gebhart/patrepeval huggingface dataset:
Synthesis and characterization of SPUU–PEO–heparin graft copolymers (1991)

Abstract A new synthetic approach for the preparation of segmented polyurethaneurea (SPUU)–PEO–Heparin graft copolymers (B–PEO–Hep) has been developed. The procedure involved the coupling of hexamethylene diisocyanate (HMDI) to soluble Biomer® (B) through an allophanate/biuret reaction. The free isocyanate (NCO) groups attached to Biomer® were then coupled to PEO terminal hydroxyl groups to form PEO grafted Biomer® (B–PEO). B–PEO free hydroxy groups were modified with HMDI to introduce terminal isocyanate groups. The NCO functionalized B–PEO was then coupled to heparin (Hep) functional groups (OH, NH 2 ) producing B–PEO–Hep graft copolymer. Synthetic intermediates were confirmed by FTIR, NCO group determination, and toluidine blue heparin assay. Physical characterization techniques, such as contact angle measurements, water swelling, light scattering measurements, and DSC thermal analysis, detailed properties of the graft copolymer containing covalently bound heparin. This new heparinized copolymer can be applied as a coating on other existing blood contacting surfaces without changing bulk properties. The heparin bioactivity observed attests to the usefulness of this new procedure as a coating to improve the blood compatibility of blood‐contacting surfaces.
Allergy and the skin (2008)

Allergic skin disorders include urticaria, angioedema, contact dermatitis and atopic dermatitis, but the model fitting most closely the systemic concept of allergy is atopic dermatitis (AD), the pathogenesis of which is linked to a complex interaction between skin barrier dysfunction and environmental factors such as allergens and microbes. In particular, an important advance was the demonstration that the mutation of the skin barrier protein filaggrin is related strictly to allergen sensitization and to the development of asthma in subjects with AD. The altered skin barrier function, caused by several factors, results in the passage of allergens through the skin and to systemic responses. A pivotal role in such a response is exerted by Langerhans cells which, via their immunoglobulin E (IgE) receptor, capture the allergens and present them to T cells. When T helper type 2 (Th2) cells are activated, the production of a proinflammatory cytokines and chemokines pattern sustains the persistence of inflammation. Known AD-related cytokines are interleukin (IL)-5, IL-13 and tumour necrosis factor (TNF)-alpha, with emerging importance for IL-17, which seems to drive airway inflammation following cutaneous exposure to antigens, and IL-31, which is expressed primarily in skin-homing Th2 cells. Skin-homing is another crucial event in AD, mediated by the cutaneous lymphocyte-associated antigens (CLA) receptor, which characterizes T cell subpopulations with different roles in AD and asthma.
Effect of Feeding Calcium Soaps of Fatty Acids on Production and Reproductive Responses in High Producing Lactating Cows (1991)

The effect of feeding Ca soaps of fatty acids for 120 d from parturition on productive and reproductive performance of dairy cows was examined, together with changes in blood lipids and progesterone. Cows fed Ca soaps received 1.5 Mcal NE1 d more than controls fed isonitrogenous and equi-forage rations. Cows fed Ca soaps produced more milk and fat for 60 d, and more FCM for 90 d after calving. In these cows, BW decreased more, and reached a minimum later than controls. Plasma free fatty acids were higher until 50 d postpartum, when phospholipid, and later triglyceride, concentrations were elevated. Cows fed soaps commenced ovarian cyclicity later than controls as shown by frequency distribution of the time required to reach cyclic plasma progesterone concentrations, 2 ng/ml progesterone in plasma, or behavioral estrus. However, once cyclicity commenced, more fat-fed cows had normal cycle length (18 to 26 d) than controls. Progesterone concentrations were higher in Ca soap-fed cows in the luteal phase before AI and were higher 9 and 24 d after AI in percent that conceived. Conception rate was higher in cows fed Ca soaps for 2nd to 4th AI, a higher proportion of cows were pregnant at 150 d after calving and number of open days was reduced. Feeding Ca soaps of fatty acids resulted in higher production at the expense of body reserves close to calving, and subsequently enhanced lipid concentrations in plasma. Higher progesterone production was accompanied by increased pregnancy rate and reduced open days.
"Human Science"-Really! (1994)

