Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the Effectiveness of Static Analysis through Defect Correlation Analysis

Assessment of code and design quality using Software Code Assessment tools is important for continuous improvement and monitoring of code quality in the software industry in general and for global software development in particular. Static Analysis is believed to help identify issues at an early stage in the software development life cycle (SDLC), however it is still under utilized in the industry. In this paper, we discuss our experiences in determining the importance of Static Analysis and the extent to which the defects (that could otherwise be slipped to later stages of SDLC) could have been reduced with the continuous use of Static Analysis. Towards this end, we have performed analysis of defects reported from testing/field by correlating the defects to Static Analysis Rules, for projects that were developed across different regions. Our focus was to gather insight into the number and type of defects that could be identified in advance through Static Analysis Rules. The purpose of gaining the insights is to justify the ROI for software quality checks, fine tune, update existing software quality practices and introduce new practices uniformly across the teams as necessary. The results substantiate the role of Static Analysis in reducing technical debt by identifying potential defects early in the SDLC.
SecWater: a multi-layer security framework for water treatment plants

A framework (SecWater) to assist in the design of secure water treatment plants is presented. SecWater enables plant designers to secure the entire Supervisory Control and Data Acquisition (SCADA) infrastructure using multi-layer security. The framework consists of seven layers labeled SL0 through SL6. Layer SL0 provides the first line of defense against cyber attacks while SL5 and SL6 provide real-time control when an attack is detected. Intermediate layers enable the detection of cyber and physical attacks. Several implementations could be derived using SecWater depending on cost constraints and risks to be tolerated. Four layers in SecWater are in use to secure an existing water treatment plant.
Making a Case for Epistemological Access in Biotechnology Education in Southern Africa

In southern Africa, biotechnology is increasingly important with regard to food security and the development of the pharmaceutical industry. Universities are tasked with providing the relevant capacity development through tertiary-level courses to meet these development needs. However, the knowledge and practices of biotechnology may be contentious as in issues related to genetically modified foods and cloning. It is also well known that in culturally diverse educational situations, students may experience epistemological challenges derived from their ontological standpoints, and that these can impact on the learning process. The purpose of this study was thus to investigate student views of biotechnology, a field of science where student ethical, religious and/or cultural beliefs may be at odds with the science that is taught in the classroom. Data was collected over a four-year period (2009–2012), from 115 students from two universities who volunteered to complete a questionnaire. Data was also collected from 70 students who volunteered to be part of focus groups during this time. Phenomenography was used as the research approach in this case study, resulting in an outcome space that produced two broad categories describing students’ responses to biotechnology. These were a theoretical and practical perspective, and a worldview perspective. The study found that students need and want to be as globally competitive as their international peers. This requires that the curriculum reflects the standard and practice of the Global North. However, in southern Africa, where the student demography in universities is typically very diverse, the findings also highlight the need for a pedagogical approach that facilitates learning through providing space for students to freely discuss and reflect on their views and concerns related to indigenous knowledge and beliefs.
Circulatory Syndrome: An Evolution of the Metabolic Syndrome Concept!

The metabolic syndrome has been a useful, though controversial construct in clinical practice as well as a valuable model in order to understand the interactions of diverse cardiovascular risk factors. However the increasing importance of the circulatory system in particular the endothelium, in both connecting and controlling organ function has underlined the limitations of the metabolic syndrome definition. The proposed “Circulatory Syndrome” is an attempt to refine the metabolic syndrome concept by the addition of recently documented markers of cardiovascular disease including renal impairment, microalbuminuria, arterial stiffness, ventricular dysfunction and anaemia to more classic factors including hypertension, dyslipidemia and abnormal glucose metabolism; all of which easily measured in clinical practice. These markers interact with each other as well as with other factors such as aging, obesity, physical inactivity, diet and smoking. The final common pathways of inflammation, oxidative stress and hypercoagulability thereby lead to endothelial damage and eventually cardiovascular disease. Nevertheless, the Circulatory (MARC) Syndrome, like its predecessor the metabolic syndrome, is only a small step toward an understanding of these complex and as yet poorly understood markers of disease.
A taxonomy of congestion control and reliability approaches in opportunistic DTNs

