bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determining True HER2 Gene Status in Breast Cancers With Polysomy by Using Alternative Chromosome 17 Reference Genes: Implications for Anti-HER2 Targeted Therapy
Authors: Tse Chun Hing , Hwang Harry C. , Goldstein Lynn C. , Kandalaft Patricia L. , Wiley Jesse C. , Kussick Steven J. , Gown Allen M. 
Published: September 2011

Purpose The ratio of human epidermal growth factor receptor 2 (HER2) to CEP17 by fluorescent in situ hybridization (FISH) with the centromeric probe CEP17 is used to determine HER2 gene status in breast cancer. Increases in CEP17 copy number have been interpreted as representing polysomy 17. However, pangenomic studies have demonstrated that polysomy 17 is rare. This study tests the hypothesis that the use of alternative chromosome 17 reference genes might more accurately assess true HER2 gene status. Patients and Methods In all, 171 patients with breast cancer who had HER2 FISH that had increased mean CEP17 copy numbers (> 2.6) were selected for additional chromosome 17 studies that used probes for Smith-Magenis syndrome (SMS), retinoic acid receptor alpha (RARA), and tumor protein p53 (TP53) genes. A eusomic copy number exhibited in one or more of these loci was used to calculate a revised HER2-to-chromosome-17 ratio by using the eusomic gene locus as the reference. Results Of 132 cases classified as nonamplified on the basis of their HER2:CEP17 ratios, 58 (43.9%) were scored as amplified by using alternative chromosome 17 reference gene probes, and 13 (92.9%) of 14 cases scored as equivocal were reclassified as amplified. Among the cases with mean HER2 copy number of 4 to 6, 41 (47.7%) of 86 had their HER2 gene status upgraded from nonamplified to amplified, and four (4.7%) of 86 were upgraded from equivocal to amplified. Conclusion Our results support the findings of recent pangenomic studies that true polysomy 17 is uncommon. Additional FISH studies that use probes to the SMS, RARA, and TP53 genes are an effective way to determine the true HER2 amplification status in patients with polysomy 17 and they have important potential implications for guiding HER2-targeted therapy in breast cancer.
Prospective Study on Incidence, Risk Factors, and Long-Term Outcome of Osteonecrosis in Pediatric Acute Lymphoblastic Leukemia
Authors: te Winkel Mariël L. , Pieters Rob , Hop Wim C.J. , de Groot-Kruseman Hester A. , Lequin Maarten H. , van der Sluis Inge M. , Bökkerink Jos P.M. , Leeuw Jan A. , Bruin Marrie C.A. , Egeler R. Maarten , Veerman Anjo J.P. , van den Heuvel-Eibrink Marry M. 
Published: September 2011

Purpose We studied cumulative incidence, risk factors, therapeutic strategies, and outcome of symptomatic osteonecrosis in pediatric patients with acute lymphoblastic leukemia (ALL). Patients and Methods Cumulative incidence of osteonecrosis was assessed prospectively in 694 patients treated with the dexamethasone-based Dutch Child Oncology Group–ALL9 protocol. Osteonecrosis was defined by development of symptoms (National Cancer Institute grade 2 to 4) during treatment or within 1 year after treatment discontinuation, confirmed by magnetic resonance imaging. We evaluated risk factors for osteonecrosis using logistic multivariate regression. To describe outcome, we reviewed clinical and radiologic information after antileukemic treatment 1 year or more after osteonecrosis diagnosis. Results Cumulative incidence of osteonecrosis at 3 years was 6.1%. After adjustment for treatment center, logistic multivariate regression identified age (odds ratio [OR], 1.47; P < .01) and female sex (OR, 2.23; P = .04) as independent risk factors. Median age at diagnosis of ALL in patients with osteonecrosis was 13.5 years, compared with 4.7 years in those without. In 21 (55%) of 38 patients with osteonecrosis, chemotherapy was adjusted. Seven patients (18%) underwent surgery: five joint-preserving procedures and two total-hip arthroplasties. Clinical follow-up of 35 patients was evaluated; median follow-up was 4.9 years. In 14 patients (40%), symptoms completely resolved; 14 (40%) had symptoms interfering with function but not with activities of daily living (ADLs; grade 2); seven (20%) had symptoms interfering with ADLs (grade 3). In 24 patients, radiologic follow-up was available; in six (25%), lesions improved/disappeared; in 13 (54%), lesions remained stable; five (21%) had progressive lesions. Conclusion Six percent of pediatric patients with ALL developed symptomatic osteonecrosis during or shortly after treatment. Older age and female sex were risk factors. After a median follow-up of 5 years, 60% of patients had persistent symptoms.
Creation of Nucleophilic Boryl Anions and Their Properties
Authors: Yamashita Makoto 
Published: September 2011

