bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of at-risk genotypes for genotoxic effects decreases with age in a randomly selected population in Flanders: a cross sectional study
Authors: Ketelslegers Hans B , Godschalk Roger WL , Gottschalk Ralph WH , Knaapen Ad M , Koppen Gudrun , Schoeters Greet , Baeyens Willy F , Nelen Vera , Geraedts Joep PM , van Delft Joost HM , Kleinjans Jos CS , van Larebeke Nicolas A 
Published: October 2011

Abstract

Background
We hypothesized that in Flanders (Belgium), the prevalence of at-risk genotypes for genotoxic effects decreases with age due to morbidity and mortality resulting from chronic diseases. Rather than polymorphisms in single genes, the interaction of multiple genetic polymorphisms in low penetrance genes involved in genotoxic effects might be of relevance.

Methods
Genotyping was performed on 399 randomly selected adults (aged 50-65) and on 442 randomly selected adolescents. Based on their involvement in processes relevant to genotoxicity, 28 low penetrance polymorphisms affecting the phenotype in 19 genes were selected (xenobiotic metabolism, oxidative stress defense and DNA repair, respectively 13, 6 and 9 polymorphisms). Polymorphisms which, based on available literature, could not clearly be categorized a priori as leading to an 'increased risk' or a 'protective effect' were excluded.

Results
The mean number of risk alleles for all investigated polymorphisms was found to be lower in the 'elderly' (17.0 ± 2.9) than the 'adolescent' (17.6 ± 3.1) subpopulation (P = 0.002). These results were not affected by gender nor smoking. The prevalence of a high (> 17 = median) number of risk alleles was less frequent in the 'elderly' (40.6%) than the 'adolescent' (51.4%) subpopulation (P = 0.002). In particular for phase II enzymes, the mean number of risk alleles was lower in the 'elderly' (4.3 ± 1.6 ) than the 'adolescent' age group (4.8 ± 1.9) P < 0.001 and the prevalence of a high (> 4 = median) number of risk alleles was less frequent in the 'elderly' (41.3%) than the adolescent subpopulation (56.3%, P < 0.001). The prevalence of a high (> 8 = median) number of risk alleles for DNA repair enzyme-coding genes was lower in the 'elderly' (37,3%) than the 'adolescent' subpopulation (45.6%, P = 0.017).

Conclusions
These observations are consistent with the hypothesis that, in Flanders, the prevalence of at-risk alleles in genes involved in genotoxic effects decreases with age, suggesting that persons carrying a higher number of at risk alleles (especially in phase II xenobiotic-metabolizing or DNA repair genes) are at a higher risk of morbidity and mortality from chronic diseases. Our findings also suggest that, regarding risk of disease associated with low penetrance polymorphisms, multiple polymorphisms should be taken into account, rather than single ones.
A binary matrix factorization algorithm for protein complex prediction
Authors: Tu Shikui , Chen Runsheng , Xu Lei 
Published: October 2011

Abstract

Background
Identifying biologically relevant protein complexes from a large protein-protein interaction (PPI) network, is essential to understand the organization of biological systems. However, high-throughput experimental techniques that can produce a large amount of PPIs are known to yield non-negligible rates of false-positives and false-negatives, making the protein complexes difficult to be identified.

Results
We propose a binary matrix factorization (BMF) algorithm under the Bayesian Ying-Yang (BYY) harmony learning, to detect protein complexes by clustering the proteins which share similar interactions through factorizing the binary adjacent matrix of a PPI network. The proposed BYY-BMF algorithm automatically determines the cluster number while this number is pre-given for most existing BMF algorithms. Also, BYY-BMF’s clustering results does not depend on any parameters or thresholds, unlike the Markov Cluster Algorithm (MCL) that relies on a so-called inflation parameter. On synthetic PPI networks, the predictions evaluated by the known annotated complexes indicate that BYY-BMF is more robust than MCL for most cases. On real PPI networks from the MIPS and DIP databases, BYY-BMF obtains a better balanced prediction accuracies than MCL and a spectral analysis method, while MCL has its own advantages, e.g., with good separation values.
ATPsite: sequence-based prediction of ATP-binding residues
Authors: Chen Ke , Mizianty Marcin J , Kurgan Lukasz 
Published: October 2011

Abstract

Background
ATP is a ubiquitous nucleotide that provides energy for cellular activities, catalyzes chemical reactions, and is involved in cellular signalling. The knowledge of the ATP-protein interactions helps with annotation of protein functions and finds applications in drug design. The sequence to structure annotation gap motivates development of high-throughput sequence-based predictors of the ATP-binding residues. Moreover, our empirical tests show that the only existing predictor, ATPint, is characterized by relatively low predictive quality.