Centrifugal trends seem to dominate the present scene in academic/ scientific/theoretical psychology, and much "post-modern" criticism would even give up the empirical enterprise aimed at cumulative understanding. I argue for a conception of "human science" that joins the interpretive and explanatory traditions and, as a central, active component of personality, developmental and social psychology, undergirds professional applications and seems unlikely to be supplanted by neuroscience or cognitive science. It ought to be distinguished from the legitimate humanistic enterprise (Geisteswissenschaft) that meets other criteria than those of natural science.
Oct-4 Knockdown Induces Similar Patterns of Endoderm and Trophoblast Differentiation Markers in Human and Mouse Embryonic Stem Cells (2004)

The transcription factor Oct-4 is a marker of pluripotency in mouse and human embryonic stem (ES) cells. Previous studies using a tetracycline-regulated Oct-4 transgene in the ZHBTc4 cell line demonstrated that downregulation of Oct-4 expression induced dedifferentiation into trophoblast, a lineage mouse ES cells do not normally generate. We found that transfection of Oct-4-specific short interfering RNA significantly reduced expression and functional activity of Oct-4 in mouse and human ES cells, enabling its role to be compared in both cell types. In mouse ES cells, Oct-4 knockdown produced a pattern of morphological differentiation and increase in expression of the trophoblast-associated transcription factor Cdx2, similar to that triggered by suppressing the Oct-4 transgene in the ZHBTc4 cell line. In addition, downregulation of Oct-4 was accompanied by increased expression of the endoderm-associated genes Gata6 and alpha-fetoprotein, and a gene trap associated with primitive liver/yolk sac differentiation. In human ES cells, Oct-4 knockdown also induced morphological differentiation coincident with the upregulation of Gata6. The induction of Cdx2 and other trophoblast-associated genes, however, was dependent on the culture conditions. These results establish the general requirement for Oct-4 in maintaining pluripotency in ES cells. Moreover, the upregulation of endoderm-associated markers in both mouse and human ES cells points to overlap between development of trophoblast and endoderm differentiation.
Cellular Processing Limits the Heterologous Expression of Secretory Component in Mammalian Cells (1997)

Recombinant vaccinia-virus-based expression systems are very popular for the overproduction of proteins in mammalian cell lines. Both the double virus T7/vaccinia hybrid system and the single recombinant strategy based on the p11 K late promoter were evaluated for their ability to govern expression and secretion of recombinant human secretory component (SC), a glycoprotein associated with IgA in mucosal secretions. We report here that, while the T7 promoter is transcriptionally 3.4-fold more active than the p11 K promoter, no difference in levels of secreted recombinant human SC is observed using either vaccinia system to infect CV-1 cells. High transcription, and thus translation levels, lead to saturation of early processing steps involved in protein export. Both systems exhibit transient accumulation of comparable amount of recombinant human SC in the endoplasmic reticulum and/or the cis Golgi network, as demonstrated by immunofluorescence and endoglycosidase H (EndoH) sensitivities. Exposure of infected cells to tunicamycin results in similar inhibition of recombinant human SC export, further arguing that N-linked glycosylation is necessary for proper folding and subsequent secretion. Moreover, pulse-chase experiments indicate that newly synthesized recombinant human SC is not completely processed in a mature glycoprotein and that a portion of overexpressed SC might be degraded before it can be secreted. Recombinant human SC behaves identically to native SC in terms of kinetics of secretion and IgA-binding capacity. Our results indicate that optimization of expression systems should not only rely on the design of effective vectors, but also on the identification and clearance of the cellular bottlenecks associated with maturation of the secreted proteins.
Angle-domain common-image gathers by wavefield continuation methods (2003)

Abstract Migration in the angle domain creates seismic images for different reflection angles. We present a method for computing angle-domain common-image gathers from seismic images obtained by depth migration using wavefield continuation. Our method operates on prestack migrated images and produces the output as a function of the reflection angle, not as a function of offset ray parameter as in other alternative approaches. The method amounts to a radial-trace transform in the Fourier domain and is equivalent to a slant stack in the space domain. We obtain the angle gathers using a stretch technique that enables us to impose smoothness through regularization. Several examples show that our method is accurate, fast, robust, and easy to implement. The main anticipated applications of our method are in the areas of migration-velocity analysis and amplitude-versus-angle analysis.
Cloning, expression, and vesicular localization of zinc transporter Dri 27/ZnT4 in intestinal tissue and cells (1999)

