Miracle-dz/UniFAR-FTUs huggingface dataset:
Vertex-Context Sampling for Weighted Network Embedding

In recent years, network embedding methods have garnered increasing attention because of their effectiveness in various information retrieval tasks. The goal is to learn low-dimensional representations of vertexes in an information network and simultaneously capture and preserve the network structure. Critical to the performance of a network embedding method is how the edges/vertexes of the network is sampled for the learning process. Many existing methods adopt a uniform sampling method to reduce learning complexity, but when the network is non-uniform (i.e. a weighted network) such uniform sampling incurs information loss. The goal of this paper is to present a generalized vertex sampling framework that works seamlessly with most existing network embedding methods to support weighted instead of uniform vertex/edge sampling. For efficiency, we propose a delicate sequential vertex-to-context graph data structure, such that sampling a training pair for learning takes only constant time. For scalability and memory efficiency, we design the graph data structure in a way that keeps space consumption low without requiring additional space. In addition to implementing existing network embedding methods, the proposed framework can be used to implement extensions that feature high-order proximity modeling and weighted relation modeling. Experiments conducted on three datasets, including a commercial large-scale one, verify the effectiveness and efficiency of the proposed weighted network embedding methods on a variety of tasks, including word similarity search, multi-label classification, and item recommendation.
Tighter Layouts of the Cube-Connected Cycles

F.P. Preparata and J. Vuillemin (1981) proposed the cube-connected cycles (CCC) and its compact layout. We give a new layout of the CCC which uses less than half the area of the Preparata-Vuillemin layout. We also give a lower bound on the layout area of the CCC. The area of the new layout deviates from this bound by a small constant factor. If we "unfold" the cycles in the CCC, the resulting structure can be laid out in optimal area.
Reduction of tertiary amine N-oxides by cytochrome P-450. Mechanism of the stimulatory effect of flavins and methyl viologen.

The stimulatory effect of flavins (riboflavin, FMN, and FAD) and viologens (methyl viologen and benzyl viologen) on the anaerobic reduction of tertiary amine N-oxides in liver microsomes was investigated. The reduced flavins or viologens hardly reduced tiaramide N-oxide and imipramine N-oxide in the absence of microsomes. The stimulatory effect of flavins or viologens was completely abolished under an atmosphere of carbon monoxide. FMN or methyl viologen added to the microsomal suspension was rapidly reduced after the addition of NADPH, probably through NADPH-cytochrome c reductase. The reduced FMN or methyl viologen was rapidly reoxidized upon addition of the N-oxides, probably through the oxidation-reduction cycle of cytochrome P-450 initiated by the N-oxides. Although a xanthine oxidase system (xanthine oxidase plus hypoxanthine) did not appreciably reduce cytochrome P-450, tiaramide N-oxide, or imipramine N-oxide, reduction of the N-oxides was markedly stimulated in the presence of flavins or viologens. FMN or methyl viologen in xanthine oxidase-containing microsomal suspensions was rapidly reduced after the addition of hypoxanthine. The reduced FMN or methyl viologen was rapidly reoxidized upon addition of the tertiary amine N-oxides concomitantly with the formation of the corresponding amines. The stimulatory effect of FMN or methyl viologen on the xanthine oxidase-supported N-oxide reduction was dependent on the amount of added xanthine oxidase and was completely blocked under an atmosphere of carbon monoxide. The maximum stimulation by FMN and methyl viologen of NADPH-supported tiaramide N-oxide reduction was about 10- and 100-fold, respectively. The maximal activity of xanthine oxidase-supported N-oxide reductase in the presence of FMN or methyl viologen was about 200 or 6000 nmoles/mg of protein per minute, respectively. Using chemically reduced FMN and methyl viologen as electron donors and tiaramide N-oxide as substrate, maximal reduction rates of 500 and 10,000 nmoles/mg of protein per minute were recorded, respectively. Therefore the maximum turnover number of cytochrome P-450 should be more than 12,000/min. These results indicate that the rate-limiting step in the reduction of N-oxides is the reduction of cytochrome P-450, and other steps seem to be very fast. It was therefore concluded that the mechanism of flavin- or viologen-induced stimulation of NADPH-dependent N-oxide reduction consists of the reduction of flavins or viologens by NADPH-cytochrome c reductase and the reduction of cytochrome P-450 by the reduced form of flavins or viologens. Experiments with purified cytochrome P-450 and NADPH-cytochrome c reductase confirmed this conclusion.
Impaired degradation of matrix collagen in human gingival fibroblasts by the antiepileptic drug phenytoin.

