We propose a method for in situ measurement of the length of kilometre-sized Fabry-Pérot cavities in laser gravitational wave detectors. The method is based on the vernier, which occurs naturally when the laser beam incident on the cavity has a sideband. By changing the length of the cavity over several wavelengths we obtain a set of carrier resonances alternating with sideband resonances. From the measurement of the separation between the carrier and a sideband resonance we determine the length of the cavity. We apply the technique to the measurement of the length of a Fabry-Pérot cavity in the Caltech 40m interferometer and discuss the accuracy of the technique.
A counter-spark-chamber experiment has been performed to measure the annihilation reactions p̅ p π+ π and p̅ p K+ K in the energy region 0.7-2.4 GeV/c. The angular region covered in the experiment was 0.65≤cosθc.m.≤1.0. The data were taken in order to study heavy bosons (mass greater than two nucleons) that might couple to the p̅ p system. Our data have been combined with data from a previous BNL-Caltech experiment to give complete folded angular distributions and total cross sections for these reactions at 12 incident momenta. The folded two-pion annihilation data have been fitted by a simple Breit-Wigner resonance model in order to explore possible resonance behavior. The extreme-angle data have been interpreted in terms of particle exchanges, and through crossing symmetry comparisons are made with backward π p and K p scattering.
The present report focuses on the source of the large difference between the theoretical strength of pure liquid  and the actual tension that is required to initiate cavitation in technical fluids such as test facilities and natural waters. This discrepancy is commonly explained by the existence of nuclei, either solid particles or vapor and gas bubbles that permit phase transition to take place near equilibrium. The existence of these nuclei, their source and lifetimes have occupied much space in the technical literature for decades [1, 2, 3, 8]. Yet, direct observations of tests in applications to naval hydrodynamics and hydraulic machinery flows has not provided much information about these nuclei. Their existence, however, and their effect on cavitation is in no doubt as is demonstrated by the series of photographs of a propeller that were taken in the 'Vacu-Tank' of NSMB  shown in Figure 1. There, addition of 'nucleating' sources to the water by electrolysis clearly increases the number of visible cavitating bubbles on the blade surfaces.
The importance of these nuclei has led to the development of several detection and observation techniques [4, 6, 10, 11]. These include the microscopic observation of water samples...
Background: Comparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes.
Results: We describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that does windowed (ungapped) comparisons of two sequences and reports all matches above a set threshold. FamilyRelationsII is a graphical viewer for comparisons that enables interactive exploration of several different kinds of comparisons. Cartwheel is a Web site and compute-cluster management system used to execute and store comparisons for display by FamilyRelationsII. These tools are specialized for the discovery of cis-regulatory regions in animal genomes. All tools and their source code are freely available at http://family.caltech.edu/.
Conclusion: These tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.
Large-amplitude drift wave fluctuations are observed to cause severe ion temperature oscillations in plasmas of the Caltech Encore tokamak [J. M. McChesney, P. M. Bellan, and R. A. Stern, Phys. Fluids B 3, 3370 (1991)]. Experimental investigations of the complete ion dynamical behavior in these waves are presented. The wave electric field excites stochastic ion orbits in the plane normal (perpendicular to) to B, resulting in rapid perpendicular to heating. Ion-ion collisions impart energy along (parallel to) B, relaxing the perpendicular to-parallel to temperature anisotropy. Hot ions with large orbit radii escape confinement, reaching the chamber wall and cooling the distribution. Cold ions from the plasma edge convect back into the plasma (i.e., recycle), causing further cooling and significantly replenishing the density depleted by orbit losses. The ion-ion collision period tau(ii)similar to Tau(3/2)/n fluctuates strongly with the drift wave phase, due to intense (approximate to 50%) fluctuations in n and Tau. Evidence for particle recycling is given by observations of bimodal ion velocity distributions near the plasma edge, indicating the presence of cold ions (0.4 eV) superposed atop the hot (4-8 eV) plasma background. These appear periodically...
