gebhart/patrepeval huggingface dataset:
Deep ocean long range underwater navigation (2020)

A long range Underwater Navigation Algorithm (UNA) is described that provides a geolocation underwater while submerged without having to surface for a Global Navigation Satellite System (GNSS) position. The UNA only uses measured acoustic travel times from a constellation of underwater acoustic sources analogous to the constellation of satellites in GNSS. The UNA positions are calculated without any a priori track, position or sound speed information, and thus provide a "Cold Start" capability. The algorithm was tested using data from the 2010-2011 Philippine Sea Experiment in which six sources were deployed in a pentagon ∼400 km on a side. 502 positions of hydrophones in a bottom-moored vertical line array at depths of 485-3037 m drifting in a tidal watch circle up to 600 m in diameter were computed. The sources were 129-450 km from the hydrophone receivers. The mean UNA position error from ground truth was 58 m with a standard deviation of 32 m. The UNA Cold Start Algorithm position can be used as the point in the ocean for calculating acoustic model runs from the source positions with a four-dimensional sound speed field from a general circulation model to improve the accuracy.
Plant antitumor agents. 29. Synthesis and biological activity of ring D and ring E modified analogs of camptothecin (1990)

The total synthesis of the pentacyclic camptothecin analogues 3 and 4 in 11 steps from p-tolualdehyde is described. The overall shape of compound 3 is the same as that of potent, naturally occurring camptothecin (1a). Despite the near spatial identity of 3 and 1b (racemic, (20RS)-camptothecin) from a three-dimensional standpoint, the 9KB and 9PS cytotoxicity assays indicate at least a 40-60-fold decrease in activity of 3 compared to that of 1b, and the isomer 4 was inactive. Similarly, studies of the inhibition of topoisomerase I activity indicated only slight activity for 3 and no activity for 4. It is evident that the pyridone ring D is essential for antitumor activity. Three E ring modified analogues of camptothecin, 2d-f, are described in which the net change is replacement of O by N in ring E. Compared to (20S)-camptothecin (1a) or (20RS)-camptothecin (1b), the ring E modified analogues 2d-f display little or no cytotoxic activity, greatly reduced effect on the inhibition of topoisomerase I, and total loss of life prolongation in the in vivo L-1210 mouse leukemia assay, indicative of the highly restricted structural and electronic requirements of ring E for biological activity in camptothecin.
Acquisition of a Potent and Selective TC-PTP Inhibitor via a Stepwise Fluorophore-Tagged Combinatorial Synthesis and Screening Strategy (2009)

Protein tyrosine phosphatases (PTPs) regulate a broad range of cellular processes including proliferation, differentiation, migration, apoptosis, and immune responses. Dysfunction of PTP activity is associated with cancers, metabolic syndromes, and autoimmune disorders. Consequently, small molecule PTP inhibitors should serve not only as powerful tools to delineate the physiological roles of these enzymes in vivo but also as lead compounds for therapeutic development. We describe a novel stepwise fluorophore-tagged combinatorial library synthesis and competitive fluorescence polarization screening approach that transforms a weak and general PTP inhibitor into an extremely potent and selective TC-PTP inhibitor with highly efficacious cellular activity. The result serves as a proof-of-concept in PTP inhibitor development, as it demonstrates the feasibility of acquiring potent, yet highly selective, cell permeable PTP inhibitory agents. Given the general nature of the approach, this strategy should be applicable to other PTP targets.
Passive Turbulence Generating Grid Arrangements in a Turbine Cascade Wind Tunnel (2015)

Abstract : Turbine cascade wind tunnels simulate Reynolds number and turbulence for the examination of flow phenomena such as boundary layer separation on the trailing portion of low pressure turbine blades. Axial chord-based Reynolds numbers considered in this study were 50k and 100k. Various passive, square-bar turbulence generating grid arrangements were explored to simulate turbulence in a turbine cascade test-section inlet, including two grid orientations: perpendicular to the inlet flow and parallel to the turbine cascade. A novel T-Bar turbulence grid configuration oriented parallel to the cascade was shown to produce better test section inlet flowfield uniformity than that produced by a perpendicular mesh grid. Improved periodicity in blade-to-blade surface pressure coefficient profiles was also observed with the parallel T-Bar grid.
Increasing Protein Production Rates Can Decrease the Rate at Which Functional Protein Is Produced and Their Steady-State Levels (2017)

