Miracle-dz/UniFAR-FTUs huggingface dataset:
Transmembrane and Coiled-Coil Domain Family 1 Is a Novel Protein of the Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a continuous membrane network in eukaryotic cells comprising the nuclear envelope, the rough ER, and the smooth ER. The ER has multiple critical functions and a characteristic structure. In this study, we identified a new protein of the ER, TMCC1 (transmembrane and coiled-coil domain family 1). The TMCC family consists of at least 3 putative proteins (TMCC1–3) that are conserved from nematode to human. We show that TMCC1 is an ER protein that is expressed in diverse human cell lines. TMCC1 contains 2 adjacent transmembrane domains near the C-terminus, in addition to coiled-coil domains. TMCC1 was targeted to the rough ER through the transmembrane domains, whereas the N-terminal region and C-terminal tail of TMCC1 were found to reside in the cytoplasm. Moreover, the cytosolic region of TMCC1 formed homo- or hetero-dimers or oligomers with other TMCC proteins and interacted with ribosomal proteins. Notably, overexpression of TMCC1 or its transmembrane domains caused defects in ER morphology. Our results suggest roles of TMCC1 in ER organization.
Sensing, modelling and closed loop control of powder feeder for laser surface modification

Powder feeder is used widely for laser surface treatment such as cladding and alloying. The stability of powder feeding is directly affecting the processing quality. This paper investigates the use of a pressure sensor for the continuous monitoring of powder flowrate and the incorporation of closed loop servo-control system for the on-line feedback control of powder flowrate. The stability of the powder feeding has been found much improved by the new feeding system especially during warm up period (about 30 minutes). The measurement of of powder particle velocity and establishment of a dynamic model of the powder feeding process are also presented.Powder feeder is used widely for laser surface treatment such as cladding and alloying. The stability of powder feeding is directly affecting the processing quality. This paper investigates the use of a pressure sensor for the continuous monitoring of powder flowrate and the incorporation of closed loop servo-control system for the on-line feedback control of powder flowrate. The stability of the powder feeding has been found much improved by the new feeding system especially during warm up period (about 30 minutes). The measurement of of powder particle velocity and establishment of a dynamic model of the powder feeding process are also presented.
Vehicle Detection and Tracking for the Urban Challenge

: The Urban Challenge 2007 was a race of autonomous vehicles through an urban environment organized by the U.S. government. During the competition the vehicles encountered various typical scenarios of urban driving. Here they had to interact with other traﬃc which was human or machine driven. This paper describes the perception approach taken by Team Tartan Racing, winner of the competition. A focus is set on the detection and tracking of other vehicles around the robot. The presented approach allows a situation speciﬁc interpretation of perception data through situation assessment algorithms keeping the perception algorithms situation independent.
Cost-Effective Design of Inverter Output Filters for AC Drives

The paper deals with the minimization of output filter cost in inverter-fed AC drives. The LC Alter design is constrained by the total harmonic distortions of the stator voltage and inverter output current, the voltage drop in the filter inductor, and the system resonance frequency. The last constraint is important from the control point of view, because the vector control requires that the sampling frequency is sufficiently higher than the resonance frequency. The design takes into account the frequency dependence of the filter resistance and inductance due to the eddy currents in the laminated iron- core inductor. The design method is further enhanced by taking into account the inverter power stage cost as a function of the switching frequency. The design minimizes the total cost of the inverter and filter, and determines the optimal switching frequency. Simulations and experiments show that the filter designed according to the proposed design procedure fulfils the design constraints, and the speed-sensorless control works well with the cost-optimized filter.
SHELLFBK: An Information Retrieval-based System For Multi-Domain Sentiment Analysis

