bluuebunny/crossref_metadata_2025_split huggingface dataset:
Invasive and Noninvasive Streptococcus pneumoniae Capsule and Surface Protein Diversity following the Use of a Conjugate Vaccine
Authors: Croney Christina M. , Nahm Moon H. , Juhn Steven K. , Briles David E. , Crain Marilyn J. 
Published: September 2013

ABSTRACT

The 13-valent pneumococcal conjugate vaccine (PCV13) was introduced in the United States in 2010 for the prevention of invasive pneumococcal disease (IPD) and otitis media. While many studies have reported its potential efficacy for IPD, not much is known about the epidemiology of noninvasive disease following its introduction. We characterized the capsular types and surface protein genes of noninvasive pediatric pneumococcal isolates collected between 2002 and 2010 (
n
= 1,058) at Children's of Alabama following the introduction of PCV7 and tested a subset of noninvasive and previously characterized IPD isolates for the presence of the
pspA
,
pspC
, and
rrgC
genes, which encode protection-eliciting proteins. PCV7 serotypes had dramatically decreased by 2010 (
P
< 0.0001), and only 50% of all noninvasive infections were caused by the PCV13 capsular serotypes. Serotype 19A accounted for 32% of the noninvasive isolates, followed by serotypes 35B (9%), 19F (7%), and 6C (6%). After 7 years of PCV7 usage, there were no changes in the frequencies of the
pspA
or
pspC
genes; 96% of the strains were positive for family 1 or 2
pspA
genes, and 81% were also positive for
pspC
. Unexpectedly, more noninvasive than invasive strains were positive for
rrgC
(
P
< 0.0001), and the proportion of
rrgC
-positive strains in 2008 to 2010 was greater than that in 2002 to 2008 (IPD,
P
< 0.02; noninvasive,
P
< 0.001). Serotypes 19F, 19A, and 35B were more frequently
rrgC
positive (
P
< 0.005) than other serotypes. A vaccine containing antigens, such as PspA, PspC, and/or RrgC, can provide coverage against most non-PCV13-type pneumococci. Continued surveillance is critical for optimal future vaccine development.
Comparison of Simplexa HSV 1 & 2 PCR with Culture, Immunofluorescence, and Laboratory-Developed TaqMan PCR for Detection of Herpes Simplex Virus in Swab Specimens
Authors: Gitman Melissa R. , Ferguson David , Landry Marie L. 
Published: September 2013

ABSTRACT

The Simplexa HSV 1 & 2 direct PCR assay was compared with conventional cell culture, cytospin-enhanced direct fluorescent antibody (DFA), and a laboratory-developed real-time TaqMan PCR (LDT HSV PCR) using extracted nucleic acid for the detection of herpes simplex virus (HSV) in dermal, genital, mouth, ocular, and other swab samples. One hundred seventy-one swabs were tested prospectively, and 58 were positive for HSV (34 HSV-1 and 24 HSV-2). Cytospin-DFA detected 50 (86.2%), conventional cell culture 51 (87.9%), Simplexa direct 55 (94.8%), and LDT HSV PCR 57 (98.3%) of 58 true positives. Simplexa direct detected more positives than DFA and culture, but the differences were not significant (
P
= 0.0736 and
P
= 0.3711, respectively, by the McNemar test). Samples that were positive by all methods (
n
= 48) were strong positives (LDT cycle threshold [

C
T

] value, 14.4 to 26.1). One strongly positive sample was falsely negative by LDT HSV PCR due to a failure of TaqMan probe binding. Three samples falsely negative by Simplexa direct had high

C
T

values by LDT HSV PCR (LDT

C
T

, 35.8 to 38.2). Omission of the DNA extraction step by Simplexa direct led to a drop in sensitivity compared to the sensitivity of LDT HSV PCR using extracted samples (94.8% versus 98.3%, respectively), but the difference was not significant (
P
= 0.6171). Simplexa HSV 1 & 2 direct PCR was the most expensive but required the least training of the assays used, had the lowest hands-on time and fastest assay time (75 min, versus 3 h by LDT HSV PCR), and provided the HSV type.
MALDI Biotyper-Based Rapid Resistance Detection by Stable-Isotope Labeling
Authors: Sparbier Katrin , Lange Christoph , Jung Jette , Wieser Andreas , Schubert Sören , Kostrzewa Markus 
Published: September 2013

