gebhart/patrepeval huggingface dataset:
Femtosecond real-time probing of reactions. I. The technique (1988)

When a chemical bond is broken in a direct dissociation reaction, the process is so rapid that it has generally been considered instantaneous and therefore unobservable. But the fragments formed interact with one another for times on the order of 10−13 s after the photon has been absorbed. On this time scale the system passes through intermediate transition configurations; the totality of such configurations have been, in the recent literature, designated as ‘‘transition states.’’ Femtosecond transition-state spectroscopy (FTS) is a real-time technique for probing chemical reactions. It allows the direct observation of a molecule in the process of falling apart or in the process of formation. In this paper, the first in a series on femtosecond real-time probing of reactions, we examine the technique in detail. The concept of FTS is explored, and the interrelationship between the dynamics of chemical reactions and molecular potential energy surfaces is considered. The experimental method, which requires the generation of spectrally tunable femtosecond optical pulses, is detailed. Illustrative results from FTS experiments for several elementary reactions are presented, and we describe methods for relating these results to the potential energy surface(s).
Expression of Erwinia uredovora Phytoene Desaturase in Synechococcus PCC7942 Leading to Resistance against a Bleaching Herbicide (1994)

The gene coding for phytoene desaturase of the bacterium Erwinia uredovora (crtI) was inserted into the chromosome of the cyanobacterium Synechococcus PCC7942 strain R2-PIM8. For expression of crtI in the heterologous host, two constructs with different promoters were introduced into Synechococcus. In the first, crtI was fused to the 5[prime] region of the psbA gene of the xanthophycean microalga Bumilleriopsis filiformis. The second construct carried crtI inserted downstream of the neomycin phosphotransferase II gene (nptII) from the transposon Tn5. Expression of crtI under the control of the respective promoter was shown by immunodetection of the gene product. The functionality of the heterologously expressed phytoene desaturase CRTI in the transformants was demonstrated by enzymic assays. The transformants acquired very strong resistance toward the bleaching herbicide norflurazon.
Fas-Mediated Apoptosis Causes Elimination of Virus-Specific Cytotoxic T Cells in the Virus-Infected Liver (2001)

Immunity to allogeneic MHC Ags is weak in rodent livers, raising questions as to the mechanisms that might control responses in this organ. Infection with an adenovirus vector reveals that T cell-mediated immunity to nonself-Ags in the liver is self-limiting. Virus-induced liver injury decreases and coincides with disappearance of virus-specific CTL, concomitant to an increase of apoptotic T cells early after infection. But whereas death in CD4 cells is independent of Fas, perforin, and TNF-alpha, that of CD8 cells requires Fas and not perforin or TNF-alpha pathways. Fas ligand is expressed on liver-infiltrating cells, pointing to death by fratricide that causes almost complete disappearance of virus-specific CTL 4 wk after infection. CTL elimination is virus dose dependent, and high doses induced high alanine aminotransferase values, elevated expression of Fas ligand on CD8 cells, and increased CD8 cell migration into the infected liver.
The pro-oligonucleotide approach: solid phase synthesis and preliminary evaluation of model pro-dodecathymidylates (1998)

A modified phosphoramidite method has been designed for the solid-phase synthesis of two dodecathymidine phosphotriesters and two dodecathymidine thionophosphotriesters. In these analogs, each internucleoside link bears an S -acyl-2-thioethyl (Me-SATE or tBu-SATE) group removable upon esterase activation. Efficient synthesis of these lipophilic analogs was achieved thanks to the use of a photolabile linker anchored to the solid support in combination with thymidine-3'- O -phosphoramidites having a SATE group in place of the regular 2-cyanoethyl one. Both dodecathymidine phosphotriester and thionophosphotriester having S -acetyl-2-thioethyl groups were found to be stable in the presence of snake venom and calf spleen phosphodiesterases whereas, upon incubation in CEM cell extracts, they were selectively hydrolyzed to the anionic parent dodecathymidylate and dodecathymidine phosphorothioate, respectively. In addition, Me-SATE-protected dodecathymidine thionophosphotriester was stable in mouse and human sera as well as in human gastric juice. These results depict the potential of SATE-protected oligonucleotides as prodrugs of antisense oligonucleotides.
4‐Fluoroindole and Derivatives (1964)

