Genomes and Genes
Experts and Doctors on algorithms in New York, United States
Locale: New York, United States
Publications297 found, 100 shown here
- Rudloff U, Bhanot U, Gerald W, Klimstra D, Jarnagin W, Brennan M, et al. Biobanking of human pancreas cancer tissue: impact of ex-vivo procurement times on RNA quality. Ann Surg Oncol. 2010;17:2229-36 pubmed publisher..This study shows the challenges and investments required to initiate and maintain high-quality tissue repositories. ..
- Needham M, Hu R, Dwarkadas S, Qiu X. Hierarchical parallelization of gene differential association analysis. BMC Bioinformatics. 2011;12:374 pubmed publisher..We believe that the principles of this hierarchical approach to parallelization can be utilized in the parallelization of other computationally demanding kernels. ..
- LAZAR A, Slutskiy Y. Channel identification machines. Comput Intell Neurosci. 2012;2012:209590 pubmed publisher..We show that our results hold for a wide class of RKHSs, including the space of finite-energy bandlimited signals. We also extend our channel identification results to noisy circuits. ..
- Bansal R, Staib L, Laine A, Hao X, Xu D, Liu J, et al. Anatomical brain images alone can accurately diagnose chronic neuropsychiatric illnesses. PLoS ONE. 2012;7:e50698 pubmed publisher..Extensions of these methods are likely to provide biomarkers that will aid in identifying biological subtypes of those disorders, predicting disease course, and individualizing treatments for a wide range of neuropsychiatric illnesses. ..
- Peerschke E. The laboratory evaluation of platelet dysfunction. Clin Lab Med. 2002;22:405-20 pubmed..It remains to be seen whether such screening tests will better predict clinical bleeding or thrombotic risk. ..
- Aronov D. Fast algorithm for the metric-space analysis of simultaneous responses of multiple single neurons. J Neurosci Methods. 2003;124:175-9 pubmed
- Lu H, Law M, Johnson G, Ge Y, van Zijl P, Helpern J. Novel approach to the measurement of absolute cerebral blood volume using vascular-space-occupancy magnetic resonance imaging. Magn Reson Med. 2005;54:1403-11 pubmed..In comparison with previous pre/postcontrast difference approaches, VASO MRI provides maximal signal difference between pre- and postcontrast situation and does not require the use of whole blood for signal normalization. ..
- Dellegrottaglie S, Sanz J, Rajagopalan S. Technology insight: Clinical role of magnetic resonance angiography in the diagnosis and management of renal artery stenosis. Nat Clin Pract Cardiovasc Med. 2006;3:329-38 pubmed..An overview of the clinical role of MRA, in conjunction with the other diagnostic modalities, in the identification and management of patients with renal artery stenosis, is also presented. ..
- Murcia M, Faraldo Gómez J, Maxfield F, Roux B. Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol. J Lipid Res. 2006;47:2614-30 pubmed
- Wright T, Massad L, Dunton C, Spitzer M, Wilkinson E, Solomon D. 2006 consensus guidelines for the management of women with abnormal cervical screening tests. J Low Genit Tract Dis. 2007;11:201-22 pubmed..The 2006 Consensus Guidelines reflect recent data from large clinical trials and advances in technology and are designed to assist clinicians of all subspecialties. ..
- Podolanczuk A, Lazarus A, Crow A, Grossbard E, Bussel J. Of mice and men: an open-label pilot study for treatment of immune thrombocytopenic purpura by an inhibitor of Syk. Blood. 2009;113:3154-60 pubmed publisher..In conclusion, inhibition of Syk was an efficacious means of increasing and maintaining the platelet count in half the patients with chronic refractory ITP. (ClinicalTrials.gov, no. NCT00706342). ..
- Xu Z, Walsh S, Telivala T, Meek A, Yang G. Evaluation of the eclipse electron Monte Carlo dose calculation for small fields. J Appl Clin Med Phys. 2009;10:2834 pubmed..However, at extended SSDs (105-110 cm), the results show good agreement (within 4 %) only for higher energies (12, 16, and 20 MeV) for a field size of 3 cm. ..
