gebhart/patrepeval huggingface dataset:
Aromatic Allylation via Diazotization:  Metal-Free C−C Bond Formation (2002)

A new method for the synthesis of allyl aromatic compounds not involving any metal-containing reagent or catalyst has been developed. Arylamines substituted with a large number of different substituents were converted via diazotizative deamination with tert-butyl nitrite in allyl bromide and acetonitrile to the corresponding allyl aromatic compounds. The allylation reaction was found to be suitable for larger scale synthesis due to short reaction times, a nonextractive workup, and robustness toward moisture, air, and type of solvent.
A Limit to the Speed of Processing in Ultra-Rapid Visual Categorization of Novel Natural Scenes (2001)

The processing required to decide whether a briefly flashed natural scene contains an animal can be achieved in 150 msec (Thorpe, Fize, & Marlot, 1996). Here we report that extensive training with a subset of photographs over a 3-week period failed to increase the speed of the processing underlying such Rapid Visual Categorizations: Completely novel scenes could be categorized just as fast as highly familiar ones. Such data imply that the visual system processes new stimuli at a speed and with a number of stages that cannot be compressed. This rapid processing mode was seen with a wide range of visual complex images, challenging the idea that short reaction times can only be seen with simple visual stimuli and implying that highly automatic feed-forward mechanisms underlie a far greater proportion of the sophisticated image analysis needed for everyday vision than is generally assumed.
Functionalized Vertically Aligned Carbon Nanofibers as Scaffolds for Immobilization and Electrochemical Detection of Redox-Active Proteins (2006)

We have investigated the functionalization of vertically aligned carbon nanofibers with the redox-active protein cytochrome c and have characterized the resulting chemical and electrochemical activity. A comparison of monolayers with different terminal groups shows that those exposing carboxylic acid groups are most effective at binding active cytochrome c to carbon nanofibers. Cyclic voltammetry (CV) measurements reveal redox peaks due to electrochemical activity of the nanofiber-bound protein. CV and chemical measurements of enzymatic activity both show that nanofibers modified with cytochrome c yield approximately 10 times more activity than similarly modified surfaces of glassy carbon and gold. However, cytochrome c-modified nanofibers yield a high capacitive background, reducing the signal-to-noise ratio of the electrical measurements. We attribute this in part to inhomogeneous functionalization of the nanofibers at edge-plane versus basal-plane sites on the nanofiber surface, leading to leaky monolayers that yield increased capacitance. Our results demonstrate the ability to link chemically and electrochemically active proteins to nanofibers in a manner that preserves their activity and provide insight into the nanometer-scale factors that control the resulting chemical and electrochemical properties of biologically modified nanostructured electrodes.
Phosphorylation-Induced Distance Change in a Cardiac Muscle Troponin I Mutant (1997)

Phosphorylation of two adjacent serine residues in the unique N-terminal extension of cardiac muscle troponin I (cTnI) is known to decrease the Ca2+-sensitivity of cardiac myofilaments. To probe the structural significance of the N-terminal extension, we have constructed two cTnI mutants each containing a single cysteine: (1) a full-length cTnI mutant (S5C/C81I/C98S) and (2) a truncated cTnI mutant (S9C/C50I/C67S) in which the N-terminal 32 amino acid residues were deleted. We determined the apparent binding constants for the complex formation between IAANS-labeled cardiac troponin C (cTnC) and the two cTnI mutants. The affinities of the cTnC for the truncated cTnI mutant were: (1) 1.5 x 10(6) M(-1) in EGTA, (2) 28.9 x 10(6) M(-1) in Mg2+, and (3) 87.5 x 10(6) M(-1) in Mg2+ + Ca2+. These binding constants were approximately 1.4-fold smaller than the corresponding values obtained with the full-length cTnI mutant, suggesting a very small contribution of the N-terminal extension to the binding of cTnI to cTnC. Cys-5 in the full-length cTnI mutant was labeled with IAANS, and the distribution of the separation between this site and Trp-192 was determined by analysis of the efficiency of fluorescence resonance energy transfer from Trp-192 to IAANS. The following mean distances were obtained with the unphosphorylated full-length mutant: 44.4 A (cTnI alone), 48.3 A (cTnI + cTnC), 46.3 A (cTnI + cTnC in Mg2+), and 51.6 A (cTnI + cTnC in Mg2+ + Ca2+). The corresponding values of the mean distance determined with the phosphorylated full-length cTnI mutant were 35.8, 36.6, 34.8, and 37.3 A. The phosphorylation of cTnI reduced the half-width of the distribution from 9.5 to 3.7 A. Similar but less pronounced decreases of the half-widths were also observed with the phosphorylated cTnI complexed with cTnC in different ionic conditions. Thus, phosphorylation of cTnI resulted in a decrease of 9-12 A in the mean distance between the sites located at the N- and C-terminal portion of cTnI. Our results indicate that phosphorylation elicits a change in the conformation of cTnI which underlies the basis of the phosphorylation-induced modulation of cTnI activity.
Group B streptococci escape host immunity by deletion of tandem repeat elements of the alpha C protein. (1996)

