gebhart/patrepeval huggingface dataset:
Pectins and pectic-oligosaccharides inhibitEscherichia coliO157:H7 Shiga toxin as directed towards the human colonic cell line HT29 (2003)

Pectins and pectic-oligosaccharides, as derived by controlled enzymatic hydrolysis, were evaluated for their ability to interfere with the toxicity of Shiga-like toxins from Escherichia coli O157:H7. Both types of material resulted in some degree of protection but this was significantly higher (P>0.01) with the oligosaccharide fractions (giving 90-100% cell survival, compared to 70-80% with the polymer). An effect of methylation on the protective effect was detected with lower degrees being more active. The pectic-oligosaccharides and galabiose, the minimum toxin receptor analogue, were shown to inhibit toxicity and were both protective at 10 mg x ml(-1), but not at lower concentrations.
Reference reconciliation in complex information spaces (2005)

Reference reconciliation is the problem of identifying when different references (i.e., sets of attribute values) in a dataset correspond to the same real-world entity. Most previous literature assumed references to a single class that had a fair number of attributes (e.g., research publications). We consider complex information spaces: our references belong to multiple related classes and each reference may have very few attribute values. A prime example of such a space is Personal Information Management, where the goal is to provide a coherent view of all the information on one's desktop.Our reconciliation algorithm has three principal features. First, we exploit the associations between references to design new methods for reference comparison. Second, we propagate information between reconciliation decisions to accumulate positive and negative evidences. Third, we gradually enrich references by merging attribute values. Our experiments show that (1) we considerably improve precision and recall over standard methods on a diverse set of personal information datasets, and (2) there are advantages to using our algorithm even on a standard citation dataset benchmark.
RNAi-mediated suppression of p -coumaroyl-CoA 3′-hydroxylase in hybrid poplar impacts lignin deposition and soluble secondary metabolism (2008)

p-Coumaroyl-CoA 3'-hydroxylase (C3'H) is a cytochrome P450-dependent monooxygenase that catalyzes the 3'-hydroxylation of p-coumaroyl shikimate and p-coumaroyl quinate. We used RNA interference to generate transgenic hybrid poplar suppressed in C3'H expression and analyzed them with respect to transcript abundance, cell wall structure and chemical composition, and soluble metabolite levels. RT-PCR expression profiles confirmed the down-regulation of C3'H in a number of lines, which generally correlated very well with reduced total cell wall lignin content. The most strongly repressed line was chosen for further analysis and compared with the wild-type trees. In-depth characterization revealed that along with the significant decrease in total lignin content, a significant shift in lignin monomer composition was observed, favoring the generation of p-hydroxyphenyl units at the expense of guaiacyl units while the proportion of syringyl moieties remained constant. Suppression of C3'H also resulted in the accumulation of substantial pools of 1-O-p-coumaroyl-beta-d-glucoside and other phenylpropanoid glycosides, and p-coumaroyl shikimate, providing further insight into the role of C3'H in the lignin biosynthetic pathway. The data presented indicate that when down-regulated, C3'H becomes a rate-limiting step in lignin biosynthesis and further support the involvement of hydroxycinnamic acid shikimate esters in the lignin biosynthetic pathway.
Mechanism of Arsenic Sorption by Hydrated Lime (1997)

Arsenic, along with mercury and selenium, represents one of the trace metallic emissions from fossil fuel-fired power plants that exhibit a tendency to remain in the gas phase. In this study, the effectiveness of some commonly used mineral sorbents is tested for the removal of arsenic from flue gas. Investigations are conducted with hydrated lime sorbent to identify the mechanism of As/Ca interaction and the chemical state and characteristics of captured species. Arsenic oxide (As2O3) is used as the representative arsenic species, and investigations are conducted in a differential fixed bed reactor at medium (400−600 °C) and high (1000−800 °C) temperature conditions. Comparison of Ca(OH)2 with three other mineral sorbents (kaolinite, alumina, and silica) reveals that calcium hydroxide is the most effective in capturing arsenic. The capture mechanism of Ca(OH)2 does not involve a simple physical adsorption but proceeds by means of an irreversible chemical reaction leading to a solid product. X-ray diffraction and ion chromatography analyses of the post-sorption sample confirm that calcium arsenate is the dominant reaction product. Sorption of arsenic by fly ash is found to be reversible and physical in nature.
&lt;italic&gt;nifH&lt;/italic&gt; Promoter Activity Is Regulated by DNA Supercoiling in &lt;italic&gt;Sinorhizobium meliloti&lt;/italic&gt; (2005)

