bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved AFLP protocol using dual‐suppression PCR and its application to species with large genomes
Authors: GUAN LANHUA , SHIRAISHI SUSUMU 
Published: June 2011

AbstractTo improve the amplified fragment length polymorphism assay, dual‐suppression PCR was introduced into the preamplification step of the assay. The dual‐suppression PCR blocked completely the amplification of fragments with the same sequence (Bsp1407I‐Bsp1407I or NlaIII‐NlaIII) at both ends and amplified selectively fragments with different adaptor sequences (Bsp1407I‐NlaIII) at each end. Two protocols, referred to as A and B, were established for species with medium‐ and large‐sized genomes, respectively. Both protocols incorporated the dual‐suppression PCR. Protocol A resulted in high‐quality electrophoretic profiles for black cottonwood and rice, which have medium‐sized genomes. In protocol B, an intensely selective PCR step was added to protocol A. Protocol B yielded profiles for Japanese black pine and Japanese cedar that were improved significantly relative to protocol A: the number of strong peaks increased and that of low peaks decreased. Japanese black pine and Japanese cedar have large genomes. The optimal profiles were generated with a total of eight or nine selective nucleotides.
Exon‐primed, intron‐crossing (EPIC) loci for five nuclear genes in deep‐sea protobranch bivalves: primer design, PCR protocols and locus utility
Authors: JENNINGS ROBERT M. , ETTER R. J. 
Published: June 2011

AbstractWe describe PCR primers and amplification protocols developed to obtain introns from conserved nuclear genes in deep‐sea protobranch bivalves. Because almost no sequence data for protobranchs are publically available, mollusk and other protostome sequences from GenBank were used to design degenerate primers, making these loci potentially useful in other invertebrate taxa. Amplification and sequencing success varied across the test group of 30 species, and we present five loci spanning this range of outcomes. Intron presence in the targeted regions also varied across genes and species, often within single genera; for instance, the calmodulin and β‐tubulin loci contained introns with high frequency, whereas the triose phosphate isomerase locus never contained an intron. In introns for which we were able to obtain preliminary estimates of polymorphism levels in single species, polymorphism was greater than traditional mitochondrial loci. These markers will greatly increase the ability to assess population structure in the ecologically important protobranchs, and may prove useful in other taxa as well.
Hypolithic communities: important nitrogen sources in Antarctic desert soils
Authors: Cowan D. A. , Sohm J. A. , Makhalanyane T. P. , Capone D. G. , Green T. G. A. , Cary S. C. , Tuffin I. M. 
Published: June 2011

SummaryHypolithic microbial communities (i.e. cryptic microbial assemblages found on the undersides of translucent rocks) are major contributors of carbon input into the oligotrophic hyper‐arid desert mineral soils of the Eastern Antarctic Dry Valleys. Here we demonstrate, for the first time, that hypolithic microbial communities possess both the genetic capacity for nitrogen fixation (i.e. the presence of nifH genes) and the ability to catalyse acetylene reduction, an accepted proxy for dinitrogen fixation. An estimate of the total contribution of these communities suggests that hypolithic communities are important contributors to fixed nitrogen budgets in Antarctic desert soils.
Distinctive Immunomodulatory and Inflammatory Properties of the Escherichia coli Type II Heat-Labile Enterotoxin LT-IIa and Its B Pentamer following Intradermal Administration
Authors: Mathias-Santos Camila , Rodrigues Juliana F. , Sbrogio-Almeida Maria Elisabete , Connell Terry D. , Ferreira Luís C. S. 
Published: June 2011

