gebhart/patrepeval huggingface dataset:
Comparison of Starch-Branching Enzyme Genes Reveals Evolutionary Relationships Among Isoforms. Characterization of a Gene for Starch-Branching Enzyme IIa from the Wheat D Genome Donor<i>Aegilops tauschii</i>  (2001)

Genes and cDNAs for starch-branching enzyme II (SBEII) have been isolated from libraries constructed from Aegilops tauschii and wheat (Triticum aestivum) endosperm, respectively. One class of genes has been termed wSBEII-DA1 and encodes the N terminus reported for an SBEII from wheat endosperm. On the basis of phylogenetic comparisons with other branching enzyme sequences, wSBEII-DA1 is considered to be a member of the SBEIIa class. The wSBEII-DA1 gene consists of 22 exons with exons 4 to 21 being identical in length to the maize (Zea mays) SBEIIb gene, and the gene is located in the proximal region of the long arm of chromosome 2 at a locus designated sbe2a. RNA encoding SBEIIa can be detected in the endosperm from 6 d after flowering and is at its maximum level from 15 to 18 d after anthesis. Use of antibodies specific for SBEIIa demonstrated that this protein was present in both the soluble and granule bound fractions in developing wheat endosperm. We also report a cDNA sequence for SBEIIa that could arise by variant transcription/splicing. A second gene, termed wSBEII-DB1, was isolated and encodes an SBEII, which shows greater sequence identity with SBEIIb-type sequences than with SBEIIa-type sequences. Comparisons of SBEII gene structures among wheat, maize, and Arabidopsis indicate the lineage of the SBEII genes.
Laser System for Dulling Work Roll by Q-Switched Nd:YAG Laser (1989)

A new dulling system for the work rolls used to roughen the surface of cold-rolled steel sheet has been developed. Such sheets are used in various products, such as outer panels of automobiles, and decorative outer plates of electric appliances. In this process, several pulsed laser beams generated by Q-switched Nd:YAG lasers produce small craters with rims around them. This process includes a longitudinal scanning system within the laser processing head and a rotation system for the work roll; consequently, the surface of the dulled roll consists of innumerable small craters. The main features of the system consist of: (1) a special way of controlling RF power applied to the acousto-optic modulator for the Q-switching to change the peak power, pulse duration, and low level CW power to fit the dulling condition, (2) a method to combine two or more pulse beams to control the profile of dulling craters. Immediate advantages of this process are: (1) timesaving (very high repetition rate of pulses by Q-switching), (2) stable operation (without a mechanical chopper which is usually used with a CO2 laser to make pulsed beam), and (3) cost-saving. This newly developed system is effectively applied to the production of cold-rolled steel sheets.
Extremely low temperature formation of silicon dioxide on gallium arsenide (1997)

This article demonstrates the growth of silicon dioxide (SiO2) on a gallium arsenide (GaAs) substrate by use of the liquid phase deposition (LPD) method at extremely low temperature (∼40 °C). This method cannot only grow SiO2 but it can also obtain good quality and reliability due to the suppression of interdiffusion in such a low temperature process. The deposition rate of LPD-SiO2 on GaAs is up to 1265 Å/h. The refractive index of the LPD-SiO2 film on GaAs is about 1.42 with growth at 40 °C. When the LPD-SiO2 film on the GaAs substrate is used to fabricate a metal–oxide–semiconductor capacitor with a device area of 0.3 cm2, the surface charge density (Qss/q) is about 3.7×1011 cm−2 and the leakage current is 43.3 pA at −5 V. A proposed mechanism for the LPD of SiO2 on GaAs is also presented.
Manganese Oxide Nanoarchitectures as Broad-Spectrum Sorbents for Toxic Gases (2016)

