bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical activity in recurrent colon cancer: Cancer and Leukemia Group B/SWOG 80702 (Alliance)
Authors: Brown Justin C. , Ma Chao , Shi Qian , Zemla Tyler , Couture Felix , Kuebler Philip , Kumar Pankaj , Tan Benjamin , Krishnamurthi Smitha , Chang Victor , Goldberg Richard M. , Venook Alan P. , Blanke Charles D. , O’Reilly Eileen M. , Shields Anthony F. , Meyerhardt Jeffrey A. 
Published: August 2023

AbstractBackgroundOne in three patients with stage III colon cancer will experience tumor recurrence. It is uncertain whether physical activity during and after postoperative chemotherapy for stage III colon cancer improves overall survival after tumor recurrence.MethodsA prospective cohort study nested within a randomized multicenter trial of patients initially diagnosed with stage III colon cancer who experienced tumor recurrence (N = 399) was conducted. Postoperative physical activity before tumor recurrence was measured. Physical activity energy expenditure was quantified via metabolic equivalent task hours per week (MET‐h/week). The primary end point was overall survival after tumor recurrence. Multivariable flexible parametric survival models estimated relative and absolute effects with two‐sided hypothesis tests.ResultsCompared with patients expending <3.0 MET‐h/week of physical activity (comparable to <1.0 h/week of brisk walking), patients with ≥18.0 MET‐h/week of physical activity (comparable to 6 h/week of brisk walking) had a 33% relative improvement in overall survival time after tumor recurrence (hazard ratio, 0.67; 95% CI, 0.42–0.96). The overall survival rate at 3 years after tumor recurrence was 61.3% (95% CI, 51.8%–69.2%) with <3.0 MET‐h/week of physical activity and 72.2% (95% CI, 63.1%–79.6%) with ≥18 MET‐h/week of physical activity (risk difference, 10.9 percentage points; 95% CI, 1.2–20.8 percentage points).ConclusionsHigher postoperative physical activity is associated with improved overall survival after tumor recurrence in patients initially diagnosed with stage III colon cancer. These data may be relevant to patients who, despite optimal postoperative medical therapy, have a high risk of tumor recurrence.
A framework to test interval arithmetic libraries and their IEEE 1788‐2015 compliance
Authors: Benet Luis , Ferranti Luca , Revol Nathalie 
Published: August 2023

SummaryAs developers of libraries implementing interval arithmetic, we faced the same difficulties when it comes to testing our libraries. What must be tested? How can we devise relevant test cases for unit testing? How can we ensure a high (and possibly 100%) test coverage? Before considering these questions, we briefly recall the main features of interval arithmetic and of the IEEE 1788‐2015 standard for interval arithmetic. After listing the different aspects that, in our opinion, must be tested, we contribute a first step towards offering a test suite for an interval arithmetic library. First we define a format that enables the exchange of test cases, so that they can be read and tried easily. Then we offer a first set of test cases, for a selected set of mathematical functions. Next, we examine how the Julia interval arithmetic library, IntervalArithmetic.jl, actually performs to these tests. As this is an ongoing work, we list extra tests that we deem important to perform.
Ambient Pressure X‐ray Photoelectron Spectroscopy Study of Oxidation Phase Transitions on Cu(111) and Cu(110)
Authors: Shi Shucheng , Han Yong , Yang Tian , Zang Yijing , Zhang Hui , Li Yimin , Liu Zhi 
Published: August 2023

