gebhart/patrepeval huggingface dataset:
ATR Mutation in Endometrioid Endometrial Cancer Is Associated With Poor Clinical Outcomes (2009)

PURPOSE Mutations in the DNA damage response gene ATR (exon 10 A10 mononucleotide repeat) have been previously described in endometrial and other cancers with defective DNA mismatch repair. In vitro studies showed that endometrial cancer cell lines with A10 repeat tract truncating mutations have a failure in the ATR-dependent DNA damage response. Cell lines carrying A10 mutations fail to trigger Chk1 activation in response to ionizing radiation and topoisomerase inhibitors. We sought to determine the frequency and clinicopathologic significance of ATR mutations in patients with endometrioid endometrial cancer. PATIENTS AND METHODS The ATR exon 10 A10 repeat was analyzed by direct sequencing in 141 tumors with microsatellite instability (MSI-positive) and 107 microsatellite stable (MSI-negative) tumors. The relationships between mutations and clinicopathologic variables, including overall and disease-free survival, were assessed using contingency table tests and Cox proportional hazard models. Results ATR mutations were identified in 12 cases (4.8%; three cases with insertions and nine cases with deletions). Mutations occurred exclusively in MSI-positive tumors (P = .02), with an overall mutation rate of 8.5%. Mutation was not associated with age, race, surgical stage, International Federation of Gynecology and Obstetrics grade, or adjuvant treatment. Multivariate analyses revealed a significant association with reduced overall survival (hazard ratio [HR] = 3.88; 95% CI, 1.64 to 9.18; P = .002) and disease-free survival (HR = 4.29; 95% CI, 1.48 to 12.45; P = .007). CONCLUSION Truncating ATR mutations in endometrial cancers are associated with biologic aggressiveness as evidenced by reduced disease-free and overall survival. Knowledge of ATR mutation status may hold promise for individualized treatment and targeted therapies in patients with endometrial cancer.
Trace elements in tissues of normal and vitamin D2-treated rats. (1975)

Comparative spectroscopic investigations were performed on 22 trace elements regarding their presence and quantitative relations in cartilages (costal cartilage, intervertebral disc) and in soft tissues most exposed to metastatic calcification (aorta, kidney) of normal, vitamin D2-treated and rachitic rats. The results revealed differences in concentration and distribution of trace elements between soft tissues and cartilages on the one hand, and untreated controls and vitamin D-treated rats on the other. On vitamin D treatment an increase in the Cr, Fe and Cu contents was noted in the soft tissues, whereas in cartilages a higher Zn content was shown. It is suggested that these trace elements may play an important role in the mechanism of calcification, some acting as challengers, others as adjuvants or inhibitors.
Beyond aerobic glycolysis: Transformed cells can engage in glutamine metabolism that exceeds the requirement for protein and nucleotide synthesis (2007)

Tumor cell proliferation requires rapid synthesis of macromolecules including lipids, proteins, and nucleotides. Many tumor cells exhibit rapid glucose consumption, with most of the glucose-derived carbon being secreted as lactate despite abundant oxygen availability (the Warburg effect). Here, we used 13C NMR spectroscopy to examine the metabolism of glioblastoma cells exhibiting aerobic glycolysis. In these cells, the tricarboxylic acid (TCA) cycle was active but was characterized by an efflux of substrates for use in biosynthetic pathways, particularly fatty acid synthesis. The success of this synthetic activity depends on activation of pathways to generate reductive power (NADPH) and to restore oxaloacetate for continued TCA cycle function (anaplerosis). Surprisingly, both these needs were met by a high rate of glutamine metabolism. First, conversion of glutamine to lactate (glutaminolysis) was rapid enough to produce sufficient NADPH to support fatty acid synthesis. Second, despite substantial mitochondrial pyruvate metabolism, pyruvate carboxylation was suppressed, and anaplerotic oxaloacetate was derived from glutamine. Glutamine catabolism was accompanied by secretion of alanine and ammonia, such that most of the amino groups from glutamine were lost from the cell rather than incorporated into other molecules. These data demonstrate that transformed cells exhibit a high rate of glutamine consumption that cannot be explained by the nitrogen demand imposed by nucleotide synthesis or maintenance of nonessential amino acid pools. Rather, glutamine metabolism provides a carbon source that facilitates the cell's ability to use glucose-derived carbon and TCA cycle intermediates as biosynthetic precursors.
A Peptide Motif Recognizing a Polymer Stereoregularity (2005)

