gebhart/patrepeval huggingface dataset:
Optically reconfigurable azobenzene polymer-based fiber Bragg filter (2005)

Optically writable, thermally erasable surface relief gratings in thin Disperse Red 1 polymethyl methacrylate azopolymer films were used to demonstrate an arbitrarily reconfigurable fiber Bragg filter. Gratings were optically written on azopolymer-coated side-polished fiber blocks, and a write-erase-write cycle was demonstrated. Finite difference time domain simulations reveal that this optically reconfigurable device concept can be optimized in a silicon-on-insulator waveguide platform.
O Rio Grande do Sul visto "de fora" (2005)

A partir dos escritos de intelectuais do final do século XIX e início do século XX, como Silvio Romero, Nina Rodrigues e Euclides da Cunha, Éder Silveira procura identificar O Rio Grande do Sul visto "de fora". Neste artigo, são discutidos os conceitos de raça e nacionalidade naquele período, a partir das visões construídas em torno dos gaúchos e suas especificidades diante do restante do Brasil.
Complete Genomic Sequence of Border Disease Virus, a Pestivirus from Sheep (1998)

The genus Pestivirus of the family Flaviviridae comprises three established species, namely, bovine viral diarrhea virus (BVDV), classical swine fever virus (CSFV), and border disease virus from sheep (BDV). In this study, we report the first complete nucleotide sequence of BDV, that of strain X818. The genome is 12,333 nucleotides long and contains one long open reading frame encoding 3, 895 amino acids. The 5' noncoding region (NCR) of BDV X818 consists of 372 nucleotides and is thus similar in length to the 5' NCR reported for other pestiviruses. The 3' NCR of X818 is 273 nucleotides long and thereby at least 32 nucleotides longer than the 3' NCR of pestiviruses analyzed thus far. Within the 3' NCR of BDV X818, the sequence motif TATTTATTTA was identified at four locations. The same repeat was found at two or three locations within the 3' NCR of different CSFV isolates but was absent in the 3' NCR of BVDV. Analysis of five additional BDV strains showed that the 3' NCR sequences are highly conserved within this species. Comparison of the deduced amino acid sequence of X818 with the ones of other pestiviruses allowed the prediction of polyprotein cleavage sites which were conserved with regard to the structural proteins. It has been reported for two BVDV strains that cleavage at the nonstructural (NS) protein sites 3/4A, 4A/4B, 4B/5A, and 5A/5B is mediated by the NS3 serine protease and for each site a conserved leucine was found at the P1 position followed by either serine or alanine at P1' (N. Tautz, K. Elbers, D. Stoll, G. Meyers, and H.-J. Thiel, J. Virol. 71:5415-5422, 1997; J. Xu, E. Mendez, P. R. Caron, C. Lin, M. A. Murcko, M. S. Collett, and C. M. Rice, J. Virol. 71:5312-5322). Interestingly, P1' of the predicted NS5A/5B cleavage site of BDV is represented by an asparagine residue. Transient expression studies demonstrated that this unusual NS5A/5B processing site is efficiently cleaved by the NS3 serine protease of BDV.
Coherence control using the ratio of Rabi frequencies for complete coherent inversion in a four-level λ system (1999)

For the purpose of an examination of coherence control, we study the dynamics of population inversion in the four-level λ system where initial populations are arbitrary coherently distributed in two lower levels. It is shown that the coherence control, which causes population transfer between the lower levels to be forbidden, is possible by using the ratio of Rabi frequencies. Under this condition, it is remarkable that the adiabatic following and the optimal detuning methods are useful to invert the four-level system completely, and it is shown that the two-photon coherences of the coupled three-level ladders are dispersive and absorptive in the former and the latter methods, respectively. From the geometrical interpretation, the Bloch vectors, describing the four-level inversions, could be defined as ones in a two-level system.
Concepts and applications of molecular similarity (1990)

