Miracle-dz/UniFAR-FTUs huggingface dataset:
Software Aging and Rejuvenation in a J2EE Application Server

Recently, software aging and software rejuvenation have been widely researched by both academic and industrial communities. Software aging is characterized by progressive performance degradation or a sudden hang/crash in a long‐running software system due to resource exhaustion of the operating system. Software rejuvenation is a proactive and preventive maintenance technique to counteract software aging. In this work, the memory leak in Java virtual machine (JVM) is firstly analyzed, and then the software aging phenomenon in a J2EE application server is investigated. To mitigate software aging effects and prevent the system from failing, the hierarchical software rejuvenation method by partial or total restarting of the system is presented. Finally, the experimental results proved that the proposed method is superior to the periodical rejuvenation method in the aspect of improving system performance. Copyright © 2014 John Wiley & Sons, Ltd.
Towards an evidence‐based process for the clinical interpretation of copy number variation

Riggs ER, Church DM, Hanson K, Horner VL, Kaminsky EB, Kuhn RM, Wain KE, Williams ES, Aradhya S, Kearney HM, Ledbetter DH, South ST, Thorland EC, Martin CL. Towards an evidence‐based process for the clinical interpretation of copy number variation.
Klebsiella aerogenes urease gene cluster: sequence of ureD and demonstration that four accessory genes (ureD, ureE, ureF, and ureG) are involved in nickel metallocenter biosynthesis

The region located immediately upstream from the Klebsiella aerogenes urease structural genes was sequenced and shown to possess an open reading frame capable of encoding a 29.8-kDa peptide. Deletions were generated in this gene, denoted ureD, and in each of the genes (ureE, ureF, and ureG) located immediately downstream of the three structural genes. Transformation of the mutated plasmids into Escherichia coli resulted in high levels of urease expression, but the enzyme was inactive (deletions in ureD, ureF, or ureG) or only partially active (deletions in ureE). Ureases were purified from the recombinant cells and shown to be identical to control enzyme when analyzed by gel filtration chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis; however, in every case the activity levels correlated to nickel contents as analyzed by atomic absorption analysis. UreD, UreE, UreF, and UreG peptides were tentatively identified by gel electrophoretic comparison of mutant and control cell extracts, by in vivo expression of separately cloned genes, or by in vitro transcription-translation analyses; the assignments were confirmed for UreE and UreG by amino-terminal sequencing. The latter peptides (apparent M(r)s, 23,900 and 28,500) were present at high levels comparable to those of the urease subunits, whereas the amounts of UreF (apparent M(r), 27,000) and UreD (apparent M(r), 29,300) were greatly reduced, perhaps because of the lack of good ribosome binding sites in the regions upstream of these open reading frames. These results demonstrate that all four accessory genes are necessary for the functional incorporation of the urease metallocenter.
Commentary: Adjusting for bias: a user's guide to performing plastic surgery on meta-analyses of observational studies.

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Mental Health, Mental Illness, and Psychological Distress: Same Continuum or Distinct Phenomena?∗

In this article, I argue that the relationships among mental health, disorder, and distress are a key source of conflict in the sociology of mental health and that the features of the conflict have the potential to call into question much of the accumulated scientific knowledge on mental health. To address this issue, I attempt to empirically assess three competing frameworks regarding these relationships: (1) the “modal perspective,” (2) the “Mirowsky and Ross perspective,” and (3) the “positive psychology perspective. ” Results, however, support a “discontinuous perspective:” no underlying continuum among any of the three concepts. These results suggest that researchers need to avoid the common practice of “lumping together” distress, disorder, and mental health and study each in their own right. Subsequent tests attempt to further specify the relationships among these concepts. Results indicate a strong positive directional association from distress to disorder, a strong negative directional association from distress to mental health, and no significant relationship between mental health and disorder. These results are used to generate a number of directions for future research.
Mediterranean Conference on Information Systems ( MCIS ) 2009 Why Do Commercial Firms Open The Source Code Of Their Products ?

