gebhart/patrepeval huggingface dataset:
Membrane properties of rat embryonic multipotent neural stem cells (2003)

We have characterized several potential stem cell markers and defined the membrane properties of rat fetal (E10.5) neural stem cells (NSC) by immunocytochemistry, electrophysiology and microarray analysis. Immunocytochemical analysis demonstrates specificity of expression of Sox1, ABCG2/Bcrp1, and shows that nucleostemin labels both progenitor and stem cell populations. NSCs, like hematopoietic stem cells, express high levels of aldehyde dehydrogenase (ALDH) as assessed by Aldefluor labeling. Microarray analysis of 96 transporters and channels showed that Glucose transporter 1 (Glut1/Slc2a1) expression is unique to fetal NSCs or other differentiated cells. Electrophysiological examination showed that fetal NSCs respond to acetylcholine and its agonists, such as nicotine and muscarine. NSCs express low levels of tetrodotoxin (TTX) sensitive and insensitive sodium channels and calcium channels while expressing at least three kinds of potassium channels. We find that gap junction communication is mediated by connexin (Cx)43 and Cx45, and is essential for NSC survival and proliferation. Overall, our results show that fetal NSCs exhibit a unique signature that can be used to determine their location and assess their ability to respond to their environment.
Face recognition in unconstrained videos with matched background similarity (2011)

Recognizing faces in unconstrained videos is a task of mounting importance. While obviously related to face recognition in still images, it has its own unique characteristics and algorithmic requirements. Over the years several methods have been suggested for this problem, and a few benchmark data sets have been assembled to facilitate its study. However, there is a sizable gap between the actual application needs and the current state of the art. In this paper we make the following contributions. (a) We present a comprehensive database of labeled videos of faces in challenging, uncontrolled conditions (i.e., `in the wild'), the `YouTube Faces' database, along with benchmark, pair-matching tests <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> . (b) We employ our benchmark to survey and compare the performance of a large variety of existing video face recognition techniques. Finally, (c) we describe a novel set-to-set similarity measure, the Matched Background Similarity (MBGS). This similarity is shown to considerably improve performance on the benchmark tests.
Reactions of some main group metals with diphenyl disulphide and diphenyl diselenide (1988)

Indium reacts with both Ph2S2 and Ph2Se2 in refluxing toluene to give the compounds In(EPh)3(E = S or Se) in high yield. Under similar conditions tin gives Sn(EPh)4. Thallium reacts with Ph2Se2 to form TI(SePh), but does not react with Ph2S2. Neither zinc nor gallium reacts with Ph2S2 or Ph2Se2. With mixtures of Ph2E2 and I2, indium yields the previously unreported InI(EPh)2 compounds. The reactions of In(SePh)3 are those of a typical indium(III) Lewis acid. Possible factors affecting the reactions of metals with Ph2S2 or Ph2Se2 are briefly discussed.
Correlation Between Surface Free Energy and Surface Constitution (1992)

Self-assembled monolayers (SAMs) of alkylsiloxanes on elastomeric PDMS (polydimethylsiloxane) were used as model systems to study interactions between surfaces. Surface free energies (gammasv) of these chemically modified surfaces were estimated by measuring the deformations that resulted from the contact between small semispherical lenses and flat sheets of the elastomer under controlled loads. The measured surface free energies correlated with the surface chemical compositions of the SAMs and were commensurate with the values estimated from the measurements of contact angles. This study provides direct experimental evidence for the validity of estimates of the surface free energies of low-energy solids obtained from contact angles.
Solid-Liquid Phase Transfer Catalysis Without Solvent: Further Improvement in SNAr Reactions (1990)

Abstract Solid-liquid PTC without added solvent efficiently promotes SNAr reactions of a variety of anionic nucleophiles generated in situ. This methodology is applied with success to some examples concerning non-activated aromatic systems. TDA-1 is the most effective catalyst.
PARP Inhibitor Development for Systemic Cancer Targeting (2007)

