pinecone/core-2020-05-10-deduplication huggingface dataset:
Polaritons in Living Systems: Modifying Energy Landscapes in
  Photosynthetic Organisms Using a Photonic Structure

Photosynthetic organisms rely on a series of self-assembled nanostructures
with tuned electronic energy levels in order to transport energy from where it
is collected by photon absorption, to reaction centers where the energy is used
to drive chemical reactions. In the photosynthetic bacteria Chlorobaculum
tepidum (Cba. tepidum), a member of the green sulphur bacteria (GSB) family,
light is absorbed by large antenna complexes called chlorosomes. The exciton
generated is transferred to a protein baseplate attached to the chlorosome,
before traveling through the Fenna-Matthews-Olson (FMO) complex to the reaction
center. The energy levels of these systems are generally defined by their
chemical structure. Here we show that by placing bacteria within a photonic
microcavity, we can access the strong exciton-photon coupling regime between a
confined cavity mode and exciton states of the chlorosome, whereby a coherent
exchange of energy between the bacteria and cavity mode results in the
formation of polariton states. The polaritons have an energy distinct from that
of the exciton and photon, and can be tuned in situ via the microcavity length.
This results in real-time, non-invasive control over the relative energy levels
within the bacteria. This demonstrates the ability to strongly influence living
biological systems with photonic structures such as microcavities. We believe
that by creating polariton states, that are in this case a superposition of a
photon and excitons within a living bacteria, we can modify energy transfer
pathways and therefore study the importance of energy level alignment on the
efficiency of photosynthetic systems
Architecting graphene oxide rolled-up micromotors : a simple paper-based manufacturing technology

A graphene oxide rolled-up tube production process is reported using wax-printed membranes for the fabrication of on-demand engineered micromotors at different levels of oxidation, thickness, and lateral dimensions. The resultant graphene oxide rolled-up tubes can show magnetic and catalytic movement within the addition of magnetic nanoparticles or sputtered platinum in the surface of graphene-oxide-modified wax-printed membranes prior to the scrolling process. As a proof of concept, the as-prepared catalytic graphene oxide rolled-up micromotors are successfully exploited for oil removal from water. This micromotor production technology relies on an easy, operator-friendly, fast, and cost-efficient wax-printed paper-based method and may offer a myriad of hybrid devices and applications
Similarities, challenges and opportunities of wikipedia content and open source projects

Copyright @ 2012 John Wiley & Sons, Ltd.Several years of research and evidence have demonstrated that Open Source Software (OSS) portals often contain a large amount of software projects that simply do not evolve, developed by relatively small communities, struggling to attract a sustained number of contributors. These portals have started to\ud
increasingly act as a storage for abandoned projects, and researchers and practitioners should try and point out how to take advantage of such content. Similarly, other online content portals (like Wikipedia) could be harvested for valuable content. In this paper we argue that, even with differences in the requested expertise, many projects reliant on content and contributions by users undergo a similar evolution, and follow similar patterns: when a project fails to attract contributors, it appears to be not evolving, or abandoned. Far from a negative finding, even those projects could provide valuable content that should be harvested and identified based on common characteristics: by using the attributes of “usefulness” and “modularity” we isolate valuable content in both Wikipedia pages and OSS projects
Improving globally distributed software development and support processes - A workflow view

We propose a new approach and related indicators for globally distributed software support and development based on a 3-year process improvement project in a globally distributed engineering company. The company develops, delivers and supports a complex software system with tailored hardware components and unique end-customer installations. By applying the domain knowledge from operations management on lead time reduction and its multiple benefits to process performance, the workflows of globally distributed software development and multitier support processes were measured and monitored throughout the company. The results show that the global end-to-end process visibility and centrally managed reporting at all levels of the organization catalyzed a change process toward significantly better performance. Due to the new performance indicators based on lead times and their variation with fixed control procedures, the case company was able to report faster bug-fixing cycle times, improved response times and generally better customer satisfaction in its global operations. In all, lead times to implement new features and to respond to customer issues and requests were reduced by 50%
Comparing text-based and dependence-based approaches for determining the origins of bugs

