Miracle-dz/UniFAR-FTUs huggingface dataset:
UvA-DARE ( Digital Academic Repository ) A Model-Driven Co-Design Framework for Fusing Control and Scheduling Viewpoints

Model-Driven Engineering (MDE) is widely applied in the industry to develop new software functions and integrate them into the existing run-time environment of a Cyber-Physical System (CPS). The design of a software component involves designers from various viewpoints such as control theory, software engineering, safety, etc. In practice, while a designer from one discipline focuses on the core aspects of his field (for instance, a control engineer concentrates on designing a stable controller), he neglects or considers less importantly the other engineering aspects (for instance, real-time software engineering or energy efficiency). This may cause some of the functional and non-functional requirements not to be met satisfactorily. In this work, we present a co-design framework based on timing tolerance contract to address such design gaps between control and real-time software engineering. The framework consists of three steps: controller design, verified by jitter margin analysis along with co-simulation, software design verified by a novel schedulability analysis, and the run-time verification by monitoring the execution of the models on target. This framework builds on CPAL (Cyber-Physical Action Language), an MDE design environment based on model-interpretation, which enforces a timing-realistic behavior in simulation through timing and scheduling annotations. The application of our framework is exemplified in the design of an automotive cruise control system.
Linking fisheries, trophic interactions and climate: threshold dynamics drive herring Clupea harengus growth in the central Baltic Sea

How multiple stressors influence fish stock dynamics is a crucial question in ecology in general and in fisheries science in particular. Using time-series covering a 30 yr period, we show that the body growth of the central Baltic Sea herring Clupea harengus, both in terms of condition and weight-at-age (WAA), has shifted from being mainly driven by hydro-climatic forces to an inter- specific density-dependent control. The shift in the mechanisms of regulation of herring growth is triggered by the abundance of sprat, the main food competitor for herring. Abundances of sprat above the threshold of ~18 × 10 10 ind. decouple herring growth from hydro-climatic factors (i.e. salin- ity), and become the main driver of herring growth variations. At high sprat densities, herring growth is considerably lower than at low sprat levels, regardless of the salinity conditions, indicative of hys- teresis in the response of herring growth to salinity changes. The threshold dynamic accurately explains the changes in herring growth during the past 3 decades and in turn contributes to elucidate the parallel drastic drop in herring spawning stock biomass. Studying the interplay between differ- ent stressors can provide fundamental information for the management of exploited resources. The management of the central Baltic herring stock should be adaptive and take into consideration the dual response of herring growth to hydro-climatic forces and food-web structure for a sound eco- system approach to fisheries.
Identifying and characterizing public science-related fears from RSS feeds

A feature of modern democracies is public mistrust of scientists and the politicization of science policy, e.g., concerning stem cell research and genetically modified food. While the extent of this mistrust is debatable, its political influence is tangible. Hence, science policy researchers and science policy makers need early warning of issues that resonate with a wide public so that they can make timely and informed decisions. In this article, a semi-automatic method for identifying significant public science-related concerns from a corpus of Internet-based RSS (Really Simple Syndication) feeds is described and shown to be an improvement on a previous similar system because of the introduction of feed-based aggregation. In addition, both the RSS corpus and the concept of public science-related fears are deconstructed, revealing hidden complexity. This article also provides evidence that genetically modified organisms and stem cell research were the two major policy-relevant science concern issues, although mobile phone radiation and software security also generated significant interest.
Mathematical modeling the neuroregulation of blood pressure using a cognitive top-down approach

