gebhart/patrepeval huggingface dataset:
Syntheses and photophysical properties of fluorescent dibenzofurans, a dibenzothiophene, and carbazoles substituted with benzoxazole and hydroxyl groups to produce excited state intramolecular proton‐transfer (1995)

Abstract Dibenzofurans, a dibenzothiophene, and carbazoles, each substituted with a 2‐benzoxazolyl group as well as an ortho ‐hydroxyl group, were synthesized to produce fluors with fluorescence due to excited‐state intramolecular proton‐transfer. The orientations for Friedel‐Crafts acylation of 3‐methoxydibenzothio‐phene and of the analogous carbazole were determined. The fluors displayed absorption peaks in the 330–385 nm region with molar extinction coefficients up to 57,000. Fluorescence quantum efficiencies of 0.17–0.44 were obtained at wavelengths that had peak values from 540–600 nm. The fluors are of potential use as wavelength shifters in scintillating polystyrene fibers.
Postsynaptic Density 95 controls AMPA Receptor Incorporation during Long-Term Potentiation and Experience-Driven Synaptic Plasticity (2004)

The regulated delivery of AMPA-type glutamate receptors (AMPARs) to synapses is an important mechanism underlying synaptic plasticity. Here, we ask whether the synaptic scaffolding protein PSD-95 (postsynaptic density 95) participates in AMPAR incorporation during two forms of synaptic plasticity. In hippocampal slice cultures, the expression of PSD-95-green fluorescent protein (PSD-95-GFP) increases AMPAR currents by selectively delivering glutamate receptor 1 (GluR1)-containing receptors to synapses, thus mimicking long-term potentiation (LTP). Mutational analysis shows that the N terminal of PSD-95 including the first two PDZ [PSD-95/Discs large (Dlg)/zona occludens-1 (ZO-1)] domains is necessary and sufficient to mediate this effect. Further supporting a role in synaptic plasticity, wild-type PSD-95 occludes LTP and dominant negative forms block LTP. Moreover, we demonstrate that PSD-95 also participates in AMPAR delivery during experience-driven plasticity in vivo. In the barrel cortex from experience-deprived animals, the expression of PSD-95-GFP selectively increases AMPAR currents, mimicking experience-driven plasticity. In nondeprived animals, PSD-95-GFP produces no additional potentiation, indicating common mechanisms between PSD-95-mediated potentiation and experience-driven synaptic strengthening. A dominant negative form of PSD-95 blocks experience-driven potentiation of synapses. Pharmacological analysis in slice cultures reveals that PSD-95 acts downstream of other signaling pathways involved in LTP. We conclude that PSD-95 controls activity-dependent AMPAR incorporation at synapses via PDZ interactions not only during LTP in vitro but also during experience-driven synaptic strengthening by natural stimuli in vivo.
Induction of ceruloplasmin gene expression in rat lung during inflammation and hyperoxia (1991)

To determine the effect of inflammation on extrahepatic ceruloplasmin gene expression we examined the ceruloplasmin mRNA content of adult rat tissues after endotoxin injection. Within 8 h of a dose of endotoxin ceruloplasmin mRNA content increased in the liver as expected and was also detectable in the lung. The effect of endotoxin was tissue specific because ceruloplasmin mRNA was not consistently detected in other extrahepatic tissues. The kinetics of ceruloplasmin mRNA accumulation in lung and liver tissue were similar with a maximum seven- to ninefold increase in ceruloplasmin mRNA content in each tissue within 24 h. The relative rate of ceruloplasmin gene transcription was increased in both tissues within 3 h of endotoxin, suggesting similar mechanisms of regulation of ceruloplasmin gene expression during inflammation. One cellular site of ceruloplasmin production in the inflamed lung was found to be the alveolar macrophage, which expressed the ceruloplasmin gene and synthesized ceruloplasmin protein in response to endotoxin in vitro. Because of these findings we also examined the effects of hyperoxia on ceruloplasmin gene expression. Exposure of adult rats to 95% O2 resulted in a five- to sixfold induction of ceruloplasmin mRNA in lung tissue within 46 h, and this response was time dependent, reaching maximum values at 86 h. Hyperoxic induction of ceruloplasmin mRNA was specific to the lung and not the result of systemic inflammation because hepatic ceruloplasmin mRNA content remained constant. These data indicate that the lung is a prominent site of ceruloplasmin gene expression during inflammation and hyperoxia and suggest that this protein may play a previously unappreciated role in pulmonary injury or repair.
Importance of Immunological and Inflammatory Processes in the Pathogenesis and THERAPY of Alzheimer's Disease (1998)

