Miracle-dz/UniFAR-FTUs huggingface dataset:
Objective quantitative analysis of eosinophils and bronchial epithelial cells in induced sputum by laser scanning cytometry

BACKGROUND Sputum induction is an important non-invasive technique for measuring airway inflammation in asthma. Cell numbers are often too low for flow cytometric analysis. Laser scanning cytometry (LSC) is a novel technique that allows objective multicolour fluorescence analysis of cells on a microscope slide. METHODS LSC was used to determine sputum eosinophil and bronchial epithelial cell counts. We first confirmed that we could measure eosinophil counts accurately in peripheral blood using α-major basic protein (MBP) immunofluorescent staining. Sputum induction was performed according to standard protocols. Sputum samples from eight normal controls and 12 asthmatic patients were analysed by LSC and manual counting by two independent observers. Octospot cytospins were fixed and stained with mouse-α-human-MBP monoclonal antibody or mouse-α-human-cytokeratin antibody and goat-α-mouse Oregon Green conjugated second antibody. RESULTS Sputum induction provided a mean (SE) of 0.99 (0.2) × 106 cells per donor. More than 3000 cells on three cytospins per slide were analysed per cell type. The intraclass correlation coefficient (R) and standard deviation (SD) of differences in eosinophils determined by manual counting and LSC were 0.9 and 2.1, respectively, and for bronchial epithelial cell counts they were 0.7 and 2.0. Selective detection of labelled cells was confirmed visually after relocation. CONCLUSION Eosinophils and bronchial epithelial cells can be accurately and reproducibly counted in an objective manner. LSC is therefore a potentially powerful new method for immunophenotyping leucocytes and epithelial cells objectively in induced sputum in patients with asthma.
GATE - a TIPSTER-based General Architecture for Text Engineering

Building on the work of the TIPSTER architecture group, the University of Sheeeld Natural Language Processing group have developed GATE, a General Architecture for Text Engineering. GATE implements the TIPSTER document manager, and adds a rich set of graphical tools for the management of modules and the data they produce and consume, and the visualisation of data. This paper classiies and reviews current approaches to software infrastructure for research, development and delivery of NLP systems. The task is motivated by a discussion of current trends in the eld of NLP and Language Engineering. The rest of the paper describes GATE and concludes with a status report on the system.
Qualtras : a Tool for Qualitative Trend Representations

This paper presents a tool developed to obtain qualitative trend representations from signals, Qualtras. The aim of such a type of description is to offer an understandable representation of process behavior based on the concept of qualitative episode. The tool is intended to be used as a numeric to qualitative interface for supervisory applications. The applicability of this tool is demonstrated in a monitoring application of a steam generator.
Upper Extremity Proprioception in Healthy Aging and Stroke Populations, and the Effects of Therapist- and Robot-Based Rehabilitation Therapies on Proprioceptive Function

The world’s population is aging, with the number of people ages 65 or older expected to surpass 1.5 billion people, or 16% of the global total. As people age, there are notable declines in proprioception due to changes in the central and peripheral nervous systems. Moreover, the risk of stroke increases with age, with approximately two-thirds of stroke-related hospitalizations occurring in people over the age of 65. In this literature review, we first summarize behavioral studies investigating proprioceptive deficits in normally aging older adults and stroke patients, and discuss the differences in proprioceptive function between these populations. We then provide a state of the art review the literature regarding therapist- and robot-based rehabilitation of the upper extremity proprioceptive dysfunction in stroke populations and discuss avenues of future research.
Ferredoxin and flavodoxin as biochemical indicators of iron limitation during open‐ocean iron enrichment

Substitution of the noniron protein flavodoxin for the iron‐sulfur protein ferredoxin is an iron‐stress response employed by a variety of unicellular organisms, including many phytoplankton. The relative abundance of these two proteins has been shown to vary with the severity of growth limitation by iron in marine diatoms. During the IronEx II mesoscale iron‐enrichment experiment, large volume (100–600 liters) phytoplankton samples were collected for analysis of community ferredoxin and flavodoxin abundance using a high‐pressure liquid chromatography (HPLC) technique. In addition, three pennate diatom species isolated from the fertilization‐induced phytoplankton bloom were used for follow‐up laboratory experiments, which examined their iron physiology.
A COMPARATIVE STUDY ON CLASSIFICATION OF IMAGE SEGMENTATION METHODS WITH A FOCUS ON GRAPH BASED TECHNIQUES