We demonstrate that sol-gel-derived manganese oxide (MnOx) nanoarchitectures exhibit broad-spectrum filtration activity for three chemically diverse toxic gases: NH3, SO2, and H2S. Manganese oxides are synthesized via the reaction of NaMnO4 and fumaric acid to form monolithic gels of disordered, mixed-valent Na-MnOx; incorporated Na(+) is readily exchanged for H(+) by subsequent acid rinsing to form a more crystalline H-MnOx phase. For both Na-MnOx and H-MnOx forms, controlled pore-fluid removal yields either densified, yet still mesoporous, xerogels or low-density aerogels (prepared by drying from supercritical CO2). The performance of these MnOx nanoarchitectures as filtration media is assessed using dynamic-challenge microbreakthrough protocols. We observe technologically relevant sorption capacities under both dry conditions and wet (80% relative humidity) for each of the three toxic industrial chemicals investigated. The Na-MnOx xerogels and aerogels provide optimal performance with the aerogel exhibiting maximum sorption capacities of 39, 200, and 680 mg g(-1) for NH3, SO2, and H2S, respectively. Postbreakthrough characterization using X-ray photoelectron spectroscopy (XPS) and diffuse-reflectance infrared Fourier transform spectroscopy (DRIFTS) confirms that NH3 is captured and partially protonated within the MnOx structure, while SO2 undergoes oxidation by the redox-active oxide to form adsorbed sulfate at the MnOx surface. Hydrogen sulfide is also oxidized to form a combination of sulfate and sulfur/polysulfide products, concomitant with a decrease in the average Mn oxidation state from 3.43 to 2.94 and generation of a MnOOH phase.
Diagnosing Cervical Cancer and High-Grade Precursors by HPV16 Transcription Patterns (2009)

Infections with high-risk human papillomaviruses (HPV), mainly HPV type 16, can cause malignant transformation of the human cervical epithelium and the development of cervical cancer (CxCa). A rapid and precise diagnosis of the precancerous lesions by conventional cytology or HPV DNA tests remains difficult and often leads to overtreatment. We quantitatively analyzed the HPV16 transcriptome of 80 HPV16 DNA-positive cervical scrapes classified as mild cytologic grade, including no intraepithelial lesion or malignancy (NIL/M; normal, n=25) and low-grade squamous intraepithelial lesion (LSIL; n=24), and severe cytologic grade, including high-grade squamous intraepithelial lesion (HSIL; n=24) and CxCa (n=7), with novel nucleic acid sequence-based amplification-Luminex assays. In severe lesions, HPV16 E6*II and E1C encoding transcripts were strongly upregulated, whereas spliced E1[SYMBOL: SEE TEXT]E4 and L1 encoding transcripts were markedly downregulated. Using a combination of the four marker transcripts, 100% of CxCa and 67% of HSIL cases were correctly identified as severe, and 74% of LSIL and 92% of NIL/M samples as mild cytologic grade. Compared with a commercially available HPV E6/E7 mRNA assay, the specificity of the marker combination for discriminating severe and mild cytologic lesions increased from 23% to 83%. In conclusion, we identified a novel HPV16 RNA pattern for grading of cervical lesions with a potentially high diagnostic value for the primary screening of CxCa precursors and the triage of cervical lesions.
Novel<i>C</i><sub>2</sub>-Symmetric Planar Chiral Diphosphine Ligands and Their Application in Pd-Catalyzed Asymmetric Allylic Substitutions (2007)

Novel C(2)-symmetric diphosphine ligands possessing only the planar chirality of ruthenocene, 1,1'-bis(diphenylphosphino)-2,2'-disubstituted-ruthenocenes (4), were prepared. With this kind of ligands, excellent enantioselectivity and especially highly catalytic activity in palladium-catalyzed asymmetric allylic substitutions of rac-1,3-diphenyl-2-propenyl acetate (9) were observed, compared to their ferrocene analogues 1. Good enantioselectivity and highly catalytic activity were also obtained with 4 in palladium-catalyzed asymmetric allylic substitutions of cyclohexen-1-yl acetate (12). Further study on the effect of R in ester group on enantioselectivity of 4 showed an opposite trend compared with their ferrocene analogues 1 in asymmetric allylic substitutions. For ruthenocene ligands 4, the one with the smaller R in the ester group gave higher enantioselectivity for the palladium-catalyzed asymmetric allylic substitutions of 9, while a converse trend had been observed with 1. However, for the palladium-catalyzed asymmetric allylic substitutions of 12, ligand 4 with a larger R in the ester group resulted in somewhat higher enantioselectivity but still an opposite trend with ligand 1. The X-ray diffraction study of crystal structures of 4 and 1 with Pd(II) was carried out and showed that the enantioselectivity was correlated to the twist angle existing in the palladium complex.
Opioid Receptor Ligands (2021)

