bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discrepancies and Rates of Publication in Orthopaedic Sports Medicine Abstracts
Authors: Kleweno Conor P. , Bryant Whitney K. , Jacir Albert M. , Levine William N. , Ahmad Christopher S. 
Published: July 2008

Background Presentations of clinically relevant data at AOSSM national meetings are presented yearly and may influence clinical decision making. Hypothesis The incidence of presentations that do not subsequently get published is high, and the numbers of major and minor inconsistencies, once published, are also high. Study Design Systematic review. Methods A database was created of all abstracts presented at AOSSM meetings from 1999 to 2001 from official program books. To assess whether each abstract had been followed by publication in a peer-reviewed journal, a PubMed search was conducted to include a 5-year follow-up for each conference. Minor inconsistencies included differences in title, authors, presentation of all outcomes, and authors’ interpretation of data. Major inconsistencies included discrepancies in study objective and/or hypothesis, study design, primary and secondary outcome measures, sample size, statistical analysis, results, and standard deviations/confidence intervals. Results Overall, 98 of the 165 abstracts presented at AOSSM national meetings from 1999 to 2001 were published in a peer-reviewed journal within 5 years, a publication rate of 59.4%. The median time to publication for all articles was 21 (range, 1–60) months. The majority of articles (61) were published in the American Journal of Sports Medicine (62.2%). The median number of major and minor inconsistencies from abstract to publication was 1 (range, 0–5) and 1 (range, 0–4), respectively. Sixty-two of the 98 published abstracts (63%) had at least 1 major inconsistency, while 79 (81 %) had at least 1 minor inconsistency. In 5 manuscripts (5%), the authors’ interpretation of the data had changed, and in 2 (2%), the change essentially invalidated the abstract. Conclusion A large number of scientific presentations do not get published in a peer-reviewed journal. In addition, those published have a significant number of changes that, in a small percentage of cases, alter the validity of the original presentation. Clinical Relevance Orthopaedic surgeons and other attendees as well as nonattendees who reference conference abstracts need to exercise good judgment when considering the implications of oral presentations of unpublished materials. When reviewing meeting presentation abstracts, readers should remember that the material being presented is often not in its definitive or ultimate form.
Hypersensitivity pneumonitis secondary to lovebirds: a new cause of bird fancier's disease
Authors: Funke M. , Fellrath J-M. 
Published: July 2008

Hypersensitivity pneumonitis (HP) is an immunologically mediated lung disease due to the repetitive inhalation of antigens. Most new cases arise from residential exposures, notably to birds, and are thus more difficult to recognise.The present authors report a 59-yr-old male who complained of dyspnoea and cough while being treated with amiodarone. Pulmonary function tests revealed restriction and obstruction with low diffusing lung capacity for carbon monoxide and partial pressure of oxygen. A high-resolution computed tomography chest scan and bronchoalveolar lavage showed diffuse bilateral ground-glass attenuation and lymphocytic alveolitis, respectively.Initial diagnosis was amiodarone pulmonary toxicity, but because of a rapidly favourable evolution, this diagnosis was questioned. A careful environmental history revealed a close contact with lovebirds shortly before the onset of symptoms. Precipitins were strongly positive against lovebird droppings, but were negative against other avian antigens. The patient was diagnosed with hypersensitivity pneumonitis to lovebirds. Avoidance of lovebirds and steroid treatment led to rapid improvement.The present observation identifies a new causative agent for hypersensitivity pneumonitis and highlights the importance of a thorough environmental history and of searching for precipitins against antigens directly extracted from the patient's environment. These two procedures should allow a more precise classification of some cases of pneumonitis, and thus might avoid progression of active undiagnosed hypersensitivity pneumonitis to irreversible fibrosis or emphysema.
Exhaled breath condensate biomarkers in COPD
Authors: Borrill Z. L. , Roy K. , Singh D. 
Published: July 2008

