gebhart/patrepeval huggingface dataset:
Ligand‐specific and non‐specific in vivo modulation of human epidermal cellular retinoic acid binding protein (CRABP) (1989)

Retinoic acid (RA) is bound intracellularly by a specific, low molecular weight protein (CRABP), that is unrelated to its nuclear receptor and whose function and regulation are still unknown. In the present study we were able to obtain an in vivo modulation of CRABP by different stimuli in one of the major target organs of RA: the human skin. We found increased CRABP after daily application during 4 days of natural or synthetic retinoids (RA, acitretin, isotretinoin, Ro137410, retinol), that have either a high affinity to CRABP or can be transformed into RA. Only Ro150778 with no affinity and no reported transformation had no effect. No macro- or microscopical changes could be observed with any of the tested compounds. Induction of inflammatory and hyperproliferative changes in the skin by topical dithranol treatment, UVB irradiation or scotch tape stripping also induced a significant increase of CRABP 3 days after exposure. Topical diflucortolone showed not only a tendancy to decrease intrinsic CRABP levels, but significantly reduced the retinoid stimulated rise of CRABP. Thus we conclude that the increase of CRABP in a fully differentiated adult tissue seems to be a biological phenomenon following processes of inflammation and proliferation with a lag of several days, while retinoids seem to be able to induce such a rise independently of, or before, the appearance of such processes. Corticosteroids seem to be inhibitors of this reaction. We discuss the hypothesis that CRABP might function as an intracellular 'buffer' in the case of RA overload.
Identification of RNA–protein interaction networks using PAR‐CLIP (2011)

All mRNA molecules are subject to some degree of post-transcriptional gene regulation (PTGR) involving sequence-dependent modulation of splicing, cleavage and polyadenylation, editing, transport, stability, and translation. The recent introduction of deep-sequencing technologies enabled the development of new methods for broadly mapping interaction sites between RNA-binding proteins (RBPs) and their RNA target sites. In this article, we review crosslinking and immunoprecipitation (CLIP) methods adapted for large-scale identification of target RNA-binding sites and the respective RNA recognition elements. CLIP methods have the potential to detect hundreds of thousands of binding sites in single experiments although the separation of signal from noise can be challenging. As a consequence, each CLIP method has developed different strategies to distinguish true targets from background. We focus on photoactivatable ribonucleoside-enhanced CLIP, which relies on the intracellular incorporation of photoactivatable ribonucleoside analogs into nascent transcripts, and yields characteristic sequence changes upon crosslinking that facilitate the separation of signal from noise. The precise knowledge of the position and distribution of binding sites across mature and primary mRNA transcripts allows critical insights into cellular localization and regulatory function of the examined RBP. When coupled with other systems-wide approaches measuring transcript and protein abundance, the generation of high-resolution RBP-binding site maps across the transcriptome will broaden our understanding of PTGR and thereby lead to new strategies for therapeutic treatment of genetic diseases perturbing these processes.
Changes in the gel properties of tracheal mucus induced by divalent cations1 (1979)

The effects of the divalent ions calcium, magnesium and copper on the rheologic and mucociliary transport properties of canine tracheal mucus have been investigated. A maximum in the viscoelastic moduli of the mucus gel was observed for each ion arou
알로에가 in vitro 에서 넙치 백혈구의 호흡폭발에 미치는 영향 (1999)

알로에가 in vitro에서 넙치의 비특이적 면역반응에 미치는 영향을 조사하기 위하여 신장으로부터 분리된 백혈구의 호흡폭발을 chemiluminescent(CL) 반응을 이용하여 측정하였다. 알로에 분말을 0.001, 0.01, 0.1, 0.5, 1.0, 10.0㎍/㎖의 농도로 MEM에 희석하여 넙치의 식세포와 함께 배양한 후 3, 6, 12, 24, 48시간째에 CL 반응을 이용하여 호흡폭발능을 측정한 결과, 알로에 0.5㎍/㎖과 1.0㎍/㎖의 농도에서 24시간 동안 배양한 실험구만이 알로에를 첨가하지 않은 대조구에 비해서 유의성 있게 호흡폭발능이 증가하였다. 이러한 결과는 알로에가 양식 넙치의 비특이적 면역능을 증강시킬 수 있음을 시사하며, 앞으로 in vivo 실험을 통한 검증이 필요할 것으로 사료된다.
Photoreactive elastin-like proteins for use as versatile bioactive materials and surface coatings (2012)

