Miracle-dz/UniFAR-FTUs huggingface dataset:
Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization

Small RNAs (sRNAs) can operate as regulatory agents to control protein expression by interaction with the 5′ untranslated region of the mRNA. We have developed a physicochemical framework, relying on base pair interaction energies, to design multi-state sRNA devices by solving an optimization problem with an objective function accounting for the stability of the transition and final intermolecular states. Contrary to the analysis of the reaction kinetics of an ensemble of sRNAs, we solve the inverse problem of finding sequences satisfying targeted reactions. We show here that our objective function correlates well with measured riboregulatory activity of a set of mutants. This has enabled the application of the methodology for an extended design of RNA devices with specified behavior, assuming different molecular interaction models based on Watson-Crick interaction. We designed several YES, NOT, AND, and OR logic gates, including the design of combinatorial riboregulators. In sum, our de novo approach provides a new paradigm in synthetic biology to design molecular interaction mechanisms facilitating future high-throughput functional sRNA design.
A Short Survey of Recommendation Technologies in Travel and Tourism

Recommendation has a long history as a successful application area of Artificial Intelligence. The demand of e-commerce platforms (e.g., amazon.com) to improve the accessibility of large productand service assortments contributed to an increased popularity of recommendation technologies. Three basic technologies supporting the personalized recommendation of products and services are presented in this paper. In order to take into account the focus of this special issue, we provide a discussion of the application of those technologies in the tourism domain (e.g., recommendation of travel destinations) with a special focus on mobile environments. Recommendation Technologies The increasing size and complexity of product assortments offered by e-commerce platforms requires appropriate technologies which alleviate the retrieval of products by online customers. Different recommendation technologies have been developed to help customers to easily find the best matching product. Those technologies have been successfully applied in different domains such as financial services, electronic goods, or movies. An overview of applications exploiting recommender technologies can be found in [16]. The most widespread technology is collaborative filtering (CF), which exploits user ratings of products in order to identify additional products that the active user may like as well [6]. User-based and item-based collaborative filtering are two basic variants of this technology. As shown in Figure 1, both variants are predicting to which extend the active user (in this case User3) would like currently unrated items. User-based approaches to collaborative filtering try to identify the k nearest neighbours of the active user (users having similar tastes), and calculate a prediction of the active user’s rating for a specific item. This rating can be defined, for example, as the weighted average of the k nearest neighbours’ ratings [6]. In the simplified example of Figure 1, User1 is found to be the nearest neighbour (k=1) of User3 (the active user) and his/her rating for the 4 product (‘Conspiracy Theory’) will be taken as prediction for the rating of User3 (rate=2). In contrast, item-based collaborative filtering is searching for items which received similar ratings from other users and were also (positively) rated by the active user. In the example
Integrating approximate depth data into dense image correspondence estimation

High-quality dense image correspondence estimation between two images is an essential prerequisite for many tasks in visual media production, one prominent example being view interpolation. Due to the ill-posed nature of the correspondence estimation problem, errors occur frequently for a number of problematic conditions, among them occlusions, large displacements and low-textured regions. In this paper, we propose to use approximate depth data from low-resolution depth sensors or coarse geometric proxies to guide the high-resolution image correspondence estimation. We counteract the effect of uncertainty in the prior by exploiting the coarse-to-fine image pyramid used in our estimation algorithm. Our results show that even with only approximate priors, visual quality improves considerably compared to an unguided algorithm or a pure depth-based interpolation.
The Effects of Science Research Based Competitions on High School Students' Responses to Science

