gebhart/patrepeval huggingface dataset:
Induction of γ-Globin by Histone Deacetylase Inhibitors (1997)

The short-chain fatty acid butyrate has been shown to elevate fetal hemoglobin (HbF) by inducing expression of the gamma-globin gene. Regulation of gene expression by butyrate is thought to proceed via inhibition of the enzyme histone deacetylase, leading to elevated levels of core histone acetylation which affect chromatin structure and transcription rates. To determine whether changes in histone acetylation are critical for the regulation of the gamma-globin gene, we tested three potent and specific inhibitors of histone deacetylase, the cyclic tetrapeptides trapoxin and Helminthsporium carbonum toxin (HC toxin), and the antifungal antibiotic trichostatin A for their ability to induce fetal hemoglobin expression in erythroid cells. These compounds induced fetal hemoglobin in both primary erythroid cell cultures and human erythroleukemia (K562) cells. A butyrate-responsive element spanning the duplicated CCAAT box region of the gamma-globin promoter has been identified in transient transfection assays using a reporter construct in K562 cells, and we show that the same promoter region is required for response to trapoxin and trichostatin. Mutational analysis of the gamma-globin promoter indicates that the distal CCAAT box and 3' flanking sequence (CCAATAGCC) is critical for activation by butyrate, trapoxin, and trichostatin, whereas the proximal element (CCAATAGTC) plays a less important role. These results show that inhibition of histone deacetylase can lead to transcriptional activation of gamma-globin promoter reporter gene constructs through proximal promoter elements, and suggest that butyrate induces gamma-globin expression via such changes in histone acetylation.
High surface area crystalline titanium dioxide: potential and limits in electrochemical energy storage and catalysis (2012)

Titanium dioxide is one of the most intensely studied oxides due to its interesting electrochemical and photocatalytic properties and it is widely applied, for example in photocatalysis, electrochemical energy storage, in white pigments, as support in catalysis, etc. Common synthesis methods of titanium dioxide typically require a high temperature step to crystallize the amorphous material into one of the polymorphs of titania, e.g. anatase, brookite and rutile, thus resulting in larger particles and mostly non-porous materials. Only recently, low temperature solution-based protocols gave access to crystalline titania with higher degree of control over the formed polymorph and its intra- or interparticle porosity. The present work critically reviews the formation of crystalline nanoscale titania particles via solution-based approaches without thermal treatment, with special focus on the resulting polymorphs, crystal morphology, surface area, and particle dimensions. Special emphasis is given to sol-gel processes via glycolated precursor molecules as well as the miniemulsion technique. The functional properties of these materials and the differences to chemically identical, non-porous materials are illustrated using heterogeneous catalysis and electrochemical energy storage (battery materials) as example.
Electron Spin Resonance Observation of Bias-Temperature Stress-Induced Interface Defects at NO/N2O-Annealed Chemical-Vapor-Deposition SiO2/(100) p-Si Substrates (2011)

Using an electron spin resonance (ESR) technique, we observed bias-temperature (BT) stress-induced interface defects at chemical-vapor-deposition (CVD) SiO 2 /(100) p-Si substrates annealed in either NO or N 2 O gas. The g -factors and peak widths detected by ESR measurements are 2.0058 and 0.35 mT, and 2.0035 and 0.40 mT for interface defects, P b0 and P b1 centers, respectively. Before BT stress application, the total density of ESR-active defects at the interface was determined to be 1.51×10 12 cm -2 for the NO-annealed sample, which is supposed to include a large number of hydrogen (H) atoms near the interface, and 1.85×10 12 cm -2 for the N 2 O-annealed sample, which is supposed to include a small amount of H atoms. After BT stress application, the total interface defect density increases with positive BT stress time monotonically, which is mainly caused by H desorption reaction. In contrast, in the case of negative BT stress application, the total density decreases first, and then increases, which might be caused by two reactions; the first reaction is [·Si\tbondSi 3 →Si\tbondSi 3 ], and the second reaction is [HSi\tbondSi 3 →H·Si\tbondSi 3 →·Si\tbondSi 3 ].
Lithium based memristive device (2015)

