bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of a Fluorescence
In Situ
Hybridization Method Using Peptide Nucleic Acid Probes for Detection of Helicobacter pylori Clarithromycin Resistance in Gastric Biopsy Specimens
Authors: Cerqueira Laura , Fernandes Ricardo M. , Ferreira Rui M. , Oleastro Mónica , Carneiro Fátima , Brandão Catarina , Pimentel-Nunes Pedro , Dinis-Ribeiro Mário , Figueiredo Céu , Keevil Charles W. , Vieira Maria J. , Azevedo Nuno F. 
Published: April 2013

ABSTRACT

Here, we evaluated a previously established peptide nucleic acid-fluorescence
in situ
hybridization (PNA-FISH) method as a new diagnostic test for
Helicobacter pylori
clarithromycin resistance detection in paraffin-embedded gastric biopsy specimens. Both a retrospective study and a prospective cohort study were conducted to evaluate the specificity and sensitivity of a PNA-FISH method to determine
H. pylori
clarithromycin resistance. In the retrospective study (
n
= 30 patients), full agreement between PNA-FISH and PCR-sequencing was observed. Compared to the reference method (culture followed by Etest), the specificity and sensitivity of PNA-FISH were 90.9% (95% confidence interval [CI], 57.1% to 99.5%) and 84.2% (95% CI, 59.5% to 95.8%), respectively. In the prospective cohort (
n
= 93 patients), 21 cases were positive by culture. For the patients harboring clarithromycin-resistant
H. pylori
, the method showed sensitivity of 80.0% (95% CI, 29.9% to 98.9%) and specificity of 93.8% (95% CI, 67.7% to 99.7%). These values likely represent underestimations, as some of the discrepant results corresponded to patients infected by more than one strain. PNA-FISH appears to be a simple, quick, and accurate method for detecting
H. pylori
clarithromycin resistance in paraffin-embedded biopsy specimens. It is also the only one of the methods assessed here that allows direct and specific visualization of this microorganism within the biopsy specimens, a characteristic that allowed the observation that cells of different
H. pylori
strains can subsist in very close proximity in the stomach.
Real-Time Optical Antimicrobial Susceptibility Testing
Authors: Fredborg Marlene , Andersen Klaus R. , Jørgensen Erik , Droce Aida , Olesen Tom , Jensen Bent B. , Rosenvinge Flemming S. , Sondergaard Teis E. 
Published: April 2013

ABSTRACT
Rapid antibiotic susceptibility testing is in high demand in health care fields as antimicrobial-resistant bacterial strains emerge and spread. Here, we describe an optical screening system (oCelloScope) which, based on time-lapse imaging of 96 bacteria-antibiotic combinations at a time, introduces real-time detection of bacterial growth and antimicrobial susceptibility with imaging material to support the automatically generated graphs. Automated antibiotic susceptibility tests of a monoculture showed statistically significant antibiotic effects within 6 min and within 30 min in complex samples from pigs suffering from catheter-associated urinary tract infections. The oCelloScope system provides a fast high-throughput screening method for detecting bacterial susceptibility that might entail an earlier diagnosis and introduction of appropriate targeted therapy and thus combat the threat from multidrug-resistant pathogenic bacteria. The oCelloScope system can be employed for a broad range of applications within bacteriology and might present new vistas as a point-of-care instrument in clinical and veterinary settings.
CDK9-Dependent Transcriptional Elongation in the Innate Interferon-Stimulated Gene Response to Respiratory Syncytial Virus Infection in Airway Epithelial Cells
Authors: Tian Bing , Zhao Yingxin , Kalita Mridul , Edeh Chukwudi B. , Paessler Slobodan , Casola Antonella , Teng Michael N. , Garofalo Roberto P. , Brasier Allan R. 
Published: April 2013