The purpose of this study is to understand the effects of Science Research Based Competitions (SRBCs) on high school students’ responses to science. SRBCs were primarily designed to develop students’ interest in science, their motivation for science learning and their science reasoning in order to provide a platform for students to show potential for carrying out research in science. But, despite their popularity, little research has so far been undertaken to evaluate the effects of SRBCs. The study explores the effects of SRBCs on students’ responses to science from the perspective of three different groups of people: key informants (government staff, SRBC funders), teachers and students. A series of case studies was carried out in six residential schools in Malaysia. Data were gathered from four key informants, six teachers and 360 sixteen-year-old student participants, divided into six groups, in Form 4 of secondary school. Students’ responses to science were explored in a number of ways. Data on attitudes towards science were gathered through the Relevance of Science Education (ROSE) questionnaire, and the findings are compared with those of the ROSE National Survey Data for Malaysia carried out in 2004. Additional data were gathered through interviews with students and from student diaries. Students in residential schools showed more positive responses to science in a number of areas when compared with the ROSE National Survey Data. In particular, students expressed a preference for jobs which favoured recognition after accomplishing challenges, and which offered creative tasks. In contrast, they shared similar views to those found in the national survey towards school science. The study indicates that SRBCs deepen students’ interest in pursuing science and create an ability to apply knowledge which is related to it. The students reported that science is much more enjoyable when it involves autonomous learning and research activity. Students were influenced by their mentors (the teachers running the SRBCs in their schools), the types of project and the degree of external involvement. The teachers reported positive developments in their students’ science processing skills, and their knowledge and awareness of science in general. The students also developed confidence in time management, communication and handling stress along with the project. This represents a revealing insight into the views of the three main components of SRBCs; the organisers/sponsors, the practitioners and the participants.
Myenteric plexus is differentially affected by infection with distinct Trypanosoma cruzi strains in Beagle dogs

Chagasic megaoesophagus and megacolon are characterised by motor abnormalities related to enteric nervous system lesions and their development seems to be related to geographic distribution of distinct Trypanosoma cruzi subpopulations. Beagle dogs were infected with Y or Berenice-78 (Be-78) T. cruzi strains and necropsied during the acute or chronic phase of experimental disease for post mortem histopathological evaluation of the oesophagus and colon. Both strains infected the oesophagus and colon and caused an inflammatory response during the acute phase. In the chronic phase, inflammatory process was observed exclusively in the Be-78 infected animals, possibly due to a parasitism persistent only in this group. Myenteric denervation occurred during the acute phase of infection for both strains, but persisted chronically only in Be-78 infected animals. Glial cell involvement occurred earlier in animals infected with the Y strain, while animals infected with the Be-78 strain showed reduced glial fibrillary acidic protein immunoreactive area of enteric glial cells in the chronic phase. These results suggest that although both strains cause lesions in the digestive tract, the Y strain is associated with early control of the lesion, while the Be-78 strain results in progressive gut lesions in this model.
Perceptions of Work Contexts: Disentangling Influences at Multiple Levels of Analysis

Individuals’ perceptions of work contexts are ine uenced by factors at both the individual level and the contextual level. However, methodological considerations have often resulted in researchers choosing a single level of analysis when studying perceptions of work environments. The current study investigated individual and contextual ine uences on teachers’ satisfaction within school districts. Hierarchical Linear Models were proposed as a useful method for simultaneously assessing variation in perceptions of community support at two levels of analysis. Perceptions of support were found to vary systematically at both the individual and the organizational level. Hypotheses about di Verent predictors of teacher perceptions at both levels of analysis and mediation across levels were supported. Implications for the assessment of employee perceptions in organizations are discussed.
Persistent audio modelling for background determination

This paper is concerned with modelling background audio online to detect foreground sounds in complex audio environments for surveillance and smart home applications. We examine and expand upon previous work in the audio and video domains, and propose a new implementation of an audio background modelling algorithm, addressing the complexities of audio data. A number of audio features characterizing different aspects of the audio content were analysed to determine the factors relevant to the determination of the background audio. We test the algorithms on three audio data sets of varying complexity. The new approach was successful in modelling the background audio for the test data.
Title page

