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https://www.readbyqxmd.com/read/29351917/a-novel-method-for-rapid-molecular-subgrouping-of-medulloblastoma
#1
Soledad Gómez, Alícia Garrido-Garcia, Laura Garcia-Gerique, Isadora Lemos, Mariona Suñol, Carmen de Torres, Marta Kulis, Sara Perez-Jaume, Angel M Carcaboso, Betty Luu, Mark W Kieran, Nada Jabado, Alexey Kozlenkov, Stella Dracheva, Vijay Ramaswamy, Volker Hovestadt, Pascal Johann, David T W Jones, Stefan M Pfister, Andrés Morales La Madrid, Ofelia Cruz, Michael D Taylor, Jose I Martín-Subero, Jaume Mora, Cinzia Lavarino
PURPOSE: The classification of medulloblastoma into WNT, SHH, Group 3 and Group 4 subgroups has become of critical importance for patient risk-stratification and subgroup-tailored clinical trials. Here, we aimed to develop a simplified, clinically applicable classification approach that can be implemented in the majority of centers treating patients with medulloblastoma. EXPERIMENTAL DESIGN: We analyzed 1,577 samples comprising previously published DNA methylation microarray data (913 medulloblastomas, 457 non-medulloblastoma tumors, 85 normal tissues), and 122 frozen and formalin-fixed paraffin-embedded medulloblastoma samples...
January 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29341697/large-scale-structure-and-hyperuniformity-of-amorphous-ices
#2
Fausto Martelli, Salvatore Torquato, Nicolas Giovambattista, Roberto Car
We investigate the large-scale structure of amorphous ices and transitions between their different forms by quantifying their large-scale density fluctuations. Specifically, we simulate the isothermal compression of low-density amorphous ice (LDA) and hexagonal ice to produce high-density amorphous ice (HDA). Both HDA and LDA are nearly hyperuniform; i.e., they are characterized by an anomalous suppression of large-scale density fluctuations. By contrast, in correspondence with the nonequilibrium phase transitions to HDA, the presence of structural heterogeneities strongly suppresses the hyperuniformity and the system becomes hyposurficial (devoid of "surface-area fluctuations")...
September 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29332804/effect-of-preprocessing-high-resolution-mass-spectra-on-the-pattern-recognition-of-cannabis-hemp-and-liquor
#3
Xinyi Wang, Peter de B Harrington, Steven F Baugh
High-resolution mass spectrometry (HRMS) combined with pattern recognition was used to discriminate among twenty-five Cannabis samples, twenty hemp samples, and eight liquor samples. The effects of preprocessing on multivariate data analysis were evaluated for Orbitrap high-resolution mass spectra. Different root transformations were evaluated with respect to the bin width and the average classification rates. In addition, linear binning and proportional binning with various resolving powers were studied with respect to the average classification rates...
April 1, 2018: Talanta
https://www.readbyqxmd.com/read/29330511/testing-density-functional-approximations-on-a-lattice-and-the-applicability-of-the-related-hohenberg-kohn-like-theorem
#4
Vivian V França, Jeremy P Coe, Irene D'Amico
We present a metric-space approach to quantify the performance of approximations in lattice density-functional theory for interacting many-body systems and to explore the regimes where the Hohenberg-Kohn-type theorem on fermionic lattices is applicable. This theorem demonstrates the existence of one-to-one mappings between particle densities, wave functions and external potentials. We then focus on these quantities, and quantify how far apart in metric space the approximated and exact ones are. We apply our method to the one-dimensional Hubbard model for different types of external potentials, and assess the regimes where it is applicable to one of the most used approximations in density-functional theory, the local density approximation (LDA)...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322937/predicting-binary-discrete-and-continued-lncrna-disease-associations-via-a-unified-framework-based-on-graph-regression
#5
Jian-Yu Shi, Hua Huang, Yan-Ning Zhang, Yu-Xi Long, Siu-Ming Yiu
BACKGROUND: In human genomes, long non-coding RNAs (lncRNAs) have attracted more and more attention because their dysfunctions are involved in many diseases. However, the associations between lncRNAs and diseases (LDA) still remain unknown in most cases. While identifying disease-related lncRNAs in vivo is costly, computational approaches are promising to not only accelerate the possible identification of associations but also provide clues on the underlying mechanism of various lncRNA-caused diseases...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322372/examination-of-patient-reported-outcomes-in-association-with-tnf-inhibitor-treatment-response-results-from-a-us-observational-cohort-study
#6
Cynthia J Larmore, Natalie N Boytsov, Carol L Gaich, Xiang Zhang, Andre B Araujo, Sabrina Rebello, Bob A Salim, George W Reed, Leslie R Harrold
INTRODUCTION: Implementation of a treat-to-target strategy is challenging when the patient and physician prioritize different goals. This study aimed to "translate" improvements in Clinical Disease Activity Index (CDAI) to concepts that resonate with patients (such as pain, fatigue, morning stiffness) by examining the association between changes in disease activity and patient-reported outcomes (PROs) in a national cohort of patients with rheumatoid arthritis (RA) initiating their first biologic treatment...
