gebhart/patrepeval huggingface dataset:
Structural and functional analysis of the nor-1 gene involved in the biosynthesis of aflatoxins by Aspergillus parasiticus (1994)

The nor-1 gene was cloned previously by complementation of a mutation (nor-1) in Aspergillus parasiticus SU-1 which blocked aflatoxin B1 biosynthesis, resulting in the accumulation of norsolorinic acid (NA). In this study, the nucleotide sequences of the cDNA and genomic DNA clones encompassing the coding region of the nor-1 gene were determined. The transcription initiation and polyadenylation sites of nor-1 were located by primer extension and RNase protection analyses and by comparison of the nucleotide sequences of the nor-1 genomic and cDNA clones. A plasmid, pNA51-82, was created for one-step disruption of the nor-1 gene by inserting a functional copy of the nitrate reductase (niaD) gene from A. parasiticus into the coding region of the nor-1 gene. Transformation of A. parasiticus NR-3 (niaD Afl+) with pNA51-82 resulted in niaD+ transformants that accumulated NA and produced reduced levels of aflatoxin as determined by thin-layer chromatography and enzyme-linked immunosorbent assay analyses of extracts from mycelia and the growth medium. Southern analysis of genomic DNA isolated from the NA-accumulating transformants indicated that the wild-type nor-1 gene in the chromosome had been replaced by the nonfunctional allele carried on pNA51-82. This recombinational inactivation event provides direct evidence that the nor-1 gene is functionally involved in aflatoxin biosynthesis. Comparison of the predicted nor-1 amino acid sequence with sequences in the GenBank and EMBL databases suggested that the protein is a member of the family of short-chain alcohol dehydrogenases, consistent with its proposed function as a keto reductase.
Aligned Li<sup>+</sup> Tunnels in Core–Shell Li(Ni<sub><i>x</i></sub>Mn<sub><i>y</i></sub>Co<sub><i>z</i></sub>)O<sub>2</sub>@LiFePO<sub>4</sub> Enhances Its High Voltage Cycling Stability as Li-ion Battery Cathode (2016)

Layered transition-metal oxides (Li[Ni<sub>x</sub>Mn<sub>y</sub>Co<sub>z</sub>]O<sub>2</sub>, NMC, or NMCxyz) due to their poor stability when cycled at a high operating voltage (>4.5 V) have limited their practical applications in industry. Earlier researches have identified Mn(II)-dissolution and some parasitic reactions between NMC surface and electrolyte, especially when NMC is charged to a high potential, as primarily factors responsible for the fading. In our previous work, we have achieved a capacity of NMC active material close to theoretical value and optimized its cycling performance by a depolarized carbon nanotubes (CNTs) network and an unique "pre-lithiation process" that generates an in situ organic coating (∼40 nm) to prevent Mn(II) dissolution and minimize the parasitic reactions. Unfortunately, this organic coating is not durable enough during a long-term cycling when the cathode operates at a high potential (>4.5 V). This work attempts to improve the surface protection of the NMC532 particles by applying an active inorganic coating consisting of nanosized- and crystal-orientated LiFePO<sub>4</sub> (LFP) (about 50 nm, exposed (010) face) to generate a core-shell nanostructure of Li(Ni<sub>x</sub>Mn<sub>y</sub>Co<sub>z</sub>)O<sub>2</sub>@LiFePO<sub>4</sub>. Transmission electron microscopy (TEM) and etching X-ray photoelectron spectroscopy have confirmed an intimate contact coating (about 50 nm) between the original structure of NMC and LFP single-particle with atomic interdiffusion at the core-shell interface, and an array of interconnected aligned Li<sup>+</sup> tunnels are observed at the interface by cross-sectional high-resolution TEM, which were formed by ball-milling and then strictly controlling the temperature below 100 °C. Batteries based on this modified NMC cathode material show a high reversible capacity when cycled between 3.0 and 4.6 V during a long-term cycling.
Translation Initiation with Initiator tRNA Charged with Exotic Peptides (2009)

