Miracle-dz/UniFAR-FTUs huggingface dataset:
Improvement of Discrimination Performance Using Temporal Smoothing for Brain – Machine Interface Based Rehabilitation System

The aim of our study is to develop a brain– machine interface rehabilitation system for patients with leg paralyzed. Using this system, the patient’s paralyzed legs are forcibly moved according to his intention of motion. This may activate a damaged neural circuit and improve the rehabilitation effect. In this study, we proposed a motion discrimination method for actual pedal exercise using electroencephalography (EEG) measured at several positions of the parietal region, and the discrimination performance was verified with healthy subjects. Although this method was uses the spatial EEG information, this often causes false detection owing to the sudden noise included in the measured EEG signals. In order to improve the discrimination performance, smoothing of the motion discriminator output was considered using temporal information. Thus, we developed a spatiotemporal filterbased discrimination method and its parameter determination method. Experimental results indicated that the discrimination performance of this method is over 10 percentage points higher than that of the general linear discriminant analysis method.
An engineered small RNA-mediated genetic switch based on a ribozyme expression platform

An important requirement for achieving many goals of synthetic biology is the availability of a large repertoire of reprogrammable genetic switches and appropriate transmitter molecules. In addition to engineering genetic switches, the interconnection of individual switches becomes increasingly important for the construction of more complex genetic networks. In particular, RNA-based switches of gene expression have become a powerful tool to post-transcriptionally program genetic circuits. RNAs used for regulatory purposes have the advantage to transmit, sense, process and execute information. We have recently used the hammerhead ribozyme to control translation initiation in a small molecule-dependent fashion. In addition, riboregulators have been constructed in which a small RNA acts as transmitter molecule to control translation of a target mRNA. In this study, we combine both concepts and redesign the hammerhead ribozyme to sense small trans-acting RNAs (taRNAs) as input molecules resulting in repression of translation initiation in Escherichia coli. Importantly, our ribozyme-based expression platform is compatible with previously reported artificial taRNAs, which were reported to act as inducers of gene expression. In addition, we provide several insights into key requirements of riboregulatory systems, including the influences of varying transcriptional induction of the taRNA and mRNA transcripts, 5′-processing of taRNAs, as well as altering the secondary structure of the taRNA. In conclusion, we introduce an RNA-responsive ribozyme-based expression system to the field of artificial riboregulators that can serve as reprogrammable platform for engineering higher-order genetic circuits.
Modeling and Optimization in Traffic Flow Management

Traffic flow management (TFM) allocates the various airport, airspace, and other resources to maintain an efficient traffic flow consistent with safety. TFM is a complex area of research involving the disciplines of operations research, guidance and control, human factors, and software engineering. Hundreds of human operators make TFM decisions that involve tens of thousands of aircraft, en route air traffic control centers, the Federal Aviation Administration's System Command Center, and many airline operation centers. This paper provides an overview of how TFM decisions are made today and challenges facing the system in the future, and reviews modeling and optimization approaches for facilitating system-wide modeling, performance assessments, and system-level optimization of the national airspace system in the presence of both en route and airport capacity constraints.
Towards a practical specification language

Recognition of the value of formal specifications in the design and verification of large software systems is becoming more widespread. Specification languages themselves, however, are difficult to develop in part because of the inherent conflict between the goals of clarity and formalism required by these languages. This paper discusses the role of specification languages, examples of specifications in two currently implemented languages, AFFIRM and SPECIAL, and makes some suggestions towards a more practical specification language.
Exploring Empirical Rank-Frequency Distributions Longitudinally through a Simple Stochastic Process

