Miracle-dz/UniFAR-FTUs huggingface dataset:
Combined Role of Seizure-Induced Dendritic Morphology Alterations and Spine Loss in Newborn Granule Cells with Mossy Fiber Sprouting on the Hyperexcitability of a Computer Model of the Dentate Gyrus

Temporal lobe epilepsy strongly affects hippocampal dentate gyrus granule cells morphology. These cells exhibit seizure-induced anatomical alterations including mossy fiber sprouting, changes in the apical and basal dendritic tree and suffer substantial dendritic spine loss. The effect of some of these changes on the hyperexcitability of the dentate gyrus has been widely studied. For example, mossy fiber sprouting increases the excitability of the circuit while dendritic spine loss may have the opposite effect. However, the effect of the interplay of these different morphological alterations on the hyperexcitability of the dentate gyrus is still unknown. Here we adapted an existing computational model of the dentate gyrus by replacing the reduced granule cell models with morphologically detailed models coming from three-dimensional reconstructions of mature cells. The model simulates a network with 10% of the mossy fiber sprouting observed in the pilocarpine (PILO) model of epilepsy. Different fractions of the mature granule cell models were replaced by morphologically reconstructed models of newborn dentate granule cells from animals with PILO-induced Status Epilepticus, which have apical dendritic alterations and spine loss, and control animals, which do not have these alterations. This complex arrangement of cells and processes allowed us to study the combined effect of mossy fiber sprouting, altered apical dendritic tree and dendritic spine loss in newborn granule cells on the excitability of the dentate gyrus model. Our simulations suggest that alterations in the apical dendritic tree and dendritic spine loss in newborn granule cells have opposing effects on the excitability of the dentate gyrus after Status Epilepticus. Apical dendritic alterations potentiate the increase of excitability provoked by mossy fiber sprouting while spine loss curtails this increase.
Robust Topology Engineering in Multiradio Multichannel Wireless Networks

Topology engineering concerns with the problem of automatic determination of physical layer parameters to form a network with desired properties. In this paper, we investigate the joint power control, channel assignment, and radio interface selection for robust provisioning of link bandwidth in infrastructure multiradio multichannel wireless networks in presence of channel variability and external interference. To characterize the logical relationship between spatial contention constraints and transmit power, we formulate the joint power control and radio-channel assignment as a generalized disjunctive programming problem. The generalized Benders decomposition technique is applied for decomposing the radio-channel assignment (combinatorial constraints) and network resource allocation (continuous constraints) so that the problem can be solved efficiently. The proposed algorithm is guaranteed to converge to the optimal solution within a finite number of iterations. We have evaluated our scheme using traces collected from two wireless testbeds and simulation studies in Qualnet. Experiments show that the proposed algorithm is superior to existing schemes in providing larger interference margin, and reducing outage and packet loss probabilities.
Deep tissue optical focusing and optogenetic modulation with time-reversed ultrasonically encoded light

Using ultrasound-guided optical wavefront shaping, the authors show enhanced optogenetic control in thick acute brain slices. Noninvasive light focusing deep inside living biological tissue has long been a goal in biomedical optics. However, the optical scattering of biological tissue prevents conventional optical systems from tightly focusing visible light beyond several hundred micrometers. The recently developed wavefront shaping technique time-reversed ultrasonically encoded (TRUE) focusing enables noninvasive light delivery to targeted locations beyond the optical diffusion limit. However, until now, TRUE focusing has only been demonstrated inside nonliving tissue samples. We present the first example of TRUE focusing in 2-mm-thick living brain tissue and demonstrate its application for optogenetic modulation of neural activity in 800-μm-thick acute mouse brain slices at a wavelength of 532 nm. We found that TRUE focusing enabled precise control of neuron firing and increased the spatial resolution of neuronal excitation fourfold when compared to conventional lens focusing. This work is an important step in the application of TRUE focusing for practical biomedical uses.
Conditions for Optimal Efficiency of Relative MDS