In the prokaryotic translation system formylmethionyl-tRNA(fMet)(CAU) acts as an exclusive initiator to yield peptides bearing formylmethionine at the N-terminus. We herein report a new methodology to initiate the translation reaction with peptidyl-tRNA(fMet)(CAU) in which the peptidyl group consists of unusual building blocks, such as D-amino acids, beta-amino acids, and N-methyl amino acids, and express peptides containing a stretch of exotic peptides at the N-terminus. Synthesis of the initiator peptidyl-tRNAs was facilitated by flexizyme, a flexible tRNA aminoacylation ribozyme, and the start codon was reprogrammed by withdrawing methionine from a reconstituted E. coli cell-free translation system to reassign the initiator from formylmethionine to exotic peptides. This represents the first demonstration for initiating the ribosomal peptide synthesis with peptides, which offers us a new tool for the synthesis of a wide variety of unusual peptides and also the mechanistic studies on the initiation and/or elongation events in translation.
Incidence of the cblA major subunit pilin gene amongst Burkholderia species (2001)

PCR-amplification has been used to screen 75 isolates of the Burkholderia cepacia complex for the cblA pilin gene. PCR-amplified products of the correct size (664 bp) were cloned and sequenced and the sequences compared. Apart from in the control, epidemic cystic fibrosis (CF)-associated B. cepacia lineage we also identified, for the first time, cblA genes in a unique, non-CF clinical isolate from France and a plant (onion) pathogenic isolate from Italy. The sequence of the cblA gene amplified from the clinical isolate was more diverged from the epidemic lineage than that amplified from the onion pathogenic isolate.
C++ Templates as Partial Evaluation (1998)

This paper explores the relationship between C++ templates and partial evaluation. Templates were designed to support generic programming, but unintentionally provided the ability to perform compile-time computations and code generation. These features are completely accidental, and as a result their syntax is awkward. By recasting these features in terms of partial evaluation, a much simpler syntax can be achieved. C++ may be regarded as a two-level language in which types are first-class values. Template instantiation resembles an offline partial evaluator. This paper describes preliminary work toward a single mechanism based on Partial Evaluation which unifies generic programming, compile-time computation and code generation. The language Catat is introduced to illustrate these ideas.
FDTD analysis of the radiometric temperature measurement of a bilayered biological tissue using a body-contacting waveguide probe (1995)

Radiometric signal received by an open-ended rectangular waveguide probe in direct contact with a bilayered biological tissue is analyzed by the FDTD method. A two-layer tissue model consists of an outer thin skin layer over a semi-infinite fat layer is analyzed for a X-band total power radiometer. A spherical tumor with same permittivity as, but slightly higher temperature than, the surrounding normal fat tissue is assumed to exist inside the fat tissue. Active probe characteristics are analyzed first using the FDTD method for a propagating, sinusoidally time-varying, TE/sub 10/ type of excitation source. For the same waveguide probe operated as the radiometer antenna, radiometric weighting factors associated with individual tissue cells are then derived from the FDTD calculated field values. Near field radiating characteristics of the probe and radiometric signals determined for tumors of various size and depth are discussed. The presence of the skin is found to result in a lower power transmission coefficient across the probe aperture and significantly lower absorbed powers by fat; both of these contribute to the much lower radiometric signals observed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Resource management issues for shared-memory multiprocessors (1998)

Shared-memory multiprocessors (SMPs) are attractive as general-purpose compute servers. On the software side, they present the same programming paradigm as uniprocessors, and they can run unmodified uniprocessor binaries. On the hardware side, the tight coupling of multiple processors, memory, and I/O provides enormous computing power in a single system, and enables the efficient sharing of these resources. As a compute server, this power can be exploited both by a collection of uniprocessor programs and by explicitly or automatically parallelized applications. This thesis addresses two important performance-related issues encountered in such systems, isolation and data locality. The solutions presented in this dissertation address these issues through careful resource management in the operating system. Current shared-memory multiprocessor operating systems provide very few controls for sharing the resources of the system among the active tasks or users. This is a serious limitation for a compute server that is to be used for multiple tasks or by multiple users. The current unconstrained sharing scheme allows the load placed by one user or task to adversely affect the seen by another. We show that this lack of isolation is caused by the resource allocation scheme (or lack thereof) carried over from single-user workstations. Multi-user multiprocessor systems require more sophisticated resource management, and we propose performance isolation, a new resource management scheme for such systems.
Frailty, Cognitive Decline, Neurodegenerative Diseases and Nutrition Interventions (2019)

