5,082 research outputs found
Processed sequence data as .csv from "Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria"
No full textThis contains all quality filtered sequence data as .csv files with each set of sequencing bins contained in a unique file.Related Publication:
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria
Nathan Belliveau Caltech
Proceedings of the National Academy of Science
2018-05-04
https://doi.org/10.1073/pnas.1722055115
engContact person: Rob Phillips [email protected]
Processed sequence data as .fastq from "Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria"
No full textThis contains all quality filtered sequence data as .fastq files (lac data are .fasta), with each sequencing bin as a unique file.Related Publication:
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria
Nathan Belliveau Caltech
Proceedings of the National Academy of Science
2018-05-04
https://doi.org/10.1073/pnas.1722055115
engContact person: Rob Phillips [email protected]
Raw mass spectrometry Thermo data from "Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria"
No full textThis contains all Thermo .raw files. The LacI target purification experiments were performed on a nanoflow LC system, EASY-nLC II coupled to a hybrid linear ion trap Orbitrap Classic mass spectrometer equipped with a Nanospray Flex Ion Source (Thermo Fisher Scientific). All other measurements were performed on a hybrid ion trap-Orbitrap Elite mass spectrometer (Thermo Fisher Scientific), which provided greater detection sensitivity and other fragmentation
techniques as described. The Orbitrap was operated in data-dependent acquisition mode to automatically alternate between a full scan (m/z=400–1,800) in the Orbitrap (resolution 120,000) and subsequent 5 MS/MS scans also acquired in Orbitrap with 15,000 resolution. The MS/MS spectra were acquired for the top 5 ions alternating between higher collision dissociation (HCD) and electron transfer dissociation (ETD) fragmentations that are well suited for higher charge peptides. Higher collision dissociation was performed at a normalized collision energy of 30% and electron transfer dissociation reaction time was set to 100 msec.Related Publication:
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria
Nathan Belliveau Caltech
Proceedings of the National Academy of Science
2018-05-04
https://doi.org/10.1073/pnas.1722055115
engContact person: Rob Phillips [email protected]
Processed data, code, and Jupiter notebooks from "Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria"
No full textThis contains all processed data sets used to construct expression shift plots and energy matrices, as well as several Jupiter notebooks associated with supplemental information of the work. Scripts used for data processing (in particular for .fastq files) are also included.Related Publication:
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria
Nathan Belliveau Caltech
Proceedings of the National Academy of Science
2018-05-04
https://doi.org/10.1073/pnas.1722055115
engContact person: Rob Phillips [email protected]
Service-oriented models for audiovisual content storage
No full textWhat are the important topics to understand if involved with storage services to hold digital audiovisual content? This report takes a look at how content is created and moves into and out of storage; the storage service value networks and architectures found now and expected in the future; what sort of data transfer is expected to and from an audiovisual archive; what transfer protocols to use; and a summary of security and interface issues
Rob Entrekin oral history interview (transcript)
No full textInterview and plant tour with Rob Entrekin, Corporate Technical Staff 2 at Phillips Ultrasound at the time of the interview. He is a biomedical engineer and this company produces medical ultrasound scanners.1 transcript: 44 page
The Molecular Switch: Signaling and Allostery/ Rob Phillips ; illustrated by Nigel Orme.
No full text4.4.1 Adaptation by HandA signature feature of living organisms is their ability to carry out purposeful actions by taking stock of the world around them. To that end, cells have an arsenal of signaling molecules linked together in signaling pathways, which switch between inactive and active conformations. The Molecular Switch articulates a biophysical perspective on signaling, showing how allostery--a powerful explanation of how molecules function across all biological domains--can be reformulated using equilibrium statistical mechanics, applied to diverse biological systems exhibiting switching behaviors, and successfully unify seemingly unrelated phenomena.Rob Phillips weaves together allostery and statistical mechanics via a series of biological vignettes, each of which showcases an important biological question and accompanying physical analysis. Beginning with the study of ligand-gated ion channels and their role in problems ranging from muscle action to vision, Phillips then undertakes increasingly sophisticated case studies, from bacterial chemotaxis and quorum sensing to hemoglobin and its role in mammalian physiology. He looks at G-protein coupled receptors as well as the role of allosteric molecules in gene regulation. Phillips concludes by surveying problems in biological fidelity and offering a speculative chapter on the relationship between allostery and biological Maxwell demons.Appropriate for