bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of microRNA expression profiles in normal and osteoarthritic human chondrocytes
Authors: Díaz-Prado Silvia , Cicione Claudia , Muiños-López Emma , Hermida-Gómez Tamara , Oreiro Natividad , Fernández-López Carlos , Blanco Francisco J 
Published: August 2012

Abstract

Background
Osteoarthritis (OA) is a multifactorial disease characterized by destruction of the articular cartilage due to environmental, mechanical and genetic components. The genetics of OA is complex and is not completely understood. Recent works have demonstrated the importance of microRNAs (miRNAs) in cartilage function. MiRNAs are a class of small noncoding RNAs that regulate gene expression and are involved in different cellular process: apoptosis, proliferation, development, glucose and lipid metabolism. The aim of this study was to identify and characterize the expression profile of miRNAs in normal and OA chondrocytes and to determine their role in the OA.

Methods
Chondrocytes were moved to aggregate culture and evaluated using histological and qPCR techniques. miRNAs were isolated and analyzed using the Agilent Human miRNA Microarray.

Results
Of the 723 miRNAs analyzed, 7 miRNAs showed a statistically significant differential expression. Amongst these 7 human miRNAs, 1 was up-regulated in OA chondrocytes (hsa-miR-483-5p) and 6 were up-regulated in normal chondrocytes (hsa-miR-149*, hsa-miR-582-3p, hsa-miR-1227, hsa-miR-634, hsa-miR-576-5p and hsa-miR-641). These profiling results were validated by the detection of some selected miRNAs by qPCR. In silico analyses predicted that key molecular pathways potentially altered by the miRNAs differentially expressed in normal and OA chondrocytes include TGF-beta, Wnt, Erb and mTOR signalling; all of them implicated in the development, maintenance and destruction of articular cartilage.

Conclusions
We have identified 7 miRNAs differentially expressed in OA and normal chondrocytes. Our potential miRNA target predictions and the signalling cascades altered by the differentially expressed miRNAs supports the potential involvement of the detected miRNAs in OA pathology. Due to the importance of miRNA in mediating the translation of target mRNA into protein, the identification of these miRNAs differentially expressed in normal and OA chondrocyte micropellets could have important diagnostic and therapeutic potential. Further studies are needed to know the function of these miRNAs, including the search of their target mRNA genes, which could lead to the development of novel therapeutic strategies for the OA treatment.
Peritumoral lymphangiogenesis induced by vascular endothelial growth factor C and D promotes lymph node metastasis in breast cancer patients
Authors: Zhao Ying-Chun , Ni Xiao-Jian , Li Yong , Dai Min , Yuan Zhong-Xu , Zhu Yong-Yun , Luo Chuan-Yu 
Published: August 2012

Abstract

Background
Mounting clinical and experimental data suggest that the migration of tumor cells into lymph nodes is greatly facilitated by lymphangiogenesis. Vascular endothelial growth factor (VEGF)-C and D have been identified as lymphangiogenic growth factors and play an important role in tumor lymphangiogenesis. The purpose of this study was to investigate the location of lymphangiogenesis driven by tumor-derived VEGF-C/D in breast cancer, and to determine the role of intratumoral and peritumoral lymphatic vessel density (LVD) in lymphangiogenesis in breast cancer.

Methods
The expression levels of VEGF-C/D were determined by immunohistochemistry, and intratumoral LVD and peritumoral LVD were assessed using immunohistochemistry and the D2-40 antibody in 73 patients with primary breast cancer. The associations of intratumoral LVD and peritumoral LVD with VEGF-C/D expression, clinicopathological features and prognosis were assessed.

Results
VEGF-C and D expression were significantly higher in breast cancer than benign disease (P < 0.01). VEGF-C (P < 0.001) and VEGF-D (P = 0.005) expression were significantly associated with peritumoral LVD, but not intratumoral LVD. Intratumoral LVD was associated with tumor size (P = 0.01). Peritumoral LVD was significantly associated with lymph node metastasis (LNM; P = 0.005), lymphatic vessel invasion (LVI; P = 0.017) and late tumor,node, metastasis (TNM) stage (P = 0.011). Moreover, peritumoral LVD was an independent risk factor for axillary lymph node metastasis, overall survival and disease-free survival in multivariate analysis.

