keyword
MENU ▼
Read by QxMD icon Read
search

Structure prediction

keyword
https://www.readbyqxmd.com/read/28651057/how-to-identify-plasmons-from-the-optical-response-of-nanostructures
#1
Runmin Zhang, Luca Bursi, Joel D Cox, Yao Cui, Caroline M Krauter, Alessandro Alabastri, Alejandro Manjavacas, Arrigo Calzolari, Stefano Corni, Elisa Molinari, Emily A Carter, F Javier Garcia de Abajo, Hui Zhang, Peter Nordlander
A promising trend in plasmonics involves shrinking the size of plasmon-supporting structures down to a few nanometers, thus enabling control over light-matter interaction at extreme-subwavelength scales. In this limit, quantum-mechanical effects, such as nonlocal screening and size quantization, strongly affect the plasmonic response, rendering it substantially different from classical predictions. For very small clusters and molecules, collective plasmonic modes are hard to distinguish from other excitations such as single-electron transitions...
June 26, 2017: ACS Nano
https://www.readbyqxmd.com/read/28650961/mfpred-rapid-and-accurate-prediction-of-protein-peptide-recognition-multispecificity-using-self-consistent-mean-field-theory
#2
Aliza B Rubenstein, Manasi A Pethe, Sagar D Khare
Multispecificity-the ability of a single receptor protein molecule to interact with multiple substrates-is a hallmark of molecular recognition at protein-protein and protein-peptide interfaces, including enzyme-substrate complexes. The ability to perform structure-based prediction of multispecificity would aid in the identification of novel enzyme substrates, protein interaction partners, and enable design of novel enzymes targeted towards alternative substrates. The relatively slow speed of current biophysical, structure-based methods limits their use for prediction and, especially, design of multispecificity...
June 26, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28650932/incremental-value-of-right-atrial-strain-for-early-diagnosis-of-hemodynamic-deterioration-in-pulmonary-hypertension-a-new-noninvasive-tool-for-a-more-comprehensive-diagnostic-paradigma
#3
Cristina Piccinino, Ailia Giubertoni, Jacopo Zanaboni, Miriam Gravellone, Daniele Sola, Roberta Rosso, Lorena Ferrarotti, Paolo Nicola Marino
AIMS: Increased right atrial size is related to adverse prognosis in pulmonary hypertension. The potential incremental value of right atrial function assessment is still unclear. We tested the relationship between right atrial two-dimensional speckle-tracking echocardiography impairment and hemodynamic, functional and clinical deterioration in patients with pulmonary hypertension. METHODS: We prospectively evaluated 36 patients (27 female, 9 male; mean age 68 ± 13 years) with suspected pulmonary hypertension undergoing right heart catheterization and 16 matched controls...
June 24, 2017: Journal of Cardiovascular Medicine
https://www.readbyqxmd.com/read/28650821/detecting-essential-proteins-based-on-network-topology-gene-expression-data-and-gene-ontology-information
#4
Wei Zhang, Jia Xu, Yuanyuan Li, Xiufen Zou
The identification of essential proteins in protein-protein interaction (PPI) networks is of great significance for understanding cellular processes. With the increasing availability of large-scale PPI data, numerous centrality measures based on network topology have been proposed to detect essential proteins from PPI networks. However, most of the current approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology annotation information. In this paper, we propose a novel centrality measure, called TEO, for identifying essential proteins by combining network topology, gene expression profiles and GO information...
October 7, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28650814/multi-label-classification-by-semi-supervised-singular-value-decomposition
#5
Liping Jing, Chenyang Shen, Liu Yang, Jian Yu, Michael K Ng
Multi-label problems arise in various domains including automatic multimedia data categorization, and have generated significant interest in computer vision and machine learning community. However, existing methods do not adequately address two key challenges: exploiting correlations between labels and making up for the lack of labeled data or even missing labeled data. In this paper, we proposed to use a semi-supervised singular value decomposition to handle these two challenges. The proposed model takes advantage of the nuclear norm regularization on the singular value decomposition to effectively capture the label correlations...
June 26, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28650727/models-for-nearly-every-occasion-part-iv-two-box-decreasing-emission-models
#6
Gary H Ganser, Paul Hewett
New two box "well-mixed room" decreasing emission (DE) models are introduced for scenarios that involve local controls, such as some form of local exhaust or local exhaust with filtered return. In addition, these models allow for the recirculation of a filtered (or cleaned) portion of the general room ventilation. For each control device scenario, a steady state and transient near and far field model is presented. The transient equations predict the concentration at time t after the application of the substance...