January 10, 2018: Rheumatology and Therapy
https://www.readbyqxmd.com/read/29320965/alterations-of-the-gut-microbiota-in-hashimoto-s-thyroiditis-patients
#7
Fuya Zhao, Jing Feng, Jun Li, Lei Zhao, Yang Liu, Huinan Chen, Ye Jin, Biqiang Zhu, Yunwei Wei
BACKGROUND: Hashimoto's thyroiditis (HT) is an organ-specific autoimmune disease in which both genetic predisposition and environmental factors serve as disease triggers. Many studies have indicated that alterations in the gut microbiota are important environmental factors in the development of inflammatory and autoimmune diseases. We systematically performed a comparative analysis of the gut microbiota in HT patients and healthy controls. METHODS: We first conducted a cross-sectional study of 28 HT patients and 16 matched healthy controls...
January 10, 2018: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/29320850/uncovering-the-origin-of-divergence-in-the-csm-cro4-2-m-la-pr-nd-sm-eu-am-family-through-examination-of-the-chemical-bonding-in-a-molecular-cluster-and-by-band-structure-analysis
#8
Shane S Galley, Alexandra A Arico, Tsung-Han Lee, Xiaoyu Deng, Yong-Xin Yao, Joseph M Sperling, Vanessa Proust, Julia S Storbeck, Vladimir Dobrosavljevic, Jennifer N Neu, Theo Siegrist, Ryan E Baumbach, Thomas E Albrecht-Schmitt, Nikolas Kaltsoyannis, Nicola Lanata
A series of f-block chromates, CsM(CrO4)2 (M = La, Pr, Nd, Sm, Eu; Am), were prepared revealing notable differences between the AmIII derivatives and their lanthanide analogs. While all compounds form similar layered structures, the americium compound exhibits polymorphism and adopts both a structure isomorphous with the early lanthanides as well as one that possesses lower symmetry. Both polymorphs are dark red and possess band gaps that are smaller than the LnIII compounds. In order to probe the origin of these differences, the electronic structure of  CsSm(CrO4)2,  CsEu(CrO4)2and  CsAm(CrO4)2 were studied using both a molecular cluster approach featuring hybrid density functional theory and QTAIM analysis, and by the periodic LDA+GA and LDA+DMFT methods...
January 10, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29315232/recognition-of-activities-of-daily-living-based-on-environmental-analyses-using-audio-fingerprinting-techniques-a-systematic-review
#9
REVIEW
Ivan Miguel Pires, Rui Santos, Nuno Pombo, Nuno M Garcia, Francisco Flórez-Revuelta, Susanna Spinsante, Rossitza Goleva, Eftim Zdravevski
An increase in the accuracy of identification of Activities of Daily Living (ADL) is very important for different goals of Enhanced Living Environments and for Ambient Assisted Living (AAL) tasks. This increase may be achieved through identification of the surrounding environment. Although this is usually used to identify the location, ADL recognition can be improved with the identification of the sound in that particular environment. This paper reviews audio fingerprinting techniques that can be used with the acoustic data acquired from mobile devices...
January 9, 2018: Sensors
https://www.readbyqxmd.com/read/29300168/electronic-properties-of-pu-sub-19-sub-os-simulating-%C3%AE-pu-the-strongly-correlated-pu-phase
#10
Ladislav Havela, Silvie Maskova, Jindrich Kolorenc, E Colineau, Jean-Christophe Griveau, Rachel Eloirdi
We established basic electronic properties of ζ-Pu<sub>19</sub>Os, which is a close analogue to β-Pu, and its low-temperature variety, η-Pu<sub>19</sub>Os. Their magnetic susceptibility is by 15% higher than for δ-Pu. Specific heat study of ζ-Pu<sub>19</sub>Os shows a soft lattice similar to δ-Pu, leading to a low Debye temperature <i>Θ</i><sub>D</sub> = 101 K. The linear electronic coefficient <i>γ</i> related to the quasiparticle density of states at the Fermi level points to a higher value, 55±2 mJ/mol Pu K<sup>2</sup>, compared to 40 mJ/mol K<sup>2</sup> for δ-Pu...
