gebhart/patrepeval huggingface dataset:
Experimental radioimmunotherapy of murine lymphoma with 131I-labeled anti-T-cell antibodies. (1986)

We have shown previously that 131I-labeled antibodies against the Thy-1.1 differentiation antigen can cure AKR/Cum (Thy-1.2+) mice bearing AKR/J (Thy-1.1+) SL2 T-cell lymphoma. In the present study we have extended these studies to the therapy of SL2 lymphoma in AKR/J mice, where 131I-anti-labeled Thy-1.1 antibodies react with both tumor and normal T-lymphocytes. A single 25-micrograms bolus of 131I-labeled anti-Thy-1.1 antibody was rapidly cleared from serum by binding to spleen cells (t1/2 less than 3 h) and only low concentrations (less than 2% injected dose/g) were present in tumor 24 h after infusion. Doses of 0.5-5.0 mg antibody saturated cells in the spleen but only slightly increased the proportion of antibody in tumor. In contrast, pretreatment of mice with 1.0 mg of unlabeled anti-Thy-1.1 antibody 24 h prior to 131I-labeled antibody resulted in a tumor concentration of 9.7% injected dose/g 24 h after infusion of the radiolabeled antibody. With this latter regimen, biodistribution approximated that seen in AKR/Cum mice, and infusion of 1,000 mu Ci would result in delivery of 16 Gy to tumor. Therapy of AKR/J mice bearing established s.c. lymphoma nodules with 1,500 mu Ci of 131I-anti-Thy-1.1 antibody given in this latter regimen resulted in complete regression of the nodule in 70% of animals and had a greater antitumor effect (27% complete regression, P less than 0.001) than 750 mu Ci of 131I-labeled irrelevant antibody, a dose that would deliver equivalent radiation to normal organs (liver, kidney, and lung). The anti-Thy-1.1 antibody had only a slightly greater antitumor effect than an equivalent mu Ci dose (1,500 mu Ci) of 131I-labeled control antibody (42% complete regression, P = 0.12). Both antibodies were marrow toxic and all animals treated with 1,500 mu Ci died of marrow aplasia. These studies suggest that radiolabeled antibodies against differentiation antigens may be useful for therapy in spite of binding to normal cell populations but curative therapy may require infusion of unirradiated bone marrow.
Induction of tissue-specific autoimmune prostatitis with prostatic acid phosphatase immunization: implications for immunotherapy of prostate cancer (1997)

Prostatic acid phosphatase (PAP) is uniquely expressed in prostatic tissue and prostate cancer. In this study, the immunogenicity of PAP was investigated in a male rat model. We show that immunization with recombinant rat or human PAP in CFA leads to a significant Ab response, but does not generate CTL or result in autoimmune prostatitis. In contrast, immunization with recombinant vaccinia expressing human PAP, but not rat PAP, generates a CTL response and tissue-specific prostatitis in the absence of detectable PAP-specific Abs. These findings suggest that a cellular immune response to PAP, rather than Abs, mediates destructive autoimmune prostatitis. Thus, xenogeneic forms of PAP are a new tool for the induction of prostate-specific immunity and may prove useful for the immunotherapy of prostate cancer.
Transactivation properties of parsley proline‐rich bZIP transcription factors (2000)

Summary Light‐responsive chalcone synthase ( CHS ) gene activation requires LRU CHS , a light regulatory promoter unit including the MYB recognition element MRE CHS and the ACGT‐containing element ACE CHS. ACE CHS is bound by the parsley basic region/leucine zipper (bZIP) factors CPRF1 and 4. Factors containing the bZIP domain exist in animals, plants and yeast, and recognize DNA sequence‐specifically after formation of homo‐ or heterodimers. To determine the potential role of CPRFs in the regulation of CHS promoter activity, we investigated the functions of distinct CPRF domains in a homologous co‐transfection system. The proline‐rich domains of CPRF1 and CPRF4 activate transcription, indicating that CPRF1 and CPRF4 have transactivating properties. Over‐expression of the CPRF1 bZIP domain caused a reduction of LRU CHS ‐mediated light inducibility, and point mutations throughout ACE CHS affected both responsiveness to UV‐containing white light and transactivation by CPRF1::VP16. The data suggest that a CPRF1‐containing bZIP heterodimer interacts with ACE CHS in vivo . We discuss regulatory steps in light‐induced CHS transcription that may be influenced by CPRF1 and/or related bZIP factors.
Analysis of altered gene expression during sustained atrial fibrillation in the goat (2002)

