gebhart/patrepeval huggingface dataset:
Rapid Transformation from Spherical Nanoparticles, Nanorods, Cubes, or Bipyramids to Triangular Prisms of Silver with PVP, Citrate, and H2O2 (2012)

Rapid sphere-to-prism (STP) transformation of silver was studied in aqueous AgNO(3)/NaBH(4)/polyvinylpyrrolidone (PVP)/trisodium citrate (Na(3)CA)/H(2)O(2) solutions by monitoring time-dependent surface plasmon resonance (SPR) bands in the UV-vis region, by examining transmission electron microscopic (TEM) images, and by analyzing emitted gases during fast reaction. Roles of PVP, Na(3)CA, and H(2)O(2) were studied without addition of a reagent, with different timing of each reagent's addition, and with addition of H(2)O(2) to mixtures of spheres and prisms. Results show that prisms can be prepared without addition of PVP, although it is useful to synthesize smaller monodispersed prisms. A new important role of citrate found in this study, besides a known role as a protecting agent of {111} facets of plates, is an assistive agent for shape-selective oxidative etching of Ag nanoparticles by H(2)O(2). The covering of Ag nanoparticles with carboxylate groups is necessary to initiate rapid STP transformation by premixing citrate before H(2)O(2) addition. Based on our data, rapid prism formation starts from the consumption of spherical Ag particles because of shape-selective oxidative etching by H(2)O(2). Oxidative etching of spherical particles by H(2)O(2) is faster than that of prisms. Therefore, spherical particles are selectively etched and dissolved, leaving only seeds of prisms to grow into triangular prisms. When pentagonal Ag nanorods and a mixture of cubes and bipyramids were used as sources of prisms, rod-to-prism (RTP), cube-to-prism (CTP), and bipyramid-to-prism (BTP) transformations were observed in Ag nanocrystals/NaBH(4)/PVP/Na(3)CA/H(2)O(2) solutions. Shape-selective oxidative etching of rods was confirmed using flag-type Ag nanostructures consisting of a triangular plate and a side rod. These data provide useful information for the size-controlled synthesis of triangular Ag prisms, from various Ag nanostructures and using a chemical reduction method, having surface plasmon resonance (SPR) bands at a desired wavelength.
Condition Monitoring of the Power Output of Wind Turbine Generators Using Wavelets (2010)

With an increasing number of wind turbines being erected offshore, there is a need for cost-effective, predictive, and proactive maintenance. A large fraction of wind turbine downtime is due to bearing failures, particularly in the generator and gearbox. One way of assessing impending problems is to install vibration sensors in key positions on these subassemblies. Such equipment can be costly and requires sophisticated software for analysis of the data. An alternative approach, which does not require extra sensors, is investigated in this paper. This involves monitoring the power output of a variable-speed wind turbine generator and processing the data using a wavelet in order to extract the strength of particular frequency components, characteristic of faults. This has been done for doubly fed induction generators (DFIGs), commonly used in modern variable-speed wind turbines. The technique is first validated on a test rig under controlled fault conditions and then is applied to two operational wind turbine DFIGs where generator shaft misalignment was detected. For one of these turbines, the technique detected a problem 3 months before a bearing failure was recorded.
CXCL1 Triggers Caspase-3 Dependent Tau Cleavage in Long-Term Neuronal Cultures and in the Hippocampus of Aged Mice: Implications in Alzheimer’s Disease (2015)

Truncation of tau protein is considered an early event in Alzheimer's disease (AD) and is believed to play a major pathogenic role in sporadic AD. However, causative factors that trigger tau truncation in AD remain poorly understood. In the present study, we demonstrate that CXCL1 (C-X-C motif ligand 1), a specific ligand for the chemokine receptor CXCR2, induced cleavage of tau at ASP421 in a caspase-3-dependent manner in long-term but not short-term cultured neurons. The cleaved tau formed varicosities or bead-like structures along the neurites, an abnormal distribution of tau induced by CXCL1 that has not been observed previously. CXCL1-induced activation of GSK3β and the subsequent phosphorylation of tau preceded and were required for caspase-3 activation and tau cleavage. Moreover, intrahippocampal microinjection of lentiviral CXCL1 induced tau cleavage in hippocampal neurons in aged (15-18 months of age) but not adult mice (5-10 months of age). Our data highlight a new role of CXCR2 in tau cleavage and suggest that targeting CXCR2 may offer therapeutic benefits to patients with AD and potentially other tauopathies.
Precise positioning of single-walled carbon nanotubes by ac dielectrophoresis (2006)

