Miracle-dz/UniFAR-FTUs huggingface dataset:
Anatomy of the rat medial geniculate body: I. Cytoarchitecture, myeloarchitecture, and neocortical connectivity

The cytoarchitecture, myeloarchitecture, and neocortical connectivity of the rat medial geniculate body (MGB) were comprehensively studied in adult and immature rats to define major anatomical divisions and nuclei. The MGB is a highly intricate structure composed of the ventral (MGv), dorsal (MGd), and medial (MGm) divisions and component nuclei, each having reciprocal connections with auditory neocortex. The MGv lies inferior to the midgeniculate bundle and extends to the rostral, but not caudal MGB tip. The MGv is composed of ventral and ovoid nuclei bounded by a marginal zone, each region containing dark staining small and medium sized, densely packed neurons shown to have tufted dendritic morphology; in contrast to the MGd, but similar to the dorsal lateral geniculate nucleus, only the perikarya of MGv neurons stain for Nissl in early postnatal material. Ventral nucleus cells align with afferent brachial axons, which penetrate the nucleus in a dorsoventral direction, whereas rostrocaudal cellular arrays are retrogradely labeled after injections of horseradish peroxidase (HRP) into auditory cortex. The ovoid nucleus is a double spiraled structure encircled and penetrated by afferent fibers that determine the orientation of constituent perikarya. Neurons in the transition zone align with a spray of axons emanating from the juncture of the ovoid and midgeniculate bundles. Marginal zone neurons are oriented in parallel to the free geniculate wall.
Transcatheter Aortic Valve Replacement: a Kidney’s Perspective

Transcatheter aortic valve replacement (TAVR) has now emerged as a viable treatment option for high-risk patients with severe aortic stenosis (AS) who are not suitable candidates for surgical aortic valve replacement (SAVR). Despite encouraging published outcomes, acute kidney injury (AKI) is common and lowers the survival of patients after TAVR. The pathogenesis of AKI after TAVR is multifactorial including TAVR specific factors such as the use of contrast agents, hypotension during rapid pacing, and embolization; preventive measures may include pre-procedural hydration, limitation of contrast dye exposure, and avoidance of intraprocedural hypotension. In recent years, the number of TAVR performed worldwide has been increasing, as well as published data on renal perspectives of TAVR including AKI, chronic kidney disease, end-stage kidney disease, and kidney transplantation. This review aims to present the current literature on the nephrology aspects of TAVR, ultimately to improve the patients’ quality of care and outcomes.
A Hybrid Genetic Search for Graph Partitioning Based on Lock Gain

A new hybrid genetic algorithm for graph bisection is proposed. The algorithm includes a new local optimization heuristic. Based on the traditional framework of the Kernighan-Lin algorithm, the local optimization uses a new type of gain as the primary measure for vertex movement. The new algorithm showed significant or dramatic improvement over the state-of-the-art algorithms.
Searching distributed collections with inference networks

The use of information retrieval systems in networked environments raises a new set of issues that have received little attention. These issues include ranking document collections for relevance to a query, selecting the best set of collections from a ranked list, and merging the document rankings that are returned from a set of collections. This paper describes methods of addressing each issue in the inference network model, dkcusses their implementation in the INQUERY system, and presents experimental results demonstrating their effectiveness.
Cohomology of Cryo-Electron Microscopy

The goal of cryo-electron microscopy (EM) is to reconstruct the 3-dimensional structure of a molecule from a collection of its 2-dimensional projected images. In this article, we show that the basic premise of cryo-EM --- patching together 2-dimensional projections to reconstruct a 3-dimensional object --- is naturally one of Cech cohomology with SO(2)-coefficients. We deduce that every cryo-EM reconstruction problem corresponds to an oriented circle bundle on a simplicial complex, allowing us to classify cryo-EM problems via principal bundles. In practice, the 2-dimensional images are noisy and a main task in cryo-EM is to denoise them. We will see how the aforementioned insights can be used towards this end.
Synthesis, Characterization, and Selected Properties of Graphene