Delay and Disruption Tolerant Networking (DTN) has been aiming to tackle the communication challenges originating from the lack of continuous end-to-end connectivity, for a diverse set of mobile/wireless networking environments and applications. Among its basic concepts, DTNs support data storage at intermediate hosts, as a means of application sessions surviving connectivity disruptions. To this end, delivery reliability can be ensured on a hop-by-hop basis for environments were the node contacts which offer communication opportunities are predetermined (scheduled). However, in a large majority of terrestrial DTN settings, the mobility patterns of the communicating peers lead to rather randomly occuring (opportunistic) contacts. In such conditions, ensuring reliable data delivery is more challenging and it might not be feasible to achieve based on the basic hop-by-hop paradigm. On top of that, buffer congestions taking place at the DTN nodes can worsen the situation. In the current report we review and classify existing congestion control and reliability approaches that exist in the literature, for opportunistic DTNs.
Eye recognition in near-infrared images for driver's drowsiness monitoring

The paper presents a system for driver's eye recognition from near infrared (NIR) images. The system is organized in a cascade of two classification modules. The first one is responsible for initial eye detection and the second one for eye validation. Detection is based on a novel eye model suited for the NIR images. This process is augmented by the background subtraction module. The subsequent stage of eye validation is performed by the second classifier based on the higher-order decomposition of a tensor with geometrically deformed prototypes. Obtained results in day and night conditions show high accuracy and real-time processing of the system in software implementation.
Towards Building Lexical Ontology via Cross-Language Matching

In this paper, we introduce a methodology for mapping linguistic ontologies lexicalized across different languages. We present a classification-based semantics for mappings of lexicalized concepts across different languages. We propose an experiment for validating the proposed cross-language mapping semantics, and discuss its role in creating a gold standard that can be used in assessing cross-language matching systems.
In Situ Electron Energy-Loss Spectroscopy in Liquids

Abstract In situ scanning transmission electron microscopy (STEM) through liquids is a promising approach for exploring biological and materials processes. However, options for in situ chemical identification are limited: X-ray analysis is precluded because the liquid cell holder shadows the detector and electron energy-loss spectroscopy (EELS) is degraded by multiple scattering events in thick layers. Here, we explore the limits of EELS in the study of chemical reactions in their native environments in real time and on the nanometer scale. The determination of the local electron density, optical gap, and thickness of the liquid layer by valence EELS is demonstrated. By comparing theoretical and experimental plasmon energies, we find that liquids appear to follow the free-electron model that has been previously established for solids. Signals at energies below the optical gap and plasmon energy of the liquid provide a high signal-to-background ratio regime as demonstrated for LiFePO4 in an aqueous solution. The potential for the use of valence EELS to understand in situ STEM reactions is demonstrated for beam-induced deposition of metallic copper: as copper clusters grow, EELS develops low-loss peaks corresponding to metallic copper. From these techniques, in situ imaging and valence EELS offer insights into the local electronic structure of nanoparticles and chemical reactions.
The Emerging Immunological Role of Post-Translational Modifications by Reactive Nitrogen Species in Cancer Microenvironment

Under many inflammatory contexts, such as tumor progression, systemic and peripheral immune response is tailored by reactive nitrogen species (RNS)-dependent post-translational modifications, suggesting a biological function for these chemical alterations. RNS modify both soluble factors and receptors essential to induce and maintain a tumor-specific immune response, creating a “chemical barrier” that impairs effector T cell infiltration and functionality in tumor microenvironment and supports the escape phase of cancer. RNS generation during tumor growth mainly depends on nitric oxide production by both tumor cells and tumor-infiltrating myeloid cells that constitutively activate essential metabolic pathways of l-arginine catabolism. This review provides an overview of the potential immunological and biological role of RNS-induced modifications and addresses new approaches targeting RNS either in search of novel biomarkers or to improve anti-cancer treatment.
Integrating RTP into the World Wide Web