The contribution of autoimmune processes or inflammatory components in the etiology and pathogenesis of Alzheimer's disease (AD) has been suspected for many years. The presence of antigen-presenting, HLA-DR-positive and other immunoregulatory cells, components of complement, inflammatory cytokines and acute phase reactants have been established in tissue of AD neuropathology. Although these data do not confirm the immune response as a primary cause of AD, they indicate involvement of immune processes at least as a secondary or tertiary reaction to the preexisting pathogen and point out its driving-force role in AD pathogenesis. These processes may contribute to systemic immune response. Thus, experimental and clinical studies indicate impairments in both humoral and cellular immunity in an animal model of AD as well as in AD patients. On the other hand, anti-inflammatory drugs applied for the treatment of some chronic inflammatory diseases have been shown to reduce risk of AD in these patients. Therefore, it seems that anti-inflammatory drugs and other substances which can control the activity of immunocompetent cells and the level of endogenous immune response can be valuable in the treatment of AD patients.
Nonclinical Testing (2004)

In the pharmaceutical development arena, Drucker's quotation represents one of the biggest challenges to be faced. One can set up many great plans and strategies, but until they are set in motion they remain abstract. Planning is one of the key steps for efficiently leading a project to a successful completion and its importance has long been recognized in many disciplines besides pharmaceutical development. Although the plan itself does not constitute a guarantee for a successful outcome, it maximizes the chances of success while attempting to minimize unexpected and unnecessary detours. Success in the pharmaceutical development process is often measured by the ability of a company to discover compounds with promising therapeutic effects and, through efficient testing in animals and humans, learn enough about their properties so they can be used in a manner such that the observed benefits outweigh the potential risks to the patient. From a business perspective, with efficiency being the key to survival, success is most often measured by the company's ability to reach its destination in the most expeditious manner while using the fewest resources and without compromising the quality of the essential information gathered along the process.
Multilayer nanocapsules of polysaccharide chitosan and alginate through layer-by-layer assembly directly on PS nanoparticles for release (2005)

Polysaccharide multilayer nanocapsules have been fabricated in aqueous media by the layer-by-layer self-assembly of chitosan (CHI) and sodium alginate (ALG) on monodisperse polystyrene (PS) nanoparticles with a diameter of 180 nm as template, followed by removal of the templates through dissolving in THF. The pH and added salt concentration of the polyelectrolyte deposition solutions were optimized to ensure the alternating deposition. Consequently, the most suitable pH values were found to be 6.0-8.0 for ALG and 3.5 for CHI and were used in the deposition. The concentration of added NaCl used in the adsorption solutions was 0.5 M, which led to an average thickness of about 13 nm for 5 bilayers of CHI/ALG shell-wall. zeta-potential indicated the stepwise and alternating adsorption of CHI and ALG to form multilayer film on the PS nanoparticles. The characteristic bands of PS residue almost disappeared in the IR spectrum of the nanocapsule after dipped in THF, confirming thorough removal of PS templates from the core-shell particles. TEM, SEM and AFM were utilized to observe the nanocapsules of about 225 nm in diameter (by TEM). A hydrophilic drug model, acridine hydrochloride (AH), was chosen to investigate the loading and release properties of the nanocapsules. The positively charged AH spontaneously deposited into the capsule due to the electrostatic interaction with the negatively charged styrene sulfonate residues from the PS template inside the capsule. The rate of AH release became slightly slower when the capsule wall was cross-linked with glutaraldehyde, but the accumulative released amount for the cross-linked capsule was obviously reduced. These nanocapsules made from nature polysaccharides have a potential application in controlled drug release.
Some Novel Applications for Wireless Inertial Sensors (2006)

