bluuebunny/crossref_metadata_2025_split huggingface dataset:
From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways
Authors: Bauer-Mehren Anna , Furlong Laura I , Rautschka Michael , Sanz Ferran 
Published: August 2009

Abstract

Background
Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understanding the differences in drug response. In this regard, it is of particular interest to study the effect of non-synonymous SNPs in the context of biological networks such as cell signalling pathways. UniProt provides curated information about the functional and phenotypic effects of sequence variation, including SNPs, as well as on mutations of protein sequences. However, no strategy has been developed to integrate this information with biological networks, with the ultimate goal of studying the impact of the functional effect of SNPs in the structure and dynamics of biological networks.

Results
First, we identified the different challenges posed by the integration of the phenotypic effect of sequence variants and mutations with biological networks. Second, we developed a strategy for the combination of data extracted from public resources, such as UniProt, NCBI dbSNP, Reactome and BioModels. We generated attribute files containing phenotypic and genotypic annotations to the nodes of biological networks, which can be imported into network visualization tools such as Cytoscape. These resources allow the mapping and visualization of mutations and natural variations of human proteins and their phenotypic effect on biological networks (e.g. signalling pathways, protein-protein interaction networks, dynamic models). Finally, an example on the use of the sequence variation data in the dynamics of a network model is presented.

Conclusion
In this paper we present a general strategy for the integration of pathway and sequence variation data for visualization, analysis and modelling purposes, including the study of the functional impact of protein sequence variations on the dynamics of signalling pathways. This is of particular interest when the SNP or mutation is known to be associated to disease. We expect that this approach will help in the study of the functional impact of disease-associated SNPs on the behaviour of cell signalling pathways, which ultimately will lead to a better understanding of the mechanisms underlying complex diseases.
Matrix gla protein (MGP): an overexpressed and migration-promoting mesenchymal component in glioblastoma
Authors: Mertsch Sonja , Schurgers Leon J , Weber Kathrin , Paulus Werner , Senner Volker 
Published: August 2009

Abstract

Background
Recent studies have demonstrated that a molecular subtype of glioblastoma is characterized by overexpression of extracellular matrix (ECM)/mesenchymal components and shorter survival. Specifically, gene expression profiling studies revealed that matrix gla protein (MGP), whose function has traditionally been linked to inhibition of calcification of arteries and cartilage, is overexpressed in glioblastomas and associated with worse outcome.

Methods
In order to analyze the role of MGP in glioblastomas, we performed expression, migration and proliferation studies.

Results
Real-time PCR and ELISA assays confirmed overexpression of MGP in glioblastoma biopsy specimens and cell lines at mRNA and protein levels as compared to normal brain tissue. Immunohistochemistry verified positivity of glial tumor cells for MGP. RNAi-mediated knockdown of MGP in three glioma cell lines (U343MG, U373MG, H4) led to marked reduction of migration, as demonstrated by wound healing and transwell assays, while no effect on proliferation was seen.

Conclusion
Our data suggest that upregulation of MGP (and possibly other ECM-related components as well) results in unfavorable prognosis via increased migration.
Body satisfaction and body weight: gender differences and sociodemographic determinants
Authors: Austin S Bryn , Haines Jess , Veugelers Paul J 
Published: August 2009

Abstract

Background
Given the documented links between body satisfaction, weight-related behaviors, and weight change in adolescents, we sought to examine the prevalence of poor body satisfaction in prepubescent girls and boys and its associations with body weight, socioeconomic factors, and rural residence.

Methods
We obtained data from 4254 girls and boys participating in a population-based survey of grade five students in the province of Nova Scotia, Canada. We examined gender specific associations between the prevalence of poor body satisfaction and body mass index (BMI) with generalized additive models and applied multilevel logistic regression methods to estimate associations of body satisfaction with BMI, rural residence, parental education and income, and neighborhood household income.

Results
We observed a linear increase in poor body satisfaction with increasing BMI in girls. Among boys, however, we found a U-shape association where boys with low BMI and those with high BMI reported higher levels of poor body satisfaction. We also found that poor body satisfaction was more prevalent among girls whose parents had lower educational attainment and among those who reside in rural areas.

