bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation and comparison of Risser sign versus bone age determination (TW3) between children with and without scoliosis in Korean population
Authors: Modi Hitesh N , Modi Chetna H , Suh Seung Woo , Yang Jae-Hyuk , Hong Jae-Young 
Published: September 2009

Abstract

Background
Most studies comparing the Risser staging for skeletal maturity are representing the American or European standards which are not always applicable to Asian population who have relatively less height and body mass. There is no article available that compares the Risser sign and bone age correlation between patients with idiopathic scoliosis and patients without scoliosis.

Materials and methods
To analyze and compare the skeletal age with the Risser sign between scoliosis and non-scoliosis group, a cross-sectional study was done in 418 scoliosis (untreated, bracing or surgically) and 256 non-scoliosis children of Korean origin. Relationship was found in both groups using Pearson correlation test.

Results
In scoliosis group, Pearson correlation exhibited significant correlation (p < 0.01) between Risser sign and chronological age (r2 = 0.791 for girls, 0.787 for boys) and Risser sign and TW3 age (r2 = 0.718 for girls, 0.785 for boys). Non-scoliosis group also showed significant relationship (p < 0.01) between Risser sign and chronological age (r2 = 0.893 for girls, 0.879 for boys) and Risser sign and TW3 age (r2 = 0.913 for girls, 0.895 for boys). Similarly, comparing Cobb angles of each patient according to their Risser staging, exhibited that if scoliosis remains untreated Cobb angle will increase with the increase in their Risser staging (r2 = 0.363 for girls, 0.443 for boys; p < 0.01).

Conclusion
Our results showed that chronological age is equally as reliable as skeletal age method to compare with Risser sign, and therefore, we do not mean to imply that only the Risser sign compared with skeletal age should be considered in the decision making in idiopathic as well as non-scoliosis patients of Korean ethnicity. Concomitant indicators such as menarchal period, secondary sex characteristics, and recent growth pattern will likely reinforce our data comparing Risser sign with skeletal age in decision making.
A method for determining the robustness of bio-molecular oscillator models
Authors: Ghaemi Reza , Sun Jing , Iglesias Pablo A , Del Vecchio Domitilla 
Published: September 2009

Abstract

Background
Quantifying the robustness of biochemical models is important both for determining the validity of a natural system model and for designing reliable and robust synthetic biochemical networks. Several tools have been proposed in the literature. Unfortunately, multiparameter robustness analysis suffers from computational limitations.

Results
A novel method for quantifying the robustness of oscillatory behavior to parameter perturbations is presented in this paper. This method relies on the combination of Hopf bifurcation and Routh-Hurwitz stability criterion, which is widely applied in control system design. The proposed method is employed to calculate the robustness of two oscillating biochemical network models previously analyzed in the literature. The robustness bounds here obtained are tighter than what was previously obtained in the literature for both models.

Conclusion
The method here proposed for quantifying the robustness of biochemical oscillator models is computationally less demanding than similar multiparamter variation techniques available in the literature. It also provides tighter bounds on two models previously analyzed in the literature.
A switchable light-input, light-output system modelled and constructed in yeast
Authors: Sorokina Oxana , Kapus Anita , Terecskei Kata , Dixon Laura E , Kozma-Bognar Laszlo , Nagy Ferenc , Millar Andrew J 
Published: September 2009

Abstract

Background
Advances in synthetic biology will require spatio-temporal regulation of biological processes in heterologous host cells. We develop a light-switchable, two-hybrid interaction in yeast, based upon the Arabidopsis proteins PHYTOCHROME A and FAR-RED ELONGATED HYPOCOTYL 1-LIKE. Light input to this regulatory module allows dynamic control of a light-emitting LUCIFERASE reporter gene, which we detect by real-time imaging of yeast colonies on solid media.

Results
The reversible activation of the phytochrome by red light, and its inactivation by far-red light, is retained. We use this quantitative readout to construct a mathematical model that matches the system's behaviour and predicts the molecular targets for future manipulation.

