gebhart/patrepeval huggingface dataset:
Nanoclay Based Composite Scaffolds for Bone Tissue Engineering Applications (2010)

Scaffolds based on chitosan/polygalacturonic acid (ChiPgA) complex containing montmorillonite (MMT) clay modified with 5-aminovaleric acid were prepared using freeze-drying technique. The MMT clay was introduced to improve mechanical properties of the scaffold. The microstructure of the scaffolds containing the modified MMT clay was influenced by the incorporation of nanoclays. The MTT assay also indicated that the number of osteoblast cells in ChiPgA scaffolds containing the modified clay was comparable to ChiPgA scaffolds containing hydroxyapatite known for its osteoconductive properties. Overall, the ChiPgA composite scaffolds were found to be biocompatible. This was also indicated by the scanning electron microscopy images of the ChiPgA composite scaffolds seeded with human osteoblast cells. Photoacoustic–Fourier transform infrared (PA-FTIR) experiments on the ChiPgA composite scaffolds indicated formation of a polyelectrolyte complex between chitosan and polygalacturonic acid. PA-FTIR studies also showed that the MMT clay modified with 5-aminovaleric acid was successfully incorporated in the ChiPgA based scaffolds. Swelling studies on ChiPgA composite scaffolds showed the swelling ability of the scaffolds that indicated that the cells and the nutrients would be able to reach the interior parts of the scaffolds. In addition to this, the ChiPgA scaffolds exhibited porosity greater than 90% as appropriate for scaffolds used in tissue engineering studies. High porosity facilitates the nutrient transport throughout the scaffold and also plays a role in the development of adequate vasculature throughout the scaffold. Compressive mechanical tests on the scaffolds showed that the ChiPgA composite scaffolds had compressive elastic moduli in the range of 4–6 MPa and appear to be affected by the high porosity of the scaffolds. Thus, the ChiPgA composite scaffolds containing MMT clay modified with 5-aminovaleric acid are biocompatible. Also, the ChiPgA scaffolds containing the modified MMT clay appears to satisfy some of the basic requirements of scaffolds for tissue engineering applications.
An Analog Modulator/Demodulator using a Programmable Arbitrary Waveform Generator (2005)

We present an analog implementation of a modulator/demodulator (programmable analog modulator/demodulator, PAMD) for analog signal processing applications. The PAMD architecture is fully programmable enabling it to be used for a variety of communication schemes and not specifically for a particular application. PAMD uses an architecture similar to a direct digital frequency synthesis implementation to generate the waveforms. We use our programmable floating-gate MOS transistors as analog memory cells to store easily programmed samples of the waveforms. Experimental results showing the programmability along with both modulation and demodulation using the presented architecture are presented. The IC prototype generating eight programmable waveforms was fabricated in a 0.5 /spl mu/m n-well CMOS process and occupies 0.95 mm/sup 2/ of area.
4-Amino-4-arylcyclohexanones and their derivatives, a novel class of analgesics. 1. Modification of the aryl ring (1980)

Investigation of central nervous system activity of phenylcyclohexylamines was continued by preparation of "reversed" analogues. Following the unexpected finding of analgesic activity with 1-(dimethylamino)-1-phenylcyclohexylamine, the SAR of the series was investigated. Synthesis starts by double Michael reaction of acrylate on arylacetonitriles. Following cyclization, decarboxylation, ketalization, and saponification, the geminally substituted acid is rearranged to the isocyanate by means of (C6H5O)2PON3. Isocyanates were then converted to the title compounds. Analgesic activity is very sensitive to the nature and position of the substitutent on the aromatic ring. The most potent compounds in this series (p-CH3, p-Br) showed 50% the potency of morphine. Deletion of the ring oxygen abolishes activity.
<i>Kluyveromyces lactis LAC4</i> Promoter Variants That Lack Function in Bacteria but Retain Full Function in <i>K. lactis</i> (2005)

