bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis
Authors: Fu Jihong , Tang Wentao , Du Peng , Wang Guanghui , Chen Wei , Li Jingming , Zhu Yunxiang , Gao Jun , Cui Long 
Published: June 2012

AbstractBackgroundMicroRNAs (miRNAs) are involved in carcinogenesis and tumor progression by regulating post-transcriptional gene expression. However, the miRNA-mRNA regulatory network is far from being fully understood. The objective of this study is to identify the colorectal cancer (CRC) specific miRNAs and their target mRNAs using a multi-step approach.ResultsA multi-step approach combining microarray miRNA and mRNA expression profile and bioinformatics analysis was adopted to identify the CRC specific miRNA-mRNA regulatory network. First, 32 differentially expressed miRNAs and 2916 mRNAs from CRC samples and their corresponding normal epithelial tissues were identified by miRNA and mRNA microarray, respectively. Secondly, 22 dysregulated miRNAs and their 58 target mRNAs (72 miRNA-mRNA pairs) were identified by a combination of Pearson’s correlation analysis and prediction by databases TargetScan and miRanda. Bioinformatics analysis revealed that these miRNA-mRNAs pairs were involved in Wnt signaling pathway. Additionally, 6 up-regulated miRNAs (mir-21, mir-223, mir-224, mir-29a, mir-29b, and mir-27a) and 4 down-regulated predicted target mRNAs (SFRP1, SFRP2, RNF138, and KLF4) were selected to validate the expression level and their anti-correlationship in an extended cohort of CRC patients by qRT-PCR. Except for mir-27a, the differential expression and their anti-correlationship were proven. Finally, a transfection assay was performed to validate a regulatory relationship between mir-29a and KLF4 at both RNA and protein levels.ConclusionsSeventy-two miRNA-mRNA pairs combined by 22 dysregulated miRNAs and their 58 target mRNAs identified by the multi-step approach appear to be involved in CRC tumorigenesis. The results in our study were worthwhile to further investigation via a functional study to fully understand the underlying regulatory mechanisms of miRNA in CRC.
An approach for jatropha improvement using pleiotropic QTLs regulating plant growth and seed yield
Authors: Sun Fei , Liu Peng , Ye Jian , Lo Loong Chuan , Cao Suying , Li Lei , Yue Gen Hua , Wang Chun Ming 
Published: June 2012

Abstract

Background
Higher seed yield is one of the objectives of jatropha breeding. However, genetic analysis of the yield traits has not been done in jatropha. Quantitative trait loci (QTL) mapping was conducted to identify genetic factors controlling growth and seed yield in jatropha, a promising biofuel crop.

Results
A linkage map was constructed consisting of 105 SSR (simple sequence repeat) markers converged into 11 linkage groups. With this map, we identified a total of 28 QTLs for 11 growth and seed traits using a population of 296 backcrossing jatropha trees. Two QTLs qTSW-5 and qTSW-7 controlling seed yield were mapped on LGs 5 and 7 respectively, where two QTL clusters controlling yield related traits were detected harboring five and four QTLs respectively. These two QTL clusters were critical with pleiotropic roles in regulating plant growth and seed yield. Positive additive effects of the two QTLs indicated higher values for the traits conferred by the alleles from J. curcas, while negative additive effects of the five QTLs on LG6, controlling plant height, branch number (in the 4th and 10th months post seed germination), female flower number and fruit number respectively, indicated higher values conferred by the alleles from J. integerrima. Therefore favored alleles from both the parents could be expected to be integrated into elite jatropha plant by further backcrossing and marker assisted selection. Efficient ways to improve the seed yield by applying the two QTL clusters are discussed.

Conclusion
This study is the first report on genetic analysis of growth and seed traits with molecular markers in jatropha. An approach for jatropha improvement is discussed using pleiotropic QTLs, which will be likely to lead to initiation of molecular breeding in jatropha by integrating more markers in the QTL regions.
MicroRNA expression signature in human abdominal aortic aneurysms
Authors: Pahl Matthew C , Derr Kimberly , Gäbel Gabor , Hinterseher Irene , Elmore James R , Schworer Charles M , Peeler Thomas C , Franklin David P , Gray John L , Carey David J , Tromp Gerard , Kuivaniemi Helena 
Published: June 2012

