Miracle-dz/UniFAR-FTUs huggingface dataset:
Segmentation of vessels: the corkscrew algorithm

Medical imaging is nowadays much more than only providing data for diagnosis. It also links 'classical' diagnosis to modern forms of treatment such as image guided surgery. Those systems require the identification of organs, anatomical regions of the human body etc., i. e. the segmentation of structures from medical data sets. The algorithms used for these segmentation tasks strongly depend on the object to be segmented. One structure which plays an important role in surgery planning are vessels that are found everywhere in the human body. Several approaches for their extraction already exist. However, there is no general one which is suitable for all types of data or all sorts of vascular structures. This work presents a new algorithm for the segmentation of vessels. It can be classified as a skeleton-based approach working on 3D data sets, and has been designed for a reliable segmentation of coronary arteries. The algorithm is a semi-automatic extraction technique requiring the definition of the start and end the point of the (centerline) path to be found. A first estimation of the vessel's centerline is calculated and then corrected iteratively by detecting the vessel's border perpendicular to the centerline. We used contrast enhanced CT data sets of the thorax for testing our approach. Coronary arteries have been extracted from the data sets using the 'corkscrew algorithm' presented in this work. The segmentation turned out to be robust even if moderate breathing artifacts were present in the data sets.
Nuclear DICKKOPF-1 as a biomarker of chemoresistance and poor clinical outcome in colorectal cancer

Sporadic colorectal cancer (CRC) insurgence and progression depend on the activation of Wnt/β-catenin signaling. Dickkopf (DKK)-1 is an extracellular inhibitor of Wnt/β-catenin signaling that also has undefined β-catenin-independent actions. Here we report for the first time that a proportion of DKK-1 locates within the nucleus of healthy small intestine and colon mucosa, and of CRC cells at specific chromatin sites of active transcription. Moreover, we show that DKK-1 regulates several cancer-related genes including the cancer stem cell marker aldehyde dehydrogenase 1A1 (ALDH1A1) and Ral-binding protein 1-associated Eps domain-containing 2 (REPS2), which are involved in detoxification of chemotherapeutic agents. Nuclear DKK-1 expression is lost along CRC progression; however, it remains high in a subset (15%) of CRC patients (n = 699) and associates with decreased progression-free survival (PFS) after chemotherapy administration and overall survival (OS) [adjusted HR, 1.65; 95% confidence interval (CI), 1.23-2.21; P = 0.002)]. Overexpression of ALDH1A1 and REPS2 associates with nuclear DKK-1 expression in tumors and correlates with decreased OS (P = 0.001 and 0.014) and PFS. In summary, our findings demonstrate a novel location of DKK-1 within the cell nucleus and support a role of nuclear DKK-1 as a predictive biomarker of chemoresistance in colorectal cancer.
Solving the Fisher ’ s Equation by Means of Variational Iteration Method

In this paper, we consider variational iteration method (VIM) to obtain exact solution to the Fisher’s equation. The variational iteration method is based on Lagrange multipliers for identification of optimal value of parameters in a functional. Using this method, it is possible to find the exact solution or an approximate solution of the problem.
TCP Testing: How Well Does ns2 Match Reality?

New transport protocols continue to appear as alternatives to the Transmission Control Protocol (TCP). Many of these are designed to address TCP’s inefficiency in operating over paths with a high bandwidth-delay product (BDP). To test these new protocols, especially comparatively, and to understand their interactions, extensions to the ns2 simulator allow real code from the linux kernel to be used within the ns2 simulations. However, how does the performance of such configurations compare to test-bed experiments of the same configuration? Although, anecdotally, there are often comments within the research community about such issues, there are no studies that quantify the differences for a specific protocol suite. Using a simple testbed, we assess four different transport protocols in a comparative study to examine how well ns2 matches reality. Our tests are all conducted at 100Mb/s over a wide range of delay and router buffer conditions: end-to-end delays from 25ms to 400ms, with end-to-end path buffering of 20% to 100% of the BDP. We find that in our simple configuration, there are significant differences in performance between ns2 and the testbed.
A complete design path for the layout of flexible macros

• A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers.
The Basics of MEMS IMU/Gyroscope Alignment