This paper surveys several recent and ongoing projects from the MIT Media Lab’s Responsive Environments Group that leverage compact, low-cost inertial sensing into scenarios that range from wearable biomotion measurement platforms to interactive badges and musical controllers.
A Hybrid Control for Autonomous Systems of Electric Power Supply (2002)

Based on regional division of state space and switching control, the problem of control for autonomous systems of electric power supply (ASES) is studied and a type of hybrid controllers is proposed. Comparing with the variable structure control strategy based on dynamic sliding mode given in recently, it is shown by simulation that the serious chattering and switching in high frequency between controllers, which are not permitted in practice applications, can be efficiently avoided and the performance of system is basically equivalent to the ones in variable structure control.
Cloning of a Differentially Expressed IκB-related Protein (1995)

We have cloned a cDNA corresponding to a novel gene from a human epithelial cell line by subtractive hybridization and polymerase chain reaction techniques. This gene is expressed at the message level and at the protein level in a lung alveolar type II-like epithelial cell line but not in lung fibroblasts. In adult human tissues, the mRNA for this gene was detected only in the heart and the skeletal muscle, but not in the brain, placenta, whole lung, liver, or kidney. We have named this gene I kappa BR (for I kappa B-related) since its 52-kDa protein product has significant homology to the I kappa B family of proteins which function as inhibitory cytoplasmic retention proteins for the vertebrate rel/NF-kappa B transcription factors. Although the important role of NF-kappa B in gene activation in cells of the immune system is now well established, a similar role in other cell types or in vertebrate development is less clear. The deduced amino acid sequence of I kappa BR has the most significant homology to the Drosophila protein Cactus which inhibits the function of the NF-kappa B-like protein Dorsal. In electrophoretic mobility shift experiments, I kappa BR inhibited the ability of the p50:p65 NF-kappa B heterodimer to bind DNA. The DNA binding ability of the p50 homodimer but not the p65 homodimer was drastically inhibited by I kappa BR. In transfection experiments, overexpression of I kappa BR significantly inhibited NF-kappa B-dependent transcription from the Ig kappa enhancer. This new member of the I kappa B family of proteins, I kappa BR, may play an important role in regulation of NF-kappa B function in epithelial cells.
Aptamer-targeted cell-specific RNA interference (2010)

This potent ability of small interfering (si)RNAs to inhibit the expression of complementary RNA transcripts is being exploited as a new class of therapeutics for a variety of diseases. However, the efficient and safe delivery of siRNAs into specific cell populations is still the principal challenge in the clinical development of RNAi therapeutics. With the increasing enthusiasm for developing targeted delivery vehicles, nucleic acid-based aptamers targeting cell surface proteins are being explored as promising delivery vehicles to target a distinct disease or tissue in a cell-type-specific manner. The aptamer-based delivery of siRNAs can often enhance the therapeutic efficacy and reduce the unwanted off-target effects of siRNAs. In particular, for RNA interference-based therapeutics, aptamers represent an efficient agent for cell type-specific, systemic delivery of these oligonucleotides. In this review, we summarize recent attractive developments in creatively using cell-internalizing aptamers to deliver siRNAs to target cells. The optimization and improvement of aptamer-targeted siRNAs for clinical translation are further highlighted.
Solubility of 2,4,6-Trinitrotoluene (TNT) in Water (1996)

Current literature values of 2,4,6-trinitrotoluene (TNT) solubility in water vary widely from 100 to 200 mg/L at room temperature. We investigated the effects of temperature and pH on the solubility of both reference TNT and field neat TNT obtained from the Alabama Army Ammunition Plant (AAAP), Childersburg, AL. The TNT solubility determined from this study was significantly lower than that of Taylor and Rinkenbach, which was cited by several reference chemical handbooks and articles. However, the values reported by the Merck Index and the Lange's Handbook of Chemistry compared well with our values. TNT solubility dropped rapidly as the pH increased. Three unknown HPLC peaks were observed at high pH, indicating a possibility of forming unknown transformation products. Both reference and field neat TNT solubility agreed well. A semiempirical solubility correlation was developed to predict the solubility of TNT at a temperature range from 6 °C to 42 °C.
Unfolding and internalization of proteins by the ATP-dependent proteases ClpXP and ClpAP (2000)

