Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Clustering of Transcription Start Site Landscapes

Genome-wide, high-throughput methods for transcription start site (TSS) detection have shown that most promoters have an array of neighboring TSSs where some are used more than others, forming a distribution of initiation propensities. TSS distributions (TSSDs) vary widely between promoters and earlier studies have shown that the TSSDs have biological implications in both regulation and function. However, no systematic study has been made to explore how many types of TSSDs and by extension core promoters exist and to understand which biological features distinguish them. In this study, we developed a new non-parametric dissimilarity measure and clustering approach to explore the similarities and stabilities of clusters of TSSDs. Previous studies have used arbitrary thresholds to arrive at two general classes: broad and sharp. We demonstrated that in addition to the previous broad/sharp dichotomy an additional category of promoters exists. Unlike typical TATA-driven sharp TSSDs where the TSS position can vary a few nucleotides, in this category virtually all TSSs originate from the same genomic position. These promoters lack epigenetic signatures of typical mRNA promoters and a substantial subset of them are mapping upstream of ribosomal protein pseudogenes. We present evidence that these are likely mapping errors, which have confounded earlier analyses, due to the high similarity of ribosomal gene promoters in combination with known G addition bias in the CAGE libraries. Thus, previous two-class separations of promoter based on TSS distributions are motivated, but the ultra-sharp TSS distributions will confound downstream analyses if not removed.
Experimental investigation of pavement behavior after embankment widening using a fiber optic sensor network

In order to investigate the actual health condition of asphalt concrete pavements on widened road embankments, a full-scale model test study was conducted. A fiber Bragg grating–based sensor network was developed to monitor the strain distributions within the pavement structure, which was subjected to differential settlements. An improved packaging and installation method of the quasi-distributed sensor system was utilized, which not only ensured a high sensor survival rate but also achieved accurate measurement of axial strains in longitudinal and transverse directions. Based on the monitoring results, the strain characteristics of the pavement structure under different settlements were analyzed in detail. It is found that in general, the top layer of the asphalt pavement structure was subject to tension stress due to the differential settlement of the embankment. Plastic deformation of the pavement was observed when the differential settlement increased to 22 cm. The base layer of the pavement had the most significant response in comparison with the top and middle layers. The geogrid reinforcement in the embankment had a positive effect to alleviate the tension stress in the pavement. This experimental study also indicates the capability of fiber optic sensor networks to monitor the performance of pavements with a high degree of accuracy.
Filtering algorithms and implementation for very fast publish/subscribe systems

Publish/Subscribe is the paradigm in which users express long-term interests (“subscriptions”) and some agent “publishes” events (e.g., offers). The job of Publish/Subscribe software is to send events to the owners of subscriptions satisfied by those events. For example, a user subscription may consist of an interest in an airplane of a certain type, not to exceed a certain price. A published event may consist of an offer of an airplane with certain properties including price. Each subscription consists of a conjunction of (attribute, comparison operator, value) predicates. A subscription closely resembles a trigger in that it is a long-lived conditional query associated with an action (usually, informing the subscriber). However, it is less general than a trigger so novel data structures and implementations may enable the creation of more scalable, high performance publish/subscribe systems. This paper describes an attempt at the construction of such algorithms and its implementation. Using a combination of data structures, application-specific caching policies, and application-specific query processing our system can handle 600 events per second for a typical workload containing 6 million subscriptions.
Applying Adaptive Algorithms to Epistatic Domains

John Holland has shown that when adaptive algorithms are used to search certain kinds of extremely large problem spaces, they will converge on a "good" solution fairly quickly. Such problem spaces are characterized by a low degree of epistasis. A host of classical search problems, however, are epistatic in nature. The present paper describes some new techniques for applying adaptive algorithms to epistatic domains, while retaining some of the strength of Holland's convergence proof. These techniques are described for two-dimensional bin-packing problems, and summarized for graph coloring problems. What makes these problems amenable to an adaptive approach is a two-stage evaluation procedure. Encodings of solutions are mutated and reproduced as they are in non-epistatic domains, but their evaluation is carried out after a decoding process. Using the techniques described, convergence is promoted in two ways: one of the natural mutation operators is a weaker version of Holland's crossover, and domain knowledge may be built into decoding processes so that the size of the search space is radically cut down.
Digitally controlled peak current mode parallel DC-DC converter for HVDC system