Conclusion
Our model, methods and materials together constitute a novel system for a eukaryotic host with the potential to convert a dynamic pattern of light input into a predictable gene expression response. This system could be applied for the regulation of genetic networks - both known and synthetic.
Discovering cancer genes by integrating network and functional properties
Authors: Li Li , Zhang Kangyu , Lee James , Cordes Shaun , Davis David P , Tang Zhijun 
Published: September 2009

Abstract

Background
Identification of novel cancer-causing genes is one of the main goals in cancer research. The rapid accumulation of genome-wide protein-protein interaction (PPI) data in humans has provided a new basis for studying the topological features of cancer genes in cellular networks. It is important to integrate multiple genomic data sources, including PPI networks, protein domains and Gene Ontology (GO) annotations, to facilitate the identification of cancer genes.

Methods
Topological features of the PPI network, as well as protein domain compositions, enrichment of gene ontology categories, sequence and evolutionary conservation features were extracted and compared between cancer genes and other genes. The predictive power of various classifiers for identification of cancer genes was evaluated by cross validation. Experimental validation of a subset of the prediction results was conducted using siRNA knockdown and viability assays in human colon cancer cell line DLD-1.

Results
Cross validation demonstrated advantageous performance of classifiers based on support vector machines (SVMs) with the inclusion of the topological features from the PPI network, protein domain compositions and GO annotations. We then applied the trained SVM classifier to human genes to prioritize putative cancer genes. siRNA knock-down of several SVM predicted cancer genes displayed greatly reduced cell viability in human colon cancer cell line DLD-1.

Conclusion
Topological features of PPI networks, protein domain compositions and GO annotations are good predictors of cancer genes. The SVM classifier integrates multiple features and as such is useful for prioritizing candidate cancer genes for experimental validations.
Intraclonal mating occurs during tsetse transmission of Trypanosoma brucei
Authors: Peacock Lori , Ferris Vanessa , Bailey Mick , Gibson Wendy 
Published: September 2009

Abstract

Background
Mating in Trypanosoma brucei is a non-obligatory event, triggered by the co-occurrence of different strains in the salivary glands of the vector. Recombinants that result from intra- rather than interclonal mating have been detected, but only in crosses of two different trypanosome strains. This has led to the hypothesis that when trypanosomes recognize a different strain, they release a diffusible factor or pheromone that triggers mating in any cell in the vicinity whether it is of the same or a different strain. This idea assumes that the trypanosome can recognize self and non-self, although there is as yet no evidence for the existence of mating types in T. brucei.

Results
We investigated intraclonal mating in T. b. brucei by crossing red and green fluorescent lines of a single strain, so that recombinant progeny can be detected in the fly by yellow fluorescence. For strain 1738, seven flies had both red and green trypanosomes in the salivary glands and, in three, yellow trypanosomes were also observed, although they could not be recovered for subsequent analysis. Nonetheless, both red and non-fluorescent clones from these flies had recombinant genotypes as judged by microsatellite and karyotype analyses, and some also had raised DNA contents, suggesting recombination or genome duplication. Strain J10 produced similar results indicative of intraclonal mating. In contrast, trypanosome clones recovered from other flies showed that genotypes can be transmitted with fidelity. When a yellow hybrid clone expressing both red and green fluorescent protein genes was transmitted, the salivary glands contained a mixture of fluorescent-coloured trypanosomes, but only yellow and red clones were recovered. While loss of the GFP gene in the red clones could have resulted from gene conversion, some of these clones showed loss of heterozygosity and raised DNA contents as in the other single strain transmissions. Our observations suggest that many recombinants are non-viable after intraclonal mating.

