Miracle-dz/UniFAR-FTUs huggingface dataset:
Six-month partial suppression of Huntingtin is well tolerated in the adult rhesus striatum

Huntington's disease is caused by expression of a mutant form of Huntingtin protein containing an expanded polyglutamine repeat. One possible treatment for Huntington's disease may be to reduce expression of mutant Huntingtin in the brain via RNA interference. Unless the therapeutic molecule is designed to be allele-specific, both wild-type and mutant protein will be suppressed by an RNA interference treatment. A key question is whether suppression of wild-type as well as mutant Huntingtin in targeted brain regions can be tolerated and result in a net benefit to patients with Huntington's disease. Whether Huntingtin performs essential functions in the adult brain is unclear. Here, we tested the hypothesis that the adult primate brain can tolerate moderately reduced levels of wild-type Huntingtin protein for an extended period of time. A serotype 2 adeno-associated viral vector encoding for a short hairpin RNA targeting rhesus huntingtin messenger RNA (active vector) was bilaterally injected into the striatum of four adult rhesus monkeys. Four additional animals received a comparable vector encoding a scrambled control short hairpin RNA (control vector). General health and motor behaviour were monitored for 6 months. Upon termination, brain tissues were sampled and assessed blindly for (i) huntingtin messenger RNA knockdown; (ii) Huntingtin protein expression; and (iii) neuropathological changes. Reduction in wild-type huntingtin messenger RNA levels averaging ∼30% was measured in the striatum of active vector recipients 6 months post-injection. A widespread reduction in Huntingtin protein levels was also observed by immunohistochemistry in these animals, with an average protein reduction of ∼45% relative to controls measured by western blot analysis in the putamen of active vector recipients. As with control vector recipients, no adverse effects were observed behaviourally, and no neurodegeneration was found on histological examination of active vector recipients. Our results suggest that long-term partial suppression of wild-type Huntingtin may be safe, and thus if a comparable level of suppression of mutant Huntingtin is beneficial, then partial suppression of both wild-type and mutant Huntingtin may result in a net benefit in patients with heterozygous Huntington's disease.
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics

DNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR‐based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross‐reactions with the predator and related species genomes. Here, we use PCR‐free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on a single pea aphid Acyrthosiphon pisum. Sequence reads were matched to three reference databases: Insecta mitogenomes of 587 species, including H. axyridis sequenced here; A. pisum nuclear genome scaffolds; and scaffolds and complete genomes of 13 potential bacterial symbionts. Immediately after feeding, multicopy mtDNA of A. pisum was detected in tens of reads, while hundreds of matches to nuclear scaffolds were detected. Aphid nuclear DNA and mtDNA decayed at similar rates (0.281 and 0.11 h−1 respectively), and the detectability periods were 32.7 and 23.1 h. Metagenomic sequencing also revealed thousands of reads of the obligate Buchnera aphidicola and facultative Regiella insecticola aphid symbionts, which showed exponential decay rates significantly faster than aphid DNA (0.694 and 0.80 h−1, respectively). However, the facultative aphid symbionts Hamiltonella defensa, Arsenophonus spp. and Serratia symbiotica showed an unexpected temporary increase in population size by 1–2 orders of magnitude in the predator guts before declining. Metagenomics is a powerful tool that can reveal complex relationships and the dynamics of interactions among predators, prey and their symbionts.
A survivability model for object-oriented software systems

In this paper, we proposed a survivability model for object-oriented software system for solving the problem of software degradation commonly caused by increasing growth in classes and methods. This is achieved through threshold scheme and software rejuvenation technique. Threshold value (TV) is set as the degradation point for the software system with consideration given to the critical region values (CV) as defined standard metrics like McCabeCyclomatic Complexity (CC) risk thresholds and NASA SATC WMC risk thresholds metrics. A mechanism is also integrated into the model to monitor and determine the continuous growth of methods and classes such that when threshold value (TV) <;= critical value (CV) set within the critical region, the software codes are refreshed and re-initiated. The model is tested using two software programs developed to implement a treemap algorithm using nine (9) attributes. It is observed that software programs with this proposed model embedded into it would prevent code degradation.
Effect of Incomplete Meta-dataset on Average Ranking Method

