gebhart/patrepeval huggingface dataset:
BET Protein Function Is Required for Inflammation: Brd2 Genetic Disruption and BET Inhibitor JQ1 Impair Mouse Macrophage Inflammatory Responses (2013)

Histone acetylation regulates activation and repression of multiple inflammatory genes known to play critical roles in chronic inflammatory diseases. However, proteins responsible for translating the histone acetylation code into an orchestrated proinflammatory cytokine response remain poorly characterized. Bromodomain and extraterminal (BET) proteins are "readers" of histone acetylation marks, with demonstrated roles in gene transcription, but the ability of BET proteins to coordinate the response of inflammatory cytokine genes through translation of histone marks is unknown. We hypothesize that members of the BET family of dual bromodomain-containing transcriptional regulators directly control inflammatory genes. We examined the genetic model of brd2 lo mice, a BET protein hypomorph, to show that Brd2 is essential for proinflammatory cytokine production in macrophages. Studies that use small interfering RNA knockdown and a small-molecule inhibitor of BET protein binding, JQ1, independently demonstrate BET proteins are critical for macrophage inflammatory responses. Furthermore, we show that Brd2 and Brd4 physically associate with the promoters of inflammatory cytokine genes in macrophages. This association is absent in the presence of BET inhibition by JQ1. Finally, we demonstrate that JQ1 ablates cytokine production in vitro and blunts the "cytokine storm" in endotoxemic mice by reducing levels of IL-6 and TNF-α while rescuing mice from LPS-induced death. We propose that targeting BET proteins with small-molecule inhibitors will benefit hyperinflammatory conditions associated with high levels of cytokine production.
A zinc-dependent adhesion module is responsible for intercellular adhesion in staphylococcal biofilms (2008)

Hospital-acquired bacterial infections are an increasingly important cause of morbidity and mortality worldwide. Staphylococcal species are responsible for the majority of hospital-acquired infections, which are often complicated by the ability of staphylococci to grow as biofilms. Biofilm formation by Staphylococcus epidermidis and Staphylococcus aureus requires cell-surface proteins (Aap and SasG) containing sequence repeats known as G5 domains; however, the precise role of these proteins in biofilm formation is unclear. We show here, using analytical ultracentrifugation (AUC) and circular dichroism (CD), that G5 domains from Aap are zinc (Zn(2+))-dependent adhesion modules analogous to mammalian cadherin domains. The G5 domain dimerizes in the presence of Zn(2+), incorporating 2-3 Zn(2+) ions in the dimer interface. Tandem G5 domains associate in a modular fashion, suggesting a "zinc zipper" mechanism for G5 domain-based intercellular adhesion in staphylococcal biofilms. We demonstrate, using a biofilm plate assay, that Zn(2+) chelation specifically prevents biofilm formation by S. epidermidis and methicillin-resistant S. aureus (MRSA). Furthermore, individual soluble G5 domains inhibit biofilm formation in a dose-dependent manner. Thus, the complex three-dimensional architecture of staphylococcal biofilms results from the self-association of a single type of protein domain. Surface proteins with tandem G5 domains are also found in other bacterial species, suggesting that this mechanism for intercellular adhesion in biofilms may be conserved among staphylococci and other Gram-positive bacteria. Zn(2+) chelation represents a potential therapeutic approach for combating biofilm growth in a wide range of bacterial biofilm-related infections.
Targeting monocyte chemoattractant protein-1 signalling in disease (2003)

Monocyte chemoattractant protein-1 (MCP-1) has been implicated in many inflammatory and autoimmune diseases. The G-protein-coupled receptor CCR-2B is probably the most important MCP-1 receptor in vivo, and loss of MCP-1 effector function alone is sufficient to impair monocytic trafficking in inflammation models. MCP-1 signalling appears to be a relevant target, especially in rheumatoid arthritis (RA). In RA patients, MCP-1 is produced by synovial cells and infiltrating monocytes, plasma MCP-1 concentrations correlate with swollen joint count, and elevated serum MCP-1 concentrations were found in juvenile RA in patients with active disease. Modulation of MCP-1 signalling in experimental RA showed beneficial effects on inflammation and joint destruction. With respect to chronic neuroinflammation, a critical role for MCP-1 has been established in animal models for multiple sclerosis. In acute neuroinflammation, experimental evidence for a detrimental role of MCP-1 in stroke and excitotoxic injury has been found. Several selective small molecular weight CCR-2B antagonists and MCP-1-blocking antibodies have been described. The proof for the validity of targeting MCP-1 signalling in disease, however, has yet to be established in clinical trials.
Subforms and In Vitro Reconstitution of the NAD-Reducing Hydrogenase of Alcaligenes eutrophus (1998)

