bluuebunny/crossref_metadata_2025_split huggingface dataset:
BreastMark: An Integrated Approach to Mining Publicly Available Transcriptomic Datasets Relating to Breast Cancer Outcome
Authors: Madden Stephen F , Clarke Colin , Gaule Patricia , Aherne Sinead T , O'Donovan Norma , Clynes Martin , Crown John , Gallagher William M 
Published: July 2013

Abstract
Introduction
Breast cancer is a complex heterogeneous disease for which a substantial resource of transcriptomic data is available. Gene expression data have facilitated the division of breast cancer into, at least, five molecular subtypes, namely luminal A, luminal B, HER2, normal-like and basal. Once identified, breast cancer subtypes can inform clinical decisions surrounding patient treatment and prognosis. Indeed, it is important to identify patients at risk of developing aggressive disease so as to tailor the level of clinical intervention.

Methods
We have developed a user-friendly, web-based system to allow the evaluation of genes/microRNAs (miRNAs) that are significantly associated with survival in breast cancer and its molecular subtypes. The algorithm combines gene expression data from multiple microarray experiments which frequently also contain miRNA expression information, and detailed clinical data to correlate outcome with gene/miRNA expression levels. This algorithm integrates gene expression and survival data from 26 datasets on 12 different microarray platforms corresponding to approximately 17,000 genes in up to 4,738 samples. In addition, the prognostic potential of 341 miRNAs can be analysed.

Results
We demonstrated the robustness of our approach in comparison to two commercially available prognostic tests, oncotype DX and MammaPrint. Our algorithm complements these prognostic tests and is consistent with their findings. In addition, BreastMark can act as a powerful reductionist approach to these more complex gene signatures, eliminating superfluous genes, potentially reducing the cost and complexity of these multi-index assays. Known miRNA prognostic markers, mir-205 and mir-93, were used to confirm the prognostic value of this tool in a miRNA setting. We also applied the algorithm to examine expression of 58 receptor tyrosine kinases in the basal-like subtype, identifying six receptor tyrosine kinases associated with poor disease-free survival and/or overall survival (EPHA5, FGFR1, FGFR3, VEGFR1, PDGFRβ, and TIE1). A web application for using this algorithm is currently available.

Conclusions
BreastMark is a powerful tool for examining putative gene/miRNA prognostic markers in breast cancer. The value of this tool will be in the preliminary assessment of putative biomarkers in breast cancer. It will be of particular use to research groups with limited bioinformatics facilities.
LUX-Lung 4: A Phase II Trial of Afatinib in Patients With Advanced Non–Small-Cell Lung Cancer Who Progressed During Prior Treatment With Erlotinib, Gefitinib, or Both
Authors: Katakami Nobuyuki , Atagi Shinji , Goto Koichi , Hida Toyoaki , Horai Takeshi , Inoue Akira , Ichinose Yukito , Koboyashi Kunihiko , Takeda Koji , Kiura Katsuyuki , Nishio Kazuto , Seki Yoko , Ebisawa Ryuichi , Shahidi Mehdi , Yamamoto Nobuyuki 
Published: July 2013

Purpose New molecular targeted agents are needed for patients with non–small-cell lung cancer (NSCLC) who progress while receiving erlotinib, gefitinib, or both. Afatinib, an oral irreversible ErbB family blocker, has preclinical activity in epidermal growth factor receptor (EGFR [ErbB1]) mutant models with EGFR-activating mutations, including T790M. Patients and Methods This was a Japanese single-arm phase II trial conducted in patients with stage IIIB to IV pulmonary adenocarcinoma who progressed after ≥ 12 weeks of prior erlotinib and/or gefitinib. Patients received afatinib 50 mg per day. The primary end point was objective response rate (complete response or partial response) by independent review. Secondary end points included progression-free survival (PFS), overall survival (OS), and safety. Results Of 62 treated patients, 45 (72.6%) were EGFR mutation positive in their primary tumor according to local and/or central laboratory analyses. Fifty-one patients (82.3%) fulfilled the criteria of acquired resistance to erlotinib and/or gefitinib. Of 61 evaluable patients, five (8.2%; 95% CI, 2.7% to 18.1%) had a confirmed objective response rate (partial response). Median PFS was 4.4 months (95% CI, 2.8 to 4.6 months), and median OS was 19.0 months (95% CI, 14.9 months to not achieved). Two patients had acquired T790M mutations: L858R + T790M, and deletion in exon 19 + T790M; they had stable disease for 9 months and 1 month, respectively. The most common afatinib-related adverse events (AEs) were diarrhea (100%) and rash/acne (91.9%). Treatment-related AEs leading to afatinib discontinuation were experienced by 18 patients (29%), of whom four also had progressive disease. Conclusion Afatinib demonstrated modest but noteworthy efficacy in patients with NSCLC who had received third- or fourth-line treatment and who progressed while receiving erlotinib and/or gefitinib, including those with acquired resistance to erlotinib, gefitinib, or both.
Staging of Ciliary Body and Choroidal Melanomas Based on Anatomic Extent
Authors: Kujala Emma , Damato Bertil , Coupland Sarah E. , Desjardins Laurence , Bechrakis Nikolaos E. , Grange Jean-Daniel , Kivelä Tero 
Published: July 2013

