Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression sequences and distribution of two primary cell adhesion molecules during embryonic development of Xenopus laevis

Studies of chicken embryos have demonstrated that cell adhesion molecules are important in embryonic induction and are expressed in defined sequences during embryogenesis and histogenesis. To extend these observations and to provide comparable evidence for heterochronic changes in such sequences during evolution, the local distributions of the neural cell adhesion molecule (N-CAM) and of the liver cell adhesion molecule (L-CAM) were examined in Xenopus laevis embryos by immunohistochemical and biochemical techniques. Because of the technical difficulties presented by the existence of multiple polypeptide forms of CAMs and by autofluorescence of yolk-containing cells, special care was taken in choosing and characterizing antibodies, fluorophores, and embedding procedures. Both N-CAM and L- CAM were found at low levels in pregastrulation embryos. During gastrulation, N-CAM levels increased in the presumptive neural epithelium and decreased in the endoderm, but L-CAM continued to be expressed in all cells including endodermal cells. During neurulation, the level of N-CAM expression in the neural ectoderm increased considerably, while remaining constant in non-neural ectoderm and diminishing in the somites; in the notochord, N-CAM was expressed transiently. Prevalence modulation was also seen at all sites of secondary induction: both CAMs increased in the sensory layer of the ectoderm during condensation of the placodes. During organogenesis, the expression of L-CAM gradually diminished in the nervous system while N- CAM expression remained high. In all other organs examined, the amount of one or the other CAM decreased, so that by stage 50 these two molecules were expressed in non-overlapping territories. Embryonic and adult tissues were compared to search for concordance of CAM expression at later stages. With few exceptions, the tissue distributions of N-CAM and L-CAM were similar in the frog and in the chicken from early times of development. In contrast to previous observations in the chicken and in the mouse, N-CAM expression was found to be high in the adult liver of Xenopus, whereas L-CAM expression was low. In the adult brain, N-CAM was expressed as three components of apparent molecular mass 180, 140, and 120 kD, respectively; in earlier stages of development only the 140- kD component could be detected. In the liver, a single N-CAM band appears at 160 kD, raising the possibility that this band represents an unusual N-CAM polypeptide. L-CAM appeared at all stages as a 124-kD molecule. (ABSTRACT TRUNCATED AT 400 WORDS)
Structure of 6‐diazo‐5‐oxo‐norleucine‐bound human gamma‐glutamyl transpeptidase 1, a novel mechanism of inactivation

Intense efforts are underway to identify inhibitors of the enzyme gamma‐glutamyl transpeptidase 1 (GGT1) which cleaves extracellular gamma‐glutamyl compounds and contributes to the pathology of asthma, reperfusion injury and cancer. The glutamate analog, 6‐diazo‐5‐oxo‐norleucine (DON), inhibits GGT1. DON also inhibits many essential glutamine metabolizing enzymes rendering it too toxic for use in the clinic as a GGT1 inhibitor. We investigated the molecular mechanism of human GGT1 (hGGT1) inhibition by DON to determine possible strategies for increasing its specificity for hGGT1. DON is an irreversible inhibitor of hGGT1. The second order rate constant of inactivation was 0.052 mM−1 min−1 and the Ki was 2.7 ± 0.7 mM. The crystal structure of DON‐inactivated hGGT1 contained a molecule of DON without the diazo‐nitrogen atoms in the active site. The overall structure of the hGGT1‐DON complex resembled the structure of the apo‐enzyme; however, shifts were detected in the loop forming the oxyanion hole and elements of the main chain that form the entrance to the active site. The structure of hGGT1‐DON complex revealed two covalent bonds between the enzyme and inhibitor which were part of a six membered ring. The ring included the OG atom of Thr381, the reactive nucleophile of hGGT1 and the α‐amine of Thr381. The structure of DON‐bound hGGT1 has led to the discovery of a new mechanism of inactivation by DON that differs from its inactivation of other glutamine metabolizing enzymes, and insight into the activation of the catalytic nucleophile that initiates the hGGT1 reaction.
Traffic Events Oriented Dynamic Traffic Assignment Model for Expressway Network: A Network Flow Approach