- Madar A, Greenfield A, Ostrer H, Vanden Eijnden E, Bonneau R. The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models. Conf Proc IEEE Eng Med Biol Soc. 2009;2009:5448-51 pubmed publisher..We show results for the prokaryote Halobacterium that demonstrate a marked improvement in our predictive performance in modeling the regulatory dynamics of the system over longer time-scales. ..
- Osteen J, Gonzalez C, Sampson K, Iyer V, Rebolledo S, Larsson H, et al. KCNE1 alters the voltage sensor movements necessary to open the KCNQ1 channel gate. Proc Natl Acad Sci U S A. 2010;107:22710-5 pubmed publisher..This work provides insight into the mechanism by which KCNE1 modulates the I(Ks) channel and presents a mechanism for distinct ?-subunit regulation of ion channel proteins. ..
- Parla J, Iossifov I, Grabill I, Spector M, Kramer M, McCombie W. A comparative analysis of exome capture. Genome Biol. 2011;12:R97 pubmed publisher..Commercial exome capture kits provide a very efficient way to sequence select areas of the genome at very high accuracy. Here we provide the data to help guide critical analyses of sequencing data derived from these products. ..
- Shen Y, Gu Y, Pe er I. A hidden Markov model for copy number variant prediction from whole genome resequencing data. BMC Bioinformatics. 2011;12 Suppl 6:S4 pubmed publisher..We applied the method to simulated data and demonstrate the power of detecting medium-size deletions is close to theoretical values. A program implemented in Java, Zinfandel, is available at http://www.cs.columbia.edu/~itsik/zinfandel/ ..
- Ma S, Kemmeren P, Aliferis C, Statnikov A. An Evaluation of Active Learning Causal Discovery Methods for Reverse-Engineering Local Causal Pathways of Gene Regulation. Sci Rep. 2016;6:22558 pubmed publisher..This study also demonstrates the feasibility of local causal pathway reconstruction in real biological systems with significant quality and low experimental cost. ..
- Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin Garcia P, Arnau V, et al. Reactome pathway analysis: a high-performance in-memory approach. BMC Bioinformatics. 2017;18:142 pubmed publisher..Reactome is an open data and open source project and all of its source code, including the one described here, is available in the AnalysisTools repository in the Reactome GitHub ( https://github.com/reactome/ ). ..
- Fai T, Leo Macias A, Stokes D, Peskin C. Image-based model of the spectrin cytoskeleton for red blood cell simulation. PLoS Comput Biol. 2017;13:e1005790 pubmed publisher..The methods presented here could form the basis of disease- and patient-specific computational studies of hereditary diseases affecting the red cell cytoskeleton...
- Atkinson P, Mills L, Starmer W, Sullivan D. Structure and evolution of the Adh genes of Drosophila mojavensis. Genetics. 1988;120:713-23 pubmed..There is a surprising and not fully explainable strong similarity of the nucleotide sequence of the 5' flanking region of the pseudogene in D. mojavensis and D. mulleri. ..
- Blumenfeld J, Laragh J. Management of hypertensive crises: the scientific basis for treatment decisions. Am J Hypertens. 2001;14:1154-67 pubmed..Based upon these considerations, a treatment algorithm is provided to guide drug selection in patients presenting with a hypertensive crisis. ..
- Ciaccio E, Chow A, Davies D, Wit A, Peters N. Localization of the isthmus in reentrant circuits by analysis of electrograms derived from clinical noncontact mapping during sinus rhythm and ventricular tachycardia. J Cardiovasc Electrophysiol. 2004;15:27-36 pubmed
- Kentsis A, Borden K. Physical mechanisms and biological significance of supramolecular protein self-assembly. Curr Protein Pept Sci. 2004;5:125-34 pubmed
- Mika S, Rost B. NLProt: extracting protein names and sequences from papers. Nucleic Acids Res. 2004;32:W634-7 pubmed..bioc.columbia.edu/services/NLProt/). Input can be PubMed/MEDLINE identifiers, authors, titles and journals, as well as collections of abstracts, or entire papers. ..
