gebhart/patrepeval huggingface dataset:
Jasmonates: Novel Anticancer Agents Acting Directly and Selectively on Human Cancer Cell Mitochondria (2005)

We reported previously that jasmonates can kill human cancer cells. Many chemotherapeutic drugs induce mitochondrial membrane permeability transition, membrane depolarization, osmotic swelling, and release of cytochrome c, involving the opening of the permeability transition pore complex (PTPC). Because jasmonates exert their cytotoxic effects independent of transcription, translation, and p53 expression, we hypothesized that these compounds may act directly on mitochondria. Mitochondrial membrane depolarization was determined by flow cytometry, and cytochrome c release by Western blotting. Mitochondria were isolated by mechanical lysis and differential centrifugation. Cytotoxicity was measured by a tetrazolium-based assay, and mitochondrial swelling by spectrophotometry. Jasmonates induced membrane depolarization and cytochrome c release in intact human cancer cell lines. Jasmonates induced swelling in mitochondria isolated from Hep 3B hepatoma cells, but not in mitochondria isolated from 3T3 nontransformed cells or from normal lymphocytes, in a PTPC-mediated manner. Methyl jasmonate induced the release of cytochrome c from mitochondria isolated from cancer cell lines in a PTPC-mediated manner, but not from mitochondria isolated from normal lymphocytes. A correlation was found between cytotoxicity of methyl jasmonate and the percentage of leukemic cells in the blood of patients with chronic lymphocytic leukemia (CLL). Jasmonates induced membrane depolarization in CLL cells, and swelling and release of cytochrome c in mitochondria isolated from these cells. In conclusion, jasmonates act directly on mitochondria derived from cancer cells in a PTPC-mediated manner, and could therefore bypass premitochondrial apoptotic blocks. Jasmonates are promising candidates for the treatment of CLL and other types of cancer.
Organization of the Motorola 88110 superscalar RISC microprocessor (1992)

Motorola's second-generation RISC microprocessor, which uses advanced techniques for exploiting instruction-level parallelism, including superscalar instruction issue, our-of-order instruction completion, speculative execution, dynamic instruction rescheduling, and two parallel, high-bandwidth, on-chip caches, is discussed. The microprocessor was designed to serve as the central processor in low-cost personal computers and workstations, and support demanding graphics and digital signal processing applications. The 88110's instruction set architecture, instruction sequencer, register files, execution units, address translation facilities, caches, and external bus interface are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Endogenous retrovirus-K promoter: a landing strip for inflammatory transcription factors? (2013)

Humans are symbiotic organisms; our genome is populated with a substantial number of endogenous retroviruses (ERVs), some remarkably intact, while others are remnants of their former selves. Current research indicates that not all ERVs remain silent passengers within our genomes; re-activation of ERVs is often associated with inflammatory diseases. ERVK is the most recently endogenized and transcriptionally active ERV in humans, and as such may potentially contribute to the pathology of inflammatory disease. Here, we showcase the transcriptional regulation of ERVK. Expression of ERVs is regulated in part by epigenetic mechanisms, but also depends on transcriptional regulatory elements present within retroviral long terminal repeats (LTRs). These LTRs are responsive to both viral and cellular transcription factors; and we are just beginning to appreciate the full complexity of transcription factor interaction with the viral promoter. In this review, an exploration into the inflammatory transcription factor sites within the ERVK LTR will highlight the possible mechanisms by which ERVK is induced in inflammatory diseases.
A Model for Human B-Chronic Lymphocytic Leukemia in Human/Mouse Radiation Chimera: Evidence for Tumor-Mediated Suppression of Antibody Production in Low-Stage Disease (1997)