Conclusions
This study suggests that tumor-derived VEGF-C/D induce peritumoral lymphangiogenesis, which may be one mechanism that leads to lymphatic invasion and metastatic spread. Peritumoral LVD has potential as an independent prognostic factor in breast cancer patients.
Malformations in a cohort of 284 women with Mayer-Rokitansky-Küster-Hauser syndrome (MRKH)
Authors: Oppelt Patricia G , Lermann Johannes , Strick Reiner , Dittrich Ralf , Strissel Pamela , Rettig Ingo , Schulze Christine , Renner Stefan P , Beckmann Matthias W , Brucker Sara , Rall Katharina , Mueller Andreas 
Published: August 2012

Abstract

Background
The aim of this retrospective study was to describe the spectrum of genital and associated malformations in women with Mayer-Rokitansky-Küster-Hauser syndrome using evaluated diagnostic procedures and the Vagina Cervix Uterus Adnex – associated Malformation classification system (VCUAM).

Methods
290 women with MRKH syndrome were clinically evaluated with using clinical examinations, abdominal and perineal/rectal ultrasound, MRI, and laparoscopy.

Results
Classification of female genital malformation according to the Vagina Cervix Uterus Adnex – associated Malformation classification system was possible in 284 women (97.9%). Complete atresia of Vagina (V5b) and bilateral atresia of Cervix (C2b) were found in 284 patients (100%). Uterus: bilateral rudimentary or a plastic uterine horns were found in 239 women (84.2%). Adnexa: normal Adnexa were found in 248 women (87.3%). Malformations: associated malformations were found in 126 of 282 evaluable women (44.7%), 84 women (29.6%) had malformations of the renal system. Of 284 women with Mayer-Rokitansky-Küster-Hauser syndrome 212 women (74.7%) could be classified as V5bC2bU4bA0. The most frequent classification was V5bC2bU4bA0M0 (46.8%) diagnosed in 133 of 284 women.

Conclusions
Complete atresia of vagina and cervix were found in all patients, variable malformations were found with uterus and adnexa. A variety of associated malformations were present, predominantly of the renal system. It is therefore recommended that all patients with genital malformations should be evaluated for renal abnormalities.
Aerobic capacity and disease activity in children, adolescents and young adults with juvenile idiopathic arthritis (JIA)
Authors: van Pelt Philomine A , Takken Tim , van Brussel Marco , de Witte Mirjam , Kruize Aike A , Wulffraat Nico M 
Published: August 2012

Abstract

Background
As patients with juvenile idiopathic arthritis (JIA) progress into adulthood, long-term outcome is determined by disease activity, physical and psychosocial development. Decreased aerobic capacity may play a critical role in health-related outcomes in JIA, since it has been linked with cardiovascular morbidity and mortality in late adulthood. The objectives of the current study are to examine the aerobic capacity and its relation to parameters of disease activity in children, adolescents and young adults with JIA.

Methods
Sixty-three patients with JIA (aged 10–27 years) were cross sectional studied regarding their aerobic capacity and correlations were made to demographic, disease-related variables, and medication utilization. in a cross-sectional study group of 63 patients of all subtypes. Patients were divided in three age groups, 10–13 years; 14–17 years and 18–27 years.

Results
Reduced aerobic capacity is found in clinical remission as well as active disease in all subtypes and all age groups. Aerobic capacity is more impaired in active disease shown by DAS 28, JADAS 27, ESR and serum thrombocyte counts. Lower haemoglobin has a negative impact. Long-term used medication including methotrexate and corticosteroids didn’t influence outcome. There is no association with current sports participation.

Conclusion
Reduced aerobic capacity is present in adolescents and young adults with JIA, both in active disease and in patients with remission. Measures of aerobic capacity may serve as important outcome measure in JIA.
Adaptive resource allocation for cognitive radio networks with multiple primary networks
Authors: Wang Ye , Zhang Qinyu , Zhang Yalin , Chen Peipei 
Published: August 2012

Abstract
In this article, adaptive resource allocation (ARA) is investigated for multiple primary networks based-cognitive radio networks under a more practical system model, where the bandwidth of each secondary user is assumed to be limited and the maximum allowable interference for each primary network is different. We first formulate the ARA as a constrained optimization problem with the objective function of maximizing the proportional fairness-based ergodic sum capacity. The multiple constraints optimization problem is NP-hard and therefore, we propose a scheme to decompose the optimization problem into two unconstrained optimization problems by designing alternative objective functions and penalty functions. Then, a suboptimal heuristic solution framework based on particle swarm optimization is proposed to solve the unconstrained optimization problems. Computation simulations are carried out and the results show that the proposed scheme outperforms traditional ARA schemes.
Alkaline phosphatase activity after cardiothoracic surgery in infants and correlation with post-operative support and inflammation: a prospective cohort study
Authors: Davidson Jesse , Tong Suhong , Hauck Amanda , Lawson D Scott , Jaggers James , Kaufman Jon , da Cruz Eduardo 
Published: August 2012

