gebhart/patrepeval huggingface dataset:
An idiotypic replica of carcinoembryonic antigen inducing cellular and humoral responses directed against human colorectal tumours (1992)

A monoclonal anti-idiotypic antibody (anti-Id MAb) 708 (IgG2b), which inhibited the binding of NCRC23 (IgG1) MAb to CEA and prevented radiolabelled CEA from binding to MAb NCRC23, was produced. No recognition of 3 other anti-CEA antibodies, 3 other IgG1 or 2 IgM MAbs was observed with this anti-idiotypic antibody. When an immunoblotting technique was used, 708 anti-Id MAb failed to bind to isolated heavy or light chains of MAb NCRC23, whereas binding was observed with intact antibody. Mouse, rat and human lymphocytes (in vitro) were immunized with 708 anti-Id MAb and the resultant Ab3 antibodies all inhibited binding of labelled 708 anti-Id MAb to MAb NCRC23 and also reacted with CEA, showing that 708 anti-Id MAb induced anti-CEA antibody responses. Similarly, mice immunized with 708 anti-Id MAb could be restimulated in vitro with either CEA or tumour cells expressing CEA which induced specific T-cell proliferative responses. Human tumour-infiltrating lymphocytes isolated from colorectal tumours or peripheral blood T cells from cancer patients were stimulated in vitro with 708 anti-Id MAb or an irrelevant IgG2b antibody. Six days later both sets of lymphocytes were restimulated with CEA, and lymphocytes primed to 708 anti-Id MAb proliferated in response to CEA. These results suggest that 708 anti-Id MAb can act as an idiotypic replica of CEA and stimulate cellular and humoral anti-CEA immune responses. It is therefore of great interest as an idiotypic vaccine against colorectal cancer.
The severity of clinical manifestations in preeclampsia correlates with the amount of placental infarction (2010)

In pregnancies with mild or severe preeclampsia, a large proportion of the placentas had histological signs of pathology, in particular signs of ischemia. The pathology was similar, but more pronounced in severe compared to mild preeclampsia, suggesting mild and severe preeclampsia to have similar underlying etiology.
PI3K-AKT Network Roles in Infectious Diseases (2008)

The PI3K-Akt network, which is activated by cytokines or growth factors, mediates intracellular signalsto regulate a variety of cellular responses, including antiapoptosis, proliferation, cell cycling, protein synthesis, glucose metabolism, and telomere activity. Genomic mutations, alterations of the PI3K-Akt regulatorynetwork, underlie such diseases as cancer, glucose intolerance (diabetes mellitus), schizophrenia, and/orautoimmune diseases. In addition to direct tumorigenesis involvement by genetically altering human cancer, the PI3K-Akt network underlies the clinical manifestation of different stages of tumorigenic viral infection, such as latent and chronic infection, and malignant transformation of Epstein-Barr, hepatitis C, hepatitis B, and human immunodeficiency virus (HIV) viruses. We summarize updated knowledge on the PI3K-AKTnetwork underlying different phathological viral and/or bacterial infections. Antiviral activity engenderedby suppressing of PI3K-Akt activity, rather than directly targeting anticancer activity via oncogenes, maythus open up ways to prevent malignant transformation by tumorigenic viral infection.
Structural perturbations in DNA caused by bis-intercalation of ditercalinium visualised by atomic force microscopy (2002)

Atomic force microscopy (AFM) has been used to examine perturbations in the tertiary structure of DNA induced by the binding of ditercalinium, a DNA bis-intercalator with strong anti-tumour properties. We report AFM images of plasmid DNA of both circular and linearised forms showing a difference in the formation of supercoils and plectonemic coils caused at least in part by alterations in the superhelical stress upon bis-intercalation. A further investigation of the effects of drug binding performed with 292 bp mixed-sequence DNA fragments, and using increment in contour length as a reliable measure of intercalation, revealed saturation occurring at a point where sufficient drug was present to interact with every other available binding site. Moment analysis based on the distribution of angles between segments along single DNA molecules showed that at this level of bis-intercalation, the apparent persistence length of the molecules was 91.7 +/- 5.7 nm, approximately twice as long as that of naked DNA. We conclude that images of single molecules generated using AFM provide a valuable supplement to solution-based techniques for evaluation of physical properties of biological macromolecules.
Aberrant Hippocampal Activity Underlies the Dopamine Dysregulation in an Animal Model of Schizophrenia (2007)