Image segmentation is the most precarious functions in image processing and analysis. Basically segmentation consequences influence all the subsequent processes of image analysis such as object description and illustration, characteristic dimension, and even the subsequent higher level tasks such as classification of object. Hence, image segmentation is the most important and critical process for assisting the, depiction, delineation and visualization of regions of interest in any image. Physical segmentation of an image is not only a tiresome and time consuming process, but also not exceptionally accurate particularly with the increasing imaging modalities and uncontrollable quantity of images that need to be observed. Therefore it becomes essential to examination current methodologies of image segmentation using computerized algorithms that are precise and entail as little user interaction as probable in particular for medical images. In the image segmentation process, the anatomical organization or the region of interest needs to be defined and extracted out so that it can be viewed independently. In this comparative paper we venture the significant place of segmentation of images in pulling out information for decision making. Afterwards we present the most relative and general methods which we have classified into three categories, first category represents pixel based, second edge based and third represents region based methods in particular graph based methods, highlighting the weaknesses and strengths according to appropriateness for image segmentation applications.
The symbiosis regulator RscS controls the syp gene locus, biofilm formation and symbiotic aggregation by Vibrio fischeri

Successful colonization of a eukaryotic host by a microbe involves complex microbe–microbe and microbe–host interactions. Previously, we identified in Vibrio fischeri a putative sensor kinase, RscS, required for initiating symbiotic colonization of its squid host Euprymna scolopes. Here, we analysed the role of rscS by isolating an allele, rscS1, with increased activity. Multicopy rscS1 activated transcription of genes within the recently identified symbiosis polysaccharide (syp) cluster. Wild‐type cells carrying rscS1 induced aggregation phenotypes in culture, including the formation of pellicles and wrinkled colonies, in a syp‐dependent manner. Colonies formed by rscS1‐expressing cells produced a matrix not found in control colonies and largely lost in an rscS1‐expressing sypN mutant. Finally, multicopy rscS1 provided a colonization advantage over control cells and substantially enhanced the ability of wild‐type cells to aggregate on the surface of the symbiotic organ of E. scolopes; this latter phenotype similarly depended upon an intact syp locus. These results suggest that transcription induced by RscS‐mediated signal transduction plays a key role in colonization at the aggregation stage by modifying the cell surface and increasing the ability of the cells to adhere to one another and/or to squid‐secreted mucus.
Realistic real-timewater effects in 2D images

This paper proposes a method of adding a realistic, real-time, water animation effect to two-dimensional images. This is in contrast to most of the other research being done which involves the realistic, real-time simulation of water surfaces in a three-dimensional space. Our method is unique in that it treats the problem as an image-processing problem, rather than a geometry problem. Our animation method allows the user to interact with the animation in real-time. This real-time processing facilitates the animation process by giving the user immediate feedback.
Towards Applying Model-based Testing in Test Case Migration

After performing migration of a software system, it must be proved that the migrated system still behaves like the legacy system regarding the functionality. As a technique to validate the migrated system, software testing is being used. According to [1], testing in software migration projects is a costly endeavor. For that reason, when existing test cases are available, their reuse should be considered. Two main things motivate their reuse: costs save and knowledge reuse. They come from the fact that the functionality of the system after the migration must stay unchanged. Hence, the existing test cases are valuable source of information about the functionality of the legacy system and consequently for the migrated system as well. Reusing test cases in a software migration scenario introduces several challenges. For example, the quality of the test cases needs to be assessed, because they might have become legacy due to the evolutionary development. The existing test case set may contain duplicate, obsolete or even erroneous test cases. Another example is the changes that happen to the system (language, framework or architectural change) may influence the existing test cases [2]. Reflecting these changes to the test cases is an important prerequisite in enabling a test case set that could validate the migrated system. Dealing with such changes on the level of test cases could be difficult and therefore we assume that abstracting from test cases and extracting test models, could ease this task. Motivated by the idea of model-driven software migration, we envision a novel test case migration method that combines reverse engineering and modelbased testing. Model-based testing(MBT) is a testing technique that relies on abstract models, which are used to derive test cases for an implementation [3]. In the literature, several different scenarios have been introduced depending on the origin of the test model [3, 4]. From our perspective, the scenario where the test models are reverse engineered from existing test cases (known as ’Models from Test Cases’ in [4]) is the most interesting one. Following the model-driven software migration horseshoe1, we first extract test models out of the test cases, then we restructure the test models by reflecting the changes from the software migration, and finally, we generate test cases for the migrated system. On the one hand, it could be seen as a test case re-engineering method that enables migration and coevolution of test cases. On the other hand, from the model-based testing perspective, it could be seen as a new scenario which is an extension of the previously mentioned scenario ’Models from Test Cases’. In this paper, we first discuss the field of modelbased testing and reverse engineering and thereafter we sketch our method and discuss how it extends the existing model-based scenario. At the end, we discuss the requirements that model-based testing imposes on our method.
An Ensemble of Competitive Learning Networks with Different Representations for Temporal Data Clustering

