gebhart/patrepeval huggingface dataset:
Effective Ways of Decreasing Acrylamide Content in Potato Crisps during Processing (2004)

The aim of this work was to examine the effect of blanching or soaking in different acid solutions on the acrylamide content in potato crisps. Furthermore, the effects of a shorter frying time and a lower frying temperature combined with a postdrying were investigated. Soaking or blanching of potato slices in acidic solutions decreased the pH of potato juice and increased the extraction of amino acids and sugars. Potato crisps obtained after such pretreatments were characterized by lower acrylamide content. The most effective extraction of free amino acids and sugars as well as the largest decrease of acrylamide content (90%) in crisps was obtained when potato slices were soaked in acetic acid solution for 60 min at 20 degrees C. Shorter frying time followed by postdrying resulted in low-moisture potato crisps. Furthermore, the postdrying treatment gave a decreases in acrylamide content of approximately 70% when potato slices were fried at 185 degrees C and approximately 80% when potato slices were fried at 160 degrees C. Effective ways of decreasing acrylamide content in crisps production have been found. Crisps with low acrylamide content and good sensory quality can be obtained either by blanching in acetic acid as pretreatment or by a short frying followed by postdrying.
Synthesis of Lignin Model Compounds -β-O-4 Linkage Compounds (1989)

This experiment was carried out to contribute to the synthetic methods of ligin model compounds. The ligin model compounds of arylglycerol--arylether structure were synthesized in high yield through three or four reaction steps. The starting compound was commercial 3, 4, 5-trimethoxyace tophenone and the final compounds were 1-(2-methoxyphenoxy)-2 - (3, 4, 5 - trimethoxyphenyl)-ethanol(IV), 1-(3, 4, 5-trimethoxyphenyl)-2-(2-methoxy-phenoxy)-propandiol-1,3 (VI), 1-(2, 6-dimethoxyphenoxy)-2-(3, 4, 5-trimethoxyphenyl)-ethanol (VIII), and 1-(3, 4, 5-trimethoxyphenyl)-2-(2, 6-dimethoxyphenoxy)-propandiol-1, 3 (X). The structures of synthetic compounds were identified by IR, -NMR spectroscopy and Mass spectrometry.
8 Recombination in Yeast (1991)

I. INTRODUCTION The exchange of information between DNA molecules is a process found in every organism that has been investigated in detail. Because recombination in eukaryotes occurs most frequently during meiosis after chromosome replication, much of our understanding of eukaryotic recombination is based on organisms (such as Saccharomyces cerevisiae) in which all products of an individual meiosis can be analyzed. In this chapter, we summarize studies of homologous recombination (meiotic and mitotic) in the yeast S. cerevisiae. We discuss less comprehensively recombination in the fission yeast Schizosaccharomyces pombe, emphasizing areas of research representing either particularly important contributions (e.g., the analysis of hot spots for meiotic recombination) or interesting contrasts with S. cerevisiae. The two goals of this chapter are (1) to introduce genetic studies of recombination and issues of interest in this area to yeast workers outside the immediate field and (2) to discuss recent recombination studies in the context of earlier work summarized in previous reviews (Esposito and Wagstaff 1981; Fogel et al. 1981; Orr-Weaver and Szostak 1985; Resnick 1987; Hastings 1988; Roeder and Stewart 1988; Thaler and Stahl 1988). This review is limited to general homologous recombination and does not concern exchanges catalyzed by specialized enzyme systems. As with other areas of yeast research, recombinant DNA procedures have had a major impact on studies of recombination (Haber et al. 1988; Petes and Hill 1988; Petes et al. 1989). Before we discuss meiotic and mitotic recombination in detail, we outline some of the general applications of this methodology to...
Extension of depth of field using amplitude and phase modulation of the pupil function (2008)

We analyze the extension of depth of field using both amplitude and phase modulation of the pupil function. In particular, we discuss the advantages and disadvantages of each approach and establish the range of applicability of each method based on the range of spatial frequencies of interest in the imaging system. To the best of our knowledge, this is the first such report on the range of applicability of amplitude and phase modulation to extend the depth of field.
Hydrocarbon Stapled Antimicrobial Peptides (2018)

