gebhart/patrepeval huggingface dataset:
Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O -phosphoseryl-tRNA Sec kinase (2008)

Selenocysteine (Sec) biosynthesis in archaea and eukaryotes requires three steps: serylation of tRNA(Sec) by seryl-tRNA synthetase (SerRS), phosphorylation of Ser-tRNA(Sec) by O-phosphoseryl-tRNA(Sec) kinase (PSTK), and conversion of O-phosphoseryl-tRNA(Sec) (Sep-tRNA(Sec)) by Sep-tRNA:Sec-tRNA synthase (SepSecS) to Sec-tRNA(Sec). Although SerRS recognizes both tRNA(Sec) and tRNA(Ser) species, PSTK must discriminate Ser-tRNA(Sec) from Ser-tRNA(Ser). Based on a comparison of the sequences and secondary structures of archaeal tRNA(Sec) and tRNA(Ser), we introduced mutations into Methanococcus maripaludis tRNA(Sec) to investigate how Methanocaldococcus jannaschii PSTK distinguishes tRNA(Sec) from tRNA(Ser). Unlike eukaryotic PSTK, the archaeal enzyme was found to recognize the acceptor stem rather than the length and secondary structure of the D-stem. While the D-arm and T-loop provide minor identity elements, the acceptor stem base pairs G2-C71 and C3-G70 in tRNA(Sec) were crucial for discrimination from tRNA(Ser). Furthermore, the A5-U68 base pair in tRNA(Ser) has some antideterminant properties for PSTK. Transplantation of these identity elements into the tRNA(Ser)(UGA) scaffold resulted in phosphorylation of the chimeric Ser-tRNA. The chimera was able to stimulate the ATPase activity of PSTK albeit at a lower level than tRNA(Sec), whereas tRNA(Ser) did not. Additionally, the seryl moiety of Ser-tRNA(Sec) is not required for enzyme recognition, as PSTK efficiently phosphorylated Thr-tRNA(Sec).
Smooth, All-Solid, Low-Hysteresis, Omniphobic Surfaces with Enhanced Mechanical Durability (2018)

The utility of omniphobic surfaces stems from their ability to repel a multitude of liquids, possessing a broad range of surface tensions and polarities, by causing them to bead up and either roll or slide off. These surfaces may be self-cleaning, corrosion-resistant, heat-transfer enhancing, stain-resistant or resistant to mineral- or biofouling. The majority of reported omniphobic surfaces use texture, lubricants, and/or grafted monolayers to engender these repellent properties. Unfortunately, these approaches often produce surfaces with deficiencies in long-term stability, durability, scalability, or applicability to a wide range of substrates. To overcome these limitations, we have fabricated an all-solid, substrate-independent, smooth, omniphobic coating composed of a fluorinated polyurethane and fluorodecyl polyhedral oligomeric silsesquioxane. Liquids of varying surface tension, including water, hexadecane, ethanol, and silicone oil, exhibit low-contact-angle hysteresis (<15°) on these surfaces, allowing liquid droplets to slide off, leaving no residue. Moreover, we demonstrate that these robust surfaces retained their repellent properties more effectively than textured or lubricated omniphobic surfaces after being subjected to mechanical abrasion.
Cerium-based metal organic frameworks with UiO-66 architecture: synthesis, properties and redox catalytic activity (2015)

A series of nine Ce(iv)-based metal organic frameworks with the UiO-66 structure containing linker molecules of different sizes and functionalities were obtained under mild synthesis conditions and short reaction times. Thermal and chemical stabilities were determined and a Ce-UiO-66-BDC/TEMPO system was successfully employed for the aerobic oxidation of benzyl alcohol.
Surfactant enhances adenovirus-mediated gene expression in rabbit lungs. (1996)

The efficiency and localization of gene transfer for gene therapy in the lung will depend on vector selection and technique used to deliver the vector. We hypothesized that surfactant might facilitate gene transfer because of its biophysical properties that enhance spreading of saline suspensions in the airways. We used a replication defective adenovirus directing the expression of the luciferase reporter gene at different virus doses and surfactant concentrations and instilled 4 ml suspensions into the lungs of adult rabbits. Transgene expression measured as luciferase-dependent light units in tissue homogenates 3 days after instillation had similar lobar distributions for surfactant-viral suspensions and for phosphate-buffered saline viral suspensions. However, total light units were four- to six-fold increased for viral doses of < 10(10) plaque forming units in 10 mg/ml or 25 mg/ml surfactant suspensions. The percentage of total transgene expression in the tracheacarina-bronchus decreased from over 50% to about 10% for virus instilled with surfactant concentrations of 2 mg/ml or greater, indicating preferential expression in airway epithelial cells located more distally in the lung. Surfactant did not enhance persistence of transgene expression 7 or 14 days after instillation. Surfactant facilitates adenovirally mediated gene transfer in the peripheral lung and enhances transgene expression.
Nucleation and crystallization process of silicon using the Stillinger-Weber potential (2005)

