Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural compounds as light stabilizer for a starch-based biodegradable polymer

Abstract The photooxidation behavior of a commercial starch-based biodegradable polymer, i.e., new generation Mater-Bi, loaded with natural stabilizers was investigated in consideration for outdoor agricultural applications. The photooxidation behavior of the biodegradable films was monitored mainly by mechanical tests and spectroscopic analysis. In order to formulate biodegradable films without any synthetic compounds, suitable for outdoor applications and with good photooxidation stability, antioxidants such as α-tocopherol and quercetin (Q) were considered. The results obtained using natural compounds were compared with those obtained by using a synthetic antioxidant and a light stabilizer. Among the investigated natural compounds, the flavonoid compound seemed to work better than the antioxidant and the improvement in the photooxidation behavior of the biodegradable film was very similar to that obtained using the synthetic light stabilizer. A flavonoid compound can be considered as an outstanding natural stabilizer to replace synthetic light stabilizers in the formulation of 100% natural compounds based films, suitable for outdoor applications.
PartFastTree: Constructing large phylogenetic trees and estimating their reliability

Inferring phylogenies from alignments of thousands of sequences is becoming a known computational problem as DNA sequencing accelerates and gene families are growing rapidly. We present a method, PartFastTree, to construct large phylogenetic trees and estimate their reliability, which is improved from FastTree, an approximate Maximum-Likelihood method for constructing phylogenetic trees. Instead of using improved Neighbor-Joining method, PartFastTree adopts PartTree method in the phase of constructing an initial tree. It reduces the memory required from O(nsa+n1.25) to O(ns) and at the same time reduces the computation time from O(n1.25sa) to O(nlog(n)s), where n is the number of sequences, s is the width of the alignment, and a is the size of the alphabet. PartFastTree and FastTree are implemented and the evaluation on them is also presented, while PartFastTree is faster than FastTree with a little reduced accuracy when running on the datasets of from 250 to 237,882 sequences.
Measuring the Pulse of the City through Shared Bicycle Programs

City-wide urban infrastructures are increasingly reliant on networked technology to improve and expand their services. As a side effect of this digitalization, large amounts of data can be sensed and analyzed to uncover patterns of human behavior. In this paper, we sense and analyze data from a new type of urban infrastructure called shared bicycling. We provide a spatio-temporal analysis of six weeks of usage data from Barcelona's shared bicycling system called Bicing. We show how these digital traces can be used to uncover daily routines, cultural influences and the role of time and space in city dynamics.
Development and characterization of EST-SSR markers for Ottelia acuminata var. jingxiensis (Hydrocharitaceae)

Premise of the study: Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. Methods and Results: Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis. One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively. Interestingly, in cross-varietal amplification, 13 out of the 16 loci were successfully amplified in O. acuminata var. acuminata, and 12 amplified in each of the other three varieties of O. acuminata. Conclusions: These newly developed SSR markers will facilitate further study of genetic variation and provide important genetic data needed for appropriate conservation of natural populations of all varieties of O. acuminata.
A New Regularized Algorithm to Calibrate Implied Volatility in Option Pricing Models

This paper discusses the problem of calibrating volatility from a finite set of observed option prices. This kind of inverse problems, where one looks for causes of observed effects, are usually ill-posed. We propose a regularized Gauss-Newton method to calibrate the implied volatility in a stable way. Bakushinskii iterative algorithm is developed for solving the regularization problem. Finally, the theoretical results are illustrated by numerical experiment.
Novel entropy based moving average refiners for HMM landmarks

The training of precise speech recognition models depends on accurate segmentation of the phonemes in a training corpus. Segmentation is typically performed using HMMs, but recent speech recognition work suggests that the transient acoustic features characteristic of manner-class phoneme boundaries (landmarks) may be more precisely localized using acoustic classifiers specifically designed for the task of landmark detection. This paper makes an empirical exploration of entropy based moving average techniques that are capable of improving the time alignment of phoneme boundaries proposed by an HMM-based speech recognizer. On a standard benchmark data set (A database of Hindi – National Language of India), we achieve new state-of-the-art performance, reducing RMS phone boundary alignment error from 28ms to 15ms.
A self-reconfiguring architecture supporting multiple objective functions in genetic algorithms

Genetic algorithms (GA) are search algorithms based on the mechanism of natural selection and genetics. FPGAs have been widely used to implement hardware-based genetic algorithms (HGA) and have provided speedups of up to three orders of magnitude as compared to their software counterparts. In this paper, we propose a parameterized partially reconfigurable HGA architecture (PPR-HGA). The novelty of this architecture is that it allows for the objective function to be updated through partial reconfiguration, and supports various genetic parameters.
Mitigating error propagation of MMSE-DFE by joint parameter optimization

