Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards automated detection of feature interactions

The feature interaction problem occurs when the addition of a new feature to a system disrupts the existing services and features This paper describes a tabular notation for specifying the functional behavior of features It also describes how four classes of feature interactions can be detected when features are speci ed in this new notation Our goal is to develop a tool that can automatically analyze feature speci cations and detect interactions at the speci cation stage of development Introduction How does one add features to a system without disrupting the services and features already provided A more di cult but related problem is how can one ensure that combinations of independently developed services and features behave as expected These questions and other variations of the feature interaction problem have plagued the telecom munications industry for several years More generally they are problems that a ect the development and evolution of all service oriented software We use the following de nitions of service and feature presented in A service provides stand alone functionality For example Plain Old Telephone Ser vice POTS is a service A feature provides added functionality to an existing feature or service a feature cannot operate stand alone For example Call Waiting adds functionality to POTS A feature interaction occurs when one feature a ects the behavior of another Sometimes feature interactions are desired and one feature is explicitly designed to interact with another In such a case one wants to determine that the features not only interact but that the interaction conforms to the speci ed behavior of the individual features In most cases one simply wants to ensure that supposedly non interacting features cannot interact This research has been supported in part by the Natural Sciences and Engineering Research Council of Canada grant FSP with matching funds from Bell Northern Research Ltd Feature1 Feature2 Featuren e1
A lacustrine record of early Holocene watershed events and vegetation history, Corvara in Badia, Dolomites (Italy)

The early–middle Holocene lacustrine succession of Corvara in Badia (Italian Dolomites, 1521 m a.s.l.) records landslides and other watershed events before the onset of human pressure. The sensitivity of this archive to relate climate change, watershed processes and vegetation dynamics in the catchment has been explored through a stratigraphic study, including the analysis of sedimentological features, magnetic properties, palaeobotanical records and radiocarbon dating. A palaeolake existed between 10.1 k and 7 k cal. yr BP and was surrounded by a dense conifer forest. Long‐term forest dynamics driven by ecological processes and by climatic conditions favourable to upward forest expansion is recorded throughout the pollen record. Within the fine clastic sedimentation, distinct layers enriched in organic debris of terrestrial origin have been attributed to instant events produced by mass movements. Their age fits the chronology of large landslide events already known in the catchment, enabling correlation of the field evidence of landslides with the lacustrine record. Landslide frequency is controlled by geological and structural factors, but it is significantly modulated by the centennial–millennial climatic phases that characterise the Holocene in the Alps. The taphonomical properties of pollen and macroremains provided valuable insight on the mechanism of watershed processes. Copyright © 2006 John Wiley & Sons, Ltd.
The persistence of drought impacts across growing seasons: a dynamic stochastic analysis

Agricultural producers throughout much of the United States experienced one of the most severe droughts in the last 100 years during the years 1999-2006. The prolonged nature of this drought highlights a need to better understand the impacts and management of drought across growing seasons, rather than just within a growing season. Producers express specific concern about the tendency of drought impacts to persist even after drought itself has subsided. The persistence of drought impacts has received limited attention in the economics literature. The objectives of this study are two-fold: 1) to determine whether inter-year dynamics, in the form of agronomic constraints and financial flows, can cause persistence of a drought's impact in years subsequent to the drought, and 2) to determine whether the impact of one year of drought can alter the impact of a subsequent year of drought. A multi-year, dynamic and stochastic decision model is developed in a discrete stochastic programming framework and solved to address the objectives. The structure and parameters of the farm-level model are based on irrigated row crop farms in eastern Oregon, USA. Analysis of the model's solution reveals the following results: 1) the impact of a drought can persist long after the drought subsides, and 2) the impact of one year of drought can alter the impact of a subsequent year of drought. Potential implications for the administration of drought-related assistance are discussed briefly.
Temperature Gradients and Materials Properties Measurements using Ultrasonic Guided Waves

