gebhart/patrepeval huggingface dataset:
Consequences of trace metal variability and supplementation on Chinese hamster ovary (CHO) cell culture performance: A review of key mechanisms and considerations (2019)

Trace metals are supplied to chemically-defined media (CDM) for optimal Chinese hamster ovary (CHO) cell culture performance during the production of monoclonal antibodies and other therapeutic proteins. However, lot-to-lot and vendor-to-vendor variability in raw materials consequently leads to an imbalance of trace metals that are supplied to CDM. This imbalance can yield detrimental effects rooted in several primary mechanisms and pathways including oxidative stress, apoptosis, lactate accumulation, and unfavorable glycan synthesis. Recent research endeavors involve supplying zinc, copper, and manganese to CDM in excess to further maximize culture productivity and product quality. These treatments significantly impact critical quality attributes and furthermore highlight the degree to which trace metal availability can affect CHO cell culture performance. This review highlights the role of trace metal variability, supplementation, and interplay on key cellular mechanisms responsible for overall culture performance and the production and quality of therapeutic proteins.
Test and verification of micro coaxial line power performance (2012)

This paper presents the characterization of rectangular micro-coaxial transmission lines assembled in a high power test system. In addition to straight transmission lines, vertical solder transitions between stacked layers of rectangular coax are presented. These test assemblies utilize standard integration techniques and components: wire bond and flip-chip transitions and edge coaxial connectors. Assembled coax lines were tested at continuous wave power levels as high as 200 W at a frequency of 2 GHz. High frequency performance of the test assemblies is maintained throughout high power testing. Thermal models developed using a 3-D finite element method are utilized to understand limitations of micro-coaxial transmission lines at higher frequencies.
Relationship Between CYP2A6 and CHRNA5-CHRNA3-CHRNB4 Variation and Smoking Behaviors and Lung Cancer Risk (2011)

Genetic variations in the CYP2A6 nicotine metabolic gene and the CHRNA5-CHRNA3-CHRNB4 (CHRNA5-A3-B4) nicotinic gene cluster have been independently associated with lung cancer. With genotype data from ever-smokers of European ancestry (417 lung cancer patients and 443 control subjects), we investigated the relative and combined associations of polymorphisms in these two genes with smoking behavior and lung cancer risk. Kruskal-Wallis tests were used to compare smoking variables among the different genotype groups, and odds ratios (ORs) for cancer risk were estimated using logistic regression analysis. All statistical tests were two-sided. Cigarette consumption (P < .001) and nicotine dependence (P = .036) were the highest in the combined CYP2A6 normal metabolizers and CHRNA5-A3-B4 AA (tag single-nucleotide polymorphism rs1051730 G>A) risk group. The combined risk group also exhibited the greatest lung cancer risk (OR = 2.03; 95% confidence interval [CI] = 1.21 to 3.40), which was even higher among those who smoked 20 or fewer cigarettes per day (OR = 3.03; 95% CI = 1.38 to 6.66). Variation in CYP2A6 and CHRNA5-A3-B4 was independently and additively associated with increased cigarette consumption, nicotine dependence, and lung cancer risk. CYP2A6 and CHRNA5-A3-B4 appear to be more strongly associated with smoking behaviors and lung cancer risk, respectively.
Microphysiometry (1998)

Microphysiometry is a non-invasive, physiological method where measurement of metabolic activity can be made on living human tumor cells. Indirect measurement of the extracellular acidification is measured over a pH-sensitive silicon membrane. In this study microphysiometry was employed for the study of cytotoxic agents used in therapy of cancer. Standard cytotoxic drugs with different postulated mechanisms of action were investigated using cell lines as well as primary cultures of patient tumor cells. Each investigated cytotoxic drug induced a characteristic pattern of metabolic activity. From these patterns, key features, like stimulation and inhibition of acidification, the time point when the response curves of the drugs fall below the control curve, and the maximum inhibition of acidification at 20 h, could be quantified. Most of the investigated drugs showed some initial stimulation of acidification rate during the experiments. For drugs producing a reduced metabolic rate at 20 h a concentration-response relationship was observed. The drug effects measured at 20 h were irreversible and correlated reasonably well with parallel measurements of membrane integrity using a standard cytotoxicity test. The results demonstrate the feasibility of 'on-line' measurements of metabolic activity using this approach and also revealed an unexpected variety of drug response profiles.
Telomerase inhibition with an oligonucleotide telomerase template antagonist: in vitro and in vivo studies in multiple myeloma and lymphoma (2003)

