Miracle-dz/UniFAR-FTUs huggingface dataset:
An Algorithm for the Extraction of DNA Fragments using Restriction Enzymes

Extraction of DNA fragments from existing base sequences is an important step in genetic manipulation. Existing tools for sequence alignment and creating the restriction map of families of restriction enzymes do not give a solution to the extraction problem. In this paper we explain why the task of choosing the most suitable enzymes for an extraction is computationally non-trivial. We present an automated algorithm for solving the extraction problem. Experimental results show that our algorithm is capable of performing extraction from large DNA sequences efficiently.
miR-501-3 p mediates the activity-dependent regulation of the expression of AMPA receptor subunit GluA 1

The Rockefeller University Press $30.00 J. Cell Biol. Vol. 208 No. 7 949–959 www.jcb. org/cgi/doi/10.1083/jcb.201404092 JCB 949 Correspondence to Zheng Li: lizheng2@mail.nih.gov; or Jun Zhu: jun.zhu@nih.gov Abbreviations used in this paper: AMPAR, -amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor; ANOVA, analysis of variance; AP5, (2R)-amino5-phosphonovaleric acid; DIV, days in vitro; NMDA, N-methyl-d-aspartate; NMDAR, NMDA receptor; qRT-PCR, quantitative RT-PCR; RISC, RNA-induced silencing complex. Introduction
Negentropic Planar Symmetry Detector

In this paper we observe that information theoretical concepts are valuable tools for extracting information from images and, in particular, information on image symmetries. It is shown that the problem of detecting reflectional and rotational symmetries in a two-dimensional image can be reduced to the problem of detecting point-symmetry and periodicity in one-dimensional negentropy functions. Based on these findings a detector of reflectional and rotational global symmetries in greyscale images is constructed. We discuss the importance of high precision in symmetry detection in applications arising from quality control and illustrate how the proposed method satisfies this requirement. Finally, a superior performance of our method to other existing methods, demonstrated by the results of a rigorous experimental verification, is an indication that our approach rooted in information theory is a promising direction in a development of a robust and widely applicable symmetry detector.
Concurrent programming in ML

Concurrent Programming ML (CML), included as part of the SML of New Jersey (SML/NJ) distribution, combines the best features of concurrent programming and functional programming. This practical, "how-to" book focuses on the use of concurrency to implement naturally concurrent applications. In addition to a tutorial introduction to programming in CML, the book presents three extended examples using CML for practical systems programming: a parallel software build system, a simple concurrent window manager, and an implementation of distributed tuple spaces. This book also illustrates advanced SML programming techniques, and includes a chapter on the implementation of concurrency using features provided by the SML/NJ system. It will be of interest to programmers, students, and professional researchers working in computer language development.
Extending BGMP for QoS-based inter-domain multicasting over the Internet

There has been active research on quality of service (QoS) multicasting. Very few, however, addresses QoS inter-domain multicasting. We present a QoS extension to BGMP (border gateway multicast protocol) which, proposed by Kumar, et al., is currently one of the most promising inter-domain multicasting proposals. With limited modification to the current BGMP, we extend it to support the so called two-bit differentiated service (including the classes of premium, assured, and best-effort services) proposed by Nichols, Jacobson, and Zhang. Detailed mechanisms of the QoS extension are described. Performance is evaluated through extensive simulation of real-network scenarios, supporting CBR, VBR, and best-effort traffic flows with the three classes of services. We believe that the work presented here is significant to the advancement of the next-generation Internet supporting QoS communications.
Validating clustering for gene expression data

MOTIVATION Many clustering algorithms have been proposed for the analysis of gene expression data, but little guidance is available to help choose among them. We provide a systematic framework for assessing the results of clustering algorithms. Clustering algorithms attempt to partition the genes into groups exhibiting similar patterns of variation in expression level. Our methodology is to apply a clustering algorithm to the data from all but one experimental condition. The remaining condition is used to assess the predictive power of the resulting clusters-meaningful clusters should exhibit less variation in the remaining condition than clusters formed by chance. RESULTS We successfully applied our methodology to compare six clustering algorithms on four gene expression data sets. We found our quantitative measures of cluster quality to be positively correlated with external standards of cluster quality.
Conference Proceedings Volume 2

— An automated method for traffic monitoring based on statistical models of sensor behavior in combination with a Markov model of monitoring points is described. A model of normal traffic flow is automatically constructed. The model's structure and parameters are optimized using a mini-batch model-merging and parameter-updating algorithm. Incoming velocity vectors are conveyed to the model and the most probable path through the tunnel's Markov model is computed. An alarm is generated when the sensor values have a low probability under the model. The performance, strengths and weaknesses of the automated traffic flow analysis system are discussed.
Automatic anatomical calibration for IMU-based elbow angle measurement in disturbed magnetic fields

