Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling the Amplification Dynamics of Human Alu Retrotransposons

Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA) that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human–chimpanzee divergence.
Analysis and Calculation of Zero-Sequence Voltage Considering Neutral-Point Potential Balancing in Three-Level NPC Converters

The neutral-point (NP) potential of the three-level neutral-point-clamped converters is needed to maintain balancing. Zero-sequence voltage is the only freedom degree when carrier-based pulsewidth modulation is utilized. Appropriate zero-sequence voltage should be identified to control the NP potential. The relationship between the neutral current and injected zero-sequence voltage is studied comprehensively, and two balancing algorithms of NP potential, respectively adopting searching-optimization and interpolation methods, are presented. The theoretical optimum zero-sequence voltage for controlling NP potential can be obtained by the latter proposed algorithm. Simulation and experimental results are shown to verify the validity and practicability of the proposed algorithms.
Synthesis, characterization, and film morphology of dodecylpolysiloxane

A novel polysiloxane softener bearing dodecyl side groups (dodecylpolysiloxane [DDPS]) was synthesized by copolymerization of octamethylcyclotetrasiloxane with dodecyltrimethoxysilane and hexamethyldisiloxane. Chemical structure and film morphology of the synthesized polysiloxane are characterized and investigated by infrared spectrum, 1H-NMR, field emission scanning electronic microscope, and atomic force microscope. The experiment results indicate that DDPS can form a hydrophobic film on both the cotton fiber and silicon wafer surface. At an amplification of 200 nm, DDPS shows a relative smooth resin film on the treated fabric/fiber surface. But as the observation rule decreases to 2 nm—almost to a molecular scale—the DDPS film mostly exhibits an inhomogeneous structure and uneven morphology in its atomic force microscope images. There are many low or high peaks that appeared in DDPS topography. Consequently in 2 μm2 scanning field, the root mean square roughness of DDPS film reaches to 0.199 nm, which is 2.46 times rougher as compared with that of polydimethylsiloxane film. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 101: 4480–4486, 2006
Yet Another Language Identifier

Language identification of written text has been studied for several decades. Despite this fact, most of the research is focused on a few most spoken languages, whereas the minor ones are ignored. The identification of a larger number of languages brings new difficulties that do not occur for a few languages. These difficulties are causing decreased accuracy. The objective of this paper is to investigate the sources of such degradation. In order to isolate the impact of individual factors, 5 different algorithms and 3 different number of languages are used. The Support Vector Machine algorithm achieved an accuracy of 98% for 90 languages and the YALI algorithm based on a scoring function had an accuracy of 95.4%. The YALI algorithm has slightly lower accuracy but classifies around 17 times faster and its training is more than 4000 times faster. Three different data sets with various number of languages and sample sizes were prepared to overcome the lack of standardized data sets. These data sets are now publicly available.
Precoding for the AWGN Channel With Discrete Interference

For a state-dependent discrete memoryless channel with input alphabet X, state alphabet S, and output alphabet Y where the independent and identically distributed (i.i.d.) state sequence is known causally at the transmitter, it is shown that by using at most min{|X||S|-|S| + 1,|Y|} out of |X||S| inputs of the Shannon's derived channel, the capacity is achievable. As an example of state-dependent channels with side information at the transmitter, M-ary signal transmission for the additive white Gaussian noise (AWGN) channel with additive Q-ary interference where the sequence of i.i. d. interference symbols is known causally at the transmitter is considered. The optimal precoding scheme is derived under the constraint that the channel input given any current interference symbol is uniformly distributed over the channel input alphabet. It is shown that at low signal-to-noise ratio (SNR) not doing precoding is optimal. For the special case where the Gaussian noise power is zero, it is shown that the rate log2 M is achievable by a one-shot coding scheme if X is an arithmetic progression.
Kleene algebra with domain

We propose Kleene algebra with domain (KAD), an extension of Kleene algebra by simple equational axioms for a domain and a codomain operation. KAD considerably augments the expressiveness of Kleene algebra, in particular for the specification and analysis of programs and state transition systems. We develop the basic calculus, present the most interesting models and discuss some related theories. We demonstrate applicability by two examples: algebraic reconstructions of Noethericity and propositional Hoare logic based on equational reasoning.
Task Lineages: Dialog State Tracking for Flexible Interaction