The frequent appearance of empirical rank-frequency laws, such as Zipf’s law, in a wide range of domains reinforces the importance of understanding and modeling these laws and rank-frequency distributions in general. In this spirit, we utilize a simple stochastic cascade process to simulate several empirical rank-frequency distributions longitudinally. We focus especially on limiting the process’s complexity to increase accessibility for non-experts in mathematics. The process provides a good fit for many empirical distributions because the stochastic multiplicative nature of the process leads to an often observed concave rank-frequency distribution (on a log-log scale) and the finiteness of the cascade replicates real-world finite size effects. Furthermore, we show that repeated trials of the process can roughly simulate the longitudinal variation of empirical ranks. However, we find that the empirical variation is often less that the average simulated process variation, likely due to longitudinal dependencies in the empirical datasets. Finally, we discuss the process limitations and practical applications.
Anion Channels, Including ClC-3, Are Required for Normal Neutrophil Oxidative Function, Phagocytosis, and Transendothelial Migration*

NADPH oxidase activity, phagocytosis, and cell migration are essential functions of polymorphonuclear leukocytes (PMNs) in host defense. The cytoskeletal reorganization necessary to perform these functions has been extensively studied, but the role of cell volume regulation, which is likely dependent upon anion channels, has not been defined. Mice lacking the anion channel ClC-3 (Clcn3(–/–)) died from presumed sepsis following intravascular catheter placement, whereas Clcn3(+/+) littermates survived. We hypothesized that ClC-3 has a critical role in host defense and reasoned that PMN function would be compromised in these mice. Clcn3(–/–) PMNs displayed markedly reduced NADPH oxidase activity in response to opsonized zymosan and modestly reduced activity after phorbol 12-myristate 13-acetate. Human PMNs treated with the anion channel inhibitors niflumic acid or 5-nitro-2-(3-phenylpropylamino)benzoic acid had a very similar defect. ClC-3 protein was detected in the secretory vesicles and secondary granules of resting PMNs and was up-regulated to the phagosomal membrane. Clcn3(–/–) PMNs and human PMNs lacking normal anion channel function both exhibited reduced uptake of opsonized zymosan at 1, 5, and 10 min in a synchronized phagocytosis assay. Niflumic acid-treated PMNs also had impaired transendothelial migration in vitro, whereas migration in vivo was not altered in Clcn3(–/–) PMNs. Selective inhibition of the swelling-activated chloride channel with tamoxifen profoundly reduced PMN migration but had no effect on NADPH oxidase activity. In summary, PMNs lacking normal anion channel function exhibited reduced NADPH oxidase activity, diminished phagocytosis, and impaired migration. ClC-3 was specifically involved in the respiratory burst and phagocytosis.
Modular Supervisory Control and Hierarchical Supervisory Control of Fuzzy Discrete-Event Systems

This paper establishes modular and hierarchical supervisory control theories of Fuzzy Discrete-Event Systems (FDES). It aims to resolve the horizontal and vertical complexities present in large-scale event-driven systems, which are affected by uncertainties in their event and state representations. The modular supervisory control architecture composed of a set of noncommunicating local supervisors, in which one supervisor is assigned for each module having its own sensing and acting capabilities. The notion of separability for languages in FDES is introduced and the property of a language specification of FDES, termed as separably-controllable-observability, is proposed to determine the existence of modular supervisors to the control problem. The hierarchical supervisory control architecture consists of multilevel supervisors assigned to detailed low-level and abstract high-level models of the plant. The notion of output-control-consistency is introduced for languages in FDES. Then, the property called strictly-output-control-consistency is defined for FDES in order to maintain the hierarchical consistency between low-level and high-level FDES modules. The property of H-fuzzy observability is introduced to ensure the hierarchical consistency under the partial observation of low-level FDES. Finally, using the established hierarchical supervisory control theory of FDES, a behavior-based mobile robot navigation example is discussed.
An algorithm for extrinsic parameters calibration of a camera and a laser range finder using line features

This paper presents an effective algorithm for calibrating the extrinsic parameters between a camera and a laser range finder whose trace is invisible. On the basis of an analysis of three possible features, we propose to design a right-angled triangular checkerboard and to employ the invisible intersection points of the laser range finder's slice plane with the edges of the checkerboard to set up the constraints equations. The extrinsic parameters are then calibrated by minimizing the algebraic errors between the measured intersections points and their corresponding projections on the image plane of the camera. We compared our algorithm with the existing methods by both simulations and the real data of a stereo measurement system. The simulation and experimental results confirmed that the proposed algorithm can yield more accurate results.
AN IMPROVED STAINING METHOD FOR ELECTRON MICROSCOPY

