gebhart/patrepeval huggingface dataset:
Grafting of “Abbreviated” Complementarity-Determining Regions Containing Specificity-Determining Residues Essential for Ligand Contact to Engineer a Less Immunogenic Humanized Monoclonal Antibody (2002)

Abstract Murine mAb COL-1 reacts with carcinoembryonic Ag (CEA), expressed on a wide range of human carcinomas. In preclinical studies in animals and clinical trials in patients, murine COL-1 showed excellent tumor localization. To circumvent the problem of immunogenicity of the murine Ab in patients, a humanized COL-1 (HuCOL-1) was generated by grafting the complementarity-determining regions (CDRs) of COL-1 onto the frameworks of the variable light and variable heavy regions of human mAbs. To minimize anti-V region responses, a variant of HuCOL-1 was generated by grafting onto the human frameworks only the “abbreviated” CDRs, the stretches of CDR residues that contain the specificity-determining residues that are essential for the surface complementarity of the Ab and its ligand. In competition RIAs, the recombinant variant completely inhibited the binding of radiolabeled murine and humanized COL-1 to CEA. The HuCOL-1 and its variant showed no difference in their binding ability to the CEA expressed on the surface of a CEA-transduced tumor cell line. Compared with HuCOL-1, the HuCOL-1 variant showed lower reactivity to patients’ sera carrying anti-V region Abs to COL-1. The final variant of the HuCOL-1, which retains its Ag-binding reactivity and shows significantly lower serum reactivity than that of the parental Ab, can serve as a prototype for the development of a potentially useful clinical reagent.
Treatment of resistant disease. (1998)

Resistant AML encompasses two groups of patients: those with refractory leukemia and those whose leukemia has relapsed. Refractory leukemia is disease that does not respond to initial induction chemotherapy with cytarabine and an anthracycline. Patients with refractory leukemia are likely to have disease with adverse cytogenetics, a history of antecedent hematologic disturbance, adverse immunophenotypic features, and expression of multiple drug resistance. On the other hand, relapsed leukemia is leukemia that recurs following a CR. The duration of CR greatly affects the patient's prognosis and response to additional treatment. Patients with relapsed leukemia are heterogeneous with variable pretreatment characteristics.
Cyclopropenimine-Catalyzed Enantioselective Mannich Reactions of tert-Butyl Glycinates with N-Boc-Imines (2013)

Cyclopropenimine 1 is shown to catalyze Mannich reactions between glycine imines and N-Boc-aldimines with high levels of enantio- and diastereocontrol. The reactivity of 1 is shown to be substantially greater than that of a widely used thiourea cinchona alkaloid-derived catalyst. A variety of aryl and aliphatic N-Boc-aldimines are effective substrates for this transformation. A preparative-scale reaction to deliver >90 mmol of product is shown using 1 mol % catalyst. The products of this transformation can be converted into several useful derivatives.
L2,3x-ray-absorption edges ofd0compounds:K+,Ca2+,Sc3+, andTi4+inOh(octahedral) symmetry (1990)

The ${L}_{2}$,3 x-ray-absorption edges of 3${d}^{0}$ compounds are calculated with use of an atomic description of the 2${p}^{6}$3${d}^{0}$ to 2${p}^{5}$3${d}^{1}$ excitation, with the inclusion of the crystal field. For reasons of clarity, we confine ourselves to ${d}^{0}$ compounds in octahedral symmetry, but the same approach is applicable to all other ${d}^{N}$ compounds in any point-group symmetry. The experimental spectra of ${\mathrm{FeTiO}}_{3}$, ${\mathrm{Sc}}_{2}$${\mathrm{O}}_{3}$, ${\mathrm{ScF}}_{3}$, ${\mathrm{CaF}}_{2}$, and the potassium halides are well reproduced by the present calculations, including the previously misinterpreted small leading peaks. The splitting between the two main peaks in both the ${L}_{3}$ and ${L}_{2}$ edge are related, though not equal, to the crystal-field splitting. Comparison to experiment showed that the broadening of the main multiplet lines is different. This can be related to Coster-Kronig Auger processes for the ${L}_{2}$ edge and to a solid-state broadening which is a combination of vibrational (phononic) and dispersional broadenings. With the full treatment of the atomic multiplets, the atomic effects can be separated from solid-state effects, which offers a better description of the latter. This includes vibrational broadenings, the covalent screening of the intra-atomic Coulomb and exchange interactions, via the position of small leading peaks, and surface effects. The same general framework can be used to discuss crystal-field effects in both lower symmetries, with the possibility of polarization-dependent spectra (e.g., ${\mathrm{TiO}}_{2}$), and partly filled d bands.
Immune responses to AAV vectors: overcoming barriers to successful gene therapy (2013)

