gebhart/patrepeval huggingface dataset:
Corrosion Passivation of Gold by n-Alkanethiol Self-Assembled Monolayers:  Effect of Chain Length and End Group (1998)

Electrochemistry, FTIR-external reflection spectroscopy (FTIR-ERS), and scanning tunneling microscopy (STM) were used to study the ability of n-alkanethiol self-assembled monolayers (SAMs) to protect Au from corrosion in aqueous Br- solutions. The thickness and terminal functional group of the SAMs were varied to determine which factors lead to the greatest corrosion passivation. SAMs prepared on Au from the following molecules were studied: HS(CH2)15CH3, HS(CH2)11CH3, HS(CH2)10COOH, and HS(CH2)11OH. The data reveal that, prior to corrosion, the SAMs are crystalline and highly ordered but that afterward they are disordered and oriented parallel to the surface plane. The results show that, for SAMs containing the same terminal functional group, corrosion resistance increases as the SAM thickness increases. For SAMs that are equal in thickness but contain different terminal functional groups, the end groups resulting in the most corrosion resistance follow the order OH > COOH > CH3. The hydrophilic SAM-modified Au surfaces corrode smoothly in a layer-by-layer fashion while the methyl-terminated, hydrophobic SAM-modified surfaces undergo localized corrosion (pitting). Since hydrophilic SAMs are generally more defective than methyl-terminated SAMs but provide the Au more protection, we conclude that initial SAM defectiveness is not a reliable predictor of its barrier properties.
Poly(I-vinyl-2-pyrrolidinone) hydrogels as vitreous substitutes: Histopathological evaluation in the animal eye (1996)

A homopolymer of 1-vinyl-2 pyrrolidinone and its copolymer with 2-hydroxyethyl methacrylate, both cross-linked with divinyl glycol, were produced as possible substitutes for the vitreous body of the eye. The hydrated polymers behaved like viscoelastic gels, displaying excellent physical and optical properties. The sterile gels (0.7-1.5 ml) were injected into the vitreous cavity of rabbits, which previously underwent gas-mediated vitrectomy. Clinically, the eyes were quiet, with the exception of transient opacities in the vitreous. After 4 weeks, the operated eyes were enucleated and subjected to histopathological analysis using light and transmission electron microscopy. The common feature in all sections was the invasion of inflammatory cells. Vacuoles containing granular material, assumed to be polymer, were seen in the intercellular spaces of the neural retina, in the retinal pigment epithelium cells, and in macrophages. These findings indicated the fragmentation and phagocytosis of synthetic gels. It appeared that the biodegradation of the internalized polymers did not proceed further, however, the fate of polymers and their usefulness as vitreous substitutes should be investigated through long-term experiments.
Still image coding based on vector quantization and fractal approximation (1996)

In this paper, we propose a coding algorithm for still images using vector quantization (VQ) and fractal approximation, in which low-frequency components of an input image are approximated by VQ, and its residual is coded by fractal mapping. The conventional fractal coding algorithms indirectly used the gray patterns of an original image with contraction mapping, whereas the proposed fractal coding method employs an approximated and then decimated image as a domain pool and uses its gray patterns. Thus, the proposed algorithm utilizes fractal approximation without the constraint of contraction mapping. For approximation of an original image, we employ the discrete cosine transform (DCT) rather than conventional polynomial-based transforms. In addition, for variable blocksize segmentation, we use the fractal dimension of a block that represents the roughness of the gray surface of a region. Computer simulations with several test images show that the proposed method shows better performance than the conventional fractal coding methods for encoding still pictures.
Chronic electromagnetic field exposure decreases HSP70 levels and lowers cytoprotection (2002)