Abstract Inertial Measurement Units (IMUs) are increasingly used for human motion analysis. However, two major challenges remain: First, one must know precisely in which orientation the sensor is attached to the respective body segment. This is commonly achieved by accurate manual placement of the sensors or by letting the subject perform tedious calibration movements. Second, standard methods for inertial motion analysis rely on a homogeneous magnetic field, which is rarely found in indoor environments. To address both challenges, we introduce an automatic calibration method for joints with two degrees of freedom such as the combined radioulnar and elbow joint. While the user performs arbitrary movements, the method automatically identifies the sensor-to-segment orientations by exploiting the kinematic constraints of the joint. Simultaneously, the method identifies and compensates the influence of magnetic disturbances on the sensor orientation quaternions and the joint angles. In experimental trials, we obtain angles that agree well with reference values from optical motion capture. We conclude that the proposed method overcomes mounting and calibration restrictions and improves measurement accuracy in indoor environments. It therefore improves the practical usability of IMUs for many medical applications.
Shallow Semantic Parsing Based on FrameNet, VerbNet and PropBank

This article describes a semantic parser based on FrameNet semantic roles that uses a broad knowledge base created by interconnecting three major resources: FrameNet, VerbNet and PropBank. We link the above resources through a mapping between Intersective Levin classes, which are part of PropBank's annotation, and the FrameNet frames. By using Levin classes, we successfully detect FrameNet semantic roles without relying on the frame information. At the same time, the combined usage of the above resources increases the verb coverage and confers more robustness to our parser. The experiments with Support Vector Machines on automatic Levin class detection suggest that (a) tree kernels are well suited for the task and (b) Intersective Levin classes can be used to improve the accuracy of semantic parsing based on FrameNet roles.
The lexicon graph model: a generic model for multimodal lexicon development

Das Lexicon Graph Model stellt ein Modell fur Lexika dar, die korpusbasiert sein konnen und multimodale Informationen enthalten. Hierbei wird die Perspektive der Lexikontheorie eingenommen, wobei die zugrundeliegenden Datenstrukturen sowohl vom Lexikon als auch von Annotationen betrachtet werden. Letztere fallen dadurch in das Blickfeld, weil sie als Grundlage fur die Erstellung von Lexika gesehen werden. Der Begriff des Lexikons bezieht sich hier sowohl auf den Bereich des Worterbuchs als auch der in elektronischen Applikationen integrierten Lexikondatenbanken. Die existierenden Formalismen und Ansatze der Lexikonentwicklung zeigen verschiedene Probleme im Zusammenhang mit Lexika auf, etwa die Zusammenfassung von existierenden Lexika zu einem, die Disambiguierung von Mehrdeutigkeiten im Lexikon auf verschiedenen lexikalischen Ebenen, die Reprasentation von anderen Modalitaten im Lexikon, die Selektion des lexikalischen Schlusselbegriffs fur Lexikonartikel, etc. Der vorliegende Ansatz geht davon aus, dass sich Lexika zwar in ihrem Inhalt, nicht aber in einer grundlegenden Struktur unterscheiden, so dass verschiedenartige Lexika im Rahmen eines Unifikationsprozesses dublettenfrei miteinander verbunden werden konnen. Hieraus resultieren deklarative Lexika. Fur Lexika konnen diese Graphen mit dem Lexikongraph-Modell wie hier dargestellt modelliert werden. Dabei sind Lexikongraphen analog den von Bird und Libermann beschriebenen Annotationsgraphen gesehen und konnen daher auch ahnlich verarbeitet werden. Die Untersuchung des Lexikonformalismus beruht auf vier Schritten. Zunachst werden existierende Lexika analysiert und beschrieben. Danach wird mit dem Lexikongraph-Modell eine generische Darstellung von Lexika vorgestellt, die auch implementiert und getestet wird. Basierend auf diesem Formalismus wird die Beziehung zu Annotationsgraphen hergestellt, wobei auch beschrieben wird, welche Masstabe an angemessene Annotationen fur die Verwendung zur Lexikonentwicklung angelegt werden mussen.
Elaeagnus angustifolia Plant Extract Inhibits Angiogenesis and Downgrades Cell Invasion of Human Oral Cancer Cells via Erk1/Erk2 Inactivation

