gebhart/patrepeval huggingface dataset:
The Receptor-DNA Complex Determines the Retinoid Response: a Mechanism for the Diversification of the Ligand Signal (1996)

To obtain insights into the principles governing the complex biological responses to retinoids, we have analyzed the ligand sensitivities of various retinoid receptor-DNA complexes. We find that different retinoid receptor heterodimers show distinct activation patterns with various response elements while a given heterodimer can be activated at different retinoic acid concentrations on different response elements. In vitro binding experiments suggest that the same retinoic acid receptor-retinoid X receptor (RAR-RXR) heterodimer can have different ligand affinities, depending on the response element it is bound to. The differential responses of a particular receptor heterodimer with various retinoic acid responsive elements can be enhanced through the use of conformationally restricted retinoids. RAR- and RXR-selective retinoids can also synergistically activate the receptor heterodimers, indicating that both partners in the heterodimer can contribute to ligand-induced transcriptional activation. However, the relative influence of the RAR or RXR partner is specific for each response element. Together, our data demonstrate that it is the receptor-DNA complex and not the receptor alone that determines the ligand response. This flexibility allows for a highly pleiotropic retinoid response. Furthermore, conformationally restricted retinoids can accentuate the differential responses and exhibit a certain degree of gene selectivity by differentially activating the RAR or RXR component in the context of a given response element.
Role of the yiaR and yiaS Genes of Escherichia coli in Metabolism of Endogenously Formed l -Xylulose (2000)

Genes yiaP and yiaR of the yiaKLMNOPQRS cluster of Escherichia coli are required for the metabolism of the endogenously formed L-xylulose, whereas yiaS is required for this metabolism only in araD mutants. Like AraD, YiaS was shown to have L-ribulose-5-phosphate 4-epimerase activity. Similarity of YiaR to several 3-epimerases suggested that this protein could catalyze the conversion of L-xylulose-5-phosphate into L-ribulose-5-phosphate, thus completing the pathway between L-xylulose and the general metabolism.
Changes in ophthalmic acid and free amino acid in rats fed with an excess methionine diet. (1989)

Met* is essential for the normal growth and development of mammals,but the consumption of excess level of Met leads to such disorders as depression in growth and tissue damage.U2) Met is metabolized via two pathways,
A Minimal Binding Domain of the Low Density Lipoprotein Receptor Family (1998)

As more relatives of the low density lipoprotein receptor (LDLR) are discovered, defining their minimal binding domain(s) becomes a challenge. Here we have chosen the multifunctional chicken oocyte receptor for yolk deposition (termed LR8), and the pan-receptor ligand, receptor associated protein (RAP), as model systems to characterize a minireceptor using the phage display approach. Displayed fragments derived from the entire 819 residue LR8 molecule, followed by selection via panning on RAP, led to the definition of an 80 residue stretch LR8 minireceptor. It contains 12 cysteines, and represents parts of the second, the entire third, and parts of the fourth, of the eight clustered 'ligand binding repeats' in LR8; only two of the eight stretches of negatively charged residues of LR8, i.e., EDGSDE and DSGEDEE, are present. The latter sequence is reminiscent of that in the fifth repeat of the human LDLR, thought to be most critical for interaction with positive charge clusters in ligands. Baculovirus-mediated expression of the soluble minireceptor in insect cells showed it to fold as a monomer, and sulfhydryl-reduction-sensitive interaction with RAP was demonstrated for immobilized as well as soluble minireceptor. Furthermore, the LR8-derived minireceptor provided a RAP-responsive surface when covalently coupled to the surface of a gold electrode. In addition to its use in defining minimal binding domains, the phage display approach provides powerful tools for dissection, and consequently, manipulation, of the function of receptors so as to direct their binding activity toward ligands of diagnostic and/or therapeutic interest.
pH-Dependent Isolations and Spectroscopic, Structural, and Thermal Studies of Titanium Citrate Complexes (2004)