Introduction to Similarity in Chemistry The Evolution of the Concept of Molecular Similarity Algorithms for the Calculation of Similarity in Chemical Structure Database Applications of Two-Dimensional Chemical Similarity Measures to Database Analysis and Querying Molecular Similarity Approaches to Property Optimization Molecular Similarity and Quantum Chemistry Molecular Shape Analysis: A Formalism to Quantitatively Establish Spatial Molecular Similarity Molecular Recognition: The Measurement and Search for Molecular Similarity in Ligand- Receptor Interaction Chemical Similarity, Chemical Distance and Computer-Assisted Formalized Reasoning by Analogy Similarity Concepts in Modeling Chemical Transformation Pathways Three- Dimensional Topological Aspects of Molecular Similarity An Approach to Molecular Similarity.
Neutralizing Monoclonal Antibody Against Ras Oncogene Product p21 Which Impairs Guanine Nucleotide Exchange (1987)

The neutralizing monoclonal antibody Y13-259 severely hampers the nucleotide exchange reaction between p21-bound and exogenous guanine nucleotides but does not interfere with the association of GDP to p21. These results suggest that the nucleotide exchange reaction is critical for p21 function. Interestingly, the v-ras p21 has a much faster dissociation rate than the p21 of the c-ras proto-oncogene.
Probing the solution structure of the DNA‐binding protein Max by a combination of proteolysis and mass spectrometry (1995)

A simple biochemical method that combines enzymatic proteolysis and matrix-assisted laser desorption ionization mass spectrometry was developed to probe the solution structure of DNA-binding proteins. The method is based on inferring structural information from determinations of protection against enzymatic proteolysis, as governed by solvent accessibility and protein flexibility. This approach was applied to the study of the transcription factor Max--a member of the basic/helix-loop-helix/zipper family of DNA-binding proteins. In the absence of DNA and at low ionic strengths, Max is rapidly digested by each of six endoproteases selected for the study, results consistent with an open and flexible structure of the protein. At physiological salt levels, the rates of digestion are moderately slowed; this and the patterns of cleavage are consistent with homodimerization of the protein through a predominantly hydrophobic interface. In the presence of Max-specific DNA, the protein becomes dramatically protected against proteolysis, exhibiting up to a 100-fold reduction in cleavage rates. Over a 2-day period, both complete and partial proteolysis of the Max-DNA complex is observed. The partial proteolytic fragmentation patterns reflect a very high degree of protection in the N-terminal and helix-loop-helix regions of the protein, correlating with those expected of a stable dimer bound to DNA at its basic N-terminals. Less protection is seen at the C-terminal where a slow, sequential proteolytic cleavage occurs, correlating to the presence of a leucine zipper. The results also indicate a high affinity of Max for its target DNA that remains high even when the leucine zipper is proteolytically removed. In addition to the study of the helix-loop-helix protein Max, the present method appears well suited for a range of other structural biological applications.
Molecular Imprinting of Macromolecules for Sensor Applications (2017)

Molecular recognition has an important role in numerous living systems. One of the most important molecular recognition methods is molecular imprinting, which allows host compounds to recognize and detect several molecules rapidly, sensitively and selectively. Compared to natural systems, molecular imprinting methods have some important features such as low cost, robustness, high recognition ability and long term durability which allows molecularly imprinted polymers to be used in various biotechnological applications, such as chromatography, drug delivery, nanotechnology, and sensor technology. Sensors are important tools because of their ability to figure out a potentially large number of analytical difficulties in various areas with different macromolecular targets. Proteins, enzymes, nucleic acids, antibodies, viruses and cells are defined as macromolecules that have wide range of functions are very important. Thus, macromolecules detection has gained great attention in concerning the improvement in most of the studies. The applications of macromolecule imprinted sensors will have a spacious exploration according to the low cost, high specificity and stability. In this review, macromolecules for molecularly imprinted sensor applications are structured according to the definition of molecular imprinting methods, developments in macromolecular imprinting methods, macromolecular imprinted sensors, and conclusions and future perspectives. This chapter follows the latter strategies and focuses on the applications of macromolecular imprinted sensors. This allows discussion on how sensor strategy is brought to solve the macromolecules imprinting.
On the Influence of Higher Excited States on the ISC Quantum Yield of Octa‐aL‐alkyloxy‐substituted Zn‐Phthalocyanine Molecules Studied by Nonlinear Absorption (1997)

