gebhart/patrepeval huggingface dataset:
From Molecules to Materials: Current Trends and Future Directions (1998)

The development, characterization, and exploitation of novel materials based on the assembly of molecular components is an exceptionally active and rapidly expanding field. For this reason, the topic of molecule-based materials (MBMs) was chosen as the subject of a workshop sponsored by the Chemical Sciences Division of the United States Department of Energy. The purpose of the workshop was to review and discuss the diverse research trajectories in the field from a chemical perspective, and to focus on the critical elements that are likely to be essential for rapid progress. The MBMs discussed encompass a diverse set of compositions and structures, including clusters, supramolecular assemblies, and assemblies incorporating biomolecule-based components. A full range of potentially interesting materials properties, including electronic, magnetic, optical, structural, mechanical, and chemical characteristics were considered. Key themes of the workshop included synthesis of novel components, structural control, characterization of structure and properties, and the development of underlying principles and models. MBMs, defined as “useful substances prepared from molecules or molecular ions that maintain aspects of the parent molecular framework” are of special significance because of the capacity for diversity in composition, structure, and properties, both chemical and physical. Key attributes are the ability in MBMs to access the additional dimension of multiple length scales and available structural complexity via organic chemistry synthetic methodologies and the innovative assembly of such diverse components. The interaction among the assembled components can thus lead to unique behavior. A consequence of the complexity is the need for a multiplicity of both existing and new tools for materials synthesis, assembly, characterization, and theoretical analysis. For some technologically useful properties, e.g., ferro- or ferrimagnetism and superconductivity, the property is not a property of a molecule or ion; it is a cooperative solid-state (bulk) property—a property of the entire solid. Hence, the desired properties are a consequence of the interactions between the molecules or ions, and understanding the solid-state structure as well as methods to predict, control, and modulate the structure are essential to understanding and manipulating such behaviors. As challenging as this is, molecules enable a substantially greater ability of control than atoms as building blocks for new materials and thus are well positioned to contribute significantly to new materials. The diversity of components and processes leads to the recognition of the critical role of cross-disciplinary research, including not only that between traditionally different areas within chemistry, but also between chemistry and biochemistry, physics, and a number of engineering disciplines. Enhancing communication and active collaboration between these groups was seen as a critical goal for the research area.
Cap-Poly(A) Synergy in Mammalian Cell-free Extracts (2000)

The 5' cap and 3' poly(A) tail of eukaryotic mRNAs cooperate to stimulate synergistically translation initiation in vivo, a phenomenon observed to date in vitro only in translation systems containing endogenous competitor mRNAs. Here we describe nuclease-treated rabbit reticulocyte lysates and HeLa cell cytoplasmic extracts that reproduce cap-poly(A) synergy in the absence of such competitor RNAs. Extracts were rendered poly(A)-dependent by ultracentrifugation to partially deplete them of ribosomes and associated initiation factors. Under optimal conditions, values for synergy in reticulocyte lysates approached 10-fold. By using this system, we investigated the molecular mechanism of poly(A) stimulation of translation. Maximal cap-poly(A) cooperativity required the integrity of the eukaryotic initiation factor 4G-poly(A)-binding protein (eIF4G-PABP) interaction, suggesting that synergy results from mRNA circularization. In addition, polyadenylation stimulated uncapped cellular mRNA translation and that driven by the encephalomyocarditis virus internal ribosome entry segment (IRES). These effects of poly(A) were also sensitive to disruption of the eIF4G-PABP interaction, suggesting that 5'-3' end cross-talk is functionally conserved between classical mRNAs and an IRES-containing mRNA. Finally, we demonstrate that a rotaviral non-structural protein that evicts PABP from eIF4G is capable of provoking the shut-off of host cell translation seen during rotavirus infection.
The flow cytometry ofBacillus anthracis spores revisited (2000)

This study shows that FCM may be an effective platform on which to perform immunological analysis for the detection and/or presumptive identification of B. anthracis spores. Published 2000 Wiley-Liss, Inc.
Improving the robustness of multivariate calibration models for the determination of glucose by near-infrared spectroscopy (2005)

