gebhart/patrepeval huggingface dataset:
The Mechanisms of Carboxyalkylpyrrole Induced Angiogenesis (2012)

amazing science.I admire their academic rigor, intelligence, and integrity.While in Dr. Salomon's lab, I had the opportunity to work alongside him to synthesize CEP.With Dr. Salomon's guidance, I was able to fully understand the mechanisms of CEP biosynthesis, and mastered a number of complex chemistry synthesis procedures.In Dr. Byzova's lab, I have been granted the great opportunity to develop my understanding of complex in vitro and in vivo models depicting angiogenesis and tumorigenesis.Under Dr. Byzova's guidance, I play a key role in elucidating the molecular mechanism of CEP-induced angiogenesis.At Cleveland Clinic, I was exposed to a tremendous amount of high-end instrumentation, surgical skills, and protocols to carry out my research.All of my biological expertise that I have gathered is accredited to Dr. Byzova.I would not be the scientist I am today without her continued support.The staffs in Dr. Byzova's lab have also provided support in the form of friendship and technical help.Dr. Malinin and Dr. Kerr are two of my closest friends, who have both supported me at every step at Cleveland Clinic.They are always encouraging
A novel method for real time quantitative RT-PCR. (1996)

A novel approach to quantitative reverse transcriptase polymerase chain reaction (QC RT-PCR) using real time detection and the 5' nuclease assay has been developed. Cystic fibrosis transmembrane transductance regulator (CFTR) target mRNA is reverse transcribed, amplified, detected, and quantitated in real time. A fluorogenic probe was designed to detect the CFTR amplicon. Relative increase in 6-carboxy-fluorescein reporter fluorescent emission is monitored during PCR amplification using an analytical thermal cycler. An internal control template containing the same primer sequences as the CFTR amplicon, but a different internal sequence, has been designed as a control. An internal control probe with a reporter fluorescent dye tetrachloro-6-carboxy-fluorescein was designed to hybridize to the internal control amplicon. The internal control template is placed in each reaction tube and is used for quantitative analysis of the CFTR mRNA. This method provides a convenient and high-throughput format for QC RT-PCR.
Nucleophilic selectivity ratios of model and clinical alkylating agents by 4-(4'-nitrobenzyl)pyridine competition. (1981)

An aqueous acetone 4-(4'-nitrobenzyl)pyridine (NBP) assay for alkylating activity was used at neutral pH to reproduce the Swain-Scott-Ogston reactivity sequence of nucleophile n constants, based on bimolecular competition between NBP and added nucleophiles for alkylation by nitrogen mustards, methanesulfonate esters, methyl iodide, epichlorohydrin, or 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU). Nucleophile concentration-dependent decreases in the 540-nm NBP product(s) permitted determination of the second-order rate constant ratio, kx / knbp , for alkylation of the competing nucleophile/NBP. The slope, s *, of several log( kx / knbp ) values versus n constants closely paralleled literature Swain-Scott s constants and could be derived from the value for thiosulfate competition, 1og( kss2oo3 / knbp ). Alkylating activity, defined by the maximal 540-nm absorbance found for reactions up to 1 hr, was clearly related to an alkylating agent’s nucleophilic sensitivity [ s, s *, or log( kss2oo3 / knbp ) value]. Values of log( kSS2oo3 / knbp ) corresponding to s constants 0.78-1.39 for clinical alkylating agents increased in the order 1-chloroethyl-3-(4-methylcyclohexyl)-1-nitrosourea ∼ streptozotocin < 1,4-bis(methanesulfonoxy)butane ∼ BCNU < 1,1',l ''-phosphinothioylidynetrisaziridine ∼ methyl-bis(2-chloroethyl)amine < 4-[bis(2-chloroethyl)amino]-L-phenylalanine. NBP competition methods for determination of nucleophilic selectivity ratios should be highly useful for rapid identification of protective nucleophile-clinical alkylating agent combinations, and for classification of alkylating agent biological mechanism of action according to recent interpretations of alkylating agent kinetic behavior.

