bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracellular matrix composition in COPD
Authors: Annoni Raquel , Lanças Tatiana , Yukimatsu Tanigawa Ryan , de Medeiros Matsushita Marcus , de Morais Fernezlian Sandra , Bruno Andreina , Fernando Ferraz da Silva Luiz , Roughley Peter J. , Battaglia Salvatore , Dolhnikoff Marisa , Hiemstra Pieter S. , Sterk Peter J. , Rabe Klaus F. , Mauad Thais 
Published: April 2012

Extracellular matrix (ECM) composition has an important role in determining airway structure. We postulated that ECM lung composition of chronic obstructive pulmonary disease (COPD) patients differs from that observed in smoking and nonsmoking subjects without airflow obstruction.We determined the fractional areas of elastic fibres, type-I, -III and -IV collagen, versican, decorin, biglycan, lumican, fibronectin and tenascin in different compartments of the large and small airways and lung parenchyma in 26 COPD patients, 26 smokers without COPD and 16 nonsmoking control subjects.The fractional area of elastic fibres was higher in non-obstructed smokers than in COPD and nonsmoking controls, in all lung compartments. Type-I collagen fractional area was lower in the large and small airways of COPD patients and in the small airways of non-obstructed smokers than in nonsmokers. Compared with nonsmokers, COPD patients had lower versican fractional area in the parenchyma, higher fibronectin fractional area in small airways and higher tenascin fractional area in large and small airways compartments. In COPD patients, significant correlations were found between elastic fibres and fibronectin and lung function parameters.Alterations of the major ECM components are widespread in all lung compartments of patients with COPD and may contribute to persistent airflow obstruction.
Thoracoscore fails to predict complications following elective lung resection
Authors: Bradley Amy , Marshall Andrea , Abdelaziz Mahmoud , Hussain Khalid , Agostini Paula , Bishay Ehab , Kalkat Maninder , Steyn Richard , Rajesh Pala , Dunn Janet , Naidu Babu 
Published: April 2012

The Thoracoscore mortality risk model has been incorporated into the British Thoracic Society guidelines on the radical management of patients with lung cancer. The discriminative and predictive ability to predict mortality and post-operative pulmonary complications (PPCs) in this group of patients is uncertain.A prospective observational study was carried out on all patients following lung resectionviathoracotomy in a regional thoracic centre over 42 months. 128 out of 703 subjects developed a PPC. 16 (2%) patients died in hospital. In a logistic regression analysis the Thoracoscore was not a significant predictor of mortality (OR 1.07, 95% CI 0.99–1.17; p=0.11) but was a significant predictor of PPCs (OR 1.08, 95% CI 1.03–1.13; p=0.002). However, the area under the receiver operator characteristic curve for the Thoracoscore was 0.68 (95% CI 0.56–0.80) for predicting mortality and 0.64 (95% CI 0.59–0.69) for PPCs, indicating limited discriminative ability.In a logistic regression analysis, another risk model, the European Society Objective Score, was predictive of mortality (OR 1.43, 95% CI 1.11–1.83; p=0.006) and PPCs (OR 1.48, 95% CI 1.30–1.68; p<0.0001).Therefore, Thoracoscore may have poor discriminative and predictive ability for mortality and PPCs following elective lung resection.
Modeling overdispersed longitudinal binary data using a combined beta and normal random-effects model
Authors: Kassahun Wondwosen , Neyens Thomas , Molenberghs Geert , Faes Christel , Verbeke Geert 
Published: April 2012

AbstractBackgroundIn medical and biomedical areas, binary and binomial outcomes are very common. Such data are often collected longitudinally from a given subject repeatedly overtime, which result in clustering of the observations within subjects, leading to correlation, on the one hand. The repeated binary outcomes from a given subject, on the other hand, constitute a binomial outcome, where the prescribed mean-variance relationship is often violated, leading to the so-called overdispersion.MethodsTwo longitudinal binary data sets, collected in south western Ethiopia: the Jimma infant growth study, where the child’s early growth is studied, and the Jimma longitudinal family survey of youth where the adolescent’s school attendance is studied over time, are considered. A new model which combines both overdispersion, and correlation simultaneously, also known as the combined model is applied. In addition, the commonly used methods for binary and binomial data, such as the simple logistic, which accounts neither for the overdispersion nor the correlation, the beta-binomial model, and the logistic-normal model, which accommodate only for the overdispersion, and correlation, respectively, are also considered for comparison purpose. As an alternative estimation technique, a Bayesian implementation of the combined model is also presented.ResultsThe combined model results in model improvement in fit, and hence the preferred one, based on likelihood comparison, and DIC criterion. Further, the two estimation approaches result in fairly similar parameter estimates and inferences in both of our case studies. Early initiation of breastfeeding has a protective effect against the risk of overweight in late infancy (p = 0.001), while proportion of overweight seems to be invariant among males and females overtime (p = 0.66). Gender is significantly associated with school attendance, where girls have a lower rate of attendance (p = 0.001) as compared to boys.ConclusionWe applied a flexible modeling framework to analyze binary and binomial longitudinal data. Instead of accounting for overdispersion, and correlation separately, both can be accommodated simultaneously, by allowing two separate sets of the beta, and the normal random effects at once.
De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode
Authors: Xu De-Lin , Long Hai , Liang Jun-Jun , Zhang Jie , Chen Xin , Li Jing-Liang , Pan Zhi-Fen , Deng Guang-Bing , Yu Mao-Qun 
Published: April 2012

