gebhart/patrepeval huggingface dataset:
Heat-Induced Gelation of Globular Proteins. 1. Model for the Effects of Time and Temperature on the Gelation Time of BSA Gels (1997)

Globular protein gels have been extensively investigated over many years, although the great majority of studies have used rather crude and/or mixed samples of protein. Moreover, most previous work has concentrated on examining structural and rheological properties of fully cured gels. In the present paper we will discuss heat-induced gelation of the typical globular protein, bovine serum albumin (BSA), not far from critical gel conditions together with aspects of kinetic gelation theory. We will concentrate on a description of the parameters that alter the gelation or gel time, tc. We will develop a new model to describe both the effect of temperature and polymer concentration on tc. Gel formation is achieved by isothermal heating. The change in rheological properties during the gelation process is monitored by dynamic shear rheometry as a function of time. The measurements are carried out at different temperatures and protein concentrations to clarify their effects on the gelation. The results are displayed in various diagrams, including a new form of sol/gel state diagram, and discussed in terms of both phase behavior and gelation kinetics.
Covalent radii revisited (2008)

A new set of covalent atomic radii has been deduced from crystallographic data for most of the elements with atomic numbers up to 96. The proposed radii show a well behaved periodic dependence that allows us to interpolate a few radii for elements for which structural data is lacking, notably the noble gases. The proposed set of radii therefore fills most of the gaps and solves some inconsistencies in currently used covalent radii. The transition metal and lanthanide contractions as well as the differences in covalent atomic radii between low spin and high spin configurations in transition metals are illustrated by the proposed radii set.
Topical aminolaevulinic acid-photodynamic therapy for the treatment of acne vulgaris: a study of clinical efficacy and mechanism of action (2004)

ALA-PDT is capable of clinically improving acne. An alternative mode of action for ALA-PDT other than direct damage to sebaceous glands or photodynamic killing of P. acnes is suggested from the results of this study.
Finite-element modeling predicts possibility of thermoelectrically cooled lead-salt diode lasers (1997)

Finite-element thermal modeling shows that thermoelectric cooled operation of IV-VI semiconductor diode lasers is possible by replacing the thermally resistive lead-salt substrate with copper. Contrasting thermal models reveal a 63 K decrease in active region temperature under normal operating conditions when PbTe is replaced with copper. This improved device structure can be obtained by using epitaxial-lift-off techniques similar to those developed for III-V semiconductor devices.
Regulation of oncogene expression in cultured aortic smooth muscle cells. Post-transcriptional control of c-myc mRNA. (1986)

Proliferation of normally quiescent vascular smooth muscle cells plays a major role in the development of an atherosclerotic lesion. Since cellular homologues of oncogenes have been implicated in the control of normal cell proliferation, we have analyzed the regulation of expression of two proto-oncogenes (c-fos and c-myc) in primary cultures of calf aortic smooth muscle cells during the transition from quiescence to proliferation. Quiescent (serum-deprived) smooth muscle cells were stimulated to proliferative by serum addition. DNA synthesis began 12 h post-serum addition and peaked between 16 and 20 h. Following addition of serum, c-fos mRNA levels increased rapidly from an undetectable amount to the maximal level at 30 min after serum addition and then rapidly returned to the levels found in quiescent cells. Changes in the rate of c-fos gene transcription, as measured by nuclear "runoff" assays, paralleled the alterations in mRNA levels, indicating that regulation of c-fos was at the level of mRNA synthesis. The mRNA for the c-myc oncogene was expressed at a detectable level in quiescent cells, peaked in abundance at approximately 2 h after stimulation, and then returned to the level found in quiescent cells. No significant change in the rate of c-myc gene transcription was detectable over the time course. The rate of decay of c-myc mRNA following the inhibition of transcription by actinomycin D was measured at the 1- and 4-h time points and in exponentially growing cells. There was a transient stabilization of the normally labile c-myc mRNA at 1 h after serum stimulation. Thus c-myc gene expression was regulated at the level of mRNA turnover.
Effect of Surface Polarity on Water Contact Angle and Interfacial Hydration Structure (2007)