Currently the human population is aging faster. This leads to higher dependency rates and the transformation of health and social care to adapt to this aged population. Among the changes developed by this population is frailty. It is defined as a clinically detectable syndrome, related to the aging of multiple physiological systems, which prompts a situation of vulnerability. The etiology of frailty seems to be multifactorial and its pathophysiology is influenced by the interaction of numerous factors. Morley et al. propose four main mechanisms triggering the frailty: atherosclerosis, sarcopenia, cognitive deterioration and malnutrition, with their respective metabolic alterations. Malnutrition is associated with cognitive impairment or functional loss, but it is also known that an inadequate nutritional status predisposes to cognitive frailty. Additionally, nutritional factors that may influence vascular risk factors will potentially have an effect on dementia decline among patients with cognitive frailty. This review aims to describe the nutritional factors that have been researched so far which may lead to the development of frailty, and especially cognitive decline.
Polarization engineered deep ultraviolet nanowire LEDs integrated on silicon and metal substrates (2015)

AlGaN nanowire heterostractures are promising for realization of efficient ultraviolet LEDs due to their tolerance to strain [1] and their ability to be grown and electronically integrated on silicon wafers. Previously we developed polarization-induced nanowire LEDs that include Al composition grading resulting in n-type and p-type doping within nanowires [2]. Because the barriers in this structure are A1N, we can incorporate AlGaN quantum disk active regions with emission tunable out to deep ultraviolet wavelengths. These nanowire heterostractures exhibit dominant N-face polarity [3] which has the advantage of allowing for n-type top contacts favorable for Nitride LEDs. However, this poses a challenge due to the difficultly of forming a bottom p-type contact to p-AlGaN.
Enhanced expression of the Escherichia coli serA gene in a plasmid vector (1989)

The serA gene of Escherichia coli strain K-12, which codes for the cooperative allosteric enzyme D-3-phosphoglycerate dehydrogenase, was inserted into an inducible expression vector which produced phosphoglycerate dehydrogenase as 8% of the soluble protein of E. coli. The purified protein was used to grow several different single crystal forms. One of these, with space group P2(1), appears to contain all four subunits of the tetrameric enzyme in the asymmetric unit and diffracts to sufficient resolution to allow determination of the structure of phosphoglycerate dehydrogenase.
Face Expression Recognition Based on Feature Fusion (2009)

The traditional Gabor transform need calculate convolution with whole image when extract expression feature. So, the feature dimensions are very large and computation complexity is very high. Though some improved methods can reduce the feature dimensions and computing cost by manually marking out the feature points, but those methods need intense human intervention and can not meet to the need of automatic recognition. In this paper, a new face expression recognition method are proposed based on feature fusion which combines the Gabor transform and ASM automatic feature orientation technology. Firstly, ASM technology is used to locate the feature point of a face shape. And then Gabor feature of feature point are extracted by using Gabor transform. Finally, the two feature sets are fused to implement the face expression recognition. The experimental results show that the proposed method can effectively utilize the local texture information and global shape information of expression and get better recognition effect.
Treatment of Adrenocorticotropin-Dependent Cushing’s Syndrome: A Consensus Statement (2008)

ACTH-dependent Cushing's syndrome is a heterogeneous disorder requiring a multidisciplinary and individualized approach to patient management. Generally, the treatment of choice for ACTH-dependent Cushing's syndrome is curative surgery with selective pituitary or ectopic corticotroph tumor resection. Second-line treatments include more radical surgery, radiation therapy (for Cushing's disease), medical therapy, and bilateral adrenalectomy. Because of the significant morbidity of Cushing's syndrome, early diagnosis and prompt therapy are warranted.
Differentiation of Clinical Mycobacterium tuberculosis Complex Isolates by gyrB DNA Sequence Polymorphism Analysis (2000)