The effects of telomerase inhibition with an oligonucleotide N3' --> P5' thiophosphoramidate (GRN163) complementary to the telomerase template region were examined on human multiple myeloma (MM) and non-Hodgkin lymphoma (NHL) cell lines, primary MM cells, and tumor xenografts. GRN163 treatment reduced telomerase levels in all cells and induced more rapid telomeric shortening. Continuous GRN163 treatment for 7 to 14 days resulted in proliferative arrest, morphologic changes, and apoptosis characteristic of cell crisis in tumor cell lines with short (1.7-5.4 kb) but not long (9-11 kb) telomeres. Intratumoral administration of GRN163 also inhibited the growth of MM and NHL xenografts established from cell lines with short telomeres (Hs602 lymphoma, 2.7 kb; CAG myeloma, 2.7 kb) and increased tumor apoptosis. However, GRN163 therapy of NHL xenografts established from cells with long telomeres (11.0 kb) had equivocal effects on tumor growth and did not induce apoptosis during this time frame. Systemic daily intraperitoneal administration of GRN163 in myeloma xenografts with short telomere lengths also decreased tumor telomerase levels and reduced tumor volumes. These data demonstrate that telomerase is important for the replication of mature B-cell neoplasia by stabilizing short telomeres, and they suggest that telomerase inhibition represents a novel therapeutic approach to MM and NHL.
Induction of chemosensitivity in human lung cancer cells in vivo by adenovirus-mediated transfer of the wild-type p53 gene. (1994)

Recombinant adenovirus-mediated transfer of the wild-type p53 gene into monolayer cultures or multicellular tumor spheroids of human non-small cell lung cancer cell line H358, which has a homozygous deletion of p53, markedly increased the cellular sensitivity of these cells to the chemotherapeutic drug cisplatin. Treated cells underwent apoptosis with specific DNA fragmentation. Direct injection of the p53-adenovirus construct into H358 tumors s.c. implanted into nu/nu mice, followed by i.p. administration of cisplatin, induced massive apoptotic destruction of the tumors. These results support the clinical application of a regimen combining gene replacement using replication-deficient wild-type p53 adenovirus and DNA-damaging drugs for treatment of human cancer.
Multiple Intestinal Neoplasia Caused by a Mutation in the Murine Homolog of the APC Gene (1992)

Germ-line mutations of the APC gene are responsible for familial adenomatous polyposis (FAP), an autosomal dominantly inherited disease in humans. Patients with FAP develop multiple benign colorectal tumors. Recently, a mouse lineage that exhibits an autosomal dominantly inherited predisposition to multiple intestinal neoplasia (Min) was described. Linkage analysis showed that the murine homolog of the APC gene (mApc) was tightly linked to the Min locus. Sequence comparison of mApc between normal and Min-affected mice identified a nonsense mutation, which cosegregated with the Min phenotype. This mutation is analogous to those found in FAP kindreds and in sporadic colorectal cancers.
[D-category VII depends on amino acid substitution Leu(110)Pro]. (1997)

A point mutation has been postulated as cause of the phenotype D category VII, based on data of 3 probands only. Repeatedly, D protein variants have been found to be due to heterogenous molecular events. Therefore, the aforementioned cause was to be tested with more probands. In a systematic study, 68 nonrelated probands with D category VII were found. 33 were selected by chance, and the nucleic acid region 280-329 was sequenced after PCR amplification. All examined probands showed the postulated Leu(110)Pro substitution. No further polymorphisms were detected. Our data show that in Southern Germany D category VII is homogenously due to the amino acid substitution Leu(110)Pro. This allows the exploitation of this polymorphism for the prenatal detection of D category VII and the related Tar antigen.
Isolation of the mouse Hox-2.9 gene; analysis of embryonic expression suggests that positional information along the anterior-posterior axis is specified by mesoderm (1990)