Gene therapy products for the treatment of genetic diseases are currently in clinical trials, and one of these, an adeno-associated viral (AAV) product, has recently been licensed. AAV vectors have achieved positive results in a number of clinical and preclinical settings, including hematologic disorders such as the hemophilias, Gaucher disease, hemochromatosis, and the porphyrias. Because AAV vectors are administered directly to the patient, the likelihood of a host immune response is high, as shown by human studies. Preexisting and/or recall responses to the wild-type virus from which the vector is engineered, or to the transgene product itself, can interfere with therapeutic efficacy if not identified and managed optimally. Small-scale clinical studies have enabled investigators to dissect the immune responses to the AAV vector capsid and to the transgene product, and to develop strategies to manage these responses to achieve long-term expression of the therapeutic gene. However, a comprehensive understanding of the determinants of immunogenicity of AAV vectors, and of potential associated toxicities, is still lacking. Careful immunosurveillance conducted as part of ongoing clinical studies will provide the basis for understanding the intricacies of the immune response in AAV-mediated gene transfer, facilitating safe and effective therapies for genetic diseases.
Plant Cell Signal Transduction (2002)

It is remarkable how 20 years have changed concepts of plant signaling—from a situation in which even the words “signal” and “transduction” received no mention to Special Issues devoted to this critical topic. In fact, signaling in its broadest sense is now a major preoccupation of plant
Regulated secretion of glycosylated human ferritin from hepatocytes (2003)

Serum ferritin has been used widely in clinical medicine chiefly as an indicator of iron stores and inflammation. Circulating ferritin also can have paracrine effects. Despite the clinical significance of serum ferritin, its secretion remains an enigma. The consensus view is that serum ferritin arises from tissue ferritins--principally ferritin light--which can be glycosylated. Ferritin heavy and light chains are cytosolic proteins that form cages of 24 subunits to store intracellular iron. We show that ferritin light is secreted when its expression is increased in stable, transfected HepG2 cells or adenovirus-infected HepG2 cells. Export occurs through the classical secretory pathway and some chains are N-glycosylated. Ferritins do not need to form cages prior to secretion. Secretion is blocked specifically, effectively, and rapidly by a factor in serum. The timing of this inhibition of ferritin secretion suggests that normally cytosolic ferritin L is targeted to the secretory pathway during translation despite the absence of a conventional signal sequence. Thus, secretion of glycosylated and unglycosylated ferritin is a regulated and not a stochastic process.
Outer Membrane Protein F (Porin) Preparation of Pseudomonas aeruginosa as a Protective Vaccine Against Heterologous Immunotype Strains in a Burned Mouse Model (1987)

Outer membrane (OM) protein F (porin) was purified by extraction from polyacrylamide gels of cell envelope proteins of the Pseudomonas aeruginosa PA01 strain. Mice were immunized intramuscularly with 10 micrograms of protein F preparation on days 1 and 14 and then subjected to burn and challenge on day 28. Protein F immunization afforded significant protection above that provided by PA01 lipopolysaccharide (LPS) immunization against subsequent challenge with six of six heterologous LPS immunotype strains of P. aeruginosa. By an ELISA, the murine immune response revealed an IgG titer of 5,120 to protein F by day 30. Immunoblot analysis of antisera from protein F-immunized mice revealed bands with both protein F and protein H of cell envelopes of all immunotypes tested. Active immunization with OM protein H did not, however, afford significant protection to mice in this burned mouse model. These data show the efficacy of OM protein F as a protective vaccine in a murine model representative of human infection.
Spatial regulation of microRNA gene expression in the Drosophila embryo (2005)