In prokaryotes, DNA supercoiling regulates the expression of many genes; for example, the expression of Klebsiella pneumoniae nifLA operon depends on DNA negative supercoiling in anaerobically grown cells, which indicates that DNA supercoiling might play a role in gene regulation of the anaerobic response. Since the expression of the nifH promoter in Sinorhizobium meliloti is not repressed by oxygen, it is proposed that the status of DNA supercoiling may not affect the expression of the nifH promoter. We tested this hypothesis by analyzing nifH promoter activity in wild-type and gyr- Escherichia coli in the presence and absence of DNA gyrase inhibitors. Our results show that gene expression driven by the S. meliloti nifH promoter requires the presence of active DNA gyrase. Because DNA gyrase increases the number of negative superhelical turns in DNA in the presence of ATP, our data indicate that negative supercoiling is also important for nifH promoter activity. Our study also shows that the DNA supercoiling-dependent S. meliloti nifH promoter activity is related to the trans-acting factors NtrC and NifA that activate it. DNA supercoiling appeared to have a stronger effect on NtrC-activated nifH promoter activity than on NifA-activated promoter activity. Collectively, these results from the S. meliloti nifH promoter model system seem to indicate that, in addition to regulating gene expression during anaerobic signaling, DNA supercoiling may also provide a favorable topology for trans-acting factor binding and promoter activation regardless of oxygen status.
Regulation of Transcription Factor Pdr1p Function by an Hsp70 Protein in Saccharomyces cerevisiae (1998)

Multiple or pleiotropic drug resistance in the yeast Saccharomyces cerevisiae requires the expression of several ATP binding cassette transporter-encoding genes under the control of the zinc finger-containing transcription factor Pdrlp. The ATP binding cassette transporter-encoding genes regulated by Pdrlp include PDR5 and YOR1, which are required for normal cycloheximide and oligomycin tolerances, respectively. We have isolated a new member of the PDR gene family that encodes a member of the Hsp70 family of proteins found in this organism. This gene has been designated PDR13 and is required for normal growth. Overexpression of Pdr13p leads to an increase in both the expression of PDR5 and YOR1 and a corresponding enhancement in drug resistance. Pdr13p requires the presence of both the PDR1 structural gene and the Pdr1p binding sites in target promoters to mediate its effect on drug resistance and gene expression. A dominant, gain-of-function mutant allele of PDR13 was isolated and shown to have the same phenotypic effects as when the gene is present on a 2microm plasmid. Genetic and Western blotting experiments indicated that Pdr13p exerts its effect on Pdr1p at a posttranslational step. These data support the view that Pdr13p influences pleiotropic drug resistance by enhancing the function of the transcriptional regulatory protein Pdr1p.
Recommendations for Intracranial Pressure Monitoring Technology (2000)

In patients who require ICP monitoring, a ventricular catheter connected to an external strain gauge transducer or catheter tip pressure transducer device is the most accurate reliable method of monitoring ICP and enables therapeutic CSF drainage. Clinically significant infections or hemorrhage associated with ICP devices causing patient morbidity are rare and should not deter the decision to monitor ICP. Parenchymal catheter tip pressure transducer devices measure ICP similar to ventricular ICP pressure but have the potential for significant measurement differences and drift due to the inability to recalibrate. These devices are advantageous when ventricular ICP is not obtained or if there is obstruction in the fluid couple. Subarachnoid or subdural fluid coupled devices and epidural ICP devices are currently less accurate.
One-Step Synthesis and Structure of an Oligo(spiro-orthocarbonate) (2002)