Conclusion
Insight into the unique relationships between body satisfaction and BMI experienced by prepubescent children, males, and populations diverse in parental education and geographic location may help to inform public health initiatives designed to improve weight-related behaviors and reduce overweight in children.
Association of a genetic polymorphism (-44 C/G SNP) in the human DEFB1 gene with expression and inducibility of multiple β-defensins in gingival keratinocytes
Authors: Kalus Andrea A , Fredericks L Page , Hacker Beth M , Dommisch Henrik , Presland Richard B , Kimball Janet R , Dale Beverly A 
Published: August 2009

Abstract

Background
Human β-defensins (hBDs) are antimicrobial peptides with a role in innate immune defense. Our laboratory previously showed that a single nucleotide polymorphism (SNP) in the 5' untranslated region of the hBD1 gene (DEFB1), denoted -44 (rs1800972), is correlated with protection from oral Candida. Because this SNP alters the putative mRNA structure, we hypothesized that it alters hBD1 expression.

Methods
Transfection of reporter constructs and evaluation of antimicrobial activity and mRNA expression levels in keratinocytes from multiple donors were used to evaluate the effect of this SNP on constitutive and induced levels of expression.

Results
Transfection of CAT reporter constructs containing the 5' untranslated region showed that the -44 G allele yielded a 2-fold increase in CAT protein compared to other common haplotypes suggesting a cis effect on transcription or translation. The constitutive hBD1 mRNA level in human oral keratinocytes was significantly greater in cells from donors with the -44 GG genotype compared to those with the common CC genotype. Surprisingly, the hBD3 mRNA level as well as antimicrobial activity of keratinocyte extracts also correlated with the -44 G allele. Induced levels of hBD1, hBD2, and hBD3 mRNA were evaluated in keratinocytes challenged with Toll-like receptor 2 and 4 ligands, interleukin-1β, TNFα, and interferon-γ (IFNγ). In contrast to constitutive expression levels, IFNγ-induced keratinocyte hBD1 and hBD3 mRNA expression was significantly greater in cells with the common CC genotype, but there was no clear correlation of genotype with hBD2 expression.

Conclusion
The DEFB1 -44 G allele is associated with an increase in overall constitutive antimicrobial activity and expression of hBD1 and hBD3 in a manner that is consistent with protection from candidiasis, while the more common C allele is associated with IFNγ inducibility of these β-defensins and is likely to be more protective in conditions that enhance IFNγ expression such as chronic periodontitis. These results suggest a complex relationship between genetics and defensin expression that may influence periodontal health and innate immune responses.
Discovery of common marburgvirus protective epitopes in a BALB/c mouse model
Authors: Kalina Warren V , Warfield Kelly L , Olinger Gene G , Bavari Sina 
Published: August 2009

AbstractBackgroundMarburg virus (MARV) causes acute hemorrhagic fever that is often lethal, and no licensed vaccines are available for preventing this deadly viral infection. The immune mechanisms for protection against MARV are poorly understood, but previous studies suggest that both antibodies and T cells are required. In our study, we infected BALB/c mice with plaque-purified, nonlethal MARV and used overlapping peptides to map H2d-restricted CD8+ T-cell epitopes.MethodsSplenocytes from mice infected with nonlethal MARV were harvested and stimulated with multiple overlapping 15-mer peptide pools, and reactive CD8+ T cells were evaluated for antigen specificity by measuring upregulation of CD44 and interferon-γ expression. After confirming positive reactivity to specific 15-mer peptides, we used extrapolated 9-mer epitopes to evaluate the induction of cytotoxic T-cell responses and protection from lethal MARV challenge in BALB/c mice.ResultsWe discovered a CD8+ T-cell epitope within both the MARV glycoprotein (GP) and nucleoprotein (NP) that triggered cytotoxic T-cell responses. These responses were also protective when epitope-specific splenocytes were transferred into naïve animals.ConclusionEpitope mapping of MARV GP, NP, and VP40 provides the first evidence that specific MARV-epitope induction of cellular immune responses is sufficient to combat infection. Establishment of CD8+ T-cell epitopes that are reactive to MARV proteins provides an important research tool for dissecting the significance of cellular immune responses in BALB/c mice infected with MARV.
Long-term results after Boston brace treatment in adolescent idiopathic scoliosis
Authors: Lange Johan Emil , Steen Harald , Brox Jens Ivar 
Published: August 2009

Abstract

Background
Few studies have evaluated long-term outcome after bracing using validated health related quality of life outcome measures. The aim of the present study was to evaluate the long-term outcome in adolescent idiopathic scoliosis (AIS) 12 years or more after treatment with the Boston brace.