Methods
We propose a novel, high-throughput machine learning-based predictor, ATPsite, which identifies ATP-binding residues from protein sequences. Our predictor utilizes Support Vector Machine classifier and a comprehensive set of input features that are based on the sequence, evolutionary profiles, and the sequence-predicted structural descriptors including secondary structure, solvent accessibility, and dihedral angles.

Results
The ATPsite achieves significantly higher Mathews Correlation Coefficient (MCC) and Area Under the ROC Curve (AUC) values when compared with the existing methods including the ATPint, conservation-based rate4site, and alignment-based BLAST predictors. We also assessed the effectiveness of individual input types. The PSSM profile, the conservation scores, and certain features based on amino acid groups are shown to be more effective in predicting the ATP-binding residues than the remaining feature groups.

Conclusions
Statistical tests show that ATPsite significantly outperforms existing solutions. The consensus of the ATPsite with the sequence-alignment based predictor is shown to give further improvements.
Hyperbaric oxygen therapy as an adjunctive treatment for sternal infection and osteomyelitis after sternotomy and cardiothoracic surgery
Authors: Yu Wen-Kuang , Chen Yen-Wen , Shie Huei-Guan , Lien Te-Cheng , Kao Hsin-Kuo , Wang Jia-Horng 
Published: October 2011

Abstract

Purpose
A retrospective study to evaluate the effect of hyperbaric oxygen (HBO2) therapy on sternal infection and osteomyelitis following median sternotomy.

Materials and methods
A retrospective analysis of patients who received sternotomy and cardiothoracic surgery which developed sternal infection and osteomyelitis between 2002 and 2009. Twelve patients who received debridement and antibiotic treatment were selected, and six of them received additional HBO2 therapy. Demographic, clinical characteristics and outcome were compared between patients with and without HBO2 therapy.

Results
HBO2 therapy did not cause any treatment-related complication in patients receiving this additional treatment. Comparisons of the data between two study groups revealed that the length of stay in ICU (8.7 ± 2.7 days vs. 48.8 ± 10.5 days, p < 0.05), duration of invasive (4 ± 1.5 days vs. 34.8 ± 8.3 days, p < 0.05) and non-invasive (4 ± 1.9 days vs. 22.3 ± 6.2 days, p < 0.05) positive pressure ventilation were all significantly lower in patients with additional HBO2 therapy, as compared to patients without HBO2 therapy. Hospital mortality was also significantly lower in patients who received HBO2 therapy (0 case vs. 3 cases, p < 0.05), as compared to patients without the HBO2 therapy.

Conclusions
In addition to primary treatment with debridement and antibiotic use, HBO2 therapy may be used as an adjunctive and safe treatment to improve clinical outcomes in patients with sternal infection and osteomyelitis after sternotomy and cardiothoracic surgery.
Pilot Induction Regimen Incorporating Pharmacokinetically Guided Topotecan for Treatment of Newly Diagnosed High-Risk Neuroblastoma: A Children's Oncology Group Study
Authors: Park Julie R. , Scott Jeffrey R. , Stewart Clinton F. , London Wendy B. , Naranjo Arlene , Santana Victor M. , Shaw Peter J. , Cohn Susan L. , Matthay Katherine K. 
Published: October 2011

Purpose To assess the feasibility of adding dose-intensive topotecan and cyclophosphamide to induction therapy for newly diagnosed high-risk neuroblastoma (HRNB). Patients and Methods Enrolled patients received two cycles of topotecan (approximately 1.2 mg/m2/d) and cyclophosphamide (400 mg/m2/d) for 5 days followed by four cycles of multiagent chemotherapy (Memorial Sloan-Kettering Cancer Center [MSKCC] regimen). Pharmacokinetically guided topotecan dosing (target systemic exposure with area under the curve of 50 to 70 ng/mL/hr) was performed. Peripheral-blood stem cell (PBSC) harvest and surgical resection of residual primary tumor occurred after cycles 2 and 5, respectively. Patients achieving at least a partial response received myeloablative chemotherapy with PBSC rescue and radiation to the presurgical primary tumor volume. Oral 13-cis-retinoic acid maintenance therapy was administered twice daily for 14 days in six 28-day cycles. Results Thirty-one patients were enrolled onto the study. No deaths related to toxicity or dose-limiting toxicities occurred during induction. Mucositis rarely occurred after topotecan cycles (9.7%) in contrast to 30% after MSKCC cycles. Thirty patients underwent PBSC collection with median 31.1 × 106 CD34+ cells/kg (range, 1.8 to 541.8 × 106 CD34+ cells/kg), all negative for tumor contamination by immunocytochemical analysis. Targeted topotecan systemic exposure was achieved in 26 (84%) of 31 patients. At the end of induction, 26 patients (84%) had tumor response and one patient had progressive disease. In the overall cohort, 3-year event-free and overall survival were 37.8% ± 9.4% and 57.1% ± 9.4%, respectively. Conclusion This pilot induction regimen was well tolerated with expected and reversible toxicities. These data support investigation of efficacy in a phase III clinical trial for newly diagnosed HRNB.
Risk of Recurrence and Chemotherapy Benefit for Patients With Node-Negative, Estrogen Receptor–Positive Breast Cancer: Recurrence Score Alone and Integrated With Pathologic and Clinical Factors
Authors: Tang Gong , Cuzick Jack , Costantino Joseph P. , Dowsett Mitch , Forbes John F. , Crager Michael , Mamounas Eleftherios P. , Shak Steven , Wolmark Norman 
Published: October 2011

