gebhart/patrepeval huggingface dataset:
In vivo protection of photoreceptors from light damage by pigment epithelium-derived factor. (2001)

The data demonstrate that PEDF protected photoreceptor cells against light damage. This is significant, because it may open new avenues for the study of molecular mechanisms underlying degenerative processes. This, in turn, may lead to the development of therapeutic strategies for the prevention and treatment of degenerative diseases of the retina.
Conditions of formation, purification, and characterization of an alpha-galactosidase of Trichoderma reesei RUT C-30 (1993)

Trichoderma reesei RUT C-30 formed an extracellular alpha-galactosidase when it was grown in a batch culture containing lactose or locust bean gum as a carbon source. Short-chain alpha-galactosides (melibiose, raffinose, stachyose), as well as the monosaccharides galactose, dulcitol, arabinose, and arabitol, also induced alpha-galactosidase activity both when they were used as carbon sources (at a concentration of 1%) in batch cultures and in resting mycelia (at concentrations in the millimolar range). The addition of 50 mM glucose did not affect the induction of alpha-galactosidase formation by galactose. alpha-Galactosidase from T. reesei RUT C-30 was purified to homogeneity from culture fluids of galactose-induced mycelia. The active enzyme was a 50 +/- 3-kDa, nonglycosylated monomer which had an isoelectric point of 5.2. It was active against several alpha-galactosides (p-nitrophenyl-alpha-D-galactoside, melibiose, raffinose, and stachyose) and galactomannan (locust bean gum) and was inhibited by the product galactose. It released galactose from locust bean gum and exhibited synergism with T. reesei beta-mannanase. Its activity was optimal at pH 4, and it displayed broad pH stability (pH 4 to 8). Its temperature stability was moderate (60 min at 50 degrees C resulted in recovery of 70% of activity), and its highest level of activity occurred at 60 degrees C. Its action on galactomannan was increased by the presence of beta-mannanase.
Identification of murine protective epitopes on the Porphyromonas gingivalis fimbrillin molecule (1996)

Fimbriae from Porphyromonas gingivalis are believed to play an important role in the pathogenesis of periodontal diseases. The aim of the present study was to identify the fimbrial protective T-cell epitopes in CBA/J mice. A truncated protein corresponding to amino acids 1 to 198, PgF1-198, was generated and allowed us to demonstrate that the N terminus of the protein contains T-cell epitopes. With synthetic peptides, an immunodominant sequence was identified between amino acids 103 and 122. The corresponding peptide, PgF-P8, induced T-cell proliferation after in vitro restimulation of in vivo-primed cells, giving a stimulation index comparable to the one obtained with r-fimbrillin, and induced production of both Th1 and Th2 cytokines. Growth supernatant contained significant levels of interleukin 2 (IL-2), gamma interferon, IL-4 (28 pg/ml), and tumor necrosis factor alpha. Immunization of mice with r-fimbrillin, PgF1-198, and PgF-P8 induced production of antibodies specific to r-fimbrillin and PgF-P8. In addition, by using the mouse chamber model we found that mice immunized with PgF-P8 were dramatically protected against a normally lethal injection of P. gingivalis. Animals immunized with PgF-P8 40 days prior to challenge showed a 60% survival rate when challenged with P. gingivalis, compared with just 25% survival in control animals and just 5% survival in mice immunized with PgF-P8 only 21 days prior to challenge. Although the protection depended on the time of immunization before the bacterial challenge, it did not correlate with in vivo local cytokine production (IL-2, IL-4, IL-6, tumor necrosis factor alpha, and gamma interferon), specific antibody levels, or the isotype of anti-PgF-P8 antibodies produced.
A neural-network-based approach for fault classification and faulted phase selection (2002)