We have identified the Dri 27 cDNA on the basis of its upregulated expression during rat intestinal development. It encodes a hydrophobic protein of 430 amino acids that shares significant homology with members of the mammalian zinc transporter family ZnT. The murine homologue of Dri 27 (named ZnT4) was recently associated with the mouse mutation "lethal milk." The primary sequence of Dri 27/ZnT4 displays features characteristic of polytopic membrane proteins. In this paper, we show that Dri 27/ZnT4 is localized in the membrane of intracellular vesicles, the majority of which concentrate in the basal cytoplasmic region of polarized enterocytes. A Dri 27/ZnT4 myc-tagged construct, transiently transfected in intestinal Caco-2 cells, partially colocalizes with the transferrin receptor and with the beta-subunits of the clathrin adaptor complexes AP-1 and AP-2 in a subpopulation of endosomal vesicles. By subcloning distinct portions of the protein in frame with glutathione-S-transferase, we also provide experimental evidence of their function as zinc-binding and protein-protein-interaction domains.
05 gigapixel microscopy using a flatbed scanner (2013)

The capability to perform high-resolution, wide field-of-view (FOV) microscopy imaging is highly sought after in biomedical applications. In this paper, we report a wide FOV microscopy system that uses a closed-circuit-television (CCTV) lens for image relay and a flatbed scanner for data acquisition. We show that such an imaging system is capable of capturing a 10 mm × 7.5 mm FOV image with 0.78 µm resolution, resulting in more than 0.5 billion pixels across the entire image. The resolution and field curve of the proposed system were characterized by imaging a USAF resolution target and a hole-array target. To demonstrate its application, 0.5 gigapixel images of histology slides were acquired using this system.
Chronic Lymphocytic Leukemia Cells Are Dependent on Autocrine VEGF and α4β1 Integrin for Chemokine-Induced Motility. (2004)

Abstract VEGF is a multifunctional cytokine involved in tumourigenesis. In chronic lymphocytic leukaemia (CLL), it is known that the malignant cells secrete VEGF and possess VEGF receptors. This suggests that an autocrine loop might be important in the pathogenesis of CLL. Here we show that, in patients with lymphadenopathy, autocrine VEGF and α4β1-integrin are involved in the chemokine-dependent motility of CLL cells on and through endothelium - processes important for the invasion of lymphoreticular tissues. In contrast, normal lymphocytes were not dependent on autocrine VEGF or α4β1 for either type of cell movement. Moreover, in contrast to normal B lymphocytes, CLL cells failed to cluster and activate αLβ2 in response to chemokines, unless VEGF receptor(s) and α4β1 were also engaged by their respective ligands. This is the first demonstration that autocrine VEGF is involved in CLL-cell motility and that the αLβ2 on the malignant cells is functionally altered in the disease. Taken together, the results suggest that VEGF and α4 blockade may be therapeutically useful in CLL patients with tissue disease.
Neural crest cell plasticity and its limits (2004)

The neural crest (NC) yields pluripotent cells endowed with migratory properties. They give rise to neurons, glia, melanocytes and endocrine cells, and to diverse 'mesenchymal' derivatives. Experiments in avian embryos have revealed that the differentiation of the NC 'neural' precursors is strongly influenced by environmental cues. The reversibility of differentiated cells (such as melanocytes or glia) to a pluripotent precursor state can even be induced in vitro by a cytokine, endothelin 3. The fate of 'mesenchymal' NC precursors is strongly restricted by Hox gene expression. In this context, however, facial skeleton morphogenesis is under the control of a multistep crosstalk between the epithelia (endoderm and ectoderm) and NC cells.
CITED4 Inhibits Hypoxia-Activated Transcription in Cancer Cells, and Its Cytoplasmic Location in Breast Cancer Is Associated with Elevated Expression of Tumor Cell Hypoxia-Inducible Factor 1α (2004)

