gebhart/patrepeval huggingface dataset:
A genetic switch : phage λ and higher organisms (1992)

1. The Master Elements of Control:Components of the SwitchThe Action of Repressor and CroInduction - Flipping the SwitchCooperativity - Switch Stability and SensitivityThe Effect of AutoregulationOther Cases2. Protein-DNA Interactions and Gene Control:The OperatorRepressorCroAmino Acid-Base Pair InteractionsThe PromoterGene Control3. Control Circuits - Setting the Switch:A Brief Overview of Lambda GrowthControl of TranscriptionThe DecisionControl of Integration and ExcisionOther PhagesThe SOS ResponsePathways and Cell Development4. How do we Know - The Key Experiments:The Repressor IdeaThe Repressor Problem in the Early 1960sRepressor Isolation and DNA-BindingMaking More RepressorThe Claims of Chapters One and Two5. Eukaryotic Gene Regulation - An Overview:IntroductionEukaryotic Genes and their PolymerasesActivationRepressionCooperativityRegulators Assembled for Non-identical ComponentsSpeculations on Development and EvolutionCaveats6. Eukaryotic Gene Regulation - Experiments and Examples:BackgroundTwo Functions of an Activator: DNA Binding and ActivationDNA Binding StructuresActivating RegionsAction at a Distance- LoopingActivation In Vivo and In VitroSquelchingRepressionRegulators Assembled from Non-identical ComponentsMore CooperativityThe Case of EveConclusion Appendix OneDesigning an Efficient DNA-binding ProteinAppendix TwoStrong and Weak InteractionsAppendix ThreeControl of Transcription in Eukaryotes and Prokaryotes - a common mechanism
Improved Synthesis of Isogranulatimide, a G2 Checkpoint Inhibitor. Syntheses of Didemnimide C, Isodidemnimide A, Neodidemnimide A, 17-Methylgranulatimide, and Isogranulatimides A−C (1999)

A concise, improved synthesis of isogranulatimide (6), a naturally occurring substance with G2 checkpoint inhibition activity, is described. Also reported are the syntheses of didemnimide C (18), isodidemnimide A (24), neodidemnimide A (36), 17-methylgranulatimide (9), and isogranulatimides A (10), B (11), and C (12). Compounds 9-12, congeners of isogranulatimide (6), are now available for biological evaluation.
Type I phosphatidylinositol 4-phosphate 5-kinase isoforms are specifically stimulated by phosphatidic acid (1994)

A phosphatidylinositol 4-phosphate (PIP) kinase was isolated and purified to near homogeneity from bovine erythrocyte membranes. The PIP kinase was extracted from bovine erythrocyte membranes with a high salt wash, followed by phosphocellulose and phenyl-Sepharose chromatography. The predominant protein after phenyl-Sepharose purification had a molecular size of 68 kDa. Renaturation of PIP kinase activity after SDS-PAGE showed that a 68-kDa protein was able to phosphorylate PIP. An antibody developed against the 68-kDa protein Western blots the 68-kDa protein and is able to immunoprecipitate the 68-kDa protein and PIP kinase activity from membrane extracts. Based on functional studies, the 68-kDa protein is indistinguishable from the type I PIP kinase previously characterized from human erythrocyte membranes (Bazenet, C. E., Ruano, A.R., Brockman, J.L., and Anderson, R.A. (1990) J. Biol. Chem. 265, 18012-18022). These studies also show that the type I PIP kinases, but not the type II PIP kinase, are stimulated by phosphatidic acid, suggesting alternative roles for these enzymes. Two immunoreactive isoforms of the type I PIP kinase, of 68 and 90 kDa, were identified in rat brain and partially purified. Both of these isoforms are also stimulated by phosphatidic acid.
A 3.3 V 32 Mb NAND flash memory with incremental step pulse programming scheme (1995)

While the performance of flash memory exceeds hard disk drives in almost every category, the cost of flash memory must come down in order to gain wider acceptance in mass storage applications. This paper describes a 3.3 V-only 32 Mb NAND flash memory that achieves not only high performance but also low cost with a 94.9 mm/sup 2/ die size, improved yields, and a simple process with 0.5 /spl mu/m CMOS technology. Die size is reduced by eliminating high voltage operation on the bitlines through a self boosted program inhibit voltage generation scheme. Incremental-step-pulse programming results in a 2.3 MB/s program data rate as well as improved process variation tolerance. Interleaved data paths and a boosted wordline results in a 25 ns burst cycle time and a 24 MB/s read data rate. Maximum operating current is less than 8 mA.
Photoaffinity labeling of thyroid hormone nuclear receptors. Influence of n-butyrate and analysis of the half-lives of the 57,000 and 47,000 molecular weight receptor forms. (1984)

