gebhart/patrepeval huggingface dataset:
Homeodomain-interacting protein kinase (Hipk) plays roles in nervous system and muscle structure and function (2020)

Homeodomain-interacting protein kinases (Hipks) have been previously associated with cell proliferation and cancer, however, their effects in the nervous system are less well understood. We have used Drosophila melanogaster to evaluate the effects of altered Hipk expression on the nervous system and muscle. Using genetic manipulation of Hipk expression we demonstrate that knockdown and over-expression of Hipk produces early adult lethality, possibly due to the effects on the nervous system and muscle involvement. We find that optimal levels of Hipk are critical for the function of dopaminergic neurons and glial cells in the nervous system, as well as muscle. Furthermore, manipulation of Hipk affects the structure of the larval neuromuscular junction (NMJ) by promoting its growth. Hipk regulates the phosphorylation of the synapse-associated cytoskeletal protein Hu-li tai shao (Hts; adducin in mammals) and modulates the expression of two important protein kinases, Calcium-calmodulin protein kinase II (CaMKII) and Partitioning-defective 1 (PAR-1), all of which may alter neuromuscular structure/function and influence lethality. Hipk also modifies the levels of an important nuclear protein, TBPH, the fly orthologue of TAR DNA-binding protein 43 (TDP-43), which may have relevance for understanding motor neuron diseases.
Potent Bivalent Smac Mimetics: Effect of the Linker on Binding to Inhibitor of Apoptosis Proteins (IAPs) and Anticancer Activity (2011)

We have synthesized and evaluated a series of nonpeptidic, bivalent Smac mimetics as antagonists of the inhibitor of apoptosis proteins and new anticancer agents. All these bivalent Smac mimetics bind to full-length XIAP with low nanomolar affinities and function as ultrapotent antagonists of XIAP. While these Smac mimetics bind to cIAP1/2 with similar low nanomolar affinities, their potencies to induce degradation of cIAP1/2 proteins in cells differ by more than 100-fold. The most potent bivalent Smac mimetics inhibit cell growth with IC(50) from 1 to 3 nM in the MDA-MB-231 breast cancer cell line and are 100 times more potent than the least potent compounds. Determination of intracellular concentrations for several representative compounds showed that the linkers in these bivalent Smac mimetics significantly affect their intracellular concentrations and hence the overall cellular activity. Compound 27 completely inhibits tumor growth in the MDA-MB-231 xenografts while causing no signs of toxicity in the animals.
Administration of Transforming Growth Factor-α Reduces Infarct Volume after Transient Focal Cerebral Ischemia in the Rat (2001)

Growth factors promote cell growth and survival and protect the brain from developing injury after ischemia. In this article, the authors examined whether transforming growth factor-alpha (TGF-alpha) was protective in transient focal ischemia and whether alteration of cerebral circulation was involved. Rats received intraventricular TGF-alpha (50 ng, either split into 2 doses given 30 minutes before and 30 minutes after middle cerebral artery occlusion (MCAO), or 1 dose given 30 minutes after MCAO) or vehicle. Rats were subjected to 1-hour intraluminal MCAO and cerebral blood flow was recorded continuously by laser-Doppler flowmetry. Infarct volume was measured 1 and 4 days later. The effects of TGF-alpha on arterial tone were assessed in isolated rabbit basilar and common carotid arteries. Transforming growth factor-alpha before and after ischemia reduced infarct volume by 70% at 1 day and 50% at 4 days. Transforming growth factor-alpha given only after ischemia also did reduce infarct volume by 70% at 1 day and 80% at 4 days. The protective effect was more marked in cortex than in striatum. Transforming growth factor-alpha did not change cortical microvascular perfusion and did not modify arterial passive tone nor agonist-induced active tone. It can be concluded that TGF-alpha reduces infarct volume, even when the factor is exclusively administered at reperfusion, and that this effect is not mediated by changes in microvascular perfusion or cerebral arteries. It is therefore suggested that TGF-alpha has a protective effect against neuronal cell death after transient focal ischemia.
[Os(bipy)(CN)4]2- and Its Relatives as Components of Polynuclear Assemblies:  Structural and Photophysical Properties (2007)

