gebhart/patrepeval huggingface dataset:
Protein evolution by codon-based random deletions (2004)

A method to delete in-phase codons throughout a defined target region of a gene has been developed. This approach, named the codon-based random deletion (COBARDE) method, is able to delete complete codons in a random and combinatorial mode. Robustness, automation and fine-tuning of the mutagenesis rate are essential characteristics of the method, which is based on the assembly of oligonucleotides and on the use of two transient orthogonal protecting groups during the chemical synthesis. The performance of the method for protein function evolution was demonstrated by changing the substrate specificity of TEM-1 beta-lactamase. Functional ceftazidime-resistant beta-lactamase variants containing several deleted residues inside the catalytically important omega-loop region were found. The results show that the COBARDE method is a useful new molecular tool to access previously unexplorable sequence space.
XL.—An investigation into the formation of 4(5)-aminoglyoxalines. Part I (1930)

I. E. Balaban, J. Chem. Soc., 1930, 268 DOI: 10.1039/JR9300000268
Carbon nanotube thin films with ordered structures (2004)

Carbon nanotube thin films with ordered structures have been developed from a highly concentrated suspension of nanotubes; this is shown to be an attractive approach to fabricating electrodes for high power density supercapacitors.
Cycloaddition Chemistry at Surfaces:  Reaction of Alkenes with the Diamond(001)-2 × 1 Surface (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTCycloaddition Chemistry at Surfaces: Reaction of Alkenes with the Diamond(001)-2 × 1 SurfaceJ. S. Hovis, S. K. Coulter, R. J. Hamers, M. P. D'Evelyn, J. N. Russell, and J. E. ButlerView Author Information Department of Chemistry University of Wisconsin, 1101 University Avenue Madison, Wisconsin 53706 GE Corp. Research and Development Schenectady, New York 12301 Chemistry Division Naval Research Laboratory Washington D.C. 20375 Cite this: J. Am. Chem. Soc. 2000, 122, 4, 732–733Publication Date (Web):January 15, 2000Publication History Received11 August 1999Published online15 January 2000Published inissue 1 February 2000https://pubs.acs.org/doi/10.1021/ja9929077https://doi.org/10.1021/ja9929077rapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views462Altmetric-Citations91LEARN 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 SUBJECTS:Addition reactions,Carbon,Hydrocarbons,Mathematical methods,Oligomers Get e-Alerts
A Novel Ganglioside Isolated from Renal Cell Carcinoma (2001)

In renal cell carcinoma (RCC), the level of higher gangliosides is correlated with degree of metastatic potential, and cell lines derived from metastatic deposits of RCC are characterized by high expression of disialogangliosides (Saito, S., Orikasa, S., Ohyama, C., Satoh, M., and Fukushi, Y. (1991) Int. J. Cancer 49, 329-334 and Saito, S., Orikasa, S., Satoh, M., Ohyama, C., Ito, A., and Takahashi, T. (1997) Jpn. J. Cancer Res. (Gann) 88, 652-659). We now report two disialogangliosides, G1 and G2, found in the RCC cell line TOS-1. G1 from TOS-1 cells was characterized as having a novel hybrid structure between ganglio-series (region I as in Structure; same as the terminal structure of ganglioside GM2), and the lacto-series type 1 (region II). The characterization was based on reactivity with various monoclonal antibodies (mAbs) with defined epitope specificity, as well as monosaccharide and fatty acid component analysis, (1)H NMR spectroscopy, and electrospray ionization mass spectrometry of the intact compound. G1 showed strong reactivity with mAb RM2, raised originally against TOS-1 cells, and weak cross-reactivity with anti-GM2 mAb MK-1-8. The antigen is hereby termed GalNAc disialosyl Lc4Cer (IV4GalNAcIV3NeuAcIII6NeuAcLc4; abbreviated GalNAcDSLc4). G2 was identified by 1H NMR and mass spectrometry as having a structure similar to Structure but without the GalNAcbeta1-->4 substitution and showed strong reactivity with mAb FH9 reported previously to be specific for disialosyl lacto-series type 1 (disialosyl Lc(4)) having vicinal alpha2-->3 and alpha2-->6 sialosyl residues, an antigen associated with human colonic cancer. Clinicopathological studies indicate that expression of these disialoganglioside antigens in RCC tissue is correlated with the metastatic potential of RCC.
Oncolytic Adenovirus Expressing Soluble TGFβ Receptor II-Fc-mediated Inhibition of Established Bone Metastases: A Safe and Effective Systemic Therapeutic Approach for Breast Cancer (2011)

