Search

Additional file 5.. Supplementary Figure 2: Kaplan-Meier Comparison of Histologic Grade vs. AI-grade in Full Train and Validation Cohort.

Supplementary Material 5

Supplementary Material 4

Supplementary Material 1

Supplementary Material 3

Supplementary Material 6

Additional file 6. Supplementary Table 3: Demographics of Combined Training and Validation Oncotype Dataset.

Supplementary Material 2

Additional file 1. Methods.

Additional file 4. Supplementary Figure 1: MindAct Clinical Risk Models vs. PDxBr in training (A) vs validation (B).

Additional file 8. Supplemental Figure 3: AUC/C-index Oncotype Models.

Additional file 7. Supplementary Table 4A-D: Oncotype models.

Additional file 3. Supplementary Table 2: PDxBr Training and Validation: Image Feature Only Model.

Additional file 2. Supplementary Table 1: PDxBr Training and Validation: Clinical Feature only model.

BACKGROUND Acceptability of digital mental health interventions is a significant predictor of treatment-seeking behavior and engagement. However, acceptability has been conceptualized and operationalized in various ways, which decreases measurement precision and leads to heterogeneous conclusions about acceptability. Standardized self-report measures of acceptability have been developed, which have the potential to ameliorate these problems, but none have demonstrated evidence for validation among Black communities, which limits our understanding of attitudes toward these interventions among racially minoritized groups with well-documented barriers to mental health treatment. OBJECTIVE This study aims to examine the psychometric validity and reliability of one of the first and most widely used measures of acceptability, the Attitudes Towards Psychological Online Interventions Questionnaire, among a Black American sample. METHODS Participants (N=254) were recruited from a large southeastern university and the surrounding metropolitan area and completed the self-report measure via a web-based survey. A confirmatory factor analysis using mean and variance adjusted weighted least squares estimation was conducted to examine the validity of the underlying hierarchical 4-factor structure proposed by the original authors of the scale. An alternative, hierarchical 2-factor structure model and bifactor model were examined for comparative fit. RESULTS The findings indicated that the bifactor model demonstrated a superior fit (comparative fit index=0.96, Tucker-Lewis index=0.94, standardized root mean squared residual=0.03, and root mean square error of approximation=0.09) compared with both 2- and 4-factor hierarchical structure models. CONCLUSIONS The findings suggest that, within a Black American sample, there may be greater utility in interpreting the Attitudes Towards Psychological Online Interventions Questionnaire subscales as attitudinal constructs that are distinct from the global acceptability factor. The theoretical and practical implications for culturally responsive measurements were explored.

This thesis investigates whether the information contained in a Vitech Genesys model can retain its informational accuracy after conversion into a Dassault Systemes’ Magic System of Systems Architect (MSOSA) model. The thesis uses a sample system model in Vitech that implements the system definition language (SDL) and converts it to MSOSA, which uses the systems modeling language (SysML). The study reviewed conversion methods available to the user and converted a Genesys model to an MSOSA model using the only available method, Excel. The study then assessed the converted model and outlined any post-migration remediation. The results of this thesis demonstrate that the currently available methods are feasible but inefficient, as only 34% of the entities and 9% of the relationships transferred successfully during the experiment. Genesys can output tabular data that represents system model entities and relationships; however, the MSOSA import function was unable to correctly import entities that had one-to-many relationships with other entities. Consequently, the user must perform manual manipulation during the conversion process. Furthermore, ontological differences between the tools prevented the complete import of behavioral data, since many SDL entities map to more than one SysML entity. Based on the results, this thesis recommends pursuing an extensible markup language–based software solution for Genesys and MSOSA and developing a formal Navy and Marine Corps ontology. Civilian, Department of the Navy Approved for public release. Distribution is unlimited.