ABSTRACT

Against the background of increasing numbers of resistant microorganisms, the fast and cost-efficient detection of microbial resistance is an important clinical requirement for optimal therapeutic intervention. Current routine assays take at least 5 h, but in most cases an overnight incubation is necessary to identify resistant isolates. The usage of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) profiling in combination with growth media containing isotopically labeled amino acids facilitates the detection of resistant microorganisms after 3 h or less directly from the profile spectrum. Growing microorganisms incorporate isotopically labeled amino acids, increasing protein masses and thereby leading to mass shifts of their corresponding peaks in the profile spectra. In the presence of antibiotics, only resistant microorganisms are able to grow and to incorporate the labeled amino acids. This leads to a difference in the mass spectra of susceptible and resistant isolates, allowing their differentiation. In the presented study, we demonstrated the applicability of this novel approach for the detection of methicillin-resistant
Staphylococcus aureus
and tested different bioinformatics approaches for automated data interpretation.
First Outbreak of KPC-2-Producing Klebsiella pneumoniae Sequence Type 258 in a Hospital in South Korea
Authors: Hong Sung Kwan , Yong Dongeun , Kim Kyeongmi , Hong Sang Sook , Hong Seong Geun , Khosbayar Tulgaa , Song Wonkeun , Roh Kyoung Ho , Jeong Seok Hoon , Lee Kyungwon , Chong Yunsop 
Published: September 2013

ABSTRACT

In this study, we report the first outbreak of KPC-2-producing
Klebsiella pneumoniae
isolates from three patients admitted to a neurosurgery department in a South Korean teaching hospital. Multilocus sequence typing showed that the isolates were identical to the previous KPC producers in South Korea and other countries, suggesting clonal spread.
Helicobacter pylori Infection in Infants and Toddlers in South America: Concordance between [
13
C]Urea Breath Test and Monoclonal H. pylori Stool Antigen Test
Authors: Queiroz Dulciene Maria Magalhães , Saito Mayuko , Rocha Gifone Aguiar , Rocha Andreia Maria Camargos , Melo Fabrício Freire , Checkley William , Braga Lúcia Libanez Bessa C. , Silva Igor Simões , Gilman Robert H. , Crabtree Jean E. 
Published: September 2013

ABSTRACT

Accurate noninvasive tests for diagnosing
Helicobacter pylori
infection in very young children are strongly required. We investigated the agreement between the [
13
C]urea breath test ([
13
C]UBT) and a monoclonal ELISA (HpSA) for detection of
H. pylori
antigen in stool. From October 2007 to July 2011, we enrolled 414 infants (123 from Brazil and 291 from Peru) of ages 6 to 30 months. Breath and stool samples were obtained at intervals of at least 3 months from Brazilian (
n
= 415) and Peruvian (
n
= 908) infants. [
13
C]UBT and stool test results concurred with each other in 1,255 (94.86%) cases (kappa coefficient = 0.90; 95% confidence interval [CI] = 0.87 to 0.92). In the
H. pylori
-positive group, delta-over-baseline (DOB) and optical density (OD) values were positively correlated (
r
= 0.62;
P
< 0.001). The positivity of the tests was higher (
P
< 0.001; odds ratio [OR] = 6.01; 95% CI = 4.50 to 8.04) in Peru (546/878; 62.2%) than in Brazil (81/377; 21.5%) and increased with increasing age in Brazil (
P
= 0.02), whereas in Peru it decreased with increasing age (
P
< 0.001). The disagreement between the test results was associated with birth in Brazil and female gender but not with age and diarrhea. Our results suggest that both [
13
C]UBT and the stool monoclonal test are reliable for diagnosing
H. pylori
infection in very young children, which will facilitate robust epidemiological studies in infants and toddlers.
“Epidemic Clones” of Listeria monocytogenes Are Widespread and Ancient Clonal Groups
Authors: Cantinelli Thomas , Chenal-Francisque Viviane , Diancourt Laure , Frezal Lise , Leclercq Alexandre , Wirth Thierry , Lecuit Marc , Brisse Sylvain 
Published: September 2013