A novel technique for the measurement of Elastic Moduli of materials as well as measurement of temperature gradients using ultrasonic waveguides is described here. The range of temperature measurement was from room temperature to maximum utility temperature of waveguides or maximum measurable value of thermocouple temperature, typically beyond 1000°C. In this work, thermocouple wires have been used as a wave guide subsequently time of flight and temperature data was collected from laboratory experiments from 45°C to 1100°C. The changes in sound speed can be determined through the time of flight variations of the wave that also depends on the particular geometry of waveguide.
Resistance of mRNAs with AUG-proximal nonsense mutations to nonsense-mediated decay reflects variables of mRNA structure and translational activity

Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that recognizes and selectively degrades mRNAs carrying premature termination codons (PTCs). The level of sensitivity of a PTC-containing mRNA to NMD is multifactorial. We have previously shown that human β-globin mRNAs carrying PTCs in close proximity to the translation initiation AUG codon escape NMD. This was called the ‘AUG-proximity effect’. The present analysis of nonsense codons in the human α-globin mRNA illustrates that the determinants of the AUG-proximity effect are in fact quite complex, reflecting the ability of the ribosome to re-initiate translation 3′ to the PTC and the specific sequence and secondary structure of the translated ORF. These data support a model in which the time taken to translate the short ORF, impacted by distance, sequence, and structure, not only modulates translation re-initiation, but also impacts on the exact boundary of AUG-proximity protection from NMD.
First Steps Toward a Motor Imagery Based Stroke BCI: New Strategy to Set up a Classifier

A new approach in motor rehabilitation after stroke is to use motor imagery (MI). To give feedback on MI performance brain–computer interface (BCIs) can be used. This requires a fast and easy acquisition of a reliable classifier. Usually, for training a classifier, electroencephalogram (EEG) data of MI without feedback is used, but it would be advantageous if we could give feedback right from the beginning. The sensorimotor EEG changes of the motor cortex during active and passive movement (PM) and MI are similar. The aim of this study is to explore, whether it is possible to use EEG data from active or PM to set up a classifier for the detection of MI in a group of elderly persons. In addition, the activation patterns of the motor cortical areas of elderly persons were analyzed during different motor tasks. EEG was recorded from three Laplacian channels over the sensorimotor cortex in a sample of 19 healthy elderly volunteers. Participants performed three different tasks in consecutive order, passive, active hand movement, and hand MI. Classifiers were calculated with data of every task. These classifiers were then used to detect event-related desynchronization (ERD) in the MI data. ERD values, related to the different tasks, were calculated and analyzed statistically. The performance of classifiers calculated from passive and active hand movement data did not differ significantly regarding the classification accuracy for detecting MI. The EEG patterns of the motor cortical areas during the different tasks was similar to the patterns normally found in younger persons but more widespread regarding localization and frequency range of the ERD. In this study, we have shown that it is possible to use classifiers calculated with data from passive and active hand movement to detect MI. Hence, for working with stroke patients, a physiotherapy session could be used to obtain data for classifier set up and the BCI-rehabilitation training could start immediately.
Tra2-Mediated Recognition of HIV-1 5′ Splice Site D3 as a Key Factor in the Processing of vpr mRNA

ABSTRACT Small noncoding HIV-1 leader exon 3 is defined by its splice sites A2 and D3. While 3′ splice site (3′ss) A2 needs to be activated for vpr mRNA formation, the location of the vpr start codon within downstream intron 3 requires silencing of splicing at 5′ss D3. Here we show that the inclusion of both HIV-1 exon 3 and vpr mRNA processing is promoted by an exonic splicing enhancer (ESE vpr ) localized between exonic splicing silencer ESSV and 5′ss D3. The ESE vpr sequence was found to be bound by members of the Transformer 2 (Tra2) protein family. Coexpression of these proteins in provirus-transfected cells led to an increase in the levels of exon 3 inclusion, confirming that they act through ESE vpr . Further analyses revealed that ESE vpr supports the binding of U1 snRNA at 5′ss D3, allowing bridging interactions across the upstream exon with 3′ss A2. In line with this, an increase or decrease in the complementarity of 5′ss D3 to the 5′ end of U1 snRNA was accompanied by a higher or lower vpr expression level. Activation of 3′ss A2 through the proposed bridging interactions, however, was not dependent on the splicing competence of 5′ss D3 because rendering it splicing defective but still competent for efficient U1 snRNA binding maintained the enhancing function of D3. Therefore, we propose that splicing at 3′ss A2 occurs temporally between the binding of U1 snRNA and splicing at D3.
Neutral Stochastic Differential Delay Equations with Markovian Switching