ABSTRACT Oral cancer is a common malignancy in both men and women worldwide; this cancer is characterized by a marked propensity for invasion and spreading to local lymph nodes. On the other hand, Elaeagnus angustifolia (EA) is a medicinal plant that has been used for centuries for treating many human diseases in the Middle East. However, the effect of EA plant extract on human cancers especially oral has not been investigated yet. Thus, first we examined the outcome of EA flower extract on angiogenesis, using the chorioallantoic membrane (CAM) of the chicken embryo; we found that EA extract reduces blood vessel development of the CAM. Then, we investigated the effect of EA flower extract on selected parameters in FaDu and SCC25 oral cancer cell lines. Our results show that EA extract inhibits cell proliferation and colony formation, in addition to the initiation of S cell cycle arrest and reduction of G1/G2 phase. In parallel, EA extract provokes differentiation to an epithelial phenotype “mesenchymal-to-epithelial transition: MET” which is the opposite of “epithelial-to-mesenchymal transition, EMT”: an important event in cell invasion and metastasis. Thus, EA plant extract causes a dramatic decrease in cell invasion and motility abilities of FaDu and SCC25 cancer cells in comparison with their controls. These changes are accompanied by an upregulation of E-cadherin expression. The molecular pathway analysis of the EA flower extract reveals that it can inhibit the phosphorylation of Erk1/Erk2, which could be behind the inhibition of angiogenesis, the initiation of MET event, and the overexpression of E-cadherin. Our findings indicate that EA plant extract can reduce human oral cancer progression by the inhibition of angiogenesis and cell invasion via Erk1/Erk2 signaling pathways.
Mental health status among rural women of reproductive age: findings from the Central Pennsylvania Women's Health Study.

OBJECTIVES We sought to examine variables associated with mental health among rural women of reproductive age, with particular attention given to rural area type and farm residence. METHODS We analyzed data from the Central Pennsylvania Women's Health Study, which included a random-digit-dialed survey of women aged 18 to 45 years. Hierarchical multiple linear and logistic regression models were estimated to predict 3 mental health outcomes: score on a mental health measure, depressive symptoms, and diagnosed depression or anxiety. RESULTS Mental health outcomes were associated with different factors. Farm residence was associated with higher mental health score, and the most isolated rural residence was associated with less diagnosed depression or anxiety. Elevated psychosocial stress was consistently significant across all models. A key stress modifier, self-esteem, was also consistently significant across models. Other variables associated with 2 of the outcomes were intimate partner violence exposure and affectionate social support. CONCLUSIONS Farm residence may be protective of general mental health for women of reproductive age, and residence in isolated rural areas may decrease access to mental health screening and treatment, resulting in fewer diagnoses of depression or anxiety.
Monte Carlo simulations of 250 keV photons effects on a 3D realistic mitochondria phantom and evaluation of radiation enhancement using gold nanoparticles

In the field of radiobiology, damage to nuclear DNA is extensively studied since it is considered as a sensitive target inside cells. Mitochondria are starting to get some attention as sensitive targets as well since they control many functions important to the cell’s survival. They are double membraned organelles mainly in charge of energy production as well as reactive oxygen species regulation, cell signaling and apoptosis control. Some experiments have shown that after exposure to ionizing radiation the mitochondrial contents are altered and their functions are affected. That is why we are interested in studying the effects of ionizing radiation on mitochondria. At the microscopic scale, Monte Carlo simulations are helpful in reproducing the tracks of ionizing particles for a close study. Therefore, we produced 3D phantoms of mitochondria starting from microscopic images of fibroblast cells. These phantoms are easily uploaded into Geant4 as tessellated and tetrahedral meshes filled with water representing the realistic geometry of these organelles. Microdosimetric analysis is performed to deposited energy by 250keV photons inside these phantoms. The Geant4-DNA electromagnetic processes are used to simulate the tracking of the produced secondary electrons. Since clustered damages are harder to repair by cells, a clustering algorithm is used to study the spatial clustering of potential radiation damages. In radiotherapy, it is a challenge to deliver an efficient dose to the tumor sites without affecting healthy surrounding tissues. The use of gold nanoparticles as radio-sensitizers seems to be promising. Their high photon absorption coefficient compared to tissues deposit a larger dose when they are preferentially absorbed in tumors. Since gold has a high atomic number, Auger electrons are produced abundantly. These electrons have lower range than photoelectrons enabling them to deposit most of their energy near the nanoparticle and thus increasing the local dose. We studied the radio-sensitizing effect of gold nanoparticles on the mitochondria phantom. The effectiveness of this method is dependent on the number, size and spatial distribution of gold nanoparticles. After exposure to ionizing radiation, reactive oxygen species are produced in the biological material that contains abundant amount of water. In this study, we simulate the chemical species produced inside the mitochondria phantom and their clustering is estimated. We take advantage of the Geant4-DNA chemistry processes libraries that is recently included in the Geant4.10. 1 release to simulate the spatial distribution of the chemicals and their evolution with time.
Application dependent FPGA testing method using compressed deterministic test vectors

