gebhart/patrepeval huggingface dataset:
Interaction of cationic porphyrins with DNA: importance of the number and position of the charges and minimum structural requirements for intercalation (1990)

Thirty-three porphyrins or metalloporphyrins corresponding to the general formula [meso-[N-methyl-4(or 3 or 2)-pyridiniumyl]n(aryl)4-nporphyrin]M (M = H2, CuII, or ClFeIII), with n = 2-4, have been synthesized and characterized by UV-visible and 1H NMR spectroscopy and mass spectrometry. These porphyrins differ not only in the number (2-4) and position of their cationic charges but also in the steric requirements to reach even temporarily a completely planar geometry. In particular, they contain 0, 1, 2, 3, or 4 meso-aryl substituents not able to rotate. Interaction of these porphyrins or metalloporphyrins with calf thymus DNA has been studied and their apparent affinity binding constants have been determined by use of a competition method with ethidium bromide which was applicable not only for all the free base porphyrins but also for their copper(II) or iron(III) complexes. Whatever their mode of binding may be, their apparent affinity binding constants were relatively high (Kapp between 1.2 x 10(7) and 5 x 10(4) M-1 under our conditions), and a linear decrease of log Kapp with the number of porphyrin charges was observed. Studies of porphyrin-DNA interactions by UV and fluorescence spectroscopy, viscosimetry, and fluorescence energy transfer experiments showed that not only the tetracationic meso-tetrakis[N-methyl-4(or 3)-pyridiniumyl]porphyrins, which both involved four freely rotating meso-aryl groups, but also the corresponding tri- and dicationic porphyrins were able to intercalate into calf thymus DNA. Moreover, the cis dicationic meso-bis(N-methyl-2-pyridiniumyl)diphenylporphyrin, which involved only two freely rotating meso-aryl groups in a cis position, was also able to intercalate. The other meso-(N-methyl-2-pyridiniumyl)n(phenyl)4-nporphyrins, which involved either zero, one, or two trans freely rotating meso-aryl groups, could not intercalate into DNA. These results show that only half of the porphyrin ring is necessary for intercalation to occur.
Angiotensin II-induced mitogenesis of spontaneously hypertensive rat-derived cultured smooth muscle cells is dependent on autocrine production of transforming growth factor-beta. (1992)

Angiotensin II (Ang II) has been implicated in the regulation of smooth muscle cell proliferation after vascular injury, but the molecular mechanisms of this effect remain obscure. The aims of the present study were 1) to determine if Ang II was mitogenic (in a defined serum-free medium) for aortic smooth muscle cells derived from spontaneously hypertensive rats, either alone or in combination with epidermal growth factor, basic fibroblast growth factor, or platelet-derived growth factor-BB; and 2) to determine if the Ang II effects were mediated by autocrine production of transforming growth factor-beta (TGF-beta). Results demonstrated that Ang II increased the proliferative response of smooth muscle cells to epidermal growth factor or platelet-derived growth factor-BB. Ang II alone and in combination with basic fibroblast growth factor induced a small delayed increase (48-72 hours after treatment) in DNA synthesis and [3H]thymidine labeling indexes without an increase in cell number. Ang II effects were at least partially mediated by autocrine production of active TGF-beta in that 1) treatment with Ang II increased TGF-beta activity in conditioned media and 2) TGF-beta neutralizing antibody inhibited Ang II-induced increases in DNA synthesis. However, treatment with exogenous TGF-beta at concentrations induced by Ang II failed to elicit a mitogenic response, thus implicating other autocrine factors in mediation of Ang II effects. Results suggest a potential mechanism whereby Ang II might regulate smooth muscle cell mitogenesis after vascular injury.
Telomerase and DNA End Replication: No Longer a Lagging Strand Problem? (1995)

UPLIN
In VitroSynthesis and Secretion of Ovine Trophoblast Protein-1 during the Period of Maternal Recognition of Pregnancy* (1985)

