Miracle-dz/UniFAR-FTUs huggingface dataset:
Recommending missing citations for newly granted patents

The U.S. recently adopted a post-grant opposition procedure to encourage third parties to challenge the validity of newly granted patents by providing relevant prior patents that are missed during patent examination (i.e., missing citations). In this paper, we propose a recommendation system for missing citations for newly granted patents. The recommendation system, based on the patent citation network of a newly granted query patent, focuses on paths that start with the references of the query patent in the network. Our approach is to identify the relevancy of a candidate patent to the query patent by its citation relationship (paths) that are distinguished based on the direction, topology and semantics of the paths in the network. We consider six different types of paths between a candidate patent and a query patent based on their citation relationship and define a relevancy score for each path type. Accordingly, we rank candidate patents via a RankSVM model learned by using those relevancy scores as features. The experimental results show our approach significantly improves the average precision and recall performance compared to two baseline methods, i.e., Katz distance and text similarity.
Comments on "Security Improvement of an RFID Security Protocol of ISO/IEC WD 29167-6"

Song et al. recently scrutinized the security of a mutual authentication protocol published as a part of ISO/IEC WD 29167-6, denoted as Protocol 1, and showed its lack of protection against man-in-the-middle attacks . In addition, they proposed an improved version, called Protocol 1+, and claimed resistance against this sort of attacks. Nevertheless, in this letter we show that the new protocol is as insecure as the original protocol against man-in-the-middle attacks.
Cross-coupling effect compensation of an AFM piezoelectric tube scanner for improved nanopositioning

The imaging performance of an atomic force microscope (AFM) at high scanning speeds is limited due to the cross-coupling properties of its scanning unit; i.e., the piezoelectric tube scanner (PTS). In order to increase the imaging speed of an AFM, a multi-input multi-output (MIMO) model predictive control (MPC) scheme is used for the PTS to reduce its cross-coupling effect. The design of this controller is based on an identified MIMO model of the AFM PTS. Also, a damping compensator is designed and included in the feedback loop with the plant to suppress the vibration of the PTS at the resonant frequency. Experimental results confirm the efficacy of the proposed controller.
cAMP-Mediated Regulation of Neurotrophin-Induced Collapse of Nerve Growth Cones

Neurotrophins are known to promote the survival, differentiation, and neurite outgrowth of developing neurons. Here we report that acutely applied brain-derived neurotrophic factor (BDNF) induces rapid growth cone collapse and neurite retraction of embryonicXenopus spinal neurons in culture. The collapsing effect of BDNF depends on the activation of Trk receptor tyrosine kinase, requires an influx of extracellular Ca2+, and is regulated by cAMP-dependent activity. Elevation of intracellular cAMP levels ([cAMP]i) by forskolin or (Sp)-cAMP completely blocked the collapsing effect, whereas inhibition of protein kinase A (PKA) by (Rp)-cAMP potentiated the collapsing action. BDNF-induced growth cone collapse was only observed in 6 hr cultures but not in 24 hr cultures. However, inhibition of PKA by (Rp)-cAMP restored the collapsing response of these “old” neurons in 24 hr cultures, suggesting that embryonic Xenopus spinal neurons may upregulate their endogenous cAMP-dependent activity during development in culture, leading to the blockade of their collapsing response to BDNF. Taken together, our results suggest the presence of cross-talk between Ca2+- and cAMP-signaling pathways involved in the collapsing action of neurotrophins, in which the cAMP-pathway regulates the Ca2+-mediated signal transduction required for BDNF-induced collapse. By modulating the cAMP-dependent activity through the intrinsic programming or interaction with other factors present in the environment, a neuron thus could respond to the same extracellular factors with different morphological and cellular changes at different stages during development.
Using gene genealogies to localize rare variants associated with complex traits in diploid populations

Background and Aims Many methods can detect trait association with causal variants in candidate genomic regions; however, a comparison of their ability to localize causal variants is lacking. We extend a previous study of the detection abilities of these methods to a comparison of their localization abilities. Methods Through coalescent simulation, we compare several popular association methods. Cases and controls are sampled from a diploid population to mimic human studies. As benchmarks for comparison, we include two methods that cluster phenotypes on the true genealogical trees, a naive Mantel test considered previously in haploid populations and an extension that takes into account whether case haplotypes carry a causal variant. We first work through a simulated dataset to illustrate the methods. We then perform a simulation study to score the localization and detection properties. Results In our simulations, the association signal was localized least precisely by the naive Mantel test and most precisely by its extension. Most other approaches had intermediate performance similar to the single-variant Fisher’s-exact test. Conclusions Our results confirm earlier findings in haploid populations about potential gains in performance from genealogy-based approaches. They also highlight differences between haploid and diploid populations when localizing and detecting causal variants.
Less frequently mutated genes in colorectal cancer: evidences from next-generation sequencing of 653 routine cases