AbstractThe surface structure effect on the oxidation of Cu has been investigated by performing ambient‐pressure X‐ray photoelectron spectroscopy (APXPS) on Cu(111) and Cu(110) surfaces under oxygen pressures ranging from 10−8 to 1 mbar and temperatures from 300 to 750 K. The APXPS results show a subsequential phase transition from chemisorbed O/Cu overlayer to Cu2O and then to CuO on both surfaces. For a given temperature, the oxygen pressure needed to induce initial formation of Cu2O on Cu(110) is about two orders of magnitude greater than that on Cu(111), which is in contrast with the facile formation of O/Cu overlayer on clean Cu(110). The depth profile measurements during the initial stage of Cu2O formation indicate the distinct growth modes of Cu2O on the two surface orientations. We attribute these prominent effects of surface structure to the disparities in the kinetic processes, such as the dissociation and surface/bulk diffusion over O/Cu overlayers. Our findings provide new insights into the kinetics‐controlled process of Cu oxidation by oxygen.
Impaired resolution of blood transcriptomes through tuberculosis treatment with diabetes comorbidity
Authors: Eckold Clare , van Doorn Cassandra L. R. , Ruslami Rovina , Ronacher Katharina , Riza Anca‐Lelia , van Veen Suzanne , Lee Ji‐Sook , Kumar Vinod , Kerry‐Barnard Sarah , Malherbe Stephanus T. , Kleynhans Léanie , Stanley Kim , Joosten Simone A. , Critchley Julia A , Hill Philip C. , van Crevel Reinout , Wijmenga Cisca , Haks Mariëlle C. , Ioana Mihai , Alisjahbana Bachti , Walzl Gerhard , Ottenhoff Tom H. M. , Dockrell Hazel M. , Vianello Eleonora , Cliff Jacqueline M. ,   the TANDEM Consortium$
Published: August 2023

AbstractBackgroundPeople with diabetes are more likely to develop tuberculosis (TB) and to have poor TB‐treatment outcomes than those without. We previously showed that blood transcriptomes in people with TB‐diabetes (TB‐DM) co‐morbidity have excessive inflammatory and reduced interferon responses at diagnosis. It is unknown whether this persists through treatment and contributes to the adverse outcomes.MethodsPulmonary TB patients recruited in South Africa, Indonesia and Romania were classified as having TB‐DM, TB with prediabetes, TB‐related hyperglycaemia or TB‐only, based on glycated haemoglobin concentration at TB diagnosis and after 6 months of TB treatment. Gene expression in blood at diagnosis and intervals throughout treatment was measured by unbiased RNA‐Seq and targeted Multiplex Ligation‐dependent Probe Amplification. Transcriptomic data were analysed by longitudinal mixed‐model regression to identify whether genes were differentially expressed between clinical groups through time. Predictive models of TB‐treatment response across groups were developed and cross‐tested.ResultsGene expression differed between TB and TB‐DM patients at diagnosis and was modulated by TB treatment in all clinical groups but to different extents, such that differences remained in TB‐DM relative to TB‐only throughout. Expression of some genes increased through TB treatment, whereas others decreased: some were persistently more highly expressed in TB‐DM and others in TB‐only patients. Genes involved in innate immune responses, anti‐microbial immunity and inflammation were significantly upregulated in people with TB‐DM throughout treatment. The overall pattern of change was similar across clinical groups irrespective of diabetes status, permitting models predictive of TB treatment to be developed.ConclusionsExacerbated transcriptome changes in TB‐DM take longer to resolve during TB treatment, meaning they remain different from those in uncomplicated TB after treatment completion. This may indicate a prolonged inflammatory response in TB‐DM, requiring prolonged treatment or host‐directed therapy for complete cure. Development of transcriptome‐based biomarker signatures of TB‐treatment response should include people with diabetes for use across populations.
Complex System Reliability Analysis using a Model‐Based Shared Systems Simulation
Authors: Ross Jeremy 
Published: August 2023

AbstractThe continued growth of system complexity is challenging traditional qualitative, heuristics‐based approaches to architecting system emergence. As these emergent attributes are products of the architecture and established early in the system development lifecycle, where ambiguity is most pronounced, a shift to a model‐based approach is viewed as essential to understanding system interdependencies and the impacts of tradeoff decisions. This paper discusses how model‐based systems engineering methods and a coupled architecture‐simulation can be used to model system reliability. Employing a probabilistic model of system element failure, the coupled simulation is shown to predict system reliability for various architecture configurations early in the system design process. The advantages this quantitative system performance assessment provide to stakeholder decision‐making are reviewed, and the simulation model is extended to demonstrate how the complexity‐resilience tradeoff can impact system reliability.
A Social Enterprise Approach for Parenting in the Japanese Society
Authors: Hoffmann Raquel , Bori Ana Maria 
Published: August 2023