Photocrosslinkable, protein-engineered biomaterials combine a rapid, controllable, cytocompatible crosslinking method with a modular design strategy to create a new family of bioactive materials. These materials have a wide range of biomedical applications, including the development of bioactive implant coatings, drug delivery vehicles, and tissue engineering scaffolds. We present the successful functionalization of a bioactive elastin-like protein with photoreactive diazirine moieties. Scalable synthesis is achieved using a standard recombinant protein expression host followed by site-specific modification of lysine residues with a heterobifunctional N-hydroxysuccinimide ester-diazirine crosslinker. The resulting biomaterial is demonstrated to be processable by spin coating, drop casting, soft lithographic patterning, and mold casting to fabricate a variety of two- and three-dimensional photocrosslinked biomaterials with length scales spanning the nanometer to millimeter range. Protein thin films proved to be highly stable over a three-week period. Cell-adhesive functional domains incorporated into the engineered protein materials were shown to remain active post-photo-processing. Human adipose-derived stem cells achieved faster rates of cell adhesion and larger spread areas on thin films of the engineered protein compared to control substrates. The ease and scalability of material production, processing versatility, and modular bioactive functionality make this recombinantly engineered protein an ideal candidate for the development of novel biomaterial coatings, films, and scaffolds.
Use of Botulinum Toxin Type A to Prevent Widening of Facial Scars (2006)

In view of the results of this study, it is considered worthwhile to offer patients with ugly scars of the face botulinum toxin injections simultaneous with revision surgery.
Contribution of the IL-2 and IL-10 genes to inflammatory bowel disease (IBD) susceptibility (1998)

Although the importance of genetic susceptibility to IBD has been established by epidemiological studies, the genes involved remain poorly characterized. Important candidate genes include those encoding the immunoregulatory cytokines IL-2 and IL-10. The aim of this study was to assess the contribution of the IL-2 and IL-10 genes to IBD susceptibility. One hundred and ninety-eight pairs of siblings with IBD were genotyped at dinucleotide repeat polymorphisms within the IL-2 and IL-10 genes, and data analysed by the affected sib-pair method of linkage analysis and the transmission disequilibrium test (TDT). A subset of 89 affected sibling pairs was genotyped at markers flanking the IL-2 gene as part of a genome-wide search. The IL-2 polymorphism showed no linkage to IBD overall, but modest evidence for linkage to the ulcerative colitis (UC) data set (P = 0.028). A microsatellite 4 cM distal to the IL-2 gene showed a similar distortion in the ulcerative colitis subgroup (P = 0.006). The TDT showed some distortion of allelic transmission for the IL-2 polymorphism in the UC group, but this did not reach statistical significance (P = 0.09). Results for the IL-10 polymorphism were not significant. Thus the gene encoding IL-2 may contribute to UC susceptibility, but the effect is modest and must await replication in other data sets. The IL-10 gene does not appear to contribute to the risk of developing UC or Crohn's disease.
Accumulation and persistence of DNA adducts in respiratory tissue of rats following multiple administrations of the tobacco specific carcinogen 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone. (1986)