Biomarkers in chronic obstructive pulmonary disease may be useful in aiding diagnosis, defining specific phenotypes of disease, monitoring exacerbations and evaluating the effects of drugs. Exhaled breath condensate is a noninvasive means of sampling the airways, allowing biomarkers of airway inflammation and oxidative stress to be measured. In the present review, the use of exhaled breath condensate biomarkers in chronic obstructive pulmonary disease is explored and potential applications in diagnosis, disease phenotyping, exacerbation monitoring and clinical trials are considered. Exhaled breath condensate biomarkers are comprehensively reviewed in terms of method validation, reproducibility, disease specificity and sensitivity to detect changes in airway inflammation.The commonly used exhaled breath condensate methodologies in chronic obstructive pulmonary disease patients are shown to have considerable variability, due to technical issues concerning both sample collection and analysis. Despite these issues, there is still data to support the use of exhaled breath condensate biomarkers for monitoring chronic obstructive pulmonary disease exacerbations and the response to pharmacological intervention. Further improvements to sample collection and analysis methods will improve the sensitivity of these biomarkers. The use of cytokine arrays, mass spectrometry and nuclear magnetic resonance profiling of exhaled breath condensate has opened a new avenue for analysis, as hypothesis generation from such profiling may lead to further selection of biomarkers for specific analysis.
Msx1 and Msx2are required for endothelial-mesenchymal transformation of the atrioventricular cushions and patterning of the atrioventricular myocardium
Authors: Chen Yi-Hui , Ishii Mamoru , Sucov Henry M , Maxson Robert E 
Published: July 2008

Abstract

Background

Msx1 and Msx2, which belong to the highly conserved Nk family of homeobox genes, display overlapping expression patterns and redundant functions in multiple tissues and organs during vertebrate development. Msx1 and Msx2 have well-documented roles in mediating epithelial-mesenchymal interactions during organogenesis. Given that both Msx1 and Msx2 are crucial downstream effectors of Bmp signaling, we investigated whether Msx1 and Msx2 are required for the Bmp-induced endothelial-mesenchymal transformation (EMT) during atrioventricular (AV) valve formation.

Results
While both Msx1-/- and Msx2-/- single homozygous mutant mice exhibited normal valve formation, we observed hypoplastic AV cushions and malformed AV valves in Msx1-/-; Msx2-/- mutants, indicating redundant functions of Msx1 and Msx2 during AV valve morphogenesis. In Msx1/2 null mutant AV cushions, we found decreased Bmp2/4 and Notch1 signaling as well as reduced expression of Has2, NFATc1 and Notch1, demonstrating impaired endocardial activation and EMT. Moreover, perturbed expression of chamber-specific genes Anf, Tbx2, Hand1 and Hand2 reveals mispatterning of the Msx1/2 double mutant myocardium and suggests functions of Msx1 and Msx2 in regulating myocardial signals required for remodelling AV valves and maintaining an undifferentiated state of the AV myocardium.

Conclusion
Our findings demonstrate redundant roles of Msx1 and Msx2 in regulating signals required for development of the AV myocardium and formation of the AV valves.
Transcriptional profiling of putative human epithelial stem cells
Authors: Koçer Salih S , Djurić Petar M , Bugallo Mónica F , Simon Sanford R , Matic Maja 
Published: July 2008

Abstract

Background
Human interfollicular epidermis is sustained by the proliferation of stem cells and their progeny, transient amplifying cells. Molecular characterization of these two cell populations is essential for better understanding of self renewal, differentiation and mechanisms of skin pathogenesis. The purpose of this study was to obtain gene expression profiles of alpha 6+/MHCI+, transient amplifying cells and alpha 6+/MHCI-, putative stem cells, and to compare them with existing data bases of gene expression profiles of hair follicle stem cells. The expression of Major Histocompatibility Complex (MHC) class I, previously shown to be absent in stem cells in several tissues, and alpha 6 integrin were used to isolate MHCI positive basal cells, and MHCI low/negative basal cells.

Results
Transcriptional profiles of the two cell populations were determined and comparisons made with published data for hair follicle stem cell gene expression profiles. We demonstrate that presumptive interfollicular stem cells, alpha 6+/MHCI- cells, are enriched in messenger RNAs encoding surface receptors, cell adhesion molecules, extracellular matrix proteins, transcripts encoding members of IFN-alpha family proteins and components of IFN signaling, but contain lower levels of transcripts encoding proteins which take part in energy metabolism, cell cycle, ribosome biosynthesis, splicing, protein translation, degradation, DNA replication, repair, and chromosome remodeling. Furthermore, our data indicate that the cell signaling pathways Notch1 and NF-κB are downregulated/inhibited in MHC negative basal cells.