Abstract 4‐Fluoroindole(VIII) has been prepared by a five‐step synthesis from 2‐fluoro‐6‐nitrotoluene (III). (VIII) has been converted into a number of N,N‐dialkylated 4‐fluorotryptamines.
The performance potential of multiple functional unit processors (1988)

In this paper, we look at the interaction of pipelining and multiple functional units in single processor machines. When implementing a high performance machine, a number of hardware techniques maybe used to improve the performance of the final system. Our goal is to gain an understanding of how each of these techniques contribute to performance improvement. As a basis for our studies we use a CRAY-like processor model and the issue rate (instructions per clock cycle) as the performance measure. We then systematically augment this base, non-pipelined, machine with more and more hardware features and evaluate the performance impact of each feature. We find, for example, that in non-vector machines, pipelining multiple function units does not provide significant performance improvements. Dataflow limits are then derived for our benchmark programs to determine the performance potential of each benchmark. In addition, other limits are computed which apply more realistic constraints on a computation. Based on these more realistic limits, we determine it is worthwhile to investigate the performance improvements that can be achieved from issuing multiple instructions each clock cycle. Several hardware approaches are evaluated for issuing multiple instructions each clock cycle.
Molecular Cloning of Human Fibroblast Hyaluronic Acid-binding Protein Confirms Its Identity with P-32, a Protein Co-purified with Splicing Factor SF2 (1996)

The purification of a 68-kDa hyaluronic acid-binding protein (HA-binding protein), a homodimer of 34 kDa that binds specifically to hyaluronic acid, has been reported earlier by us (Gupta, S., Batchu, R. B., and Datta, K. (1991) <i>Eur. J. Cell Biol.</i> 56, 58-67). Here, we report the isolation of a partial cDNA clone from a λ gt<sup>11</sup> cDNA expression library of human skin fibroblast by immunoscreening with HA-binding protein antiserum. The internal polypeptide sequence (83 residues) of the purified hyaluronic acid-binding protein is identical to the predicted protein sequence derived from hyaluronic acid-binding protein cDNA, suggesting the authenticity of the clone. Interestingly, this hyaluronic acid-binding protein cDNA sequence has complete homology with the cDNA sequence of a protein P-32, co-purified with the human pre-mRNA splicing factor SF2 (Krainer, A. R., 5eda, A., Kozak, D., and Binns, G.(1991) <i>Cell</i> 66, 383-394). Furthermore, the data on the N-terminal sequence of hyaluronic acid-binding protein and the predicted polypeptide of P-32 revealed the identical coding sequence of 209 amino acids for both the proteins. As the identity and functional characterization of P-32 have not yet been reported, P-32 cDNA was expressed in <i>Escherichia coli</i>, and the recombinant P-32 protein was purified by hyaluronic acid-Sepharose affinity chromatography. The recombinant P-32 protein showed immunocross-reactivity with the polyclonal antibodies raised against HA-binding protein. The predicted amino acid sequence of the protein fulfilled the minimal criteria for binding to hyaluronic acid, <i>i.e.</i> two basic amino acids flanking a seven-amino acid stretch, as reported for other hyaluronic acid-binding proteins. Furthermore, the hyaluronic acid affinity of the recombinant P-32 protein was confirmed by biotinylated hyaluronic acid binding assay. The binding of recombinant P-32 protein to biotinylated hyaluronic acid can be competed only with excess unlabeled hyaluronic acid, confirming its specificity toward hyaluronic acid. All these results suggest that both P-32, co-purified with the human pre-mRNA splicing factor SF2, and 34-kDa hyaluronic acid-binding protein reported by us are the same protein and that it is a new member of the hyaluronic acid- binding protein family, the "hyaladherins."
Macroporous and nanofibrous polymer scaffolds and polymer/bone‐like apatite composite scaffolds generated by sugar spheres (2006)