The discriminatory power of gyrB DNA sequence polymorphisms for differentiation of the species of the Mycobacterium tuberculosis complex (MTBC) was evaluated by sequencing and restriction fragment length polymorphism (RFLP) analysis of a 1,020-bp fragment amplified from clinical isolates of M. tuberculosis, Mycobacterium bovis (pyrazinamide [PZA] resistant as well as PZA susceptible), Mycobacterium africanum subtypes I and II, and Mycobacterium microti types vole and llama. We found sequence polymorphisms in four regions described previously and at one additional position. These differences in the gyrB sequences allow an accurate discrimination of M. bovis, M. microti, and M. africanum subtype I. The PZA-susceptible subtypes of M. bovis shared the M. bovis-specific substitution at position 756 with the PZA-resistant strains, but can be unambiguously differentiated by a characteristic substitution at position 1311. As a drawback, M. tuberculosis and M. africanum subtype II showed an identical gyrB sequence that facilitates discrimination from the other species, but not from each other. A PCR-RFLP technique applying three restriction enzymes could be shown to be a rapid and easy-to-perform tool for the differentiation of the members of the MTBC. Based on these results, we present a clear diagnostic algorithm for the differentiation of species of the MTBC.
A New Class of Zirconocene Catalysts for the Syndiospecific Polymerization of Propylene and Its Modification for Varying Polypropylene from Isotactic to Syndiotactic (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA New Class of Zirconocene Catalysts for the Syndiospecific Polymerization of Propylene and Its Modification for Varying Polypropylene from Isotactic to SyndiotacticTimothy A. Herzog, Deanna L. Zubris, and John E. BercawView Author Information Arnold and Mabel Beckman Laboratories of Chemical Synthesis California Institute of Technology Pasadena, California 91125 Cite this: J. Am. Chem. Soc. 1996, 118, 47, 11988–11989Publication Date (Web):November 27, 1996Publication History Received15 July 1996Published online27 November 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja962413zhttps://doi.org/10.1021/ja962413zrapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views964Altmetric-Citations104LEARN 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 (1)»Supporting Information Supporting Information SUBJECTS:Alkyls,Catalysts,Ligands,Sandwich compounds,Thermoresponsive polymers Get e-Alerts
Single Molecule Conductance of Porphyrin Wires with Ultralow Attenuation (2008)

A series of thioacetate-terminated butadiyne-linked porphyrin oligomers have been synthesized with one to three porphyrin repeat units. Single molecule electrical scanning tunneling microscopy measurements using the I(s) and I(t) methods were used to determine the molecule conductances for this series of oligomers. The molecular conductance shows an exponential falloff with sulfur-sulfur distance with a remarkably low attenuation factor of beta = (0.04 +/- 0.006) A-1.
Corepressor-induced organization and assembly of the biotin repressor: A model for allosteric activation of a transcriptional regulator (2001)

The Escherichia coli biotin repressor binds to the biotin operator to repress transcription of the biotin biosynthetic operon. In this work, a structure determined by x-ray crystallography of a complex of the repressor bound to biotin, which also functions as an activator of DNA binding by the biotin repressor (BirA), is described. In contrast to the monomeric aporepressor, the complex is dimeric with an interface composed in part of an extended beta-sheet. Model building, coupled with biochemical data, suggests that this is the dimeric form of BirA that binds DNA. Segments of three surface loops that are disordered in the aporepressor structure are located in the interface region of the dimer and exhibit greater order than was observed in the aporepressor structure. The results suggest that the corepressor of BirA causes a disorder-to-order transition that is a prerequisite to repressor dimerization and DNA binding.
Comparative analysis of drug response and gene profiling of HER2-targeted tyrosine kinase inhibitors (2021)

