gebhart/patrepeval huggingface dataset:
Pro‐apoptotic function of calsenilin/DREAM/KChIP3 (2001)

Apoptotic cell death and increased production of amyloid b peptide (Ab) are pathological features of Alzheimer's disease (AD), although the exact contribution of apoptosis to the pathogenesis of the disease remains unclear. Here we describe a novel pro-apoptotic function of calsenilin/DREAM/KChIP3. By antisense oligonucleotide-induced inhibition of calsenilin/DREAM/KChIP3 synthesis, apoptosis induced by Fas, Ca2+-ionophore, or thapsigargin is attenuated. Conversely, calsenilin/DREAM/KChIP3 expression induced the morphological and biochemical features of apoptosis, including cell shrinkage, DNA laddering, and caspase activation. Calsenilin/DREAM/KChIP3-induced apoptosis was suppressed by caspase inhibitor Z-VAD and by Bcl-XL, and was potentiated by increasing cytosolic Ca2+, expression of Swedish amyloid precursor protein mutant (APPSW) or presenilin 2 (PS2), but not by a PS2 deletion lacking its C-terminus (PS2/411stop). In addition, calsenilin/DREAM/KChIP3 expression increased Ab42 production in cells expressing APPsw, which was potentiated by PS2, but not by PS2/411stop, which suggests a role for apoptosis-associated Ab42 production of calsenilin/DREAM/KChIP3.
Polyoxin Analogs. I. Synthesis of Aminoacyl Derivatives of 5'-Amino-5'-deoxyuridine (1971)

5'-δ-Carbamoyloxy-L-x-aminovaleramido-5'-deoxyuridine, a polyoxin analog, was prepared by the reaction of 5'-amino-5'-deoxy-2', 3'-O-isopropylideneuridine and N-carbobenzoxy-L-α-aminovalero-δ-lactone, followed by carbamoylation and the removal of the protective groups. Several other ω-substituted aminoacyl derivatives were also prepared utilizing the activated ester method and the mixed anhydride method. All these compounds showed no polyoxin-activity.
The Relationship Between Peripheral Levels of Leukocytes and Neutrophils and Periodontal Disease Status in a Patient With Congenital Neutropenia (2000)

This report demonstrates for the first time that periodontal therapy, resulting in decreased bacterial load, may result in restoration of normal levels of circulating neutrophils in individuals with congenital neutropenia under treatment with rhG-CSF. The results also suggest that periodontal pathogens may be associated with depressed neutrophil levels, even when patients receive treatment for neutropenia.
Absence of siderophore activity in Legionella species grown in iron-deficient media (1983)

Growth of Legionella species in a defined medium deficient in iron did not result in the production of phenolic or hydroxamate siderophores which could be detected by chemical or biological assay methods. Growth of a variety of other gram-negative organisms under the same conditions resulted in the production of both hydroxamate and phenolate siderophores. The iron-deficient medium limited growth of the Legionella species more severely than it did the growth of the other gram-negative organisms. We have concluded that Legionella species do not make the commonly recognized siderophores, probably because they are restricted in their growth to those environments in which inorganic iron is readily available or is supplied in a form bound to an unknown carrier.
Exacting Public Beach Access: The Viability of Permit Conditions and Florida's State Beach Access Laws After Dolan v. City of Tigard (1997)

* J.D. with honors, Florida State University College of Law (1997), B.A., Florida State University (1994). 1. See FLA. Stat. § 161.55(6) (1995) (providing that a developer cannot interfere with existing beach access unless the developer provides a comparable alternate accessway); FLA. St AT. § 161.053(5)(e) (1995) (allowing the Department of Environmental Protection (DEP) to require an alternate accessway where the granting of a permit will cause unavoidable interference with public beach access). 2. See S.C. CODE ANN. § 48-39-150(A)(5), (B) (Law. Co-op. 1987 & Supp. 19%) (allowing DEP to consider the extent to which a proposed development will affect public beach access in granting or denying a development permit and providing that DEP may condition the permit on whatever measures it deems necessary for protection of the public interest). 3. See N.C. Gen. Stat. § 113A-120(a), (b) (1996) (providing that a development permit may be conditioned upon the applicant's amending of a proposal to protect the public interest with respect to various factors, including beach access). 303
TFIIS Enhances Transcriptional Elongation through an Artificial Arrest Site In Vivo (2001)