Purpose The 21-gene breast cancer assay recurrence score (RS) is widely used for assessing recurrence risk and predicting chemotherapy benefit in patients with estrogen receptor (ER) –positive breast cancer. Pathologic and clinical factors such as tumor size, grade, and patient age also provide independent prognostic utility. We developed a formal integration of these measures and evaluated its prognostic and predictive value. Patients and Methods From the National Surgical Adjuvant Breast and Bowel (NSABP) B-14 and translational research cohort of the Arimidex, Tamoxifen Alone or in Combination (TransATAC) studies, we included patients who received hormonal monotherapy, had ER-positive tumors, and RS and traditional clinicopathologic factors assessed (647 and 1,088, respectively). Individual patient risk assessments from separate Cox models were combined using meta-analysis to form an RS-pathology-clinical (RSPC) assessment of distant recurrence risk. Risk assessments by RS and RSPC were compared in node-negative (N0) patients. RSPC was compared with RS for predicting chemotherapy benefit in NSABP B-20. Results RSPC had significantly more prognostic value for distant recurrence than did RS (P < .001) and showed better separation of risk in the study population. RSPC classified fewer patients as intermediate risk (17.8% v 26.7%, P < .001) and more patients as lower risk (63.8% v 54.2%, P < .001) than did RS among 1,444 N0 ER-positive patients. In B-20, the interaction of RSPC with chemotherapy was not statistically significant (P = .10), in contrast to the previously reported significant interaction of RS with chemotherapy (P = .037). Conclusion RSPC refines the assessment of distant recurrence risk and reduces the number of patients classified as intermediate risk. Adding clinicopathologic measures did not seem to enhance the value of RS alone nor the individual biology RS identifies in predicting chemotherapy benefit.
Primary Stability of a Dynamic Artificial Disc Tested in a Human Cadaveric Model
Authors: Thompson R. E. , Schwarzenbach O. , Seebeck J. , Fröhlich M. 
Published: October 2011

Abstract
Sufficient anchorage of an interbody device will allow osseointegration and avoid implant migration. Shear forces in the lumbar spine are transferred across the bone/implant interface, resulting in relative motion between the implant and bone. Relative motion greater than 150 μm will have a detrimental effect on the osseointegration of titanium (Ti) implants. This study developed an in vitro, primary stability testing protocol to assess a total disc replacement (TDR). Testing was performed on seven human cadaveric L4 and L5 vertebrae. Cyclic shear loading of the prepared implant/bone interface was applied for 20 cycles in the anterior and posterior directions to ±350 N under an axial compressive load of 600 N. The relative motion was measured and the average of the last five cycles analysed. The shear force necessary to cause complete anterior migration of the TDR was also measured. The averaged cyclic motion for the last five cycles in both the anterior and posterior directions was below 85 μm for all specimens. The average yield force for complete anterior implant migration was 522.2 N (±105.9 N) and the failure force was 605.1 N (±118.4 N). A primary stability testing protocol was developed and employed to assess a TDR in human cadaveric bone. The measured relative motion for this TDR for each loading cycle was below 150 μm, which is favourable for osseointegration with the vertebral body endplates.
Acylated/unacylated ghrelin ratio in cord blood: correlation with anthropometric and metabolic parameters and pediatric lifespan comparison
Authors: Bellone S , Prodam F , Savastio S , Avanzo D , Pagani A , Trovato L , Walker G E , Genoni G , Bona G 
Published: October 2011

