gebhart/patrepeval huggingface dataset:
<title>Experimental results using vision-based control for uncalibrated robotic systems</title> (1999)

This work demonstrates a vision-based control technique that does not require robot or vision system calibration. There are two distinct advantages: first, the approach is generic and can be applied to a variety of systems; second, calibration is unnecessary after a reconfiguration or disturbance to the robotic workcell. It has the potential to provide a low-cost, low-maintenance automation solution for unstructured industries and environments. The robot end- effector tracks a moving target using a novel dynamic quasi- Newton control was formulated in the image plane and on-line Jacobian estimation using either a dynamic Broyden's method or a dynamic recursive least squares algorithm. Experimental results demonstrate convergent and stable control of an uncalibrated manipulator tracking a moving target. The method is shown to be robust to system reconfiguration such as modifications to the position and orientation of the camera.
Multiset-Partition Distribution Matching (2018)

Distribution matching is a fixed-length invertible mapping from a uniformly distributed bit sequence to shaped amplitudes and plays an important role in the probabilistic amplitude shaping framework. With conventional constant-composition distribution matching (CCDM), all output sequences have identical composition. In this paper, we propose multiset-partition distribution matching (MPDM), where the composition is constant over all output sequences. When considering the desired distribution as a multiset, MPDM corresponds to partitioning this multiset into equal-sized subsets. We show that MPDM allows addressing more output sequences and, thus, has a lower rate loss than CCDM in all nontrivial cases. By imposing some constraints on the partitioning, a constructive MPDM algorithm is proposed which comprises two parts. A variable-length prefix of the binary data word determines the composition to be used, and the remainder of the input word is mapped with a conventional CCDM algorithm, such as arithmetic coding, according to the chosen composition. Simulations of 64-ary quadrature amplitude modulation over the additive white Gaussian noise channel demonstrate that the block-length saving of MPDM over CCDM for a fixed gap to capacity is approximately a factor of 2.5-5 at medium to high signal-to-noise ratios.
Extracellular DNA promotes efficient extracellular electron transfer by pyocyanin in Pseudomonas aeruginosa biofilms (2019)

SUMMARY Extracellular electron transfer (EET), the process whereby cells access electron acceptors or donors that reside many cell lengths away, enables metabolic activity by microorganisms, particularly under oxidant-limited conditions that occur in multicellular bacterial biofilms. Although different mechanisms underpin this process in select organisms, a widespread strategy involves extracellular electron shuttles, redox-active metabolites that are secreted and recycled by diverse bacteria. How these shuttles catalyze electron transfer within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazine electron shuttles mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms, which are important in nature and disease. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by binding to eDNA. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and phenazines can participate directly in redox reactions through DNA; the biofilm eDNA can also support rapid electron transfer between redox active intercalators. Electrochemical measurements of biofilms indicate that retained PYO supports an efficient redox cycle with rapid EET and slow loss from the biofilm. Together, these results establish that eDNA facilitates phenazine metabolic processes in P. aeruginosa biofilms, suggesting a model for how extracellular electron shuttles achieve retention and efficient EET in biofilms.
Dentate gyrus volume is reduced before onset of plaque formation in PDAPP mice: A magnetic resonance microscopy and stereologic analysis (2003)

High-resolution magnetic resonance microscopy (MRM) was used to determine regional brain volumetric changes in a mouse model of Alzheimer's disease. These transgenic (Tg) mice overexpress human mutant amyloid precursor protein (APP) V717F under control of platelet-derived growth factor promoter (PDAPP mice), and cortical and hippocampal beta-amyloid (Abeta) deposits accumulate in heterozygotes after 8-10 mos. We used MRM to obtain 3D volumetric data on mouse brains imaged in their skulls to define genotype- and age-related changes. Hippocampal, cerebellar, and brain volumes and corpus callosum length were quantified in 40-, 100-, 365-, and 630-day-old mice. Measurements taken at age 100 days, before Abeta deposition, revealed a 12.3% reduction of hippocampus volume in Tg mice compared with WT controls. This reduction persisted without progression to age 21 mos. A significant 18% increase in hippocampal volume occurred between 40 and 630 days in WT mice, and no corresponding significant increase occurred in Tg mice. Cavalieri volume estimates of hippocampal subfields from 100-day-old Tg mice further localized a 28% volume deficit in the dentate gyrus. In addition, corpus callosum length was reduced by approximately 25% in Tg mice at all ages analyzed. In summary, reduced hippocampal volume and corpus callosum length can be detected by MRM before Abeta deposition. We conclude that overexpression of APP and amyloid may initiate pathologic changes before the appearance of plaques, suggesting novel targets for the treatment of Alzheimer's disease and further reinforcing the need for early diagnosis and treatment.
Internet-based system for simulation-based medical planning for cardiovascular disease (2003)

