keyword
MENU ▼
Read by QxMD icon Read
search

Computational biology

keyword
https://www.readbyqxmd.com/read/28646471/decoding-early-myelopoiesis-from-dynamics-of-core-endogenous-network
#1
Hang Su, Gaowei Wang, Ruoshi Yuan, Junqiang Wang, Ying Tang, Ping Ao, Xiaomei Zhu
A decade ago mainstream molecular biologists regarded it impossible or biologically ill-motivated to understand the dynamics of complex biological phenomena, such as cancer genesis and progression, from a network perspective. Indeed, there are numerical difficulties even for those who were determined to explore along this direction. Undeterred, seven years ago a group of Chinese scientists started a program aiming to obtain quantitative connections between tumors and network dynamics. Many interesting results have been obtained...
May 29, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28644851/comorbidities-in-the-diseasome-are-more-apparent-than-real-what-bayesian-filtering-reveals-about-the-comorbidities-of-depression
#2
Peter Marx, Peter Antal, Bence Bolgar, Gyorgy Bagdy, Bill Deakin, Gabriella Juhasz
Comorbidity patterns have become a major source of information to explore shared mechanisms of pathogenesis between disorders. In hypothesis-free exploration of comorbid conditions, disease-disease networks are usually identified by pairwise methods. However, interpretation of the results is hindered by several confounders. In particular a very large number of pairwise associations can arise indirectly through other comorbidity associations and they increase exponentially with the increasing breadth of the investigated diseases...
June 23, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28644841/low-dimensional-spike-rate-models-derived-from-networks-of-adaptive-integrate-and-fire-neurons-comparison-and-implementation
#3
Moritz Augustin, Josef Ladenbauer, Fabian Baumann, Klaus Obermayer
The spiking activity of single neurons can be well described by a nonlinear integrate-and-fire model that includes somatic adaptation. When exposed to fluctuating inputs sparsely coupled populations of these model neurons exhibit stochastic collective dynamics that can be effectively characterized using the Fokker-Planck equation. This approach, however, leads to a model with an infinite-dimensional state space and non-standard boundary conditions. Here we derive from that description four simple models for the spike rate dynamics in terms of low-dimensional ordinary differential equations using two different reduction techniques: one uses the spectral decomposition of the Fokker-Planck operator, the other is based on a cascade of two linear filters and a nonlinearity, which are determined from the Fokker-Planck equation and semi-analytically approximated...
June 23, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28644820/investigation-of-real-tissue-water-equivalent-path-lengths-using-an-efficient-dose-extinction-method
#4
Rongxiao Zhang, Esther Baer, Kyung-Wook Jee, Gregory C Sharp, Jay Flanz, Hsiao-Ming Lu
For proton therapy, an accurate conversion of CT HU to relative stopping power (RSP) is essential. Validation of the conversion based on real tissue samples is more direct than the current practice solely based on tissue substitutes and can potentially address variations over the population. Based on a novel dose extinction method, we measured water equivalent path lengths (WEPL) on animal tissue samples to evaluate the accuracy of CT HU to RSP conversion and potential variations over a population. A broad proton beam delivered a spread out Bragg peak to the samples sandwiched between a water tank and a 2D ion-chamber detector...
June 23, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28644563/gas-phase-dissociation-study-of-erythrinian-alkaloids-by-electrospray-ionization-mass-spectrometry-and-computational-methods
#5
T Guaratini, L G P Feitosa, D B Silva, N P Lopes, J L C Lopes, R Vessecchi
Alkaloids from plants of the genus Erythrina display important biological activities, including anxiolytic action. Characterization of these alkaloids by mass spectrometry (MS) has contributed to the construction of a spectral library, has improved understanding of their structures, and has supported the proposal of fragmentation mechanisms in light of density functional calculations (DFT). In this study, we have used low- and high-resolution MS(n) analyses to investigate the fragmentation patterns of erythrinian alkaloids; we have employed the B3LYP/6-31+G(d,p) model to obtain their reactive sites...
June 23, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28643930/moving-towards-precision-orthodontics-an-evolving-paradigm-shift-in-the-planning-and-delivery-of-customized-orthodontic-therapy
#6
REVIEW
A H Jheon, S Oberoi, R C Solem, S Kapila
Advances in precision medicine portend similar progress in orthodontics and will be increasingly harnessed to achieve customized treatment approaches and enhance treatment efficiencies. Our goal is to provide a background on emerging advances in computer technologies and biomedicine and highlight their current and likely future applications to precision orthodontics. A review of orthodontically relevant technologies and advances in pertinent biological research was undertaken. Innovations in computer hardware and software, and 3D imaging technologies offer the ability for customized treatment and biomechanical planning that will be more fully realized within the next few decades...
