gebhart/patrepeval huggingface dataset:
Suppression of Thermal Convection and Its Effect on Growth of GaN in Metal Organic Vapor Phase Epitaxy (1998)

Improvement of the performance of devices with group III nitrides needs advances in growth techniques. At the high temperatures required for epitaxial growth, thermal convection has to be suppressed for controlled growth of GaN. The effect of flow rate on growth rate and layer uniformity is investigated and the minimum gas velocity for suppression of thermal convection in a multiwafer, vertical reactor is determined. It is shown that, using the optimized gas velocity, high-quality GaN can be grown.
Case report: Fractional brain tumor burden magnetic resonance mapping to assess response to pulsed low-dose-rate radiotherapy in newly-diagnosed glioblastoma (2022)

This case series provides insight into the radiographic response to upfront pLDR and TMZ and the role for FTB mapping to distinguish tumor progression from treatment effect prior to redo-surgery and within 20 weeks post-radiation.
Supplementary Figure 2 from Activation of Apoptosis by 1-Hydroxy-5,7-Dimethoxy-2-Naphthalene-Carboxaldehyde, a Novel Compound from <i>Aegle marmelos</i> (2023)

Supplementary Figure 2 from Activation of Apoptosis by 1-Hydroxy-5,7-Dimethoxy-2-Naphthalene-Carboxaldehyde, a Novel Compound from &lt;i&gt;Aegle marmelos&lt;/i&gt;
Cytotoxic Terpenoids from Dasyscyphus niveus (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Correlation between immunohistochemistry (HercepTest) and fluorescence in situ hybridization (FISH) for HER‐2 in 426 breast carcinomas from 37 centres (2003)

Accurate diagnostic assessment of HER-2 is essential for the appropriate application of the humanized anti-HER-2 monoclonal antibody trastuzumab (Herceptin) to the treatment of patients with metastatic breast cancer. The diagnostic test needs to be applicable to archival, fixed tissue removed at excision, in many cases several years earlier. We compared the assessment of HER-2 by immunohistochemistry (IHC; HercepTest) and fluorescence in situ hybridization (FISH) in 426 breast carcinomas from patients being considered for trastuzumab therapy. The tumours were tested in three reference centres having been sent in from 37 hospitals. Only 2/270 (0.7%) IHC 0/1+ tumours were FISH positive. Six of 102 (5.9%) IHC 3+ tumours were FISH negative. Five of the six had between 1.75 and 2.0 HER-2 gene copies per chromosome 17 and the sixth had multiple copies of chromosome 17. Thirteen per cent of tumours were IHC 2+ and overall 48% of these were FISH positive but this proportion varied markedly between the centres. Sixty IHC-stained slides selected to be enriched with 2+ cases were circulated between the three laboratories and scored. There were 20 cases in which there was some discordance in scoring. Consideration of the FISH score in these cases led to concordance in the designation of positivity/negativity in 19 of these 20 cases. These data support an algorithm in which FISH testing is restricted to IHC 2+ tumours in reference centres. The results may not extrapolate to laboratories with less experience or using different methodologies.
Going forward (2006)

