Miracle-dz/UniFAR-FTUs huggingface dataset:
MAC/FAC Retrieval of Semantic Workflows

This paper presents a novel two-step retrieval method for semantic workflow cases, inspired by the MAC/FAC (“many are called, but few are chosen”) model proposed by Gentner and Forbus. MAC/FAC retrieval is motivated by the computational complexity of graph matching, which is usually involved in the similarity-based retrieval of workflows. An additional computationally efficient retrieval step (MAC stage) is introduced prior to the graph-based retrieval (FAC stage) to perform a pre-selection of potentially relevant cases. The MAC stage is based on a feature representation of the workflows automatically derived from the original graph-based representation. In the paper, we briefly introduce previous work on the semantic workflow retrieval and then we describe the pre-selection step in more detail. A comprehensive evaluation with case bases from the cooking domain is reported with demonstrates that the retrieval time can be significantly reduced without significant negative impact on the retrieval quality.
Cucurbitacin I Inhibits Cell Motility by Indirectly Interfering with Actin Dynamics

Background Cucurbitacins are plant natural products that inhibit activation of the Janus kinase 2 (JAK2)/signal transducer and activator of transcription 3 (STAT3) pathway by an unknown mechanism. They are also known to cause changes in the organization of the actin cytoskeleton. Methodology/Principal Findings We show that cucurbitacin I potently inhibits the migration of Madin-Darby canine kidney (MDCK) cell sheets during wound closure, as well as the random motility of B16-F1 mouse melanoma cells, but has no effect on movement of Dictyostelium discoideum amoebae. Upon treatment of MDCK or B16-F1 cells with cucurbitacin I, there is a very rapid cessation of motility and gradual accumulation of filamentous actin aggregates. The cellular effect of the compound is similar to that observed when cells are treated with the actin filament-stabilizing agent jasplakinolide. However, we found that, unlike jasplakinolide or phallacidin, cucurbitacin I does not directly stabilize actin filaments. In in vitro actin depolymerization experiments, cucurbitacin I had no effect on the rate of actin filament disassembly at the nanomolar concentrations that inhibit cell migration. At elevated concentrations, the depolymerization rate was also unaffected, although there was a delay in the initiation of depolymerization. Therefore, cucurbitacin I targets some factor involved in cellular actin dynamics other than actin itself. Two candidate proteins that play roles in actin depolymerization are the actin-severing proteins cofilin and gelsolin. Cucurbitacin I possesses electrophilic reactivity that may lead to chemical modification of its target protein, as suggested by structure-activity relationship data. However, mass spectrometry revealed no evidence for modification of purified cofilin or gelsolin by cucurbitacin I. Conclusions/Significance Cucurbitacin I results in accumulation of actin filaments in cells by a unique indirect mechanism. Furthermore, the proximal target of cucurbitacin I relevant to cell migration is unlikely to be the same one involved in activation of the JAK2/STAT3 pathway.
An improved method for rearing head lice.

Maintenance of a large colony of body lice, Pediculus humanus humanus Linn. , has evolved from feeding them, usually twice daily, on man (Moore & Hirschfelder, 1917, Res. Publ. Univ. Minn. 8 : 1–86; Culpepper, 1948, Amer. J. Trop. Med. 28 : 499–504) to feeding them once per day on laboratory rabbits (Culpepper, 1948, loc. cit.; Smith & Eddy, 1954, Bull. Wld Hlth Organ. 10 : 127–37). Large numbers of head lice were produced by feeding them once per day on rabbits (Eddy, 1973, pers. commun.). This was accomplished by initially feeding them 5 times daily on man and then slowly reducing the feedings to once per day. They were then reared on the animals. We noted, however, that when nymphal and adult stages of head lice were fed 4 to 5 times daily, molting was delayed and copulation retarded. We therefore found that head lice maintain normal rates of development and egg production when allowed access to a constant blood supply. This has also been shown when allowing them to feed on man for from 6 to 7 hr nightly with moderate success (Bacot, 1917, Parasitology 9 : 228–58) as compared to allowing them 24-hr feeding on man using a wristlet method (Nuttall, 1917, Parasitology 10 : 80–185). The greater degree of success of this latter method is reflected by improved rates of development and better egg production.
Fluid flow velocity measurement using dual-ultrasonic transducer by means of simultaneously transit time method