Abstract

Background

Aegilops variabilis No.1 is highly resistant to cereal cyst nematode (CCN). However, a lack of genomic information has restricted studies on CCN resistance genes in Ae. variabilis and has limited genetic applications in wheat breeding.

Results
Using RNA-Seq technology, we generated a root transcriptome at a sequencing depth of 4.69 gigabases of Ae. variabilis No. 1 from a pooled RNA sample. The sample contained equal amounts of RNA extracted from CCN-infected and untreated control plants at three time-points. Using the Trinity method, nearly 52,081,238 high-quality trimmed reads were assembled into a non-redundant set of 118,064 unigenes with an average length of 500 bp and an N50 of 599 bp. The total assembly was 59.09 Mb of unique transcriptome sequences with average read-depth coverage of 33.25×. In BLAST searches of our database against public databases, 66.46% (78,467) of the unigenes were annotated with gene descriptions, conserved protein domains, or gene ontology terms. Functional categorization further revealed 7,408 individual unigenes and three pathways related to plant stress resistance.

Conclusions
We conducted high-resolution transcriptome profiling related to root development and the response to CCN infection in Ae. variabilis No.1. This research facilitates further studies on gene discovery and on the molecular mechanisms related to CCN resistance.
Expression of CD39 on FoxP3+ T regulatory cells correlates with progression of HBV infection
Authors: Tang Yan , Jiang Li , Zheng Yanhua , Ni Bing , Wu Yuzhang 
Published: April 2012

Abstract

Background
Although it is known that regulatory T cells (Tregs) can suppress the function of effector T cells, and may contribute to impaired immune response, the precise role of Tregs during the course of hepatitis B virus (HBV) infection remains to be elucidated. A newly identified subset of the CD4+Foxp3+ Tregs, the CD39+ Tregs, has been associated with viral infections and autoimmune diseases. Therefore, we hypothesized that this discrete Treg subset may contribute to the chronic infection of HBV.

Results
Initial characterization studies of healthy peripheral CD39+FoxP3+CD4+ T cells revealed that the majority were CD45RA- Treg cells. Subsequent analysis of HBV-infected patients (38 asymptomatic HBV carriers (AsCs), 37 chronic active hepatitis B (CAH), 29 HBV-associated acute-on-chronic liver failure (ACLF)) and healthy individuals (25 controls) was conducted to assess association with HBV copy number and the liver injury marker alanine aminotransferase (ALT). A higher percentage of CD39+ Tregs was detected within the population of FoxP3+CD4+ T cells in peripheral blood of AsCs patients. Moreover, the percentage of CD39+ Tregs was significantly less in CAH and ACLF patients. The increased proportions of circulating CD39+ Tregs were positively correlated with serum viral load, but inversely correlated with serum ALT level.

Conclusion
These findings not only suggest that CD39+ Treg cells may be involved in HBV disease progression but also identify CD39+ Tregs as a dynamic immune regulatory cell population that may represent a new target of immunomodulatory therapeutic interventions.
QRS pattern and improvement in right and left ventricular function after cardiac resynchronization therapy: a radionuclide study
Authors: Domenichini Giulia , Burri Haran , Valzania Cinzia , Gavaruzzi Gilberto , Fallani Francesco , Biffi Mauro , Sunthorn Henri , Diemberger Igor , Martignani Cristian , Foulkes Huberdine , Fleury Eric , Boriani Giuseppe 
Published: April 2012

Abstract

Background
Predicting response to cardiac resynchronization therapy (CRT) remains a challenge. We evaluated the role of baseline QRS pattern to predict response in terms of improvement in biventricular ejection fraction (EF).