This paper is concerned with the economic trade-offs associated with open-sourcing, the business strategy of releasing the source code of a commercial software product. We model open-sourcing as a strategic option for firms that compete in the market for software products. At the core of our model is the effect of open-sourcing on customer values, as well as the relative ease of customizing the open-source products. We show that open-sourcing can arise as an equilibrium outcome in our two-stage game. If the enhancement of customer value from open-sourcing is moderate or high, in equilibrium firms may find it optimal to release the source code of their commercial software products even when this strategy may reduce their profits.
Mental Disorders as Causal Systems

Debates about posttraumatic stress disorder (PTSD) often turn on whether it is a timeless, cross-culturally valid natural phenomenon or a socially constructed idiom of distress. Most clinicians seem to favor the first view, differing only in whether they conceptualize PTSD as a discrete category or the upper end of a dimension of stress responsiveness. Yet both categorical and dimensional construals presuppose that PTSD symptoms are fallible indicators reflective of an underlying, latent variable. This presupposition has governed psychopathology research for decades, but it rests on problematic psychometric premises. In this article, we review an alternative, network perspective for conceptualizing mental disorders as causal systems of interacting symptoms, and we illustrate this perspective via analyses of PTSD symptoms reported by survivors of the Wenchuan earthquake in China. Finally, we foreshadow emerging computational methods that may disclose the causal structure of mental disorders.
Recommendations for the treatment of Crohn's disease with tumor necrosis factor antagonists: An expert consensus report

Background: Symptom relief is the traditional treatment goal in Crohn's disease (CD). New goals including mucosal healing and bowel preservation are now achievable with tumor necrosis factor (TNF) antagonists. Infliximab and adalimumab are approved as second‐line treatments for severe, active CD. Certolizumab pegol is approved only in the U.S. and Switzerland as second‐line treatment for moderate‐to‐severe, active CD. Data from trials of infliximab suggest that high‐risk patients and patients with active inflammation (CRP elevation and/or ileocolonic ulcers) may benefit from earlier use of this drug. Methods: A Delphi survey was used to obtain consensus on issues surrounding bowel preservation and use of TNF antagonists. At the time of this survey, infliximab was the only TNF antagonist approved for the treatment of CD in Europe, Canada, and Australia. An expert panel of 12 gastroenterologists with substantial clinical experience using infliximab in clinical practice and trials in these areas participated. Results: The experts agreed that bowel preservation and mucosal healing are relevant and achievable goals, and form a rationale for using TNF antagonists in CD patients. Control of inflammation and induction of mucosal healing were considered essential for bowel preservation. Consensus areas: 1) mucosal healing is predictive of improved long‐term disease course and increases the likelihood of steroid‐free remission; 2) infliximab induces sustained mucosal healing, promotes bowel preservation, and reduces hospitalizations and surgeries; 3) benefits of infliximab in relation to mucosal healing, bowel preservation, and clinical remission increase when therapy is initiated earlier. Conclusions: Treatment with TNF antagonists helps preserve the bowel in CD patients. (Inflamm Bowel Dis 2011;)
Familial association of abstinent remission from alcohol use disorder in first‐degree relatives of alcohol‐dependent treatment‐seeking probands

BACKGROUND AND AIMS Studies that have included family history of alcohol use disorder (AUD) as a predictor of remission from AUD have yielded few significant results. The goals of this study were to estimate the association of persistent AUD, non-abstinent remission and abstinent remission ('AUD/remission status') in a proband with AUD/remission status in a relative and to test whether this association differed in related and unrelated proband-relative pairs. DESIGN High-risk family study of alcohol dependence. Probands were recruited from treatment settings and relatives were invited to participate. Baseline assessments occurred between 1991 and 1998 with follow-up between 1996 and 2005. Half of probands were matched with a biological 1st-degree relative with life-time AUD (related group) and half of probands were paired with an unrelated individual with life-time AUD (unrelated group). SETTING Brooklyn, New York; Indianapolis, Indiana; Iowa City, Iowa; San Diego, California; Farmington, Connecticut; and St Louis, Missouri, USA. PARTICIPANTS A total of 606 probands (25.7% female, mean age 37.7) with baseline and follow-up data and 606 of their 1st-degree relatives who had life-ime AUDs (45.8% female, mean age 36.2 years). MEASUREMENTS Persistent AUD, non-abstinent remission and abstinent remission were based on self-report interview data on most recent AUD symptoms and alcohol consumption. Dependent variable was relatives' AUD/remission status. Independent variable was probands' AUD/remission status. FINDINGS A total of 34.6% of probands and 20.6% of relatives were abstinent and 11.1% of probands and 22.8% of relatives were in non-abstinent remission. AUD/remission status was correlated significantly in related (r = 0.23, P = 0.0037) but not in unrelated pairs. A significant interaction of probands' abstinent remission with a variable representing related (versus unrelated, P = 0.003) pairs suggested a familial association for abstinent remission. In related pairs, individuals with an abstinent proband were more likely to be abstinent themselves than were individuals whose proband had persistent AUD [relative risk ratio = 3.27, 95% confidence interval (CI) = 1.56-6.85, P = 0.002]; this association was not significant in unrelated pairs. CONCLUSIONS The likelihood of abstinent remission among people with alcohol use disorder appears to be more than three times greater for individuals who are related to an abstinent proband versus those related to a proband with persistent alcohol use disorder.
Robot introduction to cleaning work in the East Japan Railway Company

