gebhart/patrepeval huggingface dataset:
The Bacterial Origins of the CRISPR Genome-Editing Revolution (2015)

Like most of the tools that enable modern life science research, the recent genome-editing revolution has its biological roots in the world of bacteria and archaea. Clustered, regularly interspaced, short palindromic repeats (CRISPR) loci are found in the genomes of many bacteria and most archaea, and underlie an adaptive immune system that protects the host cell against invasive nucleic acids such as viral genomes. In recent years, engineered versions of these systems have enabled efficient DNA targeting in living cells from dozens of species (including humans and other eukaryotes), and the exploitation of the resulting endogenous DNA repair pathways has provided a route to fast, easy, and affordable genome editing. In only three years after RNA-guided DNA cleavage was first harnessed, the ability to edit genomes via simple, user-defined RNA sequences has already revolutionized nearly all areas of biological science. CRISPR-based technologies are now poised to similarly revolutionize many facets of clinical medicine, and even promise to advance the long-term goal of directly editing genomic sequences of patients with inherited disease. In this review, we describe the biological and mechanistic basis for these remarkable immune systems, and how their engineered derivatives are revolutionizing basic and clinical research.
Understanding image quality losses due to smear in high-resolution remote sensing imaging systems (1999)

Space-based high-resolution scanning array imaging sys- tems have the potential to introduce large amounts of image smear. When designing these systems, it is useful to understand how smear will degrade image quality. A brief description of the causes of smear and a simple mathematical model are presented. A series of image simulations (for a system in which lFN/p51.0, where l is the mean wavelength for a panchromatic system, FN is the system f number, and p is the pixel pitch of the detectors) are performed in which along scan smear (ranging from 1.0 to 8.0 pixels) is introduced. Using the National Imagery Inter- pretability Rating Scale (NIIRS), expert observers rated DNIIRS differ- ence in image quality between the images with simulated smear and the original ''unsmeared'' image. The functional relationship between smear error and image quality (in units of DNIIRS) is determined. © 1999 Society of Photo-Optical Instrumentation Engineers. (S0091-3286(99)01505-6)
Regioselective halo- and carbodesilylation of (trimethylsilyl)-1-methylpyrazoles (1984)

The isomeric 3-, 4-, and 5-(trimethylsily1)- as well as the 3,4-, 3,5-, and 4,5-bis(trimethylsilyl)-l-methylpyrazoles (2,7,3,5,9,a nd 10, respectively) are obtained by methylation of the corresponding (trimethylsily1)-1H-pyrazoles or by silylation of Grignard or lithio derivatives of appropriate 1-methylpyrazoles with chlorotrimethylsilane. 5 and 10 are halodesilylated regioselectively by Br2 or ICl in the 4-position, yielding 13 and 15. With additional bromine, these monobromo compounds suffer exclusively bromodesilylation to give 3,4- and 4,5-dibromo-lmethylpyrazole (14 and 16, respectively). These findings are in accord with the electrophilic substitution reactivity indices for 1-methylpyrazole (8) and with ipso-directing influence of the MeBSi group. The reaction of 5 with Iz, unexpectedly, attacks preferentially at the 3-position. Regioselective carbodesilylation in the 5-position is observed in the fluoride-catalyzed reactions of 3, 9, and 10 with carbon electrophiles. The high regiospecificity of this reaction is rationalized in terms of carbanion stabilization at the individual pyrazole positions.
309 Pharmacokinetic Profile of epidurally administered Methylnaltrexone, a novel peripheral opioid antagonist (1999)

Murphy, Damian MB, FFARCSI; Foss, Joseph MD; Chan, V FRCPC; El-Beheiry, Hossam PhD FRCPC Author Information
Kinetics of thermal oxidation of AlAs in water vapor (1996)

We have investigated the lateral thermal oxidation of AlAs in water vapor in vertical cavity surface emitting laser structures. At low temperatures and short oxidation times, oxide growth was found to be reaction rate limited. Conversely, diffusion across the oxide was the rate controlling mechanism at higher temperatures and longer oxidation times. Lasers are typically processed at intermediate values of temperatures and time. The observed growth can be modeled by rate equations by which the two component growth mechanisms can be separated. Activation energies of 1.6 and 0.8 eV were determined for the reaction rate and diffusion limited mechanisms, respectively.
Hybrid III-V/SOI single-mode vertical-cavity laser with in-plane emission into a silicon waveguide (2015)

