gebhart/patrepeval huggingface dataset:
Interaction Energy Analyses of Folate Analog Binding to Human Dihydrofolate Reductase: Contribution of the Antifolate Substructural Regions to Complex Stability (2000)

The three-dimensional structure of the human dihydrofolate reductase (DHFR), methotrexate tetrazole, and NADPH ternary complex was used to model the corresponding ternary complexes with methotrexate tetrazole replaced by methotrexate, methotrexate-polyglutamate with three glutamyl residues, and 5,10-deazaaminopterin, respectively. Each complex was solvated in a 60-angstrom cube of explicit water and subjected to structural minimization followed by interaction energy analyses. Interaction energy calculations were performed for the antifolate interaction with water, NADPH, the DHFR binding site residues, the entire DHFR protein, and the solvated NADPH:DHFR complex. These studies revealed that methotrexate-polyglutamate exhibited the most stable interactions and that approximately one half of antifolate:DHFR stability could be accounted for by the interaction of the antifolate with the binding site residues. The antifolate structures were also subdivided into heterocyclic, phenyl, and glutamyl substructural regions. Interaction energies were subsequently calculated for the interactions of the subregions with water, NADPH, the DHFR binding site residues, the DHFR protein, and the solvated NADPH:DHFR complex. The glutamyl substructural region showed the greatest contribution to overall antifolate binding stability due to its interaction with the DHFR protein. The heterocyclic and phenyl substructural regions generally showed much less stable interactions. These results suggest that the primary stabilizing factor of the antifolate interaction is the interaction of glutamyl with the DHFR protein. Additionally, interaction energy analyses were performed for specific groups of atoms within the substructural regions. These studies indicated that the stability of the glutamyl interaction is due to the interaction of glutamyl oxygen atoms with the DHFR protein. In the case of the methotrexate tetrazole complex, the tetrazole nitrogens also contribute significantly to the stability of the glutamyl interaction. The carbon atoms of the heterocyclic and phenyl groups both showed more stable interactions with NADPH than with water, while the nitrogen atoms showed more stable interactions with water than with NADPH. Collectively, these results indicate that the glutamyl region is the most important in antifolate binding stability.
Tri6 encodes an unusual zinc finger protein involved in regulation of trichothecene biosynthesis in Fusarium sporotrichioides (1995)

In Fusarium sporotrichioides, several genes required for biosynthesis of the trichothecene mycotoxin T-2 toxin are closely linked. Further characterization of this gene cluster has revealed a gene, Tri6, that specifies a 217-amino-acid protein with regions similar to Cys2His2 zinc finger proteins. Temporal expression of Tri6 is similar to that of trichothecene biosynthetic pathway genes. Analysis of Tri6 transcripts indicated that transcription is initiated in two regions and that within each region there may be at least four initiation sites. Disruption of Tri6 resulted in a mutant that did not produce trichothecenes but that did accumulate low levels of the trichothecene precursor trichodiene. The Tri6 mutant was unable to convert six trichothecene biosynthetic intermediates to T-2 toxin, and transcription of two biosynthetic genes, Tri4 and Tri5, was greatly reduced in the mutant relative to the wild type. In addition, the product of Tri6 functioned as a transcriptional activator in Saccharomyces cerevisiae when fused to the DNA binding region of GAL4. These results indicate that Tri6 encodes a protein involved in the transcriptional regulation of trichothecene biosynthetic genes in F. sporotrichioides.
Experimental realization of a semiconducting full-Heusler compound:Fe2TiSi (2014)

Single-phase films of the full-Heusler compound ${\mathrm{Fe}}_{2}\mathrm{TiSi}$ have been prepared by magnetron sputtering. The compound is found to be a semiconductor with a gap of 0.4 eV. The electrical resistivity has a logarithmic temperature dependence up to room temperature due to Kondo scattering of a dilute free electron gas off superparamagnetic impurities. The origin of the electron gas is extrinsic due to residual off-stoichiometry. Density functional theory calculations of the electronic structure are in excellent agreement with electron energy loss, optical, and x-ray absorption experiments. ${\mathrm{Fe}}_{2}\mathrm{TiSi}$ may find applications as a thermoelectric material.
Free Carrier Generation and Recombination in Polymer-Wrapped Semiconducting Carbon Nanotube Films and Heterojunctions (2013)

