gebhart/patrepeval huggingface dataset:
Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacteria via Dynamic RNA Nanotechnology (2019)

A guide RNA (gRNA) directs the function of a CRISPR protein effector to a target gene of choice, providing a versatile programmable platform for engineering diverse modes of synthetic regulation (edit, silence, induce, bind). However, the fact that gRNAs are constitutively active places limitations on the ability to confine gRNA activity to a desired location and time. To achieve programmable control over the scope of gRNA activity, here we apply principles from dynamic RNA nanotechnology to engineer conditional guide RNAs (cgRNAs) whose activity is dependent on the presence or absence of an RNA trigger. These cgRNAs are programmable at two levels, with the trigger-binding sequence controlling the scope of the effector activity and the target-binding sequence determining the subject of the effector activity. There are two possible logical directions for single-input cgRNAs: constitutively active cgRNAs that are conditionally inactivated by an RNA trigger (ON→OFF logic) and constitutively inactive cgRNAs that are conditionally activated by an RNA trigger (OFF→ON logic). Using an in vitro assay for cgRNA activity with synthetic trigger, in vitro transcribed cgRNA, and recombinant dCas9, we observe a conditional (ON→OFF logic) response for a set of four allosteric constitutively active cgRNAs with a median ≈6% crosstalk between noncognate cgRNA/trigger pairs. Motivated by the observed lack of conditional response of this mechanism when ported to E. coli, we describe a systematic study of unstructured sequence inserts into the standard gRNA structure and report the conditional response of a set of 34 candidate cgRNAs in living cells. Molecular mechanisms for both ON→OFF and OFF→ON cgRNAs are demonstrated in E. coli. For each mechanism, automated sequence design is performed using the reaction pathway designer within NUPACK to produce an orthogonal library of cgRNAs that respond to different RNA triggers. In E. coli expressing cgRNAs, triggers, and silencing dCas9 as the protein effector, we observe a median conditional response of ≈15-fold for a library of three orthogonal ON→OFF splinted switch cgRNA/trigger pairs, and ≈3-fold for a library of three orthogonal OFF→ON toehold switch cgRNA/trigger pairs; the median crosstalk within each library is
Speculative thread decomposition through empirical optimization (2007)

Chip multiprocessors (CMPs), or multi-core processors, have become a common way of reducing chip complexity and power consumption while maintaining high performance. Speculative CMPs use hardware to enforce dependence, allowing a parallelizing compiler to generate multithreaded code without needing to prove independence. In these systems, a sequential program is decomposed into threads to be executed in parallel; dependent threads cause performance degradation, but do not affect correctness. Thread decomposition attempts to reduce the run-time overheads of data dependence, thread misprediction, and load imbalance. Because these overheads depend on the runtimes of the threads that are being created by the decomposition, reducing the overheads while creating the threads is a circular problem. Static compile-time decomposition handles this problem by estimating the run times of the candidate threads, but is limited by the estimates' inaccuracy. Dynamic execution-time decomposition in hardware has better run-time information, but is limited by the decomposition hardware's complexity and run-time overhead. We propose a third approach where a compiler instruments a profile run of the application to search through candidate threads and pick the best threads as the profile run executes. The resultant decomposition is compiled into the application so that a production run of the application has no instrumentation and does not incurany decomposition overhead. We avoid static decomposition's estimation accuracy problem by using actual profile-run execution times to pick threads, and we avoid dynamic decomposition's overhead by performing the decomposition at profile time. Because we allow candidate threads to span arbitrary sections of the application's call graph and loop nests, an exhaustive search of the decomposition space is prohibitive, even in profile runs. To address this issue, we make the key observation that the run-time overhead of a thread depends, to the first order, only on threads that overlap with the thread inexecution (e.g., in a four-core CMP, a given thread can overlap with at most three preceding and three following threads). This observation implies that a given thread affects only a few other threads, allowing pruning of the space. Using a CMP simulator, we achieve an average speedup of 3.51 on four cores for five of the SPEC CFP2000 benchmarks, which compares favorably to recent static techniques. We also discuss experiments with CINT2000.
Canthaxanthin. A new total synthesis (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCanthaxanthin. A new total synthesisMichael Rosenberger, Patrick McDougal, and Julie BahrCite this: J. Org. Chem. 1982, 47, 11, 2130–2134Publication Date (Print):May 1, 1982Publication History Published online1 May 2002Published inissue 1 May 1982https://pubs.acs.org/doi/10.1021/jo00132a028https://doi.org/10.1021/jo00132a028research-articleACS PublicationsRequest reuse permissionsArticle Views618Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Development of continuous descent approach concepts for noise abatement [ATC] (2003)