In this paper, we focus on the dynamic traffic assignment (DTA) problem on large-scale expressway networks especially under the condition of traffic events (such as severe weather, large traffic accidents etc.). We formulate the expressway network DTA problem as a nonconvex optimization problem. Considering the difficulty of solving the problem, we put forward an approximate solution algorithm based on the network flow theory with high computational efficiency and strong applicability. Specifically, a machine learning approach and a series of customization strategies of network flow model (including multi-origin and multidestination split, flow discretization and parallel edges addition methods) are proposed to transform the DTA problem into a resoluble network flow problem. After that, in order to improve the operational efficiency of an expressway network after traffic events occurring, the proposed network flow based two-layer DTA model (NTDM) is separated into two parts-traffic flow limitation model based on maximum flow algorithm and traffic assignment model based on minimum cost flow algorithm. Experiments on real expressway network data in some provinces of China show that our method can make a significant 26.03% reduction in saturation rate in a particular scenario. In efficiency test, the NTDM is at least 600 times faster than the traditional analytic method in a network with thousands of nodes.
Unified Inference for Variational Bayesian Linear Gaussian State-Space Models

Linear Gaussian State-Space Models are widely used and a Bayesian treatment of parameters is therefore of considerable interest. The approximate Variational Bayesian method applied to these models is an attractive approach, used successfully in applications ranging from acoustics to bioinformatics. The most challenging aspect of implementing the method is in performing inference on the hidden state sequence of the model. We show how to convert the inference problem so that standard Kalman Filtering/Smoothing recursions from the literature may be applied. This is in contrast to previously published approaches based on Belief Propagation. Our framework both simplifies and unifies the inference problem, so that future applications may be more easily developed. We demonstrate the elegance of the approach on Bayesian temporal ICA, with an application to finding independent dynamical processes underlying noisy EEG signals.
Support-Based Implementation of Bayesian Data Fusion for Spatial Enhancement: Applications to ASTER Thermal Images

In this letter, a general Bayesian data fusion (BDF) approach is proposed and applied to the spatial enhancement of ASTER thermal images. This method fuses information coming from the visible or near-infrared bands (15 times 15 m pixels) with the thermal infrared bands (90 times 90 m pixels) by explicitly accounting for the change of support. By relying on linear multivariate regression assumptions, differences of support size for input images can be explicitly accounted for. Due to the use of locally varying variances, it also avoids producing artifacts on the fused images. Based on a set of ASTER images over the region of Lausanne, Switzerland, the advantages of this support-based approach are assessed and compared to the downscaling cokriging approach recently proposed in the literature. Results show that improvements are substantial with respect to both visual and quantitative criteria. Although the method is illustrated here with a specific case study, it is versatile enough to be applied to the spatial enhancement problem in general. It thus opens new avenues in the context of remotely sensed images.
Spectral Entropy Feature in Multi-stream for Robust ASR

In recent papers, entropy computed from sub-bands of the spectrum was used as a feature for automatic speech recognition. In the present paper, we further study the sub-band spectral entropy features which can give the flatness/peakiness of the sub-band spectrum and in turn the position of the formants in the spectrum. The sub-band spectral entropy features are used in hybrid hidden Markov model/artificial neural network systems and are found to be noise robust. The spectral entropy features are investigated along with PLP features in multi-stream combination. Separate multi-layer perceptrons (MLPs) are trained for PLP features, spectral entropy features and both the features concatenated. The output posteriors of the three MLPs are combined after weighting such that the weight to a particular MLP's outputs are inversely proportional to the entropy of the output posterior distributions of that MLP. In Tandem framework, the combined output, after decorrelation, is fed to standard hidden Markov model/Gaussian mixture model system. Significant improvement in performance is reported when spectral entropy features are used along with PLP features in multi-stream combination.
Organization of Cytoskeletal F‐Actin, G‐Actin, and Gelsolin in the Adhesion Structures in Cultured Osteoclast

