gebhart/patrepeval huggingface dataset:
Analytical model to describe fluorescence spectra of normal and preneoplastic epithelial tissue: comparison with Monte Carlo simulations and clinical measurements (2004)

Fluorescence spectroscopy has shown promise for the detection of precancerous changes in vivo. The epithelial and stromal layers of tissue have very different optical properties; the albedo is relatively low in the epithelium and approaches one in the stroma. As precancer develops, the optical properties of the epithelium and stroma are altered in markedly different ways: epithelial scattering and fluorescence increase, and stromal scattering and fluorescence decrease. We present an analytical model of the fluorescence spectrum of a two-layer medium such as epithelial tissue. Our hypothesis is that accounting for the two different tissue layers will provide increased diagnostic information when used to analyze tissue fluorescence spectra measured in vivo. The Beer-Lambert law is used to describe light propagation in the epithelial layer, while light propagation in the highly scattering stromal layer is described with diffusion theory. Predictions of the analytical model are compared to results from Monte Carlo simulations of light propagation under a range of optical properties reported for normal and precancerous epithelial tissue. In all cases, the mean square error between the Monte Carlo simulations and the analytical model are within 15%. Finally, model predictions are compared to fluorescence spectra of normal and precancerous cervical tissue measured in vivo; the lineshape of fluorescence agrees well in both cases, and the decrease in fluorescence intensity from normal to precancerous tissue is correctly predicted to within 5%. Future work will explore the use of this model to extract information about changes in epithelial and stromal optical properties from clinical measurements and the diagnostic value of these parameters.
Exploiting reality with multicast groups (1995)

This article describes our investigation into developing large distributed simulations. The architecture we describe logically partitions virtual environments by associating spatial, temporal, and functional classes with network multicast groups. We exploit the actual characteristics of the real-world large scale environments being simulated by focusing or restricting an entity's processing and network resources to its area of interest via a local area-of-interest manager. For example, a simulated infantryman in a virtual environment doesn't need to know the condition of a simulated truck 20 virtual kilometres away.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Detoxification of jojoba meal (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetoxification of jojoba mealAnthony J. Verbiscar, Thomas F. Banigan, Charles W. Weber, B. L. Reid, John E. Trei, Edward A. Nelson, Robert F. Raffauf, and Donald KoserskyCite this: J. Agric. Food Chem. 1980, 28, 3, 571–578Publication Date (Print):May 1, 1980Publication History Published online1 May 2002Published inissue 1 May 1980https://doi.org/10.1021/jf60229a007RIGHTS & PERMISSIONSArticle Views137Altmetric-Citations47LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
Minute Virus of Mice Small Nonstructural Protein NS2 Interacts and Colocalizes with the Smn Protein (2002)

The small nonstructural protein NS2 of the minute virus of mice (MVM) is required for efficient viral replication, although its mode of action is unclear. Here we demonstrate that NS2 and survival motor neuron protein (Smn) interact in vitro and in vivo. NS2 and Smn also colocalize in infected nuclei at late times following MVM infection.
Prostate Cancer Treatment is Enhanced by GenisteinIn VitroandIn Vivoin a Syngeneic Orthotopic Tumor Model (2006)

Pretreatment with genistein, a bioactive component of soy isoflavones, potentiated cell killing induced by radiation in human PC-3 prostate cancer cells in vitro. Using an orthotopic xenograft in nude mice, we demonstrated that genistein combined with prostate tumor irradiation caused greater inhibition of primary tumor growth and increased control of spontaneous metastasis to para-aortic lymph nodes, increasing mouse survival. Paradoxically, treatment with genistein alone increased metastasis to lymph nodes. This observation is of concern in relation to soy-based clinical trials for cancer patients. To address whether this observation is because nude mice have an impaired immune system, these studies were repeated in orthotopic RM-9 prostate tumors in syngeneic C57BL/6 mice. The combination of genistein with radiation in this model also caused a greater inhibition of primary tumor growth and spontaneous metastasis to regional para-aortic lymph nodes, whereas treatment with genistein alone showed a trend to increased lymph node metastasis. Data from the syngeneic and xenograft models are comparable and indicate that the combination of genistein with radiotherapy is more effective and safer for prostate cancer treatment than genistein alone, which promotes metastatic spread to regional lymph nodes.
DNA recombination with a heterospecific Cre homolog identified from comparison of the pac-c1 regions of P1-related phages (2004)