In this paper, we outline an architecture and an implementation which enables the real-time delivery of continuous media within the WWW, monitors QoS of data transmission, and conveys minimal session control information to all participants in an audio or a video session. We describe our current implementation of the Real-time Transport Protocol (RTP) and its associated control protocol RTCP embedded into the WWW environment. We used the Web browser, Netscape, thus allowing Netscape users to access remote realtime audio and video media using RTP. An adaptive rate-based flow controller is also included to control and reduce network congestion and to adjust the bandwidth dynamically.
The Effects of Calorie Restriction in Depression and Potential Mechanisms

Depression, also called major depressive disorder, is a neuropsychiatric disorder jeopardizing an increasing number of the population worldwide. To date, a large number of studies have devoted great attention to this problematic condition and raised several hypotheses of depression. Based on these theories, many antidepressant drugs were developed for the treatment of depression. Yet, the depressed patients are often refractory to the antidepressant therapies. Recently, increasing experimental evidences demonstrated the effects of calorie restriction in neuroendocrine system and in depression. Both basic and clinical investigations indicated that short-term calorie restriction might induce an antidepressant efficacy in depression, providing a novel avenue for treatment. Molecular basis underlying the antidepressant actions of calorie restriction might involve multiple physiological processes, primarily including orexin signaling activation, increased CREB phosphorylation and neurotrophic effects, release of endorphin and ketone production. However, the effects of chronic calorie restriction were quite controversial, in the cases that it often resulted in the long-term detrimental effects via inhibiting the function of 5-HT system and decreasing leptin levels. Here we review such dual effects of calorie restriction in depression and potential molecular basis behind these effects, especially focusing on antidepressant effects.
Analysis of payment transaction security in mobile commerce

Mobile payment is the process of two parties exchanging financial value using a mobile device in return for goods or services. This paper is an analysis of the security issues in mobile payment for m-commerce. We introduce m-commerce and mobile payment, discuss the public key infrastructure as a basis for secure mobile technologies, and study the features for different security technologies employed in current m-commerce market, including WAP, SIM application toolkit and J2M. In addition, we compare the effectiveness of these security technologies in supporting a secure mobile payment, and discuss research issues to enhance the security of mobile payment for large scale deployment of m-commerce.
Submillimeter Array 12CO (J = 3-2) Interferometric Observations of the Central Region of M51

We present the first interferometric 12CO (J = 3-2) observations (beam size of 3.″9 × 1.″6 or 160 × 65 pc) with the Submillimeter Array (SMA) toward the center of the Seyfert 2 galaxy M51. The image shows a strong concentration at the nucleus and weak emission from the spiral arm to the northwest. The integrated intensity of the central component in 12CO (J = 3-2) is almost twice as high as that in 12CO (J = 1-0), indicating that the molecular gas within an ~80 pc radius of the nucleus is warm (≳100 K) and dense (~104 cm-3). Similar intensity ratios are seen in shocked regions in our Galaxy, suggesting that these gas properties may be related to active galactic nucleus or starburst activity. The central component shows a linear velocity gradient (~1.4 km s-1 pc-1) perpendicular to the radio continuum jet, similar to that seen in previous observations and interpreted as a circumnuclear molecular disk/torus around the Seyfert 2 nucleus. In addition, we identify a linear velocity gradient (0.7 km s-1 pc-1) along the jet. Judging from the energetics, the velocity gradient can be explained by supernova explosions or energy and momentum transfer from the jet to the molecular gas via interaction, which is consistent with the high-intensity ratio.
Luteolin is a novel p90 ribosomal S6 kinase (RSK) inhibitor that suppresses Notch4 signaling by blocking the activation of Y-box binding protein-1 (YB-1)

