gebhart/patrepeval huggingface dataset:
An indolocarbazole inhibitor of human checkpoint kinase (Chk1) abrogates cell cycle arrest caused by DNA damage. (2000)

Many cancer therapies cause DNA damage to effectively kill proliferating tumor cells; however, a major limitation of current therapies is the emergence of resistant tumors following initial treatment. Cell cycle checkpoints are involved in the response to DNA damage and specifically prevent cell cycle progression to allow DNA repair. Tumor cells can take advantage of the G2 checkpoint to arrest following DNA damage and avoid immediate cell death. This can contribute to acquisition of drug resistance. By abrogating the G2 checkpoint arrest, it may be possible to synergistically augment tumor cell death induced by DNA damage and circumvent resistance. This requires an understanding of the molecules involved in regulating the checkpoints. Human Chk1 is a recently identified homologue of the Schizosaccharomyces pombe checkpoint kinase gene, which is required for G2 arrest in response to DNA damage. Chk1 phosphorylates the dual specificity phosphatase cdc25C on Ser-216, and this may be involved in preventing cdc25 from activating cdc2/cyclinB and initiating mitosis. To further study the role of Chk1 in G2 checkpoint control, we identified a potent and selective indolocarbazole inhibitor (SB-218078) of Chk1 kinase activity and used this compound to assess cell cycle checkpoint responses. Limited DNA damage induced by gamma-irradiation or the topoisomerase I inhibitor topotecan was used to induce G2 arrest in HeLa cells. In the presence of the Chk1 inhibitor, the cells did not arrest following gamma-irradiation or treatment with topotecan, but continued into mitosis. Abrogation of the damage-arrest checkpoint also enhanced the cytotoxicity of topoisomerase I inhibitors. These studies suggest that Chk1 activity is required for G2 arrest following DNA damage.
Web Service Composition as AI Planning { a Survey ⁄ (2005)

This article gives an overview of AI (Artiflcial Intelligence) planning techniques and discusses their application to the Web service composition problem.
Antiviral agents for the treatment and chemoprophylaxis of influenza --- recommendations of the Advisory Committee on Immunization Practices (ACIP). (2011)

This report updates previous recommendations by CDC's Advisory Committee on Immunization Practices (ACIP) regarding the use of antiviral agents for the prevention and treatment of influenza (CDC. Prevention and control of influenza: recommendations of the Advisory Committee on Immunization Practices [ACIP]. MMWR 2008;57[No. RR-7]).This report contains information on treatment and chemoprophylaxis of influenza virus infection and provides a summary of the effectiveness and safety of antiviral treatment medications. Highlights include recommendations for use of 1) early antiviral treatment of suspected or confirmed influenza among persons with severe influenza (e.g., those who have severe, complicated, or progressive illness or who require hospitalization); 2) early antiviral treatment of suspected or confirmed influenza among persons at higher risk for influenza complications; and 3) either oseltamivir or zanamivir for persons with influenza caused by 2009 H1N1 virus, influenza A (H3N2) virus, or influenza B virus or when the influenza virus type or influenza A virus subtype is unknown; 4) antiviral medications among children aged <1 year; 5) local influenza testing and influenza surveillance data, when available, to help guide treatment decisions; and 6) consideration of antiviral treatment for outpatients with confirmed or suspected influenza who do not have known risk factors for severe illness, if treatment can be initiated within 48 hours of illness onset. Additional information is available from CDC's influenza website at http://www.cdc.gov/flu, including any updates or supplements to these recommendations that might be required during the 2010-11 influenza season. Health-care providers should be alert to announcements of recommendation updates and should check the CDC influenza website periodically for additional information. Recommendations related to the use of vaccines for the prevention of influenza during the 2010-11 influenza season have been published previously (CDC. Prevention and control of influenza with vaccines: recommendations of the Advisory Committee on Immunization Practices [ACIP], 2010. MMWR 2010;59[No. RR-8]).
Management of Location Based Advertisement Services using Spatial Triggers in Cellular Networks (2009)