Immunofluorescence using Gc protein (group‐specific component or vitamin D binding protein [DBP]) as a marker of G‐actin showed that nonfilamentous, monomeric G‐actin is a component of the podosomes of osteoclasts cultured on glass plates or bone slices. Typical individual podosomes of the well‐spread cells on glass plates were rosette in form. When viewed from the basolateral surface, the core portion of the dotlike podosomes was associated with packed F‐actin filaments surrounded by G‐actin organized in a ringlike structure. The podosomes, when viewed perpendicular to the substrate, showed a conical shape as a bundle of short F‐actin core and a ring of G‐actin. With cell spreading on glass plates, the clustering of the podosomes formed a continuous belt of tightly packed podosomes as an adhesion structure at the paramarginal area. In addition, these structures were seen on the ventral cell surface. Similar changes in cell shape were seen in the osteoclasts when they were plated on bone slices. With the loss of dotlike podosomes, a continuous band of F‐actin was formed around the resorption lacunae. It became evident then that F‐ and G‐actin dissociated from each other in the podosomes. The staining patterns of G‐actin varied from a discrete dot to a diffuse one. Toward the nonresorption phase, the osteoclasts lost their continuous F‐actin band but dotlike podosomes appeared in the leading and the trailing edges. In such a cell undergoing translational movements, G‐actin was located diffusely in the cytoplasm behind the lamellipodia and along some segments of the leading edge. Cytochalasin B treatment caused cells to disorganize the actin cytoskeletal architecture, which indicated the disassembling of F‐actin into G‐actin in podosomes and disappearance of actin‐ring of cultured osteoclasts. Staining with polyclonal actin antibody or monoclonal β‐actin was overlapped with the distribution pattern of G‐ and F‐actin. Gelsolin was detected in the region of the adhesion area corresponding to the podosome. The observation that F‐actin, G‐actin, and gelsolin were detected in the osteoclastic adhesion structures suggests that the podosomes may represent sites where a rapid polymerization/depolymerization of actin occurs. These dynamic changes in cytoskeletal organization and reorganization of G‐actin may reflect changes in the functional polarization of the osteoclast during the bone resorption cycle and suggest the important role of G‐actin in the regulation of osteoclast adhesion.
An Efficient Three-Dimensional Localization Scheme Using Trilateration in Wireless Sensor Networks

In this letter, we propose a novel three-dimensional (3D) localization algorithm based on a simple range-based localization approach. The proposed scheme requires distance measurements associated with only three anchor nodes for a 3D location estimation using linear least squares estimation (LLSE). It uses Heron's formula of tetrahedron to calculate the target height and then transforms a two-dimensional location computed by LLSE into a 3D estimated location. Simulation results validate the accuracy of the proposed scheme.
Understanding and leveraging tag-based relations in on-line social networks

In most social networks, measuring similarity between users is crucial for providing new functionalities, understanding the dynamics of such networks, and growing them (e.g., people you may know recommendations depend on similarity, as does link prediction). In this paper, we study a large sample of Flickr user actions and compare tags across different explicit and implicit network relations. In particular, we compare tag similarities in explicit networks (based on contact, friend, and family links), and implicit networks (created by actions such as comments and selecting favorite photos). We perform an in-depth analysis of these five types of links specifically focusing on tagging, and compare different tag similarity metrics. Our motivation is that understanding the differences in such networks, as well as how different similarity metrics perform, can be useful in similarity-based recommendation applications (e.g., collaborative filtering), and in traditional social network analysis problems (e.g., link prediction). We specifically show that different types of relationships require different similarity metrics. Our findings could lead to the construction of better user models, among others.
Keys to Soil Taxonomy

