gebhart/patrepeval huggingface dataset:
Confinement of Metal–Organic Polyhedra in Silica Nanopores (2012)

Metal-organic polyhedra (MOPs) have been incorporated into silica nanopores for the first time. Three MOPs with identical geometries but different ligand functionality (namely tert-butyl, hydroxyl, and sulfonic groups) were employed. A typical mesoporous silica, SBA-15, with a two-dimensional hexagonal pore regularity was used as the host. In comparison with bulk MOPs, which prefer to aggregate, MOPs confined in silica nanopores can be well dispersed, making the active sites and pores in the MOPs accessible. These dispersed MOPs showed apparently superior H(2) adsorption capacity in comparison with aggregated bulk MOPs. Moreover, the thermal stability of the MOPs was enhanced upon their confinement in silica nanopores.
[Clinical pharmacology of prostacyclin and stable analogs]. (1992)

Prostacyclin (PGI2) has vasodilatory effects and a powerful platelet anti-aggregating action. Receptors which may be common to prostaglandin E1 have been described on the platelet membranes, the uterus and various human arterial segments. The platelet activity is linked to the activation of adenylate-cyclase, coupled with a G protein. The mechanisms of the vasorelaxant effect have still not been fully studied. PGI2 is synthesized and released in vessels by the endothelium and the smooth muscle cells, and is very unstable. Its short half-life probably restricts its role to local regulation of platelet activity and vasomotricity. The kinetics and pharmacological effects of prostaglandins have been studied during intravenous injections in healthy volunteers and patients. The synthesis of numerous stable analogues is designed to produce drugs which can be administered orally to treat arteriopathies. The side-effects linked with the vasodilatory effects restricts the use of maximally active dosage.
Single-Molecule DNA Methylation Quantification Using Electro-optical Sensing in Solid-State Nanopores (2016)

Detection of epigenetic markers, including 5-methylcytosine, is crucial due to their role in gene expression regulation and due to the mounting evidence of aberrant DNA methylation patterns in cancer biogenesis. Single-molecule methods to date have primarily been focused on hypermethylation detection; however, many oncogenes are hypomethylated during cancer development, presenting an important unmet biosensing challenge. To this end, we have developed a labeling and single-molecule quantification method for multiple unmethylated cytosine-guanine dinucleotides (CpGs). Our method involves a single-step covalent coupling of DNA with synthetic cofactor analogues using DNA methyltransferases (MTases) followed by molecule-by-molecule electro-optical nanopore detection and quantification with single or multiple colors. This sensing method yields a calibrated scale to directly quantify the number of unmethylated CpGs in the target sequences of each DNA molecule. Importantly, our method can be used to analyze ∼10 kbp long double-stranded DNA while circumventing PCR amplification or bisulfite conversion. Expanding this technique to use two colors, as demonstrated here, would enable sensing of multiple DNA MTases through orthogonal labeling/sensing of unmethylated CpGs (or other epigenetic modifications) associated with specific recognition sites. Our proof-of-principle study may permit sequence-specific, direct targeting of clinically relevant hypomethylated sites in the genome.
Mechanism and inhibition of SARS-CoV-2 PLpro (2020)

Abstract Coronaviruses, including SARS-CoV-2, encode multifunctional proteases that are essential for viral replication and evasion of host innate immune mechanisms. The papain-like protease PLpro cleaves the viral polyprotein, and reverses inflammatory ubiquitin and anti-viral ubiquitin-like ISG15 protein modifications 1,2 . Drugs that target SARS-CoV-2 PLpro (hereafter, SARS2 PLpro) may hence be effective as treatments or prophylaxis for COVID-19, reducing viral load and reinstating innate immune responses 3 . We here characterise SARS2 PLpro in molecular and biochemical detail. SARS2 PLpro cleaves Lys48-linked polyubiquitin and ISG15 modifications with high activity. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. We further exploit two strategies to target PLpro. A repurposing approach, screening 3727 unique approved drugs and clinical compounds against SARS2 PLpro, identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small molecule SARS PLpro inhibitors were able to inhibit SARS2 PLpro with high potency and excellent antiviral activity in SARS-CoV-2 infection models.
Enhanced web log based recommendation by personalized retrieval (2014)

guided me in terms of information retrieval and web log mining.Dr Ling Chen helped me by asking insightful questions, and giving me thoughtful comments on the thesis.I enjoyed working with them, and benefited enormously from my interactions with them.I spent nearly two and a half
Correlation between traditional Chinese medicine syndromes in primary immunoglobulin A nephropathy and A267G in 5'-untranslated region within exonal of megsin gene (2008)

