gebhart/patrepeval huggingface dataset:
The Insulin-like Growth Factor (IGF)Binding Protein 1 Binding Epitope on IGF-I Probed by Heteronuclear NMR Spectroscopy and Mutational Analysis (1998)

NMR spectroscopy studies and biosensor interaction analysis of native and site-directed mutants of insulin-like growth factor I (IGF-I) was applied to identify the involvement of individual residues in IGF-I binding to IGF-binding protein 1 (IGFBP-1). Backbone NMR chemical shifts were found to be affected by IGFBP-1 binding in the following residues: Pro2, Glu3, Cys6, Gly7, Gly19, Pro28-Gly30, Gly32, Arg36, Arg37, Gln40-Gly42, Pro63, Lys65, Pro66, and Lys68-Ala70. Three IGF-I arginine side chains were identified by NMR to participate in IGFBP-1 binding. All IGF-I arginine residues were replaced by alanines, using site-directed mutagenesis, in four single substituted variants, IGF-I(R21A), IGF-I(R50A), IGF-I(R55A), and IGF-I(R56A), and one double replacement mutant, IGF-I(R36A/R37A). Biosensor interaction analysis binding studies demonstrate the involvement of Arg36-Arg37 and Arg50 in IGFBP-1 binding, while experiments with the IGF-I receptor implicate Arg21, Arg36-Arg37, and Arg56 as part of the receptor binding epitope. These overlapping binding surfaces explain why IGF-I receptor and IGFBP-1 binding to IGF-I is competitive. The C terminus of free, but not IGFBP-1-bound, IGF-I is found to exist in two distinct, NMR-detectable conformations at 30 degreesC. One possible explanation for this structural heterogeneity could be cis-trans isomerization of the Cys6-Cys48 disulfide bond.
Achievable accuracy of site-specific path-loss predictions in residential environments (1999)

The design of future wireless communication systems employing microcells will require a flexible tool for determining the dependence of the coverage area on base-station antenna height and position. In this paper, the accuracy of a ray-based algorithm versus slope intercept models for propagation prediction in residential environments is investigated by comparison with measurements. The measurements were taken in two areas of Trenton, NJ, where building heights ranged from one to three stories. For base-station antennas at or above rooftop levels, the algorithm is shown to give good agreement with the measurements. For these high antennas, the average and standard deviations of the difference between the site-specific prediction and measurement are less than 1 and 5 dB, respectively. For base-station antennas below the rooftops, additional ray paths are required in order to achieve similar prediction accuracy.
Guided molecular self-assembly: a review of recent efforts (2003)

This paper serves as an introductory review of significant and novel successes achieved in the fields of nanotechnology, particularly in the formation of nanostructures using guided molecular self-assembly methods. Self-assembly is a spontaneous process by which molecules and nanophase entities may materialize into organized aggregates or networks. Through various interactive mechanisms of self-assembly, such as electrostatics, chemistry, surface properties, and via other mediating agents, the technique proves indispensable to recent functional materials and device realizations. The discussion will extend to spontaneous and Langmuir–Blodgett formation of self-assembled monolayers on various substrates, and a number of different categories of self-assembly techniques based on the type of interaction exploited. Combinatorial techniques, known as soft lithography, of micro-contact printing and dip-pen nanolithography, which can be effectively used to up-size nanostructured molecular assemblies to submicrometer and micrometer scale patterns, will also be mentioned.
Cellugyrin, a Novel Ubiquitous Form of Synaptogyrin That Is Phosphorylated by pp60c- (1998)