A joint optimization of the decision feedback equalizer (DFE) filter weights and an erasure slicer is proposed in this letter. The feedback weights of the DFE are constrained with an accurate mean square error (MSE) model as the criterion. An erasure slicer is adopted to further decrease error propagation. Two consecutive 1-D optimizations are shown as good as that of a single 2-D optimization. Simulation results verify the performance improvements of the proposed scheme.
Real-time 3D markerless multiple hand detection and tracking for human computer interaction applications

In this paper we present a purely vision based implementation of markerless hand detection and tracking system which effectively detects and tracks the hand positions irrespective of hand orientation. A shape based detection algorithm using a new line approximation technique followed by an adaptive minimum distance classifier based tracking technique is implemented. The technique is very generic and can be practically used in all types of immersive and semi-immersive environments like simulations, three-dimensional (3D) games, visually assisted medical surgery and other human-computer interactive applications. The proposed technique overcomes certain limitations of glove based, handheld object based and marker based techniques for a truly immersive experience. The technique also overcomes the main limitation of previous vision based hand tracking systems by providing much larger degrees of freedom essential for effective virtual reality systems. The novelty of the technique proposed is that it separates the detection and tracking parts and therefore allows tracking of multiple hands in a 3D space for real-time interaction.
Autostereoscopic display for radiotherapy planning

The work described here forms part of a program of research into the application of direct volume rendering methods to the visualization of radiation therapy plans. The full program covers a number of related topics, including the investigation of fast parallel algorithms for interactive rendering, the design of special protocols for communication between low-cost workstations and a parallel computer used to store data and generate images, and research into direct manipulation techniques for interaction with volume data. In this paper, however, we focus on the difficulties of visualizing 3D volume data, and we report the results of preliminary experiments designed to evaluate the utility of stereoscopic displays for this purpose. The remainder of the paper is organized as follows. In the next section we outline the specific problem we are trying to solve: the interactive visualization and manipulation of radiation therapy plans. We introduce, briefly, direct volume rendering methods outlining the approach we have taken and the reasons for this. Next, we address some of the problems which arise, and how stereoscopic displays may help to alleviate these. We then describe our experiments and their results, concluding with a discussion of their significance.
Mouse neutrophils express functional umami taste receptor T1R1/T1R3

Neutrophils play an important role in the initiation of innate immunity against infection and injury. Although many different types of G-protein coupled receptors are functionally expressed in neutrophils, no reports have demonstrated functional expression of umami taste receptor in these cells. We observed that mouse neutrophils express the umami taste receptor T1R1/T1R3 through RNA sequencing and quantitative RT-PCR analysis. Stimulation of mouse neutrophils with L-alanine or L-serine, which are ligands for the umami taste receptor, elicited not only ERK or p38 MAPK phosphorylation but also chemotactic migration. Moreover, addition of L-alanine or L-serine markedly reduced the production of several cytokines including TNF-α induced by lipopolysaccharide (LPS) through inhibition of NF-κB activity or STAT3 phosphorylation in neutrophils. Our findings demonstrate that neutrophils express the umami taste receptor, through which tastants stimulate neutrophils, resulting in chemotactic migration, and attenuation of LPS-induced inflammatory response. [BMB Reports 2014; 47(11): 649-654]
Supporting Self-Explanation in a Data Normalization

Self-explanation is one of the most effective learning strategies, resulting in deep knowledge. In this paper, we discuss how self-explanation is scaffolded in NORMIT, a data normalization tutor. Data normalization is the process of refining a relational database schema in order to ensure that all relations are of high quality. We present the system first, and then discuss how it supports self-explanation. We hypothesized the self-explanation support in NORMIT would improve students’ problem solving skills, and also result in better conceptual knowledge. A preliminary evaluation study of the system was performed in October 2002, the results of which show that both problem-solving performance and the understanding of the domain of students who self-explained increased. We also discuss our plans for future research.
Enhancing Behavior Protocols with Atomic Actions ∗ Technical report

Verification of software behavior and assuring thus its reliability is among current trends of applications’ construction. As an arbitrary application tends to yield a large state space, using software components and a suitable abstraction mechanism enables for model checking the application piecewise, thus in reasonable time. Behavior protocols [1] are one of the component behavior specification platform. During the work on the specification of Airport Internet Access Application implemented in Fractal [3] a need of specifying both component initialization and synchronization of service requests and responses arised. In this article, we introduce a behavior protocols extension called atomic actions that enables for an easy way of specification of these commonly used programming techniques.
Fabrication of a microfluidic system with integrated electrochemical pump and valves