AbstractBackgroundAbdominal aortic aneurysm (AAA) is a dilatation of the aorta affecting most frequently elderly men. Histologically AAAs are characterized by inflammation, vascular smooth muscle cell apoptosis, and extracellular matrix degradation. The mechanisms of AAA formation, progression, and rupture are currently poorly understood. A previous mRNA expression study revealed a large number of differentially expressed genes between AAA and non-aneurysmal control aortas. MicroRNAs (miRNAs), small non-coding RNAs that are post-transcriptional regulators of gene expression, could provide a mechanism for the differential expression of genes in AAA.MethodsTo determine differences in miRNA levels between AAA (n = 5) and control (n = 5) infrarenal aortic tissues, a microarray study was carried out. Results were adjusted using Benjamini-Hochberg correction (adjustedp < 0.05). Real-time quantitative RT-PCR (qRT-PCR) assays with an independent set of 36 AAA and seven control tissues were used for validation. Potential gene targets were retrieved from miRNA target prediction databases Pictar, TargetScan, and MiRTarget2. Networks from the target gene set were generated and examined using the network analysis programs, CytoScape® and Ingenuity Pathway Core Analysis®.ResultsA microarray study identified eight miRNAs with significantly different expression levels between AAA and controls (adjustedp < 0.05). Real-time qRT-PCR assays validated the findings for five of the eight miRNAs. A total of 222 predicted miRNA target genes known to be differentially expressed in AAA based on a prior mRNA microarray study were identified. Bioinformatic analyses revealed that several target genes are involved in apoptosis and activation of T cells.ConclusionsOur genome-wide approach revealed several differentially expressed miRNAs in human AAA tissue suggesting that miRNAs play a role in AAA pathogenesis.
Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics
Authors: Diez Diego , Goto Susumu , Fahy John V , Erle David J , Woodruff Prescott G , Wheelock Åsa M , Wheelock Craig E 
Published: June 2012

Abstract

Background
Asthma is a chronic inflammatory airway disease influenced by genetic and environmental factors that affects ~300 million people worldwide, leading to ~250,000 deaths annually. Glucocorticoids (GCs) are well-known therapeutics that are used extensively to suppress airway inflammation in asthmatics. The airway epithelium plays an important role in the initiation and modulation of the inflammatory response. While the role of GCs in disease management is well understood, few studies have examined the holistic effects on the airway epithelium.

Methods
Gene expression data were used to generate a co-transcriptional network, which was interrogated to identify modules of functionally related genes. In parallel, expression data were mapped to the human protein-protein interaction (PPI) network in order to identify modules with differentially expressed genes. A common pathways approach was applied to highlight genes and pathways functionally relevant and significantly altered following GC treatment.

Results
Co-transcriptional network analysis identified pathways involved in inflammatory processes in the epithelium of asthmatics, including the Toll-like receptor (TLR) and PPAR signaling pathways. Analysis of the PPI network identified RXRA, PPARGC1A, STAT1 and IRF9, among others genes, as differentially expressed. Common pathways analysis highlighted TLR and PPAR signaling pathways, providing a link between general inflammatory processes and the actions of GCs. Promoter analysis identified genes regulated by the glucocorticoid receptor (GCR) and PPAR pathways as well as highlighted the interferon pathway as a target of GCs.

Conclusions
Network analyses identified known genes and pathways associated with inflammatory processes in the airway epithelium of asthmatics. This workflow illustrated a hypothesis generating experimental design that integrated multiple analysis methods to produce a weight-of-evidence based approach upon which future focused studies can be designed. In this case, results suggested a mechanism whereby GCs repress TLR-mediated interferon production via upregulation of the PPAR signaling pathway. These results highlight the role of interferons in asthma and their potential as targets of future therapeutic efforts.
Alu expression in human cell lines and their retrotranspositional potential
Authors: Oler Andrew J , Traina-Dorge Stephen , Derbes Rebecca S , Canella Donatella , Cairns Brad R , Roy-Engel Astrid M 
Published: June 2012

Abstract

Background
The vast majority of the 1.1 million Alu elements are retrotranspositionally inactive, where only a few loci referred to as ‘source elements’ can generate new Alu insertions. The first step in identifying the active Alu sources is to determine the loci transcribed by RNA polymerase III (pol III). Previous genome-wide analyses from normal and transformed cell lines identified multiple Alu loci occupied by pol III factors, making them candidate source elements.