Transcriptional elongation by RNA polymerase II has been well studied in vitro, but understanding of this process in vivo has been limited by the lack of a direct and specific assay. Here, we designed a specific assay for transcriptional elongation in vivo that involves an artificial arrest (ARTAR) site designed from a thermodynamic theory of DNA-dependent transcriptional arrest in vitro. Transcriptional analysis and chromatin immunoprecipitation experiments indicate that the ARTAR site can arrest Pol II in vivo at a position far from the promoter. TFIIS can counteract this arrest, thereby demonstrating that it possesses transcriptional antiarrest activity in vivo. Unexpectedly, the ARTAR site does not function under conditions of high transcriptional activation unless cells are exposed to conditions (6-azauracil or reduced temperature) that are presumed to affect elongation in vivo. Conversely, TFIIS affects gene expression under conditions of high, but not low, transcriptional activation. Our results provide physical evidence for the discontinuity of transcription elongation in vivo, and they suggest that the functional importance of transcriptional arrest sites and TFIIS is strongly influenced by the level of transcriptional activation.
The Ice-Binding Site of Atlantic Herring Antifreeze Protein Corresponds to the Carbohydrate-Binding Site of C-Type Lectins (1998)

The type II antifreeze proteins (AFPs) of smelt and Atlantic herring are homologous to the carbohydrate-recognition domains (CRDs) of Ca2+-dependent (C-type) animal lectins and, like these lectins, acquire a stable and active structure upon binding Ca2+ ions. In the C-type lectin CRD, the carbohydrate-binding site is located at a Ca2+-binding site. Site-directed mutagenesis was used to test the hypothesis that the ice-binding site of the type II AFP corresponds to the carbohydrate-binding site of the lectins. To disrupt this site in the herring AFP without perturbing the Ca2+-dependent protein fold, a double mutant was constructed that changed the Ca2+- and carbohydrate-binding motif from the galactose-type of wild-type AFP containing the sequence Gln-Pro-Asp to a mannose-type that has the sequence Glu-Pro-Asn and is also known to bind Ca2+. The mutant AFP exhibited proper Ca2+ binding, folding, and stability as demonstrated by ruthenium red staining, proteolysis protection assays, and CD spectroscopy. However, it showed no antifreeze activity (thermal hysteresis) and did not alter ice crystal morphology to form bipyramidal crystals as does the active wild-type AFP. These results demonstrate that the ice-binding site of the herring type II AFP corresponds to the carbohydrate-binding site of the C-type lectin CRDs and further suggest that this ice-binding function evolved from the carbohydrate-binding site of a preexisting C-type lectin.
An Efficient Halogen‐Free Electrolyte for Use in Rechargeable Magnesium Batteries (2015)

Abstract Unlocking the full potential of rechargeable magnesium batteries has been partially hindered by the reliance on chloride‐based complex systems. Despite the high anodic stability of these electrolytes, they are corrosive toward metallic battery components, which reduce their practical electrochemical window. Following on our new design concept involving boron cluster anions, monocarborane CB 11 H 12 − produced the first halogen‐free, simple‐type Mg salt that is compatible with Mg metal and displays an oxidative stability surpassing that of ether solvents. Owing to its inertness and non‐corrosive nature, the Mg(CB 11 H 12 ) 2 /tetraglyme (MMC/G4) electrolyte system permits standardized methods of high‐voltage cathode testing that uses a typical coin cell. This achievement is a turning point in the research and development of Mg electrolytes that has deep implications on realizing practical rechargeable Mg batteries.
A historical overview of bacteriophage therapy as an alternative to antibiotics for the treatment of bacterial pathogens (2013)

The seemingly inexorable spread of antibiotic resistance genes among microbial pathogens now threatens the long-term viability of our current antimicrobial therapy to treat severe bacterial infections such as sepsis. Antibiotic resistance is reaching a crisis situation in some bacterial pathogens where few therapeutic alternatives remain and pan-resistant strains are becoming more prevalent. Non-antibiotic therapies to treat bacterial infections are now under serious consideration and one possible option is the therapeutic use of specific phage particles that target bacterial pathogens. Bacteriophage therapy has essentially been re-discovered by modern medicine after widespread use of phage therapy in the pre-antibiotic era lost favor, at least in Western countries, after the introduction of antibiotics. We review the current therapeutic rationale and clinical experience with phage therapy as a treatment for invasive bacterial infection as novel alternative to antimicrobial chemotherapy.
Antidepressant effects of an inverse agonist selective for α5 GABA-A receptors in the rat forced swim test (2014)