4-(N-Methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK), a major nitrosamine formed in tobacco smoke, induces a high incidence of lung, liver, and nasal cavity tumors in rats. Since alpha-hydroxylation of NNK by target tissues can lead to the generation of a methylating agent, the formation and removal of 7-methylguanine and the promutagenic lesions O6-methylguanine (O6mGua) and O4-methyldeoxythymidine were determined over 12 days of NNK administration to rats (100 mg/kg/day). DNA alkylation was greatest in the nasal mucosa, followed by liver and lung after 1 dose of NNK. No DNA adducts were detected in kidney and brain under these conditions. The concentration of O6mGua increased steadily in lung throughout the treatment regimen, while O6-methylguanine-DNA methyltransferase decreased to less than 5% of control. The concentration of O4-methyldeoxythymidine in lung DNA reached a steady state after 4 days of carcinogen treatment. After NNK treatment was discontinued, O6mGua persisted, while O4-methyldeoxythymidine was removed rapidly in the lung, suggesting that different repair pathways exist for the removal of these adducts in vivo. In hepatocytes, nonparenchymal cells, and nasal mucosa, O6mGua concentrations were maximal after 1-2 days and declined by 50-80% during the remaining 10 days of treatment. The decrease in O6mGua levels in nasal mucosa paralleled a decline in O6-methylguanine-DNA methyltransferase activity and was associated with marked cytotoxicity to Bowman's glands, portions of the lateral nasal gland, and the olfactory and respiratory mucosa during carcinogen treatment. In contrast, the decline in O6mGua in hepatocytes was attributed to the induction of O6-methylguanine-DNA methyltransferase activity, since an 18-fold reduction in the ratio of O6mGua:7-methylguanine was observed over the 12 days of treatment. These studies have demonstrated a marked accumulation of promutagenic DNA adducts in target tissues during repeated exposure to NNK.
Self-reforming routing for stochastic search in VLSI interconnection layout (2000)

Article Free Access Share on Self-reforming routing for stochastic search in VLSI interconnection layout Authors: Yukiko Kubo Department of Electrical and Electronic Eng., Tokyo Inst. of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan Department of Electrical and Electronic Eng., Tokyo Inst. of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, JapanView Profile , Yasuhiro Takashima Information Science, Japan Advanced Inst. of Science and Technology, Tatsunokuchi, Nomi-gun, Ishikawa 932-1292, Japan Information Science, Japan Advanced Inst. of Science and Technology, Tatsunokuchi, Nomi-gun, Ishikawa 932-1292, JapanView Profile , Shigetoshi Nakatake Faculty of International Environmental Eng., Promotion and Development Office, Kitakyushu University, Kokuraminami-ku, Kitakyushu-city, Fukuoka 802-8577, Japan Faculty of International Environmental Eng., Promotion and Development Office, Kitakyushu University, Kokuraminami-ku, Kitakyushu-city, Fukuoka 802-8577, JapanView Profile , Yoji Kajitani Department of Electrical and Electronic Eng., Tokyo Inst. of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan Department of Electrical and Electronic Eng., Tokyo Inst. of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, JapanView Profile Authors Info & Claims ASP-DAC '00: Proceedings of the 2000 Asia and South Pacific Design Automation ConferenceJanuary 2000 Pages 87–92https://doi.org/10.1145/368434.368584Published:28 January 2000Publication History 2citation128DownloadsMetricsTotal Citations2Total Downloads128Last 12 Months7Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Separation and identification of GM1b pathway Neu5Ac- and Neu5Gc gangliosides by on-line nanoHPLC-QToF MS and tandem MS: toward glycolipidomics screening of animal cell lines (2009)

Monosialoganglioside fraction of YAC-1 lymphoma cells was comprehensively analyzed and structurally defined by nano-high-performance liquid chromatography (nanoHPLC) in on-line conjunction with electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QTOF MS). An efficient separation and sensitive detection of Neu5Gc-containing gangliosides from Neu5Ac-containing analogues was for the first time accomplished in a single nanoHPLC/ESI-QTOF MS run, as demonstrated for mouse hybridoma cell GM3 fraction containing GM3(Neu5Ac) and GM3(Neu5Gc) species and further applied for the analysis of YAC-1 lymphoma cell monosialoganglioside fraction. New insights into YAC-1 monosialoganglioside mixture heterogeneity were obtained: 31 distinct species, comprising 18 Neu5Gc-containing gangliosides and 13 Neu5Ac-containing species of GM1b and GalNAc-GM1b type were found to be expressed by YAC-1 cell line. On-line structural elucidation of individually separated Neu5Ac- and Neu5Gc-containing gangliosides provided strong evidence on the "GM1b-pathway" sourcing for monosialoganglioside synthesis. Such an analytical method is documented as superior to the classical approaches by increased speed of analysis, sensitivity and level of information, being thus a viable glycolipidomic tool.
Miscibility of polymer blends of poly(styrene‐co‐4‐hydroxystyrene) with bisphenol‐A polycarbonate (1999)