Sensor misalignment is often a key consideration for high performance motion control systems that use MEMS inertial measurement units (IMUs) in their feedback loops. For the gyroscopes in the IMU, sensor misalignment describes the angular difference between each gyroscope’s axis of rotation and the system defined inertial reference frame, also known as the global frame. Managing the impact that misalignment has on sensor accuracy can require unique packaging, special assembly processes, or even complex inertial testing in the final configuration. All of these things can have a major impact on important project management metrics such as schedule, investment, and the total cost associated with the IMU in each system. Therefore, sensor alignment is a metric that warrants consideration during early stages of the design cycle, while there is time to define the system architecture around the most efficient solution. After all, nobody wants to burn through 80% of their project schedule and budget to find out that their inexpensive sensor requires hundreds, maybe even thousands, of dollars in unexpected cost adders to meet nonnegotiable deliverables to their end users. Ouch!
A statistical approach on Persian word sense disambiguation

This article studies different aspect of a new approach for resolving lexical ambiguities using statistical information gained from a monolingual corpus. The proposed approach resolves the problem of target word selection in an machine translation system. This Method is an unsupervised graph-based approach which uses a bilingual dictionary to find all possible translations of each ambiguous word in the source sentence (English) and then chooses the most appropriate alternative regarding the statistical information gathered from target language (Persian) corpora. Also, two new methods to measure the semantic similarity based on source and target language corpora are introduced. The experiments show that the unsupervised graph-based WSD which uses the proposed semantic similarity measures in the dependency graph outperforms all other methods on WSD for translating English to Persian words, significantly.
Programming parallelism with futures in lustre

Efficiently distributing synchronous programs is a challenging and long-standing subject. This paper introduces the use of futures in a LUSTRE-like language, giving the programmer control over the expression of parallelism. In the synchronous model where computations are considered instantaneous, futures increase expressiveness by decoupling the beginning from the end of a computation. Through a number of examples, we show how to desynchronize long computations and implement parallel patterns such as fork-join, pipelining and data parallelism. The proposed extension preserves the main static properties of the base language, including static resource bounds and the absence of deadlock, livelock and races. Moreover, we prove that adding or removing futures preserves the underlying synchronous semantics.
Analyzing Streams of Pseudorandom Numbers for Parallel Monte Carlo Integration

The quality of parallel substreams of pseudorandom numbers obtained from linear congruential generators as it is measured by the spectral test depends in a very sensitive and irregular way on the step size which is used. On the other hand, discrepancy estimates show that explicit inversive congruential pseudorandom number generators behave stable with respect to subsequences. The results of a sample Monte Carlo integration show the impact of these diierent theoretical ndings on the reliability of the integration results.
Dynamical systems: A tool for analysis and design of silicon half center oscillators

In this paper, a new oscillator circuit for central pattern generator systems has been proposed. Switched-capacitor technique which enables controllable, more accurate and stable resistance has been used. Oscillation frequency can be easily controlled by the frequency of switching which is very useful for global change of oscillation frequency in an array of oscillators. SPICE simulation and dynamical systems analysis have shown that when used as a single oscillator, the proposed circuit is able to produce a phase response curve (PRC) close to the one of a lamprey central pattern generator (CPG) system. Applying averaging theory to the system of coupled oscillators, we obtain averaged H and G functions for unidirectional and bidirectional coupling cases. Analysis of these functions shows our circuit's superior capability to achieve fast entrained oscillation with sensory feedback and reach equilibrium even with high frequency mismatch.
Discriminative Piecewise Linear Transformation Based on Deep Neural Networks for Noise Robust Automatic Speech Recognition

あらまし 本論文では,ディープニューラルネットワークを用いた区分的線形変換による統計的特徴量強調の 拡張を提案する. 本提案手法の目的は,雑音環境下音声認識を想定した特徴量領域における雑音除去を目的とし, 観測された音声特徴量から対応する静音環境下での音声特徴量の再現を行うことである. その際,ニューラルネッ トワークを用いて,観測された雑音環境下の音声特徴量より,ガウス混合分布でクラスタリングされた静音環境 下における音声特徴量の領域を識別する. その後,各領域に対応する線形変換をニューラルネットワークにより得 られる事後確率を重みとして足し合わせることで静音環境下での音声特徴量を推定する. これによって,ニュー ラルネットワークのもつ高い識別性能と,従来の生成モデルに基づく特徴量マッピング手法のもつ高い汎化性能 の融合を狙う. Aurora-2データベースを用いた連続音声認識実験により,提案手法は従来の区分線形変換法の一 つである Stereo-based Piecewise LInear Compensation for Environments (SPLICE) と比較して,雑音が既 知の条件では 53.72%単語誤り率を削減することができた. 更に,ニューラルネットワークを回帰モデルとして 用いたオートエンコーダと比較した場合,雑音環境が未知な条件で 26.96%の単語誤り率の削減が可能となった. キーワード 音声認識,耐雑音性,特徴量強調,ディープラーニング,ニューラルネットワーク
Research and Implementation of Ontology Conflict Detection and Reasoning Based on Description Logic for Forest Disease and Pest Diagnosis