Methods
109 (80%) of 135 patients (7 men) with AIS treated with the Boston brace at a mean of 19.2 (range 12–28) years previously responded to long-term follow-up examination.
All patients (n = 109) answered a standardised questionnaire including demographics, work status, treatment, Global Back Disability Question, Oswestry Disability Index (ODI) (100-worst possible), General Function Score (GFS) (100 – worst possible), EuroQol (EQ-5D) (1 – best possible), EQ-VAS (100 – best possible)) and Scoliosis Research Society -22 (SRS – 22) (5 – best possible). Clinical and radiological examination was obtained in 86 patients.

Results
The magnitude of the primary prebrace major curve was in average 33.4° (range 20 – 52). At weaning and at the last follow-up the corresponding values were 28.3° (9–56) and 34.2° (8 – 87), respectively. The mean age at follow-up was 35 (27 – 46) years. Work status was: full time (80%), on sick-leave (3%), on rehabilitation (4%), disability pension (4%), homemaker (7%), students (2%), 7% had changed their job because of back pain. 88% had had delivered a baby, 55% of them had pain in pregnancy. Global back status was excellent or good in 81%. The mean (standard deviation) ODI was 6.4 (9.8), GFS 5.4 (10.5), EQ-5D 0.84 (0.2), SRS-22: pain 4.2 (0.8), mental health 4.2 (0.7), self-image 3.9 (0.7), function 4.1 (0.6), satisfaction with treatment 3.7 (1.0). 28% had taken physiotherapy for back pain the last year and 12% had visited a doctor.

Conclusion
Long-term results were satisfactory in most patients with AIS treated with the Boston brace.
Emerging role of microRNAs in diagnosis and treatment of various diseases including ovarian cancer
Authors: Shah Parag P , Hutchinson Lauren E , Kakar Sham S 
Published: August 2009

Abstract
MicroRNAs (miRNAs) represent a class of small non-coding RNAs that control gene expression by targeting messenger RNA (mRNA). Recently, it has been demonstrated that miRNA expression is altered in many human diseases including cancers, suggesting that miRNA may play a potential role in the pathogenesis of different diseases. It has also been reported that there is a unique expression pattern of miRNAs in the disease state differing from the normal state. In this review, we focus on the miRNA signatures in different human diseases including cancers. Such signatures may be used as diagnostic and prognostic markers.
Knee stability assessment on anterior cruciate ligament injury: Clinical and biomechanical approaches
Authors: Lam Mak-Ham , Fong Daniel TP , Yung Patrick SH , Ho Eric PY , Chan Wood-Yee , Chan Kai-Ming 
Published: August 2009

AbstractAnterior cruciate ligament (ACL) injury is common in knee joint accounting for 40% of sports injury. ACL injury leads to knee instability, therefore, understanding knee stability assessments would be useful for diagnosis of ACL injury, comparison between operation treatments and establishing return-to-sport standard. This article firstly introduces a management model for ACL injury and the contribution of knee stability assessment to the corresponding stages of the model. Secondly, standard clinical examination, intra-operative stability measurement and motion analysis for functional assessment are reviewed. Orthopaedic surgeons and scientists with related background are encouraged to understand knee biomechanics and stability assessment for ACL injury patients.
Assisted assembly: how to improve a de novo genome assembly by using related species
Authors: Gnerre Sante , Lander Eric S , Lindblad-Toh Kerstin , Jaffe David B 
Published: August 2009

AbstractWe describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting process via a related genome. We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly.
Composite Reference Interval for Thyroid-Stimulating Hormone and Free Thyroxine, Comparison with Common Cutoff Values, and Reconsideration of Subclinical Thyroid Disease
Authors: Ross H Alec , den Heijer Martin , Hermus Ad R M M , Sweep Fred C G J 
Published: August 2009