Abstract
A series of anionic boron compounds, possessing a polarized boron–metal bond, were synthesized and structurally characterized. Detailed analyses of these boryl anions using NMR spectroscopy, X-ray crystallography, reactivity with electrophiles, and DFT calculations revealed that these compounds have anionic and nucleophilic character on the boron center in contrast to conventional boron-containing molecules with a Lewis acidic character. Some applications of boryl anions toward organic synthesis, organometallic chemistry, and main group chemistry are also described.
Development of a New System for Photocatalytic Water Splitting into H2 and O2 under Visible Light Irradiation
Authors: Abe Ryu 
Published: September 2011

Abstract
Photocatalytic water splitting using semiconductor materials has attracted considerable interest due to its potential for clean production of H2 from water by utilizing abundant solar light. The developments of water-splitting systems that can efficiently use visible light have been a major challenge for many years in order to realize efficient conversion of solar light. We have developed a new type of photocatalysis system that can split water into H2 and O2 under visible light irradiation, which was inspired by the two-step photoexcitation (Z-scheme) mechanism of natural photosynthesis in green plants. In this system, the water-splitting reaction is broken up into two stages: one for H2 evolution and the other for O2 evolution; these are combined by using a shuttle redox couple (Red/Ox) in the solution. The introduction of a Z-scheme mechanism reduces the energy required to drive each photocatalysis process, extending the usable wavelengths significantly (≈660 nm for H2 evolution and ≈600 nm for O2 evolution) from that in conventional water splitting systems (≈460 nm) based on one-step photoexcitation in single semiconductor material.
Moving out: from sterol transport to drug resistance – the ABCG subfamily of efflux pumps
Authors: Moitra Karobi , Silverton Latoya , Limpert Katy , Im Kate , Dean Michael 
Published: September 2011

Abstract
The ATP binding cassette (ABC) proteins are typically ATP-driven transmembrane pumps that have been evolutionarily conserved from bacteria to humans. In humans these transporters are subdivided into seven subfamilies, ranging from A to G. The ABCG subfamily of transporters is the primary focus of this review. This subfamily of proteins has been conserved throughout evolution and plays a central role in several cellular processes, such as sterol homeostasis and multidrug resistance. Functional polymorphisms/mutations in some of these G-subfamily transporters have clinical consequences in humans.
Prevalence of Asthma and Its Association With Glycemic Control Among Youth With Diabetes
Authors: Black Mary Helen , Anderson Andrea , Bell Ronny A. , Dabelea Dana , Pihoker Catherine , Saydah Sharon , Seid Michael , Standiford Debra A. , Waitzfelder Beth , Marcovina Santica M. , Lawrence Jean M. 
Published: September 2011

OBJECTIVE:To estimate the prevalence of asthma among youth with types 1 and 2 diabetes and examine associations between asthma and glycemic control.METHODS:This was a cross-sectional analysis of data from the SEARCH for Diabetes in Youth study, which included youth diagnosed with type 1 (n = 1683) and type 2 (n = 311) diabetes from 2002 through 2005. Asthma status and medications were ascertained from medical records and self-administered questionnaires, and glycemic control was assessed from hemoglobin A1c measured at the study visit.RESULTS:Prevalence of asthma among all youth with diabetes was 10.9% (95% confidence interval [CI]: 9.6%–12.3%). The prevalence was 10.0% (95% CI: 8.6%–11.4%) among youth with type 1 and 16.1% (95% CI: 12.0%–20.2%) among youth with type 2 diabetes and differed according to race/ethnicity. Among youth with type 1 diabetes, those with asthma had higher mean A1c levels than those without asthma, after adjustment for age, gender, race/ethnicity, and BMI (7.77% vs 7.49%; P = .034). Youth with asthma were more likely to have poor glycemic control, particularly those with type 1 diabetes whose asthma was not treated with pharmacotherapy, although this association was attenuated by adjustment for race/ethnicity.CONCLUSIONS:Prevalence of asthma may be elevated among youth with diabetes relative to the general US population. Among youth with type 1 diabetes, asthma is associated with poor glycemic control, especially if asthma is untreated. Specific asthma medications may decrease systemic inflammation, which underlies the complex relationship between pulmonary function, BMI, and glycemic control among youth with diabetes.
Infant Growth Before and After Term: Effects on Neurodevelopment in Preterm Infants
Authors: Belfort Mandy B. , Rifas-Shiman Sheryl L. , Sullivan Thomas , Collins Carmel T. , McPhee Andrew J. , Ryan Philip , Kleinman Ken P. , Gillman Matthew W. , Gibson Robert A. , Makrides Maria 
Published: September 2011