Abstract Neutral stochastic differential delay equations (NSDDEs) have recently been studied intensively (see Kolmanovskii, V.B. and Nosov, V.R., Stability and Periodic Modes of Control Systems with Aftereffect; Nauka: Moscow, 1981 and Mao X., Stochastic Differential Equations and Their Applications; Horwood Pub.: Chichester, 1997). Given that many systems are often subject to component failures or repairs, changing subsystem interconnections and abrupt environmental disturbances etc., the structure and parameters of underlying NSDDEs may change abruptly. One way to model such abrupt changes is to use the continuous‐time Markov chains. As a result, the underlying NSDDEs become NSDDEs with Markovian switching which are hybrid systems. So far little is known about the NSDDEs with Markovian switching and the aim of this paper is to close this gap. In this paper we will not only establish a fundamental theory for such systems but also discuss some important properties of the solutions e.g. boundedness and stability.
Pex9p is a new yeast peroxisomal import receptor for PTS1-containing proteins

ABSTRACT Peroxisomal proteins carrying a type 1 peroxisomal targeting signal (PTS1) are recognized by the well-conserved cycling import receptor Pex5p. The yeast YMR018W gene encodes a Pex5p paralog and newly identified peroxin that is involved in peroxisomal import of a subset of matrix proteins. The new peroxin was designated Pex9p, and it interacts with the docking protein Pex14p and a subclass of PTS1-containing peroxisomal matrix enzymes. Unlike Pex5p, Pex9p is not expressed in glucose- or ethanol-grown cells, but it is strongly induced by oleate. Under these conditions, Pex9p acts as a cytosolic and membrane-bound peroxisome import receptor for both malate synthase isoenzymes, Mls1p and Mls2p. The inducible Pex9p-dependent import pathway provides a mechanism for the oleate-inducible peroxisomal targeting of malate synthases. The existence of two distinct PTS1 receptors, in addition to two PTS2-dependent import routes, contributes to the adaptive metabolic capacity of peroxisomes in response to environmental changes and underlines the role of peroxisomes as multi-purpose organelles. The identification of different import routes into peroxisomes contributes to the molecular understanding of how regulated protein targeting can alter the function of organelles according to cellular needs. Highlighted Article: Oleate-inducible targeting of malate synthases into yeast peroxisomes is facilitated by the newly identified PTS1 receptor Pex9p, which exhibits a strong selectivity for these isoenzymes.
Paleomagnetic evidence for Cenozoic block rotations in the Tadjik depression (Central Asia)