Near-infrared spectroscopy has proven to be one of the most promising techniques for the development of a noninvasive blood glucose monitoring system for diabetic patients. In this work, Fourier transform infrared (FT-IR) transmission measurements of the combination band region (4000 – 5000 cm) were analyzed for samples containing glucose (analyte) in a matrix of bovine serum albumin and triacetin (models for proteins and fats), all spanning physiological levels relevant for a diabetic patient. The first part of the study investigated the required spectral point-spacing for accurate detection of glucose. This was studied by systematically truncating interferograms before Fourier transforming them to single-beam spectra. A set of training data (70 samples) was collected for multivariate calibration using partial least-squares (PLS) and an external prediction set was used to verify the success of modeling glucose quantitatively. It was found that a relatively large point-spacing (16 cm) was successful for prediction of glucose, meaning that a shorter interferogram could be collected. The second part of the study involved collecting interferograms such that the spectral resolution was 16 cm, and investigating methods to extend the usefulness of calibration models for long-term data collection. Near-infrared spectroscopy often suffers from weak signals that are overwhelmed by significant instrumental drift, meaning that calibration models tend to be unsuccessful for data collected several days or months outside the calibration. For updating the calibration models, a set of 50 backgrounds containing only matrix constituents without analyte was collected on each analysis day, and used to
Investigation of Experimental Parameters for Surface-Enhanced Raman Scattering (SERS) Using Silver-Coated Microsphere Substrates (1987)

The effects of experimental parameters on surface-enhanced Raman scattering (SERS) for silver-coated microsphere substrates were investigated. The parameters included sphere size, silver thickness, and excitation wavelength. The SERS signal intensity varied as each of these parameters was changed. The potential for increasing SERS sensitivity was illustrated by the detection of benzo(a)pyrene, a molecule of environmental and toxicological interest, at a concentration well below that possible for normal Raman scattering. This work describes some optimization procedures and demonstrates the possibility for further improving SERS enhancement of these silver-coated microsphere substrates by optimizing experimental parameters.
Utilizing a Kidney-Targeting Peptide to Improve Renal Deposition of a Pro-Angiogenic Protein Biopolymer (2019)

Elastin-like polypeptides (ELP) are versatile protein biopolymers used in drug delivery due to their modular nature, allowing fusion of therapeutics and targeting agents. We previously developed an ELP fusion with vascular endothelial growth factor (VEGF) and demonstrated its therapeutic efficacy in translational swine models of renovascular disease and chronic kidney disease. The goal of the current work was to refine renal targeting and reduce off-target tissue deposition of ELP-VEGF. The ELP-VEGF fusion protein was modified by adding a kidney-targeting peptide (KTP) to the N-terminus. All control proteins (ELP, KTP-ELP, ELP-VEGF, and KTP-ELP-VEGF) were also produced to thoroughly assess the effects of each domain on in vitro cell binding and activity and in vivo pharmacokinetics and biodistribution. KTP-ELP-VEGF was equipotent to ELP-VEGF and free VEGF in vitro in the stimulation of primary glomerular microvascular endothelial cell proliferation, tube formation, and extracellular matrix invasion. The contribution of each region of the KTP-ELP-VEGF protein to the cell binding specificity was assayed in primary human renal endothelial cells, tubular epithelial cells, and podocytes, demonstrating that the VEGF domain induced binding to endothelial cells and the KTP domain increased binding to all renal cell types. The pharmacokinetics and biodistribution of KTP-ELP-VEGF and all control proteins were determined in SKH-1 Elite hairless mice. The addition of KTP to ELP slowed its in vivo clearance and increased its renal deposition. Furthermore, addition of KTP redirected ELP-VEGF, which was found at high levels in the liver, to the kidney. Intrarenal histology showed similar distribution of all proteins, with high levels in blood vessels and tubules. The VEGF-containing proteins also accumulated in punctate foci in the glomeruli. These studies provide a thorough characterization of the effects of a kidney-targeting peptide and an active cytokine on the biodistribution of these novel biologics. Furthermore, they demonstrate that renal specificity of a proven therapeutic can be improved using a targeting peptide.
Observations on the onset of Torsade de Pointes arrhythmias in the acquired long QT syndrome (2000)