This paper describes the SHELLFBK system that participated in SemEval 2015 Tasks 9, 10, and 11. Our system takes a supervised approach that builds on techniques from information retrieval. The algorithm populates an inverted index with pseudo-documents that encode dependency parse relationships extracted from the sentences in the training set. Each record stored in the index is annotated with the polarity and domain of the sentence it represents. When the polarity or domain of a new sentence has to be computed, the new sentence is converted to a query that is used to retrieve the most similar sentences from the training set. The retrieved instances are scored for relevance to the query. The most relevant training instant is used to assign a polarity and domain label to the new sentence. While the results on well-formed sentences are encouraging, the performance obtained on short texts like tweets demonstrate that more work is needed in this area.
Secrecy in multiagent systems

We introduce a general framework for reasoning about secrecy requirements in multiagent systems. Because secrecy requirements are closely connected with the knowledge of individual agents of a system, our framework employs the modal logic of knowledge within the context of the well-studied runs and systems framework. Put simply, "secrets" are facts about a system that low-level agents are never allowed to know. The framework presented here allows us to formalize this intuition precisely, in a way that is much in the spirit of Sutherland's notion of nondeducibility. Several well-known attempts to characterize the absence of information flow, including separability, generalized noninterference, and nondeducibility on strategies, turn out to be special cases of our definition of secrecy. However, our approach lets us go well beyond these definitions. It can handle probabilistic secrecy in a clean way, and it suggests generalizations of secrecy that may be useful for dealing with resource-bounded reasoning and with issues such as downgrading of information.
The picture-word interference paradigm: conceptual effects in the production of verbs

In recent years, experimental research on language production has started to make increasing use of the so-called picture-word interference paradigm to explore lexical retrieval processes. While providing useful information on the production of nouns, the paradigm has not led, so far, to comparable results with respect to the production of verbs. The paper presents an experiment and provides a discussion aiming at clarifying some of the variables that affect verb production and render semantic interference effects difficult to observe. 1. Interference effects and the production of nouns Interference paradigms have long been popular among psychologists studying cognitive phenomena. The technique is simple: participants are presented with a stimulus made up of two different components. Their task is to respond to one component of the stimulus, ignoring the other. For example, they could be presented with a word such as blue written in red ink, and requested to name the ink colour as quickly as possible (Stroop 1935). When the two components of the stimulus are a picture and a word, the task is typically one of picture naming: participants are instructed to ignore the distractor word and to name the picture, producing a target word. Usually, experimental conditions are manipulated by the researcher who varies the relationship between distractor and target words or the time interval between the presentations of picture and distractor (SOA: Stimulus Onset Asynchrony). Over a decade ago, in an influential study conducted in Dutch, Schriefers et al. (1990) employed this paradigm to study the production of nouns. They found that naming a picture (e.g., a dog) takes longer when the distractor is semantically related (e.g., cat) than when it is unrelated (e.g., roof) to the target (e.g., dog). This effect is observed when the distractor is presented shortly before or at the same time as the picture (SOA = -150/0 ms), but disappears when it is presented after the picture (SOA = + 150 ms). In contrast, when target and distractor are phonologically related (e.g., dog/fog) respon
Multiple-photon excitation imaging with an all-solid-state laser

Two-photon excitation imaging is a recently described optical sectioning technique where fluorophore excitation is confined to--and therefore defines--the optical section being observed. This characteristic offers a significant advantage over laser-scanning confocal microscopy; the volume of fluorophore excited in the minimum necessary for imaging, thereby minimizing the destructive effects of fluorophore excitation in living tissues. In addition, a confocal pinhole is not required for optical scattering--thus further reducing the excitation needed for efficient photon collection. We have set up a two-photon excitation imaging system which uses an all-solid-state, short-pulse, long-wavelength laser as an excitation source. The source is a diode-pumped, mode-locked Nd:YLF laser operating in the infrared (1047nm). This laser is small, has modest power requirements, and has proven reliable and stable in operation. The short laser pulses from the laser are affected by the system optical path; this has been investigated with second harmonic generation derived from a nonlinear crystal. The system has been specifically designed for the study of live biological specimens. Two cell types especially sensitive to high-energy illumination, the developing Caenorhabditis elegans embryo and the crawling sperm of the nematode, Ascaris, were used to demonstrate the dramatic increase in viability when fluorescence is generated by two-photon excitation. The system has the capability of switching between two-photon and confocal imaging modes to facilitate direct comparison of theory of these two optical sectioning techniques on the same specimen. A heavily stained zebra fish embryo was used to demonstrate the increase in sectioning depth when fluorescence is generated by infrared two-photon excitation. Two-photon excitation with the 1047nm laser produces bright images with a variety of red emitting fluorophores, and some green emitting fluorophores, commonly used in biological research. Fortuitously, we have found that at least four blue emitting fluorophores normally excited by UV light are excited by the pulsed 1047nm laser, by what we believe to be three-photon excitation. Multi-photon excitation is demonstrated by a double labelled C. elegans embryo.
Removal of Some Heavy Metals by Electrocoagulation