This paper presents results of a paleomagnetic study of Oligo-Miocene red beds of the Tadjik depression in Central Asia. We sampled about 530 cores at 69 sites and six localities across the depression and along the western border of the Pamirs. Samples were thermally demagnetized and high-temperature components appear to predate folding of upper tertiary age. Throughout the depression, paleomagnetic inclinations are consistent with those observed on the stable Turan platform, at the western margin of the depression. However, they are shallower by about 30° than the inclination predicted from the reference apparent polar wander path. This appears to indicate a 23° difference in latitude, which is incompatible with paleogeographic reconstructions for the Tertiary. A sound interpretation of this anomaly would require a better-constrained Tertiary paleomagnetic reference for Asia. Inside the Tadjik depression, paleomagnetic declinations are all significantly rotated, counterclockwise with respect to those measured on the Turan platform. The eastern part of the depression is a domain of large rotation (52°±13° to 46°±15°), whereas smaller amounts of rotation have occurred in the western part (27°±14° to 14°±15°). The similarity between Tertiary and Cretaceous data available for the area shows that rotations have occurred since the Miocene. Little or no paleomagnetic rotations are observed in the ranges bordering the northern and western parts of the depression. Paleomagnetic and structural data suggest that block rotations in the Tadjik depression are associated with indentation of the Pamirs into stable Asia. At a larger scale, observed rotations are compatible with a model of regional sinistral wrenching, along a strip running from the Gulf of Oman to Lake Baikal.
S-nitrosylation of HDAC2 regulates the expression of the chromatin-remodeling factor Brm during radial neuron migration

Dynamic epigenetic modifications play a key role in mediating the expression of genes required for neuronal development. We previously identified nitric oxide (NO) as a signaling molecule that mediates S-nitrosylation of histone deacetylase 2 (HDAC2) and epigenetic changes in neurons. Here, we show that HDAC2 nitrosylation regulates neuronal radial migration during cortical development. Bead-array analysis performed in the developing cortex revealed that brahma (Brm), a subunit of the ATP-dependent chromatin-remodeling complex BRG/brahma-associated factor, is one of the genes regulated by S-nitrosylation of HDAC2. In the cortex, expression of a mutant form of HDAC2 that cannot be nitrosylated dramatically inhibits Brm expression. Our study identifies NO and HDAC2 nitrosylation as part of a signaling pathway that regulates cortical development and the expression of Brm in neurons.
CNS: a GPU-based framework for simulating cortically-organized networks

Computational models whose organization is inspired by the cortex are increasing in both number and popularity. Current instances of such models include convolutional networks, HMAX, Hierarchical Temporal Memory, and deep belief networks. These models present two practical challenges. First, they are computationally intensive. Second, while the operations performed by individual cells, or units, are typically simple, the code needed to keep track of network connectivity can quickly become complicated, leading to programs that are difficult to write and to modify. Massively parallel commodity computing hardware has recently become available in the form of general-purpose GPUs. This helps address the first problem but exacerbates the second. GPU programming adds an extra layer of difficulty, further discouraging exploration. To address these concerns, we have created a programming framework called CNS (’Cortical Network Simulator’). CNS models are automatically compiled and run on a GPU, typically 80-100x faster than on a single CPU, without the user having to learn any GPU programming. A novel scheme for the parametric specification of network connectivity allows the user to focus on writing just the code executed by a single cell. We hope that the ability to rapidly define and run cortically-inspired models will facilitate research in the cortical modeling community. CNS is available1 under the GNU General Public License.
A Spiral-Shaped Printed Monopole Antenna for Mobile Communications

A planar monopole antenna consisting of a printed metal strip of rectangular spiral shape is studied. The spiral generates two resonance modes and radiates at two frequency bands. An example design is given where the lower operating band covers the GSM900 band, and the upper operating band covers DCS1800, PCS 1900 and UMTS2000 bands. This multi-band antenna is compact and lightweight and it can be fabricated at very low cost by etching the spiral on an FR4/Epoxy substrate and feeding with a 50Omega microstrip line
Two-Component Systems of Corynebacterium glutamicum: Deletion Analysis and Involvement of the PhoS-PhoR System in the Phosphate Starvation Response