Sequencing of the 7 kb immC region from four P1-related phages identified a novel DNA recombinase that exhibits many Cre-like characteristics, including recombination in mammalian cells, but which has a distinctly different DNA specificity. DNA sequence comparison to the P1 immC region showed that all phages had related DNA terminase, C1 repressor and DNA recombinase genes. Although these genes from phages P7, phi(w39) and p15B were highly similar to those from P1, those of phage D6 showed significant divergence. Moreover, the D6 sequence showed evidence of DNA deletion and substitution in this region relative to the other phages. Characterization of the D6 site-specific DNA recombinase (Dre) showed that it was a tyrosine recombinase closely related to the P1 Cre recombinase, but that it had a distinct DNA specificity for a 32 bp DNA site (rox). Cre and Dre are heterospecific: Cre did not catalyze recombination at rox sites and Dre did not catalyze recombination at lox sites. Like Cre, Dre catalyzed both integrative and excisive recombination and required no other phage-encoded proteins for recombination. Dre-mediated recombination in mammalian cells showed that, like Cre, no host bacterial proteins are required for efficient Dre-mediated site-specific DNA recombination.
The Effect of Increased Tissue Pressure on Blood Flow (1975)

Theoretical consideration of the factors involved in maintaining vascular equilibrium and experimental evidence in animals and man indicate that at high tissue pressures there may be a sharp decline in blood flow and, in certain situations, complete cessation of blood flow even at tissue pressures below mean arterial pressure. At least two mechanisms appear to be involved: active closure of small arterioles under vasomotor tone when transmural pressure is lowered, either by falls in intravascular pressure or rises in tissue pressure, and passive collapse of soft-walled capillaries when tissue pressure rises above intracapillary pressure. These mechanisms are likely to assume particular importance when tissues are surrounded by non-compliant fascia and may thus be involved in compartmental syndromes.
sORFs.org: a repository of small ORFs identified by ribosome profiling (2015)

With the advent of ribosome profiling, a next generation sequencing technique providing a "snap-shot'' of translated mRNA in a cell, many short open reading frames (sORFs) with ribosomal activity were identified. Follow-up studies revealed the existence of functional peptides, so-called micropeptides, translated from these 'sORFs', indicating a new class of bio-active peptides. Over the last few years, several micropeptides exhibiting important cellular functions were discovered. However, ribosome occupancy does not necessarily imply an actual function of the translated peptide, leading to the development of various tools assessing the coding potential of sORFs. Here, we introduce sORFs.org (http://www.sorfs.org), a novel database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are provided, a default one enabling quick lookup of sORFs and a BioMart interface providing advanced query and export possibilities. At present, sORFs.org harbors 263 354 sORFs that demonstrate ribosome occupancy, originating from three different cell lines: HCT116 (human), E14_mESC (mouse) and S2 (fruit fly). sORFs.org aims to provide an extensive sORFs database accessible to researchers with limited bioinformatics knowledge, thus enabling easy integration into personal projects.
Distribution of Gustatory Sensitivities in Rat Taste Cells: Whole-Cell Responses to Apical Chemical Stimulation (2001)