We report a III-V-on-SOI vertical-cavity laser emitting into an in-plane Si waveguide fabricated by using CMOS-compatible processes. The fabricated laser operates at 1.54 µm with a SMSR of 33 dB and a low threshold.
Parathyroid hormone-related protein purified from a human lung cancer cell line. (1987)

A protein with biological activities similar to parathyroid hormone (PTH) has been purified from serum-free culture medium obtained from a human lung cancer cell line (BEN). A major protein band of 18 kDa was obtained on NaDodSO4/polyacrylamide gels, with faint bands at 35 kDa and 67 kDa. Biological activity was associated only with the 18-kDa band. Amino acid sequence analysis of the material purified by HPLC revealed that 8 of the 16 residues were identical with those of human PTH. Antibody raised to a corresponding synthetic peptide recognized the PTH-related material but showed less than 1% cross-reactivity with human PTH amino-terminal peptides. BEN cells contained PTH DNA, but not PTH messenger RNA, indicating involvement of another gene. The purified PTH-related protein had a specific biological activity approximately equal to 6 times greater than that of bovine PTH(1-34). The PTH-related protein may have a role in the syndrome of humoral hypercalcemia of malignancy.
Gene expression profile of peripheral blood in colorectal cancer (2014)

A novel gene expression profile was associated with CRC and can potentially be applied to blood-based detection assays.
Highly Immunogenic Human Immunodeficiency Viruslike Particles are Produced by Recombinant Vaccinia Virus-Infected Cells (1991)

CV-1 cells were infected with two recombinant vaccinia viruses carrying the gag gene with deletion of 231 bp from 3′ terminus (strain vC5) and env gene (strain vE234L) of human immunodeficiency virus type 1 (HIV-1). Both recombinant proteins synthesized in the cells (p508 gag and gp160/120 env ) were localized predominantly in cell membranes; however, some amount of p50 was found in cell nuclei. Thin-section immunoelectron microscopy showed accumulation of viruslike particles undistinguished from immature HIV-I virions in the culture medium of the cells infected with vC5. The similar particles containing gag and env proteins were produced into the culture medium when the cells were coinfected with vC5 and vE234L strains. The particles contained heterogeneous cellular RNA, but no virus-specific RNA as shown by Northern blot hybridization. Immunization of the rabbits with purified viruslike particles produced virus-specific antibodies against gag and env proteins. The titer of antibodies was significantly higer than after immunization with cell lysate or recombinant proteins purified from the infected cells. Highly immunogenic HIV-1-like particles containing gag and env proteins but no virus-specific RNA are good candidates for potential vaccine.
Dominant negative alleles of RAD52 reveal a DNA repair/recombination complex including Rad51 and Rad52. (1993)

Saccharomyces cerevisiae rad52 mutants are characterized by severe defects in double-strand break (DSB) repair and recombination. In this study we have identified several regions of RAD52 that are required for these biological functions. We cloned and characterized a RAD52 homolog from Kluyveromyces lactis that partially complemented S. cerevisiae rad52 mutants while exhibiting negative dominance in wild-type (RAD52) strains. The dominant negative effect was suppressed by overexpression of RAD51, an additional gene known to be required for DSB repair and recombination, indicating a genetic interaction between these loci. Furthermore, GAL4 two-hybrid analysis revealed a physical interaction between Rad51 and the carboxy-terminal one-third of Rad52. Deletion alleles of rad52 (with or without the Rad51 association domain) also produced dominant negative defects, suggesting the disruption of repair through nonfunctional interactions with other DSB repair and recombination proteins. RAD51 relieved the negative dominance of each of these alleles either by competitive titration or functional activation of mutant or heterologous Rad52 proteins. These results demonstrate the importance of Rad52-Rad51 interactions and point to the formation of a higher order repair/recombination complex potentially containing other yet unidentified components.
cAMP-inducible chloride conductance in mouse fibroblast lines stably expressing the human cystic fibrosis transmembrane conductance regulator. (1991)

