bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival
Authors: Sveen Anita , Ågesen Trude H , Nesbakken Arild , Rognum Torleiv O , Lothe Ragnhild A , Skotheim Rolf I 
Published: May 2011

Abstract
Background
Colorectal cancer (CRC) is a heterogeneous disease that, on the molecular level, can be characterized by inherent genomic instabilities; chromosome instability and microsatellite instability. In the present study we analyze genome-wide disruption of pre-mRNA splicing, and propose transcriptome instability as a characteristic that is analogous to genomic instability on the transcriptome level.

Methods
Exon microarray profiles from two independent series including a total of 160 CRCs were investigated for their relative amounts of exon usage differences. Each exon in each sample was assigned an alternative splicing score calculated by the FIRMA algorithm. Amounts of deviating exon usage per sample were derived from exons with extreme splicing scores.

Results
There was great heterogeneity within both series in terms of sample-wise amounts of deviating exon usage. This was strongly associated with the expression levels of approximately half of 280 splicing factors (54% and 48% of splicing factors were significantly correlated to deviating exon usage amounts in the two series). Samples with high or low amounts of deviating exon usage, associated with overall transcriptome instability, were almost completely separated into their respective groups by hierarchical clustering analysis of splicing factor expression levels in both sample series. Samples showing a preferential tendency towards deviating exon skipping or inclusion were associated with skewed transcriptome instability. There were significant associations between transcriptome instability and reduced patient survival in both sample series. In the test series, patients with skewed transcriptome instability showed the strongest prognostic association (P = 0.001), while a combination of the two characteristics showed the strongest association with poor survival in the validation series (P = 0.03).

Conclusions
We have described transcriptome instability as a characteristic of CRC. This transcriptome instability has associations with splicing factor expression levels and poor patient survival.
Normal inflammatory markers in appendicitis: evidence from two independent cohort studies
Authors: Vaughan-Shaw Pg , Rees Jr , Bell E , Hamdan M , Platt T 
Published: May 2011

Objectives Acute appendicitis is a common surgical condition which can lead to severe complications. Recent work suggested that patients experiencing right lower abdominal pain, with normal white cell count (WCC) and C-reactive protein (CRP) are unlikely to have acute appendicitis and can be discharged. We present two independent datasets that suggest that this strategy may not be risk-free. Design Retrospective cohort study of consecutive patients from two district general hospitals. Sensitivity and specificity of CRP, WCC and neutrophil count (NC) in predicting appendicitis were calculated. Markers were analysed using Fisher's exact test and Kruskul-Wallace test. Setting Two district general hospitals in the UK. Participants Patients undergoing appendicectomy for suspected appendicitis. Main outcome measures Inflammatory markers and appendix histology. Results A total of 297 patients were included. Appendicitis occurred in four patients with normal CRP, WCC and NC in centre A and 13 patients in centre B. The sensitivity of all three markers combined was 94% (centre A) and 92% (centre B). The specificity was 60% (centre A) and 64% (centre B). No single marker could differentiate uncomplicated and complicated appendicitis, but a raised NC or a CRP >35.5 mg/l predicted complicated appendicitis. CRP, WCC and NC combined differentiated between patients with a normal appendix, uncomplicated appendicitis and complicated appendicitis. Conclusions Appendicitis in the presence of normal inflammatory markers is not uncommon. We disagree with the view of Sengupta et al. who suggest that patients with normal WCC and CRP are unlikely to have appendicitis, and recommend that clinicians be wary of normal inflammatory markers in patients with a high clinical suspicion of appendicitis.
Chronic fatigue syndrome in the media: a content analysis of newspaper articles
Authors: Knudsen Ann Kristen , Omenås Anne Nagelgaard , Harvey Samuel B , Løvvik Camilla Ms , Lervik Linn V , Mykletun Arnstein 
Published: May 2011