This paper discusses the advent of new technologies which have emerged under the area of Location Based Services (LBS). An innovative implementation and approach has been presented for design of applications which are inventive and attractive towards the user. Spatial Trigger is one of the most promising additions to the LBS technologies. This paper describes ways in which mobile advertisement services can be introduced effectively in the cellular market by bringing innovation in them through effective usage of Spatial Triggers. Hence, opening new horizons to make the consumer cellular networks, commercially, more effective and informative.
Haem iron‐transport system in enterohaemorrhagic Escherichia coli O157:H7 (1997)

In this study, we identified the iron-transport systems of Escherichia coli O157:H7 strain EDL933. This strain synthesized and transported enterobactin and had a ferric citrate transport system but lacked the ability to produce or use aerobactin. It used haem and haemoglobin, but not transferrin or lactoferrin, as iron sources. We cloned the gene encoding an iron-regulated haem-transport protein and showed that this E. coli haem-utilization gene (chuA) encoded a 69 kDa outer membrane protein that was synthesized in response to iron limitation. Expression of this protein in a laboratory strain of E. coli was sufficient for utilization of haem or haemoglobin as iron sources. Mutation of the chromosomal chuA and tonB genes in E. coli O157:H7 demonstrated that the utilization of haemin and haemoglobin was ChuA- and TonB-dependent. Nucleotide sequence analysis of chuA revealed features characteristic of TonB-dependent, Fur-regulated, outer membrane iron-transport proteins. It was highly homologous to the shuA gene of Shigella dysenteriae and less closely related to hemR of Yersinia enterocolitica and hmuR of Yersinia pestis. A conserved Fur box was identified upstream of the chuA gene, and regulation by Fur was confirmed.
An expression signature of syndecan-1 (CD138), E-cadherin and c-met is associated with factors of angiogenesis and lymphangiogenesis in ductal breast carcinoma in situ (2007)

Syndecan-1, E-cadherin and c-met constitute a marker signature associated with angiogenic and lymphangiogenic factors in DCIS. This coexpression may reflect a state of parallel activation of different signal transduction pathways, promoting tumour cell proliferation and angiogenesis. Our findings have implications for future therapeutic approaches in terms of a multiple target approach, which may be useful early in breast cancer progression.
Large-Area Patterning by Vacuum-Assisted Micromolding (1999)

Rapid micropatterning of polymers on rigid and flexible substrates can be achieved by the method—vacuum-assisted micromolding in capillaries (MIMIC)—introduced here. The Figure shows an oblique-view SEM image of a single hexagonal cell of a pattern produced by vacuum-assisted MIMIC. The use of vacuum reduced the time taken to fill the pattern with UV-curable polyurethane from ∼30 min to ∼15 s.
Bone Marrow-Derived Mesenchymal Stem Cell Therapy as a Candidate Disease-Modifying Strategy in Parkinson's Disease and Multiple System Atrophy (2009)

Parkinson's disease (PD) and multiple system atrophy (MSA) are neurodegenerative diseases representative of alpha-synucleinopathies characterized pathologically by alpha-synuclein-abundant Lewy bodies and glial cytoplasmic inclusions, respectively. Embryonic stem cells, fetal mesencephalic neurons, and neural stem cells have been introduced as restorative strategies in PD animals and patients, but ethical and immunological problems as well as the serious side effects of tumorigenesis and disabling dyskinesia have limited clinical application of these stem cells. Meanwhile, cell therapy using mesenchymal stem cells (MSCs) is attractive clinically because these cells are free from ethical and immunological problems. MSCs are present in adult bone marrow and represent <0.01% of all nucleated bone marrow cells. MSCs are themselves capable of multipotency, differentiating under appropriate conditions into chondrocytes, skeletal myocytes, and neurons. According to recent studies, the neuroprotective effect of MSCs is mediated by their ability to produce various trophic factors that contribute to functional recovery, neuronal cell survival, and stimulation of endogenous regeneration and by immunoregulatory properties that not only inhibit nearly all cells participating in the immune response cell-cell-contact-dependent mechanism, but also release various soluble factors associated with immunosuppressive activity. However, the use of MSCs as neuroprotectives in PD and MSA has seldom been studied. Here we comprehensively review recent advances in the therapeutic roles of MSCs in PD and MSA, especially focusing on their neuroprotective properties and use in disease-modifying therapeutic strategies.
Monoclonal Antibodies with Various Reactivity to p58 Killer Inhibitory Receptors (1999)