An ultrasonic flowmeter based on transit time method (USM-TT) is often used to obtain high accuracy measurements of gas flow velocity. The working principle of an USM-TT is based on the measurements of two times of flight (TOF) of ultrasonic waves that propagate toward opposite direction. In particular, both TOFs are measured sequentially under the assumption that there exists no sudden change of flow velocity during the sampling period. When such an assumption is not fulfilled, the obtained velocity can not be assumed to be the true data. To overcome the above problem, we propose an alternative method, namely simultaneously transit time (STT), which is able to obtain both of TOFs for the same flow velocity by employing dual ultrasonic transducers that transmit and receive ultrasonic wave simultaneously. For experimental validation, two ultrasonic modules which have a transmitter and a receiver ultrasonic inside are utilized as ultrasonic transducer. In addition, microcontroller is employed for data acquisition and activating the ultrasonic devices. Based on the obtained experimental data, we found that the STT method effectively reduces the sampling period required in the conventional method up to almost 50%. Thus, because TOFs are obtained for the same flow velocity, the probability of the sudden change of flow velocity during the sampling period can be diminished.
Culture Expansion in Low-Glucose Conditions Preserves Chondrocyte Differentiation and Enhances Their Subsequent Capacity to Form Cartilage Tissue in Three-Dimensional Culture

Abstract Culture conditions that preserve a stable chondrocyte phenotype are desirable in cell-based cartilage repair to maximize efficacy and clinical outcome. This study investigates whether low-glucose conditions will preserve the chondrocyte phenotype during culture expansion. Articular chondrocytes were culture-expanded in media supplemented with either low (1 mM) or high (10 mM) glucose. The metabolic phenotype, reactive oxygen species generation, and mRNA expression of markers of differentiation or catabolism were assessed by reverse-transcription quantitative polymerase chain reaction after four population doublings (PDs) and subsequent tissue formation capacity determined using pellet cultures. Continuous monolayer culture was used to determine the population doubling limit. After expansion in monolayer for four PDs, chondrocytes expanded in low-glucose conditions exhibited higher expression of the differentiation markers SOX9 and COL2A1 and reduced expression of the catabolic metalloproteinase matrix metallopeptidase 13. When chondrocytes expanded in low glucose were cultured in micropellets, they consistently generated more cartilaginous extracellular matrix than those expanded in high glucose, as evaluated by wet weight, sulfated glycosaminoglycan content, and hydroxyproline assay for collagen content. The same pattern was observed whether high or low glucose was used during the pellet culture. During expansion, chondrocytes in high-glucose generated 50% more reactive oxygen species than low-glucose conditions, despite a lower dependence on oxidative phosphorylation for energy. Furthermore low-glucose cells exhibited >30% increased population doubling limit. These data suggests that low-glucose expansion conditions better preserve the expression of differentiation markers by chondrocytes and enhance their subsequent capacity to form cartilage in vitro. Therefore, low glucose levels should be considered for the expansion of chondrocytes intended for tissue engineering applications.
Biological pathway kinetic rate constants are scale-invariant

MOTIVATION Scale-free networks have had a profound impact in Biology. Network theory is now used routinely to visualize, navigate through, and help understand gene networks, protein-protein interactions, regulatory networks and metabolic pathways. Here we analyse the numerical rather than topological properties of biological networks and focus on the study of kinetic rate constants within pathways. RESULTS We have analysed all current entries in the BioModels database and show that the kinetic rate parameters follow Benford's; law closely. The cumulative histogram plot reveals an underlying power-law. This implies that these data are scale-invariant, thus placing biological network topology and their chemistry on an equivalent 'scale-free' power-law foundation.
KeyNet : a Secure , Byzantine Fault Tolerant Distributed Public Key Directory

KeyNet is a distributed directory for secure public key storage, modification, and lookup. Local consistency, and therefore trust, is maintained at scale through the use of byzantine fault tolerance. We discuss an emerging federated byzantine consensus protocol, Stellar, that can enable open participation without sacrificing safety, and present KeyNet’s design in that context. Our initial implementation includes a PGP key store that reaches consensus through the Practical Byzantine Fault Tolerance protocol and can successfully be used to send encrypted messages over a modern email client.
Mathematical improvements to maximum likelihood parallel factor analysis: experimental studies

In this paper, the application of a number of simplified algorithms for maximum likelihood parallel factor analysis (MLPARAFAC) to experimental data is explored. The algorithms, described in a companion paper, allow the incorporation of a variety of correlated error structures into the three‐way analysis. In this work, three experimental data sets involving fluorescence excitation‐emission spectra of synthetic three‐component mixtures of aromatic compounds are used to test these algorithms. Different experimental designs were employed for the acquisition of these data sets, resulting in measurement errors that were correlated in either two or three modes. A number of data‐analysis methods were applied to characterize the error structures of these data sets. In all cases, the introduction of statistically meaningful information translated to estimates of better quality than the conventional PARAFAC estimates of concentrations and spectra. The use of the algorithms that employ the error structure suggested by the analysis of the error covariance matrix yielded the best results for each data set. Copyright © 2005 John Wiley & Sons, Ltd.
Emotion Extractor: AI based methodology to implement prosody features in Speech Synthesis