Since this is the founding issue of “Biopolymers,” we wish to set down our thoughts on the nature and scope of the new Journal. It will be a publication devoted to high quality original research in the field of biopolymers (proteins, nucleic acids, polysaccharides, etc.) and synthetic model compounds for such substances. The emphasis of the papers sought is to be on the polymeric nature of the materials and systems investigated This Journal will include both experimental and theoretical reports. Normal length papers and “Communications to the Editor” will be rigorously judged. The latter will be limited to reports of special timeliness and originality. Subjects such as structure and function of biopolymers are suitable, as are studies on synthetic analogs of biopolymers, genetic investigations, details of biological organization, and biosynthetic pathways of polymer formation. We believe that our undertaking represents a fusion of the macromolecular research in physics, chemistry, and biology of life processes. The editorial board shall strive to remain sensitive to the most modern and up-to-date reports and modify their thinking as this hybrid science grows. Biopolymers will continue to publish original research articles and reviews in the general area of macromolecular structure and function. Even 44 years ago, the editorial team recognized what s almost dogmatic today - the study of proteins, nucleic acids, and carbohydrates is truly a multidisciplinary endeavor. In this regard, the Journal will serve as a forum to present research that draws from multiple fields for the advancement of biopolymer science. In addition to review articles from leading authors on “hot” topics familiar to our readership, the Journal now will publish reviews that approach the study of biopolymers from new and, at times, unconventional perspectives. As practitioners in the field, our entire editorial team is sensitive to the constraints that today's research environment places on authors and referees. Therefore, there are no page or color charges associated with publication in Biopolymers and full papers can be of any length (both word count and artwork). The Journal will handle all papers expeditiously, taking full advantage of web technology in submission and review of manuscripts. All papers will appear on-line within a week of acceptance. The new editorial board is excited by the technical and conceptual changes to the Journal, as well as by the commitment that our publisher, John Wiley & Sons, has made to Biopolymers. We look forward to working with you to grow the Journal and invite your comments and feedback every step along the way. For the Associate Editors and Editorial Advisory Board, Gary D. Glick Ph.D. Editor-in-Chief*, * University of Michigan.
Updating the Patent System's Novelty Requirement to Promote Small-Molecule Medicinal Progress, 45 J. Marshall L. Rev. 1151 (2012) (2012)

received a BA in Chemistry from the University of Kentucky and a MS in Chemistry from Northeastern University.He is a medicinal chemist and has worked in the field
KATP channel knockout worsens myocardial calcium stress load in vivo and impairs recovery in stunned heart (2006)

Gene knockout of the KCNJ11-encoded Kir6.2 ATP-sensitive K(+) (K(ATP)) channel implicates this stress-response element in the safeguard of cardiac homeostasis under imposed demand. K(ATP) channels are abundant in ventricular sarcolemma, where subunit expression appears to vary between the sexes. A limitation, however, in establishing the full significance of K(ATP) channels in the intact organism has been the inability to monitor in vivo the contribution of the channel to intracellular calcium handling and the superimposed effect of sex that ultimately defines heart function. Here, in vivo manganese-enhanced cardiac magnetic resonance imaging revealed, under dobutamine stress, a significantly greater accumulation of calcium in both male and female K(ATP) channel knockout (Kir6.2-KO) mice compared with sex- and age-matched wild-type (WT) counterparts, with greatest calcium load in Kir6.2-KO females. This translated, poststress, into a sustained contracture manifested by reduced end-diastolic volumes in K(ATP) channel-deficient mice. In response to ischemia-induced stunning, male and female Kir6.2-KO hearts demonstrated accelerated time to contracture and increased peak contracture compared with WT. The outcome on reperfusion, in both male and female Kir6.2-KO hearts, was a transient reduction in systolic performance, measured as rate-pressure product compared with WT, with protracted increase in left ventricular end-diastolic pressure, exaggerated in female knockout hearts, despite comparable leakage of creatine kinase across groups. Kir6.2-KO hearts were rescued from diastolic dysfunction by agents that target alternative pathways of calcium handling. Thus K(ATP) channel deficit confers a greater susceptibility to calcium overload in vivo, accentuated in female hearts, impairing contractile recovery under various conditions of high metabolic demand.
Engineering Protein Therapeutics: Predictive Performances of a Structure-Based Virtual Affinity Maturation Protocol (2012)

The implementation of a structure based virtual affinity maturation protocol and evaluation of its predictivity are presented. The in silico protocol is based on conformational sampling of the interface residues (using the Dead End Elimination/A* algorithm), followed by the estimation of the change of free energy of binding due to a point mutation, applying MM/PBSA calculations. Several implementations of the protocol have been evaluated for 173 mutations in 7 different protein complexes for which experimental data were available: the use of the Boltzamnn averaged predictor based on the free energy of binding (ΔΔG(*)) combined with the one based on its polar component only (ΔΔE(pol*)) led to the proposal of a subset of mutations out of which 45% would have successfully enhanced the binding. When focusing on those mutations that are less likely to be introduced by natural in vivo maturation methods (99 mutations with at least two base changes in the codon), the success rate is increased to 63%. In another evaluation, focusing on 56 alanine scanning mutations, the in silico protocol was able to detect 89% of the hot-spots.
Safety and Efficacy of Cryoablation of Accessory Pathways Adjacent to the Normal Conduction System (2003)

