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Informed-Proteomics: open-source software package for top-down proteomics

Jungkap Park, Paul D Piehowski, Christopher Wilkins, Mowei Zhou, Joshua Mendoza, Grant M Fujimoto, Bryson C Gibbons, Jared B Shaw, Yufeng Shen, Anil K Shukla, Ronald J Moore, Tao Liu (+6 others)
2017 Nature Methods  
The quality of top-down LC-MS/MS datasets is rapidly increasing due to advances in instrumentation and sample processing protocols.  ...  In this study, we present a new open source software suite for top-down proteomics analysis consisting of an LC-MS feature finding algorithm, a database search algorithm, and an interactive results viewer  ...  Label free quantification As a demonstration of a comparative top-down study, we applied our top-down proteomics workflow for label-free quantification of the human-in-mouse xenograft breast tumor samples  ... 
doi:10.1038/nmeth.4388 pmid:28783154 pmcid:PMC5578875 fatcat:t3r7pm2b3fhkxblnzsxuycluje

Differentiation and characterization of human iPSC-derived vascular endothelial cells under physiological shear stress

Nadia O. Abutaleb, George A. Truskey
2021 STAR Protocols  
Here, we describe a 7-day protocol to differentiate up to 55 million vascular endothelial cells (viECs) from 3.5 million human iPSCs using small molecules to regulate specific transcription factors.  ...  For complete details on the use and execution of this protocol, please refer to Atchison et al. (2020).  ...  We have also uploaded the supplemental method videos and the SolidWorks part files to Mendeley Data (  ... 
doi:10.1016/j.xpro.2021.100394 pmid:33796871 pmcid:PMC7995664 fatcat:ozxij657qrcxhkd5ljfsoe32qm

Functional Characterization of Human Stem Cell-Derived Cardiomyocytes

Glenn E. Kirsch, Carlos A. Obejero-Paz, Andrew Bruening-Wright
2000 Current Protocols in Pharmacology  
As a result, SC-hCM electrophysiology has become a valuable tool to assess cardiac risk associated with drugs.  ...  But human stem cell-derived cardiomyocytes (SC-hCM) are readily available from commercial sources and are increasingly used in academic research, drug discovery and safety pharmacology.  ...  BASIC PROTOCOL 1 MEASUREMENT OF ACTION POTENTIALS INSTEM CELL-DERIVED HUMAN CARDIOMYOCYTES Action potential recordings can be made from single stem cell-derived cardiac cells (Peng et al, 2010; Ma et  ... 
doi:10.1002/0471141755.ph1112s64 pmid:25152802 pmcid:PMC4138727 fatcat:v5b5brtiunacxoiapehwt7ud6e

A little knowledge goes a long way: knowledge-based derivations and correctness proofs for a family of protocols

Joseph Y. Halpern, Lenore D. Zuck
1992 Journal of the ACM  
A high-level, knowledge-based approach for deriving a family of protocols for the sequence transmission problem is presented.  ...  The protocols of Aho et al. [2, 3] , the Alternating Bit protocol [5], and Stenning's protocol [44] are all instances of one knowledge-based protocol that is derived.  ...  We would particularly like to thank Brent Hailpern, who started us thinking about the AUY protocols. We also thank Ron Fagin  ... 
doi:10.1145/146637.146638 fatcat:vhqwfxhmbjgrbfbnt3eegw5ske

Specification Enforcing Refinement for Convertibility Verification

Partha Roop, Alain Girault, Roopak Sinha, Gregor Goessler
2009 2009 Ninth International Conference on Application of Concurrency to System Design  
A formal solution, called convertibility verification, has been recently proposed, which produces such a glue logic, termed as a converter, so that the parallel composition of the protocols and the converter  ...  This paper formulates a generalization of this convertibility verification problem, by using a new refinement called specification enforcing refinement (SER) between a protocol composition and a desired  ...  Fig. 2 depicts the LTS of the handshake protocol to the left and that of the serial protocol at the top. The handshake protocol awaits for event b in state s 0 and outputs event a in state s 1 .  ... 
doi:10.1109/acsd.2009.25 dblp:conf/acsd/RoopGSG09 fatcat:22xxts7gxjen7inyttavhwlwh4

