gebhart/patrepeval huggingface dataset:
Nucleotidylation of unsaturated carbasugar in validamycin biosynthesis (2010)

Validamycin A is a member of microbial-derived C(7)N-aminocyclitol family of natural products that is widely used as crop protectant and the precursor of the antidiabetic drug voglibose. Its biosynthetic gene clusters have been identified in several Streptomyces hygroscopicus strains, and a number of genes within the clusters have been functionally analyzed. Of these genes, valB, which encodes a sugar nucleotidyltransferase, was found through inactivation study to be essential for validamycin biosynthesis, but its role was unclear. To characterize the role of ValB in validamycin biosynthesis, four carbasugar phosphate analogues were synthesized and tested as substrate for ValB. The results showed that ValB efficiently catalyzes the conversion of valienol 1-phosphate to its nucleotidyl diphosphate derivatives, whereas other unsaturated carbasugar phosphates were found to be not the preferred substrate. ValB requires Mg(2+), Mn(2+), or Co(2+) for its optimal activity and uses the purine-based nucleotidyltriphosphates (ATP and GTP) more efficiently than the pyrimidine-based NTPs (CTP, dTTP, and UTP) as nucleotidyl donor. ValB represents the first member of unsaturated carbasugar nucleotidyltransferases involved in natural products biosynthesis. Its characterization not only expands our understanding of aminocyclitol-derived natural products biosynthesis, but may also facilitate the development of new tools for chemoenzymatic synthesis of carbohydrate mimetics.
Automated assessment of ESOL free text examinations (2021)

In this report, we consider the task of automated assessment of English as a Second Language (ESOL) examination scripts written in response to prompts eliciting free text answers. We review and critically evaluate previous work on automated assessment for essays, especially when applied to ESOL text. We formally define the task as discriminative preference ranking and develop a new system trained and tested on a corpus of manually-graded scripts. We show experimentally that our best performing system is very close to the upper bound for the task, as defined by the agreement between human examiners on the same corpus. Finally we argue that our approach, unlike extant solutions, is relatively prompt-insensitive and resistant to subversion, even when its operating principles are in the public domain. These properties make our approach significantly more viable for high-stakes assessment.
Woven Thermal Protection System Based Heat-shield for Extreme Entry Environments Technology (HEEET) (2013)

NASA's future robotic missions utilizing an entry system into Venus and the outer planets, namely, Saturn, Uranus, Neptune, result in extremely severe entry conditions that exceed the capabilities of state of the art low to mid density ablators such as PICA or Avcoat. Therefore mission planners typically assume the use of a fully dense carbon phenolic heat shield similar to what was flown on Pioneer Venus and Galileo. Carbon phenolic (CP) is a robust TPS material however its high density and relatively high thermal conductivity constrain mission planners to steep entries, with high heat fluxes and pressures and short entry durations, in order for CP to be feasible from a mass perspective. The high entry conditions pose challenges for certification in existing ground based test facilities and the longer-term sustainability of CP will continue to pose challenges. In 2012 the Game Changing Development Program (GCDP) in NASA's Space Technology Mission Directorate funded NASA ARC to investigate the feasibility of a Woven Thermal Protection System (WTPS) to meet the needs of NASA's most challenging entry missions. This project was highly successful demonstrating that a Woven TPS solution compares favorably to CP in performance in simulated reentry environments and provides the opportunity to manufacture graded materials that should result in overall reduced mass solutions and enable a much broader set of missions than does CP. Building off the success of the WTPS project GCDP has funded a follow on project to further mature and scale up the WTPS concept for insertion into future NASA robotic missions. The matured WTPS will address the CP concerns associated with ground based test limitations and sustainability. This presentation will briefly discuss results from the WTPS Project and the plans for WTPS maturation into a heat-shield for extreme entry environment.
ChemInform Abstract: 1‐(SUBSTITUTED BENZYL)‐3,4,5,6‐TETRAHYDRO‐2(1H)‐PYRIMIDONES: A SERIES WITH STIMULANT AND DEPRESSANT ACTIVITIES (1981)