The effort of investigating memristor material continues. This paper demonstrates the latest results of such effort by our group. These include memristor device design and measurement based on stacked lithium niobate and aluminum oxide. I-V sweeping results show good switch memristive characteristic. Other preliminary results in this paper include temperature dependency study, pulse voltage write/read and retention characterization. From these results, lithium niobate based device show the temperature stability and multiple stages of write/read and long retention period. All these demonstrate its potential for the application of neuromorphic computing in the future.
The Use of a Heuristic Problem-Solving Hierarchy to Facilitate the Explanation of Hypothesis-Directed Reasoning (1986)

We examine the problem of explaining expert system recommendations derived from complex reasoning strategies. We focus on the difficulty of justifying advice generated by hypothesis-directed reasoning. In this context, we discuss research on the PATHFINDER system for the diagnosis of lymph node pathology. We present our efforts to manage the complexity of an information optimizing reasoning strategy to facilitate explanation.
Localization of Human Hair Structural Lipids Using Nanoscale Infrared Spectroscopy and Imaging (2014)

Atomic force microscopy (AFM) and infrared (IR) spectroscopy have been combined in a single instrument (AFM-IR) capable of producing IR spectra and absorption images at a sub-micrometer spatial resolution. This new device enables human hair to be spectroscopically characterized at levels not previously possible. In particular, it was possible to determine the location of structural lipids in the cuticle and cortex of hair. Samples of human hair were embedded, cross-sectioned, and mounted on ZnSe prisms. A tunable IR laser generating pulses of the order of 10 ns was used to excite sample films. Short duration thermomechanical waves, due to infrared absorption and resulting thermal expansion, were studied by monitoring the resulting excitation of the contact resonance modes of the AFM cantilever. Differences are observed in the IR absorbance intensity of long-chain methylene-containing functional groups between the outer cuticle, middle cortex, and inner medulla of the hair. An accumulation of structural lipids is clearly observed at the individual cuticle layer boundaries. This method should prove useful in the future for understanding the penetration mechanism of substances into hair as well as elucidating the chemical nature of alteration or possible damage according to depth and hair morphology.
Protein Production inAspergillus sojae (2008)

Abstract Originally published in: Production of Recombinant Proteins. Edited by Gerd Gellissen. Copyright © 2005 Wiley‐VCH Verlag GmbH &amp; Co. KGaA Weinheim. Print ISBN: 3‐527‐31036‐4 The sections in this article are Introduction Taxonomy The Expression Platform Strain Selection Transformation Protoplasting Dominant Selection Markers Auxotrophic Selection Markers Re‐usable Selection Marker Promoter Elements Aspergillus sojae as a Cell Factory for Foreign Proteins Production of Fungal Proteins Production of Non‐fungal Proteins Controlled Fermentation Strain Development Protease‐deficient Strains Ultra‐violet (UV) Mutagenesis Gene Disruption Controlled Batch Fermentations Low‐viscosity Mutants Gene Disruption Controlled Fermentations Conclusion Acknowledgments Appendix
Less Invasive Unilateral Arytenoid Lateralization: A Modified Technique for Treatment of Idiopathic Laryngeal Paralysis in Dogs: Technique Description and Outcome (2014)

LI-UCAL is a feasible surgical technique and resulted in improvement of clinical signs related to LP. Calm recoveries without adverse effects such as respiratory distress were associated with early discharge. LI-UCAL could be considered an alternative to conventional UCAL.
Performance Comparison between TEA and Rijndael Encryption Algorithm for Wireless Sensor Networks. (2002)

The sequence of the gene coding for GTP cyclohydrolase I of Escherichia coli and of the adjacent regions was determined. The open reading frame contains 669 nucleotides. The deduced amino-acid sequence represents a protein consisting of 223 amino-acid residues with a molecular mass of 24,873 Da. Partial amino-acid sequences of the N-terminal region and of 5 peptides obtained by trypsin and BrCN cleavage were determined by Edman degradation and were in full agreement with the sequence deduced from the nucleotide sequence. The starting methionine is removed by posttranslational modification. The protein shows extensive homology to the recently reported GTP cyclohydrolase from rats.
Humoral and hemodynamic responses after left ventricular assist device implantation and heart transplantation. (2006)