Cryoablation appears to be a safe and effective technique for ablation of APs close to the AV node or His bundle because of the ability to predict the acute effects of ablation with ice mapping before creation of an irreversible lesion.
Array comparative genomic hybridisation (aCGH) analysis of premenopausal breast cancers from a nuclear fallout area and matched cases from Western New York (2005)

High-resolution array comparative genomic hybridisation (aCGH) analysis of DNA copy number aberrations (CNAs) was performed on breast carcinomas in premenopausal women from Western New York (WNY) and from Gomel, Belarus, an area exposed to fallout from the 1986 Chernobyl nuclear accident. Genomic DNA was isolated from 47 frozen tumour specimens from 42 patients and hybridised to arrays spotted with more than 3000 BAC clones. In all, 20 samples were from WNY and 27 were from Belarus. In total, 34 samples were primary tumours and 13 were lymph node metastases, including five matched pairs from Gomel. The average number of total CNAs per sample was 76 (range 35-134). We identified 152 CNAs (92 gains and 60 losses) occurring in more than 10% of the samples. The most common amplifications included gains at 8q13.2 (49%), at 1p21.1 (36%), and at 8q24.21 (36%). The most common deletions were at 1p36.22 (26%), at 17p13.2 (26%), and at 8p23.3 (23%). Belarussian tumours had more amplifications and fewer deletions than WNY breast cancers. HER2/neu negativity and younger age were also associated with a higher number of gains and fewer losses. In the five paired samples, we observed more discordant than concordant DNA changes. Unsupervised hierarchical cluster analysis revealed two distinct groups of tumours: one comprised predominantly of Belarussian carcinomas and the other largely consisting of WNY cases. In total, 50 CNAs occurred significantly more commonly in one cohort vs the other, and these included some candidate signature amplifications in the breast cancers in women exposed to significant radiation. In conclusion, our high-density aCGH study has revealed a large number of genetic aberrations in individual premenopausal breast cancer specimens, some of which had not been reported before. We identified a distinct CNA profile for carcinomas from a nuclear fallout area, suggesting a possible molecular fingerprint of radiation-associated breast cancer.
DEVELOPMENT OF CONTINUOUS SOLVENT EXTRACTION PROCESSES FOR COAL DERIVED CARBON PRODUCTS (2005)

The purpose of this DOE-funded effort is to develop continuous processes for solvent extraction of coal for the production of carbon products. These carbon products include materials used in metals smelting, especially in the aluminum and steel industries, as well as porous carbon structural material referred to as ''carbon foam'' and carbon fibers. Table 1 provides an overview of the major markets for carbon products. Current sources of materials for these processes generally rely on petroleum distillation products or coal tar distillates obtained as a byproduct of metcoke production facilities. In the former case, the American materials industry, just as the energy industry, is dependent upon foreign sources of petroleum. In the latter case, metcoke production is decreasing every year due to the combined difficulties associated with poor economics and a significant environmental burden. Thus, a significant need exists for an environmentally clean process which can used domestically obtained raw materials and which can still be very competitive economically.
Measurement of isolated-photon plus two-jet production in pp collisions at $$ \sqrt{s} $$ = 13 TeV with the ATLAS detector (2020)

A bstract The dynamics of isolated-photon plus two-jet production in pp collisions at a centre-of-mass energy of 13 TeV are studied with the ATLAS detector at the LHC using a dataset corresponding to an integrated luminosity of 36 . 1 fb − 1 . Cross sections are measured as functions of a variety of observables, including angular correlations and invariant masses of the objects in the final state, γ + jet + jet. Measurements are also performed in phase-space regions enriched in each of the two underlying physical mechanisms, namely direct and fragmentation processes. The measurements cover the range of photon (jet) transverse momenta from 150 GeV (100 GeV) to 2 TeV. The tree-level plus parton-shower predictions from S herpa and P ythia as well as the next-to-leading-order QCD predictions from S herpa are compared with the measurements. The next-to-leading-order QCD predictions describe the data adequately in shape and normalisation except for regions of phase space such as those with high values of the invariant mass or rapidity separation of the two jets, where the predictions overestimate the data.
Discriminant Analysis for Helicopter Rotor Vibration Prognostics (2006)