Abstract
Introduction
Limited evidence suggests that serum alkaline phosphatase activity may decrease after cardiac surgery in adults and children. The importance of this finding is not known. Recent studies, however, have identified a potential role for alkaline phosphatase as modulator of inflammation in multiple settings, including during adult cardiopulmonary bypass. We sought to describe the change in alkaline phosphatase activity after cardiothoracic surgery in infants and to assess for a correlation with intensity and duration of post-operative support, markers of inflammation, and short-term clinical outcomes.

Methods
Sub-analysis of a prospective observational study on the kinetics of procalcitonin in 70 infants (≤90 days old) undergoing cardiothoracic surgery. Subjects were grouped based on the use of cardiopulmonary bypass and delayed sternal closure. Alkaline phosphatase, procalcitonin, and C-reactive protein (CRP) levels were obtained pre-operation and on post-operative day 1. Mean change in alkaline phosphatase activity was determined in each surgical group. Generalized linear modeling and logistic regression were employed to assess for associations between post-operative alkaline phosphatase activity and post-operative support, inflammation, and short term outcomes. Primary endpoints were vasoactive-inotropic score at 24 hours and length of intubation. Secondary endpoints included procalcitonin/CRP levels on post-operative day 1, length of hospital stay, and cardiac arrest or death.

Results
Mean decrease in alkaline phosphatase was 30 U/L (p = 0.01) in the non-bypass group, 114 U/L (p<0.0001) in the bypass group, and 94 U/L (p<0.0001) in the delayed sternal closure group. On multivariate analysis, each 10 U/L decrease in alkaline phosphatase activity on post-operative day 1 was independently associated with an increase in vasoactive-inotropic score by 0.7 (p<0.0001), intubation time by 6% (p<0.05), hospital stay by 5% (p<0.05), and procalcitonin by 14% (P<0.01), with a trend towards increased odds of cardiac arrest or death (OR 1.3; p = 0.06). Post-operative alkaline phosphatase activity was not associated with CRP (p = 0.7).

Conclusions
Alkaline phosphatase activity decreases after cardiothoracic surgery in infants. Low post-operative alkaline phosphatase activity is independently associated with increased procalcitonin, increased vasoactive/inotropic support, prolonged intubation time, and prolonged hospital stay. Alkaline phosphatase may serve as a biomarker and potential modulator of post-operative support and inflammation following cardiothoracic surgery in infants.
Partial promoter substitutions generating transcriptional sentinels of diverse signaling pathways in embryonic stem cells and mice
Authors: Serup Palle , Gustavsen Carsten , Klein Tino , Potter Leah A. , Lin Robert , Mullapudi Nandita , Wandzioch Ewa , Hines Angela , Davis Ashley , Bruun Christine , Engberg Nina , Petersen Dorthe R. , Peterslund Janny M. L. , MacDonald Raymond J. , Grapin-Botton Anne , Magnuson Mark A. , Zaret Kenneth S. 
Published: August 2012

SummaryExtracellular signals in development, physiology, homeostasis, and disease often act by regulating transcription. Herein we describe a general method and specific resources for determining where and when such signaling occurs in live animals and for being able to systematically compare the timing and extent of different signals in different cellular contexts. We used recombinase-mediated cassette exchange (RMCE) to test the effect of successively deleting conserved genomic regions of the ubiquitously active Rosa26 promoter and substituting the deleted regions for regulatory sequences that respond to diverse extracellular signals. We thereby created an allelic series of embryonic stem cells and mice, each containing a signal-responsive sentinel with different fluorescent reporters that respond with sensitivity and specificity to retinoic acids, BMPs, activin A, Wnts, or Notch, and that can be adapted to any pathway that acts via DNA elements.
Characterising the tumour morphological response to therapeutic intervention
Authors: Savage Anne , Katz Elad , Eberst Alistair , Falconer Ruth E. , Houston Alasdair , Harrison David J. , Bown James 
Published: August 2012