We study the homogeneous nucleation process in Stillinger-Weber silicon in the canonical ensemble. A clear first-order transition from the liquid to crystal phase is observed thermodynamically with kinetic and structural evidence of the transformation. At $0.75{T}_{m}$, the critical cluster size is about 175 atoms. The lifetime distribution of clusters as a function of the maximum size they reach follows an inverse Gaussian distribution as was predicted recently from the classical theory of nucleation (CNT). However, while there is a qualitative agreement with the CNT, the free-energy curve obtained from the simulations differs significantly from the theoretical predictions, suggesting that the low-density liquid phase found recently could play a role at the interface between the crystallite and the surrounding liquid during the nucleation process.
Mechanistic Aspects of Atom Transfer Radical Polymerization (1998)

Typical conditions and experimental results of Atom Transfer Radical Polymerization (ATRP) of styrene, (meth)acrylates, acrylonitrile and other monomers are reviewed which include polymerization rates, evolution of molecular weights and polydispersities with conversion. The role of all major componenents of ATRP is discussed which comprises the structure of various alkyl halides, metals, ligands, solvents, additives as well as reaction times and temperatures. Enhancement of the initiation efficiency by some special procedures such as slow addition of initiator or catalyst is described. Origins and contributions of side reactions such as bimolecular termination, electron transfer and β-H elimination are discussed.
Atomic-scale origins of bias-temperature instabilities in SiC–SiO2 structures (2011)

We find that atomic-scale mechanisms for bias-temperature instabilities (BTIs) in SiC/SiO2 structures can differ significantly from those in Si/SiO2 structures. The measured effective-activation energies for BTI in 4H-SiC metal-oxide-semiconductor capacitors, 0.23±0.02 eV for p-type and 0.12±0.02 eV for n-type, are essentially identical to the respective dopant ionization energies, which are much larger than in Si. This suggests a key role for carrier release from deep dopants for BTI in SiC. In addition, asymmetric degradation is observed under switched-bias stress in p-type and n-type SiC, as a result of the reconfiguration of O vacancies in SiO2 layer after hole capture.
PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis (2011)

The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.
Accumulation of cyclic adenosine monophosphate in incubated slices of brain tissue. 2. Effects of depolarizing agents, membrane stabilizers, phosphodiesterase inhibitors, and adenosine analogs (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAccumulation of cyclic adenosine monophosphate in incubated slices of brain tissue. 2. Effects of depolarizing agents, membrane stabilizers, phosphodiesterase inhibitors, and adenosine analogsMinta Huang, Hirotoshi Shimizu, and John W. DalyCite this: J. Med. Chem. 1972, 15, 5, 462–466Publication Date (Print):May 1, 1972Publication History Published online1 May 2002Published inissue 1 May 1972https://pubs.acs.org/doi/10.1021/jm00275a005https://doi.org/10.1021/jm00275a005research-articleACS PublicationsRequest reuse permissionsArticle Views114Altmetric-Citations86LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Lysostaphin is effective in treating methicillin-resistant Staphylococcus aureus endophthalmitis in the rabbit (2001)

Lysostaphin is effective in treating experimental endophthalmitis mediated by MRSA.
The Role of Nanoscale Seed Layers on the Enhanced Performance of Niobium doped TiO2 Thin Films on Glass (2016)

Transparent conducting oxide (TCO) coatings with decreased cost and greater process or performance versatility are needed for a variety of optoelectronic applications. Among potential new TCO candidates, doped titanium dioxide is receiving particular interest. In this study, niobium-doped titania bilayer structures consisting of a nanoscale seed layer (deposited by atomic layer deposition or RF magnetron sputtering) followed by a thick bulk-like layer were grown directly on glass in order to examine the effects of the seed layer processing on the subsequent crystallization and electrical properties of these heterostructures. Observations from Raman spectroscopy suggest that higher oxygen content in the seed layer suppresses the formation of detrimental titania polymorph phases, found in films produced by annealing directly after synthesis without any exposure to oxygen. Furthermore, our results indicate that the generation of excellent Nb:TiO2 conductors on glass (without breaking vacuum) only occurs within a narrow processing range and that the sequential deposition of oxygen-poor layers on oxygen-rich layers is a critical step towards achieving films with low resistivity.
A neural network methodology for process fault diagnosis (1989)

