Miracle-dz/UniFAR-FTUs huggingface dataset:
H. pylori: should we still be looking for it? What should we be doing about it? A case-based approach.

overview Since its discovery by Marshall and Warren in 1982, Helicobacter pylori (H. pylori) has remained an important clinical consideration for virtually everyone managing patients with GI symptoms. The discovery of H. pylori revolutionized medicine, and its identification led to the well-deserved Nobel Prize to Marshall and Warren in 2005. Sitting here now, in 2011, it is hard to recall the distant dogma that peptic ulcers were principally caused by stress and lifestyle; we now recognize that many ulcers are the result of an infection, and that stress (as important as it may be for generating some GI symptoms) did not cause ulcers. But since the discovery of H. pylori, we have also learned that the pathogen is linked with many other ailments, including marginal T cell lymphoma (aka MALT), gastric adenocarcinoma, functional dyspepsia, gastroesophageal reflux disease (GERD), lymphocytic gastritis, Menetrier’s disease, dental caries, and iron deficiency anemia, among many others. While some of these links are secure (e.g., MALT), others are speculative or controversial (e.g., GERD, caries, iron deficiency).
Supporting context-aware applications for eldercare

Extended life expectancy and a decrease in fertility rates are dramatically increasing the number of seniors who will eventually need professional care assistance. Although there is no clear technical solution to this problem, recent advances in ubiquitous computing offer opportunities to assist elders in their residence, thus reducing the need for professional assistance in special facilities. There have been several studies, but current solutions tend to address specific issues and cannot be easily extended, updated, and customized to meet the complex and evolving requirements of eldercare assistance. This study aims to bridge this gap, and this pa- per presents a context-management framework, called awareness for pervasive environments (APE), that provides easily customizable support for the development of ubiquitous eldercare services and applications.
Nuclear medicine in orofacial diagnosis : A review

Radionuclide imaging is a form of noninvasive functional imaging technique, which provides information on pathophysiological and pathobiochemical processes. The other special imaging modalities, such as computed tomography (CT), magnetic resonance imaging, and diagnostic ultrasonography, are morphologic imaging techniques. Radionuclide imaging uses radioactive isotopes that emit γ (gamma) rays. Radionuclides allow measurement of tissue function in vivo and provide an early marker of disease, through measurement of biochemical change. After the radionuclides are administered, they get distributed in the body according to their clearance kinetics of that tracer. The gamma camera detects γ-rays and forms planar images showing the locations of the radionuclides in the body. The use of a scintillation crystal for an acquisition of data for image formation has led to the labeling of this technique as scintigraphy. Radionuclide imaging faces a parallel evolutionary shift from imaging function at the organ/tissue level to detecting changes at cellular and molecular levels. Single photon emission CT imaging and positron emission tomography imaging are advanced nuclear medicine techniques. This review provides an overview of the application of modern radionuclide imaging in the diagnosis and management of oral and maxillofacial diseases.
Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data

Background The investigation of the interconnections between the molecular and genetic events that govern biological systems is essential if we are to understand the development of disease and design effective novel treatments. Microarray and next-generation sequencing technologies have the potential to provide this information. However, taking full advantage of these approaches requires that biological connections be made across large quantities of highly heterogeneous genomic datasets. Leveraging the increasingly huge quantities of genomic data in the public domain is fast becoming one of the key challenges in the research community today. Methodology/Results We have developed a novel data mining framework that enables researchers to use this growing collection of public high-throughput data to investigate any set of genes or proteins. The connectivity between molecular states across thousands of heterogeneous datasets from microarrays and other genomic platforms is determined through a combination of rank-based enrichment statistics, meta-analyses, and biomedical ontologies. We address data quality concerns through dataset replication and meta-analysis and ensure that the majority of the findings are derived using multiple lines of evidence. As an example of our strategy and the utility of this framework, we apply our data mining approach to explore the biology of brown fat within the context of the thousands of publicly available gene expression datasets. Conclusions Our work presents a practical strategy for organizing, mining, and correlating global collections of large-scale genomic data to explore normal and disease biology. Using a hypothesis-free approach, we demonstrate how a data-driven analysis across very large collections of genomic data can reveal novel discoveries and evidence to support existing hypothesis.
Preferential coreceptor utilization and cytopathicity by dual-tropic HIV-1 in human lymphoid tissue ex vivo.

