gebhart/patrepeval huggingface dataset:
Solid-Phase Nested Deletion: A New Subcloning-less Method for Generating Nested Deletions (1995)

We have developed a new subcloning-less method for generating nested deletions which we have termed Solid-Phase Nested Deletion. The basic procedure for this method is as follows. The target DNA fragment is cloned in the multiple cloning site of a cloning vector, pUC or its derivatives, and amplified by PCR using a set of primers, one of which is 5'-biotinylated. The amplified DNA is partially digested by a restriction enzyme with a 4-base recognition sequence. The digested DNA is ligated with a synthetic adapter DNA. Monodiverse beads coupled with streptavidin (Dynabeads M-280 streptavidin) are added to the mixture and the biotinylated DNA fragments are separated by applying magnetic field. The unidirectionally deleted DNA fragments are recovered by PCR from the magnetic beads, and size-fractionated by agarose gel electrophoresis. The DNA fragments are amplified by PCR and used for sequencing. We demonstrate the potential of this method using a 4878-bp EcoRI fragment of lambda phage DNA.
Polymerase chain reaction–single‐strand conformation polymorphism analysis for the VHL gene in chemically induced kidney tumors of rats using intron‐derived primers (1997)

Von Hippel-Lindau (VHL) gene mutations occur throughout three exons including the exon-intron boundaries in human VHL disease–associated and sporadic renal cell carcinomas. To explore the possible role of the VHL gene in chemically induced rat kidney tumors originating from various cell types, more than 150 bp of Fischer 344 and Noble rat VHL intron sequences flanking the three exons was determined by dideoxy sequencing. Five primer sets were selected for polymerase chain reaction amplification of the coding regions of rat VHL exons 1–3 and the exon-intron boundaries. Tissues from 10 renal eosinophilic epithelial tumors induced by N-nitrosoethyl(2-hydroxyethyl)amine, 10 nephroblastomas induced by N-nitroso-N-ethylurea, and seven renal mesenchymal tumors induced by N-nitrosomethyl(methoxymethyl)amine were examined for VHL mutations by polymerase chain reaction–single-strand conformation polymorphism analysis. No mutation was detected in any tumor type, indicating that VHL mutations are not involved in the pathogenesis of rat kidney tumors arising from the distal region of the renal tubules, the metanephric blastema, or stromal tissues of the cortex. Mol. Carcinog. 19:230–235, 1997. © 1997 Wiley-Liss, Inc. This article is a US Government work and, as such, is the public domain in the United States of America.
On‐line coupled HPLC‐HRGC: A powerful tool for vapor phase FTIR analysis (LC‐GC‐FTIR) (1991)

Abstract The design of an on‐line LC‐GC‐FTIR system using an on‐column interface and partially concurrent solvent evaporation with early vapor exit is described. The integration of LC‐GC coupling into vapor phase FTIR analysis enables problems of sensitivity encountered with HRGC‐FTIR detection to be over‐come. The applicability of the method is demonstrated by the identification and determination of citropten and bergapten in bergamot oil.
Circular polarization from a ZOR patch-coupled rectangular ring-mushroom antenna (2011)

This paper presents how to generate a circular polarization in a new microstrip Zeroth Order Resonance(ZOR) metamaterial antenna. The ZOR antenna initially has a linear polarization from a coaxial fed central patch whose edges are coupled to a rectangular ring mushroom. It is a low-profile structure with the -1st resonance as the Left-Handed(LH) region, the ZOR, and the positive resonance as the Right-Handed(RH) region. This antenna is provided with an inclined slot in the ground to form a circular polarization at the LH region, while keeping the frequency response of the antenna's return loss. So the axial ratio over the LH frequency of interest is given to show the circular polarization together with the return loss and radiation pattern to present the design result as is aimed.
OS fingerprinting: New techniques and a study of information gain and obfuscation (2017)

Passive operating system fingerprinting reveals valuable information to the defenders of heterogeneous private networks; at the same time, attackers can use fingerprinting to reconnoiter networks, so defenders need obfuscation techniques to foil them. We present an effective approach for passive fingerprinting that uses data features from TLS as well as the TCP/IP and HTTP protocols in a multi-session model, which is applicable whenever several sessions can be observed within a time window. In experiments on a real-world private network, our approach identified operating system major and minor versions with accuracies of 99.4% and 97.5%, respectively, and provided significant information gain. We also show that obfuscation strategies can often be defeated due to the difficulty of manipulating data features from all protocols, especially TLS, by studying how obfuscation affects our fingerprinting system. Because devices running unpatched operating systems on private networks create significant vulnerabilities, their detection is critical; our approach achieved over 98% accuracy at this important goal.
Synthesis of Fe‐Doped ZnO Nanorods by Rapid Mixing Hydrothermal Method and Its Application for High Performance UV Photodetector (2014)

