gebhart/patrepeval huggingface dataset:
The relationship between membrane fluidity and permeabilities to water, solutes, ammonia, and protons. (1995)

Several barrier epithelia such as renal collecting duct, urinary bladder, and gastric mucosa maintain high osmotic pH and solute gradients between body compartments and the blood by means of apical membranes of exceptionally low permeabilities. Although the mechanisms underlying these low permeabilities have been only poorly defined, low fluidity of the apical membrane has been postulated. The solubility diffusion model predicts that lower membrane fluidity will reduce permeability by reducing the ability of permeant molecules to diffuse through the lipid bilayer. However, little data compare membrane fluidity with permeability properties, and it is unclear whether fluidity determines permeability to all, or only some substances. We therefore studied the permeabilities of a series of artificial large unilamellar vesicles (LUV) of eight different compositions, exhibiting a range of fluidities encountered in biological membranes. Cholesterol and sphingomyelin content and acyl chain saturation were varied to create a range of fluidities. LUV anisotropy was measured as steady state fluorescence polarization of the lipophilic probe DPH. LUV permeabilities were determined by monitoring concentration-dependent or pH-sensitive quenching of entrapped carboxyfluorescein on a stopped-flow fluorimeter. The relation between DPH anisotropy and permeability to water, urea, acetamide, and NH3 was well fit in each instance by single exponential functions (r > 0.96), with lower fluidity corresponding to lower permeability. By contrast, proton permeability correlated only weakly with fluidity. We conclude that membrane fluidity determines permeability to most nonionic substances and that transmembrane proton flux occurs in a manner distinct from flux of other substances.
Introducing foreign genes into fish eggs with electroporated sperm as a carrier. (1993)

A new method has been developed for introduction of foreign genes into fish eggs. The procedure is based on the incubation of fish sperm cells suspended in dilute citrate solution with plasmid DNA, followed by application of high-field-strength electrical pulses (electroporation) to increase DNA binding., uptake, or both. Tissue homogenates and genomic DNA extracts of free swimming fry developed from eggs fertilized with treated sperm was tested to evaluate the efficiency of gene transfer. Dot blot hybridization and gene expression assay demonstrated the presence and expression of the reporter genes introduced in 2.6 to 4.2% of several hundreds of tested larvae of common carp (Cyprinus carpio L.), African catfish (Clarias gariepinus), and tilapia (Oreochromis niloticus). No transgene has been found in the fry resulting from parallel experiments without sperm electroporation. This is the first report on successful application of electroporated sperm cells for production of transgenic fish.
Arylboronic Acids. IV. Reactions of Boronophthalide1 (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTArylboronic Acids. IV. Reactions of Boronophthalide1W. J. Lennarz and H. R. SnyderCite this: J. Am. Chem. Soc. 1960, 82, 9, 2172–2175Publication Date (Print):May 1, 1960Publication History Published online1 May 2002Published inissue 1 May 1960https://pubs.acs.org/doi/10.1021/ja01494a021https://doi.org/10.1021/ja01494a021research-articleACS PublicationsRequest reuse permissionsArticle Views1051Altmetric-Citations33LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
An analysis of collaborative patterns in large-scale ontology development projects (2011)

Today, distributed teams collaboratively create and maintain more and more ontologies. To support this type of ontology development, software engineers are introducing a new generation of tools. However, we know relatively little about how existing large-scale collaborative ontology development works and what user workflows the tools must support. In this paper, we analyze our experience in supporting several such projects. We describe a visual and interactive project-management tool that we have developed, which helps ontology developers explore historical ontology change and discussion data. We present the results of qualitative and quantitative studies of the collaborative activity associated with three large-scale ontology-development projects. Based on the analysis, we conclude that domain and ontology experts have different patterns of ontology editing behavior, which has important implications for ontology-development tools.
The pathobiology of focal lesion development in aging human articular cartilage and molecular matrix changes characteristic of osteoarthritis (2003)

These results demonstrate that lesions seen in aging exhibit molecular changes in matrix turnover similar to those seen in OA articular cartilage at arthroplasty, but not in healthy normal aging cartilage. The direct relationships between type II collagen cleavage and denaturation and the inverse relationship between type II collagen content and cleavage or denaturation implicate collagenase activity and damage to collagen in this loss of collagen during lesion development. The lack of correlation of the increased synthesis with the degradation or content of type II collagen indicates that these aspects of turnover are not coordinated in the pathologic state. However, the direct relationship between collagen and GAG contents in and adjacent to the lesion illustrates the structural interrelationships of collagen and proteoglycan aggrecan molecules. These results suggest that these focal lesions represent the development of early OA and that this involves the progressive damage to articular cartilage surrounding the lesion as part of the process of the development of idiopathic OA.
Mechanism of oligonucleotide release from cationic liposomes. (1996)