Many HIV-1 isolates at the late stage of disease are capable of using both CXCR4 and CCR5 in transfected cell lines, and are thus termed dual-tropic. Here we asked whether these dual-tropic variants also use both coreceptors for productive infection in a natural human lymphoid tissue microenvironment, and whether use of a particular coreceptor is associated with viral cytopathicity. We used 3 cloned dual-tropic HIV-1 variants, 89.6 and its chimeras 89-v345.SF and 89-v345.FL, which use both CCR5 and CXCR4 in transfected cell lines. In human lymphoid tissue ex vivo, one variant preferentially used CCR5, another preferentially used CXCR4, and a third appeared to be a true dual-tropic variant. The 2 latter variants severely depleted CD4(+) T cells, whereas cytopathicity of the virus that used CCR5 only in lymphoid tissue was mild and confined to CCR5(+)/CD4(+) T cells. Thus, (a) HIV-1 coreceptor usage in vitro cannot be unconditionally extrapolated to natural microenvironment of human lymphoid tissue; (b) dual-tropic viruses are not homogeneous in their coreceptor usage in lymphoid tissue, but probably comprise a continuum between the 2 polar variants that use CXCR4 or CCR5 exclusively; and (c) cytopathicity toward the general CD4(+) T cell population in lymphoid tissue is associated with the use of CXCR4.
Modélisation et manipulation d'entrepôts de données complexes et historisées

Le memoire de cette these traite de la modelisation conceptuelle et de la manipulation des donnees (par des algebres) dans les systemes d'aide a la decision. Notre these repose sur la dichotomie de deux espaces de stockage : l'entrepot de donnees regroupe les extraits des bases sources utiles pour les decideurs et les magasins de donnees sont deduits de l'entrepot et dedies a un besoin d'analyse particulier. Au niveau de l'entrepot, nous definissons un modele de donnees permettant de decrire l'evolution temporelle des objets complexes. Dans notre proposition, l'objet entrepot integre des etats courants, passes et archives modelisant les donnees decisionnelles et leurs evolutions. L'extension du concept d'objet engendre une extension du concept de classe. Cette extension est composee de filtres (temporels et d'archives) pour construire les etats passes et archives ainsi que d'une fonction de construction modelisant le processus d'extraction (origine source). Nous introduisons egalement le concept d'environnement qui definit des parties temporelles coherentes de tailles adaptees aux exigences des decideurs. La manipulation des donnees est une extension des algebres objet prenant en compte les caracteristiques du modele de representation de l'entrepot. L'extension se situe au niveau des operateurs temporels et des operateurs de manipulation des ensembles d'etats. Au niveau des magasins, nous definissons un modele de donnees multidimensionnelles permettant de representer l'information en une constellation de faits ainsi que de dimensions munies de hierarchies multiples. La manipulation des donnees s'appuie sur une algebre englobant l'ensemble des operations multidimensionnelles et offrant des operations specifiques a notre modele. Nous proposons une demarche d'elaboration des magasins a partir de l'entrepot. Pour valider nos propositions, nous presentons le logiciel GEDOOH (Generateur d'Entrepots de Donnees Orientees Objet et Historisees) d'aide a la conception et a la creation des entrepots dans le cadre de l'application medicale REANIMATIC.
Multidrug intravenous anesthesia for children undergoing MRI: a comparison with general anesthesia

Background: We used a multidrug intravenous anesthesia regimen with midazolam, ketamine, and propofol to provide anesthesia for children during magnetic resonance imaging (MRI). This regimen was compared with general anesthesia in a randomized comparative study. Outcome measures were safety, side effects and recovery variables in addition to adverse events in relation to age strata.
Assessing Stereo Algorithm Accuracy