We have successfully synthesized Fe‐doped ZnO nanorods by a new and simple method in which the adopted approach is by using ammonia as a continuous source of OH − for hydrolysis instead of hexamethylenetetramine (HMT). The energy dispersive X‐ray (EDX) spectra revealed that the Fe peaks were presented in the grown Fe‐doped ZnO nanorods samples and the X‐ray photoelectron spectroscopy (XPS) results suggested that Fe 3+ is incorporated into the ZnO lattice. Structural characterization indicated that the Fe‐doped ZnO nanorods grow along the c ‐axis with a hexagonal wurtzite structure and have single crystalline nature without any secondary phases or clusters of FeO or Fe 3 O 4 observed in the samples. The Fe‐doped ZnO nanorods showed room temperature (300 K) ferromagnetic magnetization versus field (M‐H) hysteresis and the magnetization increases from 2.5 μ emu to 9.1 μ emu for Zn 0.99 Fe 0.01 O and Zn 0.95 Fe 0.05 O, respectively. Moreover, the fabricated Au/Fe‐doped ZnO Schottky diode based UV photodetector achieved 2.33 A/W of responsivity and 5 s of time response. Compared to other Au/ZnO nanorods Schottky devices, the presented responsivity is an improvement by a factor of 3.9.
Hardness reinforcement by surface engineering of soda lime silicate glass under thermal poling (2016)

Surface engineering of soda-lime silicate glass has been performed by thermal poling and the correlation between the local structure and the mechanical properties of the field-induced modified surface has been investigated. Glow Discharge Optical Emission Spectroscopy (GD-OES) demonstrates the structuring under a high electric field of a multi-layered material under the surface due to the migration of cations species. The nature of the atmosphere directly impacts on the charge compensation mechanisms involved and on the resulting mechanical properties.
Small‐Diameter Implants: Indications and Contraindications (2000)

The choice of implant diameter depends on the type of edentulousness, the volume of the residual bone, the amount of space available for the prosthetic reconstruction, the emergence profile, and the type of occlusion. Small-diameter implants are indicated in specific clinical situations, for example, where there is reduced interradicular bone or a thin alveolar crest, and for the replacement of teeth with small cervical diameter. Before using a small-diameter implant, the biomechanical risk factors must be carefully analyzed. Preliminary reports of this type of implant show good short- and medium-term results.
Nucleophilic Addition to Acetylenes in Superbasic Catalytic Systems. Part 8. Fluoride Cesium Containing Systems, Efficient Catalysts for Alkanols Vinylation. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Antimicrobial Efficacy Assessment and Rheological Investigation of Two Different Hand Sanitizers Compared with the Standard Reference WHO Formulation 1 (2023)

(1) Background: recently, the use of alcohol-based hand sanitizers (ABHSs) has become very frequent, and an evaluation of the stability and effectiveness of their formulations is a critical topic which should be carefully considered. (2) Methods: starting from the characterization of the hand sanitizers object of the study, our interest was focused on their rheological behavior in order to confirm their intrinsic features, but also the stability of each formulation in different conditions of shear and temperature; the second aspect concerns the antimicrobial assessment through a panel of in vitro and in vivo experimental trials. (3) Results: rheological investigation confirmed good stability for the two hand sanitizers in gel formula with respect to the reference in liquid formula; the antimicrobial activity evaluation showed good efficacy of each formulation both in vitro and in vivo. (4) Conclusions: altogether, our overview presents a valid quality control assessment to ensure the stability and efficacy of an alcohol-based hand sanitizer.
Positive selection of activated T cells of the T8 (CD8) sub‐type by immunomagnetic separation (1986)

By conjugating a monoclonal IgM antibody of CD8-specificity to magnetite-containing polymer particles, we have developed a rapid and simple one-step procedure for positive selection of T8 cells. The method ensured good yield and viability of pure T8 cells. The positively selected T8-fraction from MLC activated T cells retained their cytolytic capacity and gave a moderate proliferative response. Most of the proliferative response occurred in the negatively selected T4 population which showed only a marginal cytotoxic activity against PHA blasts as target cells. Transferrin receptor expression, as measured in a direct radiobinding assay, could also be demonstrated both among pure T4 and T8 cells upon MLC-activation.
A Systems Biology Approach to the Evolution of Codon Use Pattern (2011)

Abstract The genetic code is redundant as amino acids are encoded by synonymous codons that are unequally used.This codon usage bias (CUB) affects gene expression and cellular functions yet the underlying mechanisms have not been elucidated. We used a sequence-specific, stoichiometric model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655 to test the effect of randomly changed CUB on growth maximization under various environmental conditions. Amongst CUB mutant strains, we identified reduced growth phenotypes, which were caused by tRNA supply shortage. We propose, supported by computations and bibliomic data, that expansion of tRNA gene content or tRNA reading is a mechanism to respond to changes in CUB. Our systems biology modelling framework suggests that in order to maximize growth and to adapt to new environmental niches, CUB and tRNA content must co-evolve and provides further evidence for the mutation-selection-drift balance theory of CUB.
On the relation between double clausal negation and negative concord (2014)