Methods
Consecutive patients (pts) undergoing CRT implantation underwent radionuclide angiography at baseline and at mid-term follow-up. The relationship between baseline QRS pattern and mechanical dyssynchrony using phase analysis was evaluated. Changes in left and right ventricular EF (LVEF and RVEF) were analyzed with regard to baseline QRS pattern.

Results
We enrolled 56 pts, 32 with left bundle branch block (LBBB), 4 with right bundle branch block (RBBB) and 20 with non-specific intraventricular conduction disturbance (IVCD). A total of 48 pts completed follow-up. LBBB pts had significantly greater improvement in LVEF compared to RBBB or non-specific IVCD pts (+9.6 ± 10.9% vs. +2.6 ± 7.6%, p = 0.003). Response (defined as ≥ 5% increase in LVEF) was observed in 68% of LBBB vs. 24% of non-specific IVCD pts (p = 0.006). None of the RBBB pts were responders. RVEF was significantly improved in LBBB (+5.0 ± 9.0%, p = 0.007), but not in non-specific IVCD and RBBB pts (+0.4 ± 5.8%, p = 0.76). At multivariate analysis, LBBB was the only predictor of LVEF response (OR, 7.45; 95% CI 1.80-30.94; p = 0.006), but not QRS duration or extent of mechanical dyssynchrony.

Conclusions
Presence of a LBBB is a marker of a positive response to CRT in terms of biventricular improvement. Pts with non-LBBB pattern show significantly less benefit from CRT than those with LBBB.
Metal ion levels in large-diameter total hip and resurfacing hip arthroplasty-Preliminary results of a prospective five year study after two years of follow-up
Authors: Maurer-Ertl W , Friesenbichler J , Sadoghi P , Pechmann M , Trennheuser M , Leithner A 
Published: April 2012

Abstract

Background
Metal-on-metal hip resurfacing is an alternative to metal-on-metal total hip arthroplasty, especially for young and physically active patients. However, wear which might be detected by increased serum ion levels is a matter of concern.

Methods
The aims of this preliminary study were to determine the raise of metal ion levels at 2-years follow-up in a prospective setting and to evaluate differences between patients with either resurfacing or total hip arthroplasty. Furthermore we investigated if the inclination of the acetabular component and the arc of cover would influence these findings. Therefore, 36 patients were followed prospectively.

Results
The results showed increments for Co and Cr in both implant groups. Patients treated with large-diameter total hip arthroplasty showed fourfold and threefold, respectively, higher levels for Co and Cr compared to the resurfacing group (Co: p < 0,001 and Cr: p = 0,005). Nevertheless, we observed no significant correlation between serum ion levels, inclination and arc of cover.

Discussion
In order to clarify the biologic effects of ion dissemination and to identify risks concerning long-term toxicity of metals, the exposure should be monitored carefully. Therefore, long-term studies have to be done to determine adverse effects of Co and Cr following metal-on-metal hip replacement.
The effect of saponins from Ampelozizyphus amazonicus Ducke on the renal Na+ pumps’ activities and urinary excretion of natriuretic peptides
Authors: Diniz Lúcio Ricardo Leite , Portella Viviane Gomes , Cardoso Flávia Magalhães , de Souza Aloa Machado , Caruso-Neves Celso , Cassali Geovanni Dantas , dos Reis Adelina Martha , Brandão MariadasGraçasLins , Vieira Maria Aparecida Ribeiro 
Published: April 2012

Abstract

Background
In a previous study, we showed that a saponin mixture isolated from the roots of Ampelozizyphus amazonicus Ducke (SAPAa D) reduces urine excretion in rats that were given an oral loading of 0.9 % NaCl (4 ml/100 g body weight). In the present study, we investigated whether atrial natriuretic peptides (ANP) and renal ATPases play a role in the SAPAa D- induced antidiuresis in rats.