ABSTRACT

The food-borne pathogen
Listeria monocytogenes
is genetically heterogeneous. Although some clonal groups have been implicated in multiple outbreaks, there is currently no consensus on how “epidemic clones” should be defined. The objectives of this work were to compare the patterns of sequence diversity on two sets of genes that have been widely used to define
L. monocytogenes
clonal groups: multilocus sequence typing (MLST) and multi-virulence-locus sequence typing (MvLST). Further, we evaluated the diversity within clonal groups by pulsed-field gel electrophoresis (PFGE). Based on 125 isolates of diverse temporal, geographical, and source origins, MLST and MvLST genes (i) had similar patterns of sequence polymorphisms, recombination, and selection, (ii) provided concordant phylogenetic clustering, and (iii) had similar discriminatory power, which was not improved when we combined both data sets. Inclusion of representative strains of previous outbreaks demonstrated the correspondence of epidemic clones with previously recognized MLST clonal complexes. PFGE analysis demonstrated heterogeneity within major clones, most of which were isolated decades before their involvement in outbreaks. We conclude that the “epidemic clone” denominations represent a redundant but largely incomplete nomenclature system for MLST-defined clones, which must be regarded as successful genetic groups that are widely distributed across time and space.
Diagnostic Rates Differ on the Basis of the Number of Read Days with the Use of the InPouch Culture System for Trichomonas vaginalis Screening
Authors: Rivers Charles. A. , Muzny Christina A. , Schwebke Jane R. 
Published: September 2013

ABSTRACT

The InPouch
Trichomonas vaginalis
test is the gold standard for clinical culture for
Trichomonas vaginalis
screening. The current package insert recommends an examination period of 3 days. After review of 2,499 InPouch tests spanning 13 years, we observed that examination up to 3 days will detect only 82.8% (95% confidence interval [CI], 79.0% to 86.2%) of positive specimens.
Oncoprotein E7 from Beta Human Papillomavirus 38 Induces Formation of an Inhibitory Complex for a Subset of p53-Regulated Promoters
Authors: Saidj Djamel , Cros Marie-Pierre , Hernandez-Vargas Hector , Guarino Francesca , Sylla Bakary S. , Tommasino Massimo , Accardi Rosita 
Published: September 2013

ABSTRACT

Our previous studies on cutaneous beta human papillomavirus 38 (HPV38) E6 and E7 oncoproteins highlighted a novel activity of IκB kinase beta (IKKβ) in the nucleus of human keratinocytes, where it phosphorylates and stabilizes ΔNp73α, an antagonist of p53/p73 functions. Here, we further characterize the role of the IKKβ nuclear form. We show that IKKβ nuclear translocation and ΔNp73α accumulation are mediated mainly by HPV38 E7 oncoprotein. Chromatin immunoprecipitation (ChIP)/Re-ChIP experiments showed that ΔNp73α and IKKβ are part, together with two epigenetic enzymes DNA methyltransferase 1 (DNMT1) and the enhancer of zeste homolog 2 (EZH2), of a transcriptional regulatory complex that inhibits the expression of some p53-regulated genes, such as
PIG3
. Recruitment to the PIG3 promoter of EZH2 and DNMT1 resulted in trimethylation of histone 3 on lysine 27 and in DNA methylation, respectively, both events associated with gene expression silencing. Decreases in the intracellular levels of HPV38 E7 or ΔNp73α strongly affected the recruitment of the inhibitory transcriptional complex to the PIG3 promoter, with consequent restoration of p53-regulated gene expression. Finally, the ΔNp73α/IKKβ/DNMT1/EZH2 complex appears to bind a subset of p53-regulated promoters. In fact, the complex is efficiently recruited to several promoters of genes encoding proteins involved in DNA repair and apoptosis, whereas it does not influence the expression of the prosurvival factor Survivin. In summary, our data show that HPV38 via E7 protein promotes the formation of a multiprotein complex that negatively regulates the expression of several p53-regulated genes.
Expression of Betapapillomavirus Oncogenes Increases the Number of Keratinocytes with Stem Cell-Like Properties
Authors: Hufbauer Martin , Biddle Adrian , Borgogna Cinzia , Gariglio Marisa , Doorbar John , Storey Alan , Pfister Herbert , Mackenzie Ian , Akgül Baki 
Published: September 2013