Identifying bug origins – the point where erroneous code was introduced – is crucial for many software engineering activities, from identifying process weaknesses to gathering data to support bug detection tools. Unfortunately, this information is not usually recorded when fixing bugs, and recovering it later is challenging. Recently, the text approach and the dependence approach have been developed to tackle this problem. Respectively, they examine textual and dependence-related changes that occurred prior to a bug fix. However, only limited evaluation has been carried out, partially because of a lack of available implementations and of datasets linking bugs to origins. To address this, origins of 174 bugs in three projects were manually identified and compared to a simulation of the approaches. Both approaches were partially successful across a variety of bugs – achieving 29–79% precision and 40–70% recall. Results suggested the precise definition of program dependence could affect performance, as could whether the approaches identified a single or multiple origins. Some potential improvements are explored in detail and identify pragmatic strategies for combining techniques along with simple modifications. Even after adopting these improvements, there remain many challenges: large commits, unrelated changes and long periods between origins and fixes all reduce effectiveness
Towards a hybrid testing process unifying exploratory testing and scripted testing

CONTEXT Given the current state of the art in research, practitioners are faced with the challenge of choosing scripted testing (ST) or exploratory testing (ET). OBJECTIVE This study aims at systematically incorporating strengths of ET and ST in a hybrid testing process to overcome the weaknesses of each. METHOD We utilized systematic review and practitioner interviews to identify strengths and weaknesses of ET and ST. Strengths of ET were mapped to weaknesses of ST and vice versa. Noblit and Hare's lines-ofargument method was used for data analysis. The results of the mapping were used as input to codesign a hybrid process with experienced practitioners. RESULTS We found a clear need to create a hybrid process as follows: (i) both ST and ET provide strengths and weaknesses, and these depend on some particular conditions, which prevents preference of one approach to another; and (ii) the mapping showed that it is possible to address the weaknesses in one process by the strengths of the other in a hybrid form. With the input from literature and industry experts, a flexible and iterative hybrid process was designed. CONCLUSIONS Practitioners can clearly benefit from using a hybrid process given the mapping of advantages and disadvantage
Supporting Collaborative Development Using Process Models: A Tool Integration-Focused Approach

Collaboration in software engineering projects is usually intensive and requires adequate support by well-integrated tools. However, process-centered software engineering environ ments (PSEE) have traditionallybeen designed to exploit integration facilities in other tools, while offering themselves little to no such facilities.This is in line with the vision of the PSEE as the central orchestrator of project support tools. We argue that thisview has hindered the widespread adoption of process-based collaboration support tools by incurring too muchadoption and switching costs. We propose a new process-based collaboration support architecture, backed by aprocess metamodel, that can easily be integrated with existing tools. The proposed architecture revolves aroundthe central concepts of ‘deep links’ and ‘hooks’. Our approach is validated by analyzing a collection of open-source projects, and integration utilities based on the implemented process model server have been developed
Software process simulation-at a crossroads?

Software Process Simulation (SPS) has been evolving over the past two decades after being introduced to the software engineering community in the 1980s. At that time the SPS technology attracted a great deal of interest from both academics and practitioners in the software process community – even to the extent of being one of the recommended techniques for achieving the quantitative modeling KPA for CMMI Level 4. However, in recent years, the growth of SPS seems to have slowed along with the number of reported applications in industry. This article summarizes the special panel during ICSSP 2012 whose goal was to assess whether this technology remains applicable to today’s software engineering projects and challenges and point out the most beneficial opportunities for future research and industry application
Supporting requirements update during software evolution

Updating the requirements specification when software systems evolve is a manual task that is expensive and time consuming. Therefore, maintainers usually apply the changes to the code directly and leave the requirements unchanged. This results in the requirements rapidly becoming obsolete and useless. In this paper, we propose an approach that supports the maintainer in keeping the requirements specification consistent with the implementation, by identifying the requirements that are impacted whenever the code is changed. Our approach works as follows. First, we analyze the changes that have been applied to the source code and detect if they are likely to impact the requirements or not. Second, we trace the requirements-impacting changes back to the requirements specification to identify the parts that might need to be modified. The output of the tracing is a list of requirements that are sorted according to their likelihood of being impacted. Automatically identifying the parts of the requirements specification that are likely to need maintenance reduces the effort needed for keeping the requirements up-to-date and thus makes the task of the maintainer easier. When applying our approach in three cases studies, 70% to 100% of the impacted requirements were identified within a list that includes less than 20% of the total number of requirements in the specification
Assessing traceability — practical experiences and lessons learned\ud