The trophoblast of the sheep conceptus secretes a low mol wt, acidic polypeptide called ovine trophoblast protein-1 (oTP-1) from days 13-21 of pregnancy. This protein has been proposed to have an antiluteolytic role during pregnancy, since infusion of oTP-1 into the uterine lumen of nonpregnant ewes lengthened their estrous cycles. In the present study, mRNA from day 16 conceptuses was translated using a cell-free wheat germ lysate, and oTP-1 was immunoprecipitated from the translation mixture by means of a specific rabbit antiserum. The predominant protein synthesized under these conditions was oTP-1, which had a mol wt (21,000) higher than that of oTP-1 secreted by intact conceptuses into culture medium (mol wt, 17,000). In a separate experiment, in vitro secretion of oTP-1 from conceptuses on days 13, 17, and 21 of pregnancy was examined. Conceptuses were cultured for 24 h in the presence of [3H]leucine, and oTP-1 was immunoprecipitated from the culture medium. Incorporation of [3H]leucine into secreted macromolecules (mol wt, greater than 3500) increased 12-fold from days 13 to 21, while release of immunoprecipitable 3H-labeled oTP-1 increased 27-fold from days 13 to 17 and declined by over 50% from days 17 to 21. When results were expressed per microgram DNA, secretion of total macromolecules declined from days 13 to 17 and then remained constant until day 21. The pattern of oTP-1 secretion held whether results were expressed per conceptus or per unit DNA. The interestrous intervals for the donor ewes were shorter for ewes which had their conceptuses removed on day 13 than for ewes flushed on day 17 or 21. Thus, the period of oTP-1 synthesis corresponds closely to the time at which the conceptus acts to extend luteal lifespan.
Cell-free tumor antigen peptide-based cancer vaccines (1997)

The central role that tumor antigen-derived peptides play in induction of antitumor immunity makes them ideal candidates for peptide-based cancer vaccines. We have demonstrated that "transloading" is an efficient strategy for importing short peptide ligands into antigen-presenting cells in vitro. Postulating that the transloading procedure might effect peptide uptake by antigen-presenting cells in vivo as well, we tested this approach for the generation of peptide-based cancer vaccines. In the P815 mastocytoma system, we vaccinated mice by s.c. injection of a single, known natural peptide derived from JAK-1 kinase. Whereas vaccination with peptide alone or mixed with incomplete Freund's adjuvant was ineffective, application of the peptide in conjunction with the polycation poly-L-lysine protected a significant number of animals against tumor challenge. Dependent upon the type of poly-L-lysine applied, protection against tumor take was comparable to that achieved with irradiated whole-cell vaccines, genetically modified to secrete granulocyte-macrophage colony-stimulating factor. In the murine melanoma M-3, a combination of four putative tumor antigen-derived peptides was tested as a cancer vaccine. Administered in combination with polycations, these peptides evoked potent antitumor immunity that could not be obtained with the peptides alone or peptides emulsified in incomplete Freund's adjuvant. However, peptide-polycation vaccines applied to the M-3 model were not as efficient as cellular control vaccines, consisting of irradiated interleukin 2 or granulocyte-macrophage colony-stimulating factor-secreting tumor cells.
Reduced Posterior Hippocampal Volume in Posttraumatic Stress Disorder (2008)

The posterior hippocampus has been associated with storage, processing, and retrieval of spatiotemporal memories, central to the protective function of fear conditioning. Volume deficit in the posterior hippocampus may indicate malfunction in this faculty, leading to the exaggerated conditioned fear response observed in PTSD.
A Large, Antigenically Conserved Protein On The Surface Of Moraxella Catarrhalis Is A Target For Protective Antibodies (1994)