Purpose To refine the anatomic classification and staging of ciliary body and choroidal melanomas in the TNM classification. Patients and Methods Tumor largest basal diameter and thickness of 7,369 patients were analyzed based on registry data from five ocular oncology centers. T categories were derived empirically by dividing data into blocks representing 3- × 3-mm fractions. Blocks with similar survival were grouped together so that no T category comprised a large majority of tumors, and each was uniform in survival, using randomly drawn 60% building and 40% validation data sets. Presence of ciliary body involvement (CBI) and extraocular extension (EXE) was analyzed among 5,403 patients to define T subcategories. Stages were generated by iteratively combining subcategories with similar survival. Results Of the 7,369 tumors analyzed, 24% were classified as T1, 33% as T2, 31% as T3, and 12% as T4. Ten-year Kaplan-Meier survival estimates for the T categories were 89%, 77%, 58%, and 39%, respectively (P < .001). Survival of patients in four subcategories based on presence or absence of CBI and EXE differed significantly within each T category (P = .018 for T1; P < .001 for T2 to T4). EXE exceeding 5 mm in largest diameter carried a worse prognosis than smaller extensions (P < .001) and was assigned a separate subcategory. Ten-year Kaplan-Meier survival estimates for stages I, IIA to IIB, and IIIA to IIIC were 88%, 80%, 67%, 45%, 27%, 10%, respectively (P < .001). Conclusion This evidence-based anatomic classification provides a basis for staging ciliary body and choroidal melanomas in the seventh edition of the Cancer Staging Manual of the American Joint Committee on Cancer.
Serum Androgens As Prognostic Biomarkers in Castration-Resistant Prostate Cancer: Results From an Analysis of a Randomized Phase III Trial
Authors: Ryan Charles J. , Molina Arturo , Li Jinhui , Kheoh Thian , Small Eric J. , Haqq Christopher M. , Grant Russell P. , de Bono Johann S. , Scher Howard I. 
Published: July 2013

Purpose In the phase III study COU-AA-301, abiraterone acetate (AA) plus prednisone (P) prolonged overall survival (OS) in patients with metastatic castration-resistant prostate cancer (mCRPC) after docetaxel administration. In this article, we investigate the relationship between baseline serum androgen (SA) levels and OS. Patients and Methods COU-AA-301 is a randomized, double-blind study of AA (1,000 mg every day) plus P (5 mg by mouth twice daily; n = 797) versus P alone (n = 398). Randomization was stratified by Eastern Cooperative Oncology Group performance status (0 to 1 v 2), pain (Brief Pain Inventory-Short Form over past 24 hours: 4 to 10, present; v 0 to 3, absent), prior chemotherapy (1 v 2), and progression (prostate-specific antigen v radiographic). Association of baseline SA (testosterone, androstenedione, dehydroepiandrosterone sulfate), was measured by ultrasensitive liquid-liquid extraction or protein precipitation and two-dimensional liquid chromatography coupled to mass spectrometry, with OS determined by bivariate and multivariable Cox models. OS was examined with SA as greater than median and less than or equal to the median. Results Median survival increased with each quartile increase in testosterone level regardless of treatment arm. SA levels at baseline strongly associated with survival (P < .0001) in bivariate and multivariable analyses. Longer survival was observed for patients with SA above median compared with below median in both the AA and P arms (eg, testosterone, AA; hazard ratio, 0.64; 95% CI, 0.53 to 0.77; P < .0001). Treatment with AA led to longer survival versus P alone in the above- or below-median group for all androgens. Conclusion SA, measured with a novel ultrasensitive assay in COU-AA-301, is prognostic for OS and may be useful for risk stratification in mCRPC clinical trials.
Symptom Control and Quality of Life in LUX-Lung 3: A Phase III Study of Afatinib or Cisplatin/Pemetrexed in Patients With Advanced Lung Adenocarcinoma With EGFR Mutations
Authors: Yang James Chih-Hsin , Hirsh Vera , Schuler Martin , Yamamoto Nobuyuki , O'Byrne Kenneth J. , Mok Tony S.K. , Zazulina Victoria , Shahidi Mehdi , Lungershausen Juliane , Massey Dan , Palmer Michael , Sequist Lecia V. 
Published: July 2013