A combinatorial phage display method was applied to films composed of a stereoregular polymer of methacrylates. The phage clones with selective affinity for isotactic (it) poly(methyl methacrylate) (PMMA) were isolated. Greater amounts of the phage clones bound to it-PMMA, compared to other stereoregular PMMAs. The phage expressing ELWRPTR most strongly bound to the polymer, and the selectivity was also the best. The peptide motif essential for the specific interaction with the stereoregular polymer was revealed.
Bipolar disorder: leads from the molecular and cellular mechanisms of action of mood stabilisers (2001)

Background New research is dramatically altering our understanding of the molecular mechanisms underlying neuronal communication. Aim To elucidate the molecular mechanisms underlying the therapeutic effects of mood stabilisers. Method Results from integrated clinical and laboratory studies are reviewed. Results Chronic administration of lithium and valproate produced a striking reduction in protein kinase C (PKC) isozymes in rat frontal cortex and hippocampus. In a small study, tamoxifen (also a PKC inhibitor) had marked antimanic efficacy. Both lithium and valproate regulate the DNA binding activity of the activator protein 1 family of transcription factors. Using mRNA differential display, it was also shown that chronic administration of lithium and valproate modulates expression of several genes. An exciting finding is that of a robust elevation in the levels of the cytoprotective protein, bcl-2. Conclusions The results suggest that regulation of signalling pathways may play a major part in the long-term actions of mood stabilisers. Additionally, mood stabilisers may exert underappreciated neuroprotective effects.
Glutathione Restores the Mechanism of Synaptic Plasticity in Aged Mice to That of the Adult (2011)

Glutathione (GSH), the major endogenous antioxidant produced by cells, can modulate the activity of N-methyl-D-aspartate receptors (NMDARs) through its reducing functions. During aging, an increase in oxidative stress leads to decreased levels of GSH in the brain. Concurrently, aging is characterized by calcium dysregulation, thought to underlie impairments in hippocampal NMDAR-dependent long-term potentiation (LTP), a form of synaptic plasticity thought to represent a cellular model for memory. Here we show that orally supplementing aged mice with N-acetylcysteine, a precursor for the formation of glutathione, reverses the L-type calcium channel-dependent LTP seen in aged animals to NMDAR-dependent LTP. In addition, introducing glutathione in the intrapipette solution during whole-cell recordings restores LTP obtained in whole-cell conditions in the aged hippocampus. We conclude that aging leads to a reduced redox potential in hippocampal neurons, triggering impairments in LTP.
Discovery of a Potent, Orally Active, Nonsteroidal Androgen Receptor Agonist:  4-Ethyl-1,2,3,4-tetrahydro-6- (trifluoromethyl)-8-pyridono[5,6-g]- quinoline (LG121071) (1999)

ADVERTISEMENT RETURN TO ISSUEPREVLetterNEXTDiscovery of a Potent, Orally Active, Nonsteroidal Androgen Receptor Agonist: 4-Ethyl-1,2,3,4-tetrahydro-6- (trifluoromethyl)-8-pyridono[5,6-g]- quinoline (LG121071)Lawrence G. Hamann, Neelakandha S. Mani, Robert L. Davis, Xiao-Ning Wang, Keith B. Marschke, and Todd K. JonesView Author Information Departments of Medicinal Chemistry, Endocrine Research, and New Leads Discovery, Ligand Pharmaceuticals, Inc., 10275 Science Center Drive, San Diego, California 92121. Cite this: J. Med. Chem. 1999, 42, 2, 210–212Publication Date (Web):January 8, 1999Publication History Received24 November 1998Published online8 January 1999Published inissue 1 January 1999https://doi.org/10.1021/jm9806648Copyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views1174Altmetric-Citations73LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (62 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Agonists,Antagonists,Assays,Quinolines,Receptors Get e-Alerts
Metabolic Engineering of a Pentose Metabolism Pathway in Ethanologenic Zymomonas mobilis (1995)