A series of diimine-tetracyanoosmate anions [Os(diimine)(CN)4]2- [diimine=2,2'-bipyridine (bipy), 2,2'-bipyrimidine (bpym), 1,10-phenanthroline (phen), and 4,4'-tBu2-2,2'-bipyridine (tBu2bpy)] were prepared and isolated as their Na+ salts (water soluble) or PPN+ salts (soluble in organic solvents). Several examples were crystallographically characterized; the Na+ salts form a range of 1D, 2D, or 3D infinite coordination polymers via coordination of the cyanide groups to Na+ cations in either an end-on or a side-on manner. The [Os(diimine)(CN)4]2- anions are solvatochromic, showing three MLCT absorptions, which are considerably blue-shifted in water compared to organic solvents, in the same way as is well-known for the analogous [Ru(diimine)(CN)4]2- anions. Luminescence in the red region of the spectrum is very weak but (following the expected solvatochromic behavior) is higher energy and more intense in water. However, by exploiting the effect of metallochromism (ref 4), the emission from [Os(tBu2bpy)(CN)4]2- in MeCN can be very substantially boosted in energy, intensity, and lifetime in the presence of Lewis-acidic metal cations (Na+, Ba2+, Zn2+), which, in a relatively noncompetitive solvent, coordinate to the cyanide groups of [Os(tBu2bpy)(CN)4]2-. This has an effect similar in principle to hydrogen bonding of the cyanides to delta+ protons of water, but very much stronger, such that in the presence of Zn2+ ions in MeCN the 1MLCT and 3MLCT absorptions are blue-shifted by ca. 7000 cm(-1), and the luminescence moves from 970 nm (vanishingly weak) to 610 nm with a lifetime of 120 ns (dominant component). Thus, the binding of metal cations to the cyanides provides a mechanism to incorporate [Os(diimine)(CN)4]2- complexes into polynuclear assemblies and simultaneously increases their 3MLCT energy and lifetime to an extent that makes them comparable to much-stronger luminophores such as Ru(II)-polypyridines.
Characterization of human sterol 27-hydroxylase. A mitochondrial cytochrome P-450 that catalyzes multiple oxidation reaction in bile acid biosynthesis. (1991)

The enzyme sterol 27-hydroxylase catalyzes the first step in the oxidation of the side chain of sterol intermediates in the bile acid synthesis pathway. Human sterol 27-hydroxylase cDNAs were isolated from a liver cDNA library by cross-hybridization with a previously cloned rabbit cDNA probe. DNA sequence analysis of hybridization-positive clones predicted a human sterol 27-hydroxylase consisting of a 33-amino-acid mitochondrial signal sequence followed by a mature protein of 498 amino acids. RNA blotting experiments demonstrated sterol 27-hydroxylase mRNAs of approximately 1.8 to 2.2 kilobases in liver and fibroblast cells. The steady state levels of the mRNA did not change when cultured cells were grown in the presence or absence of sterols. Introduction of the sterol 27-hydroxylase cDNA into Simian COS cells resulted in the expression of active enzyme capable of catalyzing multiple oxidation reactions (R-CH3----R-CH2OH----R-COOH) at carbon 27 of sterol intermediates of the bile acid synthesis pathway.
Host-guest complexation. 1. Concept and illustration (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHost-guest complexation. 1. Concept and illustrationEvan P. Kyba, Roger C. Helgeson, Khorshed Madan, George W. Gokel, Thomas L. Tarnowski, Stephen S. Moore, and Donald J. CramCite this: J. Am. Chem. Soc. 1977, 99, 8, 2564–2571Publication Date (Print):April 1, 1977Publication History Published online1 May 2002Published inissue 1 April 1977https://pubs.acs.org/doi/10.1021/ja00450a026https://doi.org/10.1021/ja00450a026research-articleACS PublicationsRequest reuse permissionsArticle Views2861Altmetric-Citations272LEARN 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
<title>Sutureless cataract incision closure using laser-activated tissue glues</title> (1991)

