Effectiveness of spatial representation in the formation of network communities: experimental study on community organizer

In this paper, we present and discuss Community Organizer, a system designed to support network communities. The main characteristic of Community Organizer is the use of spatial representations for the relationships among community members including the communications exchanged among these members. These spatial representations reflect the degree of closeness of interests and concerns among the members, and are intended to provide users with clues on how to form network communities. In order to investigate the effectiveness of the proposed spatial representations, we conducted experiments with two different versions of the software. One version offered meaningful spatial representations while the other version did not. The subjects who used the former software version felt a greater sense of ‘community’, enjoyed using the software more, and actively used it longer than the subjects using the latter software version (control condition). These results indicated that the proposed spatial representations are effective in supporting network community formation.     

Rapid and comprehensive indicator for evaluation of performance of treatment processes and of river waters.

Naturally occurring UV active compounds, commonly present in almost all source waters, can be rapidly monitored by their ultraviolet absorbance at 260 nm (E260). Herein, the extent of correlation between the E260 and the removal efficiency of the hazardous contaminants, endocrine disrupters and dioxins, were investigated using various treatment and river source waters. The detection of various types of hazardous contaminants using sophisticated analytical methods, such as high resolution gas chromatography (HRGC)/high resolution mass spectrometry (HRMS) and high performance liquid chromatography (HPLC)/inductively coupled plasma (ICP)/mass spectrometry (MS), as well as various short-term bioassays, can require hours or even days for results to be obtained. The removal of the E260 correlated well with those of individual contaminants, such as endocrine disruptor chemicals and dioxins, with the various treatment processes employed. In the plots of the endocrine disrupters against the DOC/E260, a correlation was found with the endocrine activity of the Korean/Japanese river waters employed in this study.     

Gene regulation of trkB and trkC in the chick retina by light/darkness exposure

The trk gene family members; the neurotrophic receptors for neurotrophins, are implicated in the survival and the differentiation of neurons. The roles of these protooncogenes have been argued in the pathological conditions and in the specific developmental stage when the programmed cell death occurs to neurons. Here we studied a physiological role of the trk family members in the retina through observations of their gene regulation by light/darkness exposure. Northern blot analysis and immunohistochemistry demonstrate that trkB and trkC are up-regulated by light exposure and down-regulated by darkness in the rod/cone layer, the outer nuclear layer, and the ganglion cell layer. This physiological regulation suggests that these trk family members play a protective role from the damaging effect of light exposure in the retinal neurons.     

Temperature Dependence of Thermal Reflection Behavior of Al2O3–TiO2 Multilayer Thermal Energy Window Coating

An Al₂O₃–TiO₂ multilayer-coated sapphire thermal energy window coating has been fabricated using an ultra-high-speed vacuum sputtering method. Thermal reflection spectra of the coated material in the wavelength range from 1.43 to 3.33 μm are measured in ambient air at temperatures of 298, 773, and 1173 K. The result shows that the light reflectance of ∼70% is achieved using a layered structure and this performance continues up to 1173 K. Thermal reflection energy of the coated material at T =1173 K is estimated to be about three times higher than that of uncoated sapphire, suggesting the potential of this coating to control thermal radiation energy.     

Studying high impact fix-inducing changes

As software systems continue to play an important role in our daily lives, their quality is of paramount importance. Therefore, a plethora of prior research has focused on predicting components of software that are defect-prone. One aspect of this research focuses on predicting software changes that are fix-inducing. Although the prior research on fix-inducing changes has many advantages in terms of highly accurate results, it has one main drawback: It gives the same level of impact to all fix-inducing changes. We argue that treating all fix-inducing changes the same is not ideal, since a small typo in a change is easier to address by a developer than a thread synchronization issue. Therefore, in this paper, we study high impact fix-inducing changes (HIFCs). Since the impact of a change can be measured in different ways, we first propose a measure of impact of the fix-inducing changes, which takes into account the implementation work that needs to be done by developers in later (fixing) changes. Our measure of impact for a fix-inducing change uses the amount of churn, the number of files and the number of subsystems modified by developers during an associated fix of the fix-inducing change. We perform our study using six large open source projects to build specialized models that identify HIFCs, determine the best indicators of HIFCs and examine the benefits of prioritizing HIFCs. Using change factors, we are able to predict 56 % to 77 % of HIFCs with an average false alarm (misclassification) rate of 16 %. We find that the lines of code added, the number of developers who worked on a change, and the number of prior modifications on the files modified during a change are the best indicators of HIFCs. Lastly, we observe that a specialized model for HIFCs can provide inspection effort savings of 4 % over the state-of-the-art models. We believe our results would help practitioners prioritize their efforts towards the most impactful fix-inducing changes and save inspection effort.     