Triple-negative breast cancers (TNBC) are notoriously difficult to treat because they lack hormone receptors and have limited targeted therapies. Recently, we demonstrated that p90 ribosomal S6 kinase (RSK) is essential for TNBC growth and survival indicating it as a target for therapeutic development. RSK phosphorylates Y-box binding protein-1 (YB-1), an oncogenic transcription/translation factor, highly expressed in TNBC (~70% of cases) and associated with poor prognosis, drug resistance and tumor initiation. YB-1 regulates the tumor-initiating cell markers, CD44 and CD49f however its role in Notch signaling has not been explored. We sought to identify novel chemical entities with RSK inhibitory activity. The Prestwick Chemical Library of 1120 off-patent drugs was screened for RSK inhibitors using both in vitro kinase assays and molecular docking. The lead candidate, luteolin, inhibited RSK1 and RSK2 kinase activity and suppressed growth in TNBC, including TIC-enriched populations. Combining luteolin with paclitaxel increased cell death and unlike chemotherapy alone, did not enrich for CD44+ cells. Luteolin’s efficacy against drug-resistant cells was further indicated in the primary x43 cell line, where it suppressed monolayer growth and mammosphere formation. We next endeavored to understand how the inhibition of RSK/YB-1 signaling by luteolin elicited an effect on TIC-enriched populations. ChIP-on-ChIP experiments in SUM149 cells revealed a 12-fold enrichment of YB-1 binding to the Notch4 promoter. We chose to pursue this because there are several reports indicating that Notch4 maintains cells in an undifferentiated, TIC state. Herein we report that silencing YB-1 with siRNA decreased Notch4 mRNA. Conversely, transient expression of Flag:YB-1WT or the constitutively active mutant Flag:YB-1D102 increased Notch4 mRNA. The levels of Notch4 transcript and the abundance of the Notch4 intracellular domain (N4ICD) correlated with activation of P-RSKS221/7 and P-YB-1S102 in a panel of TNBC cell lines. Silencing YB-1 or RSK reduced Notch4 mRNA and this corresponded with loss of N4ICD. Likewise, the RSK inhibitors, luteolin and BI-D1870, suppressed P-YB-1 S102 and thereby reduced Notch4. In conclusion, inhibiting the RSK/YB-1 pathway with luteolin is a novel approach to blocking Notch4 signaling and as such provides a means of inhibiting TICs.
Comparative Analysis of Three Brevetoxin-Associated Bottlenose Dolphin (Tursiops truncatus) Mortality Events in the Florida Panhandle Region (USA)

In the Florida Panhandle region, bottlenose dolphins (Tursiops truncatus) have been highly susceptible to large-scale unusual mortality events (UMEs) that may have been the result of exposure to blooms of the dinoflagellate Karenia brevis and its neurotoxin, brevetoxin (PbTx). Between 1999 and 2006, three bottlenose dolphin UMEs occurred in the Florida Panhandle region. The primary objective of this study was to determine if these mortality events were due to brevetoxicosis. Analysis of over 850 samples from 105 bottlenose dolphins and associated prey items were analyzed for algal toxins and have provided details on tissue distribution, pathways of trophic transfer, and spatial-temporal trends for each mortality event. In 1999/2000, 152 dolphins died following extensive K. brevis blooms and brevetoxin was detected in 52% of animals tested at concentrations up to 500 ng/g. In 2004, 105 bottlenose dolphins died in the absence of an identifiable K. brevis bloom; however, 100% of the tested animals were positive for brevetoxin at concentrations up to 29,126 ng/mL. Dolphin stomach contents frequently consisted of brevetoxin-contaminated menhaden. In addition, another potentially toxigenic algal species, Pseudo-nitzschia, was present and low levels of the neurotoxin domoic acid (DA) were detected in nearly all tested animals (89%). In 2005/2006, 90 bottlenose dolphins died that were initially coincident with high densities of K. brevis. Most (93%) of the tested animals were positive for brevetoxin at concentrations up to 2,724 ng/mL. No DA was detected in these animals despite the presence of an intense DA-producing Pseudo-nitzschia bloom. In contrast to the absence or very low levels of brevetoxins measured in live dolphins, and those stranding in the absence of a K. brevis bloom, these data, taken together with the absence of any other obvious pathology, provide strong evidence that brevetoxin was the causative agent involved in these bottlenose dolphin mortality events.
Collateral Posting and Choice of Collateral Currency - Implications for Derivative Pricing and Risk Management

