Miracle-dz/UniFAR-FTUs huggingface dataset:
Increasing Sequence Search Sensitivity with Transitive Alignments

Sequence alignment is an important bioinformatics tool for identifying homology, but searching against the full set of available sequences is likely to result in many hits to poorly annotated sequences providing very little information. Consequently, we often want alignments against a specific subset of sequences: for instance, we are looking for sequences from a particular species, sequences that have known 3d-structures, sequences that have a reliable (curated) function annotation, and so on. Although such subset databases are readily available, they only represent a small fraction of all sequences. Thus, the likelihood of finding close homologs for query sequences is smaller, and the alignments will in general have lower scores. This makes it difficult to distinguish hits to homologous sequences from random hits to unrelated sequences. Here, we propose a method that addresses this problem by first aligning query sequences against a large database representing the corpus of known sequences, and then constructing indirect (or transitive) alignments by combining the results with alignments from the large database against the desired target database. We compare the results to direct pairwise alignments, and show that our method gives us higher sensitivity alignments against the target database.
Elevation of mitochondrial glutathione by γ‐glutamylcysteine ethyl ester protects mitochondria against peroxynitrite‐induced oxidative stress

Mitochondria under oxidative stress are thought to play a key role in various neurodegenerative disorders by directing neurons to cell death. Protection by antioxidants against oxidative stress to mitochondria may prove to be beneficial in delaying onset or progression of these diseases. We have investigated the ability of γ‐glutamylcysteine ethyl ester (GCEE) to upregulate mitochondrial glutathione (GSH) in vivo or in vitro and protect against subsequent in vitro peroxynitrite (ONOO−) damage. Mitochondria pretreated in vitro with GCEE were protected against oxidative damage induced by peroxynitrite, as assessed by mitochondrial swelling, changes in mitochondrial membrane potential, 3‐nitrotyrosine formation, protein carbonyl formation, and cytochrome c release. Loss of mitochondrial function in neuronal cell cultures by the oxidants 2,2,′Azobis(2‐amidino‐propane)dihydrochloride (AAPH) and ONOO− was ameliorated by treatment with GCEE. In vivo studies showed that mitochondria isolated from animals injected intraperitoneally with GCEE were protected partially against oxidative modifications induced by ONOO−. Taken together, these results suggest that GCEE may be effective in increasing mitochondrial GSH and may be prove to have therapeutic relevance in neurodegenerative disorders associated with oxidative stress and mitochondrial dysfunction. © 2003 Wiley‐Liss, Inc.
Research on Effect of Antenna Beamwidth for Compressive Sensing Based GPR Imaging

Compressive sensing (CS) techniques have been exploited in subsurface imaging owing to its reduction in detection time and high-quality performance in imaging. Generally, the received data is represented in the form of linear combination of potential targets with an over complete dictionary. In previous studies, the antennas of ground penetrating radars (GPRs) are assumed to be isotropic when generating the dictionary entries, however, the beam width of the antennas are finite in practice. Thus, modeling errors would be introduced when the interested imaging region covers a wide range in the cross-range direction. To reduce this modeling error, a modified dictionary which takes the antenna patterns into account is proposed in this work. Simulated results show that the image reconstructed by utilizing the modified dictionary achieves a superior performance compared to the classic one.
Genetic algorithms with different representation schemes for complex hybrid flexible flow line problems

This paper introduces some advanced genetic algorithms for a complex hybrid flexible flow line problem with a makespan objective that was recently formulated. General precedence constraints among jobs are taken into account, as are machine release dates, time lags and sequence dependent set-up times; both anticipatory and non-anticipatory. This combination of constraints captures many real world industrial problems; among those is the ceramic tile production that served as our inspiration. The introduced algorithms employ solution representation schemes with different degrees of directness. Several new machine assignment rules are introduced and implemented in some proposed genetic algorithms. The different genetic algorithms are compared among each other and to some heuristics as well. The results indicate that simple solution representation schemes result in the best performance, even for complex scheduling problems and that the genetic algorithms lead to a better solution quality than all tested heuristics.
The cultural and chronological context of early Holocene maize and squash domestication in the Central Balsas River Valley, Mexico