ABSTRACT Corynebacterium glutamicum contains genes for 13 two-component signal transduction systems. In order to test for their essentiality and involvement in the adaptive response to phosphate (Pi) starvation, a set of 12 deletion mutants was constructed. One of the mutants was specifically impaired in its ability to grow under Pi limitation, and therefore the genes lacking in this strain were named phoS (encoding the sensor kinase) and phoR (encoding the response regulator). DNA microarray analyses with the C. glutamicum wild type and the ΔphoRS mutant supported a role for the PhoRS system in the adaptation to Pi starvation. In contrast to the wild type, the ΔphoRS mutant did not induce the known Pi starvation-inducible (psi) genes within 1 hour after a shift from Pi excess to Pi limitation, except for the pstSCAB operon, which was still partially induced. This indicates an activator function for PhoR and the existence of at least one additional regulator of the pst operon. Primer extension analysis of selected psi genes (pstS, ugpA, phoR, ushA, and nucH) confirmed the microarray data and provided evidence for positive autoregulation of the phoRS genes.
Multi-Modal Retrieval for Multimedia Digital Libraries: Issues, Architecture, and Mechanisms

Supporting effective and efficient retrieval of multimedia data is a challenging problem in building a digital library. In this paper, we examine the issues related to accommodating multi-modal retrieval of multimedia data (text, image, video and audio), and propose 2M2Net as a generic framework for such versatile retrieval in multimedia digital libraries. The retrieval is conducted based on the integration of multi-modal features including both semantic keywords and media-specific low-level features. This framework is capable of progressive improvement of its retrieval performance, by applying the learning-from-elements strategy to propagate keyword annotations, as well as the query profiling strategy to facilitate effective retrieval using historic information of the previously processed queries.
International Conference on Engineering Design, Iced'07 a Cognitive and Computational Basis for Designing

This paper presents a set of concepts that provides the cognitive and computational foundations for answering fundamental questions about designerly behaviour. A design agent should be dynamic and able to handle changes in external representations that describe its designs and changes in how it is guided by its past experiences. Such a view of agency is afforded by situated design computing and can represent and explain much designerly behaviour. It can model how a designer can commence designing before all the requirements have been specified, how two designers presented with the same specifications produce different designs, how the same designer later confronted with the same requirements produces a different design to the previous one, and how a designer can change their design trajectory during the activity of designing. This view is built upon three foundational concepts: knowledge grounded in interaction, constructive memory, situatedness. The concepts build on notions of memory that are often traced back to Dewey and Bartlett, although we use contemporary descriptions. Memory is not understood primarily as allowing for the retrieval of an object from a data store by knowing its physical location; it is guiding an experience in a fashion similar to how past experiences progressed, and recognising that this is so. The paper explicates experiences and situations and discusses implementation requirements. 1 INTRODUCTION How is it possible that a designer can commence designing before all the requirements have been specified? How is it that two designers presented with the same specifications produce different designs? How is it that the same designer later confronted with the same requirements produces a different design to the previous design? How is it that a designer can change their design trajectory during the activity of designing. Designing is often characterized by abstractness and an incomplete understanding of the problem and solution. Designers cope with this by exploring the space of requirements as they explore the space of possible conceptual designs. A design agent should therefore be dynamic and able to handle change, both in external representations that describe its designs and in how it is guided by its past experiences. Such a view of agency is afforded by situated design computing. This is built upon three foundational concepts: knowledge grounded in interaction, constructive memory and situatedness. This paper presents a set of concepts that provide the cognitive and computational foundations for answering these fundamental questions. Their bases are experiential notions …
High-gain current amplifiers for low-power MOSFET-C filters

Current amplifiers have been proposed as alternatives for low-power MOSFET-C or active-RC filters. High gain of the proposed current amplifiers relies on internal high impedance nodes. Such high impedance is realised using positive feedback cross-coupling configuration to cancel its negative feedback counterpart. Two different output stages, namely class-A and class-AB are also introduced. Bias circuits suitable for the proposed amplifiers are also introduced where they further help minimise power consumption and silicon area in a high-order filter design. The proposed circuits employed in a simple second-order filter were compared with a conventional folded-cascode OTA amplifier under 1-V supply. Simulation results with 0.18mum CMOS process indicate correct functionalities and superior linearity performance offered by the proposed amplifiers