Evidence supports a dysregulation of subcortical dopamine (DA) system function as a common etiology of psychosis; however, the factors responsible for this aberrant DA system responsivity have not been delineated. Here, we demonstrate in an animal model of schizophrenia that a pathologically enhanced drive from the ventral hippocampus (vHipp) can result in aberrant dopamine neuron signaling. Adult rats in which development was disrupted by prenatal methylazoxymethanol acetate (MAM) administration display a significantly greater number of spontaneously firing ventral tegmental DA neurons. This appears to be a consequence of excessive hippocampal activity because, in MAM-treated rats, vHipp inactivation completely reversed the elevated DA neuron population activity and also normalized the augmented amphetamine-induced locomotor behavior. These data provide a direct link between hippocampal dysfunction and the hyper-responsivity of the DA system that is believed to underlie the augmented response to amphetamine in animal models and psychosis in schizophrenia patients.
Komplette Remission eines langjährig therapierefraktären sekundär hochmalignen Non-Hodgkin-Lymphoms nach Therapie mit Bendamustin und CD 20-Ak (Rituximab) (2001)

Hintergrund: Die CD 20-Antikörper (Ak)-Therapie gewinnt innerhalb der Behandlungskonzepte niedrigmaligner Non-Hodgkin-Lymphome zunehmend an Bedeutung. Für die Behandlung hochmaligner Non-Hodgkin-Lymphome mit dem CD 20-Ak liegen vergleichsweise wenige Daten vor. Wir beschreiben den Fall eines sechs Jahre bekannten, sekundär hochmalignen, ausgesprochen therapierefraktären, zentroblastischen B-Zell-Lymphoms im Stadium IV A, das nach CD 20-Ak Therapie in Kombination mit Bendamustin eine komplette Remission mit einem rezidivfreien Intervall von 22 Monaten aufweist. Kasuistik: Im Dezember 1994 wurde bei einem damals 47-jährigen Mann ein niedrigmalignes, zentrozytisch-zentroblastisches B-Zell-Lymphom diagnostiziert. Das erste Rezidiv im August 1995 zeigte eine Transformation in ein hochmalignes, zentroblastisches B-Zell-Lymphom. Die etablierten Rezidivtherapien führten lediglich zu einem einmaligen progressfreien Intervall von 6 Monaten unter Interferon α, bei einem ausgeprägten therapieinduzierten Nebenwirkungsspektrum im Sinne einer dosislimitierenden Panmyelopathie (WHO III), einer sensiblen peripheren Neuropathie (WHO II) sowie einer Thrombose der V. axillaris und V. brachialis (WHO III). Nach Applikation der anti-CD 20-Medikation in Standarddosierung in Kombination mit Bendamustin im Februar 1999 kann bei komplikationsloser Verträglichkeit 22 Monate nach Therapieende noch immer Rezidivfreiheit beobachtet werden. Schlussfolgerung: Der CD 20-Ak-Therapie scheint in der Behandlung therapierefraktärer hochmaligner Non-Hodgkin-Lymphome hinsichtlich des Erreichens einer länger währenden Remission eine Bedeutung zuzukommen.
Data driven mean-shift belief propagation for non-gaussian MRFs (2010)

We introduce a novel data-driven mean-shift belief propagation (DDMSBP) method for non-Gaussian MRFs, which often arise in computer vision applications. With the aid of scale space theory, optimization of non-Gaussian, multimodal MRF models using DDMSBP becomes less sensitive to local maxima. This is a significant improvement over standard BP inference, and extends the range of methods that are computationally tractable. In particular, when pair-wise potentials are Gaussians, the time complexity of DDMSBP becomes bilinear in the numbers of states and nodes in the MRF. Experimental results from simulation and non-rigid deformable neuroimage registration demonstrate that our method is faster and more accurate than state-of-the-art inference algorithms.
Mechanism of toxin secretion by Vibrio cholerae investigated in strains harboring plasmids that encode heat-labile enterotoxins of Escherichia coli. (1984)