ACKNOWLEDGMENTS I am most grateful to Drs. Charles Heidelberger and George Olah for encouragement and helpful advice, and to Dr. Michael Colvin for his stimulating review of the manuscript. I am indebted to Margaret Soh for her patient typing.
Anti-EphA2 Antibodies with Distinct In Vitro Properties Have Equal In Vivo Efficacy in Pancreatic Cancer (2009)

The EphA2 receptor tyrosine kinase is overexpressed in a variety of human epithelial cancers and is a determinant of malignant cellular behavior in pancreatic adenocarcinoma cells. Moreover, it is expressed in tumor endothelium and its activation promotes angiogenesis. To better clarify the therapeutic potential of monoclonal antibodies (mAbs) directed to the EphA2 receptor, we generated a large number of mAbs by differential screening of phage-Ab libraries by oligonucleotide microarray technology and implemented a strategy for the rapid identification of antibodies with the desired properties. We selected two high-affinity and highly specific EphA2 monoclonal antibodies with different in vitro properties on the human pancreatic tumor cell line MiaPaCa2. One is a potent EphA2-agonistic antibody, IgG25, that promotes receptor endocytosis and subsequent degradation, and the second is a ligand antagonist, IgG28, that blocks the binding to ephrin A1 and is cross-reactive with the mouse EphA2 receptor. We measured the effect of antibody treatment on the growth of MiaPaCa2 cells orthotopically transplanted in nude mice. Both IgG25 and IgG28 had strong antitumor and antimetastatic efficacy. In vivo treatment with IgG25 determined the reduction of the EphA2 protein levels in the tumor and the phosphorylation of FAK on Tyr576 while administration of IgG28 caused a decrease in tumor vascularization as measured by immunohistochemical analysis of CD31 in tumor sections. These data show that in a pancreatic cancer model comparable therapeutic efficacy is obtained either by promoting receptor degradation or by blocking receptor activation.
Encoding Reality: Prediction-Assisted Cortical Learning Algorithm in Hierarchical Temporal Memory (2015)

In the decade since Jeff Hawkins proposed Hierarchical Temporal Memory (HTM) as a model of neocortical computation, the theory and the algorithms have evolved dramatically. This paper presents a detailed description of HTM's Cortical Learning Algorithm (CLA), including for the first time a rigorous mathematical formulation of all aspects of the computations. Prediction Assisted CLA (paCLA), a refinement of the CLA is presented, which is both closer to the neuroscience and adds significantly to the computational power. Finally, we summarise the key functions of neocortex which are expressed in paCLA implementations.
Fluorescent postlabelling of modified DNA bases. (1993)

Postlabelling of modified DNA bases by methods other than the 32P method has attracted little attention to date. Three approaches using fluorescence have been made: (a) detection of a characteristic adduct-DNA functionality, e.g. reaction of cis-vicinal diols of PAH-DNA adducts with a boronate-containing fluorescent molecule; (b) reaction of modified nucleotides with a reactive fluorescent molecule, e.g. detection of 8-HOdG-5'-monophosphate by reaction with dansyl chloride; (c) reaction of modified DNA bases with reagents giving fluorescent products, e.g. derivatization of 7-MeGua with phenylmalondialdehyde (PhMal). Recent results in developing the latter approach are described. Reaction of a series of 7-alkylguanines, including 7-methyl-, 7-ethyl-, 7-(2-hydroxyethyl)-, 7-carboxymethyl-, 7-(2-carboxyethyl)- and 7-(2,3-dihydroxypropyl)-guanine, with PhMal gave fluorescent products showing similar spectral properties. The detection limit for fluorescence detection following reverse-phase HPLC separation was typically less than 1 pmol injected. In order to improve the sample clean-up before analysis, an antiserum has been prepared against the fluorescent derivative of 7-(2-carboxyethyl)guanine bound to carrier protein via the carboxyl group. The resulting antiserum cross-reacted with a number of PhMal derivatives.
Oxygen Selective Membranes for Li-Air (O2) Batteries (2012)

Lithium-air (Li-air) batteries have a much higher theoretical energy density than conventional lithium batteries and other metal air batteries, so they are being developed for applications that require long life. Water vapor from air must be prevented from corroding the lithium (Li) metal negative electrode during discharge under ambient conditions, i.e., in humid air. One method of protecting the Li metal from corrosion is to use an oxygen selective membrane (OSM) that allows oxygen into the cell while stopping or slowing the ingress of water vapor. The desired properties and some potential materials for OSMs for Li-air batteries are discussed and the literature is reviewed.
Glucagon-Like Peptides: Regulators of Cell Proliferation, Differentiation, and Apoptosis (2003)