One major problem for airports today is the noise and environmental effects of conventional aircraft approach procedures. Conventional approach procedures, for example, often descend aircraft to intermediate altitudes on the order of 2000 to 3000 feet, before transitioning onto the final approach path and final descent to the approach runway. The effect of such procedures is to spread noise and aircraft emissions onto nearby communities, sometimes as far away as 30 miles from the runway threshold. Continuous descent approach (CDA) procedures have been proposed to reduce noise and emissions by (1) delaying descent below 7000 feet as late as possible, and (2) descending at idle or near idle thrust from about 220 knots until final approach speed is reached. This paper describes near-term, mid-term, and advanced operational concepts for FMS (flight management system) based CDA system deployments.
Stable Fitted Reinforcement Learning (1995)

We describe the reinforcement learning problem, motivate algorithms which seek an approximation to the Q function, and present new convergence results for two such algorithms. 1 INTRODUCTION AND BACKGROUND Imagine an agent acting in some environment. At time t, the environment is in some state x t chosen from a finite set of states. The agent perceives x t , and is allowed to choose an action a t from some finite set of actions. The environment then changes state, so that at time (t + 1) it is in a new state x t+1 chosen from a probability distribution which depends only on x t and a t . Meanwhile, the agent experiences a real-valued cost c t , chosen from a distribution which also depends only on x t and a t and which has finite mean and variance. Such an environment is called a Markov decision process, or MDP. The reinforcement learning problem is to control an MDP to minimize the expected discounted cost P t fl t c t for some discount factor fl 2 [0; 1]. Define the function Q ...
Being the Machine (2015)

This paper details the design and evaluation of Being the Machine, a portable digital fabrication system that places digital fabrication activity outside of the traditional fab lab environment. Being the Machine invites people to (re)consider materials found in their everyday and personal environment as part of the fabrication activity. We expand the design space involving hybrid (physical-digital) fabrication by describing how our system draws from art to support critical and reflective modes of making. In interaction with our system, participants distributed control between human and machine actors to support their preferred mode of making. These patterns reveal new opportunities and challenges for future hybrid fabrication systems, and suggest that designing for qualities of experience, like meditation and reflection, could support meaningful making experiences for many different kinds of makers.
In vitro manipulation of human anti-DNA antibody production by anti-idiotypic antibodies conjugated with neocarzinostatin. (1989)

Anti-DNA Id, 0-81, consist of 5 to 51% of Id in human anti-ssDNA antibodies; NE-1-Id shares 2 to 20% of those in anti-dsDNA antibodies. Thus, both 0-81-Id and NE-1-Id are of the cross-reactive Id that are commonly present among anti-DNA antibodies. In order to manipulate the production of anti-DNA antibodies by human PBL, we used mouse antiidiotypic mAb or those conjugated with a cytotoxic agent, neocarzinostatin. Treatment with the conjugates caused profound suppression of anti-ssDNA and anti-dsDNA antibody synthesis related to 0-81- and NE-1-Id. This was attributed to the specific killing of the clones bearing anti-DNA Id among the lymphocytes, evidenced by the indirect rosette formation tests. The Id-mediated suppression was not solely due to selective elimination of Id-positive B cells, because 50 to 92% of anti-DNA antibodies were suppressed by treatment with the conjugates. This was supported by flow cytometry analysis that showed a decrease of anti-Id-reactive cells when T cells were treated with the conjugates. This method, then, will permit an analysis of the question as to whether T cells reactive to anti-idiotypic antibodies might participate in the regulatory mechanism for anti-DNA production and, in addition, may lead to a new therapy for SLE.
A floorplan-aware interactive tool flow for NoC design and synthesis (2009)