AF is accompanied by changes in expression of proteins involved in cellular structure, metabolism, gene expression regulation and (de-)differentiation. Most alterations in expression confirm or support the hypothesis of cardiomyocyte de-differentiation. Furthermore, the results suggest a role for ischemic stress in the early response of cardiomyocytes to AF, possibly via activation of hypoxia-inducible factor 1 alpha.
Glycoengineering in cancer therapeutics (2012)

Experimentally modified trastuzumab antibodies show increased cytotoxic potency when used with human effector cells against HER2-overexpressing human breast cancer cells in vitro and ex vivo. Furthermore, the superior efficacy of 'glycoengineered' trastuzumab has been confirmed in vivo utilizing a preclinical xenograft model of human HER2-amplified, trastuzumab-resistant human breast cancer. The increased cytotoxic potency coupled with other improvements are achieved by a seemingly modest change in trastuzumab's structure, that is, depletion of two α-L-fucose residues from trastuzumab's heavy chains. Fucose-free trastuzumab binds with much greater affinity to human natural killer cells. This improved binding induces much greater antibody-dependent cellular cytotoxicity against HER2-overexpressing cells. The pharmaceutical industry has recognized the advantages of fucose-free therapeutic antibodies and has developed technologies that aim to mass produce such antibodies for human use. Here, we summarize data from multiple academic and pharmaceutical laboratories highlighting fucose depletion of antibodies as a key strategy of glycoengineering in cancer therapeutics. We use fucose-depleted trastuzumab as a model to show the advantages of this new class of anticancer agents. We predict that these advantages will translate clinically into improved therapeutics for many patients including those with HER2-overexpressing neoplasms.
Space‐Projected Conductivity and Spectral Properties of the Conduction Matrix (2020)

Herein, the Kubo–Greenwood formula is utilized to project the electronic conductivity into real space, and a Hermitian positive semidefinite matrix Γ is discussed, which is called the conduction matrix , that reduces the computation of spatial conduction activity to a diagonalization. It is shown that for low‐density amorphous carbon, connected sp 2 rings and sp chains are conduction‐active sites in the network. In amorphous silicon, transport involves hopping through tail states mediated by the defects near the Fermi level. It is found that for liquid silicon, thermal fluctuations induce spatial and temporal conductivity fluctuations in the material. The frequency‐dependent absorption of light as a function of wavelength in an amorphous silicon suboxide (a‐SiO 1.3 ) is also studied. It is shown that the absorption is strongly frequency dependent and selects out different oxygen vacancy subnetworks depending on the frequency. Γ is diagonalized to obtain conduction eigenvalues and eigenvectors, and it is shown that the density of states of the eigenvalues for FCC aluminum has an extended spectral tail that distinguishes metals from insulators and semiconductors. The method is easy to implement with any electronic structure code, providing suitable estimates for single‐particle electronic states and energies.
On the conjugation length in poly(para‐phenylene)‐type polymers (1995)

The study of well‐defined, monodisperse model PPP oligomers (e.g. see Figure) has revealed that, contrary to expectations, the planarization of the π system in these oligomers leads to a decrease in the effective conjugation length. This result has profound influence on the design of conducting organic materials. magnified image
Development of seven new human prostate tumor xenograft models and their histopathological characterization. (1996)

Seven human prostate tumor models were established by transplanting tumor fragments in NMRI athymic nude mice. Once established, the tumors were serially transplantable in both NMRI and BALB/c nude mice. The xenografts originated from primary prostatic carcinomas (prostatectomy specimens), transurethral resection material, and metastatic lesions (pelvic lymph nodes and scrotal skin). Histological examination revealed that, in the course of several mouse passages (8 to 23), tumors retained their resemblance to the original patient material. The PC-295, PC-310, PC-329, and PC-346 tumors are dependent on androgens for their growth. The PC-324, PC-339, and PC-374 tumors are androgen independent, although growth of PC-374 tumors still seemed androgen sensitive. All tumors are diploid, except for the PC-374, which is tetraploid. The diploid PC-295 tumor has an additional small population of tetraploid cells. All xenografts displayed a heterogeneous expression pattern of the androgen receptor except for the PC-324 and PC-339 tumors in which the androgen receptor could not be detected. Prostatic acid phosphatase and prostate-specific antigen were retained during serial transplantation in all tumors but the PC-324 and PC-339. This panel of permanent human prostate tumor models comprises tumors representing both the androgen-dependent and -independent stages of human prostate cancer with various degrees of differentiation and, therefore, is of great value for the study of many aspects of growth and progression of human prostate cancer.
Calystegins of Physalts alkekengi var. Francheti (Solanaceae) (1995)

