gebhart/patrepeval huggingface dataset:
Embedded image coding using zerotrees of wavelet coefficients (1993)

The embedded zerotree wavelet algorithm (EZW) is a simple, yet remarkably effective, image compression algorithm, having the property that the bits in the bit stream are generated in order of importance, yielding a fully embedded code. The embedded code represents a sequence of binary decisions that distinguish an image from the "null" image. Using an embedded coding algorithm, an encoder can terminate the encoding at any point thereby allowing a target rate or target distortion metric to be met exactly. Also, given a bit stream, the decoder can cease decoding at any point in the bit stream and still produce exactly the same image that would have been encoded at the bit rate corresponding to the truncated bit stream. In addition to producing a fully embedded bit stream, the EZW consistently produces compression results that are competitive with virtually all known compression algorithms on standard test images. Yet this performance is achieved with a technique that requires absolutely no training, no pre-stored tables or codebooks, and requires no prior knowledge of the image source. The EZW algorithm is based on four key concepts: (1) a discrete wavelet transform or hierarchical subband decomposition, (2) prediction of the absence of significant information across scales by exploiting the self-similarity inherent in images, (3) entropy-coded successive-approximation quantization, and (4) universal lossless data compression which is achieved via adaptive arithmetic coding.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Estimate of the Ionization Degree of Ionic Micelles Based on Krafft Temperature Measurements (2003)

The Krafft temperature, TK, of two classical ionic surfactants, sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB), were measured by conductivity, in the absence and in the presence of added salt, to test a recent suggestion (J. Phys. Chem. B 2002, 106, 9033) that TK measurements can be used to estimate the degree of counterion dissociation of ionic micelles, α. The method is based on the fact that TK of SDS and CTAB are functions of the concentration of counterions in the aqueous phase, Caq, whether the counterions are provided by the surfactant or both the surfactant and added salt. The values of α are estimated by requiring that the values of TK fall on a common curve when plotted against any function of Caq and are found to be in good agreement with the literature. The present results confirm that the Krafft temperature of ionic surfactants is one of the properties from which α can be derived for both anionic and cationic micelles. In the case of SDS, because the aggregation number, N, is known as a function of Caq, TK may be plotted versus N. The plot showed excellent linear correlation; however, it is not yet known if the linear behavior is theoretically significant.
Complexation between milk proteins and polysaccharides via electrostatic interaction: principles and applications – a review (2008)

Summary This article details recent research conducted on the complexation between milk proteins and polysaccharides and the properties of the complexes, and the application of such relationships to the food industry. Complexation between proteins and polysaccharides through electrostatic interactions gives either soluble complexes in a stable solution or insoluble complexes, leading to phase separation. The formation and the stability of these complexes are influenced by pH, ionic strength, ratio of protein to polysaccharide, charge density of protein and polysaccharide as well as processing conditions (temperature, shearing and time). The functional properties of milk proteins, such as solubility, surface activity, conformational stability, gel‐forming ability, emulsifying properties and foaming properties, are improved through the formation of complexes with polysaccharides. These changes in the functional properties provide opportunities to create new ingredients for the food industry.
An investigation of permanganic etching of linear low-density polyethylene (1988)

Abstract Permanganic etching is a technique of removing material selectively to reveal lamellae in crystalline polymers. It is generally found that populations of lamellae with different thicknesses are removed to different depths. In linear poly-ethylene we have previously shown that this discrimination is not an inherent property but a consequence of differential deformation during cutting to expose the surface prior to etching. The work is now extended to linear low-density polyethylene to test whether the changed basis of molecular segregation (with more branched molecules crystallizing later) alters the etching behavior. It is shown that thinner lamellae are etched at a faster rate which is only slightly reduced after removing damage due to cutting. This intrinsic differentiation between crystal thicknesses accompanies faster etching rates than for the linear material. It is inferred that this is due to faster chain scission at fold surfaces which are more penetrable for the linear low-density than for the linear polymer; however, chain scission remains slow compared to stem removal. Fold stems are probably removed as entities rather than incrementally, but it is evident that a fold surface region needs to be etched away before a stem can be removed.
Tyrosine phosphorylation of the MUC1 breast cancer membrane proteins Cytokine receptor‐like molecules (1994)