In this paper we present a floorplan-aware toolchain for NoC design and synthesis integrated with a graphical front-end. The resulting design methodology is highly automated yet entails rich interaction with the user, spanning across traffic flow specification, topology synthesis and physical floorplanning, with back-annotation capabilities and opportunities for incremental design. We exploit the proposed tool to implement some NoC-based case studies. We show that not only a great amount of time and effort can be saved thanks to the easy-to-use proposed environment, but also that the quality of the final netlist improves due to the optimizations unlocked by the early-stage interaction among the designer and the proposed toolchain.
Abstract 2408: Identification of R-Spondin fusions in various types of human cancer (2014)

Abstract Autocrine or paracrine constitutive Wnt pathway activation occurs at a high frequency in several tumor types. The R-spondin (RSPO) protein family is comprised of four secreted growth factors. The four paralogs share 40-60% pairwise amino acid sequence identity and are predicted to share substantial structural homology. RSPO proteins are involved in vertebrate development and their ligand-type activities overlap substantially with those of canonical Wnt ligands. A characteristic feature of all four RSPO members is their ability to activate β-catenin signaling and enhance WNT-mediated β-catenin activation. It has recently been described that recurrent gene fusions involving RSPO family members RSPO2 and RSPO3 occur in ∼10% of colon tumors. In this study we developed a TaqMan qRT-PCR-based approach to evaluate the expression of these three (3) RSPO fusion transcripts in formalin-fixed paraffin embedded tissue (FFPET) samples. We examined 324 lung cancer, 81 colorectal cancer, 71 head & neck, 11 esophageal, 92 ovarian cancer, and 103 breast cancer FFPET samples for the presence of EIF3E(e1)-RSPO2(e1), PTPRK(e1)-RSPO3(e2), and PTPRK(e7)-RSPO3(e2). EIF3E(e1)-RSPO2(e1), a fusion which is expected to produce a functional RSPO2 protein driven by the EIF3E promoter, was identified in ∼1-2% of most of cancer types with the exception of breast cancer. The PTPRK(e1)-RSPO3(e2) fusion was expressed by ∼1-11% of the samples in the different cancers, making it the most prevalent of the fusions. PTPRK(e1)-RSPO3(e2) fusion is an in-frame fusion that preserves the entire coding sequence of RSPO3 and replaces its secretion signal sequence with that of PTPRK. The PTPRK(e7)-RSPO3(e2) fusion is also an in-frame fusion in which the RSPO3 native signal peptide is replaced by the secretion signal of PTPRK. The PTPRK(e7)-RSPO3(e2) was the least prevalent of all the fusions, positive samples were found exclusively in the head and neck (∼2%) and breast cancer samples (∼2%). All of the fusions detected were mutually exclusive. The RSPO gene fusions identified may provide new potential opportunities for therapeutic intervention. Citation Format: Gabriela Martinez Cardona, Katherine Bell, Joseph Portale, Dana Gaffney, Christopher Moy, Suso Platero, Matthew V. Lorenzi, Jayaprakash Karkera. Identification of R-Spondin fusions in various types of human cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2408. doi:10.1158/1538-7445.AM2014-2408
Experiments on Plasma-Assisted Combustion in a Supersonic Flow : Optimization of Plasma Position in Relation to the Fuel Injector (2015)