With the advent of phacoemulsification and foldable intraocular lenses, there is renewed interest in sutureless cataract wound. We report the use of laser activated tissue glues for the closure of scleral tunnel cataract incisions. Two glue mixtures were tested in enucleated porcine eyes. Glue A was composed of hyaluronic acid, human albumin, and indocyanine green dye. Glue B contained hyaluronic acid, chondroitin sulfate, human albumin, and indocyanine green dye. A Spectra Physics diode laser (808 nm) with a power density of 7-1 1 watts/cm2 was used for glue activation. Wound bursting pressures, as determined by the presence of fluid at the wound margin, was significantly higher with both glue combinations than without the glue (P<O.05). The mean wound bursting pressures for Glue A was 69.9 17.1 mm Hg, and for Glue B was 42.9 9.4 mm Hg. These results suggest that laser activated tissue glues may be an alternative to suture closure of scleral tunnel cataract incisions.
Germline DNA copy number variation in familial and early-onset breast cancer (2012)

This study is the first to explore the contribution of germline CNVs to BRCA1/2-negative familial and early-onset breast cancer. The data suggest that rare CNVs may contribute to cancer predisposition in this small cohort of patients, and this trend needs to be confirmed in larger population samples.
Trypsin as a Catalyst for Peptide Synthesis (1977)

Trypsin-catalyzed syntheses of peptides were performed using various N-acylated amino acid or peptide esters as donors and amino acid derivatives, peptides, or their derivatives as acceptors. The synthesis was almost quantitative under optimal conditions. Considerably more enzyme and a more alkaline pH were necessary for synthesis than hydrolysis. Another very important condition was the concentration of the starting materials; higher concentrations resulted in much better product yields. The nucleophile specificity for synthesis was also important; hydrophobic or bulky amino acid residues were most efficient at the P1' position, and L-proline as well as D-amino acid residues were the worst choices. The synthesis was also dependent on the solubility of the products synthesized; the yield was higher with products of lower solubility. As donor esters, good substrates were all useful. Accordingly, fragment condensation was possible using N-acylated peptide esters and various peptides. The present study suggests that trypsin may become a useful tool for peptide synthesis.
Microalgae as human food: chemical and nutritional characteristics of the thermo-acidophilic microalga Galdieria sulphuraria (2012)

The use of microalgae as a food source is still poorly developed because of the technical difficulties related to their cultivation and the limited knowledge about their chemical composition and nutritional value. The unicellular red microalga Galdieria sulphuraria has a very high daily productivity and its cultivation under acidic conditions avoided any bacterial contamination. G. sulphuraria can be cultured under autotrophic and heterotrophic conditions: in this study a screening of 43 strains showed that in the latter case a duplication of biomass production was obtained. The proximate composition (protein, carbohydrates, fiber and lipids), the micronutrient content (carotenoids, phycobiliproteins, chlorophylls and vitamins) together with the antioxidant activity of the biomass produced by a selected strain of G. sulphuraria under both cultivation conditions were determined. Results showed that the material is rich in proteins (26–32%) and polysaccharides (63–69%) and poor in lipids. Under heterotrophic cultivation conditions, the lipid moiety mainly contained monounsaturated fatty acids. Among micronutrients, some B group vitamins are present, beta-carotene is the main carotenoid and phycobiliproteins are present under both cultivating conditions. G. sulphuraria proteins are strictly associated with polysaccharide components and therefore not digestible. In the second part of the work, an extraction protocol using Viscozyme L, a commercial enzymatic preparation containing a mixture of polysaccharidases, was developed which made G. sulphuraria proteins a good substrate for human gastrointestinal enzymes. All in all, the data suggested that G. sulphuraria biomass has a potential use as food ingredients both for protein-rich or insoluble dietary fibre-rich applications. The low concentration of lipids and the absence of green color make this microalgae source particularly useful for the addition to many food preparations.
A programmable editor for developing structured documents based on bidirectional transformations (2004)

This paper presents a novel editor supporting interactive refinement in the development of structured documents. The user performs a sequence of editing operations on the document view, and the editor automatically derives an efficient and reliable document source and a transformation that produces the document view. The editor is unique in its programmability, in the sense that the transformation can be obtained through editing operations. The main tricks behind are the utilization of the view-updating technique developed in the database community, and a new bidirectional transformation language that cannot only describe the relationship between the document source and its view, but also data dependency in the view.
Interactions of the Salivary and Gastrointestinal Systems (1991)

