gebhart/patrepeval huggingface dataset:
Expression of T3 in association with a molecule distinct from the T-cell antigen receptor heterodimer. (1986)

The T-cell antigen receptor consists of a disulfide-linked heterodimer (Ti) that is associated with another set of three nonpolymorphic, noncovalently linked peptides termed "T3." The cell surface expression of T3 has been thought to depend upon association with Ti. In this study, we demonstrate that T3 can be expressed in the absence of an associated Ti molecule on a T-cell leukemic line, PEER. Instead, on this cell line, T3 appears to be expressed in association with a 55- to 60-kDa glycoprotein that has a peptide backbone of 29 kDa. PEER fails to express Ti alpha-chain transcripts but does express Ti beta- and gamma-chain transcripts. Using a monoclonal antibody that reacts with nonpolymorphic epitopes expressed on Ti, WT31, we demonstrate that PEER fails to react with this antibody but does react with three independently derived anti-T3 antibodies. Moreover, a small subpopulation of T3-positive peripheral blood lymphocytes, like PEER, fails to express the antigenic determinants recognized by WT31. These results suggest that, on these normal lymphocytes, T3 may likewise be associated with a non-Ti molecule. The possibility that the 55- to 60-kDa molecule expressed on PEER, termed "Tp55-60," represents the protein product of the previously identified Ti gamma-chain gene is discussed.
Effect of Donor Cell Cycle Stage on Chromatin and Spindle Morphology in Nuclear Transplant Rabbit Embryos1 (1992)

We investigated the influence of the cell cycle stage of the nuclear donor on prematurely condensed chromatin (PCC) and spindle morphology and on chromosome constitution in rabbit nuclear transplant embryos. The configuration of PCC following nuclear transplantation with G1, early S, and late S phase donor nuclei (G1, early S, and late S transplants, respectively) was characterized in whole mounts and chromosome spreads. In addition, the influence of the donor cell cycle stage on chromosome constitution in cleavage stage-manipulated embryos was determined. Within 2 h after fusion of the donor blastomere, the recipient oocyte cytoplasm was able to induce formation de novo of a metaphase plate associated with a spindle in G1, early S, and late S transplants. Metaphase chromosomes and spindle were intact in most cases of PCC in G1 transplants. However, these structures displayed minor abnormalities in early S transplants and gross abnormalities in late S transplants, such as incomplete or absent spindle formation and incomplete chromatin condensation. Normal chromosomes were present in G1 and early S transplants, whereas chromosome abnormalities were detected in late S transplants. The results indicate that morphology of prematurely condensed G1 and early S chromatin has a minor influence on chromosome constitution of manipulated embryos. That of late S chromatin, however, affects chromosome constitution in embryos and may account for reduced development of nuclear transplant embryos when late S phase donor nuclei are used.
A Critical Assessment of Benchmark Comparison in Planning (2002)

Recent trends in planning research have led to empirical comparison becoming commonplace. The field has started to settle into a methodology for such comparisons, which for obvious practical reasons requires running a subset of planners on a subset of problems. In this paper, we characterize the methodology and examine eight implicit assumptions about the problems, planners and metrics used in many of these comparisons. The problem assumptions are: PR1) the performance of a general purpose planner should not be penalized/biased if executed on a sampling of problems and domains, PR2) minor syntactic differences in representation do not affect performance, and PR3) problems should be solvable by STRIPS capable planners unless they require ADL. The planner assumptions are: PL1) the latest version of a planner is the best one to use, PL2) default parameter settings approximate good performance, and PL3) time cut-offs do not unduly bias outcome. The metrics assumptions are: M1) performance degrades similarly for each planner when run on degraded runtime environments (e.g., machine platform) and M2) the number of plan steps distinguishes performance. We find that most of these assumptions are not supported empirically; in particular, that planners are affected differently by these assumptions. We conclude with a call to the community to devote research resources to improving the state of the practice and especially to enhancing the available benchmark problems.
Quantification of Nitryl Chloride at Part Per Trillion Mixing Ratios by Thermal Dissociation Cavity Ring-Down Spectroscopy (2011)