We consider the gap between user demands for seamless handling of complex interactions, and recent advances in dialog state tracking technologies. We propose a new statistical approach, Task Lineage-based Dialog State Tracking (TL-DST), aimed at seamlessly orchestrating multiple tasks with complex goals across multiple domains in continuous interaction. TL-DST consists of three components: (1) task frame parsing, (2) context fetching and (3) task state update (for which TL-DST takes advantage of previous work in dialog state tracking). There is at present very little publicly available multi-task, complex goal dialog data; however, as a proof of concept, we applied TL-DST to the Dialog State Tracking Challenge (DSTC) 2 data, resulting in state-of-the-art performance. TLDST also outperforms the DSTC baseline tracker on a set of pseudo-real datasets involving multiple tasks with complex goals which were synthesized using DSTC3 data.
Phantom redundancy: a high-level synthesis approach for manufacturability

Phantom redundancy, an area-efficient technique for fabrication-time reconfigurability is presented. Phantom redundancy adds extra interconnect so as to render the resulting microarchitecture reconfigurable in the presence of any (single) functional unit failure. The proposed technique yields partially good chips in addition to perfect chips. A genetic algorithm is used to incorporate phantom redundancy constraints into microarchitecture synthesis. The algorithm minimizes tire performance degradation due to any faulty functional unit of the resulting microarchitecture. The effectiveness of the technique is illustrated on benchmark examples.
Simultaneous parameter estimation and object segmentation from image sequences

Previously (see Proc. ICIP, vol.1, p.542-5, 1995) we proposed a method for segmenting an image in a sequence of images into regions of stationary, moving, and uncovered background pixels and simultaneously estimating parameters of each region. This previous work focused on the viability of the idea and considered only moving and stationary pixels. In this paper we present an extension of the formulation to include uncovered background pixels and multiple object segmentation. We show segmentations and reconstructed image frames for synthetic image sequences.
Proofs as discourse: an empirical study

Computer-based logic proofs are a form of ’unnatural’ language discourse, but the structure and process of proof can be observed in considerable detail, and analysis is leading to a number of general insights. We have been studying how students respond to multimodal logic teaching. First, psychological measures indicate that students’ pre-existing cognitive styles have a sigaificant impact on teaching outcome. Secondly, a large corpus of proofs has been gathered via automatic logging of proof development. Frequency analysis and cluster analysis of this corpus indicate that students’ cognitive styles influence the structure of their logical discourse. Our current objective is to apply further statistical methods to the proof development logs, to derive various transition frequencies, and then construct process models which explain the differences in discourse style.
Bigger is Not Always Better: on the Quality of Hypotheses in Active Automata Learning

In Angluin’s L algorithm a learner constructs a sequence of hypotheses in order to learn a regular language. Each hypothesis is consistent with a larger set of observations and is described by a bigger model. From a behavioral perspective, however, a hypothesis is not always better than the previous one, in the sense that the minimal length of a counterexample that distinguishes a hypothesis from the target language may decrease. We present a simple modication of the L algorithm that ensures that for subsequent hypotheses the minimal length of a counterexample never decreases, which implies that the distance to the target language never increases in a corresponding ultrametric. Preliminary experimental evidence suggests that our algorithm speeds up learning in practical applications by reducing the number of equivalence queries.
CSE Framework: A UIMA-based Distributed System for Configuration Space Exploration

To efficiently build data analysis and knowledge discovery pipelines, researchers and developers tend to leverage available services and existing components by plugging them into different phases of the pipelines, and then spend hours to days seeking the right components and configurations that optimize the system performance. In this paper, we introduce the CSE framework , a distributed system for a parallel experimentation test bed based on UIMA and uimaFIT, which is general and flexible to configure and powerful enough to sift through thousands option combinations to determine which represent the best system con-
A pilot study of the purchase of manipulation services for acute low back pain in the United Kingdom.

BACKGROUND The purchasing arrangements for acute low back pain recommended to UK health ministers by the Clinical Standards Advisory Group (CSAG) in 1994 as a cost-neutral way of reducing back pain disability have not been tested in practice. OBJECTIVE To test the CSAG's recommendations in primary care, studying their cost implications and identifying the professional relationships between general practitioners (GPs) and manipulation practitioners. DESIGN Retrospective and prospective observational study with cohorts balanced for similar features in terms of age, gender, diagnosis, severity and work loss at entry point. PARTICIPANTS One hundred and ninety-four retrospective patients with acute low back pain presenting to 11 GP practices between July and October 1995. Three hundred and forty-four prospective patients with the complaint presenting to the same practices between November 1995 and March 1996. Referrals to local chiropractic, osteopathic and manipulation physiotherapy practices as well as to usual secondary care services. OUTCOME MEASURES Waiting time for first attendances, sickness certification, number of consultations, drug use and costs, recovery time, x-ray utilization, cost of care. MAIN RESULTS Substantial shift of referrals to manipulation practitioners under the scheme. Prospective patients had fewer referrals to secondary care than retrospective patients, fewer GP consultations, less drug use, fewer certified sickness days. Prospective patients had shorter waiting times to be seen by manipulating physiotherapists. Chiropractors used X-rays more often than other practitioners. Demonstrable savings in sickness incapacity benefits were evident by following CSAG recommendations. CONCLUSION GPs complied with CSAG management recommendations when funding of manipulation services was made available. Implementation was associated with better outcomes generally. A fully funded study including chronic back patients is justified.
Optimization and integration of ground vehicle systems