Background: The body′s physiological stability is maintained by the influence of the autonomic nervous system upon the dynamic interaction of multiple systems. These physiological systems, their nature and structure, and the factors which influence their function have been poorly defined. A greater understanding of such physiological systems leads to an understanding of the synchronised function of organs in each neural network i.e. there is a fundamental relationship involving sensory input and/or sense perception, neural function and neural networks, and cellular and molecular biology. Such an approach compares with the bottom-up systems biology approach in which there may be an almost infinite degree of biochemical complexity to be taken into account. Aims: The purpose of this article is to discuss a novel cognitive, top-down, mathematical model of the physiological systems, in particular its application to the neuroregulation of blood pressure. Results: This article highlights the influence of sensori-visual input upon the function of the autonomic nervous system and the coherent function of the various organ networks i.e. the relationship which exists between visual perception and pathology. Conclusions: The application of Grakov′s model may lead to a greater understanding of the fundamental role played by light e.g. regulating acidity, levels of Magnesium, activation of enzymes, and the various factors which contribute to the regulation of blood pressure. It indicates that the body′s regulation of blood pressure does not reside in any one neural or visceral component but instead is a measure of the brain′s best efforts to maintain its physiological stability.
Embedded Security for Car Telematics and Infotainment

Elliptic Curve Cryptography appeared in 1985 and since became an increasingly important crypto-system in public-key cryptography. Numerous articles have come to improve the field. One of these milestones is Edwards Curves which appeared in 2007 and proposed advantageous properties against SPA attacks. This thesis proposes the design, implementation and comparison of several small co-processors in hardware acceleration work flow. We start from scratch the software implementation of a scalar multiplication of Edwards Curves defined over FP192 in projective coordinates. In a first phase, 8-bit, 16-bit, 32-bit multipliers interfaced on the parallel port of a 8051 are successively developed. Then, the system is improved again by the implementation of a memory mapped 192-bit broadcast multiplier including a modular reduction. These five hardware configurations combined to an assembly optimization finally furnish six versions which are compared on four axes : time, energy consumption, area and security. On the one hand the side-channel attack still exposes a SPA-weakness in the implementation of all the version. On the other hand, measures show the expected results that the 192-bit multiplier provides a faster and lower power system at the expense of multiplying the silicon area by three.
Response of human macrophages to wound matrices in vitro

Chronic wounds remain a major burden to the global healthcare system. Myriad wound matrices are commercially available but their mechanisms of action are poorly understood. Recent studies have shown that macrophages are highly influenced by their microenvironment, but it is not known how different biomaterials affect this interaction. Here, it was hypothesized that human macrophages respond differently to changes in biomaterial properties in vitro with respect to phenotype, including pro‐inflammatory M1, anti‐inflammatory M2a, known for facilitating extracellular matrix deposition and proliferation, and M2c, which has recently been associated with tissue remodeling. Using multiple donors, it was found that collagen scaffolds cross‐linked with 1‐ethyl‐3‐(3‐dimethylaminopropyl) carbodiimide and N‐hydroxysuccinimide (EDC/NHS) promoted the least inflammatory phenotype in primary human macrophages compared with scaffolds cross‐linked with formaldehyde or glutaraldehyde. Importantly, gene expression analysis trends were largely conserved between donors, especially TNFa (M1), CCL22 (M2a), and MRC1 (M2a). Then the response of primary and THP1 monocyte‐derived macrophages to four commercially available wound matrices were compared—Integra Dermal Regeneration Template (Integra), PriMatrix Dermal Repair Scaffold (PriMatrix), AlloMend Acellular Dermal Matrix (AlloMend), and Oasis Wound Matrix (Oasis). Gene expression trends were different between primary and THP1 monocyte‐derived macrophages for all six genes analyzed in this study. Finally, the behavior of primary macrophages cultured onto the wound matrices over time was analyzed. Integra and Oasis caused down‐regulation of M2a markers CCL22 and TIMP3. PriMatrix caused up‐regulation of TNFa (M1) and CD163 (M2c) and down‐regulation of CCL22 and TIMP3 (both M2a). AlloMend caused up‐regulation in CD163 (M2c). Lastly, Oasis promoted the largest increase in the combinatorial M1/M2 score, defined as the sum of M1 genes divided by the sum of M2 genes. This preliminary study suggested that biomaterials influenced the wound microenvironment to affect macrophage phenotype.
Bayesian model of dynamic image stabilization in the visual system