Molecular evidence indicates that the wild ancestor of maize is presently native to the seasonally dry tropical forest of the Central Balsas watershed in southwestern Mexico. We report here on archaeological investigations in a region of the Central Balsas located near the Iguala Valley in Guerrero state that show for the first time a long sequence of human occupation and plant exploitation reaching back to the early Holocene. One of the sites excavated, the Xihuatoxtla Shelter, contains well-stratified deposits and a stone tool assemblage of bifacially flaked points, simple flake tools, and numerous handstones and milling stone bases radiocarbon dated to at least 8700 calendrical years B.P. As reported in a companion paper (Piperno DR, et al., in this issue of PNAS), starch grain and phytolith residues from the ground and chipped stone tools, plus phytoliths from directly associated sediments, provide evidence for maize (Zea mays L.) and domesticated squash (Cucurbita spp.) in contexts contemporaneous with and stratigraphically below the 8700 calendrical years B.P. date. The radiocarbon determinations, stratigraphic integrity of Xihuatoxtla's deposits, and characteristics of the stone tool assemblages associated with the maize and squash remains all indicate that these plants were early Holocene domesticates. Early agriculture in this region of Mexico appears to have involved small groups of cultivators who were shifting their settlements seasonally and engaging in a variety of subsistence pursuits.
Hokuyo URG Series Block in Matlab Simulink

Since simulink has been widely used among engineer and researcher for many aspect of digital signal processing and control theory, then we develop a block that interfaced specific hardware that also has been widely used, a Laser Range Finder (LRF) sensor. Here we interface the LRF sensor from Hokuyo, the URG family series. Hokuyo is famous with the affordable LRF sensor that they built, such as URG-04LX-UG01. This paper presents the structure and the design of block proposed. Moreover, with mathematical calculation we provide the 2D plot graph from the scanned result.
Data caching tradeoffs in client-server DBMS architectures

In this paper, we examine the performance tradeoffs that are raised by caching data in the client workstations of a client-server DBMS. We begin by presenting a range of lock-based cache consistency algorithms that arise by viewing cache consistency as a v~iant of the well-understood problem of replicated data management. We then use a detailed simulation model to study the performance of these algorithm over a wide range of workloads end system resource configurations. The results illustrate the key performance tradeoffs related to clientserver cache consistency, and should be of use to designers of next-generation DBMS prototypes and products.
Spherical Distance Transforms

We present three algorithms for computing correct distance fields on a unit sphere. These algorithms enhance conventional distance transform techniques with several extensions. The first algorithm is a wavefront scheme using quaternions. As a unit quaternion represents a single rotation corresponding to the distance on a sphere, correct distances can be evaluated. Second, we propose a Euclidean vector-based algorithm whose computation is much simpler than that of the first. In addition, we also propose sequential versions of these algorithms that take in linear time. This paper demonstrates several examples computed by these algorithms, and shows that correct distance fields can be obtained by all the methods, with the sequential algorithm being the fastest.
A discrete time queueing system with negative customers and single working vacation

In this paper, we analyze a discrete time queueing system with geometrical arrivals of both positive and negative customers in which the server works at a lower rate during working vacation. Using embedded Markov chain and the matrix analysis solution method, we derive the probability generating function (PGF) of the number of customers waiting in the system and stationary queue length. From the process of the proof and the results, we also obtain the probabilities that the server is idle, busy, in working vacation, and in regular busy period, respectively. Finally, We introduce the application of the proposed model.
Evaluation of movement generation systems using the point-light technique

We describe a comparative evaluation of different movement generation systems capable of computing articulatory trajectories from phonetic input. The articulatory trajectories here pilot the facial deformation of a 3D clone of a human female speaker. We test the adequacy of the predicted trajectories in accompanying the production of natural utterances. The performance of these predictions are compared to the ones of natural articulatory trajectories produced by the speaker and estimated by an original video-based motion capture technique. The test uses the point-light technique (Rosenblum, L.D. and Saldana, H.M., 1996; 1998).
Hedging in Academic Discourse: A Comparative Analysis of Applied Linguistics and Literary Criticism Research Articles

Předkladana disertacni prace prezentuje výsledky výzkumu zabývajiciho se prostředky vyjadřujicimi nejistotu a nepřesnost (hedges) v žanru odborných clanků v anglickem jazyce. Jedna se o komparativni studii, jejimž cilem bylo zjistit, zda existuji rozdily v cetnosti použivani a funkcich těchto prostředků v odborných clancich z oboru aplikovane lingvistiky a literarni kritiky.
Wireless video graphics array system design

A novel system design to accommodate wireless computer video (WVGA) is presented. A simple, yet efficient variable threshold frame differencing scheme is developed in this paper that allows lossless computer video compression ratio's up to 100%, depending on what occurs on the screen. Using this scheme, only the differences between frames are sent through the channel. The compressed video stream still requires a very high speed wireless link. A 360 Mbps wireless OFDM link is simulated to cover a distance of 6 m in an indoor environment. The high bit rate comes at the expense of using 1/2 of the unlicensed band from 5.15-5.35 GHz (lower UNII band) per user. There is a resulting user count of 2 per 6 meter cell. However, the data rate allows a user to play full screen video files. The scheme can be modified to accommodate a higher density network of users who spend a lot of time surfing the Internet or word processing and who are not interested in viewing full screen video files all of the time.
Concept Cartoons als diskursiv-reflexive Szenarien zur Aktivierung des Methodenwissens beim Forschenden Lernen

