Genomes and Genes
Summary: A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)
- Berjón Otero M, Lechuga A, Mehla J, Uetz P, Salas M, Redrejo Rodríguez M. Bam35 Tectivirus Intraviral Interaction Map Unveils New Function and Localization of Phage ORFan Proteins. J Virol. 2017;91: pubmed publisher..screening, and these PPIs were further supported by the results of coimmunoprecipitation assays and protein structural models. This approach allowed us to propose new functions for known proteins and hypothesize about the biological ..
- Miller K, Schamber R, Osmanagaoglu O, Ray B. Isolation and characterization of pediocin AcH chimeric protein mutants with altered bactericidal activity. Appl Environ Microbiol. 1998;64:1997-2005 pubmed..The mutations are discussed in the context of structural models that have been proposed for the bacteriocin.
- Baig A, Rana Z, Mannan M, Tariq S, Ahmad H. Antibiotic Effects of Loperamide: Homology of Human Targets of Loperamide with Targets in Acanthamoeba spp. Recent Pat Antiinfect Drug Discov. 2017;12:44-60 pubmed publisher..Amino acid sequences and structural models were compared between human and A...
- Abraham A, Betoko A, Fadrowski J, Pierce C, Furth S, Warady B, et al. Renin-angiotensin II-aldosterone system blockers and time to renal replacement therapy in children with CKD. Pediatr Nephrol. 2017;32:643-649 pubmed publisher..Both Cox proportional hazards models with time-varying RAAS exposure and Cox marginal structural models (MSM) were used to evaluate the effect of RAAS use on time to RRT...
- Logeman B, Thiele D. Reconstitution of a thermophilic Cu+ importer in vitro reveals intrinsic high-affinity slow transport driving accumulation of an essential metal ion. J Biol Chem. 2018;293:15497-15512 pubmed publisher..Given structural models for mammalian Ctr1, Ctr3a likely functions as a low-efficiency Cu+ ion channel...
- Crabtree Ramirez B, Caro Vega Y, Shepherd B, Le C, Turner M, Frola C, et al. Outcomes of HIV-positive patients with cryptococcal meningitis in the Americas. Int J Infect Dis. 2017;63:57-63 pubmed publisher..the first 2 weeks after CM diagnosis versus initiating between 2-8 weeks was assessed using dynamic marginal structural models adjusting for site, age, sex, year of CM, CD4 count, and route of HIV transmission...
- Sharafi M, Rawal S, Fernandez M, Huedo Medina T, Duffy V. Taste phenotype associates with cardiovascular disease risk factors via diet quality in multivariate modeling. Physiol Behav. 2018;194:103-112 pubmed publisher..Multivariate structural models were fitted to identify predictors of CVD risk factors...
- Chaudhary S, Kaushik M, Kukreti R, Kukreti S. Structural switch from a multistranded G-quadruplex to single strands as a consequence of point mutation in the promoter of the human GRIN1 gene. Mol Biosyst. 2017;13:1805-1816 pubmed publisher..Two structural models are propounded for a multistranded parallel G-quadruplex conformation which might be responsible for ..
- Tanaka M, Yoshida K, Fukuma S, Ito K, Matsushita K, Fukagawa M, et al. Effects of Secondary Hyperparathyroidism Treatment on Improvement in Anemia: Results from the MBD-5D Study. PLoS ONE. 2016;11:e0164865 pubmed publisher..Both conventional longitudinal models and marginal structural models were adjusted for confounding factors...
- Wahyunitisari M, Mertaniasih N, Amin M, Artama W, Koendhori E. Vitamin D, cell death pathways, and tuberculosis. Int J Mycobacteriol. 2017;6:349-355 pubmed publisher..The partial least square structural equation modeling with SmartPLS 3.2.6 software was used to analyze structural models among the variables...
- Long W, Panwar P, Witkowska K, Wong K, O Neill D, Chen X, et al. Critical Roles of Two Hydrophobic Residues within Human Glucose Transporter 9 (hSLC2A9) in Substrate Selectivity and Urate Transport. J Biol Chem. 2015;290:15292-303 pubmed publisher..Furthermore, Trp-110 is a critical site for urate transport. Two structural models of the class II glucose transporters, hSLC2A9 and hSLC2A5, based on the crystal structure of hSLC2A1 (GLUT1),..