ABSTRACT

Human papillomaviruses (HPV) of genus
Betapapillomavirus
(betaPV) are associated with nonmelanoma skin cancer development in epidermodysplasia verruciformis (EV) and immunosuppressed patients. Epidemiological and molecular studies suggest a carcinogenic activity of betaPV during early stages of cancer development. Since viral oncoproteins delay and perturb keratinocyte differentiation, they may have the capacity to either retain or confer a “stem cell-like” state on oncogene-expressing cells. The aim of this study was to determine (i) whether betaPV alters the expression of cell surface markers, such as CD44 and epithelial cell adhesion molecule (EpCAM), that have been associated with epithelial stemness, and (ii) whether this confers functional stem cell-like properties to human cutaneous keratinocytes. Fluorescence-activated cell sorter (FACS) analysis revealed an increase in the number of cells with high CD44 and EpCAM expression in keratinocyte cultures expressing HPV type 8 (HPV8) oncogenes E2, E6, and E7. Particularly through E7 expression, a distinct increase in clonogenicity and in the formation and size of tumor spheres was observed, accompanied by reduction of the epithelial differentiation marker Calgranulin B. These stem cell-like properties could be attributed to the pool of CD44
high
EpCAM
high
cells, which was increased within the E7 cultures of HPV5, -8, and -20. Enhanced EpCAM levels were present in organotypic skin cultures of primary keratinocytes expressing E7 of the oncogenic HPV types HPV5, -8, and -16 and in clinical samples from EV patients. In conclusion, our data show that betaPV may increase the number of stem cell-like cells present during early carcinogenesis and thus enable the persistence and accumulation of DNA damage necessary to generate malignant stem cells.
Hepatitis C Virus Induces Interleukin-1β (IL-1β)/IL-18 in Circulatory and Resident Liver Macrophages
Authors: Shrivastava Shubham , Mukherjee Anupam , Ray Ranjit , Ray Ratna B. 
Published: September 2013

ABSTRACT
Hepatitis C virus (HCV)-mediated chronic liver disease is a global health problem, and inflammation is believed to be an important player in disease pathogenesis. HCV infection often leads to severe fibrosis/cirrhosis and hepatocellular carcinoma, although the mechanisms for advancement of disease are not fully understood. The proinflammatory cytokines interleukin-1β (IL-1β) and IL-18 have critical roles in establishment of inflammation. In this study, we examined induction of IL-1β/IL-18 secretion following HCV infection. Our results demonstrated that monocyte-derived human macrophages (THP-1) incubated with cell culture-grown HCV enhance the secretion of IL-1β/IL-18 into culture supernatants. A similar cytokine release was also observed for peripheral blood mononuclear cell (PBMC)-derived primary human macrophages and Kupffer cells (liver-resident macrophages) upon incubation with HCV. THP-1 cells incubated with HCV led to caspase-1 activation and release of proinflammatory cytokines. Subsequent studies demonstrated that HCV induces pro-IL-1β and pro-IL-18 synthesis via the NF-κB signaling pathway in macrophages. Furthermore, introduction of HCV viroporin p7 RNA into THP-1 cells was sufficient to cause IL-1β secretion. Together, our results suggested that human macrophages exposed to HCV induce IL-1β and IL-18 secretion, which may play a role in hepatic inflammation.
HLA-DPPolymorphisms Affect the Outcomes of Chronic Hepatitis B Virus Infections, Possibly through Interacting with Viral Mutations
Authors: Zhang Qi , Yin Jianhua , Zhang Yuwei , Deng Yang , Ji Xiaowei , Du Yan , Pu Rui , Han Yifang , Zhao Jun , Han Xue , Zhang Hongwei , Cao Guangwen 
Published: September 2013