Synaptogyrin is an abundant membrane protein of synaptic vesicles containing four transmembrane regions and a C-terminal cytoplasmic tail that is tyrosine phosphorylated. We have now identified a novel isoform of synaptogyrin called cellugyrin that exhibits 47% sequence identity with synaptogyrin. In rat tissues, cellugyrin and synaptogyrins are expressed in mirror image patterns. Cellugyrin is ubiquitously present in all tissues tested with the lowest levels in brain tissue, whereas synaptogyrin protein is only detectable in brain. Transfection studies in COS cells demonstrated that both cellugyrin and synaptogyrin are tyrosine phosphorylated in vivo by pp60c-src, and experiments with recombinant proteins showed that pp60c-src phosphorylates the cytoplasmic tails of these proteins in vitro. Cellugyrin and synaptogyrin co-localize when transfected into COS cells but are differentially distributed in brain, the only tissue where both proteins are detectable. Our data suggest that the synaptic vesicle protein synaptogyrin is a specialized version of a ubiquitous protein, cellugyrin, with the two proteins sharing structural similarity but differing in localization. This finding supports the emerging concept of synaptic vesicles as the simplified and specialized form of a generic trafficking organelle. The conserved tyrosine phosphorylation of cellugyrin and synaptogyrins suggests a link between tyrosine phosphorylation via pp60c-src and membrane traffic.
Comparison of culture methods for monitoring Legionella species in hospital potable water systems and recommendations for standardization of such methods (1995)

A lack of standardization of environmental monitoring techniques for Legionella spp. complicates the interpretation of results and comparisons of results from different institutions. A comparative assessment of techniques recommended by the Centers for Disease Control and Prevention, the Hygiene Institute (Graz, Austria), and our laboratory was performed. Variables investigated were sampling method (swabbing and collection of water samples [250 ml] before and after swabbing), method of concentration (none, filtration, and centrifugation), acid buffer treatment (no acid treatment, treatment for 3 min, and treatment for 15 min), and choice of medium (five formulations of buffered charcoal yeast extract agar with glycine, vancomycin, polymyxin B, anisomycin, or cycloheximide). Thirty-three sites in seven hospital buildings were studied. Recovery by swab correlated with recovery from water after swabbing (P < 0.05). However, the quantity of Legionella spp. recovered from swab specimens (mean, 3.0 x 10(4) CFU per swab) was greater than that recovered from water (mean, 4.7 x 10(3) CFU/250 ml). Filtration resulted in recovery rates (mean, 5.2 x 10(3) CFU/250 ml) higher than those by centrifugation (mean, 2.3 x 10(3) CFU/250 ml). Three minutes of acid buffer treatment to reduce overgrowth by commensal flora did not improve selectivity or sensitivity for Legionella spp. if glycine-containing selective media were used. Fifteen minutes of acid buffer treatment reduced recovery compared with that after a 3-min treatment. All glycine-containing media tested effectively inhibited background flora, but one selective medium containing dyes, glycine, vancomycin, and polymyxin B (DGVP) resulted in the greatest quantitative recovery of Legionella pneumophila. Use of buffered charcoal yeast extract agar and the acid buffer treatment gave the greatest recovery of non-pneumophila species. A standardized protocol with an emphasis on the culturing of swab samples is presented.
Structural changes after transmitter release at the frog neuromuscular junction. (1981)

The sequence of structural changes that occur during synaptic vesicle exocytosis was studied by quick-freezing muscles at different intervals after stimulating their nerves, in the presence of 4-aminopyridine to increase the number of transmitter quanta released by each stimulus. Vesicle openings began to appear at the active zones of the intramuscular nerves within 3-4 ms after a single stimulus. The concentration of these openings peaked at 5-6 ms, and then declined to zero 50-100 ms late. At the later times, vesicle openings tended to be larger. Left behind at the active zones, after the vesicle openings disappeared, were clusters of large intramembrane particles. The larger particles in these clusters were the same size as intramembrane particles in undischarged vesicles, and were slightly larger than the particles which form the rows delineating active zones. Because previous tracer work had shown that new vesicles do not pinch off from the plasma membrane at these early times, we concluded that the particle clusters originate from membranes of discharged vesicles which collapse into the plasmalemma after exocytosis. The rate of vesicle collapse appeared to be variable because different stages occurred simultaneously at most times after stimulation; this asynchrony was taken to indicate that the collapse of each exocytotic vesicle is slowed by previous nearby collapses. The ultimate fate of synaptic vesicle membrane after collapse appeared to be coalescence with the plasma membrane, as the clusters of particles gradually dispersed into surrounding areas during the first second after a stimulus. The membrane retrieval and recycling that reverse this exocytotic sequence have a slower onset, as has been described in previous reports.
Biological and Protective Properties of Immune Sera Directed to the Influenza Virus Neuraminidase (2014)