Traditionally, preventive maintenance has the drawback of being too expensive because of unnecessary replacements. Corrective maintenance involving replacement or repair after a failure is also expensive because of down time. In this paper, we present discriminant analysis and stepwise discriminant analysis for vibration prognostics. The goal is prediction of failures in drive train components of helicopters, specifically tail rotor drive shaft or engine input shaft. The method has been applied to make predictions of vibrations in the main rotor shaft of Sikorsky helicopter UH-60, using Goodrich Health and Usage Management System (HUMS). The purpose of these predictions is to help enforce rotor vibrations below a threshold to avoid component damages and to reduce aircrew fatigue. The method is particularly useful for prediction of no increase of vibration. This is an important contribution because drive train components of helicopters are normally very robust, thereby the cost of unnecessary preventive maintenance is very high. The predictions made by the model avoid unnecessary maintenance so that costs are lower.
Multidimensional Modeling and Validation of Dual-Fuel Combustion in a Large Bore Medium Speed Diesel Engine (2015)

High fidelity, three-dimensional CFD was used to model the flow, fuel injection, combustion, and emissions in a large bore medium speed diesel engine with different levels of natural gas substitution. Detailed chemical kinetics was used to model the complex combustion behavior of the premixed natural gas, ignited via a diesel spray. The numerical predictions were compared against measured multiple cycle pressure data, to understand the possible factors affecting cyclic variation in experimental data. Under conditions with high natural gas substitution rates, diesel was injected much earlier than firing-TDC. This additional mixing time allowed the active radicals from diesel dissociation to initiate combustion from the cylinder wall and propagate inwards. 0%, 60%, and 93% natural gas substitution rates (by energy) were tested in this study to develop computational capabilities needed to accurately model and understand the underlying physics. Several innovative computational methods such as adaptive mesh refinement (which automatically refines and coarsens the mesh based on the existing solution parameters), and multi-zoning (which groups chemically similar cells together to reduce combustion calculation time) were utilized to obtain accurate predictions at a lower computational cost. Important engine emissions such as NOx, CO, unburnt HC, and soot were predicted numerically and compared against measured engine data.
Aryl hydrocarbon receptor (AHR)-regulated transcriptomic changes in rats sensitive or resistant to major dioxin toxicities (2010)

The transactivation-domain deletion in dioxin-resistant rats does not abolish global AHR transactivational activity but selectively interferes with expression of subsets of genes that are candidates to mediate or protect from major dioxin toxicities such as hepatotoxicity, wasting and death.
Tailorable infrared emission of microelectromechanical system-based thermal emitters with NiO films for gas sensing (2021)

Infrared gas sensors hold great promise in the internet of things and artificial intelligence. Making infrared light sources with miniaturized size, reliable and tunable emission is essential but remains challenging. Herein, we present the tailorability of radiant power and the emergence of new emission wavelength of microelectromechanical system (MEMS)-based thermal emitters with nickel oxide (NiO) films. The coating of NiO on emitters increases top surface emissivity and induces the appearance of new wavelengths between 15 and 19 µm, all of which have been justified by spectroscopic methods. Furthermore, a sensor array is assembled for simultaneous monitoring of concentrations of carbon dioxide (CO<sub>2</sub>), methane (CH<sub>4</sub>), humidity, and temperature. The platform shows selective and sensitive detection at room temperature toward CO<sub>2</sub> and CH<sub>4</sub> with detection limits of around 50 and 1750 ppm, respectively, and also shows fast response/recovery and good recyclability. The demonstrated emission tailorability of MEMS emitters and their usage in sensor array provide novel insights for designing and fabricating optical sensors with good performance, which is promising for mass production and commercialization.
Identification of Mycobacterium tuberculosis Peptides in Serum Extracellular Vesicles from Persons with Latent Tuberculosis Infection (2020)