Titanium(IV) citrate complexes (NH(4))(2)[Ti(H(2)cit)(3)].3H(2)O (1), (NH(4))(5)[Fe(H(2)O)(6)][Ti(H(2)cit)(3)(Hcit)(3)Ti].3H(2)O (2), Ba(2)[Ti(H(2)cit)(Hcit)(2)].8H(2)O (3), and Ba(3)(NH(4))(7)[Ti(cit)(3)H(3)(cit)(3)Ti].15H(2)O (4) (H(4)cit = citric acid) were isolated in pure form from the solutions of titanium(IV) citrate with various countercations. The isolated complexes were characterized by elemental analyses, IR spectra, and (1)H NMR and (13)C NMR spectra. The formation of titanium(IV) citrate complexes depends mainly on the pH of the solutions, that is, pH 1.0-2.8 for the formation of ammonium titanium(IV) citrate 1, pH 2.5-3.5 for ammonium iron titanium(IV) citrate 2, pH 2.8-4.0 for dibarium titanium(IV) citrate 3, and pH 5.0-6.0 for ammonium barium titanium(IV) citrate 4. X-ray structural analyses revealed that complexes 2-4 featured three different protonated forms of bidentate citrate anions that chelate to the titanium(IV) atom through their negatively charged alpha-alkoxyl and alpha-carboxyl oxygen atoms. This is consistent with the large downfield shifts of the (13)C NMR spectra for the carbon atoms bearing the alpha-alkoxyl and alpha-carboxyl groups. The typical coordination modes of the barium atoms in complexes 3 and 4 are six-coordinated, with three alpha-alkoxyl groups and three beta-carboxyl groups of citrate ions. The strong hydrogen bonding between the beta-carboxylic acid and the beta-carboxyl groups [2.634(8) A for complex 2, 2.464(7) A for complex 3, and 2.467(7) A for complex 4] may be the key factor for the stabilization of the citrate complexes. The decomposition of complex 3 results in the formation of a pure dibarium titanate phase and 4 for the mixed phases of dibarium titanate and barium titanate at 1000 degrees C.
Myers-Briggs Type Indicator (MBTI): Some Psychometric Limitations (1995)

The present paper critically reviews the psychometric adequacy of the Myers-Briggs Type Indicator (MBTI). Although the instrument is extremely popular in applied settings, there is an urgent need for the development of valid and comprehensive local norms, in order to increase its predictive validity and utility within the Australian context. In addition, there is a number of psychometric limitations pertaining to the reliability and validity of the MBTI, which raise concerns about its use by practitioners. In view of these seri- ous limitations, routine use of the MBTI is not recommended, and psychologists should be cautious as to its likely misuse in various organisational and occupational settings.
Infrared Absorption and Anharmonicity of the U‐Centre Local Mode. I. Experiments (1965)

Abstract The infrared absorption due to U‐centres (substitutional H − or D − ions) is measured in NaCl, NaBr, KCl, KBr, KI, RbCl, and RbBr between 7 and 300 °K. The oscillator strength in the infrared is independent of temperature. Below 300 °K the bandwidth decreases as approximately T 2. Near helium temperatures D − bandwidths tend to saturate at a value of about 1 cm −1 , whereas H − bands in general tend to continue to decrease with T . With increasing temperatures the peaks are shifted to higher or lower frequencies depending on the substance. In the wings of the absorption band side bands appear, which are displaced by band mode frequencies [4]. In all crystals one side band peak lies in the range of the TA frequencies (near q = (100)), in KBr, KI, and NaBr additional peaks corresponding to LA and TO phonons are observed. A discussion will be given in a subsequent paper by Bilz, Fritz, and Strauch.
Effect of the antitumor drug lonidamine on glucose metabolism of adriamycin-sensitive and -resistant human breast cancer cells. (1996)

The effect of lonidamine on glucose metabolism, hexokinase activity and adenylate pool of MCF-7 human breast cancer cells sensitive and resistant to adriamycin has been investigated. The following summarizes the results: 1. In both cell types the greatest part of glucose was metabolized to lactate, whereas only a small proportion of glucose carbon atoms was incorporated into CO2, lipids, nucleic acids, and supporting structures. 2. Glucose utilization, lactate production, and ATP content were higher in resistant cells due to a greater activity of mitochondrial hexokinase. 3. Lonidamine decreased glucose utilization, aerobic glycolysis and ATP content in both cell types and the effect was significantly higher on resistant cells. 4. The extent of inhibition in sensitive and resistant cells overlapped that found for mitochondrially bound hexokinase, thus indicating that the greater sensitivity of resistant cells to lonidamine was due to their higher amount of bound hexokinase. These findings confirmed a modified glucose metabolism in cells with resistant phenotype and suggested that lonidamine might be usefully used to reduce or overcome multidrug resistance of those cells with a reduced ability to accumulate and retain antitumor drugs.
N‐Acyl Isocyanides (1977)

