gebhart/patrepeval huggingface dataset:
Protein kinase A-catalyzed phosphorylation of heat shock protein 60 chaperone regulates its attachment to histone 2B in the T lymphocyte plasma membrane (1998)

Accumulating evidence suggests that the mitochondrial molecular chaperone heat shock protein 60 (hsp60) also can localize in extramitochondrial sites. However, direct evidence that hsp60 functions as a chaperone outside of mitochondria is presently lacking. A 60-kDa protein that is present in the plasma membrane of a human leukemic CD4(+) CEM-SS T cell line and is phosphorylated by protein kinase A (PKA) was identified as hsp60. An 18-kDa plasma membrane-associated protein coimmunoprecipitated with hsp60 and was identified as histone 2B (H2B). Hsp60 physically associated with H2B when both molecules were in their dephospho forms. By contrast, PKA-catalyzed phosphorylation of both hsp60 and H2B caused dissociation of H2B from hsp60 and loss of H2B from the plasma membrane of intact T cells. These results suggest that (i) hsp60 and H2B can localize in the T cell plasma membrane; (ii) hsp60 functions as a molecular chaperone for H2B; and (iii) PKA-catalyzed phosphorylation of both hsp60 and H2B appears to regulate the attachment of H2B to hsp60. We propose a model in which phosphorylation/dephosphorylation regulates chaperoning of H2B by hsp60 in the plasma membrane.
Cloning of chicken lysozyme structural gene sequences synthesized in vitro (1978)

Double-stranded chicken lysozyme cDNA was synthesized from an oviduct mRNA fraction enriched for lysozyme mRNA. The ds-cDNA was inserted into the BamHI site of plasmid pBR322 using chemically synthesized DNA linker molecules containing the BamHI restriction endonuclease cleavage site. After bacterial transformation, colonies carrying lysozyme DNA were identified by hybridization with highly purified lysozyme cDNA. The 555 base pairs long cloned DNA fragment of one recombinant plasmid was isolated and characterized by restriction endonuclease digestion. The DNA sequence of selected parts of the inserted DNA is as predicted from the amino acid sequence of prelysozyme. The sequence data allows the unambiguous location of the coding region within lysozyme mRNA.
FIR filter optimization as preemphasis of high-speed backplane data transmission (2004)

FIR filter preemphasis has been used to counteract intersymbol interference (ISI) in high-speed backplane data transmission. Backplane channel characteristics are first analyzed. It is found that channel group delay distortion is also a major ISI contributor in addition to amplitude attenuation. A MATLAB program is then described for optimization of the FIR filter under the LMS criterion. Both symbol-spaced FIR (SSF) and fractionally-spaced FIR (FSF) are comparatively studied at different data rates. The determination of tap number and preference of FSF to SSF are discussed.
Thermally Stable Nanocrystalline TiO2 Photocatalysts Synthesized via Sol−Gel Methods Modified with Ionic Liquid and Surfactant Molecules (2006)

Recently, sol−gel methods employing ionic liquids (ILs) have shown significant implications for the synthesis of well-defined nanostructured inorganic materials. Herein, we synthesized nanocrystalline TiO2 particles via an alkoxide sol−gel method employing a water-immiscible room temperature IL (1-butyl-3-methylimidazolium hexafluorophosphate, [bmim][PF6]) as a new solvent medium and further modified with nonionic surfactant (polyoxyethylenesorbitan monooleate) as a pore templating material. Detailed information on the preparative method, synthesis route and mechanism, crystallographic and structural properties, and photocatalytic activity of the TiO2 particles is described. The possible rationale for the formation of nanocrystalline TiO2 particles with high surface area and activity is discussed with respect to the special characteristics of [bmim][PF6] as well as the role of the surfactant self-assembly in the sol−gel network. Due to its capping effect and water immiscibility, the use of [bmim][PF6] in sol−gel synthesis of TiO2 induces controlled hydrolysis of titanium alkoxide precursor, resulting in a stable sol−gel network with an ordered array, and localized water-poor conditions, resulting in the formation of completely condensed and directly crystalline systems at ambient condition. The low surface energy and adaptability of [bmim][PF6] facilitate the generation of very small nanocrystalline TiO2 particles and then it also acts as a particles aggregation inhibitor. The ensuing TiO2 particles have good thermal stability to resist pore collapse and anatase-to-rutile crystal phase transformation during thermal treatment.
Neutrophils in Anti-Cancer Immunological Strategies: Old Players in New Games (2001)