Poly(ADP-ribose) polymerase 1 (PARP-1) is a DNA-binding enzyme that is activated by DNA breaks, converting them into an intracellular signal via poly(ADP-ribosyl)ation of nuclear proteins. Negatively charged polymers of ADP-ribose (PAR) attached to PARP-1 itself and histones lead to chromatin relaxation, facilitating the access of base excision/single strand break repair proteins and activating these repair enzymes. PARP inhibitors have been developed to investigate the role of PARP-1 in cell biology and to overcome DNA repair-mediated resistance of cancer cells to cytotoxic therapy. Since the early benzamide inhibitors of the 1980s PARP inhibitors, developed through structure-activity relationships and crystal structure-based drug design, that are 1,000 x more potent have been identified. These novel PARP inhibitors have been shown to enhance the antitumour activity of temozolomide (a DNA-methylating agent), topoisomerase poisons and ionising radiation in advanced pre-clinical studies and are now under clinical evaluation. PARP inhibitors can also selectively kill cells and tumours with homozygous defects in the hereditary breast cancer genes, BRCA1 and BRCA2.
Adenosine receptor agonists: synthesis and biological evaluation of 1-deaza analogs of adenosine derivatives (1988)

In a search for more selective A1 adenosine receptor agonists, N6-[(R)-(-)-1-methyl-2-phenethyl]-1-deazaadenosine (1-deaza-R-PIA, 3a), N6-cyclopentyl-1-deazaadenosine (1-deazaCPA, 3b), N6-cyclohexyl-1-deazaadenosine (1-deazaCHA, 3c), and the corresponding 2-chloro derivatives 2a-c were synthesized from 5,7-dichloro-3-beta-D-ribofuranosyl-3H-imidazo[4,5-b]pyridine. On the other hand, N-ethyl-1'-deoxy-1'-(1-deaza-6-amino-9H-purin-9-yl)-beta-D-ribofuranu ronamide (1-deazaNECA, 10) was prepared from 7-nitro-3-beta-D-ribofuranosyl-3H-imidazo[4,5-b]pyridine, in an attempt to find a more selective A2 agonist. The activity of all deaza analogues at adenosine receptors has been determined in adenylate cyclase and in radioligand binding studies. 1-DeazaNECA proved to be a nonselective agonist at both subtypes of the adenosine receptor. It is about 10-fold less active than NECA but clearly more active than the parent compound 1-deazaadenosine as an inhibitor of platelet aggregation and as a stimulator of cyclic AMP accumulation. The N6-substituted 1-deazaadenosines largely retain the A1 agonist activity of their parent compounds, but lose some of their A2 agonist activity. This results in A1-selective compounds, of which N6-cyclopentyl-2-chloro-1-deazaadenosine (1-deaza-2-Cl-CPA, 2b) was identified as the most selective agonist at A1 adenosine receptors so far known. The activity of all 1-deaza analogues confirms that the presence of the nitrogen atom at position 1 of the purine ring is not critical for A1 receptor mediated adenosine actions.
The preclinical pharmacology of WP1066, a potent small molecule inhibitor of the JAK2/STAT3 pathway (2006)

4853 The Stat3 pathway, constitutively activated in many cancers, is associated with the regulation of many survival proteins including survivin, Mcl-1, and the Bcl family. Inhibition of Stat3 signaling leads to an inhibition of cancer cell growth and to the induction of apoptosis. A number of attempts have been made to abrogate Stat3 activity, including the use of ligands to inhibit upstream signaling events or silencing Stat3 with oligonucleotides, none of which have been successful in vivo. We report here on the first potent small molecule inhibitor of Stat3 with demonstrated in vivo activity. Studies of WP1066 in our laboratories demonstrated proapoptotic and antiproliferative activity at concentrations of 3-5 μM, in vitro, in a variety of tumor cell types. In order to determine the utility of this compound in vivo we examined the tissue stability, pharmacokinetics, drug distribution, and bioavailability in CD1 mice. Briefly, animals (10 per timepoint) were administered WP1066 (10 and 40 mg/kg) as an IV bolus and sacrificed at various out to 24 hours post-dose. Tissues were harvested and following extraction analyzed for WP1066 content using tandem LC/MS. In vitro studies were also conducted to determine the overall stability of this molecule in rodent plasma. For oral bioavailability studies animals were dosed by gavage with 40 mg/kg and samples obtained over the same 24 hour period. The mean achieved peak plasma concentrations following 10 and 40 mg/kg IV doses were 1.05 and 4.31 μM respectively. Mean drug half life was 4.5 hours and terminal concentrations measured at 12 and 18 hours were 0.03 and 0.13 μM, at the low and high doses, respectively. Tissue stability studies demonstrated an in vitro plasma half-life of 2.6 hrs. Preliminary oral bioavailability studies yielded mean peak plasma concentrations of > 1 μM and an estimated bioavailability of 0.2. Studies of U87 tumor bearing mice given drug by IV bolus demonstrated an accumulation of WP1066 in tumor tissue many fold greater than the simultaneously measured plasma concentration. These studies coupled with our in vivo efficacy studies indicate that WP1066 is the first small molecule inhibitor of Stat3 capable of achieving and maintaining tissue concentrations associated with drug activity in vivo.
The Complete Sequence, Expression in Escherichia Coli, Purification and Some Properties of Carbonic Anhydrase from Neisseria Gonorrhoeae (1997)