Current practice in vascular surgery utilizes only diagnostic and empirical data to plan treatments, which does not enable quantitative a priori prediction of the outcomes of interventions. We have previously described simulation-based medical planning methods to model blood flow in arteries and plan medical treatments based on physiologic models. An important consideration for the design of these patient-specific modeling systems is the accessibility to physicians with modest computational resources. We describe a simulation-based medical planning environment developed for the World Wide Web (WWW) using the Virtual Reality Modeling Language (VRML) and the Java programming language.
Enantio- and diastereoselective synthesis of γ-amino alcohols (2015)

The γ-amino alcohol structural motif is often encountered in drugs and natural products. We developed two complementary catalytic diastereoselective methods for the synthesis of N-PMP-protected γ-amino alcohols from the corresponding ketones. The anti-products were obtained through Ir-catalyzed asymmetric transfer hydrogenation, the syn-products via Rh-catalyzed asymmetric hydrogenation.
Comparison of the Replication of Influenza A Viruses in Chinese Ring-Necked Pheasants and Chukar Partridges (2006)

We investigated the replication and transmission of avian influenza A viruses in two species thought to be intermediate hosts in the spread of influenza A viruses in live poultry markets: Chinese ring-necked pheasants and chukar partridges. All 15 hemagglutinin subtypes replicated in pheasants, and most subtypes transmitted to naïve contact pheasants, primarily via the fecal-oral route. Many viruses were shed from the gastrointestinal tract of experimentally inoculated pheasants for 14 days or longer. Virus was isolated from the cloacal swabs of one contact pheasant for an unprecedented 45 days. Chukar partridges were less susceptible to infection with avian influenza viruses. The viruses that replicated in chukar partridges were isolated for 7 days after experimental inoculation, predominantly from the respiratory tract. We detected high neutralizing antibody titers with correspondingly low levels of serum hemagglutination inhibition antibody titers in pheasants and chukar partridges when chicken red blood cells were used in serological analyses. When horse erythrocytes were used, antibody titers were comparable to those obtained by using the neutralization assay. More importantly, the results suggested that pheasants can serve as a reservoir of influenza virus. Because of their continuous asymptomatic infection and longer stay in the markets, pheasants are ideal "carriers" of influenza A viruses. Their continued presence in live markets contributes to the perpetuation and genetic interaction of influenza viruses there. On the basis of our findings, it does not make good sense to ban quail but not pheasants from the live markets.
Synthesis and Atomic and Electronic Structure of New Si−Ge−C Alloys and Compounds (1998)

The synthesis and characterization of completely novel binary and ternary alloy semiconductors and ordered phases based on C, Si, and Ge are discussed in this review. Metastable compound semiconductors with ordered structures, which include stoichiometric SiGe, Si4C, Si3GeC4 (sphalerite), Ge4C, (Si2Ge)Cx, and (Ge2Si)Cx (x = 5%), are described. Materials systems include diamond-structured silicon−germanium solid solutions with dissolved carbon (Si1-x-yGexCy), monocrystalline Ge1-xCx hybrids of Ge, and C-diamond and related Si-containing random alloy systems. The Si4C and Ge4C materials incorporate the corresponding tetrahedra that are linked together to form a diamond-cubic structure related to Si. The Si3GeC4 phase is related to sphalerite and (Si2Ge)Cx has a new P3̄m1 structure formed by Ge−Si−Si ordering along the diamond 〈111〉 direction. These compounds offer the prospect of band gaps wider than that of Si; in some cases, the band gaps are expected to become direct. This report emphasizes an approach that combines novel precursor chemistries and modern deposition techniques (ultrahigh-vacuum chemical-vapor deposition) to develop heteroepitaxial, device-quality inorganic materials. Important highlights of recent research based on conventional deposition methods are also summarized.
12 W peak-power 10ps duration optical pulse generation by gain switching of a single-transverse-mode GaInN blue laser diode (2008)

