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https://www.readbyqxmd.com/read/29145421/radiographic-prediction-of-meningioma-grade-by-semantic-and-radiomic-features
#1
Thibaud P Coroller, Wenya Linda Bi, Elizabeth Huynh, Malak Abedalthagafi, Ayal A Aizer, Noah F Greenwald, Chintan Parmar, Vivek Narayan, Winona W Wu, Samuel Miranda de Moura, Saksham Gupta, Rameen Beroukhim, Patrick Y Wen, Ossama Al-Mefty, Ian F Dunn, Sandro Santagata, Brian M Alexander, Raymond Y Huang, Hugo J W L Aerts
OBJECTIVES: The clinical management of meningioma is guided by tumor grade and biological behavior. Currently, the assessment of tumor grade follows surgical resection and histopathologic review. Reliable techniques for pre-operative determination of tumor grade may enhance clinical decision-making. METHODS: A total of 175 meningioma patients (103 low-grade and 72 high-grade) with pre-operative contrast-enhanced T1-MRI were included. Fifteen radiomic (quantitative) and 10 semantic (qualitative) features were applied to quantify the imaging phenotype...
2017: PloS One
https://www.readbyqxmd.com/read/29145401/anatomically-specific-intratubular-and-interstitial-biominerals-in-the-human-renal-medullo-papillary-complex
#2
Ling Chen, Ryan S Hsi, Feifei Yang, Benjamin A Sherer, Marshall L Stoller, Sunita P Ho
Limited information exists on the anatomically-specific early stage events leading to clinically detectable mineral aggregates in the renal papilla. In this study, quantitative multiscale correlative maps of structural, elemental and biochemical properties of whole medullo-papillary complexes from human kidneys were developed. Correlative maps of properties specific to the uriniferous and vascular tubules using high-resolution X-ray computed tomography, scanning and transmission electron microscopy, energy dispersive X-ray spectroscopy, and immunolocalization of noncollagenous proteins (NCPs) along with their association with anatomy specific biominerals were obtained...
2017: PloS One
https://www.readbyqxmd.com/read/29143979/analysis-of-anti-tnf-induced-skin-lesions-reveals-strong-th1-activation-with-some-distinct-immunological-characteristics
#3
E Stoffel, H Maier, E Riedl, M-C Brüggen, B Reininger, M Schaschinger, C Bangert, E Guenova, G Stingl, P M Brunner
BACKGROUND: Psoriasiform and eczematous eruptions are the most common dermatological adverse reaction linked to anti-TNF-α therapy. Yet, a detailed characterization of their immune phenotype is lacking. OBJECTIVES: We sought to characterize anti-TNF-α induced inflammatory skin lesions on a histopathologic, cellular and molecular level, compared to psoriasis, eczema (atopic dermatitis), and healthy control skin. METHODS: Histopathologic evaluation, gene expression (quantitative RT-PCR) and computer-assisted immunohistologic studies (TissueFAXS) were performed on 19 skin biopsies from IBD (n=17) and rheumatoid arthritis (n=2) patients with new-onset inflammatory skin lesions during anti-TNF-α-therapy...
November 16, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/29141314/-a-novel-compound-heterozygous-mutation-in-abca3-gene-in-a-child-with-diffuse-parenchymal-lung-disease
#4
Y M Bao, X L Liu, X L Liu, J H Chen, Y J Zheng
Objective: To summarize the clinical characteristics of the diffuse parenchymal lung diseases in a child caused by a novel compound heterozygous ABCA3 mutation and explore the association between the phenotype and ABCA3 mutation. Method: The clinical material of a patient diagnosed with diffuse parenchymal lung disease with ABCA3 mutation in December 2016 in Shenzhen Children's Hospital was analyzed. The information about ABCA3 gene mutation updated before April, 2017 was searched and collected from the gene databases (including 1000Genomes, HGMD, EXAC) and the literatures (including Wanfang Chinese database and Pubmed)...
