length scales, or forcing amplitude.
Resonant Response of Deep Convection to Surface Hot Spots
Authors: Robinson F. J. , Sherwood S. C. , Li Y. 
Published: January 2008

Abstract
Observations show substantial variations of the intensity of tropical and/or summertime deep convection on land that are not explained by standard measures of convective instability. One feature that distinguishes land surfaces is their heterogeneity. The possible importance of this is investigated here by calculating the response of a nonrotating atmosphere to localized, transient surface heating using both the linearized equations of motion and a cloud-resolving configuration of the Weather Research and Forecasting (WRF) numerical model with moist physics, each in 2D. Both models predict that the depth of the resulting surface heat low near storm center will be greatest for a particular horizontal scale of heating. The linear model reveals that this is a resonant scale determined by the product of the environmental buoyancy frequency, characteristic heating time scale, and thickness of the thermal boundary layer, and the resonance occurs when the aspect ratio of the applied heating matches the ratio of vertical and horizontal wavenumbers demanded by the dispersion relation for buoyancy (gravity) waves. For realistic conditions, the resonant horizontal scale is roughly 50 km. The numerical model indicates that other measures of convective intensity, such as updraft speed and storm height, are largely controlled by the depth of the heat low, despite the presence of conditional instability and the vigorous growth of moist convective plumes. Predictions here agree with reported observations of storm severity over islands of different sizes. These findings may help explain why observed geographical variations in storm intensity defy parcel theory and indicate that phenomena often attributed to parcel entrainment may instead be due largely to storm-scale dynamical constraints.
The Comprehensive Pacific Rainfall Database
Authors: Greene J. Scott , Klatt Michael , Morrissey Mark , Postawko Susan 
Published: January 2008

Abstract
This paper describes the Comprehensive Pacific Rainfall Database (PACRAIN), which contains daily and monthly precipitation records from the tropical Pacific basin. The database is a collection of observations from a variety of sources, including one, the Schools of the Pacific Rainfall Climate Experiment (SPaRCE), that is unique to PACRAIN. SPaRCE is a cooperative field project and involves schools from various Pacific island and atoll nations.
Recent enhancements to the database, including improved quality control, observation and data entry standardization, expansion of the network, increased collaboration with local meteorological directors, and enhanced high-resolution data (e.g., on hourly or minute time scales), are discussed. This paper also outlines some of the internal data and Web-based access specifics of the database. To illustrate the potential usefulness of the data, two examples of research using the PACRAIN database are provided and discussed. The first is an analysis of temporal changes in the extreme event characteristics of daily precipitation across the region. The second is an illustration of how the PACRAIN database can be used to analyze satellite-based precipitation algorithms.
The Effects of Strength Training on the Lower Extremity Biomechanics of Female Recreational Athletes during a Stop-Jump Task
Authors: Herman Daniel C. , Weinhold Paul S. , Guskiewicz Kevin M. , Garrett William E. , Yu Bing , Padua Darin A. 
Published: January 2008

Background Strength training is considered a strategy for anterior cruciate ligament injury prevention. Little is known about the contribution of strength training to knee and hip biomechanics. Hypothesis Lower extremity muscle strength training alters knee and hip biomechanics during a stop-jump task. Study Design Controlled laboratory study. Methods Knee and hip 3-dimensional kinematic and kinetic data were collected for 66 female recreational athletes (33 intervention and 33 control) while performing 3 stop-jump tasks before and after completing a 9-week strength-training program targeting the quadriceps, hamstrings, gluteus medius, and gluteus maximus (intervention) or a 9-week period of no strength training (control). Maximum voluntary isometric contraction strength data were also collected for each subject before the stop-jump tasks in each data collection session. Knee and hip joint angles as well as resultant forces and moments were calculated. Results The intervention group increased in strength ( P < .001 for all muscles). No significant differences were observed in knee and hip kinematics and kinetics between groups before and after the strength-training protocol. Conclusions Strength training alone does not alter knee and hip kinematics and kinetics in female recreational athletes. Further research is needed to determine the effect of strength training in combination with other intervention methods on lower extremity biomechanics. Clinical Relevance Strength training as a single intervention method may not be sufficient to reduce the risk of noncontact anterior cruciate ligament injury in female recreational athletes.
Npm1 is a haploinsufficient suppressor of myeloid and lymphoid malignancies in the mouse
Authors: Sportoletti Paolo , Grisendi Silvia , Majid Samia M. , Cheng Ke , Clohessy John G. , Viale Agnes , Teruya-Feldstein Julie , Pandolfi Pier Paolo 
Published: January 2008