Abstract— Octa‐aL‐alkyloxy‐substituted Zn‐phthalocyanines are an interesting class of far red‐absorbing photosensitizers. The chemical structure, the calculated steric conformation, the observed linear optical properties and an anomalous luminescence from a higher than S, excited state are reported. To study the optical properties of higher excited states and their occupation dynamics up to delay times of 15 ns we have carried out measurements of transient absorption spectra after 14 ps pulsed, resonant B‐band and Q‐band excitation. From these measurements the excited state singlet‐singlet and triplet‐triplet spectra as well as the intersystem crossing (ISC) quantum yields are obtained. The main result is an excitation wavelength‐dependent ISC quantum yield that can be explained by an additional ISC channel between higher excited singlet and triplet states. The large rate of this channel is justified by the resonance between higher triplet states, observed in the triplet‐triplet spectrum and the B, absorption band. Using kinetic model calculations, a lifetime of the higher excited singlet state of some picoseconds is predicted and the influence of a two‐step absorption process on the population density of this higher excited singlet state is discussed.
A Novel Procedure for the Synthesis of Libraries Containing Small Organic Molecules (1994)

Accelerated drug searches should be possible through the generation and screening of libraries of smaller organic molecules. The reaction of tetracarboxylic acid tetrachloride 1 with a mixture of 21 amines (predominantly amino acids) in solution yields a complex mixture, which can theoretically contain 97461 compounds. Compound 2, an inhibitor of trypsin-catalyzed amide hydrolysis (K1 = (9 ± 2) × 10−6M), was selected by four-step screening procedure. This result demonstrates the usefulness of libraries of molecules and the screening of these complex mixtures.
Evidence for Mycoplasma ssp., Chlamydia pneunomiae, and human herpes virus‐6 coinfections in the blood of patients with autistic spectrum disorders (2007)

We examined the blood of 48 patients from central and southern California diagnosed with autistic spectrum disorders (ASD) by using forensic polymerase chain reaction and found that a large subset (28/48 or 58.3%) of patients showed evidence of Mycoplasma spp. infections compared with two of 45 (4.7%) age-matched control subjects (odds ratio = 13.8, P < 0.001). Because ASD patients have a high prevalence of one or more Mycoplasma spp. and sometimes show evidence of infections with Chlamydia pneumoniae, we examined ASD patients for other infections. Also, the presence of one or more systemic infections may predispose ASD patients to other infections, so we examined the prevalence of C. pneumoniae (4/48 or 8.3% positive, odds ratio = 5.6, P < 0.01) and human herpes virus-6 (HHV-6, 14/48 or 29.2%, odds ratio = 4.5, P < 0.01) coinfections in ASD patients. We found that Mycoplasma-positive and -negative ASD patients had similar percentages of C. pneumoniae and HHV-6 infections, suggesting that such infections occur independently in ASD patients. Control subjects also had low rates of C. pneumoniae (1/48 or 2.1%) and HHV-6 (4/48 or 8.3%) infections, and there were no coinfections in control subjects. The results indicate that a large subset of ASD patients shows evidence of bacterial and/or viral infections (odds ratio = 16.5, P < 0.001). The significance of these infections in ASD is discussed in terms of appropriate treatment.
Anionic homopolymerization and block copolymerization of 4-vinylpyridine and its investigation by high-temperature size-exclusion chromatography in N-methyl-2-pyrrolidinone (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnionic homopolymerization and block copolymerization of 4-vinylpyridine and its investigation by high-temperature size-exclusion chromatography in N-methyl-2-pyrrolidinoneSunil K. Varshney, Xing Fu Zhong, and Adi EisenbergCite this: Macromolecules 1993, 26, 4, 701–706Publication Date (Print):February 1, 1993Publication History Published online1 May 2002Published inissue 1 February 1993https://pubs.acs.org/doi/10.1021/ma00056a022https://doi.org/10.1021/ma00056a022research-articleACS PublicationsRequest reuse permissionsArticle Views1186Altmetric-Citations52LEARN 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
Comparison of generalized Gaussian and Laplacian modeling in DCT image coding (1995)

