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https://www.readbyqxmd.com/read/28110507/computer-assisted-quantification-of-cd3-t-cells-in-follicular-lymphoma
#1
Fazly S Abas, Arwa Shana'ah, Beth Christian, Robert Hasserjian, Abner Louissaint, Michael Pennell, Berkman Sahiner, Weijie Chen, Muhammad Khalid Khan Niazi, Gerard Lozanski, Metin Gurcan
The advance of high resolution digital scans of pathology slides allowed development of computer based image analysis algorithms that may help pathologists in IHC stains quantification. While very promising, these methods require further refinement before they are implemented in routine clinical setting. Particularly critical is to evaluate algorithm performance in a setting similar to current clinical practice. In this article, we present a pilot study that evaluates the use of a computerized cell quantification method in the clinical estimation of CD3 positive (CD3+) T cells in follicular lymphoma (FL)...
January 22, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28110106/fast-learning-method-for-convolutional-neural-networks-using-extreme-learning-machine-and-its-application-to-lane-detection
#2
Jihun Kim, Jonghong Kim, Gil-Jin Jang, Minho Lee
Deep learning has received significant attention recently as a promising solution to many problems in the area of artificial intelligence. Among several deep learning architectures, convolutional neural networks (CNNs) demonstrate superior performance when compared to other machine learning methods in the applications of object detection and recognition. We use a CNN for image enhancement and the detection of driving lanes on motorways. In general, the process of lane detection consists of edge extraction and line detection...
December 10, 2016: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28110100/transport-of-outer-membrane-lipids-in-mycobacteria
#3
REVIEW
Megan H Touchette, Jessica C Seeliger
The complex organization of the mycobacterial cell wall poses unique challenges for the study of its assembly. Although mycobacteria are classified evolutionarily as Gram-positive bacteria, their cell wall architecture more closely resembles that of Gram-negative organisms. They possess not only an inner cytoplasmic membrane, but also a bilayer outer membrane that encloses an aqueous periplasm and includes diverse lipids that are required for the survival and virulence of pathogenic species. Questions surrounding how mycobacterial outer membrane lipids are transported from where they are made in the cytoplasm to where they function at the cell exterior are thus similar, and similarly compelling, to those that have driven the study of Gram-negative outer membrane transport pathways...
January 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28110091/genome-wide-association-analyses-reveal-the-genetic-basis-of-stigma-exsertion-in-rice
#4
Hao Zhou, Pingbo Li, Weibo Xie, Saddam Hussain, Yibo Li, Duo Xia, Hu Zhao, Shengyuan Sun, Junxiao Chen, Hong Ye, Jun Hou, Da Zhao, Guanjun Gao, Qinglu Zhang, Gongwei Wang, Xingming Lian, Jinghua Xiao, Sibin Yu, Xianghua Li, Yuqing He
Stigma exsertion, a key determinant of the rice mating system, greatly contributes to the application of heterosis in rice. As few QTLs have been fine mapped or cloned, the genetic architecture of stigma exsertion is quite unclear. We performed genome-wide association study of stigma exsertion and related traits using 6.5 million SNPs characterized in 533 diverse accessions of Oryza sativa. We identified 23 loci significantly associated with stigma exsertion and related traits, three of which were co-located with three major grain size genes GS3, GW5 and GW2...
January 18, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28110042/recent-advances-in-compartmentalized-synthetic-architectures-as-drug-carriers-cell-mimics-and-artificial-organelles
#5
REVIEW
M J York-Duran, M Godoy-Gallardo, C Labay, A J Urquhart, T L Andresen, L Hosta-Rigau
Compartmentalization is a key feature of biological cells which conduct their metabolic activity in individual steps isolated in distinct, separated compartments. The creation of architectures containing multiple compartments with a structure that resembles that of a biological cell has generated significant research attention and these assemblies are proposed as candidate materials for a range of biomedical applications. In this Review article, the recent successes of multicompartment architectures as carriers for the delivery of therapeutic cargo or the creation of micro- and nanoreactors that mimic metabolic activities, thus acting as artificial cells or organelles, are discussed...