Abstract Opioid agonists, exemplified by morphine, have been the most prescribed class of drugs for the management of moderate to severe pain for many years. These drugs have significant liabilities of addiction and constipation over long‐term use and acute overdoses can result in respiratory depression. For over thousands of years, opium and opium‐derived drugs have nonetheless been utilized for their therapeutic and recreational benefits. Due to their liabilities, medicinal chemists and clinicians have worked for years to discover novel agents or treatment courses that would be devoid of these side effects. Still to this day, there are no agents that meet these criteria. Therefore, efforts continue vigorously in the quest for drugs with potent analgesic effects without abuse or side‐effect potential. Many chemical classes have been sought after in this quest and the range from peptides to synthetic compounds to natural products. Morphine offered a template that was rigid and able to provide an enormous amount of structure–function relationships that many of the market analgesics are based on. To complicate matters, the endogenous opioid system is comprised of four distinct receptor subtypes. These receptors are all members of the G‐protein superfamily and are designated as mu (μ, MOP), delta (δ, DOP), kappa (κ, KOP), and nociception (ORL1, NOP). It has been realized over the years that a combination of activities at these receptors may result in agents that could be devoid of liabilities. Intensive efforts have been directed at improved probes for each receptor subtype and combinations of agonists and antagonists for combinations of these receptors. This review will discuss the structure–activity relationships, as they are currently understood, with regard to each of the major classes of compounds that interact with these protein targets.
Permeative Amine Introduction for Very Weak Acid Detection in Ion Chromatography (2016)

A permeative amine introduction device (PAID) is placed after a conventional KOH eluent-suppressed conductometric anion chromatography (SCAC) system. The PAID converts the suppressed eluites from the acid form to the corresponding ammonium salt (NR2H + HX → NR2H2(+) + X(-)) and allows very weak acids HX (pKa ≥ 7.0) that cannot normally be detected by SCAC to be measured by a second conductivity detector following the PAID. Permeative reagent introduction is dilutionless, can be operated without pumps, and provides good mixing (baseline noise 0.8 nS/cm for 27 μM diethylamine) with low band dispersion (as small as 30 μL). Diethylamine (DEA) was chosen as the amine source due to its low pKb value (3.0), high vapor pressure, low toxicity, and low odor. The eluites are thus detected against a low diethylammonium hydroxide (DEAOH) background (5-31 μS/cm) as negative peaks because the equivalent conductance of OH(-) is greater than that of X(-). Reducing the background DEA concentration enhances the detectability of traces of weak acids. Lower background [DEA] will limit the maximum concentration of analyte acids that can be determined; a general concept of peak width measurement at a fixed height is proposed as a solution. Trace impurities formed during electrodialytic suppression play a role in background noise; for the first time, we look at the nature of such impurities. The appearance of silicate in a sample put in a glass container as a function of pH can be readily followed. The maximum silica level in high purity type 1 water is 50 nM (1.40 μg/L Si), which is a measurement challenge in particular. A large injection volume (1 mL) permits detection limits of 21 nM silicate, 3 nM taurine, 3 nM sulfide, and 13 nM cyanide.
Development of an advanced power system stabilizer using a strict linearization approach (1996)

This paper presents a practical design for a power system stabilizer using the differential geometric linearization approach. This stabilizer uses the information at the secondary bus of the step-up transformer as input signals, enabling its application to multi-machine power systems. The stabilizer makes it possible to obtain all necessary information within its own power station without observing an equivalent reactance in other power systems. To evaluate the dynamic performance of this stabilizer, the authors tested it on a multimachine power system computer model. The simulation results showed that the stabilizer offered good dynamic performance and robustness compared with conventional power system stabilizers, thus confirming its very effective and practical application in power system stabilization.
AKR1C3 Promotes AR-V7 Protein Stabilization and Confers Resistance to AR-Targeted Therapies in Advanced Prostate Cancer (2019)