Carbon nanotubes (CNTs) and graphene are two of the most studied materials today. Two-dimensional graphene has specially attracted a lot of attention because of its unique electrical properties such as very high carriermobility [1–4], the quantum Hall effect at room temperature [2, 5], and ambipolar electric field effect along with ballistic conduction of charge carriers [1]. Some other properties of graphene that are equally interesting include its unexpectedly high absorption of white light [6], high elasticity [7], unusual magnetic properties [8, 9], high surface area [10], gas adsorption [11], and charge-transfer interactions with molecules [12, 13]. We discuss some of these aspects in this chapter. While graphene normally refers to a single layer of sp2 bonded carbon atoms, there are important investigations on biand few-layered graphenes (FGs) as well. In the very first experimental study on graphene by Novoselov et al. [1, 2] in 2004, graphene was prepared by micromechanical cleavage from graphite flakes. Since then, there has been much progress in the synthesis of graphene and a number of methods have been devised to prepare high-quality single-layer graphenes (SLGs) and FGs, some of which are described in this chapter. Characterization of graphene forms an important part of graphene research and involves measurements based on various microscopic and spectroscopic techniques. Characterization involves determination of the number of layers and the purity of sample in terms of absence or presence of defects. Optical contrast of graphene layers on different substrates is the most simple and effective method for the identification of the number of layers. This method is based on the contrast arising from the interference of the reflected light beams at the air-to-graphene, graphene-to-dielectric, and (in the case of thin dielectric films) dielectric-to-substrate interfaces [14]. SLG, bilayer-, and multiple-layer graphenes (<10 layers) on Si substrate with a 285 nm SiO2 are differentiated using contrast spectra, generated from the reflection light of a white-light source (Figure 1.1a) [15]. A total color difference (TCD) method, based on a combination of the reflection spectrum calculation and the International Commission on Illumination (CIE) color space
T Regulatory Cell Responses to Immunization with a Soluble Egg Antigen in Schistosoma mansoni-Infected Mice

The aim of the study is to characterize the phenotypes of CD4+ CD25+ T regulatory cells within the liver granulomas and association with both Foxp-3 gene expression and splenic cytokines. Naïve C57BL/6 mice were intravenously injected with multiple doses of the soluble egg antigen (SEA) 7 days before cercarial infection. The immunized and infected control groups were sacrificed 8 and 16 weeks post-infection (PI). Histopathology, parasitological parameters, splenic phenotypes for T regulatory cells, the FOXP-3 expression in hepatic granuloma using real-time PCR, and the associated splenic cytokines were studied. Histopathological examination of the liver revealed remarkable increase in degenerated ova within hepatic granuloma which decreased in diameter at weeks 8 and 16 PI (P<0.01). The percentage of T regulatory cells (CD4+ CD25+) increased significantly (P<0.01) in the immunized group compared to the infected control at weeks 8 and 16 PI. The FOXP-3 expression in hepatic granulomas increased from 10 at week 8 to 30 fold at week 16 PI in the infected control group. However, its expression in the immunized group showed an increase from 30 at week 8 to 70 fold at week 16 PI. The splenic cytokine levels of pro-inflammatory cytokines, IFN-γ, IL-4, and TNF-α, showed significant decreases (P<0.05) compared to the infected control group. In conclusion, the magnitude and phenotype of the egg-induced effects on T helper responses were found to be controlled by a parallel response within the T regulatory population which provides protection in worm parasite-induced immunopathology.
Norwegian Native Language Identification

We present a study of Native Language Identification (NLI) using data from learners of Norwegian, a language not yet used for this task. NLI is the task of predicting a writer’s first language using only their writings in a learned language. We find that three feature types, function words, part-of-speech n-grams and a hybrid part-of-speech/function word mixture n-gram model are useful here. Our system achieves an accuracy of 79% against a baseline of 13% for predicting an author’s L1. The same features can distinguish non-native writing with 99% accuracy. We also find that part-of-speech n-gram performance on this data deviates from previous NLI results, possibly due to the use of manually post-corrected tags.
DETECTION OF CURBSTONES IN AIRBORNE LASER SCANNING DATA