BACKGROUND Gingival overgrowth (GO) is a serious adverse effect associated with the administration of phenytoin (PHT), with PHT-induced GO characterized by a massive accumulation of extracellular matrix components, especially collagen, in gingival connective tissues. However, the etiology of such collagen accumulation is still largely unknown. We examined the effects of PHT on the collagen degradation process leading to collagen accumulation in human gingival fibroblasts (HGF). METHODS HGFs were cultured with various concentrations of PHT and viable cell numbers and collagen amounts were determined. Gene and protein expressions of matrix metalloproteinases (MMP) and tissue inhibitors of MMPs (TIMP) were quantified with reverse transcription-polymerase chain reaction (RT-PCR) analyses and Western blotting, respectively. Cellular endocytosis of collagen was assayed using flow-cytometric analysis. The effects of PHT on extracellular signal-regulated kinase 1/2 (ERK1/2) and inhibitor kappaB-alpha (IkappaB-alpha) were assayed. RESULTS The proliferation of HGFs was not affected by PHT, whereas it significantly increased collagen accumulation. Further, the expressions of MMP-1, -2, and -3 were markedly suppressed by PHT, whereas that of TIMP-1 was induced in a dose- and time-dependent manner. PHT also markedly prevented collagen endocytosis by HGFs, which was associated with the suppression of alpha2beta1-integrin expression. In addition, the phosphorylation of ERK1/2 and IkappaB-alpha degradation were suppressed by PHT. CONCLUSIONS These results suggest that PHT causes an impaired degradation of collagen by suppression of enzymatic degradation with MMPs/TIMP-1 and alpha2beta1-integrin-mediated endocytosis. Those alterations are likely mediated through the cellular signaling pathways of ERK1/2 and nuclear factor kappaB. These synergistic effects may cause collagen accumulation, leading to GO.
Detecting strongly connected components in large distributed state spaces

textabstractDetecting cycles in a state space is a key task in verification algortihms like LTL/CTL model checking and, less well known, reduction modulo branching bisimulation. This paper focuses on the problem of finding cycles (strongly connected components) in very large distributed state spaces. We present a collection of state space transformations meant as building blocks for custom algorithms. We also describe two example algorithms and show that they perform well on practical case studies
Indexing and weighting of multilingual and mixed documents

Non-English-speaking users, such as Arabic speakers, are not always able to express terminology in their native languages, especially in scientific domains. Such difficulty forces many Arabic authors and scholars to use English terms in order to explain precise concepts, particularly when they address technical topics, resulting in mixed/multilingual queries with both English and Arabic terms. Cross Language Information Retrieval (CLIR) allows users to search documents that are written in a language different from the query. However, current algorithms are optimized for monolingual queries, even if they are translated. This paper attempts to address the problem of multilingual querying in CLIR. New techniques that are better suited to the unique characteristics of this problem, in terms of indexing and weighting, are proposed. A new multilingual and mixed test collection containing mixed-language (Arabic and English) computer science documents and mixed-language queries has been created. Experimentally, results show that current CLIR techniques were not designed for these types of multilingual queries and documents and are found to perform poorly whereas the proposed techniques are found to be promising.
A Multi-strategy Query Processing Approach for Biomedical Question Answering: USTB_PRIR at BioASQ 2017 Task 5B