The results of an experimental study of plasma-induced ethylene ignition and flameholding in a supersonic model combustor are presented in the paper. The experimental combustor has a cross-section of 72 mm (width) x 60 mm (height) and length of 600 mm. The fuel is directly injected into the supersonic airflow through wall orifices. The flow parameters are : Mach number M=2, static pressure Pst=160-250 Torr, stagnation temperature T0=300 K and total air flow rate Gair0.9 kg/s. The near-surface quasi-DC electrical discharge is generated by a series of flush-mounted electrodes, providing an electrical power deposition of Wpl=3-24kW. The scope of the experiments includes the characterization of the discharge interacting with the main flow and fuel injection jet, a parametric study of ignition and flame front dynamics and a comparison of three plasma generation schemes: the first two examine upstream and downstream locations of plasma generators in relation to the fuel injectors. The third pattern follows a novel approach of a combined mixing/ignition technique, where the electrical discharge is distributed along the fuel jet, starting within the fuel injector. The last pattern demonstrates a significant advantage in terms of the flameholding limit. The experiments are supported by gas temperature and H2O vapor concentration measurements by Tunable Diode-Laser Absorption Spectroscopy (TDLAS). The technique studied in this work has weighty potential for high-speed combustion applications, including cold start/restart of scramjet engines and support of the transition regime in a dual-mode scramjet and during off-design operation.
Establishment of a Real-Time PCR-Based Approach for Accurate Quantification of Bacterial RNA Targets in Water, Using <i>Salmonella</i> as a Model Organism (2004)

Quantitative PCR (Q-PCR) is a fast and efficient tool to quantify target genes. In eukaryotic cells, quantitative reverse transcription-PCR (Q-RT-PCR) is also used to quantify gene expression, with stably expressed housekeeping genes as standards. In bacteria, such stable expression of housekeeping genes does not occur, and the use of DNA standards leads to a broad underestimation. Therefore, an accurate quantification of RNA is feasible only by using appropriate RNA standards. We established and validated a Q-PCR method which enables the quantification of not only the number of copies of target genes (i.e., the number of bacterial cells) but also the number of RNA copies. The genes coding for InvA and the 16S rRNA of Salmonella enterica serovar Typhimurium were selected for the evaluation of the method. As DNA standards, amplified fragments of the target genes were used, whereas the same DNA standards were transcribed in vitro for the development of appropriate RNA standards. Salmonella cultures and environmental water samples inoculated with bacteria were then employed for the final testing. Both experimental approaches led to a sensitive, accurate, and reproducible quantification of the selected target genes and RNA molecules by Q-PCR and Q-RT-PCR. It is the first time that RNA standards have been successfully used for a precise quantification of the number of RNA molecules in prokaryotes. This demonstrates the potential of this approach for determining the presence and metabolic activity of pathogenic bacteria in environmental samples.
Conformationally Regulated Molecular Binding and Release of Molecularly Imprinted Polypeptide Hydrogels That Undergo Helix–Coil Transition (2017)

Polypeptides have inherent secondary structures, such as α-helix, β-sheet, and random coil structures, depending on their amino acid sequence. β-Cyclodextrins (CDs) as ligands of molecular recognition sites were introduced into poly(l-lysine) (PLL), which undergoes a structural transition in response to a pH change. CD-introduced PLL (CD-PLL) hydrogels with dynamic molecular recognition sites for bisphenol A (BPA) were strategically designed by molecular imprinting, where BPA was used as a template molecule with a minute amount of cross-linkers. The resulting BPA-imprinted CD-PLL hydrogels with a random coil structure underwent a change in volume in response to the target BPA because the ligand CDs formed a complex with BPA. Additionally, a change in pH induced a structural transition of the CD-PLL chains from the random coil to an α-helix, followed by a conformational change of the molecular recognition sites within the BPA-imprinted CD-PLL hydrogels. As a result, BPA adsorption into the BPA-imprinted CD-PLL hydrogels strongly depended on pH. The molecular recognition ability of the BPA-imprinted CD-PLL hydrogels was controlled by the helix–coil transition of the PLL chains. BPA, as a model drug, was loaded within the CD-PLL hydrogel networks by molecular imprinting, and the BPA template was not extracted from the hydrogel networks. The drug release from the drug-loaded CD-PLL hydrogel was regulated by the pH-responsive structural transition of the PLL chains, which could control the stability of the inclusion complex between the drugs and CD ligands. The fascinating properties of the BPA-imprinted CD-PLL hydrogels with dynamic molecular recognition sites suggest that they exhibit potential as suitable drug carriers inspired from the allosteric effects of proteins.
Impulse Density of 155 mm Projectile as a Function of Distance (2010)

