A Framework for Catering Software Complexity Issues Using Architectural Patterns

In high-performance scientific software development, the emphasis is often on short time to first solution. Even when the development of new components mostly reuses existing components or libraries and only small amounts of new code must be created, dealing with the component glue code and software build processes to obtain complete applications is still tedious and error-prone. Component-based software meant to reduce complexity at the application level increases complexity to the extent that the user must learn and remember the interfaces and conventions of the component model itself. To address these needs, we introduce Bocca, the first tool to enable application developers to perform rapid component prototyping while maintaining robust software-engineering practices suitable to HPC environments. Bocca provides project management and a comprehensive build environment for creating and managing applications composed of Common Component Architecture components. Of critical importance for high-performance computing (HPC) applications, Bocca is designed to operate in a language-agnostic way, simultaneously handling components written in any of the languages commonly used in scientific applications: C, C++, Fortran, Python and Java. Bocca automates the tasks related to the component glue code, freeing the user to focus on the scientific aspects of the application. Bocca embraces the philosophy pioneered by Ruby on Rails for web applications: start with something that works, and evolve it to the user's purpose.

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Salivary Adenocarcinoma, Not Otherwise Specified: A Collection of Orphans

Archives of Pathology & Laboratory Medicine ◽

10.5858/2004-128-1385-sanosa ◽

2004 ◽

Vol 128 (12) ◽

pp. 1385-1394 ◽

Cited By ~ 2

Author(s):

Jiang Li ◽

Beverly Yiyao Wang ◽

Magalie Nelson ◽

Lei Li ◽

Yuhua Hu ◽

...

Keyword(s):

New York ◽

Parotid Gland ◽

Medical Center ◽

Cell Types ◽

Carcinoma Ex Pleomorphic Adenoma ◽

High Grade ◽

Not Otherwise Specified ◽

Architectural Patterns ◽

Social Security Death Index ◽

Disease Free

Abstract Context.—Salivary adenocarcinoma, not otherwise specified, refers to gland-forming malignancies that do not satisfy the diagnostic requirements of other “named” malignancies. Objective.—To review the features of 11 patients with salivary adenocarcinoma, not otherwise specified. To also compare the diagnostic frequencies of 2 databases, one from the Mount Sinai Medical Center (New York, NY), the other from the Shanghai Ninth People's Hospital (Shanghai, People's Republic of China). Design.—Pathology files were searched to establish a database of salivary tumors. All available hematoxylin-eosin– stained slides from the resection specimens diagnosed as either adenocarcinoma, not otherwise specified, or with vague or unusual diagnoses (eg, probable carcinoma-ex-pleomorphic adenoma) were pulled from our files and reexamined. Dates of death were confirmed with the Social Security Death Index. Results.—We identified 11 patients with salivary adenocarcinoma, not otherwise specified, ranging in age from 49 to 80 years (median, 67 years), with a male preponderance. The parotid gland was the most common site of tumor origin. Ten of these tumors were high grade, and 1 was intermediate grade. Two patients were diagnosed at stage II, while the remaining patients were diagnosed at stage III or IV. Histologically, all tumors were invasive, with variable glandular differentiation and diverse architectural patterns. The diverse cytologic tumor cell types included cuboidal, columnar, epithelioid, polygonal, oncocytoid, clear, melanoma-like, mucinous, sebaceous, and plasmacytoid. Four patients died after 4 to 27 months (mean, 15 months), 1 patient is alive with disease at 12 months, 1 patient is disease-free at 14 years, and 3 patients remain disease-free after short follow-ups (10, 12, and 12 months). One patient had surgery just recently, and the remaining patient had no follow-up. Conclusions.—Salivary adenocarcinoma, not otherwise specified, is an aggressive, high-grade malignancy, with a predisposition for the parotid gland. It is characterized by cytologic and architectural diversity and an invasive growth pattern.

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The novel approach to distinguish primary multiple lung adenocarcinomas from intrapulmonary metastases by next generation sequencing in Chinese patients.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e20506 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e20506-e20506

Author(s):

Lin Li ◽

Naiquan Mao ◽

Yingcheng Lyu ◽

Huayue Lin ◽

Kefeng Wang ◽

...

Keyword(s):

Clinical Practice ◽

Next Generation Sequencing ◽

Chinese Patients ◽

Comparative Genomic ◽

Genomic Profiling ◽

Next Generation ◽

Architectural Patterns ◽

Chinese Cohort ◽

Lung Adenocarcinomas ◽

Generation Sequencing

e20506 Background: Differentiation of multiple primary lung cancer (MPLC) from intrapulmonary metastasis (IPM) is critical to determine clinical stage. Although clinicopathological features could provide certain evidences, it’s still challenging to identify the tumor malignancy accurately. In General, standard histopathologic approach is adequate in most cases, but has notable limitations in the recognition of IPMs. Herein, we propose an integrated molecular algorithm to facilitate MPLCs and IPMs diagnosis in the clinical practice. Methods: 40 Chinese patients with lung adenocarcinomas were enrolled in the study, 84 tumor samples were collected for next-generation sequencing. Somatic alterations with variant allele fraction (VAF) ≥1% were taken into account for molecular algorithm. A genomic database of 2,471 Chinese lung adenocarcinomas (LUAD) was used to calculate odds of coincidental occurrence, prevalence of individual mutation prevalence. Tumor relatedness diagnosed by histopathologic assessment was contrasted with comparative genomic profiling by subsequent NGS. Moreover, the performance of molecular algorithm prediction was evaluated as well. Results: Firstly, we compared the performance of comprehensive next-generation sequencing (NGS) with standard histopathologic approaches for distinguishing NSCLC subtypes in clinical practice. The genomic profiling was described as following: EGFR alterations occurred more frequently in MPLCs compared to IPMs (77.1% vs 50.0%, P<0.05). Further analysis showed that TP53 alterations occurred less frequently in MPLCs compared to large Chinese cohort (22.9% vs 51.0%, P<0.05). TP53 alterations occurred less frequently in MPLCs compared to large Chinese cohort (P<0.05). The classifications based on the three different methodologies mentioned above were compared. Molecular algorithm prediction was concordant with NGS in 21 cases (52.5%), particularly in the prediction of MPLC. Retrospective review highlighted several histologic challenges, including morphologic progression in some IPMs. For the five undetermined cases, two showed differences in architectural patterns, and remained cases have nodules presented as adenocarcinoma in situ, or minimally invasive adenocarcinoma. Of 28 MPLC cases defined by NGS, 25 cases had unique somatic mutations per pair Based on calculation from the prevalence of EGFR L858R mutation (27%) in large Chinese cohort, the odds of coincidental occurrence of the mutation in two unrelated tumors was 7.3%. Taking together, EGFR alterations occurred more frequently in MPLCs compared to IPMs (77.1% vs 50.0%, P<0.05). Molecular algorithm prediction was concordant with NGS in 21 cases (52.5%). Conclusions: Our results support broad panel NGS to assist differential diagnosis to assist approach in clinical practice. It is necessary to conduct large clinical study to establish comprehensive algorithm models to assist diagnosis and predict clinical outcome.

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