- Singh J, Srivastava A, Jha P, Sinha K, Kundu B. L-Asparaginase as a new molecular target against leishmaniasis: insights into the mechanism of action and structure-based inhibitor design. Mol Biosyst. 2015;11:1887-96 pubmed publisher..whether this enzyme can serve as a potential drug target against the Leishmania pathogen, we obtained structural models of one of the putative Leishmania l-asparaginase I (LdAI)...
- Shafi T, Sozio S, Luly J, Bandeen Roche K, St Peter W, Ephraim P, et al. Antihypertensive medications and risk of death and hospitalizations in US hemodialysis patients: Evidence from a cohort study to inform hypertension treatment practices. Medicine (Baltimore). 2017;96:e5924 pubmed publisher..We used marginal structural models accounting for time-updated comorbidities to quantify each regimen's association with mortality (both ..
- Kadowaki M, Higasi P, de Godoy M, Prade R, Polikarpov I. Biochemical and structural insights into a thermostable cellobiohydrolase from Myceliophthora thermophila. FEBS J. 2017;: pubmed publisher..GH7 cellobiohydrolases have been studied before and structural models have been proposed...
- Gopalan A, Bhagavat R, Chandra N, Subbarao S, Raja A, Bethunaickan R. Biophysical and biochemical characterization of Rv3405c, a tetracycline repressor protein from Mycobacterium tuberculosis. Biochem Biophys Res Commun. 2018;496:799-805 pubmed publisher..Using a computational pipeline involving analysis of the structural models of the Mtb proteome and an analysis of the ATPome, followed by a series of filters to identify druggable ..
- Hofmann T, Samsonov S, Pichert A, Lemmnitzer K, Schiller J, Huster D, et al. Structural analysis of the interleukin-8/glycosaminoglycan interactions by amide hydrogen/deuterium exchange mass spectrometry. Methods. 2015;89:45-53 pubmed publisher..mass spectrometry (HDX MS) combined with molecular modeling and docking experiments was used to obtain structural models of proinflammatory chemokine interleukin-8 (IL-8) in complex with hexameric chondroitin sulfate...
- Michels K, Mumford S, Sundaram R, Bell E, Bello S, Yeung E. Differences in infant feeding practices by mode of conception in a United States cohort. Fertil Steril. 2016;105:1014-1022.e1 pubmed publisher..Modified Poisson regression was used to compare risks for feeding practices by mode of conception. Marginal structural models were used to estimate the controlled direct effects of fertility treatment on feeding, independent of ..
- Hartmann D, Sima R, Konvičková J, Perner J, Kopacek P, Sojka D. Multiple legumain isoenzymes in ticks. Int J Parasitol. 2018;48:167-178 pubmed publisher..In-silico, IsAE1 and IsAE2 protein three-dimensional structural models displayed minimal differences in overall proenzyme structures, even in comparison with recently resolved ..
- Muratcioglu S, Presman D, Pooley J, GrÃ¸ntved L, Hager G, Nussinov R, et al. Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP. Biophys J. 2015;109:1227-39 pubmed publisher..The structural models indicate that BAF57 and/or BAF250 mediate the interaction between the GR and the SWI/SNF-A complex, ..
- Chaiprasongsuk M, Zhang C, Qian P, Chen X, Li G, Trigiano R, et al. Biochemical characterization in Norway spruce (Picea abies) of SABATH methyltransferases that methylate phytohormones. Phytochemistry. 2018;149:146-154 pubmed publisher..The structural basis of PaSABATHs in discriminating various phytohormone substrates was inferred based on structural models of the enzyme-substrate complexes...
- Roy R, Samanta S, Patra S, Mahato N, Saha R. In silico identification and characterization of sensory motifs in the transcriptional regulators of the ArsR-SmtB family. Metallomics. 2018;10:1476-1500 pubmed publisher..We built structural models of the motifs to show the importance of specific residues in an individual motif...