This paper focused on ontology reasoning and conflict detection based on description logic. It presented the formal definition of forest disease and pest diagnosis ontology, which can reveal the clear hierarchy structure of knowledge. SWRL rules are built from the ontology that can have application in the reasoning of forest disease and pest diagnosis system. And ontology conflict detections of individual consistency checking and relation consistency checking are proposed and designed in this paper. The reasoning process is also designed, and can provide reference information in other domain applications.
Essential fatty acid composition of human colostrum triglycerides : its relationship with adipose tissue composition 13

The relationships between essential fatty acid (EFA) composition ofcobostrum and white adipose tissue (WAT) were examined on day 5 after delivery in 69 healthy women. Fatty acid composition was assessed by capillary gas chromatography, and 33 fatty acids were detected in cobostrum and in WAT. Total polyunsaturated fatty acid (PUFA) content was similar in cobostrum and in WAT(l5.7 ± 3.1% and 16.1 ± 3.8%, respectively), but long-chain PUFA content was higher in colostrum than in WAT (2.9 ± 0.6% and 1 ± 0.2%, respectively; P < 0.001). The concentrations oflinoleic acid were significantly correlated between cobostrum and WAT (r = 0.77, P < 0.0001). No correlation was found for a-linolenic acid. The relationships between bong-chain PUFA composition ofcolostrum and WAT suggested that individual factors along with tissue specificity of the mammary gland are involved in either the capacity of desaturating and chain-elongating pathways and/or incorporation of long-chain PUFAs into cobostrum. Am J Clin Nutr
Intraclutch Variation in Testosterone Content of Red-Winged Blackbird Eggs

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Properties of PASP: a Pseudomonas protease capable of mediating corneal erosions.

PURPOSE To analyze PASP in terms of its gene distribution and expression, its corneal pathologic effects, its enzymatic properties, and the protectiveness of the immune response to this protease. METHODS Twenty-five strains of P. aeruginosa were analyzed for the PASP gene and secreted protein by PCR and Western blot analysis, respectively. Active recombinant (r)PASP (10 microg/20 microL) or heat-inactivated rPASP was intrastromally injected into rabbit corneas. Pathologic changes were monitored by slit lamp examination (SLE) and histopathology. Purified rPASP was assayed for cleavage of collagens and susceptibility to TLCK. Rabbit antibody to rPASP was produced and tested for enzyme inactivation, and actively immunized rabbits were challenged by intrastromal injection of active rPASP (5 microg). RESULTS All 25 strains of P. aeruginosa analyzed were positive for the PASP gene and protein. SLE scores of eyes injected with active rPASP were significantly higher than control eyes at all postinjection times (PI; P <or= 0.004). Histopathologic studies documented the destruction of the corneal epithelial layer and portions of the corneal stroma at 9 hours PI, and polymorphonuclear (PMN) leukocyte infiltration into the cornea by 24 hours after active rPASP injection. PASP cleaved type I and IV collagens and was susceptible to TLCK inhibition. PASP was present in the cytoplasm and periplasm, but only secreted PASP was enzymatically active. A high antibody titer (ELISA titer >or= 10,000) was produced, but this antibody did not protect against active rPASP challenge. CONCLUSIONS PASP is a commonly produced Pseudomonas protease that can cleave collagens and cause corneal erosions.
A Pc-Based Wireless And Remote Control For Shape Judgment Equipment Using A Zigbee Module

abstract To increase manufacturing productivity, industrial automation is required. Additionally, in order to monitor the manufacturing process, a remote online monitoring and control system becomes compulsory. A conventional remote monitoring system often uses a wire connection for communication within a control center; however, it is time-consuming and inconvenient. To overcome this drawback, a wireless design is proposed for the manufacturing process. In this paper, a case study of a remote wireless monitoring network used in a shape judgment system is introduced. In order to connect the server pc and the PLC (a controller of a shape judgment system), a ZigBee wireless module in conjunction with a transparent mode is used. Additionally, the interface of the above system is established with a Visual Basic 6.0. One of the advantages in using a wireless network to connect with a server pc and a shape judgment system is that the server pc is movable. Moreover, the remote monitoring function at the client pc can also be utilized using a TCP/IP protocol. Consequently, a prototype of a wireless network and a remote control for a shape judgment system using a ZigBee module that reduces the cost in electrical power and saves time in the system’s installation is exemplified.
Microarray Image Segmentation Using Clustering Methods