RNA interference (RNAi) is a mechanism for inhibiting gene expression through the action of small, non-coding RNAs. Most existing RNAi libraries target single genes through canonical pathways. Endogenous microRNAs (miRNAs), however, often target multiple genes and can act through non-canonical pathways, including pathways that activate gene expression. To interrogate all possible functions, we designed, synthesized, and validated the first shRNA-encoding library that is completely random at the nucleotide level. Screening in an IL3-dependent cell line, FL5.12, yielded shRNA-encoding sequences that double cell survival upon IL3 withdrawal. Using random mutagenesis and re-screening under more stringent IL3-starvation conditions, we hit-optimized one of the sequences; a specific nucleotide change and the creation of a mismatch between the two halves of the stem both contributed to the improved potency. Our library allows unbiased selection and optimization of shRNA-encoding sequences that confer phenotypes of interest, and could be used for the development of therapeutics and tools in many fields of biology.
Secondary organic aerosol (SOA) formation from the photooxidation of one monoterpene (α-pinene) and two sesquiterpenes (longifolene and aromadendrene) is investigated in the Caltech environmental chambers. The effect of NOx on SOA formation for these biogenic hydrocarbons is evaluated by performing photooxidation experiments under varying NOx conditions. The NOx dependence of α-pinene SOA formation follows the same trend as that observed previously for a number of SOA precursors, including isoprene, in which SOA yield (defined as the ratio of the mass of organic aerosol formed to the mass of parent hydrocarbon reacted) decreases as NOx level increases. The NOx dependence of SOA yield for the sesquiterpenes, longifolene and aromadendrene, however, differs from that determined for isoprene and α-pinene; the aerosol yield under high-NOx conditions substantially exceeds that under low-NOx conditions. The reversal of the NOx dependence of SOA formation for the sesquiterpenes is consistent with formation of relatively low-volatility organic nitrates, and/or the isomerization of large alkoxy radicals leading to less volatile products. Analysis of the aerosol chemical composition for longifolene confirms the presence of organic nitrates under high-NOx conditions. Consequently the formation of SOA from certain biogenic hydrocarbons such as sesquiterpenes (and possibly large anthropogenic hydrocarbons as well) may be more efficient in polluted air.
A collective communication library for parallel computers includes frequently used operations such as broadcast, reduce, scatter, gather, concatenate, synchronize, and shift. Such a library provides users with a convenient programming interface, efficient communication operations, and the advantage of portability. A library of this nature, the Collective Communication Library (CCL), intended for the line of scalable parallel computer products by IBM, has been designed. CCL is part of the parallel application programming interface of the recently announced IBM 9076 Scalable POWERparallel System 1 (SP1). In this paper, we examine several issues related to the functionality, correctness, and performance of a portable collective communication library while focusing on three novel aspects in the design and implementation of CCL: 1) the introduction of process groups, 2) the definition of semantics that ensures correctness, and 3) the design of new and tunable algorithms based on a realistic point-to-point communication model.
Background: The mitotic exit network (MEN) is a group of proteins that form a signaling cascade that is essential for cells to exit mitosis in Saccharomyces cerevisiae. The MEN has also been implicated in playing a role in cytokinesis. Two components of this signaling pathway are the protein kinase Dbf2 and its binding partner essential for its kinase activity, Mob1. The components of MEN that act upstream of Dbf2-Mob1 have been characterized, but physiological substrates for Dbf2-Mob1 have yet to be identified.
Results: Using a combination of peptide library selection, phosphorylation of opitmal peptide variants, and screening of a phosphosite array, we found that Dbf2-Mob1 preferentially phosphorylated serine over threonine and required an arginine three residues upstream of the phosphorylated serine in its substrate. This requirement for arginine in peptide substrates could not be substituted with the similarly charged lysine. This specificity determined for peptide substrates was also evident in many of the proteins phosphorylated by Dbf2-Mob1 in a proteome chip analysis.
Conclusion: We have determined by peptide library selection and phosphosite array screening that the protein kinase Dbf2-Mob1 preferentially phosphorylated substrates that contain an RXXS motif. A subsequent proteome microarray screen revealed proteins that can be phosphorylated by Dbf2-Mob1 in vitro. These proteins are enriched for RXXS motifs...