Phosphorylation on tyrosine residues is a key step in signal transduction pathways mediated by membrane proteins. Although it is known that human breast cancer tissue expresses at least 2 MUC1 type 1 membrane proteins (a polymorphic high molecular weight MUC1 glycoprotein that contains a variable number of tandem 20 amino acid repeat units, and the MUC1/Y protein that is not polymorphic and is lacking this repeat array) their function in the development of human breast cancer has remained elusive. Here it is shown that these MUC1 proteins are extensively phosphorylated, that phosphorylation occurs primarily on tyrosine residues and that following phosphorylation the MUC1 proteins may potentially interact with SH2 domain-containing proteins and thereby initiate a signal transduction cascade. As with cytokine receptors, the MUC1 proteins do not harbor intrinsic tyrosine kinase activity yet are tyrosine phosphorylated and the MUC1/Y protein participates in a cell surface heteromeric complex whose formation is mediated by two cytoplasmically located MUC1 cysteine residues. Furthermore, the MUC1/Y protein demonstrates sequence similarity with sequences present in cytokine receptors that are known to be involved in ligand binding. Our results demonstrate that the two MUC1 isoforms are both likely to function in signal transduction pathways and to be intimately linked to the oncogenetic process and suggest that the MUC1/Y protein may act in a similar fashion to cytokine receptors.
Novel Selective PDE4 Inhibitors. 1. Synthesis, Structure−Activity Relationships, and Molecular Modeling of 4-(3,4-Dimethoxyphenyl)-2H-phthalazin-1-ones and Analogues (2001)

A number of 6-(3,4-dimethoxyphenyl)-4,5-dihydro-2H-pyridazin-3-ones and a novel series of 4-(3,4-dimethoxyphenyl)-2H-phthalazin-1-ones were prepared and tested on the cGMP-inhibited phosphodiesterase (PDE3) and cAMP-specific phosphodiesterase (PDE4) enzymes. All tested compounds were found to specifically inhibit PDE4 except for pyridazinone 3b, which showed moderate PDE4 (pIC(50) = 6.5) as well as PDE3 (pIC(50) = 6.6) inhibitory activity. In both the pyridazinone and phthlazinone series it was found that N-substitution is beneficial for PDE4 inhibition, whereas in the pyridazinone series it also accounts for PDE4 selectivity. In the phthalazinone series, the cis-4a,5,6,7,8,8a-hexahydrophthalazinones and their corresponding 4a,5,8,8a-tetrahydro analogues showed potent PDE4 inhibitory potency (10/11c,d: pIC(50) = 7.6-8.4). A molecular modeling study revealed that the cis-fused cyclohexa(e)ne rings occupy a region in space different from that occupied by the other fused (un)saturated hydrocarbon rings applied; we therefore assume that the steric interactions of these rings with the binding site play an important role in enzyme inhibition.
Identification of Domains and Amino Acids Essential to the Collagen Galactosyltransferase Activity of GLT25D1 (2011)

Collagen is modified by hydroxylation and glycosylation of hydroxylysine residues. This glycosylation is initiated by the β1,O galactosyltransferases GLT25D1 and GLT25D2. The structurally similar protein cerebral endothelial cell adhesion molecule CEECAM1 was previously reported to be inactive when assayed for collagen glycosyltransferase activity. To address the cause of the absent galactosyltransferase activity, we have generated several chimeric constructs between the active human GLT25D1 and inactive human CEECAM1 proteins. The assay of these chimeric constructs pointed to a short central region and a large C-terminal region of CEECAM1 leading to the loss of collagen galactosyltransferase activity. Examination of the three DXD motifs of the active GLT25D1 by site-directed mutagenesis confirmed the importance of the first (amino acids 166-168) and second motif (amino acids 461-463) for enzymatic activity, whereas the third one was dispensable. Since the second DXD motif is incomplete in CEECAM1, we have restored the motif by introducing the substitution S461D. This change did not restore the activity of the C-terminal region, thereby showing that additional amino acids were required in this C-terminal region to confer enzymatic activity. Finally, we have introduced the substitution Q471R-V472M-N473Q-P474V in the CEECAM1-C-terminal construct, which is found in most animal GLT25D1 and GLT25D2 isoforms but not in CEECAM1. This substitution was shown to partially restore collagen galactosyltransferase activity, underlining its importance for catalytic activity in the C-terminal domain. Because multiple mutations in different regions of CEECAM1 contribute to the lack of galactosyltransferase activity, we deduced that CEECAM1 is functionally different from the related GLT25D1 protein.
Differentiation of nearly identical germplasm accessions by a combination of molecular and morphologic analyses (1994)