- Mackool R, Ko W, Mackool R. Intraocular lens power calculation after laser in situ keratomileusis: Aphakic refraction technique. J Cataract Refract Surg. 2006;32:435-7 pubmed..Although the pool sample was small (12 eyes) and the range of the aphakic refraction was limited (+8.50 to 12.375 D), the technique was found to be remarkably accurate. ..
- Gu X, Ren K, Hielscher A. Frequency-domain sensitivity analysis for small imaging domains using the equation of radiative transfer. Appl Opt. 2007;46:1624-32 pubmed..These results will be useful in the design of experiments and optical tomographic imaging systems that probe small tissue volumes. ..
- Averbeck N, Keppler Ross S, Dean N. Membrane topology of the Alg14 endoplasmic reticulum UDP-GlcNAc transferase subunit. J Biol Chem. 2007;282:29081-8 pubmed..Thus, this Alg13-Alg14 UDP-GlcNAc transferase represents an unprecedented example of a bipartite glycosyltransferase that evolved by both fission and fusion. ..
- Gulotta M, Qiu L, Desamero R, ROSGEN J, Bolen D, Callender R. Effects of cell volume regulating osmolytes on glycerol 3-phosphate binding to triosephosphate isomerase. Biochemistry. 2007;46:10055-62 pubmed..Results indicate that the conformational shift hypothesis alone does not account for the effects of osmolytes on Km's. ..
- Kim N, Shin J, Elmetwaly S, Gan H, Schlick T. RagPools: RNA-As-Graph-Pools--a web server for assisting the design of structured RNA pools for in vitro selection. Bioinformatics. 2007;23:2959-60 pubmed..The web server is accessible on the web at http://rubin2.biomath.nyu.edu ..
- Fatterpekar G, Delman B, Som P. Imaging the paranasal sinuses: where we are and where we are going. Anat Rec (Hoboken). 2008;291:1564-72 pubmed publisher..In this article, we describe the various imaging techniques, concerns, advantages and disadvantages of the individual techniques, and provide an overview of the various pathologies involving the paranasal sinuses. ..
- Glykys D, Banta S. Metabolic control analysis of an enzymatic biofuel cell. Biotechnol Bioeng. 2009;102:1624-35 pubmed publisher..As increasingly complex bioelectrocatalytic systems and architectures are envisioned, MCA will be a valuable framework to facilitate their design and subsequent operation. ..
- Gonen M, Schrag D, Weiser M. Nodal staging score: a tool to assess adequate staging of node-negative colon cancer. J Clin Oncol. 2009;27:6166-71 pubmed publisher..The score we developed indicates the adequacy of nodal staging for patients with no positive nodes and can assist clinical decision making in the patient without nodal metastasis. ..
- Kurian M, Sultan S, Garg K, Youn H, Fielding G, Ren Fielding C. Evaluating gastric erosion in band management: an algorithm for stratification of risk. Surg Obes Relat Dis. 2010;6:386-9 pubmed publisher..Band revision has a greater rate of erosion than primary banding. The Vanguard band has a greater risk of erosion than the 4-cm(3) bands. ..
- Teng C, De Moraes C, Prata T, Liebmann C, Tello C, Ritch R, et al. The region of largest ?-zone parapapillary atrophy area predicts the location of most rapid visual field progression. Ophthalmology. 2011;118:2409-13 pubmed publisher..The author(s) have no proprietary or commercial interest in any materials discussed in this article. ..
- Yang A, Jensen J, Hu C, Tabesh A, Falangola M, Helpern J. Effect of cerebral spinal fluid suppression for diffusional kurtosis imaging. J Magn Reson Imaging. 2013;37:365-71 pubmed publisher..To evaluate the cerebral spinal fluid (CSF) partial volume effect on diffusional kurtosis imaging (DKI) metrics in white matter and cortical gray matter...
- Patel V, Naik S, Naidich D, Travis W, Weingarten J, Lazzaro R, et al. A practical algorithmic approach to the diagnosis and management of solitary pulmonary nodules: part 1: radiologic characteristics and imaging modalities. Chest. 2013;143:825-839 pubmed publisher..In Part 2, we will describe the determination of pretest probability of malignancy and an algorithmic approach to the diagnosis of SPN. ..