Purpose Patient-reported symptoms and health-related quality of life (QoL) benefits were investigated in a randomized, phase III trial of afatinib or cisplatin/pemetrexed. Patients and Methods Three hundred forty-five patients with advanced epidermal growth factor receptor (EGFR) mutation–positive lung adenocarcinoma were randomly assigned 2:1 to afatinib 40 mg per day or up to six cycles of cisplatin/pemetrexed. Lung cancer symptoms and health-related QoL were assessed every 21 days until progression using the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire C30 and Lung Cancer-13 questionnaires. Analyses of cough, dyspnea, and pain were preplanned, including percentage of patients who improved on therapy, time to deterioration of symptoms, and change in symptoms over time. Results Questionnaire compliance was high. Compared with chemotherapy, afatinib significantly delayed the time to deterioration for cough (hazard ratio [HR], 0.60; 95% CI, 0.41 to 0.87; P = .007) and dyspnea (HR, 0.68; 95% CI, 0.50 to 0.93; P = .015), but not pain (HR, 0.83; 95% CI, 0.62 to 1.10; P = .19). More patients on afatinib (64%) versus chemotherapy (50%) experienced improvements in dyspnea scores (P = .010). Differences in mean scores over time significantly favored afatinib over chemotherapy for cough (P < .001) and dyspnea (P < .001). Afatinib showed significantly better mean scores over time in global health status/QoL (P = .015) and physical (P < .001), role (P = .004), and cognitive (P = .007) functioning compared with chemotherapy. Fatigue and nausea were worse with chemotherapy, whereas diarrhea, dysphagia, and sore mouth were worse with afatinib (all P < .01). Conclusion In patients with lung adenocarcinoma with EGFR mutations, first-line afatinib was associated with better control of cough and dyspnea compared with chemotherapy, although diarrhea, dysphagia, and sore mouth were worse. Global health status/QoL was also improved over time with afatinib compared with chemotherapy.
APPLYING VARIOUS TRAINING ALGORITHMS IN DATA ANALYSIS OF NANO COMPOSITES
Authors: Tofigh Ali Asghar , Shabani Mohsen Ostad 
Published: July 2013

In this study, SiC nano-particles were incorporated into the A356 aluminum alloy to fabricate metal matrix nano composites (MMNCs) with uniform reinforcement distribution. The tribological and mechanical properties of A356 nano composites were experimentally investigated. It was revealed that the presence of nano-SiC reinforcement led to significant improvement in hardness, 0.2% yield strength and UTS. The highest yield strength and UTS was obtained by 3.5 vol. % of SiC nano-particles. The wear sliding test disclosed that the wear resistance of the nano SiC reinforced composites is higher than that of the unreinforced alloy. The system accuracy of each artificial neural network training algorithm in finite element technique modeling of nano composites behaviors was then investigated.
MODELING THE EFFECT OF RADIUS ON TEMPERATURE HISTORY OF TRANSIENT QUENCHED BORON STEEL
Authors: Elmaryami Abdlmanam S. A. , Omar Badrul 
Published: July 2013

One-dimensional (1D) model of an axisymmetric unsteady state industrial quenched boron steel 50B46H bar based on finite element method (FEM) has been applied to investigate the influence of process history on its material properties. The effect of four different radii on its temperature history is determined. The model can be employed as a guideline to design cooling approach to achieve desired microstructure and mechanical properties such as hardness. A computer programof the model is developed, which can be used independently or incorporated into a temperature history software named (LHP)-software to continuously calculate and display temperature history of the boron steel bar and thereby to study the effect of radius on temperature history. The developed program based on (1D) FEM model has been verified by comparing its results with commercial finite element software results. The comparison indicates its validity and reliability.
Carbothermic Reduction of Zinc Ferrite by Microwave Heating
Authors: Wang Xin , Ju Shao-Hua , Srinivasakannan C. , Yang Da-Jin , Peng Jin-Hui 
Published: July 2013