We have generated optical pulses at 405nm from a single-transverse-mode GaInN blue laser diode under intensive gain-switching operation with a minimum pulse duration of less than 8ps. The maximum optical peak power was as high as 12W with a pulse width of 10ps. The peak power obtained is the highest value for optical pulses ever generated from a single transverse-mode GaInN laser diode.
Slow Conformational Dynamics at C2′-endo Nucleotides in RNA (2008)

RNA molecules undergo local conformational dynamics on timescales spanning picoseconds to minutes. Slower local motions have the greater potential to govern RNA folding, ligand recognition, and ribonucleoprotein assembly reactions but are difficult to detect in large RNAs with complex structures. RNA SHAPE chemistry employs acylation of the ribose 2'-hydroxyl position to measure local nucleotide flexibility in RNA and is well-characterized by a mechanism in which each nucleotide samples unreactive (closed) and reactive (open) states. We monitor RNA conformational dynamics over distinct time domains by varying the electrophilicity of the acylating reagent. Select C2'-endo nucleotides are nonreactive toward fast reagents but reactive toward slower SHAPE reagents in both model RNAs and in a large RNA with a tertiary fold. We conclude, first, that the C2'-endo conformation by itself does not govern SHAPE reactivity. However, some C2'-endo nucleotides undergo extraordinarily slow conformational changes, on the order of 10(-4) s(-1). Due to their distinctive local dynamics, C2'-endo nucleotides have the potential to function as rate-determining molecular switches and are likely to play central, currently unexplored, roles in RNA folding and function.
Differentiation of Deprotonated Acyl-, N-, and O-Glucuronide Drug Metabolites by Using Tandem Mass Spectrometry Based on Gas-Phase Ion–Molecule Reactions Followed by Collision-Activated Dissociation (2019)

Glucuronidation, a common phase II biotransformation reaction, is one of the major <i>in vitro</i> and <i>in vivo</i> metabolism pathways of xenobiotics. In this process, glucuronic acid is conjugated to a drug or a drug metabolite via a carboxylic acid, a hydroxy, or an amino group to form acyl-, <i>O</i>-, and/or <i>N</i>-glucuronide metabolites, respectively. This process is traditionally thought to be a detoxification pathway. However, some acyl-glucuronides react with biomolecules <i>in vivo</i>, which may result in immune-mediated idiosyncratic drug toxicity (IDT). In order to avoid this, one may attempt in early drug discovery to modify the lead compounds in such a manner that they then have a lower probability of forming reactive acyl-glucuronide metabolites. Because most drugs or drug candidates bear multiple functionalities, e.g., hydroxy, amino, and carboxylic acid groups, glucuronidation can occur at any of those. However, differentiation of isomeric acyl-, <i>N-</i>, and <i>O</i>-glucuronide derivatives of drugs is challenging. In this study, gas-phase ion-molecule reactions between deprotonated glucuronide metabolites and BF<sub>3</sub> followed by collision-activated dissociation (CAD) in a linear quadrupole ion trap mass spectrometer were demonstrated to enable the differentiation of acyl-, <i>N-</i>, and <i>O</i>-glucuronides. Only deprotonated <i>N</i>-glucuronides and deprotonated, migrated acyl-glucuronides form the two diagnostic product ions: a BF<sub>3</sub> adduct that has lost two HF molecules, [M - H + BF<sub>3</sub> - 2HF]<sup>-</sup>, and an adduct formed with two BF<sub>3</sub> molecules that has lost three HF molecules, [M - H + 2BF<sub>3</sub> - 3HF]<sup>-</sup>. These product ions were not observed for deprotonated <i>O</i>-glucuronides and unmigrated, deprotonated acyl-glucuronides. Upon CAD of the [M - H + 2BF<sub>3</sub> - 3HF]<sup>-</sup> product ion, a diagnostic fragment ion is formed via the loss of 2-fluoro-1,3,2-dioxaborale (MW of 88 Da) only in the case of deprotonated, migrated acyl-glucuronides. Therefore, this method can be used to unambiguously differentiate acyl-, <i>N-</i>, and <i>O</i>-glucuronides. Further, coupling this methodology with HPLC enables the differentiation of unmigrated 1-β-acyl-glucuronides from the isomeric acyl-glucuronides formed upon acyl migration. Quantum chemical calculations at the M06-2X/6-311++G(d,p) level of theory were employed to probe the mechanisms of the reactions of interest.
Magnetic resonance imaging and molecular features associated with tumor-infiltrating lymphocytes in breast cancer (2018)