This paper is concerned with a new approach for fault type classification and faulted phase selection based on artificial neural networks (ANN) to be used for power transmission line protection. The proposed approach is based on a 2-level hierarchical neural network structure. Compared to other architectures, this structure would have a high learning ability and accordingly higher recall accuracy. To reach the corresponding decision, the normalized changes from prefault condition in the instantaneous phase voltages and currents at the relaying point are used. This would lead to an inherent adaptive feature of the approach.
Membrane-assisted solvent extraction of organochlorine compounds in combination with large-volume injection/gas chromatography-electron capture detection (2001)

Membrane-Assisted solvent extraction is based on a small-scale liquid-liquid extraction with a polymer membrane (low-density polyethylene, LDPE) separating the aqueous from the organic phase. The organic analytes present in the aqueous sample dissolve in the membrane material and pass through it before being enriched in a small volume of organic solvent. As the organic extract is almost completely subjected to GC-ECD using large-volume injection, the volume of both aqueous sample and organic solvent can be minimised. The method was established using chlorobenzenes and HCHs as model compounds and extraction parameters were optimised. Detection limits, the linear dynamic range and reproducibility are shown. Membrane-assisted solvent extraction was applied to the analysis of heavily contaminated groundwater samples, and results were compared to conventional liquid-liquid extraction. The advantages of using a membrane between the two phases are that emulsion formation is prevented and macromolecular compounds and particles from the organic extract are excluded. This makes this extraction technique particularly suitable for complex samples high in organic matter.
Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles (2007)

PPR (pentatricopeptide repeat) genes form a large family particularly prevalent in higher plants and targeted to organelles. They are involved in many post-transcriptional processes such as splicing, editing, processing and translation. Current data suggest that PPR proteins are involved in targeting effectors to the correct sites on the correct transcripts but the molecular mechanisms for RNA binding and effector recruitment by PPR proteins are not understood yet.
Design of Automatic Guided Vehicles Based on Computer Control (2012)

The automated Guided Vehicles is the development trend of modern automated warehousing technology, which can realize the flexible transport, the use of flexible, high transport efficiency, energy saving, no pollution, significant savings in labor costs. The paper gave a brief introduction about the structure and function of the AGV, and a detailed description about the movement mathematical model and navigation calculation of the AGV. In the end the paper designed the control system of the AGV.
Modeling of the Undular Jump for White Water Bypass (1986)

Two of the authors have reported previously on the hazard that a conventional hydraulic jump with a uniform reverse surface roller presents to white water boaters. The intent is to create a hydraulic jump that is safe for boaters. This is accomplished by maintaining a horizontal supercritical discharge at the surface, thus eliminating dangerous reverse (or upstream) surface currents. Because numerous flow conditions are typically considered, the analysis technique has been computerized. Two projects of McLaughlin Water Engineers, Ltd. , have involved modeling efforts that were very useful, both in academic terms to confirm theory, and to refine the design to achieve good initial prototype performance. Results of a modeling effort for the design of a white water bypass at a grade control structure on the Arkansas River in Pueblo, Colorado are presented herein.
MICROSTRUCTURE OF CVD - Al<sub>2</sub>O<sub>3</sub> (1989)

The reaction mechanisms of CVD-Al2O3 are briefly reviewed. Two independent reaction paths exist, one of which is rate limited by a volume reaction and the second one by a surface reaction. Al2O3 crystallizes in several different phases. The α-structure is the stable phase at normal deposition temperature (950-1050°C). The metastable ϰ-phase is the second most commonly occurring phase. It is shown that ϰ - and θ - Al2O3 nucleate on pure TiC (111) facets with well defined lattice orientation-relationships between TiC and Al2O3. In contrast, no epitaxial relationship between TiC and α-Al2O3 is found and the latter interface contains a considerable amount of porosity. The difference in the interface properties is reflected in the adhesion between TiC and Al2O3. It is concluded that the nucleation resulting in α-Al2O3 does not occur on TiC but on an intermediate thin layer of titanium oxide e.g. Ti2O3 or Ti3O5, which is dissolved during the subsequent Al2O3 growth.
Biodegradable Nanocapsules Containing a Lipophilic Immunomodulator: Drug Retention and Tolerance Towards Macrophages<i>In Vitro</i> (1993)