This paper describes the participation of USTB_PRIR team in the 2017 BioASQ 5B on question answering, including document retrieval, snippet retrieval, and concept retrieval task. We introduce different multimodal query processing strategies to enrich query terms and assign different weights to them. Specifically, sequential dependence model (SDM), pseudo-relevance feedback (PRF), fielded sequential dependence model (FSDM) and Divergence from Randomness model (DFRM) are respectively performed on different fields of PubMed articles, sentences extracted from relevant articles, the five terminologies or ontologies (MeSH, GO, Jochem, Uniprot and DO) to achieve better search performances. Preliminary results show that our systems outperform others in the document and snippet retrieval task in the first two batches.
A Decision-Error-Tolerant 45 nm CMOS 7b 1 GS/s Nonbinary 2b/Cycle SAR ADC

A compact decision-error-tolerant 2b/cycle SAR ADC architecture is presented. Two DACs with different designated functions, SIG-DAC and REF-DAC, are implemented to make the structure compact and to eliminate the sampling skew issue. Use of a nonbinary decision scheme with decision redundancies not only increases the ADC speed with a relaxed DAC settling requirement but also makes the performance robust to reference fluctuations and comparator offset variations. The proposed dynamic register and direct DAC control scheme enhance the conversion speed by minimizing logic delay in the SAR decision loop. The proposed comparator-error detection with digital error correction scheme enhances high-speed ADC performance. A prototype 7b ADC fabricated in a 45 nm CMOS process operates at a sampling rate of 1 GS/s under a 1.25 V supply while achieving a peak SNDR of 41.6 dB and maintaining an ENOB higher than 6 up to 1.3 GHz signal frequency. The FoM under a 1.25 V supply is an 80 fJ/conversion-step with a power consumption of 7.2 mW.
Failure to Regulate: Counterproductive Recruitment of Top-Down Prefrontal-Subcortical Circuitry in Major Depression

Although depressed mood is a normal occurrence in response to adversity in all individuals, what distinguishes those who are vulnerable to major depressive disorder (MDD) is their inability to effectively regulate negative mood when it arises. Investigating the neural underpinnings of adaptive emotion regulation and the extent to which such processes are compromised in MDD may be helpful in understanding the pathophysiology of depression. We report results from a functional magnetic resonance imaging study demonstrating left-lateralized activation in the prefrontal cortex (PFC) when downregulating negative affect in nondepressed individuals, whereas depressed individuals showed bilateral PFC activation. Furthermore, during an effortful affective reappraisal task, nondepressed individuals showed an inverse relationship between activation in left ventrolateral PFC and the amygdala that is mediated by the ventromedial PFC (VMPFC). No such relationship was found for depressed individuals, who instead show a positive association between VMPFC and amygdala. Pupil dilation data suggest that those depressed patients who expend more effort to reappraise negative stimuli are characterized by accentuated activation in the amygdala, insula, and thalamus, whereas nondepressed individuals exhibit the opposite pattern. These findings indicate that a key feature underlying the pathophysiology of major depression is the counterproductive engagement of right prefrontal cortex and the lack of engagement of left lateral-ventromedial prefrontal circuitry important for the downregulation of amygdala responses to negative stimuli.
Building roadmaps: a knowledge sharing perspective

Roadmapping is a process that involves many stakeholders and architects. In an industry case, we have found that a major challenge is to exchange timely knowledge between these people. We report a number of knowledge sharing scenarios in the roadmapping process. In order to address these issues, we propose a codification mechanism that makes use of a semantic wiki to facilitate knowledge sharing.
Real-time estimation of thumb-tip forces using surface electromyogram for a novel human-machine interface

Due to difficulties in measurement of muscle activities and understanding a user's intention under different configurations, controlling machine forces using surface electromyogram (SEMG) is difficult in a human-machine interface (HMI). This study describes a novel HMI using Hill-based muscle model to control the isometric force of a robotic thumb that considers the importance of the thumb in hand function. In order to estimate force intension, SEMG from the skin surface was measured and converted to muscle activation information. The activations of deep muscles were inferred from the ratios of muscle activations from earlier studies. The muscle length of each contributed muscle was obtained by using a motion capture system and musculoskeletal modeling software packages. Once muscle forces were calculated, thumb-tip force was estimated based on a mapping model from the muscle force to thumb-tip force. The proposed method was evaluated in comparisons with a linear regression and artificial neural network (ANN) under four different thumb configurations to investigate the potential for estimations under conditions in which the thumb configuration changes.
The Thioesterase Bhp is Involved in the Formation of β‐Hydroxytyrosine during Balhimycin Biosynthesis in Amycolatopsis balhimycina