Human natural killer (NK) cells have receptors that bind to HLA class I molecules. Among these receptors, p58 and p50 bind to HLA-C. P58 belongs to the killer inhibitory receptor (KIR) and p50 belongs to the killer activatory receptor (KAR). Previously, we obtained three recombinant p58 KIR or p50 KAR proteins, KAR-K1 (KIR2DS4), KIR-K6 (KIR2DL1), and KIR-K7 (KIR2DL3). In this study, we produced and characterized seven monoclonal antibodies (MAbs) to the p58 KIR and p50 KAR proteins. The MAbs were classified in three groups according to their antigen-binding specificity: 5IB103 and 26ID707 were KAR-K1-specific; A809, 190IIC311, and 197IIC611 were KIR-K7-specific; while A210 and A803g bound to all three recombinant proteins. The MAbs reactive to KIR-K7 bound to the gamma3 domain among two immunoglobulin (Ig) domains of KIR-K7. Immunofluorescence staining and flow cytometric analysis with A803g showed reactivity to about 10% of peripheral blood mononuclear cells and 35% of purified natural killer cells. Double immunofluorescence staining with A803g and anti-CD56 Ab showed that CD56 and p58 or p50 were expressed on NK cells in a mutually exclusive way. We also investigated T-cell markers in A803g+ cells. A803g+ T cells were almost CD8+ cells. MAbs produced in this study can be utilized practically in the investigation of biological characteristics of p58 KIR and p50 KAR.
Pharmacokinetics and bioavailability of the flavonol quercetin in humans. (1999)

Flavonoids are plant polyphenolic compounds present in the daily diet. Latest epidemiological studies point to a crucial role of the flavonol quercetin in the prevention of cardiovascular diseases. It is assumed that this protective effect derives from the antioxidative capacity which quercetin shows in in vitro experiments. The antiproliferative and antimutagenic activities in vitro have made it a candidate for clinical trials in cancer therapy. Quercetin is also regarded as a putative active compound in various phytopharmaceuticals. However, in vivo data on the disposition, absorption, bioavailability, and metabolism of quercetin after intravenous and oral administration in humans are scarce and contradictory. The pharmacokinetic parameters following intravenous injection were determined in two studies. The elimination half-life was reported to be 2.4 h and 0.7 h, the volume of distribution at steady-state was 92.6 l and 6.2 l, and total body clearance was 34.6 lxh(-1) and 28.1 lxh(-1), respectively. Absorption after oral administration ranged from 0 to over 50% of the dose. These inconsistencies can partly be attributed to a lack of highly sensitive and specific assay methodology. The data available so far are insufficient to clarify whether or not quercetin can be held responsible for any protective or curative effect observed after oral intake.
Recent developments in biomass pelletization – A review (2012)

The depletion of fossil fuels and the need to reduce greenhouse gas emissions has resulted in a strong growth of biomass utilization for heat and power production. Attempts to overcome the poor handling properties of biomass, i.e. its low bulk density and inhomogeneous structure, have resulted in an increasing interest in biomass densification technologies, such as pelletization and briquetting. The global pellet market has developed quickly, and strong growth is expected for the coming years. Due to an increase in demand for biomass, the traditionally used wood residues from sawmills and pulp and paper industry are not sufficient to meet future needs. An extended raw material base consisting of a broad variety of fibrous residues from agriculture and food industries, as well as thermal pre-treatment processes, provides new challenges for the pellet industry. Pellet production has been an established process for several decades, but only in the past five years has there been significant progress made to understand the key factors affecting pelletizing processes. A good understanding about the pelletizing process, especially the processing parameters and their effect on pellet formation and bonding are important for process and product optimization. The present review provides a comprehensive overview of the latest insights into the biomass pelletization processes, such as the forces involved in the pelletizing processes, modeling, bonding, and adhesive mechanisms. Furthermore, thermal pretreatment of the biomass, i.e. torrefaction and other thermal treatment to enhance the fuel properties of biomass pellets are discussed.
Cardiolipin Polyspecific Autoreactivity in Two Broadly Neutralizing HIV-1 Antibodies (2005)