In this paper, the relative multidimensional scaling method is investigated. This method is designated to visualize large multidimensional data. The method encompasses application of multidimensional scaling (MDS) to the so-called basic vector set and further mapping of the remaining vectors from the analyzed data set. In the original algorithm of relative MDS, the visualization process is divided into three steps: the set of basis vectors is constructed using the k-means clustering method; this set is projected onto the plane using the MDS algorithm; the set of remaining data is visualized using the relative mapping algorithm. We propose a modification, which differs from the original algorithm in the strategy of selecting the basis vectors. The experimental investigation has shown that the modification exceeds the original algorithm in the visualization quality and computational expenses. The conditions, where the relative MDS efficiency exceeds that of standard MDS, are estimated.
Development of a Novel Compressed Index-Query Web Search Engine Model

In this paper, the authors present a description of a new Web search engine model, the compressed index-query CIQ Web search engine model. This model incorporates two bit-level compression layers implemented at the back-end processor server side, one layer resides after the indexer acting as a second compression layer to generate a double compressed index index compressor, and the second layer resides after the query parser for query compression query compressor to enable bit-level compressed index-query search. The data compression algorithm used in this model is the Hamming codes-based data compression HCDC algorithm, which is an asymmetric, lossless, bit-level algorithm permits CIQ search. The different components of the new Web model are implemented in a prototype CIQ test tool CIQTT, which is used as a test bench to validate the accuracy and integrity of the retrieved data and evaluate the performance of the proposed model. The test results demonstrate that the proposed CIQ model reduces disk space requirements and searching time by more than 24%, and attains a 100% agreement when compared with an uncompressed model.
SOAP Processing Performance and Enhancement

The web services (WS) technology provides a comprehensive solution for representing, discovering, and invoking services in a wide variety of environments, including Service Oriented Architectures (SOA ) and grid computing systems. At the core of WS technology lie a number of XML-based standards, such as the Simple Object Access Protocol (SOAP), that have successfully ensured WS extensibility, transparency, and interoperability. Nonetheless, there is an increasing demand to enhance WS performance, which is severely impaired by XML's verbosity. SOAP communications produce considerable network traffic, making them unfit for distributed, loosely coupled, and heterogeneous computing environments such as the open Internet. Also, they introduce higher latency and processing delays than other technologies, like Java RMI and CORBA. WS research has recently focused on SOAP performance enhancement. Many approaches build on the observation that SOAP message exchange usually involves highly similar messages (those created by the same implementation usually have the same structure, and those sent from a server to multiple clients tend to show similarities in structure and content). Similarity evaluation and differential encoding have thus emerged as SOAP performance enhancement techniques. The main idea is to identify the common parts of SOAP messages, to be processed only once, avoiding a large amount of overhead. Other approaches investigate nontraditional processor architectures, including micro- and macrolevel parallel processing solutions, so as to further increase the processing rates of SOAP/XML software toolkits. This survey paper provides a concise, yet comprehensive review of the research efforts aimed at SOAP performance enhancement. A unified view of the problem is provided, covering almost every phase of SOAP processing, ranging over message parsing, serialization, deserialization, compression, multicasting, security evaluation, and data/instruction-level processing.
UNIREP: a microcomputer program to find unique and repetitive nucleotide sequences in genomes

We present a program UNIREP, written in PowerBASIC for IBM-PCs, that identifies repetitive and unique nucleotide sequences in genomes or parts of genomes. A key feature of the algorithm is an oligonucleotide representation in a numerical code to make possible a comparison of all pairs of oligonucleotides (including overlaps) occurring in the analyzed sequence. This comparison assigns a score to each oligonucleotide, reflecting its similarity/dissimilarity to other oligonucleotides of the same length in the analyzed sequence. The score is plotted along the sequence so that peaks in the plot indicate repetitive regions and very low values reflect unique sequences. The scores are filtered to suppress or enhance the unique or repetitive sequences according to the user's wish. UNIREP is extended by auxiliary programs HIGHER and LOWER to list nucleotide sequences that have scores higher or lower than given limits. The potential of UNIREP is demonstrated using several long nucleotide sequences including the complete genomic sequence of EBV.
The Iron Oxide Nanocrystalline Manufactured by IGC-PECS Process (特集 ナノ構造制御と新機能発現)