Left ventricular assist device (LVAD) implantation and heart transplantation (HTx) are established therapeutic approaches in the treatment of end-stage heart failure. The postoperative humoral responses to the two treatments have not yet been compared. All patients were treated with inhaled nitric oxide (iNO) on weaning from cardiopulmonary bypass as they presented with pulmonary hypertension. We investigated atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), cGMP, endothelin (ET)-1, big endothelin (big ET), and hemodynamic parameters after LVAD implantation (15 patients; age 51 +/- 8 years) or HTx (10 patients; age 53 +/- 6 years) preoperatively, on cardiopulmonary bypass and postoperatively up to 72 hrs after cessation of iNO. Preoperatively, cardiac index (CI), pulmonary artery pressure, pulmonary capillary wedge pressure (PCWP), central venous pressure (CVP), and mean atrial pressure (MAP) were similar for both groups. Similarly, ANP, BNP, cGMP, ET-1, and big ET were comparable before surgery. Seventy-two hours after weaning from iNO, the administered epinephrine dose was higher in the HTx group (P = 0.003); whereas the CVP (P = 0.04) and pulmonary vascular resistance (PVR; P = 0.03) were lower. The following humoral parameters differed markedly: ANP (preoperatively: LVAD, 99 +/- 123 pg/ml; HTx, 197 +/- 199 pg/ml; P = 0.14; vs. 72 hrs after iNO: LVAD, 110 +/- 106 pg/ml; HTx, > 640 +/- 0 pg/ml; P = 0.003) and cGMP (preoperatively: LVAD, 4.4 +/- 5.8 pg/ml; HTx, 5.0 +/- 3.0 pg/ml; P = 0.35; vs. 72 hrs after iNO: LVAD, 8.0 +/- 10.8 pg/ml; HTx, 26.2 +/- 15.8 pg/ml; P = 0.02). Although the hemodynamic effects of both LVAD implantation and HTx in the treatment of end-stage heart failure are comparable, except for the effects on CVP and PVR, the humoral responses with respect to ANP and cGMP were strikingly different. These effects are independent of volume status, iNO, and ETs, suggesting a physiologic response to maintain circulatory homeostasis.
Formation of organic molecular nanocrystals under soft confinement (2016)

Methods to produce nano-sized organic molecular crystals in thin films are of great interest in the pharmaceutical industry due to the potential benefit of increased solubility of poorly soluble drugs and the advantages of film-based dosage forms over traditional tablet/capsule-based dosage forms. One method to directly form organic nanocrystals is by crystallization in confined environments where the overall crystallization volume is constrained. We report the use of a novel solution impregnation method to form nanocrystals in polymer matrices with various microstructures in order to study the structure of the confined nanocrystals and the role of soft confinement and polymer chemistry on the nucleation process of nano-sized crystals. The particle diameter correlates with the microstructure of the polymer matrices and the nucleation kinetics. In addition, by carefully choosing the experimental conditions and the polymer matrix, polymorph control of nanocrystals can be achieved. Solid-state nuclear magnetic resonance (ssNMR) was used to examine the local structure of nanocrystals inside the polymer matrices and crystal polymer interactions. This method may serve as a novel formulation method to obtain nanocrystals of poorly soluble active pharmaceutical ingredients (APIs) for pharmaceutical industry.
ChemInform Abstract: The Co2(CO)8‐Catalyzed Hydrosilylation of Oxygen‐Containing Olefins: Silylmetalation as a Key Step. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Expansion of Bronchial Epithelial Cell Populations by In Vitro Culture of Explants from Dysplastic and Histologically Normal Sites (1996)