A267G in 5'-untranslated region within exonal of the megsin gene may be one of the substantial genetic basis for differentiating "deficiency of liver yin and kidney yin" syndrome and "deficiency of qi and yin" syndrome in primary IgAN.
Monitoring Natural Air Corn Drying A Demonstration Project (1988)

A demonstration project is described where natural air corn drying performance was monitored weekly and drying results were printed in a local newspaper. The newspaper articles also gave management recommen-dations for the upcoming week. Similar demonstration projects can be conducted using the procedures described in this paper.
DC conduction of Al<sub>2</sub>O<sub>3</sub> under high electric field (2007)

The experimental electrical conduction current of Al2O3 has been investigated versus applied field (up to 40 kV mm−1) and temperature (from 293 to 403 K). Different conduction theories were confronted to experimental data in order to find the most suitable one. It was found that at high electric fields, space charge limited conduction is able to describe the carrier transport mechanism in Al2O3. Estimated charge carrier mobilities seem to obey an Arrhenius law and traps are found to be shallow.
The individual core/shell silicon nanowire structure probed by Raman spectroscopy (2009)

Abstract The results of Raman scattering study of well‐separated core/shell silicon nanowires grown by CVD method and deposited on an Au surface are presented. The Raman spectra analysis indicates a presence of both crystalline (520 cm –1 ) and amorphous (470 cm –1 ) silicon phases, forming quite independent fractions. From the growth conditions, nanowires are expected to form such a core‐shell cone, with the amorphous silicon phase (aSi) outside, and the crystalline silicon phase (cSi) inside. The nanowires' diameter varies from 100 nm to 400 nm, what is seen in the SEM pictures. The Raman spectra have been acquired from the three points of the cone shaped nanowire: base, centre and tip. Based on the Stokes/anti‐Stokes (St/aSt) intensity ratios, the position and full width at half maximum of the Raman peaks temperatures of the amorphous shell and the cSi core in different nanowire's position have been determined. Against our expectations, the crystalline silicon (cSi) temperature was found lower than the amorphous silicon temperature (aSi). This suggests that the nanowire cSi core is in a good thermal contact with the metallic substrate, thus improving the heat evacuation of the SiNW core, for which the thermal conductivity is known to be low. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
<i>N</i>,<i>N</i>′-Dihydroxyamidines: A New Prodrug Principle To Improve the Oral Bioavailability of Amidines (2007)

N, N'-dihydroxybenzamdine represents a model compound for a new prodrug principle to improve the oral bioavailability of drugs containing amidine functions. The activation of the prodrug could be demonstrated in vitro by porcine and human subcellular enzyme fractions, the mitochondrial benzamidoxime reducing system, and porcine hepatocytes. In vivo, the bioavailability of benzamidine after oral application of N, N'-dihydroxybenzamidine was about 91% and exceeded that of benzamidine after oral application of benzamidoxime, being about 74% (Liu, L.; Ling, Y.; Havel, C.; Bashnick, L.; Young, W.; Rai, R.; Vijaykumar, D.; Riggs, J. R.; Ton, T.; Shaghafi, M.; Graupe, D.; Mordenti, J.; Sukbuntherng, J. Species comparison of in vitro and in vivo conversion of five N-hydroxyamidine prodrugs of fVIIA inhibitors to their corresponding active amidines. Presented at the 13th North America ISSX Meeting, Maui, HI, 2005).
The role of a superconducting seed layer in the structural and transport properties of EuBa2Cu3O7−x films (2003)

