gebhart/patrepeval huggingface dataset:
Molecular features of interaction between VEGFA and anti-angiogenic drugs used in retinal diseases: a computational approach (2015)

Anti-angiogenic agents are biological drugs used for treatment of retinal neovascular degenerative diseases. In this study, we aimed at in silico analysis of interaction of vascular endothelial growth factor A (VEGFA), the main mediator of angiogenesis, with binding domains of anti-angiogenic agents used for treatment of retinal diseases, such as ranibizumab, bevacizumab and aflibercept. The analysis of anti-VEGF/VEGFA complexes was carried out by means of protein-protein docking and molecular dynamics (MD) coupled to molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculation. Molecular dynamics simulation was further analyzed by protein contact networks. Rough energetic evaluation with protein-protein docking scores revealed that aflibercept/VEGFA complex was characterized by electrostatic stabilization, whereas ranibizumab and bevacizumab complexes were stabilized by Van der Waals (VdW) energy term; these results were confirmed by MM-PBSA. Comparison of MM-PBSA predicted energy terms with experimental binding parameters reported in literature indicated that the high association rate (Kon) of aflibercept to VEGFA was consistent with high stabilizing electrostatic energy. On the other hand, the relatively low experimental dissociation rate (Koff) of ranibizumab may be attributed to lower conformational fluctuations of the ranibizumab/VEGFA complex, higher number of contacts and hydrogen bonds in comparison to bevacizumab and aflibercept. Thus, the anti-angiogenic agents have been found to be considerably different both in terms of molecular interactions and stabilizing energy. Characterization of such features can improve the design of novel biological drugs potentially useful in clinical practice.
Differential Expression of over 60 Chromosomal Genes in Escherichia coli by Constitutive Expression of MarA (2000)

In Escherichia coli, the MarA protein controls expression of multiple chromosomal genes affecting resistance to antibiotics and other environmental hazards. For a more-complete characterization of the mar regulon, duplicate macroarrays containing 4,290 open reading frames of the E. coli genome were hybridized to radiolabeled cDNA populations derived from mar-deleted and mar-expressing E. coli. Strains constitutively expressing MarA showed altered expression of more than 60 chromosomal genes: 76% showed increased expression and 24% showed decreased expression. Although some of the genes were already known to be MarA regulated, the majority were newly determined and belonged to a variety of functional groups. Some of the genes identified have been associated with iron transport and metabolism; other genes were previously known to be part of the soxRS regulon. Northern blot analysis of selected genes confirmed the results obtained with the macroarrays. The findings reveal that the mar locus mediates a global stress response involving one of the largest networks of genes described.
Hyperpolarized Gases Set NMR World Spinning (1996)

RETURN TO ISSUEPREVNewsNEXTHyperpolarized Gases Set NMR World SpinningChemical applications of laser polarization include improved NMR sensitivityELIZABETH K. WILSONView Author Information C&EN West Coast News BureauCite this: Chem. Eng. News 1996, 74, 52, 21–24Publication Date (Print):December 23, 1996Publication History Published online12 November 2010Published inissue 23 December 1996https://pubs.acs.org/doi/10.1021/cen-v074n052.p021https://doi.org/10.1021/cen-v074n052.p021newsACS PublicationsCopyright © 1996 American Chemical SocietyArticle Views8Altmetric-Citations1LEARN 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 options SUBJECTS:Nuclear magnetic resonance spectroscopy Get e-Alerts
The guanine and cytosine content of genomic DNA and bacterial evolution. (1987)

The genomic guanine and cytosine (G + C) content of eubacteria is related to their phylogeny. The G + C content of various parts of the genome (protein genes, stable RNA genes, and spacers) reveals a positive linear correlation with the G + C content of their genomic DNA. However, the plotted correlation slopes differ among various parts of the genome or among the first, second, and third positions of the codons depending on their functional importance. Facts suggest that biased mutation pressure, called A X T/G X C pressure, has affected whole DNA during evolution so as to determine the genomic G + C content in a given bacterium. The role of A X T/G X C pressure in diversification of bacterial DNA sequences and codon usage patterns is discussed in the perspective of the neutral theory of molecular evolution.
Elimination of chemoresistant multiple myeloma clonogenic colony-forming cells by combined treatment with a plasma cell-reactive monoclonal antibody and a P-glycoprotein-reactive monoclonal antibody. (1989)