January 16, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28110033/purification-characterization-and-functional-analysis-of-the-immune-molecule-lectin-from-the-haemolymph-of-blue-swimmer-crab-portunus-pelagicus-and-their-antibiofilm-properties
#6
Sangily Jayanthi, Ramachandran Ishwarya, Mahalingam Anjugam, Arokiadhas Iswarya, Sivashanmugam Karthikeyan, Baskaralingam Vaseeharan
The present study reveals purification and characterization of immune molecule lectin from the haemolymph of blue swimmer crab Portunus pelagicus (Pp-Lec). The Pp-Lec was purified by affinity chromatography with mannose coupled sepharose CL-4B column and it exhibits single band with a molecular weight of 155 kDa in SDS-PAGE. The surface morphology of purified Pp-Lec displays the homogeneous nature of protein. A distinct peak with a retention time of 3.3 min was appeared in high performance liquid chromatography (HPLC) and X-ray diffraction (XRD) analysis expresses a single peak at 31...
January 18, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28109981/thyroid-hormone-suppresses-ischemia-reperfusion-induced-liver-nlrp3-inflammasome-activation-role-of-amp-activated-protein-kinase
#7
Romina Vargas, Luis A Videla
Thyroid hormone (T3) induces liver preconditioning (PC) against ischemia-reperfusion (IR), a response energetically supported by AMP-activated protein kinase (AMPK) upregulation. The aim of this work is to evaluate the influence of T3 on IR-induced liver NLRP3 inflammasome activation and the relevance of AMPK activity on liver injury by the use of the AMPK inhibitor compound C (CC). Male Sprague-Dawley rats were given 0.1mgT3/kg (time zero) and 10mg CC/kg (time zero and 24h) or the respective vehicles, and subjected to 1h ischemia-20h reperfusion 48h after hormone treatment...
January 18, 2017: Immunology Letters
https://www.readbyqxmd.com/read/28109958/optical-barcoding-for-single-clone-tracking-to-study-tumor-heterogeneity
#8
Malte Mohme, Cecile L Maire, Kristoffer Riecken, Svenja Zapf, Tim Aranyossy, Manfred Westphal, Katrin Lamszus, Boris Fehse
Intratumoral heterogeneity has been identified as one of the strongest drivers of treatment resistance and tumor recurrence. Therefore, investigating the complex clonal architecture of tumors over time has become a major challenge in cancer research. We developed a new fluorescent "optical barcoding" technique that allows fast tracking, identification, and quantification of live cell clones in vitro and in vivo using flow cytometry (FC). We optically barcoded two cell lines derived from malignant glioma, an exemplary heterogeneous brain tumor...
January 18, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28109806/momordica-charantia-polysaccharides-ameliorate-oxidative-stress-hyperlipidemia-inflammation-and-apoptosis-during-myocardial-infarction-by-inhibiting-the-nf-%C3%AE%C2%BAb-signaling-pathway
#9
Mohammad Raish
The polysaccharide extract of Momordica charantia has various biological activities; however, its effect on endothelial dysfunction in myocardial infarction remains unclear. To elucidate this, myocardial infarction was induced in rats using isoproterenol (ISP). Pretreatment with M. charantia polysaccharides (MCP; 150 or 300mg/kg) for 25days significantly inhibited increases in heart weight, the heart-weight-to-body-weight ratio, and infarction size, and ameliorated the increased serum levels of aspartate transaminase, creatine kinase, lactate dehydrogenase, total cholesterol, triglycerides, very-low-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol...
