bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overweight status and intrauterine exposure to gestational diabetes are associated with children's metabolic health
Authors: Chandler‐Laney P. C. , Bush N. C. , Granger W. M. , Rouse D. J. , Mancuso M. S. , Gower B. A. 
Published: December 2011

SummaryBackgroundOffspring of women with gestational diabetes (OGD) have greater risk for obesity and impaired metabolic health. Whether impaired metabolic health occurs in the absence of obesity is not clear.ObjectiveThe purpose of this study was to investigate the independent and interactive effects of intrauterine exposure to gestational diabetes and of children's current weight status on their metabolic health.MethodsChildren aged 5–10 years (n = 51) with and without intrauterine exposure to gestational diabetes (OGD vs. offspring of non‐diabetic women [CTRL]) were grouped into normal weight (body mass index [BMI] < 85th %) and overweight (BMI > 85th %) according to Centers for Disease Control growth curves. Lipid profile was obtained by fasting blood draw, insulin sensitivity (SI) and secretion by liquid meal tolerance test, and body composition by dual‐energy X‐ray absorptiometry.ResultsDespite similar average BMI percentiles among normal weight OGD versus CTRL, and overweight OGD vs. CTRL, OGD had greater total %fat and trunk fat adjusted for leg fat compared with CTRL (P < 0.05). Overweight children had lower SI (P < 0.05) and greater basal, static, and total insulin secretion independent of SI (P < 0.05). OGD was independently associated with greater static insulin secretion (P < 0.05) and the interaction between OGD and overweight was associated with greater basal insulin secretion independent of SI (P < 0.01). OGD and overweight were each associated with lower high‐density lipoprotein‐cholesterol (HDL‐C) (P < 0.05).ConclusionIntrauterine exposure to gestational diabetes was associated with greater central adiposity and insulin secretion, and lower HDL‐C, irrespective of current weight status. Future research should examine respective contributions of the intrauterine environment and of underlying genotype on children's metabolic health.
Efficient nonlinear filtering of a singularly perturbed stochastic hybrid system
Authors: Park Jun H. , Rozovskii Boris , Sowers Richard B. 
Published: December 2011

AbstractOur focus in this work is to investigate an efficient state estimation scheme for a singularly perturbed stochastic hybrid system. As stochastic hybrid systems have been used recently in diverse areas, the importance of correct and efficient estimation of such systems cannot be overemphasized. The framework of nonlinear filtering provides a suitable ground for on-line estimation. With the help of intrinsic multiscale properties of a system, we obtain an efficient estimation scheme for a stochastic hybrid system.
Fully 3D list‐mode time‐of‐flight PET image reconstruction on GPUs using CUDA
Authors: Cui Jing‐yu , Pratx Guillem , Prevrhal Sven , Levin Craig S. 
Published: December 2011