In recent years, oncolytic adenoviruses have shown some promise as a novel class of antitumor agents. However, their utility in targeting bone metastases is relatively less studied. We have examined whether the systemic therapy of oncolytic adenoviruses expressing the soluble form of transforming growth factor-β (TGFβ) receptor II fused with human immunoglobulin G1 can be developed for the treatment of established breast cancer bone metastases. MDA-MB-231-luc2 human breast cancer cells were injected in the left heart ventricle of nude mice to establish bone metastasis. Mice with hind limb tumors were administered (on days 8 and 11) oncolytic adenoviruses-Ad.sTβRFc or mhTERTAd.sTβRFc. Skeletal tumor growth was monitored weekly by bioluminescence imaging (BLI) and radiography. At the termination time on day 28, hind limb bones were analyzed for tumor burden, synchrotron micro-computed tomography, and osteoclast activation. Intravenous delivery of Ad.sTβRFc and mhTERTAd.sTβRFc induced significant inhibition of tumor growth, reduction of tumor burden, osteoclast activation, and increased animals' survival. Oncolytic adenoviruses were safer than dl309, a wild-type virus. A slight elevation of liver enzyme activity was observed after Ad.sTβRFc administration; this subsided with time. Based on these studies, we believe that Ad.sTβRFc and mhTERTAd.sTβRFc can be developed as a safe and effective approach for the treatment of established bone metastasis.
Identification of immunodominant T cell epitopes of the hepatitis B virus nucleocapsid antigen. (1991)

Several lines of experimental evidence suggest that inclusion of core sequences in the hepatitis B vaccine may represent a feasible strategy to increase the efficacy of the vaccination. In order to identify immunodominant core epitopes, peripheral blood T cells purified from 23 patients with acute hepatitis B and different HLA haplotypes were tested with a panel of 18 short synthetic peptides (15 to 20 amino acids [AA]) covering the entire core region. All patients except one showed a strong T cell proliferative response to a single immunodominant 20 amino acid sequence located within the aminoterminal half of the core molecule. Two additional important sequences were also identified at the aminoterminal end and within the carboxyterminal half of the core molecule. These sequences were able to induce significant levels of T cell proliferation in 69 and 73% of the patients studied, respectively. T cell response to these epitopes was HLA class II restricted. The observations that (a) polyclonal T cell lines produced by PBMC stimulation with native HBcAg were specifically reactive with the relevant peptides and that (b) polyclonal T cell lines produced with synthetic peptides could be restimulated with native HBcAg, provide evidence that AA sequences contained within the synthetic peptides represent real products of the intracellular processing of the native core molecule. In conclusion, the identification of immunodominant T cell epitopes within the core molecule provides the molecular basis for the design of alternative and hopefully more immunogenic vaccines.
The C-proteinase that processes procollagens to fibrillar collagens is identical to the protein previously identified as bone morphogenic protein-1. (1996)

Bone morphogenic protein-1 (BMP-1) was originally identified as one of several BMPs that induced new bone formation when implanted into ectopic sites in rodents. BMP-1, however, differed from other BMPs in that it its structure was not similar to transforming growth factor beta. Instead, it had a large domain homologous to a metalloendopeptidase isolated from crayfish, an epidermal growth-factor-like domain, and three regions of internal sequence homology referred to as CUB domains. Therefore, BMP-1 was a member of the "astacin families" of zinc-requiring endopeptidases. Many astacins have been shown to play critical roles in embryonic hatching, dorsal/ventral patterning, and early developmental decisions. Here, we have obtained amino acid sequences and isolated cDNA clones for procollagen C-proteinase (EC 3.4.24.19), an enzyme that is essential for the processing of procollagens to fibrillar collagens. The results demonstrate that procollagen C-proteinase is identical to BMP-1.
Chinese word recognition and understanding with information feedback (2002)