We propose a mechanism for oligonucleotide (ODN) release from cationic lipid complexes in cells that accounts for various observations on cationic lipid-nucleic acid-cell interactions. Fluorescent confocal microscopy of cells treated with rhodamine-labeled cationic liposome/ fluorescein-labeled ODN (F-ODN) complexes show the F-ODN separates from the lipid after internalization and enters the nucleus leaving the fluorescent lipid in cytoplasmic structures. ODN displacement from the complex was studied by fluorescent resonance energy transfer. Anionic liposome compositions (e.g., phosphatidylserine) that mimic the cytoplasmic facing monolayer of the cell membrane released ODN from the complex at about a 1:1 (-/+) charge ratio. Release was independent of ionic strength and pH. Physical separation of the F-ODN from monovalent and multivalent cationic lipids was confirmed by gel electrophoresis. Fluid but not solid phase anionic liposomes are required, whereas the physical state of the cationic lipids does not effect the release. Water soluble molecules with a high negative linear charge density, dextran sulfate, or heparin also release ODN. However, ATP, spermidine, spermine, tRNA, DNA, polyglutamic acid, polylysine, bovine serum albumin, or histone did not release ODN, even at 100-fold charge excess (-/+). Based upon these results, we propose that the complex, after internalization by endocytosis, induces flip-flop of anionic lipids from the cytoplasmic facing monolayer. Anionic lipids laterally diffuse into the complex and form a charged neutralized ion-pair with the cationic lipids. This leads to displacement of the ODN from the cationic lipid and its release into the cytoplasm.
Regulation of Vascular Genes by Glucose (2005)

Endothelial dysfunction is an early sign of diabetic vascular disease. Due to their unique position at the border between blood and vascular tissue, endothelial cells (EC) are the first vascular cells to sensor humoral changes, and they are able to transmit the information about these changes to other vascular cell types by changing their gene expression profile and producing growth factors, cytokines, adhesion molecules, and other bioactive molecules. These signals alter vascular cell dynamics and interactions, vascular tone and result in inability of the vessel to maintain athrombogenic luminal surface and in alteration of vascular permeability. Although researchers have yet to uncover the precise mechanism(s) that leads to diabetic vascular disease, hyperglycemia has been identified as an independent risk factor for micro- and macrovascular complications. Elevated levels of glucose induce the expression of a variety of genes related to atherogenesis and angiogenesis regulation. However, most of our current knowledge about the molecular mechanisms used by glucose to regulate gene expression is based on studies that used cells with insulin-dependent glucose transport (hepatocytes, adipocytes). Such cells are significantly different than vascular cells, in which glucose uptake is mostly imparted by insulin-independent mechanisms. This review summarizes current information about the effects of hyperglycemia and elevated glucose in in vitro systems on vascular gene expression and molecular transcriptional and post-transcriptional mechanisms that may regulate the changes related to diabetic vascular complications.
Accurate Eye Center Location through Invariant Isocentric Patterns (2011)

Locating the center of the eyes allows for valuable information to be captured and used in a wide range of applications. Accurate eye center location can be determined using commercial eye-gaze trackers, but additional constraints and expensive hardware make these existing solutions unattractive and impossible to use on standard (i.e., visible wavelength), low-resolution images of eyes. Systems based solely on appearance are proposed in the literature, but their accuracy does not allow us to accurately locate and distinguish eye centers movements in these low-resolution settings. Our aim is to bridge this gap by locating the center of the eye within the area of the pupil on low-resolution images taken from a webcam or a similar device. The proposed method makes use of isophote properties to gain invariance to linear lighting changes (contrast and brightness), to achieve in-plane rotational invariance, and to keep low-computational costs. To further gain scale invariance, the approach is applied to a scale space pyramid. In this paper, we extensively test our approach for its robustness to changes in illumination, head pose, scale, occlusion, and eye rotation. We demonstrate that our system can achieve a significant improvement in accuracy over state-of-the-art techniques for eye center location in standard low-resolution imagery.
Reaction of bisulfite with the 5-hydroxymethyl group in pyrimidines and in phage DNAs (1979)

5-Hydroxymethylcytosine reacted with bisulfite and, instead of undergoing usual deamination process, gave cytosine 5-methylenesulfonate as the product. The conversion was rapid and quantitative, and the optimum pH was 4.5. The product was isolated as crystals and characterized. Cytosine 5-methylenesulfonate was only very slowly deaminated by treatment with bisulfite. 5-Hydroxymethyl-2'-deoxycytidine 5'-phosphate reacted with bisulfite in the same way as 5-hydroxymethylcytosine. Residues of 5-hydroxymethylcytosine in native as well as denatured T2 DNA were convertible to those of cytosine 5-methylenesulfonate by treatment of the DNA with bisulfite. While it is known that the 5-hydroxy-methyl groups of T-even bacteriophage DNA can be enzymatically glucosylated, this observation offers chemical evidence that the 5-hydrozymethyl groups in DNA are situated in such a way that they can readily react with external agents. 5-Hydroxymethyluracil gave uracil 5-methylenesulfonate on treatment with bisulfite. This reaction was much slower than that of 5-hydroxymethylcytosine, and the optimum pH was between 6 and 7.
Chromatographic Purification and Properties of Soluble Single-Walled Carbon Nanotubes (2001)