The rate at which soluble, functional protein is produced by the ribosome has recently been found to vary in complex and unexplained ways as various translation-associated rates are altered through synonymous codon substitutions. To understand this phenomenon, here, we combine a well-established ribosome-traffic model with a master-equation model of cotranslational domain folding to explore the scenarios that are possible for the protein production rate, J, and the functional-nascent protein production rate, F, as the rates of various translation processes are altered for five different E. coli proteins. We find that while J monotonically increases as the rates of translation-initiation, -elongation, and -termination increase, F can either increase or decrease. We show that F's nonmonotonic behavior arises within the model from two opposing trends: the tendency for increased translation rates to produce more total protein but less cotranslationally folded protein. We further demonstrate that under certain conditions these nonmonotonic changes in F can result in nonmonotonic variations in post-translational, steady-state levels of functional protein. These results provide a potential explanation for recent experimental observations in which the specific activity of enzymatic proteins decreased with increased synthesis rates. Additionally our model has the potential to be used to rationally design transcripts to maximize the production of functional nascent protein by simultaneously optimizing translation initiation, elongation, and termination rates.
Metabolie Engineering of Floral Scent of Ornamentals (2006)

Abstract Flowers of many plant species emit floral scent to attract pollinators. Such scents are often complex mixtures of various small aliphatic molecules, mostly terpenoid, phenylpropanoid, and benzenoid compounds. However, a large number of commercial flower varieties have lost their scent during the traditional breeding process. This lack of scent has been recognized as one of the major problems in the floriculture industry. Recent discoveries of genes encoding enzymes catalyzing the synthesis of scent compounds, and advances in our understanding of the regulation of scent biosynthetic genes, now make it possible to engineer plants with increased scent or with newly introduced aromas. Past approaches for metabolic engineering of floral scent have used various strategies, including the introduction of new scent genes and the blockage of existing non-scent pathways to divert metabolites into scent production. However, these experiments have only been partially successful. Problems have included the lack of specificity in targeting the expression of the introduced gene to flowers and unexpected biochemical reactions that metabolized the new scent compounds into non-volatile byproducts. Future attempts at scent genetic engineering will need to utilize specific floral gene promoters and be based on a clearer understanding of metabolic fluxes.
Automatic segmentation of intra-cochlear anatomy in post-implantation CT (2013)

A cochlear implant (CI) is a neural prosthetic device that restores hearing by directly stimulating the auditory nerve with an electrode array. In CI surgery, the surgeon threads the electrode array into the cochlea, blind to internal structures. We have recently developed algorithms for determining the position of CI electrodes relative to intra-cochlear anatomy using pre- and post-implantation CT. We are currently using this approach to develop a CI programming assistance system that uses knowledge of electrode position to determine a patient-customized CI sound processing strategy. However, this approach cannot be used for the majority of CI users because the cochlea is obscured by image artifacts produced by CI electrodes and acquisition of pre-implantation CT is not universal. In this study we propose an approach that extends our techniques so that intra-cochlear anatomy can be segmented for CI users for which pre-implantation CT was not acquired. The approach achieves automatic segmentation of intra-cochlear anatomy in post-implantation CT by exploiting intra-subject symmetry in cochlear anatomy across ears. We validated our approach on a dataset of 10 ears in which both pre- and post-implantation CTs were available. Our approach results in mean and maximum segmentation errors of 0.27 and 0.62 mm, respectively. This result suggests that our automatic segmentation approach is accurate enough for developing customized CI sound processing strategies for unilateral CI patients based solely on postimplantation CT scans.
Multidimensional content eXploration (2008)

Content Management Systems (CMS) store enterprise data such as insurance claims, insurance policies, legal documents, patent applications, or archival data like in the case of digital libraries. Search over content allows for information retrieval, but does not provide users with great insight into the data. A more analytical view is needed through analysis, aggregations, groupings, trends, pivot tables or charts, and so on. Multidimensional Content eXploration (MCX) is about effectively analyzing and exploring large amounts of content by combining keyword search with OLAP-style aggregation, navigation, and reporting. We focus on unstructured data or generally speaking documents or content with limited metadata, as it is typically encountered in CMS. We formally present how CMS content and metadata should be organized in a well-defined multidimensional structure, so that sophisticated queries can be expressed and evaluated. The CMS metadata provide traditional OLAP static dimensions that are combined with dynamic dimensions discovered from the analyzed keyword search result, as well as measures for document scores based on the link structure between the documents. In addition, we provide means for multidimensional content exploration through traditional OLAP rollupdrilldown operations on the static and dynamic dimensions, solutions for multi-cube analysis and dynamic navigation of the content. We present our prototype, called DBPubs, which stores research publications as documents that can be searched and -most importantly-- analyzed, and explored. Finally, we present experimental results of the efficiency and effectiveness of our approach.
Organic transistors with low operating voltage and high mobility (2003)

Thin film transistors (TFT) comprising pentacene as the semiconductor layer and an amorphous metal oxide gate insulators with a dielectric constant around 16 were fabricated and tested. Field effect mobility values up to 0.6 cm/sup 2/ V/sup -1/ s/sup -1/ with subthreshold slopes up to 0.3 V/decade and current modulation higher than 10/sup 5/ were obtained at operating voltages ranging from 4 to 15 V. TFTs fabricated at room temperature on transparent plastic substrates and exhibiting similar transport characteristics were demonstrated.
Atropisomeric 3-(β-hydroxyethyl)-4-arylquinolin-2-ones as Maxi-K Potassium Channel Openers (2007)