It is rapidly becoming accepted that the vertebrate neural tube, in particular the hindbrain, develops into a segmented structure. After segment formation, cells in the neural tube do not cross segmental boundaries, and segment-specific gene expression is observed. However, it is not known what positional cues instruct the neural tube to express genes in this restricted manner. We have cloned a murine homeobox-containing gene, Hox-2.9, whose expression in the neural tube at E9.5 is restricted to a segment of the hindbrain known as rhombomere 4. A study of its expression pattern earlier in development revealed that prior to the start of neurulation (E7.5) Hox-2.9 is expressed within a posterior to the embryonic mesoderm that will participate in hindbrain formation. With the onset of neurulation, expression then becomes detectable in the neural plate as well, but only in the part that overlies the Hox-2.9-expressing mesoderm; it is not detected in the more anterior neuroectoderm that will form the future midbrain and forebrain. On the basis of these findings, we propose that the mesoderm is providing cues that serve to instruct the overlying neuroectoderm with respect to its position along the anteroposterior axis and that Hox-2.9 participates in or reflects this process. As neurulation continues and individual segments form, a second phase of expression is detected in the neural tube in which high levels of Hox-2.9 transcripts become restricted to rhombomere 4. Hox-2.9 expression is also detected in the developing branchial arch units of the hindbrain region, in a pattern that suggests to us that here, too, mesoderm is providing a localized signal that induces Hox-2.9 expression, in this case in endoderm of the pharynx and in superficial ectoderm. In general, we interpret the expression patterns of Hox-2.9 in the hindbrain region as suggesting that the specific mechanisms of pattern formation in mammals are fundamentally similar to those of amphibians and avians - i.e. anteroposterior positional information is acquired by mesoderm, mesoderm induces positional values within (neuro-) ectoderm and endoderm, and both events occur within a restricted window of time.
Molecular pathology of prostate cancer (2005)

The molecular pathology of prostate cancer is complex; not only are multiple genes involved in its pathogenesis, but additional environmental factors such as diet and inflammation are also involved. The exhaustive research into prostate cancer to date has demonstrated a complex interaction of multiple genes and environmental factors, some of which may be more important in individual prostate cancer cases. This is an exciting era, with the emergence of new investigative tools such as DNA microarray technology and the application of the field of proteomics to the study of human cancers. Knowledge of genetic changes underlying the initiation, development, and progression of prostate cancer is accumulating rapidly. With increasing knowledge, it may be possible to distinguish indolent from aggressive prostate tumours by molecular fingerprinting. This review discusses the most consistently reported molecular pathological findings in hereditary and sporadic prostate cancer, together with new concepts and technologies.
Cadherins, catenins and APC in pleural malignant mesothelioma (2003)

Malignant mesothelioma is an aggressive disease of the pleura, and less commonly the peritoneum, with a very poor prognosis. The present study has examined the expression of cell adhesion molecules including cadherins, catenins, and APC in order to determine whether abnormal expression of components of the Wnt signalling pathway contribute to the variable phenotype of malignant mesothelioma. Sixty-three malignant mesotheliomas and nine cases of reactive mesothelial hyperplasia were analysed by immunohistochemistry for E-cadherin, N-cadherin, alpha-catenin, beta-catenin, and the C- and N-terminals of APC. In addition, DNA was extracted from formalin-fixed, paraffin wax blocks, and a 226 bp fragment of exon 3 of the beta-catenin gene was amplified, sequenced, and screened for activating mutations in the glycogen synthase kinase 3beta (GSK-3beta) phosphorylation targets. E-cadherin expression was detected in 48% of the epithelioid mesotheliomas but was observed in only 7% of sarcomatoid mesotheliomas. N-cadherin, alpha-catenin, beta-catenin, and the C- and N-terminals of APC did not show differential expression between the mesothelioma phenotypes. Abnormal nuclear localization of beta-catenin was demonstrated in 19% of mesotheliomas. Mutations of beta-catenin phosphorylation sites were not detected in any of the 62 mesotheliomas examined. Positive staining for the N-terminal of APC was seen in all of the cases of reactive mesothelial hyperplasia, as well as in all the mesotheliomas. Staining for the C-terminal of APC was negative in 23% mesotheliomas, despite being present in all the cases of reactive hyperplasia. The present study provides the first evidence that beta-catenin accumulates in the nucleus in malignant mesotheliomas. In addition, APC expression was altered in some mesotheliomas, suggesting that a truncated APC gene product may contribute to abnormal Wnt signalling and dysregulation of cell proliferation in malignant mesothelioma.
Production and characterization of monoclonal antibodies to type 8 lipooligosaccharide of Neisseria meningitidis (1992)