Objectives Although cognitive behavioural therapy and graded exercise treatment are recognized evidence-based treatments for chronic fatigue syndrome/myalgic encephalomyelitis (ME), their use is still considered controversial by some patient groups. This debate has been reflected in the media, where many patients gather health information. The aim of this study was to examine how treatment for chronic fatigue syndrome/ME is described in the newspaper media. Design Content analysis of newspaper articles. Setting The digitalized media archive Atekst was used to identify Norwegian newspaper articles where chronic fatigue syndrome/ME was mentioned. Participants Norwegian newspaper articles published over a 20-month period, from 1 January 2008 to 31 August 2009. Main outcome measures Statements regarding efficiency of various types of treatment for chronic fatigue syndrome/ME and the related source of the treatment advice. Statements were categorized as being either positive or negative towards evidence-based or alternative treatment. Results One hundred and twenty-two statements regarding treatment of chronic fatigue syndrome/ME were identified among 123 newspaper articles. The most frequent statements were positive statements towards alternative treatment Lightning Process (26.2%), negative statements towards evidence-based treatments (22.1%), and positive statements towards other alternative treatment interventions (22.1%). Only 14.8% of the statements were positive towards evidence-based treatment. Case-subjects were the most frequently cited sources, accounting for 35.2% of the statements, followed by physicians and the Norwegian ME association. Conclusions Statements regarding treatment for chronic fatigue syndrome/ME in newspapers are mainly pro-alternative treatment and against evidence-based treatment. The media has great potential to influence individual choices. The unbalanced reporting of treatment options for chronic fatigue syndrome/ME in the media is potentially harmful.
Gender-related differences in the oxidant state of cells in Fanconi anemia heterozygotes
Authors: Petrovic Sandra , Leskovac Andreja , Kotur-Stevuljevic Jelena , Joksic Jelena , Guc-Scekic Marija , Vujic Dragana , Joksic Gordana 
Published: May 2011

Abstract
Fanconi anemia (FA) is a rare cancer-prone genetic disorder characterized by progressive bone marrow failure, chromosomal instability and redox abnormalities. There is much biochemical and genetic data, which strongly suggest that FA cells experience increased oxidative stress. The present study was designed to elucidate if differences in oxidant state exist between control, idiopathic bone marrow failure (idBMF) and FA cells, and to analyze oxidant state of cells in FA heterozygous carriers as well. The results of the present study confirm an in vivo prooxidant state of FA cells and clearly indicate that FA patients can be distinguished from idBMF patients based on the oxidant state of cells. Female carriers of FA mutation also exhibited hallmarks of an in vivo prooxidant state behaving in a similar manner as FA patients. On the other hand, the oxidant state of cells in FA male carriers and idBMF families failed to show any significant difference vs. controls. We demonstrate that the altered oxidant state influences susceptibility of cells to apoptosis in both FA patients and female carriers. The results highlight the need for further research of the possible role of mitochondrial inheritance in the pathogenesis of FA.
Cooperative and independent activities of Sgt2 and Get5 in the targeting of tail-anchored proteins
Authors: Kohl Christian , Tessarz Peter , von der Malsburg Karina , Zahn Regina , Bukau Bernd , Mogk Axel 
Published: May 2011

Abstract
TPR proteins modulate the activity of molecular chaperones. Here, we describe the S. cerevisiae TPR protein Sgt2 as interaction partner of Ssa1 and Hsp104 and as a component of the GET pathway by interacting with Get5. The GET pathway mediates the sorting of tail-anchored (TA) proteins, harboring a C-terminal trans-membrane segment, to the ER membrane. S. cerevisiae sgt2Δ cells show partial defects in TA protein sorting. Sgt2 activity in vivo relies on its N- and C-terminal domains, whereas the central TPR domain and thus chaperone interactions are dispensable. We show that TA protein sorting defects are more severe in sgt2Δ get5Δ mutants compared to single knockouts. Furthermore, overproduction of Sgt2 becomes toxic to get3Δ but not to get5Δ cells. Together, these findings indicate an additional, Get5-independent role of Sgt2 in TA protein sorting, pointing to parallel pathways of substrate delivery to Get3.
Agreement between paired blood gas values in samples transported either by a pneumatic system or by human courier
Authors: Victor Peter John , Patole Shalom , Joseph Fleming Jude , Selvakumar Ratnasamy , Graham Petra L. 
Published: May 2011

Abstract

Background: Rapid accurate assessment of metabolic derangements is crucial in the critically ill. We evaluated if arterial blood gas (ABG) samples transported through a pneumatic tube system (PTS) agreed with values transported by a human courier.

Methods: In this prospective study of 50-paired ABG samples, the couriered reference ABG was compared with those transported by PTS. Agreement was summarised by the mean difference with 95% limits of agreement (LOA) and Lin's concordance correlation (pc).