ABSTRACTThe type I and type II heat-labile enterotoxins (LT-I and LT-II) are strong mucosal adjuvants when they are coadministered with soluble antigens. Nonetheless, data on the parenteral adjuvant activities of LT-II are still limited. Particularly, no previous study has evaluated the adjuvant effects and induced inflammatory reactions of LT-II holotoxins or their B pentameric subunits after delivery via the intradermal (i.d.) route to mice. In the present report, the adjuvant and local skin inflammatory effects of LT-IIa and its B subunit pentamer (LT-IIaB5) were determined. When coadministered with ovalbumin (OVA), LT-IIa and, to a lesser extent, LT-IIaB5exhibited serum IgG adjuvant effects. In addition, LT-IIa but not LT-IIaB5induced T cell-specific anti-OVA responses, particularly in respect to induction of antigen-specific cytotoxic CD8+T cell responses. LT-IIa and LT-IIaB5induced differential tissue permeability and local inflammatory reactions after i.d. injection. Of particular interest was the reduced or complete lack of local reactions, such as edema and tissue induration, in mice i.d. inoculated with LT-IIa and LT-IIaB5,respectively, compared with mice immunized with LT-I. In conclusion, the present results show that LT-IIa and, to a lesser extent, LT-IIaB5exert adjuvant effects when they are delivered via the i.d. route. In addition, the low inflammatory effects of LT-IIa and LT-IIaB5in comparison to those of LT-I support the usefulness of LT-IIa and LT-IIaB5as parenterally delivered vaccine adjuvants.
Immunization of Teenagers with a Fifth Dose of Reduced DTaP-IPV Induces High Levels of Pertussis Antibodies with a Significant Increase in Opsonophagocytic Activity
Authors: Aase Audun , Herstad Tove Karin , Merino Samuel , Bolstad Merete , Sandbu Synne , Bakke Hilde , Aaberge Ingeborg S. 
Published: June 2011

ABSTRACTWaning vaccine-induced immunity againstBordetella pertussisis observed among adolescents and adults. A high incidence of pertussis has been reported in this population, which serves as a reservoir forB. pertussis. A fifth dose of reduced antigen of diphtheria-tetanus-acellular-pertussis and inactivated polio vaccine was given as a booster dose to healthy teenagers. The antibody activity againstB. pertussisantigens was measured prior to and 4 to 8 weeks after the booster by different assays: enzyme-linked immunosorbent assays (ELISAs) of IgG and IgA against pertussis toxin (PT) and filamentous hemagglutinin (FHA), IgG against pertactin (PRN), opsonophagocytic activity (OPA), and IgG binding to liveB. pertussis. There was a significant increase in the IgG activity against PT, FHA, and PRN following the booster immunization (P< 0.001). The prebooster sera showed a geometric mean OPA titer of 65.1 and IgG binding to live bacteria at a geometric mean concentration of 164.9 arbitrary units (AU)/ml. Following the fifth dose, the OPA increased to a titer of 360.4, and the IgG concentration against live bacteria increased to 833.4 AU/ml (P< 0.001 for both). The correlation analyses between the different assays suggest that antibodies against FHA and PRN contribute the most to the OPA and IgG binding.
Prevalence and Genetic Relatedness of Methicillin-Susceptible Staphylococcus aureus Isolates Detected by the Xpert MRSA Nasal Assay
Authors: Arbefeville Sophie S. , Zhang Kunyan , Kroeger Jennifer S. , Howard Wanita J. , Diekema Daniel J. , Richter Sandra S. 
Published: June 2011

ABSTRACT

Methicillin-susceptible
Staphylococcus aureus
(MSSA) isolates lacking
mecA
yet testing positive on the Xpert MRSA assay were recovered from culture for 7.7% of 248 Xpert-positive nasal samples. These “false-positive” Xpert results may be attributed to staphylococcal cassette chromosome (SCC) elements without the
mecA
gene. Pulsed-field gel electrophoresis (PFGE) analysis revealed a diverse population of MSSA strains.
Refractory Chronic Pleurisy Caused by Helicobacter equorum-Like Bacterium in a Patient with X-Linked Agammaglobulinemia
Authors: Funato Michinori , Kaneko Hideo , Ohkusu Kiyofumi , Sasai Hideo , Kubota Kazuo , Ohnishi Hidenori , Kato Zenichiro , Fukao Toshiyuki , Kondo Naomi 
Published: June 2011

ABSTRACT

We describe a 35-year-old man with X-linked agammaglobulinemia who had refractory chronic pleurisy caused by a
Helicobacter equorum-
like bacterium. Broad-range bacterial PCR targeting the 16S and 23S rRNA genes and
in situ
hybridization targeting the 16S rRNA gene of
H. equorum
confirmed the presence of this pathogen in a human for the first time.
Quantitation of Candida CFU in Initial Positive Blood Cultures
Authors: Pfeiffer Christopher D. , Samsa Gregory P. , Schell Wiley A. , Reller L. Barth , Perfect John R. , Alexander Barbara D. 
Published: June 2011