The mechanisms resulting in resistance to next-generation antiandrogens in castration-resistant prostate cancer are incompletely understood. Numerous studies have determined that constitutively active androgen receptor (AR) signaling or full-length AR bypass mechanisms may contribute to the resistance. Previous studies established that AKR1C3 and AR-V7 play important roles in enzalutamide and abiraterone resistance. In the present study, we found that AKR1C3 increases AR-V7 expression in resistant prostate cancer cells through enhancing protein stability via activation of the ubiquitin-mediated proteasome pathway. AKR1C3 reprograms AR signaling in enzalutamide-resistant prostate cancer cells. In addition, bioinformatical analysis of indomethacin-treated resistant cells revealed that indomethacin significantly activates the unfolded protein response, p53, and apoptosis pathways, and suppresses cell-cycle, Myc, and AR/ARV7 pathways. Targeting AKR1C3 with indomethacin significantly decreases AR/AR-V7 protein expression <i>in vitro</i> and <i>in vivo</i> through activation of the ubiquitin-mediated proteasome pathway. Our results suggest that the AKR1C3/AR-V7 complex collaboratively confers resistance to AR-targeted therapies in advanced prostate cancer.
Electrical Prism: a high quality factor filter for mm wave and terahertz frequencies (2008)

Energy direction is a function of frequency in low pass 2D lattice at frequencies close to the cut off. This property can be used to implement a high quality factor filter called electrical prism. Negative effective index was also shown to be achievable using the structure. Channeling of the signal and spatial filtering are the main reasons behind the filter having higher quality factor than component quality factor. This structure is specially interesting as it is easy to fabricate on conventional CMOS process.
Laboratory Investigation of Novel Oil Recovery Method for Carbonate Reservoirs (2010)

Abstract The impact of brine salinity and ion composition on oil recovery has been an area of research in recent years. Evidence from laboratory studies supported by some field tests targeting mainly sandstones, has distinctly shown that injecting low salinity water has a significant impact on oil recovery. Although, the potential for carbonates has not been thoroughly investigated, some reported studies have excluded carbonates from this effect. The main objective of this paper is to investigate the potential of increased oil recovery by altering the salinity and ion composition of the injection water for carbonate reservoirs, define the recovery mechanisms, and eventually transform the emerged trend to full-fledged reservoir technology. This paper presents the results of a laboratory coreflooding study conducted using composite rock samples from a carbonate reservoir to investigate the impact of salinity and ionic composition on oil/brine/rock interactions, and eventually on oil recovery. The experimental parameters and procedures were well designed to reflect the reservoir conditions and current field injection practices, including reservoir pressure, reservoir temperature, salinity and ionic content of initial formation water and current types of injected water. Also, this study provides detailed discussion and interpretation for potential mechanisms. The experimental results revealed that substantial tertiary oil recovery beyond conventional waterflooding can be achieved by altering the salinity and ionic content of field injected water. The new emerged trend is distinct from what has been addressed in previous reported studies on topics of low salinity waterflooding for sandstones, or seawater injection into high temperature chalk reservoirs. On the subject of recovery mechanisms, the results showed that altering the salinity and ionic composition of the injected water has a significant impact on the wettability of the rock surface. This was also confirmed by nuclear magnetic resonance (NMR) measurements. The results, observations, and interpretations addressed in this study provided compelling evidence to suggest that the key mechanism for the emerged trend is wettability alteration.
Text2Node: a Cross-Domain System for Mapping Arbitrary Phrases to a Taxonomy (2019)

Electronic health record (EHR) systems are used extensively throughout the healthcare domain. However, data interchangeability between EHR systems is limited due to the use of different coding standards across systems. Existing methods of mapping coding standards based on manual human experts mapping, dictionary mapping, symbolic NLP and classification are unscalable and cannot accommodate large scale EHR datasets. In this work, we present Text2Node, a cross-domain mapping system capable of mapping medical phrases to concepts in a large taxonomy (such as SNOMED CT). The system is designed to generalize from a limited set of training samples and map phrases to elements of the taxonomy that are not covered by training data. As a result, our system is scalable, robust to wording variants between coding systems and can output highly relevant concepts when no exact concept exists in the target taxonomy. Text2Node operates in three main stages: first, the lexicon is mapped to word embeddings; second, the taxonomy is vectorized using node embeddings; and finally, the mapping function is trained to connect the two embedding spaces. We compared multiple algorithms and architectures for each stage of the training, including GloVe and FastText word embeddings, CNN and Bi-LSTM mapping functions, and node2vec for node embeddings. We confirmed the robustness and generalisation properties of Text2Node by mapping ICD-9-CM Diagnosis phrases to SNOMED CT and by zero-shot training at comparable accuracy. This system is a novel methodological contribution to the task of normalizing and linking phrases to a taxonomy, advancing data interchangeability in healthcare. When applied, the system can use electronic health records to generate an embedding that incorporates taxonomical medical knowledge to improve clinical predictive models.
Single Crystalline GaN Tiles Grown on Si (111) Substrates by Confined Lateral Guided Growth to Eliminate Wafer Bowing (2015)