Patients with multiple myeloma (MM) commonly become refractory to chemotherapy despite a favorable response to induction treatment. We examined the effectiveness of a previously characterized plasma cell-reactive monoclonal antibody, MM4, in eliminating MM clonogenic colony-forming cells (CCC) with a multidrug-resistant (MDR) phenotype. Experiments were performed using MM cell lines that exhibit 6 (RPMI 8226/DOX6)- and 40 (RPMI 8226/DOX40)-fold resistance to doxorubicin (DOX). Both lines were selected from the chemosensitive MM line RPMI 8226/S and were cross-resistant to mitoxantrone, acronycine, etoposide, and vincristine. Surface marker analysis conducted in this study showed that DOX6 and DOX40 overexpressed the MDR1 gene product p170. Both MDR lines remained reactive to the plasma cell-reactive monoclonal antibodies MM4 and PCA-1 and expressed the relevant cytoplasmic immunoglobulin light chain. Treatment with MM4 and rabbit complement (C') was equally cytotoxic to RPMI 8226/S [80 +/- 5.6% (SD)], DOX6 [74 +/- 8.5], and DOX40 cells [75 +/- 11.3%], based on short-term chromium release studies. Furthermore, MM4 + C' deleted up to 3 logs of CCC colonies from chemosensitive and MDR lines (RPMI 8226/S, 99.87 +/- 0.11%; DOX6, 99.91 +/- 0.08%; DOX40, 99.55 +/- 0.44%). By comparison, the P-glycoprotein-reactive monoclonal antibody MRK-16 and C' inhibited tumor colony formation of MDR cells (8226/DOX6, 95.71 +/- 2.51%; 8226/DOX40, 99.61 +/- 0.43%) but affected that of chemosensitive cells only slightly (8.9 +/- 17.8%). In an attempt to optimize the depletion of myeloma CCC, MM4 was used together with MRK-16. This approach resulted in uniform depletion of myeloma clonogenic colony-forming cells from the chemosensitive (98.32 +/- 1.53%, n = 4) and MDR lines (8226/DOX6, 98.83 +/- 0.08%, n = 4; 8226/DOX40 99.29 +/- 0.62, n = 7) but did not result in enhanced CCC depletion. When DOX40 cells were mixed with normal bone marrow (BM) in the ratio of 90:10 (BM:MM), either MM4 or MRK-16 and C' depleted MM colonies (98.8 +/- 0.71% and 98.10 +/- 1.0%, respectively) without affecting the majority of BM progenitor cells. These observations suggest that either MM4 or MRK-16 is useful for depleting MDR myeloma clonogenic colony-forming cells.
Efectos de la exposición crónica a contaminantes ambientales sobre el olfato en dos poblaciones femeninas de España durante 2004 (2006)

RESUMEN La exposicion cronica a concentraciones industriales de sustancias como el ozono o los oxidos de azufre ynitrogeno, contaminantes ambientales habituales de las grandes ciudades, se asocia a anosmia toxica.Objetivo: el presente estudio busca evaluar el efecto de la exposicion cronica ambiental a estas sustanciassobre la sensibilidad olfatoria en las mujeres sanas de edad media. Materiales y metodos: Empleando undiseno transversal se seleccionaron dos muestras de poblacion con caracteristicas equivalentes, la primeraformada por residentes de una ciudad con altos niveles de contaminacion ambiental y la segunda formada porresidentes de una poblacion sin contaminacion ambiental. Se realizo un estudio psicofisico de la olfaccion enlas dos muestras y un analisis estadistico de las diferencias. Resultados: no se encontro diferenciaestadisticamente significativa en la puntuacion de las pruebas de olfaccion entre los dos grupos. Conclusiones:en el presente estudio, la exposicion cronica a contaminantes atmosfericos en mujeres sanas de edad mediano se asocia a una disminucion de su capacidad olfatoria. PALABRAS CLAVE: Anosmia Toxica. Contaminacion Ambiental. Prueba del CCCRC.
Processing and extraction methods of medicinal cannabis: a narrative review (2021)