Group B streptococci (GBS) are the most common cause of neonatal sepsis, pneumonia, and meningitis. The alpha C protein is a surface-associated antigen; the gene (bca) for this protein contains a series of tandem repeats (each encoding 82 aa) that are identical at the nucleotide level and express a protective epitope. We previously reported that GBS isolates from two of 14 human maternal and neonatal pairs differed in the number of repeats contained in their alpha C protein; in both pairs, the alpha C protein of the neonatal isolate was smaller in molecular size. We now demonstrate by PCR that the neonatal isolates contain fewer tandem repeats. Maternal isolates were susceptible to opsonophagocytic killing in the presence of alpha C protein-specific antiserum, whereas the discrepant neonatal isolates proliferated. An animal model was developed to further study this phenomenon. Adult mice passively immunized with antiserum to the alpha C protein were challenged with an alpha C protein-expressing strain of GBS. Splenic isolates of GBS from these mice showed a high frequency of mutation in bca--most commonly a decrease in repeat number. Isolates from non-immune mice were not altered. Spontaneous deletions in the repeat region were observed at a much lower frequency (6 x 10(-4)); thus, deletions in that region are selected for under specific antibody pressure and appear to lower the organism's susceptibility to killing by antibody specific to the alpha C protein. This mechanism of antigenic variation may provide a means whereby GBS evade host immunity.
Index selection for OLAP (2002)

On-line analytical processing (OLAP) is a recent and important application of database systems. Typically, OLAP data is presented as a multidimensional "data cube." OLAP queries are complex and can take many hours or even days to run, if executed directly on the raw data. The most common method of reducing execution time is to precompute some of the queries into summary tables (subcubes of the data cube) and then to build indexes on these summary tables. In most commercial OLAP systems today, the summary tables that are to be precomputed are picked first, followed by the selection of the appropriate indexes on them. A trial-and-error approach is used to divide the space available between the summary tables and the indexes. This two-step process can perform very poorly. Since both summary tables and indexes consume the same resource-space-their selection should be done together for the most efficient use of space. The authors give algorithms that automate the selection of summary tables and indexes. In particular, they present a family of algorithms of increasing time complexities, and prove strong performance bounds for them. The algorithms with higher complexities have better performance bounds. However, the increase in the performance bound is diminishing, and they show that an algorithm of moderate complexity can perform fairly close to the optimal.
FURTHER STUDIES ON OPIATE RECEPTORS THAT MEDIATE ANTI‐NOCICEPTION: TOOTH PULP STIMULATION IN THE DOG (1980)

1 The antinociceptive activities of morphine, codeine and dextropropoxyphene (micro-agonists), buprenorphine and Mr 2034 [(-)5,9-dimethyl-2-(tetrahydrofurfuryl)-2'-hydroxy-6,7-benzomorphan](k-agonists ) have been determined against nociceptive responses to electrical stimulation of the tooth pulp in the conscious dog. 2 Dose-dependent increases in nociceptive threshold were obtained for all of the analgesic drugs tested at doses within their antinociceptive range as determined in nociceptive pressure and chemical tests in rodents.
Formal Models for Computer Security (1981)

article Formal Models for Computer Security Share on Author: Carl E. Landwehr Code 7593, Naval Research Laboratory, Washington, D.C. Code 7593, Naval Research Laboratory, Washington, D.C.View Profile Authors Info & Claims ACM Computing SurveysVolume 13Issue 3Sept. 1981 pp 247–278https://doi.org/10.1145/356850.356852Online:01 September 1981Publication History 297citation6,307DownloadsMetricsTotal Citations297Total Downloads6,307Last 12 Months64Last 6 weeks14 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
Capture and Retention of Cryptosporidium parvum Oocysts by Pseudomonas aeruginosa Biofilms (2006)

The association of Cryptosporidium oocysts with biofilm communities can influence the propagation of this pathogen through both environmental systems and water treatment systems. We observed the capture and retention of C. parvum oocysts in Pseudomonas aeruginosa biofilms using laboratory flow cells. Biofilms were developed in two different growth media using two different strains of P. aeruginosa, a wild-type strain (PAO1) and a strain that overproduces the exopolysaccharide alginate (PDO300). Confocal laser-scanning microscopy was used in conjunction with image analysis to assess the structure of the biofilms prior to introducing oocysts into the flow cells. More oocysts were captured by the biofilm-coated surfaces than the abiotic glass surface in both media. There was no significant difference in capture across the two strains of P. aeruginosa biofilm, but the fraction of oocysts captured was positively related to biofilm roughness and surface-area-to-volume ratio. Once captured, oocysts were retained in the biofilm for more than 24 h and were not released after a 40-fold increase in the system flow rate. We believe the capture and retention of oocysts by biofilm communities can impact the environmental transmission of C. parvum, and this interaction should be taken into consideration when predicting the migration of pathogens in the environment.
Development of a Novel AAV Gene Therapy Cassette with Improved Safety Features and Efficacy in a Mouse Model of Rett Syndrome (2017)