Generalized Gaussian and Laplacian source models are compared in discrete cosine transform (DCT) image coding. A difference in peak signal to noise ratio (PSNR) of at most 0.5 dB is observed for encoding different images. We also compare maximum likelihood estimation of the generalized Gaussian density parameters with a simpler method proposed by Mallat (1989). With block classification based on AC energy, the densities of the DCT coefficients are much closer to the Laplacian or even the Gaussian.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
On the role of subtype selective adenosine receptor agonists during proliferation and osteogenic differentiation of human primary bone marrow stromal cells (2010)

Purines are important modulators of bone cell biology. ATP is metabolized into adenosine by human primary osteoblast cells (HPOC); due to very low activity of adenosine deaminase, the nucleoside is the end product of the ecto-nucleotidase cascade. We, therefore, investigated the expression and function of adenosine receptor subtypes (A(1) , A(2A) , A(2B) , and A(3) ) during proliferation and osteogenic differentiation of HPOC. Adenosine A(1) (CPA), A(2A) (CGS21680C), A(2B) (NECA), and A(3) (2-Cl-IB-MECA) receptor agonists concentration-dependently increased HPOC proliferation. Agonist-induced HPOC proliferation was prevented by their selective antagonists, DPCPX, SCH442416, PSB603, and MRS1191. CPA and NECA facilitated osteogenic differentiation measured by increases in alkaline phosphatase (ALP) activity. This contrasts with the effect of CGS21680C which delayed HPOC differentiation; 2-Cl-IB-MECA was devoid of effect. Blockade of the A(2B) receptor with PSB603 prevented osteogenic differentiation by NECA. In the presence of the A(1) antagonist, DPCPX, CPA reduced ALP activity at 21 and 28 days in culture. At the same time points, blockade of A(2A) receptors with SCH442416 transformed the inhibitory effect of CGS21680C into facilitation. Inhibition of adenosine uptake with dipyridamole caused a net increase in osteogenic differentiation. The presence of all subtypes of adenosine receptors on HPOC was confirmed by immunocytochemistry. Data show that adenosine is an important regulator of osteogenic cell differentiation through the activation of subtype-specific receptors. The most abundant A(2B) receptor seems to have a consistent role in cell differentiation, which may be balanced through the relative strengths of A(1) or A(2A) receptors determining whether osteoblasts are driven into proliferation or differentiation.
Involvement of Avidity for Major Histocompatibility Complex in Homeostasis of Naive and Memory T Cells (2003)

The requirements for survival and self-renewal of peripheral T cells and the nature of mechanisms controlling the size of the naive and memory pool are not completely understood. Here, we examine the involvement of the major histocompatibility complex (MHC) in survival and homeostatic expansion of naive and memory T cells. We show that the homeostatic behavior of naive T cell receptor (TCR)-transgenic T cells can be deduced by the expression levels of TCR and CD5, a negative regulator of TCR signaling. Both these factors determine the strength of TCR stimulation by MHC-derived signals. We further show that, similarly to naive T cells, MHC-derived signals influence the homeostatic expansion capacity of memory T cells under lymphopenic conditions. In contrast to naive T cells, however, memory T cells can reach a homeostatic equilibrium, in which survival/self-renewal of each clone is dissociated from their avidity for MHC-derived signals.
In vitro generation of hematopoietic stem cells from an embryonic stem cell line. (1995)