- Sze H, Chanroj S. Plant Endomembrane Dynamics: Studies of K+/H+ Antiporters Provide Insights on the Effects of pH and Ion Homeostasis. Plant Physiol. 2018;177:875-895 pubmed publisher..Three-dimensional structural models and mutagenesis of Arabidopsis (Arabidopsis thaliana) genes have allowed us to infer that AtCHX17 and ..
- Verma S, Sharma A, Sandhu P, Choudhary N, Sharma S, Acharya V, et al. Proteome scale identification, classification and structural analysis of iron-binding proteins in bread wheat. J Inorg Biochem. 2017;170:63-74 pubmed publisher..Out of 602 putative iron-binding proteins, 130 were able to produce reliable structural models by homology techniques and further analyzed for the presence of iron-binding structural motifs...
- Bergmann P, Huber S, Segl H, Maechler H, Reiter U, Reiter G, et al. Cardiac MR in robotic heart surgery for preoperative identification of the target vessel and precise port placement--a theoretical model. Thorac Cardiovasc Surg. 2003;51:204-10 pubmed..4+/-2.4 cm. Cardiac MR in combination with the navigation grid proved suitable for the visualization of coronary vessels for individually calculating port placement points on the thorax. ..
- Seo Y, Yoo A, Jung J, Sung S, Yang D, Kim W, et al. The active site and substrate-binding mode of 1-aminocyclopropane-1-carboxylate oxidase determined by site-directed mutagenesis and comparative modelling studies. Biochem J. 2004;380:339-46 pubmed
- Chaves L, Pascual M. Comparing models for early warning systems of neglected tropical diseases. PLoS Negl Trop Dis. 2007;1:e33 pubmed
- Bagnoli P, Vismara R, Fiore G, Costantino M. A mechanical model lung for hydraulic testing of total liquid ventilation circuits. Int J Artif Organs. 2005;28:1232-41 pubmed..Moreover, features observed in data acquired during in vivo TLV sessions, such as pressure oscillations due to fluid inertia in the upper airways, were similarly obtained in vitro thanks to the inertial element in the ML...
- Ueno J, Matsuo T, Sugiyama K, Okeda R. Mechanism underlying the prevention of aneurismal rupture by coil embolization. J Med Dent Sci. 2002;49:135-41 pubmed..2, Coil insertion obstructs intra-aneurismal flow and facilitates thrombus formation in the aneurysm. These two factors may operate synergistically to prevent aneurysm rupture. ..
- Dubois J, Klinman J. Mechanism of post-translational quinone formation in copper amine oxidases and its relationship to the catalytic turnover. Arch Biochem Biophys. 2005;433:255-65 pubmed..Ongoing work has focused on uncovering the details of the TPQ formation mechanism. A larger goal is to understand how a single active site is capable of supporting both quinone formation and subsequent catalytic turnover. ..
- Eberle S, Gerber C, von Oldenburg G, Hungerer S, Augat P. Type of hip fracture determines load share in intramedullary osteosynthesis. Clin Orthop Relat Res. 2009;467:1972-80 pubmed publisher..Thus, intramedullary implants can stabilize unstable hip fractures with almost the same amount of stiffness as seen in stable fractures, but they have to bear a higher load share, resulting in higher stresses in the implant. ..
- Martins I, Marinho S, de Oliveira D, de Araújo E. [Poverty, malnutrition and obesity: interrelationships among the nutritional status of members of the same family]. Cien Saude Colet. 2007;12:1553-65 pubmed..Children aged 24 months or less presented more severe risks of delayed growth. ..
- Bitsch R, Loidolt T, Heisel C, Schmalzried T. Cementing techniques for hip resurfacing arthroplasty: development of a laboratory model. J Bone Joint Surg Am. 2008;90 Suppl 3:102-10 pubmed publisher..This model is sensitive to differences in cementing technique. ..
- Toney M. Reaction specificity in pyridoxal phosphate enzymes. Arch Biochem Biophys. 2005;433:279-87 pubmed..Our studies with alanine racemase suggest that the enzyme selectively destabilizes the carbanionic quinonoid intermediate to promote higher racemization specificity by avoiding transamination side reactions. ..