A n a q u e o u s so lu t ion of u r a n y l ace t a t e was first e m p l o y e d as a n e l ec t ron s ta in by W a t s o n (1958). W e h a v e f o u n d t h a t this s ta in , a l t h o u g h f r e q u e n t l y effective, is capr ic ious . T h e s ta in m a y no t inc rease con t r a s t of a g iven spec imen , a n d m a y , in o the r ins tances , l eave u n d e s i r a b l e c o n t a m i n a t i o n on a s t a ined grid. W h i l e a n e x p e r i m e n t on d e h y d r a t i n g a g e n t s for e l ec t ron m i c r o s c o p y was in progress , u r a n y l ace t a t e was d issolved in m e t h a n o l in a n effort to a c c o m pl ish en bloc s ta in ing . I t was no t ed t h a t the u r a n y l a ce t a t e was ve ry soluble in m e t h a n o l in con t r a s t to its l im i t ed solubi l i ty in w a t e r a n d e thano l . A t the t ime of this obse rva t ion , it was felt t h a t a n inc reased c o n c e n t r a t i o n of u r a n y l ace t a t e m i g h t a id in s t a i n i ng some t issue c o m p o n e n t s or m i g h t s ta in t issue m o r e cons i s t en t ly t h a n the less c o n c e n t r a t e d a q u e o u s s tain.
T‐Cadherin 2: Molecular characterization, function in cell adhesion, and coexpression with T‐cadherin and N‐cadherin

Cadherins are integral membrane glycoproteins that mediate calcium‐dependent, homophilic cell‐cell adhesion and are implicated in controlling tissue morphogenesis. T‐cadherin is anchored to the membrane through a glycosyl phosphatidylinositol (Ranscht B, Dours‐Zimmermann MT: Neuron 7:391–402, 1991) and expressed in a restricted pattern in developing embryos (Ranscht B, Bronner‐Fraser M: Development 111:15–22, 1991). We report here the molecular and functional characterization of the T‐cadherin isoform, T‐cadherin 2 (Tcad‐2) and the expression of the corresponding mRNA. Tcad‐2 cDNA differs in its 3′nucleotide sequence from T‐cadherin cDNA and encodes a protein in which the carboxy terminal Leu of T‐cadherin is substituted by Lys and extended by the amino acids SerPheProTyrVal. By RNase protection, mRNAs encoding the T‐cadherin isoforms are coexpressed in heart, muscle, liver, skin, somites, and in neural tissue. Many tissues contain both T‐cadherin and Tcad‐2 mRNAs in conjunction with N‐cadherin transcripts, and T‐cadherins and N‐cadherin proteins are coexpressed on the surface of individual neurons in vitro. Expression in Chinese hamster ovary cells (CHO) revealed that Tcad‐2 is a glycosyl phosphati‐dylinositol‐anchored membrane protein that functions in calcium‐dependent, homophilic cell adhesion. The identification of a functional T‐cadherin isoform and the coexpression of T‐cadherins and N‐cadherin by individual cells suggest that specific adhesive interactions of embryonic cells may involve a complex interplay between multiple cadherins. © 1993 Wiley‐Liss, Inc.
Overexpression of the EGF receptor‐related proto‐oncogene erbB‐2 in human mammary tumor cell lines by different molecular mechanisms.

