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Principal components analysis

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https://www.readbyqxmd.com/read/29350952/fast-data-sorting-with-modified-principal-component-analysis-to-distinguish-unique-single-molecular-break-junction-trajectories
#1
J M Hamill, X T Zhao, G Mészáros, M R Bryce, M Arenz
A simple and fast analysis method to sort large data sets into groups with shared distinguishing characteristics is described and applied to single molecular break junction conductance versus electrode displacement data. The method, based on principal component analysis, successfully sorts data sets based on the projection of the data onto the first or second principal component of the correlation matrix without the need to assert any specific hypothesis about the expected features within the data. This is an improvement on the current correlation matrix analysis approach because it sorts data automatically, making it more objective and less time consuming, and our method is applicable to a wide range of multivariate data sets...
January 5, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29350879/genetic-and-chemical-diversity-in-perovskia-abrotanoides-karel-lamiaceae-populations-based-on-issrs-markers-and-essential-oils-profile
#2
Seyyed Hossein Pourhosseini, Javad Hadian, Ali Sonboli, Samad Nejad Ebrahimi, Mohammad Hossein Mirjalili
Genetic and the essential oil composition variability among twelve Perovskia abrotanoides populations (PAbPs) growing wild in Iran were assessed by ISSR markers, GC-FID and GC-MS, respectively. Nine selected ISSR primers produced 119 discernible bands, of them 96 (80.7%) being polymorphic. Genetic similarity values among populations ranged between 0.07 and 0.79 which indicated a high level of genetic variation. Polymorphic information content, resolving power and marker index generated by ISSR primers were, 0...
January 19, 2018: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/29350124/a-dimensional-approach-to-assessing-psychiatric-risk-in-adults-born-very-preterm
#3
Jasmin Kroll, Sean Froudist-Walsh, Philip J Brittain, Chieh-En J Tseng, Vyacheslav Karolis, Robin M Murray, Chiara Nosarti
BACKGROUND: Individuals who were born very preterm have higher rates of psychiatric diagnoses compared with term-born controls; however, it remains unclear whether they also display increased sub-clinical psychiatric symptomatology. Hence, our objective was to utilize a dimensional approach to assess psychiatric symptomatology in adult life following very preterm birth. METHODS: We studied 152 adults who were born very preterm (before 33 weeks' gestation; gestational range 24-32 weeks) and 96 term-born controls...
January 19, 2018: Psychological Medicine
https://www.readbyqxmd.com/read/29349544/interpretation-of-motion-analysis-of-laparoscopic-instruments-based-on-principal-component-analysis-in-box-trainer-settings
#4
Ignacio Oropesa, Fernando Pérez Escamirosa, Juan A Sánchez-Margallo, Silvia Enciso, Borja Rodríguez-Vila, Arturo Minor Martínez, Francisco M Sánchez-Margallo, Enrique J Gómez, Patricia Sánchez-González
BACKGROUND: Motion analysis parameters (MAPs) have been extensively validated for assessment of minimally invasive surgical skills. However, there are discrepancies on how specific MAPs, tasks, and skills match with each other, reflecting that motion analysis cannot be generalized independently of the learning outcomes of a task. Additionally, there is a lack of knowledge on the meaning of motion analysis in terms of surgical skills, making difficult the provision of meaningful, didactic feedback...
January 18, 2018: Surgical Endoscopy
https://www.readbyqxmd.com/read/29348723/metabolite-profiling-of-fermented-ginseng-extracts-by-gas-chromatography-mass-spectrometry
#5
Seong-Eun Park, Seung-Ho Seo, Kyoung In Lee, Chang-Su Na, Hong-Seok Son
Background: Ginseng contains many small metabolites such as amino acids, fatty acids, carbohydrates, and ginsenosides. However, little is known about the relationships between microorganisms and metabolites during the entire ginseng fermentation process. We investigated metabolic changes during ginseng fermentation according to the inoculation of food-compatible microorganisms. Methods: Gas chromatography mass spectrometry (GC-MS) datasets coupled with the multivariate statistical method for the purpose of latent-information extraction and sample classification were used for the evaluation of ginseng fermentation...
January 2018: Journal of Ginseng Research
https://www.readbyqxmd.com/read/29348591/relapsing-remitting-multiple-sclerosis-diagnosis-from-cerebrospinal-fluids-via-fourier-transform-infrared-spectroscopy-coupled-with-multivariate-analysis
#6
Dilek Yonar, Levent Ocek, Bedile Irem Tiftikcioglu, Yasar Zorlu, Feride Severcan
Multiple sclerosis (MS) is a chronic, progressive, inflammatory and degenerative disease of central nervous system. Here, we aimed to develop a method for differential diagnosis of Relapsing-Remitting MS (RRMS) and clinically isolated syndrome (CIS) patients, as well as to identify CIS patients who will progress to RRMS, from cerebrospinal fluid (CSF) by infrared (IR) spectroscopy and multivariate analysis. Spectral analyses demonstrated significant differences in the molecular contents, especially in the lipids and Z conformation of DNA of CSF from CIS, CIS to RRMS transformed (TCIS) and RRMS groups...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348443/a-general-and-flexible-method-for-signal-extraction-from-single-cell-rna-seq-data
#7
Davide Risso, Fanny Perraudeau, Svetlana Gribkova, Sandrine Dudoit, Jean-Philippe Vert
Single-cell RNA-sequencing (scRNA-seq) is a powerful high-throughput technique that enables researchers to measure genome-wide transcription levels at the resolution of single cells. Because of the low amount of RNA present in a single cell, some genes may fail to be detected even though they are expressed; these genes are usually referred to as dropouts. Here, we present a general and flexible zero-inflated negative binomial model (ZINB-WaVE), which leads to low-dimensional representations of the data that account for zero inflation (dropouts), over-dispersion, and the count nature of the data...