Studying re-opened bugs in open source software

Bug fixing accounts for a large amount of the software maintenance resources. Generally, bugs are reported, fixed, verified and closed. However, in some cases bugs have to be re-opened. Re-opened bugs increase maintenance costs, degrade the overall user-perceived quality of the software and lead to unnecessary rework by busy practitioners. In this paper, we study and predict re-opened bugs through a case study on three large open source projects—namely Eclipse, Apache and OpenOffice. We structure our study along four dimensions: (1) the work habits dimension (e.g., the weekday on which the bug was initially closed), (2) the bug report dimension (e.g., the component in which the bug was found) (3) the bug fix dimension (e.g., the amount of time it took to perform the initial fix) and (4) the team dimension (e.g., the experience of the bug fixer). We build decision trees using the aforementioned factors that aim to predict re-opened bugs. We perform top node analysis to determine which factors are the most important indicators of whether or not a bug will be re-opened. Our study shows that the comment text and last status of the bug when it is initially closed are the most important factors related to whether or not a bug will be re-opened. Using a combination of these dimensions, we can build explainable prediction models that can achieve a precision between 52.1–78.6 % and a recall in the range of 70.5–94.1 % when predicting whether a bug will be re-opened. We find that the factors that best indicate which bugs might be re-opened vary based on the project. The comment text is the most important factor for the Eclipse and OpenOffice projects, while the last status is the most important one for Apache. These factors should be closely examined in order to reduce maintenance cost due to re-opened bugs.     

Gene Expression over Time during Cell Transformation Due to Non-Genotoxic Carcinogen Treatment of Bhas 42 Cells

The Bhas 42 cell transformation assay (Bhas 42 CTA) is the first Organization for Economic Cooperation and Development (OECD)-certificated method used as a specific tool for the detection of the cell-transformation potential of tumor-promoting compounds, including non-genotoxic carcinogens (NGTxCs), as separate from genotoxic carcinogens. This assay offers the great advantage of enabling the phenotypic detection of oncotransformation. A key benefit of using the Bhas 42 CTA in the study of the cell-transformation mechanisms of tumor-promoting compounds, including non-genotoxic carcinogens, is that the cell-transformation potential of the chemical can be detected directly without treatment with a tumor-initiating compound since Bhas 42 cell line was established by transfecting the v-Ha-ras gene into a mouse fibroblast cloned cell line. Here, we analyzed the gene expression over time, using DNA microarrays, in Bhas 42 cells treated with the tumor-promoting compound 12-O-tetradecanoylphorbol-13-acetate (TPA), and NGTxC, with a total of three repeat experiments. This is the first paper to report on gene expression over time during the process of cell transformation with only a tumor-promoting compound. Pathways that were activated or inactivated during the process of cell transformation in the Bhas 42 cells treated with TPA were related not only directly to RAS but also to various pathways in the hallmarks of cancer.     

Direct Reprogramming and Induction of Human Dermal Fibroblasts to Differentiate into iPS-Derived Nucleus Pulposus-like Cells in 3D Culture

Intervertebral disc (IVD) diseases are common spinal disorders that cause neck or back pain in the presence or absence of an underlying neurological disorder. IVD diseases develop on the basis of degeneration, and there are no established treatments for degeneration. IVD diseases may therefore represent a candidate for the application of regenerative medicine, potentially employing normal human dermal fibroblasts (NHDFs) induced to differentiate into nucleus pulposus (NP) cells. Here, we used a three-dimensional culture system to demonstrate that ectopic expression of MYC, KLF4, NOTO, SOX5, SOX6, and SOX9 in NHDFs generated NP-like cells, detected using Safranin-O staining. Quantitative PCR, microarray analysis, and fluorescence-activated cell sorting revealed that the induced NP cells exhibited a fully differentiated phenotype. These findings may significantly contribute to the development of effective strategies for treating IVD diseases.     

Effects of highly hydrogenated soybean oil and cholesterol on plasma,liver cholesterol,and fecal steroids in rats

We investigated the relationship between dietary highly hydrogenated soybean oil (HSO) and cholesterol transport in rats. In the first study, to examine the effects of cholesterol transport of different concentrations of HSO in dietary oil, rats were given one of the three diets containing 0, 25, or 50% HSO in dietary oil with cholesterol (5 g/kg diet) or a diet without HSO and cholesterol for 22 d. Feeding the high concentration of HSO prevented the increase in plasma total cholesterol, hepatic total lipids, and cholesterol and the decrease in high-density lipoprotein-cholesterol, which were caused by dietary cholesterol. Moreover, HSO increased the fecal excretion, fecal lipids, and steroids in a dose-dependent manner. In the second study, to examine the effects on cholesterol transport of redistribution of stearic acid in the triacylglycerol species contained in HSO, rats were given one of the six diets containing HSO (distearoylmonoacylglycerol and tristearoylglycerol)-rich, monostearoylglycerol-rich, or palmitic acid-rich oil with/without cholesterol (5 g/kg diet), for 30 d. Whereas the accumulation of cholesterol in the body was reduced, cholesterol excretion was enhanced effectively in rats given the HSO-rich diet compared with rats given the monostearoylglycerol-rich diet. These results suggested that not only the high concentration of stearic acid but also its uneven distribution in HSO-triacylglycerol contributed to the reduction in intestinal cholesterol absorption in rats.