We perform molecular dynamics simulations of water in the presence of hydrophobic/hydrophilic walls at T = 300 K and P = 0 GPa. For the hydrophilic walls, we use a hydroxylated silica model introduced in previous simulations [Lee, S. H.; Rossky, P. J. J. Chem. Phys. 1994, 100, 3334. Giovambattista, N.; Rossky, P. J.; Debenedetti, P. G.; Phys. Rev. E 2006, 73, 041604.]. By rescaling the physical partial atomic charges by a parameter 0 <or= k <or= 1, we can continuously transform the hydrophilic walls (hydroxylated silica, k = 1) into hydrophobic apolar surfaces (k = 0). From a physical point of view, k is the normalized magnitude of a surface dipole moment, and thus it quantifies the polarity of the surface. We calculate the contact angle of water for 0 <or= k <or= 1. We find that, at least for the present homogeneous, atomically flat, and defect-free surface model, the magnitude of the surface dipole correlates with the contact angle in a one-to-one correspondence. In particular, we find that polar surfaces with 0 < k <or= kc = 0.4 are macroscopically hydrophobic; that is, the contact angle is larger than 90 degrees . For the cutoff value k = kc, the magnitude of the dipole moment of the polar silica surface unit is 41% that of the water molecule dipole moment. We also study the water orientation distributions next to the walls (a microscopic property). We find that these distributions also correlate with the contact angle in a one-to-one correspondence. Thus, the structure of confined water, the surface polarity, and the contact angle are in a direct correspondence to each other, and therefore, each quantifies the hydrophobicity/hydrophilicity of the surface.
Microencapsulation and the Grafting of Genetically Transformed Cells as Therapeutic Strategies to Rescue Degenerating Neurons of the CNS (1995)

A number of approaches have been developed to deliver growth factors within the central nervous system of adult mammals. Initially a variety of neurotrophic factors were administered either by single intracerebroventricular or local injections directly into brain tissues or via permanently installed cannulae for chronic administrations. More recently delivery systems including conjugates, biodegradable and non-biodegradable implants and microspheres as well as genetically engineered cells have been introduced in order to provide a prolonged supply of neurotrophic factors and to prevent their enzymatic degradation. In this review we examine a variety of means of delivering neurotrophic factors (mainly nerve growth factor) with the primary focus upon the use of microencapsulated neurotrophins and cells genetically modified to produce them. In addition, this review highlights some difficulties and future trends in the development of novel delivery systems hopefully more suitable for investigations in different areas of neuroscience.
Isolation and structural characterization of human lymphocyte and neutrophil gangliosides. (1981)