The ethanol-producing bacterium Zymomonas mobilis was metabolically engineered to broaden its range of fermentable substrates to include the pentose sugar xylose. Two operons encoding xylose assimilation and pentose phosphate pathway enzymes were constructed and transformed into Z. mobilis in order to generate a strain that grew on xylose and efficiently fermented it to ethanol. Thus, anaerobic fermentation of a pentose sugar to ethanol was achieved through a combination of the pentose phosphate and Entner-Doudoroff pathways. Furthermore, this strain efficiently fermented both glucose and xylose, which is essential for economical conversion of lignocellulosic biomass to ethanol.
A current view of tamoxifen for the treatment and prevention of breast cancer (1993)

Tamoxifen has been found to be a safe and effective treatment for all stages of breast cancer. Long term tamoxifen therapy is associated with some rare, but potentially serious, side effects so patients should be carefully monitored. However, long term tamoxifen therapy is also associated with a number of physiological benefits over and above its tumouristatic action. These benefits include a decrease in the development of contralateral breast cancer, the maintenance of bone density in postmenopausal women and a decrease in cardiovascular disease. The successful application of tamoxifen to treat breast cancer has increased enthusiasm to test its worth to prevent breast cancer. Although there are individual requests by patients for tamoxifen to prevent breast cancer, individual treatment is inappropriate. Tamoxifen can only be adequately evaluated as a preventive in randomized, double-blind clinical trials. These trials are in place and physicians should encourage women to participate and establish a new therapeutic option as rapidly as possible.
Lipoprotein receptor–related protein 6 is required for parathyroid hormone–induced Sost suppression (2015)

Parathyroid hormone (PTH) suppresses the expression of the bone formation inhibitor sclerostin (Sost) in osteocytes by inducing nuclear accumulation of histone deacetylases (HDACs) to inhibit the myocyte enhancer factor 2 (MEF2)-dependent Sost bone enhancer. Previous studies revealed that lipoprotein receptor-related protein 6 (LRP6) mediates the intracellular signaling activation and the anabolic bone effect of PTH. Here, we investigated whether LRP6 mediates the inhibitory effect of PTH on Sost using an osteoblast-specific Lrp6-knockout (LRP6-KO) mouse model. An increased level of Sost mRNA expression was detected in femur tissue from LRP6-KO mice, compared to wild-type littermates. The number of osteocytes expressing sclerostin protein was also increased in bone tissue of LRP6-KO littermates, indicating a negative regulatory role of LRP6 on Sost/sclerostin. In wild-type littermates, intermittent PTH treatment significantly suppressed Sost mRNA expression in bone and the number of sclerostin(+) osteocytes, while the effect of PTH was much less significant in LRP6-KO mice. Additionally, PTH-induced downregulation of MEF2C and 2D, as well as HDAC changes in osteocytes, were abrogated in LRP6-KO mice. These data indicate that LRP6 is required for PTH suppression of Sost expression.
Molecular mechanisms of acquired resistance to tyrosine kinase targeted therapy (2010)

In recent years, tyrosine kinases (TKs) have been recognized as central players and regulators of cancer cell proliferation, apoptosis, and angiogenesis, and are therefore considered suitable potential targets for anti-cancer therapies. Several strategies for targeting TKs have been developed, the most successful being monoclonal antibodies and small molecule tyrosine kinase inhibitors. However, increasing evidence of acquired resistance to these drugs has been documented, and extensive preclinical studies are ongoing to try to understand the molecular mechanisms by which cancer cells are able to bypass their inhibitory activity.This review intends to present the most recently identified molecular mechanisms that mediate acquired resistance to tyrosine kinase inhibitors, identified through the use of in vitro models or the analysis of patient samples. The knowledge obtained from these studies will help to design better therapies that prevent and overcome resistance to treatment in cancer patients.
Aluminum complexes containing salicylbenzoxazole ligands and their application in the ring-opening polymerization of rac-lactide and ε-caprolactone (2016)