Scaffolds are crucial to tissue engineering/regeneration. In this work, a technique combining a unique phase-separation process with a novel sugar sphere template leaching process has been developed to produce three-dimensional scaffolds. The resulting scaffolds possess high porosities, well connected macropores, and nanofibrous pore walls. The technique advantageously controls macropore shape and size by sugar spheres, interpore opening size by assembly conditions (time and temperature of heat treatment), and pore wall morphology by phase-separation parameters. The bioactivity of a macroporous and nanofibrous poly(L-lactic acid) (PLLA) scaffold was demonstrated by the bone-like apatite deposition throughout the scaffold in a simulated body fluid (SBF). Preincorporation of nanosized hydroxyapatite eliminated the induction period and facilitated the apatite growth in the SBF. Interestingly, the apatite growth primarily occurred on the surface of the pores (internal and external) but not the interior of the nanofibrous network away from the pore surface. It was also noticed that the macropore size did not affect the apatite growth rate, while the interpore opening size did. The compressive modulus also increased substantially when a continuous apatite layer was formed on the pore walls of the scaffold. The resulting composite scaffold mimics natural bone matrix with the combination of an organic phase (a polymer such as PLLA) and an inorganic apatite phase. The demonstrated bioactivity of apatite layer, together with well-controlled macroporous and nanofibrous structures, makes the novel nanocomposite scaffolds desirable for bone tissue engineering.
Attenuated, Replication-Competent Herpes Simplex Virus Type 1 Mutant G207: Safety Evaluation of Intracerebral Injection in Nonhuman Primates (1999)

This study examined the safety of intracerebral inoculation of G207, an attenuated, replication-competent herpes simplex virus type 1 (HSV-1) recombinant, in nonhuman primates. Sixteen New World owl monkeys (Aotus nancymae [karyotype 1, formerly believed to be A. trivirgatus]), known for their exquisite susceptibility to HSV-1 infection, were evaluated. Thirteen underwent intracerebral inoculation with G207 at doses of 10(7) or 10(9) PFU, two were vehicle inoculated, and one served as an infected wild-type control and received 10(3) PFU of HSV-1 strain F. HSV-1 strain F caused rapid mortality and symptoms consistent with HSV encephalitis, including fever, hemiparesis, meningitis, and hemorrhage in the basal ganglia. One year after G207 inoculation, seven of the animals were alive and exhibited no evidence of clinical complications. Three deaths resulted from nonneurologic causes unrelated to HSV infection, and three animals were sacrificed for histopathologic examination. Two animals were reinoculated with G207 (10(7) PFU) at the same stereotactic coordinates 1 year after the initial G207 inoculation. These animals were alive and healthy 2 years after the second inoculation. Cerebral magnetic resonance imaging studies performed both before and after G207 inoculation failed to reveal radiographic evidence of HSV-related sequelae. Despite the lack of outwardly observable HSV pathology, measurable increases in serum anti-HSV titers were detected. Histopathological examination of multiple organ tissues found no evidence of HSV-induced histopathology or dissemination. We conclude that intracerebral inoculation of up to 10(9) PFU of G207, well above the efficacious dose in mouse tumor studies, is safe and therefore appropriate for human clinical trials.
The physiology of lactoferrin (2002)

This paper reviews our current knowledge of the structure and function of the iron-binding protein lactoferrin. In particular, it attempts to relate the various proposed physiological functions of lactoferrin to its most characteristic biochemical properties, i.e. its ability to bind iron and its highly basic nature. The extent to which various physiological functions can be considered as definitely established is critically reviewed, and suggestions for future research are proposed.
Chemically Induced Nephrotoxicity: Role of Metabolic Activation (1984)

Renal xenobiotic metabolism can result in production of electrophiles or free radicals that may covalently bind macromolecules or initiate lipid peroxidation. The mechanisms of renal xenobiotic metabolism may vary in different anatomical regions. Kidney cortex contains a cytochrome P-450 system while medulla contains a prostaglandin endoperoxidase. Recently cysteine conjugated-lyase has been implicated in production of reactive intermediates. Metabolic activation may be amplified by accumulation of xenobiotics within renal cells due to tubular concentrating and/or secretory mechanisms. Additionally, renal xenobiotic detoxicification can occur by conjugation with glucuronide, sulfate or glutathione.
Contact Angle, Wettability, and Adhesion (1964)

