gebhart/patrepeval huggingface dataset:
Design and Synthesis of Tetrahydropyridothieno[2,3-d]pyrimidine Scaffold Based Epidermal Growth Factor Receptor (EGFR) Kinase Inhibitors: The Role of Side Chain Chirality and Michael Acceptor Group for Maximal Potency (2010)

HTS hit 7 was modified through hybrid design strategy to introduce a chiral side chain followed by introduction of Michael acceptor group to obtain potent EGFR kinase inhibitors 11 and 19. Both 11 and 19 showed over 3 orders of magnitude enhanced HCC827 antiproliferative activity compared to HTS hit 7 and also inhibited gefitinib-resistant double mutant (DM, T790M/L858R) EGFR kinase at nanomolar concentration. Moreover, treatment with 19 shrinked tumor in nude mice xenograft model.
Transduction of TAT-HA-β-galactosidase Fusion Protein into Salivary Gland-derived Cells and Organ Cultures of the Developing Gland, and into Rat Submandibular Gland in Vivo (2000)

We have studied the transduction of TAT-HA-beta-galactosidase fusion protein into two cell lines of rat salivary gland origin, A5 and C6-21, into cells of fetal mouse submandibular glands in organ culture, and into rat submandibular gland after retrograde duct injection, using a histochemical method to demonstrate beta-galactosidase activity. Transduction of the fusion protein into A5 and C6-21 cells was concentration- and time-dependent. Therefore, the intensity of the beta-galactosidase staining, which was cytoplasmic, was less after 1 hr of exposure compared to exposures up to 24 hr. However, the fusion protein was transduced into 100% of both types of cultured cells. When explants of mouse fetuses at 13 days of gestation were exposed to the fusion proteins, both epithelial and mesenchymal cells were stained for the enzyme, with a conspicuous accumulation of the reaction product at perinuclear cytoplasmic regions. The histochemical staining of the mesenchymal cells was more intense compared to that seen in epithelial cells. TAT-HA-beta-galactosidase fusion protein was also delivered to rat submandibular glands by retrograde duct injection. Histochemical staining for beta-galactosidase activity of cryostat sections prepared from the injected glands revealed that the transduction of the fusion protein was also time- and dose-dependent. In the glands of rats sacrificed from 10 min to 1 hr after the retrograde injection, essentially all acinar and duct cells showed cytoplasmic staining. The intensity of the staining then declined, and was not seen in the glands of rats killed 24 hr after the injection of the fusion proteins. These results indicate that a full-length, active TAT fusion protein can be targeted to salivary gland cells both in vitro and in vivo to analyze physiological, developmental, and pathophysiological processes.
No-Reflow Phenomenon (2002)

B ecause total coronary artery occlusion was found in the early hours of transmural myocardial infarction, most of our research interest and treatment strategies focus on epicardial coronary arteries. 1 Little attention, however, is paid to the coronary microvasculature. When a coronary artery is occluded, detrimental changes occur in the cardiac capillaries and arterioles. After relief of the occlusion, blood flow to the ischemic tissue may still be impeded, a phenomenon known as no reflow. This article attempts to provide an in-depth understanding of this phenomenon from the laboratory bench to the clinical arena.
Enhanced cytotoxic effect of radiation and temozolomide in malignant glioma cells: targeting PI3K-AKT-mTOR signaling, HSP90 and histone deacetylases (2014)

Our results suggest possible strategies for counteracting the pro-survival signaling from EGFR to improve the therapeutic outcome of combined radiotherapy and TMZ for high-grade gliomas.
IN VIVO ADMINISTRATION OF LYMPHOCYTE-SPECIFIC MONOCLONAL ANTIBODIES IN NONHUMAN PRIMATES (1989)