Polymerase chain reaction (PCR) based random amplified polymorphic DNA (RAPD) markers were used to study the extent of redundancy (duplication of genetic materials) within a genetic resources collection. Nine nearly phenotypically and identical accessions of butterhead lettuce (Lactuca sativa L.) were assayed for their genetic identities. A nonuniform, heterogeneous butterhead line and a crisphead cultivar were added for population comparison. PCR amplification using 13 oligonucleotide primers generated 93 polymorphic bands. The percentage of segregating bands was used to determine within-line variation; values ranged from 0.0 to 12.0%, except for the nonuniform line at 22.6%. Between-line similarity was measured using similarity coefficients and ranged from 0.919 to 0.985. The relationship between the crisphead accession and a composite of all butterhead accessions was 0.84. Selfed progeny of each line were measured for morphological uniformity. The variation obtained from these biological data was compared with variation detected at the DNA level and each was positively correlated. Results demonstrate that RAPD analyses may serve as a major source of information for separation of closely related accessions, especially when integrated with phenotypic measures.
Three classes of epidermal growth factor receptors on HeLa cells. (1991)

The kinetics of 125I-labeled epidermal growth factor (EGF) binding to receptors on HeLa cells were investigated. Scatchard analysis revealed the presence of 22,000 high affinity receptors (Kd = 0.12 nM) and 25,000 low affinity receptors per cell (Kd = 9.2 nM). The kinetic analysis of EGF binding to high affinity receptors was performed with cells pretreated with the monoclonal antibody 2E9, which prevents specifically EGF binding to low affinity receptors. The study of EGF binding to only low affinity receptors was performed with cells pretreated with the phorbol ester phorbol 12-myristate 13-acetate, which induces a conversion of high affinity receptors to low affinity receptors. This kinetic analysis of EGF binding to HeLa cells revealed the presence of three types of receptors. High affinity receptors were found to consist of one receptor type (type I) with a kinetic association constant (kass) of 6.2 x 10(5) M-1.s-1 and a kinetic dissociation constant (kdis) of 3.5 x 10(-4) s-1. The low affinity receptors were found to consist of two kinetic distinguishable sites: type II or fast sites with kass = 3.3 x 10(6) M-1.s-1 and kdis = 8.1 x 10(-3) s-1 and the type III or slow sites with kass = 3.2 x 10(4) M-1.s-1 and kdis = 1.6 x 10(-4) s-1. The regulatory mechanism which may determine the EGF binding characteristics is discussed.
Synthesis and characterization of a polyoxyethylene derivative for the affinity labeling of human hemoglobin (1988)