Antimicrobial peptides are promising candidates for anti-infective pharmaceuticals. Unfortunately, because of their low proteolytic and chemical stability, their usage is generally narrowed down to topical formulations. Until now, numerous approaches to increase peptide stability have been proposed. One of them, peptide hydrocarbon stapling, a modification based on stabilizing peptide secondary structure with a side-chain covalent hydrocarbon bridge, have been successfully applied to many peptides. Moreover, constraining secondary structure of peptides have also been proven to increase their biological activity. This review article describes studies on hydrocarbon stapled antimicrobial peptides with respect to improved drug-like properties.
Effects of cytokines combined with high‐dose gamma irradiation on the expression of major histocompatibility complex molecules and intercellular adhesion molecule‐1 in human ovarian cancers (1996)

Tumor cells from 7 freshly isolated human ovarian tumors and 2 continuous human ovarian cancer cell lines were analyzed for their surface expression of MHC class-I, class-II and ICAM-I surface antigens before and after exposure to γ-irradiation and/or the cytokines TNF-α plus IFN-γ. All 7 fresh tumors expressed high levels of MHC class-I and ICAM-I antigens, and levels were markedly up-regulated after exposure to TNF-α plus IFN-γ. Similarly, class-II antigens were either induced (3 out of 7 tumors) or significantly up-regulated by TNF-α plus IFN-γ. Exposure to high doses of γ-irradiation also increased the expression of MHC class-I and ICAM-I antigens, albeit to a modest degree. MHC class-I and ICAM-I antigen expression was much lower on continuous human ovarian cell lines than on the fresh tumors. Exposure of these cells to TNF-α plus IFN-γ markedly up-regulated antigen expression to levels comparable to those expressed on the freshly isolated tumors. With the established ovarian cell lines, removal of cytokines caused a rapid down-regulation of antigen expression to basal levels within 6 days, while in the fresh tumors a low level of upregulation was still present at this time. In contrast, exposure to cytokines followed by high-dose γ-irradiation resulted in a highly significant and long-lasting expression of each surface antigen which was either up-regulated or induced by the cytokines. These data indicate that the combination of these modalities may be beneficial in generating optimal antigen expression for use of tumor cells in vaccine studies. © 1996 Wiley-Liss, Inc.
Calorimetric heats for CO and oxygen adsorption and for the catalytic CO oxidation reaction on Pt{111} (1997)

Single crystal adsorption calorimetry was applied to investigate the heats of adsorption of CO and oxygen and the reaction heats for the CO oxidation process on Pt{111} at room temperature. Both sticking probabilities and heats of adsorption for CO and oxygen are presented as a function of coverage. These results are used to interpret the subsequent measurements taken for the CO oxidation process on the same surface. The initial heats of adsorption of CO and oxygen on Pt{111} are 180±8 and 339±32 kJ/mol, respectively. In addition the pairwise lateral repulsive interaction between CO molecules in a (√3×√3)R30° ordered layer at θ=1/3 is found to be 4 kJ/mol. A detailed Monte Carlo modeling of the dissociative adsorption and sticking probability of oxygen on Pt{111} is performed. The initial rapid fall in heat is attributed to adsorption on defect sites, and subsequent adsorption on the planar {111} surface proceeds with a third neighbor interaction energy between the oxygen adatoms ω3∼22 kJ/mol. When gaseous CO reacts with preadsorbed oxygen adatoms, the CO2 produced has an excess energy of 16±8 kJ/mol.
Allelotype of pancreatic adenocarcinoma. (1994)

Knowledge of the patterns of allelic loss has been useful in identifying the spectrum of the tumor suppressor genes involved in various tumor types. Such analyses in pancreatic carcinoma have been difficult due to the characteristic host desmoplastic reaction to the neoplasm. We have assembled the first allelotype of pancreatic adenocarcinoma, a survey for allelic loss among each chromosomal arm, using seven cryostat-dissected neoplasms. The fractional allelic loss in these seven neoplasms was 0.18, a value similar to that seen previously in colorectal carcinoma. Alleles of chromosome 18q (lost in five of six informative tumors) and of chromosome 17p (lost in four of five informative tumors) were commonly affected. Neither APC mutations (33 neoplasms), allelic shifts of dinucleotide repeats (26 neoplasms), nor immunohistochemical evidence of retinoblastoma protein underexpression (7 neoplasms) were found. Further evaluation of allelic loss in pancreatic cancer would benefit from improved methods for the analysis of lost genetic material which overcome the problems posed by the high admixture of nonneoplastic stromal and inflammatory cells in these tumors.
Effects of high-frequency alternating current on axonal conduction through the vagus nerve (2011)