Der Erwerb von Kompetenzen naturwissenschaftlicher Erkenntnisgewinnung und des Wissenschaftlichen Denkens ist ein zentrales Bildungsziel des naturwissenschaftlichen Unterrichts. Zur Forderung wird das Forschende Lernen empfohlen, jedoch bedarf dieses Unterrichtsprinzip der adaquaten Unterstutzung durch die Lehrkraft. In diesem Beitrag wird eine Studie zur Uberprufung der Wirksamkeit von diskursiv-reflexiven Szenarien (Concept Cartoons) im Rahmen des Forschenden Lernens vorgestellt. Es zeigt sich, dass das Forschende Lernen mit Concept Cartoons im Vergleich zu einer Vergleichsgruppe ohne diese Lernunterstutzung zu groseren Lernzuwachsen im Wissenschaftlichen Denken, dem Methodenwissen und dem Fachwissen fuhrt. Auserdem kann die kognitive Belastung durch Verwendung der Concept Cartoons reduziert werden. (IPN/Orig.) The acquisition of inquiry skills and scientific thinking is a central goal of science education. Inquiry learning here is a recommended teaching method, but it requires adequate support by the teacher. This paper presents a study to investigate the effectiveness of discursive-reflective scenarios (Concept Cartoons) in inquiry learning. It turns out that inquiry learning supported by Concept Cartoons leads to greater learning gains in scientific thinking, methodological knowledge (procedural understanding) and content knowledge as compared to a control group without learning support. In addition, the cognitive load could be reduced by using the Concept Cartoons. (IPN/Orig.)
Effect of Clearcutting Operations on the Survival Rate of a Small Mammal

Clearcutting is a common timber harvesting technique that represents a significant and abrupt change in habitat conditions for wildlife living in industrial forests. Most research on this type of impact has focused on comparing populations or communities in mature forests/plantations and the resulting clearcut stands. However, this approach does not separate the effect of changes in habitat attributes from direct mortality produced by the intensive use of heavy machinery required for cutting down trees and dragging them to a road. Because knowing the fate of individuals after a disturbance is important for modelling landscape-scale population dynamics in industrial forests, we conducted a study in South-Central Chile to understand the short-term response to clearcutting operations of the long-haired Akodont (Abrothrix longipillis), a forest specialist mouse. Between 2009 and 2013 we radiotracked a total of 51 adult male Akodonts, before, during and after the clearcutting of the pine plantations in which they lived. A minimum of 52.4% of the individuals died as a direct cause of the timbering operations, being crushed by vehicles or logs during logging operations. Our observations suggest that, instead of fleeing the area, the response of long-haired Akodonts to the approaching machinery is to hide under the forest litter or in burrows, which exposes them to a serious risk of death. The real mortality rate associated to clearcutting may be higher than that estimated by us because of some methodological biases (i.e. individuals with crushed radiotransmitters not recorded) and the fact that additional mortality sources may affect the population in the weeks following logging operations (e.g. higher exposure to predation, effects of site preparation for the new plantation, etc).
A power and bandwidth efficient joint source and channel coding scheme

Joint source and channel coding (JSCC) using combined trellis coded quantization (TCQ) and trellis coded continuous phase modulation (CPM) is studied. Optimal soft decoding based on the a posteriori probability (APP) algorithm for trellis coded CPM is developed for the considered systems. It has been demonstrated that the combined TCQ/CPM systems are both power and bandwidth efficient compared with the combined TCQ/TCM/8PSK systems. Furthermore, a TCQ design algorithm for the noisy channel is developed. The novelties of this work is the use of a soft decoder and the APP algorithm for combined TCQ/CPM systems.
Comparative Analysis of EM Clustering Algorithm and Density Based Clustering Algorithm Using WEKA tool

Machine learning is type of artificial intelligence wherein computers make predictions based on data. Clustering is organizing data into clusters or groups such that they have high intra-cluster similarity and low inter cluster similarity. The two clustering algorithms considered are EM and Density based algorithm. EM algorithm is general method of finding the maximum likelihood estimate of data distribution when data is partially missing or hidden. In Density based clustering , clusters are dense regions in the data space, separated by regions of lower object density. The comparison between the above two algorithms is carried out using open source tool called WEKA , with the Weather dataset as it’s input.
Mixture of Gaussian based background modelling for crowd tracking using multiple cameras

Visual surveillance system for tracking crowd using multiple cameras at dynamic backgrounds faces many challenges such as illumination variance, occultation, low spatial temporal resolution, sleeping person, shadows and camera noise. In this paper we address the issue of gradual and sudden illumination variance caused by movement of the sun and the clouds. We evaluate Mixture of Gaussian method and background modelling method for extracting foreground from the background for crowd related data base. We have evaluated the performance of the background model for sparse and dense crowds to evaluate the accuracy and efficiency of the model subjectively for crowd analytics based scenarios.
Stochastic Finite Elements with Multiple Random Non-Gaussian Properties