Peptide hormones are secreted from endocrine cells and neurons and exert their actions through activation of G protein-coupled receptors to regulate a diverse number of physiological systems including control of energy homeostasis, gastrointestinal motility, neuroendocrine circuits, and hormone secretion. The glucagon-like peptides, GLP-1 and GLP-2 are prototype peptide hormones released from gut endocrine cells in response to nutrient ingestion that regulate not only energy absorption and disposal, but also cell proliferation and survival. GLP-1 expands islet mass by stimulating pancreatic beta-cell proliferation and induction of islet neogenesis. GLP-1 also promotes cell differentiation, from exocrine cells or immature islet progenitors, toward a more differentiated beta-cell phenotype. GLP-2 stimulates cell proliferation in the gastrointestinal mucosa, leading to expansion of the normal mucosal epithelium, or attenuation of intestinal injury in experimental models of intestinal disease. Both GLP-1 and GLP-2 exert antiapoptotic actions in vivo, resulting in preservation of beta-cell mass and gut epithelium, respectively. Furthermore, GLP-1 and GLP-2 promote direct resistance to apoptosis in cells expressing GLP-1 or GLP-2 receptors. Moreover, an increasing number of structurally related peptide hormones and neuropeptides exert cytoprotective effects through G protein-coupled receptor activation in diverse cell types. Hence, peptide hormones, as exemplified by GLP-1 and GLP-2, may prove to be useful adjunctive tools for enhancement of cell differentiation, tissue regeneration, and cytoprotection for the treatment of human disease.
Monolithic integration of erbium-doped amplifiers with silicon-on-insulator waveguides (2010)

Monolithic integration of Al2O3:Er3+ amplifier technology with passive silicon-on-insulator waveguides is demonstrated. A signal enhancement of >7 dB at 1533 nm wavelength is obtained. The straightforward wafer-scale fabrication process, which includes reactive co-sputtering and subsequent reactive ion etching, allows for parallel integration of multiple amplifier and laser sections with silicon or other photonic circuits on a chip.
Isothermal versus Non-isothermal Adsorption−Desorption Cycling of Triamine-Grafted Pore-Expanded MCM-41 Mesoporous Silica for CO<sub>2</sub> Capture from Flue Gas (2010)

CO2 adsorption−desorption isotherms for triamine-grafted pore-expanded mesoporous silica (TRI-PE-MCM-41) were measured up to 25 bar using the same adsorption and pretreatment temperatures at 298, 323, and 343 K and compared to CO2 adsorption data for 13X zeolite, aminated metal organic framework (Zn-Atz MOF), and Darco activated carbon (Darco-AC). Cyclic isothermal adsorption−desorption measurements of pure CO2 and a 10:90 CO2/N2 mixture were carried out using vacuum swing (VS) and concentration swing (CS) regeneration modes at 298 and 343 K, in dry and humid conditions, and compared to cyclic non-isothermal desorption measurements, i.e., temperature swing (TS) and temperature-vacuum swing (TVS) regeneration operations. In addition to high CO2 selectivity, it was found that, in comparison to the three other adsorbents, TRI-PE-MCM-41 exhibited higher CO2 uptake in the presence of a 10:90 CO2/N2 mixture in both dry and humid conditions. Cyclic experiments using VS regeneration mode at 343 K gave a similar CO2 uptake as the TS regeneration mode. Similar to liquid-phase CO2 absorption, SO2 had a deleterious effect on CO2 adsorption.
The capacity of asynchronous m-ary time hopping PPM UWB multiple access communication systems (2005)

Scholtz in (Proc. Military Comms. Conf., vol.2, p.447-450, 1993) introduced an ultra-wide bandwidth (UWB) time-hopping spread-spectrum code division multiple-access system employing a binary PPM signaling with performance analysis based on multiple-access interference represented by a Gaussian process. In this paper, the symbol error rate and the capacity of asynchronous M-ary PPM UWB are evaluated with a more precise statistical analysis of the multiuser interference which avoids the Gaussian approximation. It is shown that there is a significant error in using the Gaussian approximation as it over estimates the capacity of the M-ary PPM modulation.
TREATMENT OF SERIOUS INFECTIONS WITH CEFTRIAXONE (1989)