- Tubert Brohman I, Sherman W, Repasky M, Beuming T. Improved docking of polypeptides with Glide. J Chem Inf Model. 2013;53:1689-99 pubmed publisher..We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach. ..
- Strino F, Parisi F, Micsinai M, Kluger Y. TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res. 2013;41:e165 pubmed publisher..Finally, we deconvolve sequencing data from eight acute myeloid leukemia patients and three distinct metastases of one melanoma patient to exhibit the evolutionary relationships of their subpopulations. ..
- Bendall S, Davis K, Amir E, Tadmor M, Simonds E, Chen T, et al. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell. 2014;157:714-25 pubmed publisher..This study provides a comprehensive analysis of human B lymphopoiesis, laying a foundation to apply this approach to other tissues and "corrupted" developmental processes including cancer. ..
- Fuller C, Cellura A, Hibler B, Burris K. Computer-assisted diagnosis of melanoma. Semin Cutan Med Surg. 2016;35:25-30 pubmed publisher..A successful model must obtain results that are on par or outperform experienced dermatologists, keep costs at a minimum, be user-friendly, and be time efficient with high sensitivity and specificity. ..
- Zanderigo F, Mann J, Ogden R. A hybrid deconvolution approach for estimation of in vivo non-displaceable binding for brain PET targets without a reference region. PLoS ONE. 2017;12:e0176636 pubmed publisher..HYDECA can provide subject-specific estimates of VND without requiring a blocking study for tracers and targets for which a valid reference region does not exist. ..
- Lui W, Lee W, Cheng C. Sertoli-germ cell adherens junction dynamics in the testis are regulated by RhoB GTPase via the ROCK/LIMK signaling pathway. Biol Reprod. 2003;68:2189-206 pubmed..In summary, this report illustrates that Sertoli germ cell AJ dynamics are regulated, at least in part, via the integrin/ROCK/LIMK/cofilin signaling pathway. ..
- Narendran R, Hwang D, Slifstein M, Talbot P, Erritzoe D, Huang Y, et al. In vivo vulnerability to competition by endogenous dopamine: comparison of the D2 receptor agonist radiotracer (-)-N-[11C]propyl-norapomorphine ([11C]NPA) with the D2 receptor antagonist radiotracer [11C]-raclopride. Synapse. 2004;52:188-208 pubmed..In conclusion, [11C]NPA might provide a superior radiotracer to probe presynaptic DA function with PET in health and disease. ..
- Furhang E, Dolan J, Sillanpaa J, Harrison L. Automating the initial physics chart checking process. J Appl Clin Med Phys. 2009;10:2855 pubmed..The length of time for the entire initial chart-checking process was reduced from about an hour to a few minutes. The code developed in this work allows the user to consider the big picture, trusting the software to track details. ..
- Carter T, Flik K, Boland P, Kennedy J. Iliac hematoma mimicking neoplasm in adolescent athletes. Orthopedics. 2008;31:1144 pubmed..Careful observation in combination with radiographic findings can yield a successful diagnosis, but the orthopedic surgeon must carefully weigh the increased risk of tumor growth against the need for biopsy. ..
- Wang K, Saito M, Bisikirska B, Alvarez M, Lim W, Rajbhandari P, et al. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol. 2009;27:829-39 pubmed publisher..MINDy is generally applicable to study the post-translational modulation of mammalian TFs in any cellular context. As such it can be used to dissect context-specific signaling pathways and combinatorial transcriptional regulation. ..
- Chen B, Causton H, Mancenido D, Goddard N, Perlstein E, PE ER D. Harnessing gene expression to identify the genetic basis of drug resistance. Mol Syst Biol. 2009;5:310 pubmed publisher..Our approach is robust, applicable to other phenotypes and species, and has potential for applications in personalized medicine, for example, in predicting how an individual will respond to a previously unseen drug. ..
- Folgar F, De Moraes C, Prata T, Teng C, Tello C, Ritch R, et al. Glaucoma surgery decreases the rates of localized and global visual field progression. Am J Ophthalmol. 2010;149:258-264.e2 pubmed publisher..1 dB/year decrease in the global rate of progression. Successful IOP reduction after glaucoma surgery greatly reduces both the number of progressing points and the localized and general rates of VF progression. ..