The miscibility of blends of bisphenol-A polycarbonate (BAPC) and tetramethyl bisphenol-A polycarbonate (TMPC) with copolymers of poly(styrene-co-4-hydroxystyrene) (PSHS) was studied in this work. It has been demonstrated that BAPC is miscible with PSHS over a region of approximately 45–75 mol % hydroxyl groups in the copolymer. TMPC has a wider miscible window than BAPC when blended with PSHS. The blend miscibility was considered to be driven by the intermolecular attractive interactions between the hydroxyl groups of the PSHS and the π electrons of the aromatic rings of both polycarbonates (PCs). As the FTIR measurements showed, after blending of BAPC with PSHS, there is no visible shift of the carbonyl band of BAPC at 1774 cm−1, whereas the stretching frequency of the free hydroxyl groups of the copoly- mers at 3523 cm−1 disappeared. The large positive values of the segment interaction energy density parameter Bst-HS calculated from the group contribution approach indicated that the intramolecular repulsive interaction may also have played a role in the promotion of the blend miscibility. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 74: 639–646, 1999
Prognostic significance of CD45RO+ memory T cells in renal cell carcinoma (2011)

CD45RO+ memory T-cell status has a significant independent prognostic value, indicating that the adaptive immune response is functionally critical in human RCC.
Fermentation and Biochemical Engineering Handbook: Principles, Process Design and Equipment (1996)

A complete reference for fermentation engineers engaged in commercial chemical and pharmaceutical production, Fermentation and Biochemical Engineering Handbook emphasizes the operation, development and design of manufacturing processes that use fermentation, separation and purification techniques. Contributing authors from companies such as Merck, Eli Lilly, Amgen and Bristol-Myers Squibb highlight the practical aspects of the processes-data collection, scale-up parameters, equipment selection, troubleshooting, and more. They also provide relevant perspectives for the different industry sectors utilizing fermentation techniques, including chemical, pharmaceutical, food, and biofuels. New material in the third edition covers topics relevant to modern recombinant cell fermentation, mammalian cell culture, and biorefinery, ensuring that the book will remain applicable around the globe. It uniquely demonstrates the relationships between the synthetic processes for small molecules such as active ingredients, drugs and chemicals, and the biotechnology of protein, vaccine, hormone, and antibiotic production. This major revision also includes new material on membrane pervaporation technologies for biofuels and nanofiltration, and recent developments in instrumentation such as optical-based dissolved oxygen probes, capacitance-based culture viability probes, and in situ real-time fermentation monitoring with wireless technology. It addresses topical environmental considerations, including the use of new (bio)technologies to treat and utilize waste streams and produce renewable energy from wastewaters. Options for bioremediation are also explained. It is fully updated to cover the latest advances in recombinant cell fermentation, mammalian cell culture and biorefinery, along with developments in instrumentation. Industrial contributors from leading global companies, including Merck, Eli Lilly, Amgen, and Bristol-Myers Squibb. It covers synthetic processes for both small and large molecules.
Cutting Edge: Anti-Tumor Necrosis Factor Therapy in Rheumatoid Arthritis Inhibits Memory B Lymphocytes via Effects on Lymphoid Germinal Centers and Follicular Dendritic Cell Networks (2008)

Rheumatoid arthritis (RA) is mediated by a proinflammatory cytokine network with TNF at its apex. Accordingly, drugs that block TNF have demonstrated significant efficacy in the treatment of RA. A great deal of experimental evidence also strongly implicates B cells in the pathogenesis of RA. Yet, it remains unclear whether these two important players and the therapies that target them are mechanistically linked. In this study we demonstrate that RA patients on anti-TNF (etanercept) display a paucity of follicular dendritic cell networks and germinal center (GC) structures accompanied by a reduction in CD38+ GC B cells and peripheral blood memory B cell lymphopenia compared with healthy controls and RA patients on methotrexate. This study provides initial evidence in humans to support the notion that anti-TNF treatment disrupts GC reactions at least in part via effects on follicular dendritic cells.
Distributed Electronic Mail Models in IMAP4 (1994)