November 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29138549/inflammation-and-chronic-colonization-of-haemophilus-influenzae-in-sputum-in-copd-patients-related-to-the-degree-of-emphysema-and-bronchiectasis-in-high-resolution-computed-tomography
#5
Ellen Tufvesson, Hanna Markstad, Gracijela Bozovic, Marie Ekberg, Leif Bjermer
The presence of bacteria in the lower airways in COPD results in inflammation, further airway structural damage, and might lead to repeated exacerbations. We have previously shown that chronic colonization of Haemophilus influenzae during stable disease is related to increased inflammation, and we now aimed to relate previous findings of bacterial colonization and inflammation to the degree of radiological findings of bronchiectasis and emphysema. Thirty-nine patients with COPD were included in their stable state, and a high-resolution computed tomography of the lung was performed...
2017: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/29127738/concerted-millisecond-timescale-dynamics-in-the-intrinsically-disordered-carboxyl-terminus-of-%C3%AE-tubulin-induced-by-mutation-of-a-conserved-tyrosine-residue
#6
Jason Harris, Maria Shadrina, Carlos Oliver, Jackie Vogel, Anthony Mittermaier
Tubulins are an ancient family of eukaryotic proteins characterized by an amino-terminal globular domain and disordered carboxyl terminus. These carboxyl termini play important roles in modulating the behavior of microtubules in living cells. However, the atomic-level basis of their function is not well understood. These regions contain multiple acidic residues and their overall charges are modulated in vivo by post-translational modifications, e.g. phosphorylation. In this study, we describe an application of NMR and computer Monte Carlo simulations to investigate how the modification of local charge alters the conformational sampling of the γ-tubulin carboxyl terminus...
November 11, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29127392/saccharomycesidentifier-sid-strain-level-analysis-of-saccharomyces-cerevisiae-populations-by-using-microsatellite-meta-patterns
#7
Irene Stefanini, Davide Albanese, Maddalena Sordo, Jean-Luc Legras, Carlotta De Filippo, Duccio Cavalieri, Claudio Donati
Saccharomyces cerevisiae is a common yeast with several applications, among which the most ancient is winemaking. Because individuals belonging to this species show a wide genetic and phenotypic variability, the possibility to identify the strains driving fermentation is pivotal when aiming at stable and palatable products. Metagenomic sequencing is increasingly used to decipher the fungal populations present in complex samples such as musts. However, it does not provide information at the strain level. Microsatellites are commonly used to describe the genotype of single strains...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29126984/osteopontin-as-a-novel-substrate-for-the-proprotein-convertase-5-6-pcsk5-in-bone
#8
Betty Hoac, Delia Susan-Resiga, Rachid Essalmani, Edwige Marcinkiweicz, Nabil G Seidah, Marc D McKee
Seven proprotein convertases cleave the basic amino acid consensus sequence K/R-Xn-K/R↓ (where n=0, 2, 4 or 6 variable amino acids) to activate precursor proteins. Despite similarities in substrate specificity, basic amino acid-specific proprotein convertases have a distinct tissue distribution allowing for enzymatic actions on tissue-resident substrates. Proprotein convertase 5/6 (PC5/6) has two splice variants - soluble PC5/6A and membrane-bound PC5/6B - and is expressed during mouse development in many tissues including bone and tooth, but little is known about the substrates for PC5/6 therein...
November 7, 2017: Bone
https://www.readbyqxmd.com/read/29126123/pedam-a-database-for-pediatric-disease-annotation-and-medicine
#9
Jinmeng Jia, Zhongxin An, Yue Ming, Yongli Guo, Wei Li, Xin Li, Yunxiang Liang, Dongming Guo, Jun Tai, Geng Chen, Yaqiong Jin, Zhimei Liu, Xin Ni, Tieliu Shi
There is a significant number of children around the world suffering from the consequence of the misdiagnosis and ineffective treatment for various diseases. To facilitate the precision medicine in pediatrics, a database namely the Pediatric Disease Annotations & Medicines (PedAM) has been built to standardize and classify pediatric diseases. The PedAM integrates both biomedical resources and clinical data from Electronic Medical Records to support the development of computational tools, by which enables robust data analysis and integration...
November 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29122081/gender-specific-differences-in-serum-immunoglobulin-e-levels-and-prevalence-of-fungus-in-sinonasal-tissue-noted-in-patients-with-chronic-rhinosinusitis-who-underwent-endoscopic-sinus-surgery
#10
Antoine Azar, Matthew A Rank, Matthew A Zarka, Yu-Hui Chang, Devyani Lal
BACKGROUND: We previously presented that women with chronic rhinosinusitis (CRS) who elected endoscopic sinus surgery (ESS) have a higher symptom burden than men. Causes of these gender-based differences warranted further study. OBJECTIVES: To study gender differences in another cohort of adult patients with CRS who underwent ESS and to compare key histopathologic and serologic features Methods: Patients with CRS who underwent ESS (from 2011 to 2014) with structured histopathology reports on surgical samples were studied...