Introduction Serious, life threatening infections, areusually due to Gram negative aerobic bac-teria. Septicaemia with shock may developunless prompt effective treatment is insti-tuted. Aminoglycosides used to be the
Translocation t(10;14)(q11.2:q22.1) fusing the kinetin to the RET gene creates a novel rearranged form (PTC8) of the RET proto-oncogene in radiation-induced childhood papillary thyroid carcinoma. (2000)

Evaluation of 20 cases of radiation-induced childhood papillary thyroid carcinoma using fluorescence in situ hybridization demonstrated the presence of clonal translocations affecting the RET locus. Semiquantitative reverse transcription-PCR indicated overexpression of the RET tyrosine kinase (TK) domain in four cases. In two cases, the RET rearrangements PTC6 and PTC7 were identified and assigned to balanced translocations t(7;10)(q32;q11.2) and t(1;10)(p13;q11.2), respectively. In one case with a balanced translocation t(10;14)(q11.2;q22.1), 5' rapid amplification of cDNA ends revealed a novel type of RET oncogenic activation (PTC8), arising from a fusion of the 5' part of the kinectin (KTN1) gene to the TK domain of the RET gene. The presence of coiled-coil domains in the resulting ktn1/ret fusion protein suggests ligand-independent dimerization and thus constitutive activation of the ret TK domain.
Moving to the cloud: developing apps in the new world of cloud computing (2012)

Moving to the Cloud provides an in-depth introduction to cloud computing models, cloud platforms, application development paradigms, concepts and technologies. The authors particularly examine cloud platforms that are in use today. They also describe programming APIs and compare the technologies that underlie them. The basic foundations needed for developing both client-side and cloud-side applications covering compute/storage scaling, data parallelism, virtualization, MapReduce, RIA, SaaS and Mashups are covered. Approaches to address key challenges of a cloud infrastructure, such as scalability, availability, multi-tenancy, security and management are addressed. The book also lays out the key open issues and emerging cloud standards that will drive the continuing evolution of cloud computing.Includes complex case studies of cloud solutions by cloud experts from Yahoo! , Amazon, Microsoft, IBM, Adobe and HP Labs. Presents insights and techniques for creating compelling rich client applications that interact with cloud services. Demonstrates and distinguishes features of different cloud platforms using simple to complex API programming examples.
The Leimgruber-Batcho Indole Synthesis (1984)

The Leimgruber-Batch0 indole synthesis, which involves the reduction of 6-dimethylamino-2-nitrostyrenes, is reviewed along with applications and modifications thereof.P r e p a r a t i o n of 4-Aminoindole (36.Table 6 , e n t r y 37): 32To a s o l u t i o n o f 106 mg (0.4 -1) of enamine 35 i n 6.0 m l o f a c e t i c acid-water (2x1.v/v) was
Hollow-anode plasma source for molecular beam epitaxy of gallium nitride (1996)

GaN films have been grown by molecular beam epitaxy (MBE) using a hollow-anode nitrogen plasma source. The source was developed to minimize defect formation as a result of contamination and ion damage. The hollow-anode discharge is a special form of glow discharge with very small anode area. A positive anode voltage drop of 30–40 V and an increased anode sheath thickness leads to ignition of a relatively dense plasma in front of the anode hole. Driven by the pressure gradient, the ‘‘anode’’ plasma forms a bright plasma jet streaming with supersonic velocity towards the substrate. Films of GaN have been grown on (0001) SiC and (0001) Al2O3 at 600–800 °C. The films were investigated by photoluminescence, cathodoluminescence, x-ray diffraction, Rutherford backscattering, and particle-induced x-ray emission. The film with the highest structural quality had a rocking curve width of 5 arcmin, the lowest reported value for MBE growth to date.
Toxin, toxin-coregulated pili, and the toxR regulon are essential for Vibrio cholerae pathogenesis in humans. (1988)

Isogenic mutant strains of V. cholerae O1 lacking elements of a genetic regulon controlled by toxR and implicated in virulence were tested in volunteers. A deletion mutation in ctxA, the gene encoding the A subunit of cholera toxin, markedly attenuated disease symptoms without affecting intestinal colonization. Deletion of toxR, the gene encoding the cholera toxin-positive regulatory protein resulted in a diminution in colonizing capacity. A deletion mutation in tcpA, encoding the major subunit of the toxin coregulated pilus (regulated by toxR), abolished the colonizing capacity of this strain. These results show for the first time the role of a specific pilus structure in colonization of the human intestine by V. cholerae O1 and exemplify the significance of a genetic regulon in pathogenesis.
A 265-Base DNA Sequencing Read by Capillary Electrophoresis with No Separation Matrix (2010)

