Scientific Software Development Research Articles

Ethiopian Health Care Workers' Insights into and Responses to Intimate Partner Violence in Pregnancy-A Qualitative Study.

Violence against women is a global pandemic, with the potential to spread through generations. Intimate partner violence has impacts on women’s sexual, reproductive, and psycho-social health. It can occur during pregnancy and adversely affect the health of both mother and child. Health care workers involved in antenatal care can have a unique role in identifying intimate partner violence and in intervening, preventing, and mitigating its consequences. In this study, the objective was to explore Ethiopian health care workers’ insights of and responses to intimate partner violence in pregnancy. Using an exploratory design, this qualitative study includes ten semi-structured interviews of health care workers representing different antenatal care centers in Jimma, Ethiopia. The content analyses of translated interview notes were conducted with Atlas.ti7 software, (Atlas.ti Scientific Software Development Gmbh, Berlin). The health care workers shared their insights of the consequences of intimate partner violence during pregnancy in addition to their experience with and responses to the victims. There was a limited understanding of the extent of the adverse impacts of intimate partner violence on pregnancy outcomes, as well as the potential long-term health implications. The informants described how they only gave medical treatment for obstetric complications or visible trauma during pregnancy. There was no formal referral to or linkages with other resources. Women’s empowerment and systemic changes in the health care, including training and capacity building, clear guidelines addressing management of intimate partner violence in pregnancy, and inclusion of intimate partner violence screening tools in the Ethiopian antenatal care chart/card, were recommended by the informants. The adverse impacts of intimate partner violence on pregnancy outcomes were poorly understood by the Ethiopian health care workers in this study. They offered limited assistance to the victims and recommended changes in the routine antenatal care (ANC) and health care systems. They identified various policy initiatives focusing on women’s empowerment to reduce intimate partner violence and its complications especially during pregnancy.

Patient and physician perceptions of lung cancer care in a multidisciplinary clinic model.

Lung cancer (lc) is a complex disease requiring coordination of multiple health care professionals. A recently implemented lc multidisciplinary clinic (mdc) at Kingston Health Sciences Centre, an academic tertiary care hospital, improved timeliness of oncology assessment and treatment. This study describes patient, caregiver, and physician experiences in the mdc. We qualitatively studied patient, caregiver, and physician experiences in a traditional siloed care model and in the mdc model. We used purposive sampling to conduct semi-structured interviews with patients and caregivers who received care in one of the models and with physicians who worked in both models. Thematic design by open coding in the ATLAS.ti software application (ATLAS.ti Scientific Software Development, Berlin, Germany) was used to analyze the data. Participation by 6 of 72 identified patients from the traditional model and 6 of 40 identified patients from the mdc model was obtained. Of 9 physicians who provided care in both models, 8 were interviewed (2 respirologists, 2 medical oncologists, 4 radiation oncologists). Four themes emerged: communication and collaboration, efficiency, quality of care, and effect on patient outcomes. Patients in both models had positive impressions of their care. Patients in the mdc frequently reported convenience and a positive effect of family presence at appointments. Physicians reported that the mdc improved communication and collegiality, clinic efficiency, patient outcomes and satisfaction, and consistency of information provided to patients. Physicians identified lack of clinic space as an area for mdc improvement. This qualitative study found that a lc mdc facilitated patient communication and physician collaboration, improved quality of care, and had a perceived positive effect on patient outcomes.

A Software Institute for Data-Intensive Sciences, Joining Computer Science Academia and Natural Science Research

With the ever-increasing size of scientific collaborations and complexity of scientific instruments, the software needed to acquire, process and analyze the gathered data is increasing in both complexity and size. Unfortunately the role and career path of scientists and engineers working on software R&D and developing scientific software are neither clearly established nor defined in many fields of natural science. In addition, the exchange of information between scientific software development and computer science departments at universities or computing schools is scattered and fragmented into individual initiatives. To address the above issues we propose a new effort on a European level, which concentrates on strengthening the role of software developers in natural sciences, acts as a hub for the exchange of ideas among different stake-holders in computer science and scientific software and forms a lobbying forum for software engineering in natural sciences on an international level. This contribution discusses in detail the motivation, role and interplay with other initiatives of a “Software Institute for Data-Intensive Sciences”, which is currently being discussed between research institutes, universities and funding agencies in Europe. In addition to the current status, an outlook on future prospects of this initiative will be given.