Eight monoclonal antibodies (MAbs) to lipooligosaccharides (LOSs) of Neisseria meningitidis were produced by immunizing mice with purified LOS from group A meningococcal strain A1. The specificities of the MAbs were examined by enzyme-linked immunosorbent assay (ELISA), immunodot assay, and ELISA inhibition by using the homologous A1 LOS, 12 immunotype LOSs of N. meningitidis (L1 through L12), and LOSs or lipopolysaccharides from other gram-negative bacteria. Two of the MAbs, 4385G7 (immunoglobulin G2b [IgG2b]) and 4387A5 (IgG2a), had the strongest reactivities with the homologous A1 LOS, moderate reactivities with the M978 (L8) LOS, but no reactivity with other LOSs. The other six MAbs (4 IgM and 2 IgG3) reacted with the A1 LOS and with several or many of the 12 LOSs. ELISA inhibition at 50% showed that the inhibitory activities of the LOSs from strains A1 and BB431 (a group B strain) to the specific MAb 4387A5 were about 10 to 20 times greater than that of the M978 (L8) LOS. When compared with MAb 2-1-L8 (L8) by Western blot (immunoblot) analysis and ELISA inhibition, the two specific MAbs recognized a different epitope in the 3.6-kDa LOSs of strains A1 and BB431. We propose that the new epitope is L8a, since the MAbs also reacted with the M978 (L8) LOS. The expression of the L8a epitope in the A1 LOS requires a few monosaccharide residues in its oligosaccharide moiety, and the fatty acid residues in its lipid A moiety also play a role. In a whole-cell ELISA, the two specific MAbs bound specifically to the homologous strain A1 and the L8 prototype strain M978 but not to any other LOS prototype strains. These results suggest that the two specific MAbs can be used for LOS typing of N. meningitidis.
Low glutelin content1: A Dominant Mutation That Suppresses the Glutelin Multigene Family via RNA Silencing in Rice[W] (2003)

Low glutelin content1 (Lgc1) is a dominant mutation that reduces glutelin content in rice grains. Glutelin is a major seed storage protein encoded by a multigene family. RNA gel blot and reverse transcriptase-mediated PCR analyses revealed that Lgc1 acts at the mRNA level in a similarity-dependent manner. In Lgc1 homozygotes, there is a 3.5-kb deletion between two highly similar glutelin genes that forms a tail-to-tail inverted repeat, which might produce a double-stranded RNA molecule, a potent inducer of RNA silencing. The hypothesis that Lgc1 suppresses glutelin expression via RNA silencing is supported by transgenic analysis using this Lgc1 candidate region, by reporter gene analysis, and by the detection of small interfering RNAs. In this context, Lgc1 provides an interesting example of RNA silencing occurring among genes that exhibit various levels of similarity to an RNA-silencing-inducing gene. Possible mechanisms for gene silencing of the glutelin multigene family by Lgc1 are discussed.
Cellular Response to an Antisense-mediated Shift of Bcl-x Pre-mRNA Splicing and Antineoplastic Agents (2002)

Overexpression of Bcl-xL, an anti-apoptotic member of the Bcl-2 family, negatively correlates with the sensitivity of various cancers to chemotherapeutic agents. We show here that high levels of expression of Bcl-xL promoted apoptosis of cells treated with an antisense oligonucleotide (5'Bcl-x AS) that shifts the splicing pattern of Bcl-x pre-mRNA from the anti-apoptotic variant, Bcl-xL, to the pro-apoptotic variant, Bcl-xS. This surprising finding illustrates the advantage of antisense-induced modulation of alternative splicing versus down-regulation of targeted genes. It also suggests a specificity of the oligonucleotide effects since non-cancerous cells with low levels of Bcl-xL should resist the treatment. 5'Bcl-x AS sensitized cells to several antineoplastic agents and radiation and was effective in promoting apoptosis of MCF-7/ADR cells, a breast cancer cell line resistant to doxorubicin via overexpression of the mdr1 gene. Efficacy of 5'Bcl-x AS combined with chemotherapeutic agents in the PC3 prostate cancer cell line may be translated to clinical prostate cancer since recurrent prostate cancer tissue samples expressed higher levels of Bcl-xL than benign prostate tissue. Treatment with 5'Bcl-x AS may enhance the efficacy of standard anti-cancer regimens and should be explored, especially in recurrent prostate cancer.
Substrate effect on the superconductivity of YBa/sub 2/Cu/sub 3/O/sub 7/ thin films (1988)