Conclusion
This study demonstrates that alpha 6+/MHCI- cells have additional characteristics attributed to stem cells. Moreover, the transcription profile of alpha 6+/MHCI- cells shows similarities to transcription profiles of mouse hair follicle bulge cells known to be enriched for stem cells. Collectively, our data suggests that alpha 6+/MHCI- cells may be enriched for stem cells. This study is the first comprehensive gene expression profile of putative human epithelial stem cells and their progeny that were isolated directly from neonatal foreskin tissue. Our study is important for understanding self renewal and differentiation of epidermal stem cells, and for elucidating signaling pathways involved in those processes. The generated data base may serve those working with other human epithelial tissue progenitors.
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis
Authors: Nelson Curtis M , Herron Michael J , Felsheim Roderick F , Schloeder Brian R , Grindle Suzanne M , Chavez Adela Oliva , Kurtti Timothy J , Munderloh Ulrike G 
Published: July 2008

Abstract

Background

Anaplasma phagocytophilum (Ap) is an obligate intracellular bacterium and the agent of human granulocytic anaplasmosis, an emerging tick-borne disease. Ap alternately infects ticks and mammals and a variety of cell types within each. Understanding the biology behind such versatile cellular parasitism may be derived through the use of tiling microarrays to establish high resolution, genome-wide transcription profiles of the organism as it infects cell lines representative of its life cycle (tick; ISE6) and pathogenesis (human; HL-60 and HMEC-1).

Results
Detailed, host cell specific transcriptional behavior was revealed. There was extensive differential Ap gene transcription between the tick (ISE6) and the human (HL-60 and HMEC-1) cell lines, with far fewer differentially transcribed genes between the human cell lines, and all disproportionately represented by membrane or surface proteins. There were Ap genes exclusively transcribed in each cell line, apparent human- and tick-specific operons and paralogs, and anti-sense transcripts that suggest novel expression regulation processes. Seven virB2 paralogs (of the bacterial type IV secretion system) showed human or tick cell dependent transcription. Previously unrecognized genes and coding sequences were identified, as were the expressed p44/msp2 (major surface proteins) paralogs (of 114 total), through elevated signal produced to the unique hypervariable region of each – 2/114 in HL-60, 3/114 in HMEC-1, and none in ISE6.

Conclusion
Using these methods, whole genome transcription profiles can likely be generated for Ap, as well as other obligate intracellular organisms, in any host cells and for all stages of the cell infection process. Visual representation of comprehensive transcription data alongside an annotated map of the genome renders complex transcription into discernable patterns.
Transcriptome analysis of a respiratory Saccharomyces cerevisiae strain suggests the expression of its phenotype is glucose insensitive and predominantly controlled by Hap4, Cat8 and Mig1
Authors: Bonander Nicklas , Ferndahl Cecilia , Mostad Petter , Wilks Martin DB , Chang Celia , Showe Louise , Gustafsson Lena , Larsson Christer , Bill Roslyn M 
Published: July 2008

Abstract

Background
We previously described the first respiratory Saccharomyces cerevisiae strain, KOY.TM6*P, by integrating the gene encoding a chimeric hexose transporter, Tm6*, into the genome of an hxt null yeast. Subsequently we transferred this respiratory phenotype in the presence of up to 50 g/L glucose to a yeast strain, V5 hxt1-7 Δ, in which only HXT1-7 had been deleted. In this study, we compared the transcriptome of the resultant strain, V5.TM6*P, with that of its wild-type parent, V5, at different glucose concentrations.

Results
cDNA array analyses revealed that alterations in gene expression that occur when transitioning from a respiro-fermentative (V5) to a respiratory (V5.TM6*P) strain, are very similar to those in cells undergoing a diauxic shift. We also undertook an analysis of transcription factor binding sites in our dataset by examining previously-published biological data for Hap4 (in complex with Hap2, 3, 5), Cat8 and Mig1, and used this in combination with verified binding consensus sequences to identify genes likely to be regulated by one or more of these. Of the induced genes in our dataset, 77% had binding sites for the Hap complex, with 72% having at least two. In addition, 13% were found to have a binding site for Cat8 and 21% had a binding site for Mig1. Unexpectedly, both the up- and down-regulation of many of the genes in our dataset had a clear glucose dependence in the parent V5 strain that was not present in V5.TM6*P. This indicates that the relief of glucose repression is already operable at much higher glucose concentrations than is widely accepted and suggests that glucose sensing might occur inside the cell.