The strong LAC4 promoter (P(LAC4)) from Kluyveromyces lactis has been extensively used to drive expression of heterologous proteins in this industrially important yeast. A drawback of this expression method is the serendipitous ability of P(LAC4) to promote gene expression in Escherichia coli. This can interfere with the process of assembling expression constructs in E. coli cells prior to their introduction into yeast cells, especially if the cloned gene encodes a protein that is detrimental to bacteria. In this study, we created a series of P(LAC4) variants by targeted mutagenesis of three DNA sequences (PBI, PBII, and PBIII) that resemble the E. coli Pribnow box element of bacterial promoters and that reside immediately upstream of two E. coli transcription initiation sites associated with P(LAC4). Mutation of PBI reduced the bacterial expression of a reporter protein (green fluorescent protein [GFP]) by approximately 87%, whereas mutation of PBII and PBIII had little effect on GFP expression. Deletion of all three sequences completely eliminated GFP expression. Additionally, each promoter variant expressed human serum albumin in K. lactis cells to levels comparable to wild-type P(LAC4). We created a novel integrative expression vector (pKLAC1) containing the P(LAC4) variant lacking PBI and used it to successfully clone and express the catalytic subunit of bovine enterokinase, a protease that has historically been problematic in E. coli cells. The pKLAC1 vector should aid in the cloning of other potentially toxic genes in E. coli prior to their expression in K. lactis.
Isolation of<i>Arabidopsis thaliana</i>cDNAs That Confer Yeast Boric Acid Tolerance (2006)

An Arabidopsis thaliana cDNA library was introduced into a Saccharomyces cerevisiae mutant that lacks ScBOR1 (YNL275W), a boron (B) efflux transporter. Five cDNAs were identified that confer tolerance to high boric acid. The nucleotide sequence analysis identified the clones as a polyadenylate-binding protein, AtPAB2; a ribosomal small subunit protein, AtRPS20B; an RNA-binding protein, AtRBP47c'; and two Myb transcription factors, AtMYB13 and AtMYB68. The expression of these five genes also conferred boric acid tolerance on wild-type yeast. Two yeast genes, ScRPS20 and ScHRB1, that are similar to the isolated clones, were necessary for this boric acid tolerance. The possible roles of these A. thaliana and S. cerevisiae genes in boric acid tolerance are discussed.
Turbo-coded pragmatic trellis coded modulation using coset mapping (2004)

This paper presents the application of turbo coding technique combined with bandwidth efficient method known as trellis coded modulation (TCM). A transformation apply to the incoming I-channel and Q-channel symbols allows to use off-the-self B/QPSK turbo decoder without any modifications. A conventional turbo decoder then operates on transformed symbols to estimate the coded bits. The uncoded bits are decoded based on the estimated coded bits and locations of the received symbols.
KNET: A General Framework for Learning Word Embedding using Morphological Knowledge (2014)

Neural network techniques are widely applied to obtain high-quality distributed representations of words, i.e., word embeddings, to address text mining, information retrieval, and natural language processing tasks. Recently, efficient methods have been proposed to learn word embeddings from context that captures both semantic and syntactic relationships between words. However, it is challenging to handle unseen words or rare words with insufficient context. In this paper, inspired by the study on word recognition process in cognitive psychology, we propose to take advantage of seemingly less obvious but essentially important morphological knowledge to address these challenges. In particular, we introduce a novel neural network architecture called KNET that leverages both contextual information and morphological word similarity built based on morphological knowledge to learn word embeddings. Meanwhile, the learning architecture is also able to refine the pre-defined morphological knowledge and obtain more accurate word similarity. Experiments on an analogical reasoning task and a word similarity task both demonstrate that the proposed KNET framework can greatly enhance the effectiveness of word embeddings.
IKK phosphorylates RelB to modulate its promoter specificity and promote fibroblast migration downstream of TNF receptors (2014)