A review of the author's investigations of the equilibrium contact angles of pure liquids on low- and high-energy solid surfaces, both bare and covered with a condensed monomolecular adsorbed film, includes the critical surface tension of wetting and the effect of homology on spreading by pure liquids, the causes of nonspreading on high-energy surfaces, and the existence and properties of autophobic liquids and oleophobic monolayers. Constitutive relationships are summarized in a table of critical surface tensions of wetting. The theory and application of the retraction method of preparing adsorbed monolayers from solution and the conditions for mixed films are presented. Studies of the wetting behavior of solutions of various surfactants and the resultant explanation of the function of a wetting agent are generalized to include nonaqueous systems. Following estimates of the reversible work of adhesion of liquids to solids, the part played by wetting in obtaining optimum adhesion by adhesives is outlined, and a fundamental explanation is given of constitutive effects in the development of strong adhesive joints. Future areas of research on wetting and adhesion are indicated.
Comparative Prime-Boost Vaccinations Using Semliki Forest Virus, Adenovirus, and ALVAC Vectors Demonstrate Differences in the Generation of a Protective Central Memory CTL Response against the P815 Tumor (2007)

Tumor-specific Ags are potential target molecules in the therapeutic treatment of cancer. One way to elicit potent immune responses against these Ags is to use recombinant viruses, which activate both the innate and the adaptive arms of the immune system. In this study, we have compared Semliki Forest virus (SFV), adenovirus, and ALVAC (poxvirus) vectors for their capacity to induce CD8(+) T cell responses against the P1A tumor Ag and to elicit protection against subsequent challenge injection of P1A-expressing P815 tumor cells in DBA/2 mice. Both homologous and heterologous prime-boost regimens were studied. In most cases, both higher CD8(+) T cell responses and better tumor protections were observed in mice immunized with heterologous prime-boost regimens, suggesting that the combination of different viral vectors is beneficial for the induction of an effective immune response. However, homologous immunization with SFV provided potent tumor protection despite a rather moderate primary CD8(+) T cell response as compared with mice immunized with recombinant adenovirus. SFV-immunized mice showed a rapid and more extensive expansion of P1A-specific CD8(+) T cells in the tumor-draining lymph node after tumor challenge and had a higher frequency of CD62L(+) P1A-specific T cells in the blood, spleen, and lymph nodes as compared with adenoimmunized mice. Our results indicate that not only the magnitude but in particular the quality of the CD8(+) T cell response correlates with tumor protection.
Selective reduction of fatty acid oxidation in colonocytes: Correlation with ulcerative colitis (1990)

Attempts were made to define which fatty acid (2:0 to 18:1) was optimally oxidized by isolated colonocytes (colonic epithelial cells) and to select inhibitors of fatty acid oxidation which would be analogous in their action to the inhibition of fatty acid oxidation observed in colonocytes involved with ulcerative colitis. Isolated colonic epithelial cells of Sprague-Dawley rats were used with 2-mercaptoacetate, dichloroacetate, 3-mercaptopropionate, 4-mercaptobutyrate, 4-sulfatebutyrate, 2-bromobutyrate, sulfite ions and nitrite ions. n-Butyrate (4:0) was maximally oxidized to CO2 and ketone bodies (mean value 5.46 mumols/min/g dry wt). Oxidation of butyrate to CO2 was diminished by 2-bromobutyrate, sulfite ions and all mercapto fatty acids. Both fatty acid oxidation and glucose oxidation were significantly inhibited by 2-bromobutyrate, while mercapto fatty acids and sulfite inhibited fatty acid oxidation (p less than 0.01) without significantly changing glucose oxidation. Observation with 2-mercaptoacetate and sulfite correlate with early changes of fatty acid oxidation observed in cases of ulcerative colitis, and warrant further study with isolated colonocytes of man.
A Novel Molecular Recognition Motif Necessary for Targeting Photoactivated Phytochrome Signaling to Specific Basic Helix-Loop-Helix Transcription Factors[W] (2004)