January 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29347852/the-patient-categorisation-tool-psychometric-evaluation-of-a-tool-to-measure-complexity-of-needs-for-rehabilitation-in-a-large-multicentre-dataset-from-the-united-kingdom
#8
Lynne Turner-Stokes, Christian U Krägeloh, Richard J Siegert
PURPOSE: This first psychometric evaluation of the Patient Categorisation Tool examined its properties as an instrument to measure complexity of needs in a mixed population of patients presenting for specialist neurorehabilitation. MATERIALS/METHODS: Analysis of a large multicentre cohort of patients (n = 5396) from the national clinical dataset representing 63 specialist rehabilitation services across England. Structural validity was examined using exploratory and confirmatory factor analysis...
January 18, 2018: Disability and Rehabilitation
https://www.readbyqxmd.com/read/29347325/two-step-relaxation-mode-analysis-with-multiple-evolution-times-applied-to-all-atom-molecular-dynamics-protein-simulation
#9
N Karasawa, A Mitsutake, H Takano
Proteins implement their functionalities when folded into specific three-dimensional structures, and their functions are related to the protein structures and dynamics. Previously, we applied a relaxation mode analysis (RMA) method to protein systems; this method approximately estimates the slow relaxation modes and times via simulation and enables investigation of the dynamic properties underlying the protein structural fluctuations. Recently, two-step RMA with multiple evolution times has been proposed and applied to a slightly complex homopolymer system, i...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346328/comparison-of-svm-rf-and-elm-on-an-electronic-nose-for-the-intelligent-evaluation-of-paraffin-samples
#10
Hong Men, Songlin Fu, Jialin Yang, Meiqi Cheng, Yan Shi, Jingjing Liu
Paraffin odor intensity is an important quality indicator when a paraffin inspection is performed. Currently, paraffin odor level assessment is mainly dependent on an artificial sensory evaluation. In this paper, we developed a paraffin odor analysis system to classify and grade four kinds of paraffin samples. The original feature set was optimized using Principal Component Analysis (PCA) and Partial Least Squares (PLS). Support Vector Machine (SVM), Random Forest (RF), and Extreme Learning Machine (ELM) were applied to three different feature data sets for classification and level assessment of paraffin...
January 18, 2018: Sensors
https://www.readbyqxmd.com/read/29346294/gc-ms-analysis-of-the-volatile-constituents-in-the-leaves-of-14-compositae-plants
#11
Yiguang Wang, Xiran Li, Qinjie Jiang, Hainan Sun, Jiafu Jiang, Sumei Chen, Zhiyong Guan, Weimin Fang, Fadi Chen
The green organs, especially the leaves, of many Compositae plants possess characteristic aromas. To exploit the utility value of these germplasm resources, the constituents, mainly volatile compounds, in the leaves of 14 scented plant materials were qualitatively and quantitatively compared via gas chromatography-mass spectrometry (GC-MS). A total of 213 constituents were detected and tentatively identified in the leaf extracts, and terpenoids (especially monoterpene and sesquiterpene derivatives), accounting for 40...
January 18, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29345906/prediction-of-hot-spots-at-myeloid-cell-leukemia-1-inhibitors-interface-using-energy-estimation-and-alanine-scanning-mutagenesis
#12
Parthiban Marimuthu, Kalaimathy Singaravelu
Myeloid cell leukemia 1 (Mcl1) is an anti-apoptotic protein that plays central role in apoptosis regulation. Also, Mcl1 has the potency to resist apoptotic cues resulting in up-regulation and cancer cell protection. A molecular probe that has the potential to specifically target Mcl1, and thereby provoke its down-regulatory activity is very essential. The aim of the current study is to probe the internal conformational dynamics of protein motions and potential binding mechanism in response to a series of picomolar range Mcl1 inhibitors using explicit-solvent molecular dynamics (MD) simulations...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345800/haplotype-based-genotyping-by-sequencing-in-oat-genome-research
#13
Wubishet A Bekele, Charlene P Wight, Shiaoman Chao, Catherine J Howarth, Nicholas A Tinker
In a de-novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker-density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel...