This article deals with the optimal design of ground vehicles and their subsystems, with particular reference to ‘active’ safety and comfort. A review of state-of-the-art optimization methods for solving vehicle system design problems, including the integration of electronic controls, is given, thus further encouraging the use of such methods as standard tools for automotive engineers. Particular attention is devoted to the class of methods pertaining to complex system design optimization, as well as approaches for the optimal design of complex systems under uncertainty. Some examples of design optimizations are given in the fields of vehicle system dynamics, powertrain/internal combustion engine design, active safety and ride comfort, vehicle system design and lightweight structures, advanced automotive electronics, and smart vehicles.
Subcellular electrical stimulation of neurons enhances the myelination of axons by oligodendrocytes

Myelin formation has been identified as a modulator of neural plasticity. New tools are required to investigate the mechanisms by which environmental inputs and neural activity regulate myelination patterns. In this study, we demonstrate a microfluidic compartmentalized culture system with integrated electrical stimulation capabilities that can induce neural activity by whole cell and focal stimulation. A set of electric field simulations was performed to confirm spatial restriction of the electrical input in the compartmentalized culture system. We further demonstrate that electrode localization is a key consideration for generating uniform the stimulation of neuron and oligodendrocytes within the compartments. Using three configurations of the electrodes we tested the effects of subcellular activation of neural activity on distal axon myelination with oligodendrocytes. We further investigated if oligodendrocytes have to be exposed to the electrical field to induce axon myelination. An isolated stimulation of cell bodies and proximal axons had the same effect as an isolated stimulation of distal axons co-cultured with oligodendrocytes, and the two modes had a non-different result than whole cell stimulation. Our platform enabled the demonstration that electrical stimulation enhances oligodendrocyte maturation and myelin formation independent of the input localization and oligodendrocyte exposure to the electrical field.
Benefits of retinal image motion at the limits of spatial vision

Even during fixation, our eyes are constantly in motion, creating an ever-changing signal in each photoreceptor. Neuronal processes can exploit such transient signals to serve spatial vision, but it is not known how our finest visual acuity—one that we use for deciphering small letters or identifying distant faces and objects—is maintained when confronted with such change. We used an adaptive optics scanning laser ophthalmoscope to precisely control the spatiotemporal input on a photoreceptor scale in human observers during a visual discrimination task under conditions with habitual, cancelled or otherwise manipulated retinal image motion. We found that when stimuli moved, acuities were about 25% better than when no motion occurred, regardless of whether that motion was self-induced, a playback of similar motion, or an external simulation. We argue that in our particular experimental condition, the visual system is able to synthesize a higher resolution percept from multiple views of a poorly resolved image, a hypothesis that might extend the current understanding of how fixational eye motion serves high acuity vision.
Chloroform Fraction of Centratherum anthelminticum (L.) Seed Inhibits Tumor Necrosis Factor Alpha and Exhibits Pleotropic Bioactivities: Inhibitory Role in Human Tumor Cells

We investigated the antioxidant potential, cytotoxic effect, and TNF-α inhibition activity with NF-κB activation response in a chloroform fraction of Centratherum anthelminticum seeds (CACF). The antioxidant property of CACF was evaluated with DPPH, ORAC, and FRAP assays, which demonstrated significant antioxidant activity. The cytotoxicity of CACF was tested using the MTT assay; CACF effective inhibitory concentrations (IC50) for A549, PC-3, MCF-7, and WRL-68 cells were 31.42 ± 5.4, 22.61 ± 1.7, 8.1 ± 0.9, and 54.93 ± 8.3 μg/mL, respectively. CACF effectively and dose-dependently inhibited TNF-α release, in vitro and in vivo. CACF inhibited TNF-α secretion in stimulated RAW264.7 macrophage supernatants with an IC50 of 0.012 μg/mL, without affecting their viability; the highest dose tested reduced serum TNF-α by 61%. Acute toxicity testing in rats revealed that CACF was non-toxic at all doses tested. Matching the cytotoxic activity towards a mechanistic approach, CACF dose-dependently exhibited in vitro inhibitory effects against the activation of NF-κB translocation in MCF-7 cells. Preliminary phytochemical screening with GC/MS analysis detected 22 compounds in CACF, of which morpholinoethyl isothiocyanate was the most abundant (29.04%). The study reveals the potential of CACF in the treatment of breast cancer and in oxidative stress conditions with associated inflammatory responses.
AutoStyle: Scale-driven Hint Generation for Coding Style

