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https://www.readbyqxmd.com/read/29665244/dafi-a-directed-recursive-data-filtering-and-clustering-approach-for-improving-and-interpreting-data-clustering-identification-of-cell-populations-from-polychromatic-flow-cytometry-data
#1
Alexandra J Lee, Ivan Chang, Julie G Burel, Cecilia S Lindestam Arlehamn, Aishwarya Mandava, Daniela Weiskopf, Bjoern Peters, Alessandro Sette, Richard H Scheuermann, Yu Qian
Computational methods for identification of cell populations from polychromatic flow cytometry data are changing the paradigm of cytometry bioinformatics. Data clustering is the most common computational approach to unsupervised identification of cell populations from multidimensional cytometry data. However, interpretation of the identified data clusters is labor-intensive. Certain types of user-defined cell populations are also difficult to identify by fully automated data clustering analysis. Both are roadblocks before a cytometry lab can adopt the data clustering approach for cell population identification in routine use...
April 17, 2018: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/29593901/frequent-benign-nontraumatic-noninflammatory-causes-of-low-back-pain-in-adolescents-mri-findings
#2
Aikaterini Solomou, Pantelis Kraniotis, Aspasia Rigopoulou, Theodore Petsas
Introduction: Low back pain (LBP) is common in children and adolescents. There are many factors that cause LBP, including structural disorders, degenerative changes, Scheuermann's disease, fractures, inflammation, and tumors. Magnetic Resonance Imaging is the gold standard for diagnosing spinal abnormalities and is mandatory when neurological symptoms exist. The study focuses on common MRI findings in adolescents with persistent LBP, without history of acute trauma or evidence of either inflammatory or rheumatic disease...
2018: Radiology Research and Practice
https://www.readbyqxmd.com/read/29590361/big-data-and-single-cell-transcriptomics-implications-for-ontological-representation
#3
Brian D Aevermann, Mark Novotny, Trygve Bakken, Jeremy A Miller, Alexander D Diehl, David Osumi-Sutherland, Roger S Lasken, Ed S Lein, Richard H Scheuermann
Cells are fundamental function units of multicellular organisms, with different cell types playing distinct physiological roles in the body. The recent advent of single cell transcriptional profiling using RNA sequencing is producing "big data", enabling the identification of novel human cell types at an unprecedented rate. In this review, we summarize recent work characterizing cell types in the human central nervous and immune systems using single cell and single nuclei RNA sequencing, and discuss the implications that these discoveries are having on the representation of cell types in the reference Cell Ontology (CL)...
March 24, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29556050/versatile-protein-recognition-by-the-encoded-display-of-multiple-chemical-elements-on-a-constant-macrocyclic-scaffold
#4
Yizhou Li, Roberto De Luca, Samuele Cazzamalli, Francesca Pretto, Davor Bajic, Jörg Scheuermann, Dario Neri
In nature, specific antibodies can be generated as a result of an adaptive selection and expansion of lymphocytes with suitable protein binding properties. We attempted to mimic antibody-antigen recognition by displaying multiple chemical diversity elements on a defined macrocyclic scaffold. Encoding of the displayed combinations was achieved using distinctive DNA tags, resulting in a library size of 35,393,112. Specific binders could be isolated against a variety of proteins, including carbonic anhydrase IX, horseradish peroxidase, tankyrase 1, human serum albumin, alpha-1 acid glycoprotein, calmodulin, prostate-specific antigen and tumour necrosis factor...
April 2018: Nature Chemistry
https://www.readbyqxmd.com/read/29413741/reciprocal-changes-in-sagittal-alignment-with-operative-treatment-of-adolescent-scheuermann-kyphosis-prospective-evaluation-of-96-patients
#5
Baron S Lonner, Stefan Parent, Suken A Shah, Paul Sponseller, Burt Yaszay, Amer F Samdani, Patrick J Cahill, Joshua M Pahys, Randal Betz, Yuan Ren, Harry L Shufflebarger, Peter O Newton
INTRODUCTION: Sagittal alignment abnormalities in Scheuermann kyphosis (SK) strongly correlate with quality of life measures. The changes in spinopelvic parameters after posterior spinal fusion have not been adequately studied. This study is to evaluate the reciprocal changes in spinopelvic parameters following surgical correction for SK. METHODS: Ninety-six operative SK patients (65% male; age 16 years) with minimum 2-year follow-up were identified in the prospective multicenter study...