Despite the large numbers of papers proposing new algorithms for the stereo matching process, there is a dearth of quantitative comparisons of proposed algorithms. Scharstein and Szeliski have recently compared area-based stereo matching algorithms on two metrics: fraction of pixels for which the disparity is not calculated correctly and the root mean square error using a small set of real images with known disparities. In this work, we start with ‘perfect’ images produced by a ray-tracer from a scene model and corrupt the images with varying amounts of additive white gaussian noise. This enables us to assess matching algorithm performance on perfect images and in the presence of defined amounts of noise. We found that the Pixel-to-Pixel algorithm, although it performs well in the absence of noise, rapidly deteriorates compared to the other algorithms. In the low noise region, there is very little difference between the algorithms we studied and thus one could chose the simplest and fastest sum of absolute differences as any benefit from others is very small. At higher noise levels (SNR ≤ 16dB), a sum of squared differences (computationally the next cheapest) performs consistently better.
Obstructive Sleep Apnea Detection Using Clustering Classification of Nonlinear Features from Nocturnal Oximetry

This study is focused on the classification of patients suspected of suffering from obstructive sleep apnea (OSA) by means of cluster analysis. We assessed the diagnostic ability of three clustering algorithms: k-means, hierarchical and fuzzy c-means (FCM). Nonlinear features of blood oxygen saturation (SaO2) from nocturnal oximetry were used as inputs to the clustering methods. Three nonlinear methods were used: approximate entropy (ApEn), central tendency measure (CTM) and Lempel-Ziv (LZ) complexity. A population of 74 subjects (44 OSA positive and 30 OSA negative) was studied. 90.5%, 87.8% and 86.5% accuracies were reached with k-means, hierarchical and FCM algorithms, respectively. The diagnostic accuracy values improved those obtained with each nonlinear method individually. Our results suggest that nonlinear analysis and clustering classification could provide useful information to help in the diagnosis of OSA syndrome.
Microsporidia Detection in Stools from Pets and Animals from the Zoo in Portugal: A Preliminary Study

MARIA LUISA LOBO, ANA TELES, MARGARIDA BARAO DA CUNHA, JOAQUIM HENRIQUES, ANA MAFALDA LOURENCO, FRANCISCO ANTUNES and OLGA MATOS Instituto de Higiene e Medicina Tropical/Unidade de Protozoarios Oportunistas/VIH e outras Protozooses/UPMM, Rua da Junqueira, 96 1349-008 Lisboa, Portugal, and Jardim Zoologico de Lisboa, and Instituto Medico Veterinario–Alameda D. Afonso Henriques, and Clinica Veterinaria Sao Macario–Lazarim, and Clinica Universitaria de Doencas Infecciosas, Faculdade de Medicina, Hospital de Santa Maria, Universidade de Lisboa, Portugal
Maximum Power Point Tracking & Efficiency Enhancements for PV Systems

This paper includes the verification of the characteristic equation for the output current generated by a solar panel. The characteristic equation is simulated by using MATLAB/Simulink. Many factors that affect the performance of the solar energy tracking system need to be considered profoundly for the complete & effective utilization of the available energy. This work deals with the study of tracking the position of the sun and positioning the solar panel to operate at the maximum power point.
Low quality of reporting adverse drug reactions in paediatric randomised controlled trials

Objective Randomised controlled trials (RCT) offer an opportunity to learn about frequency and character of adverse drug reactions. To improve the quality of reporting adverse effects, the Consort group published recommendations. The authors studied the application of these recommendations in RCTs performed in children. Design Literature search. Results The authors found 107 articles on paediatric RCTs written in English and published between 1 January 2006 and 1 April 2009. 83 articles (78%) mentioned adverse drug reactions, 36 articles (34%) used standardised methods for the disclosure of adverse drug reactions, 33 articles (31%) tabulated the reactions, and 27 (25%) stated numbers of and reasons for withdrawal. Registration of the RCT did not influence reporting. Sponsoring did lead to better reporting. According to the Consort guidelines, 19 (18%) reported safety data adequately. Conclusion Reporting of adverse drug reactions in RCTs is often inadequate. Authors should anticipate and define adverse drug reactions. During research all adverse events should be monitored and assessed actively. Monitoring and assessment should be described in articles in accordance with the extended Consort recommendations. Both authors and editors share the responsibility for the improvement of reporting safety data.
Robust Land Use Characterization of Urban Landscapes using Cell Phone Data

Mobile devices have become one of the main sensors of human behavior, and as such, can be used as proxies to study urban environments. In this paper we describe a method to automatically identify land uses from call detail record databases. Given the inherent diversity of human activities in urban landscapes, we use fuzzy clustering techniques to identify land uses in a robust way, characterizing only those geographical areas with well defined behaviors. Finally, we validate the results obtained using expert knowledge.
When Does Relay Transmission Give a More Secure Connection in Wireless Ad Hoc Networks?