Temporal data clustering provides useful techniques for condensing and summarizing information conveyed in temporal data, which is demanded in various fields ranging from time series analysis to sequential data understanding. In this paper, we propose a novel approach to temporal data clustering by an ensemble of competitive learning networks incorporated by different representations of temporal data. In our approach, competitive learning networks of the rival-penalized learning mechanism are employed for clustering analyses based on different temporal data representations while an optimal selection function is applied to find out a final consensus partition from multiple partition candidates yielded by applying alternative consensus functions to results of competitive learning on different representations. Thanks to its capability of the rival penalized learning rules in automatic model selection and the synergy of fusing diverse partitions on different representations, our ensemble approach yields favorite results, which has been demonstrated in time series and motion trajectory clustering tasks.
Sexual Abuse Prevalence Rates of Residents in Institutional Care Settings Compared with a Population Representative Sample

ABSTRACT Adolescents in residential institutions are considered to be a high-risk group for experiencing sexual abuse. The aim of this study was to provide a comparison of sexual abuse lifetime prevalence rates between residents in institutional settings and the general population. In total, 271 adolescents from 32 different institutions took part in the survey. Overall, 5.9% of the participants had experienced exhibitionism and 7.0% vaginal/anal penetration. Compared with the general population, significantly higher prevalence rates were evident for penetration. It has to be discussed whether population representative surveys should explicitly include these high-risk groups in order to avoid underestimating sexual abuse.
Association between Thrombomodulin Polymorphisms and Coronary Artery Disease Risk: A Meta-Analysis

Background The associations between the thrombomodulin (TM) polymorphisms and coronary artery disease (CAD) risk remain controversial. The aim of this study was to evaluate the association of TM polymorphisms with CAD susceptibility using a meta-analysis approach. Material/Methods All eligible studies were identified through a search of PubMed, EMBASE, and China National Knowledge Infrastructure (CNKI) before February 2014. The associations between the TM polymorphisms and CAD risk was assessed by odds ratios (ORs) and 95% confidence intervals (CIs). Results A total of 14 case-control studies, including 5493 cases and 8297 controls, were eventually collected. There was a significant association between TM -33G/A polymorphism and CAD risk (OR=1.61; 95% CI, 1.35–1.92; I2=15%). The TM Ala455Val polymorphism was also associated with a significantly increased CAD risk (OR=1.14; 95% CI, 1.05–1.24; I2=0%). These results remained statistically significant when the adjusted ORs were combined. Conclusions Our results suggest that TM-33G/A and Ala455Val polymorphisms are risk factors for CAD.
ILS with Multiple Variable Neighbourhood Descendent for the Vehicle Routing Problem with Multiple Trips

This paper describes a new approach to solving the vehicle route problem with Multiple Trips. The proposed algorithm (IVNDS) is based on the Iterative Local Search meta-heuristic which uses two consecutive Variable Neighbourhood Descendent (VND) procedures in the improvement phase. The VND procedures are differentiated by the search spaces they explore. The first VND performs moves in routes of the same vehicle and the second one relocates customers to routes of different vehicles. The algorithm has been tested against well-known benchmark instances and the results obtained are competitive with previous approaches found in the literature.
The neuron types of the glomerular layer of the olfactory bulb.