A novel concept termed confined lateral guided growth (CLGG) has been demonstrated to prepare single crystalline GaN microtiles with a goal to create high crystalline quality and strain‐free GaN on large‐sized Si (111) substrates. Uniform array of hexagonal GaN tiles has been created with a diameter of larger than 30 μm for each tile. As revealed by the surface pits density of around 2 × 10 8 cm −2 , the density of dislocations in these GaN tiles has been significantly reduced compared with that obtained typically from a GaN heteroepitaxy on Si (111). The strain in GaN tiles has been dramatically reduced to nearly zero. This approach offers a route to eliminate wafer‐bowing for growing high crystalline quality GaN on Si, especially when the substrate size scales to 12 in and beyond. The growth behavior and mechanism within these confined growth masks are investigated by both finite element modeling and experimental studying, indicating that CLGG is dominated by gas phase diffusion.
Abstract 3503: A method for quantifying soluble folate receptor 1 in IMGN853 0401 clinical trial patients. (2013)

Abstract IMGN853, an antibody-“drug” conjugate (ADC), consists of a human folate receptor 1 (FOLR1)-binding monoclonal antibody, M9346A, conjugated to the maytansinoid, DM4, via the cleavable sulfo-SPDB linker. A phase I clinical study has been initiated to identify the maximum tolerated dose, safety, pharmacokinetics (PK), and preliminary efficacy of IMGN853 in patients with FOLR1-positive tumors, including ovarian cancer, non-small cell lung cancer, and other epithelial malignancies. The levels of soluble FOLR1 antigen (sFOLR1) in plasma may vary depending on factors such as tumor antigen expression level, tumor type, and disease stage, and may affect the PK of IMGN853and response to treatment. Previously reported studies describing the detection of sFOLR1 in patient samples are limited and not quantitative. The aim of this study was to develop a sandwich ELISA to quantify levels of sFOLR1 present in plasma samples from cancer patients for use as a potential biomarker of IMGN853 PK and/or clinical response. A panel of murine anti-FOLR1 antibodies was generated at ImmunoGen by standard hybridoma technology. Two clones were chosen for use as capture (FR1-9) and detector (FR1-13) antibodies in the ELISA due to their high affinity and ability to bind to FOLR1 even in the presence of IMGN853 or the FOLR1 ligand, folate. The extracellular domain of FOLR1 fused to murine IgG2a Fc region (FOLR1-Fc) was used as a reference standard. A sandwich ELISA was developed using FR1-9 antibody to capture sFOLR1 from patient plasma, and bound sFOLR1 was detected using biotinylated FR1-13 antibody and streptavidin-HRP with TMB as the substrate. The ELISA was used to quantify sFOLR1 in ovarian carcinoma patient plasma using a reference standard curve generated with FOLR1-Fc antigen. A robust sandwich ELISA was developed to quantify sFOLR1 in patient plasma. The quantitation range of the assay was determined to be 0.2 to 90 nanomolar. Coated plates stored frozen from 0-14 days and protein reagents freeze-thawed over two cycles gave repeatable results. The ELISA was able to detect sFOLR1 in 5 of 10 ovarian cancer patient plasma samples, where the levels of detectable sFOLR1 ranged from 0.7-31 nM. This ELISA is considered suitable to quantify levels of sFOLR1 in patients enrolled in the phase 1 trial over the course of IMGN853 treatment, and resulting data will be assessed for correlations with IMGN853 PK and with clinical response. Citation Format: Nathan Testa, Laura Bartle, Olga Ab, Judy Cheng, Gillian Payne, Robert J. Lutz, Ben Wolf, Christina Carrigan. A method for quantifying soluble folate receptor 1 in IMGN853 0401 clinical trial patients. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3503. doi:10.1158/1538-7445.AM2013-3503