Conclusion
We have demonstrated intraclonal mating during fly transmission of T. b. brucei, contrary to previous findings that recombination occurs only when another strain is present. It is thus no longer possible to assume that T. b. brucei remains genetically unaltered after fly transmission.
Characterizing trends in HIV infection among men who have sex with men in Australia by birth cohorts: results from a modified back‐projection method
Authors: Wand Handan , Wilson David , Yan Ping , Gonnermann Andrea , McDonald Ann , Kaldor John , Law Matthew 
Published: September 2009

BackgroundWe set out to estimate historical trends in HIV incidence in Australian men who have sex with men with respect to age at infection and birth cohort.MethodsA modified back‐projection technique is applied to data from the HIV/AIDS Surveillance System in Australia, including “newly diagnosed HIV infections”, “newly acquired HIV infections” and “AIDS diagnoses”, to estimate trends in HIV incidence over both calendar time and age at infection.ResultsOur results demonstrate that since 2000, there has been an increase in new HIV infections in Australian men who have sex with men across all age groups. The estimated mean age at infection increased from ~35 years in 2000 to ~37 years in 2007. When the epidemic peaked in the mid 1980s, the majority of the infections (56%) occurred among men aged 30 years and younger; 30% occurred in ages 31 to 40 years; and only ~14% of them were attributed to the group who were older than 40 years of age. In 2007, the proportion of infections occurring in persons 40 years or older doubled to 31% compared to the mid 1980s, while the proportion of infections attributed to the group younger than 30 years of age decreased to 36%.ConclusionThe distribution of HIV incidence for birth cohorts by infection year suggests that the HIV epidemic continues to affect older homosexual men as much as, if not more than, younger men. The results are useful for evaluating the impact of the epidemic across successive birth cohorts and study trends among the age groups most at risk.
Clinical presentation and aetiologies of acute or complicated headache among HIV‐seropositive patients in a Ugandan clinic
Authors: Katwere Michael , Kambugu Andrew , Piloya Theresa , Wong Matthew , Hendel‐Paterson Brett , Sande Merle A , Ronald Allan , Katabira Elly , Were Edward M , Menten Joris , Colebunders Robert 
Published: September 2009

BackgroundWe set out to define the relative prevalence and common presentations of the various aetiologies of headache within an ambulant HIV‐seropositive adult population in Kampala, Uganda.MethodsWe conducted a prospective study of adult HIV‐1‐seropositive ambulatory patients consecutively presenting with new onset headaches. Patients were classified as focal‐febrile, focal‐afebrile, non‐focal‐febrile or non‐focal‐afebrile, depending on presence or absence of fever and localizing neurological signs. Further management followed along a pre‐defined diagnostic algorithm to an endpoint of a diagnosis. We assessed outcomes during four months of follow up.ResultsOne hundred and eighty patients were enrolled (72% women). Most subjects presented at WHO clinical stages III and IV of HIV disease, with a median Karnofsky performance rating of 70% (IQR 60‐80).The most common diagnoses were cryptococcal meningitis (28%, n = 50) and bacterial sinusitis (31%, n = 56). Less frequent diagnoses included cerebral toxoplasmosis (4%, n = 7), and tuberculous meningitis (4%, n = 7). Thirty‐two (18%) had other diagnoses (malaria, bacteraemia, etc.). No aetiology could be elucidated in 28 persons (15%). Overall mortality was 13.3% (24 of 180) after four months of follow up. Those without an established headache aetiology had good clinical outcomes, with only one death (4% mortality), and 86% were ambulatory at four months.ConclusionIn an African HIV‐infected ambulatory population presenting with new onset headache, aetiology was found in at least 70%. Cryptococcal meningitis and sinusitis accounted for more than half of the cases.
Suppressive effect of secretory phospholipase A2inhibitory peptide on interleukin-1β-induced matrix metalloproteinase production in rheumatoid synovial fibroblasts, and its antiarthritic activity in hTNFtg mice
Authors: Thwin Maung-Maung , Douni Eleni , Arjunan Pachiappan , Kollias George , Kumar Prem V , Gopalakrishnakone Ponnampalam 
Published: September 2009