SummaryIn cancer, morphological assessment of histological tissue samples is a fundamental part of both diagnosis and prognosis. Image analysis offers opportunities to support that assessment through quantitative metrics of morphology. The majority of morphometric analysis is carried out on two-dimensional tissue section data and so only represents a small fraction of any tumour. We present a novel application of three-dimensional (3D) morphometrics for 3D imaging data obtained from tumours grown in a culture model. Minkowski functionals, a set of measures that characterise geometry and topology in n-dimensional space are used to quantify tumour topology in the absence of and in response to therapeutic intervention. These measures are used to stratify morphological response of tumours to therapeutic intervention. Breast tumours are characterised by ER status, HER2 status and tumour grade. Previously, we have shown that ER status is associated with tumour volume in response to tamoxifen treatment ex vivo. Here, HER2 status is found to predict the changes in morphology other than volume as a result of tamoxifen treatment ex vivo. Finally, we show the extent to which Minkowski functionals may be used to predict tumour grade. Minkowski functionals are generalisable to any 3D data set, including in vivo and cellular systems. This quantitative topological analysis can provide a valuable link among biomarkers, drug intervention and tumour morphology that is complementary to existing, non-morphological measures of tumour response to intervention and may ultimately inform patient treatment.
A yeast model for amyloid-β aggregation exemplifies the role of membrane trafficking and PICALM in cytotoxicity
Authors: D'Angelo Fabien , Vignaud Hélène , Di Martino Julie , Salin Bénédicte , Devin Anne , Cullin Christophe , Marchal Christelle 
Published: August 2012

Summary
Alzheimer's disease is the most common neurodegenerative disease, associated with aggregation of amyloid-β (Aβ) peptides. The exact mechanism of neuronal cell dysfunction in Alzheimer's disease is poorly understood and numerous models have been used to decipher the mechanisms leading to cellular death. Yeast cells might be a good model to understand the intracellular toxicity triggered by Aβ peptides. Indeed, yeast has been used as a model to examine protein functions or cellular pathways that mediate the secretion, aggregation and subsequent toxicity of proteins associated with human neurodegenerative disorders. In the present study, we use the yeast Saccharomyces cerevisiae as a model system to study the effects of intracellular Aβ in fusion with green fluorescent protein. We sent this fusion protein into the secretory pathway and showed that intracellular traffic pathways are necessary for the generation of toxic species. Yeast PICALM orthologs are involved in cellular toxicity, indicating conservation of the mechanisms of toxicity from mammals to yeast. Finally, our model demonstrates the capacity for intracellular Aβ to cross intracellular membranes and target mitochondrial organelles.
Applicability of the AGREE II Instrument in Evaluating the Development Process and Quality of Current National Academy of Clinical Biochemistry Guidelines
Authors: Don-Wauchope Andrew C , Sievenpiper John L , Hill Stephen A , Iorio Alfonso 
Published: August 2012

Abstract

BACKGROUND
Laboratory medicine practice guidelines (LMPGs) are an important part of clinical laboratory medicine. The Appraisal of Guidelines for Research and Evaluation II (AGREE II) instrument has been developed to evaluate the process of practice-guideline development and the quality of reporting. We assessed the applicability of AGREE II in assessing the National Academy of Clinical Biochemistry (NACB) LMPGs.

METHODS
The NACB website was searched for all available LMPGs up to December 2011. Two independent appraisers used the AGREE II instrument to assess each LMPG identified by the search. Quality was assessed across 6 domains (scope and purpose, stakeholder involvement, rigor of development, clarity of presentation, applicability, and editorial independence), comprising a total of 23 items and 2 overall assessments, each scored on a 7-point scale (1, strongly disagree, to 7, strongly agree). All scores were expressed as AGREE II calculated percentages (100% indicates that all items scored 7 by all appraisers).

RESULTS
Eleven LMPGs were identified. All of the LMPGs provided some information seen as applicable to clinical practice by the appraisers. Only 5 of the LMPGs had overall scores ≥50%, with a median score of 42% (range: 8%–92%). Individual domain scores varied considerably from 0% to 100%. One guideline achieved a very high score on the instrument.