Findings
Analysis of the data from these genome-wide studies determined that the majority of pol III-bound Alus belonged to the older subfamilies Alu S and Alu J, which varied between cell lines from 62.5% to 98.7% of the identified loci. The pol III-bound Alus were further scored for estimated retrotransposition potential (ERP) based on the absence or presence of selected sequence features associated with Alu retrotransposition capability. Our analyses indicate that most of the pol III-bound Alu loci candidates identified lack the sequence characteristics important for retrotransposition.

Conclusions
These data suggest that Alu expression likely varies by cell type, growth conditions and transformation state. This variation could extend to where the same cell lines in different laboratories present different Alu expression patterns. The vast majority of Alu loci potentially transcribed by RNA pol III lack important sequence features for retrotransposition and the majority of potentially active Alu loci in the genome (scored high ERP) belong to young Alu subfamilies. Our observations suggest that in an in vivo scenario, the contribution of Alu activity on somatic genetic damage may significantly vary between individuals and tissues.
Variability of insulin sensitivity during the first 4 days of critical illness: implications for tight glycemic control
Authors: Pretty Christopher G , Le Compte Aaron J , Chase J Geoffrey , Shaw Geoffrey M , Preiser Jean-Charles , Penning Sophie , Desaive Thomas 
Published: June 2012

Abstract

Background
Effective tight glycemic control (TGC) can improve outcomes in critical care patients, but it is difficult to achieve consistently. Insulin sensitivity defines the metabolic balance between insulin concentration and insulin-mediated glucose disposal. Hence, variability of insulin sensitivity can cause variable glycemia. This study quantifies and compares the daily evolution of insulin sensitivity level and variability for critical care patients receiving TGC.

Methods
This is a retrospective analysis of data from the SPRINT TGC study involving patients admitted to a mixed medical-surgical ICU between August 2005 and May 2007. Only patients who commenced TGC within 12 hours of ICU admission and spent at least 24 hours on the SPRINT protocol were included (N = 164). Model-based insulin sensitivity (SI) was identified each hour. Absolute level and hour-to-hour percent changes in SI were assessed on cohort and per-patient bases. Levels and variability of SI were compared over time on 24-hour and 6-hour timescales for the first 4 days of ICU stay.

Results
Cohort and per-patient median SI levels increased by 34% and 33% (p < 0.001) between days 1 and 2 of ICU stay. Concomitantly, cohort and per-patient SI variability decreased by 32% and 36% (p < 0.001). For 72% of the cohort, median SI on day 2 was higher than on day 1. The day 1–2 results are the only clear, statistically significant trends across both analyses. Analysis of the first 24 hours using 6-hour blocks of SI data showed that most of the improvement in insulin sensitivity level and variability seen between days 1 and 2 occurred during the first 12–18 hours of day 1.

Conclusions
Critically ill patients have significantly lower and more variable insulin sensitivity on day 1 than later in their ICU stay and particularly during the first 12 hours. This rapid improvement is likely due to the decline of counter-regulatory hormones as the acute phase of critical illness progresses. Clinically, these results suggest that while using TGC protocols with patients during their first few days of ICU stay, extra care should be afforded. Increased measurement frequency, higher target glycemic bands, conservative insulin dosing, and modulation of carbohydrate nutrition should be considered to minimize safely the outcome glycemic variability and reduce the risk of hypoglycemia.
Exercise training in pulmonary arterial hypertension associated with connective tissue diseases
Authors: Grünig Ekkehard , Maier Felicitas , Ehlken Nicola , Fischer Christine , Lichtblau Mona , Blank Norbert , Fiehn Christoph , Stöckl Frank , Prange Felix , Staehler Gerd , Reichenberger Frank , Tiede Henning , Halank Michael , Seyfarth Hans-Jürgen , Wagner Simone , Nagel Christian 
Published: June 2012

Abstract
Introduction
The objective of this prospective study was to assess short- and long-term efficacy of exercise training (ET) as add-on to medical therapy in patients with connective tissue disease-associated pulmonary arterial hypertension (CTD-APAH).

Methods
Patients with invasively confirmed CTD-APAH received ET in-hospital for 3 weeks and continued at home for 12 weeks. Efficacy parameters have been evaluated at baseline and after 15 weeks by blinded-observers. Survival rate has been evaluated in a follow-up period of 2.9 ± 1.9 years.