In conclusion, based on the current knowledge, using organic solvents is the most convenient method for medicinal cannabis extraction. However, more research is needed for some of the drying and extraction methods. Also, developing a green and sustainable cannabis extraction method should be considered for future studies.
CpG Immunostimulatory Oligodeoxynucleotide 1826 Enhances Antitumor Effect of Interleukin 12 Gene-Modified Tumor Vaccine in a Melanoma Model in Mice (2004)

The results provided the evidence that the combination of IL-12 gene-modified melanoma vaccine and ODN 1826 induces synergistically systemic and local antitumor immunity.
BIND: A Fine-Grained Attestation Service for Secure Distributed Systems (2005)

In this paper we propose BIND (binding instructions and data), a fine-grained attestation service for securing distributed systems. Code attestation has recently received considerable attention in trusted computing. However, current code attestation technology is relatively immature. First, due to the great variability in software versions and configurations, verification of the hash is difficult. Second, the time-of-use and time-of-attestation discrepancy remains to be addressed, since the code may be correct at the time of the attestation, but it may be compromised by the time of use. The goal of BIND is to address these issues and make code attestation more usable in securing distributed systems. BIND offers the following properties: (1) BIND performs fine-grained attestation. Instead of attesting to the entire memory content, BIND attests only to the piece of code we are concerned about. This greatly simplifies verification. (2) BIND narrows the gap between time-of-attestation and time-of-use. BIND measures a piece of code immediately before it is executed and uses a sandboxing mechanism to protect the execution of the attested code. (3) BIND ties the code attestation with the data that the code produces, such that we can pinpoint what code has been run to generate that data. In addition, by incorporating the verification of input data integrity into the attestation, BIND offers transitive integrity verification, i.e., through one signature, we can vouch for the entire chain of processes that have performed transformations over a piece of data. BIND offers a general solution toward establishing a trusted environment for distributed system designers.
Iatrogenic Botulism in a Child With Spastic Quadriparesis (2007)

Botulinum toxins are potent neurotoxins used in a variety of neurological disorders. Few pediatric reports have been published to date regarding the potential hazards of therapeutic use of botulinum toxins. We describe the case of a 10-year-old boy who developed systemic weakness following treatment of spasticity with botulinum toxin type B. The patient developed iatrogenic botulism with ptosis, facial diplegia, neck flexor and extensor weakness, and profound hypopharyngeal laxity with respiratory compromise from which he eventually recovered. Clinicians should be mindful of the risk for systemic botulism when using local injections of the neurotoxin.
Microelectromagnets for the control of magnetic nanoparticles (2001)

A microelectromagnet matrix and a ring trap that position and control magnetic nanoparticles are demonstrated. They consist of multiple layers of lithographically defined Au wires separated by transparent, insulating polyimide layers on sapphire substrates. Magnetic field patterns produced by these devices allow microscopically precise control and manipulation of magnetic nanoparticles. A microelectromagnet matrix produces single or multiple peaks in the magnetic field magnitude, which trap, move, and rotate magnetic nanoparticles, as well as electromagnetic fields to probe and detect particles. Microelectromagnets are new tools with which to study and manipulate nanoparticles and biological entities.
Bioaccumulation of triclocarban in Lumbriculus variegatus (2009)