The cytoplasmic, NAD-reducing hydrogenase (SH) of Alcaligenes eutrophus H16 is a heterotetrameric enzyme which contains several cofactors and undergoes a complex maturation during biogenesis. HoxH is the Ni-carrying subunit, and together with HoxY it forms the hydrogenase dimer. HoxF and HoxU represent the flavin-containing diaphorase moiety, which is closely related to NADH:ubiquinone oxidoreductase and mediates NADH oxidation. A variety of mutations were introduced into the four SH structural genes to obtain mutant enzymes composed of monomeric and dimeric forms. A deletion removing most of hoxF, hoxU, and hoxY led to the expression of a HoxH monomer derivative which was proteolytically processed at the C terminus like the wild-type polypeptide. While the hydrogenase dimer, produced by a strain deleted of hoxF and hoxU, displayed H2-dependent dye-reducing activity, the monomeric form did not mediate the activation of H2, although nickel was incorporated into HoxH. Deletion of hoxH and hoxY led to the production of HoxFU dimers which displayed NADH:oxidoreductase activity. Mixing the hydrogenase and the diaphorase moieties in vitro reconstituted the structure and catalytic function of the SH holoenzyme.
Long-term in vitro culture of murine mast cells. III. Discrimination of mast cells growth factor and granulocyte-CSF. (1982)

Long-term in vitro growth of murine mast cells was dependent on the presence of a mast cell growth factor (MCGF) present in media conditioned by mitogen-activated splenic leukocytes or by various murine leukemic cell lines. MCGF shared a number of properties with granulocyte colony-stimulating factor (G-CSF). Both factors were present in media conditioned by the myelomonocytic leukemic WEHI-3 and the T cell lymphoma, LBRM-33 cell lines. They were relatively sensitive to trypsin treatment, and were resistant to boiling temperature. NZB mice that failed to respond to WEHI-3-derived G-CSF also failed to respond to MCGF. MCGF differed from G-CSF, however, in sensitivity to neuraminidase and lactoferrin, an inhibitor of macrophage CSF production, suppressed G-CSF production by WEHI-3 cells without affecting MCGF production. Furthermore, peritoneal cells produced G-CSF but not MCGF when stimulated with lipopolysaccharide. In vitro production of MCGF by normal spleen cells required the presence of T lymphocytes and is relatively macrophage-independent. The role of T cells in the maturation and growth of mast cells and the physiologic function of MCGF are discussed.
Facilitating Adolescents' Constructive Use of Time in One-Parent Families (2001)

Abstract Many adolescents in 1-parent families experience positive conditions for development. In this article, we use experience sampling data from 101 mother-only families to evaluate factors associated with adolescents' devotion of time to constructive activities, such as reading, sports, creative, and religious activities. Findings show that a set of family management variables, including firm discipline, family routines, and mothers' amount of time spent in child-supportive activities, were associated with adolescents' constructive use of free time. Adolescents' constructive time was also correlated with mothers' time spent reading, participating in religious activities, and watching TV; and with mothers' well-being and cooperation with the nonresident father. These results demonstrate how many families adjust positively to the situation of single parenthood.
Evaluation of elastic modulus of Li<sub>2</sub>S–P<sub>2</sub>S<sub>5</sub> glassy solid electrolyte by ultrasonic sound velocity measurement and compression test (2013)

Elastic modulus is an important factor of solid electrolytes for an all-solid-state battery as a next-generation battery. In this study, Young’s moduli of dense pellets of the Li2S–P2S5 glass solid electrolytes prepared by room temperature pressing and hot pressing were investigated. The Young’s moduli of Li2S–P2S5 hot-pressed pellets measured by ultrasonic sound velocity measurements were 18–25 GPa and those of cold-pressed pellets were about 14–17 GPa. The compression test was also done to determine Young’s modulus. The Young’s modulus of Li2S–P2S5 glasses increased with increasing the Li2S content in both hot press and cold press pellets. The Young’s moduli were lower than those of oxide based solid electrolytes.
Three-Dimensional Culture of Mouse Renal Carcinoma Cells in Agarose Macrobeads Selects for a Subpopulation of Cells with Cancer Stem Cell or Cancer Progenitor Properties (2011)