The precise placement of single-walled carbon nanotubes (SWCNTs) in device architectures by ac dielectrophoresis involves the optimization of the electrode geometry, applied voltage and frequency, load resistance, and type of nanotube sample used. The authors have developed a toolkit to controllably integrate SWCNTs in device structures by the use of floating potential metal posts and appropriate electrode geometries, as designed using electric field simulations, and used it to fabricate structures such as crossed nanotube junctions.
pokkuri, a Drosophila gene encoding an E-26-specific (Ets) domain protein, prevents overproduction of the R7 photoreceptor. (1992)

Studies on sevenless and bride of sevenless genes have revealed that the R8 cell plays a key role in the fate of the R7 photoreceptor cell, presenting on its surface an inductive cue to which R7 responds. sev-independent induction of R7 cells has been reported in the seven-up mutation, which appears to transform R1 and R6 cells to R7 cells. We have induced recessive mutations in a gene pokkuri (pok; pokkuri is a Japanese word that means "dropping dead") that lead to overproduction of R7 cells with rather minor effects on outer photoreceptors and R8 cells. Pok protein may function as a transcription factor, as the predicted amino acid sequence contains a region similar to the consensus established for the E-26-specific (Ets) domain.
Improving work performance of individuals with severe cognitive impairment through enabling technology (2003)

The over-arching question of this research project was: can technology i.e. the coordinator system, improve the work performance of individuals with severe cognitive impairment to levels required to obtain and maintain employment? This research project consisted of two conditions. In the first condition, two students packaged candy once weekly using matching correspondence for a five session learning phase and a two-session operant phase. They then packaged candy once weekly using the coordinator system for a five session learning phase and a two session operant phase. For condition two, two students packaged candy once every-other week using the coordinator system for a three session learning phase and a two session operant phase. The coordinator system was removed and the students packaged candy using matching correspondence for a three session learning phase and a two session operant phase. Each student was videotaped for half of each 70-90 minute work session and out of that videotape random ten-minute segments were analyzed. Out of the analyzed segments the following data were collected: the proportion of non-value added behavior per cycle of bagged candy, the number of specific type of non-value added behaviors, productivity - as defined by the time to package an individual piece of candy, the number and specific type of errors and the number and type of prompts.
Bayesian estimation of weak material dispersion: theory and experiment (2010)

This work considers the estimation of dispersion in materials via an interferometric technique. At its core, the problem involves extracting the quadratic variation in phase over a range of wavelengths based on measured optical intensity. The estimation problem becomes extremely difficult for weakly dispersive materials where the quadratic nonlinearity is very small relative to the uncertainty inherent in experiment. This work provides a means of estimating dispersion in the face of such uncertainty. Specifically, we use a Markov Chain Monte Carlo implementation of Bayesian analysis to provide both the dispersion estimate and the associated confidence interval. The interplay between various system parameters and the size of the resulting confidence interval is discussed. The approach is then applied to several different experimental samples.
Viral Persistence Alters CD8 T-Cell Immunodominance and Tissue Distribution and Results in Distinct Stages of Functional Impairment (2003)