- Kanawati B, Herrmann F, Joniec S, Winterhalter R, Moortgat G. Mass spectrometric characterization of beta-caryophyllene ozonolysis products in the aerosol studied using an electrospray triple quadrupole and time-of-flight analyzer hybrid system and density functional theory. Rapid Commun Mass Spectrom. 2008;22:165-86 pubmed
- Xiao F, Brajer V, Mead R. Blowing in the wind: the impact of China's Pearl River Delta on Hong Kong's air quality. Sci Total Environ. 2006;367:96-111 pubmed..The resulting policy implication is that Hong Kong's primary pollution control efforts should lie at the local level. ..
- Abraham A, Krzyzanski W, Mager D. Partial derivative-based sensitivity analysis of models describing target-mediated drug disposition. AAPS J. 2007;9:E181-9 pubmed..Model 3 was also sensitive to the rates of receptor degradation and internalization. These results suggest that informed sampling may be essential to accurately estimate influential parameters of target-mediated models. ..
- Collins S, Ortiz J, Maruffo F, Hruby G, Pierorazio P, Gupta M, et al. Expedited struvite-stone dissolution using a high-flow low-pressure irrigation system. J Endourol. 2007;21:1153-8 pubmed..Additionally, the system yielded lower intrarenal pressures than standard nephrostomy-tube irrigation. ..
- Chin C, Wehrli F, Hwang S, Jaggard D, Hackney D, Wehrli S. Feasibility of probing boundary morphology of structured materials by 2D NMR q-space imaging. J Magn Reson. 2003;160:20-5 pubmed..The results suggest that 2D q-space imaging may allow probing of the boundary morphology of structured materials and possibly biological cells. ..
- Sancho J, Servera E, Marin J, Vergara P, Belda F, Bach J. Effect of lung mechanics on mechanically assisted flows and volumes. Am J Phys Med Rehabil. 2004;83:698-703 pubmed
- Mercado E. Empowering the staff to assist in planning and developing a freestanding radiation oncology cancer center. J Oncol Manag. 2003;12:15-8 pubmed
- Zanuy D, Gunasekaran K, Lesk A, Nussinov R. Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices. J Mol Biol. 2006;358:330-45 pubmed
- Teraoka T, Sugai T, Nakamura S, Hirasawa H, Oda S, Shiga H, et al. Prediction of iopromide reduction rates during haemodialysis using an in vitro dialysis system. Nephrol Dial Transplant. 2005;20:754-9 pubmed..The in vitro model used in the present study provides pertinent information about CL(HD) and is helpful for predicting RR during HD in individual patients undergoing HD. ..
- Nevzorov A, Opella S. Structural fitting of PISEMA spectra of aligned proteins. J Magn Reson. 2003;160:33-9 pubmed
- Ishida T. Formal analysis of the urban 'Dutch model' with aims of re-formulating spatial quality concerns for pedestrian precincts in current New Town developments. J Physiol Anthropol Appl Human Sci. 2005;24:155-9 pubmed
- Haines R, Brooks L. The facility's role in office economics: the bottom line. J Med Pract Manage. 2005;20:305-7 pubmed..This article discusses the impact of office space configuration on these factors. Not only is profitability increased, satisfaction improves as providers can spend more face-to-face time with patients, and waits are reduced. ..
- Garcia Aymerich J, Lange P, Serra I, Schnohr P, Anto J. Time-dependent confounding in the study of the effects of regular physical activity in chronic obstructive pulmonary disease: an application of the marginal structural model. Ann Epidemiol. 2008;18:775-83 pubmed publisher..Marginal structural models (MSMs) have been proposed to address this type of confounding...
- Esnouf R, Hamer R, Sussman J, Silman I, Trudgian D, Yang Z, et al. Honing the in silico toolkit for detecting protein disorder. Acta Crystallogr D Biol Crystallogr. 2006;62:1260-6 pubmed..Finally, it presents a brief discussion as to how methods of prediction might be improved in the future. ..