In recent years, we have observed the dramatic increase of the use of collateral as an important credit risk mitigation tool. It has become even rare to make a contract without collateral agreement among the major financial institutions. In addition to the significant reduction of the counterparty exposure, collateralization has important implications for the pricing of derivatives through the change of effective funding cost. This paper has demonstrated the impact of collateralization on the derivative pricing by constructing the term structure of swap rates based on the actual market data. It has also shown the importance of the "choice" of collateral currency. Especially, when the contract allows multiple currencies as eligible collateral and free replacement among them, the paper has found that the embedded "cheapest-to-deliver" option can be quite valuable and significantly change the fair value of a trade. The implications of these findings for market risk management have been also discussed.
Mechanisms of Recurrent Functional Mitral Regurgitation After Mitral Valve Repair in Nonischemic Dilated Cardiomyopathy: Importance of Distal Anterior Leaflet Tethering

Background— Recurrent functional mitral regurgitation (MR) has been reported after mitral valve repair with annuloplasty in patients with dilated cardiomyopathy, but the mechanism is not understood completely. The authors sought to identify abnormalities of the mitral valve and left ventricle that are associated with recurrent MR after mitral annuloplasty. Method and Results— In 104 patients with idiopathic dilated cardiomyopathy who underwent annuloplasty for functional MR, basal mitral anterior leaflet angle, distal mitral anterior leaflet angle (ALAtip), posterior leaflet angle, coaptation depth, tenting area, mitral annular dimensions, left ventricular volumes, and MR severity were quantified by echocardiography before surgery and at 6-month intervals after it. Compared with patients without MR recurrence (n=79), patients with recurrent MR (defined as ≥2+) (n=25) had greater ALAtip (P<0.001) and basal mitral anterior leaflet angle (P<0.001), greater coaptation depth and tenting area (P<0.001), larger left ventricular volumes (P<0.001), and worse left ventricular ejection fraction (P<0.05) but similar mitral annular dimensions and postoperative exaggeration in posterior leaflet angle. Multivariable analysis identified postoperative ALAtip as the major determinant of postoperative MR. Receiver operator characteristic curves identified preoperative ALAtip as the best predictor of MR recurrence (area under curve, 0.98). For ALAtip >25°, the sensitivity, specificity, and positive and negative predictive values in predicting recurrent MR were 88%, 94%, 82%, and 93%, respectively. Three distinct patterns of anterior leaflet tethering (minimal, basal, and distal) with an increasing risk of recurrent MR were identified. Conclusions— Posterior leaflet tethering is invariable after mitral annuloplasty, rendering postoperative mitral competence highly dependent on distal anterior leaflet mobility.
Genomic Recombination Leading to Decreased Virulence of Group B Streptococcus in a Mouse Model of Adult Invasive Disease

Adult invasive disease caused by Group B Streptococcus (GBS) is increasing worldwide. Whole-genome sequencing (WGS) now permits rapid identification of recombination events, a phenomenon that occurs frequently in GBS. Using WGS, we described that strain NGBS375, a capsular serotype V GBS isolate of sequence type (ST)297, has an ST1 genomic background but has acquired approximately 300 kbp of genetic material likely from an ST17 strain. Here, we examined the virulence of this strain in an in vivo model of GBS adult invasive infection. The mosaic ST297 strain showed intermediate virulence, causing significantly less systemic infection and reduced mortality than a more virulent, serotype V ST1 isolate. Bacteremia induced by the ST297 strain was similar to that induced by a serotype III ST17 strain, which was the least virulent under the conditions tested. Yet, under normalized bacteremia levels, the in vivo intrinsic capacity to induce the production of pro-inflammatory cytokines was similar between the ST297 strain and the virulent ST1 strain. Thus, the diminished virulence of the mosaic strain may be due to reduced capacity to disseminate or multiply in blood during a systemic infection which could be mediated by regulatory factors contained in the recombined region.