High-frequency alternating current (HFAC) is known to disrupt axonal conduction in peripheral nerves, and HFAC has much potential as a therapeutic approach for a number of pathological conditions. Many previous studies have utilized motor output as a bioassay of effects of HFAC on conduction through medium- to large-diameter motor axons. However, little is known about the effectiveness of HFAC on smaller, more slowly conducting nerve fibres. The present study tested whether HFAC influences axonal conduction through sub-diaphragmatic levels of the rat vagus nerve, which consists almost entirely of small calibre axons. Using an isolated nerve preparation, we tested the effects of HFAC on electrically evoked compound action potentials (CAPs). We found that delivery of charge-balanced HFAC at 5000 Hz for 1 min was effective in producing reversible blockade of axonal conduction. Both Aδ and C components of the vagus CAP were attenuated, and the degree of blockade as well as time to recovery was proportional to the amount of HFAC current delivered. The Aδ waves were more sensitive than C waves to HFAC blockade, but they required more time to recover.
Toxic encephalopathy associated with use of DEET insect repellents: a case analysis of its toxicity in children (2001)

(1) Respiratory distress and seizures developed in an 18-month-old boy following brief exposure to low-strength (17.6%) N,N-diethyl-m-toluamide (DEET). A review of the literature revealed 17 reports of DEET-induced encephalopathy in children. The objective of this study was to test the hypothesis that the potential toxicity of DEET is high and that available repellents containing DEET, irrespective of their strength, are not safe when applied to children's skin. (2) Although this is a case report, we used the features of published reports of DEET-induced encephalopathy in children to support the diagnosis, since the evidence that the child's illness was caused by DEET was circumstantial. In the following case analysis, clinical reports of children < 16 years old have been reviewed and analyzed in an effort to relate direct DEET toxicity to various clinical, demographic, and toxic compound exposure factors (Fisher's exacttest and logistic regression analysis). (3) DEET-induced encephalopathy in children (56% girls) followed not only ingestion or repeated and extensive application of repellents, but also a brief exposure to DEET (45%). Of those who reported a dermal exposure, 33% reported an exposure to a product containing DEET < 20%. Seizures, the most prominent symptom (72%), were significantly more frequent when DEET solutions were applied to the skin (P<0.01). Mortality (16.6%) did not correlate significantly with the concentration of the DEET liquid used, duration of skin exposure, pattern of use, age, or sex. (4) Data of this case analysis suggest that repellents containing DEET are not safe when applied to children's skin and should be avoided in children. Additionally, since the potential toxicity of DEET is high, less toxic preparations should be probably substituted for DEET-containing repellents, whenever possible.
An Iron Oxide Nanocarrier for dsRNA to Target Lymph Nodes and Strongly Activate Cells of the Immune System (2014)

The success of nanoparticle-based therapies will depend in part on accurate delivery to target receptors and organs. There is, therefore, considerable potential in nanoparticles which achieve delivery of the right drug(s) using the right route of administration to the right location at the right time, monitoring the process by non-invasive molecular imaging. A challenge is harnessing immunotherapy via activation of Toll-like receptors (TLRs) for the development of vaccines against major infectious diseases and cancer. In immunotherapy, delivery of the vaccine components to lymph nodes (LNs) is essential for effective stimulation of the immune response. Although some promising advances have been made, delivering therapeutics to LNs remains challenging. It is here shown that iron-oxide nanoparticles can be engineered to combine in a single and small (<50 nm) nanocarrier complementary multimodal imaging features with the immunostimulatory activity of polyinosinic-polycytidylic acid (poly (I:C)). Whilst the fluorescence properties of the nanocarrier show effective delivery to endosomes and TLR3 in antigen presenting cells, MRI/SPECT imaging reveals effective delivery to LNs. Importantly, in vitro and in vivo studies show that, using this nanocarrier, the immunostimulatory activity of poly (I:C) is greatly enhanced. These nanocarriers have considerable potential for cancer diagnosis and the development of new targeted and programmable immunotherapies.
Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis (2011)