This memo provides information for the Internet community.This memo does not specify an Internet standard of any kind.
Surface Treatments of Polymers for Biocompatibility (1996)

Biological recognition mediates cell and tissue interactions with biomaterials, be the materials employed in a biotechnical environment in vitro or a biomedical environment in vivo. These interactions are typically mediated by proteins that have adsorbed to the biomaterial surface. The principles of protein adsorption and biological recognition are described. Polymer surface modifications to reduce protein adsorption upon biomaterial surfaces are summarized, as are modifications to enhance the irreversible adsorption of proteins. Using these approaches, it may be possible to reduce the extent to which the biomaterial surface and the protein-biomaterial surface are recognized by cells and tissues. Polymer surface modifications to incorporate oligopeptide-, saccharide-, and oligosaccharide-based receptor-binding sequences are described to enable direct binding of cells with the polymer surface. With use of these approaches, it is possible to endow an entirely synthetic material with the biological recognition characteristics of biological macromolecules.
Staphylococcal iron requirements, siderophore production, and iron-regulated protein expression (1994)

Despite the ability of staphylococci to grow in iron-restricted conditions in vivo, their iron requirements and the mechanisms possessed by them for the uptake of iron are poorly understood. Many bacteria are known to produce siderophores. By using the chrome azurol S universal method for the detection of siderophores, all 14 isolates of Staphylococcus aureus tested grew well under conditions of iron restriction and produced iron-regulated siderophore in large quantities, while all 19 isolates of coagulase-negative staphylococci (CoNS) grew poorly under conditions of iron restriction and produced low levels of iron chelator. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles of S. aureus isolates revealed altered protein patterns due to iron restriction, while altered profiles were not seen in the CoNS group. The ability to grow in iron-restricted conditions, possibly with the assistance of siderophore-mediated iron uptake, may contribute to the increased pathogenicity of S. aureus when compared with that of the CoNS.
Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism (2018)

Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (Rif<sup>R</sup>). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant Rif<sup>R</sup> mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of Rif<sup>R</sup> RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5'-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.
Isolation and In vitro Propagation of Tumorigenic Breast Cancer Cells with Stem/Progenitor Cell Properties (2005)

Breast cancer-initiating cells have been recently identified in breast carcinoma as CD44+/CD24(-/low) cells, which exclusively retain tumorigenic activity and display stem cell-like properties. However, at present, direct evidence that breast cancer-initiating cells can be propagated in vitro is still lacking. We report here the isolation and in vitro propagation of breast cancer-initiating cells from three breast cancer lesions and from an established breast carcinoma cell line. Our breast carcinoma-derived cultures encompassed undifferentiated cells capable of self-renewal, extensive proliferation as clonal nonadherent spherical clusters, and differentiation along different mammary epithelial lineages (ductal and myoepithelial). Interestingly, cultured cells were CD44+/CD24- and Cx43-, overexpressed neoangiogenic and cytoprotective factors, expressed the putative stem cell marker Oct-4, and gave rise to new tumors when as few as 10(3) cells were injected into the mammary fat pad of SCID mice. Long-term cultures of breast tumorigenic cells with stem/progenitor cell properties represent a suitable in vitro model to study breast cancer-initiating cells and to develop therapeutic strategies aimed at eradicating the tumorigenic subpopulation within breast cancer.
Three-dimensional structure of p21 in the active conformation and analysis of an oncogenic mutant. (1991)

The three-dimensional structure of the active guanosine triphosphate (GTP)-analogue-containing complex of the H-ras-encoded p21 has been determined. It was necessary to correct the topology of p21 as published earlier. The structure analysis shows all of the interactions between protein and GTP and how the important cofactor Mg2+ is bound. From the oncogenic mutants of p21 crystallized, a Gly12 to Arg mutation has been analyzed in detail. It shows that the overall structure of the mutant is not perturbed and that the side chain of Arg12 is coming close to the gamma-phosphate for an interaction.