gebhart/patrepeval huggingface dataset:
Effects of a soluble dietary fibre NUTRIOSE® on colonic fermentation and excretion rates in rats (2010)

The resistant dextrin NUTRIOSE®, developed from starch, is expected to act as a prebiotic. The aim of this study was to determine the effects of NUTRIOSE® on cecal parameters, short-chain fatty acid (SCFA) concentrations, and fecal excretion in rats. In an initial experiment, twenty-four male Fischer F344 rats were randomly assigned to one of the following four treatments for 14 days: G0 (control diet), G2.5 (control diet + 2.5% of dextrin), G5 (control diet + 5% of dextrin), and G10 (control diet + 10% of dextrin). After 14 days, total cecal weight, cecal content, and cecal wall weight were significantly increased in G5 and G10 compared to G0. At the same time, cecal pH was significantly lower in G10 compared to G0. Total SCFA concentration was significantly higher in G10 than in G5, G2.5, and G0, and significantly higher in G5 than in G0. Acetate, butyrate, and propionate concentrations were significantly increased in G5 and G10 compared to the controls. In a second trial based on a similar design, eighteen male Fischer F344 rats were treated with a control diet supplemented with 5% of dextrin or 5% of fructo-oligosaccharide. The results obtained with NUTRIOSE® were similar to those obtained with the fructo-oligosaccharide. In a third experiment, two groups of 5 Fischer F344 rats were orally treated with 100 and 1,000 mg/kg NUTRIOSE®, respectively, and from 18% to 25% of the dextrin was excreted in the feces. The results of these three studies show that the consumption of NUTRIOSE®, by its effects on total cecal weight, cecal content, cecal wall weight, pH, and SCFA production, could induce healthy benefits since these effects are reported to be prebiotic effects.
Two-handed endoscopic-directed vestibular nerve sectioning: case series and review of the literature (2012)

The endoscopic-directed approach represents a safe and effective method for performing vestibular nerve sectioning. Until now, the endoscope has been used primarily as an adjunct to the operating microscope in surgery at the cerebellopontine angle. In addition, previous endoscopic techniques typically require a third hand to manipulate the endoscope. With the 2-handed endoscopic-directed technique, however, the endoscope is used as the primary means of visualization, and the unique design of this endoscope allows for a bimanual procedure without the requirement of a cosurgeon. Advantages of using this technique compared with the microscope include superior brightness at close distances, greater depth of field, increased maneuverability within small regions, and an improved ability to visualize objects not in a direct line of sight. Among other things, this allows for minimally invasive openings, decreased cerebellar retraction, and better identification of nerve cleavage planes and vascular anatomy.
The Prefrontal Cortex Regulates Lateral Amygdala Neuronal Plasticity and Responses to Previously Conditioned Stimuli (2003)

The amygdala plays a role in learning and memory processes that involve an emotional component. However, neural structures that regulate these amygdala-dependent processes are unknown. Previous studies indicate that regulation of affect may be imposed by the prefrontal cortex (PFC) and its efferents to the amygdala. The presentation of conditioned affective stimuli enhances activity of neurons in the lateral nucleus of the amygdala (LAT), which is thought to drive conditioned affective responses. Moreover, plasticity of LAT neuronal responses to stimuli during the course of conditioning is believed to underlie affective learning. This study examines the role of the PFC in the regulation of affective behaviors by evaluating how the PFC affects LAT neuronal plasticity and activity that is evoked by previously conditioned stimuli. In vivo intracellular recordings were performed from the LAT of anesthetized rats during pavlovian conditioning and during the presentation of stimuli that were conditioned in the awake rat before recording. Train stimulation of the PFC suppressed LAT neuronal activity that was evoked by both previously conditioned and neutral stimuli. In addition, PFC stimulation blocked LAT neuronal plasticity associated with an affective conditioning procedure. These results indicate that the PFC has the potential to regulate affective processes by inhibition of the LAT. Patients with disruptions of the PFC-LAT interaction often display an inability to regulate affective responses. This may be attributable to the loss of PFC-imposed inhibition of the emotional response to a stimulus but may also include the formation or diminished extinction of inappropriate associations.
Polymer-protein and polymer-drug conjugates in cancer therapy. (2003)