June 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28643923/micro-anatomical-responses-in-periodontal-complexes-of-mice-to-calibrated-orthodontic-forces-on-the-crown
#7
A Pal, L Chen, L Yang, F Yang, B Meng, A H Jheon, S P Ho
OBJECTIVE: Correlating mechanical forces with quantifiable physical changes in the dentoalveolar complex. SETTING AND SAMPLE POPULATION: Male 6-week C57BL/6 mice (N=3), micro X-ray-computed tomography; post-analysis software to extract physical changes in periodontal ligament (PDL)-space. MATERIALS AND METHODS: Silicone-elastic bands were placed between maxillary molars for 1 week, with the contralateral side as internal control. Average displacements between crowns and roots, and changes in PDL-spaces were evaluated by registering X-ray tomograms of experimental and control hemi-maxillae...
June 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28643868/the-potassium-battery-a-mobile-energy-source-for-transport-processes-in-plant-vascular-tissues
#8
REVIEW
Ingo Dreyer, Judith Lucia Gomez-Porras, Janin Riedelsberger
Contents I. II. III. IV. V. VI. VII. VIII. References SUMMARY: Plant roots absorb potassium ions from the soil and transport them in the xylem via the transpiration stream to the shoots. There, in source tissues where sufficient chemical energy (ATP) is available, K(+) is loaded into the phloem and then transported with the phloem stream to other parts of the plant; in part, transport is also back to the roots. This, at first sight, futile cycling of K(+) has been uncovered to be part of a sophisticated mechanism that (1) enables the shoot to communicate its nutrient demand to the root, (2) contributes to the K(+) nutrition of transport phloem tissues and (3) transports energy stored in the K(+) gradient between phloem cytosol and the apoplast...
June 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/28643003/recent-developments-in-solution-nuclear-magnetic-resonance-nmr-based-molecular-biology
#9
REVIEW
Joshua J Ziarek, Diego Baptista, Gerhard Wagner
Visualizing post-translational modifications, conformations, and interaction surfaces of protein structures at atomic resolution underpins the development of novel therapeutics to combat disease. As computational resources expand, in silico calculations coupled with experimentally derived structures and functional assays have led to an explosion in structure-based drug design (SBDD) with several compounds in clinical trials. It is increasingly clear that "hidden" transition-state structures along activation trajectories can be harnessed to develop novel classes of allosteric inhibitors...
June 23, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28642491/a-cross-species-approach-to-identify-transcriptional-regulators-exemplified-for-dnajc22-and-hnf4a
#10
A C Aschenbrenner, K Bassler, M Brondolin, L Bonaguro, P Carrera, K Klee, T Ulas, J L Schultze, M Hoch
There is an enormous need to make better use of the ever increasing wealth of publicly available genomic information and to utilize the tremendous progress in computational approaches in the life sciences. Transcriptional regulation of protein-coding genes is a major mechanism of controlling cellular functions. However, the myriad of transcription factors potentially controlling transcription of any given gene makes it often difficult to quickly identify the biological relevant transcription factors. Here, we report on the identification of Hnf4a as a major transcription factor of the so far unstudied DnaJ heat shock protein family (Hsp40) member C22 (Dnajc22)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642368/the-influence-of-disulfide-bonds-on-the-mechanical-stability-of-proteins-is-context-dependent
#11
Aitor Manteca, Álvaro Alonso-Caballero, Marie Fertin, Simon Poly, David De Sancho, Raul Perez-Jimenez
Disulfide bonds play a crucial role in proteins, modulating their stability and constraining their conformational dynamics. A particularly important case is that of proteins that need to withstand forces arising from their normal biological function and that are often disulfide bonded. However, the influence of disulfides on the overall mechanical stability of proteins is poorly understood. Here, we used single-molecule force spectroscopy (smFS) to study the role of disulfide bonds in different mechanical proteins in terms of their unfolding forces...
June 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28642271/powerful-genetic-association-analysis-for-common-or-rare-variants-with-high-dimensional-structured-traits
#12
Xiang Zhan, Ni Zhao, Anna Plantinga, Timothy A Thornton, Karen N Conneely, Michael P Epstein, Michael C Wu
Many genetic association studies collect a wide range of complex traits. As these traits may be correlated and share a common genetic mechanism, joint analysis can be statistically more powerful and biologically more meaningful. However, most existing tests for multiple traits cannot be used for high-dimensional and possibly structured traits, such as network-structured transcriptomic pathway expressions. To overcome potential limitations, in this paper we propose the dual kernel-based association test (DKAT) for testing the association between multiple traits and multiple genetic variants, both common and rare...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28642109/neoaortic-xenoprosthetic-grafts-for-treatment-of-mycotic-aneurysms-and-infected-aortic-grafts
#13
C Anibueze, V Sankaran, U Sadat, K Tan, Y G Wilson, R E Brightwell, M S Delbridge, P W Stather
OBJECTIVE: There is no international consensus regarding the optimum management of infected aortae (mycotic aneurysms, infected aortic grafts). Neoaortoiliac reconstruction has advantages over extra anatomical bypass grafting; however use of autologous vein is associated with venous hypertension and compartment syndrome, alternatively cadaveric homografts are associated with high rates of perianastomotic haemorrhage, limb occlusion and pseudoaneurysm. Arterial repair using xenoprosthetic patches is associated with lower infection rates compared to the use of prosthetic material...