The synthesis of a series of 3-beta-hydroxyethyl-4-arylquinolin-2-ones is described. These compounds contain hydrophilic and hydrophobic substituents ortho to the phenolic OH in the C ring of the quinolinone. Electrophysiological evaluation of the panel of compounds revealed that 11 and 16 with an unbranched ortho substituent retain activity as maxi-K ion channel openers. Members of this series of compounds can exist as stable atropisomers. Calculated estimates of the energy barrier for rotation around the aryl-aryl single bond in 3 is 31 kcal/mol. The atropisomers of (+/-)-3, (+/-)-4, and (+/-)-11 were separated by chiral HPLC and tested for their effect on maxi-K mediated outward current in hSlo injected X. laevis oocytes. The (-) isomer in each case was found to be more active than the corresponding (+) isomer, suggesting that the ion channel exhibits stereoselective activation. X-ray crystallographic structures of (+)-3 and (+)-11 were determined. Evaluation of the stability of (-)-3 at 80 degrees C in n-butanol indicated a 19.6% conversion to (+)-3 over 72 h. In human serum at 37 degrees C (-)-3 did not racemize over the course of the 30 h study.
Phase Synchronization of Two Anharmonic Nanomechanical Oscillators (2014)

We investigate the synchronization of oscillators based on anharmonic nanoelectromechanical resonators. Our experimental implementation allows unprecedented observation and control of parameters governing the dynamics of synchronization. We find close quantitative agreement between experimental data and theory describing reactively coupled Duffing resonators with fully saturated feedback gain. In the synchronized state we demonstrate a significant reduction in the phase noise of the oscillators, which is key for sensor and clock applications. Our work establishes that oscillator networks constructed from nanomechanical resonators form an ideal laboratory to study synchronization--given their high-quality factors, small footprint, and ease of cointegration with modern electronic signal processing technologies.
Nanoscale Magnification and Shape Control System for Precision Overlay in Jet and Flash Imprint Lithography (2014)

Jet and flash imprint lithography steppers have demonstrated unprecedented capability for patterning of sub-25-nm features for semiconductor manufacturing. A critical requirement for such patterning is the ability to overlay one layer of a device to a previously printed layer. In this paper, the design and development of a nanoprecision mask magnification/shape control system (MSCS) for the unique requirements of imprint-based overlay is presented. Imprint specific topics such as in-liquid overlay and distortions, and on-tool overlay metrology are discussed. The MSCS presented here has demonstrated 10-nm mix and match overlay (mean + 3 sigma) capability that approaches performance of state-of-the-art photolithography tools.
Characterizing and classifying IoT traffic in smart cities and campuses (2017)

Campuses and cities of the near future will be equipped with vast numbers of IoT devices. Operators of such environments may not even be fully aware of their IoT assets, let alone whether each IoT device is functioning properly safe from cyber-attacks. This paper proposes the use of network traffic analytics to characterize IoT devices, including their typical behaviour mode. We first collect and synthesize traffic traces from a smart-campus environment instrumented with a diversity of IoT devices including cameras, lights, appliances, and health-monitors; our traces, collected over a period of 3 weeks, are released as open data to the public. We then analyze the traffic traces to characterize statistical attributes such as data rates and burstiness, activity cycles, and signalling patterns, for over 20 IoT devices deployed in our environment. Finally, using these attributes, we develop a classification method that can not only distinguish IoT from non-IoT traffic, but also identify specific IoT devices with over 95% accuracy. Our study empowers operators of smart cities and campuses to discover and monitor their IoT assets based on their network behaviour.
ILP formulation of signal power based routing for single and multilayer optical networks (2008)

In both metropolitan optical networks (MON) and long haul optical networks (LHON) the signal quality is often influenced by the physical impairments, therefore a proper impairment based routing decision is needed. In this paper we propose new routing and wavelength assignment (RWA) methods where the control plane has influence on the signal power of the Wavelength Division Multiplexed (WDM) channels. Nowadays in nearly all kinds of reconfigurable optical add-drop multiplexers (ROADM) the signal power can be tuned via variable optical attenuators (VOA) from the control plane. We give the exact integer linear programming (ILP) formulation of the method for both single and multilayer networks. In the first case we assume that no signal regeneration is allowed along the path, while in the more complex multilayer case 3R signal regeneration, grooming and wavelength conversion can all be done in the electronic layer. The proposed algorithm can be used in existing WDM optical networks where the nodes support signal power tuning. The algorithm finds the global optimum, if it exists, for a certain network topology, physical constraints and demand set.
A 3.5 GHz Digital Fractional-N PLL Frequency Synthesizer Based on Ring Oscillator Frequency-to-Digital Conversion (2015)