ABSTRACT

One potential limitation of DNA-based molecular diagnostic tests for
Candida
bloodstream infection (BSI) is organism burden, which is not sufficiently characterized. We hypothesized that the number of CFU per milliliter (CFU/ml) present in an episode of
Candida
BSI is too low for reliable DNA-based diagnostics. In this study, we determined
Candida
burden in the first positive blood culture and explored factors that affect organism numbers and patient outcomes. We reviewed records of consecutive patients with a positive blood culture for
Candida
in the lysis-centrifugation blood culture system (Isolator, Wampole Laboratories, Cranbury, NJ) from 1987 to 1991. Descriptive statistics and logistic regression analyses were performed. One hundred fifty-two episodes of
Candida
BSI were analyzed. Patient characteristics included adult age (72%), indwelling central venous catheters (83%), recent surgery (29%), neutropenia (24%), transplant (14%), and other immune suppression (21%). Rates of treatment success and 30-day mortality for candidemia were each 51%. The median CFU/ml was 1 (mode 0.1, range 0.1 to >1,000). In the multivariate analysis, pediatric patients were more likely than adults to have high organism burdens (odds ratio [OR], 10.7; 95% confidence interval [95% CI], 4.3 to 26.5). Initial organism density did not affect patient outcome.
Candida
CFU/ml in the first positive blood culture of a BSI episode varies greatly; >50% of cultures had ≤1 CFU/ml, a concentration below the experimental yeast cell threshold for reliable DNA-based diagnostics. DNA-based diagnostics for
Candida
BSI will be challenged by low organism density and the need for sufficient specimen volume; future research on alternate targets is warranted.
Cepheid GeneXpert MTB/RIF Assay for Mycobacterium tuberculosis Detection and Rifampin Resistance Identification in Patients with Substantial Clinical Indications of Tuberculosis and Smear-Negative Microscopy Results
Authors: Ioannidis Panayotis , Papaventsis Dimitrios , Karabela Simona , Nikolaou Stavroula , Panagi Marina , Raftopoulou Ekaterini , Konstantinidou Eythymia , Marinou Ioanna , Kanavaki Sofia 
Published: June 2011

ABSTRACT
The GeneXpert MTB/RIF assay was evaluated with microscopically negative and positive pulmonary and extrapulmonary specimens from patients with substantial clinical indications for tuberculosis. For the pulmonary samples, the sensitivity, specificity, and positive and negative predictive values were 90.6%, 94.3%, 93.5%, and 91.7%, and for the extrapulmonary samples, they were 100%, 91.6%, 50%, and 100%, respectively. For microscopically negative specimens, the respective values were 86.3%, 93%, 79%, and 95.6%. The assay correctly detected rifampin resistance in all but one specimen, which harbored a mixed population. The GeneXpert assay was highly effective for tuberculosis diagnosis and identification of rifampin-resistant strains in smear-negative samples.
Four Independent Molecular Prion Protein Parameters for Discriminating New Cases of C, L, and H Bovine Spongiform Encephalopathy in Cattle
Authors: Langeveld Jan P. M. , Erkens Jo H. F. , Rammel Ines , Jacobs Jorg G. , Davidse Aart , van Zijderveld Fred G. , Bossers Alex , Schildorfer Hermann 
Published: June 2011

ABSTRACT
In anticipation of the emergence of more variants of bovine spongiform encephalopathy (BSE), a semiquantitative display of the following four independent molecular diagnostic prion parameters was designed: N terminus, proteinase K (PK) resistance, glycoprofile, and mixed population. One H BSE case, three L BSE cases, six C BSE cases, and one unusual classical BSE (C BSE) case are reported.
Injury mortality indicators: recommendations from the International Collaborative Effort on Injury Statistics
Authors: Cryer Colin , Fingerhut Lois , Segui-Gomez Maria 
Published: June 2011

BackgroundThe International Collaborative Effort (ICE) on Injury Statistics called for an effort ‘to reach consensus on what are the 10 most important indicators of injury incidence that offer the potential for international comparisons and for regional or global monitoring.’ObjectivesTo describe the process of developing the ICE indicators and to present the specifications of selected injury mortality indicators, along with comparisons between selected countries for those specified indicators.MethodsParticipants on the ICE list had been asked to send to one of the authors what they considered the most important five indicators of injury incidence. These were synthesised and presented under six themes: mortality indicators (general); mortality indicators (motor vehicle); mortality indicators (other); hospital data-based (overall); hospital data-based (traumatic brain injury (TBI)); long-term disability (overall). Following two work group discussions and after drafting and revising indicator specifications, agreement was reached on mortality indicators and specifications. Specifications for those mortality indicators are presented. Morbidity indicators are still to be agreed.ResultsThe mortality indicators proposed were age-adjusted rates of injury death; motor vehicle traffic crash-related death; self-harm/suicide; assault/homicide; and TBI death. The empirical work highlighted difficulties in identifying TBI in countries where mortality data do not capture multiple injuries, prompting us to drop the mortality indicator related to TBI and moving us instead to introduce an indicator to monitor the use of undetermined intent in the classification of injury mortality.ConclusionThe ICE has reached a consensus on what injury mortality indicators should be used for comparison between countries. Specifications for each of these have been applied successfully to the mortality data of seven countries.
Occupational health impact of the 2009 H1N1 flu pandemic: surveillance of sickness absence
Authors: Torá-Rocamora Isabel , Delclos George L , Martínez José Miguel , Jardí Josefina , Alberti Constança , Manzanera Rafael , Yasui Yutaka , Clèries Ramón , Tobías Aurelio , Benavides Fernando G 
Published: June 2011