Specific MRI features of tumor and parenchyma are associated with TILs in breast cancer, and imaging may play an important role in the evaluation of TILs by providing key complementary information in equivocal cases or situations that are prone to sampling bias.
Heat Transfer Augmentation Downstream of Rows of Various Dimple Geometries on the Suction Side of a Gas Turbine Airfoil (2008)

Heat transfer coefficients were measured downstream of a row of shaped film cooling holes as well as elliptical, diffuser, and teardrop shaped dimples simulating depressions due to film coolant holes of different shapes. These features were placed on the suction side of a simulated gas turbine vane. The dimples were used as approximations to film cooling holes after the heat transfer levels downstream of active fan shaped film cooling holes was found to be independent of film cooling. The effects of the dimples were tested with varying approach boundary layers, freestream turbulence intensity, and Reynolds numbers. For the case of an untripped (transitional) approach boundary layer, all dimple shapes caused approximately a factor of two increase in heat transfer coefficient relative to the smooth baseline condition due to the dimples effectively causing boundary layer transition downstream. The exact augmentation varied depending on the dimple geometry: diffuser shapes causing the largest augmentation and teardrop shapes causing the lowest augmentation. For tripped (turbulent boundary layer) approach conditions, the dimple shapes all caused the same 20% augmentation relative to the smooth tripped baseline. The already turbulent nature of the tripped approach flow reduces the effect that the dimples have on the downstream heat transfer coefficient.
Synthesis of methyl ketones by metabolically engineered Escherichia coli (2012)

Methyl ketones are a group of highly reduced platform chemicals with widespread applications in the fragrance, flavor and pharmacological industries. Current methods for the industrial production of methyl ketones include oxidation of hydrocarbons, but recent advances in the characterization of methyl ketone synthases from wild tomato have sparked interest towards the development of microbial platforms for the industrial production of methyl ketones. A functional methyl ketone biosynthetic pathway was constructed in Escherichia coli by over-expressing two genes from Solanum habrochaites: shmks2, encoding a 3-ketoacyl-ACP thioesterase, and shmks1, encoding a beta-decarboxylase. These enzymes enabled methyl ketone synthesis from 3-ketoacyl-ACP, an intermediate in the fatty acid biosynthetic cycle. The production of 2-nonanone, 2-undecanone, and 2-tridecanone by MG1655 pTH-shmks2-shmks1 was initially detected by nuclear magnetic resonance and gas chromatography-mass spectrometry analyses at levels close to 6 mg/L. The deletion of major fermentative pathways leading to ethanol (adhE), lactate (ldhA), and acetate (pta, poxB) production allowed for the carbon flux to be redirected towards methyl ketone production, doubling total methyl ketone concentration. Variations in methyl ketone production observed under different working volumes in flask experiments led to a more detailed analysis of the effects of oxygen availability on methyl ketone concentration in order to determine optimal levels of oxygen. The methyl ketone concentration achieved with MG1655 ∆adhE ∆ldhA ∆poxB ∆pta pTrcHis2A-shmks2-shmks1, the best performer strain in this study, was approximately 500 mg/L, the highest reported for an engineered microorganism. Through the establishment of optimal operating conditions and by executing rational metabolic engineering strategies, we were able to increase methyl ketone concentrations by almost 75-fold from the initial confirmatory levels.
Phenolic Extract from Aralia nudicaulis L. Rhizomes Inhibits Cellular Oxidative Stresses (2021)