Abstract The ability of knowledge‐based expert systems to facilitate the automation of difficult problems in process engineering that require symbolic reasoning and an efficient manipulation of diverse knowledge has generated considerable interest recently. Rapid deployment of these systems, however, has been difficult because of the tedious nature of knowledge acquisition, the inability of the system to learn or dynamically improve its performance, and the unpredictability of the system outside its domain of expertise. This paper proposes a neural‐network‐based methodology for providing a potential solution to the preceding problems in the area of process fault diagnosis. The potential of this approach is demonstrated with the aid of an oil refinery case study of the fluidized catalytic cracking process. The neural‐network‐based system successfully diagnoses the faults it is trained upon. It is able to generalize its knowledge to successfully diagnose novel fault combinations it is not explicitly trained upon. Furthermore, the network can also handle incomplete and uncertain data. In addition, this approach is compared with the knowledge‐based approach.
Multiple activation pathways of benzene leading to products with varying genotoxic characteristics. (1989)

Benzene and 13 potential metabolites were investigated for genotoxicity in Salmonella typhimurium and V79 Chinese hamster cells. In the presence of NADPH-fortified hepatic postmitochondrial fraction (S9 mix), benzene reverted his- S. typhimurium strains. The effect was strongest in strain TA1535. Among the potential metabolites, only the trans-1,2-dihydrodiol, in the presence of S9 mix, and the diol epoxides, in the presence and absence of S9 mix, proved mutagenic in this strain. The anti-diol epoxide was more potent than the syn-diastereomer. Both enantiomers of the anti-diastereomer showed similar activities. S9 mix did not appreciably affect the mutagenicity of the anti-diol epoxide. However, detoxification was observed when purified rat liver dihydrodiol dehydrogenase (EC 1.3.1.20) was used at concentrations comparable to that present in the liver. The (1S)-anti-diol epoxide was a much better substrate than the (1R)-enantiomer, as was true also for (1S)-versus (1R)-trans-1,2-dihydrodiol. The anti-diol epoxide reverted all six strains of S. typhimurium used and induced all four genotoxic effects studied in V79 cells (sister chromatid exchange greater than acquisition of 6-thioguanine resistance, acquisition of ouabain resistance, micronuclei). However, other potential benzene metabolites showed genotoxic effects in V79 cells, as well: sister chromatid exchange was induced by the syn-diol epoxide, 1,2,4-trihydroxybenzene, hydroquinone, catechol, and 1,2,3-trihydroxybenzene. Elevated frequencies of micronucleated cells were observed after treatment with hydroquinone, 1,2,4-trihydroxybenzene, catechol, phenol, 1,2,3-trihydroxybenzene, and quinone. Mutations to 6-thioguanine resistance were induced by quinone, hydroquinone, 1,2,4-trihydroxybenzene, catechol, and the trans-1,2-dihydrodiol.(ABSTRACT TRUNCATED AT 250 WORDS)
Inhibitory Control of LTP and LTD: Stability of Synapse Strength (1999)

Although much is known about the induction of synaptic plasticity, the persistence of memories suggests the importance of understanding factors that maintain synaptic strength and prevent unwanted synaptic changes. Here we present evidence that recurrent inhibitory connections in the CA1 region of hippocampus may contribute to this task by modulating the relative ability to induce long-term potentiation and depression (LTP and LTD). Bath application of the gamma-aminobutyric acid (GABA) type A agonist muscimol to hippocampal slices increased the range of frequencies that produce LTD, whereas in the presence of the GABA type A antagonist picrotoxin LTD was induced only at very low stimulation frequencies (0.25-0.5 Hz). Because one source of GABAergic input to CA1 pyramidal cells is via recurrent inhibition, we tested the prediction that elevated postsynaptic spike activity would increase feedback GABA inhibition and favor the induction of LTD. By using an induction stimulation of 8 Hz, which alone produced no net change in synaptic strength, we found that stimulation presented during antidromic activation of pyramidal cell spikes induced LTD. This effect was blocked by picrotoxin. The influence of recurrent inhibition on LTP and LTD displays properties that may decrease the potential for self-reinforcing, runaway changes in synapse strength. A mechanism of this sort may help maintain patterns of synaptic strengths despite the ongoing opportunities for plasticity produced by synapse activation.
Multi-hypothesis, volumetric reconstruction of 3-D objects from multiple calibrated camera views (1999)

In this paper we present a volumetric method for the 3-D reconstruction of real world objects from multiple calibrated camera views. The representation of the objects is fully volume-based and no explicit surface description is needed. The approach is based on multi-hypothesis tests of the voxel model back-projected into the image planes. All camera views are incorporated in the reconstruction process simultaneously and no explicit data fusion is needed. In a first step each voxel of the viewing volume is filled with several color hypotheses originating from different camera views. This leads to an overcomplete representation of the 3-D object and each voxel typically contains multiple hypotheses. In a second step only those hypotheses remain in the voxels which are consistent with all camera views where the voxel is visible. Voxels without a valid hypothesis are considered to be transparent. The methodology of our approach combines the advantages of silhouette-based and image feature-based methods. Experimental results on real and synthetic image data show the excellent visual quality of the voxel-based 3-D reconstruction.
Mitochondrial DNA variation in Koryaks and Itel'men: Population replacement in the Okhotsk Sea-Bering Sea region during the neolithic (1999)