Cleaning of rolling stock and stations is very important work in supplying comfortable service to customers. However, there are some problems with cleaning work, e.g. lack of workers who are getting older. To improve these problems, the East Japan Railway has developed several kinds of robots for cleaning. Here, I explain four types of floor cleaning robots. The first is a dust-collecting robot (the sweeper-type robot) for corners of station floors, the second is a cleaning robot (the scrubber-type robot) for use throughout a station and the third is a floor cleaning robot for commuter rail cars, all of which are self-propelled. The last one is a bonnet cleaning robot for Shinkansen rolling stock which has special axis mechanisms and a running mechanism.
Data Confidentiality and Chase-Based Knowledge Discovery

This article discusses data security in Knowledge Discovery Systems (KDS). In particular, we presents the problem of confidential data reconstruction by Chase (Dardzinska and Ras, 2003c) in KDS, and discuss protection methods. In conventional database systems, data confidentiality is achieved by hiding sensitive data from unauthorized users (e.g. Data encryption or Access Control). However, hiding is not sufficient in KDS due to Chase. Chase is a generalized null value imputation algorithm that is designed to predict null or missing values, and has many application areas. For example, we can use Chase in a medical decision support system to handle difficult medical situations (e.g. dangerous invasive medical test for the patients who cannot take it). The results derived from the decision support system can help doctors diagnose and treat patients. The data approximated by Chase is particularly reliable because they reflect the actual characteristics of the data set in the information system. Chase, however, can create data security problems if an information system contains confidential data (Im and Ras, 2005) (Im, 2006). Suppose that an attribute in an information system S contains medical information about patients; some portions of the data are not confidential while others have to be confidential. In this case, part or all of the confidential data in the attribute can be revealed by Chase using knowledge extracted at S. In other words, self-generated rules extracted from non-confidential portions of data can be used to find secret data. Knowledge is often extracted from remote sites in a Distributed Knowledge Discovery System (DKDS) (Ras, 1994). The key concept of DKDS is to generate global knowledge through knowledge sharing. Each site in DKDS develops knowledge independently, and they are used jointly to produce global knowledge without complex data integrations. Assume that two sites S1 and S2 in a DKDS accept the same ontology of their attributes, and they share their knowledge in order to obtain global knowledge, and an attribute of a site S1 in a DKDS is confidential. The confidential data in S1 can be hidden by replacing them with null values. However, users at S1 may treat them as missing data and reconstruct them with Chase using the knowledge extracted from S2. A distributed medical information system is an example that an attribute is confidential for one information system while the same attribute may not be considered as secret information in another site. These examples show that hiding confidential data from an information system does not guarantee data confidentiality due to Chase, and methods that would protect against these problems are essential to build a security-aware KDS.
Simulation of the RRAM-based flip-flops with data retention

A RRAM-based non-volatile flip-flop (NYFF) is designed to meet energy efficiency requirement for standby-power-critical applications in the deployment solution of IoT (Internet of Things). Adding only a pair of 1T1R cell into slave latch of a traditional FF can cut off the standby leakage at the cost of 4pJ write energy, and 20ps data retention time upon ideal power-on. The NVFF circuit is simulated and analyzed in HSPICE with a SPICE compact model of oxide-based RRAM on the conductive filament evolution model.
Cytochrome P-450 complex formation in rat liver by the antibiotic tiamulin

Tiamulin is a semisynthetic diterpene antibiotic frequently used in farm animals. The drug has been shown to produce clinically important--often lethal--interactions with other compounds. It has been suggested that this is caused by a selective inhibition of oxidative drug metabolism via the formation of a cytochrome P-450 metabolic intermediate complex. In the present study, rats were treated orally for 6 days with tiamulin at two different doses: 40 and 226 mg/kg of body weight. For comparison, another group received 300 mg of triacetyloleandomycin (TAO) per kg, which is equivalent to the 226-mg/kg tiamulin group. Subsequently, microsomal P-450 contents, P-450 enzyme activities, metabolic intermediate complex spectra, and P-450 apoprotein concentrations were assessed. In addition, effects on individual microsomal P-450 activities were studied in control microsomes at different tiamulin and substrate concentrations. In the rats treated with tiamulin, a dose-dependent complex formation as evidenced by its absorption spectrum and an increase in cytochrome P-4503A1/2 contents as assessed by Western blotting (immunoblotting) were found. The effects were comparable to those of TAO. Tiamulin induced microsomal P-450 content, testosterone 6 beta-hydroxylation rate, erythromycin N-demethylation rate, and the ethoxyresorufin O-deethylation activity. Other activities were not affected or decreased. When tiamulin was added to microsomes of control rats, the testosterone 6 beta-hydroxylation rate and the erythromycin N-demethylation were strongly inhibited. It is concluded that tiamulin is a potent and selective inducer-inhibitor of cytochrome P-450. Though not belonging to the macrolides, the compound produces an effect on P-450 similar to those of TAO and related compounds.
Dynamic accessibility: accommodating differences in ability and situation