The neuraminidase of influenza A viruses is a sialidase that acts as a receptor-destroying enzyme facilitating the release of progeny virus from infected cells. Here, we demonstrate that monospecific anti-NA immune sera inhibited not only sialidase activity, but also influenza virus hemagglutination and infection of MDCK cells, suggesting that NA antibodies can interfere with virus attachment. Inhibition of both processes, virus release and virus binding, may explain why NA antibodies efficiently blocked virus dissemination in vitro and in vivo. Anti-NA immune sera showed broader reactivity than anti-HA sera in hemagglutination inhibition tests and demonstrated cross-subtype activity in sialidase inhibition tests. These remarkable features of NA antibodies highlight the importance of the NA antigen for the development of next-generation influenza virus vaccines.
Retrograde Transport of KDEL-bearing B-fragment of Shiga Toxin (1997)

To investigate retrograde transport along the biosynthetic/secretory pathway, we have constructed a recombinant Shiga toxin B-fragment carrying an N-glycosylation site and a KDEL retrieval motif at its carboxyl terminus (B-Glyc-KDEL). After incubation with HeLa cells, B-Glyc-KDEL was progressively glycosylated in the endoplasmic reticulum (ER) and remained stably associated with this compartment. B-fragment with a nonfunctional KDEL sequence (B-Glyc-KDELGL) was glycosylated with about the same kinetics as B-Glyc-KDEL but localized at steady state to the Golgi apparatus. Morphological studies showed that B-Glyc-KDEL was delivered from the plasma membrane, via endosomes and the cisternae of the Golgi apparatus, to the ER. Moreover, the addition of a sulfation site allowed us to show that B-Glyc-KDEL on transit to the ER entered the Golgi apparatus through the trans-Golgi network. Transport of B-Glyc-KDEL to the ER was slowed down by nocodazole, indicating that microtubules are important for the retrograde pathway. Our results document the existence of a continuous pathway from the plasma membrane to the endoplasmic reticulum via the Golgi apparatus and show that a fully folded exogenous protein arriving in the endoplasmic reticulum via this pathway can undergo N-glycosylation.
Peripheral biomarkers in Autism: secreted amyloid precursor protein-alpha as a probable key player in early diagnosis. (2008)

Autism is a pervasive developmental disorder characterized by impairments in socialization and communication. There is currently no single molecular marker or laboratory tool capable of diagnosing autism at an early age. The purpose of this study is to explore the plausible use of peripheral biomarkers in the early diagnosis of autism via a sensitive ELISA. Here, we measured plasma secreted amyloid precursor protein alpha (sAPP-alpha) levels in autistic and aged-matched control blood samples and found a significantly increased level of sAPP-alpha in 60% of the known autistic children. We then tested 150 human umbilical cord blood (HUCB) samples and found significantly elevated levels of plasma sAPP-alpha in 10 of 150 samples. As an additional confirmatory measure, we performed Western blot analysis on these samples which consistently showed increased sAPP-alpha levels in autistic children and 10 of 150 HUCB samples; suggesting a group of autistic patients which could be identified in early childhood by levels of sAPP-alpha. While there is need for further studies of this concept, the measurement of sAPP-alpha levels in serum and human umbilical cord blood by ELISA is a potential tool for early diagnosis of autism.
Crystallinity and the effect of ionizing radiation in polyethylene. III. An experiment on the irradiation‐induced crosslinking in n‐hexatriacontane (1975)

Abstract Samples of n ‐hexatriacontane irradiated in the crystalline and molten states were compared as regards the GPC chromatograms of the partially crosslinked products. From differences in the elution volumes it could be inferred that there is a greater trend for random linking along the chain in the sample irradiated in the melt as opposed to preference for end‐type linking in the samples irradiated as crystals. In the course of this work the applicability of the GPC technique for detecting short (methyl) branches and for distinguishing between the position of these branches along the chain has also become apparent.
Leptin- and Leptin Receptor-Deficient Rodent Models: Relevance for Human Type 2 Diabetes (2014)

