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Kamal Taha
This study proposes a new method to determine the functions of an unannotated protein. The proteins and amino acid residues mentioned in biomedical texts associated with an unannotated protein p can be considered as characteristics terms for p, which are highly predictive of the potential functions of p. Similarly, proteins and amino acid residues mentioned in biomedical texts associated with proteins annotated with a functional category f can be considered as characteristics terms of f. We introduce in this paper an information extraction system called IFP_IFC that predicts the functions of an unannotated protein p by representing p and each functional category f by a vector of weights...
October 6, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Marion Ortner, Lorenzo Pasquini, Martina Barat, Panagiotis Alexopoulos, Timo Grimmer, Stefan Förster, Janine Diehl-Schmid, Alexander Kurz, Hans Förstl, Claus Zimmer, Afra Wohlschläger, Christian Sorg, Henning Peters
Very early Alzheimer's disease (AD) - i.e., AD at stages of mild cognitive impairment (MCI) and mild dementia - is characterized by progressive structural and neuropathologic changes, such as atrophy or tangle deposition in medial temporal lobes, including hippocampus and entorhinal cortex and also adjacent amygdala. While progressively disrupted intrinsic connectivity of hippocampus with other brain areas has been demonstrated by many studies, amygdala connectivity was rarely investigated in AD, notwithstanding its known relevance for emotion processing and mood disturbances, which are both important in early AD...
2016: Frontiers in Neurology
Suena H Massey, Daniel Stern, Eva C Alden, Julie E Petersen, Derin J Cobia, Lei Wang, John G Csernansky, Matthew J Smith
BACKGROUND: Cognitive empathy is supported by the medial prefrontal cortex (mPFC), inferior frontal gyrus (IFG), anterior mid-cingulate cortex (aMCC), insula (INS), supplementary motor area (SMA), right temporo-parietal junction (TPJ), and precuneus (PREC). In healthy controls, cortical thickness in these regions has been linked to cognitive empathy. As cognitive empathy is impaired in schizophrenia, we examined whether reduced cortical thickness in these regions was associated with poorer cognitive empathy in this population...
September 21, 2016: Schizophrenia Research
Ting Xu, Alexander Opitz, R Cameron Craddock, Margaret J Wright, Xi-Nian Zuo, Michael P Milham
Resting state fMRI (R-fMRI) is a powerful in-vivo tool for examining the functional architecture of the human brain. Recent studies have demonstrated the ability to characterize transitions between functionally distinct cortical areas through the mapping of gradients in intrinsic functional connectivity (iFC) profiles. To date, this novel approach has primarily been applied to iFC profiles averaged across groups of individuals, or in one case, a single individual scanned multiple times. Here, we used a publically available R-fMRI dataset, in which 30 healthy participants were scanned 10 times (10 min per session), to investigate differences in full-brain transition profiles (i...
September 6, 2016: Cerebral Cortex
Holger Hennig, Paul Rees, Thomas Blasi, Lee Kamentsky, Jane Hung, David Dao, Anne E Carpenter, Andrew Filby
Imaging flow cytometry (IFC) enables the high throughput collection of morphological and spatial information from hundreds of thousands of single cells. This high content, information rich image data can in theory resolve important biological differences among complex, often heterogeneous biological samples. However, data analysis is often performed in a highly manual and subjective manner using very limited image analysis techniques in combination with conventional flow cytometry gating strategies. This approach is not scalable to the hundreds of available image-based features per cell and thus makes use of only a fraction of the spatial and morphometric information...
September 1, 2016: Methods: a Companion to Methods in Enzymology
Hongping Li, Yufeng Wu, Yali Zhao, Xiuli Hu, Jianfeng Chang, Qun Wang, Pengfei Dong, Moubiao Zhang, Chaohai Li
We have isolated a new mutation in maize, incompletely fused carpels (ifc), which results in an open stylar canal on the ovary and an incomplete pericarp at the top of the kernel. The maize ovary derives from the fusion of three carpels; however, the molecular networks regulating maize carpel fusion remain largely unclear. In this study, RNA sequencing (RNA-seq) was performed on wild-type (WT) and ifc ovaries that were collected after carpel fusion defects could be morphologically distinguished. In total, 877 differentially expressed genes were identified...