Considerable evidence now demonstrates that saliva and its components have multiple functions in the GI tract. Saliva aids in bolus formation; it lubricates, protects and cleanses the pharyngeal and esophageal mucosa. Salivary bicarbonate buffers esophageal acid in common reflux. Normal salivary flow decreases the duration of acid contact with esophageal mucosa, an important factor in the development of GERD. If salivary flow is depressed or if the esophagosalivary reflex is lost, a patient may be predisposed to develop GERD. Salivary EGF stimulates GI mucosal proliferation via a direct lumenal effect in the esophagus and stomach. The salivary enzymes LL and salivary amylase initiate fat and starch digestion. They are particularly significant in patients with pancreatic insufficiency such as neonates and patients with cystic fibrosis.
Defective IgE production by SJL mice is linked to the absence of CD4+, NK1.1+ T cells that promptly produce interleukin 4. (1995)

SJL mice produce little or no IgE in response to polyclonal stimulation with anti-IgD antibody and fail to express interleukin 4 (IL-4) mRNA in the spleen 5 days after injection of anti-IgD, in contrast to other mouse strains that produce substantial amounts of IgE and IL-4. Because IL-4 is critical in IgE production, the possibility that SJL mice are poor IgE producers because their naive T cells fail to differentiate into IL-4 producers must be seriously considered. IL-4 itself is the principal factor determining that naive T cells develop into IL-4 producers. A major source of IL-4 for such differentiation is a population of CD1-specific CD4+ T cells that express NK1.1. These cells produce IL-4 within 90 min of anti-CD3 injection. T cells from SJL mice fail to produce IL-4 in response to injection of anti-CD3. Similarly, SJL T cells and CD4+ thymocytes do not produce IL-4 in response to acute in vitro stimulation. SJL T cells show a marked deficiency in CD4+ cells that express the surface receptors associated with the NK1.1+ T-cell phenotype. This result indicates that the SJL defect in IgE and IL-4 production is associated with, and may be due to, the absence of the CD4+, NK1.1+ T-cell population.
Analyzing Image Deblurring Through Three Paradigms (2011)

To recover a sharp version from a blurred image is a long-standing inverse problem. In this paper, we analyze the research on this topic both theoretically and experimentally through three paradigms: 1) the deterministic filter; 2) Bayesian estimation; and 3) the conjunctive deblurring algorithm (CODA), which performs the deterministic filter and Bayesian estimation in a conjunctive manner. We point out the weaknesses of the deterministic filter and unify the limitation latent in two kinds of Bayesian estimators. We further explain why the CODA is able to handle quite large blurs beyond Bayesian estimation. Finally, we propose a novel method to overcome several unreported limitations of the CODA. Although extensive experiments demonstrate that our method outperforms state-of-the-art methods with a large margin, some common problems of image deblurring still remain unsolved and should attract further research efforts.
Multiscale Hybrid Linear Models for Lossy Image Representation (2006)

In this paper, we introduce a simple and efficient representation for natural images. We view an image (in either the spatial domain or the wavelet domain) as a collection of vectors in a high-dimensional space. We then fit a piece-wise linear model (i.e., a union of affine subspaces) to the vectors at each downsampling scale. We call this a multiscale hybrid linear model for the image. The model can be effectively estimated via a new algebraic method known as generalized principal component analysis (GPCA). The hybrid and hierarchical structure of this model allows us to effectively extract and exploit multimodal correlations among the imagery data at different scales. It conceptually and computationally remedies limitations of many existing image representation methods that are based on either a fixed linear transformation (e.g., DCT, wavelets), or an adaptive uni-modal linear transformation (e.g., PCA), or a multimodal model that uses only cluster means (e.g., VQ). We will justify both quantitatively and experimentally why and how such a simple multiscale hybrid model is able to reduce simultaneously the model complexity and computational cost. Despite a small overhead of the model, our careful and extensive experimental results show that this new model gives more compact representations for a wide variety of natural images under a wide range of signal-to-noise ratios than many existing methods, including wavelets. We also briefly address how the same (hybrid linear) modeling paradigm can be extended to be potentially useful for other applications, such as image segmentation.
Inhibition of a vaccine-induced anti-tumor B cell response by soluble protein antigen in the absence of continuing T cell help (2005)