Polymer conjugates are becoming established as a new approach towards improved cancer therapy. These water-soluble, hybrid constructs fall into two main categories: polymer-protein conjugates (already available as licensed products), and polymer-drug conjugates (currently in clinical development). Polyethyleneglycol conjugation of proteins is accepted as a means to reduce immunogenicity, prolong plasma half-life and enhance protein stability. Polymer-drug conjugation promotes tumor targeting by the 'enhanced permeation and retention' effect, and at the cellular level, allows lysosomotropic drug delivery. Eleven polymer-drug conjugates have entered clinical development and activity has already been observed in chemotherapy refractory patients. Certain compounds have also demonstrated a marked reduction in drug toxicity.
Structural Analysis of Residual and Technical Lignins by 1H-13C Correlation 2D NMR-Spectroscopy (2001)

Summary Structural analysis was conducted on residual lignin from pine Kraft AQ pulp, Eucalyptus Kraft lignin from Eucalyptus globulus and Repap Organosolv lignin by 2D 13 C- 1 H correlation NMR spectroscopic techniques such as HMQC sequence. These lignins contain a rather wide variety of saturated aliphatic groups. The HMQC NMR spectra of the lignins do not verify the presence of diarylmethane moieties in any lignin investigated. The type and amount of other condensed structures depend on the nature of lignin preparation. All the lignins investigated still contained β- O -4′, pino- and syringayresinol (β-β′) and phenylcoumarane (β-5′) structures. Stilbene structures were also identified. Vinyl ether structures were present only in Eucalyptus Kraft lignin. All the lignins contain α-carbonyl groups conjugated to aromatic moieties as terminal side chains rather than involving β- O -4′ structures. No coniferyl alcohol and coniferyl aldehyde type structures are detected in the lignins after pulping. The spectra of kraft lignins show some new signals, the origin of which is discussed.
Assessment of the anti-obesity effects of the TNP-470 analog, CKD-732 (2007)

The systemic treatment with angiogenesis inhibitor has been shown to result in weight reduction and adipose tissue loss in various models of obesity. To verify the mechanism of CKD-732 (TNP-470 analog) against obesity, we evaluated CKD-732's peripheral and central anti-obesity effects. CKD-732 was injected subcutaneously (s.c.) for 7 days in various animal models and intracerebroventricularly (i.c.v.) in arcuate nucleus (ARC) lesion mice, ob/ob mice, and normal littermates. Modulation of the hypothalamic neuropeptide mRNAs after i.c.v. injection was evaluated in ARC lesion mice and normal littermates. A conditioned taste aversion (CTA) was performed using lithium chloride (LiCl) as a positive control agent in Long-Evans Tokushima Otsuka and Otsuka Long-Evans Tokushima fatty (OLETF) rats. As a result, 7 days of CKD-732 s.c. injection reduced the cumulative food intake and the body weight significantly in both treated obese (e.g. 114.8 +/- 13.4 g vs 170.7 +/- 20.6 g, 7.9 +/- 0.5% decrease vs 0.3 +/- 2.2% decrease; in treated OLETF rat versus control OLETF rat, P < 0.01 respectively) and non-obese models. Epididymal and mesenteric fat pads, and the size of adipocytes were significantly decreased in treated rats. A single i.c.v. injection decreased food intake and body weight in ARC lesion mice and ob/ob mice but not in normal littermates. Unexpectedly, the hypothalamic neuropeptide mRNAs were not altered by single i.c.v. injection. CKD-732 also induced a dose-dependent CTA comparable with LiCl injection, which is a commonly used agent to produce a CTA. In conclusion, CKD-732 causes significant body weight and appetite reduction, possibly by decreasing adiposity directly and inducing central anorexia, which is partly explained by a CTA. These results should be carefully verified to assess the utility of CKD-732 as an anti-obesity drug.
Saliency filters: Contrast based filtering for salient region detection (2012)