One of the simplest metalearning methods is the average ranking method. This method uses metadata in the form of test results of a given set of algorithms on given set of datasets and calculates an average rank for each algorithm. The ranks are used to construct the average ranking. We investigate the problem of how the process of generating the average ranking is affected by incomplete metadata including fewer test results. This issue is relevant, because if we could show that incomplete metadata does not affect the final results much, we could explore it in future design. We could simply conduct fewer tests and save thus computation time. In this paper we describe an upgraded average ranking method that is capable of dealing with incomplete metadata. Our results show that the proposed method is relatively robust to omission in test results in the meta datasets.
Metric invariants of tropical conics and factorization of degree--two homogeneous tropical polynomials in three variables

To every tropical conic we associate a certain non–negative symmetric3 × 3 real matrix. The non–diagonal entries of this matrix are met ric invariants of the given tropical conic, up to translation. There exist proper and improper tropical conics, pairs of lines being a particular sort of the latter. We characterize those tropical conics whose associated matrix is tropically sing ular. Again, pairs of lines are among the latter. A tropical conic is defined by an arbitrary degree–two homoge neous tropical polynomial in three variables. The conic is a tree of a very pa rticular kind. Given such a tree, we give a procedure to obtain a defining tropical p olynomial. Finally, we give criteria to decide whether a tropical degre –two homogeneous polynomial in three variables is reducible and, if so, we find a factorization. 2000 Math. Subj. Class. : 05C05; 12K99
Modeling and Simulation for Material Selection and Mechanical Design

This reference describes advanced computer modeling and simulation procedures to predict material properties and component design including mechanical properties, microstructural evolution, and materials behavior and performance. The book illustrates the most effective modeling and simulation technologies relating to surface-engineered compounds, fastener design, quenching and tempering during heat treatment, and residual stresses and distortion during forging, casting, and heat treatment. Written by internationally recognized experts in the field, it enables researchers to enhance engineering processes and reduce production costs in materials and component development.
Image Retrieval based on the Combination of Color Histogram and Color Moment

A novel technique for Content based image retrieval (CBIR) that employs color histogram and color moment of images is proposed. The color histogram has the advantages of rotation and translation invariance and it has the disadvantages of lack of spatial information. In this paper, to improve the retrieval accuracy, a content-based image retrieval method is proposed in which color histogram and color moment feature vectors are combined. For color moment, to improve the discriminating power of color indexing techniques, a minimal amount of spatial information is encoded in the color index by dividing the image horizontally into three equal nonoverlapping regions. The three moments (mean, variance and skewness) are extracted from each region (in this case three regions), for all the color channels. Thus, for a HSV color space, 27 floating point numbers are used for indexing. The HSV (16, 4, 4) quantization scheme has been adopted for color histogram and an image is represented by a vector of 256-dimension. Weights are assigned to each feature respectively and calculate the similarity with combined features of color histogram and color moment using Histogram intersection distance and Euclidean distance as similarity measures. Experimental results show that the proposed method has higher retrieval accuracy in terms of precision than other conventional methods combining color histogram and color moments based on global features approach
How much feedback from visual cortex to lateral geniculate nucleus in cat: A perspective

Corticothalamic feedback is believed to play an important role in selectively regulating the flow of sensory information from thalamus to cortex. But despite its importance, the size and nature of corticothalamic pathway connectivity is not fully understood. In light of recent empirical data, the aim of this paper was to quantify the contribution of area 17 axon connectivity to the synaptic organization of A-laminae in dorsal lateral geniculate nucleus (dLGN) in cat, the best studied corticothalamic pathway. Numerical constraints indicate that most corticogeniculate synapses are not formed with inhibitory interneurons. However, the main finding is that there was an order of magnitude difference between estimates of the mean number of cortical synapses per A-laminae neuron based on individual corticogeniculate axon data (12,000–16,000 cortical synapses per cell) than that previously derived from partial reconstructions of the synaptic input to two physiologically identified relay cells (1200–1500 cortical synapses per cell). In an attempt to reconcile these different estimates, parameter variation and comparative analyses suggest that previous work may have overestimated the density of corticogeniculate efferent neurons and underestimated the total number of synapses per geniculate neuron. But as this analysis did not include area 18 corticogeniculate axons innervating A-laminae, the discrepancy between different estimates may be greater and require further explanation. Thus, the analysis presented here suggests geniculate neurons receive on average a greater number of cortical synapses per cell but from far fewer corticogeniculate axons than previously thought.
Determining Urban Emotion using an unsupervised learning approach: A case study around Majitar, East District, Sikkim