The thyroid hormone receptor is a nuclear-associated protein which appears to mediate the actions of 3,5,3'-triiodo-L-thyronine (L-T3) and 3,5,3',5'-tetraiodo-L-thyronine (L-T4) in mammalian cells. In a previous study we reported that N-2-diazo-3,3,3-trifluoropropionyl-3,5,3'-triiodo-L-thyronine (L-T3-PAL) serves as an effective photoaffinity label probe of the receptor in GH1 cells, a growth hormone producting rat pituitary cell line. Irradiation of cells at 254 nm covalently cross-links L-[125I]T3-PAL to two molecular weight (Mr) nuclear receptor forms, an abundant 47,000 Mr component and a less abundant 57,000 Mr species (Pascual, A., Casanova, J., and Samuels, H. H. (1982) J. Biol. Chem. 257, 9640-9647). In this study we have explored a number of possible interrelationships of the different Mr receptor forms. Denaturing gel electrophoresis and autoradiography indicates that the 57,000 Mr form is a doublet species which differ in Mr by 1,000 to 2,000. The various receptor forms are not an artifact of the L-[125I]T3-PAL probe, and identical forms can be labeled at 310 nm using underivatized L-[125I]T4 with a 15-fold lower coupling efficiency. The 57,000 and 47,000 Mr receptor forms are not generated by indiscriminate proteolysis, UV peptide cleavage, or zero length protein-protein cross-linking by irradiation at 254 nm. Micrococcal nuclease excises both the 57,000 and 47,000 Mr forms, and receptor is not identified in the residual nuclear matrix fraction. Receptor is also not detected in the cytoplasmic fraction. By coupling dense amino acid labeling and photoaffinity labeling of receptor we determined a half-life of 2.4 h for the 57,000 Mr species and 5.6 h for the 47,000 Mr form while both species have similar relative synthetic rates. n-Butyrate has been previously shown to decrease receptor levels in GH1 cells. We demonstrate that n-butyrate decreases receptor levels primarily by shortening the half-life of the 47,000 Mr form.
Microsoft Office Infopath 2003: Kick Start (2004)

Microsoft InfoPath 2003 Kick Start builds upon the reader's knowledge of the Microsoft Office system to enable them to get right to work making productive use of InfoPath. It is targeted specifically at the early adopters - developers who will use their knowledge of XML and Web development to build sophisticated applications with InfoPath ends. However it is also, carefully structured to enable front line InfoPath users to quickly glean the information they need to be productive when developing their own InfoPath forms - and when working with developers to create more involved InfoPath applications.
Chronic heart failure leads to an expanded plasma volume and pseudoanaemia, but does not lead to a reduction in the body's red cell volume (2008)

Aims Chronic heart failure (CHF) is frequently associated with a decreased haemoglobin level, whereas the mechanism remains largely unknown. Methods and results One hundred consecutive CHF patients without anaemia or renal dysfunction based on non-cardiac reasons were enrolled. We explored determinants of anaemia (as iron parameters, erythropoietin, hepcidin and kidney function) including red cell volume (RCV) (by a 51 Cr assay) as well as related markers and plasma volume. The influence of each factor on haemoglobin concentrations was determined in a multiple regression model. Mean haemoglobin concentrations were 11.7 +/- 0.8 mg/dL in anaemic CHF patients and 14.4 +/- 1.2 mg/dL in non-anaemic patients. Corrected reticulocytes were lower in anaemic patients (35.1 +/- 15.7 vs. 50.3 +/- 19.2 G/L, P = 0.001), but the RCV was not reduced (1659.3 +/- 517.6 vs. 1826.4 +/- 641.3 mL, P = 0.194). We found that plasma volumes were significantly higher in anaemic CHF patients (70.0 +/- 2.4 vs. 65.0 +/- 4.0%, P < 0.001). Plasma volume was the best predictor of haemoglobin concentrations in the regression model applied (B = -0.651, P < 0.001, R(2) = 0.769). Conclusion Haemodilution appears to be the most potent factor for the development of low haemoglobin levels in patients with CHF. Our data support an additional independent, but minor influence of iron deficiency on haemoglobin concentrations in CHF patients.
Cleansing Noisy City Names in Spatial Data Mining (2010)