The antimicrobial triclocarban (TCC) has been detected in streams and municipal biosolids throughout the United States. In addition, TCC and potential TCC transformation products have been detected at high levels (ppm range) in sediments near major cities in the United States. Previous work has suggested that TCC is relatively stable in these environments, thereby raising concerns about the potential for bioaccumulation in sediment-dwelling organisms. Bioaccumulation of TCC from sediments was assessed using the freshwater oligochaete Lumbriculus variegatus. Worms were exposed to TCC in sediment spiked to 22.4 ppm to simulate the upper bound of environmental concentrations. Uptake from laboratory-spiked sediment was examined over 56 d for TCC and 4,4'-dichlorocarbanilide (DCC), a chemical impurity in and potential transformation product of TCC. The clearance of TCC from worms placed in clean sediment was also examined over 21 d after an initial 35-d exposure to TCC in laboratory-spiked sediment. Concentrations of TCC and DCC were monitored in the worms, sediment, and the overlying water using liquid chromatography/tandem mass spectrometry. Experimental data were fitted using a standard biodynamic model to generate uptake and elimination rate constants for TCC in L. variegatus. These rate constants were used to estimate steady-state lipid (lip)- and organic carbon (OC)-normalized biota-sediment accumulation factors (BSAFs) for TCC and DCC of 2.2+/-0.2 and 0.3+/-0.1 g OC/g lip (goc/glip), respectively. Alternatively, directly measured BSAFs for TCC and DCC after 56 d of exposure were 1.6+/-0.6 and 0.5+/-0.2 goc/glip, respectively. Loss of TCC from pre-exposed worms followed first-order kinetics, and the fitted elimination rate constant was identical to that determined from the uptake portion of the present study. Overall, study observations indicate that TCC bioaccumulates from sediments in a manner that is consistent with the traditional hydrophobic organic contaminant paradigm.
α-Aminoadipate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus (2004)

The extremely thermophilic bacterium Thermus thermophilus HB27 synthesizes lysine through alpha-aminoadipate (AAA). In this study, a T. thermophilus gene encoding the enzyme that catalyses transamination of AAA was cloned as a mammalian kynurenine/AAA aminotransferase (Kat2) gene homologue. A T. thermophilus mutant with disruption of the Kat2 homologue required a longer lag phase for growth and showed slower growth in minimal medium. Furthermore, addition of AAA or lysine shortened the lag phase and improved the growth rate. The Kat2 homologue was therefore termed lysN. LysN recognizes not only 2-oxoadipate, an intermediate of lysine biosynthesis, but also 2-oxoisocaproate, 2-oxoisovalerate and 2-oxo-3-methylvalerate, intermediates of leucine, valine and isoleucine biosyntheses, respectively, along with oxaloacetate, a compound in the TCA cycle, as an amino acceptor. These results suggest multiple roles of LysN in several cellular metabolic pathways including lysine and branched-chain amino acid biosyntheses.
The likelihood of aggregation during protein renaturation can be assessed using the second virial coefficient (2003)

Protein aggregation is commonly observed during protein refolding. To better understand this phenomenon, the intermolecular interactions experienced by a protein during unfolding and refolding are inferred from second virial coefficient (SVC) measurements. It is accepted that a negative SVC is indicative of protein-protein interactions that are attractive, whereas a positive SVC indicates net repulsive interactions. Lysozyme denatured and reduced in guanidinium hydrochloride exhibited a decreasing SVC as the denaturant was diluted, and the SVC approached zero at approximately 3 M GdnHCl. Further dilution of denaturant to renaturation conditions (1.25 M GdnHCl) led to a negative SVC, and significant protein aggregation was observed. The inclusion of 500 mM L-arginine in the renaturation buffer shifted the SVC to positive and suppressed aggregation, thereby increasing refolding yield. The formation of mixed disulfides in the denatured state prior to refolding also increased protein solubility and suppressed aggregation, even without the use of L-arginine. Again, the suppression of aggregation was shown to be caused by a shift from attractive to repulsive intermolecular interactions as reflected in a shift from a negative to a positive SVC value. To the best of our knowledge, this is the first time that SVC data have been reported for renaturation studies. We believe this technique will aid in our understanding of how certain conditions promote renaturation and increase protein solubility, thereby suppressing aggregation. SVC measurements provide a useful link, for protein folding and aggregation, between empirical observation and thermodynamics.
Anti-Inflammatory and Analgesic Effects of the Marine-Derived Compound Excavatolide B Isolated from the Culture-Type Formosan Gorgonian Briareum excavatum (2015)