DCA++ project: Sustainable and scalable development of a high-performance research code

Scientific discoveries across all fields, from physics to biology, are increasingly driven by computer simulations. At the same time, the computational demand of many problems necessitates large-scale calculations on high-performance supercomputers. Developing and maintaining the underlying codes, however, has become a challenging task due to a combination of factors. Leadership computer systems require massive parallelism, while their architectures are diversifying. New sophisticated algorithms are continuously developed and have to be implemented efficiently for such complex systems. Finally, the multidisciplinary nature of modern science involves large, changing teams to work on a given codebase. Using the example of the DCA++ project, a highly scalable and efficient research code to solve quantum many-body problems, we explore how computational science can overcome these challenges by adopting modern software engineering approaches. We present our principles for scientific software development and describe concrete practices to meet them, adapted from agile software development frameworks.

Application of Fluid Dynamics in the Development of Communication Industrialization

Fluid mechanics has made great progress in recent decades, especially in the field of communication engineering, which is an important emerging direction. This paper provides an overview of the main essence and latest progress of this method. At the same time, it also discusses the development of relevant scientific and technological software and its impact on practical industrial applications.

The Historic City, Its Transmission and Perception via Augmented Reality and Virtual Reality and the Use of the Past as a Resource for the Present: A New Era for Urban Cultural Heritage and Tourism?

The objective of this study is to analyze the impact that augmented reality (AR) and virtual reality (VR) are having on our conception, appreciation, and use of urban heritage spaces. Although most evaluations that appear in the specialized literature are clearly positive in this respect, there is a critical line of thought that considers these new technologies as connected to prior theoretical assumptions about heritage, in terms of what we value, how we value it, and for what reasons. To contrast the two perspectives, we have selected and examined scientific literature evaluating the application of AR and VR in urban heritage spaces, in order to analyze whether, in addition to positive effects, certain negatives linked to the ‘virtualization’ of space are also at work. A qualitative methodology has been developed supported by the ATLAS.ti tool (Scientific Software Development GmbH, Berlin, Germany), which allows definition of the different thematic lines treated in the literature as well as the connections between them. Our main conclusion is that concerns around the critical aspects are very limited, with only a few perceiving the possible dangers of trivialization of heritage, the creation of virtual tourist worlds separate from the material space of socio-economic relations, negative effects on the way in which knowledge is constructed, or the difficulties for some user groups in accessing these technologies.

Solvent Selection Methods and Tool

An interactive tool with a browser-type interface has been developed for solvent selection using the software R. Two main classes of considerations can be taken into account: technical suitability for the intended duties, and practical considerations including costs and health, safety environment (HSE) impact. The tool builds on quantitative analyses of properties selected by the user for the application at hand. The underlying philosophy is to assist the thought processes of the tool’s users, rather than to prescribe set answers. The tool is a stepping stone toward design-of-experiment in chemical process development, enabling parameter space exploration without specialized software licenses, and grouping properties to assist the users. Six examples of use are given to illustrate various methodologies. In building the tool, scientific software development was found to be more intrinsically iterative than originally expected, with mock-ups and sharing of user stories more agile than lengthy user requireme...

Engaging Aging Individuals in the Design of Technologies and Services to Support Health and Well-Being: Constructivist Grounded Theory Study.

BackgroundChanges noted within the aging population are physical, cognitive, as well as emotional. Social isolation and loneliness are also serious problems that the aging population may encounter. As technology and apps become more accessible, many basic services, such as those offered by social services, well-being organizations, and health care institutions, have invested in the development of supportive devices, services, and Web-based interactions. Despite the perceived benefits that these devices and services offer, many aging individuals choose not to engage, or engage in a limited manner. To explore this phenomenon, we developed a theory to describe the condition for engagement.ObjectiveThe main objective of this study was to understand the perceptions of an aging South African population regarding Web-based services and technologies that could support aging in place (AiP). Although the concept of AiP speaks to a great number of everyday activities, this paper explores aspects of health and well-being as being central to AiP.MethodsThe study used a grounded theory (GT) methodology, relying on an iterative and simultaneous process of data collection, coding, category development, and data comparisons. Data were collected through qualitative methods, including interviews (13 participants aged between 64 and 85 years), 2 participatory workshops (15 participants), and observations. The study focused on Charmaz’s approach to constructivist GT, which puts forward the premise that theory or knowledge cannot take shape in a purely objective manner. Instead, theory is constructed through the interaction of the researcher and research participant. Coding and data analysis were supported with ATLAS.ti (ATLAS.ti Scientific Software Development GmbH).ResultsThe study resulted in a substantive theory exploring the process of interaction and engaging factors through user insights and experiences. The emerging design theory, Ageing User Decision-Driven Engagement (AUDDE), explored the elements that support engagement with technology and supportive apps, which could offer access to required health and wellness services.ConclusionsIn AUDDE, the perceived value of the interaction is a crucial catalyst for engagement. Aging users continuously make meaning of their experiences, which affects their current and future actions.