Aims The incidence of RAS/RAF/PI3KA and TP53 gene mutations in colorectal cancer (CRC) is well established. Less information, however, is available on other components of the CRC genomic landscape, which are potential CRC prognostic/predictive markers. Methods Following a previous validation study, ion-semiconductor next-generation sequencing (NGS) was employed to process 653 routine CRC samples by a multiplex PCR targeting 91 hotspot regions in 22 CRC significant genes. Results A total of 796 somatic mutations in 499 (76.4%) tumours were detected. Besides RAS/RAF/PI3KA and TP53, other 12 genes showed at least one mutation including FBXW7 (6%), PTEN (2.8%), SMAD4 (2.1%), EGFR (1.2%), CTNNB1 (1.1%), AKT1 (0.9%), STK11 (0.8%), ERBB2 (0.6%), ERBB4 (0.6%), ALK (0.2%), MAP2K1 (0.2%) and NOTCH1 (0.2%). Conclusions In a routine diagnostic setting, NGS had the potential to generate robust and comprehensive genetic information also including less frequently mutated genes potentially relevant for prognostic assessments or for actionable treatments.
Consensus Clustering Algorithms: Comparison and Refinement

Consensus clustering is the problem of reconciling clustering information about the same data set coming from different sources or from different runs of the same algorithm. Cast as an optimization problem, consensus clustering is known as median partition, and has been shown to be NP-complete. A number of heuristics have been proposed as approximate solutions, some with performance guarantees. In practice, the problem is apparently easy to approximate, but guidance is necessary as to which heuristic to use depending on the number of elements and clusterings given. We have implemented a number of heuristics for the consensus clustering problem, and here we compare their performance, independent of data size, in terms of efficacy and efficiency, on both simulated and real data sets. We find that based on the underlying algorithms and their behavior in practice the heuristics can be categorized into two distinct groups, with ramification as to which one to use in a given situation, and that a hybrid solution is the best bet in general. We have also developed a refined consensus clustering heuristic for the occasions when the given clusterings may be too disparate, and their consensus may not be representative of any one of them, and we show that in practice the refined consensus clusterings can be much superior to the general consensus clustering.
Algorithms for Simultaneous Localization and Mapping

Simultaneous Localization and Mapping (SLAM) is the problem in which a sensor-enabled mobile robot incrementally builds a map for an unknown environment, while localizing itself within this map. Efficient and accurate SLAM is fundamental for any mobile robot to perform robust navigation. It is also the cornerstone for higher-level tasks such as path planning and exploration. In this talk, I will survey the three major families of SLAM algorithms: parametric filter, particle filter and graph-based smoother. I will review the representative algorithms and the state-of-the-art in each family. I will also discuss issues including submapping, data association and loop closing.
Improved Video Transmission over Mobile Ad-hoc Networks using AOMDV and MDC with Path Diversity

Mobile Ad-hoc Network is capable of clearing lots of challenges involved in the real-world communication. They are used in emergency response schemes, military field operation, oil drilling and mining operations. Transmitting video over MANET is an active research area due to their potential wide spread applications. In the last decade, both mobile and multimedia communications have experienced unequal rapid growth and commercial success. However, transmitting multimedia flows over wireless Ad hoc network remains an extremely challenging issue due to the limited battery lifetime of the wireless nodes. Providing good quality end-to-end video communications over mobile ad-hoc networks is more challenging due to the dynamically changing topology of the ad-hoc networks and the unreliable wireless channels. Multiple Description Coding (MDC) is an effective coding approach to enhance the error resilience of video transmission over any lossy networks. When MDC is combined with multipath transmission, MDC enables traffic dispersion and it alleviates the error propagation caused by the packet losses and hence reduces the network congestion. The error prone nature of the adhoc network always causes the frame to get corrupted. When MDC is used with such a network, it uses these corrupted frames as a reference frame and through motion compensation it compares the current frame with the reference frame and leads to error propagation throughout the network which results in video quality degradation. So, in this work, routing messages of AOMDV is used as the feedback messages after estimating the packet loss in the network and video coding is adapted accordingly with respect to the feedback messages and thus the quality of the received video is improved. AOMDV also saves the energy of the nodes by multipath routing. This work deals with comparing video quality using MDC, MDC with feedback based SMR (Split Multipath Routing) and MDC with feedback based AOMDV (Ad-hoc On demand Multipath Distance Vector routing). The experiment has been conducted using NS2 simulator along with EvalVid for evaluating the video quality. The results demonstrate that MDC with feedback based AOMDV gives good PSNR value under different packet loss rate and guarantees good video quality for large number of users in the network and at the same time the PSNR is examined by varying the number of nodes in the network resulting in decreased PSNR while trying to increase the number of nodes involved in the network.
Provided for Non-commercial Research and Educational Use. Not for Reproduction, Distribution or Commercial Use. Author's Personal Copy Introduction Definition of Bns Building Models Using Models Special Cases Further Reading