AbstractThe kinetics of carbothermic reduction of ZnFe2O4 in the temperature range 823–1223 K, was investigated in a microwave reactor. The mechanism of formation of ZnO and Fe3O4/FeO by decomposition of ZnFe2O4 was explained using the equilibrium calculations and thermodynamics analysis using HSC chemistry software 6.0. In addition the effect of parameters such as the decomposition temperature, C/ZnFe2O4 ratio, particle size and microwave power were assessed on the decomposition kinetics. Zn recovery as high as 98.83% could be achieved at a decomposition temperature of 1023 K, C/ZnFe2O4 ratio of 1:3, particle size of +74–61 µm and microwave power of 1200 W. The kinetics of decomposition was found to be carbon gasification reaction controlled, with the activation energy of 39.21 kJ/mol.
A spherical x-ray transform and hypercube sections
Authors: Kazantsev Ivan G. , Schmidt Søren 
Published: July 2013

Abstract
We investigate the problem of sampling a unit great circle on the unit sphere 𝕊3 as a support of orientation distribution functions on which acts the discrete spherical x-ray transform. The circle's partition subsets are gnomonically mapped onto lines that constitute a convex polygon inside the bounding cubes of hypercube. Thus the problem
of the great circle tracing is reduced to the problem of the four-dimensional cube sectioning by the plane containing the circle and the intersection figure (the polygon) vertices finding. In this paper, a fast, non-combinatorial approach
for the polygon tracing within the general multi-dimensional frame is proposed.
Semismooth Newton and quasi-Newton methods in weighted ℓ1-regularization
Authors: Muoi Pham Quy , Hào Dinh Nho , Maass Peter , Pidcock Michael 
Published: July 2013

Abstract.
We investigate semismooth Newton and quasi-Newton methods for
minimization problems arising from weighted
ℓ1-regularization. We give proofs of the local convergence of
these methods and show how their interpretation as active set
methods leads to the development of efficient numerical
implementations of these algorithms. We also propose and analyze
Broyden updates for the semismooth quasi-Newton method. The
efficiency of these methods is analyzed and compared with standard
implementations. The paper concludes with some numerical examples
that include both linear and nonlinear operator equations.
Relationships Between Reactive Agility Movement Time and Unilateral Vertical, Horizontal, and Lateral Jumps
Authors: Henry Greg J. , Dawson Brian , Lay Brendan S. , Young Warren B. 
Published: July 2013

Abstract
Henry, GJ, Dawson, B, Lay, BS, and Young, WB. Relationships between reactive agility movement time and unilateral vertical, horizontal, and lateral jumps. J Strength Cond Res 30(9): 2514–2521, 2016—This study compared reactive agility movement time and unilateral (vertical, horizontal, and lateral) jump performance and kinetics between dominant and nondominant legs in Australian rules footballers (n = 31) to investigate the role of leg strength characteristics in reactive agility performance. Jumps involved jumping forward on 1 leg, then for maximum height or horizontal or lateral distance. Agility and movement time components of reactive agility were assessed using a video-based test. Correlations between each of the jumps were strong (r = −0.62 to −0.77), but between the jumps and agility movement time the relationships were weak (r = −0.25 to −0.33). Dominant leg performance was superior in reactive agility movement time (4.5%; p = 0.04), lateral jump distance (3%; p = 0.008), and lateral reactive strength index (4.4%; p = 0.03) compared with the nondominant leg. However, when the subjects were divided into faster and slower performers (based on their agility movement times) the movement time was significantly quicker in the faster group (n = 15; 12%; p < 0.001), but no differences in jump performance or kinetics were observed. Therefore, although the capacity for jumps to predict agility performance seems limited, factors involved in producing superior lateral jump performance in the dominant leg may also be associated with advantages in agility performance in that leg. However, because reactive strength as measured by unilateral jumps seems to play a limited role in reactive agility performance and other factors such as skill, balance, and coordination, and also cognitive and decision-making factors, are likely to be more important.
Inpatient Characteristics of the Child Admitted With Chronic Pain
Authors: Coffelt Thomas A. , Bauer Benjamin D. , Carroll Aaron E. 
Published: July 2013

OBJECTIVE:
To define the demographic, diagnostic, procedural, and episode of care characteristics for children admitted with chronic pain.