The synergism between ectopic beats (short-long-short sequence) and DeltaAPD create the circumstances for TdP initiation.
Phylogenetic analysis of 48 papillomavirus types and 28 subtypes and variants: a showcase for the molecular evolution of DNA viruses (1992)

Papillomaviruses are attractive models for studying the molecular evolution of DNA viruses because of the large number of isolates that exhibit genomic diversity and host species and tissue specificity. To examine their relationship, we selected two amino acid sequences, one of 52 residues within the early gene E1 and the other of 44 residues within the late gene L1, which allowed insertion- and deletion-free alignment of all accessible papillomavirus sequences. We constructed phylogenetic trees from the amino acid and corresponding nucleotide sequences from 28 published and 20 newly determined animal and human papillomavirus (HPV) genomic sequences by using distance matrix, maximum-likelihood, and parsimony methods. The trees agreed in all important topological aspects. One major branch with two clearly separated clusters contained 11 HPV types associated with epidermodysplasia verruciformis. A second major branch had all the papillomaviruses involved in genital neoplasia and, in distant relationship, the cutaneous papillomaviruses HPV type 2a (HPV-2a), HPV-3, and HPV-10 as well as the "butcher's" papillomavirus HPV-7 and two simian papillomaviruses. Four artiodactyl (even-toed hoofed mammal) papillomaviruses, the cottontail rabbit papillomavirus, and avian (chaffinch) papillomavirus type 1 formed a third major branch. Last, four papillomaviruses exhibited little affinity to any of these three branches; these were the cutaneous types HPV-1a, HPV-4, and HPV-41 and B-group bovine papillomavirus type 4. The phylogeny suggests that some branches of papillomavirus evolution are restricted to particular target tissues and that a general process of long-term papillomavirus-host coevolution has occurred. This latter hypothesis is still conjectural because of bias in the current data base for human types and the paucity of animal papillomavirus sequences. The comparison of evolutionary distances for the most closely related types with those of 28 subtypes and variants of HPV-2, HPV-5, HPV-6, HPV-16, and HPV-18 supports the type as a natural taxonomic unit, with subtypes and variants being expressions of minor intratype genomic diversity similar to that found in the natural populations of all biological species. An exception to this seems to be HPV-2c, which has an evolutionary distance from HPV-2a of the intertype magnitude and may eventually have to be regarded as a distinct type. We describe an experimental approach that estimates the taxonomic and phylogenetic positions of newly identified papillomaviruses without viral isolation and complete genomic sequencing.(ABSTRACT TRUNCATED AT 400 WORDS)
Involvement of H-cadherin (CDH13) on 16q in the region of frequent deletion in ovarian cancer. (1999)

Ovarian cancer is one of the leading causes of mortality unique to women. Deletions within chromosome 6q are the most frequent events in high-grade invasive epithelial ovarian cancer (IEOC). While previous reports seem to indicate that there is loss of 16q sequences in IOEC, only a very small number of markers (single marker in two different reports) were used. In order to more precisely define the regions of deletions on 16q, we first analyzed LOH with 13 polymorphic markers on 16q in 10 benign, 3 low-grade and 21 high-grade invasive ovarian cancer samples. There was no loss with any of the markers with the benign ovarian samples and loss of one marker in one of three low-grade tumors. In contrast, 14 of 21 (67%) high-grade invasive ovarian tumors showed loss of one or more markers. Detailed deletion mapping revealed three distinct commonly deleted regions on this chromosomal arm: 10/21 (48%) of high-grade tumors showed loss at 16q23.1-23.2 (D16S518, D16S3049 and D16S3029). The second region of loss at 16q23.3-16q24.1 (D16S3144, D16S504, HSD17B2 and D16S507) was observed in 11/21 (52%) of the tumors. The highest frequency of loss was seen at 16q24.2-16q24.3 (D16S422, D16S402 and D16S520) in 12/21 (57%) of tumors. The genomic map of CDH13 indicates that the marker D16S422 that was lost in 5 of these 12 tumors is part of this gene. Three of these 5 tumors showed very low levels of CDH13 expression. Three tumors with LOH of other markers in this region also showed lower levels of CDH13 expression. Analysis of the methylation status of CDH13 in tumors with low levels of expression with methylation-specific PCR revealed that four of six (67%) tumors had methylation of one of the CDH13 alleles. These results suggest that a combination of hyper-methylation and deletion cause the inactivation of CDH13 in ovarian tumors.
Trichophyton Antigens Associated with IgE Antibodies and Delayed Type Hypersensitivity (1998)