Gangliosides were isolated from purified preparations of human peripheral blood lymphocytes and neutrophils. Structural analyses and comparisons were performed by direct probe mass spectrometry and by degradation studies with the following enzymes: Escherichia freundii endo-beta-galactosidase; Clostridium perfringens and Arthrobacter ureafaciens neuraminidase; and jack bean beta-N-acetylhexosaminidase and beta-galactosidase. This combination of techniques allowed us to obtain carbohydrate composition and sequence information without the aid of methylation or carbohydrate compositional analyses using only 1-2 mg of purified gangliosides. On the basis of these studies we propose that human lymphocytes and neutrophils have gangliosides with the following structures. NeuAc alpha 2 leads to 3Gal beta 1 leads to 4Glc beta 1 leads to 1Cer Structure A NeuAc alpha 2 leads to ? GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc beta 1 leads to 1Cer Structure B NeuAc alpha 2 leads to ? Gal beta 1 leads to 3,4GlcNAc beta 1 leads to 3Gal beta 1 leads to 4Glc beta 1 leads to 1Cer Structure C All three compounds were isolated from both cell types with structure A being the major lymphocyte ganglioside and structure C the major neutrophil ganglioside. Structure B is a novel ganglioside and may represent a leukocyte-specific glycosphingolipid. Neuraminidase degradation studies demonstrated that only one ganglioside species of each cell type contains an internally linked sialic acid residue, and on the basis of thin layer chromatographic analysis this component is the same as the major brain ganglioside, GM1 (II3-N-acetylneuraminosyl-gangliotetraosylceramide). In addition, large gangliosides with the general structure NeuAc alpha 2 leads to ?(Gal beta 1 leads to 3,4GlcNAc beta 1 leads to 3)n Gal beta 1 leads to 4Glc beta 1 leads to 1Cer were isolated. These results are discussed as they relate to blood group antigens and specific cell surface markers in human leukocytes.
Prostaglandins and congeners. 20. Synthesis of prostaglandins via conjugate addition of lithium trans-1-alkenyltrialkylalanate reagents. A novel reagent for conjugate 1,4-additions (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProstaglandins and congeners. 20. Synthesis of prostaglandins via conjugate addition of lithium trans-1-alkenyltrialkylalanate reagents. A novel reagent for conjugate 1,4-additionsKarel F. Bernady, M. Brawner Floyd, John F. Poletto, and Martin J. WeissCite this: J. Org. Chem. 1979, 44, 9, 1438–1447Publication Date (Print):April 1, 1979Publication History Published online1 May 2002Published inissue 1 April 1979https://pubs.acs.org/doi/10.1021/jo01323a017https://doi.org/10.1021/jo01323a017research-articleACS PublicationsRequest reuse permissionsArticle Views5724Altmetric-Citations156LEARN 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
Chemical vapor deposition of titanium–silicon–nitride films (1997)

Titanium–silicon–nitride films were grown by metal-organic chemical vapor deposition. At temperatures between 300 and 450 °C, tetrakis(diethylamido)titanium, ammonia, and silane react to form films with average compositions near the TiN–Si3N4 tie line and low impurity contents (C&amp;lt;1.5 at. %, H between 5 and 15 at. %, with no other impurities present). The film resistivity is a strong function of Si content in the films, ranging continuously from 400 μΩ cm for pure TiN up to 1 Ω cm for films with 25 at. % Si. Step coverages of approximately 75% on 0.35 μm, 3:1 aspect ratio trenches, and 35%–40% on 0.1 μm/10:1 trenches are found for films with resistivities below 1000 μΩ cm. These films are promising candidates for diffusion barriers in microelectronic applications.
Wavelet analysis in coherence estimation of electroencephalographic signals in children for the detection of dyslexia-related abnormalitites (2006)

An approach based on the estimation of the coherence using wavelet analysis is applied to EEG and ERP signals for the detection of pathological patterns related with dyslexia. Coherence can be defined as the correlation of two signals in the frequency domain. The continuous wavelet transform was used for the computation of spectral characteristics since it provides highly overlapping windows which improve the reliability of the coherence estimate. This is achieved by increasing the number of segments over which the spectrum is averaged and thereby half of the amount of data is needed. Statistical analysis of the results revealed significant differences between controls and dyslexics in EEG(F3 gamma band), ERP-P50H(F3 gamma band) and attentive ERP-N100L(F3, C3 and Cz alpha band). It has also been shown that there are significant differences related with handiness and age. It is believed that signal recording from these electrodes may reflect brain areas concerning auditory and memory processing.
Prospective evaluation of the clinical utility of endoscopic submucosal dissection (ESD) in patients with Barrett’s esophagus: a Western center experience (2016)

ESD for BE with HGD/early EAC is feasible and safe with resulting very high en-bloc and R0 resection rates. ESD provided for more accurate pathologic evaluation and significant discrepancy between the pre- and post-ESD histopathological diagnosis was noted.
Mucosal immunization with a DNA vaccine induces immune responses against HIV-1 at a mucosal site (1997)