Humans can resolve the fine details of visual stimuli although the image projected on the retina is constantly drifting relative to the photoreceptor array. Here we demonstrate that the brain must take this drift into account when performing high acuity visual tasks. Further, we propose a decoding strategy for interpreting the spikes emitted by the retina, which takes into account the ambiguity caused by retinal noise and the unknown trajectory of the projected image on the retina. A main difficulty, addressed in our proposal, is the exponentially large number of possible stimuli, which renders the ideal Bayesian solution to the problem computationally intractable. In contrast, the strategy that we propose suggests a realistic implementation in the visual cortex. The implementation involves two populations of cells, one that tracks the position of the image and another that represents a stabilized estimate of the image itself. Spikes from the retina are dynamically routed to the two populations and are interpreted in a probabilistic manner. We consider the architecture of neural circuitry that could implement this strategy and its performance under measured statistics of human fixational eye motion. A salient prediction is that in high acuity tasks, fixed features within the visual scene are beneficial because they provide information about the drifting position of the image. Therefore, complete elimination of peripheral features in the visual scene should degrade performance on high acuity tasks involving very small stimuli.
Impact of prediagnostic smoking and smoking cessation on colorectal cancer prognosis: a meta-analysis of individual patient data from cohorts within the CHANCES consortium

Background Smoking has been associated with colorectal cancer (CRC) incidence and mortality in previous studies and might also be associated with prognosis after CRC diagnosis. However, current evidence on smoking in association with CRC prognosis is limited. Patients and methods For this individual patient data meta-analysis, sociodemographic and smoking behavior information of 12 414 incident CRC patients (median age at diagnosis: 64.3 years), recruited within 14 prospective cohort studies among previously cancer-free adults, was collected at baseline and harmonized across studies. Vital status and causes of death were collected for a mean follow-up time of 5.1 years following cancer diagnosis. Associations of smoking behavior with overall and CRC-specific survival were evaluated using Cox regression and standard meta-analysis methodology. Results A total of 5229 participants died, 3194 from CRC. Cox regression revealed significant associations between former [hazard ratio (HR) = 1.12; 95 % confidence interval (CI) = 1.04-1.20] and current smoking (HR = 1.29; 95% CI = 1.04-1.60) and poorer overall survival compared with never smoking. Compared with current smoking, smoking cessation was associated with improved overall (HR<10 years = 0.78; 95% CI = 0.69-0.88; HR≥10 years = 0.78; 95% CI = 0.63-0.97) and CRC-specific survival (HR≥10 years = 0.76; 95% CI = 0.67-0.85). Conclusion In this large meta-analysis including primary data of incident CRC patients from 14 prospective cohort studies on the association between smoking and CRC prognosis, former and current smoking were associated with poorer CRC prognosis compared with never smoking. Smoking cessation was associated with improved survival when compared with current smokers. Future studies should further quantify the benefits of nonsmoking, both for cancer prevention and for improving survival among CRC patients, in particular also in terms of treatment response.
Market Crashes and Investor Sentiment : The Case of Taiwan

This study examines the dynamic relations between market fluctuation and investor sentiment for the Taiwan stock market before critical crash using the LPPL (log-periodic power law) signatures. First, aftershock patterns resembling those associated with earthquakes also occurred in the Taiwan stock market before critical crashes. It exhibits the same pattern of cycles speeding up as approaching to a crash point. Second, a lead-lag relationship exists between the Taiwan stock index and investor sentiment. This study finds the variance increases of frequency on investor sentiment move ahead of the increase in stock index variance as a crash approaches. The investor sentiment variables can be used to forecast the time of a crash.
Mapping Wild Leek through the Forest Canopy Using a UAV