B-chronic lymphocytic leukemia (BCLL) is a lymphoproliferative disease that is characterized by clonal expansion of CD5+ B cells. BCLL is associated with secondary immunodeficiency and hypogammaglobulinemia. It has been suggested that T-cell dysregulation may play a role in the hypogammaglobulinemia and in the increased incidence of autoimmunity in BCLL patients. We attempted to transfer human peripheral blood mononuclear cells (PBMC) from BCLL patients in different stages of the disease into immunodeficient mice. PBMC from BCLL patients in stage 0, stages I to II, and stages III to IV were transplanted into the peritoneal cavity of lethally irradiated Balb/c or beige/nude/Xid (BNX) mice radioprotected with bone marrow (BM) from severe combined immunodeficiency (SCID) mice. Different engraftment profiles were found in the chimeric mice 2 weeks after transplantation of PBMC according to the disease stage of the BCLL donors. Infusion of PBMC from donors in stage 0 led to marked engraftment of human T cells, whereas the human tumor cells could hardly be detected. In contrast, chimeric mice receiving PBMC from patients in stage III to IV disease exhibited engraftment with a dominance of tumor cells, compared with a miniscule level of T cells. The ability of the engrafted cells to produce human Ig was also found to be correlated with the disease stage of the donor, although all donors had the same magnitude of hypogammaglobulinemia. Total human Ig production in the chimeric mice was normal in mice receiving PBMC from donors in stage 0, whereas in chimeric mice engrafted with PBMC from donors in stages III to IV almost no human Igs could be detected. This differential reconstitution of antibody production in the mouse model according to the stage of the patient's disease will allow further studies on possible cellular interactions between malignant and immune cells in BCLL.
Copper Oxide Nanoparticles Are Highly Toxic: A Comparison between Metal Oxide Nanoparticles and Carbon Nanotubes (2008)

Since the manufacture and use of nanoparticles are increasing, humans are more likely to be exposed occupationally or via consumer products and the environment. However, so far toxicity data for most manufactured nanoparticles are limited. The aim of this study was to investigate and compare different nanoparticles and nanotubes regarding cytotoxicity and ability to cause DNA damage and oxidative stress. The study was focused on different metal oxide particles (CuO, TiO2, ZnO, CuZnFe2O4, Fe3O4, Fe2O3), and the toxicity was compared to that of carbon nanoparticles and multiwalled carbon nanotubes (MWCNT). The human lung epithelial cell line A549 was exposed to the particles, and cytotoxicity was analyzed using trypan blue staining. DNA damage and oxidative lesions were determined using the comet assay, and intracellular production of reactive oxygen species (ROS) was measured using the oxidation-sensitive fluoroprobe 2',7'-dichlorofluorescin diacetate (DCFH-DA). The results showed that there was a high variation among different nanoparticles concerning their ability to cause toxic effects. CuO nanoparticles were most potent regarding cytotoxicity and DNA damage. The toxicity was likely not explained by Cu ions released to the cell medium. These particles also caused oxidative lesions and were the only particles that induced an almost significant increase (p = 0.058) in intracellular ROS. ZnO showed effects on cell viability as well as DNA damage, whereas the TiO2 particles (a mix of rutile and anatase) only caused DNA damage. For iron oxide particles (Fe3O4, Fe2O3), no or low toxicity was observed, but CuZnFe2O4 particles were rather potent in inducing DNA lesions. Finally, the carbon nanotubes showed cytotoxic effects and caused DNA damage in the lowest dose tested. The effects were not explained by soluble metal impurities. In conclusion, this study highlights the in vitro toxicity of CuO nanoparticles.
Corticostriatal connections of the superior temporal region in rhesus monkeys (1998)

Corticostriatal connections of auditory areas within the supratemporal plane and in rostral and caudal portions of the superior temporal gyrus were studied by the autoradiographic anterograde tracing technique. The results show that the primary auditory cortex has limited projections to the caudoventral putamen and to the tail of the caudate nucleus. In contrast, the second auditory area within the circular sulcus has connections to the rostral and the caudal putamen and to the body of the caudate nucleus and the tail. The association areas of the superior temporal gyrus collectively have widespread corticostriatal projections characterized by differential topographic distributions. The rostral part of the gyrus projects to ventral portions of the head of the caudate nucleus and of the body and to the tail. In addition, there are connections to rostroventral and caudoventral portions of the putamen. The mid-portion of the gyrus projects to similar striatal regions, but the connections to the head of the caudate nucleus are less extensive. Compared with the rostral and middle parts of the superior temporal gyrus, the caudal portion has little connectivity to the tail of the caudate nucleus. It projects more dorsally within the head and the body and also more dorsally within the caudal putamen. These differential patterns of corticostriatal connectivity are consistent with functional specialization at the cortical level.
The Role of Metal Site Vacancies in Promoting Li–Mn–Ni–O Layered Solid Solutions (2013)