- Bahia D, Mortara R, Kusel J, Andrade L, Ludolf F, Kuser P, et al. Schistosoma mansoni: expression of Fes-like tyrosine kinase SmFes in the tegument and terebratorium suggests its involvement in host penetration. Exp Parasitol. 2007;116:225-32 pubmed..These findings suggest that SmFes may play a role in signal transduction pathways involved in larval transformation after penetration into intermediate and definitive hosts. ..
- Savage P, Li C, Taotafa U, Ding B, Guan Q. Antibacterial properties of cationic steroid antibiotics. FEMS Microbiol Lett. 2002;217:1-7 pubmed..Studies of the mechanism of action of these antibiotics suggest that they share mechanistic aspects with cationic peptide antibiotics. ..
- Lee J, Air G. Contacts between influenza virus N9 neuraminidase and monoclonal antibody NC10. Virology. 2002;300:255-68 pubmed..We propose that the difference lies in the contribution of buried water molecules to the NA-NC10 complex. ..
- Zeng Z, Li D, Xue W, Sun L. Structural models and surface equation of state for pulmonary surfactant monolayers. Biophys Chem. 2007;131:88-95 pubmed..b>Structural models of pure protein (SP-B and SP-C) monolayer are proposed to interpret the behavior characteristics of ..
- Lagerstedt J, Voss J, Wieslander A, Persson B. Structural modeling of dual-affinity purified Pho84 phosphate transporter. FEBS Lett. 2004;578:262-8 pubmed..The line shape from labels located at both positions is consistent with the structural environment predicted by the template-generated model, thus supporting the model. ..
- Kopylov A. X-ray analysis of ribosomes: the static of the dynamic. Biochemistry (Mosc). 2002;67:372-82 pubmed..This review considers a brief history, comments, and consequences of recent remarkable achievements: X-ray analysis on the level of atomic resolution of structures of bacterial ribosomes, their subunits, and functional complexes. ..
- Boskovic J, Arnold J, Stilion R, Gordon S, Sim R, Rivera Calzada A, et al. Structural model for the mannose receptor family uncovered by electron microscopy of Endo180 and the mannose receptor. J Biol Chem. 2006;281:8780-7 pubmed..We propose a structural model for the mannose receptor family where at least two conformations exist that may serve to regulate differences in ligand selectivity. ..
- Kazantsev D, Dal Savio C, Pierz K, Güttler B, Danzebrink H. Low-temperature scanning system for near- and far-field optical investigations. J Microsc. 2003;209:199-204 pubmed..The presented results demonstrate the potential of the system. ..
- Walberer B, Cheng A, Frankel A. Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids. J Mol Biol. 2003;327:767-80 pubmed..These studies highlight some of the combinatoric and geometric versatility of base interactions and help provide a framework for analyzing and modeling isomorphic interactions and potentially for designing novel nucleic acid structures. ..
- Lewis D. Structural models for cytochrome P450-mediated catalysis. ScientificWorldJournal. 2003;3:536-45 pubmedThis review focuses on the structural models for cytochrome P450 that are improving our knowledge and understanding of the P450 catalytic cycle, and the way in which substrates bind to the enzyme leading to catalytic conversion and ..
- Sterck F, Schieving F, Lemmens A, Pons T. Performance of trees in forest canopies: explorations with a bottom-up functional-structural plant growth model. New Phytol. 2005;166:827-43 pubmed..The model successfully unravels the interaction effects of different constraints and strategies on tree growth in different canopy light environments. ..
- Torshin I, Harrison R. Protein folding: search for basic physical models. ScientificWorldJournal. 2003;3:623-35 pubmed..In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics. ..
- Mauk M, Rosell F, Mauk A. Structural modelling of metal ion binding to human haemopexin. Nat Prod Rep. 2007;24:523-32 pubmed
- Liu L, Prasad S, Bassano D. Evaluation of two water-equivalent phantom materials for output calibration of photon and electron beams. Med Dosim. 2003;28:267-9 pubmed..0% for solid water and +/- 0.5% for virtual water). We suggest that these corrections are large enough in most cases and should be applied in the calculation of beam outputs. ..