Wild leek, an endangered plant species of Eastern North America, grows on forest floors and greens up to approximately three weeks before the trees it is typically found under, temporarily allowing it to be observed through the canopy by remote sensing instruments. This paper explores the accuracy with which wild leek can be mapped with a low-flying UAV. Nadir video imagery was obtained using a commercial UAV during the spring of 2017 in Gatineau Park, Quebec. Point clouds were generated from the video frames with the Structure-from-Motion framework, and a multiscale curvature classification was used to separate points on the ground, where wild leek grows, from above-ground points belonging to the forest canopy. Five-cm resolution orthomosaics were created from the ground points, and a threshold value of 0.350 for the green chromatic coordinate (GCC) was applied to delineate wild leek from wood, leaves, and other plants on the forest floor, with an F1-score of 0.69 and 0.76 for two different areas. The GCC index was most effective in delineating bigger patches, and therefore often misclassified patches smaller than 30 cm in diameter. Although short flight times and long data processing times are presently technical challenges to upscaling, the low cost and high accuracy of UAV imagery provides a promising method for monitoring the spatial distribution of this endangered species.
Influence of polymorphisms in the factor VII gene promoter on activated factor VII levels and on the risk of myocardial infarction in advanced coronary atherosclerosis

Summary In this study, we investigate the influence of three factor VII (FVII) gene polymorphisms on activated FVII levels (FVIIa), and also on the risk of myocardial infarction (MI) in patients with advanced coronary atherosclerotic disease (CAD). The –323A2 allele in the promoter is known to be associated with low FVII levels, and has been suggested to protect against MI in some studies. The –402GA promoter polymorphism, that in vitro has been associated with having opposite effect, is less well studied clinically. For this study, plasma FVIIa levels and three FVII gene polymorphisms were assessed in 934 subjects of both sexes, all with an angiographic documentation of coronary vessels. Our results show that two promoter polymorphisms, plasma cholesterol, and gender, were significant predictors of FVIIa levels. The –402A allele was associated to a significant increase of FVIIa levels in males (by 19.2%). In a selected clinical model including the patients with severe CAD, with or without a thrombotic complication (MI), male carriers of the –402A had an increased risk of MI (OR=1.79; 95% CI 1.15-2.80). The –323A2 allele was associated to a significant decrease in FVIIa (by 36.02% in males, and 39.7% in females). Male carriers of the –323A2 were protected from MI (OR=0.6; 95% CI 0.39-0.94), but only after correction for the confounding effect of combined heterozygosity for the promoter polymorphisms. We can conclude that FVII gene polymorphisms with an opposite effect on FVIIa levels may modulate the risk of MI in males with advanced CAD. This study highlights a “within-gene” interaction, and the need to explore polymorphisms in candidate gene(s) in detail.
Frontal lobe epileptic seizures are accompanied by elevated pitch during verbal communication

The objective of our study was to assess alterations in speech as a possible localizing sign in frontal lobe epilepsy. Ictal speech was analyzed in 18 patients with frontal lobe epilepsy (FLE) during seizures and in the interictal period. Matched identical words were analyzed regarding alterations in fundamental frequency (ƒo) as an approximation of pitch. In patients with FLE, ƒo of ictal utterances was significantly higher than ƒo in interictal recordings (p = 0.016). Ictal ƒo increases occurred in both FLE of right and left seizure origin. In contrast, a matched temporal lobe epilepsy (TLE) group showed less pronounced increases in ƒo, and only in patients with right‐sided seizure foci. This study for the first time shows significant voice alterations in ictal speech in a cohort of patients with FLE. This may contribute to the localization of the epileptic focus. Increases in ƒo were interestingly found in frontal lobe seizures with origin in either hemisphere, suggesting a bilateral involvement to the planning of speech production, in contrast to a more right‐sided lateralization of pitch perception in prosodic processing.
Developer Micro Interaction Metrics for Software Defect Prediction