OBJECTIVE:
To identify sensitive periods of postnatal growth for preterm infants relative to neurodevelopment at 18 months' corrected age.

PATIENTS AND METHODS:
We studied 613 infants born at &lt;33 weeks' gestation who participated in the DHA for Improvement of Neurodevelopmental Outcome trial. We calculated linear slopes of growth in weight, length, BMI, and head circumference from 1 week of age to term (40 weeks' postmenstrual age), term to 4 months, and 4 to 12 months, and we estimated their associations with Bayley Scales of Infant Development, 2nd Edition, Mental (MDI) and Psychomotor (PDI) Development Indexes in linear regression.

RESULTS:
The median gestational age was 30 (range: 2–33) weeks. Mean ± SD MDI was 94 ± 16, and PDI was 93 ± 16. From 1 week to term, greater weight gain (2.4 MDI points per z score [95% confidence interval (CI): 0.8–3.9]; 2.7 PDI points [95% CI: 1.2–.2]), BMI gain (1.7 MDI points [95% CI: 0.4–3.1]; 2.5 PDI points [95% CI: 1.2–3.9]), and head growth (1.4 MDI points [95% CI: −0.0–2.8]; 2.5 PDI points [95% CI: 1.2–3.9]) were associated with higher scores. From term to 4 months, greater weight gain (1.7 points [95% CI: 0.2–3.1]) and linear growth (2.0 points [95% CI: 0.7–3.2]), but not BMI gain, were associated with higher PDI. From 4 to 12 months, none of the growth measures was associated with MDI or PDI score.

CONCLUSIONS:
In preterm infants, greater weight and BMI gain to term were associated with better neurodevelopmental outcomes. After term, greater weight gain was also associated with better outcomes, but increasing weight out of proportion to length did not confer additional benefit.
Molecular Assays in the Diagnosis of Neonatal Sepsis: A Systematic Review and Meta-analysis
Authors: Pammi Mohan , Flores Angela , Leeflang Mariska , Versalovic James 
Published: September 2011

BACKGROUND:
Microbial cultures for diagnosis of neonatal sepsis suffer from low sensitivity and reporting delay. Advances in molecular microbiology have fostered new molecular assays that are rapid and may improve neonatal outcomes.

OBJECTIVES:
We assessed whether molecular assays have sufficient sensitivity (&gt;0.98) and specificity (&gt;0.95) to replace microbial cultures in the diagnosis of neonatal sepsis and explored heterogeneity by use of subgroup analyses based on the type of assay, gestational age of the neonate, and type of sepsis onset.

METHODS:
We performed the systematic review as recommended by the Cochrane Diagnostic Test Accuracy Working Group. Electronic bibliographic databases, conference abstracts, personal files, and reference lists of identified articles were searched. We included studies of case-control or consecutive series design, which evaluated molecular assays (index test) in neonates with suspected sepsis (participants) in comparison with microbial cultures (reference standard). Two reviewers independently assessed the methodologic quality of the studies and extracted data.

RESULTS:
A bivariate random-effects model was used for meta-analysis of the 23 included studies, and summary estimates of sensitivity and specificity with 95% confidence intervals (CIs) were generated. Mean sensitivity and specificity were 0.90 (95% CI: 0.78–0.95) and 0.96 (95% CI: 0.94–0.97), respectively. Real-time polymerase chain reaction (PCR) and broad-range conventional PCR had higher sensitivity and specificity than other assays. Sufficient data were not available to evaluate gestational-age and sepsis-type subgroups.