Human abilities and situations are idiosyncratic and may change frequently. Static one-size-fits-many accessibility solutions miss the opportunities that arise from careful consideration of an individual's abilities and fail to address the sometimes dynamic aspect of those abilities, such as when a user's activity or context causes a "situational impairment. " The goal of this workshop is to bring together researchers and practitioners in accessibility, mobile HCI, and interactive intelligent systems who are pursuing agile, data-driven approaches that enable interactive systems to adapt or become adapted to the needs and abilities of a particular individual in a particular context.
Flow and scour around cylindrical objects in laboratory experiments

The prediction of scour and burial processes on the seafloor is the major goal of the presented investigations. As this task is extremely complex, single effects which cause scour and burial have been inspected separately. Therefore scour in the immediate vicinity of different objects and its changes under the influence of constant incident flow have been analyzed in the water channel. The observed scour patterns are the result of fluid mechanical effects. The measurements have been carried out by using the particle image velocimetry (PIV) and maintaining the Reynolds number. These investigations yield an explanation for the observed scour patterns and therewith verify the validity of the experiments in the water channel. Numerical simulations of scour around a cylindrical object are the first step to achieve the prediction of scour and burial of objects.
Concentrations and Frequencies of Polychlorinated Biphenyl Congeners in a Native American Population That Consumes Great Lakes Fish

Objective: Polychlorinated biphenyl congener profiles were examined in serum samples from 61 Native American (Ojibwa) volunteers who regularly consumed fish harvested from the Great Lakes region. A total of 93 peaks are reported which represent 126 individual chlorobiphenyls. Results: When ranked by frequency, 13 peaks comprising single or co-eluting chlorobiphenyls occurred in all 61 samples (a frequency of 100%). These included chlorobiphenyls 138 + 158 + 163, 105 + 132 + 153, 180, 118, 196 + 203, 74, 182 + 187, 199, 183, 114 + 134, 195 + 208, 206, and 194. These 13 peaks also occurred at concentrations higher than those of all other measured chlorobiphenyls, except for the addition of the peak containing chlorobiphenyls 170 and 190, which was below detection in 15% of the samples and ranked fifth in average concentration. The highly chlorinated chlorobiphenyls resembled human serum profiles previously reported in the literature. Methods: Individual chlorobiphenyls were identified using a gas chromatograph equipped with a 60-meter DB-5 capillary column and electron capture detection. Conclusion: When compared to other human residue analyses for fish-eating populations, the Ojibwa samples contained higher proportions of lightly chlorinated and labile chlorobiphenyls such as 8, 16 + 32, 17, 18, 25, 41 + 64 + 71, 33, 52, 110, and 129. These proportions were similar to those found in carp, whitefish, or whitefish livers harvested from the Great Lakes region. These data indicate that regular meals of lower trophic level fish, such as whitefish from the Great Lakes, may distort steady-state human chlorobiphenyl profiles with respect to certain lightly chlorinated or labile chlorobiphenyls.
Biorthonormal transfer-matrix renormalization-group method for general Markov random fields

We seek numerical calculations of partition functions of general Markov random fields (MRFs) by using the biorthonormal transfer-matrix renormalization-group (BTMRG) method. The BTMRG is a modification of the conventional TMRG, a variant of the density-matrix renormalization-group (DMRG), which automatically truncates the Hilbert space so that the properties of large systems can be precisely calculated while the dimensions of the renormalized transfer matrix remain constant. We apply the BTMRG to the decimation of the fundamental transfer matrix for general MRFs. Four binary 2nd-order MRFs are selected for numerical simulations. Results of simulations show that all four models exhibit the phase transition phenomenon. This work shows that our BTMRG method is superior to the conventional TMRG in accuracy, computational speed, and in the possibility of treating a much larger system.
Ultrafast optical response of a new metal organic complex-polymer composite film

A new Cu-based metal organic complex incorporated into poly (methyl mathacrylate) film exhibits large and fast offresonant optical nonlinearity in the 800 to 1550 nm wavelength range. A large χ<sup>(3)</sup> value of 1.8×10<sup>−10</sup> esu is estimated.