2016: Scientific Reports
Hans Minderman, Orla Maguire, Kieran L O'Loughlin, Jason Muhitch, Paul K Wallace, Scott I Abrams
The transcription factor interferon regulatory factor-8 (IRF8) plays an essential role in myeloid differentiation and lineage commitment, based largely on molecular and genetic studies. The detection of IRF8 in specific cell populations by flow cytometry (FCM) has the potential to provide new insights into normal and pathologic myelopoiesis, but critical validation of this protein-based approach, particularly in human samples, is lacking. In this study, the assessment of total cellular IRF8 presence was compared to its specific nuclear presence as assessed by imaging flow cytometry (IFC) analysis...
August 28, 2016: Methods: a Companion to Methods in Enzymology
K E McGrath, S C Catherman, J Palis
Adult humans need to make 2.5million red blood cells (RBCs) every second to maintain a steady state level of 25trillion circulating RBCs. Understanding normal erythropoiesis as well as diseases that afflict the erythron, such as genetic anemias, hyperproliferative disorders, and myelodysplastic syndromes, requires a robust method to delineate erythropoietic intermediates. In order to apply the power of flow cytometry to these studies, challenges of limited immunophenotypic markers, incorporation of significant changes in morphology, and maturational changes that occur along a continuum need to be met...
August 28, 2016: Methods: a Companion to Methods in Enzymology
Olli A Kajander, Natalia Pinilla-Echeverri, Sanjit S Jolly, Ravinay Bhindi, Heini Huhtala, Kari Niemelä, Anthony Fung, Ram Vijayaraghavan, Dimitrios Alexopoulos, Tej Sheth
AIMS: Our aim was to compare stenosis severity and plaque content between STEMI culprit lesions with intact fibrous cap (IFC) and those with plaque rupture (PR) in a prospective study. METHODS AND RESULTS: We evaluated 93 patients undergoing OCT and thrombectomy as part of a prospective substudy of the TOTAL (ThrOmbecTomy versus PCI ALone) trial. Culprit lesion morphology was assessable by OCT in 70/93 (75.3%). IFC was found in 31 (44.3%), PR in 34 (48.6%) and calcified nodule in five (7...
August 20, 2016: EuroIntervention
Lindsay A Beaton-Green, Matthew A Rodrigues, Sylvie Lachapelle, Ruth C Wilkins
Biodosimetry is an important tool for triage in the case of large-scale radiological or nuclear emergencies, but traditional microscope-based methods can be tedious and prone to scorer fatigue. While the dicentric chromosome assay (DCA) has been adapted for use in triage situations, it is still time-consuming to create and score slides. Recent adaptations of traditional biodosimetry assays to imaging flow cytometry (IFC) methods have dramatically increased throughput. Additionally, recent improvements in image analysis algorithms in IFC software have resulted in improved specificity for spot counting of small events...
August 11, 2016: Methods: a Companion to Methods in Enzymology
Robert van Haselen, Manuela Thinesse-Mallwitz, Vitaliy Maidannyk, Stephen L Buskin, Stephan Weber, Thomas Keller, Julia Burkart, Petra Klement
We investigated the clinical effectiveness of a homeopathic add-on therapy in a pediatric subpopulation with upper respiratory tract infections (URTI) in a randomized, controlled, multinational clinical trial. Patients received either on-demand symptomatic standard treatment (ST-group) or the same ST plus a homeopathic medication (Influcid; IFC-group) for 7 days. Outcome assessment was based on symptom and fever resolution and the Wisconsin Upper Respiratory Symptom Survey-21 (WURSS-21). A total of 261 pediatric (<12 years) patients (130 IFC-group; 131 ST-group) were recruited in Germany and the Ukraine...
2016: Global Pediatric Health
A Paul Mould, Janet A Askari, Adam Byron, Yoshikazu Takada, Thomas A Jowitt, Martin J Humphries
We previously demonstrated that Arg-Gly-Asp (RGD)-containing ligand-mimetic inhibitors of integrins are unable to dissociate pre-formed integrin-fibronectin complexes (IFCs). These observations suggested that amino acid residues involved in integrin-fibronectin binding become obscured in the ligand-occupied state. Because the epitopes of some function-blocking anti-integrin monoclonal antibodies (mAbs) lie near the ligand-binding pocket, it follows that the epitopes of these mAbs may become shielded in the ligand-occupied state...
September 30, 2016: Journal of Biological Chemistry
Orla Maguire, Paul K Wallace, Hans Minderman
The emergence of imaging flow cytometry (IFC) has brought novel applications exploiting its advantages over conventional flow cytometry and microscopy. One of the new applications is fluorescence in situ hybridization in suspension (FISH-IS). Conventional FISH is a slide-based approach in which the spotlike imagery resulting from hybridization with fluorescently tagged probes is evaluated by fluorescence microscopy. The FISH-IS approach evaluated by IFC enables the evaluation of tens to hundreds of thousands of cells in suspension and the analysis can be automated and standardized diminishing operator bias from the analysis...