The Role of Scientific Communities in Creating Reusable Software: Lessons From Geophysics

The domain of geophysics has historically been a driver of scientific software development due to the size, complexity, and societal importance of the research questions. Geophysical computation complements field observation, laboratory analysis, experiment, and theory. Specialized scientific software is regularly developed by geophysicists in collaboration with computational scientists and applied mathematicians; in this cross-disciplinary environment, reusability is critically important both to preserve the intellectual investment and to ensure the quality of the research and its replicability. The Computational Infrastructure for Geodynamics (CIG) is a “community of practice” that advances Earth science by developing and disseminating software for geophysics and related fields. We discuss CIG's best practices, lessons learned, and community practices, and highlight how development of high-quality, reusable scientific software has accelerated scientific discovery by enabling simulations of the dynamics of Earth's surface and interior across a wide spectrum of problems using resources from laptops to leadership-class supercomputers.

Metamorphic Testing: A Simple Yet Effective Approach for Testing Scientific Software

Testing scientific software is a difficult task due to their inherent complexity and the lack of test oracles. In addition, these software systems are usually developed by end-user developers who are not normally trained as professional software developers nor testers. These factors often lead to inadequate testing. Metamorphic testing (MT) is a simple yet effective testing technique for testing such applications. Even though MT is a wellknown technique in the software testing community, it is not very well utilized by the scientific software developers. The objective of this paper is to present MT as an effective technique for testing scientific software. To this end, we discuss why MT is an appropriate testing technique for scientists and engineers who are not primarily trained as software developers. Specifically, how it can be used to conduct systematic and effective testing on programs that do not have test oracles without requiring additional testing tools.

Women’s Experience with Socio-Economic Factors Associated with Perinatal Morbidity and Mortality in Lusaka and Mumbwa Districts of Zambia

Background: More than half a million women and four million infants are reported to die every year due to complications related to pregnancy and child bearing. The efforts to improve quality maternity care have been on the World Health Organization member countries’ agenda. Zambia has been striving to reduce maternal mortality by ensuring universal access to maternal and child health care services. Our study aimed to explore women’s experience with socio-economic factors associated with perinatal morbidity and mortality in Lusaka and Mumbwa districts, Zambia. Methodology: This hermeneutic phenomenological study was conducted at four health facilities in Mumbwa and Lusaka Districts of Zambia. A purposeful sample of 45 consenting women organized in four groups was selected. Each group comprised of 11 to 12 women. The focus group discussion guide was used to direct the discussion and the Olympus Digital Voice Recorder WS-852 (Olympus Corporation, Shinjuku, Tokyo, Japan) was used to record the discussions. The audio data was manually transcribed and verbatim transcript analyzed using ATLAS.ti 8.0 qualitative data software (ATLAS.ti Scientific Software Development GmbH, Berlin, Germany) to ascertain patterns of relationships between themes and quotations. Results: Money, husbands and family support, adequate health care resources, and good nurses attitude simplify the burden of pregnancy, delivery and child rearing for the health care providers, mothers and society. Conclusion: Having money and all the necessary resources during pregnancy simplifies the burden of pregnancy, delivery and child rearing for the health care providers, mothers and society. Women are still ignorant and believe in myths and need information on the dangers of depending on herbs and God in preparation for labor and care of the new born, but also seek help from qualified medical personnel when labor starts. Nurse’s attitude needs to change to ensure a reduction in women and newborn mortalities. Nurses were mentioned as the cause of mortality among women and newborn. Recommendations: There’s a need for training of nurses and other health care workers on self-awareness of attitudes. Women should be empowered with resources that facilitate labor and delivery. Midwives and health care providers should take responsibility for evaluating and correcting the beliefs and traditional practices of the community. Training should be planned for raising awareness in order to support beneficial practices and prevent harmful ones.

You Can't Have It All: The Experience of Academic Hospitalists During Pregnancy, Parental Leave, and Return to Work.