MicroRNAs (miRNAs) regulate posttranscriptional gene activity by binding to specific sequences in the 3' UTRs of target mRNAs. A number of metazoan miRNAs have been shown to exhibit tissue-specific patterns of expression. Here, we investigate the possibility that localized expression is mediated by tissue-specific enhancers, comparable to those seen for protein-coding genes. Two miRNA loci in Drosophila melanogaster are investigated, the mir-309-6 polycistron (8-miR) and the mir-1 gene. The 8-miR locus contains a cluster of eight distinct miRNAs that are transcribed in a common precursor RNA. The 8-miR primary transcript displays a dynamic pattern of expression in early embryos, including repression at the anterior and posterior poles. An 800-bp 5' enhancer was identified that recapitulates this complex pattern when attached to a RNA polymerase II core promoter fused to a lacZ-reporter gene. The miR-1 locus is specifically expressed in the mesoderm of gastrulating embryos. Bioinformatics methods were used to identify a mesoderm-specific enhancer located approximately 5 kb 5' of the miR-1 transcription unit. Evidence is presented that the 8-miR enhancer is regulated by the localized Huckebein repressor, whereas miR-1 is activated by Dorsal and Twist. These results provide evidence that restricted activities of the 8-miR and miR-1 miRNAs are mediated by classical tissue-specific enhancers.
Ferroportin1 is required for normal iron cycling in zebrafish (2005)

Missense mutations in ferroportin1 (fpn1), an intestinal and macrophage iron exporter, have been identified between transmembrane helices 3 and 4 in the zebrafish anemia mutant weissherbst (weh(Tp85c-/-)) and in patients with type 4 hemochromatosis. To explore the effects of fpn1 mutation on blood development and iron homeostasis in the adult zebrafish, weh(Tp85c-/-) zebrafish were rescued by injection with iron dextran and studied in comparison with injected and uninjected WT zebrafish and heterozygotes. Although iron deposition was observed in all iron-injected fish, only weh(Tp85c-/-) zebrafish exhibited iron accumulation in the intestinal epithelium compatible with a block in iron export. Iron injections initially reversed the anemia. However, 8 months after iron injections were discontinued, weh(Tp85c-/-) zebrafish developed hypochromic anemia and impaired erythroid maturation despite the persistence of iron-loaded macrophages and elevated hepatic nonheme iron stores. Quantitative real-time RT-PCR revealed a significant decrease in mean hepatic transcript levels of the secreted iron-regulator hepcidin and increased intestinal expression of fpn1 in anemic weh(Tp85c-/-) adults. Injection of iron dextran into WT or mutant zebrafish embryos, however, resulted in significant increases in hepcidin expression 18 hours after injection, demonstrating that hepcidin expression in zebrafish is iron responsive and independent of fpn1's function as an iron exporter.
Java security: Web browsers and beyond (1997)

The introduction of Java applets has taken the World Wide Web by storm. Java allows web creators to embellish their content with arbitrary programs which execute in the web browser, whether for simple animations or complex front-ends to other services. We examined the Java language and the Sun HotJava, Netscape Navigator, and Microsoft Internet Explorer browsers which support it, and found a significant number of flaws which compromise their security. These flaws arise for several reasons, including implementation errors, unintended interactions between browser features, differences between the Java language and bytecode semantics, and weaknesses in the design of the language and the bytecode format. On a deeper level, these flaws arise because of weaknesses in the design methodology used in creating Java and the browsers. In addition to the flaws, we discuss the underlying tension between the openness desired by web application writers and the security needs of their users, and we sug...
Cation Exchange Behavior of Bauxite Refining Residues from Western Australia (1995)

Abstract Over 60 million tonnes per year of bauxite refining residue (red mud) is produced worldwide. Its high Na concentration inhibits plant growth and hence reclamation. The cation‐exchange capacity (CEC) of red mud and the cation exchange equilibria between Na + and several other cations were measured to elucidate the mechanism of Na release from red mud. The CECs obtained by using K + and NH + 4 were significantly higher than those obtained using Ca 2+ and Ba 2+ . This unusual cation exchange phenomenon can be attributed to the presence of zeolitic minerals in red mud. Cation exchange equilibria show that Na + originally present in red mud was preferentially adsorbed by the mud over other cations. At high cation fractions in red mud (&gt;0.1), the mud selectively sorbed monovalent over divalent cations, with the following order of selectivity: K + &gt; Li + &gt; NH + 4 &gt; Ba 2+ ≥ Ca 2+ &gt; Mg 2+ . The exchange of Na + has been found to have significant negative correlations with the radius of hydration and Debye‐Huckei parameter. Divalent cations have little ability to exchange Na + from zeolitic exchange sites. Incremental extraction of Na + in red mud shows that K + and NH + 4 displaced 99 (63%) and 57 (44%) cmol c kg −1 red mud whereas Ca 2+ and Mg 2+ could only displace 33 and 29 cmol c kg −1 red mud, respectively, out of a total of 99 cmol c Na kg −1 red mud. In a reverse process 95% of K + adsorbed on red mud was readily replaced by Na + . The experimental evidence suggests that the release of Na + from red mud is due to cation exchange.
Improved detectability of VX2 carcinoma in the rabbit liver with contrast enhancement in computed tomography. (1980)