ABSTRACTRespiratory syncytial virus (RSV) is a negative-sense single-stranded RNA virus responsible for lower respiratory tract infections. During infection, the presence of double-stranded RNA (dsRNA) activates the interferon (IFN) regulatory factor 3 (IRF3) transcription factor, an event triggering expression of immediate early, IFN-stimulated genes (ISGs). We examine the role of transcriptional elongation in control of IRF3-dependent ISG expression. RSV infection induces ISG54, ISG56, and CIG5 gene expression in an IRF3-dependent manner demonstrated by IRF3 small interfering RNA (siRNA) silencing in both A549 epithelial cells and IRF3−/−MEFs. ISG expression was mediated by the recruitment of IRF3, CDK9, polymerase II (Pol II), and phospho-Ser2carboxy-terminal domain (CTD) Pol II to the IFN-stimulated response element (ISRE) binding sites of the IRF3-dependent ISG promoters in native chromatin. We find that RSV infection enhances the activated fraction of cyclin-dependent kinase 9 (CDK9) by promoting its association with bromodomain 4 (BRD4) and disrupting its association with the inhibitory 7SK small nuclear RNA. The requirement of CDK9 activity for ISG expression was shown by siRNA-mediated silencing of CDK9 and by a selective CDK9 inhibitor in A549 cells. In contrast, RSV-induced beta interferon (IFN-β) expression is not influenced by CDK9 inhibition. Using transcript-selective quantitative real-time reverse transcription-PCR (Q-RT-PCR) assays for the ISG54 gene, we observed that RSV induces transition from short to fully spliced mRNA transcripts and that this transition is blocked by CDK9 inhibition in both A549 and primary human small airway epithelial cells. These data indicate that transcription elongation plays a major role in RSV-induced ISG expression and is mediated by IRF3-dependent recruitment of activated CDK9. CDK9 activity may be a target for immunomodulation in RSV-induced lung disease.
940 nm diode laser therapy in management of recurrent apthous ulcer
Authors: Misra Neeta , Maiti Debasmita , Misra Pradyumna , Singh Ashish Kumar 
Published: April 2013

Recurrent apthous stomatitis (RAS) is one of the most common oral inflammatory diseases characterised by painful recurrent ulcerations of the orofacial region. The ulcers occur in three clinical forms: minor, major and herpetiform. Several therapies have been advocated to manage these lesions such as topical corticosteroids (triamcinolone acetonide, hydrocortisone acetate and clobetasol propionate), chlorhexidine mouth rinses, tetracycline oral rinses, thalidomide, fluocinonide, colchicines and the immune boosting agent levamosile, vitamin therapy and topical interferon α-2a. Laser therapy is used as an alternative method in treatment of RAS.In this paper one patient with RAS was treated using a 940 nm diode laser for symptomatic relief of pain and burning sensation and healing of ulcer.
Educational inequalities in mortality in northern, mid and southern Italy and the contribution of smoking
Authors: Federico Bruno , Mackenbach Johan P , Eikemo Terje A , Sebastiani Gabriella , Marinacci Chiara , Costa Giuseppe , Kunst Anton E 
Published: April 2013

BackgroundPrevious studies have shown that mortality inequalities are smaller in Italy than in most European countries. This may be due to the weak association between socioeconomic status and smoking in Italy. However, most published studies were based on data from a single city in northern Italy (Turin). In this study, we aimed to assess the size of mortality inequalities in Italy as a whole, their geographical pattern of variation within Italy, and the contribution of smoking to these inequalities.MethodsParticipants in the National Health Interview Survey 1999–2000 were followed up for mortality until 31 December 2007. Using Cox regression, we computed the age-adjusted relative index of inequality (RII) for all-cause mortality with and without controlling for smoking status and intensity. Education was used as an indicator of socioeconomic status.ResultsAmong 72 762 individuals aged 30–74 years at baseline, 4092 died during the follow-up. The age-adjusted RII of mortality was 1.69 (95% CI 1.44 to 2.00) among men and 1.43 (95% CI 1.13 to 1.82) among women. Among men, inequalities were larger in both northern and southern regions than in the middle of the country, whereas among women they were larger in the south. After controlling for smoking RII decreased to 1.63 (95% CI 1.38 to 1.92) among men and increased to 1.54 (95% CI 1.21 to 1.96) among women. The geographical variation in mortality inequalities was not affected by smoking adjustment.ConclusionsMortality inequalities in Italy are smaller than in most European countries. This is due, among other factors, to the weak socioeconomic pattern of smoking over the past decades in Italy.
New multituberculate mammal from the Early Cretaceous of eastern North America
Authors: Cifelli Richard L. , Gordon Cynthia L. , Lipka Thomas R. 
Published: April 2013

