The potential of a GIS-based scoping system: An Israeli proposal and case study

In the environmental impact assessment (EIA) lifecycle, scoping is regarded as the most important stage for the quality of the entire process. Even though many EIA methods exist, only a few of them are specifically suited for scoping. Despite the well-acknowledged potential of geographical information systems (CIS) for EIA and their seemingly widespread use, the applicability of GIS for scoping has not been analyzed sufficiently. This article advances a GIS-based scoping method and discusses the conditions necessary for its utilization. Two specific issues are addressed: the ability of a GIS-based system to identify the pertinent environmental effects on the basis of readily available information under stringent time and budget constraints, and the institutional infrastructure needed for such a system to operate effectively. These issues are analyzed in a case study conducted in Israel. In this case study, the proposed GIS-based scoping system identified all the main effects found independently in a comprehensive environmental impact statement (EIS), as well as issues not analyzed in the EIS. A centralized institutional scoping structure, whereby EIS guidelines are issued by a single entity, is found to be important for the operation of such a system, because it can enjoy the economies of scale and scope involved in setting up and operating a GIS system for scoping purposes

"We do not appreciate being experimented on": Developer and Researcher Views on the Ethics of Experiments on Open-Source Projects

A tenet of open source software development is to accept contributions from users-developers (typically after appropriate vetting). But should this also include interventions done as part of research on open source development? Following an incident in which buggy code was submitted to the Linux kernel to see whether it would be caught, we conduct a survey among open source developers and empirical software engineering researchers to see what behaviors they think are acceptable. This covers two main issues: the use of publicly accessible information, and conducting active experimentation. The survey had 224 respondents. The results indicate that open-source developers are largely open to research, provided it is done transparently. In other words, many would agree to experiments on open-source projects if the subjects were notified and provided informed consent, and in special cases also if only the project leaders agree. While researchers generally hold similar opinions, they sometimes fail to appreciate certain nuances that are important to developers. Examples include observing license restrictions on publishing open-source code and safeguarding the code. Conversely, researchers seem to be more concerned than developers about privacy issues. Based on these results, it is recommended that open source repositories and projects address use for research in their access guidelines, and that researchers take care to ask permission also when not formally required to do so. We note too that the open source community wants to be heard, so professional societies and IRBs should consult with them when formulating ethics codes.Comment: 15 pages with 42 charts and 3 tables; accepted versio

Pathogenesis of Hepatitis B Virus Associated Chronic Liver Disease

Hepatitis B virus (HBV) infection is associated with chronic liver diseases (CLD), which progress from hepatitis to fibrosis, cirrhosis, and finally hepatocellular carcinoma (HCC) over 30–50 years. The pathogenesis of CLD is immune mediated, which is characterized by persistent immune responses against virus infected hepatocytes. During bouts of CLD, the virus gene encoding the hepatitis B x antigen (HBx) is increasingly found integrated at multiple sites within the human genome. Many of these integrated templates express HBx, which is a trans-regulatory protein that supports virus gene expression and replication on one hand, but also alters patterns of gene expression in the infected cell. HBx alters gene expression by constitutively activating signal transduction pathways in the cytoplasm and promoting epigenetic mediated changes in the expression of cellular genes. In doing so, HBx contributes to the persistence of virus infected cells and to the pathogenesis of CLD by triggering multiple hallmarks which are characteristic of cancer

Energy-Aware Lease Scheduling in Virtualized Data Centers

Energy efficiency has become an important measurement of scheduling algorithms in virtualized data centers. One of the challenges of energy-efficient scheduling algorithms, however, is the trade-off between minimizing energy consumption and satisfying quality of service (e.g. performance, resource availability on time for reservation requests). We consider resource needs in the context of virtualized data centers of a private cloud system, which provides resource leases in terms of virtual machines (VMs) for user applications. In this paper, we propose heuristics for scheduling VMs that address the above challenge. On performance evaluation, simulated results have shown a significant reduction on total energy consumption of our proposed algorithms compared with an existing First-Come-First-Serve (FCFS) scheduling algorithm with the same fulfillment of performance requirements. We also discuss the improvement of energy saving when additionally using migration policies to the above mentioned algorithms.Comment: 10 pages, 2 figures, Proceedings of the Fifth International Conference on High Performance Scientific Computing, March 5-9, 2012, Hanoi, Vietna