graduate students and researchers in biophysics, physics, engineering, biology, and neuroscience, The Molecular Switch presents a unified, quantitative model for describing biological signaling phenomena.Cover -- Contents -- Preface -- PART I: THE MAKING OF MOLECULAR SWITCHES -- 1. It's An Allosteric World -- 1.1 The Second Secret of Life -- 1.2 The Broad Reach of the Allostery Concept -- 1.2.1 Sculpting Biochemistry via Allostery -- 1.2.2 One- and Two-Component Signal Transduction and the Two-State Philosophy -- 1.3 Reasoning about Feedback: The Rise of Allostery -- 1.3.1 The Puzzle -- 1.3.2 The Resolution of the Molecular Feedback Puzzle -- 1.3.3 Finding the Allosterome -- 1.4 Mathematicizing the Two-State Paradigm -- 1.4.1 Transcendent Concepts in Physics1.4.2 One Equation to Rule Them All -- 1.5 Beyond the MWC Two-State Concept -- 1.5.1 Molecular Agnosticism: MWC versus KNF versus Eigen -- 1.6 On BeingWrong -- 1.7 Summary -- 1.8 Further Reading -- 1.9 References -- 2. The Allosterician's Toolkit -- 2.1 A Mathematical Microscope: Statistical Mechanics Preliminaries -- 2.1.1 Microstates -- 2.1.2 The Fundamental Law of Statistical Mechanics -- 2.1.3 The Dimensionless Numbers of Thermal Physics -- 2.1.4 Boltzmann and Probabilities -- 2.2 Case Study in Statistical Mechanics: Ligand-Receptor Binding2.2.1 Ligand Binding and the Lattice Model of Solutions -- 2.3 Conceptual Tools of the Trade: Free Energy and Entropy -- 2.3.1 Resetting Our Zero of Energy Using the Chemical Potential -- 2.4 The MWC Concept in Statistical Mechanical Language -- 2.5 Cooperativity and Allostery -- 2.5.1 Cooperativity and Hill Functions -- 2.5.2 Cooperativity in the MWC Model -- 2.6 Internal Degrees of Freedom and Ensemble Allostery -- 2.7 Beyond Equilibrium -- 2.8 Summary -- 2.9 Further Reading -- 2.10 References -- PART II: THE LONG REACH OF ALLOSTERY -- 3. Signaling at the Cell Membrane: Ion Channels3.1 How Cells Talk to the World -- 3.2 Biological Processes and Ion Channels -- 3.3 Ligand-Gated Channels -- 3.4 Statistical Mechanics of the MWC Channel -- 3.5 Data Collapse, Natural Variables, and the Bohr Effect -- 3.5.1 Data Collapse and the Ion-Channel Bohr Effect -- 3.6 Rate Equation Description of Channel Gating -- 3.7 Cyclic Nucleotide-Gated Channels -- 3.8 Beyond the MWC Model in Ion Channelology -- 3.8.1 Conductance Substates and Conformational Kinetics -- 3.8.2 The Koshland-Némethy-Filmer Model Revealed -- 3.8.3 Kinetic Proliferation -- 3.8.4 The Question of Inactivation -- 3.9 Summary3.10 Further Reading -- 3.11 References -- 4. How Bacteria Navigate the World around Them -- 4.1 Bacterial Information Processing -- 4.1.1 Engelmann's Experiment and Bacterial Aerotaxis -- 4.1.2 Love Thy Neighbors: Signaling between Bacteria -- 4.2 Bacterial Chemotaxis -- 4.2.1 The Chemotaxis Phenomenon -- 4.2.2 Wiring Up Chemotaxis through Molecular Switching -- 4.3 MWC Models of Chemotactic Response -- 4.3.1 MWC Model of Chemotaxis Receptor Clusters -- 4.3.2 Heterogenous Clustering -- 4.3.3 Putting It All Together by Averaging -- 4.4 The Amazing Phenomenon of Physiological Adaptation1 online resource (437 p.
Letter from Hubert Phillips to American Civil Liberties Union of Northern California, August 4, 1942
No full textLetter from Hubert Phillips to American Civil Liberties Union of Northern California, enclosing checks for $57 from F. C. Kellogg, Arthur E. Geschke, Claus Bertelsen, and Hubert Phillips. The letter states that the checks represent "the contributions of about twenty-five people made at a dinner held here recently to consider the phases of the status of citizens of Japanese ancestry and is to be applied specifically to helping prosecute the case of Miss Mitsuye Endo. Mr. F. C. Kellogg of the Fowler High School faculty was the author of the idea and deserves the credit for raising the enclosed contribution."The ACLU-Northern California case file records contain legal documents and correspondence pertaining to the case Ex parte Mitsuye Endo (1944), in which the United States Supreme court unanimously ruled that the federal government could not indefinitely detain United States citizens who were loyal to the government. Files include documents related to the Gordon Hirabayashi Supreme Court case Hirabayashi v. United States
Louise Phillips scrapbooks
No full textTwo scrapbooks compiled by Louise Phillips, a University of Maryland Alumna. She graduated with a Bachelor's of Science in Early Childhood Education in 1960 and with an Med. in Curriculum and Instruction in 1991. Phillips was a Montgomery County public school teacher and is the author of children's books. In 1986 she made a documentary about her teaching experiences. The scrapbooks include statements of her philosophy on teaching, vacation photographs, and correspondence. Also included are her two books, The Bald Eagle's Flying Shadow: A Fourth of July Celebration and The First Snowflake of Winter
Caryl Phillips, Radio Plays
No full textpeer reviewedCaryl Phillips is an award-winning author best known for his fiction, essays and stage plays. But he has also written radio plays, nine of which were broadcast by the BBC between 1984 and 2016. Previously locked away in Phillips’s archives, housed at the Beinecke Library at Yale University, these hidden gems are now published in Caryl Phillips’s Radio Plays, the first collection of these important works of drama
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