The interaction of an intense laser with a solid foil target can drive $$\sim$$ ∼ TV/m electric fields, accelerating ions to MeV energies. In this study, we experimentally observe that structured targets can dramatically enhance proton acceleration in the target normal sheath acceleration regime. At the Texas Petawatt Laser facility, we compared proton acceleration from a $$1\, {\upmu }\hbox {m}$$ 1 μ m flat Ag foil, to a fixed microtube structure 3D printed on the front side of the same foil type. A pulse length (140–450 fs) and intensity ((4–10) $$\times 10^{20}$$ × 10 20 W/cm$$^2$$ 2 ) study found an optimum laser configuration (140 fs, 4 $$\times 10^{20}$$ × 10 20 W/cm$$^2$$ 2 ), in which microtube targets increase the proton cutoff energy by 50% and the yield of highly energetic protons ($$>10$$ > 10 MeV) by a factor of 8$$\times$$ × . When the laser intensity reaches $$10^{21}$$ 10 21 W/cm$$^2$$ 2 , the prepulse shutters the microtubes with an overcritical plasma, damping their performance. 2D particle-in-cell simulations are performed, with and without the preplasma profile imported, to better understand the coupling of laser energy to the microtube targets. The simulations are in qualitative agreement with the experimental results, and show that the prepulse is necessary to account for when the laser intensity is sufficiently high.

Background Acceptability of digital mental health interventions is a significant predictor of treatment-seeking behavior and engagement. However, acceptability has been conceptualized and operationalized in various ways, which decreases measurement precision and leads to heterogeneous conclusions about acceptability. Standardized self-report measures of acceptability have been developed, which have the potential to ameliorate these problems, but none have demonstrated evidence for validation among Black communities, which limits our understanding of attitudes toward these interventions among racially minoritized groups with well-documented barriers to mental health treatment. Objective This study aims to examine the psychometric validity and reliability of one of the first and most widely used measures of acceptability, the Attitudes Towards Psychological Online Interventions Questionnaire, among a Black American sample. Methods Participants (N=254) were recruited from a large southeastern university and the surrounding metropolitan area and completed the self-report measure via a web-based survey. A confirmatory factor analysis using mean and variance adjusted weighted least squares estimation was conducted to examine the validity of the underlying hierarchical 4-factor structure proposed by the original authors of the scale. An alternative, hierarchical 2-factor structure model and bifactor model were examined for comparative fit. Results The findings indicated that the bifactor model demonstrated a superior fit (comparative fit index=0.96, Tucker-Lewis index=0.94, standardized root mean squared residual=0.03, and root mean square error of approximation=0.09) compared with both 2- and 4-factor hierarchical structure models. Conclusions The findings suggest that, within a Black American sample, there may be greater utility in interpreting the Attitudes Towards Psychological Online Interventions Questionnaire subscales as attitudinal constructs that are distinct from the global acceptability factor. The theoretical and practical implications for culturally responsive measurements were explored.

In an electron wakefield accelerator, an intense laser pulse or charged particle beam excites plasma waves. Under proper conditions, electrons from the background plasma are trapped in the plasma wave and accelerated to ultra-relativistic velocities. We present recent results from a proof-of-principle wakefield acceleration experiment that reveal a unique synergy between a laser-driven and particle-driven accelerator: a high-charge laser-wakefield accelerated electron bunch can drive its own wakefield while simultaneously drawing energy from the laser pulse via direct laser acceleration. This process continues to accelerate electrons beyond the usual decelerating phase of the wakefield, thus reaching much higher energies. We find that the 10-centimeter-long nanoparticle-assisted wakefield accelerator can generate 340 pC, 10.4+-0.6 GeV electron bunches with 3.4 GeV RMS convolved energy spread and 0.9 mrad RMS divergence. It can also produce bunches with lower energy, a few percent energy spread, and a higher charge. This synergistic mechanism and the simplicity of the experimental setup represent a step closer to compact tabletop particle accelerators suitable for applications requiring high charge at high energies, such as free electron lasers or radiation sources producing muon beams.

Methods

Additional file 1: Figure S1. Subcellular localization of ABC. Magnified images demonstrating subcellular localization of ABC.