November 1, 2017: American Journal of Rhinology & Allergy
https://www.readbyqxmd.com/read/29121144/positron-emission-tomography-computed-tomography-based-assessments-of-androgen-receptor-expression-and-glycolytic-activity-as-a-prognostic-biomarker-for-metastatic-castration-resistant-prostate-cancer
#11
Josef J Fox, Somali C Gavane, Estelle Blanc-Autran, Sadek Nehmeh, Mithat Gönen, Brad Beattie, Hebert A Vargas, Heiko Schöder, John L Humm, Samson W Fine, Jason S Lewis, Stephen B Solomon, Joseph R Osborne, Darren Veach, Charles L Sawyers, Wolfgang A Weber, Howard I Scher, Michael J Morris, Steven M Larson
Importance: Androgen receptor-signaling inhibitor (ARSi) drugs prolong life in metastatic castration-resistant prostate cancer (mCRPC), but such tumors eventually become resistant and progress. Comprehensive positron emission tomography/computed tomography (PET/CT) imaging using fluoro-2-D-deoxyglucose F 18 ([18F]-FDG) for glycolysis (Glyc) and fluorodihydrotestosterone F 18 ([18F]-FDHT) for androgen receptor (AR) expression determine heterogeneity of imaging phenotypes, which may be useful in distinguishing patients who will benefit from ARSi drugs from those who need alternative treatments...
November 9, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/29119102/the-transcriptional-network-structure-of-a-myeloid-cell-a-computational-approach
#12
Jesús Espinal-Enríquez, Daniel González-Terán, Enrique Hernández-Lemus
Understanding the general principles underlying genetic regulation in eukaryotes is an incomplete and challenging endeavor. The lack of experimental information regarding the regulation of the whole set of transcription factors and their targets in different cell types is one of the main reasons to this incompleteness. So far, there is a small set of curated known interactions between transcription factors and their downstream genes. Here, we built a transcription factor network for human monocytic THP-1 myeloid cells based on the experimentally curated FANTOM4 database where nodes are genes and the experimental interactions correspond to links...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29118821/tasselnet-counting-maize-tassels-in-the-wild-via-local-counts-regression-network
#13
Hao Lu, Zhiguo Cao, Yang Xiao, Bohan Zhuang, Chunhua Shen
Background: Accurately counting maize tassels is important for monitoring the growth status of maize plants. This tedious task, however, is still mainly done by manual efforts. In the context of modern plant phenotyping, automating this task is required to meet the need of large-scale analysis of genotype and phenotype. In recent years, computer vision technologies have experienced a significant breakthrough due to the emergence of large-scale datasets and increased computational resources...
2017: Plant Methods
https://www.readbyqxmd.com/read/29118820/non-destructive-high-content-analysis-of-wheat-grain-traits-using-x-ray-micro-computed-tomography
#14
Nathan Hughes, Karen Askew, Callum P Scotson, Kevin Williams, Colin Sauze, Fiona Corke, John H Doonan, Candida Nibau
Background: Wheat is one of the most widely grown crop in temperate climates for food and animal feed. In order to meet the demands of the predicted population increase in an ever-changing climate, wheat production needs to dramatically increase. Spike and grain traits are critical determinants of final yield and grain uniformity a commercially desired trait, but their analysis is laborious and often requires destructive harvest. One of the current challenges is to develop an accurate, non-destructive method for spike and grain trait analysis capable of handling large populations...
2017: Plant Methods
https://www.readbyqxmd.com/read/29118113/measurement-of-micro-scale-soil-deformation-around-roots-using-four-dimensional-synchrotron-tomography-and-image-correlation
#15
S D Keyes, L Cooper, S Duncan, N Koebernick, D M McKay Fletcher, C P Scotson, A van Veelen, I Sinclair, T Roose
This study applied time lapse (four-dimensional) synchrotron X-ray computed tomography to observe micro-scale interactions between plant roots and soil. Functionally contrasting maize root tips were repeatedly imaged during ingress into soil columns of varying water content and compaction. This yielded sequences of three-dimensional densiometric data, representing time-resolved geometric soil and root configurations at the micronmetre scale. These data were used as inputs for two full-field kinematic quantification methods, which enabled the analysis of three-dimensional soil deformation around elongating roots...