This review highlights the new "immunological identity" of neutrophils within the cytokine network and their role in biology of diseases, particularly in tumor biology. The latest preclinical evidence of their involvement in anti-cancer immunotherapeutic and prophylactic strategies will be discussed with particular reference to the real possibilities of transferring experimental results to a clinical setting.
Cloning and nucleotide sequence of the gene (amyP) for maltotetraose-forming amylase from Pseudomonas stutzeri MO-19 (1989)

The gene (amyP) coding for maltotetraose-forming amylase (exo-maltotetraohydrolase) of Pseudomonas stutzeri MO-19 was cloned. Its nucleotide sequence contained an open reading frame coding for a precursor (547 amino acid residues) of secreted amylase. The precursor had a signal peptide of 21 amino acid residues at its amino terminus. An extract of Escherichia coli carrying the cloned amyP had amylolytic activity with the same mode of action as the extracellular exo-maltotetraohydrolase obtained from P. stutzeri MO-19. A region in the primary structure of this amylase showed homology with those of other amylases of both procaryotic and eucaryotic origins. The minimum 5' noncoding region necessary for the expression of amyP in E. coli was determined, and the sequence of this region was compared with those of Pseudomonas promoters.
Cellular localization of the chemokine receptor CCR5. Correlation to cellular targets of HIV-1 infection. (1997)

The chemokine receptor CCR5 has recently been described as a co-receptor for macrophage-tropic strains of human immunodeficiency virus (HIV)-1. In this study, using a panel of monoclonal antibodies specific for human CCR5, we show by immunohistochemistry and flow cytometry that CCR5 is expressed by bone-marrow-derived cells known to be targets for HIV-1 infection, including a subpopulation of lymphocytes and monocyte/macrophages in blood, primary and secondary lymphoid organs, and noninflamed tissues. In the central nervous system, CCR5 is expressed on neurons, astrocytes, and microglia. In other tissues, CCR5 is expressed on epithelium, endothelium, vascular smooth muscle, and fibroblasts. Chronically inflamed tissues contain an increased number of CCR5+ mononuclear cells, and the number of immunoreactive cells is directly associated with a histopathological correlate of inflammatory severity. Collectively, these results suggest that CCR5+ cells are recruited to inflammatory sites and, as such, may facilitate transmission of macrophage-tropic strains of HIV-1.
Macrophage-Induced Genes ofLegionella pneumophila:Protection from Reactive Intermediates and Solute Imbalance during Intracellular Growth (2002)

A promoter-probe strategy was devised to identify genes specifically expressed by Legionella pneumophila during growth within the macrophage. Random fragments from the L. pneumophila chromosome were inserted upstream of a promoterless phage T4 td gene, and fragments that led to complementation of thymine auxotrophy during intracellular growth of the bacterium were identified. Two different selection strategies were employed to eliminate promoters that were also active during extracellular growth of the bacterium. Some of these genes were identified independently by using both of the selection strategies. The factors identified include orthologs of efflux-mediated resistance determinants and transporters, a transporter involved in protection from osmotic stress, a stress response GTP-binding protein, a response regulator, a sensor kinase, and two systems that increase the reducing potential of the bacterium, one of which encodes the L. pneumophila ortholog of ahpC. Five of the clones analyzed here were fusions to promoters that were closely linked to genes encoding three-component chemiosmotic efflux pumps that export heavy metals or toxic organic compounds. Analysis of ahpC gene expression indicates that levels increased at least sevenfold during intracellular growth of the bacterium. Inactivation of several of the genes at their chromosomal loci had no effect on the intracellular growth rate of L. pneumophila in cultured macrophages. This suggests that a number of genes with increased expression during intracellular growth may be part of redundant systems that allow survival and growth under the conditions encountered within host cells.
Autophagy in Cancer: Good, Bad, or Both? (2006)