ContextGhrelin is a peptide with multiple functions that circulates in acylated (AG) and unacylated (UAG) forms. However, the role of ghrelin in neonates (NN) remains to be clarified.ObjectiveThe aim of this study was to determine ghrelin concentrations of the two forms in NN to clarify their biological roles. As such, ghrelin levels at birth were compared with those in later life.Setting and designTertiary Care Center. In this cross-sectional study, we evaluated AG, UAG, AG/UAG ratio, and insulin levels in venous cord blood from NN and in fasted normal weight (NW) and obese (OB) children, both prepubertal and pubertal.SubjectsWe studied 82 NN, 82 NW, and 58 OB children.ResultsAG levels were lower in NN than in NW and OB children (P<0.0001), more specifically the prepubertal NW and OB children (P<0.0001). UAG levels were higher in NN than in NW and OB children (P<0.0001). Therefore, the AG/UAG ratio was lower in NN than in NW and OB children (P<0.0001). NN showed insulin levels similar to NW and lower than OB children (P<0.0001). At birth UAG was positively correlated with AG (Pearson: 0.425; P<0.0001) and negatively with insulin (−0.253; P<0.02). In NW and OB, UAG and AG were positively correlated to each other and negatively correlated with insulin and body mass index (−0.566; P<0.0001).ConclusionsNN compared with children, showed higher UAG and lower AG levels. The AG/UAG ratio showed a very different profile in NN, being lower than in NW and OB children, thus suggesting a different metabolic function for the two forms in NN. Further studies are needed to clarify the exact role of the different ghrelin forms in NN.
Spread of Methicillin-ResistantStaphylococcus aureusin a Large Tertiary NICU: Network Analysis
Authors: Geva Alon , Wright Sharon B. , Baldini Linda M. , Smallcomb Jane A. , Safran Charles , Gray James E. 
Published: October 2011

OBJECTIVE:Methicillin-resistant Staphylococcus aureus (MRSA) colonization in NICUs increases the risk of nosocomial infection. Network analysis provides tools to examine the interactions among patients and staff members that put patients at risk of colonization.METHODS:Data from MRSA surveillance cultures were combined with patient room locations, nursing assignments, and sibship information to create patient- and unit-based networks. Multivariate models were constructed to quantify the risk of incident MRSA colonization as a function of exposure to MRSA-colonized infants in these networks.RESULTS:A MRSA-negative infant in the NICU simultaneously with a MRSA-positive infant had higher odds of becoming colonized when the colonized infant was a sibling, compared with an unrelated patient (odds ratio: 8.8 [95% confidence interval [CI]: 5.3–14.8]). Although knowing that a patient was MRSA-positive and was placed on contact precautions reduced the overall odds of another patient becoming colonized by 35% (95% CI: 20%–47%), having a nurse in common with that patient still increased the odds of colonization by 43% (95% CI: 14%–80%). Normalized group degree centrality, a unitwide network measure of connectedness between colonized and uncolonized patients, was a significant predictor of incident MRSA cases (odds ratio: 18.1 [95% CI: 3.6–90.0]).CONCLUSIONS:Despite current infection-control strategies, patients remain at significant risk of MRSA colonization from MRSA-positive siblings and from other patients with whom they share nursing care. Strategies that minimize the frequency of staff members caring for both colonized and uncolonized infants may be beneficial in reducing the spread of MRSA colonization.
Effectiveness of a School Nurse–Delivered Smoking-Cessation Intervention for Adolescents
Authors: Pbert Lori , Druker Susan , DiFranza Joseph R. , Gorak Diane , Reed George , Magner Robert , Sheetz Anne H. , Osganian Stavroula 
Published: October 2011

OBJECTIVE:
To evaluate the effectiveness of a school nurse–delivered smoking-cessation intervention in increasing abstinence among adolescent smokers.

METHODS:
Thirty-five high schools were pair-matched and randomly assigned to 1 of 2 conditions, each of which consisted of 4 visits with the school nurse: (1) counseling intervention using the 5 A's model and cognitive-behavioral techniques; or (2) an information-attention control condition. Adolescents (n = 1068) who reported past 30-day smoking and interest in quitting completed surveys at baseline and at 3 and 12 months and provided saliva samples for biochemical validation of reported smoking abstinence.

RESULTS:
Intervention condition participants were almost twice as likely to be abstinent per self-report at 3 months (odds ratio: 1.90 [95% confidence interval: 1.12–3.24]; P = .017) compared with control participants; at 12 months there were no differences. The difference at 3 months was driven by quit rates in male students (15.0% [intervention] vs 4.9% [control]; odds ratio: 3.23 [95% confidence interval: 1.63–6.43]; P = .001); there was no intervention effect in female students at either time point (6.6% vs 7.0% at 3 months and 16.6% vs 15.5% at 12 months) and no intervention effect in male students at 12 months (13.9% vs 13.2%). Smoking amount and frequency decreased significantly in intervention compared with control schools at 3 but not at 12 months.