The purpose of this paper is to present the demonstration of digitally controlled peak current mode parallel dc-dc converter for the higher voltage direct current (HVDC) system. The peak current mode control circuit is only composed of the RC integrator and comparator. It can detect the peak current in real time. A prototype uses 800W phase-shifted full-bridge zero volt switching (ZVS) dc-dc converter. The digital control circuit is implemented by the field programmable gate array (FPGA) except the A-D conversion of output voltage. In this paper, the prototype tests the transient response by the experiment. Experimental results show that the prototype has superior transient response and it is suitable for switching power supplies for the HVDC system.
Space-Division Multiple-Access for Wireless MIMO Networks : A Game Theoretic Approach

Optimized Space-Division Multiple-Access (SDMA) strategies for Multiple-Input Multiple-Output (MIMO) Ad-hoc wireless networks are proposed in this paper, where noncooperating transmit/receive nodes are assumed to be affected by spatially colored Multiple Access Interference (MAI). The final task is to maximize the information throughput (in bits/slot) conveyed by each peer-to-peer link active in the network. For this purpose, the SDMA problem is modelled as an uncooperative strategic game, and the Game Theory approach is adopted for characterizing the nodes’ interactions and deriving out the conditions for the ”Nash Equilibrium” of the overall Ad-hoc networking game. The main contributions of this paper may be so summarized. Firstly, we develop a fully distributed scalable and asynchronous SDMA scheme combining both power-allocation and spatial data-shaping that maximizes (in a competitive sense) the information throughput sustained by each active peer-to-peer link under both Best-Effort and Contracted QoS access policies. Secondly, we characterize the convergence property of the proposed SDMA scheme under low and high traffic load offered to the network. Thirdly, based on the proposed SDMA scheme, we present two Connection Admission Procedures (CAPs) attaining an optimized (in a competitive sense) trade-off between number of allowed connections and throughput requested by each connection. Finally, for corroborating the carried out performance analysis, we present several numerical tests supporting superiority (in terms of conveyed peer-to-peer throughput) of the proposed SDMA scheme over more conventional collision-avoiding MAC schemes, such as TDMA and CSMA/CA.
Recognition of Human Action Using Moment-Based Features

Abstract The performance of different classification approaches is evaluated using a view-based approach for motion representation. The view-based approach uses computer vision and image processing techniques to register and process the video sequence. Two motion representations called Motion Energy Images and Motion History Image are then constructed. These representations collapse the temporal component in a way that no explicit temporal analysis or sequence matching is needed. Statistical descriptions are then computed using moment-based features and dimensionality reduction techniques. For these tests, we used 7 Hu moments, which are invariant to scale and translation. Principal Components Analysis is used to reduce the dimensionality of this representation. The system is trained using different subjects performing a set of examples of every action to be recognized. Given these samples, K-nearest neighbor, Gaussian, and Gaussian mixture classifiers are used to recognize new actions. Experiments are conducted using instances of eight human actions (i.e., eight classes) performed by seven different subjects. Comparisons in the performance among these classifiers under different conditions are analyzed and reported. Our main goals are to test this dimensionality-reduced representation of actions, and more importantly to use this representation to compare the advantages of different classification approaches in this recognition task.
A stack multilayer high reflectance optical filter produced on polyester substrate with the PECVD technique

The present work reports results of an eﬀort to produce a stack multilayer optical ﬁlter on a poly(ethylene terephtalate) (PET) substrate, using a PECVD technique. Titanium dioxide type of material (n 550 = 2 . 3 ) has been selected for high refractive index layers while that of silicon dioxide type (n 550 = 1 . 4 ) served as low refractive index ﬁlms. For a synthesis of the former material, titanium tetrachloride with an excess of gaseous oxygen was taken as a precursor system, and a mixture of oxygen and hexamethyldisiloxane (HMDSO) was used as a precursor system for a deposition of the latter one. The entire deposition process was carried out in the same parallel plate PECVD reactor, with all the consecutive layers being synthesized in one vacuum run. In the ﬁrst part of the work, the deposition processes of both types of materials were optimized separately using polyester ﬁlm as a substrate. The main goal of this step was to obtain high refractive index and low refractive index materials of good optical quality, remaining as close as possible to that of, respectively, titanium dioxide and silicon dioxide, without jeopardizing the optical quality of the polymer support. Aconstruction of the ﬁlter was the next stage of the work. The design concerned high reﬂectance (HR) type ﬁlter consisting of ﬁve high refractive index layers, separated by four low refractive index ﬁlms. Before an actual deposition, a performance of such system had been simulated, using the TFCalc TM 3.5 optical software. As a ﬁnal step, the real structure, consisting of nine ﬁlms, was produced, and the optical properties of the so obtained ﬁlter have been compared with those of the simulated system.
Randomised controlled trials investigating pharmacological and psychological interventions for treatment-refractory depression