METHODS:
We used the Pediatric Health Information System database to obtain data on demographic characteristics, length of stay, readmission rates, diagnoses, and procedures for children admitted with chronic pain. Patients with sickle cell disease, cancer, burns, cerebral palsy, transplants, and ventilator-dependent children were excluded.

RESULTS:
A total of 3752 patients with chronic pain were identified from 2004 through 2010. Admissions increased by 831% over this time period. The mean age of these patients was 13.5 years, the most common race was white (79%), and female subjects outnumbered male subjects by 2.41 to 1. The most common admission and principal discharge diagnosis was abdominal pain; comorbid diagnoses were common, with a mean of 10 diagnoses per patient. In total, 65% of patients had a comorbid gastrointestinal diagnosis and 44% had a psychiatric diagnosis. The mean length of stay was 7.32 days, with an expected length of stay of 4.24 days; 12.5% were readmitted at least once within 1 year. They underwent a mean of 3.18 procedures per patient.

CONCLUSIONS:
The average child admitted with chronic pain is a teenaged female with a wide variety of comorbid conditions, many of which are gastrointestinal and psychiatric in nature. Admissions for chronic pain are rising and account for substantial resource utilization. Future studies should further characterize this population, with the overall objective of improving outcomes and optimizing cost-effective care.
Health Care Costs Associated With Child Maltreatment: Impact on Medicaid
Authors: Florence Curtis , Brown Derek S. , Fang Xiangming , Thompson Hope F. 
Published: July 2013

OBJECTIVE:
To estimate the increased Medicaid expenditures associated with child maltreatment.

METHODS:
Data on child maltreatment were collected from the National Survey of Child and Adolescent Well-Being, a nationally representative sample of cases investigated or assessed by local Child Protective Services agencies between October 1999 and December 2000. Medicaid claims data for 2000 to 2003 were obtained from the Medicaid Analytic Extract (MAX). Children from the National Survey of Child and Adolescent Well-Being who had Medicaid were matched to the MAX data by Social Security number or birthdate, gender, and zip code. Propensity score matching was used to select a comparison group from the MAX data. Two-part regression models were used to estimate the impact of child maltreatment on expenditures. Data with individual identifiers were obtained under confidentiality agreements with the collecting agencies.

RESULTS:
Children who were identified as maltreated or as being at risk of maltreatment incurred, on average, Medicaid expenditures that were &gt;$2600 higher per year compared with children not so identified. This finding accounted for ∼9% of all Medicaid expenditures for children.

CONCLUSIONS:
Child maltreatment imposes a substantial financial burden on the Medicaid system. These expenses could be partially offset by increased investment in child maltreatment prevention.
Patterns of Care and Persistence After Incident Elevated Blood Pressure
Authors: Daley Matthew F. , Sinaiko Alan R. , Reifler Liza M. , Tavel Heather M. , Glanz Jason M. , Margolis Karen L. , Parker Emily , Trower Nicole K. , Chandra Malini , Sherwood Nancy E. , Adams Kenneth , Kharbanda Elyse O. , Greenspan Louise C. , Lo Joan C. , O’Connor Patrick J. , Magid David J. 
Published: July 2013

BACKGROUND AND OBJECTIVE:Screening for hypertension in children occurs during routine care. When blood pressure (BP) is elevated in the hypertensive range, a repeat measurement within 1 to 2 weeks is recommended. The objective was to assess patterns of care after an incident elevated BP, including timing of repeat BP measurement and likelihood of persistently elevated BP.METHODS:This retrospective study was conducted in 3 health care organizations. All children aged 3 through 17 years with an incident elevated BP at an outpatient visit during 2007 through 2010 were identified. Within this group, we assessed the proportion who had a repeat BP measured within 1 month of their incident elevated BP and the proportion who subsequently met the definition of hypertension. Multivariate analyses were used to identify factors associated with follow-up BP within 1 month of initial elevated BP.RESULTS:Among 72 625 children and adolescents in the population, 6108 (8.4%) had an incident elevated BP during the study period. Among 6108 with an incident elevated BP, 20.9% had a repeat BP measured within 1 month. In multivariate analyses, having a follow-up BP within 1 month was not significantly more likely among individuals with obesity or stage 2 systolic elevation. Among 6108 individuals with an incident elevated BP, 84 (1.4%) had a second and third consecutive elevated BP within 12 months.CONCLUSIONS:Whereas &gt;8% of children and adolescents had an incident elevated BP, the great majority of BPs were not repeated within 1 month. However, relatively few individuals subsequently met the definition of hypertension.