The high point densities obtained by today’s airborne laser scanners enable the extraction of various features that are traditionally mapped by photogrammetry or land surveying. While significant progress has been made in the extraction of buildings and trees from dense point clouds, little research has been performed on the extraction of roads. In this paper it is analysed to what extent road sides can be mapped in point clouds of high point density (20 pts/m 2 ). In urban areas curbstones often separate the road surface from the adjacent pavement. These curbstones are mapped in a three step procedure. First, the locations with small height jumps near the terrain surface are detected. Second, midpoints of high and low points on either side of the height jump are generated, put in a sequence, and used to fit a smooth curve. Third, small gaps between nearby and collinear line segments are closed. GPS measurements were taken to analyse the performance of the road side detection. The analysis showed that the completeness varied between 50 and 86%, depending on the amount of parked cars occluding the curbstones. The RMSE in the comparison with the GPS measurements was 0.18 m.
Simulation of Fuel Temperature of Diesel Engine Heating by PTC Materials

The PTC materials, as a kind of positive temperature coefficient materials, are used to heat diesel fuel in the high-pressure fuel pipe near the injector in Diesel engine, which have a lot of advantages, such as simple structure, safe and rapid heating, and fixed heating temperature around its Curie point. In order to study its heating effect on diesel fuel of the high pressure fuel pipe, the dynamical models for both the controlled object and PTC heater are presented by the way of lumped parameter, and the heating effects are also simulated and analyzed. The calculation results show that the diesel temperature is heated by the PTC materials effectively. Meanwhile, the heating law by PTC materials heating diesel fuel in the high pressure fuel pipe of engine is also summarized.
Global analysis of functional surfaces of core histones with comprehensive point mutants

The core histones are essential components of the nucleosome that act as global negative regulators of DNA‐mediated reactions including transcription, DNA replication and DNA repair. Modified residues in the N‐terminal tails are well characterized in transcription, but not in DNA replication and DNA repair. In addition, roles of residues in the core globular domains are not yet well characterized in any DNA‐mediated reactions. To comprehensively understand the functional surface(s) of a core histone, we constructed 320 yeast mutant strains, each of which has a point mutation in a core histone, and identified 42 residues responsible for the suppressor of Ty (Spt‐) phenotypes, and 8, 30 and 61 residues for sensitivities to 6‐azauracil (6AU), hydroxyurea (HU) and methyl‐methanesulfonate (MMS), respectively. In addition to residues that affect one specific assay, residues involved in multiple reactions were found, and surprisingly, about half of them were clustered at either the nucleosome entry site, the surface required for nucleosome–nucleosome interactions in crystal packing or their surroundings. This comprehensive mutation approach was proved to be powerful for identification of the functional surfaces of a core histone in a variety of DNA‐mediated reactions and could be an effective strategy for characterizing other evolutionarily conserved hub‐like factors for which surface structural information is available.
Learning to Estimate and Remove Non-uniform Image Blur

This paper addresses the problem of restoring images subjected to unknown and spatially varying blur caused by defocus or linear (say, horizontal) motion. The estimation of the global (non-uniform) image blur is cast as a multi-label energy minimization problem. The energy is the sum of unary terms corresponding to learned local blur estimators, and binary ones corresponding to blur smoothness. Its global minimum is found using Ishikawa's method by exploiting the natural order of discretized blur values for linear motions and defocus. Once the blur has been estimated, the image is restored using a robust (non-uniform) deblurring algorithm based on sparse regularization with global image statistics. The proposed algorithm outputs both a segmentation of the image into uniform-blur layers and an estimate of the corresponding sharp image. We present qualitative results on real images, and use synthetic data to quantitatively compare our approach to the publicly available implementation of Chakrabarti~et al.
Controlled-source interferometric redatuming by crosscorrelation and multidimensional deconvolution in elastic media

