gebhart/patrepeval huggingface dataset:
Specificity of 14-3-3 isoform dimer interactions and phosphorylation (2002)

Proteins that interact with 14-3-3 isoforms are involved in regulation of the cell cycle, intracellular trafficking/targeting, signal transduction, cytoskeletal structure and transcription. Recent novel roles for 14-3-3 isoforms include nuclear trafficking the direct interaction with cruciform DNA and with a number of receptors, small G-proteins and their regulators. Recent findings also show that the mechanism of interaction is also more complex than the initial finding of the novel phosphoserine/threonine motif. Non-phosphorylated binding motifs that can also be of high affinity may show a more isoform-dependent interaction and binding of a protein through two distinct binding motifs to a dimeric 14-3-3 may also be essential for full interaction. Phosphorylation of specific 14-3-3 isoforms can also regulate interactions. In many cases, they show a distinct preference for a particular isoform(s) of 14-3-3. A specific repertoire of dimer formation may influence which of the 14-3-3-interacting proteins could be brought together. Mammalian and yeast 14-3-3 isoforms show a preference for dimerization with specific partners in vivo.
Formation and Reduction of Intermediate Acyladenylate by Aryl‐Aldehyde (1972)

The enzyme aryl‐aldehyde: NADP oxidoreductase catalyzes a rapid exchange of PPi and ATP. The reaction requires the presence of an aromatic acid and Mg 2+ ions. The exchange reaction has a pH‐optimum of approx. 8.5 and is inhibited by NADPH. The inhibition of the exchange reaction by hydroxylamine as well as the enzymic formation of benzoylhydroxamate confirm that an activated intermediate is involved in the reduction of aromatic acids. This compound was identified as acyladenylate which, however, is assumed not to exist in the free state under normal conditions. In a subsequent step the acyladenylate is reduced to aldehyde. This reaction depends on the presence of sulfhydryls and does not require Mg 2+ ions. Both the activating and the reductive step are catalyzed by one enzyme.
Synthesis and antiviral activity of various 3'-azido, 3'-amino, 2',3'-unsaturated, and 2',3'-dideoxy analogs of pyrimidine deoxyribonucleosides against retroviruses (1987)

Various 3'-azido, 3'-amino, 2',3'-unsaturated, 2',3'-dideoxy, and 5-substituted analogues of pyrimidine deoxyribonucleosides have been prepared and tested against Moloney-murine leukemia virus (M-MULV), a mammalian T-lymphotropic retrovirus in vitro. Among these compounds, the 3'-azido analogues of thymidine, 2'-deoxy-5-bromouridine, and 2'-deoxy-5-iodouridine, the 2',3'-unsaturated analogue of thymidine and and 2'-deoxycytidine, and 2',3'-dideoxycytidine were found to be most active, with ED50 values of 0.02, 1.5, 3.0, 2.5, 3.7, and 4.0 microM, respectively. These active compounds were nontoxic to the host SC-1 cells up to 100 microM concentration. The 3'-azido analogues of thymidine and 2'-deoxy-5-bromouridine were also tested in vitro against HTLV-III/LAV/AAV ("AIDS" virus) and found to be significantly active, with ED50 values of 0.23 and 2.3 microM, respectively. The structure-activity relationships are discussed.
Influence of grain size, shape and compaction on georadar waves: examples of aeolian dunes (2012)

Many ground penetrating radar (GPR) profiles acquired in dry aeolian environment have shown good reflectivity inside present-day dunes. We show that the origin of this reflectivity is related to changes in grain size distribution, packing and/or grain shape in a sandy material. We integrate these three parameters into analytical models for bulk permittivity in order to predict the reflections and the velocity of GPR waves. We consider two GPR cross-sections acquired over aeolian dunes in the Chadian desert. The 2D migration of GPR data suggests that dunes contain different kinds of bounding surfaces. We discuss and model three kinds of reflections using reasonable geological hypothesis about aeolian sedimentation processes. The propagation and the reflection of radar waves are calculated using the 1D wavelet modelling method in spectral domain. The results of the forward modelling are in good accordance with real observed data.
Ribosomal binding to the internal ribosomal entry site of classical swine fever virus (2000)