March 2018: Spine Deformity
https://www.readbyqxmd.com/read/29327948/effects-of-lumacaftor-ivacaftor-therapy-on-cftr-function-in-phe508del-homozygous-patients-with-cystic-fibrosis
#6
Simon Y Graeber, Christian Dopfer, Lutz Naehrlich, Lena Gyulumyan, Heike Scheuermann, Stephanie Hirtz, Sabine Wege, Heimo Mairbäurl, Marie Dorda, Rebecca Hyde, Azadeh Bagheri-Hanson, Claudia Rueckes-Nilges, Sebastian Fischer, Marcus A Mall, Burkhard Tümmler
RATIONALE: The combination of the CFTR corrector lumacaftor with the potentiator ivacaftor has been approved for the treatment of patients with cystic fibrosis (CF) homozygous for the Phe508del CFTR mutation. The phase 3 trials examined clinical outcomes, but did not evaluate CFTR function in patients. OBJECTIVES: To examine the effect of lumacaftor-ivacaftor on biomarkers of CFTR function in Phe508del homozygous CF patients aged 12 years and older. METHODS: This prospective observational study assessed clinical outcomes including FEV1 % predicted and BMI, and CFTR biomarkers including sweat chloride concentration, nasal potential difference (NPD) and intestinal current measurement (ICM) before and 8-16 weeks after initiation of lumacaftor-ivacaftor...
January 12, 2018: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29322913/cell-type-discovery-and-representation-in-the-era-of-high-content-single-cell-phenotyping
#7
Trygve Bakken, Lindsay Cowell, Brian D Aevermann, Mark Novotny, Rebecca Hodge, Jeremy A Miller, Alexandra Lee, Ivan Chang, Jamison McCorrison, Bali Pulendran, Yu Qian, Nicholas J Schork, Roger S Lasken, Ed S Lein, Richard H Scheuermann
BACKGROUND: A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and therapeutic/vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery...
December 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29322068/measuring-temporal-stability-of-positron-emission-tomography-standardized-uptake-value-bias-using-long-lived-sources-in-a-multicenter-network
#8
Darrin Byrd, Rebecca Christopfel, Grae Arabasz, Ciprian Catana, Joel Karp, Martin A Lodge, Charles Laymon, Eduardo G Moros, Mikalai Budzevich, Sadek Nehmeh, Joshua Scheuermann, John Sunderland, Jun Zhang, Paul Kinahan
Positron emission tomography (PET) is a quantitative imaging modality, but the computation of standardized uptake values (SUVs) requires several instruments to be correctly calibrated. Variability in the calibration process may lead to unreliable quantitation. Sealed source kits containing traceable amounts of [Formula: see text] were used to measure signal stability for 19 PET scanners at nine hospitals in the National Cancer Institute's Quantitative Imaging Network. Repeated measurements of the sources were performed on PET scanners and in dose calibrators...
January 2018: Journal of Medical Imaging
https://www.readbyqxmd.com/read/29290534/selection-of-distal-fusion-level-in-terms-of-distal-junctional-kyphosis-in-scheuermann-kyphosis-a-comparison-of-3-methods
#9
Fatih Dikici, Turgut Akgul, Kerim Sariyilmaz, Murat Korkmaz, Okan Ozkunt, Cuneyt Sar, Unsal Domanic
OBJECTIVE: The aim of this study was to investigate the effect of distal fusion level selection on the distal junctional kyphosis (DJK) in Scheuermann kyphosis (SK) patients who underwent posterior fusion. METHODS: Thirty-nine SK patients who underwent posterior fusion with a minimum follow-up of 3 years were retrospectively evaluated. According to the distal fusion level, patients were divided into 3 groups. Group S; lowest instrumented vertebra (LIV) was the sagittal stable vertebra (SSV), Group F; LIV was the first lordotic vertebra (FLV) and, Group L; LIV was the lower end vertebra (LEV)...
January 2018: Acta Orthopaedica et Traumatologica Turcica
https://www.readbyqxmd.com/read/29275006/altered-myofilament-structure-and-function-in-dogs-with-duchenne-muscular-dystrophy-cardiomyopathy
#10
Younss Ait Mou, Alain Lacampagne, Thomas Irving, Valérie Scheuermann, Stéphane Blot, Bijan Ghaleh, Pieter P de Tombe, Olivier Cazorla
AIM: Duchenne Muscular Dystrophy (DMD) is associated with progressive depressed left ventricular (LV) function. However, DMD effects on myofilament structure and function are poorly understood. Golden Retriever Muscular Dystrophy (GRMD) is a dog model of DMD recapitulating the human form of DMD. OBJECTIVE: The objective of this study is to evaluate myofilament structure and function alterations in GRMD model with spontaneous cardiac failure. METHODS AND RESULTS: We have employed synchrotron X-rays diffraction to evaluate myofilament lattice spacing at various sarcomere lengths (SL) on permeabilized LV myocardium...