Relay transmission can enhance coverage and throughput, whereas it can be vulnerable to eavesdropping attacks due to the additional transmission of the source message at the relay. Thus, whether or not one should use relay transmission for secure communication is an interesting and important problem. In this paper, we consider the transmission of a confidential message from a source to a destination in a decentralized wireless network in the presence of randomly distributed eavesdroppers. The source-destination pair can be potentially assisted by randomly distributed relays. For an arbitrary relay, we derive exact expressions of secure connection probability for both colluding and noncolluding eavesdroppers. We further obtain lower bound expressions on the secure connection probability, which are accurate when the eavesdropper density is small. Using these lower bound expressions, we propose a relay selection strategy to improve the secure connection probability. By analytically comparing the secure connection probability for direct transmission and relay transmission, we address the important problem of whether or not to relay and discuss the condition for relay transmission in terms of the relay density and source-destination distance. These analytical results are accurate in the small eavesdropper density regime.
Patwin Phonemics, Phonetics, and Phonotactics

This paper provides an overview of the phonemics, phonetics, and phonotactics of the Patwin language, using archival data sources. Patwin is a member of the small and underdescribed Wintuan language family. Although there is extensive archival material available for the Patwin language, little has been published about Patwin and there are no publications at all which deal with Patwin phonetics, phonemics, or phonotactics in a detailed way. It is therefore desirable to analyze the available archival data in the light of modern methodology and scholarship, and to create a defnitive description of Patwin phonemics and phonetics. The goal of this paper is similar to the goals of the “Phonetic Structures of. ” papers by Matthew Gordon, Peter Ladefoged, and colleagues, but with an archival data source and therefore a more philological methodology.
CONVERGENT PATTERNS IN THE SELECTION MOSAIC FOR TWO NORTH AMERICAN BIRD-DISPERSED PINES

The strength and outcome of interspecific interactions often vary across the landscape because of differences in community context. We investigated how the presence or absence of pine squirrels (Tamiasciurus spp.) influences the ecology and (co)evolution of seed-dispersal mutualisms between Clark's Nutcrackers (Nucifraga columbiana) and limber (Pinus flexilis) and whitebark (P. albicaulis) pines. Nutcrackers are the primary seed dispersers of these pines. Therefore both nutcrackers and pines potentially benefit from the evolution of a cone structure that enhances seed harvest by nutcrackers. Pine squirrels are the dominant predispersal seed predator of these pines throughout the Sierra Nevada–Cascades and Rocky Mountains and do not disperse seeds, so that pines benefit from deterring seed harvest by pine squirrels. To determine whether pines have evolved in response to selection by nutcrackers and pine squirrels, we conducted studies in ranges with pine squirrels and in ranges in the Great Basin and north.
Role of dendritic cells in the pathogenesis of systemic lupus erythematosus

Given their crucial role in immunologic tolerance and immune activation, dendritic cells are considered important orchestrators of autoimmunity. Research over the past decade has revealed multiple potential mechanisms by which dendritic cells contribute to the immunopathogenesis of systemic lupus erythematosus. Genetic abnormalities in systemic lupus erythematosus can result in dendritic cells with aberrant uptake, maturation and presentation capabilities. Dysregulated apoptosis in lupus can provide a source of autoantigens for uptake by inappropriately activated dendritic cells. These cells then present autoantigen to autoreactive lymphocytes, stimulating autoantibody and immune complex formation. In addition to depositing in tissues and causing damage, these immune complexes can stimulate plasmacytoid dendritic cells via Toll-like receptors 7 and 9 to synthesize IFN-α. This cytokine exerts a host of pathogenic effects on various effector cells, including myeloid dendritic cells, generating a feedback lo.
Konventionelles und unkonventionelles Organisationslernen: Literaturreport und Ergänzungsvorschlag