The iron oxide nanocrystalline were manufactured by a Inert Gas Condensation - Pulse Electric Current Sintering (IGC-PECS) process. The IGC method involves condensation of vapors of metallic or nonmetallic powders with a controlled residence time in a low pressure environment. The particle size was controlled by pressure of inert gas (He). The smallest average size of powders, 8 nm and the largest average size of powders, 28 nm, were used as a starting precursors for PECS. The smallest average grain size of sintered pellets is 33 nm under the condition at 1073 K with applied pressure of 100 MPa.
Effect of Casting Condition on Density and Hardness Gradients of Al-Al2Cu Alloy FGM Fabricated by Centrifugal In Situ Method

Functionally graded material (FGM) is a combined material that has a component gradient from one material at one surface to another material at the opposite surface. As one of the fabrication processes of FGM, centrifugal in-situ method has been proposed. Centrifugal in-situ method is a casting that centrifugal force is applied during solidification to both the primary crystal and the matrix. In a previous study, the density and hardness gradients of Al-3mass%Cu FGM ring fabricated by centrifugal in-situ method have been investigated. According to the study, Cu concentration within the FGM ring monolithically increases towards the ring's inner position, and its density also increases toward inner region. This is because the density of the primary -Al crystal is larger than that of the molten Al-Cu alloy in the early stage of solidification. Based on this solidification process, it is considered that the casting condition and the initial Cu concentration of Al-Cu master alloy affect on the density and hardness gradients in the Al-Cu FGM ring. In this study, effects of the casting condition on the density and hardness gradients of Al-Al2Cu FGM rings fabricated by the centrifugal in-situ method were investigated. It was found that density gradient of the Al-Al2Cu FGM rings increases with increasing Cu concentration of Al-Cu master alloys. Also, processing temperature for Al-Cu master alloy can control density gradient of Al-Al2Cu FGM rings. These phenomena were explained by variation of the densities of primary -Al and the molten Al matrix during the solidification.
An LMI optimization approach to Lyapunov stability analysis for linear time-invariant systems

Theorem of alternatives based on the separation theorems are proposed to provide systematic and unified proofs of necessary and sufficient conditions for solvability of Lyapunov inequality on P. As an application of the theorem of alternatives, we investigate the conditions for the existence of feasible solutions to Lyapunov inequality on P and obtain a restatement of the celebrated Lyapunov stability theorem for linear time-invariant systems. Furthermore, the effectiveness of the proposed method is illustrated by a numerical example.
Analysis of Copy Number Variations in Patients with Autism Using Cytogenetic and MLPA Techniques: Report of 16p13.1p13.3 and 10q26.3 Duplications

Autism is a common neuropsychiatric disorder affecting 1 in 68 children. Copy number variations (CNVs) are known to be major contributors of autism spectrum disorder (ASD). There are different whole genome or targeted techniques to identify CNVs in the patients including karyotyping, multiplex ligation-dependent probe amplification (MLPA) and array CGH. In this study, we used karyotyping and MLPA to detect CNVs in 50 Iranian patients with autism. GTG banding and 4 different MLPA kits (2 subtelomeric and 2 autism kits) were utilized. To elevate our detection rate, we selected the sporadic patients who had additional clinical features including intellectual disability, seizure, attention deficit hyperactivity disorder, and abnormal head circumference. Two out of 50 patients (4%) showed microscopic chromosome abnormalities and 5 out of 50 (10%) demonstrated copy number gains or losses using MLPA kits. Including one overlapping result between karyotype and MLPA techniques, our overall detection rate was 6 out of 50 (12%). Three out of 6 CNVs were de novo and three others were paternally inherited. Two of CNVs detected by karyotyping and MLPA tests were 16p13.1q13. 3 and 10q26.3 duplications, respectively. For these two CNVs genotype and phenotype of the patients were compared with other studies. Although the pathogenicity of cytogenetic results was certain, most of MLPA results needed to be better refined using other more accurate techniques such as array CGH. Our findings suggest that it might be possible to obtain some useful information using MLPA technique but it cannot be used as a single diagnostic tool for the autism.
Riac: a Rule Induction Algorithm Based on Approximate Classiication Riac: a Rule Induction Algorithm Based on Approximate Classiication