Two series of four-coordinate aluminum () and five-coordinate aluminum () complexes were successfully synthesized via the reactions between the corresponding salicylbenzoxazole ligands and 1 or 0.5 equivalents of AlMe3, respectively. The synthesized aluminum complexes were characterized by (1)H and (13)C NMR spectroscopy and elemental analysis. The solid-state structures of complexes and were determined using single crystal X-ray diffraction. Upon addition of 1 equivalent of benzyl alcohol, all complexes were efficient initiators for the ring-opening polymerization (ROP) of rac-lactide (rac-LA) and ε-caprolactone (ε-CL). The polymerizations were living with a good control over molecular weights and molecular weight distributions. Under immortal polymerization conditions, all four-coordinate aluminum complexes () exhibited a living polymerization with the obtained molecular weights proportional to the ratio of monomer/benzyl alcohol and the PDIs were narrow. Kinetic studies revealed that both rac-LA and ε-CL polymerizations mediated by all complexes were first-order in monomers. The effects of ligand structure and coordination geometry on the catalytic activity and stereoselectivity were discussed. A good isoselectivity control was achieved for the polymerizations mediated by complexes (Pm = 0.75), (Pm = 0.74), and (Pm = 0.74).
Optimal Design of Monolithic Integrated DC-DC Converters (2006)

Increasing supply current of high-performance microprocessors and limited real-estate available for power delivery in mobile platforms have spurred research of monolithic integrated DC-DC converters. Based on a model for the three key power loss mechanisms we derive an analytical solution for the optimal DC-DC converter design, linking power efficiency directly to CMOS front-end parameters and inductor technology. Further analysis shows that source-drain leakage, skin effect, eddy currents, and routing parasitics, although significant, don't change the optimal design
Morbidity and mortality of chronic GVHD after hematopoietic stem cell transplantation from HLA-identical siblings for patients with aplastic or refractory anemias (2002)

We analyzed effects of successive changes in prevention and treatment of chronic GVHD in 405 patients with aplastic anemia and refractory anemia given HLA-matched hematopoietic stem cell transplantation (HSCT) from 1970-1997. For analysis, patients were divided into group I, transplantations from 1970-1976; group II, 1977-1983; group III, 1984-1990; and group IV, 1991-1997. The overall incidence of chronic GVHD was 28%. Incidences of chronic GVHD for groups I through IV were 20%, 46%, 41%, and 22%, respectively, reflecting added buffy coat infusions in groups II and III. Five-year survival rates of patients with chronic GVHD for groups I through IV were 58%, 74%, 82%, and 76%, respectively (NS). Among group I patients, 50% were alive off immunosuppression, none were alive on immunosuppression, and 50% died. These figures were 76%, 0%, and 24% in group II; 80%, 10%, and 10% in group III; and 64%, 21%, and 14% in group IV patients. More serious infections and skin contractures were seen in group I than in groups II, III, and IV (P = .0001, .02, .01 and P =.0003, .001, .05, respectively). Lung complications, aseptic necroses, depression, and Karnofsky scores were comparable among groups. Gastrointestinal complications seemed less frequent among groups II through IV. Diabetes mellitus was more frequent in group IV than in groups I through III (P = .008). Secondary malignancies occurred in 33%, 6%, 3%, and 0% of patients in the 4 groups, respectively. In conclusion, over 28 years, chronic GVHD has remained challenging, with only slight improvements in quality of life. Decisive improvements in therapy and survival will have to await both a better understanding of the immunological events underlying chronic GVHD and better infection prevention and control.
Vaccination with Plasmid DNA Activates Dendritic Cells via Toll-Like Receptor 9 (TLR9) but Functions in TLR9-Deficient Mice (2003)