Among the most widely used animal models in obesity-induced type 2 diabetes mellitus (T2DM) research are the congenital leptin- and leptin receptor-deficient rodent models. These include the leptin-deficient ob/ob mice and the leptin receptor-deficient db/db mice, Zucker fatty rats, Zucker diabetic fatty rats, SHR/N-cp rats, and JCR:LA-cp rats. After decades of mechanistic and therapeutic research schemes with these animal models, many species differences have been uncovered, but researchers continue to overlook these differences, leading to untranslatable research. The purpose of this review is to analyze and comprehensively recapitulate the most common leptin/leptin receptor-based animal models with respect to their relevance and translatability to human T2DM. Our analysis revealed that, although these rodents develop obesity due to hyperphagia caused by abnormal leptin/leptin receptor signaling with the subsequent appearance of T2DM-like manifestations, these are in fact secondary to genetic mutations that do not reflect disease etiology in humans, for whom leptin or leptin receptor deficiency is not an important contributor to T2DM. A detailed comparison of the roles of genetic susceptibility, obesity, hyperglycemia, hyperinsulinemia, insulin resistance, and diabetic complications as well as leptin expression, signaling, and other factors that confound translation are presented here. There are substantial differences between these animal models and human T2DM that limit reliable, reproducible, and translatable insight into human T2DM. Therefore, it is imperative that researchers recognize and acknowledge the limitations of the leptin/leptin receptor- based rodent models and invest in research methods that would be directly and reliably applicable to humans in order to advance T2DM management.
Isolation, Structure, Synthesis, and Antimitotic Properties of Combretastatins B-3 and B-4 from Combretum caffrum (1988)

Further investigation of a CH2Cl2 fraction prepared from the South African tree Combretum caffrum for substances inhibitory to the murine P-388 lymphocytic leukemia (PS system) cell line has led to the isolation of two new bibenzyls, designated combretastatins B-3 and B-4, accompanied by the previously known bibenzyls 7, 8, and 9. The structure of each substance was ascertained by results of mass and nmr spectral analyses and confirmed by crystal structure determination (for 7) or synthesis. Combretastatins B-3 and B-4 gave PS ED50 values of 0.4 and 1.7 micrograms/ml, respectively, and bibenzyls 7, 8, and 9 were comparably cell growth inhibitory against the PS cell line with ED50 results of 1.7, 2.5, and 0.25 ug/ml, respectively. All the bibenzyls caused leukemia cells to accumulate in mitosis at cytotoxic drug concentrations; however, a wide range of in vitro activity against the protein tubulin (the major component of the mitotic spindle) was observed.
The Extended Amygdala: Are the Central Nucleus of the Amygdala and the Bed Nucleus of the Stria Terminalis Differentially Involved in Fear versus Anxiety? (1999)

Although there is a close correspondence between fear and anxiety, and the study of fear in animals has been extremely valuable for understanding the neural basis of anxiety, it is also clear that a richer animal model of human anxiety disorders would include measures of both stimulus-specific fear and something less stimulus specific, more akin to anxiety. Patients with posttraumatic stress syndrome seem to show normal fear reactions but abnormal anxiety measured with the acoustic startle reflex. Studies in rats, also using the startle reflex, indicate that highly processed explicit cue information (lights, tones) activates the central nucleus of the amygdala, which projects to and modulates the acoustic startle pathway in the brain stem. Less explicit information, such as that produced by exposure to a threatening environment or by intraventricular administration of corticotropin-releasing hormone, may activate another part of the extended amygdala, the bed nucleus of the stria terminalis, which also projects to the startle pathway. Because this information may be less specific and of long duration, activation of the bed nucleus of the stria terminalis may mediate anxiety, whereas activation of the central nucleus of the amygdala may mediate stimulus-specific fear.
Endothelial cell signaling and cytoskeletal changes in response to shear stress. (1993)

Endothelial cells exposed to a fluid shear stress both in vivo and in vitro show an alignment with the direction of flow and an elongation of cells with a concomitant reorganization of their F-actin microfilament network. Specialized regions of the plasma membrane known as focal contacts are sites of transmembrane linkages between the actin microfilament bundles and the extracellular matrix (ECM) where cytoskeletal organization and, hence, cellular morphological changes may be modulated. Focal contact-associated proteins such as fibronectin receptors, vitronectin receptors and vinculin were shown in this study to play specific roles in the modulation of the cytoskeletal and cell shape changes. Data is also presented suggesting that protein kinase C is part of the cellular signaling system involved in shear stress-induced cytoskeletal reorganization.
Amelioration of rat antigen-induced arthritis by liposomally conjugated methotrexate is accompanied by down-regulation of cytokine mRNA expression (2001)