November 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29117580/discovery-and-visualization-of-structural-biomarkers-from-mri-using-transport-based-morphometry
#16
Shinjini Kundu, Soheil Kolouri, Kirk I Erickson, Arthur F Kramer, Edward McAuley, Gustavo K Rohde
Disease in the brain is often associated with subtle, spatially diffuse, or complex tissue changes that may lie beneath the level of gross visual inspection, even on magnetic resonance imaging (MRI). Unfortunately, current computer-assisted approaches that examine pre-specified features, whether anatomically-defined (i.e. thalamic volume, cortical thickness) or based on pixelwise comparison (i.e. deformation-based methods), are prone to missing a vast array of physical changes that are not well-encapsulated by these metrics...
November 5, 2017: NeuroImage
https://www.readbyqxmd.com/read/29116519/upgrading-affinity-screening-experiments-by-analysis-of-next-generation-sequencing-data
#17
Christian Grohmann, Michael Blank
Computational analysis of next-generation sequencing data (NGS; also termed deep sequencing) enables the analysis of affinity screening procedures (or biopanning experiments) in an unprecedented depth and therewith improves the identification of relevant peptide or antibody ligands with desired binding or functional properties. Virtually any selection methodology employing the direct physical linkage of geno- and phenotype to select for desired properties can be leveraged by computational analysis. This article describes a concept how relevant ligands can be identified by harnessing NGS data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29114909/an-ancestry-based-approach-for-detecting-interactions
#18
Danny S Park, Itamar Eskin, Eun Yong Kang, Eric R Gamazon, Celeste Eng, Christopher R Gignoux, Joshua M Galanter, Esteban Burchard, Chun J Ye, Hugues Aschard, Eleazar Eskin, Eran Halperin, Noah Zaitlen
BACKGROUND: Epistasis and gene-environment interactions are known to contribute significantly to variation of complex phenotypes in model organisms. However, their identification in human association studies remains challenging for myriad reasons. In the case of epistatic interactions, the large number of potential interacting sets of genes presents computational, multiple hypothesis correction, and other statistical power issues. In the case of gene-environment interactions, the lack of consistently measured environmental covariates in most disease studies precludes searching for interactions and creates difficulties for replicating studies...
November 8, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/29114575/prediction-of-a-highly-deleterious-mutation-e17k-in-akt-1-gene-an-in-silico-approach
#19
Imran Khan, Irfan A Ansari
The AKT1 (v-akt murine thymoma viral oncogene homologue 1) kinase is a member of most frequently activated proliferation and survival signaling pathway in cancer. Recently, hyperactivation of AKT1, due to functional point mutation in the pleckstrin homology (PH) domain of AKT1 gene, has been found to be associated with human colorectal, breast and ovarian cancer. Thus, considering its crucial role in cellular signaling pathway, a functional analysis of missense mutations of AKT1 gene was undertaken in this study...
July 2017: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/29109795/the-use-of-pet-imaging-for-prognostic-integrin-%C3%AE-2%C3%AE-1-phenotyping-to-detect-non-small-cell-lung-cancer-and-monitor-drug-resistance-responses
#20
Chiun-Wei Huang, Wen-Chuan Hsieh, Shih-Ting Hsu, Yi-Wen Lin, Yi-Hsiu Chung, Wen-Chi Chang, Han Chiu, Yun Han Lin, Chung-Pu Wu, Tzu-Chen Yen, Feng-Ting Huang
PURPOSE: Growing evidence has demonstrated that aberrant expression of integrin α2β1 might contribute to the invasion, metastasis and drug resistance of non-small cell lung cancer (NSCLC). Thus, the integrin α2β1 targeting (68)Ga-DOTA-A2B1 tracer was validated in NSCLC in contrast to accumulation of the clinically used (18)F-FDG PET tracer to see if (68)Ga-DOTA-A2B1-PET imaging can offer a valuable and critical diagnostic imaging criterion for the identification of phenotypes of aggressive lung cancer...
2017: Theranostics
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