Methods
To evaluate the effect of SAPAa D on furosemide-induced diuresis, Wistar rats (250-300 g) were given an oral loading of physiological solution (0.9 % NaCl, 4 ml/100 g body weight) to impose a uniform water and salt state. The solution containing furosemide (Furo, 13 mg/kg) was given 30 min after rats were orally treated with 50 mg/kg SAPAa D (SAPAaD + Furo) or 0.5 ml of 0.9 % NaCl (NaCl + Furo). In the SAPAaD + NaCl group, rats were pretreated with SAPAa D and 30 min later they received the oral loading of physiological solution. Animals were individually housed in metabolic cages, and urine volume was measured every 30 min throughout the experiment (3 h). To investigate the role of ANP and renal Na+ pumps on antidiuretic effects promoted by SAPAa D, rats were given the physiological solution (as above) containing SAPAa D (50 mg/kg). After 90 min, samples of urine and blood from the last 30 min were collected. Kidneys and atria were also removed after previous anesthesia. ANP was measured by radioimmunoassay (RIA) and renal cortical activities of Na+- and (Na+,K+)-ATPases were calculated from the difference between the [32P] Pi released in the absence and presence of 1 mM furosemide/2 mM ouabain and in the absence and presence of 1 mM ouabain, respectively.

Results
It was observed that SAPAa D inhibited furosemide-induced diuresis (at 90 min: from 10.0 ± 1.0 mL, NaCl + Furo group, n = 5, to 5.9 ± 1.0 mL, SAPAaD + Furo group n = 5, p < 0.05), increased both Na+-ATPase (from 25.0 ± 5.9 nmol Pi.mg-1.min-1, control, to 52.7 ± 8.9 nmol Pi.mg-1.min-1, p < 0.05) and (Na+,K+)-ATPase (from 47.8 ± 13.3 nmol Pi.mg-1.min-1, control, to 79.8 ± 6.9 nmol Pi .mg-1.min-1, p < 0.05) activities in the renal cortex. SAPAa D also lowered urine ANP (from 792 ± 132 pg/mL, control, to 299 ± 88 pg/mL, p < 0.01) and had no effect on plasma or atrial ANP.

Conclusion
We concluded that the SAPAa D antidiuretic effect may be due to an increase in the renal activities of Na+- and (Na+,K+)-ATPases and/or a decrease in the renal ANP.
Molecular network profiling of U373MG human glioblastoma cells following induction of apoptosis by novel marine-derived anti-cancer 1,2,3,4-tetrahydroisoquinoline alkaloids
Authors: Tabunoki Hiroko , Saito Naoki , Suwanborirux Khanit , Charupant Kornvika , Satoh Jun-ichi 
Published: April 2012

AbstractBackgroundGlioblastoma is the most aggressive form of brain tumors showing resistance to treatment with various chemotherapeutic agents. The most effective way to eradicate glioblastoma requires the concurrent inhibition of multiple signaling pathways and target molecules involved in the progression of glioblastoma. Recently, we obtained a series of 1,2,3,4-tetrahydroisoquinoline alkaloids with potent anti-cancer activities, including ecteinascidin-770 (ET-770; the compound 1a) and renieramycin M (RM; the compound 2a) from Thai marine invertebrates, together with a 2’-N-4”-pyridinecarbonyl derivative of ET-770 (the compound 3). We attempted to characterize the molecular pathways responsible for cytotoxic effects of these compounds on a human glioblastoma cell line U373MG.MethodsWe studied the genome-wide gene expression profile on microarrays and molecular networks by using pathway analysis tools of bioinformatics.ResultsAll of these compounds induced apoptosis of U373MG cells at nanomolar concentrations. The compound 3 reduced the expression of 417 genes and elevated the levels of 84 genes, while ET-770 downregulated 426 genes and upregulated 45 genes. RM decreased the expression of 274 genes and increased the expression of 9 genes. The set of 196 downregulated genes and 6 upregulated genes showed an overlap among all the compounds, suggesting an existence of the common pathways involved in induction of apoptosis. We identified the ErbB (EGFR) signaling pathway as one of the common pathways enriched in the set of downregulated genes, composed of PTK2, AKT3, and GSK3B serving as key molecules that regulate cell movement and the nervous system development. Furthermore, a GSK3B-specific inhibitor induced apoptosis of U373MG cells, supporting an anti-apoptotic role of GSK3B.ConclusionMolecular network analysis is a useful approach not only to characterize the glioma-relevant pathways but also to identify the network-based effective drug targets.
Anticonvulsant and analgesic activities of crude extract and its fractions of the defensive secretion from the Mediterranean sponge, Spongia officinalis
Authors: Dellai Afef , Mansour Hedi Ben , Clary-Laroche Audrey , Deghrigue Monia , Bouraoui Abderrahman 
Published: April 2012