January 4, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29299925/a-chiral-sensor-array-for-peptidoglycan-biosynthesis-monitoring-based-on-mos2-nanosheets-supported-host-guest-recognitions
#11
Feng Zhang, Chenwei Lu, Min Wang, Xinsheng Yu, Weili Wei, Zhining Xia
Monitoring the dynamic change in respects of chirality and species of amino acids in bacterial peptidoglycan (PG) during cell wall biosynthesis is correlating with bacterial taxonomy, physiology, micropathology and antibacterial mechanism. However, this is challenging because ever reported methods are usually lack of the ability of chiral analysis with the co-existence of D- and L-amino acids in PG. Here we report a chiral sensor array for PG biosynthesis monitoring through chiral amino acids recognition. Multi-types of host molecules modified MoS2 nanosheets (MNSs) were used as receptor units to achieve more accurate and specific sensing...
January 4, 2018: ACS Sensors
https://www.readbyqxmd.com/read/29298045/volatile-compound-fingerprinting-by-headspace-gas-chromatography-ion-mobility-spectrometry-hs-gc-ims-for-the-authenticity-assessment-of-honey-as-benchtop-alternative-to-1h-nmr-profiling
#12
Natalie Gerhardt, Markus Birkenmeier, Sebastian Schwolow, Sascha Rohn, Philipp Weller
This work describes a simple approach of untargeted profiling of volatile compounds for the authentication of the botanical origin of honey based on resolution-optimized HS-GC-IMS, combined with optimized chemometric techniques, namely PCA, LDA and kNN. A direct comparison of the PCA-LDA models between HS-GC-IMS and 1H-NMR data demonstrated that HS-GC-IMS profiling could be used as a complementary tool to the NMR-based profiling of honey samples. While NMR profiling still requires compara-tively precise sample preparation, in particular, pH adjustment, HS-GC-IMS fingerprinting may be considered as an alternative approach for a truly fully automatable, cost-efficient and in particular, highly sensitive method...
January 3, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29297944/solvent-effects-on-differentiation-of-mouse-brain-tissue-using-laser-microdissection-cut-and-drop-sampling-with-direct-mass-spectral-analysis
#13
John F Cahill, Vilmos Kertesz, Tiffany Porta, J C Yves LeBlanc, Ron M A Heeren, Gary J Van Berkel
RATIONALE: Laser microdissection-liquid vortex capture/electrospray ionization mass spectrometry (LMD-LVC/ESI-MS) has potential for on-line classification of tissue but an investigation into what analytical conditions provide best spectral differentiation has not been conducted. The effects of solvent, ionization polarity, and spectral acquisition parameters on differentiation of mouse brain tissue regions are described. METHODS: Individual 40 × 40 μm microdissections from cortex, white, grey, granular, and nucleus regions of mouse brain tissue were analyzed using different capture/ESI solvents, in positive and negative ion mode ESI, using time-of-flight (TOF)-MS and sequential window acquisitions of all theoretical spectra (SWATH)-MS (a permutation of tandem-MS), and combinations thereof...
January 3, 2018: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/29290635/on-the-rearrangement-of-n-aryl-n-boc-phosphoramidates-to-n-boc-protected-o-aminoarylphosphonates
#14
Edyta Kuliszewska, Friedrich Hammerschmidt
Abstract: Various arylamines were converted in two steps to N-Boc-N-arylphosphoramidates. LiTMP and LDA induced directed ortho-metalation at temperatures from -78 to 0 °C. The ensuing [1,3]-migration of the phosphorus atom with its substituents from the nitrogen to the ortho-carbanionic carbon atom gave N-Boc-protected o-aminoarylphosphonates. The nature of the substituent of 3-substituted phenylphosphoramidates strongly influenced the regioselectivity of phosphonate formation. A crossover experiment with a deuterated phosphoramidate proved the intramolecular course of the rearrangement...
2018: Monatshefte Für Chemie
https://www.readbyqxmd.com/read/29279759/a-standardization-model-based-on-image-recognition-for-performance-evaluation-of-an-oral-scanner
#15
Sang-Wan Seo, Wan-Sun Lee, Jae-Young Byun, Kyu-Bok Lee
PURPOSE: Accurate information is essential in dentistry. The image information of missing teeth is used in optically based medical equipment in prosthodontic treatment. To evaluate oral scanners, the standardized model was examined from cases of image recognition errors of linear discriminant analysis (LDA), and a model that combines the variables with reference to ISO 12836:2015 was designed. MATERIALS AND METHODS: The basic model was fabricated by applying 4 factors to the tooth profile (chamfer, groove, curve, and square) and the bottom surface...