Autophagy has been recognized as an important cellular process for at least 50 years; however, it is only with the recent identification of key regulators of autophagy (Atg genes) that we have begun a mechanistic exploration of its importance in cancer. Recent studies suggest that autophagy may be important in the regulation of cancer development and progression and in determining the response of tumor cells to anticancer therapy. However, the role of autophagy in these processes is complicated and may, depending on the circumstances, have diametrically opposite consequences for the tumor. In this article, we discuss recent discoveries regarding autophagy in cancer.
Internal wave tunnelling: Laboratory experiments (2010)

Heuristics based upon ray theory are often used to predict the propagation of internal gravity waves in non-uniform media. In particular, they predict that waves reflect from weakly stratified regions where the local buoyancy frequency is less than the wave frequency. However, if the layer of weak stratification is sufficiently thin, waves can partially transmit through it in a process called tunnelling. The first laboratory evidence of internal wave tunnelling through a weakly stratified region is analysed using the synthetic schlieren technique and the Hilbert transform is applied to filter the wavefield into upward- and downward-propagating components. Transmission is calculated as the squared ratio of transmitted and incident wave amplitude and using an appropriate superposition of plane waves to reproduce the structure of the incident wave beam, a corresponding weighted sum of transmissions can be used to predict the beam transmission. These transmission predictions are compared with experimental measurements.
Curative cancer chemotherapy. (1985)

Cancer chemotherapy provides variably effective treatment for the majority of forms of human cancer and curative treatment for some 12 categories of cancer. Curative treatment is defined as the proportion of patients who survive beyond the time after which the risk of treatment failure approaches zero, i.e., the disease-free survival plateau. This progress has resulted from a closely integrated scientific effort, including drug development, pharmacology, preclinical modeling, experimental design with respect to clinical trials, quantitative criteria for response, and a series of clinical trials (initially in children with acute lymphocytic leukemia) in which the importance of complete remission, of dose and schedule, of sequencing chemotherapeutic agents, of pharmacological sanctuaries, and particularly of combination chemotherapy was studied. The principles derived from these studies, particularly those relating to combination chemotherapy, resulted in curative treatment for disseminated Hodgkin's disease, non-Hodgkin's lymphoma, pediatric solid tumors, testicular cancer, and limited small cell lung cancer. Many patients with certain stages of solid tumors, such as breast cancer and osteogenic sarcoma, are at high risk of having disseminated microscopic disease. Experimental studies indicate that treatment which is only partially effective against macroscopic disease is much more effective against microscopic tumors. Therefore chemotherapy is administered immediately following control of the primary tumor in patients at high risk of having disseminated microscopic disease, a treatment known as adjuvant chemotherapy. This program has been highly successful in increasing the cure rate in patients with pediatric solid tumors and in prolonging disease-free survival in patients with premenopausal breast cancer. Given dissemination of the technology, it is estimated that 15,000-30,000 patients per year are potentially curable in the United States. Curability of cancer by chemotherapy generally is inversely related to age, i.e., the above tumors are most common in children and young adults. There are new and promising treatment strategies, such as neoadjuvant chemotherapy and autologous bone marrow transplantation. The revolution in molecular and cellular biology is providing an increase in targets, rationale, and opportunity for more effective and novel chemotherapeutic approaches.
Isoforms of Vascular Endothelial Growth Factor Act in a Coordinate Fashion To Recruit and Expand Tumor Vasculature (2000)

Vascular endothelial growth factor (VEGF) is an essential regulator of vascularization. It is expressed as several splice variants; the major forms contain 120 amino acids, 164 amino acids, and 188 amino acids. We utilized transformed cells nullizygous for VEGF to specifically express each of these isoforms in isolation, in order to determine the role of each in tumorigenic neo-vascularization. We found that only the intermediate isoform, VEGF164, could fully rescue tumor growth; VEGF120 partially rescued tumor growth, and VEGF188 failed completely to rescue tumor expansion. Surprisingly, the vascular density of VEGF188 isoform-expressing tumors is significantly greater than that of wild-type VEGF cells and the other isoform-specific tumors. The failure of the hypervascular VEGF188-expressing tumors to grow may be due to inadequate perfusion of the massive number of microvessels in these tumors; three-dimensional imaging of the tumorigenic vasculature indicated little or no recruitment of the peripheral vasculature. This demonstrates that the VEGF isoforms perform unique functions which together enable tumorigenic vascularization.
Combining genetic engineering and traditional breeding to provide elevated resistance in potatoes to Colorado potato beetle (2004)