The Li–Mn–Ni-O system has received much attention for potential positive electrode materials in lithium-ion batteries. Recent work mapping the phase diagrams of the entire pseudo-ternary system showed that the layered solid-solution region extends to compositions with both less and more lithium than the well-known lithium-rich layered composition line that joins Li2MnO3 to LiNi0.5Mn0.5O2. The part of this solid-solution region that is lithium deficient has a “bump” feature in the single-phase boundary, which could not be explained until now. The current study explores this part of the phase diagram with the use of X-ray diffraction, helium pycnometry measurements, redox titrations, and a Monte Carlo simulation. Results show that metal site vacancies are present in the structures in increasing amounts as the lithium content of the samples decreases. A Ni2+ ion and a vacancy can replace two Li+ ions in Li[Li1/3Mn2/3]O2 to make the solid solution series Li[Li(1/3)–xNix/2□x/2Mn2/3]O2 with 0 < x < 1/3. The most lithium-deficient structures contain sufficient vacancies to allow manganese to form on two-thirds (2/3) of the transition-metal layer, such that the ordering of manganese on two √3 × √3 lattices yields a structure with low internal energy and sharp superlattice peaks in XRD patterns. The material with the maximum theoretical vacancy fraction that still has two-thirds of the transition-metal layer filled with manganese, Li[Ni1/6□1/6Mn2/3]O2, was also synthesized. Both XRD and electrochemical data regarding this new material are presented.
Natural killer T cell-mediated immunotherapy for malignant diseases (2009)

Ischemia/reperfusion (I/R) injury remains a major problem in solid organ transplantation, as it adversely impacts both short and long term outcomes. It has been well established that the innate immune system plays a significant role in the pathogenesis of I/R injury. In contrast, the proximal molecular signaling events that initiate activation of the innate immune system are less clear. Recent findings have demonstrated that Toll-like receptors (TLR) play a role in I/R injury. Specifically, TLR4 is central to early activation of the innate immune response in the setting of I/R. Furthermore, recent evidence has shown that endogenous molecules, such as high mobility group box-1 (HMGB1) and others that are released from ischemic, damaged, or dying cells and tissues in the setting I/R, can serve as triggers for activation of the innate immune system and exacerbate tissue injury. This evolving body of literature, which has provided insight into the early molecular events that activate the innate system after I/R, is reviewed here.
Recombination Proteins in Yeast (2004)

The process of homologous recombination promotes error-free repair of double-strand breaks and is essential for meiosis. Central to the process of homologous recombination are the RAD52 group genes (RAD50, RAD51, RAD52, RAD54, RDH54/TID1, RAD55, RAD57, RAD59, MRE11, and XRS2), most of which were identified by their requirement for the repair of ionizing radiation-induced DNA damage in Saccharomyces cerevisiae. The Rad52 group proteins are highly conserved among eukaryotes. Recent studies showing defects in homologous recombination and double-strand break repair in several human cancer-prone syndromes have emphasized the importance of this repair pathway in maintaining genome integrity. Herein, we review recent genetic, biochemical, and structural analyses of the genes and proteins involved in recombination.
Vasoactive Intestinal Peptide: A Novel Stimulator of Steroidogenesis by Cultured Rat Granulosa Cells1 (1985)