Abstract The possibility of preparing a polyoxyethylene derivative containing only one active group per chain, and with a narrow distribution of molecular size, was investigated. The aim of this investigation was to obtain a polymeric derivative of benzenehexacarboxylate (BHC) capable of interacting specifically inside the polyphosphate binding site of human hemoglobin (Hb) and which, after covalent coupling with this protein, could lead to conjugates with well‐defined oxygen‐binding properties. Such conjugates could be of interest in the field of blood substitutes. To minimize the percentage of high‐molecular‐weight products resulting from the fact that, on one hand, commercial monomethoxypolyoxyethylene (MPOE 5000) contained a considerable amount of difunctional and high‐molecular‐weight species, and on the other hand that several reactions were likely to lead to cross‐linked products, fractionation steps and/or chromatographic steps were carried out. The final compound obtained under these conditions (83,5% of BHC‐mono substituted polyoxyethylene, 8,5% of BHC disubstituted and 8% MPOE) was found to interact with the polyphosphate binding site of Hb, as it was capable of lowering its affinity for oxygen. After covalent coupling with deoxy‐Hb under defined conditions, this effect was strengthened, which means that the binding was probably formed with an amine of the Hb polyphosphate binding site.
Anabolic Actions of Parathyroid Hormone on Bone* (1993)

PHYSICIANS have traditionally considered PTH to be an agent that is catabolic to the skeleton. However, as early as 60 yr ago, Albright and his colleagues (1) and later Selye (2) noted that the peptide extract could also be anabolic to the skeleton, producing increases in bone tissue in animals. The potential for an agent that can increase bone mass and hence reverse the skeletal defect in patients with osteoporosis is great, particularly if in doing so it also repairs microarchitectural damage. The agents currently available in the United States for treatment of osteoporosis, estrogens and salmon calcitonin, primarily stabilize bone mass and prevent further loss of bone, although a transient small increment in mass is often reported, particularly in patients with elevated levels of bone remodeling. This increase is not a true anabolic effect but is related to the temporal effects on turnover in which resorption declines initially followed by a reduction in formation that may take several months. Fluoride, in contrast, does increase bone mass by a true anabolic action, but there is controversy about the quality of the bone formed. Two recent controlled studies failed to find a reduction in fracture recurrence (3, 4), although the dose may have been excessive, and consequently, fluoride is currently not approved for treatment of osteoporosis in the United States. Thus, if PTH is capable of improving bone mass and quality, the peptide will have a potential therapeutic role in osteoporosis. This review summarizes the data available to date, starting at the cellular level.
The Telomerase Picture Fills In (1997)

Cell BiologyResearchers may finally have nailed a long-sought quarry: a catalytic protein that helps rebuild the chromosome ends after each cell division. In work described on page [561][1], researchers report that they have isolated a catalytic component of the enzyme telomerase from both a ciliated protozoan called Euplotes aediculatus and yeast. Although there are other candidates for the protein, other telomerase researchers find the evidence for this one particularly convincing. If so, the discovery will not only provide a boost to researchers trying to understand how it does its crucial job, but could also lead to insights into aging and cancer.

 [1]: http://www.sciencemag.org/cgi/content/full/276/5312/561
The MDM2 RING Domain and Central Acidic Domain Play Distinct Roles in MDM2 Protein Homodimerization and MDM2-MDMX Protein Heterodimerization (2015)