Monoclonal antibodies, either alone or conjugated to toxins, hold promise as important therapeutic agents. However, the immune response to these foreign protein agents may markedly limit their therapeutic utility in vivo. We have administered both an interleukin-2 receptor-specific monoclonal antibody (anti-IL-2R) and a CD2-specific monoclonal antibody linked to the ribosome-inactivating protein gelonin to macaque monkeys. The monkeys developed high-titer antibody responses to mouse Ig and, when immunotoxin was administered, to the toxin gelonin. Their antimouse Ig antibody responses were broadly reactive with mouse Ig of differing idiotypes and isotypes. Furthermore, sera from these monkeys blocked the in vitro cytotoxic effect of anti-IL-2R or immunotoxin. This blocking was mediated by both the antimouse Ig and the antigelonin antibodies. Serum from a monkey infused with one CD2-specific monoclonal antibody blocked the in vitro cytotoxicity of two other isotypically different CD2-specific monoclonal antibody conjugates. In addition, this serum blocked the in vitro cytotoxicity of a gelonin-monoclonal antibody conjugate of an unrelated specificity. These data indicate that the immune response to some monoclonal antibodies and toxins might preclude the later use of this class of substances in an individual. Therefore, strategies for the parental therapeutic use of monoclonal antibodies and immunotoxins must take into consideration the possible limiting effects of the humoral immune response to these agents.
Developments in liposomal drug delivery systems (2001)

Liposomes are the leading drug delivery systems for the systemic (iv.) administration of drugs. There are now liposomal formulations of conventional drugs that have received clinical approval and many others in clinical trials that bring benefits of reduced toxicity and enhanced efficacy for the treatment of cancer and other life-threatening diseases. The mechanisms giving rise to the therapeutic advantages of liposomes, such as the ability of long-circulating liposomes to preferentially accumulate at disease sites including tumours, sites of infection and sites of inflammation are increasingly well understood. Further, liposome-based formulations of genetic drugs such as antisense oligonucleotides and plasmids for gene therapy that have clear potential for systemic utility are increasingly available. This paper reviews the liposomal drug delivery field, summarises the success of liposomes for the delivery of small molecules and indicates how this success is being built on to design effective carriers for genetic drugs.
CSF-1 receptor structure/function in MacCsf1r–/– macrophages: regulation of proliferation, differentiation, and morphology (2008)

CSF-1 is the major regulator of tissue macrophage development and function. A GM-CSF-dependent, CSF-1 receptor (CSF-1R)-deficient F4/80(hi)Mac-1(+)Gr1(-)CD11c(+) bone marrow macrophage (BMM) line (MacCsf1r-/-) was developed to study the roles of the eight intracellular CSF-1R tyrosines phosphorylated upon receptor activation. Retroviral expression of the wild-type CSF-1R rescued the CSF-1-induced survival, proliferation, differentiation, and morphological characteristics of primary BMM. Mutation of all eight tyrosines failed to rescue, whereas the individual Y --> F mutants (544, 559, 697, 706, 721, 807, 921, 974) rescued these CSF-1-inducible phenotypes to varying degrees. The juxtamembrane domain Y559F and activation loop Y807F mutations severely compromised proliferation and differentiation, whereas Y706, Y721F, and Y974F mutations altered morphological responses, and Y706F increased differentiation. Despite their retention of significant in vitro tyrosine kinase activity, Y559F and Y807F mutants exhibited severely impaired in vivo receptor tyrosine phosphorylation, consistent with the existence of cellular mechanisms inhibiting CSF-1R tyrosine phosphorylation that are relieved by phosphorylation of these two sites. The MacCsf1r-/- macrophage line will facilitate genetic and proteomic approaches to CSF-1R structure/function studies in the major disease-related CSF-1R-expressing cell type.
Spatial prediction based on self-similarity compensation for 3D holoscopic image and video coding (2011)

Holoscopic imaging, also known as integral imaging, provides a solution for glassless 3D, and is promising to change the market for 3D television. To start, this paper briefly describes the general concepts of holoscopic imaging, focusing mainly on the spatial correlations inherent to this new type of content, which appear due to the micro-lens array that is used for both acquisition and display. The micro-images that are formed behind each micro-lens, from which only one pixel is viewed from a given observation point, have a high cross-correlation between them, which can be exploited for coding. A novel scheme for spatial prediction, exploring the particular arrangement of holoscopic images, is proposed. The proposed scheme can be used for both still image coding and intra-coding of video. Experimental results based on an H.264/AVC video codec modified to handle 3D holoscopic images and video are presented, showing the superior performance of this approach.
IL-10-Dependent Suppression of Experimental Allergic Encephalomyelitis by Th2-Differentiated, Anti-TCR Redirected T Lymphocytes (2005)