A cAMP-inducible chloride permeability has been detected in mouse fibroblast (L cell) lines upon stable integration of a full-length cDNA encoding the human cystic fibrosis transmembrane conductance regulator (CFTR). As indicated by a Cl(-)-indicator dye, the Cl- permeability of the plasma membrane increases by 10- to 30-fold within 2 min after treatment of the cells with forskolin, an activator of adenylyl cyclase. The properties of the conductance are similar to those described in secretory epithelial cells; the whole-cell current-voltage relationship is linear and there is no evidence of voltage-dependent inactivation or activation. In contrast, this cAMP-dependent Cl- flux is undetectable in the untransfected cells or cells harboring defective cDNA constructs, including one with a phenylalanine deletion at amino acid position 508 (delta F508), the most common mutation causing cystic fibrosis. These observations are consistent with the hypothesis that the CFTR is a cAMP-dependent Cl- channel. The availability of a heterologous (nonepithelial) cell type expressing the CFTR offers an excellent system to understand the basic mechanisms underlying this CFTR-associated ion permeability and to study the structure and function of the CFTR.
Notch Signaling Proteins: Legitimate Targets for Cancer Therapy (2010)

Proteins and small peptides (growth factors and hormones) are key molecules in maintaining cellular homeostasis. To that end, Notch signaling pathway proteins are known to play critical roles in maintaining the balance between cell proliferation, differentiation and apoptosis, and thus it has been suggested that Notch may be responsible for the development and progression of human malignancies. Therefore, the Notch signaling pathway proteins may present novel therapeutic targets, which could have promising therapeutic impact on eradicating human malignancies. This review describes the role of Notch signaling pathway proteins in cancer and how its deregulation is involved in tumor development and progression leading to metastasis and the ultimate demise of patients diagnosed with cancer. Further, we summarize the role of several Notch inhibitors especially "natural agents" that could represent novel therapeutic strategies targeting Notch signaling toward better treatment outcome of patients diagnosed with cancer.
Coengagement of CD2 with LFA-1 or VLA-4 by bispecific ligand fusion proteins primes T cells to respond more effectively to T cell receptor-dependent signals (1994)

To examine the effects of ligand engagement and accessory molecule juxtaposition on T cell receptor (TCR) signaling, we prepared LFA-3/ICAM-1 Rg and LFA-3/VCAM-1 Rg bispecific immunoglobulin fusion proteins (Rg, recombinant globulin). These novel fusion proteins allowed us to examine the effects of ligand driven co-engagement of T cell proteins CD2 and LFA-1 or CD2 and VLA-4 on TCR-dependent mobilization of intracellular Ca2+. We observed that preincubation of resting T cells with LFA-3/ICAM-1 Rg or LFA-3/VCAM-1 Rg fusion proteins resulted in significantly enhanced mobilization of intracellular Ca2+ following TCR-accessory molecule cross-linking relative to T cells preincubated with each of the monospecific Rgs alone or with combinations of the monospecific Rg fusion proteins. In addition, such coengagement stimulated TCR-dependent activation and tyrosine phosphorylation of phospholipase C gamma 1 (PLC gamma 1). These results suggest that when T cells interact with antigen presenting cells the engagement of multiple cell adhesion molecules such as CD2, LFA-1, and VLA-4 primes the T cell to respond more effectively to signals delivered through the TCR.
Bioavailability of Single and Multiple Doses of Enteric-Coated Mesalamine and Sulphasalazine (1990)

The bioavailibity of mesalamine from enteric-coated mesalamine and sulphasalazine was determined following a single dose and at steady state in healthy subjects in crossover studies. Plasma concentrations and urinary excretion of mesalamine and its major metabolite, N-acetyl-5-aminosalicylic acid, were measured. After a single dose of enteric-coated mesalamine, about 10 h elapsed before the onset of measurable plasma drug concentrations, probably representing gastro-intestinal transit prior to drug release near the ileocaecal junction. The elimination kinetics were similar for a single oral dose and steady state using enteric-coated mesalamine, but after both single and multiple administration of enteric-coated mesalamine only about 20% of the mesalamine given was absorbed, with about 80% estimated to remain for colon therapeutic activity. It is concluded that, despite different mechanisms of mesalamine release, enteric-coated mesalamine and sulphasalazine produced similar mesalamine absorption.
VIP and Drug Design (2003)

The following review outlines the physiological outcome of VIP and VIP gene manipulations. Previously, we reviewed the various VIP receptors associated with biological functions ranging from growth regulation, sexual function, bronchodilation, vasodilation and immune interactions to neurotrophism. VIP-based drug design is discussed below.
B cell stimulating factor 2/interleukin 6 is a costimulant for human thymocytes and T lymphocytes. (1988)