The dermatophyte fungus <i>Trichophyton</i>exhibits unique immunologic properties by its ability to cause both immediate and delayed type hypersensitivity. An 83-kDa<i>Trichophyton tonsurans</i> allergen (Tri t 4) was previously shown to elicit distinct T lymphocyte cytokine profiles <i>in vitro</i>. The homologous protein, Tri r 4, was cloned from a<i>Trichophyton rubrum</i> cDNA library, and the recombinant protein was expressed in <i>Pichia pastoris</i>. This 726-amino acid protein contained an arrangement of catalytic triad residues characteristic of the prolyl oligopeptidase family of serine proteinases (Ser-Asp-His). In addition, a novel<i>Trichophyton</i> allergen, encoding 412 amino acids, was identified by its human IgE antibody-binding activity. Sequence similarity searches showed that this allergen, designated Tri r 2, contained all of the conserved residues characteristic of the class D subtilase subfamily (41–58% overall sequence identity). Forty-two percent of subjects with immediate hypersensitivity skin test reactions to a <i>Trichophyton</i> extract exhibited IgE antibody binding to a recombinant glutathione <i>S</i>-transferase fusion protein containing the carboxyl-terminal 289 amino acids of Tri r 2. Furthermore, this antigen was capable of inducing delayed type hypersensitivity skin test reactions. Our results define two distinct antigens derived from the dermatophyte <i>Trichophyton</i> that serve as targets for diverse immune responses in humans.
Development of the First Potent and Selective Inhibitor of the Zinc Endopeptidase Neurolysin Using a Systematic Approach Based on Combinatorial Chemistry of Phosphinic Peptides (1996)

A new systematic approach, based on combinatorial chemistry of phosphinic peptides, is proposed for rapid development of highly potent and selective inhibitors of zinc metalloproteases. This strategy first evaluates the effects on the inhibitory potency and selectivity of the following parameters: 1) size of the phosphinic peptides, 2) position of the phosphinic bond in the sequence, and 3) the state (free or blocked) of the peptide extremities. After this selection step, the influence of the inhibitor sequence is analyzed in order to determine the identity of the residues that optimized both the potency and the selectivity. We demonstrate the efficiency of this novel approach in rapid identification of the first potent inhibitor of the mammalian zinc endopeptidase neurolysin(24-16), able to discriminate between this enzyme and the related zinc endopeptidase thimet oligopeptidase(24-15). The most potent and selective inhibitor developed in this study, Pro-LPhePsi(PO2CH2)Gly-Pro, displays a Ki value of 4 nM for 24-16 and is 2000 times less potent on 24-15. The specific recognition of such a free phosphinic tetrapeptide by 24-16, as well as the unique specificity of the 24-16 S2 and S2' subsites for proline, unveiled by this study, are discussed in terms of their possible significance for the function of this enzyme and its related zinc endopeptidase activities.
Definition and Functional Implications of Gibberellin and Abscisic Acid cis-Acting Hormone Response Complexes (1992)

John C. Rogers, Sally W. Rogers, Definition and Functional Implications of Gibberellin and Abscisic Acid cis-Acting Hormone Response Complexes, The Plant Cell, Vol. 4, No. 11 (Nov., 1992), pp. 1443-1451
Early Contact Interactions between Mammalian Gametes In Vitro: Evidence That the Vitellus Influences Adherence between Sperm and Zona Pellucida (1972)

A study in vitro of interactions between gametes of the golden hamster showed that the spermatozoon associates with the zona pellucida, or outer coat of the ovum, by two successive steps termed attachment and binding. Attachment, apparently the first step in fertilization, is not species-specific; it is insensitive to temperature (2 degrees ) and is reversible. Binding, on the other hand, is species-specific, temperature-sensitive, and irreversible. Experiments with isolated zonae pellucidae indicated that the vitellus (cellular portion of the ovum) influences the interaction between the sperm and the zona pellucida by increasing the time required for the sperm to bind. This effect is exerted on the sperm while they are attached to the zona pellucida.
DNAzyme-based fluorescent microarray for highly selective and sensitive detection of lead(ii) (2011)