- Agius P, Bennett K, Zuker M. Comparing RNA secondary structures using a relaxed base-pair score. RNA. 2010;16:865-78 pubmed publisher..Our results indicate that relaxed measures give more stable and more meaningful clusters than the BP metric. We also use the RBP score to compute representative foldings for each cluster. ..
- Cheong F, Krishnatreya B, Grier D. Strategies for three-dimensional particle tracking with holographic video microscopy. Opt Express. 2010;18:13563-73 pubmed publisher..The two techniques agree quantitatively on colloidal spheres' in-plane positions. Their systematic differences in axial tracking can be explained in terms of the illuminated objects' light scattering properties. ..
- Maisto S, Krenek M, Chung T, Martin C, Clark D, Cornelius J. Comparison of the concurrent and predictive validity of three measures of readiness to change marijuana use in a clinical sample of adolescents. J Stud Alcohol Drugs. 2011;72:592-601 pubmed..The ruler emerged as the measure with the most clinical utility when brevity and ease of administration are taken into account. Research and clinical implications of the findings are discussed. ..
- Vilar S, Harpaz R, Chase H, Costanzi S, Rabadan R, Friedman C. Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis. J Am Med Inform Assoc. 2011;18 Suppl 1:i73-80 pubmed publisher..Various data mining approaches have been developed that use AERS to detect signals identifying associations between drugs and ADE. The signals must then be monitored further by domain experts, which is a time-consuming task...
- Parasoglou P, Xia D, Regatte R. Spectrally selective 3D TSE imaging of phosphocreatine in the human calf muscle at 3 T. Magn Reson Med. 2013;69:812-7 pubmed publisher..The mean ± standard deviation of the phosphocreatine concentration measured in five healthy volunteers was 29.4 ± 2.5 mM with signal-to-noise ratio of 14:1 and voxel size of 0.52 mL. ..
- Greenfield A, Hafemeister C, Bonneau R. Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. Bioinformatics. 2013;29:1060-7 pubmed publisher..Code, datasets and networks presented in this article are available at http://bonneaulab.bio.nyu.edu/software.html. Supplementary data are available at Bioinformatics online. ..
- Mazaheri Y, Vargas H, Nyman G, Akin O, Hricak H. Image artifacts on prostate diffusion-weighted magnetic resonance imaging: trade-offs at 1.5 Tesla and 3.0 Tesla. Acad Radiol. 2013;20:1041-7 pubmed publisher..Therefore, to take full advantage of the benefits of 3.0 T, further improvements in acquisition techniques are needed to address DW-MRI artifacts corresponding to higher field strengths. ..
- Altieri M, Pryor A, Telem D, Hall K, Brathwaite C, Zawin M. Algorithmic approach to utilization of CT scans for detection of internal hernia in the gastric bypass patient. Surg Obes Relat Dis. 2015;11:1207-11 pubmed publisher..CT scans will not detect IH in 1:4 patients; despite negative findings, surgical exploration should remain the gold standard for patients with acute abdominal pain after LRYGB or biliopancreatic diversion when IH is a consideration. ..
- Rizvi A, Camara P, Kandror E, Roberts T, Schieren I, Maniatis T, et al. Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development. Nat Biotechnol. 2017;35:551-560 pubmed publisher..scTDA can be applied to study asynchronous cellular responses to either developmental cues or environmental perturbations. ..
- Holler S, Mansley E, Mazzeo C, Donovan M, Sobrero M, Miles B. Raman Spectroscopy of Head and Neck Cancer: Separation of Malignant and Healthy Tissue Using Signatures Outside the "Fingerprint" Region. Biosensors (Basel). 2017;7: pubmed publisher..Preliminary multivariate statistical analyses of the Raman spectra indicate that discrimination between diseased and healthy tissue is possible based on these peaks. ..