Saliency estimation has become a valuable tool in image processing. Yet, existing approaches exhibit considerable variation in methodology, and it is often difficult to attribute improvements in result quality to specific algorithm properties. In this paper we reconsider some of the design choices of previous methods and propose a conceptually clear and intuitive algorithm for contrast-based saliency estimation. Our algorithm consists of four basic steps. First, our method decomposes a given image into compact, perceptually homogeneous elements that abstract unnecessary detail. Based on this abstraction we compute two measures of contrast that rate the uniqueness and the spatial distribution of these elements. From the element contrast we then derive a saliency measure that produces a pixel-accurate saliency map which uniformly covers the objects of interest and consistently separates fore- and background. We show that the complete contrast and saliency estimation can be formulated in a unified way using high-dimensional Gaussian filters. This contributes to the conceptual simplicity of our method and lends itself to a highly efficient implementation with linear complexity. In a detailed experimental evaluation we analyze the contribution of each individual feature and show that our method outperforms all state-of-the-art approaches.
Mutants of the major ryegrass pollen allergen, Lol p 5, with reduced IgE-binding capacity: candidates for grass pollen-specific immunotherapy (2002)

More than 400 million individuals are sensitized to grass pollen allergens. Group 5 allergens represent the most potent grass pollen allergens recognized by more than 80 % of grass pollen allergic patients. The aim of our study was to reduce the allergenic activity of group 5 allergens for specific immunotherapy of grass pollen allergy. Based on B- and T-cell epitope mapping studies and on sequence comparison of group 5 allergens from different grasses, point mutations were introduced by site-directed mutagenesis in highly conserved sequence domains of Lol p 5, the group 5 allergen from ryegrass. We obtained Lol p 5 mutants with low IgE-binding capacity and reduced allergenic activity as determined by basophil histamine release and by skin prick testing in allergic patients. Circular dichroism analysis showed that these mutants exhibited an overall structural fold similar to the recombinant Lol p 5 wild-type allergen. In addition, Lol p 5 mutants retained the ability to induce proliferation of group 5 allergen-specific T cell lines and clones. Our results demonstrate that a few point mutations in the Lol p 5 sequence yield mutants with reduced allergenic activity that represent potential vaccine candidates for immunotherapy of grass pollen allergy.
A bacterial enzyme degrading the model lignin compound β‐etherase is a member of the glutathione‐S‐transferase superfamily (1993)

Cleavage of beta-aryl ether linkages is essential in lignin degradation. We identified another beta-etherase gene (ligF), which contains an open reading frame of 771 bp and lies between genes coding C alpha-dehydrogenase (ligD) and beta-etherase (ligE). The beta-etherase activity of LigF expressed in Escherichia coli was more than 80 times as high as that of LigE. ligF and ligE are homologous to glutathione-S-transferase, and upon addition of glutathione a remarkable acceleration of beta-etherase activity was found in E. coli carrying ligF. It is concluded that LigF plays a central role in beta-aryl ether cleavage and that glutathione is the hydrogen donor in this reaction.
A Network Analysis of the Human T-Cell Activation Gene Network Identifies Jagged1 as a Therapeutic Target for Autoimmune Diseases (2007)

Understanding complex diseases will benefit the recognition of the properties of the gene networks that control biological functions. Here, we set out to model the gene network that controls T-cell activation in humans, which is critical for the development of autoimmune diseases such as Multiple Sclerosis (MS). The network was established on the basis of the quantitative expression from 104 individuals of 20 genes of the immune system, as well as on biological information from the Ingenuity database and Bayesian inference. Of the 31 links (gene interactions) identified in the network, 18 were identified in the Ingenuity database and 13 were new and we validated 7 of 8 interactions experimentally. In the MS patients network, we found an increase in the weight of gene interactions related to Th1 function and a decrease in those related to Treg and Th2 function. Indeed, we found that IFN-ss therapy induces changes in gene interactions related to T cell proliferation and adhesion, although these gene interactions were not restored to levels similar to controls. Finally, we identify JAG1 as a new therapeutic target whose differential behaviour in the MS network was not modified by immunomodulatory therapy. In vitro treatment with a Jagged1 agonist peptide modulated the T-cell activation network in PBMCs from patients with MS. Moreover, treatment of mice with experimental autoimmune encephalomyelitis with the Jagged1 agonist ameliorated the disease course, and modulated Th2, Th1 and Treg function. This study illustrates how network analysis can predict therapeutic targets for immune intervention and identified the immunomodulatory properties of Jagged1 making it a new therapeutic target for MS and other autoimmune diseases.
Primary Differentiation in the Human Blastocyst: Comparative Molecular Portraits of Inner Cell Mass and Trophectoderm Cells (2005)