Nanocapsules (250 nm diameter) were prepared from poly (D, L-lactide) containing a lipophilic immunomodulator: MDP-L-alanyl cholesterol (MTP-Chol). High encapsulation rates were obtained at 37 degrees C in culture medium or in buffers imitating phagosomes and lysosomes. The tolerance of these particles by rat alveolar macrophages in vitro was tested. A slight toxicity was observed which was the result of two factors: the capacity of the immunomodulator to stimulate the generation of nitrite oxide by the L-arginine-dependent pathway and the polymer itself. The latter toxicity seemed to be mediated by a different mechanism.
The Wnt5a/Ror2 pathway is associated with determination of the differentiation fate of bone marrow mesenchymal stem cells in vascular calcification (2013)

Accumulating evidence have demonstrated that mesenchymal stem cells (MSCs) are involved in the initiation and progression of various vascular diseases. Canonical Wnt signaling controls the fate of MSCs, and plays an important role in vascular calcification. However, vascular calcification can be inhibited by the non-canonical Wnt signaling pathway Wnt5a/Ror2. This study aimed to investigate whether the Wnt5a/Ror2 pathway is associated with determination of the differentiation fate of MSCs in vascular calcification. Direct co-cultures were established by seeding smooth muscle cells (SMCs) or calcified SMCs and MSCs together at ratios of SMCs or calcified SMCs 15x104; SMCs or calcified SMCs 5x104: MSCs 10x104, SMCs or calcified SMCs 10x104: MSCs 5x104. Osteosynthesis-inducing medium (OS) was added to the culture medium in the groups of MSCs with non-calcified SMCs. Cells were cultured for nine days. Osteoblastic differentiation was evaluated by cell morphology and the activity of alkaline phosphatase (ALP) in cell lysates and ALP staining. Furthermore, we investigated the inhibition of Wnt signaling, and observed that the members of the non-canonical signaling pathway Wnt5a/Ror2 were expressed in each group. Additionally, MSCs cultured in culture media with OS did not differentiate into an osteoblast phenotype when in direct contact with non-calcified SMCs, irrespective of the number of MSCs. However, an osteoblast phenotype was observed when MSCs were cultured in media without OS differentiation towards direct contact with calcified SMCs, and the levels of osteoblastic markers had a direct correlation with the number of MSCs. Of note, the Wnt5a protein was associated with the levels of calcification, thus, although rarely detected in non-calcification, Ror2 mRNA in the non-calcified groups was significantly higher compared to that in the calcified groups. Therefore, the Wnt5a/Ror2 pathway is associated with determination of the differentiation fate of bone marrow mesenchymal stem cells in vascular calcification.
A personalized, multiomics approach identifies genes involved in cardiac hypertrophy and heart failure (2018)

A traditional approach to investigate the genetic basis of complex diseases is to identify genes with a global change in expression between diseased and healthy individuals. However, population heterogeneity may undermine the effort to uncover genes with significant but individual contribution to the spectrum of disease phenotypes within a population. Here we investigate individual changes of gene expression when inducing hypertrophy and heart failure in 100 + strains of genetically distinct mice from the Hybrid Mouse Diversity Panel (HMDP). We find that genes whose expression fold-change correlates in a statistically significant way with the severity of the disease are either up or down-regulated across strains, and therefore missed by a traditional population-wide analysis of differential gene expression. Furthermore, those "fold-change" genes are enriched in human cardiac disease genes and form a dense co-regulated module strongly interacting with the cardiac hypertrophic signaling network in the human interactome. We validate our approach by showing that the knockdown of <i>Hes1</i>, predicted as a strong candidate, induces a dramatic reduction of hypertrophy by 80-90% in neonatal rat ventricular myocytes. Our results demonstrate that individualized approaches are crucial to identify genes underlying complex diseases as well as to develop personalized therapies.
Provenance for Computational Tasks: A Survey (2008)