Amplification of the erbB/EGF receptor and a structurally related gene, designated erbB‐2, have previously been detected in a variety of human tumors. In a series of human mammary tumor cell lines, analysis of transcripts of these genes revealed elevated levels of one or the other in more than 60% of tumors analyzed. Eight cell lines demonstrated erbB‐2 mRNA levels ranging from 4‐ to 128‐fold above those of normal controls. erbB‐2 expression was evaluated in comparison to the expression level of actin observed in these cell lines. There was no evidence of an aberrantly sized erbB‐2 transcript in any of these lines. Immunoblot analysis indicated elevation in levels of the 185‐kd product of the erbB‐2 gene expressed by these cells. In four lines erbB‐2 gene amplification in the absence of an apparent gene rearrangement was demonstrated. In a representative cell line of this type, SK‐BR‐3, the amplified erbB‐2 gene copies were located in an aberrant chromosomal location. Four additional cell lines, which demonstrated 4‐ to 8‐fold overexpression of erbB‐2 mRNA, did not exhibit gene amplification. In a representative cell line of this type ZR‐75‐1, an apparently normal chromosomal location was found for the erbB‐2 gene. Our findings indicate that overexpression of the erbB‐2 gene in mammary tumor cell lines is frequent and associated with different genetic abnormalities.
Meaning, misinterpretations, and medicine : A cognitive-behavioral approach to understanding health anxiety and hypochondriasis

The cognitive-behavioral theory of hypochondriasis is firmly rooted in current cognitive approaches to emotional disorders in general. Moreover, it assumes that hypochondriasis represents the extreme (and handicapping) end of a continuum of normal health anxiety. This emphasis inevitably has a powerful normalizing influence reflected not only in the treatment but also in the fact that the approach can readily be applied to understanding health anxiety in the context of somatic problems and the psychological reaction to health screening. A growing body of empirical evidence supports this view. The authors argue here that the combination of further theoretical development and refinement will inevitably lead to more effective and efficient treatment.
Differential Entrainment and Learning-Related Dynamics of Spike and Local Field Potential Activity in the Sensorimotor and Associative Striatum

Parallel cortico-basal ganglia loops are thought to have distinct but interacting functions in motor learning and habit formation. In rats, the striatal projection neuron populations (MSNs) in the dorsolateral and dorsomedial striatum, respectively corresponding to sensorimotor and associative regions of the striatum, exhibit contrasting dynamics as rats acquire T-maze tasks (Thorn et al., 2010). Here, we asked whether these patterns could be related to the activity of local interneuron populations in the striatum and to the local field potential activity recorded simultaneously in the corresponding regions. We found that dorsolateral and dorsomedial striatal fast-spiking interneurons exhibited task-specific and training-related dynamics consistent with those of corresponding MSN populations. Moreover, both MSNs and interneuron populations in both regions became entrained to theta-band (5–12 Hz) frequencies during task acquisition. However, the predominant entrainment frequencies were different for the sensorimotor and associative zones. Dorsolateral striatal neurons became entrained mid-task to oscillations centered ∼5 Hz, whereas simultaneously recorded neurons in the dorsomedial region became entrained to higher frequency (∼10 Hz) rhythms. These region-specific patterns of entrainment evolved dynamically with the development of region-specific patterns of interneuron and MSN activity, indicating that, with learning, these two striatal regions can develop different frequency-modulated circuit activities in parallel. We suggest that such differential entrainment of sensorimotor and associative neuronal populations, acquired through learning, could be critical for coordinating information flow throughout each trans-striatal network while simultaneously enabling nearby components of the separate networks to operate independently.
A Fast, Practical Algorithm for the Trapezoidation of Simple Polygons

A fast, practical, deterministic algorithm for the horizontal trapezoidation of simple polygons is presented. The polygon is decomposed into a minimal collection of trapezoid sequences, such that two trapezoids adjacent within a sequence always share a common horizontal border. Such trapezoid sequences are a convenient data structure in a display list for a collection of polygonal objects to be filled/rendered. A linear traversal of the polygon outline identifies a subset of critical vertices, which are then processed in sweep order. Horizontal as well as vertical edges—very common in practical polygons—are handled explicitly. Complexity is linear for most ‘practical’ polygons, with non-linear running times being required only for much less frequently occurring geometries. A straightforward extension allows trapezoidation of simple polygons with holes.
Structural Classifier Ensembles for Vector Space Embedded Graphs

The motivation of classifier ensembles is that errors of an individual classifier can often be compensated by the other ensemble members. In the present paper we introduce a general approach to building structural classifier ensembles, i.e. classifiers that make use of graphs as representation formalism and include strings and trees as special cases. The proposed methodology is based on graph embedding in real vector spaces by means of prototype selection. This selection is performed randomized eta times such that the procedure leads to eta different graph embeddings. Hence, a classifier can be trained for each embedding and the results of the individual classifiers can be combined in an appropriate way. In the present paper we take into account that not only the prototypes themselves but also their number has a critical impact on the classification accuracy in the resulting vector space. In several experimental results we make investigations on the classification accuracy of the resulting classifier ensembles and compare them with single classifier systems.
Sodium/calcium exchange: its physiological implications.