It is the one of tasks of a Chinese speech understanding system that the Chinese syllable produced by the Chinese speech recognition system is translated into a correct Chinese word, and the Chinese speech understanding system will implement the task of transformation from speech to text together with the Chinese speech recognition system. This paper describe the design of a Chinese word recognition and understanding system based on a new approach with information feedback, that is different from the traditional scheme of speech recognition and understanding, using both linguistic and statistical methods. Finally, an analysis is included an experimental system with a summary of this new approach.
Cerebral monitoring during cardiovascular surgery (2008)

Neuromonitoring tools may guide both intervention and treatment, and are aimed at reducing brain damage during cardiovascular surgery, especially when combined in multimodality monitoring. Further prospective, double-blind, randomized outcome studies are needed to determine the optimal neurologic monitoring modality (or modalities) in specific surgical settings.
A Highly Specific Inhibitor of Matrix Metalloproteinase-9 Rescues Laminin from Proteolysis and Neurons from Apoptosis in Transient Focal Cerebral Ischemia (2005)

Neuronal cell death occurs during many neurodegenerative disorders and stroke. The aberrant, excessive activity of matrix metalloproteinases (MMPs), especially MMP-9, contributes directly to neuron apoptosis and brain damage (Rosenberg et al., 1996; Asahi et al., 2001; Gu et al., 2002; Horstmann et al., 2003). We determined that MMP-9 degrades the extracellular matrix protein laminin and that this degradation induces neuronal apoptosis in a transient focal cerebral ischemia model in mice. We also determined that the highly specific thiirane gelatinase inhibitor SB-3CT blocks MMP-9 activity, including MMP-9-mediated laminin cleavage, thus rescuing neurons from apoptosis. We conclude that MMP-9 is a highly promising drug target and that SB-3CT derivatives have significant therapeutic potential in stroke patients.
Task Decomposition of Laparoscopic Surgery for Objective Evaluation of Surgical Residents' Learning Curve Using Hidden Markov Model (2002)

Objective: Evaluation of the laparoscopic surgical skills of surgical residents is usually a subjective process carried out in the operating room by senior surgeons. The two hypotheses of the current study were: (1) haptic information and tool/tissue interactions (types and transitions) performed in laparoscopic surgery are skill-dependent, and (2) statistical models (Hidden Markov Models—HMMs) incorporating these data are capable of objectively evaluating laparoscopic surgical skills.Materials and Methods: Eight subjects (six residents—two first-year (R1), two third-year (R3), and two fifth-year (R5)—and two expert laparoscopic surgeons) performed laparoscopic cholecystectomy on pigs using an instrumented grasper equipped with force/torque (F/T) sensors at the hand/tool interface, and F/T data was synchronized with video of the operative maneuvers. Fourteen types of tool/tissue (T/T) interactions, each associated with unique F/T signatures, were defined from frame-by-frame video analysis. HMMs for each subject and step of the operation were compared to evaluate the statistical distance between expert surgeons and residents with different skill levels.Results: The statistical distances between HMMs representing expert surgeons and residents were significantly different (α < 0.05). Major differences occurred in: (1) F/T magnitudes; (2) type of T/T interactions and transitions between them; and (3) time intervals for each T/T interaction and overall completion time. The greatest difference in performance was between Rl (junior trainee) and R3 (midlevel trainee). Smaller changes were seen as expertise increased beyond the R3 level.Conclusion: HMMs incorporating haptic and visual information provide an objective tool for evaluating surgical skills. Objective evidence for a “learning curve” suggests that surgical residents acquire a major portion of their laparoscopic skill between year 1 and year 3 of training.
Transform Audio Coding with Arithmetic-Coded Scalar Quantization and Model-Based Bit Allocation (2007)