Background About 30% of people with depression do not respond to an antidepressant at the recommended dose and can be described as having treatment-refractory depression. Aims To summarise the findings from all randomised controlled trials (RCTs) that have assessed the efficacy of a pharmacological or psychological intervention for treatment-refractory depression. Method We used a systematic search strategy to identify RCTs that included adults aged 18–75 years with a diagnosis of unipolar depression that had not responded to a 4-week course of a recommended dose of an antidepressant. Results We identified 16 RCTs. None of the included trials assessed the efficacy of psychotherapy. All the trials were too small to detect an important clinical response. We found only two trials on lithium augmentation, which randomised 50 subjects in total. Conclusions There is little evidence to guide the management of depression that has not responded to a course of antidepressants. Treatment-refractory depression is an important public health problem and large pragmatic trials are needed to inform clinical practice.
Efficient High-Performance ASIC Implementation of JPEG-LS Encoder

This paper introduces an innovative design which implements a high-performance JPEG-LS encoder. The encoding process follows the principles of the JPEG-LS lossless mode. The proposed implementation consists of an efficient pipelined JPEG-LS encoder, which operates at a significantly higher encoding rate than any other JPEG-LS hardware or software implementation while keeping area small
Epigenetic Differences in Normal Colon Mucosa of Cancer Patients Suggest Altered Dietary Metabolic Pathways

We have compared DNA methylation in normal colon mucosa between patients with colon cancer and patients without cancer. We identified significant differences in methylation between the two groups at 114 to 874 genes. The majority of the differences are in pathways involved in the metabolism of carbohydrates, lipids, and amino acids. We also compared transcript levels of genes in the insulin signaling pathway. We found that the mucosa of patients with cancer had significantly higher transcript levels of several hormones regulating glucose metabolism and significantly lower transcript levels of a glycolytic enzyme and a key regulator of glucose and lipid homeostasis. These differences suggest that the normal colon mucosa of patients with cancer metabolizes dietary components differently than the colon mucosa of controls. Because the differences identified are present in morphologically normal tissue, they may be diagnostic of colon cancer and/or prognostic of colon cancer susceptibility. Cancer Prev Res; 5(3); 374–84. ©2012 AACR.
Performance Analysis of Optical Flow : High Definition Video . vs . Regular Video

This paper presents a preliminary result on the performance evaluation of a robust optical flow algorithm using a high definition video and a regular video. The hypothesis is that, because of its higher resolution, a high definition video can yield better optical flow data, which is critical for the motion-based face recognition research. The experiment was designed to capture the facial motion of human subjects in a video sequence, which was then broken into individual frames. A series of frame pairs of different frame intervals were then processed by an optical flow algorithm to generate dense optical flow images. Analysis of those images based on both qualitative visual examination and quantitative violation percentages indicates that a high definition video is superior to a regular video.
Towards geographical referencing of monocular SLAM reconstruction using 3D city models: Application to real-time accurate vision-based localization

In the past few years, lots of works were achieved on Simultaneous Localization and Mapping (SLAM). It is now possible to follow in real time the trajectory of a moving camera in an unknown environment. However, current SLAM methods are still prone to drift errors, which prevent their use in large-scale applications. In this paper, we propose a solution to reduce those errors a posteriori. Our solution is based on a postprocessing algorithm that exploits additional geometric constraints, relative to the environment, to correct both the reconstructed geometry and the camera trajectory. These geometric constraints are obtained through a coarse 3D modelisation of the environment, similar to those provided by GIS database. First, we propose an original articulated transformation model in order to roughly align the SLAM reconstruction with this 3D model through a non-rigid ICP step. Then, to refine the reconstruction, we introduce a new bundle adjustment cost function that includes, in a single term, the usual 3D point/ID observation consistency constraint as well as the geometric constraints provided by the 3D model. Results on large-scale synthetic and real sequences show that our method successfully improves SLAM reconstructions. Besides, experiments prove that the resulting reconstruction is accurate enough to be directly used for global relocalization applications.
CL for CALL in the Primary School