Five calystegins were extracted from the roots of Physalis alkekengi var. francheti (Solanaceae) with hot water and purified to homogeneity by the combination of a variety of ion-exchange column chromatographies. Their structures have been determined from the 1H- and 13C-NMR spectral data, and two of the compounds were identified as calystegins A3 and B2, which have been isolated from the roots of Calystegia sepium (Convolvulaceae). Two of the remaining three were found to be 1 alpha, 3 alpha, 4 beta-trihydroxy-nor-tropane and 1 alpha, 2 alpha, 3 alpha, 4 beta-tetrahydroxy-nor-tropane and given the trivial name calystegins A5 and B3, respectively. The last calystegin was assigned as 1 alpha, 2 beta, 3 alpha, 6 alpha-tetrahydroxy-nor-tropane, which was the same as the relative configuration proposed in the literature for calystegin B1 isolated from C. sepium. However, the 13C-NMR spectral data for the compound from C. sepium differed substantially from our results. From a personal communication with the authors of the original paper on calystegins, it was clarified that the 13C-NMR chemical shifts of calystegin B1 in the original paper had been erroneous. Since their corrected 13C-NMR data of calystegin B1 and its 1H-NMR chemical shifts in the original paper are very close to our present data, we concluded that both compounds from C. sepium and P. alkekengi are identical. Calystegin B2 has been known to be a potent competitive inhibitor of almond beta-glucosidase (Ki = 1.2 microM) and coffee bean alpha-galactosidase (Ki = 0.86 microM). In this study calystegin B1 (1 alpha, 2 beta, 3 alpha, 6 alpha-tetrahydroxy-nor-tropane) proved to be a potent competitive inhibitor of almond beta-glucosidase (Ki = 1.9 microM) and bovine liver beta-galactosidase (Ki = 1.6 microM), but not an inhibitor of alpha-galactosidases. Calystegin A3 was found to be a weaker inhibitor compared to calystegin B2 but with the same inhibitory spectrum. Calystegin A5, a 2-deoxy derivative of calystegin B2, showed no activity against any glycosidases tested. Since calystegin B3, a 2-epimer of calystegin B2, also exhibited only a weak inhibitory activity, it was concluded that the equatorially oriented OH group at C2 is the essential feature for recognition and strong binding by the active site of glycosidases.(ABSTRACT TRUNCATED AT 400 WORDS)
HER3 Comes of Age: New Insights into Its Functions and Role in Signaling, Tumor Biology, and Cancer Therapy (2010)

The human epidermal growth family (HER) of tyrosine kinase receptors underlies the pathogenesis of many types of human cancer. The oncogenic functions of three of the HER proteins can be unleashed through amplification, overexpression, or mutational activation. This has formed the basis for the development of clinically active targeted therapies. However, the third member HER3 is catalytically inactive, not found to be mutated or amplified in cancers, and its role and functions have remained shrouded in mystery. Recent evidence derived primarily from experimental models now seems to implicate HER3 in the pathogenesis of several types of cancer. Furthermore, the failure to recognize the central role of HER3 seems to underlie resistance to epidermal growth factor receptor (EGFR)- or HER2-targeted therapies in some cancers. Structural and biochemical studies have now greatly enhanced our understanding of signaling in the HER family and revealed the previously unrecognized activating functions embodied in the catalytically impaired kinase domain of HER3. This renewed interest and mechanistic basis has fueled the development of new classes of HER3-targeting agents for cancer therapy. However, identifying HER3-dependent tumors presents a formidable challenge and the success of HER3-targeting approaches depends entirely on the development and power of predictive tools.
Sequence and Expression of Human Estrogen Receptor Complementary DNA (1986)