The Laser Interferometer Gravitational Wave Observatory (LIGO) operates a 40m prototype interferometer on the Caltech campus. The primary mission of the prototype is to serve as an experimental testbed for upgrades to the LIGO interferometers and for gaining experience with advanced interferometric techniques, including detuned resonant sideband extraction (i.e. signal recycling) and dc readout (optical homodyne detection). The former technique will be employed in Advanced LIGO, and the latter in both Enhanced and Advanced LIGO. Using dc readout for gravitational wave signal extraction has several technical advantages, including reduced laser and oscillator noise couplings as well as reduced shot noise, when compared to the traditional rf readout technique (optical heterodyne detection) currently in use in large-scale ground-based interferometric gravitational wave detectors. The Caltech 40m laboratory is currently prototyping a dc readout system for a fully suspended interferometric gravitational wave detector. The system includes an optical filter cavity at the interferometer's output port, and the associated controls and optics to ensure that the filter cavity is optimally coupled to the interferometer. We present the results of measurements to characterize noise couplings in rf and dc readout using this system.
We constructed a 24-pixel bolometer camera operating in the 350- and 450-µm atmospheric windows for the Caltech Submillimeter Observatory (CSO). This instrument uses a monolithic silicon bolometer array that is cooled to approximately 300 mK by a single-shot 3 He refrigerator. First-stage amplification is provided by field-effect transistors at approximately 130 K. The sky is imaged onto the bolometer array by means of several mirrors outside the Dewar and a cold off-axis elliptical mirror inside the cryostat. The beam is defined by cold aperture and field stops, which eliminates the need for any condensing horns. We describe the instrument, present measurements of the physical properties of the bolometer array, describe the performance of the electronics and the data-acquisition system, and demonstrate the sensitivity of the instrument operating at the observatory. Approximate detector noise at 350 µm is 5 x 10^-15 W/√Hz, referenced to the entrance of the Dewar, and the CSO system noise-equivalent flux density is approximately 4 Jy/√Hz. These values are within a factor of 2.5 of the background limit.
We have developed a foreoptics module that converts the Submillimeter High Angular Resolution Camera generation II (SHARC-II) camera at the Caltech Submillimeter Observatory into a sensitive imaging polarimeter at wavelengths of 350 and 450 μm. We refer to this module as "SHARP." SHARP splits the incident radiation into two orthogonally polarized beams that are then reimaged onto opposite ends of the 32×12 pixel detector array in SHARC-II. A rotating half-wave plate is used just upstream from the polarization-splitting optics. The effect of SHARP is to convert SHARC-II into a dual-beam 12×12 pixel polarimeter. A novel feature of SHARP's design is the use of a crossed grid in a submillimeter polarimeter. Here we describe the detailed optical design of SHARP and present results of tests carried out during our first few observing runs. At 350 μm, the beam size (9 arc sec), throughput (75%), and instrumental polarization (<1%) are all very close to our design goals.
The Sindbis virus envelope contains two species of integral membrane glycoproteins, E1 and E2. These proteins form heterodimers, and three dimeric units assemble to form spikes incorporated into the viral surface which play an important role in the specific attachment of Sindbis virus to host cells. To map the neutralization epitopes on the surface of the virus, we constructed a lambda gt11 expression library with cDNA inserts 100 to 300 nucleotides long obtained from randomly primed synthesis on Sindbis virus genomic RNA. This library was screened with five different neutralizing monoclonal antibodies (MAbs) specific for E2 (MAbs 50, 51, 49, 18, and 23) and with one neutralizing MAb specific for E1 (MAb 33). When 10(6) lambda gt11 plaques were screened with each antibody, four positive clones that reacted with E2-specific MAb 23 were found. These four clones contained overlapping inserts from glycoprotein E2; the domain from residues 173 to 220 of glycoprotein E2 was present in all inserts, and we concluded that this region contains the neutralization epitope recognized by the antibody. No clones that reacted with the other antibodies examined were found, and we concluded that these antibodies probably recognize conformational epitopes not present in the lambda gt11 library. We suggest that the E2 domain from residues 173 to 220 is a major antigenic determinant of Sindbis virus and that this domain is important for virus attachment to cells.