A genetically engineered Vibrio cholerae strain from which the cholera toxin genes had previously been deleted was used as a host in which to study the expression and secretion of related toxins and their subunits. Recombinant plasmids encoding heat-labile enterotoxins (LTs) from Escherichia coli of human and porcine origin were expressed in the V. cholerae host, and this resulted in the secretion of the LTs into the extracellular milieu. The secreted LTs were isolated and it was found that the A subunits of human and porcine LT were "unnicked" polypeptides, which indicates that nicking is not obligatory for toxin secretion. V. cholerae strains were also constructed that harbored plasmids encoding either the A or the B subunits of human LT (A+B-, or A-B+). Approximately 90% of the B subunits were secreted from the A-B+ strain, while all of the A subunits expressed by the A+B- strain remained cell associated. This implies that strains synthesizing both subunits assemble the A and B subunits prior to their secretion. We propose that the entry of the toxin into the secretory step of the export pathway is mediated by a secretory apparatus that recognizes structural domains within the B subunit of LT.
Chromosomal localization of the genes for the vitronectin and fibronectin receptors alpha subunits and for platelet glycoproteins IIb and IIIa. (1988)

The integrins, a family of related membrane receptors involved in cell-cell and cell-matrix interactions, are heterodimeric complexes of alpha and beta subunits. To begin to understand the evolution of these complexes, we studied the genomic organization of several alpha and beta integrin subunits. Using both somatic cell hybrids and an in situ hybridization technique, we have determined the chromosomal location of the genes for the alpha subunits of the vitronectin receptor (VNR alpha), the fibronectin receptor (FNR alpha), and for the alpha subunit of the platelet glycoprotein IIb/IIIa complex, GPIIb. In addition, we have determined the chromosomal location of the gene for the beta subunit of the GPIIb/IIIa heterodimer, GPIIIa. Our studies indicate that the alpha subunits do not localize to a single locus, but that each is found on a different chromosome. The gene for VNR alpha is located on chromosome 2, the gene for FNR alpha is on chromosome 12q11----13, and the gene for GPIIb is on chromosome 17q21----23. In contrast to the chromosomal dispersion of the alpha subunits, the genes for GPIIb and GPIIIa are physically close, with the gene for GPIIIa also located on chromosome 17q21----23. These studies indicate that the genes for the alpha subunits of the integrin family have been dispersed during evolution while GPIIb and GPIIIa are in close physical proximity. This physical proximity of GPIIb and GPIIIa may be involved in the concurrent expression of these proteins by megakaryocytes, and may result in linkage disequilibrium between these two genes, which would limit the use of restriction length polymorphisms in linkage studies of GPIIb/IIIa abnormalities in small kindreds.
Experimental investigation of three-dimensional dynamic stall model oscillating in pitch (1995)

The ONERA semiempirical theoretical model for unsteady aerodynamics in the stall regime has been extended to three-dimensi onal flow. Parameter identification for the model is obtained from experimental dynamic stall data for a low AR rectangular wing with a NACA 0012 airfoil profile oscillating in pitch. Excellent correlations were obtained with the measured data for a three-dimensional linear aerodynamic model and reasonable agreement between theory and test data were obtained for a nonlinear (stalled) aerodynamic model. Qualitatively, the results obtained for this simple three-dimensional wing are similar to the corresponding data for the twodimensional airfoil.
Robust web extraction (2009)

On script-generated web sites, many documents share common HTML tree structure, allowing wrappers to effectively extract information of interest. Of course, the scripts and thus the tree structure evolve over time, causing wrappers to break repeatedly, and resulting in a high cost of maintaining wrappers. In this paper, we explore a novel approach: we use temporal snapshots of web pages to develop a tree-edit model of HTML, and use this model to improve wrapper construction. We view the changes to the tree structure as suppositions of a series of edit operations: deleting nodes, inserting nodes and substituting labels of nodes. The tree structures evolve by choosing these edit operations stochastically.
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract (2002)