Prostate cancer; Systems pathology; Wnt/β-catenin pathway Càncer de pròstata; Patologia de sistemes; Via Wnt/β-catenina Cáncer de próstata; Patología de sistemas; Vía Wnt/β-catenina OBJECTIVES: To apply a systems pathology-based approach to the quantification of nuclear Active β-catenin and human leukocyte antigen class I, and assess the biomarker involvement in a cohort of prostate tumor patients. RESULTS: The systems pathology approach applied allows a precise quantification of the marker expression in the different cell compartments as well as the determination of the areas that coexpress two markers. Our data shows that the accumulation of β-catenin in the nuclear compartment is significantly decreased in the adjacent normal areas when compared to tumor of the same patients (p

Figure S1. Images of the changes in the physical traits (normalised z-score values) associated with each CNV and their 95% confidence intervals (95%CI). (XLSX 335 kb) (DOCX 1040 kb)

Figures S1-S8. All supplementary figures. (PDF 1212 kb)

A quantitative ethogram was developed for the Zebra finch, using one-zero focal animal sampling on an ethologically comprehensive checklist of 52 behavioral items, and was assessed for both interobserver reliability and construct validity. Interobserver reliabilities were highly acceptable (an eta-squared of, 923 for aggregation periods of 5 minutes). Nine common factors (Singing & Parenting, Social Proximity, Social Contact, Social Submission, Social Aggression, Sex & Violence, Object Handling, Surface Foraging, and General Activity) produced highly acceptable convergent validities (high factor loadings for most behavioral items) and discriminant validities (low factor intercorrelations). Applying the quantitative methods of psychometrics thus permits the verification of ethological theory and the testing of diverse hypotheses with a high degree of sophistication.

Supplementary Material: Supplementary Results, Supplementary Methods, Supplementary Table legends. (DOCX 67 kb)

Comparison of weighed correlations of log2ratio (a, data from Additional file 7: Figure S4) and log2mBAF (b, data from Additional file 8: Figure S5) for assays on FFPE- versus frozen-derived tumor DNA material. D statistic and p-value from 2-sided KS test are shown for FFPE- versus frozen-derived correlation distributions (see "Methods" for details on KS test). (PPTX 76 kb)

Detailed workflow of an integrative genomic approach in personalized cancer therapy. (PPTX 303 kb)

Correlation of somatic CNA heterozygosity change (median â log2mBAFâ segment statistic from saasCNV of tumor with respect to normal) between WES and array data. The same partitions are used as in Additional file 7: Figure S4, and weighed correlation in the lower right corner is also computed in the same way. (PPTX 981 kb)

Distribution of somatic mutation allelic fractions in patient P0011, by mutation type. (PPTX 191 kb)

A decision tree approach to predict drug response based on genetic alterations. (PPTX 96 kb)

A decision tree approach to predict drug response based on genetic alterations. (PPTX 96 kb)

Sanger sequencing validation results of novel somatic EGFR mutation p.D587H (chr7:55233009G>C) in patient P0015. Sanger sequencing was carried out on normal and tumor DNA from this patient using forward and reverse primers (Beckman Coulter Genomics, Danvers, Massachusetts). Traces shown are as displayed by 4Peaks visualization software for Mac OS X ( http://nucleobytes.com/4peaks ). Two replicate sequencing reactions were carried out for each primer and sample combination, yielding the same result (second replicate not shown). Base numbering shown is relative to priming site. The allelic fraction of p.D587H in tumor was 19.4 % (387/1998 reads have variant) in targeted panel sequencing, explaining the relatively small size of the Sanger peak for the alternate allele. (PPTX 240 kb)

A scatter plot of CCND1 gene expression versus log2 copy number ratio (tumor/normal). Each dot represents a patient tumor sample. Tumor types are color-coded. The two breast cancer patients where we reported CCND1 amplification are P0002 and P0040. (PPTX 112 kb)

Correlation of somatic CNA fold-change (median “log2ratio” segment statistic from saasCNV of tumor with respect to normal) between WES and array data. The genome was split into non-overlapping partitions such that each partition begins and ends on a CNA segment break from either assay, but no CNA segment breaks occur inside any partition (“partition” feature of “bedops” software tool v2.4.14, https://github.com/bedops/bedops ). Thus, each partition overlaps exactly one segment from WES data and exactly one segment from array data. Each point is a partition, with plotted values taken from the pair of segments that overlap it. Lower right corner shows the weighed (by partition length) Pearson correlation between WES- and array-derived log2ratio values for partitions, computed using the “corr” function from R (v3.2.1) package “boot” (v1.3-17). “FFPE” and “frozen” in all plots refers to tissue source of tumor DNA. (PPTX 1114 kb)