Abstract Aus dem Pyrimidonhydrochlorid (I) und den Benzylchloriden (II) entstehen die Benzylpyrimidone (III), die zu den Benzyltetrahydropyrimidonen (IV) hydriert werden.
Down-conversion en-face optical coherence tomography (2019)

We present an optical coherence tomography (OCT) method that can deliver an <i>en-face</i> OCT image from a sample in real-time, irrespective of the tuning speed of the swept source. The method, based on the master slave interferometry technique, implements a coherence gate principle by requiring that the optical path difference (OPD) between the arms of an imaging interferometer is the same with the OPD in an interrogating interferometer. In this way, a real-time <i>en-face</i> OCT image can originate from a depth in the sample placed in the imaging interferometer, selected by actuating on the OPD in the interrogating interferometer, while laterally scanning the incident beam over the sample. The generation of the <i>en-face</i> image resembles time domain OCT, with the difference that here the signal is processed based on spectral domain OCT. The optoelectronic processor operates down-conversion of the chirped radio frequency signal delivered by the photo-detector. The down-conversion factor is equal to the ratio of the maximum frequency of the photo-detected signal due to an OPD value matching the coherence length of the swept source, to the sweeping rate. This factor can exceed 10<sup>6</sup> for long coherence swept sources.
Human-computer interaction for hybrid carving (2013)

In this paper we explore human-computer interaction for carving, building upon our previous work with the FreeD digital sculpting device. We contribute a new tool design (FreeD V2), with a novel set of interaction techniques for the fabrication of static models: personalized tool paths, manual overriding, and physical merging of virtual models. We also present techniques for fabricating dynamic models, which may be altered directly or parametrically during fabrication. We demonstrate a semi-autonomous operation and evaluate the performance of the tool. We end by discussing synergistic cooperation between human and machine to ensure accuracy while preserving the expressiveness of manual practice.
Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates (2021)

A primary goal of HIV-1 vaccine development is the consistent elicitation of protective, neutralizing antibodies. While highly similar neutralizing antibodies (nAbs) have been isolated from multiple HIV-infected individuals, it is unclear whether vaccination can consistently elicit highly similar nAbs in genetically diverse primates. Here, we show in three outbred rhesus macaques that immunization with Env elicits a genotypically and phenotypically conserved nAb response. From these vaccinated macaques, we isolated four antibody lineages that had commonalities in immunoglobulin variable, diversity, and joining gene segment usage. Atomic-level structures of the antigen binding fragments of the two most similar antibodies showed nearly identical paratopes. The Env binding modes of each of the four vaccine-induced nAbs were distinct from previously known monoclonal HIV-1 neutralizing antibodies, but were nearly identical to each other. The similarities of these antibodies show that the immune system in outbred primates can respond to HIV-1 Env vaccination with a similar structural and genotypic solution for recognizing a particular neutralizing epitope. These results support rational vaccine design for HIV-1 that aims to reproducibly elicit, in genetically diverse primates, nAbs with specific paratope structures capable of binding conserved epitopes.
Multiplex dosage pyrophosphorolysis-activated polymerization: application to the detection of heterozygous deletions (2006)

Large heterozygous chromosomal deletions and gene duplications are important classes of mutations that are generally missed by standard PCR amplification and sequencing. Multiplex dosage pyrophosphorolysis-activated polymerization (MD-PAP), a derivative of PAP, was utilized to detect these types of mutations. PAP is a method for nucleic acid amplification in which 3' blocked oligonucleotides (P*) are activated by pyrophosphorolysis when annealed to the target template and subsequently extended. A key advantage to this technology is that PAP reactions produce little or no primer-dimer or false priming. As a result of this enhanced specificity, MD-PAP is easy to optimize. Herein, we utilize MD-PAP to determine gene dosage of each exon of the human factor IX gene by comparison with one endogenous internal control from the ATM gene. Estimated dosage is proportional to the actual template copy number over a minimum dynamic range from 1 to 16 copies. A blinded analysis detected 100% of 43 heterozygous deletions of exons in the human factor IX gene.
Reduction of nitrosamines in cosmetic products (1995)