Electrophoretic DNA sequencing without a polymer matrix is currently possible only with the use of some kind of "drag-tag" as a mobility modifier. In free-solution conjugate electrophoresis (FSCE), a drag-tag attached to each DNA fragment breaks linear charge-to-friction scaling, enabling size-based separation in aqueous buffer alone. Here we report a 265-base read for free-solution DNA sequencing by capillary electrophoresis using a random-coil protein drag-tag of unprecedented length and purity. We identified certain methods of protein expression and purification that allow the production of highly monodisperse drag-tags as long as 516 amino acids, which are almost charge neutral (+1 to +6) and yet highly water-soluble. Using a four-color LIF detector, 265 bases could be read in 30 min with a 267-amino acid drag-tag, on par with the average read of current next-gen sequencing systems. New types of multichannel systems that allow much higher throughput electrophoretic sequencing should be much more accessible in the absence of a requirement for viscous separation matrix.
Functional Testing of Human Dopamine D <sub>1</sub> And D <sub>5</sub> Receptors Expressed in Stable camp-Responsive Luciferase Reporter Cell Lines (1993)

A large number of G-protein coupled receptors are known to modulate adenylyl cyclase activity. In order to find new compounds modulating the activity of specific receptor subtypes we developed a cellular screening system that measures the biological activity of drugs acting on receptors rather than merely their binding characteristics. The activity of the receptor coupling to the cAMP signal transduction pathway was measured via transcriptional activation of a reporter gene. A chinese hamster ovary cell line was stably transformed with a reporter plasmid containing the firefly luciferase gene under the transcriptional control of multiple cAMP responsive elements (CRE). This CRE reporter cell line exhibited 20 to 30-fold induction of luciferase activity upon stimulation of adenylyl cyclase with forskolin, but did not respond to dopamine agonists. Stable test cell lines were developed by transfecting reporter cell lines with human dopamine D1 and D5 receptor genes, respectively. Treatment of these test cell lines with dopamine receptor agonists and antagonists modulated the luciferase expression in a dose-dependent manner. The rank of potency of dopamine receptor agonists and antagonists was in agreement with reported data obtained from binding studies. The non-isotopic assay can be performed in microtiter plate format and is far less work intensive than the determination of adenylyl cyclase activity by direct cAMP measurement. This technology could also be utilized for discovery of new classes of compounds, e.g. allosteric effectors or non competitive ligands.
Metadata driven seamless content handover in ubiquitous environment (2004)

Seamless content handover across different terminal devices achieved by the association of metadata and network functions is discussed in terms of service, architecture and prototype system (MetaPORT). A network recognizes the context so that the content is automatically adapted to handovered terminal device. This is achieved by using TV-Anytime server-type broadcasting infrastructure as well as IETF presence management infrastructure as underlying capabilities. In order to deliver broadcast content over ubiquitous network, usage environment metadata (UEM) that describes terminal capabilities and presence is introduced and managed by UEM server, in addition to content metadata. The network recognizes terminal state and content at the same time to enable user-friendly content handover.
Monoclonal antibodies as tools in membrane biochemistry. Identification and partial characterization of the dicarboxylate transporter from pea leaf mitochondria. (1988)

Monoclonal antibodies specific for the dicarboxylate transporter of pea mitochondria were prepared and used to identify this substrate carrier. The hybridoma library was derived from mice that had been immunized with total mitochondrial membranes. The monoclonal antibodies specific for the dicarboxylate transporter were selected by screening hybridoma supernatants for their ability to inhibit malate- and succinate-dependent oxalacetate reduction by osmotically shocked pea leaf mitochondria. Three monoclonal antibodies were shown to be specific for the dicarboxylate transporter by their ability to 1) inhibit malate and succinate metabolism without affecting alpha-ketoglutarate, citrate, pyruvate, glycine, glutamate, or aspartate metabolism by mitochondria and 2) inhibit malate uptake by a partially purified transporter fraction reconstituted into asolectin vesicles. The dicarboxylate transporter was identified by Western blotting and immunoprecipitation and had an apparent molecular mass of 26,000 Da. The techniques described should prove useful for identifying a number of membrane proteins that can be assayed in situ but are difficult to assay following dissolution of the membrane.