Results
Twenty-one consecutive patients were included and assessed at baseline, and after 3 weeks, 14 after 15 weeks. Patients significantly improved the mean distance walked in 6 minutes compared to baseline by 67 ± 52 meters after 3 weeks (p < 0.001) and by 71 ± 35 meters after 15 weeks (p = 0.003), scores of quality of life (p < 0.05), heart rate at rest, peak oxygen consumption, oxygen saturation and maximal workload. Systolic pulmonary artery pressure and diastolic systemic blood pressure improved significantly after 3 weeks of ET. The 1- and 2-year overall-survival rates were 100%, the 3-year survival 73%. In one patient lung transplantation was performed 6 months after ET.

Conclusion
ET as add-on to medical therapy is highly effective in patients with CTD-APAH to improve work capacity, quality of life and further prognostic relevant parameters and possibly improves the 1-, 2- and 3-year survival rate. Further randomized controlled studies are needed to confirm these results.

Trial registration
ClinicalTrials.gov: NCT00491309.
Hydroxychloroquine is associated with impaired interferon-alpha and tumor necrosis factor-alpha production by plasmacytoid dendritic cells in systemic lupus erythematosus
Authors: Sacre Karim , Criswell Lindsey A , McCune Joseph M 
Published: June 2012

Abstract
Introduction
Plasmacytoid dendritic cells (pDCs) constitutively express two members of the Toll-like receptor (TLR) family, TLR-9 and TLR-7, through which they can be stimulated to produce high levels of interferon (IFN)-α, a key mediator of the pathogenesis of systemic lupus erythematosus (SLE). Given the known efficacy of hydroxychloroquine (HCQ) in the treatment of SLE, we examined its ability to inhibit such pDC function in vivo.

Methods
Peripheral blood mononuclear cells (PBMCs) from SLE subjects treated or not with HCQ and from healthy controls were stimulated with the TLR-9 agonist, CpG oligodeoxynucleotides (CpG-A ODN)-2216, and the TLR-7 agonist, imiquimod. The proportion of monocytes, B cells, myeloid dendritic cells, pDCs, and natural killer (NK) cells producing IFN-α and tumor necrosis factor alpha (TNF-α) was then analyzed by multiparameter flow cytometry.

Results
After TLR-9/7 stimulation in both SLE and healthy subjects, significant production of IFN-α and TNF-α was only observed in pDCs. TLR-7 and TLR-9 induced IFN-α and TNF-α production by pDCs from subjects with SLE was decreased relative to that found in controls (TLR-9/IFN-α, P < 0.0001; TLR-9/TNF-α P < 0.0001; TLR-7/TNF-α P = 0.01). TLR-9 and TLR-7 induced IFN-α and TNF-α production by pDCs was severely impaired in 36% (TLR-9) and 33% (TLR-7) of SLE subjects. In almost all cases, these subjects were being treated with HCQ (HCQ vs. no HCQ: impaired TLR-9/IFN-α, P = 0.0003; impaired TLR-7/IFN-α, P = 0.07; impaired TLR-9/TNF-α, P < 0.009; impaired TLR-7/TNF-α, P < 0.01).

Conclusions
Treatment with HCQ is associated with impaired ability of pDCs from subjects with SLE to produce IFN-α and TNF-α upon stimulation with TLR-9 and TLR-7 agonists.
Centromere protein-A, an essential centromere protein, is a prognostic marker for relapse in estrogen receptor-positive breast cancer
Authors: McGovern Susan L , Qi Yuan , Pusztai Lajos , Symmans William F , Buchholz Thomas A 
Published: June 2012

Abstract
Introduction
Centromere protein A (CENP-A), an essential centromere protein, has been associated with high grade cancers. This study was undertaken to determine if CENP-A is a prognostic factor for breast cancer patients not receiving systemic therapy or predictive of response to tamoxifen or neoadjuvant chemotherapy.

Methods
mRNA levels of CENP-A and CENP-B, a centromere protein that binds independently of CENP-A, were measured in breast cancer specimens from 484 patients receiving no systemic therapy, 276 patients receiving tamoxifen, and 233 patients treated with neoadjuvant chemotherapy. Associations between CENP-A, CENP-B, Ki-67, relapse, and chemotherapy response were determined.