Abstract Electromagnetic field (EMF) exposures have been shown to induce heat shock proteins (HSPs), which help to maintain the conformation of cellular proteins during periods of stress. We have previously reported that short‐term exposure of chick embryos to either 60 Hz (extremely low frequency: ELF), or radio‐frequency (RF: 915 MHz) EMFs induce protection against hypoxia. Experiments presented in the current report are based on a study in which long‐term (4 days), continuous exposure to ELF‐EMFs decreased protection against ultraviolet radiation. Based on this result, it was hypothesized that de‐protection against hypoxia should also occur following long‐term, continuous, or daily, repeated exposures to EMFs. To test this hypothesis, chick embryos were exposed to ELF‐EMFs (8 μT) continuously for 4 days, or to ELF or RF (3.5 mW incident power)‐EMFs repeated daily (20, 30, or 60 min once or twice daily for 4 days). Several of the exposure protocols yielded embryos that had statistically significant decreases in protection against hypoxic stress (continuous and 30 or 60 min ELF twice daily; or 30 or 60 min once daily RF). This is consistent with our finding that following 4 days of ELF‐EMF exposure, HSP70 levels decline by 27% as compared to controls. In addition, the superposition of ELF‐EM noise, previously shown to minimize ELF‐EMF induced hypoxia protection, inhibited hypoxia de‐protection caused by long term, continuous ELF or daily, repeated RF exposures. This EMF‐induced decrease in HSP70 levels and resulting decline in cytoprotection suggests a mechanism by which daily exposure (such as might be experienced by mobile phone users) could enhance the probability of cancer and other diseases. J. Cell. Biochem. 84: 447–454, 2002. © 2001 Wiley‐Liss, Inc.
The Effect of Co-Substrate Feeding on Polyhydroxyalkanoate (PHA) Homopolymer and Copolymer Production in Recombinant Escherichia coli LS5218 (2012)

Polyhydroxyalkanoates (PHAs) are aliphatic polyesters produced by a wide variety of bacteria as carbon and energy storage sources. Copolymers of the short chain length (SCL) 3-hydroxybutyrate (3HB) repeating unit and medium chain length hydroxyalkanoate (MCL-HA) repeating units have better thermal and mechanical properties than poly-3HB homopolymers. In this study, a MCL monomer supplier gene phaJ4 from Pseudomonas putida KT2440, an engineered PHA synthase gene (phaC1) from Pseudomonas sp. 61-3, and the SCL monomer supplier genes, phaA and phaB from Ralstonia eutropha, were coexpressed under the lac promoter in recombinant E. coli LS5218 to produce SCL-MCL copolymers. The recombinant strains were co-fed lauric acid (a fatty acid) and glucose as a carbon source and the ratio of SCL to MCL monomers varied dependant on differences in the timing of the addition of each carbon source during the fermentation. The PHA copolymers produced exhibited a range from 0.4 mol% to 35 mol% MCL repeating units giving rise to wide range of physical properties. The molecular weights and thermal properties of different polymers were studied by gel permeation chromatography (GPC) and differential scanning calorimetry (DSC). The results suggested the polymers produced by co-feeding with lauric acid and glucose were mixtures of 3HB homopolymers and 3HB-co-MCL copolymers. This conclusion was confirmed by acetone fractionation.
A Crucial Role of MafA as a Novel Therapeutic Target for Diabetes*♦ (2005)

MafA, a recently isolated pancreatic beta-cell-specific transcription factor, is a potent activator of insulin gene transcription. In this study, we show that MafA overexpression, together with PDX-1 (pancreatic and duodenal homeobox factor-1) and NeuroD, markedly increases insulin gene expression in the liver. Consequently, substantial amounts of insulin protein were induced by such combination. Furthermore, in streptozotocin-induced diabetic mice, MafA overexpression in the liver, together with PDX-1 and NeuroD, dramatically ameliorated glucose tolerance, while combination of PDX-1 and NeuroD was much less effective. These results suggest a crucial role of MafA as a novel therapeutic target for diabetes.
Histones and Basic Polyamino Acids Stimulate the Uptake of Albumin by Tumor Cells in Culture (1965)

Basic proteins and polyamino acids are taken up by mammalian cells at rates up to 3000 times greater than serum albumin. When given together with serum albumin they increase the albumin uptake by a factor that correlates with their own rate of uptake and can reach more than 50-fold. The lowest threshold of activity detected (10(-10)M)is comparable to the activities of the most potent membrane-active agents.
Electromagnetically induced localized ignition in secondary high explosives: Experiments and numerical verification (2011)