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Predicting Information Flows in Network Traffic

In optimizing information flows in networks, it would be useful to predict aspects of the network traffic. Yet, the notion of predicting network traffic does not appear in the relevant literature reporting analysis of network traffic. This literature is both well developed and skeptical about the value of traditional time series analysis on network data. It has consistently reported three "traffic invariants" in the analysis of network and Internet traffic. This study uses such time series analysis on a day's worth of Internet log data and finds poor support for one of the invariants. In the preliminary analysis, evidence of nonlinearity was discovered in these data and the analysis presented here examines this question further. This study posits that nonlinear events may be a traffic invariant although this hypothesis would have to be investigated further. The appearance of nonlinear structures is important to the question of predicting network traffic because there are currently no methods to predict time series with nonlinear structures. The discovery of non-linear structures, then, may mean that developing a predictive model is impossible with current techniques. On the other hand, these nonlinearities may result from interactions from other OSI Layers than the one studied.
An improved hidden vector state model approach and its adaptation in extracting protein interaction information from biomedical literature

Large quantity of knowledge, which is important for biological researchers to unveil the mechanism of life, often hides in the literature, such as journal articles, reports, books and so on. Many approaches focusing on extracting information from unstructured text, such as pattern matching, shallow and full parsing, have been proposed especially for biomedical applications. In this paper, we present an information extraction system employing a semantic parser using the Hidden Vector State (HVS) model for protein-protein interactions. We found that it performed better than other established statistical methods and achieved 58.3% and 76.8% in recall and precision respectively. Moreover, the pure data-driven HVS model can be easily adapted to other domains, which is rarely mentioned and possessed by other approaches. Experimental results prove that the model trained on one domain can still generate satisfactory results when shifting to another domain with a small amount of adaptation training data.
Design of a Dexterous Force Controllable Humanoid

Why: Dexterous manipulation allows a humanoid robot to actively explore its world. Through exploratory acts such as touching, poking, pushing, and holding, the robot can physically ground its sensory experiences. A humanoid which is capable of manipulating its world can move from a passive sensing of the world to an active and directed perception. Developing a mechanically robust manipulator which can be force controlled will allows us explore long-term interactions with an unfamiliar environment.
A 17.7Mpixel 120fps CMOS image sensor with 34.8Gb/s readout

Recently, the demands to achieve both high-speed and high-quality imaging — including high A/D resolution — have increased. The new target specification is 60fps Ultra-High-Definition with 12b resolution. This imaging requires 24Gb/s, while reported CMOS image sensors have reached up to 6.5Gb/s [1–4]. This paper presents a 34.8Gb/s CMOS image sensor with high image quality, which realizes 17.7M pixels at 120fps with 12b resolution and a dynamic range of over 75dB (one of the highest image qualities, compared with data from [2]). Generally there exists a trade-off between high-speed imaging and high image quality. This is because high-speed imaging brings high power with high thermal noise, which also degrades the signal quality, and because fast data transfer may require more output pins, bringing more interference.
Color Image Classification Using Block Matching and Learning

In this paper, we propose block matching and learning for color image classification. In our method, training images are partitioned into small blocks. Given a test image, it is also partitioned into small blocks, and mean-blocks corresponding to each test block are calculated with neighbor training blocks. Our method classifies a test image into the class that has the shortest total sum of distances between mean blocks and test ones. We also propose a learning method for reducing memory requirement. Experimental results show that our classification outperforms other classifiers such as support vector machine with bag of keypoints.
Exploiting Task-Level Parallelism Using pTask

This paper presents pTask— a system that allows users to automatically exploit dynamic task-level parallelism in sequential array-based C programs. The system employs compiler analysis to extract data usage information from the program, then uses this information at run-time to dynamically exploit concurrency and to enforce data-dependences. Experimental results using a prototype of the system show scaling performance and low overhead on a 32-processor KSR1 multiprocessor for a number of applications.
Oxidation of the antihistaminic drug terfenadine in human liver microsomes. Role of cytochrome P-450 3A(4) in N-dealkylation and C-hydroxylation.