The oncoprotein murine double minute 2 (MDM2) is an E3 ligase that plays a prominent role in p53 suppression by promoting its polyubiquitination and proteasomal degradation. In its active form, MDM2 forms homodimers as well as heterodimers with the homologous protein murine double minute 4 (MDMX), both of which are thought to occur through their respective C-terminal RING (really interesting new gene) domains. In this study, using multiple MDM2 mutants, we show evidence suggesting that MDM2 homo- and heterodimerization occur through distinct mechanisms because MDM2 RING domain mutations that inhibit MDM2 interaction with MDMX do not affect MDM2 interaction with WT MDM2. Intriguingly, deletion of a portion of the MDM2 central acidic domain selectively inhibits interaction with MDM2 while leaving intact the ability of MDM2 to interact with MDMX and to ubiquitinate p53. Further analysis of an MDM2 C-terminal deletion mutant reveals that the C-terminal residues of MDM2 are required for both MDM2 and MDMX interaction. Collectively, our results suggest a model in which MDM2-MDMX heterodimerization requires the extreme C terminus and proper RING domain structure of MDM2, whereas MDM2 homodimerization requires the extreme C terminus and the central acidic domain of MDM2, suggesting that MDM2 homo- and heterodimers utilize distinct MDM2 domains. Our study is the first to report mutations capable of separating MDM2 homo- and heterodimerization. The oncoprotein murine double minute 2 (MDM2) is an E3 ligase that plays a prominent role in p53 suppression by promoting its polyubiquitination and proteasomal degradation. In its active form, MDM2 forms homodimers as well as heterodimers with the homologous protein murine double minute 4 (MDMX), both of which are thought to occur through their respective C-terminal RING (really interesting new gene) domains. In this study, using multiple MDM2 mutants, we show evidence suggesting that MDM2 homo- and heterodimerization occur through distinct mechanisms because MDM2 RING domain mutations that inhibit MDM2 interaction with MDMX do not affect MDM2 interaction with WT MDM2. Intriguingly, deletion of a portion of the MDM2 central acidic domain selectively inhibits interaction with MDM2 while leaving intact the ability of MDM2 to interact with MDMX and to ubiquitinate p53. Further analysis of an MDM2 C-terminal deletion mutant reveals that the C-terminal residues of MDM2 are required for both MDM2 and MDMX interaction. Collectively, our results suggest a model in which MDM2-MDMX heterodimerization requires the extreme C terminus and proper RING domain structure of MDM2, whereas MDM2 homodimerization requires the extreme C terminus and the central acidic domain of MDM2, suggesting that MDM2 homo- and heterodimers utilize distinct MDM2 domains. Our study is the first to report mutations capable of separating MDM2 homo- and heterodimerization.
Humanizing the yeast telomerase template (1998)

Saccharomyces cerevisiae contains an irregular telomere sequence (TG1-3)n, which differs from the regular repeat (TTAGGG)n found at the telomeres of higher organisms including humans. We have modified the entire 16-nt template region of the S. cerevisiae telomerase RNA gene (TLC1) to produce (TTAGGG)n repeats, the human telomere sequence. Haploid yeast strains with the tlc1-human allele are viable with no growth retardation and express the humanized gene at a level comparable to wild type. Southern hybridization demonstrates that (TTAGGG)n repeats are added onto the yeast chromosome ends in haploid strains with the tlc1-human allele, and sequencing of rescued yeast artificial chromosome ends has verified the addition of human telomeric repeats at the molecular level. These data suggest that the irregularity of the yeast telomere sequence is because of the template sequence of the yeast telomerase RNA. Haploid strains with the tlc1-human allele will provide an important tool for studying the function of telomerase and its regulation by telomere-binding proteins, and these strains will serve as good hosts for human artificial chromosome assembly and propagation.
Inhibition of fibrinogen binding to GP IIb-IIIa by a GP IIIa peptide (1991)

The glycoprotein IIb-IIIa complex (GP IIb-IIIa) mediates platelet aggregation and is a member of the cytoadhesin family of receptors that bind adhesive proteins such as fibrinogen, fibronectin, and von Willebrand factor. Despite the wide range of cell-substrate interactions mediated by these receptors, ligand binding domains have not yet been identified on any of the integrins. The present study was designed to determine potential fibrinogen binding domain(s) on the GP IIb-IIIa complex. Synthetic peptides derived from residues 1-288 of the amino-terminal portion of GP IIIa were tested for their abilities to block the binding of fibrinogen to purified GP IIb-IIIa in a solid-phase microtiter assay. Two overlapping peptides encompassing residues 204-229 of GP IIIa were identified which blocked fibrinogen binding in this assay. Polyclonal antibodies to these peptides blocked fibrinogen binding to purified GP IIb-IIIa as well as platelet aggregation. The overlapping residues of these two peptides GP IIIa (211-222), SVSRNRDAPEGG-NH2, blocked the binding of fibronectin, von Willebrand factor, and vitronectin to purified GP IIb-IIIa. Finally, direct binding of GP IIIa (204-229) to fibrinogen and fibronectin was demonstrated by enzyme-linked immunosorbent assay. We conclude from these studies that the amino acid sequence 211-222 of GP IIIa is critically involved in adhesive protein binding, and may represent an important portion of the GP IIb-IIIa ligand binding domain.