gebhart/patrepeval huggingface dataset:
Native Design of Soluble, Aggregation-Resistant Bioactive Peptides: Chemical Evolution of Human Glucagon (2016)

Peptide-based therapeutics commonly suffer from biophysical properties that compromise pharmacology and medicinal use. Structural optimization of the primary sequence is the usual route to address such challenges while trying to maintain as much native character and avoiding introduction of any foreign element that might evoke an immunological response. Glucagon serves a seminal physiological role in buffering against hypoglycemia, but its low aqueous solubility, chemical instability, and propensity to self-aggregate severely complicate its medicinal use. Selective amide bond replacement with metastable ester bonds is a preferred approach to the preparation of peptides with biophysical properties that otherwise inhibit synthesis. We have recruited such chemistry in the design and development of unique glucagon prodrugs that have physical properties suitable for medicinal use and yet rapidly convert to native hormone upon exposure to slightly alkaline pH. These prodrugs demonstrate in vitro and in vivo pharmacology when formulated in physiological buffers that are nearly identical to native hormone when solubilized in conventional dilute hydrochloric acid. This approach provides the best of both worlds, where the pro-drug delivers chemical properties supportive of aqueous formulation and the native biological properties.
Control of the Size and Distribution of Gold Nanoparticles by Unmodified Cyclodextrins (2003)

We report and discuss how gold nanoparticles were synthesized by the reduction of hydrogen tetrachloroaurate(III) trihydrate by sodium citrate in the presence of unmodified α-cyclodextrin (CD), β-CD, and γ-CD. Gold nanoparticles were immobilized on poly(diallyldimethylammonium) chloride (PDDA) modified glass slides to enable AFM measurements. The particle size was dependent upon the type and concentration of cyclodextrin used as well as the sodium citrate concentration. An increase in the cyclodextrin concentration effected a shift of the particle size range from 12−15 to 4−6 nm with uniform particle size distribution. The homogeneity of the synthesized gold nanoparticles was also evident from transmission electron micrographs (TEMs). Synthesis of gold nanoparticles by the reduction of hydrogen tetrachloroaurate(III) trihydrate by sodium borohydride in the presence of cyclodextrins also reduced the particle size from 6−8 to 2−4 nm. The consecutive particle growth due to the mutual coalescence between nanoclusters and their neighboring free gold atoms was limited in the presence of CDs. FT-Raman, FT-IR spectroscopy, and mass spectrometry (MS) indicated that the synthesis procedure exhibited no effect on the cyclodextrins. There was no evidence that gold nanoparticles were included in the CD cavities.
Designing and Evaluating Calmer, a Device for Simulating Maternal Skin-to-Skin Holding for Premature Infants (2020)

We describe the design and deployment of Calmer, a technology that simulates key aspects of maternal skin-to-skin holding for prematurely born infants: its inspiration, approach, physical design, and introduction into the Neonatal Intensive Care Unit. Maternal skin-to-skin holding can mitigate neonatal pain during medical procedures by as much as 50%, which can improve weight gain, sleep and later development. However, parents cannot always be present, and some infants are too fragile to be held. Interventions targeting this gap could be perceived as supplanting the mother in this intimate role, exposing her to depression and endangering her maternal bond. Over 10 years, we iteratively developed Calmer and demonstrated infant health benefit in a randomized clinical trial. Here, we report and reflect on pursuing this goal in a socially and technologically complex context: constraints, strategies, features, reception of the device, and surprises, such as leading to mothers feeling channeled rather than replaced.
Visual ego-vehicle lane assignment using Spatial Ray features (2013)

Assigning the ego-vehicle to a lane is not only beneficial for navigation but will be an essential element in future Advanced Driver Assistance Systems. This paper describes an approach for ego-lane index estimation using only a monocular camera and no additional sensing equipment like, e.g., the typically employed GPS and Inertial Measurement Unit. Key aspect of the approach are SPatial RAY (SPRAY) features which represent the spatial layout of the road in the visual scene. The proposed method perceives a variety of local visual properties of the scene by means of base classifiers operating on patches extracted from camera images. The spatial arrangement of these local visual properties are captured using SPRAY features. With a boosting classifier trained on these features the ego-lane index is obtained. The system is evaluated on low traffic density and complementary to an object-based approach suitable for heavy traffic. In the conducted experiments, the proposed approach reaches recognition rates of 93% to 97% on individual highway images without applying any kind of temporal filtering.
Methoxy-Functionalized <i>N</i>-Heterocyclic Carbenes (2014)

