gebhart/patrepeval huggingface dataset:
mTOR Kinase Inhibitor AZD8055 Enhances the Immunotherapeutic Activity of an Agonist CD40 Antibody in Cancer Treatment (2011)

mTOR is a central mediator of cancer cell growth, but it also directs immune cell differentiation and function. On this basis, we had explored the hypothesis that mTOR inhibition can enhance cancer immunotherapy. Here, we report that a combination of αCD40 agonistic antibody and the ATP-competitive mTOR kinase inhibitory drug AZD8055 elicited synergistic antitumor responses in a model of metastatic renal cell carcinoma. In contrast to the well-established mTOR inhibitor rapamycin, AZD8055 increased the infiltration, activation, and proliferation of CD8(+) T cells and natural killer cells in liver metastatic foci when combined with the CD40 agonist. AZD8055/αCD40-treated mice also display an increased incidence of matured macrophages and dendritic cells compared with that achieved in mice by αCD40 or AZD8055 treatment alone. We found that the combination treatment also increased macrophage production of TNFα, which played an indispensable role in activation of the observed antitumor immune response. Levels of Th1 cytokines, including interleukin 12, IFN-γ, TNFα, and the Th1-associated chemokines RANTES, MIG, and IP-10 were each elevated significantly in the livers of mice treated with the combinatorial therapy versus individual treatments. Notably, the AZD8055/αCD40-induced antitumor response was abolished in IFN-γ(-/-) and CD40(-/-) mice, establishing the reliance of the combination therapy on host IFN-γ and CD40 expression. Our findings offer a preclinical proof of concept that, unlike rapamycin, the ATP-competitive mTOR kinase inhibitor AZD8055 can contribute with αCD40 treatment to trigger a restructuring of the tumor immune microenvironment to trigger regressions of an established metastatic cancer.
Making journals (2009)

Creating your own journals and diaries encourages your group to think about their environment and the day-to-day events in their lives. The following activities also help the children to discover the purpose of journals and diaries and explore different ways of using them.
The brain tissue response to implanted silicon microelectrode arrays is increased when the device is tethered to the skull (2007)

The influence of tethering silicon microelectrode arrays on the cortical brain tissue reaction was compared with that of untethered implants placed in the same location by identical means using immunoflourescent methods and cell type specific markers over indwelling periods of 1-4 weeks. Compared with untethered, freely floating implants, tethered microelectrodes elicited significantly greater reactivity to antibodies against ED1 and GFAP over time. Regardless of implantation method or indwelling time, retrieved microelectrodes contained a layer of attached macrophages identified by positive immunoreactivity against ED1. In the tethered condition and in cases where the tissue surrounding untethered implants had the highest levels of ED1+ and GFAP+ immunoreactivity, the neuronal markers for neurofilament 160 and NeuN were reduced. Although the precise mechanisms are unclear, the present study indicates that simply tethering silicon microelectrode arrays to the skull increases the cortical brain tissue response in the recording zone immediately surrounding the microelectrode array, which signals the importance of identifying this important variable when evaluating the tissue response of different device designs, and suggests that untethered or wireless devices may elicit less of a foreign body response.
Role of Genotype in the Cycle of Violence in Maltreated Children (2002)

We studied a large sample of male children from birth to adulthood to determine why some children who are maltreated grow up to develop antisocial behavior, whereas others do not. A functional polymorphism in the gene encoding the neurotransmitter-metabolizing enzyme monoamine oxidase A (MAOA) was found to moderate the effect of maltreatment. Maltreated children with a genotype conferring high levels of MAOA expression were less likely to develop antisocial problems. These findings may partly explain why not all victims of maltreatment grow up to victimize others, and they provide epidemiological evidence that genotypes can moderate children's sensitivity to environmental insults.
Complex transgene locus structures implicate multiple mechanisms for plant transgene rearrangement (2002)