Results
CENP-A but not CENP-B was higher in estrogen receptor (ER)-negative tumors than ER-positive tumors and positively correlated with Ki-67 expression. Among patients with ER-positive disease who received no systemic therapy or tamoxifen, higher levels of CENP-A were associated with lower rates of 5-year distant relapse free survival (DRFS). On multivariate analyses including Ki-67, high CENP-A expression had a hazard ratio of 10.9 for relapse in patients with ER-positive disease not receiving systemic therapy (95% CI, 2.86 to 41.78; P = 0.00047) and 1.64 for patients with ER-positive disease receiving tamoxifen (95% CI, 0.99 to 2.71; P = 0.054). CENP-A was not an independent prognostic marker in ER-negative tumors. For both ER-positive and ER-negative tumors, CENP-A was not a significant independent predictor of chemotherapy response.

Conclusions
CENP-A was a significant independent prognostic marker for patients with ER-positive breast cancer not treated with systemic therapy but had limited predictive value in tamoxifen treated patients and was not predictive of response to neoadjuvant chemotherapy.
Four hour creatinine clearance is better than plasma creatinine for monitoring renal function in critically ill patients
Authors: Pickering John W , Frampton Christopher M , Walker Robert J , Shaw Geoffrey M , Endre Zoltán H 
Published: June 2012

Abstract
Introduction
Acute kidney injury (AKI) diagnosis is based on an increase in plasma creatinine, which is a slowly changing surrogate of decreased glomerular filtration rate. We investigated whether serial creatinine clearance, a direct measure of the glomerular filtration rate, provided more timely and accurate information on renal function than serial plasma creatinine in critically ill patients.

Methods
Serial plasma creatinine and 4-hour creatinine clearance were measured 12-hourly for 24 hours and then daily in 484 patients. AKI was defined either as > 50% increase in plasma creatinine from baseline, or > 33.3% decrease in creatinine clearance. The diagnostic and predictive performance of the two AKI definitions were compared.

Results
Creatinine clearance decrease diagnosed AKI in 24% of those not diagnosed by plasma creatinine increase on entry. These patients entered the ICU sooner after insult than those diagnosed with AKI by plasma creatinine elevation (P = 0.0041). Mortality and dialysis requirement increased with the change in creatinine clearance-acute kidney injury severity class (P = 0.0021). Amongst patients with plasma creatinine < 1.24 mg/dl on entry, creatinine clearance improved the prediction of AKI considerably (Net Reclassification Improvement 83%, Integrated Discrimination Improvement 0.29). On-entry, creatinine clearance associated with AKI severity and duration (P < 0.0001) predicted dialysis need (area under the curve: 0.75) and death (0.61). A > 33.3% decrease in creatinine clearance over the first 12 hours was associated with a 2.0-fold increased relative risk of dialysis or death.

Conclusions
Repeated 4-hour creatinine clearance measurements in critically ill patients allow earlier detection of AKI, as well as progression and recovery compared to plasma creatinine.

Trial Registration
Australian New Zealand Clinical Trials Registry ACTRN012606000032550.
Estrogen Promotes Prostate Cancer Cell Migration via Paracrine Release of ENO1 from Stromal Cells
Authors: Yu Lin , Shi Jiandang , Cheng Sa , Zhu Yan , Zhao Xiulan , Yang Kuo , Du Xiaoling , Klocker Helmut , Yang Xiaoli , Zhang Ju 
Published: June 2012

Abstract
As a key glycolytic enzyme, enolase 1 (ENO1) is critical for cellular energy metabolism. Recent studies have revealed its important role in growth and metastasis of lung, head and neck, and breast cancer. However, the regulatory mechanisms of ENO1 expression and secretion remain unclear. We observed that conditioned medium from estradiol-stimulated prostate stromal cells significantly promoted the migration of prostate cancer (PCa) cells. Two-dimensional protein electrophoresis, mass spectrometry, and immunodepletion assays identified one of the major active factors in the conditioned medium as α-type enolase (α-enolase, or ENO1). Moreover, in prostate stromal cells, estradiol not only enhanced the stability of ENO1 at the protein level in an estrogen receptor-α-dependent manner but also promoted its secretion to the extracellular matrix. Furthermore, recombinant ENO1 bound to the surface of PCa cells and promoted cell migration via their plasminogen receptor activity in a paracrine manner. Immunohistochemistry suggested that stromal ENO1 levels increased in PCa compared with those in normal tissue.