Abstract
Background: Examination of the 2-dimensional probability distribution of thyroid-stimulating hormone (TSH) and free thyroxine (FT4) shows that the widths of the TSH and FT4 reference intervals derived from this bivariate distribution are mutually interdependent, an aspect commonly ignored when interpreting thyroid testing results with separate reference intervals for TSH and FT4. We desired to establish and critically evaluate a composite reference interval for TSH and FT4 to allow bivariate classification of biochemical thyroid conditions.
Methods: FT4 and TSH results of 871 healthy individuals [361 women and 510 men, 18–40 years old, without history of thyroid-related disease or medication, negative for anti–thyroid peroxidase (anti-TPO) antibody] were transformed to standard normal variables by logarithmic transformation with correction for skewness and subsequent normalization. We established a 95% reference interval of the distance of each FT4/TSH pair of values to the center of the 2-dimensional probability distribution.
Results: The bivariate 95% reference interval is enclosed by a circular profile with radius 2.45 SD. By contrast, conventional reference intervals comprise a square with the boundaries of −1.96 and +1.96 SD for both FT4 and TSH that enclose only 90% of all data. Compared with the ±1.96 SD square, the bivariate reference interval classified 4% fewer of 3651 healthy individuals older than 40 years as subclinically hyperthyroid and 14% fewer of 712 anti-TPO–positive healthy individuals as subclinically hypothyroid.
Conclusions: Conventional application of separate cutoff values for FT4 and TSH leads to overestimation of the incidence of subclinical thyroid disease. Application of a composite overall reference interval is recommended.
Cystatin C and Cardiovascular Risk
Authors: Taglieri Nevio , Koenig Wolfgang , Kaski Juan Carlos 
Published: August 2009

Abstract
Background: Patients with chronic kidney disease (CKD) are at high risk for developing cardiovascular disease (CVD) and cardiovascular events. Cystatin C, a protease inhibitor synthesized in all nucleated cells, has been proposed as a replacement for serum creatinine for the assessment of renal function, particularly to detect small reductions in glomerular filtration rate.
Content: This report presents a review of the role of cystatin C as a predictor of cardiovascular risk.
Summary: Patients with higher circulating cystatin C concentrations appear to have an increased cardiovascular risk profile, i.e., they are older and have a higher prevalence of systemic hypertension, dyslipidemia, documented CVD, increased body mass index, and increased concentrations of C-reactive protein. Prospective studies have shown, in various clinical scenarios, that patients with increased cystatin C are at a higher risk of developing both CVD and CKD. Importantly, cystatin C appears to be a useful marker for identifying individuals at a higher risk for cardiovascular events among patients belonging to a relatively low-risk category as assessed by both creatinine and estimated glomerular filtration rate values. Of interest, elastolytic proteases and their inhibitors, in particular cystatin C, have been shown to be directly involved in the atherosclerotic process. Increased concentrations of cystatin C appear to be indicative of preclinical kidney disease associated with adverse outcomes. Clinical studies involving direct glomerular filtration rate measurements are required to ascertain both the true role of this promising marker in renal disease and whether atherogenic factors like inflammation can account for increases in cystatin C concentrations, thus explaining its predictive value in CVD.
Formation and Propagation of Gel Aggregates Using Partially Hydrolyzed Polyacrylamide and Aluminum Citrate
Authors: Al-Assi A. A. , Willhite G. P. , Green D. W. , McCool C. S. 
Published: August 2009