Synthesis of communications protocol converters using the timed Petri net model

Mansour Jaragh, Kassem Saleh
1999 Journal of Systems and Software  
The paper also highlights the dynamicity of the derived converter. We illustrate the converter design method using an example showing the dynamicity and timeliness features of the converter.  ...  Moreover, a reliable converter must perform its conversion functions in a timely manner satisfying the timing constraints of both protocol architectures.  ...  The greatest common service de®nition (gcsd) is the basis of most top-down converter synthesis methods.  ... 
doi:10.1016/s0164-1212(99)00024-2 fatcat:3a4szigqtzgkljyq5ywbxt7wru

Spectral correlation control in down-converted photon pairs

Andrzej Gajewski, Piotr Kolenderski
2016 Physical Review A  
Sources of photon pairs based on the spontaneous parametric down conversion process are commonly used for long distance quantum communication.  ...  Our analysis shows a way for full control of spectral correlation within a fiber-coupled photon pair simultaneously with optimal brightness.  ...  This, seemingly, energy conservation relation breaking, is a result of a pump pulse spectral width and characteristics of down conversion process.  ... 
doi:10.1103/physreva.94.013838 fatcat:7rc3npcxdfcvtdjzqtkjy7swr4

Automated Synthesis of Protocol Converters with BALM-II [chapter]

Giovanni Castagnetti, Matteo Piccolo, Tiziano Villa, Nina Yevtushenko, Robert Brayton, Alan Mishchenko
2015 Lecture Notes in Computer Science  
The largest solution of the defined language equations includes all protocol converters that solve the problem; this is a strong advantage over computational techniques that deliver only one or a few solutions  ...  For illustration we show examples of setting up and solving language equations for classical protocol mismatch problems, aiming at the design of protocol converters to interface an alternating-bit (AB)  ...  The ability to derive all protocol converters that solve the problem is an advantage over computational techniques that deliver only one or a few solutions (which might yield inferior implementations,  ... 
doi:10.1007/978-3-662-49224-6_23 fatcat:tyl54ylkzvbi7kp2clpifrboh4

Performance Evaluation of Wave Energy Converters [chapter]

Arthur Pecher
2013 Performance Evaluation of Wave Energy Converters  
Guidelines for the development of wave energy converters recommend the use of different prototypes, having different sizes, which have to perform tank tests or sea trials.  ...  However, each concept is expected to require a thorough development process, involving different phases and prototypes.  ...  The paper is an elaboration of the EquiMar D4.2 protocol on Data Analysis & Presentation of Marine Energy Converters based on Sea trials [28] .  ... 
doi:10.13052/rp-9788792982278 fatcat:ymiotqzc5bg3vhqape7ppxdkqi

Verifying the Function and Localization of Genetically Encoded Ca2+Sensors and Converting FRET Ratios to Ca2+Concentrations

J. Genevieve Park, Amy E. Palmer
2015 Cold Spring Harbor Protocols  
This protocol describes how to perform a calibration of a Ca 2+ sensor expressed in cultured mammalian cells as images are acquired using a widefield fluorescence microscope.  ...  This protocol also explains how to calculate Förster Resonance Energy Transfer (FRET) ratios from acquired images and how to convert FRET ratios to Ca 2+ concentrations.  ...  Step 3: Place a glass coverslip on top of the glue. Step 4: Gently press down on the glass coverslip to remove air bubbles and to spread out the glue.  ... 
doi:10.1101/pdb.prot076547 pmid:25561614 pmcid:PMC4968932 fatcat:z66d7fvpqjecnlhrtrak73zna4

Wave-to-wire Modelling of Wave Energy Converters [chapter]