AbstractJapan has one of the world's most family‐friendly parental leave systems. However, a government survey conducted in 2020 found that less than 13 percent of male respondents exercised their right to take paternity leave, leaving the burden of child‐rearing to the mothers. Although Japan's Government has made parental leave a top priority, the effects on society are still modest. Work culture, labor regulation, and gender bias are some of the challenges in the imbalanced parenting problem. Solving a society‐related issue requires a holistic approach that considers complex multidimensional aspects. This paper uses the Unified Architecture Framework to model a Social Enterprise by investigating the Japanese parenting problem. We use the challenges and drivers identified in the Japanese case to explore viewpoints that place the human aspect of parenting together with business and policymaking. Lastly, we introduce the next parenting phase considering principles from Society 5.0.
Proposing a DEI Strategy for INCOSE Based on the Diversity and Inclusion Progression Framework 2.0
Authors: Squires Alice F. , Harding Alan 
Published: August 2023

AbstractInstitutions that embody diversity, equity, and inclusion (DEI) as a key value and key objective of the organization better understand the positive and negative impacts of strategic decisions on the communities they serve. This paper describes a process for developing a DEI strategy for the International Council on Systems Engineering (INCOSE) based on the Royal Academy of Engineering and Science Council's Diversity and Inclusion Progression Framework 2.0. The paper investigates four of the eleven areas of the framework, benchmarking INCOSE's progress and developing a set of initiatives to support INCOSE's DEI progression. Based on this paper's research, and confirmed by dozens of other societies in similar exercises, DEI progression requires careful planning and proactive steps, as part of a comprehensive strategy consistently implemented over time. But most of all, success in transforming into a diverse, equitable, and inclusive institution requires the passion and motivation of the organizational members to change.
MBFHA: A Framework for Model‐Based Functional Hazard Assessment for Aircraft Systems
Authors: Lai Kimberly , Robert Thomas , Shindman David , Olechowski Alison 
Published: August 2023

AbstractTo address growing system complexity in the aerospace industry, a Model‐Based Systems Engineering (MBSE) approach has been increasingly adopted for the development of aircraft systems. This calls for a corresponding approach for performing safety assessment to maintain consistency between the system and safety domains. One of the key safety assessment processes for aircraft development is the Functional Hazard Assessment (FHA). The purpose of this paper is to build upon previously published works and introduce the MBFHA framework which describes the language, method, and tool needed for implementing a model‐based approach to performing FHA and integrating it into MBSE activities. A customised FHA profile is introduced for the modelling language, an overall workflow along with processes for FHA report and safety requirements generation is presented for the method, and a list of tool constraints is provided. A proof‐of‐concept is subsequently presented using safety data for the landing gear extension and retraction system of a generic business aircraft.
Physics‐Informed Gas Lifting Oil Well Modelling using Neural Ordinary Differential Equations
Authors: Ban Zhe , Pfeiffer Carlos 
Published: August 2023

AbstractModelling of oil well systems is important for a wide range of petroleum scientific and oil industrial processes. Considering the uncertainty of the measurements and the demand for empirical knowledge, a purely first‐principle model and a black‐box model based on data are not sufficient for accurately describing an oil well system. Thus, there is a growing body of literature that recognizes the importance of data‐driven methods combined with physical knowledge. However, the application of combination methods for dynamic nonlinear systems is still challenging. In this work, we demonstrate the application of a physics‐informed neural network to a gas lifting oil well system. The neural ordinary differential equation is the main tool for the modeling and the simulation is examined in Julia programming language. The advantage and drawbacks of the physics‐informed data‐driven method are analyzed.
Phased Demonstrations of MBSE in Small Demonstration Satellite Series: Development of System Model and Environment for Full Application of MBSE
Authors: Wada Atsushi , Komatsu Yutaka , Tate Daiki , Katsumata Haruhi , Shirasawa Yoji , Fujimoto Keiichiro , Kakehashi Yuya , Nakamura Kengo , Kaneko Yutaka , Suzuki Shinichi , Iwata Takanori 
Published: August 2023