Most existing software systems that lack explicit traceability links between artefacts, or if implemented, are often not leveraged to take advantage of the information it can provide to a development or validation team. Within the medical device domain, as in other safety critical domains, regulation normally requires such systems that are certified before entering service. This involves submission of a safety case (a reasoned argument that the system is acceptably safe) to the regulator. A safety case should include evidence that the organisation has established effective software development processes. At the heart of such processes, they must incorporate traceability. However, numerous barriers such as a lack of awareness of traceability and a lack of guidance as to how to implement traceability hamper its effective implementation. In this paper, we address the lack of guidance on traceability implementation by presenting our experience of developing and trialling a traceability assessment model in two medical device organisations. We show that the assessment model was successful in identifying strengths and weaknesses in both organisations' implementation of traceability. Through experience of trialling the model, we propose an idea to improve it by automation, using the Open Services for Lifecycle Collaboration initiative
On the Use of Variability Operations in the V-Modell XT Software Process
  Line

Software process lines provide a systematic approach to develop and manage
software processes. It defines a reference process containing general process
assets, whereas a well-defined customization approach allows process engineers
to create new process variants, e.g., by extending or modifying process assets.
Variability operations are an instrument to realize flexibility by explicitly
declaring required modifications, which are applied to create a procedurally
generated company-specific process. However, little is known about which
variability operations are suitable in practice. In this article, we present a
study on the feasibility of variability operations to support the development
of software process lines in the context of the V-Modell XT. We analyze which
variability operations are defined and practically used. We provide an initial
catalog of variability operations as an improvement proposal for other process
models. Our findings show that 69 variability operation types are defined
across several metamodel versions of which, however, 25 remain unused. The
found variability operations allow for systematically modifying the content of
process model elements and the process documentation, and they allow for
altering the structure of a process model and its description. Furthermore, we
also find that variability operations can help process engineers to compensate
process metamodel evolution.Comment: Journal of Software: Evolution and Process, 201
The MedITNet Assessment Framework: Development and Validation of a Framework for Improving Risk Management of Medical IT Networks\ud

Medical devices are increasingly designed for incorporation into a hospital’s IT network allowing devices to exchange critical information. However, connecting devices in this way can introduce risks potentially negating the benefits to patients. While the IEC 80001-1 standard has been developed to aid Healthcare Delivery Organisations (HDOs) in addressing these risks, HDOs often struggle to understand and implement the requirements. The MedITNet framework has been developed to allow HDOs to assess the capability of their risk management processes against the requirements of IEC 80001-1. MedITNet provides a flexible assessment framework enabling HDOs to gain a understanding of the requirements of the standard and to improve risk management processes by determining their current state and highlighting areas for improvement. This paper examines the challenges faced by HDOs in the risk management of medical IT networks and explains the components of the MedITNet framework and how the framework addresses these challenges. The use of Action Design Research (ADR) in the development and validation of MedITNet are also discussed focusing on a pilot implementation of the assessment method and expert review of the overall framework. The changes to the framework and its components as a result of the validation process are also discussed
The Relationship between Evolutionary Coupling and Defects in Large Industrial Software

This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.Evolutionary coupling (EC) is defined as the implicit relationship between 2 or more software artifacts that are frequently changed together. Changing software is widely reported to be defect-prone. In this study, we investigate the effect of EC on the defect proneness of large industrial software systems and explain why the effects vary. We analysed 2 large industrial systems: a legacy financial system and a modern telecommunications system. We collected historical data for 7 years from 5 different software repositories containing 176 thousand files. We applied correlation and regression analysis to explore the relationship between EC and software defects, and we analysed defect types, size, and process metrics to explain different effects of EC on defects through correlation. Our results indicate that there is generally a positive correlation between EC and defects, but the correlation strength varies. Evolutionary coupling is less likely to have a relationship to software defects for parts of the software with fewer files and where fewer developers contributed. Evolutionary coupling measures showed higher correlation with some types of defects (based on root causes) such as code implementation and acceptance criteria. Although EC measures may be useful to explain defects, the explanatory power of such measures depends on defect types, size, and process metrics
Mobile medical app development with a focus on traceability