The genetic and phenotypic properties of cells which ultimately give rise to carcinoma of the lung are not well defined in part because of unavailability of preneoplastic cells from well-characterized dysplastic sites. In order to expand bronchial epithelial cell populations from patients at high risk for lung cancer, endobronchial biopsy specimens were explanted onto collagen- and fibronectin-coated dishes and cultured in serum-free, chemically defined media. One hundred forty-nine biopsy pairs were obtained from smokers and from healthy volunteers for culture and histologic evaluation. The histologic appearances of mucosa adjacent to the site of the cultured biopsies ranged from normal through varying degrees of noninvasive squamous dysplasia to invasive carcinoma. Confluent monolayers of pure epithelial cells were obtained from 68% of the cultured explants. Sites exhibiting high-grade dysplasia were 51% more likely to yield successful cultures than sites exhibiting normal histology (13 of 14 cultures successful versus 52 of 83 cultures successful, P < 0.02). Cultures had a maximum proliferative life span of 81 days and none of the cultures spontaneously became immortalized. Immunolabeling studies revealed that all cultured epithelial cells, regardless of the in situ histologic appearances of the mucosa at the biopsy site, strongly expressed keratin and epidermal growth factor receptor, weakly expressed transferrin receptor and human folate receptor, and were negative for neural cell adhesion molecule and human leukocyte antigen DR (HLADR). Ploidy and karyotypic analyses were performed in a limited number of explants from normal and dysplastic sites and all were found to be diploid without karyotypic abnormality. We conclude that pure bronchial epithelial cell populations can be routinely expanded from histologically normal and dysplastic sites by tissue culture of biopsy explants and that the expanded cell populations may represent a library of normal and preneoplastic cells which are suitable for immunophenotypic, ploidy, genetic, or functional analyses.
T cells infiltrating non-Hodgkin's B cell lymphomas show altered tyrosine phosphorylation pattern even though T cell receptor/CD3-associated kinases are present (1995)

Although tumor infiltrating lymphocytes (T-TIL) from B cell non-Hodgkins lymphoma patients contain tumor-reactive T cells, they display poor proliferation and IFN-gamma production when stimulated through the TCR-CD3. To determine if there was altered signaling linked to TCR-CD3 ligation, tyrosine phosphorylation was examined in T-TIL because it represents an early and critical event in T cell activation. After stimulation with anti-CD3 Ab, Western blotting with anti-phosphotyrosine showed reduced phosphorylation in T-TIL when compared with peripheral blood-derived T cells from normal individuals. The altered phosphorylation was not due to the reduced expression of signaling elements linked to the TCR-CD3 complex. T-TIL expressed normal levels of CD3 epsilon, TCR zeta chain, and the three tyrosine kinases, p56lck (Lck), p59fyn, and ZAP-70. However, in T-TIL, anti-Lck Ab reacted with a 60-kDa protein, which appears to be the phosphorylated form of Lck. Binding of anti-Lck Ab to the 60-kDa protein was blocked by Lck peptide. In addition, anti-Lck Ab immunoprecipitated a phosphorylated 60-kDa protein from gamma-32P-labeled T-TIL that was not seen in normal resting T cells. In vitro kinase assay studies also demonstrated that TCR-CD3 engagement increased the kinase activity of Lck in normal T cells but not in T-TIL. These results suggest that although T-TIL from B cell non-Hodgkins lymphoma patients contain the signal transduction molecules associated with TCR-CD3 activation pathway, they are impaired in tyrosine phosphorylation and Lck activity, which may contribute to the functional defects of these cells.
Stable polarons in polyacetylene oligomers: optical spectra of long polyene radical cations (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStable polarons in polyacetylene oligomers: optical spectra of long polyene radical cationsThomas Bally, Kuno Roth, W. Tang, Richard R. Schrock, Konrad Knoll, and Lee Y. ParkCite this: J. Am. Chem. Soc. 1992, 114, 7, 2440–2446Publication Date (Print):March 1, 1992Publication History Published online1 May 2002Published inissue 1 March 1992https://doi.org/10.1021/ja00033a020RIGHTS & PERMISSIONSArticle Views242Altmetric-Citations77LEARN 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 InReddit PDF (905 KB) Get e-Alerts Get e-Alerts
Inhibition of Amyloid-β Aggregation by Cobalt(III) Schiff Base Complexes: A Computational and Experimental Approach (2019)

Coordination complexes have emerged as prominent modulators of amyloid aggregation via their interaction with the N-terminal histidine residues of amyloid-β (Aβ). Herein, we report the synthesis and characterization of a novel cobalt(III) Schiff base complex with methylamine axial ligands, and we present both computational and experimental data demonstrating the reduction of β-sheet formation by this complex. The computations include molecular dynamics simulations of both monomeric and pentameric Aβ, which demonstrate decreased formation of β-sheet structures, destabilization of preformed β-sheets, and suppression of aggregation. These results are consistent with a dose dependence in experimental bulk aggregation data using thioflavin T fluorescence, and overall this study demonstrates useful drug activity of the cobalt complex.
Numerical simulation of the air-conditioning environment in a computer room (1998)