Mucosal immunity is the first defense system in protection against mucosal infection by sexually transmitted diseases and subsequent systemic dissemination of infection. Development of vaccines which can induce protective mucosal immunity would have great promise for preventing sexually transmitted diseases including AIDS. DNA vaccines have recently shown certain advantages over other types of vaccines in safety and elicitation of specific immune responses. We have hypothesized that direct delivery of a DNA plasmid coding the HIV-1 envelope (pcMN160) via mucosal routes will stimulate mucosal immunity against HIV-1. The expression of DNA plasmid inoculated intravaginally was detected in various tissues. Intravaginal inoculation of pcMN160 elicits production of vaginal immunoglobulins which specifically bind to the HIV-1 envelope and neutralize HIV-1 infectivity in vitro. These results indicate the feasibility of inducing mucosal immunity following mucosal inoculation of DNA vaccines. When coupled with systemic inoculation of appropriate DNA constructs, effective mucosal and systemic immunity may be generated.
Specific sequence-specific recognition of right-handed double-helical DNA by (2S,3S)- and (2R,3R)-dihydroxybis(netropsin)succinamide (1986)

We report a class of chiral sequence-specific DNA binding molecules based on two netropsin analogues and the enantiomers of dl-tartaric acid: (2R,3R)- and (2S,3S)-dihydroxybis(netropsin)succinamide-EDTA [(R,R)- and (S,S)-1, respectively] (Figures 1 and 2). The enantiomeric threo-(R,R)1 and -(SS)-1 should afford diastereomeric complexes at common binding sites on double-helical DNA (Figure 1). Attachment of EDTA to one terminus of the crescent-shaped hexamides allows use of the affinity cleaving method to determine the differences between (R,R)-1•Fe^(II) and (S,S)-1•Fe^(II) with regard to relative binding affinities, sequence specificities, and orientations by analysis of the DNA-cleavage patterns on a 32P end-labeled DNA restriction fragment using high-resolution gel electrophoresis. For comparison to the enantiomers of 1, bis(netropsin)succinamide-EDTA (2) was synthesized (Figure 2).
The Role of Activin A in Regulation of Hemopoiesis (2002)

Activin A, a cytokine member of the transforming growth factor-beta superfamily, is expressed locally by the mesenchymal component of the hemopoietic microenvironment. Its expression is regulated on the mRNA level by different cytokines, and the biological activity of the protein is tightly controlled by several inhibitory molecules. Activin A affects hemopoietic cells of various lineages, as evidenced by in vitro studies of leukemia and lymphoma cell lines, which were used to elucidate the mechanism of its action. In the B-cell lineage, activin A is a cell cycle inhibitor, a mediator of apoptosis, and a cytokine antagonist. Limited information is available on the effects of activin A on normal hemopoietic cells. Recent studies suggest that it might be a negative regulator of normal B lymphopoiesis. Whereas the functions of activin A in vitro are well established, further research tools are needed to elucidate its role within specific hemopoietic microenvironments in vivo.
Flow Injection Chemiluminescent Immunoassay for Carcinoembryonic Antigen Using Boronic Immunoaffinity Column (2009)

A flow injection chemiluminescence immunoassay for rapid and sensitive detection of carcinoembryonic antigen (CEA) by using a phenylboronic acid-based immunoaffinity column as a glycoprotein collector was proposed in this paper. The column was prepared by coupling of 3-aminophenylboronic acid on the glass beads through a γ-glycidoxypropyltrimethoxysilane (GPMS) linkage. Based on an indirect competitive immunoreaction, the mixture of CEA sample and enzyme conjugated CEA antibody (HRP-anti-CEA) was incubated in advance, followed by direct injection to the column to capture free HRP-labeled CEA antibody in the column. The trapped HRP-labeled antibody was detected by flow inject chemiluminescence in the presence of luminol and hydrogen peroxide. The decreased chemiluminescent signal was proportional to the concentration of CEA in the range of 3.0-30.0 ng/mL with a correlation coefficient of 0.998. The column showed an acceptable reproducibility and stability and is potentially used for practical clinical detection of the serum CEA level.
Expression and Clinical Significance of Matrix Metalloproteinase-9 in Lymphatic Invasiveness and Metastasis of Breast Cancer (2014)