The complete nucleotide sequence of the carbonic anhydrase gene from Neisseria gonorrhoeae has been determined. The gene encodes a 252-residue polypeptide with a molecular mass of 28085 Da. The gene has been cloned and overexpressed in Escherichia coli, and the enzyme has been purified. A 26-residue signal peptide is cleaved off by the E. coli processing machinery. Thus, the isolated enzyme contains 226 amino acid residues with a molecular mass of 25314 Da. Most of the enzyme seems to be produced as a soluble protein located in the periplasm of E. coli. The enzyme is homologous to carbonic anhydrases from the animal kingdom; it is an alpha-carbonic anhydrase. A comparison with the amino acid sequences of human carbonic anhydrases I and II suggests that the secondary structures are essentially intact in the bacterial enzyme but that several loops are much shorter than in the human forms. Most of the active-site residues are identical to those found in the high-activity human isozyme II. The bacterial enzyme has a high CO2 hydration activity with a k(cat) of 1.1 x 10(6) s(-1) and Km of 20 mM at pH 9 and 25 degrees C. The enzyme also catalyzes the hydrolysis of 4-nitrophenyl acetate. The pH/rate profile can be described as a titration curve with pKa of 6.7 and a maximal value of the catalytic second-order rate constant, k(enz), of 130 M(-1) x s(-1).
Nonchromosomal Antibiotic Resistance in Bacteria: Genetic Transformation of Escherichia coli by R-Factor DNA (1972)

Transformation of E. coli cells treated with CaCl(2) to multiple antibiotic resistance by purified R-factor DNA is reported. Drug resistance is expressed in a small fraction of the recipient bacterial population almost immediately after uptake of DNA, but full genetic expression of resistance requires subsequent incubation in drugfree medium before antibiotic challenge. Transformed bacteria acquire a closed circular, transferable DNA species having the resistance, fertility, and sedimentation characteristics of the parent R factor. Covalently-closed, catenated, and open (nicked) circular forms of R-factor DNA are all effective in transformation, but denaturation and sonication abolish the transforming ability of R-factor DNA in this system.
Planning for Semantic Web Services. (2004)

Using Semantic Web ontologies to describe Web Services has proven to be useful for various different tasks including service discovery and composition.
Beta 2-microglobulin is not required for cell surface expression of the murine class I histocompatibility antigen H-2Db or of a truncated H-2Db. (1986)

beta 2-Microglobulin (beta 2m) has been thought essential for transport of all major histocompatibility complex class I antigens to the cell surface. Here, we show that the mouse class I antigen H-2Db is expressed at the cell surface even when there is no beta 2m present within the cell. This was established by transfecting the H-2Db gene into the R1E cell line, which lacks beta 2m. The conformation of the Db antigen expressed by the R1E transfectant is very different from that of the native molecule. This Db antigen is not recognized by Db-allospecific and Db-restricted cytotoxic T lymphocytes or by most monoclonal antibodies to the native Db. We show further that a deletion construct of the Db gene, which consists of exon 1 linked to exons 4-8, expresses a truncated Db antigen lacking domains 1 and 2 [Db-(1 + 2)] at the cell surface after transfection into the R1E line. Previous biochemical and crystallographic data have indicated that domain 3 is associated with beta 2m; unexpectedly, Db-(1 + 2) does not associate with beta 2m when the mouse beta 2mb gene is transfected into the R1E transfectant expressing the truncated Db. This suggests that interactions with domains 1 and 2 are important for the paired association of domain 3 and beta 2m in the native Db antigen.
Synthesis and Aminoacylation of 3′-Amino-3′-deoxy Transfer RNA and Its Activity in Ribosomal Protein Synthesis (1973)