December 2017: Journal of Advanced Prosthodontics
https://www.readbyqxmd.com/read/29278006/relationship-between-disease-activity-and-patient-reported-outcomes-in-rheumatoid-arthritis-post-hoc-analyses-of-overall-and-japanese-results-from-two-phase-3-clinical-trials
#16
Naoki Ishiguro, Maxime Dougados, Zhihong Cai, Baojin Zhu, Masato Ishida, Masayo Sato, Carol Gaich, Amanda Quebe, Ivaylo Stoykov, Yoshiya Tanaka
OBJECTIVE: To examine patient-reported outcomes (PROs) in patients with different rheumatoid arthritis (RA) disease activity levels and identify residual symptoms. METHODS: Post hoc analyses of overall and Japanese data from two randomized controlled trials including RA patients with previous inadequate responses to methotrexate (NCT01710358) or no/minimal previous disease-modifying antirheumatic drug treatment (NCT01711359) (sponsor: Eli Lilly and Company). Week 24 assessments were disease activity (Simplified Disease Activity Index, Disease Activity Score/Disease Activity Score 28 joints-erythrocyte sedimentation rate) and PROs (pain visual analog scale [VAS], morning joint stiffness [MJS], Health Assessment Questionnaire-Disability Index, Functional Assessment of Chronic Illness Therapy-Fatigue, and Medical Outcomes Study Short Form 36 Health Survey Physical and Mental Component Scores)...
December 26, 2017: Modern Rheumatology
https://www.readbyqxmd.com/read/29274736/can-we-accurately-classify-schizophrenia-patients-from-healthy-controls-using-magnetic-resonance-imaging-and-machine-learning-a-multi-method-and-multi-dataset-study
#17
Julie L Winterburn, Aristotle N Voineskos, Gabriel A Devenyi, Eric Plitman, Camilo de la Fuente-Sandoval, Nikhil Bhagwat, Ariel Graff-Guerrero, Jo Knight, M Mallar Chakravarty
Machine learning is a powerful tool that has previously been used to classify schizophrenia (SZ) patients from healthy controls (HC) using magnetic resonance images. Each study, however, uses different datasets, classification algorithms, and validation techniques. Here, we perform a critical appraisal of the accuracy of machine learning methodologies used in SZ/HC classifications studies by comparing three machine learning algorithms (logistic regression [LR], support vector machines [SVMs], and linear discriminant analysis [LDA]) on three independent datasets (435 subjects total) using two tissue density estimates and cortical thickness (CT)...
December 20, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/29274674/comparative-study-between-obstetric-antiphospholipid-syndrome-and-obstetric-morbidity-related-with-antiphospholipid-antibodies
#18
Jaume Alijotas-Reig, Enrique Esteve-Valverde, Raquel Ferrer-Oliveras, Elisa LLurba, Amelia Ruffatti, Angela Tincani, Elmina Lefkou, Mª Tiziana Bertero, Gerard Espinosa, Sara de Carolis, Patrizia Rovere-Querini, Krista Lundelin, Elisa Picardo, Arsene Mekinian
BACKGROUND AND OBJECTIVES: To compare clinical, laboratory, treatment and live birth rate data between women with aPL-related obstetric complications (OMAPS) not fulfilling the Sydney criteria and women fulfilling them (OAPS). MATERIALS AND METHODS: Retrospective and prospective multicentre study. Data comparison between groups from The European Registry on Antiphospholipid Syndrome included within the framework of the European Forum on Antiphospholipid Antibody projects...
December 20, 2017: Medicina Clínica
https://www.readbyqxmd.com/read/29274343/psychological-stress-level-detection-based-on-electrodermal-activity
#19
Yun Liu, Du Siqing
This paper presents a method for detecting psychological stress levels. It aims to explore the feasibility of using a single physiological signal to create a more practical alternative for detecting stress in people than current multiple physiological signals approaches involve. In particular, the approach explored uses linear discriminant analysis (LDA) based on the electrodermal activity (EDA) signal which aims at discriminating between three stress levels: low, medium and high. We used the MIT Media lab 'stress database' from which we selected eleven 'foot' based EDA data sets for our experiments...
December 20, 2017: Behavioural Brain Research
https://www.readbyqxmd.com/read/29251034/residual-symptoms-and-disease-burden-among-patients-with-rheumatoid-arthritis-in-remission-or-low-disease-activity-a-systematic-literature-review
#20
Masato Ishida, Yuki Kuroiwa, Emiko Yoshida, Masayo Sato, Dominika Krupa, Nathaniel Henry, Kei Ikeda, Yuko Kaneko
OBJECTIVES: To identify, describe and summarize evidence on residual symptoms and disease burdens in rheumatoid arthritis (RA) patients qualified as being in remission or low disease activity (LDA). METHODS: A systematic literature review (SLR) was conducted according to Cochrane collaboration guidelines. The population of interest was adult patients with RA in remission or LDA. The reported outcomes of interest were any symptoms or burdens. RESULTS: 51 publications were identified through an e-database search...
December 18, 2017: Modern Rheumatology
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