Semiconducting single-walled carbon nanotubes (s-SWCNTs) are promising for solution-processed, thin film photovoltaics due to their strong near-infrared absorptivity and excellent transport properties. We report on the generation yield and recombination kinetics of free charge carriers in photoexcited thin films of polymer-wrapped s-SWCNTs with and without an overlying electron-accepting C60 layer, using time-resolved microwave photoconductivity (TRMC). Free carriers are generated in neat s-SWCNT films, even without an obvious driving force for exciton dissociation. However, most carriers recombine in <10 ns. Adding C60 increases the yield and extends the lifetime of a significant fraction of free carriers to ≫100 ns via interfacial charge separation. Spectral dependencies indicate that the driving force for interfacial electron transfer vanishes for large-diameter SWCNTs, from which we approximate (9,7) s-SWCNT energetics. We estimate a free carrier generation yield of ∼6% in neat s-SWCNT films and 9 GHz SWCNT hole mobility of >1.3 cm2 V–1 s–1. These studies improve understanding of s-SWCNT photoresponses in solar cells and photodetectors.
Ultraviolet-induced Photochemical Damage in Ocular Tissues (1989)

Exposure to ultraviolet (UV) lasers may result in pathology to either the cornea, lens or retina of the primate eye. The particular combination of exposure parameters (wavelength, peak power, pulsewidth, pulse repetition rate, and total energy delivered) determines the primary target tissue(s) in each instance. The effect may be acute or chronic, and the implicated damage mechanism may be categorized as photochemical, photoablative or thermal. This paper summarizes a number of specific cases where UV laser radiation affected one or more of the ocular tissues, describes the nature of the pathologies, and indicates what is known about the damage mechanism in each case. Ranges of exposure parameters where each ocular tissue is the most sensitive are defined. The cornea is most sensitive via a photochemical damge mechanism in the 260- to 280-nm range, where the threshold dose is approximately 5 mJ cm-2. For near-UV wavelengths (320-400 nm), different target molecules absorb the radiation and are susceptible to less efficient photochemical damage mechanism yielding corneal thresholds in the range of 10-100 J cm-2. However, we report acute cataract induction following exposure to a 337-nm nitrogen laser at 1 J cm-2 when the energy is delivered in a 10-ns pulse. Further, with longer pulsewidths (approximately 1 s) of comparable wavelength, retinal lesions were induced when 0.28 J was delivered to the eye. The data suggest that the acute lens effect is the result of a thermal mechanism, whereas the UV-induced retinal lesions result from a photochemical insult to the photoreceptors. Data presented include the action spectra for far- and near-UV-induced ocular damage, the pulsewidth and total energy dependencies of ocular thresholds, cumulative effects of repeated exposures, and repair or recovery rates.
Oral Candida albicans isolates from nonhospitalized normal carriers, immunocompetent hospitalized patients, and immunocompromised patients with or without acquired immunodeficiency syndrome (1989)

A total of 128 human oral isolates of Candida albicans were collected from asymptomatic healthy carriers (64 isolates); asymptomatic, nonimmunosuppressed, hospitalized patients (25 isolates); immunosuppressed transplant patients (19 isolates); and human immunodeficiency virus-infected patients with symptoms of acquired immunodeficiency syndrome and oral candidiasis (20 isolates). Isolates were serotyped as A or B and tested for reactivity with an agglutinating immunoglobulin M monoclonal antibody (H9). Immunocompetent individuals colonized by oral C. albicans were almost equally likely to carry serotype A as serotype B cells, while immunocompromised individuals were at least twice as likely to be infected by serotype B than serotype A strains. The reactivity of isolates with H9 antibody followed a similar but more distinctive pattern. Approximately half of the strains from immunocompetent individuals reacted strongly with H9, and the remainder reacted weakly. However, up to 75% of the isolates from immunocompromised patients reacted weakly with H9, while the remainder reacted strongly. A correlation between H9 reactivity and the serotypes of these isolates existed (P = 0.16). The correlation between H9 reactivity and immune status was even stronger (P = 0.025). The monoclonal antibody activities described above were determined by agglutination tests during defined phases of C. albicans growth. Expression of antigen at various times during growth of several isolates was confirmed at the cellular level by analysis using fluorescence-activated cell sorting. Despite the correlation between serotype A and H9 reactivity, H9 antigen was not identical to the serotype A antigen because four serotype A strains reacted only weakly with H9 antibody, and one strain reacted strongly with H9 but was serotype B. These data indicate that oral strains of C. albicans from immunocompetent individuals differ as a group from C. albicans isolated from those who are immunosuppressed.
On-chip detection of non-classical light by scalable integration of single-photon detectors (2015)