Supplementary data are available at Bioinformatics online.
Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. (1994)

The maintenance of transcriptional silencing at HM mating-type loci and telomeres in yeast requires the SIR2, SIR3, and SIR4 proteins, none of which appear to be DNA-binding proteins. Here we show that SIR3 and SIR4 interact with a carboxy-terminal domain of the silencer, telomere, and UAS-binding protein RAP1. We identified SIR3 and SIR4 in a two-hybrid screen for RAP1-interacting factors and showed that SIR3 interacts both with itself and with SIR4. The interaction between RAP1 and SIR3 can be observed in vitro in the absence of other yeast proteins. Consistent with the notion that native SIR proteins interact with the RAP1 carboxyl terminus, we show that mutation of the endogenous SIR3 and SIR4 genes increases transcriptional activation by LexA/RAP1 hybrids. To test the importance of the RAP1-SIR3 interaction for silencing, we identified mutations in the RAP1 carboxyl terminus that either diminish or abolish this interaction. When introduced into the native RAP1 protein, these mutations cause corresponding defects in silencing at both HMR and telomeres. We propose that RAP1 acts in the initiation of transcriptional silencing by recruiting a complex of SIR proteins to the chromosome via protein-protein interactions. These data are consistent with a model in which SIR3 and SIR4 play a structural role in the maintenance of silent chromatin and indicate that their action is initiated at the silencer itself.
A Comparison of Methods for Plasmid Delivery into Plant Protoplasts (1984)

Three methods of plasmid delivery to mesophyll protoplasts of Nicotiana tabacum cv. Xanthi have been evaluated. Specifically; a) chemically stimulated uptake of isolated plasmid, b) delivery of plasmid encapsulated in liposomes, and c) fusion of plasmid-containing spheroplasts, were combined with divalent cation (Ca2+ and Mg2+) or polyalcohol [polyethylene glycol (PEG) and polyvinyl alcohol (PVA)] treatments. The quantity and quality of plasmid associated with intact protoplasts, was assessed by DNA-DNA blot hybridisation analysis, following stringent washing to separate intact protoplasts from non-viable protoplasts and debris. Treatments which increased association of plasmid with protoplasts decreased protoplast viability. Optimum association of plasmid with protoplasts, in the context of acceptable loss of viability, was achieved when protoplasts were interacted with either naked plasmid or liposomeencapsulated DNA in the presence of 15% w/v PEG 6000, or with Escherichia coli spheroplasts containing chloramphenicol-amplified plasmid in the presence of 25% w/v PEG 6000. Divalent cations did not stimulate significant plasmid delivery without unacceptable loss of protoplast viability. Strategies to further increase the efficiency of plasmid delivery are discussed.
Site‐directed mutagenesis of rabbit LAT1 at amino acids 219 and 234 (2003)

The availability of amino acids in the brain is regulated by the blood-brain barrier (BBB) large neutral amino acid transporter type 1 (LAT1) isoform, which is characterized by a high affinity (low Km) for substrate large neutral amino acids. The hypothesis that brain amino acid transport activity can be altered with single nucleotide polymorphisms was tested in the present studies with site-directed mutagenesis of the BBB LAT1. The rabbit has a high Km LAT1 large neutral amino acid transporter, as compared to the low Km neutral amino acid transporter at the human or rat BBB. The rabbit LAT1 was cloned from a rabbit brain capillary cDNA library. Alignment of the amino acid sequences of rabbit, human, and rat LAT1 revealed two radical amino acid residues that differ in the rabbit relative to the rat or human LAT1. The G219D mutation had a modest effect on the Km and Vmax of tryptophan transport via cloned rabbit LAT1 in frog oocytes, but the W234L variant reduced the Km by 64% and the Vmax by 96%. Conversely, LAT1 transport of either tryptophan or phenylalanine was nearly normalized when the double mutation W234L/G219D variant was produced. These studies show that marked changes in the affinity and capacity of the LAT1 are caused by single nucleotide polymorphisms and that phenotype can be restored with a double mutation.
A Geometric Programming Framework for Optimal Multi-Level Tiling (2005)