2016: Methods in Molecular Biology
Andrew Filby, William Day, Sukhveer Purewal, Nuria Martinez-Martin
Measuring cellular DNA content by conventional flow cytometry (CFC) and fluorescent DNA-binding dyes is a highly robust method for analysing cell cycle distributions within heterogeneous populations. However, any conclusions drawn from single-parameter DNA analysis alone can often be confounded by the asynchronous nature of cell proliferation. We have shown that by combining fluorescent DNA stains with proliferation tracking dyes and antigenic staining for mitotic cells one can elucidate the division history and cell cycle position of any cell within an asynchronously dividing population...
2016: Methods in Molecular Biology
David A Basiji
Over the last decade imaging flow cytometry (IFC) has become an established technique, as evidenced by its use in over 500 peer-reviewed scientific articles. Nevertheless, it is still an emerging technique with an installed base of less than 5 % that of conventional flow cytometers. In parallel with its adoption, the technology has evolved rapidly, increasing in speed, sensitivity, and real-time data analysis capacity by over an order of magnitude since its introduction. This chapter summarizes IFC's basic principles of operation and describes the current state of the art...
2016: Methods in Molecular Biology
Ivan A Vorobjev, Natasha S Barteneva
This chapter describes advantages and limitations of imaging flow cytometry (IFC) based on Imagestream instrumentation using a hybrid approach of morphometric measurement and quantitation of multiparametric fluorescent intensities' distribution in cells and particles. Brief comparison is given of IFC with conventional flow cytometry and fluorescent microscopy. Some future directions of the IFC technology are described and discussed.
2016: Methods in Molecular Biology
Philippe Pfeifer, Oliver Tüscher, Hans Georg Buchholz, Gerhard Gründer, Ingo Vernaleken, Michael Paulzen, Ulrich S Zimmermann, Stephan Maus, Klaus Lieb, Thomas Eggermann, Christoph Fehr, Mathias Schreckenberger
Investigations on the acute effects of alcohol in the human mesolimbic dopamine D2 /D3 receptor system have yielded conflicting results. With respect to the effects of alcohol on extrastriatal D2 /D3 dopamine receptors no investigations have been reported yet. Therefore we applied PET imaging using the postsynaptic dopamine D2 /D3 receptor ligand [(18) F]fallypride addressing the question, whether intravenously applied alcohol stimulates the extrastriatal and striatal dopamine system. We measured subjective effects of alcohol and made correlation analyses with the striatal and extrastriatal D2 /D3 binding potential...
July 11, 2016: Addiction Biology
Concepcion Parrado, Marta Mascaraque, Yolanda Gilaberte, Angeles Juarranz, Salvador Gonzalez
Healthier life styles include increased outdoors time practicing sports and walking. This means increased exposure to the sun, leading to higher risk of sunburn, photoaging and skin cancer. In addition to topical barrier products, oral supplementations of various botanicals endowed with antioxidant activity are emerging as novel method of photoprotection. Polypodium leucotomos extract (PL, commercial name Fernblock(®), IFC Group, Spain) is a powerful antioxidant due to its high content of phenolic compounds...
2016: International Journal of Molecular Sciences
Véronique Cabaret
This article aims at introducing an educational sequence completed at l'Institut de Formation des Cadres de Santé (IFCS) at the CHRU in Lille in France, entitled "training project and educational project" present in the "training duties" module whose goal is to generate students'knowledge through co-operative education programmes. By creating this innovative sequence, the educational aim is to use the Institut ground as a ground of learning, associated with the various internship grounds, in order to get the most of co-operative education programmes...
March 2016: Journal International de Bioéthique, International Journal of Bioethics
Jing Zhao, Lo-Yi Lin, Chih-Min Lin
The diversity of medical factors makes the analysis and judgment of uncertainty one of the challenges of medical diagnosis. A well-designed classification and judgment system for medical uncertainty can increase the rate of correct medical diagnosis. In this paper, a new multidimensional classifier is proposed by using an intelligent algorithm, which is the general fuzzy cerebellar model neural network (GFCMNN). To obtain more information about uncertainty, an intuitionistic fuzzy linguistic term is employed to describe medical features...
2016: Computational Intelligence and Neuroscience
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