To more fully characterize the internal structure of transgene loci and to gain further understanding of mechanisms of transgene locus formation, we sequenced more than 160 kb of complex transgene loci in two unrelated transgenic oat (Avena sativa L.) lines transformed using microprojectile bombardment. The transgene locus sequences from both lines exhibited extreme scrambling of non-contiguous transgene and genomic fragments recombined via illegitimate recombination. A perfect direct repeat of the delivered DNA, and inverted and imperfect direct repeats were detected in the same transgene locus indicating that homologous recombination and synthesis-dependent mechanism(s), respectively, were also involved in transgene locus rearrangement. The most unexpected result was the small size of the fragments of delivered and genomic DNA incorporated into the transgene loci via illegitimate recombination; 50 of the 82 delivered DNA fragments were shorter than 200 bp. Eleven transgene and genomic fragments were shorter than the DNA lengths required for Ku-mediated non-homologous end joining. Detection of these small fragments provided evidence that illegitimate recombination was most likely mediated by a synthesis-dependent strand-annealing mechanism that resulted in transgene scrambling. Taken together, these results indicate that transgene locus formation involves the concerted action of several DNA break-repair mechanisms.
Targeting distinct tumor-infiltrating myeloid cells by inhibiting CSF-1 receptor: combating tumor evasion of antiangiogenic therapy (2009)

Tumor-infiltrating myeloid cells (TIMs) support tumor growth by promoting angiogenesis and suppressing antitumor immune responses. CSF-1 receptor (CSF1R) signaling is important for the recruitment of CD11b(+)F4/80(+) tumor-associated macrophages (TAMs) and contributes to myeloid cell-mediated angiogenesis. However, the impact of the CSF1R signaling pathway on other TIM subsets, including CD11b(+)Gr-1(+) myeloid-derived suppressor cells (MDSCs), is unknown. Tumor-infiltrating MDSCs have also been shown to contribute to tumor angiogenesis and have recently been implicated in tumor resistance to antiangiogenic therapy, yet their precise involvement in these processes is not well understood. Here, we use the selective pharmacologic inhibitor of CSF1R signaling, GW2580, to demonstrate that CSF-1 regulates the tumor recruitment of CD11b(+)Gr-1(lo)Ly6C(hi) mononuclear MDSCs. Targeting these TIM subsets inhibits tumor angiogenesis associated with reduced expression of proangiogenic and immunosuppressive genes. Combination therapy using GW2580 with an anti-VEGFR-2 antibody synergistically suppresses tumor growth and severely impairs tumor angiogenesis along with reverting at least one TIM-mediated antiangiogenic compensatory mechanism involving MMP-9. These data highlight the importance of CSF1R signaling in the recruitment and function of distinct TIM subsets, including MDSCs, and validate the benefits of targeting CSF1R signaling in combination with antiangiogenic drugs for the treatment of solid cancers.
The effect of islet amyloid polypeptide (amylin) and calcitonin gene-related peptide on glucose removal in the anaesthetized rat and on insulin secretion from rat pancreatic isletsin vitro (1990)

The effect of intravenous infusion of islet amyloid polypeptide (IAPP/amylin) and calcitonin gene-related peptide (CGRP) on blood glucose and plasma insulin in the basal and glucose-stimulated state was investigated in the anaesthetized rat. Both peptides had no effect on basal blood glucose or plasma insulin but following an intravenous bolus of glucose, CGRP-treated rats were hyperglycaemic and hyperinsulinaemic compared with control animals which were similar to IAPP-treated rats. IAPP had no effect on glucose-stimulated islet insulin secretion. These results suggest that CGRP, but not IAPP, alters glucose removal in vivo.
Monoclonal Antibody Expression in Mammalian Cells (2012)