Conclusion
Our dataset gives a remarkably complete view of the involvement of genes in the TCA cycle, glyoxylate cycle and respiratory chain in the expression of the phenotype of V5.TM6*P. Furthermore, 88% of the transcriptional response of the induced genes in our dataset can be related to the potential activities of just three proteins: Hap4, Cat8 and Mig1. Overall, our data support genetic remodelling in V5.TM6*P consistent with a respiratory metabolism which is insensitive to external glucose concentrations.
Genetic variation in the invasive avian parasite, Philornis downsi (Diptera, Muscidae) on the Galápagos archipelago
Authors: Dudaniec Rachael Y , Gardner Michael G , Donnellan Steve , Kleindorfer Sonia 
Published: July 2008

Abstract

Background
Understanding the dispersal and genetic structure of invasive insects across islands is important for designing management plans that are appropriate at spatial and temporal scales. For invasive parasites, population dynamics are largely determined by the distribution and density of their host species. The introduced parasitic fly, Philornis downsi, parasitises nestlings of endemic birds on all major islands of the Galápagos archipelago. The fly's high mortality and fitness impacts are of conservation concern for vulnerable and declining species of Darwin's finches. Using microsatellite data in Bayesian clustering and landscape genetic analyses, we examine gene flow and dispersal in P. downsi between three islands and across habitats (highlands, lowlands) and examine for the presence of population bottlenecks. We also examine variation at the mitochondrial gene CO1 across islands to establish if cryptic species were present.

Results
Both the mitochondrial and microsatellite data were consistent with there being a single species across islands. We found low genetic differentiation between islands and strong evidence for inter-island gene flow, or shared recent ancestry among individuals. Landscape genetic analysis identified two genetic clusters: one encompassing Santa Cruz and Isabela, and one on Floreana Island. There was no evidence of genetic differentiation between habitats and molecular variance was mainly attributable to within individuals. The combined P. downsi population was found to have undergone a population bottleneck.

Conclusion

Philornis downsi populations have high connectivity within and between islands, with low levels of genetic differentiation between Floreana and the other two islands examined. The genetic bottleneck found across islands suggests there was a small founding population or few introduction events of P. downsi. The high dispersal capacity and wide habitat use of P. downsi highlights the significant threat that this parasite poses to the Galápagos avifauna. Our findings are relevant for assessing the viability of methods to control P. downsi on Galápagos, such as the sterile insect technique.
Family physician and endocrinologist coordination as the basis for diabetes care in clinical practice
Authors: Duran Alejandra , Runkle Isabelle , Matía Pilar , de Miguel Maria P , Garrido Sofia , Cervera Emilio , Fernandez Maria D , Torres Pilar , Lillo Tomas , Martin Patricia , Cabrerizo Lucio , de la Torre Nuria Garcia , Calle Jose R , Ibarra Jose , Charro Aniceto L , Calle-Pascual Alfonso L 
Published: July 2008

Abstract

Background
To estimate the proportion of diabetic patients (DPts) with peripheral vascular disease treated at a primary health care site after an endocrinologist-based intervention, who meet ATP III and Steno targets of metabolic control, as well as to compare the outcome with the results of the patients treated by endocrinologists.

Methods
A controlled, prospective over 30-months period study was conducted in area 7 of Madrid. One hundred twenty six eligible diabetic patients diagnosed as having peripheral vascular disease between January 2003 and June 2004 were included in the study. After a treatment period of three months by the Diabetes team at St Carlos Hospital, 63 patients were randomly assigned to continue their follow up by diabetes team (Group A) and other 63 to be treated by the family physicians (FP) at primary care level with continuous diabetes team coordination (Group B). 57 DPts from Group A and 59 from Group B, completed the 30 months follow-up period. At baseline both groups were similar in age, weight, time from diagnosis and metabolic control. The main outcomes of this study were the proportion of patients meeting ATP III and Steno goals for HbA1c (%), Cholesterol, HDL cholesterol, LDL cholesterol, triglycerides, blood pressure, albumine-to-creatinine excretion ratio (ACR), body mass index (BMI), waist circumference (WC), anti-aggregation treatment and smoking status.