Objectives. We examined the temporal changes in the expression of interleukin 1b (IL-1b), tumour necrosis factor a (TNF-a) and interleukin 6 (IL-6) in the rat antigen-induced arthritis (AIA) model and investigated how their expression was modulated following disease amelioration by liposomally conjugated methotrexate (G-MLV).
Über Aminosäuren und Peptide, XI. Hydroxylsubstituierte Cyclodipeptide durch Ringschluß von Pyruvoylaminosäure‐amiden (1974)

Abstract Mit Hilfe von energiereichen Brenztraubensäure‐Verbindungen (Brenztraubensäure‐chlorid, ‐ p ‐nitrophenylester und Hydroxymaleinsäure‐anhydrid) werden Pyruvoylaminosäure‐amide aufgebaut. Sie cyclisieren — am schnellsten bei pH 7.5 in Wasser‐Zu den Hydroxycyclodipeptiden 13 , 14 , 15 und 17 . Unabhängig von der Struktur der Brenztraubensäure‐Verbindung liegt das Gleichgewicht vollständig auf der Seite der Ringverbindung. Beim Prolinderivat 11 führt, der Ringschluß mit hoher optischer Induktion kinetisch Kontrolliert zum Isomeren 13a , das sich in saurer und alkalischer wäßriger Lösung mit hoher optischer Induktion in das thermodynamisch stabilere Isomere 13b umwandelt. Unter Mercaptalisierungsbedingungen läßt sich die Hydroxygruppe mit meist hoher optischer Induktion durch schwefel haltige Gruppen ersetzen.
Shear Effects on Stability of DNA Complexes in the Presence of Serum (2017)

The behavior of nanocarriers, even though they are well-defined at equilibrium conditions, is unpredictable in living system. Using the complexes formed by plasmid DNA (pDNA) and K<sub>20</sub> (K: lysine), protamine, or polylysine (PLL) as models, we studied the dynamic behavior of gene carriers in the presence of fetal bovine serum (FBS) and under different shear rates, a condition mimicking the internal physical environment of blood vessels. Without shear, all the positively charged complexes bind to the negatively charged proteins in FBS, leading to the formation of large aggregates and even precipitates. The behaviors are quite different under shear. The shear generates two effects: a mechanical force to break down the complex into smaller size particles above a critical shear rate and a stirring effect leading to secondary aggregation of complexes below the critical shear rate. In the studied shear rate from 100 to 3000 s<sup>-1</sup>, the mechanical force plays a key role in K<sub>20</sub>/pDNA and protamine/pDNA, while the stirring effect is dominant in PLL/pDNA. A model study shows that the interfacial tension, the chain density, and the elasticity of the complexes determine their responsiveness to shear force. This study is helpful to understand the fate of drug/gene carriers under physiological conditions. It also gains insight in designing drug/gene carriers with desirable properties for in vivo applications.
An advanced detrending method with application to HRV analysis (2002)

An advanced, simple to use, detrending method to be used before heart rate variability analysis (HRV) is presented. The method is based on smoothness priors approach and operates like a time-varying finite-impulse response high-pass filter. The effect of the detrending on time- and frequency-domain analysis of HRV is studied.
Optimal pricing of water rights for efficient use (2000)

Based on a dynamic optimization model, this paper develops a socially optimal pricing scheme of water rights to enhance efficiency of water use. The pricing model is characterized by several important features. Important factors such as the integrated use of surface water and groundwater, alternative incentive instruments, government budget constraint, and restrictions on hydraulic head to prevent ecosystem from catastrophe are taken into account in the model. It is shown that the optimal charges might be different from the conventional shadow price of water resources. The comparative static analysis also indicates how the optimal charge should be adjusted in response to changes in water-rights allocation and geographic parameters such as hydraulic head, etc. The comparative dynamic analysis, on the other hand, reveals that the time path of the optimal charge for the surface water rights is different from that of the ground water rights.