We analyzed whether the immunobiology of vaccinating plasmid DNA containing a transcription unit for OVA is influenced by immunostimulatory CpG motifs in the plasmid backbone. Indeed, plasmid DNA differentially activated in vitro myeloid and plasmacytoid dendritic cells (DCs) provided they expressed the CpG-DNA receptor, Toll-like receptor 9 (TLR9). Dependent on the DC subset, activation resulted in type 1 IFN production, while both DC subsets produced IL-6 and up-regulated expression of costimulatory molecules CD40 and CD86. In vivo, however, even upon repeated vaccination with plasmid DNA, priming of OVA-specific CTL and clonal expansion of SIINFEKL-specific CD8 T cells were equal in TLR9-positive and TLR9- or MyD88-negative mice. Overall, these results negate a dominant role of CpG-DNA/TLR9 interactions in long-term vaccination protocols.
Plastid‐localised seed acyl‐carrier protein of Brassica napus is encoded by a distinct, nuclear multigene family (1988)

Acyl-carrier protein (ACP) is a key component involved in the regulation of fatty acid biosynthesis in plants. cDNA clones encoding ACP from Brassica napus (oil seed rape) embryos have been isolated using oligonucleotide probes derived from heterologous ACPs. Analysis of the DNA sequence data, in conjunction with N-terminal amino acid sequence data, revealed ACP to be synthesized from nuclear DNA as a precursor containing a 51-amino-acid N-terminal extension. Immunocytochemical studies showed ACP to be localised solely within the plastids of B. napus seed tissue and it would therefore appear that the N-terminal extension functions as a transit peptide to direct ACP into these organelles. Analysis of several cDNA clones revealed sequence heterogeneity and thus evidence for an ACP multigene family. From ten cDNA clones, six unique genes, encoding five different mature ACP polypeptides, were identified. Northern blot hybridisation studies provide evidence that the seed and leaf forms of rape ACP are encoded by structurally distinct gene sets.
Rapid analysis of gene expression (RAGE) facilitates universal expression profiling (1999)

Current techniques for analysis of gene expression either monitor one gene at a time, for example northern hybridization or RT-PCR methods, or are designed for the simultaneous analysis of thousands of genes, for example microarray hybridization or serial analysis of gene expression. To provide a flexible, intermediate scale alternative, a PCR-based method for the rapid analysis of gene expression has been developed which allows expression changes to be determined in either a directed search of known genes, or an undirected survey of unknown genes. A single set of reagents and reaction conditions allows analyses of most genes in any eukaryote. The method is useful for assaying on the order of tens to hundreds of genes in multiple samples. Control experiments indicate reliable detection of changes in gene expression 2-fold and greater, and sensitivity of detection better than 1 in 10 000. Analyses of over 400 genes in a mouse system transgenic for the E2F1 gene have identified several new downstream targets of E2F1, including Brca1 and Cdk7, in addition to several unidentified genes that are upregulated in the transgenic mice. Changes in expression of several genes related to apoptosis suggest a possible potentiation of apoptotic pathways in the transgenic keratinocytes.
Structural basis for ineffective T‐cell responses to MHC anchor residue‐improved “heteroclitic” peptides (2014)

MHC anchor residue-modified "heteroclitic" peptides have been used in many cancer vaccine trials and often induce greater immune responses than the wild-type peptide. The best-studied system to date is the decamer MART-1/Melan-A26-35 peptide, EAAGIGILTV, where the natural alanine at position 2 has been modified to leucine to improve human leukocyte antigen (HLA)-A*0201 anchoring. The resulting ELAGIGILTV peptide has been used in many studies. We recently showed that T cells primed with the ELAGIGILTV peptide can fail to recognize the natural tumor-expressed peptide efficiently, thereby providing a potential molecular reason for why clinical trials of this peptide have been unsuccessful. Here, we solved the structure of a TCR in complex with HLA-A*0201-EAAGIGILTV peptide and compared it with its heteroclitic counterpart , HLA-A*0201-ELAGIGILTV. The data demonstrate that a suboptimal anchor residue at position 2 enables the TCR to "pull" the peptide away from the MHC binding groove, facilitating extra contacts with both the peptide and MHC surface. These data explain how a TCR can distinguish between two epitopes that differ by only a single MHC anchor residue and demonstrate how weak MHC anchoring can enable an induced-fit interaction with the TCR. Our findings constitute a novel demonstration of the extreme sensitivity of the TCR to minor alterations in peptide conformation.
SPRING: a kinetic interface for visualizing high dimensional single-cell expression data (2017)

Supplementary data are available at Bioinformatics online.