A facile microarray-based fluorescent sensor for the detection of lead (II) was developed based on the catalytic cleavages of the substrates by a DNAzyme upon its binding to Pb(2+). The release of the fluorophore labelled substrates resulted in the decrease of fluorescence intensity. The sensor had a quantifiable detection range from 1 nM to 1 μM and a selectivity of >20 fold for Pb(2+) over other metal ions.
Amorphization-decomposition behavior of HfW2O8 at high pressure (2008)

Structural stability of HfW2O8 is investigated at high pressure using Raman spectroscopy. Irreversible amorphization is found to occur when pressurized to above 3 GPa under hydrostatic conditions. The Raman spectrum of the pressure-amorphized sample closely resembles that of amorphous WO3. On the other hand, spectrum of the recovered sample subjected to uniaxial compression of about 5 GPa showed bands characteristic of crystalline HfO2 besides the parent cubic phase and amorphous phase. Ex situ x-ray diffraction measurements on the pressure-cycled samples also indicated the presence of monoclinic HfO2. These results suggest that the observed pressure-induced amorphization (PIA) under hydrostatic compression is indeed due to hindered decomposition, which is facilitated under uniaxial compression. Thus, the behavior of HfW2O8 appears to be different from that of ZrW2O8, which exhibited only PIA and not pressure-induced decomposition at ambient temperature.
N-(sulfonyloxy)phthalimides and analogues are potent inactivators of serine proteases. (1994)

A series of 2-(sulfonyloxy) and 2-(acyloxy)-1H-isoindole-1,3(2H)-diones and analogous 1H-benz[de]isoquinoline-1,3(2H)-diones was prepared, and their potential to inactivate chymotrypsin was investigated. The N-(sulfonyloxy) and N-(acyloxy)phthalimides were found to be potent inactivators of chymotrypsin and related serine proteinases. For the most active compounds, N-(dansyloxy)phthalimide and N-(tosyloxy)phthalimide, the second-order rate constant of chymotrypsin inactivation was in the range of 250,000 m-1 s-1. N-(Mesyloxy)-phthalimide was the most active compound for inactivation of leukocyte elastase. It was shown that these compounds act as true suicide substrates. Enzyme-catalyzed opening of the heterocyclic ring results in the formation of an acyl-enzyme with attached O-acyl or O-sulfonylhydroxamic acid moiety. Subsequent Lossen rearrangement leads to the formation of a highly reactive isocyanate, which irreversibly modifies the target protease.
Shadow Detection and Sun Direction in Photo Collections (2015)

Modeling the appearance of outdoor scenes from photo collections is challenging because of appearance variation, especially due to illumination. In this paper we present a simple and robust algorithm for estimating illumination properties-shadows and sun direction-from photo collections. These properties are key to a variety of scene modeling applications, including outdoor intrinsic images, realistic 3D scene rendering, and temporally varying (4D) reconstruction. Our shadow detection method uses illumination ratios to analyze lighting independent of camera effects, and determines shadow labels for each 3D point in a reconstruction. These shadow labels can then be used to detect shadow boundaries and estimate sun direction, as well as to compute dense shadow labels in pixel space. We demonstrate our method on large Internet photo collections of scenes, and show that it outperforms prior multi-image shadow detection and sun direction estimation methods.
Dendritic Cells Exposed to Human Immunodeficiency Virus Type-1 Transmit a Vigorous Cytopathic Infection to CD4 + T Cells (1992)

The paucity of virus-laden CD4+ cells in individuals infected with human immunodeficiency virus type-1 (HIV-1) contrasts with the greatly reduced numbers and function of these lymphocytes. A pathway is described whereby dendritic cells carry HIV-1 to uninfected T cells, amplifying the cytopathic effects of small amounts of virus. After exposure to HIV-1, dendritic cells continue to present superantigens and antigens, forming clusters with T cells that are driven to replicate. Infection of the dendritic cells cannot be detected, but the clustered T cells form syncytia, release virions, and die. Carriage of HIV-1 by dendritic cells may facilitate the lysis and loss of antigen specific CD4+ T cells in acquired immunodeficiency syndrome.