AbstractIntroductionSecretory phospholipase A2(sPLA2) and matrix metalloproteinase (MMP) inhibitors are potent modulators of inflammation with therapeutic potential, but have limited efficacy in rheumatoid arthritis (RA). The objective of this study was to understand the inhibitory mechanism of phospholipase inhibitor from python (PIP)-18 peptide in cultured synovial fibroblasts (SF), and to evaluate its therapeutic potential in a human tumor necrosis factor (hTNF)-driven transgenic mouse (Tg197) model of arthritis.MethodsGene and protein expression of sPLA2-IIA, MMP-1, MMP-2, MMP-3, MMP-9, tissue inhibitor of metalloproteinase (TIMP)-1, and TIMP-2 were analyzed by real time PCR and ELISA respectively, in interleukin (IL)-1β stimulated rheumatoid arthritis (RA) and osteoarthritis (OA) synovial fibroblasts cells treated with or without inhibitors of sPLA2 (PIP-18, LY315920) or MMPs (MMP Inhibitor II). Phosphorylation status of mitogen-activated protein kinase (MAPK) proteins was examined by cell-based ELISA. The effect of PIP-18 was compared with that of celecoxib, methotrexate, infliximab and antiflamin-2 in Tg197 mice after ip administration (thrice weekly for 5 weeks) at two doses (10, 30 mg/kg), and histologic analysis of ankle joints. Serum sPLA2and cytokines (tumor necrosis factor (TNF)α, IL-6) were measured byEscherichia coli(E coli) assay and ELISA, respectively.ResultsPIP-18 inhibited sPLA2-IIA production and enzymatic activity, and suppressed production of MMPs in IL-1β-induced RA and OA SF cells. Treatment with PIP-18 blocked IL-1β-induced p38 MAPK phosphorylation and resulted in attenuation of sPLA2-IIA and MMP mRNA transcription in RA SF cells. The disease modifying effect of PIP-18 was evidenced by significant abrogation of synovitis, cartilage degradation and bone erosion in hTNF Tg197 mice.ConclusionsOur results demonstrate the benefit that can be gained from using sPLA2inhibitory peptide for RA treatment, and validate PIP-18 as a potential therapeutic in a clinically relevant animal model of human arthritis.
The role of patient expectations in predicting outcome after total knee arthroplasty
Authors: Mannion Anne F , Kämpfen Stephane , Munzinger Urs , Kramers-de Quervain Ines 
Published: September 2009

Abstract
Introduction
Patient's expectations are variably reported to influence self-rated outcome and satisfaction after medical treatment; this prospective study examined which of the following was the most important unique determinant of global outcome/satisfaction after total knee arthroplasty (TKA): baseline expectations; fulfilment of expectations; or current symptoms and function.

Methods
One hundred and twelve patients with osteoarthritis of the knee (age, 67 ± 9 years) completed a questionnaire about their expectations regarding months until full recovery, pain, and limitations in everyday activities after TKA surgery. Two years postoperatively, they were asked what the reality was for each of these domains, and rated the global outcome and satisfaction with surgery. Multivariable regression analyses using forward conditional selection of variables (and controlling for age, gender, other joint problems) identified the most significant determinants of outcome.

Results
Patients significantly underestimated the time for full recovery (expected 4.7 ± 2.8 months, recalled actual time, 6.1 ± 3.7 months; P = 0.005). They were also overly optimistic about the likelihood of being pain-free (85% expected it, 43% were; P < 0.05) and of not being limited in usual activities (52% expected it, 20% were; P < 0.05). Global outcomes were 46.2% excellent, 41.3% good, 10.6% fair and 1.9% poor. In multivariable regression, expectations did not make a significant unique contribution to explaining the variance in outcome/satisfaction; together with other joint problems, knee pain and function at 2 years postoperation predicted global outcome, and knee pain at 2 years predicted satisfaction.