Several taste transduction mechanisms have been demonstrated in mammals, but little is known about their distribution within and across receptor cells. We recorded whole-cell responses of 120 taste cells of the rat fungiform papillae and soft palate maintained within the intact epithelium in a modified Ussing chamber, which allowed us to flow tastants across the apical membrane while monitoring the activity of the cell with a patch pipette. Taste stimuli were: 0.1 m sucrose, KCl, and NH(4)Cl, 0.032 m NaCl, and 3.2 mm HCl and quinine hydrochloride (QHCl). When cells were held at their resting potentials, taste stimulation resulted in conductance changes; reversible currents >5 pA were considered reliable responses. Sucrose and QHCl produced a decrease in outward current and membrane conductance, whereas NaCl, KCl, NH(4)Cl, and HCl elicited inward currents accompanied by increased conductance. Combinations of responses to pairs of the four basic stimuli (sucrose, NaCl, HCl, and QHCl) across the 71-84 cells tested with each pair were predictable from the probabilities of responses to individual stimuli, indicating an independent distribution of sensitivities. Of 62 cells tested with all four basic stimuli, 59 responded to at least one of the stimuli; 16 of these (27.1%) responded to only one, 20 (33.9%) to two, 15 (25.4%) to three, and 8 (13.6%) to all of the basic stimuli. Cells with both inward (Na(+)) and outward (K(+)) voltage-activated currents were significantly more broadly tuned to gustatory stimuli than those with only inward currents.
Bone development and its relation to fracture repair. The role of mesenchymal osteoblasts and surface osteoblasts (2008)

Bone development occurs by two mechanisms: intramembranous bone formation and endochondral bone formation. Bone tissue forms by eventual differentiation of osteoprogenitor cells into either mesenchymal osteoblasts (MOBL), which synthesize woven bone in random orientation, or surface osteoblasts (SOBL), which synthesize bone on surfaces in a well oriented lamellar array. Bone repair uses the same formation patterns as bone development but the specific mechanism of repair is determined by the biomechanical environment provided. Bone synthesis and maintenance are highly dependent on the blood supply of bone and on cell-cell communication via the lacunar-canalicular system. Recent investigations highlight the molecular cascades leading to cell differentiation, the components of the structural proteins such as the various collagens, and tissue vascularization. The patterning of bone matrix from an initial woven to an eventual lamellar orientation is essential for bone to develop its maximum strength. This review demonstrates the repetitive nature of woven to lamellar bone formation as mediated by MOBLs and SOBLs in both normal vertebrate bones and bone repair. Repair, using endochondral, primary, direct and distraction osteogenesis mechanisms, is reviewed along with the associated molecular, vascular, and biophysical features.
Altered Adhesion Molecule Expression and Endothelial Cell Activation Accompany the Recruitment of Human Granulocytes to the Lung after Segmental Antigen Challenge (1992)

Mounting evidence suggests that inflammatory cells recruited to the lung can contribute to the pathogenesis of asthma. The factors governing the activation and recruitment of circulating cells to the lung remain unknown, but an early step in this process is the interaction of adhesion molecules on circulating cells with those on endothelial cells. We used a segmental antigen challenge model followed 18 h later by bronchoalveolar lavage (BAL) to study granulocyte recruitment to the lung in 14 allergic subjects. Using immunofluorescence and flow cytometry, we determined the expression of the adhesion molecules CD11b, L-selectin (LECAM-1), and VLA-4 on BAL and peripheral blood granulocytes. Total cell count and percentages of recovered eosinophils and basophils were significantly increased in BAL fluids from antigen-challenged segments. Compared with their peripheral blood counterparts, CD11b expression was increased 2- to 3-fold on BAL eosinophils, basophils, and neutrophils (n = 9, P less than 0.05). In contrast, L-selectin expression was significantly decreased on BAL cells (n = 3 to 4, P less than 0.05). Similar phenotypic changes were observed on all three cell types, and on neutrophils recovered from saline-challenged control lung segments. In two subjects, VLA-4 alpha (CD49d) expression on BAL eosinophils was 78 +/- 5% of that seen on peripheral blood eosinophils. Because ELAM-1 (endothelial leukocyte adhesion molecule-1, E-selectin) expression occurs during allergic inflammation and is shed after endothelial activation, we used a sensitive enzyme-linked immunosorbent assay to analyze BAL supernatants for a soluble form of this molecule (sELAM-1).(ABSTRACT TRUNCATED AT 250 WORDS)
The Role of Individual Cysteine Residues in the Structure and Function of the v- sis Gene Product (1987)