Purpose:List‐mode processing is an efficient way of dealing with the sparse nature of positron emission tomography (PET) data sets and is the processing method of choice for time‐of‐flight (ToF) PET image reconstruction. However, the massive amount of computation involved in forward projection and backprojection limits the application of list‐mode reconstruction in practice, and makes it challenging to incorporate accurate system modeling.Methods:The authors present a novel formulation for computing line projection operations on graphics processing units (GPUs) using the compute unified device architecture (CUDA) framework, and apply the formulation to list‐mode ordered‐subsets expectation maximization (OSEM) image reconstruction. Our method overcomes well‐known GPU challenges such as divergence of compute threads, limited bandwidth of global memory, and limited size of shared memory, while exploiting GPU capabilities such as fast access to shared memory and efficient linear interpolation of texture memory. Execution time comparison and image quality analysis of the GPU‐CUDA method and the central processing unit (CPU) method are performed on several data sets acquired on a preclinical scanner and a clinical ToF scanner.Results:When applied to line projection operations for non‐ToF list‐mode PET, this new GPU‐CUDA method is >200 times faster than a single‐threaded reference CPU implementation. For ToF reconstruction, we exploit a ToF‐specific optimization to improve the efficiency of our parallel processing method, resulting in GPU reconstruction >300 times faster than the CPU counterpart. For a typical whole‐body scan with 75 × 75 × 26 image matrix, 40.7 million LORs, 33 subsets, and 3 iterations, the overall processing time is 7.7 s for GPU and 42 min for a single‐threaded CPU. Image quality and accuracy are preserved for multiple imaging configurations and reconstruction parameters, with normalized root mean squared (RMS) deviation less than 1% between CPU and GPU‐generated images for all cases.Conclusions:A list‐mode ToF OSEM library was developed on the GPU‐CUDA platform. Our studies show that the GPU reformulation is considerably faster than a single‐threaded reference CPU method especially for ToF processing, while producing virtually identical images. This new method can be easily adapted to enable more advanced algorithms for high resolution PET reconstruction based on additional information such as depth of interaction (DoI), photon energy, and point spread functions (PSFs).
Draft Genome Sequence of Penicillium marneffei Strain PM1
Authors: Woo Patrick C. Y. , Lau Susanna K. P. , Liu Bin , Cai James J. , Chong Ken T. K. , Tse Herman , Kao Richard Y. T. , Chan Che-Man , Chow Wang-Ngai , Yuen Kwok-Yung 
Published: December 2011

ABSTRACT

Penicillium marneffei
is the most important thermal dimorphic, pathogenic fungus endemic in China and Southeast Asia and is particularly important in HIV-positive patients. We report the 28,887,485-bp draft genome sequence of
P. marneffei
, which contains its complete mitochondrial genome, sexual cycle genes, a high diversity of Mp1p homologues, and polyketide synthase genes.
Direct Analysis and Identification of Pathogenic Lichtheimia Species by Matrix-Assisted Laser Desorption Ionization–Time of Flight Analyzer-Mediated Mass Spectrometry
Authors: Schrödl Wieland , Heydel Tilo , Schwartze Volker U. , Hoffmann Kerstin , Große-Herrenthey Anke , Walther Grit , Alastruey-Izquierdo Ana , Rodriguez-Tudela Juan Luis , Olias Philipp , Jacobsen Ilse D. , de Hoog G. Sybren , Voigt Kerstin 
Published: December 2011

ABSTRACT

Zygomycetes of the order Mucorales can cause life-threatening infections in humans. These mucormycoses are emerging and associated with a rapid tissue destruction and high mortality. The resistance of Mucorales to antimycotic substances varies between and within clinically important genera such as
Mucor
,
Rhizopus
, and
Lichtheimia
. Thus, an accurate diagnosis before onset of antimycotic therapy is recommended. Matrix-assisted laser desorption ionization (MALDI)–time of flight (TOF) mass spectrometry (MS) is a potentially powerful tool to rapidly identify infectious agents on the species level. We investigated the potential of MALDI-TOF MS to differentiate
Lichtheimia
species, one of the most important agents of mucormycoses. Using the Bruker Daltonics FlexAnalysis (version 3.0) software package, a spectral database library with
m/z
ratios of 2,000 to 20,000 Da was created for 19 type and reference strains of clinically relevant Zygomycetes of the order Mucorales (12 species in 7 genera). The database was tested for accuracy by use of 34 clinical and environmental isolates of
Lichtheimia
comprising a total of five species. Our data demonstrate that MALDI-TOF MS can be used to clearly discriminate
Lichtheimia
species from other pathogenic species of the Mucorales. Furthermore, the method is suitable to discriminate species within the genus. The reliability and robustness of the MALDI-TOF-based identification are evidenced by high score values (above 2.3) for the designation to a certain species and by moderate score values (below 2.0) for the discrimination between clinically relevant (
Lichtheimia corymbifera
,
L. ramosa
, and
L. ornata
) and irrelevant (
L. hyalospora
and
L. sphaerocystis
) species. In total, all 34 strains were unequivocally identified by MALDI-TOF MS with score values of >1.8 down to the generic level, 32 out of 34 of the
Lichtheimia
isolates (except CNM-CM 5399 and FSU 10566) were identified accurately with score values of >2 (probable species identification), and 25 of 34 isolates were identified to the species level with score values of >2.3 (highly probable species identification). The MALDI-TOF MS-based method reported here was found to be reproducible and accurate, with low consumable costs and minimal preparation time.
Diagnosis of Tuberculosis by Trained African Giant Pouched Rats and Confounding Impact of Pathogens and Microflora of the Respiratory Tract
Authors: Mgode Georgies F. , Weetjens Bart J. , Nawrath Thorben , Cox Christophe , Jubitana Maureen , Machang'u Robert S. , Cohen-Bacrie Stéphan , Bedotto Marielle , Drancourt Michel , Schulz Stefan , Kaufmann Stefan H. E. 
Published: December 2011