This paper presents the methodology to extract emotion from the text at real time and add the expression to the documents contents during speech synthesis. To understand the existence of emotions self assessment test was carried out on set of documents and preliminary rules were formulated for three basic emotions: Pleasure, Arousal and Dominance. These rules are used in an automated procedure that assigns emotional state values to document contents. These values are then used by speech synthesizer to add emotions to speech. The system is language independent and content free.
One-Class Classification of Mammograms Using Trace Transform Functionals

Mammography is one of the first diagnostic tests to prescreen breast cancer. Early detection of breast cancer has been known to improve recovery rates to a great extent. In most medical centers, experienced radiologists are given the responsibility of analyzing mammograms. But, there is always a possibility of human error. Errors can frequently occur as a result of fatigue of the observer, resulting in interobserver and intraobserver variations. The sensitivity of mammographic screening also varies with image quality. To offset different kinds of variability and to standardize diagnostic procedures, efforts are being made to develop automated techniques for diagnosis and grading of breast cancer images. This paper presents a one-class classification pipeline for the classification of breast cancer images into benign and malignant classes. Because of the sparse distribution of abnormal mammograms, the two-class classification problem is reduced to a one-class outlier identification problem. Trace transform, which is a generalization of the Radon transform, has been used to extract the features. Several new functionals specific to mammographic image analysis have been developed and implemented to yield clinically significant features. Classifiers such as the linear discriminant classifier, quadratic discriminant classifier, nearest mean classifier, support vector machine, and the Gaussian mixture model (GMM) were used. For automated diagnosis, the classification pipeline was tested on a set of 313 mammograms provided by the Singapore Anti-Tuberculosis Association CommHealth. A maximum accuracy rate of 92.48% has been obtained using GMMs.
Space-scale diagrams: understanding multiscale interfaces

Big information worlds cause big problems for interfaces. There is too much to see. They are hard to navigate. An armada of techniques has been proposed to present the many scales of information needed. Space-scale diagrams provide an analytic framework for much of this work. By representing both a spatial world and its different magnifications explicitly, the diagrams allow the direct visualization and analysis of important scale related issues for interfaces.
diets containing soy protein isolate Differentially abundant mRNAs in rat liver in response to

24 times a year (twice monthly) by the American Physiological Society, 9650 Rockville Pike, Bethesda MD systems with techniques linking genes and pathways to physiology, from prokaryotes to eukaryotes. It is published publishes results of a wide variety of studies from human and from informative model Physiological Genomics
False data injection attacks against state estimation in electric power grids

A power grid is a complex system connecting electric power generators to consumers through power transmission and distribution networks across a large geographical area. System monitoring is necessary to ensure the reliable operation of power grids, and state estimation is used in system monitoring to best estimate the power grid state through analysis of meter measurements and power system models. Various techniques have been developed to detect and identify bad measurements, including the interacting bad measurements introduced by arbitrary, non-random causes. At first glance, it seems that these techniques can also defeat malicious measurements injected by attackers. In this paper, we present a new class of attacks, called false data injection attacks, against state estimation in electric power grids. We show that an attacker can exploit the configuration of a power system to launch such attacks to successfully introduce arbitrary errors into certain state variables while bypassing existing techniques for bad measurement detection. Moreover, we look at two realistic attack scenarios, in which the attacker is either constrained to some specific meters (due to the physical protection of the meters), or limited in the resources required to compromise meters. We show that the attacker can systematically and efficiently construct attack vectors in both scenarios, which can not only change the results of state estimation, but also modify the results in arbitrary ways. We demonstrate the success of these attacks through simulation using IEEE test systems. Our results indicate that security protection of the electric power grid must be revisited when there are potentially malicious attacks.
Kleene algebra modulo theories: a framework for concrete KATs

Kleene algebras with tests (KATs) offer sound, complete, and decidable equational reasoning about regularly structured programs. Interest in KATs has increased greatly since NetKAT demonstrated how well extensions of KATs with domain-specific primitives and extra axioms apply to computer networks. Unfortunately, extending a KAT to a new domain by adding custom primitives, proving its equational theory sound and complete, and coming up with an efficient implementation is still an expert’s task. Abstruse metatheory is holding back KAT’s potential. We offer a fast path to a “minimum viable model” of a KAT, formally or in code through our framework, Kleene algebra modulo theories (KMT). Given primitives and a notion of state, we can automatically derive a corresponding KAT’s semantics, prove its equational theory sound and complete with respect to a tracing semantics (programs are denoted as traces of states), and derive a normalization-based decision procedure for equivalence checking. Our framework is based on pushback, a generalization of weakest preconditions that specifies how predicates and actions interact. We offer several case studies, showing tracing variants of theories from the literature (bitvectors, NetKAT) along with novel compositional theories (products, temporal logic, and sets). We derive new results over unbounded state, reasoning about monotonically increasing, unbounded natural numbers. Our OCaml implementation closely matches the theory: users define and compose KATs with the module system.
Expression of the hilA Salmonella typhimurium gene in a poultry Salm. enteritidis isolate in response to lactate and nutrients