The v-sis oncogene encodes a platelet-derived growth factor (PDGF)-related product whose transforming activity is mediated by its functional interaction with the PDGF receptor. PDGF, as well as processed forms of the v-sis gene product, is a disulfide-linked dimer with eight conserved cysteine residues in the minimum region necessary for biologic activity. Site-directed mutagenesis of the v-sis gene revealed that each conserved cysteine residue was required directly or indirectly for disulfide-linked dimer formation. However, substitution of serine for cysteine codons at any of four positions had no detrimental effect on transforming activity of the encoded v-sis protein. These results establish that interchain disulfide bonds are not essential in order for this protein to act as a functional ligand for the PDGF receptor. The remaining four substitutions of serine for cysteine each inactivated transforming function of the molecule. In each case this was associated with loss of a conformation shown to involve intramolecular disulfide bonds. These studies provide insight into the role of individual cysteine residues in determining the structure of the sis/PDGF molecule critical for biological activity.
Repression of the ovalbumin gene involves multiple negative elements including a ubiquitous transcriptional silencer. (1995)

Most eukaryotic genes are controlled by a complex array of cis-acting regulatory elements that modulate transcriptional activity. Two major regulatory elements reside in the chicken ovalbumin gene, a steroid-dependent regulatory element (SDRE, -892 to -780) and a negative regulatory element (NRE, -308 to -88). The SDRE is required for responsiveness to estrogen and glucocorticoid. The NRE appears to have the dual role of repressing transcription in the absence of steroids and of cooperating with the SDRE to activate transcription in the presence of steroids. The experiments described herein were designed to investigate the role of the NRE in repressing gene expression. Transfection of OvCAT fusion genes containing deletions in the NRE into primary oviduct cell cultures identified three elements (-308 to -256, -239 to -220, and -174 to -88) that repress transcription. Oligomers corresponding to portions of these elements also independently repress the viral thymidine kinase promoter. Interestingly, the element from -239 to -220 functions mechanistically as a silencer and shares sequence identity with silencers in other genes (TCTCTCCNA). Mobility shift studies indicated that all of the negative elements bind specific protein complexes from oviduct, none of which is appreciably affected by treatment with steroid hormones. However, oviduct-specific proteins bind to the regions from -280 to -252 and from -134 to -88, providing the first identification of potential tissue-specific elements in the ovalbumin gene. These results demonstrate that the region of DNA originally called the NRE is a multifunctional regulatory element that may be involved in several diverse regulatory activities.
Local administration of uridine suppresses the cardinal features of asthmatic airway inflammation (2010)

In summary, we were able to show that uridine inhibits the classical features of asthmatic airway inflammation. As uridine supplementation is well tolerated in humans, it might be a new therapeutic approach for the treatment of bronchial asthma.
Regulation of Macrophage Colony-Stimulating Factor (M-CSF) Production in Cultured Human Synovial Fibroblasts (1993)

These results suggest that cytokine-stimulated synovial fibroblasts may be a source of M-CSF production in the joints of patients with inflammatory arthritis; as a result, monocyte/macrophages may be activated, leading to perpetuation of the inflammation and destructive events occurring in these lesions.
Natramune and PureWay-C reduce xenobiotic-induced human T-cell alpha5beta1 integrin-mediated adhesion to fibronectin. (2008)

These data demonstrate that xenobiotic-induced alpha5beta1 integrin mediated T-cell adhesion to fibronectin is reduced by nutritional supplementation with Natramune (PDS-2865) and PureWay-C. These data suggest the possibility that inflammatory responses associated with exposure to pollutants can be mitigated by nutritional supplementation.
Albumin Binding to FcRn:  Distinct from the FcRn−IgG Interaction (2006)