The primary differentiation event during mammalian development occurs at the blastocyst stage and leads to the delineation of the inner cell mass (ICM) and the trophectoderm (TE). We provide the first global mRNA expression data from immunosurgically dissected ICM cells, TE cells, and intact human blastocysts. Using a cDNA microarray composed of 15,529 cDNAs from known and novel genes, we identify marker transcripts specific to the ICM (e.g., OCT4/POU5F1, NANOG, HMGB1, and DPPA5) and TE (e.g., CDX2, ATP1B3, SFN, and IPL), in addition to novel ICM- and TE-specific expressed sequence tags. The expression patterns suggest that the emergence of pluripotent ICM and TE cell lineages from the morula is controlled by metabolic and signaling pathways, which include inter alia, WNT, mitogen-activated protein kinase, transforming growth factor-beta, NOTCH, integrin-mediated cell adhesion, phosphatidylinositol 3-kinase, and apoptosis. These data enhance our understanding of the first step in human cellular differentiation and, hence, the derivation of both embryonic stem cells and trophoblastic stem cells from these lineages.
Preparation and Characterization of Nanocomposite Films from Chitin Whisker and Waterborne Poly(ester-urethane) With or Without Ultra-Sonification Treatment (2010)

Two series of nanocomposite films were prepared from waterborne poly(ester-urethane) and chitin whisker with and without ultrasound treatment coded as CW/WPU and CHW/WPU, respectively. The effects of ultra-sonification method and chitin whisker content on the chemical compositions, crystallization behavior and miscibility were studied by attenuated total reflection Fourier transform infrared (ATR-FTIR), wide-angle X-ray diffraction (WXRD), dynamic mechanical analysis (DMA) and scanning electron microscopy (SEM). Thermal stability and mechanical properties of the films were measured by thermogravimetric analysis (TGA) and tensile test, respectively. The results revealed that both nanocomposite films exhibited a certain degree of miscibility when chitin whisker content was lower than 30 wt%, resulting in higher thermal stability and tensile strength than the pure waterborne poly(ester-urethane) film. Interestingly, the composite films CW/WPU with ultrasound treatment possessed better miscibility, storage modulus, thermal stability and tensile strength than those without ultrasound treatment over the entire composition range studied here. The difference can be attributed to the relatively higher dispersion level of whisker within poly(ester-urethane) matrix resulting in relatively stronger entanglement and interaction between both components. The ultrasound treatment can effectively improve the miscibility and mechanical properties of the casting nanocomposite films with nano-meter size chitin whisker added. This indicated that the structure, miscibility and mechanical properties of the nanocomposite films depended significantly on the preparation method.
Endocytic sorting motif interactions involved in Nef-mediated downmodulation of CD4 and CD3 (2017)

Lentiviral Nefs recruit assembly polypeptide complexes and target sorting motifs in cellular receptors to induce their internalization. While Nef-mediated CD4 downmodulation is conserved, the ability to internalize CD3 was lost in HIV-1 and its precursors. Although both functions play key roles in lentiviral replication and pathogenicity, the underlying structural requirements are poorly defined. Here, we determine the structure of SIV<sub>mac239</sub> Nef bound to the ExxxLM motif of another Nef molecule at 2.5 Å resolution. This provides a basis for a structural model, where a hydrophobic crevice in simian immunodeficiency virus (SIV) Nef targets a dileucine motif in CD4 and a tyrosine-based motif in CD3. Introducing key residues into this crevice of HIV-1 Nef enables CD3 binding but an additional N-terminal tyrosine motif is required for internalization. Our resolution of the CD4/Nef/AP2 complex and generation of HIV-1 Nefs capable of CD3 downregulation provide insights into sorting motif interactions and target discrimination of Nef.HIV and simian immunodeficiency virus (SIV) Nef proteins both stimulate the clathrin-mediated endocytosis of CD4 but differ in downmodulation of the immune receptor CD3. Here, the authors present the structure of SIV Nef bound to the ExxxLM motif of another Nef molecule, which allows them to propose a model how Nef recognizes these motifs in CD3 and CD4.
Properties of Novel Hydroxypropyl Methylcellulose Films Containing Chitosan Nanoparticles (2008)