The first acyl isocyanides have now become available. The pronounced carbonyl‐activation of benzoyl isocyanide (1) is manifested, e.g. , in the acylation of ynamines; in contrast, (1) undergoes cycloaddition with acetylenedicarboxylates. equation image
Synthetic electric sounding surveys over known oil fields (1984)

Abstract The possibility of using various types of electrical methods to locate oil or gas fields has been proposed in recent years. In an effort to quantify the anomaly to be expected with electrical sounding methods, average geoelectrical parameters have been determined by studying electrical well logs from several oil fields characterized by different geoelectrical sections. The dc resistivity anomaly due to the presence of an oil-bearing layer at depth depends upon the sequence of resistivities above and below and the electrode array employed. The radial dipole array gives the largest anomaly values, and is followed by other arrays such as the Schlumberger and Wenner arrays. The maximum anomaly in apparent resistivity is observed when the resistivity beneath the target zone is lower than that above; the relative anomaly in apparent resistivity is almost the same as the contrast ratio of the transverse resistance of the oil-bearing layer to the overlying beds. When the radial dipole array is used, a limited areal extent of the oil-bearing layer does not cause a significant change from the anomaly value due to a layer of infinite lateral extent. In that case the least dimension is about four times the depth. Use of one buried current electrode in the vicinity of the oil-bearing layer increases the amplitude of the anomaly; the maximum anomaly appears at a separation comparable to the depth.Typical anomalies in apparent resistivity caused by these oil fields range from less than 0.1 percent to more than 10 percent. Such anomalies would be detectable only with an order of magnitude improvement in the capabilities of electrical sounding methods, or with considerably larger oil field targets.
Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome (2009)

By comparing the sequences of tumor and skin genomes of a patient with AML-M1, we have identified recurring mutations that may be relevant for pathogenesis.
Does Beano prevent gas? A double-blind crossover study of oral alpha-galactosidase to treat dietary oligosaccharide intolerance. (1994)

Oral alpha-galactosidase solution is efficacious, at least in some patients, for the prophylaxis of gastrointestinal intolerance of oligosaccharides.
CD1d-dependent Activation of NKT Cells Aggravates Atherosclerosis (2004)

Adaptive and innate immunity have been implicated in the pathogenesis of atherosclerosis. Given their abundance in the lesion, lipids might be targets of the atherosclerosis-associated immune response. Natural killer T (NKT) cells can recognize lipid antigens presented by CD1 molecules. We have explored the role of CD1d-restricted NKT cells in atherosclerosis by using apolipoprotein E-deficient (apoE-/-) mice, a hypercholesterolemic mouse model that develops atherosclerosis. ApoE-/- mice crossed with CD1d-/- (CD1d-/-apoE-/-) mice exhibited a 25% decrease in lesion size compared with apoE-/- mice. Administration of alpha-galactosylceramide, a synthetic glycolipid that activates NKT cells via CD1d, induced a 50% increase in lesion size in apoE-/- mice, whereas it did not affect lesion size in apoE-/-CD1d-/- mice. Treatment was accompanied by an early burst of cytokines (IFNgamma, MCP-1, TNFalpha, IL-2, IL-4, IL-5, and IL-6) followed by sustained increases in IFNgamma and IL-4 transcripts in the spleen and aorta. Early activation of both T and B cells was followed by recruitment of T and NKT cells to the aorta and activation of inflammatory genes. These results show that activation of CD1d-restricted NKT cells exacerbates atherosclerosis.
A kallikrein-like serine protease in prostatic fluid cleaves the predominant seminal vesicle protein. (1985)