The MHC-related Fc receptor for IgG (FcRn) protects albumin and IgG from degradation by binding both proteins with high affinity at low pH in the acid endosome and diverting both from a lysosomal pathway, returning them to the extracellular compartment. Immunoblotting and surface plasmon resonance studies show that both IgG and albumin bind noncooperatively to distinct sites on FcRn, that the affinity of FcRn for albumin decreases approximately 200-fold from acidic to neutral pH, and that the FcRn-albumin interaction shows rapid association and dissociation kinetics. Isothermal titration calorimetry shows that albumin binds FcRn with a 1:1 stoichiometry and the interaction has hydrophobic features as evidenced by a large positive change in entropy upon binding. Our results suggest that the FcRn-albumin interaction has unique features distinct from FcRn-IgG binding despite the overall similarity in the pH-dependent binding mechanism by which both ligands are protected from degradation.
Layered Double Hydroxides for CO2 Capture: Structure Evolution and Regeneration (2006)

Mg−Al−CO3 layered double hydroxide (LDH) was synthesized, and its thermal evolution was investigated using X-ray diffraction, FTIR spectroscopy, and thermogravimetric analysis (TGA). The resultant LDH derivatives showed excellent CO2 adsorption capabilities, especially suitable for high-temperature CO2 separation from flue gases. Calcination of crystalline LDHs at 400 °C led to phase transformation yielding amorphous Mg−Al mixed oxides having a CO2 sorption capacity of 0.49 mmol/g at 200 °C. Reversible and irreversible CO2 sorption was determined to be ∼88% and ∼12% of the total CO2 sorption, respectively. Regeneration restored the Mg−Al mixed oxide to 98% of its initial CO2 sorption after several cycles of CO2 adsorption testing. This clearly indicates the desirable properties of Mg−Al mixed oxide for CO2 capture from flue gases at high temperatures (up to 200 °C).
Colony‐stimulating factor‐1 receptor (c‐fms) (1988)

The macrophage colony-stimulating factor, CSF-1 (M-CSF), is a homodimeric glycoprotein required for the lineage-specific growth of cells of the mononuclear phagocyte series. Apart from its role in stimulating the proliferation of bone marrow-derived precursors of monocytes and macrophages, CSF-1 acts as a survival factor and primes mature macrophages to carry out differentiated functions. Each of the actions of CSF-1 are mediated through its binding to a single class of high-affinity receptors expressed on monocytes, macrophages, and their committed progenitors. The CSF-1 receptor (CSF-1R) is encoded by the c-fms proto-oncogene, and is one of a family of growth factor receptors that exhibits an intrinsic tyrosine-specific protein kinase activity. Transduction of c-fms sequences as a viral oncogene (v-fms) in the McDonough (SM) and HZ-5 strains of feline sarcoma virus has resulted in alterations in receptor coding sequences that affect its activity as a tyrosine kinase and provide persistent signals for cell growth in the absence of its ligand. The genetic alterations in the c-fms gene that unmask its latent transforming potential abrogate its lineage-specific activity and enable v-fms to transform a variety of cells that do not normally express CSF-1 receptors.
Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes (1995)

The thermodynamic parameters (delta H degree, delta S degree, and delta G degree 37) for 16 nearest-neighbor sets and one initiation factor are presented here in order to predict stability of RNA/DNA hybrid duplexes. To determine the nearest-neighbor parameters, thermodynamics for 68 different hybrid sequences (136 single-stranded oligonucleotides) with 5-13 nucleotide length including several duplexes with identical nearest-neighbors were measured by UV melting procedure. These sequences were selected to have many different combinations of nearest-neighbor pairs, and so that the number of the 16 nearest-neighbor sequences in the oligomers were as equal as possible. The structures of the hybrids were also investigated by measuring circular dichroism spectra. Comparing delta G degree 37 values of the hybrids with DNA/DNA and RNA/RNA parameters reported previously (Breslauer, K.J., Frank, R., Blöcker, H., & Marky, L.A. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750; Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T., & Turner, D.H. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 9373-9377), RNA/RNA double helix is the most stable of the three kinds of helixes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA hybrid duplexes depends on its sequence. Calculated thermodynamic values of hybrid formation with the present parameters reproduce the experimental values within reasonable errors.