Abstract
Nucleophosmin (NPM1) gene has been heavily implicated in cancer pathogenesis both as a putative proto-oncogene and tumor suppressor gene. NPM1 is the most frequently mutated gene in acute myeloid leukemia (AML), while deletion of 5q, where NPM1 maps, is frequent in patients with myelodysplastic syndromes (MDS). We have previously shown that mice heterozygous for Npm1 (Npm1+/−) develop a hematologic syndrome with features of human MDS. Here we analyzed Npm1+/− mutants to determine their susceptibility to cancer. Npm1+/− mice displayed a greater propensity to develop malignancies compared with Npm1+/+ mice. The Npm1+/− cohort frequently developed hematologic malignancies of both myeloid and lymphoid origin with myeloid malignancies displaying the highest incidence. Malignant cells retained the wild-type allele with normal localization and expression of Npm1 at the protein level, suggesting that complete Npm1 loss is not a prerequisite for tumorigenesis. Our results conclusively demonstrate that Npm1 acts as a haploinsufficient tumor suppressor in the hematopoietic compartment.
Antigen-induced clustering of surface CD38 and recruitment of intracellular CD38 to the immunologic synapse
Authors: Muñoz Pilar , Mittelbrunn María , de la Fuente Hortensia , Pérez-Martínez Manuel , García-Pérez Angélica , Ariza-Veguillas Adriana , Malavasi Fabio , Zubiaur Mercedes , Sánchez-Madrid Francisco , Sancho Jaime 
Published: January 2008

AbstractDuring immunologic synapse (IS) formation, human CD38 redistributes to the contact area of T cell–antigen-presenting cell (APC) conjugates in an antigen-dependent manner. Confocal microscopy showed that CD38 preferentially accumulated along the contact zone, whereas CD3-ζ redistributed toward the central zone of the IS. APC conjugates with human T cells or B cells transiently expressing CD38–green fluorescent protein revealed the presence of 2 distinct pools of CD38, one localized at the cell membrane and the other in recycling endosomes. Both pools were recruited to the T/APC contact sites and required antigen-pulsed APCs. The process appeared more efficient in T cells than in APCs. CD38 was actively recruited at the IS of T cells by means of Lck-mediated signals. Overexpression of CD38 in T cells increased the levels of antigen-induced intracellular calcium release. Opposite results were obtained by down-regulating surface CD38 expression by means of CD38 siRNA. CD38 blockade in influenza HA-specific T cells inhibited IL-2 and IFN-γ production, PKCθ phosphorylation at Thr538, and PKCθ recruitment to the IS induced by antigen-pulsed APCs. These results reveal a new role for CD38 in modulating antigen-mediated T-cell responses during IS formation.
New evidence of risk factors for community-acquired pneumonia: a population-based study
Authors: Almirall J. , Bolíbar I. , Serra-Prat M. , Roig J. , Hospital I. , Carandell E. , Agustí M. , Ayuso P. , Estela A. , Torres A. ,   the Community-Acquired Pneumonia in Catalan Countries (PACAP) Study Group
Published: January 2008

The aim of the present study was to identify risk factors for community-acquired pneumonia (CAP), with special emphasis on modifiable risk factors and those applicable to the general population.A population-based, case–control study was conducted, with a target population of 859,033 inhabitants aged >14 yrs. A total of 1,336 patients with confirmed CAP were matched to control subjects by age, sex and primary centre over 1 yr.In the univariate analysis, outstanding risk factors were passive smoking in never-smokers aged >65 yrs, heavy alcohol intake, contact with pets, households with >10 people, contact with children, interventions on the upper airways and poor dental health. Risky treatments included amiodarone,N-acetylcysteine and oral steroids. Influenza and pneumococcal vaccine, and visiting the dentist were protective factors. Multivariable analysis confirmed cigarette smoking, usual contact with children, sudden changes of temperature at work, inhalation therapy (particularly containing steroids and using plastic pear-spacers), oxygen therapy, asthma and chronic bronchitis as independent risk factors.Interventions for reducing community-acquired pneumonia should integrate health habits and lifestyle factors related to household, work and community, together with individual clinical conditions, comorbidities and oral or inhaled regular treatments. Prevention would include vaccination, dental hygiene and avoidance of upper respiratory colonisation.