The spectral formulation of the stochastic finite-element method is applied to the problem of heat conduction in a random medium. Specifically, the conductivity of the medium, as well as its heat capacity are treated as uncorrelated random processes with spatial random fluctuations. Using the spectral stochastic finite-element method, this paper analyzes the sensitivity of heat conduction problems to probabilistic models of random data. In particular, both the thermal conductivity and the heat capacity of the medium are assumed to be uncertain. The implementation of the method is demonstrated for both Gaussian and lognormal material properties, modeled either as random variables or random processes.
FPGA implementation of spectrum sensing based on energy detection for Cognitive Radio

Spectrum sensing is a critical component of the Cognitive Radio that detects the presence of primary user signal in a channel. In this paper energy detection technique based on Neyman-pearson criterion is used to detect the presence of deterministic primary user (PU) signals in the channel. We have considered three different kinds of modulated signal such as BPSK, QPSK, DVB-T (2K mode) under additive white Gaussian noise (AWGN) and Rayleigh fading channel environment as specified in IEEE 802.22 standard for validating the algorithm. The simulation result shows that the energy detector achieves the desired probability of detection (≥0.9) with probability of false alarm (≤0.1) at low signal to noise ratio (SNR) up to −8dB for QPSK and DVB-T modulated signal with sample size of 64. The algorithm is also implemented in Xilinx Virtex2pro XC2VP30 (FFG896-7) Field Programmable Gate Array (FPGA). Hardware in loop (HIL) technique is used for verifying the algorithm in FPGA. The implementation result reveals that the algorithm fits into the Virtex2pro FPGA and can execute with operating frequency between 110 to 138 MHz for different sample size of primary user signals.
Vocational rehabilitation following traumatic brain injury: what is the evidence for clinical practice?

Traumatic brain injury (TBI) typically affects young adults with potentially many years of working life ahead of them. For people who were in work prior to their injury, return to work (RTW) is a common goal. However, a systematic review of RTW rates for people with TBI who were in work prior to their injury found that approximately 41% were in work at one and two years post TBI [1]. Since TBI is a leading cause of morbidity worldwide in young adults [2], this discrepancy between what people with TBI want and what they achieve is important. The question is does the research evidence inform clinicians how to help a person with TBI return to work?
A study on a system for measuring curvature and slope through edge information extraction of an electric pole partially hidden by an obstacle

Since the service life of utility poles is limited, utility poles need to be regularly maintained. For this purpose, this paper proposes an algorithm developed to determine whether a utility pole needs to be discarded or how much it is cracked, using curvature information (curvature angle) thereof obtained from an image thereof. In particular, the curvature angle of a utility pole partially hidden by an obstacle is easily measured by setting environments (e.g., user pointer) of a program to extract edge information of the utility pole. An error between a theoretical value of a left or right curvature angle of a utility pole and a measured value thereof is 0.2°(degree), and when the utility pole is divided into 3 sections, i.e., an upper section, a middle section, and a lower section, corresponding errors are 0.42°, 0.28°, and 0.26°, respectively, and a mean error value is 0.32°. Even if this system is used in a real site, these error values are rarely influenced and therefore there may be little problem to employ the system.
Changing Perspectives : A Look at Unsociability on Facebook

We propose unsociability as a novel perspective to approach and support online social interactions. With examples taken from focus group discussions, we highlight the need of users to save face in their online interactions within social network sites. We claim that people follow a “social-over-technical” pattern on Facebook, as they base their interactions on their social understanding of this site instead of on its technical capabilities. These social norms and patterns challenge social translucence which has for more than a decade been recognized as one of the cornerstones of social computing systems.
La medición de la producción intelectual: Retos, Mitos y Complejidades

2014 13 De forma general, la medición de productos, inves-tigadores o grupos es un proceso que puede generar tensiones, más aún si se tiene en cuenta que estas mediciones tienen implicaciones económicas e institucionales. Editorial La medición de la producción intelectual: Retos, Mitos y Complejidades
Theory Research on NC Instruction Interpretation for Trajectory Trace

Based on the global optimization design method of Mechatronics, from the perspective of the performance optimization of the overall CNC equipment, the dynamic model of the controlled mechanism is built, and then which is used to research on the error-free trajectory tracking for the controlled mechanism. Based on the model of the error-free trajectory tracking, NC instruction interpretation with high-order differentiability is proposed, and then relevant in-depth research is performed. NC instruction interpretation with high-order differentiability is pointed out. Finally, it is achieved on the multi-axis system with the same cycle control has been successfully developed by the author. The result demonstrates that NC instruction interpretation with high-order differentiability is useful to improve the error of trajectory tracking.