June 26, 2017: Journal of Occupational and Environmental Hygiene
https://www.readbyqxmd.com/read/28650714/models-for-nearly-every-occasion-part-iii-one-box-decreasing-emission-models
#7
Paul Hewett, Gary H Ganser
New one box "well-mixed room" decreasing emission (DE) models are introduced that allow for local exhaust or local exhaust with filtered return, as well the recirculation of a filtered (or cleaned) portion of the general room ventilation. For each control device scenario, a steady state and transient model is presented. The transient equations predict the concentration at any time t after the application of a known mass of a volatile substance to a surface, and can be used to predict the task exposure profile, the average task exposure, as well as peak and short-term exposures...
June 26, 2017: Journal of Occupational and Environmental Hygiene
https://www.readbyqxmd.com/read/28650586/a-complete-thermodynamic-analysis-of-enzyme-turnover-links-the-free-energy-landscape-to-enzyme-catalysis
#8
Hannah Bl Jones, Stephen A Wells, Erica J Prentice, Anthony Kwok, Liyin L Liang, Vickery L Arcus, Christopher R Pudney
Our understanding of how enzymes work is colored by static structure depictions where the enzyme scaffold is presented as either immobile, or in equilibrium between well-defined static conformations. Proteins however exhibit a large degree of motion over a broad range of timescales and magnitudes and this is defined thermodynamically by the enzyme free energy landscape (FEL). The role and importance of enzyme motion is extremely contentious. Much of the challenge is in the experimental detection of so called 'conformational sampling' involved in enzyme turnover...
June 26, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28650512/elucidating-sequence-and-solvent-specific-design-targets-to-protect-and-stabilize-enzymes-for-biocatalysis-in-ionic-liquids
#9
K G Sprenger, J G Plaks, J L Kaar, J Pfaendtner
For many different frameworks, the structure, function, and dynamics of an enzyme is largely determined by the nature of its interactions with the surrounding host environment, thus a molecular level understanding of enzyme/host interactions is essential to the design of new processes and applications. Ionic liquid (IL) solvents are a popular class of solvents in which to study enzyme behavior, yet it is still not possible to predict how a given enzyme will behave in a given IL solvent. Furthermore, a dearth of experimental data with which to evaluate simulation force fields has prevented the full integration of experimental and computational techniques to gain a complete picture of enzyme/IL interactions...
June 26, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28650199/an-initial-application-of-a-biopsychosocial-framework-to-predict-posttraumatic-stress-following-pediatric-injury
#10
Meghan L Marsac, Nancy Kassam-Adams, Douglas L Delahanty, Jeffrey Ciesla, Danielle Weiss, Keith F Widaman, Lamia P Barakat
OBJECTIVE: Each year millions of children suffer from unintentional injuries that result in poor emotional and physical health. This study examined selected biopsychosocial factors (i.e., child heart rate, peritrauma appraisals, early coping, trauma history) to elucidate their roles in promoting emotional recovery following injury. The study evaluated specific hypotheses that threat appraisals (global and trauma-specific) and coping would predict subsequent posttraumatic stress symptoms (PTSS), that coping would mediate the association between early and later PTSS, and that heart rate would predict PTSS and appraisals would mediate this association...
June 26, 2017: Health Psychology: Official Journal of the Division of Health Psychology, American Psychological Association
https://www.readbyqxmd.com/read/28650197/anger-hostility-and-hospitalizations-in-patients-with-heart-failure
#11
Felicia Keith, David S Krantz, Rusan Chen, Kristie M Harris, Catherine M Ware, Amy K Lee, Paula G Bellini, Stephen S Gottlieb
OBJECTIVE: Heart failure patients have a high hospitalization rate, and anger and hostility are associated with coronary heart disease morbidity and mortality. Using structural equation modeling, this prospective study assessed the predictive validity of anger and hostility traits for cardiovascular and all-cause rehospitalizations in patients with heart failure. METHOD: 146 heart failure patients were administered the STAXI and Cook-Medley Hostility Inventory to measure anger, hostility, and their component traits...