Tests that exercise complete FPGA resources are often more time and memory consuming than application dependent tests due to the high number of reconfigurations required for complete test. Presented application dependent test does not require reconfiguration of the tested hardware, thus it preserves conditions that led to the erroneous behavior of the FPGA device. The test method saves time and memory requirements of the test by storing compressed test patterns into the internal structure of the FPGA. The patterns are obtained with the help of the improved COMPAS algorithm – compression system based on test pattern overlapping. The COMPAS requires unused scan chains for the test pattern decompression. This is well suited for nowadays FPGAs which contain high number of LUT based shift registers. The neighborhood of the tested circuit is dynamically reconfigured into TPG and ORA. The TPG contains compressed test patterns which allow fast test pattern decompression. The paper demonstrates efficiency of this approach on experimental results.
A Conceptual History of the Emergence of Bounded Rationality

Whereas multiple interpretations of the concept of bounded rationality are currently enthusiastically employed by a wide range of academics, their colleagues of one hundred years ago did not have this concept available, but made use of related notions. This paper traces the history of the emergence of ‘bounded rationality’ from the first appearance of ‘limited intelligence’ in 1840 and ‘finite intelligence’ in 1880 through related concepts such as ‘incomplete’, ‘limited’, ‘administrative’, and ‘approximate’ rationality during the first half of the twentieth century to its inception in 1957 at the hands of Herbert Simon. In the process, it locates the semantic field from which the notion of bounded rationality emerged and attends to the co-emergence of terms such as ‘limited rationality’. This allows us to analyse the process of metaphorical crystallisation in which ‘bounded rationality’ assumed the dominant position within its semantic field.
Two energy-efficient and timesaving improvement mechanisms for network reprogramming in wireless sensor network

Network Reprogramming is very necessary to wireless sensor networks. We give two mechanisms, sender selection mechanism and permanent mechanism, making Network Reprogramming timesaving and energy-efficient. Network Reprogramming usually includes three processes which are image pretreatment, image distribution and image reloading. To make the image distribution more efficient, we give a sender selection algorithm based on Influence, Distance and residual Energy. Simulation reveals that after adopting this algorithm, the classic code distribution protocol Deluge has almost the same completion time as before, but produces less messages and saves more energy. On the other hand, completion time and energy cost has direct ratio with the image size to transmit. In order to reduce the image size, we keep some universal functions such as the image distribution fixed in the sensor nodes and design the permanent mechanism sending only application module and relative basic function modules. Simulation shows that this mechanism remarkably reduces the energy cost and completion time.
Multiuser decoding for multibeam systems

An iterative multiuser decoding algorithm for co-channel BPSK/QPSK users in a multibeam system is presented. The approach can be applied to the return link of multibeam satellites and to terrestrial systems with sectored base-station antennas. It allows the reuse of the same spectrum in each beam. The algorithm is based on the extension of turbo-decoding techniques to the iterative decoding of parallel users. Simulation results show one can asymptotically achieve single user performance in a high multiuser interference environment; often this includes some diversity gain. The complexity of the algorithm is approximately O(2/sup K/+2/sup /spl kappa//) operations per bit per iteration where K is the number of co-channel users and /spl kappa/ is the constraint length of the forward error correction code.
Hand Shape Recognition Using Fingertips

Recently the importance of studies to recognize the shape of human hands in realtime is being more stressed to implement the user-friendly user interface. However, human hands have a large degree of freedom and thus it is very difficult to accurately recognize the hand shape, especially in a complicated background of the color same as the skin color. In this study, we detect the fingertip, without any special sensors, by using the hand shape based on the skin color information detected by a camera. This paper describes an algorithm to show directions using the detected fingertip. This algorithm is used to detect the fingertip through template matching and then detect forward, backward, left and right directions based on the detected fingertip and wrist center information. We applied the algorithm to navigation in 3D virtual-reality space, and achieved a very good result in an experiment on the change of directions to forward, backward, left and right. It is expected that this algorithm can provide more natural interaction between man and computer by allowing the user to instruct change of directions intuitively without the aid of a mouse, a keyboard or a joystick.
Mechanizing the Metatheory of LF

LF is a dependent type theory in which many other formal systems can be conveniently embedded. However, correct use of LF relies on nontrivial metatheoretic developments such as proofs of correctness of decision procedures for LF's judgments. Although detailed informal proofs of these properties have been published, they have not been formally verified in a theorem prover. We have formalized these properties within Isabelle/HOL using the nominal datatype package, closely following a recent article by Harper and Pfenning. In the process, we identified and resolved a gap in one of the proofs and a small number of minor lacunae in others. Besides its intrinsic interest, our formalization provides a foundation for studying the adequacy of LF encodings, the correctness of Twelf-style metatheoretic reasoning, and the metatheory of extensions to LF.