In order to more fully understand the factors that influence the thermal “hot-spot” initiation of high explosives, we have chosen a model system for study that uses the internal and localized dissipation of long wavelength electromagnetic energy (microwaves). High purity organic crystals generally interact weakly with microwave energy. Therefore, the addition of electromagnetically absorbing inclusions of silicon carbide provides a tractable system for the study of hot-spot ignition phenomena. Previously, we developed a simple analytic model that illuminates the important physical factors. In this work, we verify the relationships of the analytic model using a series of experiments and a numerical model.
Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities (2008)

Viruses shape microbial community structure and function by altering the fitness of their hosts and by promoting genetic exchange. The complexity of most natural ecosystems has precluded detailed studies of virus-host interactions. We reconstructed virus and host bacterial and archaeal genome sequences from community genomic data from two natural acidophilic biofilms. Viruses were matched to their hosts by analyzing spacer sequences that occur among clustered regularly interspaced short palindromic repeats (CRISPRs) that are a hallmark of virus resistance. Virus population genomic analyses provided evidence that extensive recombination shuffles sequence motifs sufficiently to evade CRISPR spacers. Only the most recently acquired spacers match coexisting viruses, which suggests that community stability is achieved by rapid but compensatory shifts in host resistance levels and virus population structure.
FXR agonist obeticholic acid reduces hepatic inflammation and fibrosis in a rat model of toxic cirrhosis (2016)

Hepatic inflammation drives hepatic stellate cells (HSC), resulting in liver fibrosis. The Farnesoid-X receptor (FXR) antagonizes inflammation through NF-κB inhibition. We investigated preventive and therapeutic effects of FXR agonist obeticholic acid (OCA) on hepatic inflammation and fibrosis in toxic cirrhotic rats. Cirrhosis was induced by thioacetamide (TAA) intoxication. OCA was given during or after intoxication with vehicle-treated rats as controls. At sacrifice, fibrosis, hemodynamic and biochemical parameters were assessed. HSC activation, cell turn-over, hepatic NF-κB activation, pro-inflammatory and pro-fibrotic cytokines were determined. The effect of OCA was further evaluated in isolated HSC, Kupffer cells, hepatocytes and liver sinusoidal endothelial cells (LSEC). OCA decreased hepatic inflammation and fibrogenesis during TAA-administration and reversed fibrosis in established cirrhosis. Portal pressure decreased through reduced intrahepatic vascular resistance. This was paralleled by decreased expression of pro-fibrotic cytokines (transforming growth-factor β, connective tissue growth factor, platelet-derived growth factor β-receptor) as well as markers of hepatic cell turn-over, by blunting effects of pro-inflammatory cytokines (e.g. monocyte chemo-attractant protein-1). In vitro, OCA inhibited both LSEC and Kupffer cell activation; while HSC remained unaffected. This related to NF-κB inhibition via up-regulated IκBα. In conclusion, OCA inhibits hepatic inflammation in toxic cirrhotic rats resulting in decreased HSC activation and fibrosis.
Viable but non‐culturable and persistence describe the same bacterial stress state (2018)

Bacteria are often thought of as having two dormant phenotypes: the viable but non-culturable (VBNC) state and the persister state. Here we investigate the relatedness of the two stress-induced phenotypes at the single-cell level and examine cell morphology and quantify cell resuscitation. Using the classic starvation conditions to create VBNC cells, we found that the majority of the remaining Escherichia coli population are spherical, have empty cytosol and fail to resuscitate; however, some of the spherical cells resuscitate immediately (most probably those with dense cytosol). Critically, all the culturable cells in this starved population became persister cells within 14 days of starvation. We found that the persister cells initially are rod-like, have clear but limited membrane damage, can resuscitate immediately and gradually become spherical by aging. After 24 h, only rod-shaped persister cells survive, and all the spherical cells lyse. Both cell populations formed under the VBNC-inducing conditions and the persister conditions are metabolically inactive. Therefore, the bacterial population consists of dead cells and persister cells in the VBNC-inducing conditions; that is, the non-lysed particles that do not resuscitate are dead, and the dormant cells that resuscitate are persister cells. Hence, 'VBNC' and 'persister' describe the same dormant phenotype.
Intra-articular corticosteroid for knee osteoarthritis (2015)