A monoclonal antibody (MAb) to Moraxella catarrhalis O35E bound to a surface-exposed epitope of a proteinaceous antigen of this organism. The antigen, designated UspA, was present in every strain of the pathogen tested in a colony blot RIA. UspA had a molecular mass on SDS-PAGE that varied between 300 and 400 kDa, depending on the individual M. catarrhalis strain. Passive immunization of mice with the UspA-reactive Mab enhanced pulmonary clearance of M. catarrhalis. Use of this Mab to screen a M. catarrhalis genomic DNA library permitted identification of a recombinant bacteriophage expressing the M. catarrhalis UspA protein. The recombinant UspA protein was used in Western blot analysis with sera from patients with M. catarrhalis pneumonia. Convalescent-phase sera but not acute-phase sera from these patients contained antibodies to this M. catarrhalis surface protein, indicating that M. catarrhalis strains growing in vivo express this molecule.
BIOELECTROCHEMISTRY. I. ENZYME UTILIZING BIO-FUEL CELL STUDIES. (1964)

Electron transfer as opposed to hydrogen transfer was demonstrated to be involved in the oxidation-reduction of the flavoprotein enzyme system. A bioelectrochemical investigation of glucose oxidase (EC 1.1.3.4), d -amino acid oxidase (EC 1.4.3.3), and yeast alcohol dehydrogenase (EC 1.1.1.1) systems was conducted in an attempt to utilize the electron-transferring process as a potential anodic reaction in a biochemical fuel cell. Utilizing a bio-fuel cell constructed of plexiglass, platinum-foil electrodes, and an ion-exchange membrane for conduction between the anolyte and catholyte, the flavoprotein enzymes, both glucose oxidase and d -amino acid oxidase systems in conjunction with an O 2 cathode, generated 175–350 mV. In contrast, alcohol dehydrogenase (yeast), a pyridinoprotein enzyme which requires coenzyme I (NAD+), did not produce any electrical voltage. Elemental iron was found to potentiate the flavoprotein enzyme reaction yielding voltages ranging from 625 to 750 mV. The potentiating effect was probably due to a faster turnover rate of FADH to FAD+ coupled with the additional net oxidation potential of iron.
Antiproliferative effect of retinoic acid in intravitreous silicone oil in an animal model of proliferative vitreoretinopathy. (1993)

The in vivo data suggest that retinoic acid might be useful as an antiproliferative agent in human eyes.
Effects of Blood-Processing Protocols on Cell-free DNA Quantification in Plasma (2003)

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Macrophage populations in the human placenta and amniochorion. (1984)

Fetal and maternal macrophage populations in human utero-placental tissues at different stages of gestation have been studied using immunohistological and histochemical techniques. A large population of macrophages has been identified within maternal decidualized endometrium in both term and first trimester tissues, although lymphoid cells also constitute a major component of the bone marrow derived cells in the decidua of early pregnancy. In contrast, fetal macrophages have been shown to contribute nearly all of the substantial bone marrow derived cell population within placental chorionic villous mesenchyme and within the mesenchyme of the term amniochorion. Apart from a small population of stellate intensely HLA-DR positive cells in term placental villous stroma, these extra-embryonic fetal macrophages could be shown consistently to express both the leu-M3 tissue macrophage antigen and lysosomal enzyme activities. It is suggested that the major HLA-DR positive cell population of fetal amniochorion comprises 'classical' macrophages rather than dendritic type cells. These various macrophage populations may perform vital phagocytic and degradative functions within utero-placental tissues and amniochorion.
Generalized Theory of Acoustic Propagation in Porous Dissipative Media (1962)

The theory of acoustic propagation in porous media is extended to include anisotropy, viscoelasticity, and solid dissipation. A more refined analysis of the relative motion of the fluid in the pores is also developed by introducing the concept of viscodynamic operational tensor. The nature of this operator is analyzed by applying variational and Lagrangian methods. Viscoelasticity and solid dissipation are introduced by applying the correspondence principle as derived from thermodynamics in earlier work by the author. Various dissipative models are discussed and the corresponding operators and relaxation spectra are derived. The physical chemistry of the multiphase porous medium including surface effects lies within the scope of the thermodynamic theory. The nature of thermoelastic dissipation and electrokinetic effects in relation to the thermodynamic theory is also brought out.
Fetal origins of hyperphagia, obesity, and hypertension and postnatal amplification by hypercaloric nutrition (2000)