January 18, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28109442/label-free-and-standard-free-absolute-quantitative-proteomics-using-the-total-protein-and-proteomic-ruler-approaches
#10
J R Wiśniewski
Understanding biological systems and their variation upon stimuli requires knowledge on their composition, primarily including information on organization and dynamics of proteomes. The total protein approach (TPA) is a label- and standard-free method for absolute protein quantitation of proteins using large-scale proteomic data. The method relies on the assumption that the total MS signal from all identified proteins in the dataset reflects-in a biochemical sense-the total protein and the MS signal from a single protein corresponds its abundance in the studied sample...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28109330/the-structure-of-mammalian-prions-and-their-aggregates
#11
E Vázquez-Fernández, H S Young, J R Requena, H Wille
Prion diseases, such as Creutzfeldt-Jakob disease in humans, bovine spongiform encephalopathy in cattle, chronic wasting disease in cervids (i.e., deer, elk, moose, and reindeer), and sheep scrapie, are caused by the misfolding of the cellular prion protein (PrP(C)) into a disease-causing conformer (PrP(Sc)). PrP(C) is a normal, GPI-anchored protein that is expressed on the surface of neurons and other cell types. The structure of PrP(C) is well understood, based on studies of recombinant PrP, which closely mimics the structure of native PrP(C)...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28109225/effects-of-stereochemistry-and-copolymerization-on-the-lcst-of-pnipam
#12
Tiago E de Oliveira, Debashish Mukherji, Kurt Kremer, Paulo A Netz
Poly(N-isopropylacrylamide) (PNIPAm) is a smart polymer that presents a lower critical transition temperature (LCST) of 305 K. Interestingly, this transition point falls within the range of the human body temperature, making PNIPAm a highly suitable candidate for bio-medical applications. However, it is sometimes desirable to have a rather flexible tuning of the LCST of these polymers to further increase their range of applications. In this work, we use all-atom molecular dynamics simulations to study the LCST of PNIPAm-based (co-)polymers...
January 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28109062/fibroblasts-as-maestros-orchestrating-tissue-regeneration
#13
REVIEW
Raquel Costa-Almeida, Raquel Soares, Pedro L Granja
Fibroblasts constitute a dynamic and versatile population of cells of mesenchymal origin, implicated in both regenerative strategies and pathological conditions. Despite being frequently associated to disease development, particularly through the establishment of fibrotic tissue, fibroblasts hold great potential for tissue engineering and regenerative medicine applications. They are responsible for synthesizing and depositing extracellular matrix components, allowing other cells to settle and migrate along a three-dimensional support and thereby generating an organ-specific architecture...
January 20, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/28108584/astrocytic-transporters-in-alzheimer-s-disease
#14
REVIEW
Chris Ugbode, Yuhan Hu, Benjamin Whalley, Chris Peers, Marcus Rattray, Mark L Dallas
Astrocytes play a fundamental role in maintaining the health and function of the central nervous system. Increasing evidence indicates that astrocytes undergo both cellular and molecular changes at an early stage in neurological diseases, including Alzheimer's disease (AD). These changes may reflect a change from a neuroprotective to a neurotoxic phenotype. Given the lack of current disease-modifying therapies for AD, astrocytes have become an interesting and viable target for therapeutic intervention. The astrocyte transport system covers a diverse array of proteins involved in metabolic support, neurotransmission and synaptic architecture...
February 1, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28108555/immune-dysregulation-may-contribute-to-disease-pathogenesis-in-spinal-muscular-atrophy-mice
#15
Marc-Olivier Deguise, Yves De Repentigny, Emily McFall, Nicole Auclair, Subash Sad, Rashmi Kothary
Spinal muscular atrophy (SMA) has long been solely considered a neurodegenerative disorder. However, recent work has highlighted defects in many other cell types that could contribute to disease aetiology. Interestingly, the immune system has never been extensively studied in SMA. Defects in lymphoid organs could exacerbate disease progression by neuroinflammation or immunodeficiency. Smn depletion led to severe alterations in the thymus and spleen of two different mouse models of SMA. The spleen from Smn depleted mice was dramatically smaller at a very young age and its histological architecture was marked by mislocalization of immune cells in the Smn(2B/-) model mice...