Chronic viral infections often result in ineffective CD8 T-cell responses due to functional exhaustion or physical deletion of virus-specific T cells. However, how persisting virus impacts various CD8 T-cell effector functions and influences other aspects of CD8 T-cell dynamics, such as immunodominance and tissue distribution, remains largely unknown. Using different strains of lymphocytic choriomeningitis virus (LCMV), we compared responses to the same CD8 T-cell epitopes during acute or chronic infection. Persistent infection led to a disruption of the normal immunodominance hierarchy of CD8 T-cell responses seen following acute infection and dramatically altered the tissue distribution of LCMV-specific CD8 T cells in lymphoid and nonlymphoid tissues. Most importantly, CD8 T-cell functional impairment occurred in a hierarchical fashion in chronically infected mice. Production of interleukin 2 and the ability to lyse target cells in vitro were the first functions compromised, followed by the ability to make tumor necrosis factor alpha, while gamma interferon production was most resistant to functional exhaustion. Antigen appeared to be the driving force for this loss of function, since a strong correlation existed between the viral load and the level of exhaustion. Further, epitopes presented at higher levels in vivo resulted in physical deletion, while those presented at lower levels induced functional exhaustion. A model is proposed in which antigen levels drive the hierarchical loss of different CD8 T-cell effector functions during chronic infection, leading to distinct stages of functional impairment and eventually to physical deletion of virus-specific T cells. These results have implications for the study of human chronic infections, where similar T-cell deletion and functional dysregulation has been observed.
Comparative pharmacology of endothelium‐derived relaxing factor, nitric oxide and prostacyclin in platelets (1987)

1 The pharmacological effects of endothelium-derived relaxing factor (EDRF), nitric oxide (NO) and prostacyclin on human and rabbit platelets were examined. 2 EDRF is released from porcine aortic endothelial cells, cultured on microcarriers and treated with indomethacin, in sufficient quantities to inhibit platelet aggregation induced by 9,11-dideoxy-9 alpha, 11 alpha-methano epoxy-prostaglandin F2 alpha (U46619) and collagen. 3 The anti-aggregating activity of EDRF was potentiated by M&B 22948, a selective inhibitor of cyclic GMP phosphodiesterase, and by superoxide dismutase (SOD) and was inhibited by haemoglobin and Fe2+. 4 Both NO and prostacyclin inhibited platelet aggregation. 5 The anti-aggregatory activity of NO, but not that of prostacyclin, was potentiated by M&B 22948 and by SOD and was inhibited by haemoglobin and Fe2+. Thus NO is a potent inhibitor of platelet aggregation whose activity on platelets mimics that of EDRF. 6 It is likely that the inhibitory effect of NO on platelets represents the action of endogenous EDRF and therefore this substance, together with prostacyclin, is a regulator of platelet-vessel wall interactions.
Bonelike apatite growth on hydroxyapatite–gelatin sponges from simulated body fluid (2001)

In vitro bioactivity of gelatin sponges and hydroxyapatite-enriched gelatin sponges was tested through evaluation of the variations in their composition and morphology after soaking in simulated body fluid (1.5) for periods up to 21 days at 37 degrees C. The presence of hydroxyapatite inside the sponges promotes the deposition of bonelike apatite crystals. The deposits are laid down as spherical aggregates, with mean diameters increasing from about 1-2 microm, after 4 days of soaking in simulated body fluid solution, up to about 3.5 microm in the samples soaked for 21 days. Simultaneously, the relative amount of inorganic phase increases up to about 56% wt, leading to a composite material with a composition quite close to that of bone tissue. The inorganic phase is a poor crystalline carbonated apatite similar to trabecular bone apatite.
Dysregulation of the fibroblast growth factor system in major depression (2004)

In this report we describe findings that imply dysregulation of several fibroblast growth factor (FGF) system transcripts in frontal cortical regions of brains from human subjects with major depressive disorder (MDD). This altered gene expression was discovered by microarray analysis of frontal cortical tissue from MDD, bipolar, and nonpsychiatric control subjects and was verified by quantitative real-time PCR analysis and, importantly, in a separate cohort of MDD subjects. Furthermore, we show, through a separate analysis of specific serotonin reuptake inhibitor (SSRI)-treated and non-SSRI-treated MDD subjects that the observed changes in expression of FGF transcripts are not secondary to drug treatment. Rather, changes in specific FGF transcripts are attenuated by SSRIs and may thus be partially responsible for the mechanism of action of these drugs. We also make available the gene-expression profile of all of the other growth factors and growth factor receptors detected in these postmortem samples.
In vivo optical biopsy of hamster oral cavity with epi-third-harmonic-generation microscopy (2006)