’ 黒 ボ ク 上 に お け る デ ン ト ー = 一ソ の 全 量基肥 ・接触 施肥 ・不 耕 起栽培 (第 2報) 研 究 の 経 費 の 一部 は ,日 本 学 術 振興 会 未 来 開拓 学術 研 究 推 進事 業 「植 物 の 環 境 応 答 機 構 とバ イ オ テ ク ノ 卩 ジ ー 」 (RFTF 9700604 ) の 一 貫 と し て 行 わ れた もの で あ る . 榊 東北大学大 学院農学研 究科 (989−6711 宮城 県玉 造郡 鳴子 町 大 口 字蓬 田 2323 ) 2000年 1 月 14H 受 付 ・200U年 3 月 14 口 受 理 日本土 壌肥料学雑誌 第 71巻 第 5号 p.674〜681(2000) 肥効 調 節 型 肥料 を 用 い た 全量 基 肥 ・接触施肥 法 は , 施 用量 の 全量 を基肥 と し て種子 と接触 させ て 施用す る方法 で あ り, Shoji and Gandeza9 に よ っ て 提唱 され た 新 し
SV MIXTURE, CLASSIFICATION USING EM ALGORITHM

The present paper presents a theoretical extension of our earlier work entitled“A comparative study of two models SV with MCMC algorithm” cited, Rev Quant Finan Acc (2012) 38:479-493 DOI 10.1007/s11156-011-0236-1 where we propose initially a mixture stochastic volatility model providing a tractable method for capturing certain market characteristics. To estimate the parameter of a mixture stochastic volatility model, we first use the Expectation-Maximisation (EM) algorithm. The second step is to adopt the clustering approach to classify the database into subsets (clusters).
A Policy-Based Approach for Managing Ubiquitous Networks in Urban Spaces

Modern cities are becoming increasingly networked environments and a plethora of computing equipment interacts with today's urban citizens. We refer to these ubiquitous networked environments as "urban spaces" and attempt to manage these under a unified framework based on policies. Since users actively participate in urban spaces with their owned devices and demand more control and privacy, we introduce a scheme to protect user privacy and respect their preferences. We adopt a multiple manager paradigm to enable more entities to offer their services and cooperatively shape management logic based on their objectives. Detailed policy examples illustrate the concepts and simulation results measure the effect of policies on network performance.
Identification of Nucleic Acid Binding Sites on Translin-Associated Factor X (TRAX) Protein

Translin and TRAX proteins play roles in very important cellular processes such as DNA recombination, spatial and temporal expression of mRNA, and in siRNA processing. Translin forms a homomeric nucleic acid binding complex and binds to ssDNA and RNA. However, a mutant translin construct that forms homomeric complex lacking nucleic acid binding activity is able to form fully active heteromeric translin-TRAX complex when co-expressed with TRAX. A substantial progress has been made in identifying translin sites that mediate its binding activity, while TRAX was thought not to bind DNA or RNA on its own. We here for the first time demonstrate nucleic acid binding to TRAX by crosslinking radiolabeled ssDNA to heteromeric translin-TRAX complex using UV-laser. The TRAX and translin, photochemically crosslinked with ssDNA, were individually detected on SDS-PAGE. We mutated two motifs in TRAX and translin, designated B2 and B3, to help define the nucleic acid binding sites in the TRAX sequence. The most pronounced effect was observed in the mutants of B3 motif that impaired nucleic acid binding activity of the heteromeric complexes. We suggest that both translin and TRAX are binding competent and contribute to the nucleic acid binding activity.
Neuronal-Derived Nitric Oxide and Somatodendritically Released Vasopressin Regulate Neurovascular Coupling in the Rat Hypothalamic Supraoptic Nucleus