In this paper we present a new model-based method to code the transform coefficients of audio signals. The histogram of transform coefficients is approximated by a generalized Gaussian model for efficient model-based bit allocation and the spectrum is coded by scalar quantization followed by arithmetic coding. An example coder operating at 16 kHz and using predictive modified discrete cosine transform (MDCT) coding is described. We compare the performance of the proposed coder with ITU-T G.722.1. Objective and subjective quality results are presented. The proposed coder is better than ITU-T G.722.1 at 24 kbit/s and equivalent at 32 kbit/s.
Crystal and Molecular Structure of Double Macrocyclic Inclusion Complexes, γ-Cyclodextrin·12-Crown-4·NaCl, a Model for the Transport of Ions through Membranes (1988)

Abstract The crystal structure of a γ-cyclodextrin·12-crown-4·NaCl (3 : 3 : 1) inclusion complex was determined by an X-ray method to be space group P4212, a=b=23.816(3) Å, c=23.072(3) Å. The inclusion complex has a C4 symmetry, and the cation, Na+, is coordinated by two 12-crown-4 molecules in a hydrophobic channel formed by tail-to-tail oriented two γ-cyclodextrin molecules.
Solar wind parameters and magnetospheric coupling studies (1986)

This paper presents distributions, means, and standard deviations of the fluxes of solar wind protons, momentum, and energy as observed near earth during the solar quiet and active years 1976 and 1979. Distributions of ratios of energies (Alfven Mach number, plasma beta) and distributions of interplanetary magnetic field orientations are also given. Finally, the uncertainties associated with the use of the libration point orbiting ISEE-3 spacecraft as a solar wind monitor are discussed.
Barroco, Símbolo e Alegoria em Walter Benjamin (2007)

O presente artigo discute os conceitos de simbolo, alegoria e barroco a partir de Walter Benjamin. Investiga, portanto, a relacao que esses conceitos mantem com a concepcao de historia do mesmo autor. Isso implica demonstrar de que maneira o modo de ser barroco se assemelha qualitativamente ao modo de ser do individuo na era moderna.
A closed tube format for amplification and detection of DNA based on energy transfer (1997)

A new method for the direct detection of PCR-amplified DNA in a closed system is described. The method is based on the incorporation of energy transfer-labeled primers into the amplification product. The PCR primers contain hairpin structures on their 5'ends with donor and acceptor moieties located in close proximity on the hairpin stem. The primers are designed in such a way that a fluorescent signal is generated only when the primers are incorporated into an amplification product. A signal to background ratio of 35:1 was obtained using the hairpin primers labeled with fluorescein as a donor and 4-(4'-dimethylaminophenylazo) benzoic acid (DABCYL) as a quencher. The modified hairpin-primers do not interfere with the activity of DNA polymerase, and both thermostable Pfu and Taq polymerase can be used. This method was applied to the detection of cDNA for prostate specific antigen. The results demonstrate that the fluorescent intensity of the amplified product correlates with the amount of incorporated primers, and as few as 10 molecules of the initial template can be detected. This technology eliminates the risk of carry-over contamination, simplifies the amplification assay and opens up new possibilities for the real-time quantification of the amplified DNA over an extremely wide dynamic range.
Isolation of temperature-sensitive pantothenate kinase mutants of Salmonella typhimurium and mapping of the coaA gene (1979)

Temperature-sensitive pantothenate kinase mutants of Salmonella typhimurium LT2 were selected by using the excretion of pantothenate at the nonpermissive temperature as a screening method. Thermolability of the pathothenate kinase activity in extracts of the mutants was demonstrated. The mutations were mapped at min 89 of the Salmonella chromosome, near rpoB, by transduction. As pantothenate kinase catalyzes the first step in the biosynthesis of coenzyme A from pantothenate, the new genetic locus has been designated coaA.
Soft-tissue aging and musculoskeletal function. (1993)

Buckwalter, J A; Woo, S L; Goldberg, V M; Hadley, E C; Booth, F; Oegema, T R; Eyre, D R Author Information
Urodilatin and four cardiac hormones decrease human renal carcinoma cell numbers (2006)