January 19, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28108553/the-bright-fluorescent-protein-mneongreen-facilitates-protein-expression-analysis-in-vivo
#16
Lola Hostettler, Laura Grundy, Stéphanie Käser-Pébernard, Chantal Wicky, William R Schafer, Dominique A Glauser
The Green Fluorescent Protein (GFP) has been tremendously useful to investigate cell architecture, protein localization, and protein function. While recent developments in transgenesis and genome editing methods enable working with few transgene copies and, consequently, with physiological expression levels, lower signal intensity might become a limiting factor. The recently developed mNeonGreen protein is a brighter alternative to GFP in vitro The goal of the present study was to determine how mNeonGreen performs in vivo in Caenorhabditis elegans, a model extensively used for fluorescence imaging in intact animals...
January 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28107913/quantitative-structure-retention-relationship-model-for-the-determination-of-naratriptan-hydrochloride-and-its-impurities-based-on-artificial-neural-networks-coupled-with-genetic-algorithm
#17
Mikołaj Mizera, Anna Krause, Przemysław Zalewski, Robert Skibiński, Judyta Cielecka-Piontek
Mathematical modeling of Quantitative Structure - Property Relationships met great interest in fields of in silico drug design and more recently, pharmaceutical analysis. In our approach we proposed automated method of creation Quantitative Structure-Retention Relationship (QSRR) for analysis of triptans, selective serotonin 5-HT1 receptor agonists used for the treatment of acute headache. The method was created using hybrid machine learning approach, namely Genetic algorithm (GA) coupled with artificial neutral networks (ANN)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107810/hierarchically-ordered-porous-and-high-volume-poly-caprolactone-pcl-microchannel-scaffolds-enhanced-axon-growth-in-transected-spinal-cords
#18
Dena Shahriari, Jacob Y Koffler, Mark H Tuszynski, Wendy M Campana, Jeff S Sakamoto
The goal of this work was to design nerve guidance scaffolds with a unique architecture to maximize the open volume available for nerve growth. Poly caprolactone (PCL) was selected as the scaffold material based on its biocompatibility and month-long degradation. Yet, dense PCL does not exhibit suitable properties such as porosity, stiffness, strength and cell adhesion to function as an effective nerve guidance scaffold. To address these shortcomings, PCL was processed using a modified salt-leaching technique to create uniquely controlled interconnected porosity...
January 20, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28107619/peptide-based-stealth-nanoparticles-for-targeted-and-ph-triggered-delivery
#19
Alessandro Ranalli, Melissa Santi, Luigi Capriotti, Valerio Voliani, David Porciani, Fabio Beltram, Giovanni Signore
Stealth agents are extensively investigated as means to prolong nanostructures residence time in the bloodstream by avoiding uptake by the reticuloendothelial system. Unfortunately, commonly used agents such as poly(ethylene glycol) can adversely impact on targeting efficiency and promote immune reaction by the host organism. Therefore, there is an increasing interest in developing biocompatible, non-PEGylated organic nanostructures able to perform targeted delivery, to increase the efficacy of liposomal technology...
January 20, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28107481/bet-inhibitors-disrupt-rad21-dependent-conformational-control-of-kshv-latency
#20
Horng-Shen Chen, Alessandra De Leo, Zhuo Wang, Andrew Kerekovic, Robert Hills, Paul M Lieberman
Kaposi's Sarcoma-associated Herpesvirus (KSHV) establishes stable latent infection in B-lymphocytes and pleural effusion lymphomas (PELs). During latency, the viral genome persists as an epigenetically constrained episome with restricted gene expression programs. To identify epigenetic regulators of KSHV latency, we screened a focused small molecule library containing known inhibitors of epigenetic factors. We identified JQ1, a Bromodomain and Extended Terminal (BET) protein inhibitor, as a potent activator of KSHV lytic reactivation from B-cells carrying episomal KSHV...
January 20, 2017: PLoS Pathogens
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