Summary From initial rate studies of morpholine nitrosation in aqueous media by nitrite ion in the presence of formaldehyde at pH 5-7 and 25 degrees C, four potential pathways are revealed for the concurrent formation of nitrosamine contaminants in cosmetic and toiletry products. Three of the pathways involve conventional electrophilic nitrosation by XNO reagents of both neutral amine and N-hydroxymethylamine compounds obtained by prior reaction with formaldehyde. The fourth pathway involves a nucleophilic reaction by nitrite ion with the iminium ion derived from N-hydroxymethylamine. For morpholine, reaction via XNO reagents is substantial at pH 5 only, whereas the iminium ion pathway is pre-eminent at pH 7. The concurrent formation of nitrosamines by mechanistically different pathways implies that combinations of nitrosation inhibitors are necessary to minimize contamination of cosmetic and toiletry products. For these different pathways, novel inhibitory compounds are described which fulfil the usual acceptance criteria for cosmetic and toiletry materials. The efficacy of these compounds is assessed against N-nitrosomorpholine formation in the presence of formaldehyde. These include erythorbate, ascorbate, pentanedione and pyranone compounds for the XNO pathways (pH 6) and neutral organic and inorganic salts for the iminium ion pathways (pH 7). Preliminary results for both a bath gel and a cream-base formulation deliberately adulterated with morpholine, diethanolamine, nitrite and a preservative which releases low levels of formaldehyde on decomposition show better than 90% inhibition of nitrosamines by selected pairs of inhibitor compounds on storage at 40 degrees C over several months. This novel technology is the subject of a worldwide patent application.
Spatio‐temporal characterizations of non‐linear changes in intracranial activities prior to human temporal lobe seizures (2000)

Recent studies have shown that non-linear analysis of intracranial activities can detect a 'pre-ictal phase' preceding the epileptic seizure. Nevertheless, the dynamical nature of the underlying neuronal process and the spatial extension of this pre-ictal phase still remain unknown. In this paper, we address these aspects using a new non-linear measure of dynamic similarity between different parts of intracranial recordings of nine patients with medial temporal lobe epilepsy recorded during transitions to seizure. Our results confirm that non-linear changes in neuronal dynamics allow, in most cases (16 out of 17), a seizure anticipation several minutes in advance. Furthermore, we show that the spatial distribution of pre-ictal changes often involves an extended network projecting beyond the limits of the epileptogenic region. Finally, the pre-ictal phase could frequently (13 out of 17) be characterized with a marked shift toward slower frequencies in upper delta or theta frequency range.
How to use current-mode control with capacitively coupled half-bridge converters (1987)

Switch-peak-current commanding current-mode control produces asymmetrical operation when used in capacitively coupled symmetrical dc/dc converters. This paper discusses the causes and effects of asymmetry, gives an analytical model, and proposes a negative-feedback corrector to eliminate the asymmetry. Test results on a 150-W off-line halfbridge converter prove the effectiveness of the recommended solution.
Transesophageal magnetic resonance imaging (1999)

The purpose of this study was to develop a non-invasive method of imaging the thoracic aorta that would provide both morphological detail within the aortic wall and information about regional aortic wall motion. An esophageal probe is described that allows transesophageal MR imaging (TEMRI) of the thoracic aorta and has several potential advantages over the competing non-vasculoinvasive techniques of transesophageal echocardiography (TEE) or standard MRI. The probe consists of a loopless antenna housed inside a modified Levin gastric tube, with external matching and tuning circuitry. Using this probe, the thoracic aorta has been imaged in longitudinal and cross-sectional views. Details of the aortic wall were readily seen. Tissue tagging for measurement of focal stress/strain relationships was demonstrated to be feasible. TEMRI avoids the risks inherent in intravascular MRI yet provides comparable image quality. Potential applications of the device are discussed. Magn Reson Med 41:722–726, 1999. © 1999 Wiley-Liss, Inc.
Development of a Molecular Signature to Monitor Pharmacodynamic Responses Mediated by In Vivo Administration of Glucocorticoids (2018)