One of the biggest adversaries to data mining from a large data warehouse is poor data quality. It is because most data mining algorithms have been designed based on the assumption that the data is clean and meaningful. Hence, poor data quality may lead to completely unexpected results. In this paper, an automatic city name correction algorithm is proposed to cleanse a large spatial database without requiring human intervention or a prior knowledge of the context. The algorithm achieves a precision of 96.6% which is significantly better than the 86.6% of the traditional Levenshtein distance and the 92% of the Longest Common Subsequence algorithm.
Vaccination with myelin oligodendrocyte glycoprotein adsorbed to alum effectively protects DBA/1 mice from experimental autoimmune encephalomyelitis (2003)

To prevent an organism from developing autoimmunity the body limits the number of autoreactive cells through thymic negative selection and regulates their activity through induction of suppressor T cells. Development of antigen-specific therapies provides an interesting opportunity to imitate the body's own, often effective, method of protection. Our study demonstrates that DBA/1 mice could be protected from experimental autoimmune encephalomyelitis induced through injection of recombinant myelin oligodendrocyte glycoprotein (rMOG) when they were previously immunized intraperitoneally with rMOG adsorbed to aluminium hydroxide. This protection was associated with a decreased IFN-gamma production by rMOG-specific cells, but not a decreased proliferative response. Protection was long lasting, indicating that MOG-alum vaccination might be developed as a prophylactic therapy in multiple sclerosis.
LIGHT CONTROL OF PLANT DEVELOPMENT (1997)

To grow and develop optimally, all organisms need to perceive and process information from both their biotic and abiotic surroundings. A particularly important environmental cue is light, to which organisms respond in many different ways. Because they are photosynthetic and non-motile, plants need to be especially plastic in response to their light environment. The diverse responses of plants to light require sophisticated sensing of its intensity, direction, duration, and wavelength. The action spectra of light responses provided assays to identify three photoreceptor systems absorbing in the red/far-red, blue/near-ultraviolet, and ultraviolet spectral ranges. Following absorption of light, photoreceptors interact with other signal transduction elements, which eventually leads to many molecular and morphological responses. While a complete signal transduction cascade is not known yet, molecular genetic studies using the model plant Arabidopsis have led to substantial progress in dissecting the signal transduction network. Important gains have been made in determining the function of the photoreceptors, the terminal response pathways, and the intervening signal transduction components.
Peripheral-Type Benzodiazepine Receptor Function in Cholesterol Transport. Identification of a Putative Cholesterol Recognition/Interaction Amino Acid Sequence and Consensus Pattern (1998)

In steroid-synthesizing cells, like the MA-10 mouse tumor Leydig cells, the peripheral-type benzodiazepine receptor (PBR) is an outer mitochondrial membrane protein involved in the regulation of cholesterol transport from the outer to the inner mitochondrial membrane, the rate-determining step in steroid biosynthesis. Expression of PBR in Escherichia coli DE3 cells, which have no PBR, no cholesterol, and do not make steroids, induced the ability to take up cholesterol in a time-dependent, temperature-sensitive, and energy- independent manner. These cells took up no other steroids tested. Addition of the high affinity PBR ligand PK 11195 to cholesterol-loaded membranes, obtained from cells transfected with PBR, resulted in the release of the uptaken cholesterol. Expression in DE3 cells of mutant PBRs demonstrated that deletions in the cytoplasmic carboxy-terminus dramatically reduced the cholesterol uptake function of PBR, although it retained full capacity to bind PK 11195. Site-directed mutagenesis in the carboxy-terminal region of PBR demonstrated that bacteria expressing the mutant PBR proteins PBR(Y153S) and PBR(R156L) do not accumulate cholesterol, suggesting that amino acids Y153 and R156 are involved in the interaction of the receptor with cholesterol. Considering these results, we postulate the existence of a common cholesterol recognition/interaction amino acid consensus pattern (–L/V-(X)1–5-Y-(X)1–5-R/K-). Indeed, we found this amino acid consensus pattern in all proteins shown to interact with cholesterol. In conclusion, these data suggest that the expression of PBR confers the ability to take up and release, upon ligand activation, cholesterol. Considering the widespread occurrence of this protein and its tissue and cell specific subcellular localization, these results suggest a more general role of PBR in intracellular cholesterol transport and compartmentalization.
Parathyroid Hormone Bone Anabolic Action Requires Cbfa1/Runx2-Dependent Signaling (2003)