Whether there are clinically important benefits of intra-articular corticosteroids after one to six weeks remains unclear in view of the overall quality of the evidence, considerable heterogeneity between trials, and evidence of small-study effects. A single trial included in this review described adequate measures to minimise biases and did not find any benefit of intra-articular corticosteroids.In this update of the systematic review and meta-analysis, we found most of the identified trials that compared intra-articular corticosteroids with sham or non-intervention control small and hampered by low methodological quality. An analysis of multiple time points suggested that effects decrease over time, and our analysis provided no evidence that an effect remains six months after a corticosteroid injection.
A multispectral LED array for the reduction of background autofluorescence in brain tissue (2013)

The presence of fixative-induced and cellular-derived artifactual autofluorescences (AAFs) presents a challenge in histological analysis involving immunofluorescence. We have established a simple and highly effective method for the reduction of AAFs that are ubiquitous in fixed mammalian brain and other tissues. A compact AAF-quenching photo-irradiation device was constructed using a commercially available light emitting diode (LED) array, cooling unit, and supporting components. The LED panel is comprised of an array of multispectral high intensity LEDs which serve as the illumination source for the photo-irradiation process. Rabbit and cat brain specimens of 5 μm- and 40 μm-thicknesses, respectively, were photo-irradiated for various durations. The AAFs were reduced to near tissue background levels after 24h of treatment for both deparaffinized and paraffinized rabbit brain specimens, and for the free-floating cat brain specimens. Subsequent immunofluorescence staining using primary antibodies against GFAP, NeuN, Iba-1, and MAP-2, and the corresponding Qdot(®) and Alexafluor(®) fluoroconjugates confirmed that the LED photo-irradiation treatment did not compromise the efficiency of the immunofluorescence labeling. The use of the device is not labor intensive, and only requires minimal tissue processing and experimental set-up time, with very low maintenance and operating costs. Finally, multiple specimens, in both slide and well-plate format, can be simultaneously photo-irradiated, thus, allowing for scalable batch processing.
Chromatin-Dependent Cooperativity between Constitutive and Inducible Activation Domains in CREB (2001)

The cyclic AMP (cAMP)-responsive factor CREB induces target gene expression via constitutive (Q2) and inducible (KID, for kinase-inducible domain) activation domains that function synergistically in response to cellular signals. KID stimulates transcription via a phospho (Ser133)-dependent interaction with the coactivator paralogs CREB binding protein and p300, whereas Q2 recruits the TFIID complex via a direct association with hTAF(II)130. Here we investigate the mechanism underlying cooperativity between the Q2 domain and KID in CREB by in vitro transcription assay with naked DNA and chromatin templates containing the cAMP-responsive somatostatin promoter. The Q2 domain was highly active on a naked DNA template, and Ser133 phosphorylation had no additional effect on transcriptional initiation in crude extracts. Q2 activity was repressed on a chromatin template, however, and this repression was relieved by the phospho (Ser133) KID-dependent recruitment of p300 histone acetyltransferase activity to the promoter. In chromatin immunoprecipitation assays of NIH 3T3 cells, cAMP-dependent recruitment of p300 to the somatostatin promoter stimulated acetylation of histone H4. Correspondingly, overexpression of hTAFII130 potentiated CREB activity in cells exposed to cAMP, but had no effect on reporter gene expression in unstimulated cells. We propose that cooperativity between the KID and Q2 domains proceeds via a chromatin-dependent mechanism in which recruitment of p300 facilitates subsequent interaction of CREB with TFIID.
A Universal Quantum Dots-Aptamer Probe for Efficient Cancer Detection and Targeted Imaging (2012)

Targeted quantum dots have shown as an analytical and imaging tool for cancer detection and molecular imaging. Aptamers have recently been demonstrated as ideal candidates for molecular targeting applications. In the present work, quantum dots (QDs) were encapsulated with functional poly(ethylene glycol)-phospholipids to improve their solubility in water solution. The as-prepared QDs were then conjugated with the AS1411 aptamer recognizing the nucleolin overexpressed on cancer cell surface. The recognition of QD-Aptamer nanocomplex to breast cancer cells was demonstrated using confocal microscopy, and the viability of QDs-aptamer bioconjugate bound cells were not affected within 24 h, indicating that the probe was biocompatible and suitable for in vitro diagnostic assays and live cell imaging. Such well-defined aptamer-conjugated QDs nanoprobe was simple and universal to be extended to prepare various aptamer-nanoparticles hybrid systems for cancer targeting and molecular imaging applications.
Copper-controllable gene expression system for whole plants. (1993)