Most eukaryotic mRNAs require the cap-binding complex elF4F for efficient initiation of translation, which occurs as a result of ribosomal scanning from the capped 5' end of the mRNA to the initiation codon. A few cellular and viral mRNAs are translated by a cap and end-independent mechanism known as internal ribosomal entry. The internal ribosome entry site (IRES) of classical swine fever virus (CSFV) is approximately 330 nt long, highly structured, and mediates internal initiation of translation with no requirement for elF4F by recruiting a ribosomal 43S preinitiation complex directly to the initiation codon. The key interaction in this process is the direct binding of ribosomal 40S subunits to the IRES to form a stable binary complex in which the initiation codon is positioned precisely in the ribosomal P site. Here, we report the results of analyses done using enzymatic footprinting and mutagenesis of the IRES to identify structural components in it responsible for precise binding of the ribosome. Residues flanking the initiation codon and extending from nt 363-391, a distance equivalent to the length of the 40S subunit mRNA-binding cleft, were strongly protected from RNase cleavage, as were nucleotides in the adjacent pseudoknot and in the more distal subdomain IIId1. Ribosomal binding and IRES-mediated initiation were abrogated by disruption of helix 1b of the pseudoknot and very severely reduced by mutation of the protected residues in IIId1 and by disruption of domain IIIa. These observations are consistent with a model for IRES function in which binding of the region flanking the initiation codon to the decoding region of the ribosome is determined by multiple additional interactions between the 40S subunit and the IRES.
BlackSea TeleDiab: Diabetes computer system with communication technology for black sea region (1998)

BlackSea TeleDiab (BSTD) is a multidisciplinary research project whose aim is to promote the exchange of healthcare information between clinicians and scientists in countries of the Black Sea area to provide a means by which the care of patients with diabetes may be enhanced. The project is built on an existing organizational framework provided by the WHO Diabcare Quality Network (Q-Net) and the Black Sea Diab Action Project. The aim is to develop a standardized software package (in the national languages of the CCE/NIS Black Sea partners) for the storage and transfer of medical information and healthcare data between participating institutions. It will utilize a standard format for medical records based on the Good European Health Record (GEHR), a project within the Advanced Informatics in Medicine (AIM) program, which aims to develop and propagate a common architecture for computerized health records across Europe that can be used across clinical domains, countries, and computer systems.
Restricted localization of L1 and N‐CAM at sites of contact between Schwann cells and neurites in culture (1994)

Schwann cell-axon contacts in developing and regenerating peripheral nerve in situ contain high levels of the recognition molecules L1 and N-CAM, while the molecules are not detectable at the ab-axonal cell surface of Schwann cells. To investigate whether Schwann cells, axons, or both contribute to the localization of the molecules at Schwann cell-axon contacts, a heterologous cell culture system consisting of Schwann cells from mice and neurons from chicken was investigated by immunoelectron microscopy using species-specific L1 and N-CAM antibodies. We showed that Schwann cells expressed both molecules only at sites of contact between Schwann cells and neurites and other Schwann cells. Schwann cells not in contact with other cells expressed both molecules on their entire cell surface. In contrast, neurites expressed G4, an L1-related molecule in chicken, on their entire cell surface independently of whether they were in contact with other cells or not. Thus, cultured Schwann cells localize L1 and N-CAM selectively at cell contact sites and may thereby stabilize their attachment to the neighboring cellular partners.
On bending invariant signatures for surfaces (2003)