Perception and expectation of citizens is an important factor in urban settlement, planning and management. Hence, there is a need of a participatory citizen centric planning of urban settlement based on spatial data. These perception and expectation may be represented in terms of emotions. Determining Urban Emotions is an approach which can be used to map different types of emotions associated with urbanization. In the recent years, some new methods have been presented for the area of urban and spatial planning that resulted in a fundamental change of the understanding of urban planning. Geographical information system acts as a tool for analyzing urban emotions from various types of data. This paper presents the unsupervised learning approach for determining urban emotions using K-Means algorithm.
A new lip-automatic detection and location algorithm in lip-reading system

This article realized a method applying Haar features to train Adaboost classifier, and combined skin and lip color separation algorithm to form a self-adaptive skin and lip color separation model, which can dynamically adjust constant parameters of skin and lip separation algorithm based on the result of applying Haar features to train Adaboost classifier. The model can dynamically acquire distribution range of skin color and lip color, and improve the effectiveness and robustness of lip-reading deletion. Applying the method to deal with 4000 image in GENKI database, it successfully detected lip area and had the smaller deviation. Lastly, curve fitting for the edge of the lip region was made to locate lip. The results showed that the method was more effective.
Transfer-based statistical translation of Taiwanese sign language using PCFG

This article presents a transfer-based statistical model for Chinese to Taiwanese sign-language (TSL) translation. Two sets of probabilistic context-free grammars (PCFGs) are derived from a Chinese Treebank and a bilingual parallel corpus. In this approach, a three-stage translation model is proposed. First, the input Chinese sentence is parsed into possible phrase structure trees (PSTs) based on the Chinese PCFGs. Second, the Chinese PSTs are then transferred into TSL PSTs according to the transfer probabilities between the context-free grammar (CFG) rules of Chinese and TSL derived from the bilingual parallel corpus. Finally, the TSL PSTs are used to generate the possible translation results. The Viterbi algorithm is adopted to obtain the best translation result via the three-stage translation. For evaluation, three objective evaluation metrics including AER, Top-N, and BLUE and one subjective evaluation metric using MOS were used. Experimental results show that the proposed approach outperforms the IBM Model 3 in the task of Chinese to sign-language translation.
Toward Fault-Tolerant Atomic Data Access in Mutable Distributed Hash Tables

Though the peer-to-peer network based on distributed hash table have scalability and availability features, but most of the distributed hash tables lack the support for the atomic data accessing, this ability is important to build data structures on distributed system. This paper gives the design and implementation of an atomic accessible mutable distributed hash table - FamDHT. The FamDHT use the Paxos distributed consensus protocol to ensure that the simultaneous access to data is executed under a total order agreement. The FamDHT is build on top of the Bamboo DHT, a robust, open-source DHT implementation. At the end of the paper, an evaluation was given
Energy-Efficient Data Aggregation Hierarchy for Wireless Sensor Networks

A network of sensors can be used to obtain state-based data from the area in which they are deployed. To reduce costs, the data, sent via intermediate sensors to a sink, is often aggregated (or compressed). This compression is done by a subset of the sensors called aggregators. Since sensors are usually equipped with small and unreplenishable energy reserves, a critical issue is to strategically deploy an appropriate number of aggregators so as to minimize the amount of energy consumed by transporting and aggregating the data. In this paper, we first study single-level aggregation and propose an Energy-Efficient Protocol for Aggregator Selection (EPAS). Then, we generalize it to an aggregation hierarchy and extend EPAS to a Hierarchical Energy-Efficient Protocol for Aggregator Selection (hEPAS). We derive the optimal number of aggregators with generalized compression and power-consumption models, and present fully distributed algorithms for aggregator deployment. Simulation results show that our algorithms significantly reduce the energy consumption for data collection in wireless sensor networks. Moreover, the algorithms do not rely on particular routing protocols, and are thus applicable to a broad spectrum of application environments.
Low-density polymer gel dosimeters for 3D radiation dosimetry in the thoracic region: A preliminary study