Nitryl chloride (ClNO(2)) is an important nocturnal nitrogen oxide reservoir species in the troposphere. Here, we report a novel method, thermal dissociation cavity ring-down spectroscopy (TD-CRDS), to quantify ClNO(2) mixing ratios with tens of parts-per-trillion by volume (pptv) sensitivity. The mixing ratios of ClNO(2) are determined by blue diode laser CRDS of NO(2), produced from quantitative thermal dissociation of ClNO(2) in an inlet heated to 450 °C, relative to NO(2) observed in an unheated reference channel. ClNO(2) was generated by passing Cl(2) gas over a slurry containing a 1:10 mixture of NaNO(2) and NaCl. The TD-CRDS response was evaluated using parallel measurements of ClNO(2) by chemical ionization mass spectrometry (CIMS) using I(-) as the reagent ion and NO(y) (= NO + NO(2) + HNO(3) + ΣRO(2)NO(2) + ΣRONO(2) + HONO + 2N(2)O(5) + ClNO(2) + ...) chemiluminescence (CL). The linear dynamic range extends from the detection limit of 20 pptv (1 σ, 1 min) to 30 parts-per-billion by volume (ppbv), the highest mixing ratio tested. The ClNO(2) TD profile overlaps with those of alkyl nitrates, which has implications for nocturnal measurements of total alkyl nitrate (ΣAN = ΣRONO(2)) abundances by thermal dissociation (with detection as NO(2)) in ambient air.
GENETICS OF SOMATIC MAMMALIAN CELLS. IV. PROPERTIES OF CHINESE HAMSTER CELL MUTANTS WITH RESPECT TO THE REQUIREMENT FOR PROLINE (1967)

HILE the availability of the single cell plating technique has facilitated study of some aspects of the genetic biochemistry of mammalian cells in vitro (PUCK and FISHER 1956;TJIO and PUCK 1958;PUCK, CIECIURA and ROBINSON 1958), other:; like mutagenesis and recombination have progressed slowly, largely because of the difficulty in securing adequate genetic markers.In contrast to the abundance in microorganisms of many stable markers such as those involving nutritional deficiency and virus-, drug-and radiation-resistance, the markers available for genetic studies in mammalian cells have been limited in number; their expression is often variable from day to day; and the spontaneous reversion rate is often so high as to make the resolving power of genetic experiments much less than that attainable with fungi, bacteria and bacteriophage.A program was begun in this laboratory to attempt isolation of nutritional markers in mammalian cells cultivated in vitro.To this end, the molecular requirements for single-cell plating were first defined for the S3 HeLa cell (FISHER, PUCK and SATO 1959).However, the high degree of chromosomal instability and polyploidy characteristic of this heteroploid cell line made it disadvantageous for genetic experiments.Consequently, attention was turned to the Chinese hamster cells which had been introduced into in vitro culture in this laboratory (PUCK, CIECIURA and ROBINSON 1958).While these cells also have a small degree of variability in chromosome number presumably due to spontaneous lag or nondisjunction, the modal number is usually diploid and relatively constant, and karyotypic analysis is possible with only small uncertainty, at least as compared with the HeLa or similar cells.Moreover, the low chromosome number of Chinese hamster cells makes karyotype analysis feasible and their rapid growth (1 0-hour generation time) is favorable for experimentation.A defined medium for single cell plating of Chinese hamster cells was developed (HAM 1962).One subclone derived from a Chinese hamster ovary which had
Twilight spectral dynamics and the coral reef invertebrate spawning response (2011)