Isometric surfaces share the same geometric structure, also known as the "first fundamental form." For example, all possible bendings of a given surface that includes all length preserving deformations without tearing or stretching the surface are considered to be isometric. We present a method to construct a bending invariant signature for such surfaces. This invariant representation is an embedding of the geometric structure of the surface in a small dimensional Euclidean space in which geodesic distances are approximated by Euclidean ones. The bending invariant representation is constructed by first measuring the intergeodesic distances between uniformly distributed points on the surface. Next, a multidimensional scaling technique is applied to extract coordinates in a finite dimensional Euclidean space in which geodesic distances are replaced by Euclidean ones. Applying this transform to various surfaces with similar geodesic structures (first fundamental form) maps them into similar signature surfaces. We thereby translate the problem of matching nonrigid objects in various postures into a simpler problem of matching rigid objects. As an example, we show a simple surface classification method that uses our bending invariant signatures.
Formation of liquid core–polymer shell microcapsules (2006)

Polymer shell microcapsules with liquid cores are used in a wide variety of industries, from food and flavour protection to inkless paper. There is a number of production methods, each with different characteristics and this article reviews a number of them. The methods considered are colloidosome formation, polymer precipitation by phase separation, polycondensation interfacial polymerisation, layer-by-layer polyelectrolyte deposition, polymer growth by surface polymerisation and copolymer vesicle formation. Each production method is described and the relative strength of each is outlined.
Introduction of disease-related mitochondrial DNA deletions into HeLa cells lacking mitochondrial DNA results in mitochondrial dysfunction. (1991)

Mutant mitochondrial DNA with large-scale deletions (delta-mtDNA) has been frequently observed in patients with chronic progressive external ophthalmoplegia (CPEO), a subgroup of the mitochondrial encephalomyopathies. To exclude involvement of the nuclear genome in expression of the mitochondrial dysfunction characteristic of CPEO, we introduced the mtDNA of a CPEO patient into clonal mtDNA-less HeLa cells and isolated cybrid clones. Quantitation of delta-mtDNA in the cybrids revealed that delta-mtDNA was selectively propagated with higher levels of delta-mtDNA correlating with slower cellular growth rate. In these cybrid clones, translational complementation of the missing tRNAs occurred only when delta-mtDNA was less than 60% of the total mtDNA, whereas accumulation of delta-mtDNA to greater than 60% resulted in progressive inhibition of overall mitochondrial translation as well as reduction of cytochrome c oxidase activity throughout the organelle population. Because these cybrids shared the same nuclear background as HeLa cells, these results suggest that large-scale deletion mutations of mtDNA alone are sufficient for the mitochondrial dysfunction characteristic of CPEO.
Transforming growth factor-beta and breast cancer: Tumor promoting effects of transforming growth factor-β (2000)

The transforming growth factor (TGF)-betas are potent growth inhibitors of normal epithelial cells. In established tumor cell systems, however, the preponderant experimental evidence suggests that TGF-betas can foster tumor-host interactions that indirectly support the viability and/or progression of cancer cells. The timing of this 'TGF-beta switch' during the progressive transformation of epithelial cells is not clear. More recent evidence also suggests that autocrine TGF-beta signaling is operative in some tumor cells, and can also contribute to tumor invasiveness and metastases independent of an effect on nontumor cells. The dissociation of antiproliferative and matrix associated effects of autocrine TGF-beta signaling at a transcriptional level provides for a mechanism(s) by which cancer cells can selectively use this signaling pathway for tumor progression. Data in support of the cellular and molecular mechanisms by which TGF-beta signaling can accelerate the natural history of tumors will be reviewed in this section.
Comparison of different cultivation modes and light intensities using mono‐cultures and co‐cultures of Haematococcus pluvialis and Chlorella zofingiensis (2010)