19 Stopping performance is known to depend on low-level motion features, such as 20 movement velocity. It is not known, however, whether it is also subject to high-level 21 motion constraints. Here, we report results of fifteen subjects instructed to connect 22 four target points depicted on a digitizing tablet and stop 'as rapidly as possible' upon 23 hearing a 'stop' cue (tone). Five subjects connected target points with straight paths 24 while eleven subjects generated movements corresponding to coarticulation 25 between adjacent movement components. For the non-coarticulating and 26 coarticulating subjects, stopping performance was not correlated or only weakly 27 correlated with motion velocity, respectively. The generation of a straight point-to28 point movement or a smooth, curved trajectory was not disturbed by the occurrence 29 of a 'stop' cue. Overall, the results indicate that stopping performance is subject to 30 high-level motion constraints, such as the completion of a geometrical plan and that 31 globally planned movements, once started, must run to completion providing 32 evidence for the definition of a motion primitive as an unstoppable motion element. 33 34
Attenuation-Predistortion Linearization of CMOS OTAs With Digital Correction of Process Variations in OTA-C Filter Applications

An architectural attenuation-predistortion linearization scheme for a wide range of operational transconductance amplifiers (OTAs) is proposed and demonstrated with a transconductance-capacitor (G<sub>m</sub>-C) filter. The linearization technique utilizes two matched OTAs to cancel output harmonics, creating a robust architecture. Compensation for process variations and frequency-dependent distortion based on Volterra series analysis is achieved by employing a delay equalization scheme with on-chip programmable resistors. An OTA design with the proposed broadband linearization method has third-order inter-modulation (IM3) distortion better than -74 dB up to 350 MHz with 0.2V¿¿ input, 70 dB signal-to-noise ratio (SNR) in 1 MHz bandwidth, and 5.2 mW power consumption. The distortion-cancellation technique enables an IM3 improvement of up to 22 dB compared to a commensurate OTA without linearization. A proof-of-concept low-pass filter with the linearized OTAs has a measured IM3 < - 70 dB and 54.5 dB dynamic range over its 195 MHz bandwidth. The standalone OTAs and the filter were fabricated on a 0.13 ¿m CMOS test chip with 1.2 V supply.
Understanding phases and styles of object-oriented systems' evolution

Understanding the phases and styles of evolution of software systems can provide valuable insight in support of project management. We present a method for studying the evolution of object-oriented software at system/subsystem level and analyzing the underlying factors that drive its unfolding over time. This method relies on analyzing the design-level structural changes between two subsequent software versions to identify additions, removals, moves, renamings and signature-changes of classes, interfaces, and their methods and fields, represented as change trees. A sequence of such change trees constitutes the system's evolution profile. Based on discrete system evolution profiles, three types of analyses: phasic analysis, gamma analysis, and optimal matching analysis, are applied, to abstract an overall sequential pattern and structural properties of system evolution phases and to develop the typology of system evolution styles. We report on two case studies evaluating our approach.
Sub-Micrometer Anatomical Models of the Sarcolemma of Cardiac Myocytes Based on Confocal Imaging

We describe an approach to develop anatomical models of cardiac cells. The approach is based on confocal imaging of living ventricular myocytes with submicrometer resolution, digital image processing of three-dimensional stacks with high data volume, and generation of dense triangular surface meshes representing the sarcolemma including the transverse tubular system. The image processing includes methods for deconvolution, filtering and segmentation. We introduce and visualize models of the sarcolemma of whole ventricular myocytes and single transversal tubules. These models can be applied for computational studies of cell and sub-cellular physical behavior and physiology, in particular cell signaling. Furthermore, the approach is applicable for studying effects of cardiac development, aging and diseases, which are associated with changes of cell anatomy and protein distributions.
SINGLE-SHOT LONGITUDINAL BUNCH PROFILE MEASUREMENTS AT FLASH USING ELECTRO-OPTIC DETECTION: EXPERIMENT, SIMULATION, AND VALIDATION.