Multituberculates, though among the most commonly encountered mammalian fossils of the Mesozoic, are poorly known from the North American Early Cretaceous, with only one taxon named to date. Herein we describe Argillomys marylandensis, gen. et sp. nov., from the Early Cretaceous of Maryland, based on an isolated M2. Argillomys represents the second mammal known from the Arundel Clay facies of the Patuxent Formation (Lower Cretaceous: Aptian). Though distinctive in its combination of characters (e.g., enamel ornamentation consisting of ribs and grooves only, cusp formula 2:4, presence of distinct cusp on anterobuccal ridge, enlargement of second cusp on buccal row, central position of ultimate cusp in lingual row, great relative length), the broader affinities of Argillomys cannot be established because of non-representation of the antemolar dentition. Based on lack of apomorphies commonly seen among Cimolodonta (e.g., three or more cusps present in buccal row, fusion of cusps in lingual row, cusps strongly pyramidal and separated by narrow grooves), we provisionally regard Argillomys as a multituberculate of “plagiaulacidan” grade. Intriguingly, it is comparable in certain respects to some unnamed Paulchoffatiidae, a family otherwise known from the Late Jurassic – Early Cretaceous of the Iberian Peninsula.
A CONTINUATION METHOD AND ITS CONVERGENCE FOR SOLVING NONLINEAR EQUATIONS IN BANACH SPACES
Authors: PRASHANTH M. , GUPTA D. K. 
Published: April 2013

A continuation method is a parameter based iterative method establishing a continuous connection between two given functions/operators and used for solving nonlinear equations in Banach spaces. The semilocal convergence of a continuation method combining Chebyshev's method and Convex acceleration of Newton's method for solving nonlinear equations in Banach spaces is established in [J. A. Ezquerro, J. M. Gutiérrez and M. A. Hernández [1997] J. Appl. Math. Comput.85: 181–199] using majorizing sequences under the assumption that the second Frechet derivative satisfies the Lipschitz continuity condition. The aim of this paper is to use recurrence relations instead of majorizing sequences to establish the convergence analysis of such a method. This leads to a simpler approach with improved results. An existence–uniqueness theorem is given. Also, a closed form of error bounds is derived in terms of a real parameter α ∈ [0, 1]. Four numerical examples are worked out to demonstrate the efficacy of our convergence analysis. On comparing the existence and uniqueness region and error bounds for the solution obtained by our analysis with those obtained by using majorizing sequences, it is found that our analysis gives better results in three examples, whereas in one example it gives the same results. Further, we have observed that for particular values of the α, our analysis reduces to those for Chebyshev's method (α = 0) and Convex acceleration of Newton's method (α = 1) respectively with improved results.
The Epidemic of Non–Hodgkin Lymphoma in the United States: Disentangling the Effect of HIV, 1992–2009
Authors: Shiels Meredith S. , Engels Eric A. , Linet Martha S. , Clarke Christina A. , Li Jianmin , Hall H. Irene , Hartge Patricia , Morton Lindsay M. 
Published: April 2013

Abstract
Background: For decades, non–Hodgkin lymphoma (NHL) incidence has been increasing worldwide. NHL risk is strongly increased among HIV-infected people. Our understanding of trends in NHL incidence has been hampered by difficulties in separating HIV-infected NHL cases from general population rates.
Methods: NHL incidence data during 1992–2009 were derived from 10 U.S. SEER cancer registries with information on HIV status at NHL diagnosis. The CDC estimated the number of people living with HIV in the registry areas. The proportion of NHL cases with HIV and NHL rates in the total and the HIV-uninfected populations were estimated. Time trends were assessed with Joinpoint analyses.
Results: Of 115,643 NHL cases diagnosed during 1992–2009, 5.9% were HIV-infected. The proportions of NHL cases with HIV were highest for diffuse large B-cell (DLBCL; 7.8%), Burkitt (26.9%), and peripheral T-cell lymphomas (3.2%) with low proportions (≤1.1%) in the other subtypes. NHL rates in the total population increased 0.3% per year during 1992–2009. However, rates of NHL in HIV-uninfected people increased 1.4% per year during 1992–2003, before becoming stable through 2009. Similar trends were observed for DLBCLs and follicular lymphoma in HIV-uninfected people; rates increased 2.7% per year until 2003 and 1.7% per year until 2005, respectively, before stabilizing.
Conclusions: NHL incidence rates in the United States have plateaued over the last 5–10 years, independent of HIV infection.
Impact: Although the causes of the long-term increase in NHL incidence rates in the United States remain unknown, general population rates of NHL have stabilized since the early 2000s, independent of HIV. Cancer Epidemiol Biomarkers Prev; 22(6); 1069–78. ©2013 AACR.
Alcohol intake and risk of venous thromboembolism
Authors: Gaborit Freja , Overvad Kim , Nørgaard Mette , Kristensen Søren , Tjønneland Anne , Severinsen Marianne 
Published: April 2013