January 2018: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/29225115/thoracic-disc-herniation-surgical-treatment
#11
REVIEW
C Court, E Mansour, C Bouthors
Thoracic disc herniation is rare and mainly occurs between T8 and L1. The herniation is calcified in 40% of cases and is labeled as giant when it occupies more than 40% of the spinal canal. A surgical procedure is indicated when the patient has severe back pain, stubborn intercostal neuralgia or neurological deficits. Selection of the surgical approach is essential. Mid-line calcified hernias are approached from a transthoracic incision, while lateralized soft hernias can be approached from a posterolateral incision...
February 2018: Orthopaedics & Traumatology, Surgery & Research: OTSR
https://www.readbyqxmd.com/read/29208285/hybrid-nanofibers-based-on-poly-caprolactone-gelatin-hydroxyapatite-nanoparticles-loaded-doxycycline-effective-anti-tumoral-and-antibacterial-activity
#12
Ricardo Ramírez-Agudelo, Karina Scheuermann, Alfonso Gala-García, Ana Paula F Monteiro, Ana Delia Pinzón-García, Maria E Cortés, Rubén D Sinisterra
Cancer is one of the leading causes of morbidity and mortality Worldwide, 19.3 million new cancer cases are expected to be identified in 2025. Among the therapeutic arsenal to cancer control one could find the Doxycycline and the nano hydroxyapatite. The Doxycycline (Dox) not only shown antibiotic effect but also exhibits a wide range of pleiotropic therapeutic properties as the control of the invasive and metastatic cancer cells characteristics. The purpose of the present study was to evaluate both cytotoxicity in vitro and antibacterial activity of electrospun Dox-loaded hybrid nanofibrous scaffolds composed by hydroxyapatite nanoparticles (nHA), poly-ε-caprolactone (PCL) and gelatin (Gel) polymers...
February 1, 2018: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/29189571/adding-satellite-rods-to-standard-2-rod-construct-with-the-use-of-duet-screws-an-effective-technique-to-improve-surgical-outcomes-and-preventing-proximal-junctional-kyphosis-in-posterior-only-correction-of-scheuermann-kyphosis
#13
Ze-Zhang Zhu, Xi Chen, Yong Qiu, Zhong-Hui Chen, Song Li, Liang Xu, Xu Sun
STUDY DESIGN: Retrospective matched-cohort comparative study. OBJECTIVE: To compare the surgical results after the use of duet screw based satellite rods plus bilateral satellite rods (S-RC) versus a standard 2-rod construct (2-RC) across osteotomy sites in a matched-cohort with Scheuermann kyphosis (SK). SUMMARY OF BACKGROUND DATA: Multiple Ponte osteotomies are frequently employed to correct SK via a posterior-only approach, with a 2-RC across the osteotomy sites...
November 17, 2017: Spine
https://www.readbyqxmd.com/read/29171067/toward-scintillator-high-gain-avalanche-rushing-photoconductor-active-matrix-flat-panel-imager-sharp-amfpi-initial-fabrication-and-characterization
#14
James R Scheuermann, Adrian Howansky, Marc Hansroul, Sébastien Léveillé, Kenkichi Tanioka, Wei Zhao
PURPOSE: We present the first prototype Scintillator High-Gain Avalanche Rushing Photoconductor Active Matrix Flat Panel Imager (SHARP-AMFPI). This detector includes a layer of avalanche amorphous Selenium (a-Se) (HARP) as the photoconductor in an indirect detector to amplify the signal and reduce the effects of electronic noise to obtain quantum noise-limited images for low-dose applications. It is the first time avalanche a-Se has been used in a solid-state imaging device and poses as a possible solution to eliminate the effects of electronic noise, which is crucial for low-dose imaging performance of AMFPI...
February 2018: Medical Physics
https://www.readbyqxmd.com/read/29150740/severe-rigid-scheuermann-kyphosis-in-adult-patients-correction-with-posterior-only-approach
#15
B Mirzashahi, M Chehrassan, A Arfa, M Farzan
PURPOSE: Scheuermann kyphosis is the most common structural kyphosis among adolescence and young people. Surgical treatment may be performed through combined anterior and posterior or posterior-only approaches; to our knowledge, the efficacy of posterior-only approach as less invasive procedure is not well studied in case of severe rigid Scheuermann kyphosis. MATERIALS AND METHODS: Eighteen patients with severe rigid Scheuermann kyphosis operated through only posterior approach from 2013 to 2016 were evaluated...