January 18, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29345556/positional-differences-in-elite-basketball-selecting-appropriate-training-load-measures
#14
Luka Svilar, Julen Castellano, Igor Jukic, David Casamichana
PURPOSE: The purpose of this paper was to study the structure of interrelationships among external training load measures and how these vary among different positions in elite basketball. METHODS: Eight external variables of jumping (JUMP), acceleration (ACC), deceleration (DEC) and change of direction (COD), and two internal load variables (RPE and sRPE) were collected from 13 professional players with 300 session records. Three playing positions were considered: guards (n=4), forwards (n=4) and centers (n=5)...
January 18, 2018: International Journal of Sports Physiology and Performance
https://www.readbyqxmd.com/read/29344957/rapid-differentiation-of-chinese-hops-varieties-humulus-lupulus-using-volatile-fingerprinting-by-hs-spme-gc-ms-combined-with-multivariate-statistical-analysis
#15
Zechang Liu, Liping Wang, Yumei Liu
BACKGROUND: Hops imparts flavor to beer, and its volatile components characterize the various hops varieties and qualities. The volatile components of hops are used for distinguishing between its various varieties and qualities. Fingerprinting, especially flavor fingerprinting, is often used to identify "flavor products", since inconsistencies in the description of flavor may lead to incorrect definition of beer quality. Compared to flavor fingerprinting, volatile fingerprinting is simpler and easier...
January 18, 2018: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/29344947/genome-wide-population-structure-and-admixture-analysis-reveals-weak-differentiation-among-ugandan-goat-breeds
#16
R B Onzima, M R Upadhyay, R Mukiibi, E Kanis, M A M Groenen, R P M A Crooijmans
Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei...
January 17, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29344732/recognition-of-the-importance-of-geogenic-sources-in-the-content-of-metals-in-pm2-5-collected-in-the-mexico-city-metropolitan-area
#17
Ofelia Morton-Bermea, Rodrigo Garza-Galindo, Elizabeth Hernández-Álvarez, Omar Amador-Muñoz, Maria Elena Garcia-Arreola, Sara L Ordoñez-Godínez, Laura Beramendi-Orosco, Graciela L Santos-Medina, Javier Miranda, Irma Rosas-Pérez
The study of airborne metals in urban areas is relevant due to their toxic effects on human health and organisms. In this study, we analyzed metals including rare earth elements (REE) in particles smaller than 2.5 μm (PM2.5), collected at five sites around the Mexico City Metropolitan Area (MCMA), during three periods in 2011: April (dry-warm season, DW), August (rainy season, R), and November (dry-cold season, DC). Principal component analysis allowed identifying factors related to geogenic sources and factors related to anthropogenic sources...
January 17, 2018: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/29343737/moderate-decline-in-select-synaptic-markers-in-the-prefrontal-cortex-ba9-of-patients-with-alzheimer-s-disease-at-various-cognitive-stages
#18
Odile Poirel, Sébastien Mella, Catherine Videau, Lauriane Ramet, Maria Antonietta Davoli, Etienne Herzog, Pavel Katsel, Naguib Mechawar, Vahram Haroutunian, Jacques Epelbaum, Stéphanie Daumas, Salah El Mestikawy
Synaptic loss, plaques and neurofibrillary tangles are viewed as hallmarks of Alzheimer's disease (AD). This study investigated synaptic markers in neocortical Brodmann area 9 (BA9) samples from 171 subjects with and without AD at different levels of cognitive impairment. The expression levels of vesicular glutamate transporters (VGLUT1&2), glutamate uptake site (EAAT2), post-synaptic density protein of 95 kD (PSD95), vesicular GABA/glycine transporter (VIAAT), somatostatin (som), synaptophysin and choline acetyl transferase (ChAT) were evaluated...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343701/alanine-mutation-of-the-catalytic-sites-of-pantothenate-synthetase-causes-distinct-conformational-changes-in-the-atp-binding-region
#19
Bharati Pandey, Sonam Grover, Sukriti Goyal, Anchala Kumari, Aditi Singh, Salma Jamal, Jagdeep Kaur, Abhinav Grover
The enzyme Pantothenate synthetase (PS) represents a potential drug target in Mycobacterium tuberculosis. Its X-ray crystallographic structure has demonstrated the significance and importance of conserved active site residues including His44, His47, Asn69, Gln72, Lys160 and Gln164 in substrate binding and formation of pantoyl adenylate intermediate. In the current study, molecular mechanism of decreased affinity of the enzyme for ATP caused by alanine mutations was investigated using molecular dynamics (MD) simulations and free energy calculations...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343650/decoder-calibration-with-ultra-small-current-sample-set-for-intracortical-brain-machine-interface
#20
Peng Zhang, Xuan Ma, Luyao Chen, Jin Zhou, Changyong Wang, Wei Li, Jiping He
OBJECTIVE: Intracortical brain-machine interfaces (iBMIs) aim to restore efficient communication and movement ability for paralyzed patients. However, frequent recalibration is required for consistency and reliability, and every recalibration will require relatively large most current sample set. The aim in this study is to develop an effective decoder calibration method that can achieve good performance while minimizing recalibration time. APPROACH: Two rhesus macaques implanted with intracortical microelectrode arrays were trained separately on movement and sensory paradigm...
January 18, 2018: Journal of Neural Engineering
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