To facilitate software quality assurance, defect prediction metrics, such as source code metrics, change churns, and the number of previous defects, have been actively studied. Despite the common understanding that developer behavioral interaction patterns can affect software quality, these widely used defect prediction metrics do not consider developer behavior. We therefore propose micro interaction metrics (MIMs), which are metrics that leverage developer interaction information. The developer interactions, such as file editing and browsing events in task sessions, are captured and stored as information by Mylyn, an Eclipse plug-in. Our experimental evaluation demonstrates that MIMs significantly improve overall defect prediction accuracy when combined with existing software measures, perform well in a cost-effective manner, and provide intuitive feedback that enables developers to recognize their own inefficient behaviors during software development.
Changes in PGE2 signaling after submandibulectomy alter post–tooth extraction socket healing

Saliva is very important to oral health, and a salivary deficit has been shown to bring serious problems to oral health. There is scant information about the mechanisms through which salivary glands participate in post–tooth extraction socket healing. Therefore, the aim of the present study was to investigate the effect of submandibulectomy (SMx), consisting of the ablation of submandibular and sublingual glands (SMG and SLG, respectively), on PGE2 signaling and other bone regulatory molecules, such as OPG and RANKL, involved in tooth extraction socket healing. Male Wistar rats, 70 g body weight, were assigned to an experimental (subjected to SMx) or a control group (sham operated). One week later, the animals in both groups underwent bilateral extraction of the first mandibular molars. The effect of SMx on different stages of socket healing after tooth extraction (7, 14, and 30 days) was studied by evaluating some parameters of inflammation, including PGE2 and its receptors, and of bone metabolism, as well as by performing bone biomechanical studies. SMx increased TNFα and PGE2 content as well as cyclooxygenase‐II (COX‐II) expression in tooth socket tissue at almost all the studied time points. SMx also had an effect on mRNA expression of PGE2 receptors at the different time points, but did not significantly alter osteoprotegerin (OPG) and RANKL mRNA expression at any of the studied time points. In addition, an increase in bone mass density was observed in SMx rats compared with matched controls, and the structural and mechanical bone properties of the mandibular socket bone were also affected by SMx. Our results suggest that the SMG/SLG complex regulates cellular activation and differentiation by modulating the production of molecules intervening in tooth extraction socket repair, including the PGE2 signaling system, which would therefore account for the higher density and resistance of the newly formed bone in SMx rat.
Towards Clarity in Research on “Non-Cognitive” Skills: Linking Executive Functions, Self-Regulation, and Economic Development to Advance Life Outcomes for Children, Adolescents and Youth Globally

Human development and economic development are intrinsically linked. Guided by human capital theory, economists are increasingly recognizing the importance of a range of other skills – in addition to intelligence and technical skills – for economic success. Until fairly recently, years of education completed, literacy, numeracy and IQ – often used as proxies for cognitive ability – were the main measures used to assess the relationship between human capital and economic development. More recently, researchers and practitioners have acknowledged that skills such as the ability to work in groups, maintain good interpersonal relations and a positive attitude, control impulses and demonstrate goal-directed behavior are all critical to economic productivity and individual success. The economist James Heckman highlighted the importance of these skills, which he originally called “non-cognitive” skills, for economic development in 2006 [Heckman, Stixrud, & Urza, 2006]. Since that time, there has been considerable interest among the international development community in these skills, but also confusion as to how to conceptualize, define, and assess this set of skills, and above all, how to foster them. Recent writings by Heckman refer to these skills as “character skills” while others have termed them “life skills,” “21st century skills,” “socio-emotional skills,” or “soft skills. ” Regardless of the term used, many of these skills fall under the more clearly defined umbrella of executive functions and self-regulation. While these skills, or more aptly, competencies necessary for healthy and productive lives have been referred to as “non-cognitive,” in fact cognitive processes are at the heart of self-regulation. Such brain processes allow us to flexibly regulate emotions, control anger or strong emotional reactions and maintain calm under pressure according to the demands of a particular context. These domains of