We report on the structural and transport properties of EuBa2Cu3O7−x (Eu123) films on SrTiO3 substrates. A substrate temperature 100 °C higher than that used to deposit YBa2Cu3O7−x (Y123) is needed to grow high-performance Eu123 films directly on SrTiO3 substrates. However, this high-temperature restriction can be circumvented by inserting a seed layer (∼12 nm) of Y123, Gd123, or Dy123 between the substrate and the Eu123. A structural analysis reveals that a transition region that promotes the growth of the a-axis is first formed on the surface of the substrate if the Eu123 is deposited directly on SrTiO3 at a temperature of less than 800 °C. On the other hand, the use of a seed layer of another superconducting material restructures the Eu123 to the right phase without forming this transition region. Eu123 films with critical temperatures of 94 K and critical current densities of 5.8×106 A/cm2 at 75.5 K have been deposited under standard deposition conditions using such an approach.
Multiple recombination pathways for sister chromatid exchange in Saccharomyces cerevisiae: role of RAD1 and the RAD52 epistasis group genes (2003)

Sister chromatid exchange (SCE) can occur by several recombination mechanisms, including those directly initiated by double-strand breaks (DSBs), such as gap repair and break-induced replication (BIR), and those initiated when DNA polymerases stall, such as template switching. To elucidate SCE recombination mechanisms, we determined whether spontaneous and DNA damage-associated SCE requires specific genes within the RAD52 and RAD3 epistasis groups in Saccharomyces cerevisiae strains containing two his3 fragments, his3-Delta5' and his3-Delta3'::HOcs. SCE frequencies were measured after cells were exposed to UV, X-rays, 4-nitroquinoline 1-oxide (4-NQO) and methyl methanesulfonate (MMS), or when an HO endonuclease-induced DSB was introduced at his3-Delta3'::HOcs. Our data indicate that genes involved in gap repair, such as RAD55, RAD57 and RAD54, are required for DNA damage-associated SCE but not for spontaneous SCE. RAD50 and RAD59, genes required for BIR, are required for X-ray-associated SCE but not for SCE stimulated by HO-induced DSBs. In comparison with wild type, rates of spontaneous SCE are 10-fold lower in rad51 rad1 but not in either rad51 rad50 or rad51 rad59 double mutants. We propose that gap repair mechanisms are important in DNA damage-associated recombination, whereas alternative pathways, including a template switch pathway, play a role in spontaneous SCE.
Low sludge carbohydrate content: a prerequisite for enhanced biological phosphate removal (1997)

The relationship between sludge carbohydrate (CH) content and phosphate (P) removal performance has been studied in two sequencing batch reactors (SBRs) exhibiting enhanced biological phosphorus removal (EBPR). Glucose and acetate were used as the main organic substrates for the two SBRs, respectively. The phosphorus removal performance was excellent when the sludge CH content ranged from 8 to 10% (CH/mixed liquor suspended solids), but it declined concomitantly as the sludge CH content increased beyond this range. The sludge CH content was found to be a reliable parameter representing its capacity for phosphorus removal. The change of the sludge CH content was mainly influenced by the characteristics of the substrates, as well as by the operation modes. The study, as a whole, suggests that the control of sludge CH content to low levels is a prerequisite for achieving enhanced phosphorus removal in EBPR process.
3D Map Creation using the Structured Light Technique for Obstacle Avoidance (2011)

Obstacle avoidance is an essential part of robotic navigation in which the robot, based on some global path planning strategy, has to reach a certain goal position. In robotic navigation the problem of obstacle avoidance refers to the determination of a local navigationstrategy. Here, the navigation strategy is based on the detection ofobstacles which is made depending on the local environment of the robot. This thesis presents the development and implementation of anovel obstacle avoidance system in which the detection of obstaclesis based on the use of computer vision implemented using the principle of structured light based depth map creation. This allows the detection of an obstacle of at least 20mm x 18mm at the projection distance of 675mm. The obstacle avoidance system consists of a robotic platform called Create from iRobot with a vision system, made up of acamera-projector pair, all controlled by an embedded computing unitcalled BeagleBoard. The BeagleBoard, based on inputs from the vision system, computes a depth map of the observed environment relativeto the robotic platform. This depth map is then used to determine the 3D coordinates of the observable environment which define the presence or absence of obstacles. An obstacle is defined taking into account the physical parameters of the entire system, which then governs the movements of the entire robotic platform. The system is testedon a number of real world obstacles and a variety of tests are carried to determine the system performance for varying distances, undervarying ambient light conditions and different obstacle surfaces.The deviations obtained with respect to the real world depths areless than 10mm for the depth range between 600 to 800mm.
Improved micro-flow regulator for drug delivery systems (2002)