There are dramatic and physiologically relevant changes in both skylight color and intensity during evening twilight as the pathlength of direct sunlight through the atmosphere increases, ozone increasingly absorbs long wavelengths and skylight becomes increasingly blue shifted. The moon is above the horizon at sunset during the waxing phase of the lunar cycle, on the horizon at sunset on the night of the full moon and below the horizon during the waning phase. Moonlight is red shifted compared with daylight, so the presence, phase and position of the moon in the sky could modulate the blue shifts during twilight. Therefore, the influence of the moon on twilight color is likely to differ somewhat each night of the lunar cycle, and to vary especially rapidly around the full moon, as the moon transitions from above to below the horizon during twilight. Many important light-mediated biological processes occur during twilight, and this lunar effect may play a role. One particularly intriguing biological event tightly correlated with these twilight processes is the occurrence of mass spawning events on coral reefs. Therefore, we measured downwelling underwater hyperspectral irradiance on a coral reef during twilight for several nights before and after the full moon. We demonstrate that shifts in twilight color and intensity on nights both within and between evenings, immediately before and after the full moon, are correlated with the observed times of synchronized mass spawning, and that these optical phenomena are a biologically plausible cue for the synchronization of these mass spawning events.
Epigenetic profiling at mouse imprinted gene clusters reveals novel epigenetic and genetic features at differentially methylated regions (2009)

Genomic imprinting arises from allele-specific epigenetic modifications that are established during gametogenesis and that are maintained throughout somatic development. These parental-specific modifications include DNA methylation and post-translational modifications to histones, which create allele-specific active and repressive domains at imprinted regions. Through the use of a high-density genomic tiling array, we generated DNA and histone methylation profiles at 11 imprinted gene clusters in the mouse from DNA and from chromatin immunoprecipitated from sperm, heart, and cerebellum. Our analysis revealed that despite high levels of differential DNA methylation at non-CpG islands within these regions, imprinting control regions (ICRs) and secondary differentially methylated regions (DMRs) were identified by an overlapping pattern of H3K4 trimethylation (active chromatin) and H3K9 trimethylation (repressive chromatin) modifications in somatic tissue, and a sperm differentially methylated region (sDMR; sperm not equal somatic tissue). Using these features as a common signature of DMRs, we identified 11 unique regions that mapped to known imprinted genes, to uncharacterized genes, and to intergenic regions flanking known imprinted genes. A common feature among these regions was the presence of a CpG island and an array of tandem repeats. Collectively, this study provides a comprehensive analysis of DNA methylation and histone H3K4me3 and H3K9me3 modifications at imprinted gene clusters, and identifies common epigenetic and genetic features of regions regulating genomic imprinting.
Expression of a hybrid Cu/Zn-type superoxide dismutase which has high affinity for heparin-like proteoglycans on vascular endothelial cells. (1991)

Since plasma levels of enzymes, such as superoxide dismutase (SOD), that scavenge reactive oxygen species are low, surface membranes of endothelial and parenchymal cells of various tissues are often exposed to oxidative stress. To dismutase superoxide radicals efficiently in and around vascular endothelial cells, we constructed a fusion gene encoding a hybrid SOD (HB-SOD) consisting of human Cu/Zn-SOD and a C-terminal basic peptide that binds to heparin-like proteoglycans. The fusion gene was expressed in yeast, and the resulting HB-SOD was highly purified. Upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis, HB-SOD revealed a protein band with an apparent molecular weight of 20,000. HB-SOD bound to endothelial cells of aortic segments by a mechanism which was inhibited by heparin but not by antithrombin III. When injected intravenously to rats, 125I-labeled HB-SOD rapidly disappeared from the circulation; the rate of disappearance was decreased by heparin. Less than 1% of the injected HB-SOD was found in the urine 20 min after administration at which time more than 70% of SOD was excreted in its intact form. Immunohistochemical studies revealed that HB-SOD predominantly bound to heparin-like proteoglycans on endothelial cells of the artery and other tissues. HB-SOD might permit studies on pathophysiological roles of superoxide radicals in and around vascular endothelial cells in vivo.
Apolipoprotein E Genotypes in Patients with Prostate Cancer. (2016)

E3/E3 genotype may be a potential risk factor for prostate cancer and high Gleason scoring. The E4 allele maybe a risk-reducing factor for prostate cancer.
A Polymer‐Supported Salen‐Type Palladium Complex as a Catalyst for the Suzuki—Miyaura Cross‐Coupling Reaction. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Role of Postnatal Acquisition of the Intestinal Microbiome in the Early Development of Immune Function (2010)