In the past two decades, the production levels for monoclonal antibodies in mammalian expression systems have improved dramatically. Single cell productivity for monoclonal antibodies has increased 20-50 fold due to the improvements in expression hosts, expression vectors, cell culture media, and production processes. However, most of these improvements are proprietary to large pharmaceutical/biotech companies and involve large steel-tank bioreactors. Therefore, these processes are difficult for small companies and academic labs to reproduce. Transient expression in mammalian cells has recently been used very widely for monoclonal antibody expression. Cell line and expression vector engineering increased expression levels to several hundred milligrams per liter. The availability of highly effective transfection reagents and disposable bioreactors make the transient expression process an efficient and cost-effective way to make recombinant antibodies in large quantity. Here, we describe the protocols for small- to mid-scale transient expression of monoclonal antibodies in shake-flasks and for large-scale production in WAVE bioreactors.
Prevalence of Dry Eye Among the Elderly (1997)

Symptoms and signs of dry eye are common among the elderly but were not associated with age, race, or sex in this population-based sample of elderly Americans. Extrapolating to the United States population aged 65 to 84 years, the study yields an estimate of 4.3 million who experience symptoms of ocular irritation often or all the time.
An alternative pathway of vitamin D2 metabolism (2006)

We report an alternative, hydroxylating pathway for the metabolism of vitamin D2 in a cytochrome P450 side chain cleavage (P450scc; CYP11A1) reconstituted system. NMR analyses identified solely 20-hydroxyvitamin D2 and 17,20-dihydroxyvitamin D2 derivatives. 20-Hydroxyvitamin D2 was produced at a rate of 0.34 mol x min(-1) x mol(-1) P450scc, and 17,20-dihydroxyvitamin D2 was produced at a rate of 0.13 mol x min(-1) x mol(-1). In adrenal mitochondria, vitamin D2 was metabolized to six monohydroxy products. Nevertheless, aminoglutethimide (a P450scc inhibitor) inhibited this adrenal metabolite formation. Initial testing of metabolites for biological activity showed that, similar to vitamin D2, 20-hydroxyvitamin D2 and 17,20-dihydroxyvitamin D2 inhibited DNA synthesis in human epidermal HaCaT keratinocytes, although to a greater degree. 17,20-Dihydroxyvitamin D2 stimulated transcriptional activity of the involucrin promoter, again to a significantly greater extent than vitamin D2, while the effect of 20-hydroxyvitamin D2 was statistically insignificant. Thus, P450scc can metabolize vitamin D2 to generate novel products, with intrinsic biological activity (at least in keratinocytes).
PREPARATION OF 2-SUBSTITUTED OXAZOLES (2002)

ABSTRACT A simple and economical method for 2-substituted oxazole synthesis and its scope are described. ACKNOWLEDGMENTS We thank Dr. Kumar Gadamasetti for technical assistance with the preparation of substrates 3f and 3i.
Dietary fat intake and the risk of incident dementia in the Rotterdam study (1997)

A high intake of saturated fat and cholesterol and a low intake of polyunsaturated fatty acids have been related to an increased risk of cardiovascular disease. Cardiovascular disease has been associated with dementia. We investigated the association between fat intake and incident dementia among participants, age 55 years or older, from the population-based prospective Rotterdam Study. Food intake of 5,386 nondemented participants was assessed at baseline with a semiquantitative food-frequency questionnaire. At baseline and after an average of 2.1 years of follow-up, we screened for dementia with a three-step protocol that included a clinical examination. The risk of dementia at follow-up (RR [95% CI]) was assessed with logistic regression. After adjustment for age, sex, education, and energy intake, high intakes of the following nutrients were associated with an increased risk of dementia: total fat (RR = 2.4 [1.1-5.2]), saturated fat (RR = 1.9 [0.9-4.0]), and cholesterol (RR = 1.7 [0.9-3.2]). Dementia with a vascular component was most strongly related to total fat and saturated fat. Fish consumption, an important source of n-3 polyunsaturated fatty acids, was inversely related to incident dementia (RR = 0.4 [0.2-0.91), and in particular to Alzheimer's disease (RR = 0.3 [0.1-0.9]). This study suggests that a high saturated fat and cholesterol intake increases the risk of dementia, whereas fish consumption may decrease this risk.
Astrocyte activation in vivo during graded photic stimulation (2007)