Abstract BACKGROUND: Recent studies indicate that microalgal cultivation using organic carbon sources has the potential to provide high yields. Haematococcus pluvialis and Chlorella zofingiensis, two important carotenoid producers, were selected for co‐culture cultivations to utilize the unique advantages of both organisms. A co‐culture production process was investigated in terms of the effects of organic carbon source, co‐cultivation method, and light intensity on carotenoid production. RESULTS: The addition of 5 g L −1 glucose resulted in a growth rate of 0.60 day −1 for H. pluvialis and 0.59 day −1 for C. zofingiensis , which were higher than those for other carbon sources tested and the control group. Incremental increase of light intensity instead of direct increase to 170 µE m −2 s − prevented cell loss in both cultures. Co‐cultivation based on cell numbers (60% H. pluvialis and 40% C. zofingiensis ) prevented population domination of one microalgae over the other. The biomass production rate of the co‐culture was higher (0.61 g L −1 day −1 ) in glucose‐enriched medium. The total carotenoid content of the co‐culture in the control culture was higher (0.83 mg total carotenoids g −1 cell) than that obtained in glucose‐enriched medium (0.54 mg total carotenoids g −1 cell) but not as high as the amounts reached in mono‐cultures. CONCLUSION: Total carotenoid content of the mono‐cultures gave higher yields in standard bold basal medium (BBM). Preliminary high performance liquid chromatography (HPLC) studies indicated a variation in the amounts of astaxanthin isomers produced. Further studies are in progress to determine the effects of carbon‐enriched media and co‐cultivation on the type of isomers and caretenoids produced. Copyright © 2010 Society of Chemical Industry
Early appearing gamma/delta-bearing T cells during infection with Calmétte Guérin bacillus (1991)

To search for a potential role of TCR gamma/delta T cells in host-defense against mycobacterial infection, we analyzed the kinetics, repertoire, specificity, and cytokine production of gamma/delta T cells in the peritoneal exudate cells (PEC), lymph node (LN) cells and spleen cells during an i.p. infection with a sublethal dose (5 x 10(5) of viable Bacillus Calmétte-Guérin (BCG) in mice. In the PEC on day 7 after infection, approximately 26% of the CD3+ cells were CD4-CD8-, most of which expressed TCR gamma/delta on their surface. However, the PEC on day 28 contained an increased number of alpha/beta T cells that were CD4+8- or CD4-8+ and the proportion of gamma/delta T cells in the PEC reciprocally decreased to 18% of the CD3+ cells. The kinetics of gamma/delta and alpha/beta T cells in the LN during BCG infection showed in much the same pattern as that seen in the PEC. When purified CD4-CD8- cells in the LN on day 7 after BCG infection were cultured with sonicated BCG lysate, PPD derived from Mycobacterium tuberculosis or recombinant 65 kDa heat shock protein derived from Mycobacterium bovis, the gamma/delta T cells on this stage significantly proliferated and secreted IL-2 in response to sonicated BCG lysate and PPD but not to 65 kDa heat shock protein. V gene segment usage analysis with PCR method revealed that purified protein derivative-reactive gamma/delta T cells preferentially used V gamma 1/2/V delta 6, whereas gamma/delta T cells polyclonally expanded in response to the BCG lysate. These results suggest that gamma/delta T cells specific for mycobacterial antigens preceding alpha/beta T cells in appearance during infection may serve as a first line of defense against mycobacterial infection.
The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins (2014)

Sharks and other cartilaginous fish are the phylogenetically oldest living organisms that rely on antibodies as part of their adaptive immune system. They produce the immunoglobulin new antigen receptor (IgNAR), a homodimeric heavy chain-only antibody, as a major part of their humoral adaptive immune response. Here, we report the atomic resolution structure of the IgNAR constant domains and a structural model of this heavy chain-only antibody. We find that despite low sequence conservation, the basic Ig fold of modern antibodies is already present in the evolutionary ancient shark IgNAR domains, highlighting key structural determinants of the ubiquitous Ig fold. In contrast, structural differences between human and shark antibody domains explain the high stability of several IgNAR domains and allowed us to engineer human antibodies for increased stability and secretion efficiency. We identified two constant domains, C1 and C3, that act as dimerization modules within IgNAR. Together with the individual domain structures and small-angle X-ray scattering, this allowed us to develop a structural model of the complete IgNAR molecule. Its constant region exhibits an elongated shape with flexibility and a characteristic kink in the middle. Despite the lack of a canonical hinge region, the variable domains are spaced appropriately wide for binding to multiple antigens. Thus, the shark IgNAR domains already display the well-known Ig fold, but apart from that, this heavy chain-only antibody employs unique ways for dimerization and positioning of functional modules.
Bystander Activation of CD8+ T Cells Contributes to the Rapid Production of IFN-γ in Response to Bacterial Pathogens (2001)