CONCLUSION:
Molecular assays do not have sufficient sensitivity to replace microbial cultures in the diagnosis of neonatal sepsis but may perform well as “add-on” tests.
Atomistically informed continuum model for body centered cubic iron
Authors: Koester Aenne , Ma Anxin , Hartmaier Alexander 
Published: September 2011

ABSTRACTPlastic deformation in body centered cubic iron is dominated by glide of screw dislocations with non-planar dislocation cores. This causes a strong strain rate and temperature dependence of flow stress, the breakdown of Schmid’s law and a dependence of dislocation mobility on shear stress components that do not contribute to the mechanical driving force for dislocation glide. Based on the framework of crystal plasticity, we developed a constitutive plasticity model that takes all these phenomena into account. To parameterize this continuum plasticity model molecular statics simulations using a semi-empirical potential have been performed. These atomistic calculations yielded quantitative relationships for the influence of all components of the local stress tensor on dislocation mobility. Together with experimental data from the literature on the kinetics of screw dislocations in bcc iron the constitutive relation presented here has been developed. As application example of the model, we calculated the tension compression asymmetry and the strain rate dependence of the hardening behavior within a bcc iron crystal.
Mapping Nanomechanical Properties near Internal Interfaces in Biological Materials
Authors: Zlotnikov Igor , Drezner Haika , Shilo Doron , Aichmayer Barbara , Dauphin Yannicke , Zolotoyabko Emil , Fratzl Peter 
Published: September 2011

ABSTRACTModulus mapping using nanoDMA (Dynamic Mechanical Analysis) is a recently developed technique based on a nanoindentation instrument equipped with an AFM-like piezoscanner and dynamic force modulation system. The surface properties, storage and loss moduli are quantified based on the Hertz model for the contact mechanics of the sample-tip configuration. In this approach, the applied load, topography features, and their size may have a pronounced effect on the obtained results. In order to demonstrate that, internal interfaces of deep sea sponge (Monorhaphis chuni), which comprises alternating layers of relatively thick (4 μm in average) biosilica and thin (60 nm) organic material, were characterized using the nanoDMA modulus mapping technique. Experimental data were analyzed in tight interrelation with finite element simulations. This combination allowed us to evaluate elastic modulus of a 60 nm wide organic layers in M. chuni.
Zinc and Zinc Oxide Nanowires Grown on PEDOT:PSS/SiO2 Conductive Polymer Thin Films by Vapor Phase Transport Deposition
Authors: Chamberlin Matthew P. , Constantin Costel 
Published: September 2011

ABSTRACTEasily available spin coating and vapor phase transport deposition techniques offer tremendous possibilities in fabricating inorganic/organic heterojunctions. We present here preliminary results from different thin film growth mechanisms including: i) PEDOT:PSS/Zn-nanowires/SiO2, ii) Zn-nanowires/PEDOT:PSS/SiO2, and iii) ZnO-nanowires/PEDOT:PSS/SiO2. The preliminary scanning electron microscopy and energy dispersive spectroscopy results show that Zn nanowires bond better to the non-annealed PEDOT:PSS thin films. It was also found that ZnO nanowires grow homogeneously on annealed PEDOT:PSS surfaces with colloidal Au nanoparticles as bonding reaction catalysts.
In Vitro Evaluation of the Effect of Delaying Toothbrushing With Toothpaste on Enamel Microhardness Subsequent to Bleaching the Teeth With 15% Carbamide Peroxide
Authors: Navimipour EJ , Kimyai S , Nikazar S , Ghojazadeh M 
Published: September 2011

Clinical Relevance
Delaying oral hygiene procedures during bleaching does not seem to cause any change in enamel microhardness.
Treatment of Invasive Cervical Resorption With Sandwich Technique Using Mineral Trioxide Aggregate: A Case Report
Authors: Kqiku L , Ebeleseder KA , Glockner K 
Published: September 2011

Clinical Relevance
MTA combined with glass ionomer cement and composite resin in a “sandwich technique” showed a favourable clinical outcome for treatment of invasive cervical resorption lesions.
An innovative image fusion algorithm based on wavelet transform and discrete fast curvelet transform
Authors: Sumathi T. , Hemalatha M. 
Published: September 2011