An integrated microfluidic system with a check valve and a micropump based on electrochemical actuation was designed and fabricated using UV-LIGA microfabrication technologies. The main components of the system include two electrochemical (ECM) actuators, a polydimethylsiloxane (PDMS) membrane, and multi levels of covers. The thickness of the membrane is 100 &mgr;m thick and the thickness of the PDMS structure is 1000 &mgr;m. Hydrogen gas bubbles were generated from Pt black electrodes with 1M of NaCl solution in the valve chamber. Experimental results proved that the system can be operated by controlling the electrical signals supplied to the ECM actuators.
Adaptive Algorithms for Online Convex Optimization with Long-term Constraints

We present an adaptive online gradient descent algorithm to solve online convex optimization problems with long-term constraints , which are constraints that need to be satisfied when accumulated over a finite number of rounds T , but can be violated in intermediate rounds. For some user-defined trade-off parameter $\beta$ $\in$ (0, 1), the proposed algorithm achieves cumulative regret bounds of O(T^max{$\beta$,1--$\beta$}) and O(T^(1--$\beta$/2)) for the loss and the constraint violations respectively. Our results hold for convex losses and can handle arbitrary convex constraints without requiring knowledge of the number of rounds in advance. Our contributions improve over the best known cumulative regret bounds by Mahdavi, et al. (2012) that are respectively O(T^1/2) and O(T^3/4) for general convex domains, and respectively O(T^2/3) and O(T^2/3) when further restricting to polyhedral domains. We supplement the analysis with experiments validating the performance of our algorithm in practice.
Planning motion compliant to complex contact states

In robotic tasks and in mechanism design, planning motion compliant to contacts is often desired, but planning such motion poses special challenges not present in collision-free motion planning. One challenge is how to achieve exactness, i.e., how to make sure that a planned path is exactly compliant to a desired contact state, especially when the configuration manifold of such a contact state is hard to describe analytically due to high geometrical complexity and/or high dimensionality. We tackle the problem with a hybrid approach of direct computation to exploit contact constraints and randomized planning. We describe such a planner for planning motion compliant to a contact formation between two arbitrary polyhedra and present results of implementation.
Single‐Channel Analysis of Glutamate Receptors

This is a companion to UNIT 11.16 : Single‐Channel Recording of Glutamate Receptors. Described here are techniques for analyzing single‐channel currents recorded from glutamate receptors to characterize their properties. In addition, issues that need to be taken into account when analyzing glutamate receptor single‐channel recording results are discussed. © 2015 by John Wiley & Sons, Inc.
Simultaneous Tracking of the Best Basis in Reduced-Rank Wiener Filter

A new on-line learning algorithm that yields a reduced-rank Wiener filter (RRWF) is proposed. The RRWF is defined as the matrix of prescribed rank that provides the best least-squares approximation of a given signal. This implies that an RRWF determines only a subspace, but is not endowed with information of basis functions or axes for the subspace. In other words, even if we want to reduce the rank of the estimated RRWF, we should learn another RRWF of "more reduced rank" again. Our goal in this paper is therefore to establish a learning rule that simultaneously tracks basis functions yielding a matrix that gives an RRWF. To this end, we reformulate the optimization problem of RRWFs, which will be solved by a gradient-based algorithm derived within the framework of differential geometry. Numerical examples are illustrated to support the proposals in the paper
Fairness in Assignment Markets with Dual Decomposition

In this work, we present a market design for assignment problems that computes a globally optimal solution by adjusting incentives. Such markets can help in settings such as the assignment of peer-reviewers to submitted academic articles, assignment of tutors to students, or online matchmaking services. In these settings, each assignment has some reward value, and existing strategies for achieving high global reward involve either adjustments to greedy choices by agents or global optimization of estimated reward values. The benefit of maintaining a market is that we combine benefits from these methods in a principled way. The agents make incentivized greedy decisions, which is ideal because they understand their reward functions best, while the incentives push their decisions toward the global optimum. We update the incentives by relating the assignment market to a dual decomposition of the (b-) matching linear programming relaxation. We evaluate our proposed system on simulations, demonstrating that the market quickly improves the global reward.
Comparison of the optical gain of wurtzite GaN/AlGaN quantum well lasers grown on (0001)- and (1010)-oriented substrates

We calculate the optical gain of wurtzite (WZ) GaN/AlGaN QWs grown on the (0001) and (1010) oriented substrates, taking into account the valence subband structure modification due to the crystal orientation effect and the pseudomorphic strain which is anisotropic in the QW plane. We show that, for the (1010) GaN/AlGaN quantum well (QW), the two topmost valence subbands are more widely separated than the HH1 and LH1 subbands in the (0001) GaN/AlGaN QW. The in-plane energy dispersion of the (1010) QW also becomes anisotropic, giving rise to a reduced band-edge density-of-states in comparison with the (0001) QW. Moreover, states constituting the topmost valence subband at the (Gamma) point favor TE mode gain. A combination of the reduced band-edge density-of- states and the existence of the preferred symmetry at the valence band maximum contributes to an improvement of the TE optical gain. A comparison of the QWs of both orientations shows that the (1010) QW is capable of achieving lower transparency current densities. Therefore, the (1010) orientation is promising in improving the threshold performance of WZ GaN-based QW lasers.
Modeling gunshot bruises in soft body armor with an adaptive fuzzy system