We describe a system for gene expression in plants based on the regulation mechanism of the yeast metallothionein (MT) gene. The system consists of two elements: (i) the yeast ace1 (activating copper-MT expression) gene encoding a transcription factor under control of the cauliflower mosaic virus (CaMV) 35S RNA promoter, and (ii) a gene of interest under control of a chimeric promoter consisting of the 90-base-pair domain A of the CaMV 35S RNA promoter linked to the ACE1 transcription factor-binding site. At elevated copper ion concentrations, the ACE1 protein changes conformation, binds to, and activates transcription from the chimeric promoter. To test the functioning of the system in plants, a construct containing the beta-glucuronidase (GUS) reporter gene under control of the chimeric promoter was prepared, and transgenic tobacco plants were produced. It was shown that GUS activity in the leaves of transgenic plants increased up to 50-fold, either after addition of 50 microM CuSO4 to the nutrient solution or after application of 0.5 microM CuSO4 to the plants in a foliar spray. This GUS expression was repressed after the removal of copper ions. The results show that the activity of the described chimeric promoter directly depends on copper ion concentration and that this system can be used in experiments that demand precise timing of expression.
Highly Efficient Multiple Exciton Generation in Colloidal PbSe and PbS Quantum Dots (2005)

We report ultra-efficient multiple exciton generation (MEG) for single photon absorption in colloidal PbSe and PbS quantum dots (QDs). We employ transient absorption spectroscopy and present measurement data acquired for both intraband as well as interband probe energies. Quantum yields of 300% indicate the creation, on average, of three excitons per absorbed photon for PbSe QDs at photon energies that are four times the QD energy gap. Results indicate that the threshold photon energy for MEG in QDs is twice the lowest exciton absorption energy. We find that the biexciton effect, which shifts the transition energy for absorption of a second photon, influences the early time transient absorption data and may contribute to a modulation observed when probing near the lowest interband transition. We present experimental and theoretical values of the size-dependent interband transition energies for PbSe QDs. We present experimental and theoretical values of the size-dependent interband transition energies for PbSe QDs, and we also introduce a new model for MEG based on the coherent superposition of multiple excitonic states.
Performance of a New, Low-volume, High-Surface Area Aqueous Shunt in Normal Rabbit Eyes (2000)

As a consequence of Laplace's law, reduction in bleb diameter reduces surface tension on the bleb, reducing capsular fibrosis and consequently capsule thickness, thus increasing hydraulic conductivity. Increased hydraulic conductivity increases the effectiveness of the filtering surface. Cylindrical geometry allows reduced bleb volume yet maintains total surface area that is proportional to the length of the implant, which is unlimited and customizable for each eye by simply cutting the length of implant needed.
Analysis of Flanking Sequences fromDissociationInsertion Lines: A Database for Reverse Genetics in Arabidopsis (1999)

We have generated Dissociation (Ds) element insertions throughout the Arabidopsis genome as a means of random mutagenesis. Here, we present the molecular analysis of genomic sequences that flank the Ds insertions of 931 independent transposant lines. Flanking sequences from 511 lines proved to be identical or homologous to DNA or protein sequences in public databases, and disruptions within known or putative genes were indicated for 354 lines. Because a significant portion (45%) of the insertions occurred within sequences defined by GenBank BAC and P1 clones, we were able to assess the distribution of Ds insertions throughout the genome. We discovered a significant preference for Ds transposition to the regions adjacent to nucleolus organizer regions on chromosomes 2 and 4. Otherwise, the mapped insertions appeared to be evenly dispersed throughout the genome. For any given gene, insertions preferentially occurred at the 5' end, although disruption was clearly possible at any intragenic position. The insertion sites of >500 lines that could be characterized by reference to public databases are presented in a tabular format at http://www.plantcell. org/cgi/content/full/11/12/2263/DC1. This database should be of value to researchers using reverse genetics approaches to determine gene function.