Results: The mean (±SD) time from sampling to analysis was 35.7±23.2 (courier) and 38.6±22.1 (PTS) minutes. Agreement was good between courier and PTS for pH, PaCO2, bicarbonate, oxygen saturation and PaO2 values (pc>0.97). Although the mean difference in PaO2 values between PTS and courier was small (–0.9 mm Hg) and the agreement was good, individual differences were clinically significant (95% LOA –40.8 to 39.0). For PaO2 <160 mm Hg, analysis of PTS samples yielded erroneously high PaO2 values and vice versa for PaO2>160 mm Hg compared to manual courier. This suggested exaggerated oxygen movement between the blood sample and air in the PTS.

Conclusions: In this study, analysis of samples transported through the PTS resulted in clinically unacceptable PaO2 values. Delay in transport and analysis of ABG samples should be avoided and samples transported manually if they cannot be assessed on-site.
Improving clinical laboratory efficiency: a time-motion evaluation of the Abbott m2000 RealTime and Roche COBAS AmpliPrep/COBAS TaqMan PCR systems for the simultaneous quantitation of HIV-1 RNA and HCV RNA
Authors: Amendola Alessandra , Coen Sabrina , Belladonna Stefano , Pulvirenti F. Renato , Clemens John M. , Capobianchi M. Rosaria 
Published: May 2011

Abstract

Background: Diagnostic laboratories need automation that facilitates efficient processing and workflow management to meet today's challenges for expanding services and reducing cost, yet maintaining the highest levels of quality.

Methods: Processing efficiency of two commercially available automated systems for quantifying HIV-1 and HCV RNA, Abbott m2000 system and Roche COBAS Ampliprep/COBAS TaqMan 96 (docked) systems (CAP/CTM), was evaluated in a mid/high throughput workflow laboratory using a representative daily workload of 24 HCV and 72 HIV samples. Three test scenarios were evaluated: A) one run with four batches on the CAP/CTM system, B) two runs on the Abbott m2000 and C) one run using the Abbott m2000 maxCycle feature (maxCycle) for co-processing these assays. Cycle times for processing, throughput and hands-on time were evaluated.

Results: Overall processing cycle time was 10.3, 9.1 and 7.6 h for Scenarios A), B) and C), respectively. Total hands-on time for each scenario was, in order, 100.0 (A), 90.3 (B) and 61.4 min (C).

Conclusions: The interface of an automated analyzer to the laboratory workflow, notably system set up for samples and reagents and clean up functions, are as important as the automation capability of the analyzer for the overall impact to processing efficiency and operator hands-on time.
Evaluation of two automated chemiluminescence immunoassays, the LIAISON Treponema Screen and the ARCHITECT Syphilis TP, and the Treponema pallidum particle agglutination test for laboratory diagnosis of syphilis
Authors: Wellinghausen Nele , Dietenberger Hanna 
Published: May 2011

Abstract

Background: Automated Treponema pallidum-specific chemi-luminescence immunoassays (CLIA) run on random-access analyzers allow for rapid diagnosis of syphilis infection.

Methods: We evaluated the LIAISON Treponema Screen (LIA) and the ARCHITECT Syphilis TP (ARCH) in comparison to the Treponema pallidum particle agglutination (TPPA) test, as a screening test for syphilis. We performed a prospective study using 577 sera submitted for diagnosis of syphilis, including 318 samples from pregnant women. In addition, 42 stored sera from 32 patients with clinically and serologically characterized syphilis infection were investigated.

Results: In the prospective study, the sensitivity and specificity of LIA, ARCH, and TPPA were 100% (18/18), 100% (17/17), and 100% (18/18), and 100% (558/558), 99.8% (552/553), and 99.6% (556/558), respectively. In pregnant women, the specificity of LIA and ARCH was 100% (317/317) and of TPPA 99.7% (316/317). One sample from a child with assumed exposure to maternal antitreponemal antibodies was omitted from analysis. LIA, ARCH, and TPPA were also positive in all investigated sera from patients with known syphilis.

Conclusions: Both automated CLIA demonstrated excellent diagnostic sensitivity and specificity when evaluated as a screening test for syphilis under routine conditions of a diagnostic laboratory. Thus, these may be used independently as an alternative to the manual TPPA screen.
Racial trends in sugar-sweetened beverage consumption among US adolescents: 1988–2004
Authors: Bremer Andrew A. , Byrd Robert S. , Auinger Peggy 
Published: June 2011

Abstract

Background: Increased consumption of sugar-sweetened beve­rages (SSBs) over the past two decades has been implicated in the increased incidence of metabolic disorders in the pediatric population, but whether racial differences exist with regard to SSB intake among adolescents is unknown.