DNA vaccination can elicit the production of anti-tumor antibodies, thus obviating the need to continuously administer passive antibody. This vaccination strategy is particularly important where antibodies have proven to be effective anti-tumor agents. To amplify antibody responses against weak tumor antigens, we previously designed DNA-fusion vaccines incorporating tumor sequences linked to microbial genes. By using a safe idiotypic (Id) antigen from a B cell tumor fused to a fragment C (FrC) sequence from tetanus toxin, we induced both anti-Id and anti-FrC antibodies. It was important to determine whether the antigen itself, either injected or released from residual tumor cells, would boost the antibody response. Id protein not only failed to boost the response, but permanently and rapidly inhibited it by ablating Id-specific memory B cells. In contrast, an Id protein-FrC conjugate boosted both Id-specific and FrC-specific responses. Strikingly, the depletion of CD4+ T cells converted the Id protein-FrC conjugate vaccine into an inhibitor. These findings support the hypothesis that the activation of memory B cells by a DNA vaccine encoding a protein antigen, in the presence of the protein itself, depends completely on T cell help. Furthermore, by using knockout mice, we have shown that inhibition of the Id-specific memory B cells by the Id protein is largely independent of the FcgammaRIIB and, hence, independent of immune complexes. The principles revealed by using a DNA vaccine have implications for all cancer vaccines designed to induce and maintain antibody responses against weak autologous tumor antigens.
A METHOD FOR DETERMINING THE OXYGEN CONSUMPTION OF A SINGLE CELL (1931)

1. A method for measuring the O(2) consumption of a single cell is described. The cell is placed in a capillary tube adjacent to a bubble of air. KOH (5 per cent) is drawn in on the opposite side of the air and both ends of the tube are sealed with mineral oil. The decrease in the volume of the gas, representing the O(2) consumed, is followed. 2. The possible errors of the technique are appraised. 3. A single Actinosphaerium eichhornii consumes 0.00113 mm.(3) of O(2) per hour. A single Paramecium caudatum consumes 0.00049 mm.(3) of O(2) per hour. 4. The significance of the results and the limitations of the method are discussed.
The Complete Amino Acid Sequence of a Human Folate Binding Protein from KB Cells Determined from the cDNA (1989)

Two species of folate binding protein (FBP), an integral membrane-associated form and a soluble secreted form, have been previously purified from cultured human KB cells. The complete nucleotide sequence of the complementary DNA (cDNA) clone for the coding region of the mature membrane-associated FBP has now been determined, and the deduced amino acid sequence has been computer-analyzed for a prediction of the secondary structure of the protein. The clone has 857 nucleotides of which 678 comprise the coding region for 226 amino acids. The deduced amino sequence contains the identical sequence of the published 18 NH2-terminal amino acids of the purified FBP from KB cells and the published partial amino acid sequence of the human milk FBP except for 1 residue. There was also over 90% homology with the published amino acid sequence of the bovine milk FBP. A total of 16 cysteine residues has been conserved in the three proteins indicating that this amino acid may provide a tertiary structure which is required for its ligand binding function. Northern blot analysis using the cDNA probe identified a single band of 1.28-kilobase pair mRNA in KB cells which was 4.7-fold more intense in folate-depleted cells than in normal cells. These results indicate that the membrane FBP and the soluble FBP in the medium are translation products of the same gene. Computer analysis of the deduced amino acid sequence indicates that there is only one stretch of amino acids of sufficient hydrophobicity and length to span the lipid bilayer of the plasma membrane, but it lacked a predictable helical structure. Those regions of the sequence which did have a predictable helical structure lacked sufficient hydrophobicity required for a membrane anchor. Thus, it is likely that the fatty acids previously reported to be present in the membrane-associated FBP from these cells rather than a peptide sequence provide an important membrane anchoring function.