Results
At the end of the follow up, no differences were found between the groups. More than 37% of diabetic patients assigned to be treated by FP achieved a HbA1c < 6.5%, more than 50% a ACR < 30 mg/g, and more than 80% reached low risk values for cholesterol, LDL cholesterol, triglycerides, diastolic blood pressure and were anti-aggregated, and 12% remained smokers. In contrast, less than 45% achieved a systolic blood pressure < 130 mm Hg, less than 12% had a BMI < 25 Kg.m-2 (versus 23% in group A; p < 0.05) and 49%/30% (men/women) had a waist circumference of low risk.

Conclusion
Improvements in metabolic control among diabetic patients with peripheral vascular disease treated at a primary health care setting is possible, reaching similar results to the patients treated at a specialized level. Despite such an improvement, body weight control remains more than poor in both levels, mainly at primary care level. General practitioner and endocrinologist coordination care may be important to enhance diabetes management in primary care settings.

Trial registration
Clinical Trial number ISRCTN75037597
Polymorphisms in IL12A and cockroach allergy in children with asthma
Authors: Pistiner Michael , Hunninghake Gary M , Soto-Quiros Manuel E , Avila Lydiana , Murphy Amy , Lasky-Su Jessica , Schuemann Brooke , Klanderman Barbara J , Raby Benjamin A , Celedón Juan C 
Published: July 2008

AbstractBackgroundIL12A has been implicated in T-cell development and may thus influence the development of atopy and allergic diseases.MethodsWe tested for association between four linkage disequilibrium (LD)-tagging SNPs (rs2243123, rs2243151, rs668998, and rs17826053) inIL12Aand asthma and allergy-related (serum total and allergen-specific IgE, and skin test reactivity [STR] to two common allergens) phenotypes in two samples: 417 Costa Rican children with asthma and their parents, and 470 families of 503 white children in the Childhood Asthma Management Program (CAMP). The analysis was conducted using the family-based association test (FBAT) statistic implemented in the PBAT program.ResultsAmong Costa Rican children with asthma, homozygosity for the minor allele of each of two SNPs inIL12A(rs2243123 and rs2243151) was associated with increased risks of STR to American cockroach (P ≤ 0.03 for both SNPs), STR to German cockroach (P ≤ 0.01 for both SNPs), and having a positive IgE to German cockroach (P < 0.05 for both SNPs). Among children in CAMP, homozygosity for the minor allele of SNP rs2243151 inIL12Awas inversely associated with STR to German cockroach (P = 0.03) and homozygosity for the minor allele of SNP rs17826053 inIL12Awas associated with increased risks of STR to American cockroach (P = 0.01) and STR to German cockroach (P = 0.007). There was no significant association between any SNP inIL12Aand asthma, STR to dust mite, or total IgE in Costa Rica or CAMP.ConclusionOur findings suggest that variants inIL12Ainfluence cockroach allergy among children with asthma.
Oral acantholytic squamous cell carcinoma shares clinical and histological features with angiosarcoma
Authors: Driemel Oliver , Müller-Richter Urs DA , Hakim Samer G , Bauer Richard , Berndt Alexander , Kleinheinz Johannes , Reichert Torsten E , Kosmehl Hartwig 
Published: July 2008

Abstract

Background
acantholytic squamous cell carcinomas (ASCC) and intraoral angiosarcoma share similar histopathological features. Aim of this study was to find marker for a clear distinction.

Methods
Four oral acantholytic squamous cell carcinomas and one intraoral angiosarcoma are used to compare the eruptive intraoral growth-pattern, age-peak, unfavourable prognosis and slit-like intratumorous spaces in common histological staining as identical clinical and histopathological features. Immunohistochemical staining for pancytokeratin, cytokeratin, collagen type IV, γ2-chain of laminin-5, endothelial differentiation marker CD31 and CD34, F VIII-associated antigen, Ki 67-antigen, β-catenin, E-cadherin, α-smooth-muscle-actin and Fli-1 were done.

Results
Cytokeratin-immunoreactive cells can be identified in both lesions. The large vascularization of ASCC complicates the interpretation of vascular differential markers being characteristic for angiosarcoma. Loss of cell-cell-adhesion, monitored by loss of E-cadherin and β-catenin membrane-staining, are indetified as reasons for massive expression of invasion-factor ln-5 in ASCC and considered responsible for unfavourable prognosis of ASCC. Expression of Fli-1 in angiosarcoma and cellular immunoreaction for ln-5 in ASCC are worked out as distinguishing features of both entities.

Conclusion
Fli-1 in angiosarcoma and ln-5 in ASCC are distinguishing features.