Comparison of weighed correlations of log2ratio (a, data from Additional file 7: Figure S4) and log2mBAF (b, data from Additional file 8: Figure S5) for assays on FFPE- versus frozen-derived tumor DNA material. D statistic and p-value from 2-sided KS test are shown for FFPE- versus frozen-derived correlation distributions (see "Methods" for details on KS test). (PPTX 76 kb)

Correlation of somatic CNA fold-change (median “log2ratio” segment statistic from saasCNV of tumor with respect to normal) between WES and array data. The genome was split into non-overlapping partitions such that each partition begins and ends on a CNA segment break from either assay, but no CNA segment breaks occur inside any partition (“partition” feature of “bedops” software tool v2.4.14, https://github.com/bedops/bedops ). Thus, each partition overlaps exactly one segment from WES data and exactly one segment from array data. Each point is a partition, with plotted values taken from the pair of segments that overlap it. Lower right corner shows the weighed (by partition length) Pearson correlation between WES- and array-derived log2ratio values for partitions, computed using the “corr” function from R (v3.2.1) package “boot” (v1.3-17). “FFPE” and “frozen” in all plots refers to tissue source of tumor DNA. (PPTX 1114 kb)

Correlation of somatic CNA heterozygosity change (median â log2mBAFâ segment statistic from saasCNV of tumor with respect to normal) between WES and array data. The same partitions are used as in Additional file 7: Figure S4, and weighed correlation in the lower right corner is also computed in the same way. (PPTX 981 kb)

Example PDF document of genomic findings returned to patients and their treating physicians in this study. Each section of this document was taken from an actual returned document, but to protect patient privacy, different sections were taken from different patient documents and information identifying the patient and specimens was removed. (PDF 367 kb)

Detailed workflow of an integrative genomic approach in personalized cancer therapy. (PPTX 303 kb)

This paper synthesizes and extends the results of urban land market studies carried out in three Brazilian cities – Brasília, Curitiba and Recife. The purpose of the studies is to empirically assess the performance of urban land markets in different cities and to gauge the feasibility of applying the Land Market Assessment methodology in Brazil. The project involved the collaboration of several organizations: The World Bank, Instituto de Pesquisa Econômica Aplicada (IPEA), Secretaria de Estado de Desenvolvimento Urbano e Habitação (SEDUH), Instituto de Pesquisa e Planejamento Urbano de Curitiba (IPPUC), and Fundação de Desenvolvimento Municipal (FIDEM). The field research was carried out in 2003. Este trabalho sintetiza e expande os resultados dos estudos sobre mercados de terras realizados em três cidades brasileiras – Brasília, Curitiba e Recife. O objetivo desses estudos era avaliar empiricamente a performance dos mercados de terras urbanas em diferentes cidades e verificar a viabilidade de se aplicar a “Metodologia de Avaliação do Mercado de Terras” para o Brasil. O projeto envolveu a colaboração de diversas instituições: Banco Mundial, Instituto de Pesquisa Econômica Aplicada (IPEA), Secretaria de Estado de Desenvolvimento Urbano e Habitação (SEDUH), Instituto de Pesquisa e Planejamento Urbano de Curitiba (IPPUC), e Fundação de Desenvolvimento Municipal (FIDEM). O trabalho de campo foi realizado em 2003.

We modify a classical construction of Bousfield and Kan to define the Adams tower of a simplicial nonunital commutative algebra over a field k. We relate this construction to Radulescu-Banu's cosimplicial resolution, and prove that all connected simplicial algebras are complete with respect to Andr��-Quillen homology. This is a convergence result for the unstable Adams spectral sequence for commutative algebras over k., 10 pages

We present data for relativistic hot electron production by the Texas Petawatt Laser irradiating solid Au targets with thickness between 1 and 4 mm. The experiment was performed at the short focus target chamber TC1 in July 2011, with laser energies around 50 J. We measured hot electron spectra out to 50 MeV which show a narrow peak around 10 - 20 MeV plus high energy exponential tail. The hot electron spectral shape differs from those reported for other PW lasers. We did not observe direct evidence of positron production above background., Comment: HEDLA 2012 Conference Paper. submitted to HEDP. revised 1/28/2013. 18 pages. 10 figures