gebhart/patrepeval huggingface dataset:
COMBINES-CID: An Efficient Method for De Novo Engineering of Highly Specific Chemically Induced Protein Dimerization Systems (2019)

Chemically induced dimerization (CID) systems, in which two proteins dimerize only in the presence of a small molecule ligand, offer versatile tools for small molecule sensing and actuation. However, only a handful of CID systems exist and creating one with the desired sensitivity and specificity for any given ligand is an unsolved problem. Here, we developed a <u>com</u>binatorial <u>bin</u>ders-<u>e</u>nabled <u>s</u>election of CID (COMBINES-CID) method broadly applicable to different ligands. We demonstrated a proof-of-principle by generating nanobody-based heterodimerization systems induced by cannabidiol with high ligand selectivity. We applied the CID system to a sensitive sandwich enzyme-linked immunosorbent assay-like assay of cannabidiol in body fluids with a detection limit of ∼0.25 ng/mL. COMBINES-CID provides an efficient, cost-effective solution for expanding the biosensor toolkit for small molecule detection.
The bone marrow microenvironment and leukemia: biology and therapeutic targeting (2011)

Multiple studies have demonstrated that interaction with the bone marrow stromal microenvironment contributes to the survival of leukemia cells. One explanation for this phenomenon is the interaction between the cell surface receptors CXCR4 and CXCL12. Through CXCL12/CXCR4-mediated chemotaxis, leukemia cells migrate to microscopic niches within the bone marrow, which leads to increased proliferation and survival. Several studies have suggested that increased CXCR4 expression may portend a poor prognosis in various types of leukemia, possibly due to increased protection of leukemia cells by bone marrow stroma. A potential therapeutic strategy to overcome this stromal-mediated survival advantage is to target CXCR4. Inhibition of CXCR4 may allow leukemia cells to be released from bone marrow niches that confer resistance to chemotherapy and negate the survival benefit imparted by bone marrow stroma.
Abberations in Phospholipase D Activity‐A Pharmacological Target for Cancer Detection (2006)

Understanding molecular targets and developing novel molecular imaging agents can improve early cancer detection. Radioiodinated NM404, a phospholipid ether analog in clinical trials, displays selective and prolonged retention in 28/28 xenograft and spontaneous tumor models. This specificity for malignant tumors is apparently due to prolonged and selective retention of NM404 in cancer cells having reduced ability to metabolize NM404. Prior in vitro studies implicate phospholipase D (PLD) in NM404 metabolism. PLD is a critical regulator of cell proliferation, survival signaling, cell transformation and tumor progression. Decreased expression of PLD in numerous tumors has been reported, and thus, reduced PLD levels in malignant cells may result in prolonged retention of NM404. PLD activity and expression were evaluated to assess the mechanism of action of NM404 and possibly identify novel drug development targets. Fluorescent enzyme assay and RT‐PCR were used to quantify PLD in mouse and human malignant cell lines and solid tumors compared to normal host tissue. PLD activity and mRNA levels were significantly lower (p&lt;0.05, T‐test) in malignant cells compared to the respective normal host tissues. The data strongly suggest decreased PLD activity in malignant cells may result in selective retention of NM404 and that malignancy maybe associated with aberrations in PLD activity. Supported by NCI grant CA95240
Polycyclic Aromatic Hydrocarbon Removal from Soil by Surfactant Solubilization and Phanerochaete chrysosporium Oxidation (2002)

Surfactant soil washing can remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soil, and the white rot fungus, Phanerochaete chrysosporium Burdsall in Burdsall & Eslyn, can oxidize PAHs. The objective of this study was to develop a novel bioremediation technology using a combination of abiological surfactant soil washing followed by PAH biological oxidation in soil washwater using P. chrysosporium in a rotating biological contactor (RBC) reactor. Soil used for experimentation was an 11-month aged contaminated soil spiked with a total of nine PAHs: acenaphthene, fluorene, phenanthrene, fluoranthene, pyrene, chrysene, benzo(a)pyrene, dibenz(a-h)anthracene, and benzo(ghi)perylene. After 11 months of aging, recovery percentages of high molecular weight PAHs [i.e., from chrysene to benzo(ghi)perylene] were greater than 86%, while those of low molecular weight PAHs (i.e., from acenaphthene to pyrene) were less than 19%. Total removal efficiency for any of the nine PAHs was greater than 90% using a combination of surfactant soil washing and P. chrysosporium oxidation of soil washwater in the RBC reactor when used in batch operation, and greater than 76% when used in continuous operation. The treatment of PAH-contaminated soil using a combination of surfactant soil washing and subsequent PAH removal from the resultant washwater in an RBC reactor, in the presence of immobilized P. chrysosporium, permits (i) a rapid abiological cleanup of soil for compliance with relevant soil quality standards and (ii) PAH biological removal in soil washwater for compliance with aqueous discharge standards.
Precursor sequence, processing, and urothelium-specific expression of a major 15-kDa protein subunit of asymmetric unit membrane. (1994)