3'-amino-3'-deoxy adenosine was enzymatically converted into 3'-amino-3'-deoxy ATP. This ATP analogue was incorporated into the 3'-terminal adenosine position of Escherichia coli tRNA. The modified tRNA was aminoacylated with phenylalanine by use of E. coli phenylalanyl tRNA synthetase. The phenylalanine was attached to the 3'-amino group of the tRNA, as shown by its high resistance to base-catalyzed hydrolysis in contrast with the normal lability of phenylalanyl-tRNA. Aminoacyl tRNA synthetases charge the 3'-amino-3'-deoxy tRNA with kinetics that are similar to those of the charging reaction in which normal tRNA is the substrate. When phenylalanyl-3'-amino-3'-deoxy tRNA is used in a protein-synthesizing system directed by poly(U) in vitro, this molecule is capable of receiving an acetyl-phenylalanine from the donor site of the ribosome. However, the ribosome is unable to cleave the amide bond connecting phenylalanine to the tRNA molecule; hence, the phenylalanyl-3'-amino-3'-deoxy tRNA has acceptor but not donor activity in protein synthesis. Failure of the ribosome to cleave the amide bond may be due to its greater stability relative to the normal ester bond. However, it may also be due to the fact that the isomerization of the peptidyl chain between the 2' and 3' positions of adenosine is prevented due to the amide bond at the 3' position, and cleavage may normally occur with the peptidyl chain on the 2' position of adenosine.
The gene specifying RNase E (rne) and a gene affecting mRNA stability (ams) are the same gene (1991)

A DNA clone complementing the rne-3071 mutation has been expressed and localized in the physical map of Escherichia coli. The DNA fragment from this clone was localized to the region of the E. coli chromosome where the rne-3071 mutation has been mapped. The position of this DNA fragment in the E. coli chromosome, the size of the product directed by this DNA fragment (110,000 Da), the restriction map of this fragment, the fact that the same clone complements the ams mutation, and the observation that the rne-3071 and the ams mutations cause similar patterns of RNA synthesis, show that the rne gene--a gene specifying the processing endonuclease RNase E--and the ams gene--a gene that affects mRNA stability--are identical.
Tumor Necrosis Factor α-dependent Drug Resistance to Purine and Pyrimidine Analogues in Human Colon Tumor Cells Mediated through IKK (2004)

Development of drug resistance in cancer is one of the main challenges in chemotherapy, and many mechanisms are still unknown. In this study, we show that tumor necrosis factor alpha (TNFalpha) increases postdrug survival from 5-fluoro-2'-deoxyuridine (FdUrd) in two human colon tumor cell lines. This resulted in the development of drug-resistant cells in a TNFalpha-dependent manner. Interestingly, although the drug-resistant cells were selected using FdUrd, they are also resistant to a number of other antimetabolites in the DNA synthesis pathway in a TNFalpha-dependent manner. Only in the drug-resistant cells (p35-colo201) TNFalpha treatment resulted in G(0)-G(1) arrest but not in the parental colo201 and other cell types. Blocking TNFalpha-induced cell cycle arrest sensitized drug-resistant cells to FdUrd. TNFalpha-induced cell cycle arrest required IKK. IKK inhibition by a small molecule inhibitor or by the knockdown of IKKalpha, IKKbeta, or RelA/p65 using siRNA, but not the inhibition of JNK, MEK, p38, or caspase-8 pathways, blocked TNFalpha-induced G(0)-G(1) arrest and restored sensitivity to FdUrd of drug-resistant cells. TNFalpha reduced the transcripts and protein levels of phosphorylated retinoblastoma protein (Rb), Rb, E2F1, and Cdk4 only in drug-resistant p35-colo201 cells. This effect of TNFalpha was reversed by IKK inhibitor, suggesting that TNFalpha-induced cell cycle arrest is probably due to the reduction of Rb, E2F1, and Cdk4. Taken together, this study shows that, in vitro, TNFalpha-induced cell cycle arrest through IKK can provide a mechanism for the development of drug resistance to anti-cancer drugs, purine and pyrimidine analogues.
Alkylating Polymers: Resin-Released Carbenium Ions as Versatile Reactive Intermediates in Polymer-Assisted Solution-Phase Synthesis (2001)

Solid-supported diazoalkane analogues for the smooth and clean esterifications of carboxylic acids [Eq. (1)] as well as of complex compound mixtures: the alkylating polymers presented here were synthesized as solid-supported 3-alkyl-1-aryltriazenes and are capable of releasing carbenium ions following acidic activation.
Substance p and arthritis: analysis of plasma and synovial fluid levels (1990)