Vasoactive intestinal peptide (VIP) and VIPergic nerve fibers are present in the ovaries of several mammalian species, suggesting a possible ovarian action of VIP. We have investigated the direct effects of synthetic porcine VIP on rat granulosa cell steroidogenesis in vitro. The cells were obtained from immature, hypophysectomized, estrogen-primed rats, and cultured in a serum-free medium for 24 h in the absence or presence of varying amounts of VIP. Medium steroids were then determined by specific radioimmunoassay. Vasoactive intestinal peptide dose-dependently stimulated progesterone, 20 alpha-hydroxypregn-4-ene-3-one (20 alpha-OH-progesterone), and estrogen production with an approximate ED50 value of 3 X 10(-8) M. Maximum steroid production induced by VIP ranged from 15% to 28% of that seen with maximal follicle-stimulating hormone (FSH) stimulation. In contrast to the ability of FSH to induce luteinizing hormone (LH) receptor formation, treatment with VIP did not increase [125I]iodo-human chorionic gonadotropin (hCG) binding to granulosa cells. The ability of several gastrointestinal peptides, having 17-44% sequence identity to VIP, to stimulate granulosa cell steroidogenesis was also tested. The most closely related peptide, PHM-27 was less effective than VIP, and the least closely related, secretin and glucagon, were ineffective at 10(-6) M. Vasoactive intestinal peptide seems to act at least partly through cyclic 3',5'-adenosine monophosphate (cAMP)-dependent processes: addition of a phosphodiesterase inhibitor significantly potentiated the VIP stimulation of granulosa cell steroidogenesis, and VIP was capable of producing a dose- and time-dependent increase in both intracellular and medium cAMP levels. Vasoactive intestinal peptide stimulation of estrogen production seemed to be a result of increased aromatase activity. The increased progesterone production was associated with increased pregnenolone production, increased rate of conversion of pregnenolone to progesterone via 3 beta-hydroxysteroid dehydrogenase, and decreased metabolism of progesterone via 20 alpha-hydroxysteroid dehydrogenase. These results indicate that VIP exerts a specific action on granulosa cells to increase estrogen and progestin production. The observed direct effects of VIP, coupled with its identification in the ovary, suggest that VIP may be a physiologically important regulator of ovarian activity.
Engineered Monoclonal Antibody with Novel Antigen-Sweeping Activity In Vivo (2013)

Monoclonal antibodies are widely used to target disease-related antigens. However, because conventional antibody binds to the antigen but cannot eliminate the antigen from plasma, and rather increases the plasma antigen concentration by reducing the clearance of the antigen, some clinically important antigens are still difficult to target with monoclonal antibodies because of the huge dosages required. While conventional antibody can only bind to the antigen, some natural endocytic receptors not only bind to the ligands but also continuously eliminate them from plasma by pH-dependent dissociation of the ligands within the acidic endosome and subsequent receptor recycling to the cell surface. Here, we demonstrate that an engineered antibody, named sweeping antibody, having both pH-dependent antigen binding (to mimic the receptor-ligand interaction) and increased binding to cell surface neonatal Fc receptor (FcRn) at neutral pH (to mimic the cell-bound form of the receptor), selectively eliminated the antigen from plasma. With this novel antigen-sweeping activity, antibody without in vitro neutralizing activity exerted in vivo efficacy by directly eliminating the antigen from plasma. Moreover, conversion of conventional antibody with in vitro neutralizing activity into sweeping antibody further potentiated the in vivo efficacy. Depending on the binding affinity to FcRn at neutral pH, sweeping antibody reduced antigen concentration 50- to 1000-fold compared to conventional antibody. Thereby, sweeping antibody antagonized excess amounts of antigen in plasma against which conventional antibody was completely ineffective, and could afford marked reduction of dosage to a level that conventional antibody can never achieve. Thus, the novel mode of action of sweeping antibody provides potential advantages over conventional antibody and may allow access to the target antigens which were previously undruggable by conventional antibody.
Self-Assembly Approach toward Magnetic Silica-Type Nanoparticles of Different Shapes from Reverse Block Copolymer Mesophases (2003)

In the present study poly(isoprene-block-ethylene oxide), PI-b-PEO, block copolymers are used to structure iron oxide and silica precursors into reverse mesophases, which upon dissolution of the organic matrix lead to well-defined nanoparticles of spheres, cylinders, and plates based on the original structure of the mesophase prepared. The hybrid mesophases with sphere, cylinder, and lamellar morphologies containing the inorganic components in the minority phases are characterized through a combination of small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM), and electron energy loss spectroscopy (EELS). After heat treatments the respective nanoparticles on mica surfaces are characterized by scanning force microscopy (SFM). X-ray diffraction (XRD) and superconducting quantum interference device (SQUID) magnetometer measurements are performed to demonstrate that the heat treatment leads to the formation of a magnetic gamma-Fe2O3 crystalline phase within the amorphous aluminosilicate. The results pave the way to functional, i.e., magnetic nanoparticles where the size, shape, and iron oxide concentration can be controlled opening a range of possible applications.
Shortened telomeres in the expanded CD28-CD8+ cell subset in HIV disease implicate replicative senescence in HIV pathogenesis (1996)