The asymmetric unit membrane (AUM) is a highly specialized biomembrane elaborated by terminally differentiated urothelial cells. It contains quasi-crystalline arrays of 12-nm protein particles each of which is composed of six dumbbell-shaped subdomains. In this paper we describe the precursor sequence, processing and in vitro membrane insertion properties of bovine uroplakin II (UPII), a 15-kDa major protein component of AUM. The cDNA-deduced amino acid sequence revealed that UPII is synthesized as a precursor protein containing a cleavable signal peptide of approximately 26 amino acids, a long pro-sequence of approximately 59 residues harboring three potential N-glycosylation sites, and the mature polypeptide of 100 residues. In vitro translation of UPII mRNA demonstrated that UPII is indeed first synthesized as a 19-kDa precursor, which loses its signal peptide upon insertion into added microsomes; this process is accompanied by the acquisition of high mannose-type oligosaccharides giving rise to a 28-kDa precursor which is completely protected from the digestion by exogenous proteases. These results, together with the presence of a stretch of 25 hydrophobic amino acids at the C terminus, suggest that UPII protein is anchored to the lipid bilayer via its C-terminal membrane-spanning domain with its major N-terminal domain exposed luminally. The formation of the 15-kDa mature UPII requires the removal of the pro-sequence by a furin-like endoprotease. Since only mature UPII devoid of this pro-sequence can interact with 27-kDa uroplakin I, the proteolytic processing of UPII precursor may play an important role in regulating the assembly of AUM. Finally, we showed that genomic sequences cross-hybridizing with bovine UPII cDNA are present in many mammals suggesting that UPII performs a highly conserved function in the terminally differentiated cells of mammalian urinary bladder epithelium.
Cytogenetic analysis of 57 primary prostatic adenocarcinomas (1992)

Cytogenetic analysis after short-term culture in vitro of primary tumor samples was attempted in 82 patients with prostatic cancer. Tumor material was obtained by radical prostatectomy or transurethral resection. Successful cytogenetic studies were performed on 57 tumors of which five were well, 30 moderately, and 22 poorly differentiated adenocarcinomas. Only normal karyotypes were found in 24 tumors. Structural nonclonal aberrations were detected in 18 and clonal karyotypic abnormalities in 15 tumors. The most common clonal numerical aberration was loss of the Y chromosome; a missing Y was found in six tumors, in three of these as the sole anomaly. Clonal structural chromosomal rearrangements, usually accompanied by numerical changes, were detected in 12 tumors. The rearrangements involved 18 of the 22 autosomes and the X chromosome. Chromosomes 1, 7, and 10 were most frequently affected. Deletions, duplications, inversions, insertions, and balanced as well as unbalanced translocations were represented. The breakpoints in chromosome 1 were scattered along both the short and long arms with no obvious clustering, whereas those in chromosomes 7 and 10 were clustered at bands 7q22 (two deletions and two duplications in four different tumors) and 10q24 (two translocations, one deletion, and one inversion in four tumors). One additional tumor displayed a derivative chromosome 10 with a breakpoint in 10q23, and one had monosomy 10. Altogether, these abnormalities resulted in loss of 10q24----qter in five tumors. Monosomy 8 and rearrangements of the short arm of chromosome 8 leading to loss of 8p21----pter were seen in four tumors. Double minute chromosomes were found in two tumors.
Electronic passivation of GaAs surfaces through the formation of arsenic—sulfur bonds (1989)

X-ray photoelectron spectroscopy reveals that the remarkable electronic quality of GaAs/sulfide interfaces can be ascribed to the formation of AsxSy phases which grow on an oxide-free GaAs surface. While one of these phases is akin to As2S3, another shows significant in-plane S—S bonding. Raman experiments indicate that the band bending on this disulfide- terminated surface has been reduced to 0.12 eV.
Lymphotoxin (1988)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Aldose reductase induction: a novel response to oxidative stress of smooth muscle cells (1997)

Hydrogen peroxide (H2O2) or 4-hydroxy-2,3-trans-nonenal (HNE) treatment of rat vascular smooth muscle cells (A7r5) caused induction of aldose reductase mRNA. Induction was dose (10-100 microM H2O2, 1-10 microM HNE) and time dependent, reaching a maximum (three- to fourfold) after 7-12 h. Treatment of cells with actinomycin D confirmed de novo synthesis of aldose reductase mRNA. H2O2-induced expression was prevented by catalase but unaffected by Desferal, indicating that metal catalyzed degradation of peroxide was not involved. Induction of enzymatically active aldose reductase by H2O2 and HNE was confirmed using Western blotting and enzyme assays. Aldose reductase can metabolize several aldehyde compounds including HNE, a major toxic product of lipid peroxidation. Inclusion of Sorbinil, an aldose reductase inhibitor, in toxicity assays resulted in a significant (twofold) enhancement of HNE-mediated killing of A7r5 cells, suggesting a protective role of aldose reductase against HNE-induced cell death. These data indicate that the induction of aldose reductase during oxidative stress might represent an important cellular antioxidant defense mechanism.
Organization of Endothelial Cells, Pericytes, and Astrocytes into a 3D Microfluidicin VitroModel of the Blood–Brain Barrier (2016)