The effect of methoxy functionalization of three N-heterocyclic carbene ligands was assessed using a variety of methods. The steric environment of each carbene has been assessed in various coordination environments. The electronic properties, specifically the electron-donating character and π-accepting ability, have been evaluated using nickel and iridium complexes and selenium adducts, respectively. Comparisons with the parent systems have been made with respect to both electronic and steric properties. The carbenes IPrOMe, SIPrOMe, and IPr*OMe have been found to be more electron donating than the parent systems IPr, SIPr, and IPr* and only slightly less π accepting, yet they exhibit similar steric properties.
High efficiency inversion layer solar cells on polycrystalline silicon by the application of silicon nitride (1981)

Plasma enhanced CVD silicon nitride is introduced for the fabrication of inversion layer solar cells on p-type polycrystalline silicon. The same high interface quality as obtained for Si-nitride on monocrystalline silicon could also be achieved for polycrystalline silicon. This includes high interface charge densities up to 6.6 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> and high UV sensitivity of the cells. For 4-cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> polycrystalline metal-insulator-semiconductor inversion layer (MIS/IL) solar cells active area efficiencies up to 13.4 percent (12.3-percent total area efficiency) under AM1 illumination could be reached, the highest values yet reported for polycrystalline silicon inversion layer solar cells on a total area basis. For the coprocessed MIS/IL cells on monocrystalline 0.7-ω. cm p-Si
Cover Picture: Identification of Pharmacological Chaperones for Gaucher Disease and Characterization of Their Effects on β‐Glucocerebrosidase by Hydrogen/Deuterium Exchange Mass Spectrometry (ChemBioChem 16/2008) (2008)

The cover picture shows the regions (shades of blue) on human lysosomal glucocerebrosidase (green) that undergo a significant reduction in hydrogen–deuterium exchange (denoted by loss of blurriness) upon binding a 2,4-diamino-5-substituted quinazoline (MWP; red). MWP was identified in a high-throughput screen of the Maybridge library of 50 000 small molecule drug-like compounds (grey structures) for inhibitors. The confocal images immediately below the 3D structures of the enzyme are patient fibrobroblasts homozygous for the common N370S Gaucher disease type I allele, stained with an antibody against glucocerebrosidase (green); these show increased levels of the enzyme in MWP treated (+MWP) cells in comparison with untreated control (−MWP) cells. This study has identified pharmacological chaperones (PC) that are not based on the structure of the glycolipid substrate of the enzyme. These new compounds increase the repertoire of chemical frameworks available for the construction of efficient PCs for the treatment of Gaucher disease. For more details, see the article by M. B. Tropak, D. J. Mahuran et al. on p. 2650 ff.
An approach to remove homoepitaxially grown GaN layers by cleavage from the substrate surface (2020)

We demonstrate removal of homoepitaxially grown semi-polar gallium nitride (GaN) layers from the native substrates. The weak link at the interface of the epitaxial lateral overgrowth and cleavable m-plane of the respective native semi-polar plane is used to separate homoepitaxial GaN from its native substrate. Homoepitaxial GaN layers of the semi-polar planes, (101), (201), (301), (10), (20), and (30) are successfully removed. This approach allows the reuse of expensive semi-polar GaN substrates, eliminating one barrier to market introduction of superior optoelectronic devices grown with semi-polar orientations.
Production of docosahexaenoic acid by <i>Crypthecodinium cohnii</i> grown in a pH‐auxostat culture with acetic acid as principal carbon source (2001)