Photonic-integrated circuits have emerged as a scalable platform for complex quantum systems. A central goal is to integrate single-photon detectors to reduce optical losses, latency and wiring complexity associated with off-chip detectors. Superconducting nanowire single-photon detectors (SNSPDs) are particularly attractive because of high detection efficiency, sub-50-ps jitter and nanosecond-scale reset time. However, while single detectors have been incorporated into individual waveguides, the system detection efficiency of multiple SNSPDs in one photonic circuit-required for scalable quantum photonic circuits-has been limited to <0.2%. Here we introduce a micrometer-scale flip-chip process that enables scalable integration of SNSPDs on a range of photonic circuits. Ten low-jitter detectors are integrated on one circuit with 100% device yield. With an average system detection efficiency beyond 10%, and estimated on-chip detection efficiency of 14-52% for four detectors operated simultaneously, we demonstrate, to the best of our knowledge, the first on-chip photon correlation measurements of non-classical light.
Human Papillomavirus and Papanicolaou Tests to Screen for Cervical Cancer (2007)

The addition of an HPV test to the Pap test to screen women in their mid-30s for cervical cancer reduces the incidence of grade 2 or 3 cervical intraepithelial neoplasia or cancer detected by subsequent screening examinations. (ClinicalTrials.gov number, NCT00479375 [ClinicalTrials.gov].).
Ablation of Perivascular Hepatic Malignant Tumors with Irreversible Electroporation (2012)

This early analysis of IRE treatment of perivascular malignant hepatic tumors demonstrates safety for treating liver malignancies. Larger studies and longer follow-up are necessary to determine long-term efficacy.
Drug Transport into the Mammalian Brain: The Nasal Pathway and its Specific Metabolic Barrier (2002)

It is generally accepted that the rate of entry into and distribution of drugs and other xenobiotics within the central nervous system (CNS) depends on the particular anatomy of the brain microvessels forming the blood-brain barrier (BBB), and of the choroid plexus forming the blood-cerebrospinal fluid barrier (CSF), which possess tight junctions preventing the passage of most polar substances. Drug entry to the CNS also depends on the physicochemical properties of the substances, which can be metabolised during this transport to pharmacologically inactive, non-penetrating polar products. Finally, the entry of drugs may be prevented by multiple complex specialized carriers, which are able to catalyse the active transport of numerous drugs and xenobiotics out of the CNS. Nasal delivery is currently considered as an efficient tool for systemic administration of drugs that are poorly absorbed via the oral route, and increasing evidence suggests that numerous drugs and potentially toxic xenobiotics can reach the CNS by this route. This short review summarizes recent knowledge on factors controlling the nasal pathway, focusing on drug metabolising enzymes in olfactory mucosa, olfactory bulb and brain, which should constitute a CNS metabolic barrier.
Ubiquitin-aldehyde: a general inhibitor of ubiquitin-recycling processes. (1987)