TNFα is a potent cytokine that plays a critical role in numerous cellular processes, particularly immune and inflammatory responses, programmed cell death, angiogenesis, and cell migration. Thus, understanding the molecular mechanisms that mediate TNFα-induced cellular responses is a crucial issue. It is generally accepted that global DNA binding activity of the NF-κB avian reticuloendotheliosis viral (v-rel) oncogene related B (RelB) subunit is not induced upon TNFα treatment in fibroblasts, despite its TNFα-induced nuclear accumulation. Here, we demonstrate that RelB plays a critical role in promoting fibroblast migration upon prolonged TNFα treatment. We identified the two kinases IκB kinase α (IKKα) and IκB kinase β (IKKβ) as RelB interacting partners whose activation by TNFα promotes RelB phosphorylation at serine 472. Once phosphorylated on serine 472, nuclear RelB dissociates from its interaction with the inhibitory protein IκBα and binds to the promoter of critical migration-associated genes, such as the matrix metallopeptidase 3 (MMP3). Further, we show that RelB serine 472 phosphorylation status controls MMP3 expression and promigration activity downstream of TNF receptors. Our findings provide new insights into the regulation of RelB activity and reveal a novel link between selective NF-κB target gene expression and cellular response in response to TNFα.
CONCRETE BRIDGE PROTECTION, REPAIR, AND REHABILITATION RELATIVE TO REINFORCEMENT CORROSION: A METHODS APPLICATION MANUAL (1993)

This manual is a practical guide for state highway agency personnel who are faced with the day-to-day task of cost-effectively protecting repairing, and rehabilitating concrete bridges exposed to chloride laden environments. The manual addresses the chloride induced corrosion of reinforcing steel. Methods are presented to estimate the service life and remaining service life of concrete bridge components. Economic models are presented to enable selection of the most cost effective methods. These methods include standard physical, chemical, and experimental protection, repair, and rehabilitation. Also, rapid bridge deck protection, repair, and rehabilitation methods are presented. Two mechanized concrete removal methods, milling and hydrodemolition, are compared to the traditional method, pneumatic breakers. The advantages of combining the strengths of the three removal methods are also presented.
New approaches towards automated oligoribonucleotide synthesis. (1991)

Several protecting group combinations have been investigated to achieve an automated oligoribonucleotide synthesis on a solid support. The use of 2'-O-tert-butyldimethylsilyl-5'-O-monomethoxytrityl-ribonucleoside -3'-(p-nitrophenylethyl, N,N-diethyl)-phosphoramidites in conjunction with beta-eliminating blocking groups at the aglycone gave satisfactory results. An inverse protecting group strategy based upon analogously substituted 5'-O-2-dansylethoxycarbonyl-2'-O-4- methoxytetrahydropyran-4-yl-phosphoramidites can be regarded as another promising approach.
Simultaneous false‐colour imaging of birefringence, extinction and transmittance at camera speed (2007)

A polarized light imaging technique is introduced that simultaneously captures and unfolds transmittance, fast/slow axes directions and birefringence or linear dichroism from single camera exposures. The technique, based on the rotating polarizer method, is capable of sampling an object through polarizers at four different angles in a single image with the use of an image multiplexer. The range of possible applications is demonstrated with examples from the fields of biology, medicine, forensics and material sciences.
Upgrade of Highly Available Systems: Formal Methods at the Rescue (2017)

High Availability (HA) is a quality of service that is required for many services, e.g. carrier grade services. Systems providing such services undergo upgrades, e.g. software version upgrade, like any other system. Avoiding/limiting service outage during these upgrades is of critical importance to meet the HA requirement. Thus, the upgrade campaign specifications, which drive the process need to be designed and evaluated properly. In this paper we discuss how modeling, automation and formal methods can help to design appropriate upgrade campaigns. We discuss our methods for upgrade campaign specification generation and evaluation with respect to the execution time and induced service outage.
Identification of a site on herpes simplex virus type 1 glycoprotein D that is essential for infectivity (1990)

Herpes simplex virus glycoprotein D (gD) plays an essential role during penetration of the virus into cells. There is evidence that it recognizes a specific receptor after initial attachment of virions to cell surface heparan sulfate and also that gD-1, gD-2, and gp50 (the pseudorabies virus gD homolog) bind to the same receptor. Although the antigenic structure of gD has been studied intensively, little is known about functional regions of the protein. Antigenic site I is a major target for neutralizing antibodies and has been partially mapped by using deletion mutants and neutralization-resistant viruses. Working on the assumption that such a site may overlap with a functional region of gD, we showed previously that combining two or more amino acid substitutions within site I prevents gD-1 from functioning and is therefore lethal. We have now used a complementation assay to measure the functional activity of a panel of deletion mutants and compared the results with an antigenic analysis. Several mutations cause gross changes in protein folding and destroy functional activity, whereas deletions at the N and C termini have little or no effect on either. In contrast, deletion of residues 234 to 244 has only localized effects on antigenicity but completely abolishes functional activity. This region, which is part of antigenic site Ib, is therefore essential for gD-1 function. The complementation assay was also used to show that a gD-negative type 1 virus can be rescued by gD-2 and by two gD-1-gD-2 hybrids but not by gp50, providing some support for the existence of a common receptor for herpes simplex virus types 1 and 2 but not pseudorabies virus. Alternatively, gp50 may lack a signal for incorporation into herpes simplex virions.
<title>Interactive electronic biopsy for 3D virtual colonscopy</title> (2001)