Abstract It has been shown in electrophysiological studies that the ligand L-655,708 possesses a binding selectivity and a moderate inverse agonist functional selectivity for α5-containing GABA-A receptors. The present study is aimed to investigate the antidepressant effects of the ligand L-655,708 in the forced swim test (FST) and its impact on locomotor activity in rats. The behavior of the animals was recorded with a digital camera, and the data were analyzed by one-way ANOVA, followed by Dunnett’s test. In FST, L-655,708 significantly decreased immobility time at a dose of 3 mg/kg after a single and repeated administration (p<0.05), exerting acute and chronic antidepressant effects. However, it did not induce significant differences in the time of struggling behavior during FST. Furthermore, L-655,708 did not show a significant effect on locomotor activity (p>0.05). These data suggest that negative modulation at GABA-A receptors containing the α5 subunit may produce antidepressant effects in rats. These effects were not confounded by locomotor influences.
Deep-tissue anatomical imaging of mice using carbon nanotube fluorophores in the second near-infrared window (2011)

Fluorescent imaging in the second near-infrared window (NIR II, 1-1.4 μm) holds much promise due to minimal autofluorescence and tissue scattering. Here, using well-functionalized biocompatible single-walled carbon nanotubes (SWNTs) as NIR II fluorescent imaging agents, we performed high-frame-rate video imaging of mice during intravenous injection of SWNTs and investigated the path of SWNTs through the mouse anatomy. We observed in real-time SWNT circulation through the lungs and kidneys several seconds postinjection, and spleen and liver at slightly later time points. Dynamic contrast-enhanced imaging through principal component analysis (PCA) was performed and found to greatly increase the anatomical resolution of organs as a function of time postinjection. Importantly, PCA was able to discriminate organs such as the pancreas, which could not be resolved from real-time raw images. Tissue phantom studies were performed to compare imaging in the NIR II region to the traditional NIR I biological transparency window (700-900 nm). Examination of the feature sizes of a common NIR I dye (indocyanine green) showed a more rapid loss of feature contrast and integrity with increasing feature depth as compared to SWNTs in the NIR II region. The effects of increased scattering in the NIR I versus NIR II region were confirmed by Monte Carlo simulation. In vivo fluorescence imaging in the NIR II region combined with PCA analysis may represent a powerful approach to high-resolution optical imaging through deep tissues, useful for a wide range of applications from biomedical research to disease diagnostics.
Delaying Caspase Activation by Bcl-2: A Clue to Disease Retardation in a Transgenic Mouse Model of Amyotrophic Lateral Sclerosis (2000)

Molecular mechanisms of apoptosis may participate in motor neuron degeneration produced by mutant copper/zinc superoxide dismutase (mSOD1), the only proven cause of amyotrophic lateral sclerosis (ALS). Consistent with this, herein we show that the spinal cord of transgenic mSOD1 mice is the site of the sequential activation of caspase-1 and caspase-3. Activated caspase-3 and its produced beta-actin cleavage fragments are found in apoptotic neurons in the anterior horn of the spinal cord of affected transgenic mSOD1 mice; although such neurons are few, their scarcity should not undermine the potential importance of apoptosis in the overall mSOD1-related neurodegeneration. Overexpression of the anti-apoptotic protein Bcl-2 attenuates neurodegeneration and delays activation of the caspases and fragmentation of beta-actin. These data demonstrate that caspase activation occurs in this mouse model of ALS during neurodegeneration. Our study also suggests that modulation of caspase activity may provide protective benefit in the treatment of ALS, a view that is consistent with our recent demonstration of caspase inhibition extending the survival of transgenic mSOD1 mice.
A high frequency iron loss measuring system (1984)

A high performance iron loss measuring system is introduced by using an 8-bit microcomputer, a two-channel memory device with high speed A/D converters and a wide band power amplifier. A required time to obtain a datum of one experimental point is about one minute when the error between the desired maximum flux density and the settled one is allowed within 0.5%. This system makes it possible to measure iron losses in the frequency range up to 1MHz. The results have a good correlation to the measured results by using the U-Function Meter.
A Geometry-Based Welding Distortion Prediction Tool (2021)