The GC gene signature identified in this study represents a pharmacodynamic marker of GC exposure.
Use of CereportTM (RMP-7) to Increase Delivery of Carboplatin to Gliomas: Insight and Parameters for Intracarotid Infusion Via a Single-Lumen Cannula (1999)

CereportTM (RMP-7) is a selective bradykinin B receptor ago2 nist that increases the permeability of the blood-brain tumor barrier (BBTB) to increase delivery of chemotherapeutic agents to brain tumors. Two experiments were performed in a rat glioma model to evaluate and refine intra-arterial dosing parameters using Cereport. The first experiment investigated whether desensitization or tachyphylaxis to the effects of Cereport on vascular permeability can be avoided during the course of super-selective, intracarotid drug administration. Super-selective administration may be used when two different arterial branches supply a single tumor in order to ensure that enough of the drug reaches the entire tumor. In this instance, the chemotherapeutic drug is infused separately and sequentially into each branch. This procedure necessitates an infusion duration that is sufficiently long to raise concerns that tachyphylaxis to B2 receptor stimulation might occur during the Cereport infusion. To study this possibility, relative concentrations, timing, and duration of Cereport were selected to mimic those encountered during super-selective drug administration.Cereport increased the uptake of carboplatin into gliomas to a similar extent as that achieved under more conventional intra-arterial procedures, suggesting that significant tachyphylaxis was not induced. A second experiment tested several alternative dosing paradigms to determine whether a single-lumen cannula could be employed when using Cereport to enhance delivery of carboplatin into a cerebral artery. Mixing carboplatin and Cereport prior to intracarotid infusion through a single-lumen cannula did not reduce the ability of Cereport to increase the permeability of the BBTB. Equivalent effects in carboplatin uptake into a tumor were also seen when the two drugs were co-infused and their infusions sequentially alternated. Finally, Cereport pretreatment did not offer any advantage, indicating very rapid effects of Cereport on the BBTB. Collectively, these data (1) establish a range of dosing paradigms wherein Cereport significantly increases delivery of chemotherapeutic drugs via a single-lumen, arterial cannula, (2) define some of the parameters required to do so successfully, and (3) further elucidate the pharmacodynamic effects of bradykinin B2 receptor-mediated changes in permeability of the BBTB.
A novel method of formant analysis and glottal inverse filtering (1998)

This paper presents a class of methods for automatically extracting formant parameters from speech. The methods rely on an iterative optimization algorithm. It was found that formant parameter data derived with these methods was less prone to discontinuity errors than conventional methods. Also, experiments were conducted that demonstrated that these methods are capable of better accuracy in formant estimation than LPC, especially for the first formant. In some cases, the analytic (non-iterative) solution has been derived, making real time applications feasible. The main target that we have been pursuing is text-to-speech (TTS) conversion. These methods are being used to automatically analyze a concatenation database, without the need for a tuning phase to fix errors. In addition, they are instrumental in realizing high quality pitch tracking, and pitch epoch marking.
Performance of antenna array receiver algorithms for CDMA (2002)

This paper considers a number of algorithms that could be used for antenna array receivers in the mobile-to-base station link of a cellular code division multiple access (CDMA) system, Two classes of algorithms are considered: (1) algorithms that estimate spatially matched filter solutions and (2) adaptive techniques for suppressing interference. In the simulations that were conducted, the "matched filter" algorithms provide more consistent performance than the "adaptive" algorithms, and required less computation. This is due to the fact that CDMA interference is comprised of a large number of small interference contributions from throughout the cell.
A universal 3.3 V 1 GHz BiCMOS transceiver (driver/receiver) (2002)

A universal BiCMOS low-voltage-swing transceiver (driver/receiver) with low on-chip power consumption is reported. Operating at 3.3 V, it can drive/receive low-voltage-swing signals with termination voltages ranging from 5 V down to 2 V without using any external reference voltages.
Optical isolator with TiO<sub>2</sub>/magnetic garnet waveguide employing nonreciprocal phase shift (2008)