ClpX and ClpA are molecular chaperones that interact with specific proteins and, together with ClpP, activate their ATP-dependent degradation. The chaperone activity is thought to convert proteins into an extended conformation that can access the sequestered active sites of ClpP. We now show that ClpX can catalyze unfolding of a green fluorescent protein fused to a ClpX recognition motif (GFP-SsrA). Unfolding of GFP-SsrA depends on ATP hydrolysis. GFP-SsrA unfolded either by ClpX or by treatment with denaturants binds to ClpX in the presence of adenosine 5'-O-(3-thiotriphosphate) and is released slowly (t(1/2) approximately 15 min). Unlike ClpA, ClpX cannot trap unfolded proteins in stable complexes unless they also have a high-affinity binding motif. Addition of ATP or ADP accelerates release (t(1/2) approximately 1 min), consistent with a model in which ATP hydrolysis induces a conformation of ClpX with low affinity for unfolded substrates. Proteolytically inactive complexes of ClpXP and ClpAP unfold GFP-SsrA and translocate the protein to ClpP, where it remains unfolded. Complexes of ClpXP with translocated substrate within the ClpP chamber retain the ability to unfold GFP-SsrA. Our results suggest a bipartite mode of interaction between ClpX and substrates. ClpX preferentially targets motifs exposed in specific proteins. As the protein is unfolded by ClpX, additional motifs are exposed that facilitate its retention and favor its translocation to ClpP for degradation.
Robot-arm pick and place behavior programming system using visual perception (2002)

This paper presents the programming of a robot-arm system for carrying out flexible pick and place behavior using visual perception. Object manipulation from visual data involves determining the pose of the object with respect to the manipulator. Taking into account that visual positioning is an ill-posed problem due to the perspective projection, this system uses a camera and a sensor distance, and both of them mounted on a robot-arm tool adapter for locating (positioning and orienting) objects. On the other hand, this programming system is modular, composed of different dynamic link libraries to be independent with the hardware and offers a friendly graphic interface where the user can define pick and place object locations on the image space.
Novel Substrate Specificity of the Histone Acetyltransferase Activity of HIV-1-Tat Interactive Protein Tip60 (1997)

Tip60, originally isolated as an HIV-1-Tat interactive protein, contains an evolutionarily conserved domain with yeast silencing factors. We demonstrate here direct biochemical evidence that this domain of Tip60 has histone acetyltransferase activity. The purified recombinant effectively acetylates H2A, H3, and H4 but not H2B of core histone mixtures. This substrate specificity has not been observed among histone acetyltransferases analyzed to date. These results indicate that Tip60 is a histone acetyltransferase with a novel property, suggesting that Tip60 and its related factors may introduce a distinct alteration on chromatin.
Developing a Heme Iron Database for Meats According to Meat Type, Cooking Method and Doneness Level (2012)

Although heme iron levels varied, there was no clear effect of cooking method or doneness level. We outline the methods used to create a heme iron database to be used in conjunction with food frequency questionnaires to estimate heme iron intake in relation to disease outcome.
Analogy retrieval and processing with distributed vector representations (2000)

Holographic reduced representations (HRRs) are a method for encoding nested relational structures in fixed‐width vector representations. HRRs encode relational structures as vector representations in such a way that the superficial similarity of the vectors reflects both superficial and structural similarity of the relational structures. HRRs also support a number of operations that could be very useful in psychological models of human analogy processing: fast estimation of superficial and structural similarity via a vector dot‐product; finding corresponding objects in two structures; and chunking of vector representations. Although similarity assessment and discovery of corresponding objects both theoretically take exponential time to perform fully and accurately, with HRRs one can obtain approximate solutions in constant time. The accuracy of these operations with HRRs mirrors patterns of human performance on analog retrieval and processing tasks.
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions (2006)