June 19, 2017: Annals of Vascular Surgery
https://www.readbyqxmd.com/read/28641555/supervised-machine-learning-methods-applied-to-predict-ligand-binding-affinity
#14
Gabriela Sehnem Heck, Val Oliveira Pintro, Richard Rene Pereira, Mauricio Boff de Ávila, Nayara Maria Bernhardt Levin, Walter Filgueira de Azevedo
BACKGROUND: Calculation of ligand-binding affinity is an open problem in computational medicinal chemistry. The ability to computationally predict affinities has a beneficial impact in the early stages of drug development, since it allows a mathematical model to assess protein-ligand interactions. Due to the availability of structural and binding information, machine learning methods have been applied to generate scoring functions with good predictive power. OBJECTIVE: Our goal here is to review recent developments in the application of machine learning methods to predict ligand- binding affinity...
June 22, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28641485/microarray-based-gene-expression-analysis-for-veterinary-pathologists-a-review
#15
Barbara B Raddatz, Ingo Spitzbarth, Katja A Matheis, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich
High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms...
January 1, 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/28641440/accurate-excitation-energies-of-molecules-and-oligomers-from-a-semilocal-density-functional
#16
Guocai Tian, Yuxiang Mo, Jianmin Tao
Excitation energy plays an important role in energy conversion, biological processes, and optical devices. In this work, we apply the Tao-Mo (TM) nonempirical meta-generalized gradient approximation and the combination TMTPSS (TMx + TPSSc), with TPSSc being the correlation part of the original TPSS (Tao-Perdew-Staroverov-Scuseria) to study excitation energies of small molecules and oligomers. Our test set consists of 17 molecules with 134 total excited states, including singlet, triplet, valence, and Rydberg excited states...
June 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28641268/newgoa-predicting-new-go-annotations-of-proteins-by-bi-random-walks-on-a-hybrid-graph
#17
Guoxian Yu, Guangyuan Fu, Jun Wang, Yingwen Zhao
A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many of them are incomplete. We proposed a method called NewGOA to predict new Gene Ontology (GO) annotations for incompletely annotated proteins and for completely un-annotated ones. NewGOA employs a hybrid graph, composed of two types of nodes (proteins and GO terms), to encode interactions between proteins, hierarchical relationships between terms and available annotations of proteins...
June 15, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28641043/radiogenomics-of-high-grade-serous-ovarian-cancer-multireader-multi-institutional-study-from-the-cancer-genome-atlas-ovarian-cancer-imaging-research-group
#18
Hebert Alberto Vargas, Erich P Huang, Yulia Lakhman, Joseph E Ippolito, Priya Bhosale, Vincent Mellnick, Atul B Shinagare, Maria Anello, Justin Kirby, Brenda Fevrier-Sullivan, John Freymann, C Carl Jaffe, Evis Sala
Purpose To evaluate interradiologist agreement on assessments of computed tomography (CT) imaging features of high-grade serous ovarian cancer (HGSOC), to assess their associations with time-to-disease progression (TTP) and HGSOC transcriptomic profiles (Classification of Ovarian Cancer [CLOVAR]), and to develop an imaging-based risk score system to predict TTP and CLOVAR profiles. Materials and Methods This study was a multireader, multi-institutional, institutional review board-approved, HIPAA-compliant retrospective analysis of 92 patients with HGSOC (median age, 61 years) with abdominopelvic CT before primary cytoreductive surgery available through the Cancer Imaging Archive...
June 22, 2017: Radiology
https://www.readbyqxmd.com/read/28640862/a-biosystems-approach-to-identify-the-molecular-signaling-mechanisms-of-tmem30a-during-tumor-migration
#19
Jiao Wang, Qian Wang, Dongfang Lu, Fangfang Zhou, Dong Wang, Ruili Feng, Kai Wang, Robert Molday, Jiang Xie, Tieqiao Wen
Understanding the molecular mechanisms underlying cell migration, which plays an important role in tumor growth and progression, is critical for the development of novel tumor therapeutics. Overexpression of transmembrane protein 30A (TMEM30A) has been shown to initiate tumor cell migration, however, the molecular mechanisms through which this takes place have not yet been reported. Thus, we propose the integration of computational and experimental approaches by first predicting potential signaling networks regulated by TMEM30A using a) computational biology methods, b) our previous mass spectrometry results of the TMEM30A complex in mouse tissue, and c) a number of migration-related genes manually collected from the literature, and subsequently performing molecular biology experiments including the in vitro scratch assay and real-time quantitative polymerase chain reaction (qPCR) to validate the reliability of the predicted network...
2017: PloS One
https://www.readbyqxmd.com/read/28640810/lassim-a-network-inference-toolbox-for-genome-wide-mechanistic-modeling
#20
Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets...
June 22, 2017: PLoS Computational Biology
keyword
keyword
20301
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"