We propose an interactive electronic biopsy technique for more accurate colon cancer diagnoses by using advanced volume rendering technologies. The volume rendering technique defines a transfer function to map different ranges of sample values of the original volume data to different colors and opacities, so that the interior structure of the polyps can be clearly recognized by human eyes. Specifically, we provide a user- friendly interface for physicians to modify various parameters in the transfer function, so that the physician can interactively change the transfer function to observe the interior structures inside the abnormalities. Furthermore, to speed up the volume rendering procedure, we propose an efficient space-leaping technique by observing that the virtual camera parameters are often fixed when the physician modifies the transfer function. In addition, we provide an important tool to display the original 2D CT image at the current 3D camera position, so that the physician is able to double check the interior structure of a polyp with the density variation in the corresponding CT image for confirmation. Compared with the traditional biopsy in the procedure of optical colonoscopy, our method is more flexible, noninvasive, and therefore without risk.
Process for the preparation of acetic acid, acetaldehyde and ethanol from synthesis gas. Verfahren zur Herstellung von Essigsaeure, Acetaldehyd und Ethanol aus Synthesegas (1982)

For an improvement of the service life of catalysts employed for converting synthesis gas to acetic acid, acetaldehyde and ethanol, temperature will be increased in small steps only within 100-1,000 h on reaching a temperature range of 75-125/sup 0/C below operation temperature. This measure will also result in an increased selectivity for the oxygen-containing compounds desired for production and will remain so on reaching operation temperature. The catalysts consist of rhodium with promoters added if necessary.
Effect of impurities in wet-process phosphoric acids on DAP grades. [Diammonium phosphate] (1980)

Results of this study identify the main problems in meeting diammonium phosphate (DAP) grade specifications and suggest some possible solutions to these problems as follows: 1. The major source of grade deficiency in the commercial samples which were investigated was calcium. Some solutions to this problem are to maintain filter cloths in the phosphoric acid unit in good condition, operate the phosphoric acid unit at as low an acid temperature as consistent with good operation of this unit, and partially clarify the acid before it is used. 2. In the DAP unit the amount of Fe/sub 2/O/sub 3/ and F in the acid affects the content of C.I. P/sub 2/O/sub 5/ in the product. If the F:Fe/sub 2/O/sub 3/ wt ratio in the product can be kept above 2.3:1, probably the C.I.-P/sub 2/O/sub 5/ content of the product will be less than 0.1 percent. At lower F:Fe/sub 2/O/sub 3/ wt ratios, it is advantageous to have low retention times in the preneutralizer and ammoniator-granulator when the N:P mole ratio is 1.4:1 or higher. 3. Other data show that the N:P mole ratio in the slurry from the preneutralizer to the granulator must be above 1.4:1 to avoid nitrogen deficiencies. Atmore » lower ratios the product will contain some MAP; this causes nitrogen deficiency in the products. 4. The Mg and Al contents of the acids have less effect on grade deficiency than Ca and Fe. 5. To avoid highly viscous preneutralizer slurries when low preneutralizer retention times are used, ensure that there is sufficient F available (F:Fe/sub 2/O/sub 3/ wt ratio > 2.0:1) to combine with the Fe/sub 2/O/sub 3/ to form coarse crystals. An alternative to this latter suggestion is to replace the preneutralizer with a TVA pipe reactor which is partially installed in the granulator and discharges viscous slurry directly onto the bed of material in the granulator.« less
Discriminability Objective for Training Descriptive Captions (2018)