In this study, chitosan nanoparticles were prepared and incorporated in hydroxypropyl methylcellulose (HPMC) films under different conditions. Mechanical properties, water vapor and oxygen permeability, water solubility, and scanning and transmission electron microscopy (SEM and TEM) results were analyzed. Incorporation of chitosan nanoparticles in the films improved their mechanical properties significantly, while also improving film barrier properties significantly. The chitosan poly(methacrylic acid) (CS-PMAA) nanoparticles tend to occupy the empty spaces in the pores of the HPMC matrix, inducing the collapse of the pores and thereby improving film tensile and barrier properties. This study is the first to investigate the use of nanoparticles for the purpose of strengthening HPMC films.
A fibroblast chondroitin sulfate proteoglycan core protein contains lectin-like and growth factor-like sequences. (1987)

We have isolated cDNA clones that code for a proteoglycan-related polypeptide with unique properties. A lambda gt11 expression library made from human fibroblast mRNA was screened with an antiserum made against a proteoglycan fraction from human fetal membranes. One group of positive clones revealed an open reading frame coding for 685 amino acids from the COOH terminus of a polypeptide. This amino acid sequence contains a domain that is strongly homologous with the COOH-terminal core protein domain of the large aggregating cartilage proteoglycan. This domain also contains sequences that are homologous with vertebrate lectins that bind terminal galactosyl, N-acetyl-glucosaminyl or mannosyl residues. On the NH2-terminal side of the lectin-like domain the cDNA-derived amino acid sequence contains two epidermal growth factor-related segments. The cDNA clones were shown to belong to a chondroitin sulfate proteoglycan by using antisera made against two peptides predicted from the cDNA sequence. These antisera were reactive with a proteoglycan fraction from fibroblasts after chondroitinase treatment of the fraction but not after treatment with heparinase or no treatment. Among the several polypeptides reactive with the anti-peptide antibodies the largest one, corresponding to a molecular weight of about 400,000, is likely to be the intact core protein, whereas the smaller polypeptides may be processing products or products of artifactual proteolysis. These results show that the amino acid sequence belongs to a proteoglycan core protein, and the sequence, therefore, provides a molecular definition to this proteoglycan. The lectin-related and growth factor-like sequences in the core protein of this proteoglycan suggest that it may play a role in intercellular signaling.
Kinetics of cytokine and NFAT gene expression in human interleukin‐2‐dependent T lymphoblasts stimulated via T‐cell receptor (1998)

T cells respond to mitogenic or antigenic stimulation by proliferation and by turning on cytokine gene expression. Here we have analysed the kinetics and nature of cytokine production in human peripheral blood-derived T lymphoblasts stimulated with anti-CD3 antibodies or Lens culinaris lectin (LCL). T cells were purified from peripheral blood mononuclear cells (PBMC) and primarily activated with anti-CD3 antibodies and cultured in the presence of interleukin-2 (IL-2). Anti-CD3-restimulated T cells (mainly CD8+) produced IL-2, interferon-gamma (IFN-gamma) and tumour necrosis factor-alpha (TNF-alpha) and low levels of IL-4 and IL-10 transcripts and proteins. No IL-6 gene expression was observed. In LCL-stimulated cells the cytokine production pattern was very similar. Steady-state mRNA levels of IL-2, IL-10 and IFN-gamma peaked at 3 hr after anti-CD3 stimulation and declined rapidly thereafter. The kinetics of TNF-alpha mRNA expression was faster, being at its peak level 1 hr after stimulation. Anti-CD3-stimulated IL-2 gene expression was down-regulated by protein synthesis inhibitor, whereas IL-10, IFN-gamma and TNF-alpha genes were readily induced independent of ongoing protein synthesis. T-cell receptor stimulation also induced a very rapid expression of c-jun, c-fos and NFATc1 (NFATc) genes, the gene products of which are involved in cytokine gene expression. In conclusion, the cytokines synthesized by IL-2-dependent T cells were predominantly IL-2, IFN-gamma and TNF-alpha.