Various researchers have shown that accurate redatuming of controlled seismic sources to downhole receiver locations can be achieved without requiring a velocity model. By placing receivers in a horizontal or deviated well and turning them into virtual sources, accurate images can be obtained even below a complex near-subsurface. Examples include controlled-source interferometry and the virtual-source method, both based on crosscorrelated signals at two downhole receiver locations, stacked over source locations at the surface. Because the required redatuming operators are taken directly from the data, even multiple scattered waveforms can be focused at the virtual-source location, and accurate redatuming can be achieved. To reach such precision in a solid earth, representations for elastic wave propagation that require multicomponent sources and receivers must be implemented. Wavefield decomposition prior to crosscorrelation allows us to enforce virtual sources to radiate only downward or only upward. Virtual-source focusing and undesired multiples from the overburden can be diagnosed with the interferometric point-spread function (PSF), which can be obtained directly from the data if an array of subsurface receivers is deployed. The quality of retrieved responses can be improved by filtering with the inverse of the PSF, a methodology referred to as multidimensional deconvolution.
Minimizing Makespan in Distributed Blocking Flowshops Using Hybrid Iterated Greedy Algorithms

This paper studies the distributed blocking flow shop scheduling problem (DBFSP) using meta-heuristics. A mixed integer programming model for solving the problem is proposed, and then three versions of the hybrid iterated greedy algorithm (HIG1, HIG2, and HIG3) are developed, combining the advantages of an iterated greedy algorithm with the operators of the variable Tabu list, the constant Tabu list, and the cooling schedule. A benchmark problem set is used to assess empirically the performance of the HIG1, HIG2, and HIG3 algorithms. Computational results show that all the three versions of the proposed algorithm can efficiently and effectively minimize the maximum completion time among all factories of the DBFSP, and HIG1 is the most effective.
Semi-supervised learning for relation extraction in Vietnamese text

Relation extraction (RE) is the task of finding semantic relations between entities from text. As the supervised learning method requires a large amount of labeled training data, the semi-supervised learning method is the topics of interest. This paper presents a semi-supervised learning approach to relation extraction for Vietnamese text using bootstrapping. As the accuracy of syntactic parsing in Vietnamese text is still not high, we used Shallow Linguistic Kernel (SLK) which combines global kernel and local kernel to present sentences. The differences between our SLK and Giuliano et al.'s SLK [5] are: our global kernel not only use bags of words but also use part of speech, another entities type, a dictionary of compound verbs; The window size of right kernel of our local context starts from the beginning of the sentence to the word immediately before the second entity, the window size of left kernel start from the word immediately after the first entity to the end of the sentence. Our experimental results show that the supervised method using our SKL can achieve higher accuracy than the one used by Giuliano et al. [5]. And the system's accuracy when applying the bootstrapping method is higher than when applying the supervised one.
Dynamic multi-hop switch handoffs in Software Defined Wireless Mesh Networks

Software Defined Networking (SDN) allows network administrators to customize the network according to the requirements. The centralized control plane in SDN finds its application in several areas of networking, especially in Wireless Mesh Networks (WMNs). In this paper we propose two dynamic switch handoff schemes for Software Defined Wireless Mesh Networks (SDWMNs) with multiple controller architectures. We use the metrics end-to-end Round-Trip-Time (RTT) and multi-hop Expected Transmission Count (ETX) for computing the handoff decision. Two schemes are analyzed by deploying a testbed consisting of mobile routers and multiple controllers. Our results show that ETX is a better metric for switch handoffs compared to RTT in mobile environments. Further, we propose an anticipatory handoff algorithm, based on multi-hop ETX, which predicts the near future of network behavior and makes the handoff decision prior to actual handoff. Finally, we observe significant performance improvement with our ETX-based handoff scheme as compared to architectures with a single controller.
Blood flow dynamics in heart failure.