In vitro selection targeting an anti-polyhistidine monoclonal antibody was performed using mRNA display with a random, unconstrained 27-mer peptide library. After six rounds of selection, epitope-like peptides were identified that contain two to five consecutive, internal histidines and are biased for arginine residues, without any other identifiable consensus. The epitope was further refined by constructing a high-complexity, unidirectional fragment library from the final selection pool. Selection by mRNA display minimized the dominant peptide from the original selection to a 15-residue functional sequence (peptide Cmin: RHDAGDHHHHHGVRQ; K-D = 38 nM). Other peptides recovered from the fragment library selection revealed a separate consensus motif (ARRXA) C-terminal to the histidine track. Kinetics measurements made by surface plasmon resonance, using purified Fab (antigen-binding fragment) to prevent avidity effects, demonstrate that the selected peptides bind with 10- to 75-fold higher affinities than a hexahistidine peptide. The highest affinity peptides (K-D approximate to 10 nM) encode both a short histidine track and the ARRXA motif, suggesting that the motif and other flanking residues make important contacts adjacent to the core polyhistidine-binding site and can contribute > 2.5 kcal/mol of binding free energy. The fragment library construction methodology described here is applicable to the development of high-complexity protein or cDNA expression libraries for the identification of protein-protein interaction domains.
Analysis of large-scale gene expression studies usually begins with gene clustering. A ubiquitous problem is that different algorithms applied to the same data inevitably give different results, and the differences are often substantial, involving a quarter or more of the genes analyzed. This raises a series of important but nettlesome questions: How are different clustering results related to each other and to the underlying data structure? Is one clustering objectively superior to another? Which differences, if any, are likely candidates to be biologically important? A systematic and quantitative way to address these questions is needed, together with an effective way to integrate and leverage expression results with other kinds of large-scale data and annotations. We developed a mathematical and computational framework to help quantify, compare, visualize and interactively mine clusterings. We show that by coupling confusion matrices with appropriate metrics (linear assignment and normalized mutual information scores), one can quantify and map differences between clusterings. A version of receiver operator characteristic analysis proved effective for quantifying and visualizing cluster quality and overlap. These methods, plus a flexible library of clustering algorithms...
Treiman, S. B.; Kruse, U. E.; Frazer, W. R.; Berger, E. L.; Feynman, R. P.; Lai, K. W.; Barnham, K. W. J.; Flatte, S. M.; Ozaki, S.; Gettner, M.; Rosner, J. L.; Steiner, H.; Cutkosky, R. E.; Musgrave, B.; Leith, D. W. G. S.; Dick, L.; Yokosawa, A.; Schmid
Fonte: California Institute of TechnologyPublicador: California Institute of Technology
What is phenomenology? Reach not for your dictionary; make no vain efforts to pronounce it; we will come clean and explain all.
Science is noted for a competitive and helpful interaction between theorists and experimentalists. Unfortunately in almost all developing sciences, the moving hand of time drives a widening wedge between theory and experiment. Thus theorists are fully occupied in the mathematical and philosophical intricacies of their latest ideas. Again, experimentalists must concentrate on the design of their apparatus to insure they will get the best possible results current technology will allow. Phenomenology seeks to close the gap between those once close friends, theory and experiment, and so restore the interaction which is both vital to and characteristic of science. Although a classical concept, phenomenology is best known in its second-quantized form.
The basic tool of the phenomenologist is, first, the construction of simple models that embody important theoretical ideas, and then, the critical comparison of these models with all relevant experimental data. It follows that a phenomenologist must combine a broad understanding of theory with a complete knowledge of current and future feasible experiments in order to allow him to interact meaningfully with both major branches of a science. The impact of phenomenology is felt in both theory and experiment. Thus it can pinpoint unexpected experimental observations and so delineate areas where new theoretical ideas are needed. Further...