This paper describes the development of software for simulating the air-conditioning environment in a computer room. This software uses a finite volume method combined with a rectangular structured mesh system and a {kappa}-{epsilon} two-equation model for turbulence. Some special modeling techniques are also used. This software has two purposes: (1) to optimize the layout of a computer room, thus minimizing the electric power used for air conditioning, and (2) to reproduce the situation in which an accident is caused by an air-conditioning problem and to assist in an investigation of the problem. Measurements and simulation tests on the flow and temperature distribution in computer rooms confirm the accuracy and usefulness of this simulator.
Small-scale Aeroelastic Rotor Simulation, Design and Fabrication (2005)

Efficient, small-scale fixed-pitch rotor blades are essential for miniature rotorcraft. Extremely thin blade sections are required for highly efficient rotor performance that leads to acceptable mission endurance. Such rotor blades are difficult to manufacture from sufficiently rigid material to avoid significant torsional deformation in operating conditions. In practice, it is necessary to trade-off manufacturing simplicity and mechanical rigidity of a blade design against aerodynamic performance. This paper presents a design methodology for this problem, based on development of a simulator for steady-state rotor performance along with a search algorithm to find the ideal taper and twist geometry for a specified motor torque. The approach is demonstrated on the design of rotors for a small scale quad-rotor unmanned aerial vehicle under development at the Australian National University. Experimental thrust tests indicate good correspondence with theoretical predications. Nomenclature A Rotor disc area, m2 AoA Angle of Attack, rad c Blade chord, m cd Non-dimensional drag coefficient cl Non-dimensional lift coefficient cm Non-dimensional moment coefficient
Antibody Probes of Module 1 of the 6-Deoxyerythronolide B Synthase Reveal an Extended Conformation During Ketoreduction (2020)

The 6-deoxyerythronolide B synthase (DEBS) is a prototypical assembly line polyketide synthase (PKS) that synthesizes the macrocyclic core of the antibiotic erythromycin. Each of its six multidomain modules presumably sample distinct conformations, as biosynthetic intermediates tethered to their acyl carrier proteins interact with multiple active sites during the courses of their catalytic cycles. The spatiotemporal details underlying these protein dynamics remain elusive. Here, we investigate one aspect of this conformational flexibility using two domain-specific monoclonal antibody fragments (F<sub>ab</sub>s) isolated from a very large naïve human antibody library. Both F<sub>ab</sub>s, designated 1D10 and 2G10, were bound specifically and with high affinity to the ketoreductase domain of DEBS module 1 (KR1). Comparative kinetic analysis of stand-alone KR1 as well as a truncated bimodular derivative of DEBS revealed that 1D10 inhibited KR1 activity whereas 2G10 did not. Co-crystal structures of each KR1-F<sub>ab</sub> complex provided a mechanistic rationale for this difference. A hybrid PKS module harboring KR1 was engineered, whose individual catalytic domains have been crystallographically characterized at high resolution. Size exclusion chromatography coupled to small-angle X-ray scattering (SEC-SAXS) of this hybrid module bound to 1D10 provided further support for the catalytic relevance of the "extended" model of a PKS module. Our findings reinforce the power of monoclonal antibodies as tools to interrogate structure-function relationships of assembly line PKSs.
Novel multiphase optical nanodomains, metamaterials, and their role into molecular imaging, endocrinology, nanophotonics, and optical microfluidics (2008)

This paper reports new discoveries in the area of molecular optics and nanophotonics with potential applications in the areas of imaging, molecular imaging, endocrinology, optical microfluidics, and biomedical microdevices. The outcome of this study suggests that liquid multiphase macromolecules and liquid colloids give rise to the formation of molecular heterogeneous structures, and multiphase nanodomains, with enhanced index of refraction contrast, and pronounced metamaterial characteristics, which contribute significantly to the enhancement of interacting optical fields.