ABSTRACT

Trained African giant-pouched rats (
Cricetomys gambianus
) can detect
Mycobacterium tuberculosis
and show potential for the diagnosis of tuberculosis (TB). However, rats' ability to discriminate between clinical sputum containing other
Mycobacterium
spp. and nonmycobacterial species of the respiratory tract is unknown. It is also unknown whether nonmycobacterial species produce odor similar to
M. tuberculosis
and thereby cause the detection of smear-negative sputum. Sputum samples from 289 subjects were analyzed by smear microscopy, culture, and rats.
Mycobacterium
spp. were isolated on Lowenstein-Jensen medium, and nonmycobacterial species were isolated on four different media. The odor from nonmycobacterial species from smear- and
M. tuberculosis
culture-negative sputa detected by ≥2 rats (“rat positive”) was analyzed by gas chromatography-mass spectrometry and compared to the
M. tuberculosis
odor. Rats detected 45 of 56 confirmed cases of TB, 4 of 5 suspected cases of TB, and 63 of 228 TB-negative subjects (sensitivity, 80.4%; specificity, 72.4%; accuracy, 73.9%; positive predictive value, 41.7%; negative predictive value, 93.8%). A total of 37 (78.7%) of 47 mycobacterial isolates were
M. tuberculosis
complex, with 75.7% from rat-positive sputa. Ten isolates were nontuberculous mycobacteria, one was
M. intracellulare
, one was
M. avium
subsp.
hominissuis
, and eight were unidentified. Rat-positive sputa with
Moraxella catarrhalis
,
Streptococcus pneumoniae
,
Staphylococcus
spp., and
Enterococcus
spp. were associated with TB.
Rhodococcus
,
Nocardia
,
Streptomyces
,
Staphylococcus
, and
Candida
spp. from rat-positive sputa did not produce
M. tuberculosis
-specific volatiles (methyl nicotinate, methyl
para
-anisate, and
ortho
-phenylanisole). Prevalence of
Mycobacterium
-related
Nocardia
and
Rhodococcus
in smear-negative sputa did not equal that of smear-negative mycobacteria (44.7%), of which 28.6% were rat positive. These findings and the absence of
M. tuberculosis
-specific volatiles in nonmycobacterial species indicate that rats can be trained to specifically detect
M. tuberculosis
.
Prosthetic Joint Infection Caused by Helcococcus kunzii
Authors: Pérez-Jorge Conchita , Cordero José , Marin Mercedes , Esteban Jaime 
Published: December 2011

ABSTRACTHelcococcus kunziiwas isolated by sonication and conventional cultures obtained from a case of infection following total knee prosthesis in an immunocompetent patient. The patient recovered uneventfully. This is the first known case of anH. kunziiprosthetic joint infection.
Characterization of Ertapenem-Resistant Enterobacter cloacae in a Taiwanese University Hospital
Authors: Yang Fu-Chen , Yan Jing-Jou , Hung Kuei-Hsiang , Wu Jiunn-Jong 
Published: December 2011