Detection of liver metastases by CT scanning depends on both size and difference in attenuation between the metastasis and the surrounding liver parenchyma. VX2 carcinoma cells were injected into the liver parenchyma of rabbits which were subsequently scanned under suspended respiration before, during and after infusion of iothalamate ethyl ester, a particulate contrast agent. The results demonstrate the greater attenuation difference between tumor and parenchyma required for the detection of smaller lesions. Contrast enhancement was most beneficial in the detection of tumors having diameters less than the scan section width.
.ALPHA.-Solanine Inhibits Human Melanoma Cell Migration and Invasion by Reducing Matrix Metalloproteinase-2/9 Activities (2010)

α-Solanine, a naturally occurring steroidal glycoalkaloid in potato sprouts, was found to possess anti-carcinogenic properties, such as inhibiting proliferation and inducing apoptosis of tumor cells. However, the effect of α-solanine on cancer metastasis remains unclear. In the present study, we examined the effect of α-solanine on metastasis in vitro. Data demonstrated that α-solanine inhibited proliferation of human melanoma cell line A2058 in a dose-dependent manner. When treated with non-toxic doses of α-solanine, cell migration and invasion were markedly suppressed. Furthermore, α-solanine reduced the activity of matrix metalloproteinase-2 (MMP-2) and MMP-9, which are involved in the migration and invasion of cancer cells. Our biochemical assays indicated that α-solanine potently suppressed the phosphorylation of c-Jun N-terminal kinase (JNK), phosphatidylinositide-3 kinase (PI3K) and Akt, while it did not affect phosphorylation of extracellular signal regulating kinase (ERK). In addition, α-solanine significantly decreased the nuclear level of nuclear factor kappa B (NF-κB), suggesting that α-solanine inhibited NF-κB activity. Taken together, the results suggested that α-solanine inhibited migration and invasion of A2058 cells by reducing MMP-2/9 activities. It also inhibited JNK and PI3K/Akt signaling pathways as well as NF-κB activity. These findings reveal new therapeutic potential for α-solanine in anti-metastatic therapy.
Expression of Shigella dysenteriae serotype 1 O-antigenic polysaccharide by Shigella flexneri aroD vaccine candidates and different S. flexneri serotypes (1995)

The potential utility of Shigella flexneri aroD vaccine candidates for the development of bi- or multivalent vaccines has been explored by the introduction of the genetic determinants rfp and rfb for heterologous O antigen polysaccharide from Shigella dysenteriae serotype 1. The serotype Y vaccine strain SFL124 expressed the heterologous antigen qualitatively and quantitatively well, qualitatively in the sense of the O antigen polysaccharide being correctly linked to the S. flexneri lipopolysaccharide R3 core oligosaccharide and quantitatively in the sense that typical yields were obtained, with ratios of homologous to heterologous O antigen being 4:1 for one construct and 1:1 for another. Moreover, both polysaccharide chains were shown to be linked to position O-4 of the subterminal D-glucose residue of the R3 core. In contrast to the hybrid serotype Y SFL124 derivatives, analogous derivatives of serotype 2a vaccine strain SFL1070 did not elaborate a complete heterologous O antigen. Such derivatives, and analogous derivatives of rough, O antigen-negative mutants of SFL1070, formed instead a hybrid lipopolysaccharide molecule consisting of the S. flexneri lipid A R3 core with a single repeat unit of the S. dysenteriae type 1 O antigen. Introduction of the determinants for the S. dysenteriae type 1 O antigen into a second serotype 2a strain and into strains representing other serotypes of S. flexneri, revealed the following for the expression of the heterologous O antigen: serotypes 1a, 1b, 2a, and 5a did not produce the heterologous O antigen, whereas serotypes 2b, 3a, 3b, 4a, 4b, 5b, and X did.
Differential Expression of MicroRNAs in Tumors from Chronically Inflamed or Genetic (APCMin/+) Models of Colon Cancer (2011)