Francesco Ferri Dréau
2014 Wave-to-wire Modelling of Wave Energy Converters  
The work load, in terms of numerical simulation and analysis, have been equally shared between Francesco Ferri, Boris Fischer and Simon Ambühl, who had a fundamental role in the model development too.  ...  It uses a non-standard method for deriving the time discrete model from the time continuous model in Equation (5) .  ...  Fig. 4.5 sketches the flow diagram of the proposed method, going from the WEC and location definitions, down to the identification of the minimum CF. The definition of the AEP Fig. 4.5.  ... 
doi:10.13052/rp-9788793237247 fatcat:53fqyt5lsbehncj35it32jq5li

Decoding neuronal diversity by single-cell Convert-seq [article]

Joachim Luginbuhl, Tsukasa Kouno, Rei Nakano, Thomas E Chater, Divya M Sivaraman, Mami Kishima, Filip Roudnicky, Piero Carninci, Charles Plessy, Jay W Shin
2019 bioRxiv   pre-print
Here we present Convert-seq, combining single-cell RNA sequencing (scRNA-seq) and pooled ectopic gene expression with a new strategy to discriminate sequencing reads derived from exogenous and endogenous  ...  Functional validation of iN subtypes generated by novel combinations of exogenous transcription factors establish Convert-seq as a broadly applicable workflow to rapidly identify key transcription factors  ...  We tested Convert-seq in a droplet based 3'-seq platform, 332 however, detection of exogenous transcripts was inefficient, possibly due to the strong 3' bias of the 333 protocol.  ... 
doi:10.1101/600239 fatcat:ee2gkauhqbbkbesn6nfnxvzvue

Renoprotective Effect of Combined Inhibition of Angiotensin-Converting Enzyme and Histone Deacetylase

Y. Zhong, E. Y. Chen, R. Liu, P. Y. Chuang, S. K. Mallipattu, C. M. Tan, N. R. Clark, Y. Deng, P. E. Klotman, A. Ma'ayan, J. C. He
2013 Journal of the American Society of Nephrology  
We predicted that the combination of an angiotensin-converting enzyme (ACE) inhibitor and a histone deacetylase inhibitor would maximally reverse the disease-associated expression of genes in the kidneys  ...  The Connectivity Map database contains microarray signatures of gene expression derived from approximately 6000 experiments that examined the effects of approximately 1300 single drugs on several human  ...  Light cycler analysis software was used to determine crossing points using the second derivative method.  ... 
doi:10.1681/asn.2012060590 pmid:23559582 pmcid:PMC3636790 fatcat:2fsmqgq3dve4hpqr72pj2626uq

eGaN FETs in Low Power Wireless Energy Converters

M. A. de Rooij, J. T. Strydom
2013 ECS Transactions  
An amplifier (a.k.a. a power converter). 2. A transmit coil including matching network. 3. A receive coil including matching network. 4. A rectifier with high frequency filtering.  ...  Most of the wireless power solutions have focused on tight coupling with induction coil solutions at operating frequencies around 200 kHz, and Class E, F and S amplifier converter topologies.  ...  This is the most popular method of control for wireless converters that typically operate in the 100 kHz to 200 kHz range and is popular for wireless converters because it results in a power converter  ... 
doi:10.1149/05003.0377ecst fatcat:g3k4dalhbrcmbp3ay5aofy7f2u

Angiotensin-converting enzyme and male fertility

J. R. Hagaman, J. S. Moyer, E. S. Bachman, M. Sibony, P. L. Magyar, J. E. Welch, O. Smithies, J. H. Krege, D. A. O'Brien
1998 Proceedings of the National Academy of Sciences of the United States of America  
The angiotensin-converting enzyme (ACE; EC gene (Ace) encodes both a somatic isozyme found in blood and several other tissues, including the epididymis, and a testis-specific isozyme (testis  ...  Furthermore, male and female mice lacking angiotensinogen have normal fertility, indicating that angiotensin I is not a necessary substrate for testis ACE.  ...  ACE activities were assayed by using a scaled-down reaction with a commercially available kit (Sigma) with activities expressed as units͞liter. Fertility Tests.  ... 
doi:10.1073/pnas.95.5.2552 pmid:9482924 pmcid:PMC19410 fatcat:je3nn4fssfgt5palnsuqosjsz4
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