The Cbfa1/Runx2 (referred to herein as Cbfa1) transcription factor has been shown to be essential for osteoblast differentiation and bone formation during embryogenesis. PTH given intermittently is a proven bone anabolic agent. Here, we investigated whether PTH regulates the expression and/or activity of Cbfa1 in osteoblastic cells and in a rat metatarsal organ culture assay. PTH was found to regulate Cbfa1 mRNA in the rat osteosarcoma cell line UMR106 in a concentration-dependent manner. The effect of PTH was mimicked by forskolin, an activator of adenylate cyclase leading to the protein kinase A pathway. PTH administered intermittently for 5 d in vivo was found to stimulate Cbfa1 protein in the rat proximal tibiae metaphysis. To demonstrate PTH regulation of Cbfa1 activity, a construct containing six tandem Cbfa1 binding elements fused to luciferase was shown to be rapidly stimulated in response to PTH. This stimulation preceded the effects on mRNA regulation and resulted from a protein kinase A-mediated increase in Cbfa1 activity. Finally, using a neonate rat metatarsal organ culture system, we demonstrated dose-dependent anabolic responsiveness to PTH and to Cbfa1 overexpression from an adenoviral construct. We further showed that Cbfa1 antisense oligonucleotides that blocked adenoviral Cbfa1-induced anabolic effects in this organ culture model also abolished the PTH-mediated anabolic increase. These findings suggest a requirement for Cbfa1 in mediating the anabolic effects of PTH. Thus, regulation of Cbfa1 expression or activity is an important mechanism by which PTH controls osteoblast function.
Substituent effects of the trifluoromethyl group on electrophilic additions to alkenes. Solvolysis of the trifluoromethyl group. Protonation of alkenes less basic than ethylene, .rho.+ values of deactivated styrenes, and reactivity-selectivity effects (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSubstituent effects of the trifluoromethyl group on electrophilic additions to alkenes. Solvolysis of the trifluoromethyl group. Protonation of alkenes less basic than ethylene, .rho.+ values of deactivated styrenes, and reactivity-selectivity effectsK. M. Koshy, Danielle Roy, and Thomas T. TidwellCite this: J. Am. Chem. Soc. 1979, 101, 2, 357–363Publication Date (Print):January 1, 1979Publication History Published online1 May 2002Published inissue 1 January 1979https://pubs.acs.org/doi/10.1021/ja00496a014https://doi.org/10.1021/ja00496a014research-articleACS PublicationsRequest reuse permissionsArticle Views406Altmetric-Citations36LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Platelet storage for transfusion. (1986)

An overview is given about the different variables which are of influence during platelet storage. After reinfusion of 51Cr-labeled platelets of PRP stored in first generation containers and evaluation of in vivo recovery and half life optimum, range of storage temperature was found to be 20-24 degrees C. Storage of PC in first generation containers showed a significant fall of pH which was in a clear relationship to platelet concentration, lactate production, and glucose consumption. If pH fell below 6.0 irreversible morphological changes and decrease of in vivo recovery/survival was observed. The second generation containers (PL-732, CLX, PL-1240) resulted in superior pH maintenance which was due to superior O2 and CO2 transport through the walls of the bags and a lower rate of glycolysis. In vivo recovery showed a gradual decline from 57% for fresh platelets to 42% after 7-day-storage. Platelet survival curves after 7-day-storage lay just at the lower limit of the range for fresh platelets. The success of prolonged storage depends critically on the mode of agitation used which was demonstrated by comparing three different agitators. A lot of questions remain still to be answered concerning the substrates of the oxidative metabolism, the morphological changes, and especially the in vitro function of platelets after prolonged storage.
Helper T Cell Recognition of Respiratory Syncytial Virus in Mice (1988)