Abstract The sustainable deployment of resistant crop varieties is a critical issue for the implementation of biotechnology in crop pest management. Feeding, biomass accumulation, and mortality were evaluated for susceptible, insecticide‐resistant, and Bacillus thuringiensis (Bt) Cry 3A‐selected Colorado potato beetle ( Leptinotarsa decemlineata Say) (Coleoptera, Chrysomelidae) larvae fed on: cultivated potato, a Solanum chacoense line expressing leptine glycoalkaloids, a transformed line expressing Bt toxin, or the leptine line transformed to express Bt toxin. Larvae selected for resistance to Bt‐Cry3A performed better on Bt foliage, but not as well on the leptine foliage, compared to susceptible or insecticide‐resistant larvae. Neither leptine nor Bt toxin completely inhibited the feeding and growth of 3rd and 4th instars of all three strains of Colorado potato beetle. However, for all three strains of Colorado potato beetle on leptine + Bt foliage, feeding was almost zero, growth was zero or negative, and mortality was near 100%.
Mechanically Strong, Flexible Polyimide Aerogels Cross-Linked with Aromatic Triamine (2012)

Polyimide gels are produced by cross-linking anhydride capped polyamic acid oligomers with aromatic triamine in solution and chemically imidizing. The gels are then supercritically dried to form nanoporous polyimide aerogels with densities as low as 0.14 g/cm(3) and surface areas as high as 512 m(2)/g. To understand the effect of the polyimide backbone on properties, aerogels from several combinations of diamine and dianhydride, and formulated oligomer chain length are examined. Formulations made from 2,2'-dimethylbenzidine as the diamine shrink the least but have among the highest compressive modulus. Formulations made using 4,4'-oxydianiline or 2,2'dimethylbenzidine can be fabricated into continuous thin films using a roll to roll casting process. The films are flexible enough to be rolled or folded back on themselves and recover completely without cracking or flaking, and have tensile strengths of 4-9 MPa. Finally, the highest onset of decomposition (above 600 °C) of the polyimide aerogels was obtained using p-phenylene diamine as the backbone diamine with either dianhydride studied. All of the aerogels are suitable candidates for high-temperature insulation with glass transition temperatures ranging from 270-340 °C and onsets of decomposition from 460-610 °C.
A Thermoanaerobacter ethanolicus secondary alcohol dehydrogenase mutant derivative highly active and stereoselective on phenylacetone and benzylacetone (2007)

The secondary alcohol dehydrogenase from Thermoanaerobacter ethanolicus 39E (TeSADH) is highly thermostable and solvent-stable, and it is active on a broad range of substrates. These properties make TeSADH an excellent template to engineer an industrial catalyst for chiral chemical synthesis. (S)-1-Phenyl-2-propanol was our target product because it is a precursor to major pharmaceuticals containing secondary alcohol groups. TeSADH has no detectable activity on this alcohol, but it is highly active on 2-butanol. The structural model we used to plan our mutagenesis strategy was based on the substrate's orientation in a horse liver alcohol dehydrogenase*p-bromobenzyl alcohol*NAD(+) ternary complex (PDB entry 1HLD). The W110A TeSADH mutant now uses (S)-1-phenyl-2-propanol, (S)-4-phenyl-2-butanol and the corresponding ketones as substrates. W110A TeSADH's kinetic parameters on these substrates are in the same range as those of TeSADH on 2-butanol, making W110A TeSADH an excellent catalyst. In particular, W110A TeSADH is twice as efficient on benzylacetone as TeSADH is on 2-butanol, and it produces (S)-4-phenyl-2-butanol from benzylacetone with an enantiomeric excess above 99%. W110A TeSADH is optimally active at 87.5 degrees C and remains highly thermostable. W110A TeSADH is active on aryl derivatives of phenylacetone and benzylacetone, making this enzyme a potentially useful catalyst for the chiral synthesis of aryl derivatives of alcohols. As a control in our engineering approach, we used the TbSADH*(S)-2-butanol binary complex (PDB entry 1BXZ) as the template to model a mutation that would make TeSADH active on (S)-1-phenyl-2-propanol. Mutant Y267G TeSADH did not have the substrate specificity predicted in this modeling study. Our results suggest that (S)-2-butanol's orientation in the TbSADH*(S)-2-butanol binary complex does not reflect its orientation in the ternary enzyme-substrate-cofactor complex.
High-Speed Laser Transmitters Using Cascaded Optical Injection Locking (2007)