The phytochrome (phy) family of sensory photoreceptors (phyA to phyE) in Arabidopsis thaliana control plant developmental transitions in response to informational light signals throughout the life cycle. The photoactivated conformer of the photoreceptor Pfr has been shown to translocate into the nucleus where it induces changes in gene expression by an unknown mechanism. Here, we have identified two basic helix-loop-helix (bHLH) transcription factors, designated PHYTOCHROME-INTERACTING FACTOR5 (PIF5) and PIF6, which interact specifically with the Pfr form of phyB. These two factors cluster tightly with PIF3 and two other phy-interacting bHLH proteins in a phylogenetic subfamily within the large Arabidopsis bHLH (AtbHLH) family. We have identified a novel sequence motif (designated the active phytochrome binding [APB] motif) that is conserved in these phy-interacting AtbHLHs but not in other noninteractors. Using the isolated domain and site-directed mutagenesis, we have shown that this motif is both necessary and sufficient for binding to phyB. Transgenic expression of the native APB-containing AtbHLH protein, PIF4, in a pif4 null mutant, rescued the photoresponse defect in this mutant, whereas mutated PIF4 constructs with site-directed substitutions in conserved APB residues did not. These data indicate that the APB motif is necessary for PIF4 function in light-regulated seedling development and suggest that conformer-specific binding of phyB to PIF4 via the APB motif is necessary for this function in vivo. Binding assays with the isolated APB domain detected interaction with phyB, but none of the other four Arabidopsis phys. Collectively, the data suggest that the APB domain provides a phyB-specific recognition module within the AtbHLH family, thereby conferring photoreceptor target specificity on a subset of these transcription factors and, thus, the potential for selective signal channeling to segments of the transcriptional network.
Metabolic engineering of Clostridium acetobutylicum ATCC 824 for increased solvent production by enhancement of acetone formation enzyme activities using a synthetic acetone operon (1993)

The ability to genetically alter the product-formation capabilities of Clostridium acetobutylicum is necessary for continued progress toward industrial production of the solvents butanol and acetone by fermentation. Batch fermentations at pH 4.5, 5.5, or 6.5 were conducted using C. acetobutylicum ATCC 824 (pFNK6). Plasmid pFNK6 contains a synthetic operon (the "ace operon") in which the three homologous acetone-formation genas (adc, ctfA, and ctfB) are transcribed from the adc promoter. The corresponding enzymes (acetoacetate decarboxylase and CoA-transferase) were best expressed in pH 4.5 fermentations. However, the highest levels of solvents were attained at pH 5.5. Relative to the plasmid-free control strain at pH 5.5, ATCC 824 (pFNK6) produced 95%, 37%, and 90% higher final concentrations of acetone, butanol, and ethanol, respectively; a 50% higher yield (g/g) of solvents on glucose; and a 22-fold lower mass of residual carboxylic acids. At all pH values, the acetone-formation enzymes were expressed earlier with ATCC 824 (pFNK6) than in control fermentations, leading to earlier induction of acetone formation. Furthermore, strain ATCC 824 (pFNK6) produced butanol significantly earlier in the fermentation and produced significant levels of solvents at pH 6.5. Only trace levels of solvents were produced by strain ATCC 824 at pH 6.5. Compared with ATCC 824, a plasmid-control strain containing a vector without the ace operon also produced higher levels of solvents [although lower than those of strain ATCC 824 (pFNK6)] and lower levels of acids. Strains containing plasmid-borne derivatives of the ace operon, in which either the acetoacetate decarboxylase or CoA-transferase alone were expressed at elevated levels, produced acids and solvents at levels similar to those of the plasmid-control strain.
Valving in Microchannels via Electrodeposition on Solid Electrolytes (2005)

Microfluidic technology is currently being applied to analytical systems but suitable valving elements are proving to be difficult to implement. We have recently developed a novel way to electrically regulate flow through microchannels via a structure that can be made using readily available microfabrication techniques. An electrical signal is used to stimulate silver deposition on a thin AgGe-Se solid electrolyte layer in a small region of a channel. The electrodeposited silver, which is a high surface area fractal structure less than 1 Pm in height and several hundred Pm long, changes the fluid-surface interaction. In this paper we demonstrate that this effect can be used to regulate pressure-driven flow in a microchannel.
A Role for DNA-PK in Retroviral DNA Integration (1999)

Retroviral DNA integration is catalyzed by the viral protein integrase. Here, it is shown that DNA-dependent protein kinase (DNA-PK), a host cell protein, also participates in the reaction. DNA-PK-deficient murine scid cells infected with three different retroviruses showed a substantial reduction in retroviral DNA integration and died by apoptosis. Scid cell killing was not observed after infection with an integrase-defective virus, suggesting that abortive integration is the trigger for death in these DNA repair-deficient cells. These results suggest that the initial events in retroviral integration are detected as DNA damage by the host cell and that completion of the integration process requires the DNA-PK-mediated repair pathway.