ObjectivesWorkplace absences due to illness can disrupt usual operations and increase costs for businesses. This study of sickness absence due to influenza and influenza-related illness presents a unique opportunity to characterise and measure the impact of the 2009 (H1N1) pandemic, by comparing trends during the pandemic to those of previous years, and adding this information to that obtained by traditional epidemiological surveillance systems.MethodsWe compared the numbers of cases of sickness absence due to illness caused by influenza and influenza-related illness in 2007–2009, and in the first 3 months of 2010 in Catalonia (n=811 940) using a time series approach. Trends were examined by economic activity, age and gender. The weekly endemic-epidemic index (EEI) was calculated and its 95% CI obtained with the delta method, with observed and expected cases considered as independent random variables.ResultsInfluenza activity peaked earlier in 2009 and yielded more cases than in previous years. Week 46 (in November 2009) had the highest number of new cases resulting in sickness absence (EEI 20.99; 95% CI 9.44 to 46.69). Women and the ‘education, health and other social activities’ sector were the most affected.ConclusionsResults indicate that the new H1N1 pandemic had a significant impact on business, with shifts in the timing of peak incidence, a doubling in the number of cases, and changes in the distribution of cases by economic activity sector and gender. Traditional epidemiological surveillance systems could benefit from the addition of information based on sickness absence data.
Conflict of interest and FCTC implementation in China
Authors: Wan Xia , Ma Shaojun , Hoek Janet , Yang Jie , Wu Lanyan , Zhou Jiushun , Yang Gonghuan 
Published: June 2011

ObjectiveTo critically review the structure of tobacco control policy making in China, examine conflicts of interest within this structure, and consider how these affected the introduction of on-pack warnings.MethodsGovernment policy documents and warning labels were obtained and critically reviewed.ResultsFew differences exist between the on-pack warnings formerly used in China and those introduced ostensibly to meet Framework Convention on Tobacco Control (FCTC) obligations. Comparison with tobacco manufactured for export or overseas consumption shows the new Chinese domestic on-pack warnings are demonstrably inferior to those required internationally. The inherent conflict of interest in the Chinese tobacco control agency structure, which must meet commercial and public health objectives, undermined the introduction of new health warnings.ConclusionsTo promote more effective tobacco control policies, the conflict of interest inhibiting the public health function of the State Tobacco Monopoly Administration (STMA) must be removed. Specifically, the public health function must be separated from oversight of commercial production, and packaging must be redesigned with pictorial warnings and messages compliant with Article 11 of the FCTC.
Exempting casinos from the Smoke-free Illinois Act will not bring patrons back: they never left: Figure 1
Authors: Harris Jenine K , Carothers Bobbi J , Luke Douglas A , Silmere Hiie , McBride Timothy D , Pion Martin 
Published: June 2011

ObjectiveThe Smoke-free Illinois Act was implemented in January 2008, one month after the beginning of a national recession. In December 2010, the Illinois legislature proposed new legislation that would provide an exemption for casinos from the act until neighbouring states also implement smoke-free casino policies. Lobbyists and gaming commission representatives argued that Illinois casinos were losing patrons to casinos in neighbouring states that allow smoking. This study examined the influence of the act on casino admissions in Illinois and neighbouring states in light of the economy.MethodsA multilevel model was developed to examine monthly casino admissions from January 2007 to December 2008.ResultsThere was no difference in changes in admissions across the four states over time after accounting for the economic downturn.ConclusionsThe Smoke-Free Illinois Act did not have a detectable effect on Illinois casino admissions.
Efficient and effective misaligned data access handling in a dynamic binary translation system
Authors: Li Jianjun , Wu Chenggang , Hsu Wei-Chung 
Published: June 2011