Abstract The bacterium Burkholderia pseudomallei causes a life-threatening disease called melioidosis. In vivo experiments in mice have identified that a rapid IFN-γ response is essential for host survival. To identify the cellular sources of IFN-γ, spleen cells from uninfected mice were stimulated with B. pseudomallei in vitro and assayed by ELISA and flow cytometry. Costaining for intracellular IFN-γ vs cell surface markers demonstrated that NK cells and, more surprisingly, CD8+ T cells were the dominant sources of IFN-γ. IFN-γ+ NK cells were detectable after 5 h and IFN-γ+ CD8+ T cells within 15 h after addition of bacteria. IFN-γ production by both cell populations was inhibited by coincubation with neutralizing mAb to IL-12 or IL-18, while a mAb to TNF had much less effect. Three-color flow cytometry showed that IFN-γ-producing CD8+ T cells were of the CD44high phenotype. The preferential activation of NK cells and CD8+ T cells, rather than CD4+ T cells, was also observed in response to Listeria monocytogenes or a combination of IL-12 and IL-18 both in vitro and in vivo. This rapid mechanism of CD8+ T cell activation may be an important component of innate immunity to intracellular pathogens.
Increased levels of human papillomavirus type 16 DNA in a subset of prostate cancers. (1999)

Whether oncogenic human papilloma viruses (HPVs) are involved in the pathogenesis of prostate cancers has been a subject of great controversy. To clarify the contradictory results of investigations, with the aim of detecting viral nucleic acids in prostate cancers, we have carried out a comparative quantitation of the HPV16-E6 sequence in 84 prostate specimens. Using single-tube quantitative competitive PCR, we characterized 47 prostate cancers and 37 control tissues of benign prostatic hyperplasia. A subgroup of the prostate tumors (10 of 47; 21%) was detected as having significantly higher copy numbers of HPV16-E6 sequences when compared to the control tissue (1 of 37; 3%), using a cutoff value of 300 copies per 12,500 diploid cells (two-sided Fisher's exact test, P = 0.02). Our results indicate that the oncogenic HPV16 might contribute to the development of a subset of prostate tumors.
Human Fetal Dopamine Neurons Grafted Into the Striatum in Two Patients With Severe Parkinson's Disease (1989)

By using stereotaxic surgical techniques, ventral mesencephalic tissues from aborted human fetuses of 8 to 10 weeks' gestational age were implanted unilaterally into the striata in two patients with advanced Parkinson's disease. The patients were treated with a cyclosporine, azathioprine, and steroid regimen to minimize the risk for graft rejection. They were examined for 6 months preoperatively and 6 months postoperatively and continued to receive the same doses of antiparkinsonian medication. There were no significant postoperative complications. No major therapeutic effect from the operation was observed. However, in the clinical tests, both patients showed small but significant increases of movement speed for repeated pronation-supination, fist clenching, and foot lifting. The rate of walking also increased in the one patient tested. For both patients, there was an initial worsening postoperatively, followed by improvement vs preoperative performance at 1 to 3 months. Both patients also showed significant improvement in the magnitude of response to a single dose of levodopa (L-dopa), but there was no increase in the duration of drug action. The motor readiness potential increased in both patients postoperatively, primarily over the operated hemisphere. Neurophysiological measurements also showed a more rapid performance of simple and complex arm and hand movements on the side contralateral to transplantation in one patient at 5 months postoperatively. Positron emission tomography demonstrated no increased uptake of 6-L-(18F)-fluorodopa in the transplanted striatum at 5 and 6 months. Taken together, these results suggest that the fetal nigral implants may have provided a modest improvement in motor function, consistent with the presence of small surviving grafts. Although our results support further scientific experimentation with transplantation in Parkinson's disease, widespread clinical trials with this procedure are probably not warranted at this time.