BACKGROUND Exercise intolerance in heart failure (HF) may be due to inadequate vasodilation, augmented vasoconstriction, and/or altered muscle metabolic responses that lead to fatigue. METHODS AND RESULTS Vascular and metabolic responses to rhythmic forearm exercise were tested in 9 HF patients and 9 control subjects (CTL) during 2 protocols designed to examine the effect of HF on the time course of oxygen delivery versus uptake (protocol 1) and on vasoconstriction during exercise with 50 mm Hg pressure about the forearm to evoke a metaboreflex (protocol 2). In protocol 1, venous lactate and H+ were greater at 4 minutes of exercise in HF versus CTL (P<0.05) despite similar blood flow and oxygen uptake responses. In protocol 2, mean arterial pressure increased similarly in each group during ischemic exercise. In CTL, forearm blood flow and vascular conductance were similar at the end of ischemic and ambient exercise. In HF, forearm blood flow and vascular conductance were reduced during ischemic exercise compared with the ambient trial. CONCLUSIONS Intrinsic differences in skeletal muscle metabolism, not vasodilatory dynamics, must account for the augmented glycolytic metabolic responses to moderate-intensity exercise in class II and III HF. The inability to increase forearm vascular conductance during ischemic handgrip exercise, despite a normal pressor response, suggests that enhanced vasoconstriction of strenuously exercising skeletal muscle contributes to exertional fatigue in HF.
Ordering Policies in an environment of Stochastic Yields and Substitutable Demands

In this paper, we model production problems where yields are stochastic, demands are substitutable, and several items are jointly produced. We formulate this problem as a profit maximizing convex program, and study two approximation procedures. The first method solves finite horizon stochastic programs on a rolling horizon basis. We develop a decomposition algorithm for solving the finite horizon problems. The finite horizon problems are linear programs. Our algorithm utilizes the network-like structure of the coefficient matrix of the linear programs. The second method is a heuristic procedure that is based on the structure of the optimal policy for two-period problems. The heuristic parallels the decision rules used by managers in practice. The computational results suggest that the performance of this heuristic is comparable to that of the rolling horizon approach.
Querying XML Data on a Structured P2P Network

In this paper, we present solutions that enable efficient XML data querying on a structured P2Pnetwork. In particular, our solutions rely on a distributed index technique which indexes both the string values and structure summary of any XML document over the P2P network. With such kind of distributed indices, we may find the relevant results by a limiting number of peer lookups. To improve the efficiency of data querying, we also present a method that enables performing a query in parallelization. In addition, we use Bloom Filter to reduce the size of the candidate document lists exchanging between peers and improve the network traffic. Our simulation results show that our solutions can achieve major performance gains in terms of network bandwidth and execution time.
Feldspar: A domain specific language for digital signal processing algorithms

A new language, Feldspar, is presented, enabling high-level and platform-independent description of digital signal processing (DSP) algorithms. Feldspar is a pure functional language embedded in Haskell. It offers a high-level dataflow style of programming, as well as a more mathematical style based on vector indices. The key to generating efficient code from such descriptions is a high-level optimization technique called vector fusion. Feldspar is based on a low-level, functional core language which has a relatively small semantic gap to machine-oriented languages like C. The core language serves as the interface to the back-end code generator, which produces C. For very small examples, the generated code performs comparably to hand-written C code when run on a DSP target. While initial results are promising, to achieve good performance on larger examples, issues related to memory access patterns and array copying will have to be addressed.
Scalable ultrapeer-based DHT protocol for file sharing

In this paper, we present a novel file searching protocol to structure a DHT ring consisting of only ultrapeers, not all the nodes. The DHT ring in this protocol is much less sensitive to the churn rate because ultrapeers have much longer uptime compared with leaf nodes. Thus, this feature makes the protocol more scalable and efficient than the previous DHT ones in terms of costs of file search, node join and leave operations and the number of routing table entries each node should maintain. Moreover, it is more effective for locating rare files than Gnutella-like searching protocols.