Binary Translation (BT) has been commonly used to migrate application software across Instruction Set Architectures (ISAs). Some architectures, such as X86, allow Misaligned Data Accesses (MDAs), while most modern architectures require natural data alignments. In a binary translation system, where the source ISA allows MDA and the target ISA does not, memory operations must be carefully translated. Naive translation may cause frequent misaligned data access traps to occur at runtime on the target machine and severely slow down the migrated application.
This article evaluates different approaches in handling MDA in a binary translation system including how to identify MDA candidates and how to translate such memory instructions. This article also proposes some new mechanisms to more effectively deal with MDAs. Extensive measurements based on SPEC CPU2000 and CPU2006 benchmarks show that the proposed approaches are more effective than existing methods and getting close to the performance upper bound of MDA handling.
Genetic Variation in an miRNA-1827 Binding Site in MYCL1 Alters Susceptibility to Small-Cell Lung Cancer
Authors: Xiong Fang , Wu Chen , Chang Jiang , Yu Dianke , Xu Binghe , Yuan Peng , Zhai Kan , Xu Jian , Tan Wen , Lin Dongxin 
Published: June 2011

Abstract
Genetic variations in microRNAs (miRNA) that affect control of their target genes may alter individual susceptibilities to cancer. In this study, we took an in silico approach to identify single-nucleotide polymorphisms (SNP) within the 3′-untranslated region (UTR) of miRNA genes deregulated in human small-cell lung cancer (SCLC), and then investigated their associations with SCLC susceptibility in 666 SCLC patients and 758 controls. Odds ratios (OR) were estimated by multivariate logistic regression, and biochemical assays were conducted to investigate SNP functions. We identified 2 SNPs, rs3134615 and rs2291854, which were located in the 3′-UTR of the L-MYC gene MYCL1 and the neuronal development Achaete-Scute Complex homolog ASCL1. Case–control analyses showed that the rs3134615T allele was associated with a significantly increased risk of SCLC, with the OR for carrying the GT or TT genotype being 2.08 (95% confidence interval, 1.39–3.21; P = 0.0004) compared with the GG genotype. In support of the likelihood that these 3′-UTR SNPs may directly affect miRNA-binding sites, reporter gene assays indicated MYCL1 as the target of hsa-miR-1827 and the rs3134615 G&gt;T change resulted in altered regulation of MYCL1 expression. Our findings define a 3′-UTR SNP in the human L-MYC oncogene that may increase susceptibility to SCLC, possibly resulting from attenuated interaction with the miRNA hsa-miR-1827. Cancer Res; 71(15); 5175–81. ©2011 AACR.
MicroRNA Replacement Therapy for miR-145 and miR-33a Is Efficacious in a Model of Colon Carcinoma
Authors: Ibrahim Ahmed Fawzy , Weirauch Ulrike , Thomas Maren , Grünweller Arnold , Hartmann Roland K. , Aigner Achim 
Published: June 2011

AbstractMicroRNAs (miRNA) aberrantly expressed in tumors may offer novel therapeutic approaches to treatment. miR-145 is downregulated in various cancers including colon carcinoma in which in vitro studies have established proapoptotic and antiproliferative roles. miR-33a was connected recently to cancer through its capacity to downregulate the oncogenic kinase Pim-1. To date, miRNA replacement therapy has been hampered by the lack of robust nonviral delivery methods for in vivo administration. Here we report a method of miRNA delivery by using polyethylenimine (PEI)-mediated delivery of unmodified miRNAs, using miR-145 and miR-33a to preclinically validate the method in a mouse model of colon carcinoma. After systemic or local application of low molecular weight PEI/miRNA complexes, intact miRNA molecules were delivered into mouse xenograft tumors, where they caused profound antitumor effects. miR-145 delivery reduced tumor proliferation and increased apoptosis, with concomitant repression of c-Myc and ERK5 as novel regulatory target of miR-145. Similarly, systemic injection of PEI-complexed miR-33a was validated as a novel therapeutic targeting method for Pim-1, with antitumor effects comparable with PEI/siRNA-mediated direct in vivo knockdown of Pim-1 in the model. Our findings show that chemically unmodified miRNAs complexed with PEI can be used in an efficient and biocompatible strategy of miRNA replacement therapy, as illustrated by efficacious delivery of PEI/miR-145 and PEI/miR-33a complexes in colon carcinoma. Cancer Res; 71(15); 5214–24. ©2011 AACR.