The reaction of pentaerythritol and tetraethylorthocarbonate at 260 degrees C for 12 h yields a white crystalline material that was characterized by 13C CPMAS NMR, CHN analysis, FT-IR, electron and X-ray powder diffraction, and Rietveld analysis. The white crystalline material was found to have the formula C6H8O4 and a crystal structure with a monoclinic cell [a = 9.167 A, b = 5.681 A, c = 5.880 A, beta = 90.0 degrees , space group I2] of hexagonally arranged spiro-oligomeric chains.
Allelic variation of the inducible costimulator (ICOS) gene: detection of polymorphisms, analysis of the promoter region, and extended haplotype estimation (2003)

The human chromosome region 2q33 including the three costimulatory molecules CD28, CTLA-4 and ICOS, has been subject to much attention due to its linkage to a number of autoimmune diseases. The search for the causal relationship of this linkage has revealed several polymorphisms, but no variations in the amino acid sequences, except for one polymorphism in the leader sequence of CTLA-4. In the present study, we examined the ICOS gene of an unrelated group of healthy donors from the Danish population. We were able to report 16 intronic SNP, one intronic G-insert and two repeat regions in intron 4, consistent with the [T]n and the [GT]n regions reported in a Japanese study. Putative haplotypes for the established SNP and repeat polymorphisms have been estimated by computational analysis. Sequencing of approximately 3500 bp of the upstream region of ICOS revealed an additional eight SNP of which two resided in putative NF-kB and Sp1 sites. In accordance with previous studies we detected no variations in the coding regions except for a rare polymorphism that was found in one donor in the last codon of exon 5, which lead to a heterozygous genotype, but no amino acid change. This suggests that regulation of transcription rather than protein structure could be a possible mechanism in the explanation of linkage.
On IEEE 802.14 medium access control protocol (1998)

In this article we present a comprehensive survey on the architecture, protocol issues, and standard of the hybrid fiber coaxial (HFC) networks which are evolving from the existing residential CATV networks. We first describe the HFC architecture and discuss the problems in providing two-way communication. Then, we identify three important medium access control (MAC) issues in designing the IEEE 802.14 standard; namely, synchronization, upstream channel access modes, and collision resolution. Resolutions adopted by the IEEE 802.14 Committee are illustrated after giving a protocol overview. Key resolutions include compensating round trip correction (RTC), interleaving minislots of data and request concurrently, and resolving collisions by multiple collision resolution engines, using the n-ary tree plus p-persistence algorithm with a first transmission rule. A comparative summary of some draft proposals that lead to the standard is given. Finally, we pinpoint two headend algorithms, minislot allocation and request scheduling, which are left open in the standard. They do not affect interoperability but may have a critical impact on performance.
Centralized marine control system (1986)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1986Centralized marine control systemAuthors: David E. AllenJeffrey W. CunkelmanWilliam M. KellyDavid E. AllenGSI, Jeffrey W. CunkelmanGSI, and William M. KellyGSIhttps://doi.org/10.1190/1.1892981 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1892981FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 1986ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1986 Pages: 715 publication data© 1986 Copyright © 1986 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 07 Mar 2005 CITATION INFORMATION David E. Allen, Jeffrey W. Cunkelman, and William M. Kelly, (1986), "Centralized marine control system," SEG Technical Program Expanded Abstracts : 643-644. https://doi.org/10.1190/1.1892981 Plain-Language Summary PDF DownloadLoading ...
Short Interfering RNA against Transient Receptor Potential Vanilloid 1 Attenuates Cisplatin-Induced Hearing Loss in the Rat (2008)