The culture of tumor cell lines in three-dimensional scaffolds is considered to more closely replicate the in vivo tumor microenvironment than the standard method of two-dimensional cell culture. We hypothesized that our method of encapsulating and maintaining viable and functional pancreatic islets in agarose-agarose macrobeads (diameter 6-8 mm) might provide a novel method for the culture of tumor cell lines. In this report we describe and characterize tumor colonies that form within macrobeads seeded with mouse renal adenocarcinoma cells. Approximately 1% of seeded tumor cells survive in the macrobead and over several months form discrete elliptical colonies appearing as tumor cell niches with increasing metabolic activity in parallel to colony size. The tumor colonies demonstrate ongoing cell turnover as shown by BrdU incorporation and activated caspase-3 and TUNEL staining. Genes upregulated in the tumor colonies of the macrobead are likely adaptations to this novel environment, as well as an amplification of G(1)/S cell-cycle checkpoints. The data presented, including SCA-1 and Oct4 positivity and the upregulation of stem cell-like genes such as those associated with the Wnt pathway, support the notion that the macrobead selects for a subpopulation of cells with cancer stem cell or cancer progenitor properties.
Adipose conversion of 3T3 cells depends on a serum factor. (1978)

The adipose conversion of 3T3-F442A cells depends on an adipogenic factor in serum. In the presence of this factor, cells grown to confluence become spherical, greatly increase the activity of their lipogenic enzymes, and accumulate triglyceride. In the absence of the adipogenic factor, the cells grow normally, but when they reach confluence they do not become spherical, do not accumulate triglyceride, and do not undergo any increase in activity of lipogenic enzymes. In cattle there is a great deal more of the adipogenic factor in the serum before birth than in the serum of grown animals. The nature of the adipogenic factor suggests that it may play an important role in the development of adipose tissue.
Combustion synthesis of silicon nanopowders (2010)

Silicon nanopowders with high surface area were synthesized by reduction-type combustion reaction between silicon oxide and magnesium. Main advantages of the method are its simplicity and uniqueness of product characteristics. Microstructural analysis of the powders synthesized from different raw materials allowed us to suggest the mechanism of structural transformations taking place in the combustion wave. Based on this mechanism, an effective approach to controlling the microstructure of final product was proposed.
Macrophage CD74 contributes to MIF-induced pulmonary inflammation (2009)

MIF-induced neutrophil accumulation in the alveolar space results from interaction with CD74 expressed on the surface of alveolar macrophage cells. This interaction induces p44/p42 MAPK activation and chemokine release. The data suggest that MIF and its receptor, CD74, may be useful targets to reduce neutrophilic lung inflammation, and acute lung injury.
Atomically Precise Growth of Catalytically Active Cobalt Sulfide on Flat Surfaces and within a Metal–Organic Framework via Atomic Layer Deposition (2015)

Atomic layer deposition (ALD) has been employed as a new synthetic route to thin films of cobalt sulfide on silicon and fluorine-doped tin oxide platforms. The self-limiting nature of the stepwise synthesis is established through growth rate studies at different pulse times and temperatures. Additionally, characterization of the materials by X-ray diffraction and X-ray photoelectron spectroscopy indicates that the crystalline phase of these films has the composition Co9S8. The nodes of the metal-organic framework (MOF) NU-1000 were then selectively functionalized with cobalt sulfide via ALD in MOFs (AIM). Spectroscopic techniques confirm uniform deposition of cobalt sulfide throughout the crystallites, with no loss in crystallinity or porosity. The resulting material, CoS-AIM, is catalytically active for selective hydrogenation of m-nitrophenol to m-aminophenol, and outperforms the analogous oxide AIM material (CoO-AIM) as well as an amorphous CoSx reference material. These results reveal AIM to be an effective method of incorporating high surface area and catalytically active cobalt sulfide in metal-organic frameworks.
Pancreatic elastase IIIA and its variants are expressed in pancreatic carcinoma cells. (2002)