November 17, 2017: Musculoskeletal Surgery
https://www.readbyqxmd.com/read/29128077/automated-analysis-of-clinical-flow-cytometry-data-a-chronic-lymphocytic-leukemia-illustration
#16
REVIEW
Richard H Scheuermann, Jack Bui, Huan-You Wang, Yu Qian
Flow cytometry is used in cell-based diagnostic evaluation for blood-borne malignancies including leukemia and lymphoma. The current practice for cytometry data analysis relies on manual gating to identify cell subsets in complex mixtures, which is subjective, labor-intensive, and poorly reproducible. This article reviews recent efforts to develop, validate, and disseminate automated computational methods and pipelines for cytometry data analysis that could help overcome the limitations of manual analysis and provide for efficient and data-driven diagnostic applications...
December 2017: Clinics in Laboratory Medicine
https://www.readbyqxmd.com/read/29035089/intent-to-quit-quit-attempts-and-perceived-health-risk-reduction-among-african-american-latino-and-white-nondaily-and-daily-smokers-in-the-united-states
#17
Taneisha S Scheuermann, Nicole L Nollen, Xianghua Luo, Lisa Sanderson Cox, Jasjit S Ahluwalia
OBJECTIVE: Ethnic and racial differences in smoking patterns and behaviors have been well documented and most African American and Latino smokers are nondaily or light smokers. However, differences within smoking levels are understudied. Our primary aim was to determine whether there are racial and ethnic differences among African American, Latino, and White nondaily, light daily, and moderate to heavy daily smokers on (1) perceived health risk reduction, (2) intentions to quit, and (3) past year quit attempts...
October 16, 2017: Ethnicity & Health
https://www.readbyqxmd.com/read/29020925/vdjpipe-a-pipelined-tool-for-pre-processing-immune-repertoire-sequencing-data
#18
Scott Christley, Mikhail K Levin, Inimary T Toby, John M Fonner, Nancy L Monson, William H Rounds, Florian Rubelt, Walter Scarborough, Richard H Scheuermann, Lindsay G Cowell
BACKGROUND: Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perform multiple pre-processing tasks with just a single pass over the data files. RESULTS: Processing tasks provided by VDJPipe include base composition statistics calculation, read quality statistics calculation, quality filtering, homopolymer filtering, length and nucleotide filtering, paired-read merging, barcode demultiplexing, 5' and 3' PCR primer matching, and duplicate reads collapsing...
October 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28964216/the-new-versatile-general-purpose-surface-muon-instrument-gps-based-on-silicon-photomultipliers-for-%C3%AE-sr-measurements-on-a-continuous-wave-beam
#19
A Amato, H Luetkens, K Sedlak, A Stoykov, R Scheuermann, M Elender, A Raselli, D Graf
We report on the design and commissioning of a new spectrometer for muon-spin relaxation/rotation studies installed at the Swiss Muon Source (SμS) of the Paul Scherrer Institute (PSI, Switzerland). This new instrument is essentially a new design and replaces the old general-purpose surface-muon (GPS) instrument that has been for long the workhorse of the μSR user facility at PSI. By making use of muon and positron detectors made of plastic scintillators read out by silicon photomultipliers, a time resolution of the complete instrument of about 160 ps (standard deviation) could be achieved...
September 2017: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28944578/impact-of-a-central-scaffold-on-the-binding-affinity-of-fragment-pairs-isolated-from-dna-encoded-self-assembling-chemical-libraries
#20
Martina Bigatti, Alberto Dal Corso, Sara Vanetti, Samuele Cazzamalli, Ulrike Rieder, Jörg Scheuermann, Dario Neri, Filippo Sladojevich
The screening of encoded self-assembling chemical libraries allows the identification of fragment pairs that bind to adjacent pockets on target proteins of interest. For practical applications, it is necessary to link these ligand pairs into discrete organic molecules, devoid of any nucleic acid component. Here we describe the discovery of a synergistic binding pair for acid alpha-1 glycoprotein and a chemical strategy for the identification of optimal linkers, connecting the two fragments. The procedure yielded a set of small organic ligands, the best of which exhibited a dissociation constant of 9...
November 8, 2017: ChemMedChem
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