The RAIN project is a research collaboration between Caltech and NASA-JPL on distributed computing and data-storage systems for future spaceborne missions. The goal of the project is to identify and develop key building blocks for reliable distributed systems built with inexpensive off-the-shelf components. The RAIN platform consists of a heterogeneous cluster of computing and/or storage nodes connected via multiple interfaces to networks configured in fault-tolerant topologies. The RAIN software components run in conjunction with operating system services and standard network protocols. Through software-implemented fault tolerance, the system tolerates multiple node, link, and switch failures, with no single point of failure. The RAIN-technology has been transferred to Rainfinity, a start-up company focusing on creating clustered solutions for improving the performance and availability of Internet data centers. In this paper, we describe the following contributions: 1) fault-tolerant interconnect topologies and communication protocols providing consistent error reporting of link failures, 2) fault management techniques based on group membership, and 3) data storage schemes based on computationally efficient error-control codes. We present several proof-of-concept applications: a highly-available video server...
Wrublewski, Donna T.; Porter, George S.; Painter, Joy; Buxton, Kristin; Cleary, Lindsay B.
Fonte: Instituto de Tecnologia da CalifórniaPublicador: Instituto de Tecnologia da Califórnia
Tipo: Conference or Workshop Item; NonPeerReviewedFormato: application/pdf
Publicado em /08/2014
Relevância na Pesquisa
Access to chem. information has evolved dramatically over the past 50 years, from printed to electronic to networked. Channeling and focusing this torrent of information to meet the specific needs of researchers has increased exponentially over time, and has required librarians to become beta testers, instructors, and negotiators. Dana Roth's contributions to chem. information, and to the field of librarianship as a whole, cannot be overestimated. This talk will highlight key contributions that Roth has made to the relationships between the Caltech Library and publishers, and between the Library and the campus research community. These relationships continue to flourish and expand, and examples of past efforts and current projects from across the Caltech Library will be discussed.
Several clones hybridizing with a bovine ADP/ATP translocase cDNA were isolated from an adult human liver cDNA library in the vector pEX1. DNA sequence analysis revealed that these clones encode two distinct forms of translocase. In particular, two clones specifying the COOH-end-proximal five-sixths of the protein exhibit a 9% amino acid sequence divergence and totally dissimilar 3' untranslated regions. One of these cDNAs is nearly identical in sequence to an ADP/ATP translocase clone (hp2F1) recently isolated from a human fibroblast cDNA library [Battini, R., Ferrari, S., Kaczmarek, L., Calabretta, B., Chen, S. & Baserga, R. (1987) J. Biol. Chem. 262, 4355-4359], with three amino acid changes and a few differences in the 3' untranslated region. Another clone isolated from the pEX1 library contains a reading frame encoding the remaining, NH2-end-proximal, 37 amino acids of the translocase. This sequence differs significantly (14% amino acid sequence divergence) from the corresponding segment of hp2F1, and the 5' untranslated regions of the two clones are totally dissimilar. RNA transfer hybridization experiments utilizing the clones isolated from the pEX1 library revealed the presence in HeLa cells of three distinct mRNA species. The pattern of hybridization and the sizes of these mRNAs suggest a greater complexity of organization and expression of the ADP/ATP translocase genes in human cells than indicated by the analysis of the cDNA clones.
We introduce a challenging set of 256 object categories containing a total of 30607 images. The original Caltech-101  was collected by choosing a set of object categories, downloading examples from Google Images and then manually screening out all images that did not fit the category. Caltech-256 is collected in a similar manner with several improvements: a) the number of categories is more than doubled, b) the minimum number of images in any category is increased from 31 to 80, c) artifacts due to image rotation are avoided and d) a new and larger clutter category is introduced for testing background rejection. We suggest several testing paradigms to measure classification performance, then benchmark the dataset using two simple metrics as well as a state-of-the-art spatial pyramid matching  algorithm. Finally we use the clutter category to train an interest detector which rejects uninformative background regions.