SummaryKnowledge about the influence of alcohol intake on the risk of venous thromboembolism (VTE) is limited. We investigated the risk of VTE according to alcohol intake and drinking pattern among 27,178 men and 29,876 women participating in the Danish follow-up study Diet, Cancer and Health. Information on alcohol exposure and potential confounders were obtained from baseline questionnaires. We used Cox proportional hazard models to assess the association between VTE and alcohol intake. We performed separate analyses for the two sexes. During follow-up 619 incidents VTE events were verified. The lowest incidence rates of VTE were found for an average weekly intake of 3.9–13.9 standard drinks per weeks both for men and women. The adjusted hazard ratio (HR) was 0.91 [95%CI: 0.69–1.19] for women and 0.75 [95%CI: 0.56–1.02] for men according to an average alcohol intake of 3.9–13.9 standard drinks per week compared with low alcohol intake. In men, alcohol intake 2–6 times per week was associated with a lower risk of VTE compared to once per week (HR 0.77 [95%CI: 0.59–0.99]), but the difference disappeared after adjustment for total alcohol intake. We found no difference in the risk of VTE according to wine and beer intake. In conclusion, we found no consistent or statistically significant association between VTE and alcohol intake. Our data showed a u-formed association between alcohol intake and VTE, indicating that moderate alcohol intake may lower the risk of VTE with 10–30% in men.
Human Rights Treaty Bodies and the Jurisdiction of the International Court of Justice
Authors: Zimmermann Andreas 
Published: April 2013

Abstract
In recent years, the ICJ has had to deal more and more often with alleged violations of major human rights treaties and the respective compromissory clauses contained in such treaties. Yet, the interrelationship between the Court’s treaty-based jurisdiction under such clauses and State complaint mechanisms, as provided for in human rights treaties, has not yet been fully considered and analysed. Moreover, there might also be interlinkages between the ICJ’s contentious jurisdiction under Article 36 (2) of the ICJ Statute and such State complaint procedures.
Procedural Developments at the International Court of Justice
Authors: Bordin Fernando Lusa 
Published: April 2013

Abstract
The present column covers procedural developments at the International Court of Justice in the period spanning from 1 April 2012 to 31 January 2013. These include: the consideration by the Court of the critical date to ascertain the existence of a dispute, and of the locus standi of States to bring claims in the collective interest, in the Questions relating to the Obligation to Prosecute or Extradite case; questions arising from the decision that a new claim was admissible but could not be upheld in the Territorial and Maritime Dispute case; and proof and quantification of material and moral damages in the Diallo/Compensation case.
Social Participation in Indonesian Media and Art: Echoes from the Past, Visions for the Future
Authors: Jurriëns Edwin 
Published: April 2013

Abstract
This article uses a critical and historical perspective to examine some of the achievements of Indonesian community media, the problems they have encountered, as well as the solutions they are offering. It analyses the similarities and differences with earlier genres with an explicit participatory agenda, including certain forms of LEKRA literature and art of the 1950s and 1960s, ‘people’s theatre’ since the 1970s, and ‘conscientization art’ since the 1980s. One of the main challenges for contemporary community media has been to reconcile class differences in the collaboration between media or art facilitators and local communities. These and other factors have affected the accessibility, distribution, sustainability and reach of their ideas, activities and outputs. The article demonstrates how facilitators and practitioners have tried to solve some of these problems through the exploration of alternative media networks, formats and content.
Modern Hindu Intellectuals and Ancient Texts: Reforming Śaiva Yoga in Bali
Authors: Acri Andrea 
Published: April 2013