Zusammenfassung Mit der Renaissance von Akteurtheorien in Analysen der modernen „Organisationsgesellschaft“ erfahren auch das Steuerungsvermögen kollektiver Akteure und ihre Fähigkeit zu Kompetenzgewinnen vermehrte Aufmerksamkeit. Der Beitrag vermittelt - in Form eines systematisierten Literaturberichts - einen Überblick über die Angebote der empirischen Organisationsforschung im Themenbereich „Organisationslernen“ und beleuchtet weitere, organisationswissenschaftlich weniger prominente Phänomene kollektiven „Lernens“. Im ersten Teil werden typische Lernmodi vorgestellt, die nach Argyris (1976) und Argyris/ Schön (1978) als einfaches (single-loop), komplexes (double-loop) und reflexives (deutero-) Lernen identifizierbar sind. Im Kontrast zu diesen „konventionellen“ Lern typen kommen im zweiten Teil des Papiers „unkonventionelle“ Lernmodi zur Sprache. Sie beruhen auf Intrusionsprozessen, wie sie als Invasion, Dissidenz oder Intersektion zu beobachten sind. Während konventionelles Organisationslernen pfadabhängig verläuft, sind beim unkonventionellen Lernen auch abrupte Kognitions- und Strategiewechsel erwartbar. Eine Bedingung ihrer Möglichkeit ist, daß die Organisation keine vollständige Kontrolle über ihre Grenze zur Umwelt ausübt. Beispiele zeigen, daß diese Voraussetzung, die organisationssoziologischen Prämissen zuwiderläuft, nicht selten erfüllt ist. Abschließend werden einige typische Lernresultate skizziert: Erfahrungsgewinn, Personalaustausch, Orientierungswandel und multiple Identität.
Probing of C‐terminal lysine variation in a recombinant monoclonal antibody production using Chinese hamster ovary cells with chemically defined media

C‐terminal lysine (C‐K) variants are commonly observed in therapeutic monoclonal antibodies and recombinant proteins. Heterogeneity of C‐K residues is believed to result from varying degree of proteolysis by endogenous carboxypeptidase(s) during cell culture production. The achievement of batch‐to‐batch culture performance and product quality reproducibility is a key cell culture development criterion. Understanding the operational parameters affecting C‐K levels provides valuable insight into the cell culture process. A CHO cell line X expressing a recombinant antibody was selected as the model cell line due to the exhibited sensitivity of its C‐K level to the process conditions. A weak cation exchange chromatography (WCX) method with or without carboxypeptidase B (CpB) treatment was developed to monitor the C‐K level for in‐process samples. The effects of operating conditions (i.e., temperature and culture duration) and media trace elements (copper and zinc) on C‐K variants were studied. The dominant effect on C‐K level was identified as the trace elements concentration. Specifically, increased C‐K levels were observed with increase of copper concentration and decrease of zinc concentration in chemically defined medium. Further, a hypothesis for C‐K processing with intracellular and extracellular carboxypeptidase activity was proposed, based on preliminary intracellular carboxypeptidase Western blot results and the extracellular HCCF holding study. Biotechnol. Bioeng. 2012;109: 2306–2315. © 2012 Wiley Periodicals, Inc.
Melody, bass line, and harmony representations for music version identification

In this paper we compare the use of different musical representations for the task of version identification (i.e. retrieving alternative performances of the same musical piece). We automatically compute descriptors representing the melody and bass line using a state-of-the-art melody extraction algorithm, and compare them to a harmony-based descriptor. The similarity of descriptor sequences is computed using a dynamic programming algorithm based on nonlinear time series analysis which has been successfully used for version identification with harmony descriptors. After evaluating the accuracy of individual descriptors, we assess whether performance can be improved by descriptor fusion, for which we apply a classification approach, comparing different classification algorithms. We show that both melody and bass line descriptors carry useful information for version identification, and that combining them increases version detection accuracy. Whilst harmony remains the most reliable musical representation for version identification, we demonstrate how in some cases performance can be improved by combining it with melody and bass line descriptions. Finally, we identify some of the limitations of the proposed descriptor fusion approach, and discuss directions for future research.