Crypthecodinium cohnii, a marine alga used for the commercial production of docosahexaenoic acid (DHA), was cultivated in medium containing sodium acetate as principal carbon source; the pH was maintained at a constant value by addition of acetic acid, which also provided an additional carbon source in a controlled manner. The accumulation of lipid by C. cohnii in this pH-auxostat culture was significantly greater than previously reported for batch cultures using glucose as principal carbon source. Of six strains tested in pH-auxostat cultures, C. cohnii ATCC 30772 was the best, with the cells reaching 20 to 30 g dry weight per liter after 98 to 144 h and containing in excess of 40% (w/w) total lipid, with DHA representing approximately half of the total fatty acids in the triacylglycerol fraction. A productivity of 36 mg DHA L(-1) h(-1) was achieved during cultivation for 98 h using a 5% (vol/vol) inoculum, and DHA production was in excess of 3 g per liter of culture. Most of the DHA was present in neutral lipids.
Anisotropic conductivity tensor imaging in MREIT using directional diffusion rate of water molecules (2014)

Magnetic resonance electrical impedance tomography (MREIT) is an emerging method to visualize electrical conductivity and/or current density images at low frequencies (below 1 KHz). Injecting currents into an imaging object, one component of the induced magnetic flux density is acquired using an MRI scanner for isotropic conductivity image reconstructions. Diffusion tensor MRI (DT-MRI) measures the intrinsic three-dimensional diffusion property of water molecules within a tissue. It characterizes the anisotropic water transport by the effective diffusion tensor. Combining the DT-MRI and MREIT techniques, we propose a novel direct method for absolute conductivity tensor image reconstructions based on a linear relationship between the water diffusion tensor and the electrical conductivity tensor. We first recover the projected current density, which is the best approximation of the internal current density one can obtain from the measured single component of the induced magnetic flux density. This enables us to estimate a scale factor between the diffusion tensor and the conductivity tensor. Combining these values at all pixels with the acquired diffusion tensor map, we can quantitatively recover the anisotropic conductivity tensor map. From numerical simulations and experimental verifications using a biological tissue phantom, we found that the new method overcomes the limitations of each method and successfully reconstructs both the direction and magnitude of the conductivity tensor for both the anisotropic and isotropic regions.
<i>N</i>‐Bromoacetamide—A New Nitrogen Source for the Catalytic Asymmetric Aminohydroxylation of Olefins (1997)

The efficient large-scale synthesis (see below) of an enantiomerically pure Taxol side chain precursor—3-phenylisoserine (1)—highlights the potential of the third modification of the asymmetric aminohydroxylation (AA). The use of N-bromoacetamide as the nitrogen source is the latest advance in the osmium-catalyzed AA of olefins.
Antigen-specific antibody and polyfunctional T cells generated by respiratory immunization with protective Burkholderia ΔtonB Δhcp1 live attenuated vaccines (2021)

Melioidosis, caused by Burkholderia pseudomallei (Bpm), lacks a vaccine. We identify the immune correlates of protection induced by B. mallei ΔtonB Δhcp1 (CLH001) and Bpm ΔtonB Δhcp1 (PBK001) vaccines against inhalational melioidosis. Mucosal immunization with either vaccine generates Bpm-specific IgM and IgG (IgG<sub>2</sub><sub>b/c </sub>> IgG<sub>1</sub> > IgG<sub>3</sub>) antibodies in sera and lungs, and lung IgA antibodies. Sera confers complement-independent bactericidal activity and macrophages opsonophagocytic uptake but is insufficient in passive transfer experiments to provide significant protection. Both vaccines elicit memory Th1 and Th17 CD4<sup>+</sup> T-cell responses in lung and spleen after Bpm antigen-specific recall. The PBK001 vaccine is superior in generating respiratory IgA post-boost, anamnestic IgG at challenge, T-cell recall to specific antigen, and development of diverse polyfunctional memory T-cell pools. Analysis of lung histology suggests that potent polyfunctional T-cell memory and/or IL-17 signatures generated with PBK001 vaccination may be associated with moderate lung inflammation post vaccination.
Efficacy of Intravenous and Oral Sotalol in Pharmacologic Conversion of Atrial Fibrillation: A Systematic Review and Meta-Analysis (2016)

Sotalol is as effective as class IA and class IC antiarrhythmic agents, and it is also as effective as amiodarone for pharmacologic conversion of AF. Only ibutilide at a high dose showed a greater conversion rate of AF.
Providing Oligonucleotides with Steric Selectivity by Brush-Polymer-Assisted Compaction (2015)