The generation and characterization of ubiquitin (Ub)-aldehyde, a potent inhibitor of Ub-C-terminal hydrolase, has previously been reported. We now examine the action of this compound on the Ub-mediated proteolytic pathway using the system derived from rabbit reticulocytes. Addition of Ub-aldehyde was found to strongly inhibit breakdown of added 125I-labeled lysozyme, but inhibition was overcome by increasing concentrations of Ub. The following evidence shows the effect of Ub-aldehyde on protein breakdown to be indirectly caused by its interference with the recycling of Ub, leading to exhaustion of the supply of free Ub: Ub-aldehyde markedly increased the accumulation of Ub-protein conjugates coincident with a much decreased rate of conjugate breakdown. release of Ub from isolated Ub-protein conjugates in the absence of ATP (and therefore not coupled to protein degradation) is markedly inhibited by Ub-aldehyde. On the other hand, the ATP-dependent degradation of the protein moiety of Ub conjugates, which is an integral part of the proteolytic process, is not inhibited by this agent. Direct measurement of levels of free Ub showed a rapid disappearance caused by the inhibitor. The Ub is found to be distributed in derivatives of a wide range of molecular weight classes. It thus seems that Ub-aldehyde, previously demonstrated to inhibit the hydrolysis of Ub conjugates of small molecules, also inhibits the activity of a series of enzymes that regenerate free Ub from adducts with proteins and intermediates in protein breakdown.
Therapeutic effect of recombinant vaccinia virus expressing the 60‐kd heat‐shock protein on adjuvant arthritis (1994)

Our results suggest novel avenues of therapeutic intervention in autoimmune arthritis associated with immunity to hsp60.
Genes coding for the benzoyl‐CoA pathway of anaerobic aromatic metabolism in the bacterium Thauera aromatica (1998)

Many aromatic compounds are anaerobically oxidized to CO2 via benzoyl-CoA as the common aromatic intermediate. In Thauera aromatica, the central benzoyl-CoA pathway comprises the ATP-driven two-electron reduction of the benzene ring; this reaction uses a ferredoxin as electron donor and is catalyzed by benzoyl-CoA reductase. The first intermediate, cyclohex-1,5-diene-1-carboxyl-CoA, is subsequently hydrated by dienoyl-CoA hydratase to 6-hydroxycyclohex-1-ene-1-carboxyl-CoA. Formation of the main product produced by cell extracts, 3-hydroxypimelyl-CoA, requires at least two further steps; the oxidation of a hydroxyl group and the hydrolytic carbon ring cleavage of a CoA-activated beta-oxoacid. In addition, enoyl-CoA hydratase may come into play. A cluster of eight adjacent genes, which are transcribed in the same direction and may form an operon, was found in this bacterium. The cluster codes for proven and postulated enzymes of the benzoyl-CoA pathway. The genes for the enzymes code for ferredoxin, four subunits of benzoyl-CoA reductase, dienoyl-CoA hydratase, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase (NAD+), and the ring hydrolyzing enzyme. The deduced amino acid sequences of these proteins were 35-86% similar to the corresponding sequences found in Rhodopseudomonas palustris. Benzoyl-CoA reductase subunits exhibit distinct similarities with 2-hydroxyglutaryl-CoA dehydratase and its ATP-hydrolysing activase protein of Acidaminococcus fermentans as well as with open reading frames of unknown function in other bacteria. Conversion of benzoyl-CoA to 3-hydroxypimelyl-CoA can be explained by a minimal model of the benzoyl-CoA pathway assuming the four enzymes whose genes were characterized and an additional enoyl-CoA hydratase. In R. palustris the dienoyl-CoA hydratase gene is lacking suggesting the operation of a modified benzoyl-CoA pathway with cyclohex-1-ene-1-carboxyl-CoA as intermediate.
Cloning, sequencing, and mapping of the bacterioferritin gene (bfr) of Escherichia coli K-12 (1989)

The bacterioferritin (BFR) of Escherichia coli K-12 is an iron-storage hemoprotein, previously identified as cytochrome b1. The bacterioferritin gene (bfr) has been cloned, sequenced, and located in the E. coli linkage map. Initially a gene fusion encoding a BFR-lambda hybrid protein (Mr 21,000) was detected by immunoscreening a lambda gene bank containing Sau3A restriction fragments of E. coli DNA. The bfr gene was mapped to 73 min (the str-spc region) in the physical map of the E. coli chromosome by probing Southern blots of restriction digests of E. coli DNA with a fragment of the bfr gene. The intact bfr gene was then subcloned from the corresponding lambda phage from the gene library of Kohara et al. (Y. Kohara, K. Akiyama, and K. Isono, Cell 50:495-508, 1987). The bfr gene comprises 474 base pairs and 158 amino acid codons (including the start codon), and it encodes a polypeptide having essentially the same size (Mr 18,495) and N-terminal sequence as the purified protein. A potential promoter sequence was detected in the 5' noncoding region, but it was not associated with an "iron box" sequence (i.e., a binding site for the iron-dependent Fur repressor protein). BFR was amplified to 14% of the total protein in a bfr plasmid-containing strain. An additional unidentified gene (gen-64), encoding a relatively basic 64-residue polypeptide and having the same polarity as bfr, was detected upstream of the bfr gene.
Characterization of Sputter‐Deposited LiMn2 O 4 Thin Films for Rechargeable Microbatteries (1994)