One property that remains lacking in image captions generated by contemporary methods is discriminability: being able to tell two images apart given the caption for one of them. We propose a way to improve this aspect of caption generation. By incorporating into the captioning training objective a loss component directly related to ability (by a machine) to disambiguate image/caption matches, we obtain systems that produce much more discriminative caption, according to human evaluation. Remarkably, our approach leads to improvement in other aspects of generated captions, reflected by a battery of standard scores such as BLEU, SPICE etc. Our approach is modular and can be applied to a variety of model/loss combinations commonly proposed for image captioning.
Abstract IA29: Peptide-TLR-7/8 agonist conjugate vaccines chemically programmed for nanoparticle self-assembly to enhance the magnitude and breadth of anticancer neoantigen CD8 T cell immunity (2019)

Abstract T cells recognizing tumor-specific neoantigens can mediate effective anti-tumor immunity and provide the rationale for personalized cancer vaccines (PCVs). Current approaches for PCVs include synthetic long peptides given with adjuvants or RNA vaccines. Such approaches induce de novo CD8 T cell responses in ~10% or less of predicted neoantigens. Here, we focused on how peptide based neoantigen vaccines could be altered to enhance the magnitude and breadth of CD8 T cells. A key finding was that particulate peptide antigens, unlike soluble peptide antigens, are more efficiently taken up by dendritic cells in draining lymphoid tissue for increasing CD8 T cell expansion. However, due to the broad range of neoantigen physicochemical properties, ensuring consistent particle vaccine formulations with neoantigen peptides is a major challenge. Therefore, we developed a new PCV platform based on charge-modified peptide-TLR-7/8 agonist conjugates that are chemically programmed for self-assembling into nanoparticles (“SNP-7/8a”) of a defined size (20–50 nm) irrespective of the underlying neoantigen peptide composition. Bioinformatics analysis of 72 million human genome-derived neoantigens shows that SNP-7/8a ensures consistent nanoparticle formation with neoantigens at extremes of charge and hydropathy. Vaccination of mice with SNP-7/8a using predicted neoantigens (n = 179) from three tumor models induced CD8 T cells in ~50% of those with high predicted MHC-I binding affinity (IEDB consensus score &lt; 0.5). Moreover, therapeutic vaccination with SNP-7/8a enhanced tumor clearance in tumor models using neoantigens, self-antigens or viral antigens. Overall, the SNP-7/8a PCV is a universal approach for co-delivering peptide antigens and immune adjuvants in nanoparticles to enhance anticancer T cell immunity. Citation Format: Geoffrey M. Lynn, Faezzah Baharom, Yaling Zhu, Vincent Coble, Andrei Ramirez-Valdez, Hide Yamane, Kennedy Tobin, Brennan Decker, Andrew Ishizuka, Robert Seder. Peptide-TLR-7/8 agonist conjugate vaccines chemically programmed for nanoparticle self-assembly to enhance the magnitude and breadth of anticancer neoantigen CD8 T cell immunity [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr IA29.
Mass Analysis of Mobility-Selected Ion Populations Using Dual Gate, Ion Mobility, Quadrupole Ion Trap Mass Spectrometry (2005)

An electrospray ionization, dual gate, ion mobility, quadrupole ion trap mass spectrometer (ESI-DG-IM-QIT-MS) was constructed and evaluated for its ability to select mobility-filtered ions prior to mass analysis. While modification of the common signal-averaged ion mobility experiment was required, no modifications to the QIT were necessary. The dual gate scanning mode of operation was used to acquire mobility spectra, whereas the single mobility monitoring experiment selectively filtered ions for concentration and subsequent fragmentation within the QIT. Ion mobility separation of positively charged peptides and negatively charged carbohydrates, followed by MS fragmentation, was demonstrated. For a 1-min acquisition time, it was possible to obtain complete de novo sequence information for the examined peptides. Fragmentation of the negative carbohydrate chlorine adducts yielded ions characteristic of cross-ring and glycosidic bond cleavage. Previous unions of atmospheric pressure ion mobility and mass spectrometry have been limited in their ability to reproducibly obtain MSn data for mobility separation ions. The union of high-pressure ion mobility with quadrupole ion trap mass spectrometry presents the unique opportunity to obtain more detailed information regarding the chemistries of gas-phase ions.