ABSTRACTGenetic polymorphisms ofHLA-DPhave been associated with hepatitis B virus (HBV) persistence. We aimed to determine the effect ofHLA-DPpolymorphisms on the generation of HBV mutations and their interactions on the outcomes of HBV infection. rs3077, rs3135021, rs9277535, and rs2281388 were genotyped in 1,342 healthy controls, 327 HBV clearance subjects, and 2,736 HBV-positive subjects, including 1,108 hepatocellular carcinoma (HCC) patients, using quantitative PCR. HBV mutations were determined by sequencing. Multiplicative interactions ofHLA-DPpolymorphisms and viral mutations were assessed by multivariate logistic regression. rs3077 (from subjects with genotype CT combined with those from subjects with genotype TT [CT+TT] versus CC), rs3135021 (GA+AA versus GG), rs9277535 (GA+AA versus GG), and rs2281388 (CC versus CT+TT) significantly decreased HBV persistence. This effect was found only in genotype B HBV-infected subjects compared to HBV clearance subjects.HLA-DPpolymorphisms promoting HBV clearance were associated with a lower prevalence of mutations increasing HCC risk (C1653T, T1674C/G, A1846T, G1896A and pre-S2 mutations and pre-S deletion in genotype C) and a higher prevalence of mutations decreasing HCC risk (G1652A, T1673C, T1674C, G1719T, G1730C, and G1799C in genotype B and A1727T in genotype C). Significant effects of viral mutations on cirrhosis and HCC were selectively evident in those withHLA-DPpolymorphisms promoting HBV persistence. The interactions of C1653T, T1674C/G, and G1896A mutations withHLA-DPpolymorphisms promoting HBV clearance significantly decreased cirrhosis risk. The interaction of rs9277535 AA with the T1674C/G or G1719T mutation in genotype C significantly decreased HCC risk. In conclusion,HLA-DPpolymorphisms affect genotype B HBV clearance, regulate immune selection of viral mutations, and influence cirrhosis and HCC risks contributed by HBV mutations.
Inverse intubation in entrapped trauma casualties: a simulator based, randomised cross-over comparison of direct, indirect and video laryngoscopy
Authors: Schober Patrick , Krage Ralf , van Groeningen Dick , Loer Stephan A , Schwarte Lothar A 
Published: September 2013

BackgroundAirway management in entrapped casualties with restricted access to the head is challenging. If tracheal intubation is required and conventional laryngoscopy is not possible, intubation must be attempted in a face-to-face approach. Traditionally, this is performed with a standard laryngoscope held in the right hand with the blade facing upward. Recently, alternative methods have been developed to facilitate difficult intubations, and we hypothesised that such techniques are also useful for face-to-face intubations.Methods24 (trainee) anaesthesiologists attempted tracheal intubation in a patient simulator (SimMan, Laerdal, Norway) using three techniques in random order: (1) direct laryngoscopy (Macintosh blade #3), (2) indirect optical laryngoscopy (Airtraq, Prodol, Spain) and (3) video laryngoscopy (McGrath, Aircraft Medical, UK). The manikin was sitting with the neck immobilised and only accessible from the left anterolateral side. Success rate (percentage (95% CI)) and tube insertion time (median (IQR)) were recorded.ResultsSuccess rate did not differ significantly (Airtraq and McGrath 100% (84% to 100%), direct laryngoscopy 88% (68% to 96%)). Intubation was faster with Airtraq (25 s (22–34), p<0.001) and direct laryngoscopy (34 s (22–48), p<0.05) compared with the McGrath technique (55 s (37–96)).ConclusionsAll three techniques have a high success rate, but the usefulness of the video laryngoscope is limited due to longer intubation duration. Inverse direct laryngoscopy showed reasonable intubation times and, given the widespread availability of Macintosh laryngoscopes, seems a useful technique. Intubation was always successful and tended to be fastest with the Airtraq device, suggesting that this technique may be a promising alternative.
Increasing chlamydia screening tests in general practice: a modified Zelen prospective Cluster Randomised Controlled Trial evaluating a complex intervention based on the Theory of Planned Behaviour
Authors: McNulty Cliodna A M , Hogan Angela H , Ricketts Ellie J , Wallace Louise , Oliver Isabel , Campbell Rona , Kalwij Sebastian , O'Connell Elaine , Charlett Andre 
Published: September 2013