Objective: To evaluate racial trends in SSB consumption in US adolescents.

Study group: In total, 10,201 individuals aged 12–19 years from the National Health and Nutrition Examination Survey (NHANES) during the years 1988–1994 and 1999–2004 were included in the study.

Methods: Multivariate linear regression analyses were performed to determine SSB consumption trends.

Results: From 1988 to 2004, SSB intake increased more in adolescents from racial minorities than in their Caucasian counterparts. Although other Hispanics and non-Hispanic whites consumed more SSBs than other racial groups at the beginning of the study, the amount of SSBs consumed by other racial groups increased in the interval time such that total SSB consumption in each racial group was comparable by the end of the study period. Sex-related differences in SSB consumption trends among racial groups were also observed.

Conclusions: SSB consumption trends have differed among racial groups and between the sexes over the past two decades, with SSB intake having increased more dramatically in racial minorities during this time than in non-Hispanic whites. Although other Hispanics and non-Hispanic whites consumed more SSBs than other racial groups in 1988–1991, SSB consumption among adolescents from all racial groups was comparable by 2003–2004. Furthermore, adolescents from most racial groups consumed more SSBs in 1994–2004 than in 1988–1994, paralleling the increase in pediatric obesity and metabolic syndrome.
The Application and Early-Age Behaviors of Continuously Reinforced Bonded Concrete Overlay of Distressed Jointed Concrete Pavements
Authors: Sun RenJuan , Won Hoonill , Won Moon. C. 
Published: June 2011

Abstract
Considerable efforts and money are spent to maintain and repair the distressed jointed concrete pavement (JCP) sections by providing partial-/full-depth repair, under sealing, and patching; however, a lot of distresses reoccur frequently. For severe distresses, overlay was constructed on the JCP. Resurfacing with a bonded concrete overlay (BCO) over the existing pavement to form a monolithic structure has proven to be a cost-effective rehabilitation strategy. Continuously reinforced concrete pavement (CRCP) bonded overlay was constructed for the rehabilitation of a 2000 ft long JCP section on U.S.75 in Sherman, Texas, United States which had been subjected to numerous rehabilitations to construct the guidelines of the CRCP bonded overlay. The pavement design and concrete mix design selected are discussed and introduced in this article. In order to reduce the reflective cracking at the location of the JCP joints, geotextile was placed at the joint location before the overlay construction. For the study on the function of the geotextile, the geotextile was not placed at 20 JCP joints for the comparison. One week after the BCO construction, the investigation for the CRCP cracking was carried out at three stages. The investigated results revealed that the cracks at the transverse steel location are much more than those between the transverse steel. Falling weight deflectometer testing was run on the pavement surface before and after the overlay construction to measure the deflection behavior of the pavement. The performance of the overlay shows that the bonded CRCP is appropriate for the JCP resurfacing.
A combination of polymorphisms in HSD11B1 associates with in vivo 11β-HSD1 activity and metabolic syndrome in women with and without polycystic ovary syndrome
Authors: Gambineri Alessandra , Tomassoni Federica , Munarini Alessandra , Stimson Roland H , Mioni Roberto , Pagotto Uberto , Chapman Karen E , Andrew Ruth , Mantovani Vilma , Pasquali Renato , Walker Brian R 
Published: May 2011