A 33-kD glycoprotein, known as the "prostate-specific antigen," was purified to homogeneity from human seminal plasma. The prostatic protein was identified as a serine protease, and its NH2-terminal sequence strongly suggests that it belongs to the family of glandular kallikreins. The structural protein of human seminal coagulum, the predominant protein in seminal vesicle secretion, was rapidly cleaved by the prostatic enzyme, which suggests that this seminal vesicle protein may serve as the physiological substrate for the protease. The prostatic enzyme hydrolyzed arginine- and lysine-containing substrates with a distinct preference for the former. All synthetic substrates tested were poor substrates for the enzyme. Synthetic Factor XIa substrate (pyro-glutamyl-prolyl-arginine-p-nitroanilide), and the synthetic kallikrein substrate (H-D-prolyl-phenylalanyl-arginine-p-nitroanilide) were hydrolyzed with maximum specific activities at 23 degrees C of 79 and 34 nmol/min per mg and Km values of 1.0 and 0.45 mM, respectively. Synthetic substrates for plasmin, chymotrypsin, and elastase were either not hydrolyzed by the enzyme at all, or only hydrolyzed very slowly.
Deep Watershed Transform for Instance Segmentation (2017)

Most contemporary approaches to instance segmentation use complex pipelines involving conditional random fields, recurrent neural networks, object proposals, or template matching schemes. In this paper, we present a simple yet powerful end-to-end convolutional neural network to tackle this task. Our approach combines intuitions from the classical watershed transform and modern deep learning to produce an energy map of the image where object instances are unambiguously represented as energy basins. We then perform a cut at a single energy level to directly yield connected components corresponding to object instances. Our model achieves more than double the performance over the state-of-the-art on the challenging Cityscapes Instance Level Segmentation task.
Preparation and screening of an arrayed human genomic library generated with the P1 cloning system. (1994)

We describe here the construction and initial characterization of a 3-fold coverage genomic library of the human haploid genome that was prepared using the bacteriophage P1 cloning system. The cloned DNA inserts were produced by size fractionation of a Sau3AI partial digest of high molecular weight genomic DNA isolated from primary cells of human foreskin fibroblasts. The inserts were cloned into the pAd10sacBII vector and packaged in vitro into P1 phage. These were used to generate recombinant bacterial clones, each of which was picked robotically from an agar plate into a well of a 96-well microtiter dish, grown overnight, and stored at -70 degrees C. The resulting library, designated DMPC-HFF#1 series A, consists of approximately 130,000-140,000 recombinant clones that were stored in 1500 microtiter dishes. To screen the library, clones were combined in a pooling strategy and specific loci were identified by PCR analysis. On average, the library contains two or three different clones for each locus screened. To date we have identified a total of 17 clones containing the hypoxanthine-guanine phosphoribosyltransferase, human serum albumin-human alpha-fetoprotein, p53, cyclooxygenase I, human apurinic endonuclease, beta-polymerase, and DNA ligase I genes. The cloned inserts average 80 kb in size and range from 70 to 95 kb, with one 49-kb insert and one 62-kb insert.
Sorting of Furin in Polarized Epithelial and Endothelial Cells: Expression Beyond the Golgi Apparatus (2004)

The conversion of proteins into their mature forms underlies the functionality of many fundamental cellular pathways. One posttranslational modification leading to maturation of precursor proteins consists of the cleavage of their prodomain at pairs of basic amino acids by enzymes of the subtilisin-like mammalian proprotein convertase family. One of these enzymes, furin, acts in the constitutive secretory pathway of almost every cell type. However, in spite of furin's major roles in many pathophysiological processes, the exact subcellular sites of processing and activation of its substrates remain elusive. In this study, furin antigenic sites were tracked in subcellular compartments of various tissues and corresponding cell lines by high-resolution immunogold electron microscopy, Western blotting, cell transfection, and in vivo gene delivery of the furin cDNA. In addition to the Golgi apparatus, furin was assigned to endosomes and plasma membranes of polarized intestinal and renal epithelial cells and endothelial cells of the continuous, fenestrated, and discontinuous capillaries. Roles of furin in endothelial permeability, basement membrane turnover, and shedding of transmembrane proteins are supported by our data.
Generic Self Repair Architecture with Multiple Fault Handling Capability (2015)

Built-in self-repair (BISR) approach utilized mostly in regular structures of memory cores has been a promising approach to increase the reliability of any type of integrated circuit. BISR considers spare blocks which in the case of a fault occurrence are used to replace defected circuit parts. A new fault detection and repair procedure with a generic BISR architecture for logic cores is presented in this paper. The architecture is able to localize and repair multiple faults (both permanent and transient), to identify faulty functional blocks, to detect faulty backup blocks, and to repair the core function by employing backup blocks if possible. The number of repairable faults is determined by the number of reconfigurable logic blocks (RLBs) in the core. The whole repair procedure needs only 4 test runs. Experimental results show an additional area of approximately 140% which is still within acceptable level compared to other redundant methods (TMR overhead is 200% without the voter area).
Structure-Function Studies of Human Leptin (1998)