Growth and differentiation of thymocytes and mature T lymphocytes is regulated by cellular interactions that are in part mediated by soluble factors. We identify IL-6, formerly called B cell stimulating factor (BSF-2). IFN-beta 2, or hybridoma-plasmacytoma growth factor (HPGF) as a novel T cell costimulant rIL-6 induced a six-to seven-fold increase in proliferation of human thymocytes stimulated with suboptimal doses of PHA. A similar effect with added IL-6 could be observed using peripheral blood T lymphocytes, but only if the cultures were first rigorously depleted of monocytes that release high levels of IL-6. Analysis of the mechanism of the IL-6 effect on thymocytes and T lymphocytes showed that IL-6 did not lead to an increase in IL-2-R expression. Concentrations of antibody to IL-2-R inhibiting IL-2 effects did not block the IL-6-induced proliferation, indicating that the IL-6 effect was relatively IL-2 independent. These results identify IL-6 as a novel costimulant of human thymocytes and mature T lymphocytes, and suggest that IL-6 is also an important regulatory of cellular immunity.
Distribution of fetal bovine serum fibronectin and endogenous rat cell fibronectin in extracellular matrix. (1979)

Normal rat kidney cells were cultured in medium supplemented with normal fetal bovine serum (FBS) or FBS depleted of fibronectin. The cell surface fibronectin of these cultures was visualized by indirect immunofluorescence using species-specific antisera for either rat fibronectin or bovine fibronectin. Anti-rat-fibronectin revealed fibrillar structures on the cells grown in either normal medium or fibronectin-depleted medium. Anti-bovine fibronectin revealed similar fibrillar networks, but only on the cells grown in medium containing bovine fibronectin. Staining in each case was abolished by absorption with the homologous antigen. It appears that exogenous fibronectin was incorporated into the same structures as endogenous fibronectin. This finding suggests that circulating fibronectin may serve as a building block for the assembly of extracellular matrix, possibly by cells which are incapable of synthesizing it.
Synergistic Action of an X-Prolyl Dipeptidyl Aminopeptidase and a Non-Specific Aminopeptidase in Protein Hydrolysis (2001)

Non-specific monoaminopeptidase (AP; E.C. 3.4.11) and X-prolyl dipeptidyl aminopeptidase (X-PDAP; E.C. 3.4.14.5), both from Aspergillus oryzae, demonstrate strong synergism in hydrolyzing proline-containing peptides. Incubation of AP alone with the peptide Ala-Pro-Gly-Asp-Arg-Ile-Tyr-Val-His-Pro-Phe does not generate free amino acids. However, when AP and X-PDAP are added in combination, complete and immediate hydrolysis of all peptide bonds, other than X-Pro bonds, is observed. In the enzymatic hydrolysis of casein, soy, and gluten, degree of hydrolysis (DH) values of 54, 54, and 47% were achieved, respectively, when subtilisin (E.C. 3.4.21.62) was supplemented with AP. Addition of a third enzyme, X-PDAP, resulted in significantly higher DH values of 69, 72, and 64%, respectively, establishing the utility of this synergism in protein hydrolysis.
Prognostic Significance of Ror2 and Wnt5a Expression in Medulloblastoma (2012)

Medulloblastoma (MB) is a clinically and biologically heterogeneous group of tumors, and currently classified into four molecular subgroups (Wnt, Shh, Group 3 and Group 4). Intracellular signaling of the Wnt pathway has been divided into two classes: the "canonical" and the "non-canonical" signaling pathway. The canonical signaling pathway is a well-established, β-catenin-dependent signaling pathway in MB. In contrast, very little research about the non-canonical WNT signaling pathway in MB exists. In order to identify the roles of Wnt-5a and Ror2, two non-canonical WNT pathway-related genes, we studied 76 cases of MB with immunohistochemistry and quantitative real-time PCR and correlated the results with clinicopathological and other molecular parameters and prognosis. Wnt5a and Ror2 were immunopositive in 20 (29.4%) and 35 (51.5%) of 68 cases, respectively. There were positive associations among protein expressions of Wnt5a, Ror2 and β-catenin. Ror2 mRNA levels were well correlated with immunoexpression. Ror2 mRNA expression was significantly associated with CTNNB1 mutation. High Ror2 mRNA expression was an independent favorable prognostic factor. In conclusion, our study demonstrates the first attempt to identify Wnt5a and Ror2 as additional mechanisms contributing to dysregulation of the non-canonical WNT signaling pathway in MB. Ror2 may play a role as an oncosuppressor in MB.
Novel Design Architecture for Genetic Stability of Recombinant Poliovirus: the Manipulation of G/C Contents and Their Distribution Patterns Increases the Genetic Stability of Inserts in a Poliovirus-Based RPS-Vax Vector System (2002)