Negative concord and double clausal negation are separate phenomena, which show some striking similarities, the main similarity being the fact that negation is formally expressed more than once, but semantically only once. These similarities have led scholars to hypothesize on whether and how these two are related. In this chapter some issues in the diachrony of both processes are discussed. On the basis of a survey of 103 non-European languages it is concluded that NC cannot be considered to be a necessary condition for DN nor for preverbal negation, thus refuting claims that have been proposed in the literature. The peculiar constellation found in French, in which a new negator grew out of NC concord, was not found in any other language of the sample, not even Ewe and Karok, the two other languages that have both NC and DN. It is further suggested that DN may be more frequent than NC and it is argued, against other claims in the literature, that the strategy of expressing clausal negation with only negative pronouns or adverbs is not only typical for Europe but also for the Americas and that it is also found in verb-initial languages.
Modeling the Similarity and Divergence of Dopamine D2-like Receptors and Identification of Validated Ligand−Receptor Complexes (2005)

Focusing on the similarity and divergence of GPCR subtypes and their ligand interactions, we generated dopamine D2, D3, and D4 receptor models based on the rhodopsin crystal structure and refined these with an extensive MM/MD protocol. After validation by diagnostic experimental data, subtype-specific relative positions of TM1, 2, 6, and 7 and bending angles of TM7 were found. To sample the conformational space of the complex, we performed simulated-annealing runs of the receptor protein with the sub-nanomolar antagonist spiperone. Docking a representative set of ligands, we were able to identify one superior model for each subtype when excellent correlations between predicted energies of binding and experimental affinities (r2 = 0.72 for D2, 0.91 for D3 and 0.77 for D4) could be observed. Further analysis revealed general ligand interactions with ASP3.32 and aromatic residues in TM6/7 and individual key interactions with TM1 and TM2 residues of the D3 and D4 receptor models, respectively.
High-performance thin-layer chromatography fingerprinting, total phenolic and total flavonoid contents and anti-platelet-aggregation activities of Prosopis farcta extracts (2020)

Cardiovascular diseases are a leading cause of worldwide death and excessive platelet is closely related with their pathogenesis. Different plants and natural compounds have demonstrated anti-platelet effects. The aim of this study was to report the high-performance thin-layer chromatography (HPTLC) fingerprinting and anti-platelet-aggregation activities of different leaf extracts (n-hexane, chloroform, ethyl acetate, methanol and aqueous) of Prosopis farcta (Syrian mesquite) plant. The results showed a 100% inhibition of aggregation activity after plasmatic adenosine diphosphate (ADP) aggregation activation of ethyl acetate, ethanolic, methanolic and aqueous extracts, at 60 mg/mL concentration. The IC50 ADP value of these extracts ranged between 4.07 and 11.39 mg/mL. Moreover, these extracts reported the highest amounts of phenolic and flavonoid contents. In conclusion, phytochemicals present in P. farcta leaves have anti-platelet-aggregation activities. Future studies are needed to identify the compounds with anti-platelet potential present in P. farcta.
Mechanism of Formation of Platinum(0) Complexes Containing Silicon-Vinyl Ligands (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism of Formation of Platinum(0) Complexes Containing Silicon-Vinyl LigandsLarry N. Lewis, Robert E. Colborn, Hans Grade, Garold L. Bryant Jr., Chris A. Sumpter, and Robert A. ScottCite this: Organometallics 1995, 14, 5, 2202–2213Publication Date (Print):May 1, 1995Publication History Published online1 May 2002Published inissue 1 May 1995https://pubs.acs.org/doi/10.1021/om00005a021https://doi.org/10.1021/om00005a021research-articleACS PublicationsRequest reuse permissionsArticle Views982Altmetric-Citations54LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
The effects of a concurrent task on walking in persons with transfemoral amputation compared to persons without limb loss (2015)

The addition of a concurrent task did not differentially affect walking outcomes in people with and without transfemoral amputation. However, compared to people without limb loss, people with transfemoral amputation adopted a conservative walking strategy. This strategy may reduce the need to concentrate on walking but also contributed to notable gait deviations.
Enhanced efficacy and limited systemic cytokine exposure with membrane-anchored interleukin-12 T-cell therapy in murine tumor models (2020)

Expression of aIL-12 by tumor-targeting therapeutic T cells demonstrated low systemic exposure and improved efficacy. This treatment strategy may have broad applications to cellular therapy with tumor-infiltrating lymphocytes, chimeric antigen receptor T cells, and TCR T cells.
Discovery of PDK1 Kinase Inhibitors with a Novel Mechanism of Action by Ultrahigh Throughput Screening (2010)