To elucidate the structural requirement of human leptin for its functions, the wild-type, mutant-type, C-terminal deletion, and N-terminal deletion were expressed in Escherichia coli and purified in soluble forms. These leptin analogs were intracerebroventrically injected into C57BL/6J ob/ob mice, and their in vivo biological activities were evaluated. The mutant-type leptin lacking a C-terminal disulfide bond reduced food intake at doses of more than 15 pmol/mouse, which was as effective as the wild-type leptin. C-terminal deletion without the loop structure, also significantly, but to a lesser extent, reduced food intake at doses of more than 90 pmol/mouse. However, N-terminal deletions showed no effect on food intake. We also evaluated the effects of the leptin analogs on radiolabeled leptin binding to its receptor in the choroid plexus using autoradiography. An excess of unlabeled mutant-type leptin as well as wild-type leptin led to complete inhibition of binding. C-terminal deletions led to weak inhibitory activity, whereas N-terminal deletions caused no inhibitory activity. These results clearly demonstrate that the N-terminal region of leptin is essential for both its biological and receptor binding activities. The amino acid sequence of the C-terminal loop structure is also important for enhancing these actions, whereas the C-terminal disulfide bond is not needed.
Molecular Characterization of Circulating Tumor Cells in Breast Cancer by a Liquid Bead Array Hybridization Assay (2011)

The expression of 6 genes in CTCs can be measured simultaneously and reliably, thereby saving precious sample and reducing the costs and time of analysis.
IL-33 amplifies both Th1- and Th2-type responses through its activity on human basophils, allergen-reactive Th2 cells, iNKT and NK Cells (2008)

IL-33 is an IL-1 family member recently identified as the ligand for T1/ST2 (ST2), a member of the IL-1 receptor family. ST2 is stably expressed on mast cells and T(h)2 effector T cells and its function has been studied in the context of T(h)2-associated inflammation. Indeed, IL-33 induces T(h)2 cytokines from mast cells and polarized mouse T cells and leads to pulmonary and mucosal T(h)2 inflammation when administered in vivo. To better understand how this pathway modulates inflammatory responses, we examined the activity of IL-33 on a variety of human immune cells. Human blood-derived basophils expressed high levels of ST2 receptor and responded to IL-33 by producing several pro-inflammatory cytokines including IL-1 beta, IL-4, IL-5, IL-6, IL-8, IL-13 and granulocyte macrophage colony-stimulating factor. Next, utilizing a human T(h)2-polarized T cell culture system derived from allergic donor blood cells, we found that IL-33 was able to enhance antigen-dependent and -independent T cell responses, including IL-5, IL-13 and IFN-gamma production. IL-33 activity was also tested on V alpha 24-positive human invariant NKT (iNKT) cells. In the presence of alpha-galactosylceramide antigen presentation, IL-33 dose dependently enhanced iNKT production of several cytokines, including both IL-4 and IFN-gamma. IL-33 also directly induced IFN-gamma production from both iNKT and human NK cells via cooperation with IL-12. Taken together, these results indicate that in addition to its activity on human mast cells, IL-33 is capable of activating human basophils, polarized T cells, iNKT and NK cells. Moreover, the nature of the responses elicited by IL-33 suggests that this axis may amplify both T(h)1- and T(h)2-oriented immune responses.
Treatment of Parkinson's Disease (1993)

Parkinson's disease (idiopathic parkinsonism or paralysis agitans) is characterized clinically by progressive tremor, bradykinesia, and rigidity and pathologically by degeneration of the dopaminergic nigrostriatal pathway, decreases in the striatal concentration of dopamine, and the presence of laminated inclusions (Lewy bodies) in neurons of the substantia nigra. The cause (or causes) of Parkinson's disease is not known, and the pathophysiology is poorly understood. However, there is a considerable body of knowledge concerning the disturbances of synaptic function. Degeneration of the nigrostriatal pathway leads to the depletion of the neurotransmitter dopamine. Since dopamine does not readily cross the blood-brain barrier, the major . . .