These results indicate that urodilatin and the four cardiac hormones have potent anti-cancer effects by eliminating up to 81% of renal carcinoma cells within 24 h of treatment.
Carcinogens are Mutagens: A Simple Test System Combining Liver Homogenates for Activation and Bacteria for Detection (1973)

18 Carcinogens, including aflatoxin B(1), benzo(a)pyrene, acetylaminofluorene, benzidine, and dimethylamino-trans-stilbene, are shown to be activated by liver homogenates to form potent frameshift mutagens. We believe that these carcinogens have in common a ring system sufficiently planar for a stacking interaction with DNA base pairs and a part of the molecule capable of being metabolized to a reactive group: these structural features are discussed in terms of the theory of frameshift mutagenesis. We propose that these carcinogens, and many others that are mutagens, cause cancer by somatic mutation. A simple, inexpensive, and extremely sensitive test for detection of carcinogens as mutagens is described. It consists of the use of a rat or human liver homogenate for carcinogen activation (thus supplying mammalian metabolism) and a set of Salmonella histidine mutants for mutagen detection. The homogenate, bacteria, and a TPNH-generating system are all incubated together on a petri plate. With the most active compounds, as little as a few nanograms can be detected.
Not All Immune Checkpoints Are Created Equal (2018)

Antibodies that block T cell inhibition via the immune checkpoints CTLA-4 and PD-1 have revolutionized cancer therapy during the last 15 years. T cells express additional inhibitory surface receptors that are considered to have potential as targets in cancer immunotherapy. Antibodies against LAG-3 and TIM-3 are currently clinically tested to evaluate their effectiveness in patients suffering from advanced solid tumors or hematologic malignancies. In addition, blockade of the inhibitory BTLA receptors on human T cells may have potential to unleash T cells to effectively combat cancer cells. Much research on these immune checkpoints has focused on mouse models. The analysis of animals that lack individual inhibitory receptors has shed some light on the role of these molecules in regulating T cells, but also immune responses in general. There are current intensive efforts to gauge the efficacy of antibodies targeting these molecules called immune checkpoint inhibitors alone or in different combinations in preclinical models of cancer. Differences between mouse and human immunology warrant studies on human immune cells to appreciate the potential of individual pathways in enhancing T cell responses. Results from clinical studies are not only highlighting the great benefit of immune checkpoint inhibitors for treating cancer but also yield precious information on their role in regulating T cells and other cells of the immune system. However, despite the clinical relevance of CTLA-4 and PD-1 and the high potential of the emerging immune checkpoints, there are still substantial gaps in our understanding of the biology of these molecules, which might prevent the full realization of their therapeutic potential. This review addresses PD-1, CTLA-4, BTLA, LAG-3, and TIM-3, which are considered major inhibitory immune checkpoints expressed on T cells. It provides summaries of our current conception of the role of these molecules in regulating T cell responses, and discussions about major ambiguities and gaps in our knowledge. We emphasize that each of these molecules harbors unique properties that set it apart from the others. Their distinct functional profiles should be taken into account in therapeutic strategies that aim to exploit these pathways to enhance immune responses to combat cancer.
Characterization and cellular localization of human myristoyl-CoA: protein N-myristoyltransferase (1995)

Conference Article| August 01 1995 Characterization and cellular localization of human myristoyl-CoA: protein N-myristoyltransferase R. A.J. McIlhinney R. A.J. McIlhinney 1Medical Research Council Anatomical Neuropharmacology Unit, Mansfield Road, Oxford OX1 3TH, UK Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1995) 23 (3): 549–553. https://doi.org/10.1042/bst0230549 Article history Received: March 02 1995 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation R. A.J. McIlhinney; Characterization and cellular localization of human myristoyl-CoA: protein N-myristoyltransferase. Biochem Soc Trans 1 August 1995; 23 (3): 549–553. doi: https://doi.org/10.1042/bst0230549 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: MARCKS, myristoylated alaninerich C kinase substrate, NMT, myristoyl-CoA:protein N-myristoyltransferase © 1995 Biochemical Society1995 Article PDF first page preview Close Modal You do not currently have access to this content.