At the superconducting linac of FLASH at DESY, we have installed an electro-optic (EO) experiment for singleshot, non-destructive measurements of the longitudinal electric charge distribution of individual electron bunches. The time profile of the electric bunch field is electrooptically encoded onto a chirped titanium-sapphire laser pulse. In the decoding step, the profile is retrieved either from a cross-correlation of the encoded pulse with a 30 fs laser pulse, obtained from the same laser (electrooptic temporal decoding, EOTD), or from the spectral intensity of the transmitted probe pulse (electro-optic spectral decoding, EOSD). At FLASH, the longitudinally compressed electron bunches have been measured during FEL operation with a resolution of better than 50 fs. The electrooptic process in gallium phosphide was numerically simulated using as input data the bunch shapes determined with a transverse-deflecting RF structure. In this contribution, we present electro-optically measured bunch profiles and compare them with the simulation.
A Digital Signature Scheme Based on CV P∞

In Crypto 1997, Goldreich, Goldwasser and Halevi (GGH) proposed a lattice analogue of McEliece public key cryptosystem, which security is related to the hardness of approximating the closest vector problem (CVP) in a lattice. Furthermore, they also described how to use the same principle of their encryption scheme to provide a signature scheme. Practically, this cryptosystem uses the euclidean norm, l 2 - norm, which has been used in many algorithms based on lattice theory. Nonetheless, many drawbacks have been studied and these could lead to cryptanalysis of the scheme. In this paper, we present a novel method of reducing a vector under the l ∞ -norm and propose a digital signature scheme based on it. Our scheme takes advantage of the l ∞ -norm to increase the resistance of the GGH scheme and to decrease the signature length. Furthermore, after some other improvements, we obtain a very eﬃcient signature scheme, that trades the security level, speed and space.
A spectroscopic study of some suspected chemically peculiar stars

Time-resolved spectra in the 410 - 700 nm range havebeenobtainedtoinvestigate10starswhichareclassiedas suspected chemically peculiar stars in The General Catalogue of Ap and Am stars by Renson et al. (1991) or in the latest literature. Among the studied stars, HD20629 presents metal abun- dances which are signicantly different from main sequence star values and it should be classied as Silicon star. From the Hei587.6nmline,weconcludethatHD35575isaheliumweak star. Because of the found radial velocity variability and the de- rived abundances, the periodic photometric variable HD38602 could be an ellipsoidal variable.
A novel reduced switch count single-phase to three-phase AC/AC converter

Recently, reduced-switch-count converters have garnered particular attention in power electronic systems due to the numerous advantages such as low cost, low weight and volume, and high reliability offered by them. In this paper, a new reduced-switch-count converter topology is proposed as a single-phase to three-phase ac/ac converter. This converter employs less number of semiconductor devices compared to former single-phase to three-phase ac/ac converters. The modulation scheme of the novel converter is developed and two methods are devised for enhancing DC bus voltage utilization and hence minimizing the output voltage THD and the switching loss. The proposed converter features sinusoidal input and output, unity input power factor, and more importantly, low manufacturing cost. The validity of theoretical issues is confirmed by simulation results.
Essential fatty acid requirements in human nutrition.

Arachidonic acid (20:4 omega-6) and docosahexaenoic acid (22:6 omega-3) are major acyl components of cell membrane phospholipids, and are particularly enriched in the nonmyelin membranes of the central nervous system. Dietary deficiency of linoleic acid (18:2 omega-6) and linolenic acid (18:3 omega-3) during development has been shown to result in reduced levels of 20:4 omega-6 and 22:6 omega-3 in the developing central nervous system, and this has been associated with altered learning behaviour and visual function. Synthesis of 20:4 omega-6 and 22:6 omega-3 depends on the dietary intake of 18:2 omega-6 and 18:3 omega-3, respectively, and the activity of the fatty acid desaturase-elongase enzymes. Oxidation of 18:2 omega-6 and 18:3 omega-3 for energy, or direct acylation of 18:2 omega-6 into triglycerides, cholesteryl esters, and phospholipids, could also influence the amount of 20:4 omega-6 and 22:6 omega-3 formed. The tissue levels of 20:4 omega-6 and 22:6 omega-3, or other (omega-6) and (omega-3) fatty acids, compatible with optimum growth and development or health are not known. The amount of preformed 22:6 omega-3 in the diet of adults, infants fed various milks or formulae, or animals is reflected in the circulating lipid levels of 22:6 omega-3. Human milk levels of (omega-6) and (omega-3) fatty acids vary, depending in part on the mother's diet. A valid, scientific approach to extrapolate dietary essential fatty acid requirements from the composition of human milk or the circulating lipids of infants fed different diets has not been agreed on. (ABSTRACT TRUNCATED AT 250 WORDS)
PARP and RIP 1 are required for autophagy induced by 11'-deoxyverticillin A, which precedes caspase-dependent apoptosis