While the use of autograders for code correctness is widespread, less e ↵ ort has focused on automating feed-back for good programming style: the tasteful use of language features and idioms to produce code that is not only correct, but also concise, elegant, and revealing of design intent. We present a system that can provide real-time actionable code style feedback to students in large introductory computer science classes. We demonstrate that in a randomized controlled trial, 70% of students using our system achieved the best style solution to a coding problem in less than an hour, while only 13% of students in the control group achieved the same. Students using our system also showed a statistically-signiﬁcant greater improvement in code style than students in the control group. We also present experiments to demonstrate the e � cacy and relevance of each of the di ↵ erent types of hints generated by our system.
A multi-resolution ICP with heuristic closest point search for fast and robust 3D registration of range images

The iterative closest point (ICP) algorithm is widely used for the registration of 3D geometric data. One of the main drawbacks of the algorithm is its quadratic time complexity O(N/sup 2/) with the number of points N. Consequently, several methods have been proposed to accelerate the process. We present a new solution for the speeding up of the ICP algorithm and special care is taken to avoid any tradeoff with the quality of the registration. The proposed solution combines a coarse to fine multiresolution approach with the neighbor search algorithm. The multiresolution approach permits to successively improve the registration using finer levels of representation and the neighbor search algorithm speeds up the closest point search by using a heuristic approach. Both multiresolution scheme and neighbor search algorithm main features are presented. Confirming the success of the proposed solution, typical results show that this combination permits to create a very fast ICP algorithm, with a closest point search complexity of O(N), while preserving the matching quality.
Role of the small GTPase RhoA in the hypoxia-induced decrease of plasma membrane Na,K-ATPase in A549 cells

Hypoxia impairs alveolar fluid reabsorption by promoting Na,K-ATPase endocytosis, from the plasma membrane of alveolar epithelial cells. The present study was designed to determine whether hypoxia induces Na,K-ATPase endocytosis via reactive oxygen species (ROS)-mediated RhoA activation. In A549 cells, RhoA activation occurred within 15 minutes of cells exposure to hypoxia. This activation was inhibited in cells infected with adenovirus coding for gluthatione peroxidase (an H2O2 scavenger), in mitochondria depleted (ρ0) cells or cells expressing decreased levels of the Rieske iron-sulfur protein (inhibitor of mitochondrial complex III), which suggests a role for mitochondrial ROS. Moreover, exogenous H2O2 treatment during normoxia mimicked the effects of hypoxia on RhoA, further supporting a role for ROS. Cells expressing dominant negative RhoA failed to endocytose the Na,K-ATPase during hypoxia or after H2O2 treatment. Na,K-ATPase endocytosis was also prevented in cells treated with Y-27632, a Rho-associated kinase (ROCK) inhibitor, and in cells expressing dominant negative ROCK. In summary, we provide evidence that in human alveolar epithelial cells exposed to hypoxia, RhoA/ROCK activation is necessary for Na,K-ATPase endocytosis via a mechanism that requires mitochondrial ROS.
Design of modified Sierpinski fractal based miniaturized patch antenna

Miniaturization of microstrip patch antenna by incorporating fractal geometry is presented in this paper. The unique space-filling property of fractals is explored to develop a novel patch antenna operating at 2.45 GHz with significant size reduction than its conventional counterpart. An inset-fed patch antenna is taken as initiator of proposed fractal design. The fractal iteration of Sierpinski Carpet in modified form is performed up to 2nd iteration. The antennas are designed using finite element method based HFSS and their performances are demonstrated in terms of Return loss, radiation pattern, gain plot, smith chart, and VSWR. Experimental results of Sierpinski Carpet iterations and their comparison with the generator shows size reduction of 31% and 32% in 1st and 2nd iteration correspondingly, without affecting antenna performances such as reflection loss, impedance matching and antenna gain.
Design of a Modified Concolic Testing Algorithm with Smaller Constraints

Concolic testing is a well-known unit test generation technique. However, bottlenecks such as constraint solving prevents concolic testers to be used in large projects. We propose a modification to a standard concolic tester. Our modification makes more but smaller queries to the constraint solver, i.e. ignores some path conditions. We show that it is possible to reach the same branch coverage as the standard concolic tester while decreasing the burden on the constraint solver. We support our claims by testing several C programs with our method. Experimental results show that our modification improves runtime performance of the standard concolic tester in half of the experiments and results in more than 5x speedup when the unit under test has many infeasible paths.