Rett syndrome (RTT), caused by loss-of-function mutations in the <i>MECP2</i> gene, is a neurological disorder characterized by severe impairment of motor and cognitive functions. The aim of this study was to investigate the impact of vector design, dosage, and delivery route on the efficacy and safety of gene augmentation therapy in mouse models of RTT. Our results show that AAV-mediated delivery of <i>MECP2</i> to <i>Mecp2</i> null mice by systemic administration, and utilizing a minimal endogenous promoter, was associated with a narrow therapeutic window and resulted in liver toxicity at higher doses. Lower doses of this vector significantly extended the survival of mice lacking MeCP2 or expressing a mutant T158M allele but had no impact on RTT-like neurological phenotypes. Modifying vector design by incorporating an extended <i>Mecp2</i> promoter and additional regulatory 3' UTR elements significantly reduced hepatic toxicity after systemic administration. Moreover, direct cerebroventricular injection of this vector into neonatal <i>Mecp2-</i>null mice resulted in high brain transduction efficiency, increased survival and body weight, and an amelioration of RTT-like phenotypes. Our results show that controlling levels of MeCP2 expression in the liver is achievable through modification of the expression cassette. However, it also highlights the importance of achieving high brain transduction to impact the RTT-like phenotypes.
Identification of Dipeptidyl Nitriles as Potent and Selective Inhibitors of Cathepsin B through Structure-Based Drug Design (2001)

Cathepsin B is a member of the papain superfamily of cysteine proteases and has been implicated in the pathology of numerous diseases, including arthritis and cancer. As part of an effort to identify potent, reversible inhibitors of this protease, we examined a series of dipeptidyl nitriles, starting with the previously reported Cbz-Phe-NH-CH(2)CN (19, IC(50) = 62 microM). High-resolution X-ray crystallographic data and molecular modeling were used to optimize the P(1), P(2), and P(3) substituents of this template. Cathepsin B is unique in its class in that it contains a carboxylate recognition site in the S(2)' pocket of the active site. Inhibitor potency and selectivity were enhanced by tethering a carboxylate functionality from the carbon alpha to the nitrile to interact with this region of the enzyme. This resulted in the identification of compound 10, a 7 nM inhibitor of cathepsin B, with excellent selectivity over other cysteine cathepsins.
Birth of a Healthy Infant after Preimplantation Confirmation of Euploidy by Comparative Genomic Hybridization (2001)

Embryos that are transferred after in vitro fertilization frequently fail to implant in the uterus; in many cases, this failure is due to chromosomal abnormalities in the embryo. The current methods of diagnosis of aneuploidy cannot detect many chromosomal abnormalities. This report on the case of a 38-year-old woman with a long history of infertility describes the use of comparative genomic hybridization to determine that all the chromosomes of a single embryo were free of aneuploidy, resulting in the birth of a healthy infant.
Porous Graphitic Carbon Loading Ultra High Sulfur as High-Performance Cathode of Rechargeable Lithium–Sulfur Batteries (2013)

Porous graphitic carbon of high specific surface area of 1416 m(2) g(-1) and high pore volume of 1.11 cm(3) g(-1) is prepared by using commercial CaCO3 nanoparticles as template and sucrose as carbon source followed by 1200 °C high-temperature calcination. Sulfur/porous graphitic carbon composites with ultra high sulfur loading of 88.9 wt % (88.9%S/PC) and lower sulfur loading of 60.8 wt % (60.8%S/PC) are both synthesized by a simple melt-diffusion strategy, and served as cathode of rechargeable lithium-sulfur batteries. In comparison with the 60.8%S/PC, the 88.9%S/PC exhibits higher overall discharge capacity of 649.4 mAh g(-1)(S-C), higher capacity retention of 84.6% and better coulombic efficiency of 97.4% after 50 cycles at a rate of 0.1C, which benefits from its remarkable specific capacity with such a high sulfur loading. Moreover, by using BP2000 to replace the conventional acetylene black conductive agent, the 88.9% S/PC can further improve its overall discharge capacity and high rate property. At a high rate of 4C, it can still deliver an overall discharge capacity of 387.2 mAh g(-1)(S-C). The porous structure, high specific surface area, high pore volume and high electronic conductivity that is originated from increased graphitization of the porous graphitic carbon can provide stable electronic and ionic transfer channel for sulfur/porous graphitic carbon composite with ultra high sulfur loading, and are ascribed to the excellent electrochemical performance of the 88.9%S/PC.
Distribution pattern of tumor associated macrophages predicts the prognosis of gastric cancer (2017)