CONCLUSIONS:
A school nurse–delivered smoking-cessation intervention proved feasible and effective in improving short-term abstinence among adolescent boys and short-term reductions in smoking amount and frequency in both genders. Additional research is needed to enhance both cessation and maintained abstinence.
Effects of Oxygen and Forming Gas Annealing on ZnO TFTs
Authors: Huang Jiaye , Radhakrishna Ujwal , Lemberger Martin , Jank Michael P.M. , Polster Sebastian , Ryssel Heiner , Frey Lothar 
Published: October 2011

ABSTRACTZnO TFTs with bottom gate top S/D contact architecture were fabricated by sputtering of ZnO with layer thicknesses from 30 nm to 100 nm. The effect of post deposition annealing in oxygen and forming gas atmospheres at 400°C to 500°C on the devices was investigated. The tendencies of a lower threshold voltage Vth and a higher saturation mobility μsat for higher annealing temperature can be observed for both oxygen and forming gas annealing. Reduction of trap density in oxygen annealing and additional hydrogen incorporation in forming gas annealing play an important role for these electrical parameters. Morphological changes of increased grain size and fewer grain boundaries in the channel also contribute to tendencies in electrical characteristics of ZnO TFTs.
Characteristics of OTFTs Using Olefin-polymer Gate Insulator and Their Application to a 5-in. OTFT-driven Flexible AMOLED Display
Authors: Nakajima Yoshiki , Fujisaki Yoshihide , Takei Tatsuya , Sato Hiroto , Nakata Mitsuru , Suzuki Mitsunori , Fukagawa Hirohiko , Motomura Genichi , Shimizu Takahisa , Sugitani Koichi , Isogai Yukie , Katoh Takeyoshi , Yamamoto Toshihiro , Fujikake Hideo , Tokito Shizuo 
Published: October 2011

ABSTRACTOrganic thin-film transistors (OTFTs) using cross-linked olefin polymer as a gate insulator were fabricated on a plastic film. An olefin polymer layer was formed by spin-coating and baking at temperatures below 150°C. Pentacene was used as an organic semiconductor layer. The fabricated OTFTs with a short 5-μm-long channel showed a mobility of 0.1-0.2 cm2/Vs and a current ON/OFF ratio of 107. These OTFTs also exhibited good stable performance in the atmosphere. On the basis of the results, we fabricated a 5 inches OTFT-driven flexible active-matrix organic light emitting diode (AMOLED) display. The gate insulator, some metal wirings and electrodes on the OTFT backplane were formed on the plastic film by photolithography. After fabrication of the OTFT backplane, OLED layers were formed by vacuum deposition through a shadow-mask. Clear color moving images were observed on the flexible display even when it was bent.
Pulsed Laser Deposition of Silicon Nanostructures
Authors: Bruno P. , Salve T. , Russo V. , Dellasega D. , Filoni G. , Casari C.S. , Bottani C.E. , Bassi A. Li 
Published: October 2011

ABSTRACTSilicon nanostructures embedded in an amorphous matrix have been synthesized by Pulsed Laser Deposition (PLD) at room temperature. The structural and optical properties of the materials were tailored by varying deposition parameters; attention has been devoted to the nanoscale morphology of the Si layers which has been varied from compact to open-porous by changing background gas (Ar) pressure (1-100 Pa). An adopted simple-minded strategy of a compact Si layer deposited on top of nanostructured layers showed to reduce quite successfully ex-situ oxidation. Raman spectroscopy suggests that as deposited samples are mainly constituted by amorphous silicon with nanocrystals (NCs) inclusions. The results indicate that the average size of the Si NCs varies in the range 2-6 nm. Photoluminescence (PL) responses are found to be strictly dependent on morphology and strengthen up the idea of the quantum confinement effect in the obtained nanostructured material. The results are interpreted in terms of particle size distribution, crystallinity and partial surface oxidation of the silicon nanostructures.
Non-idealities in Graphene/p-silicon Schottky-barrier Solar Cells
Authors: Lin Derek Y.T. , Shambayati Shabnam , Kiasari Nima Mohseni , Pulfrey David L. , Servati Peyman 
Published: October 2011

ABSTRACTThis paper presents fabrication details and preliminary experimental results for graphene/p-silicon Schottky-barrier solar cells, where graphene is used as a transparent electrode and forms a rectifying junction with silicon wafer. Deviations from expected Schottky behavior in the form of large diode-ideality factors and s-shaped current-voltage curves observed in measurements are reported and analyzed.