AbstractThe Japan Aerospace Exploration Agency (JAXA) has been implementing phased and progressive demonstrations of the Model‐Based Systems Engineering (MBSE) applications, using small demonstration satellite series, so called the Rapid Innovative Payload Demonstration Satellite (RAISE), as a demonstration pre‐cursor. The purpose of the activity is to establish a practical methodology of the MBSE application to satellite projects, to promote its practices, and to infuse MBSE to the Japanese space community. These RAISE satellites are 100kg‐class flagships in the Innovative Satellite Technology Demonstration Program, which provides on‐orbit demonstration opportunities for new technologies and key‐components. This paper presents the phased demonstration strategy, an overall approach, and the technology development of a system model being built for the full application of MBSE to RAISE‐4. For the technology development, the paper covers framework, modeling scope, system model building, system model collaboration with analysis/simulation tool, introduction of design rationale and concerns, information sharing through OpenMBEE, for our full application of MBSE.
Value‐driven Optimization Campaign Addressing Manufacturing, Supply Chain and Overall Aircraft Design Domains in the Early Development Stage
Authors: Merola Umberto , Donelli Giuseppa , Lefebvre Thierry , Bartoli Nathalie , Mello João M.G.D. , Odaguil Felipe I.K. , van der Laan Ton , Björn Nagel 
Published: August 2023

AbstractIn the last decades, several studies demonstrate how the integration of manufacturing and supply chain in the early design phase brings significant advantages to industries. Within the European Project (AGILE 4.0, 2022), a value‐driven methodology concurrently coupling design, manufacturing and supply chain has been developed. This study aims at addressing a new challenge: the identification of non‐dominated solutions simultaneously accounting for manufacturing, design and supply chain variables. For this purpose, an optimization design campaign has been addressed in this research activity and the main results are‐here presented.
A Systems View of Career Development for Systems Engineering Leadership
Authors: Gupta Stueti , Keim Jonathan , Kennedy Grace , Opland Brandi , Sigterman Yoeri , Wingate Brandi 
Published: August 2023

AbstractSE leaders' career development journeys are primarily driven by their experiences that shape their capability, qualities, and perspective; however, the pathways that individuals take are not only broad and varied, but also equally affected by personal life decisions and external factors. This paper describes a two‐fold study that aimed to: a) provide insight into commonalities in the career journeys of SE leaders, and b) ascertain how key areas affect career development. Five key areas were explored: education, technical experience, soft skills experience, job satisfaction and work‐life balance. A mixed and multi‐method approach was taken, gathering data from sixty‐one participants through interviews, surveys and facilitated workshop. The study found that although there was no ‘blueprint’ that yields successful SE leadership, there were themes/trends that were common. An influence model was developed to highlight these trends in the form of the key areas, factors affecting them, and the interrelationships between them.
An Empirical Survey on the Prevalence of Technical Debt in Systems Engineering
Authors: Kleinwaks Howard , Batchelor Ann , Bradley Thomas 
Published: August 2023

AbstractThe technical debt metaphor is used within software engineering to describe technical concessions that produce a short‐term benefit but result in long‐term consequences. Systems engineering is subject to these concessions, yet there is a limited amount of research associating technical debt with systems engineering. This paper provides the results of an empirical survey investigating the prevalence of technical debt in systems engineering, including the occurrence of technical debt, the use of the metaphor, and the distribution of technical debt within the systems engineering lifecycle. The results of the survey show that while technical debt is common in systems engineering and occurs throughout the lifecycle, the metaphor and terminology of technical debt is not consistently applied. These results emphasize the need to enrich the usage of the technical debt metaphor within systems engineering to enable the management of technical debt and to reduce the risk of technical bankruptcy.
From Requirements to Product: an MBSE Approach for the Digitalization of the Aircraft Design Process
Authors: Bruggeman Anne‐Liza M.R.M. , La Rocca Gianfranco 
Published: August 2023