Cisplatin, a chemotherapeutic agent of choice for the treatment of solid tumors, produces hearing loss in approximately half a million new cancer patients annually in the United States. The hearing loss is due, in part, to increased generation of reactive oxygen species (ROS) in the cochlea, leading to lipid peroxidation and damage or death of outer hair cells in the organ of Corti. The cochlea expresses the transient receptor potential vanilloid 1 (TRPV1), which are normally expressed on small diameter neurons in the peripheral nervous system and mediate thermal sensitivity, but whose role in the cochlea is unclear. In this study, we show that TRPV1 is coregulated along with the NADPH oxidase isoform, NOX3, by cisplatin. Induction of these proteins by cisplatin is dependent on ROS generation, since it is reversed by systemic lipoic acid administration. In organ of Corti hair cell cultures (UB/OC-1 cells), cisplatin activates and induces TRPV1 and NOX3, leading to apoptosis of these cells. Inhibition of TRPV1 by capsazepine or ruthenium red reduced the apoptosis, implicating TRPV1 in this process. Treatment of UB/OC-1 cultures with short interfering RNA (siRNA) against either TRPV1 or NOX3 reduced cisplatin-induced apoptosis, while round window application of TRPV1 siRNA to rats reduced TRPV1 expression, decreased damage to outer hair cells and reduced cisplatin-induced hearing loss. These data provide a link between NOX3 and TRPV1 in cisplatin-induced hearing loss and suggest that targeting these proteins for knockdown by siRNA could serve as a novel approach in treating cisplatin ototoxicity.
Significant Breakthroughs in Search for Anti-Infectious Agents Derived from Erythromycin A (2011)

As a well-established class, macrolide antibiotics continue to enjoy a remarkable interest within pharmaceutical industry. Several stunning breakthroughs in semi-synthetic study of erythromycin A (EMA) contribute to the important role played by the macrolide class in search for new anti-infectious agents. Earlier structural modifications of EMA to address the issue of acid instability resulted in the first breakthrough in search for anti-infectious agents derived from EMA. Clarithromycin (CAM) and azithromycin (AZM) are two representative antibacterials commercialized during this period. Afterwards, continued research on the modifications of EMA to combat bacterial resistance culminated in the second breakthrough in this field. Telithromycin and cethromycin are two innovative antibacterials discovered in this period for treating community-acquired pneumonia (CAP). Recently, further structural modifications of EMA generate promising antibacterials endlessly, which will hopefully arouse another breakthrough in the near future. In this review, we will give an account of these breakthroughs and discuss the future directions of semi-synthetic research on EMA. In particular, the design and synthesis of some distinguished or promising antibacterials derived from EMA will be highlighted.
A novel adenosine triphosphate analog with a heavy atom to target the nucleotide binding site of proteins (1995)

We have synthesized 2'-deoxy-2'-iodoadenosine-5'-triphosphate (2'-IATP), a heavy-atom analog of adenosine-5'-triphosphate. This compound was made for X-ray structural studies to target the nucleotide site of ATP binding proteins. It was diffused successfully into crystals of the microtubule-based motor proteins ncd (non-claret disjunctional protein from Drosophila melanogaster) and kinesin. With ncd, the nucleotide binding site was 70% occupied and the crystals were able to diffract X-rays to 2.5 A. The iodo-analog provided a useful isomorphous derivative with overall phasing power 1.89 in the range of 25.0-2.5 A. With kinesin, 2'-IATP co-crystallized with the protein. The crystals diffracted to at least 2.8 A with a phasing power of 1.73 in the range of 20.0-5.0 A. The analog was also found to be a substrate for all of the enzymes tested, including creatine kinase, pyruvate kinase, hexokinase, and myosin, with values of Km and Vmax that were within a factor of 10 of those for ATP. The analog supported muscle contraction, relaxing fibers, and producing active tension with values not statistically different from those obtained with ATP. These results all suggest that this analog should be useful for providing a heavy-atom derivative for crystals of enzymes that bind ATP.
"Crossed-Field" and "EH" Antennas Including Radiation from the Feed Lines and Reflection from the Earth's Surface (2010)

An ongoing challenge in electrical engineering is the design of antennas whose size is small compared to the broadcast wavelength λ. One difficulty is that the radiation resistance of a small antenna is small compared to that of the typical transmission lines that feed the antenna,1 so that much of the power in the feed line is reflected off the antenna rather than radiated unless a matching network is used at the antenna terminals (with a large inductance for a small dipole antenna and a large capacitance for a small loop antenna). The radiation resistance of an antenna that emits dipole radiation is proportional to the square of the peak (electric or magnetic) dipole moment of the antenna. This dipole moment is roughly the product of the peak charge times the length of the antenna in the case of a linear (electric) antenna, and is the product of the peak current times the area of the antenna in the case of a loop (magnetic) antenna. Hence, it is hard to increase the radiation resistance of small linear or loop antennas by altering their shapes.2 One suggestion for a small antenna is the so-called “crossed-field ” antenna [2]. Its pro-ponents are not very explicit as to the design of this antenna, so this problem is based on a conjecture as to its motivation.3
Characterization of T Lymphocyte Responses During Primary Infection with Human Immunodeficiency Virus (1988)