This paper looks at how Computational Linguistics (CL) and Natural Language Processing (NLP) resources can be deployed in Computer-Assisted Language Learning (CALL) materials for primary school learners. We draw a broad distinction between CL and NLP technology and briefly review the use of CL/NLP in e-Learning in general, how it has been deployed in CALL to date and specifically in the primary school context. We outline how CL/NLP resources can be used in a project to teach Irish and German to primary school children in Ireland. This paper focuses on the use of Finite State morphological analysis (FST) resources for Irish and Part of Speech (POS) taggers for German.
Neural Networks with Few Multiplications

For most deep learning algorithms training is notoriously time consuming. Since most of the computation in training neural networks is typically spent on floating point multiplications, we investigate an approach to training that eliminates the need for most of these. Our method consists of two parts: First we stochastically binarize weights to convert multiplications involved in computing hidden states to sign changes. Second, while back-propagating error derivatives, in addition to binarizing the weights, we quantize the representations at each layer to convert the remaining multiplications into binary shifts. Experimental results across 3 popular datasets (MNIST, CIFAR10, SVHN) show that this approach not only does not hurt classification performance but can result in even better performance than standard stochastic gradient descent training, paving the way to fast, hardware-friendly training of neural networks.
VDCBPI: an Approximate Scalable Algorithm for Large POMDPs

Existing algorithms for discrete partially observable Markov decision processes can at best solve problems of a few thousand states due to two important sources of intractability: the curse of dimensionality and the policy space complexity. This paper describes a new algorithm (VDCBPI) that mitigates both sources of intractability by combining the Value Directed Compression (VDC) technique [13] with Bounded Policy Iteration (BPI) [14]. The scalability of VDCBPI is demonstrated on synthetic network management problems with up to 33 million states.
Bond-Sequential Search ( BSS )

—This paper presents a new search algorithm for searching a list or array for two or more keys at the same time. The new algorithm is named Bond Sequential Search (BSS), and the objective in this algorithm is to search for two keys in one array using sequential search with some enhancements. The classic sequential search is one of the easiest and cheapest search techniques, but it is very slow and requires comparing each element in the array until finding the desired element. This process is time consuming, and in the worst case when the element is at the end of the array or when it does not exist in the array, the number of comparisons required will be equal to the array size. Thus, the complexity of the sequential search will be equal to the length of the search array, and if two keys are searched this complexity will double. There are other faster search methods used like the binary search and the parallel sequential search. However, each of the two methods has its own disadvantages; binary search requires sorting the data, and parallel search requires the use of multiple processors, and both methods will require additional cost compared to sequential search. Bond Sequential search (BSS) introduced in this paper is based on sequential search. Simple logic gates were added to the classic sequential search in order to combine two or more searches on one cycle, which enhanced the performance of classic sequential search without any need for data sorting as in the binary search or using multiple processors as in the parallel search. The BSS algorithm is discussed and explained in details in this paper. The BSS is also compared to the classic sequential search, and the results showed that our algorithm is two times faster than the classic sequential search.
Stability of time-delay reset systems with a nonlinear and time-varying base system

This work is devoted to investigate the stability properties of time-delay reset systems. We present a Lyapunov-Krasovskii proposition, which generalizes the available results in the literature, providing results for verifying the stability of time-delay reset systems with nonlinear and time-varying base system. We demonstrate the applicability of the proposed results in the analysis of time-delay reset control systems, and an illustrative example with nonlinear, time-varying base system.
Autistic traits modulate frontostriatal connectivity during processing of rewarding faces

Deficits in facial mimicry have been widely reported in autism. Some studies have suggested that these deficits are restricted to spontaneous mimicry and do not extend to volitional mimicry. We bridge these apparently inconsistent observations by testing the impact of reward value on neural indices of mimicry and how autistic traits modulate this impact. Neutral faces were conditioned with high and low reward. Subsequently, functional connectivity between the ventral striatum (VS) and inferior frontal gyrus (IFG) was measured while neurotypical adults (n = 30) watched happy expressions made by these conditioned faces. We found greater VS–IFG connectivity in response to high reward vs low reward happy faces. This difference was negatively proportional to autistic traits, suggesting that reduced spontaneous mimicry of social stimuli seen in autism, may be related to a failure in the modulation of the mirror system by the reward system rather than a circumscribed deficit in the mirror system.