- Jordan P, Christini D. Characterizing the contribution of voltage- and calcium-dependent coupling to action potential stability: implications for repolarization alternans. Am J Physiol Heart Circ Physiol. 2007;293:H2109-18 pubmed
- Zhu D. Mathematical modeling of blood coagulation cascade: kinetics of intrinsic and extrinsic pathways in normal and deficient conditions. Blood Coagul Fibrinolysis. 2007;18:637-46 pubmed..6 s for the extrinsic pathway using normal protein concentrations in plasma. Various prolonged clotting times were observed in different factor-deficient disorders using this model. ..
- Hielscher A, Bartel S. Parallel programming of gradient-based iterative image reconstruction schemes for optical tomography. Comput Methods Programs Biomed. 2004;73:101-13 pubmed..The resulting algorithms are shown to accelerate the reconstruction process to various degrees, substantially reducing the computation times for clinically relevant problems. ..
- Iacobas D, Suadicani S, Spray D, Scemes E. A stochastic two-dimensional model of intercellular Ca2+ wave spread in glia. Biophys J. 2006;90:24-41 pubmed..Such modeling is expected to be useful for testing phenomenological hypotheses and in understanding consequences of alteration of system components under experimental or pathological conditions. ..
- Li Y. Using the open-source statistical language R to analyze the dichotomous Rasch model. Behav Res Methods. 2006;38:532-41 pubmed..The use of R is encouraged because it is free, supported by a network of peer researchers, and covers both basic and advanced topics in statistics frequently used by psychologists. ..
- Kim D, Kellman P. Improved cine displacement-encoded MRI using balanced steady-state free precession and time-adaptive sensitivity encoding parallel imaging at 3 T. NMR Biomed. 2007;20:591-601 pubmed..The combined implementation of b-SSFP imaging, 3T imaging, echo-combination image reconstruction, and TSENSE parallel imaging can be used to incrementally improve the cine displacement-encoded MRI pulse sequence. ..
- Wang S, Haynes C, Barany F, Ott J. Genome-wide autozygosity mapping in human populations. Genet Epidemiol. 2009;33:172-80 pubmed publisher..We illustrate the advantage of the algorithm with its application to a genome-wide association study on Parkinson's disease. ..
- Gusev A, Lowe J, Stoffel M, Daly M, Altshuler D, Breslow J, et al. Whole population, genome-wide mapping of hidden relatedness. Genome Res. 2009;19:318-26 pubmed publisher..This finding is supported by concordance of detected deletions with other evidence from independent databases and statistical analyses of fluorescence intensity not used by GERMLINE. ..
- Wiesel J, Fitzig L, Herschman Y, Messineo F. Detection of atrial fibrillation using a modified microlife blood pressure monitor. Am J Hypertens. 2009;22:848-52 pubmed publisher..Use of this device by patients who monitor their blood pressure at home may help detect asymptomatic AF and allow for treatment prior to the development of a stroke. ..
- Wang K, Yorke E, Nehmeh S, Humm J, Ling C. Modeling acute and chronic hypoxia using serial images of 18F-FMISO PET. Med Phys. 2009;36:4400-8 pubmed..This is the first effort to separate acute and chronic hypoxia from serial PET images of cancer patients. ..
- Scott M, Wilcox H, Huo Y, Turner J, Fisher P, Shaffer D. School-based screening for suicide risk: balancing costs and benefits. Am J Public Health. 2010;100:1648-52 pubmed publisher..We examined the effects of a scoring algorithm change on the burden and sensitivity of a screen for adolescent suicide risk...
- Lundbaek J, Koeppe R, Andersen O. Amphiphile regulation of ion channel function by changes in the bilayer spring constant. Proc Natl Acad Sci U S A. 2010;107:15427-30 pubmed publisher..The use of gA channels as molecular force probes provides a tool for quantitative, predictive studies of bilayer-mediated regulation of membrane protein function by amphiphiles...
- Speiser P, Azziz R, Baskin L, Ghizzoni L, Hensle T, Merke D, et al. Congenital adrenal hyperplasia due to steroid 21-hydroxylase deficiency: an Endocrine Society clinical practice guideline. J Clin Endocrinol Metab. 2010;95:4133-60 pubmed publisher..At the transition to adulthood, we recommend monitoring for potential complications of CAH. Finally, we recommend judicious use of medication during pregnancy and in symptomatic patients with nonclassic CAH. ..