The phosphoinositide 3-kinase/AKT signaling pathway plays a key role in cancer cell growth, survival, and angiogenesis. Phosphoinositide-dependent protein kinase-1 (PDK1) acts at a focal point in this pathway immediately downstream of phosphoinositide 3-kinase and PTEN, where it phosphorylates numerous AGC kinases. The PDK1 kinase domain has at least three ligand-binding sites: the ATP-binding pocket, the peptide substrate-binding site, and a groove in the N-terminal lobe that binds the C-terminal hydrophobic motif of its kinase substrates. Based on the unique PDK1 substrate recognition system, ultrahigh throughput TR-FRET and Alphascreen screening assays were developed using a biotinylated version of the PDK1-tide substrate containing the activation loop of AKT fused to a pseudo-activated hydrophobic motif peptide. Using full-length PDK1, K(m) values were determined as 5.6 mum for ATP and 40 nm for the fusion peptide, revealing 50-fold higher affinity compared with the classical AKT(Thr-308)-tide. Kinetic and biophysical studies confirmed the PDK1 catalytic mechanism as a rapid equilibrium random bireactant reaction. Following an ultrahigh throughput screen of a large library, 2,000 compounds were selected from the reconfirmed hits by computational analysis with a focus on novel scaffolds. ATP-competitive hits were deconvoluted by dose-response studies at 1x and 10x K(m) concentrations of ATP, and specificity of binding was assessed in thermal shift assay. Inhibition studies using fusion PDK1-tide1 substrate versus AKT(Thr-308)-tide and kinase selectivity profiling revealed a novel selective alkaloid scaffold that evidently binds to the PDK1-interacting fragment pocket. Molecular modeling suggests a structural paradigm for the design of inhibitory versus activating allosteric ligands of PDK1.
Performance enhancement of iterative learning control system using disturbance observer (2009)

Iterative learning control (ILC) has been widely used in industrial applications. However, there are two critical assumptions that limit the use of ILC: a) no non-repetitive disturbance is present; and b) the trajectory needs to be the same every iteration. This paper proposes a control scheme based on the combination of ILC and disturbance observer (DOB) to relax these assumptions. First, the use of DOB attenuates the effects of non-repetitive disturbance on ILC systems. Second, the proposed control scheme can decouple tracking error into two parts: tracking error due to disturbances and tracking error due to a trajectory. The decoupled tracking error then is utilized to properly initialize the ILC for a new trajectory so as to speed up the convergence rate. Simulation results and experimental results of a prototype wafer scanner system demonstrate the effectiveness of the proposed control scheme.
Sulfuric Acid Decomposition for the Sulfur-Based Thermochemical Cycles (2012)

In this work, we describe a novel design for a H2SO4 decomposer. The decomposition of H2SO4 to produce SO2 is a common processing operation in the sulfur-based thermochemical cycles for hydrogen production where acid decomposition takes place at 850°C in the presence of a catalyst. The combination of a high temperature and sulfuric acid creates a very corrosive environment that presents significant design challenges. The new decomposer design is based on a bayonet-type heat exchanger tube with the annular space packed with a catalyst. The unit is constructed of silicon carbide and other highly corrosion-resistant materials. The new design integrates acid boiling, superheating, decomposition, and heat recuperation into a single process and eliminates problems of corrosion and failure of high-temperature seals encountered in previous testing using metallic construction materials. The unit was tested by varying the acid feed rate and decomposition temperature and pressure.
<title>Spyrobenzopyran-doped core PMMA fibers</title> (1999)

Cylindrical PMMA filters with core regions doped with spirobenzopyran molecules have been fabricated. Spirobenzopyran is a photochromic molecule with two forms: spiropyran and merocyanine. In the fibers, one state could be reverted to the other either by a photo-initiated reaction or by thermal excitation. The fluorescence from the merocyanine form could be generated by exciting the core with a 543nm laser. For spirobenzopyran, higher temperatures favor the reaction form spiropyran form to merocyanine form, hence as temperature increases the merocyanine from concentration in the core increase causing the fluorescence intensity to increase. It was observed that the fluorescence increased fairly linearly over a certain range and started rolling off as the temperature approached to 60 degrees C. Refractive index and material dispersion characteristics of SP/PMMA was also measured. Fluorescence generation in the core by two-photon absorption from 40 ps pulses at 1064 nm has been demonstrated. The energy of the pulses was 1.8 uJ, which gave a peak intensity of 5GW/cm<SUP>2</SUP> in 33um core. A portion of the emitted fluorescence was guided to the end of the fiber and a portion of it escaped the cladding and radiated into the air.