The paper reports on the design, manufacturing, and experimental testing of a micromachined pressure compensating flow regulator. This device was designed to provide a constant liquid flow rate of 1 ml/hr within a pressure difference of 100 to 600 mbar. At pressures higher than 600 mbar the device is designed to block the flow, preventing an over-delivery of medicine. Structural and fluidic simulations were used to design the geometry of the device before manufacturing. After devices have been characterized experimental results demonstrate the credibility of the design, the accuracy of the flow rate and the long-term stability of the device. One application of this device is the replacement of the flow restrictor in an elastomeric infusion system, which will increase the accuracy and safety of the drug delivery system. This pressure compensating flow regulator is passive, hence it needs no external energy source. The device is relatively inexpensive to manufacture and is therefore, potentially a disposable unit in a microfluidic system. Finally, it is small and lightweight, ideal for portable applications.
In vivo production of non-glycosylated recombinant proteins in Nicotiana benthamiana plants by co-expression with Endo-β-N-acetylglucosaminidase H (Endo H) of Streptomyces plicatus (2017)

A plant transient expression system, with eukaryotic post-translational modification machinery, offers superior efficiency, scalability, safety, and lower cost over other expression systems. However, due to aberrant N-glycosylation, this expression system may not be a suitable expression platform for proteins not carrying N-linked glycans in the native hosts. Therefore, it is crucial to develop a strategy to produce target proteins in a non-glycosylated form while preserving their native sequence, conformation and biological activity. Previously, we developed a strategy for enzymatic deglycosylation of proteins in planta by co-expressing bacterial peptide-N-glycosidase F (PNGase F). Though PNGase F removes oligosaccharides from glycosylated proteins, in so doing it causes an amino acid change due to the deamidation of asparagine to aspartate in the N-X-S/T site. Endo-β-N-acetylglucosaminidase (EC3.2.1.96, Endo H), another deglycosylating enzyme, catalyzes cleavage between two N-Acetyl-D-glucosamine residues of the chitobiose core of N-linked glycans, leaving a single N-Acetyl-D-glucosamine residue without the concomitant deamidation of asparagine. In this study, a method for in vivo deglycosylation of recombinant proteins in plants by transient co-expression with bacterial Endo H is described for the first time. Endo H was fully active in vivo. and successfully cleaved N-linked glycans from glycoproteins were tested. In addition, unlike the glycosylated form, in vivo Endo H deglycosylated Pfs48/45 was recognized by conformational specific Pfs48/45 monoclonal antibody, in a manner similar to its PNGase F deglycosylated counterpart. Furthermore, the deglycosylated PA83 molecule produced by Endo H showed better stability than a PNGase F deglycosylated counterpart. Thus, an Endo H in vivo deglycosylation approach provides another opportunity to develop vaccine antigens, therapeutic proteins, antibodies, and industrial enzymes.
Overview of the epidemiology and the threat of Klebsiella pneumoniae carbapenemases (KPC) resistance (2012)

Klebsiella pneumoniae carbapenemases (KPCs) confer resistance to nearly all β-lactams. This broad-spectrum drug resistance mechanism has rapidly spread in the United States and is reportedly increasing elsewhere in the world. Thus, the emergence of KPC resistance is a major threat to global health. This article reviews the epidemiology and provides an overview of the dissemination of KPC-producing organisms.
Regulation of MMP-1 and MMP-2 production through CD147/extracellular matrix metalloproteinase inducer interactions. (2001)

Extracellular matrix metalloproteinase inducer (EMMPRIN; CD147) is a heavily glycosylated protein containing two immunoglobulin superfamily domains. It is enriched on the surface of tumor cells and stimulates the production of matrix metalloproteinases (MMPs) by adjacent stromal cells. Here we use CD147 transfectants and immobilized recombinant CD147-Fc fusion protein to show that CD147/FMMPRIN engages in a homophilic interaction, predominantly through the first immunoglobulin domain. Anti-CD147 antibody 8G6 and recombinant CD147-Fc fusion protein markedly inhibited not only homophilic interaction, but also the production of secreted MMP-2 by breast cancer cell line MDA-435 and the MMP-2-dependent invasion of MDA-435 cells through reconstituted basement-membrane Matrigel. Purified native CD147 induced the production of secreted MMP not only by dermal fibroblasts (MMP-1) but also by MDA-435 cells themselves (MMP-2), suggesting homophilic CD147-binding may occur in the context of both heterotypic and homotypic cell-cell interactions. Purified deglycosylated CD147 failed to induce MMP-1 or MMP-2, but instead antagonized the MMP-1-inducing activity of purified native CD147. Our results suggest that homophilic CD147 interactions may play a key role in MMP-2 production and tumor cell invasion, and that perturbation of this molecule may have potential therapeutic uses in the prevention of MMP-2 and MMP-1-dependent cancer metastasis.
Expression of pY397 FAK promotes the development of non-small cell lung cancer (2015)