155 mm projectiles are detonated in a test arena with steel momentum plates of 30x50x2cm3 with 23.55 kg weight, positioned 1.25m above the ground where their achieved velocities are measured by the displacement distance on the ground. Although the impulse density results show a large scatter, they can be roughly described as exponential equations of the scaled displacements.
Nanostructured Thermosetting Blends of Epoxy Resin and Amphiphilic Poly(ε-caprolactone)-<i>b</i><i>lock</i>-polybutadiene-<i>b</i><i>lock</i>-poly(ε-caprolactone) Triblock Copolymer (2005)

The amphiphilic triblock copolymer poly(ε-caprolactone)-b-polybutadiene-b-poly(ε-caprolactone) (PCL−PB−PCL) was synthesized via the ring-opening polymerization of ε-caprolactone in the presence of a hydroxyl-terminated polybutadiene (HTPB), which was catalyzed by stannous octanoate [Sn(Oct)2]. The amphiphilic triblock copolymer was further used to prepare the nanostructured epoxy thermosets. The in situ polymerization of epoxy monomers in the presence of PCL−PB−PCL started from the homogeneous solutions composed of the block copolymer and the monomers of epoxy at the temperature above the upper critical solution temperature (UCST) of diglycidyl ether of bisphenol A (DGEBA) and HTPB blends. The transmission electronic microscopy (TEM), small-angle X-ray scattering (SAXS), and atomic force microscopy (AFM) showed that the nanostructured thermosets were successfully obtained. Depending on the content of the block copolymer in the thermosets, the PB domains can display spherical and interconnected nanoobjects with the size of 10−20 nm. It is judged that the nanostructures are formed on the basis of the mechanism of polymerization-induced microphase separation, which is in a marked contrast to the approach in which some equilibrium self-organized structures were preformed and the microphases were fixed via subsequent curing reaction.
Multiple Functional Domains and Complexes of the Two Nonstructural Proteins of Human Respiratory Syncytial Virus Contribute to Interferon Suppression and Cellular Location (2011)

Human respiratory syncytial virus (RSV), a major cause of severe respiratory diseases, efficiently suppresses cellular innate immunity, represented by type I interferon (IFN), using its two unique nonstructural proteins, NS1 and NS2. In a search for their mechanism, NS1 was previously shown to decrease levels of TRAF3 and IKKε, whereas NS2 interacted with RIG-I and decreased TRAF3 and STAT2. Here, we report on the interaction, cellular localization, and functional domains of these two proteins. We show that recombinant NS1 and NS2, expressed in lung epithelial A549 cells, can form homo- as well as heteromers. Interestingly, when expressed alone, substantial amounts of NS1 and NS2 localized to the nuclei and to the mitochondria, respectively. However, when coexpressed with NS2, as in RSV infection, NS1 could be detected in the mitochondria as well, suggesting that the NS1-NS2 heteromer localizes to the mitochondria. The C-terminal tetrapeptide sequence, DLNP, common to both NS1 and NS2, was required for some functions, but not all, whereas only the NS1 N-terminal region was important for IKKε reduction. Finally, NS1 and NS2 both interacted specifically with host microtubule-associated protein 1B (MAP1B). The contribution of MAP1B in NS1 function was not tested, but in NS2 it was essential for STAT2 destruction, suggesting a role of the novel DLNP motif in protein-protein interaction and IFN suppression.