The interaction between the substrate and YBa/sub 2/Cu/sub 3/O/sub 7/ films made by ion beam sputtering and e-beam evaporation is found to significantly influence the superconducting transition temperature, T/sub c/. The substrates investigated are Al/sub 2/O/sub 3/, MgO, SrTiO/sub 3/, ZrO/sub 2/-9% Y/sub 2/O/sub 3/ (YSZ), and BaF/sub 2/. In the case of Al/sub 2/O/sub 3/, a spinel is formed at the interface and Al is found to be present in solution in the YBa/sub 2/Cu/sub 3/O/sub 7/. This reaction significantly depresses T/sub c/. For SrTiO/sub 3/, both Sr and Ti are found in the film without severely depressing the T/sub c/; this, however, depends on the annealing conditions. Although under similar conditions little interaction was observed for the MgO substrates, a moderate reduction in T/sub c/ was observed. An interaction zone of BaZrO/sub 3/ perovskite is formed at the interface between the YSZ substate and the 123 structure. In addition, Zr is found in solution in the 123 film. The presence of Zr has little effect on the T/sub c/. The films were characterized using Rutherford backscattering spectroscopy (RBS), transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), secondary ion mass spectroscopy (SIMS), x-ray and electron diffraction and resistance vsmore » temperature measurements.« less
Enzyme Activity in Invasive Tumors of Human Breast and Colon (1974)

Elevated levels of glycoprotein:sialyltransferase activity (EC 2.4.99.1; CMP-N-acetylneuraminate: D-galactosyl-glycoprotein N-acetylneuraminyltransferase) were found in human malignant neoplastic tissues compared to normal, benign, and "preneoplastic" tissues. This increase was not due to the cell density of the tissue. Elevated levels of certain proteases and glycosidases were also found. The increase in transferase activity may be associated with altered membrane synthesis in the neoplastic state; changes in the activity of degradative enzymes may be associated with tumor invasiveness and maintenance of the neoplastic state. Measurements on human tumors are possibly more directly relevant to cancer than those described for transformed fibroblastic cells in vitro.
Regulation of Sp2 DNA-Binding Activity and trans-Activation (2005)

Regulated transcription requires the collaboration of a variety of transcription factors, including sequence-specific DNA-binding proteins. The Sp-family of DNA-binding proteins governs the expression of a wide variety of mammalian genes, including housekeeping, cell cycle-regulated, and developmentally regulated genes. A wealth of information has been obtained about the functional and biochemical properties of two Sp-family members, Sp1 and Sp3, whereas studies of other Sp proteins have been limited. The purpose of this research has been to characterize the functional and biochemical properties of Sp2, and to provide insights into mechanisms regulating Sp2 DNA-binding activity and trans-activation.\n\n\tTo initiate my analysis of Sp2 I first identified its consensus DNA-binding sequence (5'-GGGCGGGAC-3') using a PCR-based protocol, and determined that Sp2 binds this sequence with high affinity in vitro (225 pM). Despite the incorporation of this consensus sequence within the promoter of a well-characterized Sp-dependent gene, I found that Sp2 was a relatively weak activator of transcription compared with Sp1 and Sp3. To begin to define mechanisms limiting Sp2 function, chimeric proteins carrying portions of Sp2 and Sp1 were created and analyzed. These studies demonstrated that Sp2 DNA-binding activity and trans-activation are each negatively regulated in mammalian cells.\n\nIn mixing experiments I detected an activity in mammalian extracts that abrogates Sp2 DNA-binding activity. I showed further that an 84 kDa mammalian protein bound to the trans-activation domain of Sp2, but not that of Sp1 or Sp3. Phosphatase treatment revealed that Sp2 DNA-binding activity requires phosphorylation, and phosphoamino acid analysis confirmed that Sp2 is phosphorylated in vivo. Size-exclusion chromatography indicated that Sp2 is specifically phosphorylated in vitro by an activity in fractions carrying high-molecular weight proteins or protein complexes. Indirect immunofluorescence studies indicated that, unlike other Sp proteins, the vast majority of Sp2 localizes to sub-nuclear foci associated with the nuclear matrix. The data reported herein indicates that Sp2 is functionally distinct from other Sp proteins, and provides insight into mechanisms that negatively regulate Sp2-mediated transcription. Taken together, my results suggest that Sp2 may perform a highly specialized role in the regulation of gene expression.