Abstract An interferometric optical isolator, with a TiO 2 /magnetic garnet waveguide, employing a nonreciprocal phase shift was studied. The nonreciprocal phase shift in the magneto‐optic waveguide was calculated at a wavelength of 1.55 μm. The large nonreciprocal phase shift was obtained when the magneto‐optic waveguide had a TiO 2 /magnetic garnet guiding layer. An optical isolator which could be operated in a unidirectional magnetic field was also discussed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Saturation-compensated measurements for fluorescence lifetime imaging microscopy (2016)

Fluorophore saturation is the key factor limiting the speed and excitation range of fluorescence lifetime imaging microscopy (FLIM). For example, fluorophore saturation causes incorrect lifetime measurements when using conventional frequency-domain FLIM at high excitation powers. In this Letter, we present an analytical theoretical description of this error and present a method for compensating for this error in order to extract correct lifetime measurements in the limit of fluorophore saturation. We perform a series of simulations and experiments to validate our methods. The simulations and experiments show a 13.2× and a 2.6× increase in excitation range, respectively. The presented method is based on algorithms that can be easily applied to existing FLIM setups.
Rate-distortion optimized video coding considering frameskip (2002)

The general problem of optimized video encoding has received a great deal of attention in recent years. This paper focuses on the optimization of video coding with frameskip. We propose models that estimate the distortion for coded frames as well as non-coded frames. Using these models in conjunction with well-know models that estimate the rate allows us to formulate a rate control problem that trades-off spatial and temporal quality. Simulation results indicate moderate improvements for low motion test sequences.
Temperature-Sensitive Mutants of Influenza A Virus: Production and Characterization of A/Victoria/3/75- <i>ts</i> -1[E] Recombinants (1978)

The Hong Kong/68-ts-1[E] virus, which has a 38 degrees C shutoff temperature for plaque formation, has been proposed as a donor of its two ts lesions to new variants of influenza A virus that pose an epidemic threat. To further examine whether the acquisition of the two ts-1[E] lesions will predictably attenuate new influenza A variants, the HK/68-ts-1[E] virus was mated with the A/Vic/3/75 wild-type virus. The Vic/75-ts-[E] recombinants that had the two ts-1[E] lesions also had a 38 degrees C shutoff temperature. Two Vic/75-ts-1[E] recombinants (clones 81 and 113) that had the two ts-1[E] lesions, a 38 degrees C shutoff temperature, and the Vic/75 hemagglutinin and neuraminidase glycoproteins were similar to each other and to their ts-1[E] parent in the pattern of replication and genetic stability in hamsters. These findings support the hypothesis that the acquisition of the two ts-1[E] lesions will predictably attenuate wild-type influenza A virus. Each Vic/75-ts-1[E] recombinant virus that possessed only the group 1 ts-1[E] lesion had a 39 degrees C shutoff temperature. Two of three of the Vic/75-ts-1[E] recombinants that had only the group 2 ts-1[E] lesion had a 39 degrees C shutoff temperature. This suggests that the HK/68-ts-1[E] donor virus contains two ts genes each of which by itself restricts plaque formation at 39 degrees C and above. The HK/68-ts-1[E] parent virus and its Vic/75 recombinant clones 81 and 113 were evaluated in ferret tracheal organ cultures maintained at permissive and restrictive temperatures. The Vic/75-ts-1[E] clone 81 differed from its parent and sister clone 113 in that it replicated readily and caused ciliostasis at 37 degrees C, a temperature restrictive for the replication of other ts-1[E] recombinants with a 38 degrees C shutoff temperature. The genetic basis underlying this difference was not elucidated.
Elemental surface analysis at ambient pressure by electron-induced x-ray fluorescence (2003)

The development of a portable surface elemental analysis tool, based on the excitation of characteristic x rays from samples at ambient pressure with a focused electron beam is described. This instrument relies on the use of a thin electron transmissive membrane to isolate the vacuum of the electron source from the ambient atmosphere. The major attributes of this instrument include rapid (several minutes) spectrum acquisition, nondestructive evaluation of elemental composition, no sample preparation, and high-to-medium (several hundreds μm) spatial resolution. The instrument proof-of-principle has been demonstrated in a laboratory setup by obtaining energy dispersive x-ray spectra from metal and mineral samples.