The United States lags behind most other countries regarding the support for working mothers and parental leave. Data are limited to describe the experience of female hospital medicine physicians during pregnancy, parental leave, and their return to work in academic hospital medicine. We conducted a qualitative descriptive study including interviews with 10 female academic hospitalists chosen from institutions across the country that are represented in Society of Hospital Medicine (SHM) Committees. Interview guides were based on the following domains: experience in pregnancy, parental leave, and return to work. Interviews were recorded, transcribed verbatim, and analyzed using a general inductive approach to theme analysis using the ATLAS.ti software (Scientific Software Development GmbH, Berlin, Germany). Women in hospital medicine experience the following six common challenges in their experience as new parents, each of which has the potential to impact their career trajectory, wellness, and are associated with areas for institutional improvement: (1) access to paid parental leave, (2) physical challenges, (3) breastfeeding, (4) career opportunities, (5) colleague responses, and (6) empathy in patient care.

Tending the \u2018monthly flower:\u2019 a qualitative study of menstrual beliefs in Tigray, Ethiopia

BackgroundMenstruation is a universal aspect of human female reproductive life. Management of menstrual flow presents hygiene challenges to girls and women in low-income countries, especially when they first start their periods. As part of a project to improve menstrual hygiene management in the Tigray Region of Ethiopia, we explored the local understanding of menstruation through focus-group discussions and individual interviews.MethodsA detailed ethnographic survey of menstrual beliefs was carried out through 40 focus group discussions, 64 in-depth key informant interviews, and 16 individual case histories in the Tigray Region of northern Ethiopia. A total of 240 individuals participated in six types of focus groups (pre-menarchal girls, menstruating adolescents, married women of reproductive age, post-menopausal women, adolescent males, and married men). In-depth interviews were also carried out with 80 individuals, including Orthodox Christian priests, imams from the Muslim community, principals of primary and secondary schools, teachers and nurses, as well as menstruating schoolgirls and women. Audio data were transcribed and translated, then broken down into discrete codes using Atlas Ti software (version 7.5.4, Atlas.ti Scientific Software Development Mnbh, Berlin) and further grouped into related families and sub-families based on their content. The results were then synthesized to produce a cohesive narrative concerning menstruation in Tigray.ResultsRecurrent themes identified by participants included descriptions of the biology of menstruation (which were sometimes fanciful); the general unpreparedness of girls for menarche; cultural restrictions imposed by menstruation on females (particularly the stigma of ritual uncleanliness in both Christian and Muslim religious traditions); the prevalence and challenges of unmet menstrual hygiene needs at schools (including lack of access to sanitary pads and the absence of acceptable toilet/washing facilities); and the stigma and shame associated with menstrual hygiene accidents in public.ConclusionsChanges in the educational system in northern Ethiopia are required to improve student understanding of the biology of menstruation, to foster gender equity, to overcome the barriers to school attendance presented by poor menstrual hygiene management, and to create a society that is more understanding and more accepting of menstruation.

GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components.

Modern bioinformatics and computational biology are fields of study driven by the availability of effective software required for conducting appropriate research tasks. Apart from providing reliable and fast implementations of different data analysis algorithms, these software applications should also be clear and easy to use through proper user interfaces, providing appropriate data management and visualization capabilities. In this regard, the user experience obtained by interacting with these applications via their Graphical User Interfaces (GUI) is a key factor for their final success and real utility for researchers. Despite the existence of different packages and applications focused on advanced data visualization, there is a lack of specific libraries providing pertinent GUI components able to help scientific bioinformatics software developers. To that end, this paper introduces GC4S, a bioinformatics-oriented collection of high-level, extensible, and reusable Java GUI elements specifically designed to speed up bioinformatics software development. Within GC4S, developers of new applications can focus on the specific GUI requirements of their projects, relying on GC4S for generalities and abstractions. GC4S is free software distributed under the terms of GNU Lesser General Public License and both source code and documentation are publicly available at http://www.sing-group.org/gc4s

Test-Driven Development in HPC Science: A Case Study

Many scientific software developers have applied software engineering practices in their work in recent years. Agile methods are gaining increased interest from both industry and academia, including scientific application domains. Test-driven development (TDD) and refactoring practices are critical to the success of agile methods. Although many scientific projects employ agile practices, the effect of TDD on scientific software development remains unknown and should thus be investigated. The authors investigated the effects of using TDD to develop scientific software in a high-performance computing environment, finding both advantages and disadvantages. In particular, they observed that developers face problems with writing unit tests and with a lack of experience with software engineering practices.