Environmental factors and diet are generally believed to be accelerators of obesity and hypertension, but they are not the underlying cause. Our animal model of obesity and hypertension is based on the observation that impaired fetal growth has long-term clinical consequences that are induced by fetal programming. Using fetal undernutrition throughout pregnancy, we investigated whether the effects of fetal programming on adult obesity and hypertension are mediated by changes in insulin and leptin action and whether increased appetite may be a behavioral trigger of adult disease. Virgin Wistar rats were time mated and randomly assigned to receive food either ad libitum (AD group) or at 30% of ad libitum intake, or undernutrition (UN group). Offspring from UN mothers were significantly smaller at birth than AD offspring. At weaning, offspring were assigned to one of two diets [a control diet or a hypercaloric (30% fat) diet]. Food intake in offspring from UN mothers was significantly elevated at an early postnatal age. It increased further with advancing age and was amplified by hypercaloric nutrition. UN offspring also showed elevated systolic blood pressure and markedly increased fasting plasma insulin and leptin concentrations. This study is the first to demonstrate that profound adult hyperphagia is a consequence of fetal programming and a key contributing factor in adult pathophysiology. We hypothesize that hyperinsulinism and hyperleptinemia play a key role in the etiology of hyperphagia, obesity, and hypertension as a consequence of altered fetal development.
Deposition of Gold Nanoparticles onto Thiol-Functionalized Multiwalled Carbon Nanotubes (2005)

Gold nanoparticles were deposited on the surface of multiwalled carbon nanotubes (MWNTs) functionalized with aliphatic bifunctional thiols (1,4-butanedithiol, 1,6-hexanedithiol, 1,8-octanedithiol, and 2-aminoethanethiol) through a direct solvent-free procedure. Small gold particles, with a narrow particle size distribution around 1.7 nm, were obtained on 1,6-hexanedithiol-functionalized MWNTs. For MWNTs functionalized with the aminothiol, the average Au particle size was larger, 5.5 nm, apparently due to a coalescence phenomenon. Gatan image filter (GIF) observations show that sulfur is at the nanotube surface with a non-homogeneous distribution. A higher sulfur concentration was observed around the gold nanoparticles' location.
Hospitalization by cytotoxic chemotherapy regimen among older women with stage IV breast cancer (2018)

Treatment regimen was associated with significant variation in 30-day hospitalization or death among older women receiving cytotoxic chemotherapy for stage IV de novo breast cancer.
The Institute for Genomic Research Osa1 Rice Genome Annotation Database (2005)

We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 non-transposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.
Using co‐occurrence models for placename disambiguation (2008)

This paper describes the generation of a model capturing information on how placenames co‐occur together. The advantages of the co‐occurrence model over traditional gazetteers are discussed and the problem of placename disambiguation is presented as a case study. We begin by outlining the problem of ambiguous placenames. We demonstrate how analysis of Wikipedia can be used in the generation of a co‐occurrence model. The accuracy of our model is compared to a handcrafted ground truth; then we evaluate alternative methods of applying this model to the disambiguation of placenames in free text (using the GeoCLEF evaluation forum). We conclude by showing how the inclusion of placenames in both the text and geographic parts of a query provides the maximum mean average precision and outline the benefits of a co‐occurrence model as a data source for the wider field of geographic information retrieval (GIR).
Integration of mammalian circadian clock signals: from molecule to behavior (2003)

The core oscillatory mechanism consisting of gene transcription and translation is a unique feature and the astonishing discovery in circadian biology is that the rhythm of gene transcription reflects the behavioral rhythm almost perfectly. This means that the clock gene oscillation generated by the core loop in each suprachiasmatic nucleus neuron is coupled and amplified, and harmonized strongly so that oscillating activities are spread into the whole brain and to all those peripheral organs which contain peripheral clocks. Additionally, circadian changes are induced in behavior and hormone secretion. Investigations of biological clocks open the fascinating perspective to analyze the integrational mechanism of 'time', providing a bridge between single genes and the living organism as a whole.
Wandering behaviour in people with dementia (2003)