The epipolythiodioxopiperazines (ETPs) are fungal secondary metabolites proven to trigger both apoptotic and necrotic cell death of tumor cells. However, the underlying mechanism of their regulatory role in macroautophagy and the interplay between autophagy and apoptosis initiated by the ETPs, remain unexplored. In the current work, we found that 11'-deoxyverticillin A (C42), a member of the ETPs, induces autophagosome formation, accumulation of microtubule-associated protein 1 light chain 3-II (LC3-II ) and degradation of sequestosome 1 (SQSTM1/p62). In addition, the LC3-II accrual and p62 degradation occur prior to caspase activation and coincide with PARP activation. Inhibition of autophagy by either chemical inhibitors or by RNA interference single knockdown of essential autophagic genes partially reduces the cell death and the cleavage of both caspase 3 and PARP. Necrostatin-1, a specific inhibitor of necroptosis, inhibits both the augmentation of LC3-II and the cleavage of caspase 3, which was confirmed by depletion of receptor-interacting protein 1 (RIP-1), a crucial necrostatin-1-targeted adaptor kinase mediating cell death and survival. Moreover, inhibition of PARP by either chemical inhibitors or RNA interference provides obvious protection for cell viability and suppresses the LC3-II accretion caused by C42 treatment. Interestingly, double silencing of LC3 and p62 completely suppressed PARP cleavage and concurrently and maximally augmented the PAR formation induced by C42. Collectively, we have demonstrated that C42 enhances the cellular autophagic process, which requires both PARP and RIP-1 participation, preceding and possibly augmenting, the caspase-dependent apoptotic cell death.
Naproxen and Diclofenac Attenuate Atorvastatin-induced Preconditioning of the Myocardium

Statins reduce infarct size (IS) in ischemia-reperfusion injury of the myocardium. Inhibition of cyclooxygenase-2 (COX-2) attenuates this benefit. We investigated the effect of two widely used non-selective non-steroidal anti-inflammatory drugs (NSAIDs) with different degree of anti-COX-2 activity on atorvastatin-mediated preconditioning. Wistar rats received oral atorvastatin (10 mg∙kg-1∙day-1), naproxen (10 mg∙kg-1∙day-1), diclofenac (8 mg∙kg-1∙day-1), atorvastatin+naproxen, atorvastatin+diclofenac or water for three days. Hearts were then excised and perfused in the Langendorff system. Area at risk (AR) and IS were determined after 30 min of regional ischemia and 120 min of reperfusion. Atorvastatin reduced IS by 51.3% compared with controls (14.7 ± 3.9% vs. 30.2 ± 4.6% of the AR; P < 0.001). Naproxen and diclofenac alone did not alter IS compared to control. Diclofenac completely abrogated atorvastatin-mediated protection of the myocardium. Naproxen significantly attenuated but did not eliminate the IS reducing the effect of atorvastatin when compared with controls (P = 0.038). The difference in IS between the atorvastatin+naproxen group and the atorvastatin+diclofenac group showed a strong trend in reaching statistical significance (P = 0.058), but was not found to be significant. Our results suggest relatively small, but noticeable differences among non-selective NSAIDs in their potential to attenuate statin-mediated preconditioning.