Ninety percent of pancreatic cancers are classified as ductal adenocarcinoma and are not known to secrete pancreatic elastases of the acinar enzymes. In the present study, we investigated the expression and the changes in elastase genes expressed in pancreatic ductal carcinoma cells. The expression of elastase gene family molecules in pancreatic cancer cells was analyzed by reverse transcription-polymerase chain reaction (RT-PCR) method using primer sets for conservative active domains among pancreatic elastases (PEs) and neutrophil elastase (NE). The PCR products were subcloned, sequenced and analyzed. Three distinct products were isolated in pancreatic carcinoma cells using the RT-PCR analyses. The sequencing revealed that one was identical with the PE IIIA isoform, and the remaining two were alternatively splicing forms of the PE IIIA. Four of five pancreatic cell lines expressed these splicing variants in a cell-dependent manner. The present study is the first report to demonstrate the expression of PE IIIA and its splicing variants in pancreatic carcinoma cells might represent another infiltrative feature of the pancreatic ductal cell carcinoma.
ChemInform Abstract: SYNTHESIS OF 4‐SUBSTITUTED β‐CARBOLINES (1983)

Abstract Es wird auf verschiedenen Wegen eine Reihe von Indol‐Derivaten (I) hergestellt, mit Aldiminen (II) und Nitroessigsäureethylester (IV) kondensiert und zu Tryptophan‐Derivaten (VI) reduziert.
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria (2008)

Bioinformatics searches of eubacterial genomes have yielded many riboswitch candidates where the identity of the ligand is not immediately obvious on examination of associated genes. One of these motifs is found exclusively in the family Streptococcaceae within the 5' untranslated regions (UTRs) of genes encoding the hypothetical membrane protein classified as COG4708 or DUF988. While the function of this protein class is unproven, a riboswitch binding the queuosine biosynthetic intermediate pre-queuosine(1) (preQ(1)) has been identified in the 5' UTR of homologous genes in many Firmicute species of bacteria outside of Streptococcaceae. Here we show that a representative of the COG4708 RNA motif from Streptococcus pneumoniae R6 also binds preQ(1). Furthermore, representatives of this RNA have structural and molecular recognition characteristics that are distinct from those of the previously described preQ(1) riboswitch class. PreQ(1) is the second metabolite for which two or more distinct classes of natural aptamers exist, indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known. Additionally, the association of preQ(1) binding RNAs with most genes encoding proteins classified as COG4708 strongly suggests that these proteins function as transporters for preQ(1) or another queuosine biosynthetic intermediate.
Upper airway {middle dot} 1: Allergic rhinitis and asthma: united disease through epithelial cells (2009)

The relationship between allergic rhinitis and asthma is now established, and most of the clinical, epidemiological and biological data recommend integrated management. Epithelial cells represent the first barrier of the upper and lower respiratory tracts and thus are logical targets for a comprehensive integrated therapeutic approach. This review discusses rhinosinusitis as a co-morbid condition, a precipitating or triggering condition, and an epiphenomenon as an integrated part of the disease. A better understanding and a more pragmatic method of diagnosis and management is needed using cost-effective long-term strategies.
Targeted delivery of interferon-alpha via fusion to anti-CD20 results in potent antitumor activity against B-cell lymphoma (2010)

The anti-CD20 antibody rituximab has substantially improved outcomes in patients with B-cell non-Hodgkin lymphomas. However, many patients are not cured by rituximab-based therapies, and overcoming de novo or acquired rituximab resistance remains an important challenge to successful treatment of B-cell malignancies. Interferon-alpha (IFNalpha) has potent immunostimulatory properties and antiproliferative effects against some B-cell cancers, but its clinical utility is limited by systemic toxicity. To improve the efficacy of CD20-targeted therapy, we constructed fusion proteins consisting of anti-CD20 and murine or human IFNalpha. Fusion proteins had reduced IFNalpha activity in vitro compared with native IFNalpha, but CD20 targeting permitted efficient antiproliferative and proapoptotic effects against an aggressive rituximab-insensitive human CD20(+) murine lymphoma (38C13-huCD20) and a human B-cell lymphoma (Daudi). In vivo efficacy was demonstrated against established 38C13-huCD20 grown in syngeneic immunocompetent mice and large, established Daudi xenografts grown in nude mice. Optimal tumor eradication required CD20 targeting, with 87% of mice cured of rituximab-insensitive tumors. Gene knockdown studies revealed that tumor eradication required expression of type I IFN receptors on the tumor cell surface. Targeting type I IFNs to sites of B-cell lymphoma by fusion to anti-CD20 antibodies represents a potentially useful strategy for treatment of B-cell malignancies.
Dipolar interactions in arrays of nickel nanowires studied by ferromagnetic resonance (2001)