We previously showed that transgenically expressed chimeric Ag-MHC-zeta receptors can Ag-specifically redirect T cells against other T cells. When the receptor's extracellular Ag-MHC domain engages cognate TCR on an Ag-specific T cell, its cytoplasmic zeta-chain stimulates the chimeric receptor-modified T cell (RMTC). This induces effector functions such as cytolysis and cytokine release. RMTC expressing a myelin basic protein (MBP) 89-101-IAs-zeta receptor can be used therapeutically, Ag-specifically treating murine experimental allergic encephalomyelitis (EAE) mediated by MBP89-101-specific T cells. In initial studies, isolated CD8+ RMTC were therapeutically effective whereas CD4+ RMTC were not. We re-examine here the therapeutic potential of CD4+ RMTC. We demonstrate that Th2-differentiated, though not Th1-differentiated, CD4+ MBP89-101-IAs-zeta RMTC prevent actively induced or adoptively transferred EAE, and treat EAE even after antigenic diversification of the pathologic T cell response. The Th2 RMTC both Th2-deviate autoreactive T cells and suppress autoantigen-specific T cell proliferation. IL-10 is critical for the suppressive effects. Anti-IL-10R blocks RMTC-mediated modulation of EAE and suppression of autoantigen proliferation, as well as the induction of IL-10 production by autoreactive T cells. In contrast to IL-10, IL-4 is required for IL-4 production by, and hence Th2 deviation of autoreactive T cells, but not the therapeutic activity of the RMTC. These results therefore demonstrate a novel immunotherapeutic approach for the Ag-specific treatment of autoimmune disease with RMTC. They further identify an essential role for IL-10, rather than Th2-deviation itself, in the therapeutic effectiveness of these redirected Th2 T cells.
Proximity breeds danger: emerging threats in metro-area wireless networks (2007)

The growing popularity of wireless networks and mobile devices is starting to attract unwanted attention especially as potential targets for malicious activities reach critical mass. In this study, we try to quantify the threat from large-scale distributed attacks on wireless networks, and, more specifically, wifi networks in densely populated metropolitan areas. We focus on three likely attack scenarios: “wildfire ” worms that can spread contagiously over and across wireless LANs, coordinated citywide phishing campaigns based on wireless spoofing, and rogue systems for compromising location privacy in a coordinated fashion. The first attack illustrates how dense wifi deployment may provide opportunities for attackers who want to quickly compromise large numbers
The role of carbon dioxide in host-finding by mosquitoes (Diptera: Culicidae): a review (1980)

Abstract From a critical review of the literature, it is concluded that the role of carbon dioxide in host-seeking by mosquitoes comprises two distinct actions. Firstly, it acts as an ‘attractant’, orientation towards the host being mediated by kinesis and optomotor anemotaxis. When tested in the absence of moving air currents, orientation to the source is not possible and only the kinetic or ‘activating’ effect is manifested. Moreover, in the absence of other host factors, sustained flight takes place only in response to intermittent pulses of carbon dioxide; this response is not elicited in uniformly permeated airstreams. Secondly, carbon dioxide has a combined action with warm moist convection currents at close range and with odour factors at a distance from the host.
Dna Sequence Specificity of Antitumor Agents: Oncogenes as possible targets for cancer therapy (1988)

An examination of the DNA sequence specificity of guanine-N7 alkylation for nitrogen mustards and chlorethylnitrosoureas revealed that large variations in alkylation intensities existed among different guanines in the DNA sequence. The most striking finding was that most agents reacted preferentially at runs of G's, the degree of preference being much greater than would be expected from the number of G's alone. This correlated with the molecular electrostatic potential induced at the guanine-N7 position by the nearest neighbor base pairs. Uracil and quinacrine mustards, however, showed distinctly different reaction patterns from other mustards and a detailed examination has led to structural hypotheses to account for the differences. Certain regions of the genome including regions in some oncogenes and the Epstein-Barr virus have unusually high GC contents (greater than 80% GC) which suggests that the antitumor effectiveness of alkylating agents may in part be due to selective reaction at certain regions in the genome. In fact certain mustards have been shown to exhibit enhanced reactivities with such regions in DNA fragments derived from the c-H-ras oncogene. The above findings point to the possibility of design of alkylating agents to optimise the selectivity of reaction with critical DNA regions. An alternative approach presently under investigation has emerged from an understanding of the characteristics of the sequence specific interaction of the natural oligopeptide antibiotics netropsin and distamycin in the minor groove of DNA. This has led to the synthesis of novel agents (lexitropsins) in which the binding specificity can be shifted from (AT)n in (GC)n in a predictable fashion. Thus the rational design of DNA sequence specific vectors linked to DNA reactive groups, such as alkylating or cleaving agents, could enable DNA damage to be delivered selectively to predetermined critical sites on the genome.
Effect of Acute Reamed Versus Unreamed Intramedullary Nailing on Compartment Pressure When Treating Closed Tibial Shaft Fractures: A Randomized Prospective Study (2000)