The first in vivo optical virtual biopsy based on epi-third-harmonic-generation (THG) microscopy is successfully demonstrated using Syrian hamster oral mucosa as a model system. Without complex physical biopsy procedures, epi-THG microscopy can provide high spatial resolution dynamic images of oral mucosa and sub-mucosa in all three dimensions. The demonstrated intra-vital epi-THG microscopy provide high resolution observation of blood flow in the capillary and could be a promising tool to image angiogenesis, which is an important feature for many human diseases including malignancies. The system setup of epi-THG microscopy can be easily integrated with other nonlinear optical microscopy such as second-harmonic generation and multi-photon fluorescence microscopy by using the same laser system to provide better integrated molecular and structural information for future clinical diagnosis. By adding 6% acetic acid solution on the mucosa, THG contrast on the borders of nuclei was found to be greatly enhanced due to the alterations of their linear and nonlinear THG susceptibilities. With a virtual-transition-based technology without using fluorescence, the optical epi-THG biopsy we demonstrated shows promise for future noninvasive in vivo diseases examinations.
DNA sequence evolution: the sounds of silence (1995)

Silent sites (positions that can undergo synonymous substitutions) in protein-coding genes can illuminate two evolutionary processes. First, despite being silent, they may be subject to natural selection. Among eukaryotes this is exemplified by yeast, where synonymous codon usage patterns are shaped by selection for particular codons that are more efficiently and/or accurately translated by the most abundant tRNAs; codon usage across the genome, and the abundance of different tRNA species, are highly co-adapted. Second, in the absence of selection, silent sites reveal underlying mutational patterns. Codon usage varies enormously among human genes, and yet silent sites do not appear to be influenced by natural selection, suggesting that mutation patterns vary among regions of the genome. At first, the yeast and human genomes were thought to reflect a dichotomy between unicellular and multicellular organisms. However, it now appears that natural selection shapes codon usage in some multicellular species (e.g. Drosophila and Caenorhabditis), and that regional variations in mutation biases occur in yeast. Silent sites (in serine codons) also provide evidence for mutational events changing adjacent nucleotides simultaneously.
Dual PD-1 and CTLA-4 Checkpoint Blockade Promotes Antitumor Immune Responses through CD4+Foxp3− Cell–Mediated Modulation of CD103+ Dendritic Cells (2018)

Immunotherapy is widely accepted as a powerful new treatment modality for the treatment of cancer. The most successful form of immunotherapy to date has been the blockade of the immune checkpoints PD-1 and CTLA-4. Combining inhibitors of both PD-1 and CTLA-4 increases the proportion of patients who respond to immunotherapy. However, most patients still do not respond to checkpoint inhibitors, and prognostic biomarkers are currently lacking. Therefore, a better understanding of the mechanism by which these checkpoint inhibitors enhance antitumor immune responses is required to more accurately predict which patients are likely to respond and further enhance this treatment modality. Our current study of two mouse tumor models revealed that CD4<sup>+</sup>Foxp3<sup>-</sup> cells activated by dual PD-1/CTLA-4 blockade modulated the myeloid compartment, including activation of conventional CD103<sup>+</sup> dendritic cells (DC) and expansion of a myeloid subset that produces TNFα and iNOS (TIP-DCs). CD4<sup>+</sup>Foxp3<sup>-</sup> T cell-mediated activation of CD103<sup>+</sup> DCs resulted in enhanced IL12 production by these cells and IL12 enhanced the therapeutic effect of dual PD-1/CTLA-4 blockade. Given the importance of these myeloid subsets in the antitumor immune response, our data point to a previously underappreciated role of CD4<sup>+</sup>Foxp3<sup>-</sup> cells in modulating this arm of the antitumor immune response. <i>Cancer Immunol Res; 6(9); 1069-81. ©2018 AACR</i>.
Convection‐Enhanced Drug Delivery to the Brain: Therapeutic Potential and Neuropathological Considerations (2013)