We demonstrate high-speed laser transmitters with relatively low-frequency devices using cascaded optical injection locking. Tailorable frequency response with a bandwidth of 52 GHz is obtained by adjusting locking parameters of the two slave lasers independently.
Pharmacokinetic study to optimize the intravesical administration of gemcitabine (2010)

The most commonly reported administration scheme of gemcitabine produced the lowest tissue bioavailability of dFdC. Other combinations of pH, dilution volume and duration of instillation proved more advantageous and merit testing in clinical trials.
Structure, function, self-assembly, and applications of bottlebrush copolymers (2015)

Bottlebrush polymers are a type of branched or graft polymer with polymeric side-chains attached to a linear backbone, and the unusual architectures of bottlebrushes provide a number of unique and potentially useful properties. These include a high entanglement molecular weight, enabling rapid self-assembly of bottlebrush block copolymers into large domain structures, the self-assembly of bottlebrush block copolymer micelles in a selective solvent even at very low dilutions, and the functionalization of bottlebrush side-chains for recognition, imaging, or drug delivery in aqueous environments. This review article focuses on recent developments in the field of bottlebrush polymers with an emphasis on applications of bottlebrush copolymers. Bottlebrush copolymers contain two (or more) different types of polymeric side-chains. Recent work has explored the diverse properties and functions of bottlebrush polymers and copolymers in solutions, films, and melts, and applications explored include photonic materials, bottlebrush films for lithographic patterning, drug delivery, and tumor detection and imaging. We provide a brief introduction to bottlebrush synthesis and physical properties and then discuss work related to: (i) bottlebrush self-assembly in melts and bulk thin films, (ii) bottlebrushes for photonics and lithography, (iii) bottlebrushes for small molecule encapsulation and delivery in solution, and (iv) bottlebrush micelles and assemblies in solution. We briefly discuss three potential areas for future research, including developing a more quantitative model of bottlebrush self-assembly in the bulk, studying the properties of bottlebrushes at interfaces, and investigating the solution assembly of bottlebrush copolymers.
Shotgun Alanine Scanning Shows That Growth Hormone Can Bind Productivelyto Its Receptor through a Drastically MinimizedInterface (2005)

The high affinity binding site (Site1) of the human growth hormone (hGH) binds to its cognate receptor (hGHR) via a concave surface patch containing about 35 residues. Using 167 sequences from a shotgun alanine scanning analysis of Site1, we have determined that over half of these residues can be simultaneously changed to an alanine or a non-isosteric amino acid while still retaining a high affinity interaction. Among these hGH variants the distribution of the mutation is highly variable throughout the interface, although helix 4 is more conserved than the other binding elements. Kinetic and thermodynamic analyses were performed on 11 representative hGH Site1 variants that contained 14-20 mutations. Generally, the tightest binding variants showed similar associated rate constants (k(on)) as the wild-type (wt) hormone, indicating that their binding proceeds through a similar transition state intermediate. However, calorimetric analyses indicate very different thermodynamic partitioning: wt-hGH binding exhibits favorable enthalpy and entropy contributions, whereas the variants display highly favorable enthalpy and highly unfavorable entropy contributions. The heat capacities (DeltaCp) on binding measured for wt-hGH and its variants are significantly larger than normally seen for typical protein-protein interactions, suggesting large conformational or solvation effects. The multiple Site1 mutations are shown to indirectly affect binding of the second receptor at Site2 through an allosteric mechanism. We show that the stability of the ternary hormone-receptor complex reflects the affinity of the Site2 binding and is surprisingly exempt from changes in Site1 affinity, directly demonstrating that dissociation of the active signaling complex is a stepwise process.
A Deficiency Disease of Foxes (1940)

A common and highly destructive dietary disease of silver foxes in captivity is pathologically the counter-part of Wernicke's hemorrhagic polioencephalitis of man. The disease in foxes is caused by feeding fish as 10 per cent., or more, of the diet. It is probable that the fish induce a B(1) avitaminosis which causes the characteristic pathology and the resultant symptoms.