The neurons of the glomerular layer of the rat olfactory bulb have been studied using Nissl staining and Golgi-Kopsch impregnation in light microscopy to define the size, shape and morphological features of individual cell somata, dendrites and axons; these have been correlated with electron-microscopic material in which fine-structural characteristics were also noted for each cell type, particularly synaptic specializations. Three neuron types are described: the external tufted and periglomerular cells of classical microscopy, and additional, superficial short-axon cells; a description of the glomerular arborizations of the mitral and deep tufted cells is also included. The tufted and mitral cells show large, non-spiny glomerular dendritic arborizations, having terminal varicosities, the external tufted cells being more limited in their branching than the deeper cells. External tufted cells have large somata and abundant cytoplasm containing stacks of Nissl material; their main dendrites are characterized by pale cytoplasm and a regular array of neurotubules. Reciprocal dendro-dendritic and somato-dendritic synapses are commonly found, the tufted/mitral cells containing spherical vesicles and contacting by means of asymmetrical membrane thickenings; the other profile involved is a gemmule containing large flattened vesicles and associated with a symmetrical thickening. The periglomerular cells are smaller, with a spiny glomerular arborization, as well as some other dendrites; all the dendrites of these cells tend to be of irregular outline. They have a dark nucleus and very little somatic cytoplasm; somatic and dendritic appendages are common and often contain large flattened vesicles. Synapses oriented from the dendritic shaft or gemmule also show such vesicles, invariably associated with symmetrical thickenings. The superficial short-axon cells are characterized by the entirely periglomerular distribution of their dendrites, which are varicose and rarely branch. Of intermediate soma dimensions, but containing dispersed Nissl material, these cells and their stem dendrites show no regions that can be designated as presynaptic. Features of axon initial segments, axo-somatic and axo-dendritic synapses are also described for each cell, as well as some unusual glial relationships. Reasons are adduced for relating the superficial short-axon cell to the axon terminal type containing small flattened vesicles, as well as for considering that the external tufted and periglomerular cells show the same synaptic specializations at their axon terminals as at their dendritic and somatic synapses. The cells of the glomerular layer are compared with those of the deeper layers of the bulb and atypical synaptic specializations discussed; some physiological implications of these findings are considered.
Dam tailwaters compound the effects of reservoirs on the longitudinal transport of organic carbon in an arid river

Abstract. Reservoirs on rivers can disrupt organic carbon (OC) transport and transformation, but less is known how river reaches directly below dams contribute to OC processing. We compared how reservoirs and their associated tailwaters affected OC quantity and quality by calculating particulate OC (POC) and dissolved OC (DOC) fluxes, and measuring composition and bioavailability of DOC. We sampled the Yampa River near Maybell, Colorado, USA, and the Green River above and below Fontenelle and Flaming Gorge reservoirs as well as their respective tailwaters from early snowmelt to base flow hydrological conditions. In unregulated reaches (Yampa River, Green River above Fontenelle reservoir), DOC and POC concentrations increased with snowmelt discharge. POC and DOC concentrations also increased with stream discharge below Fontenelle reservoir, but there was no relationship between DOC and stream flow below Flaming Gorge reservoir. The annual load of POC was 3-fold lower below Fontenelle Reservoir and nearly 7-fold lower below Flaming Gorge reservoir, compared to their respective upstream sampling sites. DOC exported to downstream reaches from both reservoirs was less bioavailable, as measured with bioassays, than DOC upriver of the reservoirs. Lastly, tailwater reaches below the reservoirs generated OC, exporting potentially 1.6–2.2 g C m−2 d−1 of OC to downstream ecosystems. Therefore, the effect of impounding rivers on C fluxes is greater than the impact of the reservoirs alone given the additive effect of tailwater reaches below dams, which may produce and export comparable amounts of likely autochthonous carbon to downstream reaches.
Ensemble Clustering for Result Diversification

This paper describes the participation of the University of Twente in the Web track of TREC 2012. Our baseline approach uses the Mirex toolkit, an open source tool that sequantially scans all the documents. For result diversification, we experimented with improving the quality of clusters through ensemble clustering. We combined clusters obtained by different clustering methods (such as LDA and K-means) and clusters obtained by using different types of data (such as document text and anchor text). Our two-layer ensemble run performed better than the LDA based diversification and also better than a non-diversification run.
Halting type I planet migration in non-isothermal disks

Aims. We investigate the effect of including a proper energy balance on the interaction of a low-mass planet with a protoplanetary disk. Methods. We use a three-dimensional version of the RODEO method to perform hydrodynamical simulations including the energy equation. Radiation is included in the flux-limited diffusion approach. Results. The sign of the torque is sensitive to the ability of the disk to radiate away the energy generated in the immediate surroundings of the planet. In the case of high opacity, corresponding to the dense inner regions of protoplanetary disks, migration is directed outward , instead of the usual inward migration that was found in locally isothermal disks. For low values of the opacity we recover inward migration and show that torques originating in the coorbital region are responsible for the change in migration direction.
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee. org and its main mirror http://tcoffee.crg. cat.
Hybrid Content-Based Trademark Retrieval Using Region and Contour Features

The number of registered trademarks is increasing tremendously in recent years. In order to retrieve a similar looking trademark from a large trademark database, we propose a hybrid content based trademark retrieval method using region and contour features. Experiments have been conducted on the MPEG-7 Core Experiment CE-Shape-1 database of 1400 images and a collected trademark database of 2000 images. The retrieval results are very encouraging.