MMP-9 was overexpressed in breast cancer specimens compared with peritumoral benign breast epithelium and lymph nodes. Moreover, its expression in the matched epithelium and lymph nodes was positively associated with lymph node metastasis, and its expression in lymph nodes was positively associated with lymphangiogenesis in breast cancer. Thus, MMP-9 is a potential marker for breast cancer progression.
N‐polarity GaN on sapphire substrate grown by MOVPE (2006)

Abstract N‐polar GaN was grown on (0001) sapphire using two‐step growth technique by MOVPE. In the growth, the key points were the controlling of the density of nuclei in a buffer layer and promoting lateral growth at high temperature. The grown GaN films had mirror‐like smooth surfaces and were proved to have N‐polarity using convergent‐beam electron diffraction and coaxial impact‐collision ion spectroscopy. The FWHM of this GaN in the ω ‐scan was also much narrower than the previous reports. The density of threading dislocations was much less than for usual Ga‐polar GaN grown with a GaN or AlN buffer layer by MOVPE and MBE. In PL at room temperature, the strong edge emission was observed as Ga‐polarity. The p‐type conduction in Mg‐doped GaN was also realized by the same methods as for Ga‐polarity. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Cloning and characterization of tfdS, the repressor-activator gene of tfdB, from the 2,4-dichlorophenoxyacetic acid catabolic plasmid pJP4 (1990)

Plasmid pRO101, a derivative of plasmid pJP4 which contains Tn1721 inserted into a nonessential region, is inducible for 2,4-dichlorophenol hydroxylase (DCPH) encoded by tfdB. Plasmid pRO103, which has a deletion in the BamHI-F--BamHI-E region of plasmid pRO101, has elevated basal levels of DCPH but is uninducible. The regulatory gene for tfdB, designated tfdS, was cloned as an 8.3-kilobase-pair EcoRI-E fragment. When the cloned tfdS gene was in trans with plasmid pRO103, the baseline DCPH levels were repressed to normal uninduced levels and were fully induced when this strain was grown in the presence of 2,4-dichlorophenoxyacetic acid, 2,4-dichlorophenol, or 4-chlorocatechol. However, when tfdS was in trans with tfdB in the absence of tfdCDEF, tfdB was repressed but could not be induced. When tfdS and tfdC1, which encodes chlorocatechol 1,2-dioxygenase, are in trans with tfdB, tfdB remained uninduced, indicating that a downstream metabolite of chloro-cis,cis-muconate, either 2-cis-chlorodiene lactone or chloromaleylacetic acid, is the effector. Collectively, these data demonstrate that the gene product of tfdS acts as a repressor of tfdB in the absence of an effector and as an activator of tfdB when an effector is present.
Mutations in a Peptidylprolyl-cis/trans-isomerase Gene Lead to a Defect in 3′-End Formation of a Pre-mRNA inSaccharomyces cerevisiae (1999)

In a genetic screen aimed at the identification of trans-acting factors involved in mRNA 3'-end processing of budding yeast, we have previously isolated two temperature-sensitive mutants with an apparent defect in the 3'-end formation of a plasmid-derived pre-mRNA. Surprisingly, both mutants were rescued by the essential gene ESS1/PTF1 that encoded a putative peptidylprolyl-cis/trans-isomerase (PPIase) (Hani, J., Stumpf, G., and Domdey, H. (1995) FEBS Lett. 365, 198-202). Such enzymes, which catalyze the cis/trans-interconversion of peptide bonds N-terminal of prolines, are suggested to play a role in protein folding or trafficking. Here we report that Ptf1p shows PPIase activity in vitro, displaying an unusual substrate specificity for peptides with phosphorylated serine and threonine residues preceding proline. Both mutations were found to result in amino acid substitutions of highly conserved residues within the PPIase domain, causing a marked decrease in PPIase activity of the mutant enzymes. Our results are suggestive of a so far unknown involvement of a PPIase in mRNA 3'-end formation in Saccharomyces cerevisiae.