Gunshots produce bruise patterns on persons who wear soft body armor when shot even though the armor stops the bullets. An adaptive fuzzy system modeled these bruise patterns based on the depth and width of the deformed armor given a projectile's mass and momentum. The fuzzy system used rules with sinc-shaped if-part fuzzy sets and was robust against random rule pruning: Median and mean test errors remained low even after removing up to one fifth of the rules. Handguns shot different caliber bullets at armor that had a 10%-ordnance gelatin backing. The gelatin blocks were tissue simulants. The gunshot data tuned the additive fuzzy function approximator. The fuzzy system's conditional variance V[Y|X=x] described the second-order uncertainty of the function approximation. Handguns with different barrel lengths shot bullets over a fixed distance at armor-clad gelatin blocks that we made with Type 250 A Ordnance Gelatin. The bullet-armor experiments found that a bullet's weight and momentum correlated with the depth of its impact on armor-clad gelatin (R/sup 2/=0.881 and p-value <0.001 for the null hypothesis that the regression line had zero slope). Related experiments on plumber's putty showed that highspeed baseball impacts compared well to bullet-armor impacts for large-caliber handguns. A baseball's momentum correlated with its impact depth in putty (R/sup 2/=0.93 and p-value <0.001). A bullet's momentum similarly correlated with its armor-impact in putty (R/sup 2/=0.97 and p-value <0.001). A Gujarati-Chow test showed that the two putty-impact regression lines had statistically indistinguishable slopes for p-value =0.396. Baseball impact depths were comparable to bullet-armor impact depths: Getting shot with a . 22 caliber bullet when wearing soft body armor resembles getting hit in the chest with a 40-mph baseball. Getting shot with a . 45 caliber bullet resembles getting hit with a 90-mph baseball.
454 Pyrosequencing of Olive (Olea europaea L.) Transcriptome in Response to Salinity

Olive (Olea europaea L.) is one of the most important crops in the Mediterranean region. The expansion of cultivation in areas irrigated with low quality and saline water has negative effects on growth and productivity however the investigation of the molecular basis of salt tolerance in olive trees has been only recently initiated. To this end, we investigated the molecular response of cultivar Kalamon to salinity stress using next-generation sequencing technology to explore the transcriptome profile of olive leaves and roots and identify differentially expressed genes that are related to salt tolerance response. Out of 291,958 obtained trimmed reads, 28,270 unique transcripts were identified of which 35% are annotated, a percentage that is comparable to similar reports on non-model plants. Among the 1,624 clusters in roots that comprise more than one read, 24 were differentially expressed comprising 9 down- and 15 up-regulated genes. Respectively, inleaves, among the 2,642 clusters, 70 were identified as differentially expressed, with 14 down- and 56 up-regulated genes. Using next-generation sequencing technology we were able to identify salt-response-related transcripts. Furthermore we provide an annotated transcriptome of olive as well as expression data, which are both significant tools for further molecular studies in olive.
High throughput architecture for packet classification using FPGA

To avoid packet classification from being the performance bottleneck in network devices, one-chip solution hardware packet classifier based on HiCuts algorithm is designed and implemented in single chip of FPGA. The compact data structure and the optimized combination of memory organization with high degree parallel and pipeline architecture make the classifier running at very high speed. The simulation and implementation tests show our design reaches OC-768 throughput even for a large rule set with 26K rules while only consuming limited logic resource of the FPGA. This low cost one-chip hardware solution can effectively off-load data processing burden from the CPU of data path in network devices.
On the Linkages between the Tropospheric Isentropic Slope and Eddy Fluxes of Heat during Northern Hemisphere Winter

AbstractPrevious studies have demonstrated the key role of baroclinicity and thus the isentropic slope in determining the climatological-mean distribution of the tropospheric eddy fluxes of heat. Here the authors examine the role of variability in the isentropic slope in driving variations in the tropospheric eddy fluxes of heat about their long-term mean during Northern Hemisphere winter.On month-to-month time scales, the lower-tropospheric isentropic slope and eddy fluxes of heat are not significantly correlated when all eddies are included in the analysis. But the isentropic slope and heat fluxes are closely linked when the data are filtered to isolate the fluxes due to synoptic ( 10 days) time scale waves. Anomalously steep isentropic slopes are characterized by anomalously poleward heat fluxes by synoptic eddies but anomalously equatorward heat fluxes by low-frequency eddies. Lag regressions based on daily data reveal that 1) variations in the isentropic slope precede by .