The endothelial cells lining the capillaries supplying the brain with oxygen and nutrients form a formidable barrier known as the blood-brain barrier (BBB), which exhibits selective permeability to small drug molecules and virtually impermeable to macromolecular therapeutics. Current in vitro BBB models fail to replicate this restrictive behavior due to poor integration of the endothelial cells with supporting cells (pericytes and astrocytes) following the correct anatomical organization observed in vivo. We report the coculture of mouse brain microvascular endothelial cells (b.End3), pericytes, with/without C8-D1A astrocytes in layered microfluidic channels forming three-dimensional (3D) bi- and triculture models of the BBB. The live/dead assay indicated high viability of all cultured cells up to 21 days. Trans-endothelial electrical resistance (TEER) values confirmed the formation of intact monolayers after 3 days in culture and showed statistically higher values for the triculture model compared to the single and biculture models. Screening the permeability of [(14)C]-mannitol and [(14)C]-urea showed the ability of bi- and triculture models to discriminate between different markers based on their size. Further, permeability of [(14)C]-mannitol across the triculture model after 18 days in culture matched its reported permeability across the BBB in vivo. Mathematical calculations also showed that the radius of the tight junctions pores (R) in the triculture model is similar to the reported diameter of the BBB in vivo. Finally, both the bi- and triculture models exhibited functional expression of the P-glycoprotein efflux pump, which increased with the increase in the number of days in culture. These results collectively indicate that the triculture model is a robust in vitro model of the BBB.
Differentially regulated NADPH:cytochrome P450 oxidoreductases in parsley (1997)

Two NADPH:cytochrome P450 oxidoreductases (CPRs) from parsley (Petroselinum crispum) were cloned, and the complete proteins were expressed and functionally identified in yeast. The two enzymes, designated CPR1 and CPR2, are 80% identical in amino acid sequence with one another and about 75% identical with CPRs from several other plant species. The mRNA accumulation patterns for CPR1 and CPR2 in fungal elicitor-treated or UV-irradiated cultured parsley cells and in developing or infected parsley plants were compared with those for cinnamate 4-hydroxylase (C4H), one of the most abundant CPR-dependent P450 enzymes in plants. All treatments strongly induced the mRNAs for C4H and CPR1 but not for CPR2, suggesting distinct metabolic roles of CPR1 and CPR2 and a functional relationship between CPR1 and C4H.
Temperature dependence of the piezoelectric response in lead zirconate titanate films (2004)

The temperature dependence of the effective transverse piezoelectric coefficient (e31,f) in lead zirconate titanate (PZT) thin films was measured between −55 and 85 °C. e31,f was calculated by simultaneously monitoring the piezoelectric charge output and strain in the film during wafer flexure. This method was used to characterize the temperature dependence of e31,f in PZT films with 2, 4, and 6 μm thickness and 40/60, 52/48, and 60/40 Zr/Ti ratios. |e31,f| was found to increase with temperature and average increases were 46%, 32%, and 12% for films with PZT 60/40, 52/48, and 40/60 compositions, respectively. Measurement uncertainty ranged from ±3%–12%. The measured temperature dependences of e31,f were consistent with the rapid rise in intrinsic d31 as Tc is approached, suggesting that they were controlled by intrinsic contributions. Additional contributors to the measured variation in the PZT film piezoelectric response over the measured temperature range were identified. Changes in film elastic properties could have decreased measured e31,f values by to 1%–4% in heating from −55 to 85 °C. Changes in the biaxial film stress with temperature were expected to account for 1%–3% of the measured increase in e31,f from −55 to 85 °C.
Long-Term, Six-Dimensional Live-Cell Imaging for the Mouse Preimplantation Embryo That Does Not Affect Full-Term Development (2009)