The putative hydrolase gene bhp from the balhimycin biosynthetic gene cluster has been cloned and overexpressed in Escherichia coli. The corresponding enzyme Bhp was purified to homogeneity by nickel‐chelating chromatography and characterized. Although Bhp has sequence similarities to hydrolases with “haloperoxidase”/perhydrolase activity, it did not show any enzymatic activity with standard “haloperoxidase”/perhydrolase substrates (e.g., monochlorodimedone and phenol red), nonspecific esterase substrates (such as p‐nitrophenyl acetate, p‐nitrophenyl phosphate and S‐thiophenyl acetate) or the model lactonase substrate dihydrocoumarin. However, Bhp could be shown to catalyse the hydrolysis of S‐β‐hydroxytyrosyl‐N‐acetyl cysteamine thioester (β‐OH‐Tyr‐SNAC) with 15 times the efficiency of S‐L‐tyrosyl‐N‐acetyl cysteamine thioester (L‐Tyr‐SNAC). This is in agreement with the suggestion that Bhp is involved in balhimycin biosynthesis, during which it was supposed to catalyse the hydrolysis of β‐OH‐Tyr‐S‐PCP (PCP=peptidyl carrier protein) to free β‐hydroxytyrosine (β‐OH‐Tyr) and strongly suggests that Bhp is a thioesterase with high substrate specificity for PCP‐bound β‐OH‐Tyr and not a “haloperoxidase”/perhydrolase or nonspecific esterase.
Centre for Theoretical Neuroscience Technical Report Dynamic Scaling for Efficient, Low-cost Control of High-precision Movements in Large Environments Dynamic Scaling for Efficient, Low-cost Control of High-precision Movements in Large Environments

This paper presents the dynamic scaling technique (DST), a method for control in large environments that dramatically reduces the resources required to achieve highly accurate movements. The DST uses a low resolution representation of the environment to calculate an initial approximately optimal trajectory and refines the control signal as the target is neared. Simulation results are presented and the effect of representation resolution on accuracy and computational efficiency is analyzed.
A Next-Generation Design Framework for Platform-Based Design

The platform-based design methodology [1] is based on the usage of formal modeling techniques, clearly defined abstraction levels and the separation of concerns to enable an effective design process. The METROPOLIS framework embodies the platform-based design methodology and has been applied to a number of case studies across multiple domains. Based on these experiences, we have identified three key features that need to be enhanced: heterogeneous IP import, orthogonalization of performance from behavior, and design space exploration. The next generation METRO II framework incorporates these advanced features. The main concepts underlying METRO II are described in this paper and illustrated with a small example.
Visual Deficit Interventions in Adult Stroke and Brain Injury: A Systematic Review

Riggs RV, Andrews K, Roberts P, Gilewski: Visual deficit interventions in adult stroke and brain injury: a systematic review. Am J Phys Med Rehabil 2007;86:853–860. Visual deficits after cerebral injury are common. The variability in the types of injury sustained as well as their impact on function in the environment have produced multiple approaches at corrective intervention. To assess the effectiveness of these vision interventions, an extensive literature search was completed. The analysis of this review revealed some success with visual neglect disorders, but not enough evidence to comment definitively on interventions for hemianopsia, quadrantonopsia, diplopia, or convergence insufficiency. A lack of follow-up also limited efforts to assess the durability of documented gains. Additional research is necessary to clarify, quantify, and measure treatment outcomes for acquired visual dysfunction as well as to link laboratory testing to improvement in actual functioning for individuals in their environment.
An adaptive trajectory control for UAV using a real-time architecture