Poliovirus has been studied as a live recombinant vaccine vector because of its attractive characteristics. The genetic instability, however, has hampered recombinant polioviruses (PVs) from being developed as an appropriate vaccine. A variety of different foreign inserts were cloned directly into our poliovirus Sabin 1-based RPS-Vax vector system, resulting in the production of recombinant PVs. The genetic stability of each recombinant PV was examined during 12 rounds of consecutive passage. It was found that the genetic stability of the recombinants was not well correlated with their insert size. Instead, elevated stability was frequently observed in recombinants with inserts of high G/C contents. Furthermore, a comparative study using different constructs of the human immunodeficiency virus env gene revealed that the internal deletion of the unstable insert was seemingly caused by the presence of the adjacent A/T-rich region. The instability of these inserts was completely remedied by (i) increasing the G/C contents and (ii) replacing the local A/T-rich region with the G/C-rich codon without a change of the amino acid. This means that stability is closely associated with the G/C content and the G/C distribution pattern. To see whether these findings can be applied to the design of genetically stable recombinant PV, we have reconstructed the heteromultimeric insert based on our design architecture, including the above-mentioned G/C rules and the template/ligation-free PCR protocol. The heteromultimeric insert was very unstable, as expected, but the manipulated insert with the same amino acid sequence showed complete genetic stability, not only in vitro, but also in vivo. Even though this guideline was established with our RPS-Vax vector system, to some extent, it can also be applied to other live viral vaccine vectors.
A Conceptual Framework for Computer Architecture (1976)

article A Conceptual Framework for Computer Architecture Share on Authors: S. S. Reddi W. W. Gaertner Research, Inc., 1492 High Ridge Road, Stamford, Connecticut W. W. Gaertner Research, Inc., 1492 High Ridge Road, Stamford, ConnecticutView Profile , E. A. Feustel Laboratory for Computer Science and Engineering, Department of Electrical Engineering, Rice University, Houston, Texas Laboratory for Computer Science and Engineering, Department of Electrical Engineering, Rice University, Houston, TexasView Profile Authors Info & Claims ACM Computing SurveysVolume 8Issue 2June 1976 pp 277–300https://doi.org/10.1145/356669.356673Online:01 June 1976Publication History 20citation1,334DownloadsMetricsTotal Citations20Total Downloads1,334Last 12 Months33Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Circular Micro-Proteins and Mechanisms of Cyclization (2011)

Transpeptidation reactions result in the formation of new peptide bonds and this can occur between two separate peptides or within the one peptide. These reactions are catalyzed by enzymes and when the N- and C-terminus of the one peptide are joined it results in the formation of cyclic proteins. Cyclization via head-to-tail linkage of the termini of a peptide chain occurs in only a small percentage of proteins but gives the resultant cyclic proteins exceptional stability. The mechanisms are not well understood and this review documents what is known of the events that lead to cyclization. Gene encoded cyclic proteins are found in both prokaryotic and eukaryotic species. The prokaryotic circular proteins include the bacteriocins and pilins. The eukaryotic circular proteins in mammals include the θ-defensins and retrocyclins. Small cyclic proteins are also found in fungi and a large range of cyclic proteins are expressed in cyanobacteria. Three types of cyclic proteins have been found in plants, the small cyclic proteins of 5-12 amino acids, the cyclic proteins from sunflower which are made up of 12-14 amino acids, and the larger group known as cyclotides which contain 28-37 amino acids. Three classes of enzymes are able to catalyse transpeptidation reactions, these include the cysteine, serine and threonine proteases. However only cysteine and serine proteases have been documented to cyclize proteins. The cyclotides from Oldenlandia affinis, the plant in which cyclotides were first discovered, are processed by an asparaginyl endopeptidase which is a cysteine protease. These proteases cleave an amide bond and form an acyl enzyme intermediate before nucleophilic attack of the amine group of the N-terminal residue to form a peptide bond, resulting in a cyclic peptide.