The design of a human immunodeficiency virus-1 (HIV-1) immunogen that can induce broadly reactive neutralizing antibodies is a major goal of HIV-1 vaccine development. Although rare human monoclonal antibodies (mAbs) exist that broadly neutralize HIV-1, HIV-1 envelope immunogens do not induce these antibody specificities. Here we demonstrate that the two most broadly reactive HIV-1 envelope gp41 human mAbs, 2F5 and 4E10, are polyspecific autoantibodies reactive with the phospholipid cardiolipin. Thus, current HIV-1 vaccines may not induce these types of antibodies because of autoantigen mimicry of the conserved membrane-proximal epitopes of the virus. These results may have important implications for generating effective neutralizing antibody responses by using HIV-1 vaccines.
Reconstruction of glucose uptake and phosphorylation in a glucose-negative mutant of Escherichia coli by using Zymomonas mobilis genes encoding the glucose facilitator protein and glucokinase (1994)

Expression of the Zymomonas mobilis glf (glucose facilitator protein) and glk (glucokinase) genes in Escherichia coli ZSC113 (glucose negative) provided a new functional pathway for glucose uptake and phosphorylation. Both genes were essential for the restoration of growth in glucose minimal medium and for acid production on glucose-MacConkey agar plates.
Modeling of continental weathering under high-CO2atmospheres during Precambrian times (2011)

Batch experiments were conducted to simulate abiotic weathering of the continental crust under high-CO 2 atmospheric conditions during Precambrian times, i.e., corresponding to the general Archaean conditions as well as to the immediate aftermath of the Neoproterozoic Snowball Earth ice ages. Three types of rock (basalt, granodiorite and tonalite) representative of the Archaean to Proterozoic continental crust were reacted in the form of powders for 1 year at 40C with pure water under various water/rock ratios, in oxic and anoxic atmospheres containing 10% CO 2 , that is, under conditions assumed to characterize the greenhouse effect which prevailed at that time. Chemical and mineralogical data collected during the course of the experiments reflect alteration phenomena occurring in two steps: (1) rapid leaching of the fresh surfaces, probably related to the proton-donor capacity of the CO 2 and (2) a steady state reaction under near-neutral conditions. These observed dissolution rates can be satisfactorily modeled by kinetic data available in the literature. Using a 1-D weathering model reproducing the two steps, we evaluate the atmospheric CO 2 consumption rate at the Snowball Earth aftermath, focusing on the relative contribution of surface leaching versus steady state reaction. The results show that the process is dominated by surface exchange.
Microscopic observations of the different morphological changes caused by anti-bacterial peptides onKlebsiella pneumoniae and HL-60 leukemia cells (1998)

Natural anti-bacterial peptides cecropin B (CB) and its analogs cecropin B-1 (CB-1), cecropin B-2 (CB-2) and cecropin B-3 (CB-3) were prepared. The different characteristics of these peptides, with amphipathic/hydrophobic alpha-helices for CB, amphipathic/amphipathic alpha-helices for CB-1/CB-2, and hydrophobic/hydrophobic alpha-helices for CB-3, were used to study the morphological changes in the bacterial cell, Klebsiella pneumoniae and the leukemia cancer cell, HL-60, by scanning and transmission electron microscopies. The natural and analog peptides have comparable secondary structures as shown by circular dichroism measurements. This indicates that the potency of the peptides on cell membranes is dependent of the helical characteristics rather than the helical strength. The microscopic results show that the morphological changes of the cells treated with CB are distinguishably different from those treated with CB-1/CB-2, which are designed to have enhanced anti-cancer properties by having an extra amphipathic alpha-helix. The morphological differences may be due to their different modes of action on the cell membranes resulting in the different potencies with lower lethal concentration and higher concentration of 50% inhibition (IC50) of CB on bacterium and cancer cell, respectively, as compared with CB-1/:CB-2 (Chen et al. 1997. Biochim. Biophys. Acta 1336, 171-179). In contrast, CB-3 has little effect on either the bacterium or the cancer cell. These results provide microscopic evidence that different killing pathways are involved with the peptides.
Cell-free hemoglobin augments acute kidney injury during experimental sepsis (2019)