The interaction of hypoxia-inducible factor 1alpha and the CH1 domain of the transcriptional coactivator p300/CBP is necessary for the expression of hypoxia responsive genes and tumor angiogenesis. The transcription factor CITED2 binds p300/CBP at the CH1 domain and functions as a negative regulator of hypoxia signaling by competing with hypoxia-inducible factor 1alpha. CITED4, a recently identified member of the CITED family, binds p300/CBP via the CH1 domain and functions as a coactivator for transcription factor AP-2. Here, we show that CITED4 blocks the binding of hypoxia-inducible factor 1alpha to p300 in vitro and inhibits hypoxia-inducible factor-1alpha transactivation and hypoxia-mediated reporter gene activation. These studies suggest that CITED4 might function as an inhibitor of hypoxia-inducible factor 1alpha. To explore the function of CITED4 in breast cancer, we determined its expression in normal, in situ and invasive breast cancers. We also correlated its expression in 286 invasive breast tumors with clinicopathological, hypoxia markers and survival. In contrast to the nuclear localization of CITED4 in normal breast tissue, breast tumors were characterized by cytoplasmic and nuclear localization. Nuclear CITED4 expression was significantly inversely associated with tumor hypoxia-inducible factor 1alpha (P < 0.05), tumor size (P = 0.03), tumor grade (P = 0.0001), and Chalkley vessel count (P = 0.04). CITED4 showed no significant correlation with patient age (P = 0.45), estrogen receptor (P = 0.11), or epidermal growth factor receptor (P = 0.48). These results show that breast cancer development is characterized by either nuclear loss or cytoplasmic translocation of CITED4, with consequent loss of hypoxia-inducible factor-1alpha transcriptional antagonist activity. This may be an important mechanism by which tumors enhance hypoxia-inducible factor expression and result in an aggressive phenotype.
Integrated Microfluidic Device for Automated Single Cell Analysis Using Electrophoretic Separation and Electrospray Ionization Mass Spectrometry (2010)

A microfabricated fluidic device was developed for the automated real-time analysis of individual cells using capillary electrophoresis (CE) and electrospray ionization-mass spectrometry (ESI-MS). The microfluidic structure incorporates a means for rapid lysis of single cells within a free solution electrophoresis channel, where cellular constituents were separated, and an integrated electrospray emitter for ionization of separated components. The eluent was characterized using mass spectrometry. Human erythrocytes were used as a model system for this study. In this monolithically integrated device, cell lysis occurs at a channel intersection using a combination of rapid buffer exchange and an increase in electric field strength. An electroosmotic pump is incorporated at the end of the electrophoretic separation channel to direct eluent to the integrated electrospray emitter. The dissociated heme group and the alpha and beta subunits of hemoglobin from individual erythrocytes were detected as cells continuously flowed through the device. The average analysis throughput was approximately 12 cells per minute, demonstrating the potential of this method for high-throughput single cell analysis.
Interferon-α and granulocyte-macrophage colony-stimulating factor differentiate peripheral blood monocytes into potent antigen-presenting cells (1998)

The diverse roles of interferon-alpha (IFN-alpha) in regulating the immune response to infectious agents suggested that it might affect dendritic cell (DC) development. Peripheral blood mononuclear cells cultured with IFN-alpha and granulocyte-macrophage colony-stimulating factor (GM-CSF) developed a dendritic morphology and expressed high levels of the class I and II human leukocyte antigens (HLA), B7 co-stimulatory molecules, adhesion proteins, and CD40. Elevated DC expression of B7-2 and HLA-DR was observed with increasing IFN-alpha concentrations up to 5000 U/mL. The effects of IFN-alpha on DC immunophenotype were not reversed by adding neutralizing antibodies against interleukin-4 (IL-4) or tumor necrosis factor alpha to the cell cultures or by eliminating lymphocytes from the cultures. The addition of IFN-alpha to cultures containing optimal concentrations of IL-4 and GM-CSF significantly increased the B7-2 and HLA-DR levels above those present on DCs grown in two cytokines. The DCs generated with IFN-alpha and GM-CSF were potent antigen-presenting cells in allogeneic mixed leukocyte reactions. They also were capable of taking up, processing, and presenting tetanus toxin to autologous T lymphocytes. These results demonstrate an important role for IFN-alpha in the generation of DCs with potent antigen-presenting capabilities from peripheral blood monocytes.
Harnessing RNA interference for the treatment of viral infections (2010)