AbstractDuring the aircraft conceptual design phase, many different design options need to be explored and compared in a short time frame. To speed up this process, efforts have been made in the past decades to digitalize parts of the design process, with a focus on the automation of the repetitive and non‐creative tasks inherent to the iterative design process. Whilst many of the newly developed methodologies focus on specific parts of the design process, a holistic model‐based design framework, incorporating the latest design technology developments, is lacking. To fill this gap, this paper presents the latest version of the Design and Engineering Engine (DEE) framework, originally proposed in the early 2000s and progressively matured through the experience of several international research collaborations. The DEE enables the setup and execution of Multidisciplinary Design Analysis and Optimization (MDAO) problems for aircraft (sub)systems, leveraging the automated, rule‐based modeling capabilities offered by Knowledge‐Based Engineering (KBE) and recent developments in the automatic formulation and integration of MDAO workflows. While the traditional MDAO process focuses on a given product architecture, the DEE allows also architectural design studies and makes use of Model‐Based Systems Engineering (MBSE) principles to address the whole design process, from requirements modeling up to the automatic verification of the requirements. In practice, the DEE provides a single conceptual framework or template from which specific design framework instances can be formulated and executed, according to the user's needs. This paper describes the DEE architecture and its implementation concepts. Furthermore, it demonstrates the application of the DEE template to four different scenarios, ranging from a simple requirement verification study, up to the simultaneous synthesis and optimization of an aircraft system and its production process, including multiple system architecture options.
ScRNAPip: A systematic and dynamic pipeline for single‐cell RNA sequencing analysis
Authors: Xu Limin , Zhang Jing , He Yiqian , Yang Qianqian , Mu Tianhao , Guo Qiushi , Li Yingqiang , Tong Tian , Chen Shifu , Ye Richard D. 
Published: August 2023

AbstractWith the advancement of sequencing technology, cell separation, and whole‐genome amplification techniques, single cell technology for genome sequencing is emerging gradually. In comparison to traditional genome sequencing at the multi‐cellular level, single‐cell sequencing can not only measure the gene expression level more accurately but also can detect a small amount of gene expression or rare noncoding RNA. This technology has garnered increasing interest among researchers engaged in single‐cell studies in recent years. Here, we developed a reproducible computational workflow for scRNA‐seq data analysis which including tasks like quality control, normalization, data correction, pseudotime analysis, copy number analysis, etc. We illustrate the application of these steps using publicly available datasets and provide practical recommendations for their implementation. This study serves as a comprehensive tutorial for researchers keen on single‐cell data analysis, aiding users in constructing and refining their own analysis pipelines.
Design of subsurface drainage network with minimum overall cost using Lagrange multiplier optimization
Authors: Gabr Mohamed Elsayed , Fattouh Ehab , Eltarabily Mohamed Galal 
Published: August 2023

AbstractSubsurface drainage is effective for not only controlling groundwater levels in agricultural lands but also alleviating soil salinity localized at the root zone, especially for arid and semi‐arid agro‐ecosystems. In this research, an optimization model that minimizes the overall costs of subsurface drainage systems subjected to design constraints was formulated. The Lagrange multiplier method for optimization was utilized to derive a general differential equation for obtaining the most economical design of the subsurface drainage system. Design charts for the minimum cost of the subsurface drainage network ($ ha−1) for lateral diameters (dL) of 2.5, 5, 7.5, 10 and 12.5 cm; hydraulic conductivities (K) of 0.5, 1, 2, 3 and 4 m day−1; different lateral lengths (LL) of 100, 150, 200, 250, and 300 m; a constant collector length (LC) of 1000 m (assuming laterals join the collector from both sides); drainage recharge (q) values of 1, 2, 3, 4 and 5 mm day−1; and excavation depths of 1.5 and 2.0 m were developed. The minimum computed subsurface drainage network (SSDN) costs observed at a lateral length (LL) of 300 m were 205, 246, 288, 331 and 374 ($ ha−1) for lateral diameters of 2.5, 5, 7.5, 10 and 12.5 cm, respectively, corresponding to lateral spacing of 175, 176, 177, 178 and 179 m. The suggested charts for the optimum design of a subsurface drainage system have lower overall costs than using conventional design approaches for pipelines and tube wells. The results will support solutions for designers to implement subsurface drainage systems with less and more affordable expenses in the old lands of the Nile delta of Egypt and other regions with similar agrosystems. Quality control during construction is very necessary for guaranteeing the effective and sustainable performance of subsurface drainage systems for many years.