We report an improved chromatographic purification of soluble single-walled carbon nanotubes (s-SWNTs) using gel permeation chromatography. Three fractions are separated by gel permeation chromatography, and the first fraction contains 74% of the s-SWNTs as detected by atomic force microscopy and UV and near-infrared spectroscopy.
Not Christian, but Nonetheless Qualified: The Secular Workplace - Whose Hardship? (2012)

This paper examines the uneven history of the U.S. as a haven for religious freedom and links it to the challenges being confronted today in incorporating into U.S. society the influx of immigrants from non-Christian, non-Western cultures. Focusing on the workplace, the author argues that non-Christian employees are at a disadvantage in the so-called secular U.S. workplace because it in truth represents a bastion of secularized Christianity. That is to say, an institutionalization of Christianity in the civil laws and public institutions of the U.S. has allowed religiously embedded practices to masquerade as secular norms. To overcome the Christian presumption in the U.S. workplace, the author argues for making religious accommodation a "fundamental right" that can be denied by an employer only upon a showing of business necessity. Thus, the "business necessity" standard would replace the "undue hardship" standard currently applied in religious accommodation cases -- a standard that the author argues allows the employer too much discretion in terms of its ability to ban bona fide religious practices, such as the wearing of religious garb, from the workplace.
The Eifel algorithm (2000)

We propose an enhancement to TCP's error recovery scheme, which we call the Eifel algorithm . It eliminates the retransmission ambiguity, thereby solving the problems caused by spurious timeouts and spurious fast retransmits. It can be incrementally deployed as it is backwards compatible and does not change TCP's congestion control semantics. In environments where spurious retransmissions occur frequently, the algorithm can improve the end-to-end throughput by several tens of percent. An exact quantification is, however, highly dependent on the path characteristics over time. The Eifel algorithm finally makes TCP truly wireless-capable without the need for proxies between the end points. Another key novelty is that the Eifel algorithm provides for the implementation of a more optimistic retransmission timer because it reduces the penalty of a spurious timeout to a single (in the common case) spurious retransmission.
Gadolinium and nephrogenic systemic fibrosis: Association or causation (Review Article) (2008)

With widespread availability of magnetic resonance imaging (MRI), it has become standard practice for patients with severe renal impairment or previous severe reactions to iodine-containing contrast media to receive gadolinium-based MRI contrast agents instead of traditional radiographic contrast agents, particularly for magnetic resonance angiography. However, there is growing concern about the use of gadolinium contrast agents in the presence of severe renal insufficiency, because of increasing reports of nephrogenic fibrosing dermopathy (NFD)/nephrogenic systemic fibrosis (NSF), associated with the exposure to certain gadolinium-containing contrast agents. In this review we explore the causal link between gadolinium exposure and NSF, using an established system of epidemiological criteria proposed by Bradford Hill. Though the current evidence makes gadolinium a strong suspect as an aetiologic agent for NSF in the presence of severe renal failure, the die is not cast yet. At this stage there needs to be cautious approach to the use of gadolinium-containing contrast agents in the presence of severe renal failure (glomerular filtration rate <30 mL/min per 1.73 m(2)).
Fuzzy semi-topogenous orders and fuzzy supra topologies (2003)

We investigate the properties of fuzzy (semi-)topogenous orders in the framework of fuzzy (supra) topologies and fuzzy (supra) interior operators. We study the relationship between fuzzy (semi-)topogenous structures, fuzzy (supra)topologies and fuzzy (supra)interior operators.
Synergy of Two Assembly Languages in DNA Nanostructures: Self-Assembly of Sequence-Defined Polymers on DNA Cages (2016)

DNA base-pairing is the central interaction in DNA assembly. However, this simple four-letter (A-T and G-C) language makes it difficult to create complex structures without using a large number of DNA strands of different sequences. Inspired by protein folding, we introduce hydrophobic interactions to expand the assembly language of DNA nanotechnology. To achieve this, DNA cages of different geometries are combined with sequence-defined polymers containing long alkyl and oligoethylene glycol repeat units. Anisotropic decoration of hydrophobic polymers on one face of the cage leads to hydrophobically driven formation of quantized aggregates of DNA cages, where polymer length determines the cage aggregation number. Hydrophobic chains decorated on both faces of the cage can undergo an intrascaffold "handshake" to generate DNA-micelle cages, which have increased structural stability and assembly cooperativity, and can encapsulate small molecules. The polymer sequence order can control the interaction between hydrophobic blocks, leading to unprecedented "doughnut-shaped" DNA cage-ring structures. We thus demonstrate that new structural and functional modes in DNA nanostructures can emerge from the synergy of two interactions, providing an attractive approach to develop protein-inspired assembly modules in DNA nanotechnology.
Identification of the membrane receptor for the complement fragment C3d by means of a monoclonal antibody. (1983)