The uncadecapeptide substance P (SP), which is localized in peripheral and central terminals of afferent nerve fibers with polymodal nociceptors, has recently been implicated as having a neurogenic, inflammatory role in experimental arthritis. We used a radioimmunoassay to measure SP levels in plasma and synovial fluid samples from patients with rheumatoid arthritis (RA), osteoarthritis (OA), Reiter's syndrome (RS), and posttraumatic arthritis, as well as in plasma samples from 13 normal subjects. Plasma SP levels in RS patients exceeded levels in RA and OA patients, which in turn exceeded levels in posttrauma patients and in normal subjects. Synovial fluid SP levels exceeded respective plasma levels for all groups, except in RS patients, in whom the plasma level was not significantly different from that in synovial fluid. SP levels in synovial fluid of RA, OA, and RS patients did not differ significantly from each other, but the level in posttrauma patients was higher than in all other groups (P less than 0.005). These studies demonstrate localized intraarticular SP release, and significant plasma/synovial fluid SP concentration gradients in several forms of arthritis.
Premixed burner experiments: Geometry, mixing, and flame structure issues (1995)

This research program is exploring techniques for improved fuel-air mixing, with the aim of achieving combustor operations up to stoichiometric conditions with minimal NO{sub x} and maximum efficiency. The experimental studies involve the use of a double-concentric natural gas burner that is operable in either premixed or non-premixed modes, and the system allows systematic variation of equivalence ratio, swirl strength shear length region and flow momentum in each annulus. Flame structures formed with various combinations of swirl strengths, flow throughput and equivalence ratios in premixed mode show the significant impact of swirl flow distribution on flame structure emanating from the mixedness. This impact on flame structure is expected to have a pronounced effect on the heat release rate and the emission of NO{sub x}. Thus, swirler design and configuration remains a key factor in the quest for completely optimized combustion. Parallel numerical studies of the flow and combustion phenomena were carried out, using the RSM and the k-E turbulence models. These results have not only indicated the strengths and limitations of CFD in performance and pollutants emission predictions, but have provided guidelines on the size and strength of the recirculation produced and the spatio-temporal structure of the combustion flowfield. The first stage of parametric studies on geometry and operational parameters at Morgan State University have culminated in the completion of a one-dimensional flow code that is integrated with a solid, virtual model of the existing premixed burner. This coupling will provide the unique opportunity to study the impact of geometry on the flowfield and vice-versa, with particular emphasis on concurrent design optimization.
A physical model to predict stiction in MEMS (2002)

One of the most important reliability problems in micro-electromechanical systems (MEMSs) is stiction, the adhesion of contacting surfaces due to surface forces. After reviewing the known physical theory, and the measurement method commonly used to investigate stiction, we present a model that can be used to investigate the sensitivity of MEMS to stiction. It quantitatively predicts the surface interaction energy of surfaces in contact. Included in the model is the roughness of the contacting surfaces and the environmental conditions (humidity and temperature). This is done by describing the surface interaction energy as a function of the distance between the surfaces. This distance is not a unique number, but rather a distribution of distances. It is shown that, if we know this distribution, we can calculate the surface interaction energy. The model is suitable for the prediction of forces due to capillary condensation and molecular interactions.
Large-Area Graphene Films by Simple Solution Casting of Edge-Selectively Functionalized Graphite (2011)

We report edge-selective functionalization of graphite (EFG) for the production of large-area uniform graphene films by simply solution-casting EFG dispersions in dichloromethane on silicon oxide substrates, followed by annealing. The resultant graphene films show ambipolar transport properties with sheet resistances of 0.52-3.11 kΩ/sq at 63-90% optical transmittance. EFG allows solution processing methods for the scalable production of electrically conductive, optically transparent, and mechanically robust flexible graphene films for use in practice.
The Lateral Amygdaloid in Fear Conditioning Nucleus: Sensory Interface Amygdala (1990)

Previous work has implicated projections from the acoustic thalamus to the amygdala in the classical conditioning of emotional responses to auditory stimuli. The purpose of the present studies was to determine whether the lateral amygdaloid nucleus (AL), which is a major subcortical target of projections from the acoustic thalamus, might be the sensory interface of the amygdala in emotional conditioning. Lesions were placed in AL of rats and the effects on emotional conditioning were examined. Lesions of AL, but not lesions of the striatum above or the cortex adjacent to the AL, interfered with emotional conditioning. Lesions that only partially destroyed AL or lesions placed too ventrally that completely missed AL had no effect. AL lesions did not affect the responses elicited following nonassociative (random) training. AL is thus an essential link in the circuitry through which