Pathogens express virulence genes in response to the combination of environmental conditions present in the host environment. The crop is the first gastrointestinal environment encountered in birds. However, feed withdrawal alters the crop environment resulting in an increased pH, and decreased concentrations of lactate, glucose and amino acids compared with unmoulted birds. Salmonella enteritidis infections increase significantly in hens that have been force moulted by feed withdrawal. The present study examined the effects of pH, carbohydrate sources, amino acids and lactate on expression of Salm. enteritidis virulence by measuring expression of hilA. The hilA gene encodes a transcriptional activator that regulates expression of Salmonella virulence genes in response to environmental stimuli. HilA expression was determined using a poultry isolate of Salm. enteritidis carrying a hilA‐lacZY transcriptional fusion from Salm. typhimurium. The media used were Luria Bertani (LB) broth and LB broth diluted 1 : 5 (DLB). The expression of hilA was 2·9‐fold higher in DLB broth compared with LB broth which suggested that there is a nutritional component to the regulation of hilA. Addition of 0·2% glucose, fructose or mannose to LB and DLB reduced hilA expression 1·5 to twofold. Addition of 0·2% Casaminoacids, arabinose, fucose, or lactose had little effect on hilA expression. Lactate (25 and 50 mmmol l−1) reduced hilA expression at pH 6, 5 and 4, with the lowest expression occurring at pH 4. Based on these results it appears that the composition of the crop lumen could potentially influence Salm. enteritidis virulence expression.
Streptococcus suis: an important zoonotic pathogen for human prevention aspects -

Streptococcus suis is a major porcine pathogen, causing economical health worldwide problems in the global swine industry. It is also emerging as a zoonotic agent capable of causing severe invasive disease in humans exposed to pigs or pork products. The most important clinical sign in swine and human is meningitis, but other pathological conditions have also been described. Serotype 2 is the most commonly associated with diseases in pigs and humans, and also the most frequently reported serotype isolated from diseased animals worldwide. The majority of human infection occurs in pork handlers, particularly in slaughterhouse workers and by minor wounds or skin abrasions contaminated by raw pork or viscera of pigs. Veterinarians should also be aware that a low but real risk may be present when manipulating S. suis-diseased animals that are probably shedding high numbers of this pathogen. Up today, in Greece there is no published epidemiological data for S. suis serotypes in swine herds and the zoonotic risk of S. suis infection in human with daily contact with pigs and pork meat. However, in our experience clinical forms of S. suis infection are common in most greek swine farms. The aim of this review study is to perform recent information about S. suis infection in swine
Neural Network Control of a Flexible Robotic Manipulator Using the Lumped Spring-Mass Model

Adaptive neural networks (NNs) are employed for control design to suppress vibrations of a flexible robotic manipulator. To improve the accuracy in describing the elastic deflection of the flexible manipulator, the system is modeled via the lumped spring-mass approach. Full-state feedback control as well as output feedback control are proposed separately. Aiming at achieving the control objective, uniform ultimate boundedness of the closed-loop system is ensured. Numerical simulations for the lumped model of the flexible robotic system are carried out to verify the performance of the NN control. Finally, the experiments are given to further validate the feasibility of the proposed NN controllers on the Quanser platform.
Dopamine systems adaptation during acquisition and consolidation of a skill

The striatum plays a key role in motor learning. Striatal function depends strongly on dopaminergic neurotransmission, but little is known about neuroadaptions of the dopamine system during striatal learning. Using an established task that allows differentiation between acquisition and consolidation of motor learning, we here investigate D1 and D2-like receptor binding and transcriptional levels after initial and long-term training of mice. We found profound reduction in D1 binding within the dorsomedial striatum (DMS) after the first training session on the accelerated rotarod and a progressive reduction in D2-like binding within the dorsolateral striatum (DLS) after extended training. Given that similar phase- and region-specific striatal neuroadaptations have been found also during learning of complex procedural tasks including habit formation and automatic responding, the here observed neurochemical alterations are important for our understanding of neuropsychiatric disorders that show a dysbalance in the function of striatal circuits, such as in addictive behaviors.