CONCLUSIONS
The AGREE II instrument is applicable and useful to evaluate LMPGs. All domains were evaluated as being useful to assess LMPGs, some were addressed well (e.g., clarity of presentation), whereas others could be improved (e.g., applicability).
Pathways of Genetic Adaptation: Multistep Origin of Mutants Under Selection Without Induced Mutagenesis inSalmonella enterica
Authors: Quiñones-Soto Semarhy , Reams Andrew B , Roth John R 
Published: August 2012

AbstractIn several bacterial systems, mutant cell populations plated on growth-restricting medium give rise to revertant colonies that accumulate over several days. One model suggests that nongrowing parent cells mutagenize their own genome and thereby create beneficial mutations (stress-induced mutagenesis). By this model, the first-order induction of new mutations in a nongrowing parent cell population leads to the delayed accumulation of visible colonies. In an alternative model (selection only), selective conditions allow preexisting small-effect mutants to initiate clones that grow and give rise to faster-growing mutants. By the selection-only model, the delay in appearance of revertant colonies reflects (1) the time required for initial clones to reach a size sufficient to allow the second mutation plus (2) the time required for growth of the improved subclone. We previously characterized a system in which revertant colonies accumulate slowly and contain cells with two mutations, one formed before plating and one after. This left open the question of whether mutation rates increase under selection. Here we measure the unselected formation rate and the growth contribution of each mutant type. When these parameters are used in a graphic model of revertant colony development, they demonstrate that no increase in mutation rate is required to explain the number and delayed appearance of two of the revertant types.
SACY-1 DEAD-Box Helicase Links the Somatic Control of Oocyte Meiotic Maturation to the Sperm-to-Oocyte Switch and Gamete Maintenance inCaenorhabditis elegans
Authors: Kim Seongseop , Govindan J Amaranath , Tu Zheng Jin , Greenstein David 
Published: August 2012

AbstractIn sexually reproducing animals, oocytes arrest at diplotene or diakinesis and resume meiosis (meiotic maturation) in response to hormones. In Caenorhabditis elegans, major sperm protein triggers meiotic resumption through a mechanism involving somatic Gαs–adenylate cyclase signaling and soma-to-germline gap-junctional communication. Using genetic mosaic analysis, we show that the major effector of Gαs–adenylate cyclase signaling, protein kinase A (PKA), is required in gonadal sheath cells for oocyte meiotic maturation and dispensable in the germ line. This result rules out a model in which cyclic nucleotides must transit through sheath-oocyte gap junctions to activate PKA in the germ line, as proposed in vertebrate systems. We conducted a genetic screen to identify regulators of oocyte meiotic maturation functioning downstream of Gαs–adenylate cyclase–PKA signaling. We molecularly identified 10 regulatory loci, which include essential and nonessential factors. sacy-1, which encodes a highly conserved DEAD-box helicase, is an essential germline factor that negatively regulates meiotic maturation. SACY-1 is a multifunctional protein that establishes a mechanistic link connecting the somatic control of meiotic maturation to germline sex determination and gamete maintenance. Modulatory factors include multiple subunits of a CoREST-like complex and the TWK-1 two-pore potassium channel. These factors are not absolutely required for meiotic maturation or its negative regulation in the absence of sperm, but function cumulatively to enable somatic control of meiotic maturation. This work provides insights into the genetic control of meiotic maturation signaling in C. elegans, and the conserved factors identified here might inform analysis in other systems through either homology or analogy.
Why Transcription Factor Binding Sites Are Ten Nucleotides Long
Authors: Stewart Alexander J , Hannenhalli Sridhar , Plotkin Joshua B 
Published: August 2012

Abstract
Gene expression is controlled primarily by transcription factors, whose DNA binding sites are typically 10 nt long. We develop a population-genetic model to understand how the length and information content of such binding sites evolve. Our analysis is based on an inherent trade-off between specificity, which is greater in long binding sites, and robustness to mutation, which is greater in short binding sites. The evolutionary stable distribution of binding site lengths predicted by the model agrees with the empirical distribution (5–31 nt, with mean 9.9 nt for eukaryotes), and it is remarkably robust to variation in the underlying parameters of population size, mutation rate, number of transcription factor targets, and strength of selection for proper binding and selection against improper binding. In a systematic data set of eukaryotic and prokaryotic transcription factors we also uncover strong relationships between the length of a binding site and its information content per nucleotide, as well as between the number of targets a transcription factor regulates and the information content in its binding sites. Our analysis explains these features as well as the remarkable conservation of binding site characteristics across diverse taxa.