Determining the optimal tile size-one that minimizes the execution time-is a classical problem in compilation and performance tuning of loop kernels. Designing a model of the overall execution time of a tiled loop nest is an important subproblem. Both problems become harder when tiling is applied at multiple levels. We present a framework for determining the optimal tile sizes for a fully permutable, perfectly nested, rectangular loop with uniform dependences. Our framework supports multiple levels of tiling and uses a BSP style high level model for estimating the overall execution time of a loop program. In our framework, the problem of determining the optimal tile sizes, subject to memory capacity and bandwidth constraints, is modeled as a geometric program and transformed into a convex optimization problem, which can be solved efficiently. The model is validated through experimental results obtained by running twenty loop programs for different levels of tiling and different program and tile parameters. Our framework is very general and can also be used to solve the optimal tile size problem with many other models of execution time.
The Localization of the Specific Antigenic Protein in the Tissue of Paragonimus westermani Metacercaria (1997)

In order to observe the localization of the specific antigenic protein in the tissue of Paragonimus westermani metacercaria, immunogoldlabeling method was applied using IgG of the dog which were infected with Paragonimus westermani metacercaria and IgG of rabbits which were immunized with purified 23 kDa protein from metacercaria of the Paragenimus westermani. The metacercaria worm tissues obtained from Cambaroides similis were embedded in Lowicryl HM20 medium, treated with infected and immunized IgG and protein A gold complex (particle size; 12 nm) and observed by electron microscope. In the tissue antigen of Paragonimus westermani metacercaria, the content of excretory bladder which was highly dense electron density was constituted in the excretory bladder of the parenchymal tissue. In the metacercaria tissues antigen reacted with IgG of infected dog. Labeled gold particles distributed on the interstitial matrix of parenchymal cells, fibrous granules of parenchymal tissue and the content of excretory bladder. High antigenicity was observed on content of excretory bladder. It was found to be specifically distributed at the tissue of Paragonimus westermani metacercaria. In the tissues antigen reacted with IgG of immunized rabbit. Labeled gold particles randomly distributed on the interstitial matrix and fibrous granules of parenchymal tissue but in the content of excretory bladder of Paragonimus westermani metacercaria, gold particles were richly labeled. Therefore, the 23 kDa protein contained with Paragonimus westermani metacercaria was found protein which was specifically constituted at the content of excretory bladder of Paragonimum westermani metacercaria. The 23 kDa protein was commonly contained from of Paragonimus westermani metacercaria to adult and showed strong antigenicity against the immunized and infected IgG.
Siderophore-Based Iron Acquisition and Pathogen Control (2007)

High-affinity iron acquisition is mediated by siderophore-dependent pathways in the majority of pathogenic and nonpathogenic bacteria and fungi. Considerable progress has been made in characterizing and understanding mechanisms of siderophore synthesis, secretion, iron scavenging, and siderophore-delivered iron uptake and its release. The regulation of siderophore pathways reveals multilayer networks at the transcriptional and posttranscriptional levels. Due to the key role of many siderophores during virulence, coevolution led to sophisticated strategies of siderophore neutralization by mammals and (re)utilization by bacterial pathogens. Surprisingly, hosts also developed essential siderophore-based iron delivery and cell conversion pathways, which are of interest for diagnostic and therapeutic studies. In the last decades, natural and synthetic compounds have gained attention as potential therapeutics for iron-dependent treatment of infections and further diseases. Promising results for pathogen inhibition were obtained with various siderophore-antibiotic conjugates acting as "Trojan horse" toxins and siderophore pathway inhibitors. In this article, general aspects of siderophore-mediated iron acquisition, recent findings regarding iron-related pathogen-host interactions, and current strategies for iron-dependent pathogen control will be reviewed. Further concepts including the inhibition of novel siderophore pathway targets are discussed.