Heavy metal removal by electrocoagulation using iron electrodes material was investigated in this paper. Several working parameters, such as pH, current density and heavy metal ions concentration were studied in an attempt to achieve a higher removal capacity. A simple and efficient treatment process for removal of heavy metals is essentially necessary. The performance of continuous flow electrocoagulation system, with reactor consists of a ladder series of twelve electrolytic cells, each cell containing stainless steel cathode and iron anode. The treatment of synthetic solutions containing Zn 2+,Cu 2+,Ni 2+,Cr 3+,Cd 2+ and Co 2+ ,has been investigated. Results showed that iron is very effective as sacrificial electrode material for heavy metals removal efficiency and cost points. Also it was concluded that the chromium has lower efficient removal as compared to zinc, copper and nickel. At the same time cadmium and cobalt have minimum removal efficiency.
K-associated optimal network for graph embedding dimensionality reduction

In machine learning, dimensionality reduction aims at reducing the dimension of the input data in order to achieve a small set of features that keeps the most important original relationships among data samples. In this paper, we investigate the usage of a non-parametric network formation algorithm into a graph embedding framework to perform supervised dimensionality reduction. Specifically, our technique maps data into networks and constructs two network adjacency matrices which convey information about intra-class components and inter-class penalty connections. Both matrices are inserted into an optimization framework in order to achieve a projection vector that is used to project high-dimension data samples into a low-dimensional space. One advantage of the technique is that no parameter is required, that is, there is no need to select a model for the input data. Computer simulations on real-world data sets have been performed to compare the proposed technique to some classical network formation methods such as k-NN and e-radius, and to well-known dimensionality reduction algorithms such as PCA and LDA. Statistical tests have shown that our approach outperforms those algorithms.
A dynamic programming approach to sequencing problems

This paper explores a dynamic programming approach to the solution of three sequencing problems: a scheduling problem involving arbitrary cost functions, the traveling-salesman problem, and an assembly line balancing problem. Each of the problems is shown to admit of numerical solution through the use of a simple recursion scheme; these recursion schemes also exhibit similarities and contrasts in the structures of the three problems. For large problems, direct solution by means of dynamic programming is not practical, but procedures are given for obtaining good approximate results by solving sequences of smaller derived problems. Experience with a computer program for the solution of traveling-salesman problems is presented.
Inferring and visualizing social networks on Internet relay chat

Internet relay chat is a system that allows groups of people to collaborate and chat from anywhere in the world. Clearly defined by several RFC documents, it is arguably the most standard real-time chat system currently in use. This work describes a method of inferring the social network of a group of IRC users in a channel. An IRC bot is used to monitor a channel and perform a heuristic analysis of events to create a mathematical approximation of the social network. From this, the bot can produce a visualization of the inferred social network on demand. These visualizations reveal the structure of the social network, highlighting connectivity, clustering and strengths of relationships between users. Animated output allows viewers to see the evolution of the social network over time. Some novel ideas for future work are discussed, showing other useful applications of this system.
Defective CFTR Expression and Function Are Detectable in Blood Monocytes: Development of a New Blood Test for Cystic Fibrosis