June 26, 2017: Health Psychology: Official Journal of the Division of Health Psychology, American Psychological Association
https://www.readbyqxmd.com/read/28650175/bioactive-peptide-natural-products-as-lead-structures-for-medicinal-use
#12
Tam Dang, Roderich D Süssmuth
The need for new drugs for the treatment of various diseases is enormous. From the previous century until the present, numerous peptide and peptide-derived natural products have been isolated from bacteria and fungi. Hence, microorganisms play a pivotal role as sources for novel drugs with an emphasis on anti-infective agents. Various disciplines from biology, chemistry, and medicine are involved in early stages of the search for peptide natural products including taxonomy, microbiology, bioanalytics, bioinformatics, and medicinal chemistry...
June 26, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28650154/interrogating-detergent-desolvation-of-nanopore-forming-proteins-by-fluorescence-polarization-spectroscopy
#13
Aaron J Wolfe, Yi-Ching Hsueh, Adam R Blanden, Mohammad M Mohammad, Bach Pham, Avinash Kumar Thakur, Stewart N Loh, Min Chen, Liviu Movileanu
Understanding how membrane proteins interact with detergents is of fundamental and practical significance in structural and chemical biology as well as in nanobiotechnology. Current methods for inspecting protein-detergent complex (PDC) interfaces require high concentrations of protein and are of low throughput. Here, we describe a scalable, spectroscopic approach that uses nanomolar protein concentrations in native solutions. This approach, which is based on steady-state fluorescence polarization (FP) spectroscopy, kinetically resolves the dissociation of detergents from membrane proteins and protein unfolding...
June 26, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28650016/prediction-of-1-h-nmr-chemical-shifts-for-clusters-of-imidazolium-based-ionic-liquids
#14
Su Chen, Ekaterina I Izgorodina
Nuclear magnetic resonance (NMR) has been widely used to elucidate the bulk structure of ionic liquids. In this work, we calculated (1)H NMR chemical shifts of 1-ethyl-3-methylimidazolium (C2mim(+)) ionic liquids combined with various anions such as chloride (Cl), tetrafluoroborate (BF4), hexafluorophosphate (PF6), acetate (OAc), trifluoroacetate (TFA), and dicyanamide (DCA). The previously established level of theory, HF/6-311G+(3df,2p), was used for the accurate prediction of NMR chemical shifts both in gas phase and in solvents with varying dielectric constant such as CHCl3 and ethanol...
June 26, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28649831/non-abelian-parton-fractional-quantum-hall-effect-in-multilayer-graphene
#15
Yinghai Wu, Tao Shi, Jainendra K Jain
The current proposals for producing non-Abelian anyons and Majorana particles, which are neither fermions nor bosons, are primarily based on the realization of topological superconductivity in two dimensions. We show theoretically that the unique Landau level structure of bilayer graphene provides a new possible avenue for achieving such exotic particles. Specifically, we demonstrate the feasibility of a ``parton" fractional quantum Hall (FQH) state, which supports non-Abelian particles without the usual topological superconductivity...
June 26, 2017: Nano Letters
https://www.readbyqxmd.com/read/28649677/outcome-prediction-for-patient-with-high-grade-gliomas-from-brain-functional-and-structural-networks
#16
Luyan Liu, Han Zhang, Islem Rekik, Xiaobo Chen, Qian Wang, Dinggang Shen
High-grade glioma (HGG) is a lethal cancer, which is characterized by very poor prognosis. To help optimize treatment strategy, accurate preoperative prediction of HGG patient's outcome (i.e., survival time) is of great clinical value. However, there are huge individual variability of HGG, which produces a large variation in survival time, thus making prognostic prediction more challenging. Previous brain imaging-based outcome prediction studies relied only on the imaging intensity inside or slightly around the tumor, while ignoring any information that is located far away from the lesion (i...