Convection-enhanced delivery (CED) describes a direct method of drug delivery to the brain through intraparenchymal microcatheters. By establishing a pressure gradient at the tip of the infusion catheter in order to exploit bulk flow through the interstitial spaces of the brain, CED offers a number of advantages over conventional drug delivery methods-bypass of the blood-brain barrier, targeted distribution through large brain volumes and minimization of systemic side effects. Despite showing early promise, CED is yet to fulfill its potential as a mainstream strategy for the treatment of neurological disease. Substantial research effort has been dedicated to optimize the technology for CED and identify the parameters, which govern successful drug distribution. It seems likely that successful clinical translation of CED will depend on suitable catheter technology being used in combination with drugs with optimal physicochemical characteristics, and on neuropathological analysis in appropriate preclinical models. In this review, we consider the factors most likely to influence the success or failure of CED, and review its application to the treatment of high-grade glioma, Parkinson's disease (PD) and Alzheimer's disease (AD).
Sequence requirement for peptide recognition by rat brain p21ras protein farnesyltransferase. (1991)

We tested 42 tetrapeptides for their ability to bind to the rat brain p21ras protein farnesyltransferase as estimated by their ability to compete with p21Ha-ras in a farnesyltransfer assay. Peptides with the highest affinity had the structure Cys-A1-A2-X, where positions A1 and A2 are occupied by aliphatic amino acids and position X is occupied by a COOH-terminal methionine, serine, or phenylalanine. Charged residues reduced affinity slightly at the A1 position and much more drastically at the A2 and X positions. Effective inhibitors included tetrapeptides corresponding to the COOH termini of all animal cell proteins known to be farnesylated. In contrast, the tetrapeptide Cys-Ala-Ile-Leu (CAIL), which corresponds to the COOH termini of several neural guanine nucleotide binding (G) protein gamma subunits, did not compete in the farnesyl-transfer assay. Inasmuch as several of these proteins are geranylgeranylated, the data suggest that the two isoprenes (farnesyl and geranylgeranyl) are transferred by different enzymes. A biotinylated heptapeptide corresponding to the COOH terminus of p21Ki-rasB was farnesylated, suggesting that at least some of the peptides serve as substrates for the transferase. The data are consistent with a model in which a hydrophobic pocket in the protein farnesyltransferase recognizes tetrapeptides through interactions with the cysteine and the last two amino acids.
Pichia Protocols (1998)

David Higgins and James Cregg compile for the first time an all-inclusive collection of key experimental procedures to manipulate Pichia pastoris for gene expression purposes. The methods-developed by
Range-only SLAM for robots operating cooperatively with sensor networks (2006)

A mobile robot we have developed is equipped with sensors to measure range to landmarks and can simultaneously localize itself as well as locate the landmarks. This modality is useful in those cases where environmental conditions preclude measurement of bearing (typically done optically) to landmarks. Here we extend the paradigm to consider the case where the landmarks (nodes of a sensor network) are able to measure range to each other. We show how the two capabilities are complimentary in being able to achieve a map of the landmarks and to provide localization for the moving robot. We present recent results with experiments on a robot operating in a randomly arranged network of nodes that can communicate via radio and range to each other using sonar. We find that incorporation of inter-node measurements helps reduce drift in positioning as well as leads to faster convergence of the map of the nodes. We find that addition of a mobile node makes the SLAM feasible in a sparsely connected network of nodes
Interspersed repeated sequences in the African green monkey genome that are homologous to the human Alu family (1981)

The dominant family of interspersed repetitive DNA sequences in the human genome has been termed the Alu family. We have found that more than 75% of the lambda phage in a recombinant library representing an African green monkey genome hybridize with a human Alu sequence under stringent conditions. A group of clones selected from the monkey library with probes other than the Alu sequence were analyzed for the presence and distribution of Alu family sequences. The analyses confirm the abundance of Alu sequences and demonstrate that more than one repeat unit is present in some phages. In the clones studied, the Alu units are separated by an average of 8 kilobase pairs of unrelated sequences. The nucleotide sequence of one monkey Alu sequence is reported and shown to resemble the human Alu sequences closely. Hence, the sequence, dispersion pattern, and copy number of the Alu family members are very similar in the African green monkey and human genomes. Among the clones investigated were two that contain segments of the satellite DNA term alpha-component joined to non alpha-component DNA. The experiments indicate that in the monkey genome Alu sequences can occur close to regions of alpha-component DNA.