These data support acute (within three days of injury) reamed intramedullary nailing of closed, displaced tibial shaft fractures without the use of a fracture table.
Regulation of the threshold for lipoprotein-induced acyl-CoA:cholesterol O-acyltransferase stimulation in macrophages by cellular sphingomyelin content. (1994)

Macrophage acyl-CoA:cholesterol O-acyltransferase (ACAT), a key enzyme in atheroma foam cell formation, is stimulated by lipoproteins only after a "threshold" amount of cholesterol has accumulated in the cell. The present study explores the hypothesis that cellular sphingomyelin, by increasing the capacity of the cell to accommodate excess cholesterol, can influence the threshold of ACAT stimulation by lipoproteins. When the sphingomyelin content of macrophages was increased by either incubation with exogenous sphingomyelin or ceramide (a stimulator of endogenous sphingomyelin synthesis), the ability of acetyl-LDL to stimulate whole-cell ACAT activity was substantially reduced despite similar lipoprotein uptake and total cholesterol accumulation as in control cells. When the sphingomyelin content of macrophages was decreased by sphingomyelinase treatment, the ability of acetyl-LDL to stimulate whole-cell ACAT activity was enhanced despite no change in lipoprotein uptake. Importantly, microsomes isolated from control, sphingomyelin-, or sphingomyelinase-treated macrophages showed no difference in ACAT activity when assayed in vitro in the presence of exogenous cholesterol, suggesting that these treatments affected cholesterol trafficking. Lastly, a corollary of the hypothesis, that cells might adapt to a large increase in free cholesterol by increasing their sphingomyelin content, was supported by showing that the sphingomyelin content of macrophages increased 2.6-fold when the cells were induced to accumulate free cholesterol by incubation with acetyl-LDL plus an ACAT inhibitor. Thus, the sphingomyelin content of macrophages can influence the threshold at which ACAT is stimulated by lipoprotein delivery of cholesterol, and the cholesterol content of macrophages can influence the sphingomyelin content of the cell. These findings are consistent with a model in which cellular sphingomyelin plays an important role in accommodating pools of cellular cholesterol that result from the uptake of atherogenic lipoproteins by macrophages.
Palmitoyl-Acyl Carrier Protein (ACP) Thioesterase and the Evolutionary Origin of Plant Acyl-ACP Thioesterases (1995)

Aubrey Jones, H. Maelor Davies, Toni A. Voelker, Palmitoyl-Acyl Carrier Protein (ACP) Thioesterase and the Evolutionary Origin of Plant Acyl-ACP Thioesterases, The Plant Cell, Vol. 7, No. 3 (Mar., 1995), pp. 359-371
Genomic and Functional Analysis of the Type VI Secretion System in Acinetobacter (2013)

The genus Acinetobacter is comprised of a diverse group of species, several of which have raised interest due to potential applications in bioremediation and agricultural purposes. In this work, we show that many species within the genus Acinetobacter possess the genetic requirements to assemble a functional type VI secretion system (T6SS). This secretion system is widespread among Gram negative bacteria, and can be used for toxicity against other bacteria and eukaryotic cells. The most studied species within this genus is A. baumannii, an emerging nosocomial pathogen that has become a significant threat to healthcare systems worldwide. The ability of A. baumannii to develop multidrug resistance has severely reduced treatment options, and strains resistant to most clinically useful antibiotics are frequently being isolated. Despite the widespread dissemination of A. baumannii, little is known about the virulence factors this bacterium utilizes to cause infection. We determined that the T6SS is conserved and syntenic among A. baumannii strains, although expression and secretion of the hallmark protein Hcp varies between strains, and is dependent on TssM, a known structural protein required for T6SS function. Unlike other bacteria, A. baumannii ATCC 17978 does not appear to use its T6SS to kill Escherichia coli or other Acinetobacter species. Deletion of tssM does not affect virulence in several infection models, including mice, and did not alter biofilm formation. These results suggest that the T6SS fulfils an important but as-yet-unidentified role in the various lifestyles of the Acinetobacter spp.
Dendritic cells and macrophages are required for Th1 development of CD4+ T cells from αβ TCR transgenic mice: IL-12 substitution for macrophages to stimulate IFN-γ production is IFN-γ-dependent (1993)