Exploiting the RNA interference (RNAi) pathway to inhibit viral gene expression has become an active field of research. The approach has potential for therapeutic application and several viruses are susceptible to RNAi-mediated knockdown. Differences in the characteristics of individual viruses require that viral gene silencing be tailored to specific infections. Important considerations are viral tissue tropism, acute or chronic nature of the infection and the efficiency with which antiviral sequences can be delivered to affected tissue. Both synthetic short interfering RNAs (siRNAs) and expressed RNAi activators are being developed for viral therapy. The sustained silencing of expressed antiviral sequences is useful for countering chronic viral infection. siRNAs, which may be chemically modified to improve specificity and stability, are being developed for knockdown of viruses that cause acute or chronic infections. Preventing viral escape from silencing is important and overcoming this problem using combinatorial RNAi or through silencing of host dependency factors is promising. Although improving delivery efficiency and limiting off-target effects remain obstacles, rapid progress continues to be made in the field and it is likely that the goal of achieving licensed RNAi-based viral therapies will soon be realized.
Clays as a Host Matrix in the Synthesis of Organic Macrocycles (2003)

A new approach for the synthesis of amide macrocycles, based on the use of organo-clay derivatives as controlling template, is proposed as an alternative to the rotaxane method. Dications of p-xylylene diamine inserted in the clay interlayer space act as molding pillars around which neutral diamine molecules are erected via hydrogen bonding and pi-pi interactions to form supramolecular arrays. Condensation of diamines in the supramolecular arrays with diacetyl dichlorides yields various tetramide macrocycles in good yields. Shape, aromaticity and dimensions of the reactants are factors affecting the condensation reaction.
Average Core Structures and Variability Measures for Protein Families: Application to the Immunoglobulins (1995)

A variety of methods are currently available for creating multiple alignments, and these can be used to define and characterize families of related proteins, such as the globins or the immunoglobulins. We have developed a method for using a multiple alignment to identify an average structural "core", a subset of atoms with low structural variation. We show how the means and variances of core-atom positions summarize the commonalities and differences with a family, making them particularly useful in compiling libraries of protein folds. We show further how it is possible to describe the rotation and translation relating two core structures, as in two domains of a multi-domain protein, in a consistent fashion in terms of a "mean" transformation and a deviation about this mean. Once determined, our average core structures (with their implicit measure of structural variation) allow us to define a measure of structural similarity more informative than the usual root-mean-square (RMS) deviation in atomic position, i.e. a "better RMS." Our average structures also permit straightforward comparisons between variation in structure and sequence at each position in a family. We have applied our core-finding methodology in detail to the immunoglobulin family. We find that the structural variability we observe just within the VL and VH domains anticipates the variability that others have observed throughout the whole immunoglobulin superfamily; that a core definition based on sequence conservation, somewhat surprisingly, does not agree with one based on structural similarity; and that the cores of the VL and VH domains vary about 5 degrees in relative orientation across the known structures.
Identification of a Caenorhabditis elegans Δ6-fatty-acid-desaturase by heterologous expression in Saccharomyces cerevisiae (1998)

We identified a cDNA expressed sequence tag from an animal (the nematode worm Caenorhabditis elegans) that showed weak similarity to a higher-plant microsomal Delta6-desaturase. A full-length cDNA clone was isolated and expressed in the yeast Saccharomyces cerevisiae. This demonstrated that the protein encoded by the C. elegans cDNA was that of a fatty acid Delta6-desaturase, as determined by the accumulation of gamma-linolenic acid. The C. elegans Delta6-desaturase contained an N-terminalcytochrome b5 domain, indicating that it had a similar structure to that of the higher-plant Delta6-desaturase. The C. elegans Delta6-desaturase mapped to cosmid W08D2, a region of chromosome III. This is the first example of a Delta6-desaturase isolated from an animal and also the first example of an animal desaturase containing a cytochrome b5 domain.