Acute kidney injury is a common complication of severe sepsis and contributes to high mortality. The molecular mechanisms of acute kidney injury during sepsis are not fully understood. Because hemoproteins, including myoglobin and hemoglobin, are known to mediate kidney injury during rhabdomyolysis, we hypothesized that cell-free hemoglobin (CFH) would exacerbate acute kidney injury during sepsis. Sepsis was induced in mice by intraperitoneal injection of cecal slurry (CS). To mimic elevated levels of CFH observed during human sepsis, mice also received a retroorbital injection of CFH or dextrose control. Four groups of mice were analyzed: sham treated (sham), CFH alone, CS alone, and CS + CFH. The addition of CFH to CS reduced 48-h survival compared with CS alone (67% vs. 97%, <i>P</i> = 0.001) and increased the severity of illness. After 24 and 48 h, CS + CFH mice had a reduced glomerular filtration rate from baseline, whereas sham, CFH, and CS mice maintained baseline glomerular filtration rate. Biomarkers of acute kidney injury, neutrophil gelatinase-associated lipocalin (NGAL) and kidney injury molecule-1 (KIM-1), were markedly elevated in CS+CFH compared with CS (8-fold for NGAL and 2.4-fold for KIM-1, <i>P</i> < 0.002 for each) after 48 h. Histological examination showed a trend toward increased tubular injury in CS + CFH-exposed kidneys compared with CS-exposed kidneys. However, there were similar levels of renal oxidative injury and apoptosis in the CS + CFH group compared with the CS group. Kidney levels of multiple proinflammatory cytokines were similar between CS and CS + CFH groups. Human renal tubule cells (HK-2) exposed to CFH demonstrated increased cytotoxicity. Together, these results show that CFH exacerbates acute kidney injury in a mouse model of experimental sepsis, potentially through increased renal tubular injury.
Biology of Gastrointestinal Stromal Tumors: KIT Mutations and Beyond (2004)

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors in the digestive tract. Aspects of the morphology and immunophenotype in GISTs resemble those in the interstitial cells of Cajal (ICC), which are a specialized cell type responsible for coordinating peristaltic activity throughout the gastrointestinal tract. Therefore, it is possible that GISTs result from transformation of nonneoplastic progenitor cells that would normally differentiate towards an ICC endpoint. Activation of the KIT receptor tyrosine kinase is required for differentiation and proliferation of nonneoplastic ICC, and oncogenic KIT mutations are a crucial event in the development of most GISTs. These mutations can involve either the extracellular or intracellular domains of the KIT receptor, giving rise to conformational changes that enable constitutive, ligand-independent, activation of the KIT protein. Oncogenic KIT activation leads to phosphorylation of various substrate proteins and, in turn, to activation of signal transduction cascades regulating cell proliferation, apoptosis, chemotaxis, and adhesion. Recently, a small molecule tyrosine kinase inhibitor (STI571, imatinib mesylate, Gleevec) directed against the enzymatic (kinase) domain of the KIT protein was found to produce dramatic clinical responses as monotherapy for metastatic GISTs. This review focuses on the biological and molecular genetic principles of GISTs, and particularly the role of mutant KIT as a therapeutic target.
Functional Interaction between Angiotensin II Receptor Type 1 and Chemokine (C-C Motif) Receptor 2 with Implications for Chronic Kidney Disease (2015)

Understanding functional interactions between G protein-coupled receptors is of great physiological and pathophysiological importance. Heteromerization provides one important potential mechanism for such interaction between different signalling pathways via macromolecular complex formation. Previous studies suggested a functional interplay between angiotensin II receptor type 1 (AT 1 ) and Chemokine (C-C motif) Receptor 2 (CCR2). However the molecular mechanisms are not understood. We investigated AT 1 -CCR2 functional interaction in vitro using bioluminescence resonance energy transfer in HEK293 cells and in vivo using subtotal-nephrectomized rats as a well-established model for chronic kidney disease. Our data revealed functional heteromers of these receptors resulting in CCR2-Gi1 coupling being sensitive to AT 1 activation, as well as apparent enhanced -arrestin2 recruitment with agonist co-stimulation that is synergistically reversed by combined antagonist treatment. Moreover, we present in vivo findings where combined treatment with AT 1 -and CCR2-selective inhibitors was synergistically beneficial in terms of decreasing proteinuria, reducing podocyte loss and preventing renal injury independent of blood pressure in the subtotal-nephrectomized rat model. Our findings further support a role for G protein-coupled receptor functional heteromerization in pathophysiology and provide insights into previous observations indicating the importance of AT 1 -CCR2 functional interaction in inflammation, renal and hypertensive disorders.