ObjectiveRegeneration of cortisol by 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) within liver and adipose tissue may be of pathophysiological importance in obesity and the metabolic syndrome. single nucleotide polymorphisms (SNPs) in HSD11B1, the gene encoding 11β-HSD1, have been associated with type 2 diabetes and hypertension in population-based cohort studies, and with hyperandrogenism in patients with the polycystic ovary syndrome (PCOS). However, the functional consequences of these SNPs for in vivo 11β-HSD1 expression and activity are unknown.MethodsWe explored associations of well-characterised hormonal and metabolic phenotypes with two common SNPs (rs846910 and rs12086634) in HSD11B1 in 600 women (300 with PCOS) and investigated 11β-HSD1 expression and activity in a nested study of 40 women from this cohort.ResultsHSD11B1 genotypes (as single SNPs and as the combination of the two minor allele SNPs) were not associated with PCOS. Women who were heterozygous for rs846910 A and homozygous for rs12086634 T (GA, TT genotype) had a higher risk of metabolic syndrome, regardless of the diagnosis of PCOS (odds ratio in the whole cohort=2.77 (95% confidence interval (CI) 1.16–6.67), P=0.023). In the nested cohort, women with the GA, TT genotype had higher HSD11B1 mRNA levels in adipose tissue, and higher rates of appearance of cortisol and d3-cortisol (16.1±0.7 nmol/min versus 12.1±1.1, P=0.044) during 9,11,12,12-2H4-cortisol (d4-cortisol) steady-state infusion.ConclusionsWe conclude that, in a population of Southern European Caucasian women with and without PCOS, alleles of HSD11B1 containing the two SNPs rs846910 A and rs12086634 T confer increased 11β-HSD1 expression and activity, which associates with the metabolic syndrome.
Estimating the Risk of Developing Type 2 Diabetes: A Comparison of Several Risk Scores
Authors: Schmid Rémy , Vollenweider Peter , Waeber Gérard , Marques-Vidal Pedro 
Published: June 2011

OBJECTIVE
To compare in the Swiss population the results of several scores estimating the risk of developing type 2 diabetes.

RESEARCH DESIGN AND METHODS
This was a single-center, cross-sectional study conducted between 2003 and 2006 in Lausanne, Switzerland. Overall, 3,251 women and 2,937 men, aged 35–75 years, were assessed, of which 5,760 (93%) were free from diabetes and included in the current study. The risk of developing type 2 diabetes was assessed using seven different risk scores, including clinical data with or without biological data. Participants were considered to be eligible for primary prevention according to the thresholds provided for each score. The results were then extrapolated to the Swiss population of the same sex and age.

RESULTS
The risk of developing type 2 diabetes increased with age in all scores. The prevalence of participants at high risk ranged between 1.6 and 24.9% in men and between 1.1 and 15.7% in women. Extrapolated to the Swiss population of similar age, the overall number of participants at risk, and thus susceptible to intervention, ranged between 46,708 and 636,841. In addition, scores that included the same clinical variables led to a significantly different prevalence of participants at risk (4.2% [95% CI 3.4–5.0] vs. 12.8% [11.5–14.1] in men and 2.9% [2.4–3.6] vs. 6.0% [5.2–6.9] in women).

CONCLUSIONS
The prevalence of participants at risk for developing type 2 diabetes varies considerably according to the scoring system used. To adequately prevent type 2 diabetes, risk-scoring systems must be validated for each population considered.
Synthesis, UV/vis spectra and electrochemical characterisation of arylthio and styryl substituted ferrocenes
Authors: Sørensen Thomas , Nielsen Merete 
Published: June 2011

Abstract
Two series of substituted ferrocenes were synthesised using either the Horner-Wadsworth-Emmons reaction or monolithiation of ferrocene. The series consist of arylthio- and styryl-ferrocenes with different substituents in the para position of the aryl rings of the systems. The electronic communication was investigated by comparing the substituent effects in absorption spectroscopy and in cyclic voltammetry. A small substituent effect was found in the electronic transitions of the styryl substituted ferrocenes. The oxidation of the ferrocene derivatives showed clear substituent effects as illustrated by the linear Hammett plots. The effect was shown to be an order of magnitude larger in the arylthio-systems than in the styryl systems. It is suggested that the reason behind the large effect is a direct sulfur-iron orbital overlap.
A study of nucleic acid base-stacking by the Monte Carlo method: Extended cluster approach
Authors: Danilov Victor , Dailidonis Vladimir , Mourik Tanja , Früchtl Herbert 
Published: June 2011

Abstract
The adenine-thymine (AT), adenine-uracil (AU) and guanine-cytosine (GC) base associates in clusters containing 400 water molecules were studied using a newly implemented Metropolis Monte Carlo algorithm based on the extended cluster approach. Starting from the hydrogen-bonded Watson-Crick geometries, all three base pairs are transformed into more favorable stacked configurations during the simulation. The obtained results show, for the first time, the transition from planar base pairs to stacked base associates in the Monte Carlo framework. Analysis of the interaction energies shows that, in the water cluster, the stacked dimers are energetically preferable compared to the corresponding Watson-Crick base pairs. This is due to the larger base-water interaction in the stacked structures. The water-water interaction is one of the main factors promoting the formation of stacked dimers, and the obtained data confirm the crucial role of the water-water interactions in base stacking.