The prediction of welding distortion requires expertise in computer simulation programs, a clear definition of the nonlinear material properties, and mesh settings together with the nonlinear solution settings of a coupled thermal-structural analysis. The purpose of this paper is to present the validation of an automatic simulation tool implemented in Ansys using Python scripting. This tool allows users to automate the preparation of the simulation model with a reduced number of inputs. The goal was, based on some assumptions, to provide an automated simulation setup that enables users to predict accurate distortion during the welding manufacturing process. Any geometry prepared in a CAD software can be used as the input, which gave us much geometrical flexibility in the shapes and sizes to be modeled. A thermomechanical loosely coupled analysis approach together with element birth and death technology was used to predict the distortions. The automation of the setup enables both simulation and manufacturing engineers to perform welding-induced distortion prediction. The results showed that the method proposed predicts distortion with 80-98% accuracy.
Control of Emission Color of High Quantum Yield CH<sub>3</sub>NH<sub>3</sub>PbBr<sub>3</sub> Perovskite Quantum Dots by Precipitation Temperature (2015)

<b>Emission color controlled, high quantum yield CH<sub>3</sub>NH<sub>3</sub>PbBr<sub>3</sub> perovskite quantum dots</b> are obtained by changing the temperature of a bad solvent during synthesis. The products for temperatures between 0 and 60 °C have good spectral purity with narrow emission line widths of 28-36 nm, high absolute emission quantum yields of 74% to 93%, and short radiative lifetimes of 13-27 ns.
Phase I Trial of Lenalidomide in Pediatric Patients With Recurrent, Refractory, or Progressive Primary CNS Tumors: Pediatric Brain Tumor Consortium Study PBTC-018 (2010)

Lenalidomide was tolerable in children with CNS tumors at doses of 116 mg/m(2)/d during the initial dose-finding period. The primary toxicity is myelosuppression. Antitumor activity, defined by both objective responses and long-term stable disease, was observed, primarily in patients with low-grade gliomas.
An artificial oral environment for testing dental materials (1991)

Two servo-hydraulic actuators were combined to produce the force movement cycle of human mastication. A closed-loop method of control was used which functions in a manner similar to the human neuromuscular system. The horizontal closed-loop uses a linearly variable differential amplifier (LVDT) to monitor the position. The vertical closed-loop uses both an LVDT to monitor position and a load cell to monitor force with a "mode switch" being made between the two mechanisms of control. A function generator is used to produce a sine wave which is modified to produce the movement and force programs for the two servo-hydraulic actuators. An acrylic chamber was constructed which contains the test samples and maintains an environment similar to that which occurs in the mouth. Natural or artificial saliva maintained at 37 degrees C is continuously circulated through the chamber. The time to complete a single chewing cycle was decreased by eliminating that part of the cycle where no force is produced. This enables the chewing rate to be increased to four cycles per second. The wear produced in the artificial mouth was found to have a high correlation with clinical wear if 250,000 cycles in the artificial mouth are assumed to be equivalent to one year in the human mouth.
Enhanced binding and uptake of remnant lipoproteins by hepatic lipase-secreting hepatoma cells in culture. (1994)