TAMs distribution pattern could be an independent prognostic factor for the OS of GC patients, and patients with MF/MS dominant pattern had worse outcomes.
Arthrodesis by the Distraction-Compression Method Using a Stainless Steel Implant (1988)

A new process for arthrodesis in humans is presented. The process has been used successfully in the cervical spine of horses and has potential for human use. The concept is encompassed in the process of an anterior cervical fusion and is an adaptation of that established practice but using an implant of stainless steel containing autogenous bone graft to encourage through-the-implant growth of bone. In the future, it may have use in the human spine and other joints.
Metabolic Engineering of Saccharomyces cerevisiae (2000)

Comprehensive knowledge regarding Saccharomyces cerevisiae has accumulated over time, and today S. cerevisiae serves as a widley used biotechnological production organism as well as a eukaryotic model system. The high transformation efficiency, in addition to the availability of the complete yeast genome sequence, has facilitated genetic manipulation of this microorganism, and new approaches are constantly being taken to metabolicially engineer this organism in order to suit specific needs. In this paper, strategies and concepts for metabolic engineering are discussed and several examples based upon selected studies involving S. cerevisiae are reviewed. The many different studies of metabolic engineering using this organism illustrate all the categories of this multidisciplinary field: extension of substrate range, improvements of producitivity and yield, elimination of byproduct formation, improvement of process performance, improvements of cellular properties, and extension of product range including heterologous protein production.
Remodeling of Yeast Genome Expression in Response to Environmental Changes (2001)

We used genome-wide expression analysis to explore how gene expression in Saccharomyces cerevisiae is remodeled in response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity. The results demonstrate that more than half of the genome is involved in various responses to environmental change and identify the global set of genes induced and repressed by each condition. These data implicate a substantial number of previously uncharacterized genes in these responses and reveal a signature common to environmental responses that involves approximately 10% of yeast genes. The results of expression analysis with MSN2/MSN4 mutants support the model that the Msn2/Msn4 activators induce the common response to environmental change. These results provide a global description of the transcriptional response to environmental change and extend our understanding of the role of activators in effecting this response.
Imaging elastic properties of biological tissues by low-frequency harmonic vibration (2003)

The elastic properties of soft tissues are closely related to their structure, biological conditions, and pathology. For years, physicians have used palpation as a crude elasticity measurement tool to diagnose diseases in the human body. Based on this simple concept, but using modern technology, several elasticity imaging schemes have been developed during the past two decades. In this paper, we present two elasticity imaging methods that use a low-frequency (Hz to kHz range) harmonic force to excite the tissue. The first method, called magnetic resonance elastography (MRE), uses a phase sensitive magnetic resonance technique to detect tissue motion. Excitation is usually performed with a mechanical actuator on the surface of the body, although other excitation methods are possible. In the second method, called vibro-acoustography, the radiation force from focused ultrasound is used for excitation in a limited region within the tissue. Tissue motion is detected by measuring the acoustic field emitted by the object in response to the vibration. The resulting images in both methods can be related to the dynamics of the object at the excitation frequency. The spatial resolution of MRE and vibro-acoustography images is in the millimeter and sub-millimeter ranges, respectively. Here, we present the theory and physical principles of MRE and vibro-acoustography and describe their performances. We also present results of experiments on various human tissues, including breast, brain, and vessels. Finally, we discuss potential clinical application of these two imaging methods.
Dephosphorylation of the C-terminal Tyrosyl Residue of the DNA Damage-related Histone H2A.X Is Mediated by the Protein Phosphatase Eyes Absent (2009)

In mammalian cells, the DNA damage-related histone H2A variant H2A.X is characterized by a C-terminal tyrosyl residue, Tyr-142, which is phosphorylated by an atypical kinase, WSTF. The phosphorylation status of Tyr-142 in H2A.X has been shown to be an important regulator of the DNA damage response by controlling the formation of gammaH2A.X foci, which are platforms for recruiting molecules involved in DNA damage repair and signaling. In this work, we present evidence to support the identification of the Eyes Absent (EYA) phosphatases, protein-tyrosine phosphatases of the haloacid dehalogenase superfamily, as being responsible for dephosphorylating the C-terminal tyrosyl residue of histone H2A.X. We demonstrate that EYA2 and EYA3 displayed specificity for Tyr-142 of H2A.X in assays in vitro. Suppression of eya3 by RNA interference resulted in elevated basal phosphorylation and inhibited DNA damage-induced dephosphorylation of Tyr-142 of H2A.X in vivo. This study provides the first indication of a physiological substrate for the EYA phosphatases and suggests a novel role for these enzymes in regulation of the DNA damage response.