Neratinib was the most effective HER2-targeted TKI against HER2-amplified, -mutant, and EGFR-mutant cell lines. This analysis revealed novel resistance mechanisms that may be exploited using combinatorial strategies.
A macrophage migration inhibitory factor-like tautomerase from Teladorsagia circumcincta (Nematoda: Strongylida) (2010)

A macrophage migration inhibitory factor (MIF)-like molecule, Tci-MIF-1, was isolated from Teladorsagia circumcincta and subjected to detailed characterization. A cDNA representing Tci-mif-1 was isolated following its identification in third-stage larvae (L3)-enriched cDNA population. Sequencing of the cDNA indicated a 348-bp open reading frame (ORF) with the closest orthologue being a MIF derived from the human hookworm Ancylostoma ceylanicum. Messenger RNA (mRNA) representing the Tci-MIF-1 transcript was detected in eggs, L3 and adult stages of T. circumcincta. The transcript was also present, but to a lesser extent in fourth-stage larvae (L4). Detection of Tci-MIF-1 protein in T. circumcincta developmental stages reflected the transcript levels identified by reverse transcriptase-PCR. Using immunohistochemistry, the Tci-MIF-1 protein was shown to have a diffuse distribution in L3 tissue, and in L4 and adult stages, the protein was localized to the nematode gut. A recombinant version of Tci-MIF-1 was produced, and enzymic assays indicated that this recombinant protein and a somatic extract of L3 possessed dopachrome tautomerase activity as has been observed previously in other MIF-like molecules. Neither native, purified Tci-MIF nor recombinant Tci-MIF-1 dramatically influenced the in vitro migration of sheep monocytes.
Fluid Characterization of an Iranian Carbonate Oil Reservoir Using Different PVT Packages (2001)

Abstract Precise and accurate characterization of a reservoir fluid is a very important factor in reservoir simulation studies. PVT experiments are usually expensive and performed in limited conditions. Therefore Computer EOS based PVT packages are used widely for the prediction and evaluation of fluid properties at reservoir, well and surface conditions over a wide range of temperature, pressure and composition1,2,3,4. In this work different PVT packages that are available in National Iranian Oil Company (NIOC) have been used to complete fluid analysis and experiment simulation of an Iranian oil reservoir and PVT model preparation for the reservoir simulators. This reservoir is a medium size, highly fractured carbonate reservoir located in southwest of Iran. The carbonate formation has dense matrix with improved permeability by presence of fracture network. This reservoir was initially highly undersaturated and after 5 years of oil production the oil pressure reached to the saturation pressure and gas injection was started into the reservoir5. In this work different equation of states, different regression methods and correlations were analyzed for the prediction of fluid properties. Considering the results of this work in general good agreement was obtained for the experimental and calculated data for used packages. However, the method used for tuning the equation of states is critical in getting good agreement.
ChemInform Abstract: Toluene Isopropylation over Zeolite β and Metallosilicates of MFI Structure. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Halloysite Clay Nanotubes for Enzyme Immobilization (2015)

Halloysite clay is an aluminosilicate nanotube formed by rolling flat sheets of kaolinite clay. They have a 15 nm lumen, 50-70 nm external diameter, length of 0.5-1 μm, and different inside/outside chemistry. Due to these nanoscale properties, they are used for loading, storage, and controlled release of active chemical agents, including anticorrosions, biocides, and drugs. We studied the immobilization in halloysite of laccase, glucose oxidase, and lipase. Overall, negatively charged proteins taken above their isoelectric points were mostly loaded into the positively charged tube's lumen. Typical tube loading with proteins was 6-7 wt % from which one-third was released in 5-10 h and the other two-thirds remained, providing enhanced biocatalysis in nanoconfined conditions. Immobilized lipase showed enhanced stability at acidic pH, and the optimum pH shifted to more alkaline pH. Immobilized laccase was more stable with respect to time, and immobilized glucose oxidase showed retention of enzymatic activity up to 70 °C, whereas the native sample was inactive.