We conclude that these four miRNAs are dysregulated at some very early stage in transformation of colonic epithelial cells. This response is not dependent on the mechanism of initiation of transformation (inflammation versus germline mutation), suggesting that the miRNAs that we have identified are likely to regulate critical signaling pathways that are central to early events in transformation of colonic epithelial cells.
Cytotoxic and Insecticidal Activities of Derivatives of Harmine, a Natural Insecticidal Component Isolated from Peganum harmala (2010)

In a continuing effort to develop novel β-carbolines endowed with better insecticidal activity, a simple high-yielding method for the synthesis of harmine compounds starting from L-tryptophan has been developed and a series of 1,3-substituted β-carboline derivatives have been synthesized and evaluated for their cytotoxicity against insect cultured Sf9 cell line in vitro and insecticidal activities against 4th instar larvae of mosquitos, Culex pipiens quinquefasciatus and mustard aphid, Lipaphis erysimi. The results demonstrated that 1-phenyl-1,2,3,4-tetrahydro-β-carboline-3-carboxylic acid (compound 2) and methyl 1-phenyl-β-carboline-3-carboxylate (compound 13) represented the best potential compounds, with Sf9 cells inhibition rates of 71.55% and 60.21% after 24 h treatment at concentrations of 50-200 mg/L, respectively. Both compounds 2 and 13 also showed strong insecticidal activity towards 4th instar larvae of mosquitos with LC(50) values of 20.82 mg/L and 23.98 mg/L, and their LC(90) values were 88.29 mg/L and 295.13 mg/L, respectively. Furthermore, the LC(50) values of compounds 2 and 13 against mustard aphids were 53.16 mg/L and 68.05 mg/L, and their LC(90) values were 240.10 mg/L and 418.63 mg/L after 48 h treatment. The in vitro cytotoxicity of these compounds was consistent with the insecticidal activity in vivo. The results indicated that the 1- and 3-positions of the β-carboline ring deserve further investigation to develop biorational insecticides based on the natural compound harmine as a lead compound.
Eicosapentaenoic acid inhibits cholesterol esterification in cultured parenchymal cells and isolated microsomes from rat liver. (1988)

The effects of eicosapentaenoic acid on synthesis and secretion of cholesterol and cholesterol ester by cultured rat hepatocytes were studied. In the presence of eicosapentaenoic acid cellular cholesterol esterification was decreased by 50-75% compared to oleic acid as measured by radioactive precursors and mass. Secretion of cholesterol ester was reduced by 50-60% in the presence of eicosapentaenoic acid as evaluated by radiolabeled fatty acids, mevalonolactone, and mass measurement. Oleic, palmitic, and stearic acid increased, whereas eicosapentaenoic and docosahexaenoic acid decreased synthesis and secretion of cholesterol ester as compared to a fatty acid-free control. Cellular and secreted free cholesterol were unaffected by eicosapentaenoic acid in comparison with oleic acid. The reduced cholesterol esterification was observed within 1 h and lasted for at least 20 h. Eicosapentaenoic acid caused lower cholesterol esterification than oleic acid in the concentration range 0.2-1.0 mM fatty acid and reduced the stimulatory effect of oleic acid on cholesterol ester formation. Cholesterol esterification and release of cholesterol ester were markedly increased by 25-hydroxycholesterol in the presence of eicosapentaenoic acid as well as oleic acid. Experiments with liver microsomes revealed that radioactive eicosapentaenoic acid and eicosapentaenoyl-CoA were poorer substrates (7-30%) for cholesterol esterification than oleic acid and oleoyl-CoA. Reduced formation of cholesterol ester was also observed when eicosapentaenoyl-CoA was given together with labeled oleoyl-CoA, whereas palmitoyl-CoA, stearoyl-CoA, linolenoyl-CoA, and arachidonoyl-CoA had no inhibitory effect. In conclusion, eicosapentaenoic acid reduced cellular cholesterol esterification by inhibiting the activity of acyl-CoA:cholesterol acyltransferase. The lowered cholesterol esterification caused by eicosapentaenoic acid secondly decreased secretion of very low density lipoprotein cholesterol ester.