October 2016: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/28649659/inflammation-of-mammary-adipose-tissue-occurs-in-overweight-and-obese-patients-exhibiting-early-stage-breast-cancer
#17
Charlotte Vaysse, Jon Lømo, Øystein Garred, Frøydis Fjeldheim, Trygve Lofteroed, Ellen Schlichting, Anne McTiernan, Hanne Frydenberg, Anders Husøy, Steinar Lundgren, Morten W Fagerland, Elin Richardsen, Erik A Wist, Catherine Muller, Inger Thune
Growing evidence indicates that adiposity is associated with breast cancer risk and negatively affects breast cancer recurrence and survival, a paracrine role of mammary adipose tissue being very likely in this process. In contrast to other adipose depots, occurrence of a sub-inflammatory state of mammary adipose tissue defined by dying adipocytes surrounded by macrophages forming crown-like structures in overweight and obese subjects, remains only partially described. In a general population of breast cancer patients (107 patients) mostly undergoing breast-conserving surgery, we found a positive association between patient's body composition, breast adipocytes size, and presence of crown-like structures in mammary adipose tissue close to the tumor...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/28649444/reverse-engineering-highlights-potential-principles-of-large-gene-regulatory-network-design-and-learning
#18
Clément Carré, André Mas, Gabriel Krouk
Inferring transcriptional gene regulatory networks from transcriptomic datasets is a key challenge of systems biology, with potential impacts ranging from medicine to agronomy. There are several techniques used presently to experimentally assay transcription factors to target relationships, defining important information about real gene regulatory networks connections. These techniques include classical ChIP-seq, yeast one-hybrid, or more recently, DAP-seq or target technologies. These techniques are usually used to validate algorithm predictions...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649312/the-eu-aims-longitudinal-european-autism-project-leap-design-and-methodologies-to-identify-and-validate-stratification-biomarkers-for-autism-spectrum-disorders
#19
Eva Loth, Tony Charman, Luke Mason, Julian Tillmann, Emily J H Jones, Caroline Wooldridge, Jumana Ahmad, Bonnie Auyeung, Claudia Brogna, Sara Ambrosino, Tobias Banaschewski, Simon Baron-Cohen, Sarah Baumeister, Christian Beckmann, Michael Brammer, Daniel Brandeis, Sven Bölte, Thomas Bourgeron, Carsten Bours, Yvette de Bruijn, Bhismadev Chakrabarti, Daisy Crawley, Ineke Cornelissen, Flavio Dell' Acqua, Guillaume Dumas, Sarah Durston, Christine Ecker, Jessica Faulkner, Vincent Frouin, Pilar Garces, David Goyard, Hannah Hayward, Lindsay M Ham, Joerg Hipp, Rosemary J Holt, Mark H Johnson, Johan Isaksson, Prantik Kundu, Meng-Chuan Lai, Xavier Liogier D'ardhuy, Michael V Lombardo, David J Lythgoe, René Mandl, Andreas Meyer-Lindenberg, Carolin Moessnang, Nico Mueller, Laurence O'Dwyer, Marianne Oldehinkel, Bob Oranje, Gahan Pandina, Antonio M Persico, Amber N V Ruigrok, Barbara Ruggeri, Jessica Sabet, Roberto Sacco, Antonia San José Cáceres, Emily Simonoff, Roberto Toro, Heike Tost, Jack Waldman, Steve C R Williams, Marcel P Zwiers, Will Spooren, Declan G M Murphy, Jan K Buitelaar
BACKGROUND: The tremendous clinical and aetiological diversity among individuals with autism spectrum disorder (ASD) has been a major obstacle to the development of new treatments, as many may only be effective in particular subgroups. Precision medicine approaches aim to overcome this challenge by combining pathophysiologically based treatments with stratification biomarkers that predict which treatment may be most beneficial for particular individuals. However, so far, we have no single validated stratification biomarker for ASD...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28649242/an-approach-for-a-synthetic-ctl-vaccine-design-against-zika-flavivirus-using-class-i-and-class-ii-epitopes-identified-by-computer-modeling
#20
Edecio Cunha-Neto, Daniela S Rosa, Paul E Harris, Tim Olson, Alex Morrow, Serban Ciotlos, Charles V Herst, Reid Martin Rubsamen
The threat posed by severe congenital abnormalities related to Zika virus (ZKV) infection during pregnancy has turned development of a ZKV vaccine into an emergency. Recent work suggests that the cytotoxic T lymphocyte (CTL) response to infection is an important defense mechanism in response to ZKV. Here, we develop the rationale and strategy for a new approach to developing cytotoxic T lymphocyte (CTL) vaccines for ZKV flavivirus infection. The proposed approach is based on recent studies using a protein structure computer model for HIV epitope selection designed to select epitopes for CTL attack optimized for viruses that exhibit antigenic drift...
2017: Frontiers in Immunology
keyword
keyword
59621
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"