ABSTRACT

The emergence of carbapenem resistance in
Enterobacteriaceae
has become a great concern. The aim of this study was to characterize ertapenem-resistant
Enterobacter cloacae
isolates from a Taiwanese university hospital. A total of 355 nonduplicated
E. cloacae
isolates collected in 2007 were analyzed by antimicrobial susceptibility testing with and without an inhibitor of efflux pumps and AmpC β-lactamase. The phenotype of extended-spectrum β-lactamase (ESBL), profile of outer membrane proteins (OMPs), and clonal relatedness were investigated by the double-disk synergy test, urea/SDS-PAGE, and pulsed-field gel electrophoresis (PFGE), respectively. β-Lactamase genes were examined by PCR and sequencing, and the expression of efflux pump gene
acrB
was evaluated by reverse transcription-PCR. The contribution of porin deficiency to resistance was investigated by restoring functional porin genes on plasmids. We demonstrated that ertapenem resistance was prevalent (53/355; 14.9%) in
E. cloacae
. Among the strains, IMP-8, SHV-12, and TEM-1 β-lactamases were identified in 3 (5.7%), 40 (75.5%), and 46 (86.8%) isolates, respectively. PFGE showed clonal diversity among these isolates. Phenotypes of ESBL, AmpC β-lactamase overproduction, an active efflux pump, and change in the expression of OMPs were found in 18 (34%), 11 (20.8%), 51 (96.2%), and 23 (43.4%) of ertapenem-resistant strains, respectively. Ertapenem MICs were restored in strains with OmpC and OmpF expression plasmids. This study suggests that ESBL, AmpC β-lactamase overproduction, and decreased OMP expression combined with an active efflux pump contribute to the ertapenem resistance of
E. cloacae
. The presence of IMP-8 may also play a partial role in ertapenem resistance in Taiwan.
Preparation and Evaluation of Recombinant Severe Fever with Thrombocytopenia Syndrome Virus Nucleocapsid Protein for Detection of Total Antibodies in Human and Animal Sera by Double-Antigen Sandwich Enzyme-Linked Immunosorbent Assay
Authors: Jiao Yongjun , Zeng Xiaoyan , Guo Xiling , Qi Xian , Zhang Xiao , Shi Zhiyang , Zhou Minghao , Bao Changjun , Zhang Wenshuai , Xu Yan , Wang Hua 
Published: December 2011

ABSTRACT
The recent emergence of the human infection confirmed to be caused by severe fever with thrombocytopenia syndrome virus (SFTSV) in China is of global concern. Safe diagnostic immunoreagents for determination of human and animal seroprevalence in epidemiological investigations are urgently needed. This paper describes the cloning and expression of the nucleocapsid (N) protein of SFTSV. An N-protein-based double-antigen sandwich enzyme-linked immunosorbent assay (ELISA) system was set up to detect the total antibodies in human and animal sera. We reasoned that as the double-antigen sandwich ELISA detected total antibodies with a higher sensitivity than traditional indirect ELISA, it could be used to detect SFTSV-specific antibodies from different animal species. The serum neutralization test was used to validate the performance of this ELISA system. All human and animal sera that tested positive in the neutralization test were also positive in the sandwich ELISA, and there was a high correlation between serum neutralizing titers and ELISA readings. Cross-reactivity was evaluated, and the system was found to be highly specific to SFTSV; all hantavirus- and dengue virus-confirmed patient samples were negative. SFTSV-confirmed human and animal sera from both Anhui and Hubei Provinces in China reacted with N protein in this ELISA, suggesting no major antigenic variation between geographically disparate virus isolates and the suitability of this assay in nationwide application. ELISA results showed that 3.6% of the human serum samples and 47.7% of the animal field serum samples were positive for SFTSV antibodies, indicating that SFTSV has circulated widely in China. This assay, which is simple to operate, poses no biohazard risk, does not require sophisticated equipment, and can be used in disease surveillance programs, particularly in the screening of large numbers of samples from various animal species.
Liquid-Based Urine Cytology as a Tool for Detection of Human Papillomavirus, Mycoplasma spp., and Ureaplasma spp. in Men
Authors: Kawaguchi Shohei , Shigehara Kazuyoshi , Sasagawa Toshiyuki , Shimamura Masayoshi , Nakashima Takao , Sugimoto Kazuhiro , Nakashima Kazufumi , Furubayashi Keiichi , Namiki Mikio 
Published: December 2011