The problem of systematically capturing and managing provenance for computational tasks has recently received significant attention because of its relevance to a wide range of domains and applications. The authors give an overview of important concepts related to provenance management, so that potential users can make informed decisions when selecting or designing a provenance solution.
Platinum Acetylide Materials for Optical Limiting (2006)

This project explored linear and non-linear optical structure-property relationships for Pt-acetylide oligomers and polymers. These materials show promise for application in laser protection via the reverse saturable absorption (RSA) mechanism. This basic science program had the following primary objectives: 1) Chemical synthesis and purification of new pi-conjugated Pt-acetylide oligomers and polymers. 2) Characterization of the ground and excited state properties of the new materials, with emphasis placed on measurement of parameters that are important to reverse saturable absorption. These parameters include ground state absorption spectra, singlet-triplet intersystem crossing yields, triplet excited state cross sections, and triplet excited state quenching via triplet-triplet annihilation. 3) Evaluate new materials for application as reverse saturable absorbers. The project also explored other key issues, including tuning the spectral region where the ground state and triplet excited states absorb for series of structurally-related Pt- acetylide materials, development of materials that are liquids at ambient temperature, and study of triplet excited state quenching in the solid state.
Activation of STAT3 induced by cerebral ischemia in rat hippocampus and its possible mechanisms. (2003)

It has been demonstrated that signal transducer and activator of transcription-3 (STAT3) is activated after cerebral ischemia/reperfusion (I/R) in cortex and striatum. In this study, we investigated whether STAT3 was rapidly activated in hippocampus by cerebral ischemia without reperfusion in four-vessel occlusion (4-VO) model of Sprague-Dawley (SD) rats. The results showed that tyrosine phosphorylation and DNA binding activity of STAT3 was rapidly increased by ischemia. The p-STAT3 level in cytoplasm increased 5 min after occlusion and reached a peak at 10 min following ischemia (1.7 folds vs sham) by means of immunoblotting (IB). P-STAT3 in nucleus was gradually enhanced with its peak activity occurring at 30 min of ischemia (2.3 folds vs sham). Electrophoretic mobility shift assay (EMSA) with STAT3 probe demonstrated that DNA binding activity of STAT3 in nuclear extracts increased from 5 min and peaked at 30 min of ischemia (3.2 folds vs sham). These changes were prevented by genistein (a protein tyrosine kinase inhibitor) and antioxidant N-acetyl-L-cysteine (NAC), but promoted by sodium orthovanadate (a protein phosphatase inhibitor), which were administered to the SD rats 20 min before ischemia. These results indicate that the activation of STAT3 following cerebral ischemia may be modulated by PTK/PTP, and that this pathway may be of benefit to the adaptation of the hippocampal neurons to oxidative stress.
The effect of weak dispersion on stimulated Raman scattering (1985)

The Raman gain of an undepleted plane-wave multimode pump laser is calculated. The Stokes and pump fields are represented as vector states in a Hilbert space, and the Dirac bracket notation is introduced to simplify the form of the equations. It is shown that in the absence of dispersion the Stokes vector component correlated with the pump grows exponentially with the monochromatic-pump gain, while all other Stokes components experience zero growth. Perturbation theory is used to second order to determine the gain decrease resulting from relative dispersion between pump and Stokes, and the results are compared with previous works.
Distinguishing roles for norepinephrine and serotonin in the behavioral effects of antidepressant drugs. (2004)