The present study shows that intestinal commensal microbiota have an influence on early postnatal immune development. Determining specific bacteria and/or bacterial ligands critical for this development could provide insight into the mechanisms by which broad-spectrum antibiotics and/or probiotic therapy influence the development of the mucosal immune system and mucosal-related diseases.
Structure of heparin-binding EGF-like growth factor. Multiple forms, primary structure, and glycosylation of the mature protein. (1992)

Heparin-binding epidermal growth factor-like growth factor (HB-EGF) is a newly described member of the epidermal growth factor (EGF) family that is mitogenic for BALB/c 3T3 cells, inhibits the binding of 125I-EGF to its receptor, and triggers autophosphorylation of the EGF receptor. HB-EGF was purified from the conditioned medium of U-937 cells using cation exchange, copper affinity, heparin affinity, and two rounds of C4 reversed phase liquid chromatography. The elution profile of the first round of C4 column chromatography contained four growth factor activity peaks with similar specific biological activities. N-terminal and tryptic fragment microsequencing demonstrated that these peaks contained different structural forms of the HB-EGF protein. Some of the differences in the various forms of HB-EGF were found to be due to N-terminal heterogeneity. Microsequencing of tryptic fragments indicated that the mature HB-EGF polypeptide can contain at least 86 of the 208 amino acids predicted by nucleotide sequence to be the HB-EGF precursor molecule. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis indicated that the various forms of HB-EGF have apparent molecular masses of 19-23 kDa. Further analysis of the most predominant form of HB-EGF found in U-937 cell conditioned medium indicated that it has a pI of 7.2-7.8 and is O-glycosylated.
Applications of Polarography for Assessment of Fish Freshness (1991)

ABSTRACT Fish freshness was assessed with an enzymatic method using a polarographic probe at 0.7 volt (platinum vs silver) to monitor degradation of inosine monophosphate (IMP), inosine (H × R), and hypoxanthine (Hx). The K‐value, a ratio of H × R + Hx/IMP + H × R + Hx, was determined in Sockeye salmon, Pacific cod and Pacific herring in ice and at 12°C. Results were compared with those from HPLC and sensory scores. K‐values by polarography correlated well with HPLC. Loss of freshness accompanied rise in K‐value in all studies. Sensory scores correlated relatively well with K‐values in Sockeye salmon and Pacific herring but less with Pacific cod. K‐value did not reflect eating quality of Pacific cod.
An unreported variation of the cervical vagus nerve: anatomical and histological observations. (2007)

Variations involving the cervical portion of the vagus nerve are seemingly very rare. We report an adult male found to harbour a right cervical vagus nerve that crossed anterior to the right common carotid artery to terminate in the lateral aspect of the thyroid gland. A very small continuation of this nerve was found to continue distally into the thorax. Histologically, this part of the vagus nerve did not contain ganglion or other cell bodies. There were no heterologous inclusions (thyroid, parathyroid, thymus, salivary gland or branchial cleft remnants) present. Although grossly there was a connection into the thyroid gland, this was not observed histologically. No signs of trauma were found to the ipsilateral neck region. We hypothesise that this variation is due to entanglement between the thyroid gland and cervical vagus nerve during development. This rare variation might be considered by the clinician who operates in the cervical region or interprets imaging of the neck. To our knowledge, a vagus nerve with the above described morphology has not been described.
Ionization Yield of Radiations. II. The Fluctuations of the Number of Ions (1947)

The ionization produced by individual fast charged particles is frequently used as a measure of their initial energy; fluctuation effects set a theoretical limit to the accuracy of this method. Formulas are derived here to estimate the statistical fluctuations of the number of ions produced by constant amounts of radiation energy. The variance of the number of ionizations is found to be two or three times smaller than if this number were governed by a Poisson distribution. An improved understanding is gained of the statistical treatment of fluctuation phenomena.
Operational and Topological Analyses of Antigenic Sites on Influenza C Virus Glycoprotein and Their Dependence on Glycosylation (1988)