Summary
A study of the formation of gel aggregates in systems containing partially hydrolyzed polyacrylamide and aluminum citrate was completed. Under certain conditions, this system forms gel aggregates, commonly referred to as colloidal dispersion gels. Systems that formed aggregates on the exit screen of a screen viscometer also developed flow resistance when displaced through slimtubes and sandpacks.
A gel system containing 1000 ppm polymer and 33.3 ppm aluminum citrate was studied in 10-darcy sandpacks 2 ft and 4 ft long. In the 2-ft sandpack, the gelant showed no significant difference in the flow resistance when compared to polymer injection when 8.7 pore volumes (PV) were injected with at residence time 0.83 hours after mixing the gelant inline prior to injection. However, a high flow resistance developed after the sandpack was shut in for 31.4 hours. The development of the high flow resistance is consistent with viscosity measurements approximately 28 hours after mixing the gelant and transistion pressures measured using the screen viscometer.
In the 4-ft sandpack, gelant was injected at an interstitial velocity of 5 ft/D so that the residence time was 19.2 hours, well beyond the time where substantial gel structure was identified in screen viscometer tests. A high flow resistance developed slowly across the sandpack, beginning at the inlet section, demonstrating the formation and retention of gel aggregates in the sandpack. Our experimental data demonstrate that gel aggregates can be formed by reaction of partially hydrolyzed polyacrylamide with aluminum citrate and propagated through sandpacks. We estimate that indepth treatment of a 10-darcy porous matrix at interstitial velocities of 5 ft/D using this gel system is limited to approximately 12 feet because retention of gel aggregates causes the permeability to decrease leading to reduction in flowrate.
Inhibitor Selection for Iron-Scale Control in MEG Regeneration Process
Authors: Guan Hua , Cole George , Clark Paul 
Published: August 2009

Summary
The formation of iron-containing scale because of highly dissolved iron content and increased pH (≥ 8.5) has been observed in a monoethylene glycol (MEG) regeneration system. The control of iron-scale deposition under these harsh conditions causes recurring problems in the reboilers, requires frequent filter change-outs, and remains a challenge to the field. To investigate this problem, a modified corrosion-testing apparatus was employed to replicate the iron-scale formation. It evaluates the performance of selected chemicals under realistic field conditions (specifically, low pH caused by carbon dioxide dissolution; higher pH because of carbon dioxide boiling off from the reboiler; and alkali addition for corrosion control). Both pH and iron levels (including dissolved iron, ferrous iron Fe2+, and total iron) were closely monitored. Additional digital photos were taken at various stages.
There are several challenges associated with the inhibition of iron scale in systems with a high iron level (≥ 150 ppm), high MEG content (≥ 60%), and high pH (≥ 8.5). These factors contribute to incompatibility and poor inhibition by conventional inhibitor species. A number of scale-inhibitor (SI) products, scale dissolvers, and blends were tested under aerobic or anaerobic conditions. One product greatly reduced the rate of scale formation and indefinitely delayed scale formation at higher dosage. This product also showed the capability to redissolve deposits already present in the system.
Evaluation of iron-scale inhibitor is a challenge because of the debatable iron-poisoning effect and the lack of a standard laboratory method. In this paper, the propensity of various iron deposits (e.g., iron carbonate and insoluble iron/inhibitor complex) is discussed. Moreover, the formation of a soluble iron/inhibitor complex is quantified. This could have important implications for the remediation of iron-containing scale.
Coupled tensorial form for atomic relativistic two-particle operator given in second quantization representation
Authors: Juršėnas Rytis , Merkelis Gintaras 
Published: August 2009

Abstract
General formulas of the two-electron operator representing either atomic or effective interactions are given in a coupled tensorial form in relativistic approximation. The alternatives of using uncoupled, coupled and antisymmetric two-electron wave functions in constructing coupled tensorial form of the operator are studied. The second quantization technique is used. The considered operator acts in the space of states of open-subshell atoms.
Accuracy Assessment of Digital Elevation Models Using GPS
Authors: Farah Ashraf , Talaat Ashraf , Farrag Farrag 
Published: August 2009

Accuracy Assessment of Digital Elevation Models Using GPSA Digital Elevation Model (DEM) is a digital representation of ground surface topography or terrain with different accuracies for different application fields. DEM have been applied to a wide range of civil engineering and military planning tasks. DEM is obtained using a number of techniques such as photogrammetry, digitizing, laser scanning, radar interferometry, classical survey and GPS techniques. This paper presents an assessment study of DEM using GPS (Stop&Go) and kinematic techniques comparing with classical survey. The results show that a DEM generated from (Stop&Go) GPS technique has the highest accuracy with a RMS error of 9.70 cm. The RMS error of DEM derived by kinematic GPS is 12.00 cm.