ABSTRACT

Liquid-based urine cytology (LB-URC) was evaluated for cytological diagnosis and detection of human papillomavirus (HPV),
Mycoplasma
, and
Ureaplasma
. Midstream urine samples were collected from 141 male patients with urethritis and 154 controls without urethritis, and sediment cells were preserved in liquid-based cytology solution. Urethral swabs from urethritis patients were tested for the presence of
Neisseria gonorrhoeae
and
Chlamydia trachomatis
. Papanicolaou tests were performed for cytological evaluation. HPV,
Mycoplasma
, and
Ureaplasma
genomes were determined by PCR-based methods, and localization of HPV DNA in urothelial cells was examined by
in situ
hybridization (ISH). The β-globin gene was positive in 97.9% of LB-URC samples from urethritis patients and in 97.4% of control samples, suggesting that high-quality cellular DNA was obtained from the LB-URC samples. HPV DNA was detected in 29 (21.0%) urethritis cases and in five (3.3%) controls (
P
< 0.05). HPV type 16 (HPV 16) was most commonly found in urethritis patients. Cytological evaluations could be performed for 92.1% of urethritis patients and 64.3% of controls. Morphological changes suggestive of HPV infection were seen in 20.7% of the HPV-positive samples, and ISH demonstrated the presence of HPV DNA in both squamous and urothelial cells in HPV-positive samples.
Mycoplasma genitalium
,
Mycoplasma hominis
,
Ureaplasma parvum
, and
Ureaplasma urealyticum
were detected in 14.5%, 10.9%, 6.5%, and 12.3% of urethritis patients, respectively. The prevalence rates of these microorganisms (except
Ureaplasma parvum
) were significantly higher in urethritis cases than controls (
P
< 0.05). LB-URC is applicable for detection of HPV,
Mycoplasma
, and
Ureaplasma.
HPV infection occurs in urothelial cells, especially in gonococcal urethritis.
Evaluation of the VersaTREK System Compared to the Bactec MGIT 960 System for First-Line Drug Susceptibility Testing of Mycobacterium tuberculosis
Authors: Espasa M. , Salvadó M. , Vicente E. , Tudó G. , Alcaide F. , Coll P. , Martin-Casabona N. , Torra M. , Fontanals D. , González-Martín J. 
Published: December 2011

ABSTRACT

The aim of this study was to evaluate the reliability of the VersaTREK system for
Mycobacterium tuberculosis
drug susceptibility testing compared with results obtained with the Bactec MGIT 960 system. A total of 67 strains were evaluated. Overall agreement was at 98.5%. Kappa indexes were 1.0 for isoniazid, rifampin, and ethambutol, 0.937 for pyrazinamide, and 0.907 for streptomycin. The VersaTREK system is validated for
M. tuberculosis
drug susceptibility testing.
A Non-Mouse-Adapted Enterovirus 71 (EV71) Strain Exhibits Neurotropism, Causing Neurological Manifestations in a Novel Mouse Model of EV71 Infection
Authors: Khong Wei Xin , Yan Benedict , Yeo Huimin , Tan Eng Lee , Lee Jia Jun , Ng Jowin K. W. , Chow Vincent T. , Alonso Sylvie 
Published: December 2011