The mechanism by which the estrogen receptor and other steroid hormone receptors regulate gene expression in eukaryotic cells is not well understood. In this study, a complementary DNA clone containing the entire translated portion of the messenger RNA for the estrogen receptor from MCF-7 human breast cancer cells was sequenced and then expressed in Chinese hamster ovary (CHO-K1) cells to give a functional protein. An open reading frame of 1785 nucleotides in the complementary DNA corresponded to a polypeptide of 595 amino acids and a molecular weight of 66,200, which is in good agreement with published molecular weight values of 65,000 to 70,000 for the estrogen receptor. Homogenates of transformed Chinese hamster ovary cells containing a protein that bound [3H]estradiol and sedimented as a 4S complex in salt-containing sucrose gradients and as an 8 to 9S complex in the absence of salt. Interaction of this receptor-[3H]estradiol complex with a monoclonal antibody that is specific for primate ER confirms the identity of the expressed complementary DNA as human estrogen receptor. Amino acid sequence comparisons revealed significant regional homology among the human estrogen receptor, the human glucocorticoid receptor, and the putative v-erbA oncogene product. This suggests that steroid receptor genes and the avian erythroblastosis viral oncogene are derived from a common primordial gene. The homologous region, which is rich in cysteine, lysine, and arginine, may represent the DNA-binding domain of these proteins.
New insights in the molecular biology and physiology of revealed by comparative genomics (2005)

Streptococcus thermophilus is a major dairy starter used for the manufacture of yoghurt and cheese. The access to three genome sequences, comparative genomics and multilocus sequencing analyses suggests that this species recently emerged and is still undergoing a process of regressive evolution towards a specialised bacterium for growth in milk. Notably, S. thermophilus has maintained a well-developed nitrogen metabolism whereas its sugar catabolism has been subjected to a high level of degeneracy due to a paucity of carbon sources in milk. Furthermore, while pathogenic streptococci are recognised for a high capacity to expose proteins at their cell surface in order to achieve cell adhesion or to escape the host immune system, S. thermophilus has nearly lost this unique feature as well as many virulence-related functions. Although gene decay is obvious in S. thermophilus genome evolution, numerous small genomic islands, which were probably acquired by horizontal gene transfer, comprise important industrial phenotypic traits such as polysaccharide biosynthesis, bacteriocin production, restriction-modification systems or oxygen tolerance.
Synthesis, reactions and biological activity of some new thieno[2,3-f]-1,3-benzodioxoles. (1999)

The reaction of 7-chlorothieno[2,3-f]-1,3-benzodioxole-6-carbonyl chloride (2) with some aromatic or heterocyclic amines gave the corresponding 6-(aryl or heterocyclyl) carbamoyl-7-chlorothieno [2,3-f]-1,3-benzodioxoles (3a-c, 4a, b and 5). Compound 2 was also reacted with potassium thiocyanate, ethanol or sodium azide to afford the isothiocyanto compound 6, the ester 7 and the acid azide 9, respectively. Hydrazinolysis of 7 gave the carbohydrazide 8. The compounds 6, 8 and 9 were used as precursors in the synthesis of the target heterocycles, 7-chlorothieno[2,3-f]-1,3-benzodioxoles substituted with a variety of moieties at position-6 (10-15, 17, 19-26, 28-31). Also, 2-methyl-1,3-dixolo[5,6][1]benzothieno[2,3-c]quinolin- 6(5 H)-one (33) was prepared. The antibacterial and antifungal activities of some selected compounds were also reported.
Preferential Growth of Semiconducting Single-Walled Carbon Nanotubes by a Plasma Enhanced CVD Method (2004)

Single-walled carbon nanotubes (SWNT) are grown by a plasma enhanced chemical vapor deposition (PECVD) method at 600 °C. The nanotubes are of high quality as characterized by microscopy, Raman spectroscopy, and electrical transport measurements. High performance field effect transistors are obtained with the PECVD nanotubes. Interestingly, electrical characterization reveals that nearly 90% of the nanotubes are semiconductors and thus highly preferential growth of semiconducting over metallic tubes in the PECVD process. Control experiments with other nanotube materials find that HiPco nanotubes consist of ∼61% semiconductors, while laser ablation preferentially grows metallic SWNTs (∼70%). The characterization method used here should also be applicable to assessing the degree of chemical separation of metallic and semiconducting nanotubes.
Therapeutic Potential and Challenges of Targeting Receptor Tyrosine Kinase ROR1 with Monoclonal Antibodies in B-Cell Malignancies (2011)

Owing to its relatively low cell surface density, ROR1 may be a preferred target for armed rather than naked mAbs. Provided is a panel of fully sequenced and thoroughly characterized anti-ROR1 mAbs suitable for conversion to antibody-drug conjugates, immunotoxins, chimeric antigen receptors, and other armed mAb entities for preclinical and clinical studies.
Hydration Enthalpy Measurement and Evaluation as Heat Exchangers of Allophane and Imogolite. (2001)