Abstract
This article aims at providing a fresh perspective on the modern, reformed version of ‘Balinese Hinduism’ that came to the fore on the island since the early 20th century. It describes certain important elements of doctrinal continuity and change in the light of the pre-colonial Śaiva religious discourse, on the basis of textual and historical data that have so far been neglected. It attempts to show that the Javano-Balinese theological tradition is characterized by a remarkable continuity, especially when it comes to its exegetical and text-building practices, but also by important elements of changes. To investigate the nature of such changes—in particular the treatment of Yoga in selected textual sources—and the historical and cultural dynamics behind them is the main concern of this article.
Dutch Colonial Containment of Islam in Manggarai, West-Flores, in Favour of Catholicism, 1907-1942
Authors: Steenbrink Karel 
Published: April 2013

Abstract
West Flores or Manggarai was until 1900 known as territory of the Muslim Sultan of Bima. In 1907 the Dutch effectively took possession of the region and after 1910 they entrusted the introduction of schools to the Catholic missionaries. The coastal Muslim settlements were neglected in favour of the mountain region, where finally one local chief, mission-educated Alexander Baroek became the most important native counterpart of the colonial rule. The ties with Bima were formally broken in the 1920s. Herewith Catholicism gained political and social influence to the detriment of the expansion of Islam and Manggarai joined the rest of Flores to become a majority Catholic society. There was no overall strategy to destroy Muslim influence, but it was simply the result of a longer chain of not always related decisions. This choice was in line with the colonial strategy of creating a prosperous Flores.
Multiple mismatches at the low expression HLA loci DP, DQ, and DRB3/4/5 associate with adverse outcomes in hematopoietic stem cell transplantation
Authors: Fernández-Viña Marcelo A. , Klein John P. , Haagenson Michael , Spellman Stephen R. , Anasetti Claudio , Noreen Harriet , Baxter-Lowe Lee Ann , Cano Pedro , Flomenberg Neal , Confer Dennis L. , Horowitz Mary M. , Oudshoorn Machteld , Petersdorf Effie W. , Setterholm Michelle , Champlin Richard , Lee Stephanie J. , de Lima Marcos 
Published: April 2013

Key PointsThree or more mismatches at the Low Expression Loci may adversely affect clinical outcome after 7/8 matched transplantation. Match grade at the Low Expression HLA Loci may be considered to select 7/8 donors with potentially lower posttransplant risks.
Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses
Authors: Yang Jun-Bo , Tang Min , Li Hong-Tao , Zhang Zhi-Rong , Li De-Zhu 
Published: April 2013

Abstract

Background

Cymbidium orchids, including some 50 species, are the famous flowers, and they possess high commercial value in the floricultural industry. Furthermore, the values of different orchids are great differences. However, species identification is very difficult. To a certain degree, chloroplast DNA sequence data are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. However, there is no evidence that a short sequence can distinguish all plant species from each other in order to infer phylogenetic relationships. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution.

Results
The complete nucleotide sequences of eight individuals from a total of five Cymbidium species’ chloroplast (cp) genomes were determined using Illumina sequencing technology of the total DNA via a combination of de novo and reference-guided assembly. The length of the Cymbidium cp genome is about 155 kb. The cp genomes contain 123 unique genes, and the IR regions contain 24 duplicates. Although the genomes, including genome structure, gene order and orientation, are similar to those of other orchids, they are not evolutionarily conservative. The cp genome of Cymbidium evolved moderately with more than 3% sequence divergence, which could provide enough information for phylogeny. Rapidly evolving chloroplast genome regions were identified and 11 new divergence hotspot regions were disclosed for further phylogenetic study and species identification in Orchidaceae.

Conclusions
Phylogenomic analyses were conducted using 10 complete chloroplast genomes from seven orchid species. These data accurately identified the individuals and established the phylogenetic relationships between the species. The results reveal that phylogenomics based on organelle genome sequencing lights the species identification—organelle-scale “barcodes”, and is also an effective approach for studying whole populations and phylogenetic characteristics of Cymbidium.