Conclusions
In this group, preoperative expectations of TKA surgery were overly optimistic. The routine analysis of patient-orientated outcomes in practice should assist the surgeon to convey more realistic expectations to the patient during the preoperative consultation. In multivariable regression, expectations did not predict global outcome/satisfaction; the most important determinants were other joint problems and the patient's pain and functional status 2 years postoperatively.
Comparative evaluation of cell-free tumor DNA in blood and disseminated tumor cells in bone marrow of patients with primary breast cancer
Authors: Schwarzenbach Heidi , Pantel Klaus , Kemper Birthe , Beeger Cord , Otterbach Friedrich , Kimmig Rainer , Kasimir-Bauer Sabine 
Published: September 2009

Abstract
Introduction
The origin and clinical relevance of circulating cell-free tumor DNA in the blood of cancer patients is still unclear. Here we investigated whether the detection of this DNA is related to bone marrow (BM) micrometastasis and tumor recurrence in breast cancer patients.

Methods
BM aspirates of 81 primary breast cancer patients were analyzed for the presence of disseminated tumor cells (DTC) by immunocytochemistry using the pan-cytokeratin antibody A45-B/B3. PCR-based fluorescence microsatellite analysis was performed for detection of loss of heterozygosity (LOH) at 6 polymorphic markers using cell-free serum DNA. The data were correlated with established risk factors, and patients were followed-up over 6-10 years.

Results
LOH was detected in 33.5% of blood samples. The occurrence of LOH at the entire microsatellite marker set correlated with histopathology (P = 0.05) and grading (P = 0.006) of the primary tumor. The genomic region characterized by marker D9S171 was only affected by LOH in patients with increased tumor stages (pT2-4, P < 0.05) and older age (≥ 55 years, P = 0.05). Kaplan-Meier analysis showed that LOH at D3S1255 (P = 0.009) and D9S171 (P = 0.001) were significantly associated with tumor relapse. In BM, DTC were detected in 39.5% of the patients, and this finding correlated with distant metastases (P < 0.05). Patients with DTC-positive BM had higher DNA yields in their blood than patients with DTC-negative BM (P < 0.05). However, no significant correlations were found between the presence of DTC in BM and the detection of marker-specific LOH on blood DNA.

Conclusions
The detection of LOH on cell-free tumor DNA in blood is unrelated to BM micrometastasis and provides independent information on breast cancer progression.
Simultaneous alignment of short reads against multiple genomes
Authors: Schneeberger Korbinian , Hagmann Jörg , Ossowski Stephan , Warthmann Norman , Gesing Sandra , Kohlbacher Oliver , Weigel Detlef 
Published: September 2009

AbstractGenome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be identified by alignments against the reference alone. Download GenomeMapper at http://1001genomes.org.
A cell surface interaction network of neural leucine-rich repeat receptors
Authors: Söllner Christian , Wright Gavin J 
Published: September 2009

Abstract
Background
The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families of neural orphan receptor proteins have been identified and are likely to contribute to these recognition processes but due to the technical difficulty in identifying novel extracellular interactions of membrane-embedded proteins, their ligands remain unknown.

Results
To identify novel neural recognition signals, we performed a large systematic protein interaction screen using an assay capable of detecting low affinity extracellular protein interactions between the ectodomains of 150 zebrafish receptor proteins containing leucine-rich-repeat and/or immunoglobulin superfamily domains. We screened 7,592 interactions to construct a network of 34 cell surface receptor-ligand pairs that included orphan receptor subfamilies such as the Lrrtms, Lrrns and Elfns but also novel ligands for known receptors such as Robos and Unc5b. A quantitative biochemical analysis of a subnetwork involving the Unc5b and three Flrt receptors revealed a surprising quantitative variation in receptor binding strengths. Paired spatiotemporal gene expression patterns revealed dynamic neural receptor recognition maps within the developing nervous system, providing biological support for the network and revealing likely functions.

Conclusions
This integrated interaction and expression network provides a rich source of novel neural recognition pathways and highlights the importance of quantitative systematic extracellular protein interaction screens to mechanistically explain neural wiring patterns.