Bifidobacteria are Gram-positive prokaryotes that naturally colonize the human gastrointestinal tract (GIT) and vagina. Although not numerically dominant in the complex intestinal microflora, they are considered as key commensals that promote a healthy GIT. We determined the 2.26-Mb genome sequence of an infant-derived strain of Bifidobacterium longum, and identified 1,730 possible coding sequences organized in a 60%-GC circular chromosome. Bioinformatic analysis revealed several physiological traits that could partially explain the successful adaptation of this bacteria to the colon. An unexpectedly large number of the predicted proteins appeared to be specialized for catabolism of a variety of oligosaccharides, some possibly released by rare or novel glycosyl hydrolases acting on "nondigestible" plant polymers or host-derived glycoproteins and glycoconjugates. This ability to scavenge from a large variety of nutrients likely contributes to the competitiveness and persistence of bifidobacteria in the colon. Many genes for oligosaccharide metabolism were found in self-regulated modules that appear to have arisen in part from gene duplication or horizontal acquisition. Complete pathways for all amino acids, nucleotides, and some key vitamins were identified; however, routes for Asp and Cys were atypical. More importantly, genome analysis provided insights into the reciprocal interactions of bifidobacteria with their hosts. We identified polypeptides that showed homology to most major proteins needed for production of glycoprotein-binding fimbriae, structures that could possibly be important for adhesion and persistence in the GIT. We also found a eukaryotic-type serine protease inhibitor (serpin) possibly involved in the reported immunomodulatory activity of bifidobacteria.
Selective Estrogen-Receptor Modulators — Mechanisms of Action and Application to Clinical Practice (2003)

The selective estrogen-receptor modulators, or SERMs, chemically diverse nonsteroid compounds, have tertiary structures that permit binding to the estrogen receptor. These compounds have either selective agonist or antagonist effects, depending on the target tissue. This article reviews current information concerning the molecular basis of SERM action and the tissue-selective agonist–antagonist effects of this class of medication. The article also offers a perspective on the therapeutic uses of SERMs and compares the SERMs with estrogen and nonestrogen alternatives.
Inhibition of platelet heparitinase by phosphorothioate DNA oligonucleotides. (1995)

In view of the role that heparitinase and heparanase enzymes are thought to play in regulating the proliferation of smooth muscle cells, inhibitors of these enzymes may have therapeutic value in the treatment of vascular hyperplasia. Here we report that phosphorothioate oligodeoxynucleotides inhibit platelet heparitinase and related enzymes in vitro. The inhibition is greatly enhanced by the presence of a GGG motif in the oligonucleotide, and also increases with oligonucleotide for two phosphorothioate DNA 30-mers consisting solely of guanosine and thymidine nucleotides. Their inhibitory efficacy was greater when heparan sulphate was used as substrate.
Smart Drug‐Loaded Polymer Gold Nanoshells for Systemic and Localized Therapy of Human Epithelial Cancer (2009)

Near-infrared-light-sensitive multifunctional smart drug-loaded polymer gold nanoshells are fabricated as advanced prototypes, composed of chemotherapeutic agents (therapeutic antibody and anticancer drug-loaded polymeric nanoparticles) for systemic chemotherapy of human epithelial cancer and a polymer-based gold nanoshell for localized photothermal treatment by NIR light.
Adjuvant chemotherapy with CEF versus CMF for node-positive breast cancer. (1998)

Article Tools Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.1998.16.12.3916 Journal of Clinical Oncology - published online before print September 21, 2016 PMID: 9850039 Adjuvant chemotherapy with CEF versus CMF for node-positive breast cancer. C D AtkinsxC D AtkinsSearch for articles by this author https://doi.org/10.1200/JCO.1998.16.12.3916 First Page PDF © 1998 by American Society of Clinical Oncology
Long-Term Developmental Outcome of Infants with Iron Deficiency (1991)

Children who have iron-deficiency anemia in infancy are at risk for long-lasting developmental disadvantage as compared with their peers with better iron status.
Remodeling of HDL by CETP in vivo and by CETP and hepatic lipase in vitro results in enhanced uptake of HDL CE by cells expressing scavenger receptor B-I (1999)