Knowledge generated through research remains insufficient to explain fully why and when wandering occurs. Variability in how the phenomenon was defined and studied, and the small size of the samples made generalizability of findings difficult. Future research should incorporate a clearer definition of wandering; a specific targeted population with representative sample size; appropriate subject identification strategies; focussed interventions, and better control conditions.
Mesalazine (5‐aminosalicylic acid) alters faecal bacterial profiles, but not mucosal proteolytic activity in diarrhoea‐predominant irritable bowel syndrome (2011)

Mesalazine treatment is associated with a decrease in faecal bacteria abundance and rebalancing of the major constituents of the microbiota. Further study of the bacteriological and anti-inflammatory properties of mesalazine in IBS is warranted.
Lnk Inhibits Tpo–mpl Signaling and Tpo-mediated Megakaryocytopoiesis (2004)

Thrombopoietin (Tpo) is the primary cytokine regulating megakaryocyte development and platelet production. Tpo signaling through its receptor, c-mpl, activates multiple pathways including signal transducer and activator of transcription (STAT)3, STAT5, phosphoinositide 3-kinase-Akt, and p42/44 mitogen-activated protein kinase (MAPK). The adaptor protein Lnk is implicated in cytokine receptor and immunoreceptor signaling. Here, we show that Lnk overexpression negatively regulates Tpo-mediated cell proliferation and endomitosis in hematopoietic cell lines and primary hematopoietic cells. Lnk attenuates Tpo-induced S-phase progression in 32D cells expressing mpl, and Lnk decreases Tpo-dependent megakaryocyte growth in bone marrow (BM)-derived megakaryocyte culture. Consistent with this result, we found that in both BM and spleen, Lnk-deficient mice exhibited increased numbers of megakaryocytes with increased ploidy compared with wild-type mice. In addition, Lnk-deficient megakaryocytes derived from BM and spleen showed enhanced sensitivity to Tpo during culture. The absence of Lnk caused enhanced and prolonged Tpo induction of STAT3, STAT5, Akt, and MAPK signaling pathways in CD41+ megakaryocytes. Furthermore, the Src homology 2 domain of Lnk is essential for Lnk's inhibitory function. In contrast, the conserved tyrosine near the COOH terminus is dispensable and the pleckstrin homology domain of Lnk contributes to, but is not essential for, inhibiting Tpo-dependent 32D cell growth or megakaryocyte development. Thus, Lnk negatively modulates mpl signaling pathways and is important for Tpo-mediated megakaryocytopoiesis in vivo.
The effects of keratinocyte growth factor in preclinical models of mucositis (2002)

The epithelium of the oral cavity and small intestine of the gastrointestinal tract have a high rate of cell renewal and as such, are sensitive to cytotoxic therapies that kill rapidly dividing cells. Mucositis is a complication of cancer therapy where impairment of the regenerative capacity of the epithelium leads to atrophy, ulceration and a loss of barrier function. Keratinocyte growth factor (KGF) is an epithelial cell-specific growth and differentiation factor that is trophic for the mucosal epithelium of the gastrointestinal tract. In this study, KGF in normal animals caused epithelial thickening in the squamous epithelium of the oral cavity and increased crypt depth and villus height of the small intestine. It also appeared to regulate gene expression in these tissues including that of some antioxidant enzymes and intestinal trefoil protein. KGF has been shown to be efficacious in several preclinical models of mucositis where KGF pretreatment reduced weight loss typically seen during and after the course of therapy and significantly improved survival. At a tissue level KGF reduced atrophy, accelerated regrowth, and decreased ulcer formation of the oral epithelium after irradiation, and improved crypt survival and prevented villus atrophy in the small intestine of irradiated or chemotherapy-treated mice. Preliminary studies suggest that its efficacy may be partly a consequence of the growth and differentiation effect, and also partly due to regulation of the expression of genes that play a role in mucosal protection. These data suggest that KGF may be useful for the prevention or treatment of mucositis in patients treated with regimens of cancer therapy that have gastrointestinal toxicity.