Background Evaluation of cystic fibrosis transmembrane conductance regulator (CFTR) functional activity to assess new therapies and define diagnosis of cystic fibrosis (CF) is cumbersome. It is known that leukocytes express detectable levels of CFTR but the molecule has not been characterized in these cells. In this study we aim at setting up and validating a blood test to evaluate CFTR expression and function in leukocytes. Description Western blot, PCR, immunofluorescence and cell membrane depolarization analysis by single-cell fluorescence imaging, using the potential-sensitive DiSBAC2(3) probe were utilized. Expression of PKA phosphorylated, cell membrane-localized CFTR was detected in non-CF monocytes, being undetectable or present in truncated form in monocytes derived from CF patients presenting with nonsense mutations. CFTR agonist administration induced membrane depolarization in monocytes isolated from non-CF donors (31 subjects) and, to a lesser extent, obligate CFTR heterozygous carriers (HTZ: 15 subjects), but it failed in monocytes from CF patients (44 subjects). We propose an index, which values in CF patients are significantly (p<0.001) lower than in the other two groups. Nasal Potential Difference, measured in selected subjects had concordant results with monocytes assay (Kappa statistic 0.93, 95%CI: 0.80–1.00). Results and Significance CFTR is detectable and is functional in human monocytes. We also showed that CFTR-associated activity can be evaluated in 5 ml of peripheral blood and devise an index potentially applicable for diagnostic purposes and both basic and translational research: from drug development to evaluation of functional outcomes in clinical trials.
Periodic Discharges: Insight From Magnetoencephalography

Purpose: This study used magnetoencephalography (MEG) dipole localization and coherence measurement to evaluate the magnetic fields associated with periodic discharges. The primary goal of the study was to evaluate whether MEG could consistently localize quasiperiodic discharges that were observed on the EEG portion of the recording. The secondary objective was to evaluate whether coherence measurements would correlate with topographic maxima of epileptiform activity. Methods: A total of 13 inpatients, whose electrographic records demonstrated lateralized periodic discharges (LPDs), were recruited from Henry Ford Hospital neurology and intensive care units. Nine patients were found clinically to be in status epilepticus before the EEG determination of LPDs. Spontaneous cortical brain activity was recorded with 148-channel MEG for 10 minutes. Data were sampled at 508 Hz and DC-100 Hz and filtered from 1 Hz to 40 Hz. Interictal events were imaged with single equivalent current dipole localization. Magnetoencephalography coherence source imaging analysis was performed and compared with the cortical topography of LPD patterns and with the focal lesions seen on the MRI (9 patients) or computed tomography (5 patients) imaging modalities. Results: The morphology of periodic waveforms was similar between EEG and MEG portions of the study. In patients with substrate positivity on imaging studies, coherence analysis revealed a tendency for LPDs to arise from the interface between the lesion and the surrounding, uncompromised cortex rather than from the lesion itself. In nonlesional patients with recent status epilepticus, the localization of maximal coherence was in the temporal lobes. Conclusions: This study demonstrated that MEG is able to detect and localize LPDs arising from damaged and adjacent cortex. The MEG coherence source imaging measurements also suggest the presence of epileptogenic networks perilesionally in cases with focal lesions on imaging. In patients without acute anatomic abnormality, the MEG coherence identified the epileptogenic networks in temporal lobe structures. Magnetoencephalography coherence source imaging may provide physicians with markers for differentiating between LPDs arising from acute injury currents versus LPDs arising from prolonged status epilepticus.
Virulence Markers in Staphylococcus aureus Strains Isolated from Hemodialysis Catheters of Mexican Patients