We have examined the antigen presenting cell (APC) requirements for primary T cell activation and T helper (Th) cell phenotype differentiation using naive CD4+ T cells from alpha beta TCR transgenic mice. Purified dendritic cells were the principal cell required for induction of primary ovalbumin peptide specific T cell activation and clonal expansion. However, dendritic cells did not induce differentiation of T cells toward Th1 or Th2 phenotype. Addition of IL-4 during primary dendritic cell stimulations of T cells resulted in the development of a Th2 phenotype which produced high levels of IL-4 during secondary and tertiary stimulation. In contrast, development of Th1 cells producing high levels of IFN-gamma could not be induced with dendritic cells alone but required the addition of appropriately activated macrophages. Addition of splenic or peritoneal B cells did not induce Th1 development. Activated splenic macrophages induced Th1 development via a non-MHC restricted mechanism. Thus, requirements for induction of proliferation of naive CD4+ T cells are distinct from those directing Th1 phenotype development. IL-12 could replace the requirement for macrophages to induce Th1 development when T cells were activated with dendritic cells. Furthermore, this IL-12 mediated development of Th1 cells producing high levels of IFN-gamma was dependent on IFN-gamma.
Production of Liquid Hydrocarbons from Biomass (2005)

Sugar in the gas tank?! Biomass is the only practical source of renewable liquid fuel (see picture). In research worldwide, new technologies are being developed for the generation of liquid fuels from renewable resources. One example is the reduction of polyols, such as sorbitol, which can be obtained from carbohydrates, into alkanes in an aqueous-phase reforming process.
Glycolysis and the pentose phosphate pathway are differentially associated with the dichotomous regulation of glioblastoma cell migration versus proliferation (2016)

Cell function and metabolic state are coupled independently of hypoxia, and glucose metabolic pathways are causatively involved in regulating "go or grow" cellular programs.
Cell adhesion and proteoglycans: I. the effect of exogenous proteoglycans on the attachment of chick embryo fibroblasts to tissue culture plastic and collagen (1979)

Proteoglycan was isolated from cartilage and freed from contaminating glycoproteins and hyaluronic acid. The macromolecule consists of a protein core covalently linked to a number of glycosaminoglycan side chains, namely chondroitin sulphate and keratan sulphate. This proteoglycan retards the attachment of a variety of cell types to tissue culture plastic and to collagen. Glycosaminoglycans alone, have no significant effect on rates of attachment. Similarly, trypsinized proteoglycan is without effect. It is concluded that the structural integrity of the proteoglycan macromolecule is essential for its effect on cell adhesion.
Ice Nucleation Activity in Fusarium acuminatum and Fusarium avenaceum (1992)

Twenty fungal genera, including 14 Fusarium species, were examined for ice nucleation activity at -5.0 degrees C, and this activity was found only in Fusarium acuminatum and Fusarium avenaceum. This characteristic is unique to these two species. Ice nucleation activity of F. avenaceum was compared with ice nucleation activity of a Pseudomonas sp. strain. Cumulative nucleus spectra are similar for both microorganisms, while the maximum temperatures of ice nucleation were -2.5 degrees C for F. avenaceum and -1.0 degrees C for the bacteria. Ice nucleation activity of F. avenaceum was stable at pH levels from 1 to 13 and tolerated temperature treatments up to 60 degrees C, suggesting that these ice nuclei are more similar to lichen ice nuclei than to bacterial ones. Ice nuclei of F. avenaceum, unlike bacterial ice nuclei, pass through a 0.22-mum-pore-size filter. Fusarial nuclei share some characteristics with the so-called leaf-derived nuclei with which they might be identified: they are cell free and stable up to 60 degrees C, and they are found in the same kinds of environment. Highly stable ice nuclei produced by fast-growing microorganisms have potential applications in biotechnology. This is the first report of ice nucleation activity in free-living fungi.