The B2 antigen characterized by means of a monoclonal antibody (14) is a 140,000 Mr protein expressed only in certain stages of the differentiation of lymphocytes of the B lineage. Here we examine the relationship between B2 and the membrane complement receptor type 2 (CR2) for the complement fragment C3d (11, 12), which is also associated only with B cells. Both phenotypic markers are distributed in a similar manner among B cell malignancies and, as shown here, among established cell lines. A polypeptide with binding affinity for C3d was isolated from the membrane of B2-positive cells, i.e., tonsil lymphocytes and Raji cells. We found that this C3d-binding protein not only had the same Mr and isoelectric point (pI) as the B2 antigen, but that it was recognized by the monoclonal antibody to B2. However, anti-B2 does not mask the ligand-binding site of CR2 since it does not prevent the interaction of the purified 140,000 Mr polypeptide with immobilized C3d. Rosette formation between tonsil lymphocytes and erythrocyte intermediates bearing C3d was specifically inhibited by anti-B2. In the case of Raji cells, rosette formation was strongly inhibited only when the lymphocytes were sequentially treated with anti-B2 and with a polyclonal antibody against mouse Ig. In short, B2 and CR2 have a similar distribution among normal and malignant cells, have the same Mr and pI under denaturing conditions, and react with a single monoclonal antibody. We conclude that B2 is identical to CR2.
Visual Observation of Oscillating Heat Pipes Using Neutron Radiography (2008)

Qualitative observation of flow patterns in water and nanofluid oscillating heat pipes was conducted at various heat inputs and condenser temperatures. Images of the liquid flow within the copper tubing were first captured at 30 frames per second using neutron radiography. Neutron radiography allows direct observation of a fluid position because liquid water is hydrogen rich and opaque while water vapor (because it is much less dense) and the other materials in the oscillating heat pipes are transparent. Flow visualization was conducted on an 8-turn water oscillating heat pipe, an 8-turn nanofluid oscillating heat pipe, and a 12-turn nanofluid oscillating heat pipe. The water oscillating heat pipe was filled with high performance liquid chromatography grade water. The 12-turn nanofluid oscillating heat pipe was filled with 1% by volume (35.0 g-ml -1 ) diamond nanoparticles in high performance liquid chromatography water and the 8-turn oscillating heat pipe contained 0.016% by volume (0.5 mg ml -1 ) diamond nanoparticles high performance liquid chromatography water. The diamond nanoparticles were 5 to 50 nm in diameter. All oscillating heat pipes were charged at a filling ratio of 50%. Visual observation shows for all heat pipes that at low heat inputs, fluid oscillation is very random and intermittent. Increasing the heat input causes a steady flow pattern to appear. For all tested oscillating heat pipes, increased heat load or operating temperature resulted in an increased fluid velocity. Also, nucleation was never observed in the tested oscillating heat pipes.
Design of efficient erasure codes with differential evolution (2002)

The design of practical and powerful codes for protection against erasures can be reduced to optimizing solutions of a highly nonlinear constraint satisfaction problem. In this paper we will attack this problem using the differential evolution approach and significantly improve results previously obtained using classical optimization procedures.
Prediction of permeability for porous media reconstructed using multiple-point statistics (2004)

To predict multiphase flow through geologically realistic porous media, it is necessary to have a three-dimensional (3D) representation of the pore space. We use multiple-point statistics based on two-dimensional (2D) thin sections as training images to generate geologically realistic 3D pore-space representations. Thin-section images can provide multiple-point statistics, which describe the statistical relation between multiple spatial locations and use the probability of occurrence of particular patterns. Assuming that the medium is isotropic, a 3D image can be generated that preserves typical patterns of the void space seen in the thin sections. The method is tested on Berea sandstone for which a 3D image from micro-CT (Computerized Tomography) scanning is available and shows that the use of multiple-point statistics allows the long-range connectivity of the structure to be preserved, in contrast to two-point statistics methods that tend to underestimate the connectivity. Furthermore, a high-resolution 2D thin-section image of a carbonate reservoir rock is used to reconstruct 3D structures by the proposed method. The permeabilities of the statistical images are computed using the lattice-Boltzmann method (LBM). The results are similar to the measured values, to the permeability directly computed on the micro-CT image for Berea and to predictions using analysis of the 2D images and the effective medium approximation.