Abstract
Image fusion is the method of combining relevant information from two or more images into a single image resulting in an image that is more informative than the initial inputs. Methods for fusion include discrete wavelet transform, Laplacian pyramid based transform, curvelet based transform etc. These methods demonstrate the best performance in spatial and spectral quality of the fused image compared to other spatial methods of fusion. In particular, wavelet transform has good time-frequency characteristics. However, this characteristic cannot be extended easily to two or more dimensions with separable wavelet experiencing limited directivity when spanning a one-dimensional wavelet. This paper introduces the second generation curvelet transform and uses it to fuse images together. This method is compared against the others previously described to show that useful information can be extracted from source and fused images resulting in the production of fused images which offer clear, detailed information.
Fitts’ law to the rescue: A comparison of graph tables
Authors: Hedman Anna , Alm Håkan 
Published: September 2011

Abstract
In this paper we investigate image browsing as an interactive method for visualizing line graphs. We have compared two interfaces that both presented exactly identically looking tables, but while one version was an overview+detail interface, the other one was a distortion-oriented interface of bifocal type. We expected there to be no difference in task completion times, and found none in our first statistical evaluation. Users preferred the static overview+detail interface to the distortion-oriented, which was motivated by complaints about the changed appearance of the distortion-oriented table. The empirical results were compared to theoretical results obtained using Fitts’ law, which showed a difference in task completion time for a certain task type. A second statistical analysis included only data from task type for which a difference could be expected. The new results supported the theoretical model, saying that users were faster with the overview+detail interface. In this paper we discuss problems with image browsing tests, and suggest some ideas for future research topics and designs.
Tigecycline attenuates polymorphonuclear leukocyte (PMN) receptors but not functions
Authors: Naess Are , Andreeva Hristina , Sørnes Steinar 
Published: September 2011

Tigecycline attenuates polymorphonuclear leukocyte (PMN) receptors but not functionsTigecycline achieves high intracellular concentrations in polymorphonuclear leukocytes (PMNs). To evaluate the effects of tigecycline on human PMNs, PMNs were incubated with tigecycline dilutions (0.1 to 100 mg L-1). Phagocytosis-associated PMN Fcγ- and complement receptors as well as phagocytosis and oxidative burst induced byStaphylococcus aureuswere measured by flow cytometry. Incubation with tigecycline caused small but significant decreases in the density of complement receptors CD11b and CD35 (all concentrations) and Fcγ receptors CD16 and CD32 (high concentrations), but not in the percentages of receptor-bearing cells, except for small reductions in the proportions of CD16 positive cells at high concentrations. Tigecycline had no effect on phagocytosis or oxidative burst induced byS. aureus. Tigecycline was thus associated with decreased density of PMN complement and (at high concentrations) Fcγ receptors. Although statistically significant, the differences were small and did not influence the PMN function as measured by phagocytosis and oxidative burst.
Simultaneous estimation of ramipril, acetylsalicylic acid and atorvastatin calcium by chemometrics assisted UV-spectrophotometric method in capsules
Authors: Sankar A. , Vetrichelvan Thangarasu , Venkappaya Devashya 
Published: September 2011

Simultaneous estimation of ramipril, acetylsalicylic acid and atorvastatin calcium by chemometrics assisted UV-spectrophotometric method in capsulesIn the present work, three different spectrophotometric methods for simultaneous estimation of ramipril, aspirin and atorvastatin calcium in raw materials and in formulations are described. Overlapped data was quantitatively resolved by using chemometric methods,viz.inverse least squares (ILS), principal component regression (PCR) and partial least squares (PLS). Calibrations were constructed using the absorption data matrix corresponding to the concentration data matrix. The linearity range was found to be 1-5, 10-50 and 2-10 μg mL-1for ramipril, aspirin and atorvastatin calcium, respectively. The absorbance matrix was obtained by measuring the zero-order absorbance in the wavelength range between 210 and 320 nm. A training set design of the concentration data corresponding to the ramipril, aspirin and atorvastatin calcium mixtures was organized statistically to maximize the information content from the spectra and to minimize the error of multivariate calibrations. By applying the respective algorithms for PLS 1, PCR and ILS to the measured spectra of the calibration set, a suitable model was obtained. This model was selected on the basis of RMSECV and RMSEP values. The same was applied to the prediction set and capsule formulation. Mean recoveries of the commercial formulation set together with the figures of merit (calibration sensitivity, selectivity, limit of detection, limit of quantification and analytical sensitivity) were estimated. Validity of the proposed approaches was successfully assessed for analyses of drugs in the various prepared physical mixtures and formulations.