Different low-density polymer gel dosimeters have been constructed that can be used to acquire the radiation dose distribution of IMRT treatments in the thoracic region. A heterogeneous phantom consisting of a low density polymer gel dosimeter sandwiched between two layers of soft tissue equivalent gel has been constructed. As a proof-of-principle, the phantom has been irradiated with a square 4 cm × 4 cm beam. The dose distribution is read out by use of both quantitative NMR spin-spin (R2) and magnetization transfer (MT) imaging. Sources of error in the dose readout have been assessed and are discussed.
Layered dynamic control for interactive character swimming

This paper proposes a layered strategy for controlling character motion in a dynamically varying environment. We illustrate this approach in the context of a physically simulated human swimmer. The swimmer attempts to follow a dynamic target by augmenting cyclic stroke control with a set of pre-specified variations, based on the current state of the character and its environment. Control of a given swim stroke is decomposed into three layers: a basic stroke sequence, a set of per-stroke control variations, and a set of continuously applied control variations. Interactive control of the swimmer is possible as a result of an efficient physical simulation using a simplified fluid model. Our results show layered dynamic control to be an effective adaptive control technique in well conditioned physical simulations such as swimming, where simulation states resulting from control errors are recoverable.
INSTITUTIONALIZATION OF AN INFORMATION SYSTEM THROUGH THE EXERCISE OF POWER

The institutionalisation of an information system is possible only if it is sustained and legitimated by organizational actors and individuals. The system reviewed in this study, the SIAFEM - Integrated System for State Financial Administration, is a large governmental system adopted by the State of Sao Paulo as an accounting and cash management system. Once implemented, it became institutionalized and, subsequently, underwent an expansion as a result of new requirements and following the intervention of powerful actors who made use of it as a control and surveillance tool, thus sustaining its expansion. This study intends to provide a better understanding of the process through which an information system can become institutionalised and subsequently expanded as a consequence of the exercise of power. The expansion of an information system sustained by actors who use it as an instrument to increase their power is a theme underdeveloped in the literature. Therefore, this study could represent a step further in the analysis of an institutionalised system.
Cheminformatics-Based Drug Design Approach for Identification of Inhibitors Targeting the Characteristic Residues of MMP-13 Hemopexin Domain

Background MMP-13, a zinc dependent protease which catalyses the cleavage of type II collagen, is expressed in osteoarthritis (OA) and rheumatoid arthritis (RA) patients, but not in normal adult tissues. Therefore, the protease has been intensively studied as a target for the inhibition of progression of OA and RA. Recent reports suggest that selective inhibition of MMP-13 may be achieved by targeting the hemopexin (Hpx) domain of the protease, which is critical for substrate specificity. In this study, we applied a cheminformatics-based drug design approach for the identification and characterization of inhibitors targeting the amino acid residues characteristic to Hpx domain of MMP-13; these inhibitors may potentially be employed in the treatment of OA and RA. Methodology/Principal Findings Sequence-based mutual information analysis revealed five characteristic (completely conserved and unique), putative functional residues of the Hpx domain of MMP-13 (these residues hereafter are referred to as HCR-13pf). Binding of a ligand to as many of the HCR-13pf is postulated to result in an increased selective inhibition of the Hpx domain of MMP-13. Through the in silico structure-based high-throughput virtual screening (HTVS) method of Glide, against a large public library of 16908 molecules from Maybridge, PubChem and Binding, we identified 25 ligands that interact with at least one of the HCR-13pf. Assessment of cross-reactivity of the 25 ligands with MMP-1 and MMP-8, members of the collagenase family as MMP-13, returned seven lead molecules that did not bind to any one of the putative functional residues of Hpx domain of MMP-1 and any of the catalytic active site residues of MMP-1 and -8, suggesting that the ligands are not likely to interact with the functional or catalytic residues of other MMPs. Further, in silico analysis of physicochemical and pharmacokinetic parameters based on Lipinski's rule of five and ADMET (absorption, distribution, metabolism, excretion and toxicity) respectively, suggested potential utility of the compounds as drug leads. Conclusions/Significance We have identified seven distinct drug-like molecules binding to the HCR-13pf of MMP-13 with no observable cross-reactivity to MMP-1 and MMP-8. These molecules are potential selective inhibitors of MMP-13 that can be experimentally validated and their backbone structural scaffold could serve as building blocks in designing drug-like molecules for OA, RA and other inflammatory disorders. The systematic cheminformatics-based drug design approach applied herein can be used for rational search of other public/commercial combinatorial libraries for more potent molecules, capable of selectively inhibiting the collagenolytic activity of MMP-13.