Focal adhesion kinase (FAK) expression has been identified as associated with cancer development and metastasis. Autophosphorylation of FAK at tyrosine (Y) 397 (pY397) performs a critical role in tumor cell signaling. However, few studies have evaluated the expression of pY397 FAK in non-small cell lung cancer (NSCLC). In the present study, pY397 FAK expression in NSCLC was investigated using immunohistochemistry. pY397 FAK staining scores were compared between various groups of specimens and the associations between clinical and pathological characteristics were investigated. A Kaplan-Meier survival curve was used to determine the association between pY397 FAK expression and the prognosis of NSCLC patients. The results of the present study revealed that pY397 FAK expression was localized to the cytoplasm of lung cells, and that pY397 FAK was overexpressed in NSCLC tissues, as well as associated metastatic tissues, when compared with the corresponding non-tumor tissues. However, no significant difference was identified between the pY397 FAK expression in primary lesions and lymph node metastases. Furthermore, pY397 FAK staining scores were not found to be associated with the tumor size, gender, degree of differentiation, histotypes, presence of lymph node metastases or survival rate of NSCLC patients. These results indicate that pY397 FAK is involved with the development of NSCLC, but is not a prognostic marker for the disease.
Characterization of hemin antibacterial action on<i>Staphylococcus aureus</i> (1987)

The mechanism of inactivation of Staphylococcas aureus cells by hemin is described. Protection experiments by sulfhydryl reagents such as cysteine, mercaptoethanol, glutathione or thioglycolate in their reduced form prevent S. aureus bacteria from inactivation by hemin (1.5 × 10−5 M). The treatment of bacteria by hemin in the presence of one of those reagents (1 × 10−2 M) showed that the growth rate and viability of the culture remained unchaged. On the other hand sulfhydryl reagents did not prevent the binding of hemin to the bacteria. When cysteine or glutathione were introduced to a culture after exposure to hemin it could neither reverse the damage done to the cells nor shorten the time of the culture's recovery. Another type of protection was obtained by addition of serum albumin which prevented hemin molecules from binding to the bacterial envelopes. Furthermore, when albumin was introduced after the bacteria were treated by hemin it prevented further damage to the survivors and thus shortened the time required for recovery. None of the singlet oxygen quenchers or hydroxyl radical scavengers could protect the bacteria from hemin inactivation. The mechanism by which hemin affects S. aureus is assumed to be by oxidizing a major system within the cell.
Photosensitive poly(urethane acylsemicarbazide)s with azobenzene chromophores in the main chain (2004)

Abstract Poly(urethane acylsemicarbazide)s were synthesized with a two‐step process: (1) the in situ generation of diisocyanate through the thermal decomposition of an azobenzene‐containing precursor diazide and a reaction with ester/ether polyols to form an isocyanate‐terminated prepolymer and (2) chain extension in N,N ‐dimethylacetamide with aliphatic or aromatic dihydrazides. Films cast from N,N ‐dimethylacetamide solutions were characterized with attenuated total reflection/Fourier transform infrared spectroscopy, and the thermal properties were studied with thermogravimetric analysis and differential scanning calorimetry. The effects of the hard‐segment content and chain extenders on the static and dynamic mechanical properties were investigated. The photoresponsive behavior of the polymers and the effects of variations in the chromophore concentration and chemical composition on the kinetics of photoisomerization were investigated with ultraviolet–visible spectroscopy, which revealed that the rates were independent of the chromophore concentration. The photomechanical behavior, assessed with creep‐recovery measurements, proved that the systems underwent photochemical isomerization upon irradiation with ultraviolet light. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 444–454, 2004