Microarray image processing is a technology for viewing and computationally measuring thousands of genes at the same time. Gene expressions provide information about the cell activity in an organism. Observing a substantial change in gene expressions between the cDNA (complementary DNA) microarray experiments of an organism can be a sign of a disease. The goal of this study is to make a fine distinction against the gene expressions in the microarray image processing. For this reason, two clustering methods have been experimented and compared. In this study we have specifically investigated the segmentation step of the microarray image. Other than the segmentation methods used in commercial packages we have used the clustering techniques. We have applied fuzzy c–means and k-means methods and observed the results.
Multi-Messenger Astronomy with GRBs: A White Paper for the Astro2010 Decadal Survey

Gamma-ray Bursts (GRBs) are relativistic cosmological beacons of transient high energy radiation whose afterglows span the electromagnetic spectrum. Theoretical expectations of correlated neutrino and/or gravitational wave (GW) emission position GRBs at an astrophysical nexus for a metamorphosis in our understanding of the Cosmos. This new dawn in the era of experimental (particle) astrophysics and cosmology is afforded by current and planned facilities enabling the novel astronomies of high energy neutrinos and gravitational waves, in concert with unprecedented electromagnetic coverage. In this white paper, we motivate GRBs as a compelling scientific theme and highlight key technical advances that may facilitate fundamental breakthroughs in the context of Swift, Fermi, IceCube and LIGO (Laser Interferometer Gravitational Wave Observatory), whose capabilities would be augmented with JANUS (Joint Astrophysics Nascent Universe Satellite), EXIST (Energetic X-ray Imaging Survey Telescope) and LISA (Laser Interferometer Space Antenna). Scientific synergy will be achieved by leveraging the combined sensitivity of contemporaneous ground-based and satellite observatories, thus optimizing their collective discovery potential for: (i) revealing the origin(s) and acceleration mechanism(s) of cosmic rays, (ii) exposing GRB progenitor(s) and (iii) exploring the high-z Cosmos. Hence, the advent of GRB multi-messenger astronomy may cement an explicit connection to fundamental physics, via nascent cosmic windows, throughout the next decade and beyond.
State estimation for delayed neural networks

In this letter, the state estimation problem is studied for neural networks with time-varying delays. The interconnection matrix and the activation functions are assumed to be norm-bounded. The problem addressed is to estimate the neuron states, through available output measurements, such that for all admissible time-delays, the dynamics of the estimation error is globally exponentially stable. An effective linear matrix inequality approach is developed to solve the neuron state estimation problem. In particular, we derive the conditions for the existence of the desired estimators for the delayed neural networks. We also parameterize the explicit expression of the set of desired estimators in terms of linear matrix inequalities (LMIs). Finally, it is shown that the main results can be easily extended to cope with the traditional stability analysis problem for delayed neural networks. Numerical examples are included to illustrate the applicability of the proposed design method.
Equilibrium Bank Runs

We analyze a banking system in which the class of feasible deposit contracts, or mechanisms, is broad. The mechanisms must satisfy a sequential service constraint, but partial or full suspension of convertibility is allowed. Consumers must be willing to deposit, ex ante. We show, by examples, that under the so‐called “optimal contract,” the postdeposit game can have a run equilibrium. Given a propensity to run, triggered by sunspots, the optimal contract for the full predeposit game can be consistent with runs that occur with positive probability. Thus the Diamond‐Dybvig framework can explain bank runs as emerging in equilibrium under the optimal deposit contract.
Fast Image-based Chinese Calligraphic Character Retrieval on Large Scale Data

Chinese calligraphy is the art of handwriting, it draws a lot of attention for its beauty and elegance. In CADAL, a Calligraphic Character Dictionary (CCD) which contains hundreds of thousands of character images labeled with semantic meaning has been constructed and provided online to common users. It is a great challenge to perform quick and accurate image-based calligraphic character retrieval on CCD. In this paper, a novel shape descriptor, Oriented Shape Context (OSC) is proposed basing on the tranditional Shape Context (SC) to perform similarity searching. Together with GIST, GIST-OSC descriptor is proposed to represent calligraphic character image for efficient and effective retrieval. In addition, an effective retrieval schema is proposed. The retrieval schema works in two steps. Firstly approximate nearest neighbors of the query image are found quickly using GIST and then one-to-one fine matching between approximate nearest neighbors and the query image is performed using OSC. Our experiments show that the GIST-OSC descriptor and the retrieval schema are efficient and effective for Chinese calligraphic character retrieval on large scale data.