Rat hepatoma McA-RH7777 cells transfected with a human hepatic lipase (HL) cDNA synthesized and secreted 50-80 ng of human HL/mg of cell protein at 4 h, approximately 50% of which was bound to cell-surface heparan sulfate proteoglycans (HSPG). The newly synthesized HL possessed enzymatic activity. When rabbit beta-very low density lipoproteins (beta-VLDL) and canine chylomicrons or chylomicron remnants were incubated with HL-secreting cells, remnant binding and uptake were enhanced 3-fold compared with nontransfected cells. Furthermore, fluorescence microscopy showed enhanced uptake of 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine-labeled beta-VLDL by the HL-transfected cells. When 125I-beta-VLDL were added to conditioned medium from HL-secreting cells, the HL in the media enhanced the binding and uptake of the remnant lipoproteins by nontransfected cells about 3-fold. Likewise, surface-bound HL (without HL in the medium) also was able to mediate the enhanced binding of the remnants. This HL-enhanced binding was shown to be mediated by an interaction with cell-surface HSPG. Heparinase treatment to remove cell-surface HSPG or chlorate treatment to prevent HSPG sulfation of the HL-secreting cells abolished all the HL-mediated enhanced binding and uptake. Furthermore, heparinase pretreatment of nontransfected cells prevented the enhanced binding and uptake of beta-VLDL incubated with conditioned medium from HL-secreting cells. As binding was not enhanced in the absence of HSPG, an HL-HSPG initial interaction appears essential. Addition of apolipoprotein (apo) E to the beta-VLDL did not facilitate HL-mediated binding and uptake; in fact, beta-VLDL from apoE-null mice demonstrated a similar degree of enhanced binding as did rabbit beta-VLDL with or without added apoE. On the other hand, beta-VLDL from transgenic mice overexpressing binding-defective apoE(Arg142-->Cys) did not display any enhanced binding and uptake by the HL-secreting cells, and it appears that the apoE(Arg142-->Cys) actually inhibited the HL-mediated interaction. This mutant form of apoE is associated with a dominant mode of expression of type III hyperlipoproteinemia in contrast to the more commonly occurring recessive disorder. Impaired HL interaction with the apoE(Arg142-->Cys) beta-VLDL may contribute to remnant lipoprotein accumulation in the plasma of patients with this mutant form of apoE. Thus, HL contributes to the enhanced cell association of specific types of remnant lipoproteins by initiating their binding to cell-surface HSPG.
The cleavage site of the R<i>sa</i>I isoschizomer,<i>C</i>vill, is GITAC (1987)

Journal Article The cleavage site of the R sa I isoschizomer, C vill, is GITAC Get access Yuannan Xia, Yuannan Xia Department of Plant Pathology, University of NebraskaLincoln, NE 68583-0722, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Kenneth E. Narva, Kenneth E. Narva Department of Plant Pathology, University of NebraskaLincoln, NE 68583-0722, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar L. Van Etten L. Van Etten Department of Plant Pathology, University of NebraskaLincoln, NE 68583-0722, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 15, Issue 23, 10 December 1987, Page 10063, https://doi.org/10.1093/nar/15.23.10063 Published: 10 December 1987 Article history Received: 05 October 1987 Published: 10 December 1987
Marker exchange mutagenesis of the <i>hydN</i> genes in <i>Desulfovibrio fructosovorans</i> (1991)

A strain of Desulfovibrio fructosovorans deleted from the hydN [NiFe]hydrogenase structural gene was constructed. A plasmid carrying a 7 kb DNA fragment on which the hydN gene had been replaced by the npt reporter gene (kanamycin-resistant, KnR) was introduced into D. fructosovorans by electroporation. Southern analysis of one KnR clone demonstrated that the hydN gene had been eliminated by marker exchange. This mutant, which was devoid of the [NiFe]hydrogenase gene, still showed a 10% residual hydrogenase activity. Its ability to grow efficiently with H2 as sole energy source is discussed. This is the first report, in a member of the sulphate-reducing bacteria, of a successful transformation and concomitant homologous recombination leading to a fully controlled genotype.
Further characterization of human myeloid antigens (gp160,95; gp150; gp67): investigation of epitopic heterogeneity and non‐haemopoietic distribution using panels of monoclonal antibodies belonging to CD‐11b, CD‐13 and CD‐33 (1988)

We have investigated the binding of over 30 different monoclonal antibodies (MAB) belonging to three distinct clusters of differentiation (CD-11b; CD-13; CD-33; as defined by the Third International Workshop on Leucocyte Differentiation Antigens (ILWS), 1986), and which are reactive with three distinct myeloid restricted surface antigens ('gp160,95'; 'gp150'; 'gp67'). By investigating reactivity with non-haemopoietic cells, we have confirmed that CD-11b and CD-33 MAB reactivity is largely restricted to haemopoietic cells, whilst CD-13 MAB showed additional binding to a wide range of non-haemopoietic cells. Epitopic heterogeneity was also investigated within each cluster of differentiation. Tested anti-CR3 (CD-11b) MAB varied in their ability to block the binding of complement coated sheep red blood cells and zymosan particles. A more detailed analysis of MAB binding heterogeneity was performed by competitive inhibition assays. It was demonstrated that MAB from both CD-11b and CD-13 bind to several distinct epitopes (at least six and five respectively) on their respective antigen molecules. In contrast, CD-33 MAB appear to bind to only a single site on 'gp67'. These data may allow for a clearer appreciation of the disparate functional effects obtained using different MAB reagents to individual myeloid antigens, as reported by a number of workers.