Difficult biopharmaceutical characteristics of oligonucleotides, such as poor enzymatic stability, rapid clearance by reticuloendothelial organs, immunostimulation, and coagulopathies, limit their application as therapeutics. Many of these side effects are initiated via sequence-specific or nonsequence-specific interactions with proteins. Herein, we report a novel form of brush-polymer/DNA conjugate that provides the DNA with nanoscale steric selectivity: Hybridization kinetics with complementary DNA remains nearly unaffected, but interactions with proteins are significantly retarded. The relative lengths of the brush side chain and the DNA strand are found to play a critical role in the degree of selectivity. Being able to evade protein adhesion also improves in vivo biodistribution, thus making these molecular nanostructures promising materials for oligonucleotide-based therapies.
Variable operation of Hall thruster with multiple segmented electrodes (2000)

Variable plasma jet velocity with low beam divergence over a range of mass flow rates can be achieved through segmented electrode operation of Hall plasma accelerator. With the use of just a cathode side electrode at the cathode potential, the beam divergence can be decreased substantially, at some cost in efficiency. However, the additional use of an anode side electrode retains the same reduced plume divergence, but at efficiencies comparable to the non-segmented operation. The high efficiency persists also when the anode side electrode is biased at an intermediate potential, thus producing two-stage Hall accelerator operation.
Eliminating Space Scanning: Fast mmWave Beam Alignment with UWB Radios (2023)

Due to their large bandwidth and impressive data speed, millimeter-wave (mmWave) radios are expected to play a key role in the 5G and beyond (e.g., 6G) communication networks. Yet, to release mmWave’s true power, the highly directional mmWave beams need to be aligned perfectly. Most existing beam alignment methods adopt an exhaustive or semi-exhaustive space scanning, which introduces up to seconds of delays. To eliminate the need for complex space scanning, this article presents an Ultra-wideband (UWB)-assisted mmWave communication framework, which leverages the co-located UWB antennas to estimate the best angles for mmWave beam alignment. One major challenge of applying this idea in the real world is the barrier of limited antenna numbers. Commercial-Off-The-Shelf (COTS) devices are usually equipped with only a small number of UWB antennas, which are not enough for the existing algorithms to provide an accurate angle estimation. To solve this challenge, we design a novel Multi-Frequency MUltiple SIgnal Classification (MF-MUSIC) algorithm, which extends the classic MUltiple SIgnal Classification (MUSIC) algorithm to the frequency domain and overcomes the antenna limitation barrier in the spatial domain. Extensive real-world experiments and numerical simulations illustrate the advantage of the proposed MF-MUSIC algorithm. MF-MUSIC uses only three antennas to achieve an accurate angle estimation, which is a mere 0.15° (or a relative difference of 3.6%) different from the state-of-the-art 16-antenna-based angle estimation method.
L‐carnitine effect on plasma lipoproteins of hyperlipidemic fat‐loaded rats (1987)

The effect of oral L-carnitine administration to rats fed olive oil has been studied. Carnitine significantly decreased triglyceride, cholesterol and phospholipid levels. Particularly, the levels of chylomicron and very low density lipoproteins in the blood were lowered. Low density lipoprotein levels were not affected, and high density lipoproteins were found to be decreased by 20%. Because carnitine did not change the composition of chylomicron and very low density lipoproteins fraction or affect the gastrointestinal triglyceride residue (about 1/3 of the original load), an effect of carnitine on hepatic fatty acid handling is most likely. The lowering of plasma free fatty acid levels by carnitine administration is in favor of an effect of carnitine on fatty acid handling. The effect on the liver is illustrated by the study of acetoacetate formation in in vitro perfused livers from previously olive oil loaded +/- carnitine-treated rats. Carnitine pretreatment stimulated ketogenesis. It is speculated that carnitine administration, by promoting beta-oxidation, lowers the production of very low density lipoproteins. This may be accomplished partly by an increase in the hepatic level of fatty acid binding protein, which also has been observed.
Inhibition of gastric H<sup>+</sup>,K<sup>+</sup>‐ATPase and <i>Helicobacter pylori</i> growth by phenolic antioxidants of<i> Zingiber officinale</i> (2007)