When Are Names Similar Or the Same? Introducing the Code Names Matcher Library

Program code contains functions, variables, and data structures that are represented by names. To promote human understanding, these names should describe the role and use of the code elements they represent. But the names given by developers show high variability, reflecting the tastes of each developer, with different words used for the same meaning or the same words used for different meanings. This makes comparing names hard. A precise comparison should be based on matching identical words, but also take into account possible variations on the words (including spelling and typing errors), reordering of the words, matching between synonyms, and so on. To facilitate this we developed a library of comparison functions specifically targeted to comparing names in code. The different functions calculate the similarity between names in different ways, so a researcher can choose the one appropriate for his specific needs. All of them share an attempt to reflect human perceptions of similarity, at the possible expense of lexical matching.Comment: 20 pages. Download from https://pypi.org/project/namecompare

The Resource Usage Aware Backfilling

Abstract. Job scheduling policies for HPC centers have been extensively stud-ied in the last few years, especially backfilling based policies. Almost all of these studies have been done using simulation tools. All the existent simulators use the runtime (either estimated or real) provided in the workload as a basis of their sim-ulations. In our previous work we analyzed the impact on system performance of considering the resource sharing (memory bandwidth) of running jobs including a new resource model in the Alvio simulator. Based on this studies we proposed the LessConsume and LessConsume Threshold resource selection policies. Both are oriented to reduce the saturation of the shared resources thus increasing the performance of the system. The results showed how both resource allocation poli-cies shown how the performance of the system can be improved by considering where the jobs are finally allocated. Using the LessConsume Threshold Resource Selection Policy, we propose a new backfilling strategy: the Resource Usage Aware Backfilling job scheduling policy. This is a backfilling based scheduling policy where the algorithms which decide which job has to be executed and how jobs have to be backfilled are based on a different Threshold configurations. This backfilling variant that considers how the shared resources are used by the scheduled jobs. Rather than backfilling the first job that can moved to the run queue based on the job arrival time or job size, it looks ahead to the next queued jobs, and tries to allocate jobs that would experience lower penalized runtime caused by the resource sharing saturation. In the paper we demostrate how the exchange of scheduling information between the local resource manager and the scheduler can improve substantially the per-formance of the system when the resource sharing is considered. We show how it can achieve a close response time performance that the shorest job first Back-filling with First Fit (oriented to improve the start time for the allocated jobs) providing a qualitative improvement in the number of killed jobs and in the per-centage of penalized runtime.

Sampling bias does not exaggerate climate–conflict claims

This correspondence is a response to Courtland Adams, Tobias Ide, Jon Barnett & Adrien Detges (2018), "Sampling bias in climate–conflict research" Nature Climate Change 8 (200–203) doi:10.1038/s41558-018-0068-2. Adams et al argue that claims regarding climate-conflict links are overstated because of sampling bias. However, this conclusion rests on logical fallacies and conceptual misunderstanding. There is some sampling bias, but it does not have the claimed effect

Role of miR-148a in hepatitis B associated hepatocellular carcinoma

Hepatitis B virus encoded X antigen (HBx) is a trans-regulatory protein that alters the activity of selected transcription factors and cytoplasmic signal transduction pathways. HBx transcriptionally up-regulates the expression of a unique gene, URG11, which in turn transcriptionally up-regulates beta-catenin, thereby contributing importantly to hepatocarcinogenesis. HBx and URG11 also alter the expression of multiple microRNAs, and by miRNA array analysis, both were shown to promote the expression of miR-148a. Elevated miR-148a was also seen in HBx positive liver samples from infected patients. To study the function of miR-148a, anti-148a was introduced into HepG2 and Hep3B cells stably expressing HBx or stably over-expressing URG11. Anti-miR-148a suppressed cell proliferation, cell cycle progression, cell migration, anchorage independent growth in soft agar and subcutaneous tumor formation in SCID mice. Introduction of anti-miR-148a increased PTEN protein and mRNA expression, suggesting that PTEN was targeted by miR-148a. Anti-miR-148a failed to suppress PTEN expression when co-transfected with reporter gene mutants in the 3'UTR of PTEN mRNA. Introduction of anti-miR-148a also resulted in depressed Akt signaling by HBx and URG11, resulting in decreased expression of beta-catenin. Thus, miR-148a may play a central role in HBx/URG11 mediated HCC, and may be an early diagnostic marker and/or therapeutic target associated with this tumor type.published_or_final_versio