The hydration enthalpies of allophane and imogolite have been measured by means of the adiabatic vapor absorption calorimeter. The hydration enthalpy (ΔHh) of allophane and imogolite were -63.2kJ/mol and -59.8kJ/mol, respectively, which were almost the same as those of a zeolite group. The total heat of hydration (Q) of allophane was 409kJ/kg at the dehydration temperature of 80°C, and was 1.5 times larger than that of the Mg-A type zeolite, The Q-value of imogolite was 405kJ/kg at the dehydration temperature of 40°C, and was 2.2 times larger than that of the Mg-A type zeolite. Allophane and imogolite are thus characterized by larger Q-values than that of Mg-A type zeolite when they are dehydrated at low temperature below 100°C. This shows that allophane and imogolite are suitable for heat exchange absorbents of zeolite-water heat pumps for low temperature heat sources.
Molecular genetics of a biological clock in Drosophila (1984)

Ninety kilobase pairs (kb) of DNA have been isolated from the 3B region of the X chromosome of Drosophila melanogaster. Previous cytogenetic analyses have placed a gene required for rhythmic behavior (per) in this chromosomal interval. Physical characterization of a series of chromosomal rearrangements altering per locus activity indicates that DNA affecting behavioral rhythms is found in a 7.1-kb HindIII fragment. A single 4.5-kb poly(A)(+) RNA is transcribed from this DNA in wild-type pupae and adult flies. The transcript is eliminated by a per mutant that retains some rhythmic activity, but this mutant substitutes two novel transcripts, 11.5 kb and 0.9 kb. It is suggested that the new poly(A)(+) transcripts provide residual per locus activity.
Cytotoxic T lymphocytes recognize an HLA-A2-restricted epitope within the hepatitis B virus nucleocapsid antigen. (1991)

The absence of readily manipulable experimental systems to study the cytotoxic T lymphocyte (CTL) response against hepatitis B virus (HBV) antigens has thus far precluded a definitive demonstration of the role played by this response in the pathogenesis of liver cell injury and viral clearance during HBV infection. To circumvent the problem that HBV infection of human cells in vitro for production of stimulator/target systems for CTL analysis is not feasible, a panel of 22 overlapping synthetic peptides covering the entire amino acid sequence of the HBV core (HBcAg) and e (HBeAg) antigens were used to induce and to analyze the HBV nucleocapsid-specific CTL response in nine patients with acute hepatitis B, six patients with chronic active hepatitis B, and eight normal controls. By using this approach, we have identified an HLA-A2-restricted CTL epitope, located within the NH2-terminal region of the HBV core molecule, which is shared with the e antigen and is readily recognized by peripheral blood mononuclear cells from patients with self-limited acute hepatitis B but less efficiently in chronic HBV infection. Our study provides the first direct evidence of HLA class I-restricted T cell cytotoxicity against HBV in humans. Furthermore, the different response in HBV-infected subjects who successfully clear the virus (acute patients) in comparison with patients who do not succeed (chronic patients) suggests a pathogenetic role for this CTL activity in the clearance of HBV infection.
MDA-7/IL-24 as a cancer therapeutic: from bench to bedside (2010)

The novel cytokine melanoma differentiation associated gene-7 (mda-7) was identified by subtractive hybridization in the mid-1990s as a protein whose expression increased during the induction of terminal differentiation, and that was either not expressed or was present at low levels in tumor cells compared with non-transformed cells. On the basis of conserved structure, chromosomal location and cytokine-like properties, MDA-7, has now been classified as a member of the expanding interleukin (IL)-10 gene family and designated as MDA-7/IL-24. Multiple studies have shown that the expression of MDA-7/IL-24 in a wide variety of tumor cell types, but not in the corresponding equivalent non-transformed cells, causes their growth arrest and ultimately cell death. In addition, MDA-7/IL-24 has been noted to be a radiosensitizing cytokine, which is partly because of the generation of reactive oxygen species and ceramide that cause endoplasmic reticulum stress. Phase I clinical trial data has shown that a recombinant adenovirus expressing MDA-7/IL-24 [Ad.mda-7 (INGN-241)] was safe and had measurable tumoricidal effects in over 40% of patients, which strongly argues that MDA-7/IL-24 may have significant therapeutic value. This review describes what is known about the impact of MDA-7/IL-24 on tumor cell biology and its potential therapeutic applications.