The antihistaminic drug terfenadine, alpha-[4-(1,1-dimethylethyl)phenyl]-4-(hydroxydiphenylmethyl)-1- piperidinebutanol (Seldane), is of interest because of its lack of sedative properties. Major routes of metabolism include oxidative N-dealkylation to 4-(hydroxydiphenylmethyl)-piperidine (1) and oxidation of a tert-butyl methyl group to a primary alcohol (2), which is subsequently oxidized to a carboxylic acid. Rates of formation of 1 and 2 varied approximately 30-fold in the 17 human liver microsomal samples examined and were highly correlated with each other, suggesting that the same enzyme may be involved in both oxidations. The rates of formation of 1 and 2 were both correlated with rates of nifedipine oxidation (a marker of cytochrome P-450 (P-450) 3A4) but not with markers for other human P-450s. Microsomal oxidation of (both enantiomers of) terfenadine to 1 and 2 was markedly inhibited by gestodene, a selective mechanism-based inactivator of P-450 3A enzymes but not by any of several other P-450 inhibitors. Antibodies raised against P-450 3A4 could inhibit most of the oxidation of (both enantiomers of) terfenadine to 1 and 2 in a microsomal sample having high catalytic activity but antibodies recognizing other P-450s had no effect. The oxidation of terfenadine to 1 and 2 was catalyzed by purified human liver microsomal P-450 3A4 and by partially purified yeast recombinant P-450 3A4. These results provide evidence that P-450 3A4 (and possibly other P-450 3A enzymes) play a major role in the oxidation of (both enantiomers of) terfenadine to both of its major oxidation products. (ABSTRACT TRUNCATED AT 250 WORDS)
Endothelial cells

Allergic reactions are characterized by a prominent exudation of fluid and cellular components from the blood into the bronchial mucosa. Evaluation of endothelial cells (EC) in asthma stems from the idea that some of the features of asthma may be caused or made worse by EC that modify both plasma exudation and/or cell emigration into the airways [1,2]. Moreover, EC are not only a passive barrier: they play a role in leucocyte adherence, act as accessory cells in the immune response and are also able to produce some mediators like PAF acether or cytokines. It seems interesting to evaluate the possible role of EC endothelial cells in the pathogenesis of bronchial asthma. As it is impossible to access to the airways endothelium itself directly, two different ways of investigation were developed: (i) The demonstration of autoantibodies against EC structures in various allergic disorders like vasculitis and some cases of severe asthma. Characterization of EC antigens involved is presently in progress [3]. (ii) The potential implication of EC in the pathogenesis of asthma. In asthmatics, bronchial biopsies showed that eosinophils, monocytes and platelets plugs are found in contact with the vascular endothelium, contrary to the data observed in control group. Cytokines, namely tumour necrosis factor-alpha are released during bronchial allergen challenge in asthmatics and act on EC through the induction of surface adhesion molecules like ICAM-1 [4]. Thus, in addition to their well-known role in microvascular leakage, EC are able to amplify the local recruitment of inflammatory cells, and might also act as target cells for auto immune processes possibly implicated in some features of severe asthma.
DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models

SUMMARY Differential Identification using Mixtures Ensemble (DIME) is a package for identification of biologically significant differential binding sites between two conditions using ChIP-seq data. It considers a collection of finite mixture models combined with a false discovery rate (FDR) criterion to find statistically significant regions. This leads to a more reliable assessment of differential binding sites based on a statistical approach. In addition to ChIP-seq, DIME is also applicable to data from other high-throughput platforms. AVAILABILITY AND IMPLEMENTATION DIME is implemented as an R-package, which is available at http://www.stat.osu.edu/~statgen/SOFTWARE/DIME. It may also be downloaded from http://cran.r-project.org/web/packages/DIME/.
Querying for video events by semantic signatures from few examples

We aim to query web video for complex events using only a handful of video query examples, where the standard approach learns a ranker from hundreds of examples. We consider a semantic signature representation, consisting of off-the-shelf concept detectors, to capture the variance in semantic appearance of events. Since it is unknown what similarity metric and query fusion to use in such an event retrieval setting, we perform three experiments on unconstrained web videos from the TRECVID event detection task. It reveals that: retrieval with semantic signatures using normalized correlation as similarity metric outperforms a low-level bag-of-words alternative, multiple queries are best combined using late fusion with an average operator, and event retrieval is preferred over event classification when less than eight positive video examples are available.