NESSie.jl – Efficient and intuitive finite element and boundary element methods for nonlocal protein electrostatics in the Julia language

The development of scientific software can be generally characterized by an initial phase of rapid prototyping and the subsequent transition to computationally efficient production code. Unfortunately, most programming languages are not well-suited for both tasks at the same time, commonly resulting in a considerable extension of the development time. The cross-platform and open-source Julia language aims at closing the gap between prototype and production code by providing a usability comparable to Python or MATLAB alongside high-performance capabilities known from C and C++ in a single programming language. In this paper, we present efficient protein electrostatics computations as a showcase example for Julia. More specifically, we present both finite element and boundary element solvers for computing electrostatic potentials of proteins in structured solvents. By modeling the latter in an implicit but nonlocal fashion, we account for correlation of molecular polarization due to the solvent structure around the solute and sustain accuracy without suffering from infeasible runtimes as compared to the explicit case. In this context, we show that our implementation is on par with optimized C code and highlight the components of the implementation that can be transferred to more general tasks.

The Role of the Nurse Leader in Advancing the Quadruple Aim

Nursing constitutes the greatest segment of the health care workforce. The 400,000 nurses serving in leadership positions influence practice environments, patient experience, health care quality, and cost per capita. Sixteen expert panelists met last winter to discuss the role of the nurse leader in support of the Quadruple Aim. A secondary analysis of discussion transcriptions was managed using Atlas.ti data management software (ATLAS.ti Scientific Software Development GmbH, Berlin, Germany) for content analysis to identify categories, codes, and themes.

THE USE OF THE UAV IMAGES FOR THE BUILDING 3D MODEL GENERATION

Abstract. The growing interest in recent years in Unmanned Aerial Vehicles (UAVs) by the scientific community, software developers, and geomatics professionals, has led these systems to be used more and more widely, in different fields of engineering and architecture. This is thanks, above all, to their flexibility of use and low cost compared to traditional photogrammetric flights using expensive metric digital cameras or LiDAR sensors. In recent years, UAVs have also been used in the field of monitoring and inspection of public or private buildings that are remarkable in terms of size and architecture. This is mainly due to the focus a sustainability and resource efficiency in the building and infrastructure sector, which aims to extend their lifetimes. Through the use of remote checking using UAVs, the monitoring and inspection of buildings can be brought to a new level of quality and saving. This paper focuses on the processing and study of 3D models obtained from images captured by an UAV. In particular, the authors wanted to study the accuracy gains achieved in the building 3D model obtained with both nadir and oblique UAV flights. The images from the flights were processed using Structure-for Motion-based approach for point cloud generation using dense image-matching algorithms implemented in an open source software. We used the open source software VisualSfM, developed by Chanchang Wu in collaboration with the University of Washington and Google. The dense matching plug-in integrated in its interface, PMVS/CMVS, made by Yasutaka Furukawa, was employed to generate the dense cloud. The achieved results were compare with those gained by Photoscan software by Agisoft and with 3D model from the Terrestrial Laser Scanner (TLS) survey.

The new direction of computational fluid dynamics and its application in industry

Computational fluid dynamics has made considerable progress in the last decade or so, and it is worth mentioning that an important emerging direction in this field is the formation and development of the so-called lattice Boltzmann method. The main essence and latest progress provide an overview. At the same time, it also discusses related scientific and technological software development and its impact in practical industrial applications.

Understanding the types of fraud in claims to South African medical schemes

Medical schemes play a significant role in funding private healthcare in South Africa (SA). However, the sector is negatively affected by the high rate of fraudulent claims. To identify the types of fraudulent activities committed in SA medical scheme claims. A cross-sectional qualitative study was conducted, adopting a case study strategy. A sample of 15 employees was purposively selected from a single medical scheme administration company in SA. Semi-structured interviews were conducted to collect data from study participants. A thematic analysis of the data was done using ATLAS.ti software (ATLAS.ti Scientific Software Development, Germany). The study population comprised the 17 companies that administer medical schemes in SA. Data were collected from 15 study participants, who were selected from the medical scheme administrator chosen as a case study. The study found that medical schemes were defrauded in numerous ways. The perpetrators of this type of fraud include healthcare service providers, medical scheme members, employees, brokers and syndicates. Medical schemes are mostly defrauded by the submission of false claims by service providers and syndicates. Fraud committed by medical scheme members encompasses the sharing of medical scheme benefits with non-members (card farming) and non-disclosure of pre-existing conditions at the application stage. The study concluded that perpetrators of fraud have found several ways of defrauding SA medical schemes regarding claims. Understanding and identifying the types of fraud events facing medical schemes is the initial step towards establishing methods to mitigate this risk. Future studies should examine strategies to manage fraudulent medical scheme claims.