ABSTRACT
Enterovirus 71 (EV71) is a neurotropic pathogen that has been consistently associated with the severe neurological forms of hand, foot, and mouth disease. The lack of a relevant animal model has hampered our understanding of EV71 pathogenesis, in particular the route and mode of viral dissemination. It has also hindered the development of effective prophylactic and therapeutic approaches, making EV71 one of the most pressing public health concerns in Southeast Asia. Here we report a novel mouse model of EV71 infection. We demonstrate that 2-week-old and younger immunodeficient AG129 mice, which lack type I and II interferon receptors, are susceptible to infection with a non-mouse-adapted EV71 strain via both the intraperitoneal (i.p.) and oral routes of inoculation. The infected mice displayed progressive limb paralysis prior to death. The dissemination of the virus was dependent on the route of inoculation but eventually resulted in virus accumulation in the central nervous systems of both animal groups, indicating a clear neurotropism of the virus. Histopathological examination revealed massive damage in the limb muscles, brainstem, and anterior horn areas. However, the minute amount of infectious viral particles in the limbs from orally infected animals argues against a direct viral cytopathic effect in this tissue and suggests that limb paralysis is a consequence of EV71 neuroinvasion. Together, our observations support that young AG129 mice display polio-like neuropathogenesis upon infection with a non-mouse-adapted EV71 strain, making this mouse model relevant for EV71 pathogenesis studies and an attractive platform for EV71 vaccine and drug testing.
Sequencing of 21 Varicella-Zoster Virus Genomes Reveals Two Novel Genotypes and Evidence of Recombination
Authors: Zell Roland , Taudien Stefan , Pfaff Florian , Wutzler Peter , Platzer Matthias , Sauerbrei Andreas 
Published: December 2011

ABSTRACT
Genotyping of 21 varicella-zoster virus (VZV) strains using a scattered single nucleotide polymorphism (SNP) method revealed ambiguous SNPs and two nontypeable isolates. For a further genetic characterization, the genomes of all strains were sequenced using the 454 technology. Almost-complete genome sequences were assembled, and most remaining gaps were closed with Sanger sequencing. Phylogenetic analysis of 42 genomes revealed five established and two novel VZV genotypes, provisionally termed VIII and IX. Genotypes VIII and IX are distinct from the previously reported provisional genotypes VI and VII as judged from the SNP pattern. The alignments showed evidence of ancient recombination events in the phylogeny of clade 4 and recent recombinations within single strains: 3/2005 (clade 1), 11 and 405/2007 (clade 3), 8 and DR (clade 4), CA123 and 413/2000 (clade 5), and strains of the novel genotypes VIII and IX. Bayesian tree inference of the thymidine kinase and the polymerase genes of the VZV clades and other varicelloviruses revealed that VZV radiation began some 110,000 years ago, which correlates with the out-of-Africa dispersal of modern humans. The split of ancestral clades 2/4 and 1/3/5/VIII/IX shows the greatest node height.
Complete Genome Sequence of the Giant Virus OBP and Comparative Genome Analysis of the Diverse ϕKZ-Related Phages
Authors: Cornelissen Anneleen , Hardies Stephen C. , Shaburova Olga V. , Krylov Victor N. , Mattheus Wesley , Kropinski Andrew M. , Lavigne Rob 
Published: December 2011

ABSTRACT

The 283,757-bp double-stranded DNA genome of
Pseudomonas fluorescens
phage OBP shares a general genomic organization with
Pseudomonas aeruginosa
phage EL. Comparison of this genomic organization, assembled in syntenic genomic blocks interspersed with hyperplastic regions of the ϕKZ-related phages, supports the proposed division in the “EL-like viruses,” and the “phiKZ-like viruses” within a larger subfamily. Identification of putative early transcription promoters scattered throughout the hyperplastic regions explains several features of the ϕKZ-related genome organization (existence of genomic islands) and evolution (multi-inversion in hyperplastic regions). When hidden Markov modeling was used, typical conserved core genes could be identified, including the portal protein, the injection needle, and two polypeptides with respective similarity to the 3′-5′ exonuclease domain and the polymerase domain of the T4 DNA polymerase. While the N-terminal domains of the tail fiber module and peptidoglycan-degrading proteins are conserved, the observation of C-terminal catalytic domains typical for the different genera supports the further subdivision of the ϕKZ-related phages.