UV-B and IR-A radiation are important inducers of biological changes in skin involving ROS generation. The overloading of antioxidant defense mechanisms by ROS production could lead to photoaging and photocarcinogenesis processes. Various traditional usages are reported for <i>Aralia nudicaulis</i> L. extracts, including treatment of dermatological disorders. Antioxidant and anti-inflammatory properties have already been reported for other <i>Aralia</i> species possibly due to the presence of phenolic compounds. However, the phenolic composition and the potential activity of <i>A. nudicaulis</i> rhizomes extract against oxidative stress and UV/IR damages have not been investigated. The main aims of this study were to prepare a fraction enriched in phenolic compounds (FEPC) from <i>A. nudicaulis</i> rhizomes, to identify its major phenolic compounds and to assess its potential for protective effects against oxidative stress induced by UV-B, IR-A or inflammation. A quantitative LC-MS study of FEPC shows that chlorogenic, caffeic and protocatechuic acids are the main phenolic compounds present, with concentrations of 15.6%, 15.3% and 4.8% of the total composition, respectively. With a validated analytical method, those compounds were quantified over different stages of the growing period. As for biological potential, first this extract demonstrates antioxidant and anti-inflammatory activities. Furthermore, ROS generation induced by IR-A and UV-B were strongly inhibited by <i>A. nudicaulis</i> extract, suggesting that <i>Aralia nudicaulis</i> L. rhizome extract could protect dermal cells against oxidative stress induced by UV-B and IR-A.
The Effects of Thermophysical Properties and Environmental Conditions on Fire Performance of Intumescent Coatings on Glass Fibre-Reinforced Epoxy Composites (2015)

Intumescent coatings are commonly used as passive fire protection systems for steel structures. The purpose of this work is to explore whether these can also be used effectively on glass fibre-reinforced epoxy (GRE) composites, considering the flammability of the composites compared to non-flammable steel substrate. The thermal barrier and reaction-to-fire properties of three commercial intumescent coatings on GRE composites have been studied using a cone calorimeter. Their thermophysical properties in terms of heating rate and/or temperature dependent char expansion ratios and thermal conductivities have been measured and correlated. It has been suggested that these two parameters can be used to design coatings to protect composite laminates of defined thicknesses for specified periods of time. The durability of the coatings to water absorption, peeling, impact, and flexural loading were also studied. A strong adhesion between all types of coatings and the substrate was observed. Water soaking had a little effect on the fire performance of epoxy based coatings. All types of 1 mm thick coatings on GRE helped in retaining ~90% of the flexural property after 2 min exposure to 50 kW/m² heat flux whereas the uncoated laminate underwent severe delamination and loss in structural integrity after 1 min.
SYNTHESIS OF NEW HETEROCYCLIC ANALOGUES OF ISOCOUMESTANE (1999)

The synthesis of substituted Isocoumestan and heterocyclic analogues, obtained by replacing ring by thiophene and selenophene, is reported.
Optimization of long range potential interaction parameters in ion mobility spectrometry (2018)

The problem of optimizing Lennard-Jones (L-J) potential parameters to perform collision cross section (CCS) calculations in ion mobility spectrometry has been undertaken. The experimental CCS of 16 small organic molecules containing carbon, hydrogen, oxygen, nitrogen, and fluoride in N2 was compared to numerical calculations using Density Functional Theory (DFT). CCS calculations were performed using the momentum transfer algorithm IMoS and a 4-6-12 potential without incorporating the ion-quadrupole potential. A ceteris paribus optimization method was used to optimize the intercept σ and potential well-depth ϵ for the given atoms. This method yields important information that otherwise would remain concealed. Results show that the optimized L-J parameters are not necessarily unique with intercept and well-depth following an exponential relation at an existing line of minimums. Similarly, the method shows that some molecules containing atoms of interest may be ill-conditioned candidates to perform optimizations of the L-J parameters. The final calculated CCSs for the chosen parameters differ 1% on average from their experimental counterparts. This result conveys the notion that DFT calculations can indeed be used as potential candidates for CCS calculations and that effects, such as the ion-quadrupole potential or diffuse scattering, can be embedded into the L-J parameters without loss of accuracy but with a large increase in computational efficiency.