Mammalian preimplantation embryonic development is achieved by tightly coordinated regulation of a great variety of temporal and spatial changes. Therefore, it would be valuable to analyze these events three-dimensionally and dynamically. We have previously developed a live-cell imaging method based on the expression of fluorescent proteins, using mRNA injection and time-lapse florescence microscopy. However, with conventional fluorescent microscopy, three-dimensional images could not be obtained due to the thickness of the embryos and the optical problem in which ;out-of focus blur' cannot be eliminated. Moreover, as the repeated exposure of intense excitation light to the cell yields phototoxicity, long-term observation was detrimental to embryonic development. Here, we improved our imaging system to enable six-dimensional live-cell imaging of mouse preimplantation embryos (x, y and z axes, time-lapse, multicolor and multisample). Importantly, by improving the imaging devices and optimizing the conditions for imaging, such as intensity of excitation and time intervals for image acquisition, the procedure itself was not detrimental to full-term development, although it is a prolonged imaging process. For example, live pups were obtained from embryos to which two different wavelengths of excitation (488 and 561 nm) were applied at 7.5-min intervals for about 70 h, and 51 images were acquired in the z axis at each time point; thus, a total of 56,814 fluorescent images were taken. All the pups were healthy, reproductively normal and not transgenic. Thus, this live-cell imaging technology is safe for full-term mouse development. This offers a novel approach for developmental and reproductive research in that it enables both retrospective and prospective analyses of development. It might also be applicable to assessment of embryo quality in fields such as human reproductive technology and production animal research.
Inductively coupled argon plasma as an ion source for mass spectrometric determination of trace elements (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInductively coupled argon plasma as an ion source for mass spectrometric determination of trace elementsRobert S. Houk, Velmer A. Fassel, Gerald D. Flesch, Harry J. Svec, Alan L. Gray, and Charles E. TaylorCite this: Anal. Chem. 1980, 52, 14, 2283–2289Publication Date (Print):December 1, 1980Publication History Published online1 May 2002Published inissue 1 December 1980https://pubs.acs.org/doi/10.1021/ac50064a012https://doi.org/10.1021/ac50064a012research-articleACS PublicationsRequest reuse permissionsArticle Views3719Altmetric-Citations574LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Bias-Dependent Admittance in Hybrid Bilayer Membranes (2006)

Artificial bilayer membranes provide a platform for bioelectronic devices based on their structural, sensing, and transport functions. In this letter, we report on the impedance response of an engineered membrane with a lower leaflet of octadecanethiol on gold and an outer leaflet of dioleoylphosphatidylcholine with the monomeric channel protein gramicidin. This hybrid bilayer exhibits an electrical response analogous to a solid-state diode: the admittance is very low (<10(-)(7) Omega(-)(1) cm(-)(2)) over a wide potential range but increases exponentially at negative potentials.
Sepsis Research in the Next Millennium: Concentrate on the Software Rather than the Hardware (2002)

Today the basic principles of septic conditions are understood. Nevertheless, sepsis research has reached a critical point. To integrate our knowledge towards a consistent theory of the disease process and to derive effective therapies, new perspectives for future research that fit the complexity of the problem have to be found. We conducted a review of the literature concerning systemic inflammatory response syndrome (SIRS) and sepsis with particular reference to liver pathophysiology. And compared our findings with characteristic features of complex systems. The complexity of sepsis is broadly recognized. A review of the different aspects of liver inflammation during SIRS and sepsis, i.e. endotoxin challenge, cytokine induced dysfunction, the mechanisms of leukocyte transmigration, and hormonal and neuroendocrine regulatory mechanisms is given. Key aspects of complex systems, including parallelism, locality, emergence, and cross-scale interactions are introduced. We conclude that sepsis research needs new perspectives that allow us to handle the complex interactions occurring during the disease process. We propose to focus research on the interactions between the constituents of the system rather than only describing isolated aspects of the disease process. We also conclude that the ideas and techniques of non-linear systems theory are suitable tools for the analysis of complex and dynamic diseases like SIRS and sepsis.
Switchable Static and Dynamic Self-Assembly of Magnetic Droplets on Superhydrophobic Surfaces (2013)

Self-assembly is a process in which interacting bodies are autonomously driven into ordered structures. Static structures such as crystals often form through simple energy minimization, whereas dynamic ones require continuous energy input to grow and sustain. Dynamic systems are ubiquitous in nature and biology but have proven challenging to understand and engineer. Here, we bridge the gap from static to dynamic self-assembly by introducing a model system based on ferrofluid droplets on superhydrophobic surfaces. The droplets self-assemble under a static external magnetic field into simple patterns that can be switched to complicated dynamic dissipative structures by applying a time-varying magnetic field. The transition between the static and dynamic patterns involves kinetic trapping and shows complexity that can be directly visualized.
Gingival Fibroblasts as a Promising Source of Induced Pluripotent Stem Cells (2010)

These results suggest that GFs from the easily obtainable gingival tissues can be readily reprogrammed into iPS cells, thus making them a promising cell source for investigating the basis of cellular reprogramming and pluripotency for future clinical applications. In addition, high-quality iPS cells were generated from mouse GFs without Myc transduction or a specific system for reprogrammed cell selection.