We present the RIAC (Rule Induction through Approximate Classiication) method for inducing rules from examples, based on the theory of rough sets. Imprecise data are generalized using a rough-sets based approximation technique. Positive, boundary and negative regions of the target concept are deened using statistical information. Then, if the concept is learnable, superruous attributes are eliminated and rules are generated. Each classiication rule generated by the RIAC algorithm is tagged with a certainty factor, which is the observed probability that an object matching the condition part of the rule belongs to the concept. Our approach treats each rule as a piece of uncertain evidence, which by itself is of little value with respect to classiication. Our classiication procedure combines as many pieces of evidence (rules) as possible. Experimental results indicate that RIAC produces fewer rules that give more accurate predictions than C4.5.
A New Method and Toolbox for Easily Calibrating Omnidirectional Cameras

In this paper, we focus on calibration of central omnidirectional cameras, both dioptric and catadioptric. We describe our novel camera model and algorithm and provide a practical Matlab Toolbox, which implements the proposed method. Our method relies on the use of a planar grid that is shown by the user at different unknown positions and orientations. The user is only asked to click on the corner points of the images of this grid. Then, calibration is quickly and automatically performed. In contrast with previous approaches, we do not use any specific model of the omnidirectional sensor. Conversely, we assume that the imaging function can be described by a polynomial approximation whose coefficients are estimated by solving a linear least squares minimization problem followed by a non-linear refinement. The performance of the approach is shown through several calibration experiments on both simulated and real data. The proposed algorithm is implemented as a Matlab Toolbox, which allows any inexpert user to easily calibrate his own camera. The toolbox is completely Open Source and is freely downloadable from the author's Web page.
SLE coordinate changes

The purpose of this note is to describe a framework which unifies radial, chordal and dipolar SLE. When the definition of SLE(κ; ρ) is extended to the setting where the force points can be in the interior of the domain, radial SLE(κ) becomes chordal SLE(κ; ρ), with ρ = κ − 6, and vice versa. We also write down the martingales describing the Radon-Nykodim derivative of SLE(κ; ρ1 ,.,ρ n) with respect to SLE(κ).
Divergent regulation of 92-kDa gelatinase and TIMP-1 by HBECs in response to IL-1β and TNF-α.

In this study, we addressed the question of whether human bronchial epithelial cells (HBECs) contribute to the regulation of 92-kDa gelatinase activity by secreting tissue inhibitor of metalloproteinase (TIMP)-1. We investigated expression of 92-kDa gelatinase and TIMP-1 in response to lipopolysaccharide (LPS) and to the proinflammatory cytokines interleukin (IL)-1β and tumor necrosis factor (TNF)-α. Confluent HBECs from explants were cultured in plastic dishes coated with type I and III collagen. We demonstrated that TIMP-1 was expressed at both the protein and mRNA levels by primary cultures of HBECs. Gelatin zymography of HBEC-conditioned media showed that exposure of HBECs to LPS, IL-1β, or TNF-α induced a twofold increase in the latent form of 92-kDa gelatinase production, as well as its activation. Also, quantitative reverse transcriptase (RT)-polymerase chain reaction (PCR) demonstrated a twofold increase in the 92-kDa mRNA level in response to both cytokines. In contrast, TIMP-1 production evaluated by immunoblotting was unchanged in the presence of LPS and IL-1β and was clearly decreased in the presence of TNF-α. Quantitative RT-PCR demonstrated that TIMP-1 mRNA levels remained unchanged in response to LPS or IL-1β but decreased by 70% in the presence of TNF-α. All of these results strongly suggest that the control mechanisms regulating the expression of 92-kDa gelatinase and TIMP-1 by HBECs in response to inflammatory stimuli are divergent and result in an imbalance between 92-kDa gelatinase and TIMP-1 in favor of the metalloproteinase. Such an imbalance may contribute significantly to acute airway inflammation.
An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase

The observation of O2 in a time-frozen structure using serial femtosecond rotation crystallography of the as-isolated oxidized enzyme provides long-awaited clear-cut evidence for the mode of O2 binding in CuNiRs. This provides an insight into how CuNiR from A. xylosoxidans can function as an oxidase, reducing O2 to H2O2, or as a superoxide dismutase (SOD) since it was shown to have ∼56% of the dismutase activity of the bovine SOD enzyme some two decades ago.
Hi-fi playback: Tolerating position errors in shift operations of racetrack memory

Racetrack memory is an emerging non-volatile memory based on spintronic domain wall technology. It can achieve ultra-high storage density. Also, its read/write speed is comparable to that of SRAM. Due to the tape-like structure of its storage cell, a “shift” operation is introduced to access racetrack memory. Thus, prior research mainly focused on minimizing shift latency/energy of racetrack memory while leveraging its ultra-high storage density. Yet the reliability issue of a shift operation, however, is not well addressed. In fact, racetrack memory suffers from unsuccessful shift due to domain misalignment. Such a problem is called “position error” in this work. It can significantly reduce mean-time-to-failure (MTTF) of racetrack memory to an intolerable level. Even worse, conventional error correction codes (ECCs), which are designed for “bit errors”, cannot protect racetrack memory from the position errors. In this work, we investigate the position error model of a shift operation and categorize position errors into two types: “stop-in-middle” error and “out-of-step” error. To eliminate the stop-in-middle error, we propose a technique called sub-threshold shift (STS) to perform a more reliable shift in two stages. To detect and recover the out-of-step error, a protection mechanism called position error correction code (p-ECC) is proposed. We first describe how to design a p-ECC for different protection strength and analyze corresponding design overhead. Then, we further propose how to reduce area cost of p-ECC by leveraging the “overhead region” in a racetrack memory stripe. With these protection mechanisms, we introduce a position-error-aware shift architecture. Experimental results demonstrate that, after using our techniques, the overall MTTF of racetrack memory is improved from 1. 33μs to more than 69 years, with only 0.2% performance degradation. Trade-off among reliability, area, performance, and energy is also explored with comprehensive discussion.
Statistical hypothesis testing in intraspecific phylogeography: nested clade phylogeographical analysis vs. approximate Bayesian computation

Nested clade phylogeographical analysis (NCPA) and approximate Bayesian computation (ABC) have been used to test phylogeographical hypotheses. Multilocus NCPA tests null hypotheses, whereas ABC discriminates among a finite set of alternatives. The interpretive criteria of NCPA are explicit and allow complex models to be built from simple components. The interpretive criteria of ABC are ad hoc and require the specification of a complete phylogeographical model. The conclusions from ABC are often influenced by implicit assumptions arising from the many parameters needed to specify a complex model. These complex models confound many assumptions so that biological interpretations are difficult. Sampling error is accounted for in NCPA, but ABC ignores important sources of sampling error that creates pseudo‐statistical power. NCPA generates the full sampling distribution of its statistics, but ABC only yields local probabilities, which in turn make it impossible to distinguish between a good fitting model, a non‐informative model, and an over‐determined model. Both NCPA and ABC use approximations, but convergences of the approximations used in NCPA are well defined whereas those in ABC are not. NCPA can analyse a large number of locations, but ABC cannot. Finally, the dimensionality of tested hypothesis is known in NCPA, but not for ABC. As a consequence, the ‘probabilities’ generated by ABC are not true probabilities and are statistically non‐interpretable. Accordingly, ABC should not be used for hypothesis testing, but simulation approaches are valuable when used in conjunction with NCPA or other methods that do not rely on highly parameterized models.