Antidepressant drugs have typically been classified into sets of compounds with actions targeted at serotonin (selective serotonin reuptake inhibitors [SSRIs]), norepinephrine (norepinephrine reuptake inhibitors [NRIs]), or both neurotransmitters (serotonin-norepinephrine reuptake inhibitors). Their classification has been based predominantly on their acute pharmacologic effects, usually determined by in vitro radioligand binding assays. The pharmacologic selectivity of antidepressants can be altered after their systemic administration, however, by dose, drug metabolism, physiologic interactions between neurotransmitters, and adaptive effects that emerge after chronic administration. This review examines whether pharmacologic selectivity is maintained by different types of antidepressants in vivo and whether pharmacologic selectivity matters for the production of their behavioral effects. Antidepressants increase extracellular levels of neurotransmitters according to their ability to inhibit presynaptic transporters, although physiologic interactions among neurotransmitters can influence antidepressants' selectivity in certain brain regions. Chronic administration of many antidepressants also causes down-regulation of postsynaptic and presynaptic receptors. The pattern of responses of presynaptic markers suggests that pharmacologic selectivity is maintained after chronic administration of many antidepressants. Behavioral tests indicate that depletion of serotonin (5-HT) is capable of preventing the effects produced by SSRIs but not NRIs. The depletion of catecholamines also inhibits the effects of NRIs, although test results can be complicated by inhibition of motor activity. Depletion of norepinephrine may also inhibit the effects of some SSRIs, but not highly selective SSRIs like citalopram. Although the pattern of results from in vivo tests supports the concept that parallel neurotransmitter mechanisms lead to antidepressant activity, norepinephrine may participate in the effects of some SSRIs. It is also possible that compounds with dual actions at 5-HT and norepinephrine systems may be effective under circumstances in which selective antidepressants are ineffective.
Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats (2018)

Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection. Comparative genomic analysis showed that many of them had conserved backbones. Plasmid coding sequences corresponding to plasmid specific functions were bioinformatically and functionally analyzed. Replication initiation protein analysis revealed the predominance of the Rep_3 superfamily. The phylogenetic tree constructed from all Acinetobacter Rep_3 superfamily plasmids showed 16 intermingled clades originating from nosocomial and environmental habitats. Phylogenetic analysis of relaxase proteins revealed the presence of a new sub-clade named MOBQ<sub>Aci</sub>, composed exclusively of Acinetobacter relaxases. Functional analysis of proteins belonging to this group showed that they behaved differently when mobilized using helper plasmids belonging to different incompatibility groups.
A Full-Bridge Resonant Inverter With Modified Phase-Shift Modulation for High-Frequency AC Power Distribution Systems (2007)

The design of a resonant inverter for high-frequency ac (HFAC) power distribution systems is complicated by the following three factors: 1) A number of electronic loads located in different locations are connected to the resonant inverter, the impedance, and the power factor of the equivalent load of which varies over a wider range than a system with a certain load; 2) the resonant inverter is subject to an input-line voltage varying over a wide range; and 3) the characteristics of the resonant inverter depend on the load impedance. It is mandatory to operate the inverter with zero-voltage switching under various load conditions of different power factors and over wide input variations. It is further desirable that multiple resonant inverters can be paralleled with simple current-sharing control (CSC). A phase-shift- modulation (PSM)-controlled full-bridge series-parallel resonant inverter is proposed for the HFAC power distribution architectures. A new PSM method is proposed with which the phase angle of the inverter output voltage is independent of the modulation signal of the phase-shift modulator. Such a feature allows multiple resonant inverters to operate in parallel with a magnitude CSC. The resonant inverter is analyzed with a general nonresistive load model, and the design curves are developed. A prototype resonant inverter system is designed and implemented with an operation frequency of 1 MHz, a rated output power of 150 W, and a sinusoidal output voltage of 1-MHz 28-V rms. The proposed resonant inverter has the advantages of high efficiency over wide input/output line variations, high waveform quality of the output voltage, and phase-angle independence of the voltage-feedback/feed-forward control and CSC.
Thermal lens coupled magneto-optical effect in a ferrofluid (1994)

A magnetic-field-induced diffraction pattern was studied by a new technique: thermal lens coupled magneto-optical effect. In low fields, the diffraction angle has an almost quadratic dependence: θ∝H2. This effect can be used as an all optical magnetic field sensor with a resolution of 0.5 Oe, with a potential for further improvement. The method can also lead to the measurement of the onset of agglomeration in the sample.