ObjectiveTo determine if a structured complex intervention increases opportunistic chlamydia screening testing of patients aged 15–24 years attending English general practitioner (GP) practices.MethodsA prospective, Cluster Randomised Controlled Trial with a modified Zelen design involving 160 practices in South West England in 2010. The intervention was based on the Theory of Planned Behaviour (TPB). It comprised of practice-based education with up to two additional contacts to increase the importance of screening to GP staff and their confidence to offer tests through skill development (including videos). Practical resources (targets, posters, invitation cards, computer reminders, newsletters including feedback) aimed to actively influence social cognitions of staff, increasing their testing intention.ResultsData from 76 intervention and 81 control practices were analysed. In intervention practices, chlamydia screening test rates were 2.43/100 15–24-year-olds registered preintervention, 4.34 during intervention and 3.46 postintervention; controls testing rates were 2.61/100 registered patients prior intervention, 3.0 during intervention and 2.82 postintervention. During the intervention period, testing in intervention practices was 1.76 times as great (CI 1.24 to 2.48) as controls; this persisted for 9 months postintervention (1.57 times as great, CI 1.27 to 2.30). Chlamydia infections detected increased in intervention practices from 2.1/1000 registered 15–24-year-olds prior intervention to 2.5 during the intervention compared with 2.0 and 2.3/1000 in controls (Estimated Rate Ratio intervention versus controls 1.4 (CI 1.01 to 1.93).ConclusionsThis complex intervention doubled chlamydia screening tests in fully engaged practices. The modified Zelen design gave realistic measures of practice full engagement (63%) and efficacy of this educational intervention in general practice; it should be used more often.Trial registrationThe trial was registered on the UK Clinical Research Network Study Portfolio database. UKCRN number 9722.
Lithotherapeutical research sources from antiquity to the mid-eighteenth century
Authors: Duffin Christopher J. 
Published: September 2013

Abstract

Geopharmaceuticals have a recorded history of use by a wide range of cultures for over 3000 years. The history of geological simples is written in the leaves of a diversity of literary sources, an overview of which is attempted for the first time. Egyptian medical papyri, Assyrian and Babylonian clay tablets, Indian
Puranas
, plus ancient Chinese, classical Greek and Roman writings all preserve a folk tradition of therapeutic earths, rocks, minerals and fossils. Anglo-Saxon
Laeceboc
, medieval Islamic writings, and Western medieval bestiaries all contain scattered references to geological simples. A surge of appreciation for geopharmaceuticals took place with the onset of the Western medieval lapidary tradition, which influenced the writings of the early encyclopaedists and writers of herbals. With the advent of printing, many classical and newly translated Islamic texts were made more readily available, stimulating a burst of scholarship by early modern scientists of the Renaissance. Increasingly detailed illustrations were used to embellish the catalogues of Renaissance
Wunderkammern
. By the late eighteenth century, the use of geological materials was declining, and being replaced by a more empirical approach to pharmacology.