In this study, we analyzed the mitochondrial DNA (mtDNA) variation in 202 individuals representing one Itel'men and three Koryak populations from different parts of the Kamchatka peninsula. All mtDNAs were subjected to high resolution restriction (RFLP) analysis and control region (CR) sequencing, and the resulting data were combined with those available for other Siberian and east Asian populations and subjected to statistical and phylogenetic analysis. Together, the Koryaks and Itel'men were found to have mtDNAs belonging to three (A, C, and D) of the four major haplotype groups (haplogroups) observed in Siberian and Native American populations (A-D). In addition, they exhibited mtDNAs belonging to haplogroups G, Y, and Z, which were formerly called "Other" mtDNAs. While Kamchatka harbored the highest frequencies of haplogroup G mtDNAs, which were widely distributed in eastern Siberian and adjacent east Asian populations, the distribution of haplogroup Y was restricted within a relatively small area and pointed to the lower Amur River-Sakhalin Island region as its place of origin. In contrast, the pattern of distribution and the origin of haplogroup Z mtDNAs remained unclear. Furthermore, phylogenetic and statistical analyses showed that Koryaks and Itel'men had stronger genetic affinities with eastern Siberian/east Asian populations than to those of the north Pacific Rim. These results were consistent with colonization events associated with the relatively recent immigration to Kamchatka of new tribes from the Siberian mainland region, although remnants of ancient Beringian populations were still evident in the Koryak and Itel'men gene pools.
Human chorionic gonadotropin in human neoplastic cells. (1976)

Peroxidase-labeled antibody against the beta chain of human chorionic gonadotropin was used to demonstrate that 25 human malignant tumors contained this antigen. The antigen was localized both in the cytoplasm and on the surface of the malignant cells. Human chorionic gonadotropin may be responsible for both selective maternal immuno-suppression by fetal tissue and host immunosuppression by tumors.
Phase III Trial Comparing Doxorubicin Plus Cyclophosphamide With Docetaxel Plus Cyclophosphamide As Adjuvant Therapy for Operable Breast Cancer (2006)

At 5 years, TC was associated with a superior DFS and a different toxicity profile compared with AC.
High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography (2012)

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.
Overview of Recombinant Human Hyaluronidase-facilitated Subcutaneous Infusion of IgG in Primary Immunodeficiencies (2014)

Subcutaneous administration of immunoglobulin (IGSC) in a home setting, compared with intravenous administration, can improve patient quality of life. During IGSC, however, the subcutaneous extracellular matrix inhibits flow and fluid entry into the vascular compartment, which limits the amount of drug delivered. Recombinant human hyaluronidase (rHuPH20) increases the absorption and dispersion of infused fluids and drugs. Results from a Phase III, prospective, open-label, noncontrolled study of patients with primary immunodeficiencies indicated that IGSC infusion, facilitated by rHuPH20, is well tolerated and delivers infusion volumes at treatment intervals and rates equivalent to intravenous administration. This drug evaluation provides an overview of rHuPH20 and results of clinical studies of IGSC infusion facilitated by rHuPH20 in patients with primary immunodeficiencies.
Engineering Plant Shikimate Pathway for Production of Tocotrienol and Improving Herbicide Resistance (2004)

Tocochromanols (tocopherols and tocotrienols), collectively known as vitamin E, are essential antioxidant components of both human and animal diets. Because of their potential health benefits, there is a considerable interest in plants with increased or customized vitamin E content. Here, we have explored a new strategy to reach this goal. In plants, phenylalanine is the precursor of a myriad of secondary compounds termed phenylpropanoids. In contrast, much less carbon is incorporated into tyrosine that provides p-hydroxyphenylpyruvate and homogentisate, the aromatic precursors of vitamin E. Therefore, we intended to increase the flux of these two compounds by deriving their synthesis directly at the level of prephenate. This was achieved by the expression of the yeast (Saccharomyces cerevisiae) prephenate dehydrogenase gene in tobacco (Nicotiana tabacum) plants that already overexpress the Arabidopsis p-hydroxyphenylpyruvate dioxygenase coding sequence. A massive accumulation of tocotrienols was observed in leaves. These molecules, which were undetectable in wild-type leaves, became the major forms of vitamin E in the leaves of the transgenic lines. An increased resistance of the transgenic plants toward the herbicidal p-hydroxyphenylpyruvate dioxygenase inhibitor diketonitril was also observed. This work demonstrates that the synthesis of p-hydroxyphenylpyruvate is a limiting step for the accumulation of vitamin E in plants.