Using a planar microstrip transmission line, the dipolar interactions in electrodeposited Ni nanowires arrays are characterized as a function of the membrane porosity (4% to 38%) and the wire diameter (56 to 250 nm). The dipolar interactions between the wires can be modeled in a mean-field approach as an effective uniaxial anisotropy field oriented perpendicular to the wire axis and proportional to the membrane porosity. The dipolar interaction field opposes the self-demagnetization field of an isolated single wire which keeps the magnetization parallel to the wire axis. An increase in the porosity therefore induces a switching of the effective anisotropy easy axis from parallel to perpendicular to the wire axis above a critical porosity of 35-38% independent of the wire diameter.
Drug Induced Weight Gain, an Impediment to Successful Pharmacotherapy: Focus on Antipsychotics (2004)

The antipsychotic drugs (APDs) are fundamental tools in current psychiatric practice. A new generation of agents, the atypical APDs, represents an important progress in the treatment of psychotic disorders. Unfortunately, some of them induce excessive body weight gain (BWG), obesity, hyperglycemia and dyslipidemia in the following order: clozapine approximately equal to olanzapine > quetiapine > risperidone > ziprasidone = aripiprazole. Appetite stimulation is probably the main mechanism of BWG and this is strongly correlated with the APD affinity for H1 (histaminergic) and alpha1 (adrenergic) receptors. A composed ratio of the APD affinity for diverse neurotransmitters involved in food intake (FI) regulation correlates with BWG as well. Endocrine/metabolic mechanisms, such as the activation of the hypothalamus-pituitary-adrenal axis, changes in insulin sensitivity (by conventional and atypical agents), hyperprolactinemia and gonadal dysfunction (by conventional APDs and risperidone) may also be involved. Importantly, patients with schizophrenia may have a genetically-based predisposition to appetite dysregulation, insulin resistance and endocrine imbalance involving gonadal steroids. Excessive BWG must be prevented or attenuated by proper drug selection, combining or switching agents, nutritional assistance and physical exercise. Amantadine. metformin and reboxetine proved to significantly lessen APD-induced BWG. Notwithstanding this, novel strategies are necessary to treat this side effect in a clinical population particularly prone to poor compliance and under a high risk of negative drug interaction.
Islet amyloid polypeptide: pinpointing amino acid residues linked to amyloid fibril formation. (1990)

Islet amyloid polypeptide (IAPP), a putative polypeptide hormone, is a product of pancreatic beta-cells and the major constituent of the amyloid deposits seen mainly in islets of type 2 diabetic humans and diabetic cats. The connection between IAPP amyloid formation and diabetes is unknown, but a limited segment of the IAPP molecule, positions 20-29, seems responsible for the aggregation to fibrils. Differences in the amino acid sequence of this region probably determine whether or not islet amyloid can develop in a particular species. Amyloid fibril formation can be mimicked in vitro with the aid of synthetic peptides. With this technique we show that peptides corresponding to IAPP positions 20-29 of human and cat, species that develop IAPP-derived islet amyloid, form amyloid-like fibrils in vitro. The corresponding IAPP segment from three rodent species that do not develop IAPP-derived amyloid did not give rise to fibrils. Substitution of the human IAPP-(20-29) decapeptide with one or two amino acid residues from species without islet amyloid generally reduced the capacity to form fibrils. We conclude that the sequence Ala-Ile-Leu-Ser-Ser, corresponding to positions 25-29 of human IAPP, is strongly amyloidogenic and that a proline-for-serine substitution in position 28, as in several rodents, almost completely inhibits formation of amyloid fibrils.
Failure of the competitive N-methyl-d-aspartate antagonist Selfotel (CGS 19755) in the treatment of severe head injury: results of two Phase III clinical trials (1999)

Subsequently, more complete data analysis revealed no statistically significant difference in mortality rates in all cases between the two treatment groups in the head injury trials. In this report the authors examine the studies in detail and discuss the potential application of the data to future trial designs.