Ulcer is a common global problem characterized by acute gastric irritability, bleeding, etc. due to either increased gastric cell proton potassium ATPase activity (PPA) or perturbation of mucosal defence. Helicobacter pylori has been identified as a major ulcerogen in addition to oxidative stress and nonsteroidal anti-inflammatory drugs. In this paper, we report ginger-free phenolic (GRFP) and ginger hydrolysed phenolic (GRHP) fractions of ginger (Zingiber officinale) as potent inhibitors of PPA and H. pylori growth. GRFP and GRHP inhibited PPA at an IC(50) of 2.9 +/- 0.18 and 1.5 +/- 0.12 microg/mL, exhibiting six- to eight-fold better potency over lansoprazole. GRFP is constituted by syringic (38%), gallic (18%) and cinnamic (14%) acids and GRHP by cinnamic (48%), p-coumaric (34%) and caffeic (6%) acids as major phenolic acids. GRFP and GRHP further exhibited free radical scavenging (IC(50) 1.7 +/- 0.07 and 2.5 +/- 0.16), inhibition of lipid peroxidation (IC(50) 3.6 +/- 0.21 and 5.2 +/- 0.46), DNA protection (80% at 4 microg) and reducing power abilities (80-338 U/g) indicating strong antioxidative properties. GRFP and GRHP may thus be potential in-expensive multistep blockers against ulcer.
Incremental learning of system log formats (2010)

System logs come in a large and evolving variety of formats, many of which are semi-structured and/or non-standard. As a consequence, off-the-shelf tools for processing such logs often do not exist, forcing analysts to develop their own tools, which is costly and timeconsuming. In this paper, we present an incremental algorithm that automatically infers the format of system log files. From the resulting format descriptions, we can generate a suite of data processing tools automatically. The system can handle large-scale data sources whose formats evolve over time. Furthermore, it allows analysts to modify inferred descriptions as desired and incorporates those changes in future revisions.
IPF: In-Place X-Filling Algorithm for the Reliability of Modern FPGAs (2013)

Modern SRAM-based field-programmable gate arrays (FPGAs) are prone to single event upsets compared to application-specific integrated circuits. We propose a synthesis-based in-place x-filling algorithm by utilizing don't cares to augment the reliability of FPGA-based designs. Compared to circuit- and architecture-based solutions, our algorithm is in place, and does not incur area, power, performance, and design time overheads. Compared to other synthesis-based algorithms, we take into account widely accepted interconnect architecture. For the 10 largest combinational MCNC benchmark circuits mapped to 6-LUT architecture, our approach achieves up to 37% greater failure rate reduction, and up to 7 × runtime speedup, compared to the best known synthesis-based in-place algorithm, namely the in-place decomposition algorithm.
Abstract 1511: Stromal gene signature regulated by TGFβ signaling predicts poor clinical outcome in ovarian cancer . (2013)

Abstract Despite the clinical and histopathological similarities in initial disease presentation, patients with advanced ovarian cancer rapidly develop chemoresistance and succumb to the disease. In order to identify genes that are associated with poor patient survival, we analyzed microarray datasets of 795 advanced ovarian cancer patients and correlated gene expression levels with clinical data. We identified a 60-gene signature that was strongly associated with poor survival. Many genes in the signature were stromal genes, including POSTN, FN1, COL11A1, COL6A1, COL3A1, LOX, TIMP3, and VCAN. The same stromal signature was enriched in ovarian cancer metastases and in a cisplatin-resistant A2780 human ovarian cancer cell line. Expression of many stromal genes was induced by TGFβ1 and the effect was reversed by A83-01, a potent TGFβ1 inhibitor. Interestingly, we found that ovarian cancer stem cells (CSC) also express TGFβR2 and several TGFβ1-target genes, including COL6A1 and COL3A1, which were previously implicated in cisplatin resistance. Culturing of A2780 cells on collagen substrate resulted in increased cisplatin resistance and expansion of the CSC population. Our results suggest that TGFβ1 signaling induces stromal gene expression and forms a favorable microenvironment for ovarian CSC, thereby leading to cisplatin resistance and poor patient survival. Citation Format: Dong-Joo Cheon, Yunguang Tong, Myung-Shin Sim, Xiaojiang Cui, Dror Berel, Mourad Tighiouart, Wolf Ruprecht Wiedemeyer, Beth Karlan, Sandra Orsulic. Stromal gene signature regulated by TGFβ signaling predicts poor clinical outcome in ovarian cancer . [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 1511. doi:10.1158/1538-7445.AM2013-1511