- Menzel E, Bouldin K, Murdock R. Trace explosives detection by photoluminescence. ScientificWorldJournal. 2004;4:55-66 pubmed
- Rumak I, Gieczewska K, Kierdaszuk B, Gruszecki W, Mostowska A, Mazur R, et al. 3-D modelling of chloroplast structure under (Mg2+) magnesium ion treatment. Relationship between thylakoid membrane arrangement and stacking. Biochim Biophys Acta. 2010;1797:1736-48 pubmed publisher..Moreover, we showed that stacking processes always affect the structural changes of chloroplast as a whole...
- Heise M, Schmidt S, Kruger U, Pfitzmann R, Scholz H, Neuhaus P, et al. Local haemodynamics and shear stress in cuffed and straight PTFE-venous anastomoses: an in-vitro comparison using particle image velocimetry. Eur J Vasc Endovasc Surg. 2003;26:367-73 pubmed..Sites of high shear stress correlated well with the known sites of intimal hyperplasia. A cuffed anastomosis type may be favourable in terms of local haemodynamics so enhancing the long-term patency of PTFE-venous grafts. ..
- Zastrow E, Davis S, Lazebnik M, Kelcz F, Van Veen B, Hagness S. Development of anatomically realistic numerical breast phantoms with accurate dielectric properties for modeling microwave interactions with the human breast. IEEE Trans Biomed Eng. 2008;55:2792-800 pubmed publisher..The comprehensive collection of numerical phantoms is made available to the scientific community through an online repository. ..
- Kim J, Brienza D, Lynch R, Cooper R, Boninger M. Effectiveness evaluation of a remote accessibility assessment system for wheelchair users using virtualized reality. Arch Phys Med Rehabil. 2008;89:470-9 pubmed publisher..This system could become an efficient tool for the service provider and can provide expert service to underserved clients that would otherwise be unavailable. ..
- Carey R, Kyle C, Carey D, Leveillee R. Preparation of artificial kidney stones of reproducible size, shape, and mass by precision injection molding. J Endourol. 2008;22:127-32 pubmed publisher..These stones are intended for use in standardized experiments of lithotripsy efficiency in which the shape of the stone as well as the mass can be predetermined and precisely controlled. ..
- Abdulla Y, Amin Y, Khoo H. Determination of percentage depth dose for 6 and 10 MV x-rays using Ge-doped optical fibre and TLD-100. J Radiol Prot. 2002;22:417-21 pubmed..For 6 MV x-ray beams we observe that the depth of maximum dose d(max) is 1.5 and 2 cm for field sizes of 5 x 5 and 10 x 10 cm2 respectively. For 10 MV d(max) is 2 cm for a field size of 5 x 5 cm2 and 2.5 cm for a 10 x 10 cm2 field. ..
- Klarica M, Rados M, Draganic P, Erceg G, Oreskovic D, Marakovic J, et al. Effect of head position on cerebrospinal fluid pressure in cats: comparison with artificial model. Croat Med J. 2006;47:233-8 pubmed..Thus, it seems that the changes in the CSF pressure occur due to the biophysical characteristics of the CSF system rather than the displacement of the blood and CSF volumes from the cranium to the lower part of body. ..
- Ayar L, Love R. Shaping ability of ProFile and K3 rotary Ni-Ti instruments when used in a variable tip sequence in simulated curved root canals. Int Endod J. 2004;37:593-601 pubmed..05) between the instruments in 30 degrees canals. Within the limitation of this study, both rotary nickel-titanium instruments prepared a well-shaped root canal with minimal canal transportation. ..
- Stavropoulos S, Itkin M, Trerotola S. In vitro study of guide wire entrapment in currently available inferior vena cava filters. J Vasc Interv Radiol. 2003;14:905-10 pubmed..5-mm J-tipped guide wires, whereas the Vena Tech LP and Günther Tulip filters did not. This study corroborates previously described wire entrapment by the stainless-steel Greenfield and Vena Tech LGM devices. ..
- Gavranic T. Practice tip. Basic black. Aust Fam Physician. 2006;35:51 pubmed
- Puniene J, Punys V, Punys J, Jurkevicius R. Myocardium structure analysis on echocardiographic images. Stud Health Technol Inform. 2003;95:39-43 pubmed..The statistical analysis was limited to the measurements of the most informative position of the transducer from the compiled database. ..