The glmS ribozyme is a riboswitch class that occurs in certain Gram-positive bacteria, where it resides within mRNAs encoding glucosamine 6-phosphate synthase. Members of this self-cleaving ribozyme class rapidly catalyze RNA transesterification upon binding GlcN6P, and genetic evidence suggests that this cleavage event is important for down-regulating GlmS protein expression. In this report, we present a refined secondary structure model of the glmS ribozyme and determine the importance of a conserved pseudoknot structure for optimal ribozyme function. Analyses of deletion constructs demonstrate that the pseudoknot, together with other structural elements, permits the ribozyme to achieve maximum rate constants for RNA cleavage at physiologically relevant Mg2+ concentrations. In addition, we show that substantial rate enhancements are supported by an exchange-inert cobalt (III) complex and by molar concentrations of monovalent ions. Our findings indicate that the glmS ribozyme forms a complex structure to employ catalytic strategies that do not require the direct participation of divalent metal ions.
Treatment of levodopa-induced motor complications (2008)

Chronic levodopa treatment for Parkinson's disease patients is frequently associated with the development of motor complications such as end-of-dose wearing-off and dyskinesias. In this review, we provide an overview of the strategies available for dealing with these problems. Medical management includes manipulation of levodopa dosing to establish the optimum treatment schedule, improving levodopa absorption, catechol-O-methyl transferase-inhibition (COMT), Monoamine oxidase-B (MAO-B) inhibition, dopaminergic agonists, amantadine, and continuous dopaminergic infusions. Surgical procedures and particularly deep brain stimulation are also reviewed. It should be noted that none of these treatments has been shown to provide anti-parkinsonian efficacy that is greater than what can be achieved with levodopa. We highlight the importance of initiating therapy with a treatment strategy that reduces the risk that a Parkinson's disease patient will develop motor complications in the first place. Key Words: Advanced PD, dyskinesias, motor fluctuations, levodopa, dopamine agonists, COMT inhibitors, MAO-B inhibitors.
Theory of Elastic Mechanisms in Fibrous Proteins (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheory of Elastic Mechanisms in Fibrous ProteinsPaul J. FloryCite this: J. Am. Chem. Soc. 1956, 78, 20, 5222–5235Publication Date (Print):October 1, 1956Publication History Published online1 May 2002Published inissue 1 October 1956https://pubs.acs.org/doi/10.1021/ja01601a025https://doi.org/10.1021/ja01601a025research-articleACS PublicationsRequest reuse permissionsArticle Views812Altmetric-Citations428LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Patterns of adherence of diarrheagenic Escherichia coli to HEp-2 cells (1987)

A total of 516 Escherichia coli strains randomly isolated from coprocultures of 154 Chilean children with diarrhea and 66 controls were examined with DNA probes and tested for adherence to HEp-2 cells. Three adherence patterns were distinguished, localized, true diffuse and "aggregative." Enteropathogenic E. coli (EPEC) were detected by EPEC adherence factor probe among 86 of the 372 isolates (23%) from patients with diarrhea vs. 14 of 144 (10%) strains from controls (P less than 0.0002). Of 95 strains that manifested localized adherence, 97% were EPEC adherence factor probe-positive; thus the HEp-2 assay may serve as an alternative to the probe in identifying EPEC adherence factor-positive EPEC. True diffuse adherence was not associated with diarrhea. In contrast the aggregative pattern appears to signify a new, distinct class of diarrheagenic E. coli (enteroadherent-aggregative E. coli). The aggregative pattern was found in only 3 of 27 enterotoxigenic, 0 of 4 enteroinvasive, 0 of 2 enterohemorrhagic and 2 of 86 EPEC strains but in 84 of 253 probe-negative strains (P less than 0.00001) from patients with diarrhea; in comparison only 20 of 134 probe-negative strains from controls were aggregative E. coli (P less than 0.00001 vs. probe-negative strains from diarrhea patients).