The classical model of neurovascular coupling (NVC) implies that activity-dependent axonal glutamate release at synapses evokes the production and release of vasoactive signals from both neurons and astrocytes, which dilate arterioles, increasing in turn cerebral blood flow (CBF) to areas with increased metabolic needs. However, whether this model is applicable to brain areas that also use less conventional neurotransmitters, such as neuropeptides, is currently unknown. To this end, we studied NVC in the rat hypothalamic magnocellular neurosecretory system (MNS) of the supraoptic nucleus (SON), in which dendritic release of neuropeptides, including vasopressin (VP), constitutes a key signaling modality influencing neuronal and network activity. Using a multidisciplinary approach, we investigated vasopressin-mediated vascular responses in SON arterioles of hypothalamic brain slices of Wistar or VP-eGFP Wistar rats. Bath-applied VP significantly constricted SON arterioles (Δ−41 ± 7%) via activation of the V1a receptor subtype. Vasoconstrictions were also observed in response to single VP neuronal stimulation (Δ−18 ± 2%), an effect prevented by V1a receptor blockade (V2255), supporting local dendritic VP release as the key signal mediating activity-dependent vasoconstrictions. Conversely, osmotically driven magnocellular neurosecretory neuronal population activity leads to a predominant nitric oxide-mediated vasodilation (Δ19 ± 2%). Activity-dependent vasodilations were followed by a VP-mediated vasoconstriction, which acted to limit the magnitude of the vasodilation and served to reset vascular tone following activity-dependent vasodilation. Together, our results unveiled a unique and complex form of NVC in the MNS, supporting a competitive balance between nitric oxide and activity-dependent dendritic released VP, in the generation of proper NVC responses.
On -Kernel Construction

15th ACM Symposium on Operating System Principles (SOSP) December 3-6, Copper Mountain Resort, Colorado From a software-technology point of view, the kernel concept is superior to large integrated kernels. On the other hand, it is widely believed that (a) kernel based systems are inherently ine cient and (b) they are not su ciently exible. Contradictory to this belief, we show and support by documentary evidence that ine ciency and in exibility of current -kernels is not inherited from the basic idea but mostly from overloading the kernel and/or from improper implementation. Based on functional reasons, we describe some concepts which must be implemented by a -kernel and illustrate their exibility. Then, we analyze the performance critical points. We show what performance is achievable, that the e ciency is su cient with respect to macro-kernels and why some published contradictory measurements are not evident. Furthermore, we describe some implementation techniques and illustrate why -kernels are inherently not portable, although they improve portability of the whole system.
Expert Finding for Community-Based Question Answering via Ranking Metric Network Learning

Expert finding for question answering is a challenging problem in Community-based Question Answering (CQA) site, arising in many applications such as question routing and the identification of best answers. In order to provide high-quality experts, many existing approaches learn the user model mainly from their past question-answering activities in CQA sites, which suffer from the sparsity problem of CQA data. In this paper, we consider the problem of expert finding from the viewpoint of learning ranking metric embedding. We propose a novel ranking metric network learning framework for expert finding by exploiting both users' relative quality rank to given questions and their social relations. We then develop a random-walk based learning method with recurrent neural networks for ranking metric network embedding. The extensive experiments on a large-scale dataset from a real world CQA site show that our method achieves better performance than other state-of-the-art solutions to the problem.
A Neural Adaptive Controller in Flapping Flight

In this paper, we propose a neural adaptive controller for attitude control in a flapping-wing insect model. The model is nonlinear and subjected to periodic force/torque generated by nominal wing kinematics. Two sets of model parameters are obtained from the fruit fly Drosophila melanogaster and the honey bee Apis mellifera. Attitude control is achieved by modifying the wing kinematics on a stroke-by-stroke basis. The controller is based on filtered-error with neural network models approximating system nonlinearities. Lyapunov-based stability analysis shows the asymptotic convergence of system outputs. We present simulation results for angular position stabilization and trajectory tracking. Trajectory tracking is illustrated by two cases: saccadic turning and sinusoidal variation in the yaw angle. The proposed controller successfully regulates flight orientation – roll, pitch and yaw angles – by generating desired torque resulting from tuning parameterized wing motion. Results furthermore show similarities between simulated and observed turning from real insects, suggesting some inherent properties in insect flight dynamics and control. The proposed controller has potential applications in future flapping-wing Micro Air Vehicles (MAVs).