In this study we aimed to define the protein and viral subtype specificities of helper Th cells to respiratory syncytial virus (RSV). BALB/c mice were primed by infection with RSV, or with vaccinia viruses (VV) containing genes encoding several individual RSV proteins. Priming for Th cell memory was assayed by stimulating spleen cells in vitro with different RSV isolates and measuring RSV-specific interleukin 2 (IL-2) release by T cells into supernatants using an IL-2-dependent CTLL cell line. Splenocytes from mice primed intranasally with RSV exhibited RSV-specific Th cell memory, whereas those from unprimed mice did not. Th cell recognition was in part specific to the strain of RSV used in priming and in part cross-reactive between RSV strains. Intraperitoneal priming with RSV fusion protein-expressing VV or nucleoprotein-expressing VV induced a stronger RSV-specific Th cell response than the attachment glycoprotein-expressing VV which produced only slight Th recognition. No Th cell recognition of two non-structural proteins (1A and 1B) could be demonstrated.
Intake of polyunsaturated fatty acids and vitamin E reduces the risk of developing amyotrophic lateral sclerosis (2006)

A high intake of PUFAs and vitamin E is associated with a 50-60% decreased risk of developing ALS, and these nutrients appear to act synergistically.
PDX-1 and Cell-Cell Contact Act in Synergy to Promote δ-Cell Development in a Human Pancreatic Endocrine Precursor Cell Line (2000)

Cell lines from the fetal and adult pancreas that were developed by retroviral transfer of the SV40T and ras(val12) oncogenes lose insulin expression but retain extremely low levels of somatostatin and glucagon mRNA. In contrast to expanded populations of primary human islet cells, none of them express the homeodomain transcription factor PDX-1. When that factor was expressed in the cell lines by retroviral-mediated gene transfer, one of the cell lines, TRM-6, derived from human fetal islets, exhibited a 10- to 100-fold increase in somatostatin gene expression. This is the first report of induction of the endogenous somatostatin gene by PDX-1. Promotion of cell-cell contact by aggregation of TRM-6/PDX-1 into islet-like clusters produced a further 10- to 100-fold increase in somatostatin mRNA, to a level similar to that of freshly isolated islets, which resulted in production of somatostatin protein. Thus, we demonstrate here that signals induced by cell-cell contact act in synergy with PDX-1 to up-regulate the endogenous somatostatin promoter in an immortalized cell line from human fetal islets. This system provides a powerful model for studying human islet cell development and, particularly, the role of cell-cell contact in the differentiation process.
Radiofrequency Ablation of Unresectable Hepatic Malignancies: Lessons Learned (2001)

Radiofrequency ablation (RFA) is increasingly used for the local destruction of unresectable hepatic malignancies. Relative contraindications include tumors in proximity to vital structures that may be injured by RFA and lesions whose size exceeds the ablation capabilities of the probe system employed. Given current technology, we believe that RFA should be cautiously utilized for lesions greater than 5 cm in diameter. Open (celiotomy) and laparoscopic approaches to RFA allow intraoperative ultrasonography, which may demonstrate occult hepatic disease. In addition, RFA performed via celiotomy can be accompanied by resection or cryosurgical ablation, and isolation of the liver from adjacent organs. Percutaneous RFA should be reserved for patients who cannot undergo general anesthesia, those with recurrent or progressive lesions, and those with smaller lesions sufficiently isolated from adjacent organs. Complications may be minimized when these approaches are selectively applied.
Can radiation-induced apoptosis be modulated by inhibitors of energy metabolism? (2007)

Both 2DG and azide can influence radiation-induced apoptosis possibly through their effects on glycolysis and ATP levels. We suggest that modulation of energy metabolism provides mechanistic insight into radiation-induced apoptotic pathways.
A restriction endonuclease analysis of the bacterial plasmid controlling the ecoRI restriction and modification of DNA. (1976)

Genetic analyses of DNA restriction and modification mechanisms have been encumbered by the inability to rigorously select for mutant phenotypes associated with these systems. The application of restriction endonucleases has now proved to be a successful approach to the genetic analyses of small genomes that are recalcitrant to the more standard genetic techniques. Restriction endonucleases EcoRI and HindIII were used to analyze the structure of the plasmid genome responsible for the EcoRI restriction endonuclease and modification methylase. This plasmid in the original clinical isolate of Escherichia coli appears to be identical to the ColE 1 plasmid except for a 1.95 kilobase pair segment which contains these genes. A preliminary restriction map of this plasmid is presented.