The transport of HDL cholesteryl esters (CE) from plasma to the liver involves a direct uptake pathway, mediated by hepatic scavenger receptor B-I (SR-BI), and an indirect pathway, involving the exchange of HDL CE for triglycerides (TG) of TG-rich lipoproteins by cholesteryl ester transfer protein (CETP). We carried out HDL CE turnover studies in mice expressing human CETP and/or human lecithin:cholesterol acyltransferase (LCAT) transgenes on a background of human apoA-I expression. The fractional clearance of HDL CE by the liver was delayed by LCAT transgene, while the CETP transgene increased it. However, there was no incremental transfer of HDL CE radioactivity to the TG-rich lipoprotein fraction in mice expressing CETP, suggesting increased direct removal of HDL CE in the liver. To evaluate the possibility that this might be mediated by SR-BI, HDL isolated from plasma of the different groups of transgenic mice was incubated with SR-BI transfected or control CHO cells. HDL isolated from mice expressing CETP showed a 2- to 4-fold increase in SR-BI-mediated HDL CE uptake, compared to HDL from mice lacking CETP. The addition of pure CETP to HDL in cell culture did not lead to increased selective uptake of HDL CE by cells. However, when human HDL was enriched with TG by incubation with TG-rich lipoproteins in the presence of CETP, then treated with hepatic lipase, there was a significant enhancement of HDL CE uptake. Thus, the remodeling of human HDL by CETP, involving CE;-TG interchange, followed by the action of hepatic lipase (HL), leads to the enhanced uptake of HDL CE by cellular SR-BI. These observations suggest that in animals such as humans in which both the selective uptake and CETP pathways are active, the two pathways could operate in a synergistic fashion to enhance reverse cholesterol transport.
Defining Lipid Transport Pathways in Animal Cells (1985)

A new technique for studying the metabolism and intracellular transport of lipid molecules in living cells based on the use of fluorescent lipid analogs is described. The cellular processing of various intermediates (phosphatidic acid and ceramide) and end products (phosphatidylcholine and phosphatidylethanolamine) in lipid biosynthesis is reviewed and a working model for compartmentalization during lipid biosynthesis is presented.
Robust water desalination membranes against degradation using high loads of carbon nanotubes (2018)

Chlorine resistant reverse osmosis (RO) membranes were fabricated using a multi-walled carbon nanotube-polyamide (MWCNT-PA) nanocomposite. The separation performance of these membranes after chlorine exposure (4800 ppm·h) remained unchanged (99.9%) but was drastically reduced to 82% in the absence of MWCNT. It was observed that the surface roughness of the membranes changed significantly by adding MWCNT. Moreover, membranes containing MWCNT fractions above 12.5 wt.% clearly improved degradation resistance against chlorine exposure, with an increase in water flux while maintaining salt rejection performance. Molecular dynamics and quantum chemical calculations were performed in order to understand the high chemical stability of the MWCNT-PA nanocomposite membranes, and revealed that high activation energies are required for the chlorination of PA. The results presented here confirm the unique potential of carbon nanomaterials embedded in polymeric composite membranes for efficient RO water desalination technologies.
Altered DNA methylation and genome instability: A new pathway to cancer? (1997)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Targeting the Purinome (2009)

Purines are critical cofactors in the enzymatic reactions that create and maintain living organisms. In humans, there are approximately 3,266 proteins that utilize purine cofactors and these proteins constitute the so-called purinome. The human purinome encompasses a wide-ranging functional repertoire and many of these proteins are attractive drug targets. For example, it is estimated that 30% of modern drug discovery projects target protein kinases and that modulators of small G-proteins comprise more than 50% of currently marketed drugs. Given the importance of purine-binding proteins to drug discovery, the following review will discuss the forces that mediate protein:purine recognition, the factors that determine druggability of a protein target, and the process of structure-based drug design. A review of purine recognition in representatives of the various purine-binding protein families, as well as the challenges faced in targeting members of the purinome in drug discovery campaigns will also be given.