Hematopoietic stem cells (HSC) are unique in that they give rise both to new stem cells (self-renewal) and to all blood cell types. The cellular and molecular events responsible for the formation of HSC remain unknown mainly because no system exists to study it. Embryonic stem (ES) cells were induced to differentiate by coculture with the stromal cell line RP010 and the combination of interleukin (IL) 3, IL-6, and F (cell-free supernatants from cultures of the FLS4.1 fetal liver stromal cell line). Cell cytometry analysis of the mononuclear cells produced in the cultures was consistent with the presence of PgP-1+ Lin- early hematopoietic (B-220- Mac-1- JORO 75- TER 119-) cells and of fewer B-220+ IgM- B-cell progenitors and JORO 75+ T-lymphocyte progenitors. The cell-sorter-purified PgP-1+ Lin- cells produced by induced ES cells could repopulate the lymphoid, myeloid, and erythroid lineages of irradiated mice. The ES-derived PgP-1+ Lin- cells must possess extensive self-renewal potential, as they were able to produce hematopoietic repopulation of secondary mice recipients. Indeed, marrow cells from irradiated mice reconstituted (15-18 weeks before) with PgP-1+ Lin- cell-sorter-purified cells generated by induced ES cells repopulated the lymphoid, myeloid, and erythroid lineages of secondary mouse recipients assessed 16-20 weeks after their transfer into irradiated secondary mice. The results show that the culture conditions described here support differentiation of ES cells into hematopoietic cells with functional properties of HSC. It should now be possible to unravel the molecular events leading to the formation of HSC.
Synthetic Receptors for the Differentiation of Phosphorylated Peptides with Nanomolar Affinities (2008)

Artificial ditopic receptors for the differentiation of phosphorylated peptides varying in i+3 amino acid side chains were synthesized, and their binding affinities and selectivities were determined. The synthetic receptors show the highest binding affinities to phosphorylated peptides under physiological conditions (HEPES, pH 7.5, 154 mM NaCl) reported thus far for artificial systems. The tight and selective binding was achieved by high cooperativity of the two binding moieties in the receptor molecules. All receptors interact with phosphorylated serine by bis(ZnII-cyclen) complex coordination and a second binding site recognizing a carboxylate or imidazole amino acid side chain functionality.
Chemokines in Allergy (2002)

Allergic diseases such as atopic dermatitis, asthma, and allergic rhinitis represent a significant healthcare problem. Understanding these diseases as dysregulated inflammatory responses has led to many new targets for therapeutic intervention. Recent data concerning soluble IL-4 receptor, monoclonal antibodies against IL-5 and an antibody toward IgE have lead to an appreciation of the crucial role played by Th2 subset of CD4(+) T cells and their corresponding cytokines. While these potential drugs are presently in clinical trials and may be valuable therapeutics, orally bioavailable small molecule inhibitors of Th2 cell responses would be desirable for treatment of these chronic diseases. One strategy is to prevent effector cell migration (Th2 cells, mast cells, and eosinophils) via chemokine receptor antagonism with a suitable small molecule. Chemokine receptors are a subset of the seven transmembrane-spanning family, which mediate their effects through interaction with heterotrimeric G-proteins. The ligands are a structurally related set of proteins that are selectively expressed in certain disease settings. Three chemokine receptors CCR3, CCR4, and CCR8 are preferentially expressed by Th2 cells, mast cells and eosinophils and therefore represent therapeutic targets for allergy. This mini-review will focus on new research involving CCR3, CCR4 and CCR8. The cellular distribution of each receptor, the corresponding chemokine ligands, and various validation studies are discussed. Recent drug discovery advances concerning pharmacological tools and small molecule receptor antagonists will also be presented.
Movement Intention Is Better Predicted than Attention in the Posterior Parietal Cortex (2006)

We decoded on a trial-by-trial basis the location of visual targets, as a marker of the locus of attention, and intentions to reach and to saccade in different directions using the activity of neurons in the posterior parietal cortex of two monkeys. Predictions of target locations were significantly worse than predictions of movement plans for the same target locations. Moreover, neural signals in the parietal reach region (PRR) gave better predictions of reaches than saccades, whereas signals in the lateral intraparietal area (LIP) gave better predictions of saccades than reaches. Taking together the activity of both areas, the prediction of either movement in all directions became nearly perfect. These results cannot be explained in terms of an attention effect and support the idea of two segregated populations in the posterior parietal cortex, PRR and LIP, that are involved in different movement plans.