Abstract
This study progresses in the direction of identifying component(s) from the Mediterranean sponge, Spongia officinalis with anticonvulsant and analgesic activities. We investigated the efficacy of crude extract and its semi-purified fractions (F1-F3) of the defensive secretion from Spongia officinalis for their in vivo anticonvulsant activity using the pentylenetetrazole (PTZ) seizure model and analgesic activity using the writhing test in mice. Among the series the crude extract exhibited interesting analgesic activity in a dose dependent manner. Similarly the fraction F2 showed a partial protection of mice from PTZ-induced seizure and interesting analgesic activity in a dose dependent manner. The purification and the determination of chemical structure(s) of compound(s) of this active fraction are under investigation.
A reinvestigation of somatic hypermethylation at the PTEN CpG island in cancer cell lines
Authors: Hesson Luke B , Packham Deborah , Pontzer Emily , Funchain Pauline , Eng Charis , Ward Robyn L 
Published: April 2012

Abstract

Background

PTEN is an important tumour suppressor gene that is mutated in Cowden syndrome as well as various sporadic cancers. CpG island hypermethylation is another route to tumour suppressor gene inactivation, however, the literature regarding PTEN hypermethylation in cancer is controversial. Furthermore, investigation of the methylation status of the PTEN CpG island is challenging due to sequence homology with the PTEN pseudogene, PTENP1. PTEN shares a CpG island promoter with another gene known as KLLN. Here we present a thorough reinvestigation of the methylation status of the PTEN CpG island in DNA from colorectal, breast, ovarian, glioma, lung and haematological cancer cell lines.

Results
Using a range of bisulphite-based PCR assays we investigated 6 regions across the PTEN CpG island. We found that regions 1-4 were not methylated in cancer cell lines (0/36). By allelic bisulphite sequencing and pyrosequencing methylation was detected in regions 5 and 6 in colorectal, breast and haematological cancer cell lines. However, methylation detected in this region was associated with the PTENP1 promoter and not the PTEN CpG island.

Conclusions
We show that methylation of the PTEN CpG island is a rare event in cancer cell lines and that apparent methylation most likely originates from homologous regions of the PTENP1 pseudogene promoter. Future studies should utilize assays that reliably discriminate between PTEN and PTENP1 to avoid data misinterpretation.
Glutathione S-transferase omega genes in Alzheimer and Parkinson disease risk, age-at-diagnosis and brain gene expression: an association study with mechanistic implications
Authors: Allen Mariet , Zou Fanggeng , Chai High Seng , Younkin Curtis S , Miles Richard , Nair Asha A , Crook Julia E , Pankratz V Shane , Carrasquillo Minerva M , Rowley Christopher N , Nguyen Thuy , Ma Li , Malphrus Kimberly G , Bisceglio Gina , Ortolaza Alexandra I , Palusak Ryan , Middha Sumit , Maharjan Sooraj , Georgescu Constantin , Schultz Debra , Rakhshan Fariborz , Kolbert Christopher P , Jen Jin , Sando Sigrid B , Aasly Jan O , Barcikowska Maria , Uitti Ryan J , Wszolek Zbigniew K , Ross Owen A , Petersen Ronald C , Graff-Radford Neill R , Dickson Dennis W , Younkin Steven G , Ertekin-Taner Nilüfer 
Published: April 2012

Abstract

Background
Glutathione S-transferase omega-1 and 2 genes (GSTO1, GSTO2), residing within an Alzheimer and Parkinson disease (AD and PD) linkage region, have diverse functions including mitigation of oxidative stress and may underlie the pathophysiology of both diseases. GSTO polymorphisms were previously reported to associate with risk and age-at-onset of these diseases, although inconsistent follow-up study designs make interpretation of results difficult. We assessed two previously reported SNPs, GSTO1 rs4925 and GSTO2 rs156697, in AD (3,493 ADs vs. 4,617 controls) and PD (678 PDs vs. 712 controls) for association with disease risk (case-controls), age-at-diagnosis (cases) and brain gene expression levels (autopsied subjects).

Results
We found that rs156697 minor allele associates with significantly increased risk (odds ratio = 1.14, p = 0.038) in the older ADs with age-at-diagnosis > 80 years. The minor allele of GSTO1 rs4925 associates with decreased risk in familial PD (odds ratio = 0.78, p = 0.034). There was no other association with disease risk or age-at-diagnosis. The minor alleles of both GSTO SNPs associate with lower brain levels of GSTO2 (p = 4.7 × 10-11-1.9 × 10-27), but not GSTO1. Pathway analysis of significant genes in our brain expression GWAS, identified significant enrichment for glutathione metabolism genes (p = 0.003).

Conclusion
These results suggest that GSTO locus variants may lower brain GSTO2 levels and consequently confer AD risk in older age. Other glutathione metabolism genes should be assessed for their effects on AD and other chronic, neurologic diseases.