In our previous study, seven monoclonal antibodies specific for influenza C virus glycoprotein (gp88) were prepared and tentatively classified into two groups: group A (J14, J9, Q5, K16) has neutralization activity whereas group B (S16, J6, J15) does not. These antibodies were used to analyse the antigenic structure of gp88 and to examine the effect of glycosylation on the antigenicity of the glycoprotein. Operational analysis with a panel of antigenic variants selected with each of the group A antibodies identified two non-overlapping antigenic sites on the gp88 molecules, site A-1 recognized by J14, J9 and Q5 and site A-2 by K16. Sites A-1 and A-2 were shown, however, to be topographically overlapping by competitive binding assays. Competitive binding analysis with group B antibodies identified two additional non-over-lapping antigenic sites, site B-1 recognized by S16 and site B-2 by J6 and J15. It was found in radioimmunoprecipitation experiments that antibodies to sites B-1 and B-2 were reactive not only with gp88 but with its non-glycosylated form (T76) synthesized in the presence of tunicamycin. Antibodies to sites A-1 and A-2, in contrast, immunoprecipitated the T76 polypeptide in only trace amounts or not at all. Additionally, Western blot analysis showed that denatured gp88 blotted on nitrocellulose was reactive with antibodies to sites B-1 and B-2 but not with those to sites A-1 and A-2. These observations suggest that glycosylation of gp88 selectively influences the integrity of antigenic sites A-1 and A-2 which are composed of conformation-dependent epitopes.
Mapping of the Active Site of Proteases in the 1960s and Rational Design of Inhibitors/Drugs in the 1990s (2005)

For several decades the specificity of proteases has been presented as an active site divided into subsites, using the nomenclature of Schechter & Berger from 1967 (S1, S2... for subsites of the active site; P1, P2... for residues of the substrate occupying the corresponding subsites). At early stages of the research (1960s) it was realized that the size of the active site was larger than expected and important interactions occur in regions remote from the catalytic site. Since the active site was found to be large it was divided into subsites, and a procedure to map it up was developed. The map provides information on the size of the active site (number of subsites), the properties of each subsite (free energy of ligand binding, nature of binding forces, etc.), and it enables rational design of new substrates and inhibitors. Already in 1968 inhibitors with binding constants ten thousand fold higher than available inhibitors, were prepared. The model of a large active site was initially met with strong opposition. Before long, however, predictions of the model (size of the active site, interactions in subsites remote from the catalytic site) were confirmed by X-ray crystallography (1970). During the 1990s proteolytic enzymes received renewed attention in biology and medicine, they became therapeutic targets, and protease inhibitors were successfully applied in the treatment of AIDS and hypertension. The model of large active site divided into subsites, proposed 38 years ago, stood the test of time. This model is still in use in basic research to evaluate enzyme activity, and in pharmaceutical research for the development of inhibitors/drugs.
Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes (2003)

This study evaluates the potential of pseudocomplementary peptide nucleic acids (pcPNAs) for sequence-specific modification of enzyme activity towards double-stranded DNA (dsDNA). To this end, we analyze the ability of pcPNA-dsDNA complexes to site-selectively interfere with the action of four type IIs restriction enzymes. We have found that pcPNA-dsDNA complexes exhibit a different degree of DNA protection against cleaving/nicking activity of various isoschizomeric endonucleases under investigation (PleI, MlyI and N.BstNBI) depending on their type and mutual arrangement of PNA-binding and enzyme recognition/cleavage sites. We have also found that the pcPNA targeting to closely located PleI or BbsI recognition sites on dsDNA generates in some cases the nicking activity of these DNA cutters. At the same time, MlyI endonuclease, a PleI isoschizomer, does not exhibit any DNA nicking/cleavage activity, being completely blocked by the nearby pcPNA binding. Our results have general implications for effective pcPNA interference with the performance of DNA-processing proteins, thus being important for prospective applications of pcPNAs.