The shortened telomeres in the CD28-CD8+ cells in HIV-infected subjects and the poor proliferative potential of these cells identifies CD8+ cell replicative senescence as a newly described feature of HIV disease. Our results provide a mechanism for the loss of CD8+ cell control of viral replication that accompanies advanced HIV disease. Replicative senescence may contribute to exhaustion of the T-cell response as a result of chronic HIV disease. Whether this phenomenon occurs in other chronic viral infections is unknown.
Kinoform using an electrically controlled birefringent liquid-crystal spatial light modulator (1991)

A programmable kinoform using an electrically controlled birefringent liquid-crystal spatial modulator (ECB-LCSLM) is discussed. The LCSLM is capable of continuous phase modulation from 0 to 2piFor the kinoform generation, the phase distribution is calculated by iterative methods and recorded on the LCSLM with 16 quantizing levels. We discuss the characteristics and the structure of the LCSLM for the implementation of the programmable kinoform while comparing the computed results and optical reconstructions.
Enantioselective Organocatalytic Aminomethylation of Aldehydes:  A Role for Ionic Interactions and Efficient Access to β2-Amino Acids (2006)

Organocatalytic Mannich addition of aldehydes to a formaldehyde-derived iminium species catalyzed by proline-derived chiral pyrrolidines provides beta-amino aldehydes with >/=90% ee. Mechanistic analysis of the proline-catalyzed reactions suggests that non-hydrogen-bonded ionic interactions at the Mannich reaction transition state can influence stereochemical outcome. The beta-amino aldehydes from our process bear a substituent adjacent to the carbonyl and can be efficiently converted to protected beta2-amino acids, which are important building blocks for beta-peptide foldamers that display useful biological activities.
Inactivation of phytochrome- and phycobiliprotein-chromophore precursors by rat liver biliverdin reductase. (1993)

The phytochrome chromophore precursor, 3E-phytochromobilin, and the phycobiliprotein chromophore precursors, 3E-phycocyanobilin and 3E-phycoerythrobilin, are enzymatically converted to novel rubinoid products by purified rat liver biliverdin reductase. Phytochromobilin and phycocyanobilin are particularly good substrates for biliverdin reductase with Km and Vmax values very similar to those of the natural substrate, biliverdin IX alpha. Phycoerythrobilin is the least preferred of the three bilin substrates. 1H NMR spectroscopy of phycocyanorubin, the product of phycocyanobilin catalysis by biliverdin reductase, and comparison of absorption spectra of all three rubinoid products reveal that the C10 methine bridge is selectively reduced by biliverdin reductase without altering the A-ring ethylidene substituent. In vitro phytochrome assembly experiments demonstrate that the phytorubin products do not form photoactive adducts with recombinant apophytochrome. These results suggest that ectopic expression of biliverdin reductase in plants will prevent assembly of the functional photoreceptor and thus will potentially alter light-mediated plant growth and development.
Determination of urinary acylcarnitines by ESI‐MS coupled with solid‐phase microextraction (SPME) (1997)

The determination of selected short-, medium- and long-chain acylcarnitines by electrospray ionization mass spectrometry (ESI-MS) is discussed. The differences in fragmentation behaviour and ionization efficiency are described in dependence on collision induced dissociation (CID) conditions and mixture composition. A new method combination, solid-phase microextraction (SPME)-ESI-MS, is introduced to characterize acylcarnitines in body fluids. This method utilizes SPME for pre-concentration of acylcarnitines from complex biological samples and ESI-MS for a selective and sensitive detection. The method is presented by standard experiments determining of acylcarnitines in aqueous solutions and urine samples from patients with secondary carnitine deficiency syndromes or related disorders. © 1997 John Wiley & Sons, Ltd.
Primary cutaneous B-cell lymphoma is associated with somatically hypermutated immunoglobulin variable genes and frequent use of VH1-69 and VH4-59 segments (2009)

Data indicate that neoplastic B cells of PBCBL have experienced germinal centre reaction and also suggest that the involvement of IgVH genes is not entirely random in PCBCL and that common antigen epitopes could be pathologically relevant in cutaneous lymphomagenesis.
Opening the window for aqueous electrolytes (2015)

Lithium batteries can operate with a safer “water-in-salt” electrolyte [Also see Research Article by Suo et al. ]