Today, the growth of medical devices and mobile medical applications is increasing enormously, thanks to the efficiency and enhancement of new technology. When it comes to mobile medical apps, developers need to understand what is required when a mobile application fulfils the definition of a medical device. Such applications have to be developed in compliance with medical device regulations. This can be a challenge for mobile medical application developers, as medical device software is normally developed in a manner that will also ensure the production of regulatory documentation that is essential to market such devices. In this paper, we identify the need for a mobile medical application development framework, the key criteria for such a framework, and describe how the results were collected through performing a Medical Device Software Development workshop. Furthermore, we describe how MDevSPICE together with an agile software development approach can be tailored to support a mobile medical applications development framework. We detail one of the key criteria for mobile medical application development framework—traceability
Formal Verification of Probabilistic SystemC Models with Statistical
  Model Checking

Transaction-level modeling with SystemC has been very successful in
describing the behavior of embedded systems by providing high-level executable
models, in which many of them have inherent probabilistic behaviors, e.g.,
random data and unreliable components. It thus is crucial to have both
quantitative and qualitative analysis of the probabilities of system
properties. Such analysis can be conducted by constructing a formal model of
the system under verification and using Probabilistic Model Checking (PMC).
However, this method is infeasible for large systems, due to the state space
explosion. In this article, we demonstrate the successful use of Statistical
Model Checking (SMC) to carry out such analysis directly from large SystemC
models and allow designers to express a wide range of useful properties. The
first contribution of this work is a framework to verify properties expressed
in Bounded Linear Temporal Logic (BLTL) for SystemC models with both timed and
probabilistic characteristics. Second, the framework allows users to expose a
rich set of user-code primitives as atomic propositions in BLTL. Moreover,
users can define their own fine-grained time resolution rather than the
boundary of clock cycles in the SystemC simulation. The third contribution is
an implementation of a statistical model checker. It contains an automatic
monitor generation for producing execution traces of the
model-under-verification (MUV), the mechanism for automatically instrumenting
the MUV, and the interaction with statistical model checking algorithms.Comment: Journal of Software: Evolution and Process. Wiley, 2017. arXiv admin
  note: substantial text overlap with arXiv:1507.0818
Database Engines: Evolution of Greenness

Context: Information Technology consumes up to 10\% of the world's
electricity generation, contributing to CO2 emissions and high energy costs.
Data centers, particularly databases, use up to 23% of this energy. Therefore,
building an energy-efficient (green) database engine could reduce energy
consumption and CO2 emissions.
  Goal: To understand the factors driving databases' energy consumption and
execution time throughout their evolution.
  Method: We conducted an empirical case study of energy consumption by two
MySQL database engines, InnoDB and MyISAM, across 40 releases. We examined the
relationships of four software metrics to energy consumption and execution time
to determine which metrics reflect the greenness and performance of a database.
  Results: Our analysis shows that database engines' energy consumption and
execution time increase as databases evolve. Moreover, the Lines of Code metric
is correlated moderately to strongly with energy consumption and execution time
in 88% of cases.
  Conclusions: Our findings provide insights to both practitioners and
researchers. Database administrators may use them to select a fast, green
release of the MySQL database engine. MySQL database-engine developers may use
the software metric to assess products' greenness and performance. Researchers
may use our findings to further develop new hypotheses or build models to
predict greenness and performance of databases
Software architectures for health care cyber-physical systems: A systematic literature review

Cyber‐physical systems (CPS) refer to the next generation of Information and Communication Technology systems that mainly integrate sensing, computing, and communication to monitor, control, and interact with a physical process to provide citizens and businesses with smart applications and services: health care, smart homes, smart cities, and so on. In recent years, health care has become one of the most important services due to the continuous increases in its costs. This has motivated extensive research on health care CPS, and some of that research has focused on describing the software architecture behind these systems. However, there is no secondary study to consolidate the research. This paper aims to identify and compare existing research on software architectures for health care CPS in order to determine successful solutions that could guide other architects and practitioners in their health care projects. We conducted a systematic literature review and compared the selected studies based on a characterization schema. The research synthesis results in a knowledge base of software architectures for health care CPS, describing their stakeholders, functional and non‐functional features, quality attributes architectural views and styles, components, and implementation technologies. This systematic literature review also identifies research gaps, such as the lack of open common platforms, as well as directions for future research