Thin films of spinel were fabricated by RF magnetron sputtering. The as‐deposited films were amorphous but could be crystallized into a spinel structure by rapid thermal annealing in an oxygen atmosphere. The electrochemical performance of 2000 Å thick thin‐film cathodes were tested in a in cell. spinel films prepared at 750°C showed good intercalation kinetics and very promising cycling behavior. Room temperature cycling of these films had capacities of about 50 μAh/cm2·μm at 200 μA/cm2 and maintained more than 98% of their original capacity after more than 1000 cycles.
Biological Characteristics and Biomedical Applications of the Squid Sepioteuthis lessoniana Cultured Through Multiple Generations (1994)

Providing squids--especially their giant axons--for biomedical research has now been achieved in 10 mariculture trials extending through multiple generations. The noteworthy biological characteristics of Sepioteuthis lessoniana are (1) this species is behaviorally and morphologically well suited to the laboratory environment; (2) the life cycle is completed in 4-6 months; (3) growth is rapid (12% and 5% wet body weight d-1 for 100 d and for the life span, respectively), with adult size ranging from 0.4-2.2 kg; (4) feeding rates are high (30% wet body weight d-1), and a variety of live crustaceans and fishes are eaten; (5) crowding is tolerated (about 4 squids m-3); (6) the incidence of disease and cannibalism is low; and (7) reproduction in captivity allows culture through three successive generations. Engineering factors contributed to culture success: (1) physical design (i.e., size, shape, and painted pattern) of the culture tanks; (2) patterns of water flow in the culture tanks; (3) water filtration systems; and (4) spawning substrates. Initial production (a few hundred squids per year) suggests that large-scale culture will be able to supply the needs of the biomedical research community. The size (> 400 microns in diameter) and characteristics of the giant axons of Sepioteuthis are appropriate for experimentation, and other studies indicate that the eye, oculomotor/equilibrium system, olfactory system, blood, and ink are equally suitable for research.
Examination of the thermal decomposition of kraft pine lignin by Fourier transform infrared evolved gas analysis (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExamination of the thermal decomposition of kraft pine lignin by Fourier transform infrared evolved gas analysisRobert A. Fenner and John O. LephardtCite this: J. Agric. Food Chem. 1981, 29, 4, 846–849Publication Date (Print):July 1, 1981Publication History Published online1 May 2002Published inissue 1 July 1981https://doi.org/10.1021/jf00106a042RIGHTS & PERMISSIONSArticle Views573Altmetric-Citations100LEARN 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 InReddit PDF (458 KB) Get e-Alerts Get e-Alerts
Production and characterization of monoclonal antibodies with therapeutic potential against Shiga toxin. (1990)

Four monoclonal antibodies (T2D1, T3B1, T7B2 and T4C4) were produced and characterized against Sh. dysenteriae type 1. These monoclonal antibodies (McAbs) were shown to be directed against the same or adjacent determinants on the A-subunit of the Shiga toxin. All the anti-Shiga toxin McAbs are IgG1 (kappa) antibodies and have the capacity to neutralize the cytotoxic and neurotoxic effects of the Shiga toxin: the data strongly suggest that both of the activities, associated with the toxin, are due to the same molecule. In addition, the McAbs were found to be highly protective, at low dose, when administered therapeutically to lethally-treated animals.
A Convenient Synthesis of 1-Chloro-2-allkanones (1987)

1-Chloro-2-alkanones (α-chloromethylketones) were conveniently prepared by chlorination of methyl β-ketoesters and subsequent demethoxycarbonylation using 50% sulfuric acid.