Identification of biomarkers for latent <i>Mycobacterium tuberculosis</i> infection and risk of progression to tuberculosis (TB) disease are needed to better identify individuals to target for preventive therapy, predict disease risk, and potentially predict preventive therapy efficacy. Our group developed multiple reaction monitoring mass spectrometry (MRM-MS) assays that detected <i>M. tuberculosis</i> peptides in serum extracellular vesicles from TB patients. We subsequently optimized this MRM-MS assay to selectively identify 40 <i>M. tuberculosis</i> peptides from 19 proteins that most commonly copurify with serum vesicles of patients with TB. Here, we used this technology to evaluate if <i>M. tuberculosis</i> peptides can also be detected in individuals with latent TB infection (LTBI). Serum extracellular vesicles from 74 individuals presumed to have latent <i>M. tuberculosis</i> infection (LTBI) based on close contact with a household member with TB or a recent tuberculin skin test (TST) conversion were included in this study. Twenty-nine samples from individuals with no evidence of TB infection by TST and no known exposure to TB were used as controls to establish a threshold to account for nonspecific/background signal. We identified at least one of the 40 <i>M. tuberculosis</i> peptides in 70 (95%) individuals with LTBI. A single peptide from the glutamine synthetase (GlnA1) enzyme was identified in 61/74 (82%) individuals with LTBI, suggesting peptides from <i>M. tuberculosis</i> proteins involved in nitrogen metabolism might be candidates for pathogen-specific biomarkers for detection of LTBI. The detection of <i>M. tuberculosis</i> peptides in serum extracellular vesicles from persons with LTBI represents a potential advance in the diagnosis of LTBI.
Crossed-beam superluminescent diode (2005)

We investigate a novel surface-emitting superluminescent diode configuration that uses two detuned grating outcouplers to suppress lasing. This device exhibits a shaped beam with a peak power of 1.5 W quasi-continuous wave with an 11 nm bandwidth centered on 970 nm.
Auxin Deprivation Induces Synchronous Golgi Differentiation in Suspension-Cultured Tobacco BY-2 Cells1 (1998)

To date, the lack of a method for inducing plant cells and their Golgi stacks to differentiate in a synchronous manner has made it difficult to characterize the nature and extent of Golgi retailoring in biochemical terms. Here we report that auxin deprivation can be used to induce a uniform population of suspension-cultured tobacco (Nicotiana tabacum cv BY-2) cells to differentiate synchronously during a 4-d period. Upon removal of auxin, the cells stop dividing, undergo elongation, and differentiate in a manner that mimics the formation of slime-secreting epidermal and peripheral root-cap cells. The morphological changes to the Golgi apparatus include a proportional increase in the number of trans-Golgi cisternae, a switch to larger-sized secretory vesicles that bud from the trans-Golgi cisternae, and an increase in osmium staining of the secretory products. Biochemical alterations include an increase in large, fucosylated, mucin-type glycoproteins, changes in the types of secreted arabinogalactan proteins, and an increase in the amounts and types of molecules containing the peripheral root-cap-cell-specific epitope JIM 13. Taken together, these findings support the hypothesis that auxin deprivation can be used to induce tobacco BY-2 cells to differentiate synchronously into mucilage-secreting cells.
Fluorescent Cyanoacrylate Monomers and Polymers for Fingermark Development (2013)

Cyanoacrylate esters with fluorescent side groups were synthesized and tested as agents for latent fingerprint development. Reactive monomers with benzyl, anthracyl, naphthyl, fluorenyl, propagyl, and cyanomethyl side groups were synthesized using the formation of an ethyl cyanoacrylate, anthracene adduct, followed by hydrolysis of the ethyl ester to the acid and esterification with a desired alcohol, and finally release of the monomer by retro-Diels–Alder with maleic anhydride. Monomers were prepared in high yield and purity as determined by spectral analysis. Attempts to synthesize these monomers from poly(ethyl cyanoacrylate) by transesterification and depolymerization resulted in low yields and low purity. The synthesized fluorescent monomers were found to be effective for latent fingerprint development in solution forming clear fluorescent fingerprint images suitable for forensic fingerprint comparison. These monomers can complement the current use of the commonly used nonfluorescent ethyl cyanoacrylate monomers for fingerprint development.