In recent years, several marine-derived compounds have been clinically evaluated. Diterpenes are secondary metabolites from soft coral that exhibit anti-inflammatory, anti-tumor and cytotoxic activities. In the present study, we isolated a natural diterpene product, excavatolide B, from cultured Formosan gorgonian Briareum excavatum and investigated its anti-inflammatory activities. We found that excavatolide B significantly inhibited the mRNA expression of the proinflammatory mediators, inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2), in lipopolysaccharide (LPS)-challenged murine macrophages (RAW 264.7). We also examined the anti-inflammatory and anti-nociceptive effects of excavatolide B on intraplantar carrageenan-induced inflammatory responses. Excavatolide B was found to significantly attenuate carrageenan-induced nociceptive behaviors, mechanical allodynia, thermal hyperalgesia, weight bearing deficits and paw edema. In addition, excavatolide B inhibited iNOS, as well as the infiltration of immune cells in carrageenan-induced inflammatory paw tissue.
Dialog state tracking with attention-based sequence-to-sequence learning (2016)

We present an advanced dialog state tracking system designed for the 5th Dialog State Tracking Challenge (DSTC5). The main task of DSTC5 is to track the dialog state in a human-human dialog. For each utterance, the tracker emits a frame of slot-value pairs considering the full history of the dialog up to the current turn. Our system includes an encoder-decoder architecture with an attention mechanism to map an input word sequence to a set of semantic labels, i.e., slot-value pairs. This handles the problem of the unknown alignment between the utterances and the labels. By combining the attention-based tracker with rule-based trackers elaborated for English and Chinese, the F-score for the development set improved from 0.475 to 0.507 compared to the rule-only trackers. Moreover, we achieved 0.517 F-score by refining the combination strategy based on the topic and slot level performance of each tracker. In this paper, we also validate the efficacy of each technique and report the test set results submitted to the challenge.
[Culture of human melanocytes. Its contribution to the knowledge of melanocyte physiology]. (1992)

Culture techniques for normal human melanocytes have been developed over the last ten years. This in vitro model for studying pigment-producing cells can be expected to provide major advances in the knowledge of cell-to-cell anc cell-to-matrix interactions, melanocyte and melanin biology, pathophysiology of pigment disorders, and malignant melanomas. Melanocyte cultures have already shed new light on keratinocyte-melanocyte interactions within the epidermal melanin unit by showing that keratinocytes produce "melanotrophic factors" which modulate growth, melanin production, and dendricity of melanocytes. Melanocyte cultures also enable in vitro studies of melanocyte responses to ultraviolet radiations and of the biologic messengers involved in these responses. Lastly, they provide a means for investigating endocrine and paracrine mechanisms involved in the regulation of melanogenesis, including the role of melanotropins, estrogens and vitamin D. Improved knowledge of the molecular biology of melanocytes provides hope for rapid advances in the understanding of tyrosinase and posttyrosinase regulation of melanogenesis. Lastly, melanocyte cultures can be expected to find useful applications in the pathophysiologic study of pigment disorders and of pharmacologic modulation of skin pigmentation.
Distinct signals control the hematopoiesis of lymphoid-related dendritic cells (2000)

The molecular and cellular requirements for the development of different populations of human dendritic cells (DC) were studied. Conditions were defined that support DC production from lymphoid progenitors but that fail to induce DC formation from peripheral monocytes. The production of these lymphoid-related DC was severely blocked when hematopoietic progenitors overexpressed Ik7, a mutant dominant-negative Ikaros protein. In contrast, Ik7 did not block the formation of DC in conditions supporting the development of monocyte-derived DC. Furthermore, Ik7 did not block the formation of monocyte/macrophages and enhanced granulopoiesis. One of the molecular mechanisms mediated by Ik7 appears to be down-regulation of the flt3-receptor mRNA. Thus, distinct signals control the formation of DC demonstrating that some aspects of DC diversity are determined in part by distinct molecular cues at the hematopoietic level. (Blood. 2000;95:128-137)