Methicillin-resistant Staphylococcus aureus is an increasingly important cause of nosocomial bacterial infections worldwide. S. aureus is responsible for several pathologies, including skin infections, endocarditis, meningitis, deep-tissue ulcers, and sepsis. S. aureus biofilm formation on catheters and other medical devices is a major post-operative concern, because biofilms are often the source of persistent and difficult to treat bacterial infections. While catheter-related S. aureus infections have been reported, the strains responsible for these infections have not been genetically characterized. We genetically characterized S. aureus strains isolated from hemodialysis catheters in Mexican patients. The frequency of 35 genes coding for adhesins, toxins, and other virulence-associated products in the 55 isolated S. aureus strains was determined using PCR, while real-time PCR was used to examine the level of gene expression. Of the 55 S. aureus strains isolated from 109 patients, 45 (81.8%) were determined to be methicillin-resistant. The icaA, rbf, sarA, and agr genes are involved in biofilm formation and bacterial dispersion and were detected in 96.3%, 40.0%, 74.5%, and 100% of S. aureus strains, respectively, and 70.9% of the strains formed a detectable biofilm. Interestingly, 67.2% of the strains contained the icaA, agr, spa, clfA, sdrC, sdrD, sdrE, seg, seh, and sei genes, suggesting that this gene combination is important for successful catheter colonization. The results of this study provide significant insight into the virulence gene make-up of catheter-colonizing S. aureus strains, and will assist in developing a more targeted treatment approach for persistent S. aureus biofilm contamination of medical devices.
State lattice with controllers: Augmenting lattice-based path planning with controller-based motion primitives

State lattice-based planning has been used in navigation for ground, water, aerial and space robots. State lattices are typically constructed of simple motion primitives connecting one state to another. There are situations where these metric motions may not be available, such as in GPS-denied areas. In many of these cases, however, the robot may have some additional sensing capability that is not being fully utilized by the planner. For example, if the robot has a camera it may be able to use simple visual servoing techniques to navigate through a GPS-denied region. Likewise, a LIDAR may allow the robot to skirt along an environmental feature even if there is not enough information to generate an accurate pose estimate. In this paper we present an expansion of the state lattice framework that allows us to incorporate controller-based motion primitives and external perceptual triggers directly into the planning process. We provide a formal description of our method of constructing the search graph in these cases as well as presenting real-world and simulated testing data showing the practical application of this approach.
Surveillance of avian and swine influenza in the swine population in Taiwan, 2004.

BACKGROUND AND PURPOSE We conducted serological and virological surveillance of pig farms in Taiwan from areas epidemic for low pathogenic avian influenza virus (AIV), H5N2 subtype, in order to determine the prevalence of AIV and swine influenza virus (SIV) in 2004. METHODS Pig sera from 9833 animals from 1974 farms in 9 counties were examined using agar gel precipitation (AGP) to screen for the presence of antibody against influenza A virus. AGP-positive sera were subjected to hemagglutination-inhibition test against H1, H3, H5 and H7 AIV subtypes and H1 and H3 SIV subtypes. Nasal swabs from 881 pigs were also examined for the presence of SIV by virus isolation in specific pathogen-free embryonated chicken eggs. Virus isolates were identified by reverse transcriptase-polymerase chain reaction followed by DNA sequencing of hemagglutinin and neuraminidase genes. RESULTS The AGP test on sera revealed the presence of antibodies against influenza A virus in 62.6% of farms and in 37.7% of pig sera. SIV antibodies to subtype H1 and H3 were found in 10.8% and 65.8% of sera, respectively. There were two peaks of the serological prevalence of SIV in pigs: one between January and February, and the other in October. By contrast, hemagglutinin tests against H5 and H7 AIV subtypes were negative in all sera, while there was a very low positive rate against H1 and H3 AIV subtypes. One H1N2 and one H3N1 viral isolate were obtained from nasal swabs of pigs. Phylogenetic analysis of hemagglutinin and neuraminidase genes revealed both isolates were reassortants of both classical and recent SIVs. CONCLUSIONS Different subtypes of SIV co-circulate among swine from different farms within the same county and may cause clinical outbreaks of the disease in Taiwan.