Multirotor helicopter have generated much interest in recent years as a powerful tool both for civil and military applications. The trajectory of the aircraft is controlled by modifying the angular velocity of the rotors. Among different control techniques the PID controller finds great application due to its simplicity. It uses proportional, integral and derivative regulator to control one or more input signal. In this paper a novel real-time system, based on a real-time Neural Network, is presented to propose an alternative control technique to the PID. In order to prove the validity of the proposed approach simulations are performed through a real experimental test-bed.
Expensive Multiobjective Optimization by MOEA/D With Gaussian Process Model

In some expensive multiobjective optimization problems (MOPs), several function evaluations can be carried out in a batch way. Therefore, it is very desirable to develop methods which can generate multipler test points simultaneously. This paper proposes such a method, called MOEA/D-EGO, for dealing with expensive multiobjective optimization. MOEA/D-EGO decomposes an MOP in question into a number of single-objective optimization subproblems. A predictive model is built for each subproblem based on the points evaluated so far. Effort has been made to reduce the overhead for modeling and to improve the prediction quality. At each generation, MOEA/D is used for maximizing the expected improvement metric values of all the subproblems, and then several test points are selected for evaluation. Extensive experimental studies have been carried out to investigate the ability of the proposed algorithm.
Silver nanoflowers for single-particle SERS with 10 pM sensitivity

Surface-enhanced Raman scattering (SERS) has received considerable attention as a noninvasive optical sensing technique with ultrahigh sensitivity. While numerous types of metallic particles have been actively investigated as SERS substrates, the development of new SERS agents with high sensitivity and their reliable characterization are still required. Here we report the preparation and characterization of flower-shaped silver (Ag) nanoparticles that exhibit high-sensitivity single-particle SERS performance. Ag nanoflowers (NFs) with bud sizes in the range 220–620 nm were synthesized by the wet synthesis method. The densely packed nanoscale petals with thicknesses in the range 9–22 nm exhibit a large number of hot spots that significantly enhance their plasmonic activity. A single Ag NF particle (530–620 nm) can detect as little as 10−11 M 4-mercaptobenzoic acid, and thus provides a sensitivity three orders of SERS magnitude greater than that of a spherical Ag nanoparticle. The analytical enhancement factors for single Ag NF particles were found to be as high as 8.0 × 109, providing unprecedented high SERS detectivity at the single particle level. Here we present an unambiguous and systematic assessment of the SERS performances of the Ag NFs and demonstrate that they provide highly sensitive sensing platforms by single SERS particle.
Coarse‐grained models and collective phenomena in membranes: Computer simulation of membrane fusion

We discuss the role coarse-grained models play in in- vestigating collective phenomena in bilayer membranes and place them in the context of alternative approaches. By reducing the de- grees of freedom and applying simple effective potentials, coarse- grained models can address the large time scales and length scales of collective phenomena in mem- branes. Although the mapping from a coarse-grained model onto chemi- cally realistic models is a challenge, such models provide a direct view on the phenomena that occur on the length scales of a few tens of nano- meters. Their relevance is exempli- ied by the study of fusion of model membranes. ' 2003 Wiley Periodicals,
Assessment of Wooded Area Reduction by Airborne Laser Scanning

Airborne Laser Scanning (ALS) data hold a great deal of promise in monitoring the reduction of single trees and forests with high accuracy. In the literature, the canopy height model (CHM) is the main input used frequently for forest change detection. ALS also has the key capability of delivering 3D point clouds, not only from the top canopy surface, but also from the entire canopy profile and also from the terrain. We investigated the use of two additional parameters, which exploit these capabilities for assessing the reduction of wooded area: Slope-adapted echo ratio (sER) and Sigma0. In this study, two ALS point cloud data sets (2005 and 2011) were used to calculate Digital Surface Model (DSM), sER, and Sigma0 in 1.5 km2 forest area in Vorarlberg, Austria. Image differencing was applied to indicate the change in the three difference models individually and in their combinations. Decision trees were used to classify the area of removed trees with the minimum mapping unit of 13 m2. The final results were evaluated by a knowledge-based manual digitization using completeness and correctness measures. The best result is achieved using the combination of sER and DSM, namely a correctness of 92% and a completeness of 85%.