The present study was undertaken to determine T cell response to primary human immunodeficiency virus (HIV) infection. No significant difference in T cell subsets was found between subjects who later seroconverted and a group of controls. Six subjects had multiple enumerations of T cell subsets done at the time of seroconversion. Initially, total lymphocyte and T cell subset counts were reduced. An inversion of the CD4+:CD8+ ratio due to a rise in the level of CD8+ cells was found later, followed by an appreciable increase in the number of CD8+ cells and further inversion of the CD4+:CD8+ ratio. Finally, the CD8+ cell count returned toward normal but remained higher than the CD4+ cell count; the inverted ratio was maintained. Lymphocyte hyporesponsiveness to mitogens and antigens was found during the seroconversion illness in one subject. In three of five subjects for whom data were available, an increase in the absolute number of CD8+ cells followed a decrease in the serum HIV antigen level.
Properties of carbon onions produced by an arc discharge in water (2002)

A simple method to fabricate high-quality nanoparticles including spherical carbon onions and elongated fullerene-like nanoparticles similar to nanotubes in large quantities without the use of vacuum equipment is reported. The nanoparticles are obtained in the form of floating powder on the water surface following an arc discharge between two graphite electrodes submerged in water. High-resolution transmission electron microscopy (HRTEM) and scanning electron microscopy images confirm the presence of spherical carbon onions with diameters ranging from 4 to 36 nm. The specific surface area of the floating powder was found to be very large, 984.3 m2/g, indicating that the material is promising for gas storage. From the surface area measurements, the mean particle diameter was calculated to be 3.7 nm. This value is close to the lower limit of the carbon onions observed in HRTEM. However, closer HRTEM observations also reveal that some carbon onions are not well crystallized. The large specific surface area can be attributed to the “surface roughness” induced by the defective nature of the carbon onion shells. To explain the formation mechanism of the carbon onions, a model of arc discharge in water with two quenching zones is proposed: (1) the presence of ion current conducive for elongated nanoparticles growth and (2) the absence of ion current for isotropic growth of carbon onions. Based on this model, we propose that the physical characteristics of the product can be controlled.
Epidermal Growth Factor Receptor Protein Expression and Gene Amplification in Small Cell Carcinoma of the Urinary Bladder (2007)

EGFR is expressed in a subset of urinary bladder small cell carcinomas; however, expression of EGFR does not correlate with clinicopathologic variables. At the molecular level, EGFR overexpression in small cell carcinoma of the urinary bladder does not seem to be caused by gene amplification. The expression of EGFR raises the possibility that EGFR may be a potential therapeutic target in the treatment of this malignancy.
Prevention of Bioprosthetic Heart Valve Calcification: Strategies and Outcomes (2014)

Despite the significant advances in cardiac surgery, heart valve replacement still faces a dilemma. While mechanical valves offer lifelong durability they also commit patients to anticoagulation treatment for the rest of their life. On the other hand, bioprosthetic valves have superior hemodynamic performance but durability of the bioprosthesis limits their use to the elderly, with early onset calcification being the primary cause of biomaterial breakdown. Considering that bioprosthetic valves are not reliant upon anticoagulation, there has been much focus on measures to overcome their issues with durability. Firstly, the calcification process has been studied and factors such as young patient age, use of glutaraldehyde fixative, the presence of phospholipids along with cell debris in the valve tissue and mechanical stress have been identified to influence tissue mineralization. Therefore different calcification reduction strategies are being sought: new fixatives have been developed and tested and post-treatments have been added to tissue processing. This review presents the pathophysiology of tissue valve calcification and focuses on the multiple approaches developed to prevent bioprosthetic heart valve calcification, as well as on their general outcomes and translation to clinical applications.