A 3.5 GHz digital fractional-N PLL in 65 nm CMOS technology is presented that achieves phase noise and spurious tone performance comparable to those of a high-performance analog PLL. It is enabled by a new second-order frequency-to-digital converter that uses a dual-mode ring oscillator and digital logic instead of a charge pump and ADC. It also incorporates a new technique to reduce excess phase noise that would otherwise be caused by component mismatches when the DCO input is near integer boundaries. The PLL's largest in-band fractional spur is -60 dBc, its worst-case reference spur is -81 dBc, and its phase noise is -93, -126, and -151 dBc/Hz at offsets of 100 kHz, 1 MHz, and 20 MHz, respectively. Its active area is 0.34 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and it dissipates 15.6 mW from a 1 V supply.
1077. Sequences from the Human Type 1α2 Procollagen Promoter Mediate Osteoblast- Specific Plasmid Nuclear Import (2006)

Two major problems limiting the use of non-viral gene therapy include the low efficiency of gene transfer seen with non-viral vectors and limited methods for cell-specific targeting and expression. We and others have shown that translocation of plasmid DNA into the nucleus is an important rate-limiting step in gene transfer that affects transgene expression levels in non-dividing cells. Further, we have identified several DNA sequences that mediate the nuclear import of plasmids in non-dividing cells, thereby acting as DNA nuclear targeting sequences. These sequences contain multiple binding sites for transcription factors that allow for the formation of protein- DNA complexes in the cytoplasm that are actively transported into the nucleus of the non-dividing cell using nuclear localization signals present on the transcription factors, and hence the protein-DNA complex. We have previously identified both a universal sequence that acts in all cell types (the SV40 enhancer) and sequences that act in specific cell types based on the property that they bind cell- specific transcription factors (e.g., the SMGA promoter for use in smooth muscle cells). In order to identify a DNA nuclear targeting sequence that is restricted to osteoblast lineage cells, we tested a number of osteoblast-specific promoters for nuclear import activity, including those from osteocalcin, collagen, BSP and Runx2 genes. Although all of these promoters showed robust expression of reporter genes following transfection into dividing osteoblasts, when microinjected into the cytoplasm of human or rat osteoblast cell lines, only the human type Iα2 procollagen (hcolIα2) promoter had the ability to mediate nuclear import of the plasmid in the absence of cell division. This sequence did not support DNA nuclear import in chondrocytes, fibroblasts and marrow stromal cells, suggesting that it is osteoblast-specific. Site-directed mutagenesis of putative transcription factor binding sites indicated that multiple response elements were required for osteoblast specific nuclear targeting, including those for AP-1, AP-2, Nkx3, SRF, Krox20, and an E-box binding protein. Taken together, these results suggest that the hCol1α2 promoter contains a novel osteoblast-specific DNA nuclear targeting sequence that can be used to increase nonviral gene transfer and transgene expression uniquely in osteoblasts, thereby increasing the safety profile by specifically targeting osteoblasts in skeletal tissue for gene therapy. The research reported in this abstract was supported by the Dept of the Army Cooperative Agreement # (DAMD17-97-2-7016). The views and content of the information does not necessarily reflect the position or the policy of the government or NMTB, and that no official endorsement should be inferred.
Development of digital stroke sensing cylinder and its performance evaluation (1996)

Automation of heavy construction machinery needs sensors that can detect each position under severe construction fields. Motivated by this need a hydraulic cylinder equipped with Hall sensors of Ga-As type has been developed. However, this sensor device has some problems associated with incorrect detection of positions owing to the existence of some magnetic slope and electric noises. To solve these problems, this paper proposes a digital stroke sensing cylinder enhanced by digital signal processing. An apparatus of two hydraulic systems coupled with each other is installed in an experimental setup to evaluate the performance of the developed digital stroke sensing cylinder. In order to control the position of a cylinder rod, a PWM method is used. Evaluation of the performance is carried out under artificial disturbances such as an impulse, addition of some magnetic slope, and additional noises.
Super-insulating gas-filled panels (1990)

This paper presents the design, materials characteristics, and thermal performance of a new insulating material. Development of this material is motivated by the need for non-CFC based high performance insulations with applications for refrigerator/freezer and building walls. This super insulating gas filled panel technology achieves R-values of between 8 hr-ft{sup 2}-F/Btu per inch and 15 hr-ft{sup 2}-F/Btu per inch (one to two times that of CFC blown foams and two to four times that of fiberglass insulations) at estimated costs of $0.40--$1.50/in-ft{sup 2}. Prototypes have been built using commercially available materials and components, tested by the developers, and sent to an independent laboratory for independent thermal performance testing. 2 refs., 4 figs., 1 tab.