- Roychoudhury A, Thompson E. Ascertainment correction for a population tree via a pruning algorithm for likelihood computation. Theor Popul Biol. 2012;82:59-65 pubmed publisher..A modification of a pruning algorithm is introduced so that the inclusion probability can be computed with a single run of the algorithm. Our computation is exact and avoids Monte-Carlo based methods. ..
- Dmochowski J, Datta A, Huang Y, Richardson J, Bikson M, Fridriksson J, et al. Targeted transcranial direct current stimulation for rehabilitation after stroke. Neuroimage. 2013;75:12-19 pubmed publisher..These results demonstrate that MRI-based models of current flow yield maximal stimulation of target structures, and as such, may aid in reliably assessing the efficacy of tDCS in neuro-rehabilitation. ..
- Zhao B, Tan Y, Bell D, Marley S, Guo P, Mann H, et al. Exploring intra- and inter-reader variability in uni-dimensional, bi-dimensional, and volumetric measurements of solid tumors on CT scans reconstructed at different slice intervals. Eur J Radiol. 2013;82:959-68 pubmed publisher..The 2.5mm slice interval provides the least measurement variability. Among the three techniques, 2D has the greatest measurement variability compared to 1D and 3D. ..
- Sharma P, Zardus J, Boyle E, González V, Jennings R, McIntyre E, et al. Into the deep: a phylogenetic approach to the bivalve subclass Protobranchia. Mol Phylogenet Evol. 2013;69:188-204 pubmed publisher..Estimation of divergence times in concert with analyses of diversification rates demonstrate the signature of the end-Permian mass extinction in the phylogeny of extant protobranchs. ..
- Kim N, Laing C, Elmetwaly S, Jung S, Curuksu J, Schlick T. Graph-based sampling for approximating global helical topologies of RNA. Proc Natl Acad Sci U S A. 2014;111:4079-84 pubmed publisher..The efficiency in graph sampling, however, implies an additional step of translating candidate graphs into atomic models. Such models can be built with the same idea of graph partitioning and build-up procedures we used for RNA design. ..
- Moroz L, Simpson L, Rochelson B. Management of severe hypertension in pregnancy. Semin Perinatol. 2016;40:112-8 pubmed publisher..With heightened surveillance and prompt evaluation of signs and symptoms of worsening hypertension, maternal morbidity and mortality can be decreased. ..
- Madiraju S, Catino J, Kokaram C, Genuit T, Bukur M. In by helicopter out by cab: the financial cost of aeromedical overtriage of trauma patients. J Surg Res. 2017;218:261-270 pubmed publisher..Revision of trauma activation protocols may result in more judicious air transport use and significant reductions in health care costs. ..
- Todd A, Carroll S, Godbold J, Moshier E, Khan F. Variability in XRF-measured tibia lead levels. Phys Med Biol. 2000;45:3737-48 pubmed
- Ford E, Mageras G, Yorke E, Rosenzweig K, Wagman R, Ling C. Evaluation of respiratory movement during gated radiotherapy using film and electronic portal imaging. Int J Radiat Oncol Biol Phys. 2002;52:522-31 pubmed..However, systematic displacements were observed in some cases between the location of an anatomic feature at simulation and its location during treatment. Frequent monitoring is advisable with film or portal imaging. ..
- Rust N, Mante V, Simoncelli E, Movshon J. How MT cells analyze the motion of visual patterns. Nat Neurosci. 2006;9:1421-31 pubmed
- Ryan P, Kirk B, Euler C, Schuch R, Fischetti V. Novel algorithms reveal streptococcal transcriptomes and clues about undefined genes. PLoS Comput Biol. 2007;3:e132 pubmed publisher..Neighbor clustering provides a more comprehensive view of the molecular responses of streptococci during pharyngeal cell adherence...
- Lisanby S, Sampson S, Husain M, Petrides G, Knapp R, McCall W, et al. Toward individualized post-electroconvulsive therapy care: piloting the Symptom-Titrated, Algorithm-Based Longitudinal ECT (STABLE) intervention. J ECT. 2008;24:179-82 pubmed publisher..Here we back-test STABLE to optimize the algorithm for subsequent testing in a prospective trial...