The Na+/Ca2+ exchanger, an ion transport protein, is expressed in the plasma membrane (PM) of virtually all animal cells. It extrudes Ca2+ in parallel with the PM ATP-driven Ca2+ pump. As a reversible transporter, it also mediates Ca2+ entry in parallel with various ion channels. The energy for net Ca2+ transport by the Na+/Ca2+ exchanger and its direction depend on the Na+, Ca2+, and K+ gradients across the PM, the membrane potential, and the transport stoichiometry. In most cells, three Na+ are exchanged for one Ca2+. In vertebrate photoreceptors, some neurons, and certain other cells, K+ is transported in the same direction as Ca2+, with a coupling ratio of four Na+ to one Ca2+ plus one K+. The exchanger kinetics are affected by nontransported Ca2+, Na+, protons, ATP, and diverse other modulators. Five genes that code for the exchangers have been identified in mammals: three in the Na+/Ca2+ exchanger family (NCX1, NCX2, and NCX3) and two in the Na+/Ca2+ plus K+ family (NCKX1 and NCKX2). Genes homologous to NCX1 have been identified in frog, squid, lobster, and Drosophila. In mammals, alternatively spliced variants of NCX1 have been identified; dominant expression of these variants is cell type specific, which suggests that the variations are involved in targeting and/or functional differences. In cardiac myocytes, and probably other cell types, the exchanger serves a housekeeping role by maintaining a low intracellular Ca2+ concentration; its possible role in cardiac excitation-contraction coupling is controversial. Cellular increases in Na+ concentration lead to increases in Ca2+ concentration mediated by the Na+/Ca2+ exchanger; this is important in the therapeutic action of cardiotonic steroids like digitalis. Similarly, alterations of Na+ and Ca2+ apparently modulate basolateral K+ conductance in some epithelia, signaling in some special sense organs (e.g., photoreceptors and olfactory receptors) and Ca2+-dependent secretion in neurons and in many secretory cells. The juxtaposition of PM and sarco(endo)plasmic reticulum membranes may permit the PM Na+/Ca2+ exchanger to regulate sarco(endo)plasmic reticulum Ca2+ stores and influence cellular Ca2+ signaling.
An autologistic model for the spatial distribution of wildlife

1. A new method for estimating the geographical distribution of plant and animal species from incomplete field survey data is developed. 2. Wildlife surveys are often conducted by dividing a study region into a regular grid and collecting data on abundance or on presence/absence from some or all of the squares in the grid. Generalized linear models (GLMs) can be used to model the spatial distribution of a species within such a grid by relating the response variable (abundance or presence/absence) to spatially referenced covariates. 3. Such models ignore or at best indirectly model dependence on unmeasured covariates, and the intrinsic spatial autocorrelation arising for example in gregarious populations. 4. We describe a procedure for use with presence/absence data in which spatial autocorrelation is modelled explicitly. We achieve this by extending a logistic model to include an extra covariate which is derived from the responses at neighbouring squares. The extended model is known as an autologistic model. 5. To allow fitting of the autologistic model when only a random sample of squares is surveyed, we use the Gibbs sampler to predict presence/absence at unsurveyed squares. 6. We compare the autologistic model with the ordinary logistic model using red deer census data. Both models are fitted to a subsample of 20% of the data and results are compared with the 'true' abundance and spatial distribution indicated by the full census. We conclude that the autologistic model is superior for estimating the spatial distribution of the deer, whereas the ordinary logistic model yields more precise estimates of the overall number of squares occupied by deer at the time of the survey.