Astrocytes have important roles in control of extracellular environment, de novo synthesis of neurotransmitters, and regulation of neurotransmission and blood flow. All of these functions require energy, suggesting that astrocytic metabolism should rise and fall with changes in neuronal activity and that brain imaging can be used to visualize and quantify astrocytic activation in vivo. A unilateral photic stimulation paradigm was used to test the hypothesis that graded sensory stimuli cause progressive increases in the uptake coefficient of [2-(14)C]acetate, a substrate preferentially oxidized by astrocytes. The acetate uptake coefficient fell in deafferented visual structures and it rose in intact tissue during photic stimulation of conscious rats; the increase was highest in structures with monosynaptic input from the eye and was much smaller in magnitude than the change in glucose utilization (CMR(glc)) by all cells. The acetate uptake coefficient was not proportional to stimulus rate and did not correlate with CMR(glc) in resting or activated structures. Simulation studies support the conclusions that acetate uptake coefficients represent mainly metabolism and respond to changes in metabolism rate, with a lower response at high rates. A model portraying regulation of acetate oxidation illustrates complex relationships among functional activation, cation levels, and astrocytic metabolism.
Bausteine von Oligosacchariden, CIII. Synthese von modifizierten Derivaten des Disaccharides β‐D‐Gal‐(1 → 3)‐α‐D‐GalNAc zur Untersuchung der Substratspezifität der Core‐2‐β6‐GlcNAc‐Transferase und α‐3‐Sialyltransferase der Biosynthese von O‐Glycoproteinen (1992)

Building Units of Oligosaccharides, CIII. — Synthesis of Modified Derivatives of the Disaccharide β‐ D ‐Gal‐(→3)‐α‐ D ‐GalNAc for the Examination of Substrate Specificities of Core 2‐β6‐GlcNAc‐Transferase and α‐3‐Sialyltransferase Involved in the Biosynthesis of O ‐Glycoproteins Derivatives of benzyl β‐ D ‐galactopyranosyl‐(1→3)‐2‐acet‐amido‐2‐deoxy‐α‐ D ‐galactopyranoside have been synthesized. The 6′‐, 4′‐ and 3′‐OH group of the galactose moiety as well as the 6‐ and 4‐OH and the 2‐acetamido group of the 2‐acet‐amido‐2‐deoxy‐ D ‐galactose moiety have been selectively substituted by the corresponding deoxy function. The compounds are useful in studies of the substrate specificities of the core 2‐β6‐GlcNAc‐transferase and the α3‐sialyltransferase involved in the biosynthesis of O ‐glycoproteins.
Investigation of Transactional Memory Using FPGAs (2006)

The following outlines an effort to speedup the evaluation of a transactional memory system without loosing accuracy. Instead of using the traditional software simulation techniques we build our system within a large FPGA device. The system elements are a mix of commercially available IP cores and our own design. Together with appropriate runtime monitoring this approach yields a powerful substitute to simulation.
UBB pseudogene 4 encodes functional ubiquitin variants (2020)

Pseudogenes are mutated copies of protein-coding genes that cannot be translated into proteins, but a small subset of pseudogenes has been detected at the protein level. Although ubiquitin pseudogenes represent one of the most abundant pseudogene families in many organisms, little is known about their expression and signaling potential. By re-analyzing public RNA-sequencing and proteomics datasets, we here provide evidence for the expression of several ubiquitin pseudogenes including UBB pseudogene 4 (UBBP4), which encodes Ub<sup>KEKS</sup> (Q2K, K33E, Q49K, N60S). The functional consequences of Ub<sup>KEKS</sup> conjugation appear to differ from canonical ubiquitylation. Quantitative proteomics shows that Ub<sup>KEKS</sup> modifies specific proteins including lamins. Knockout of UBBP4 results in slower cell division, and accumulation of lamin A within the nucleolus. Our work suggests that a subset of proteins reported as ubiquitin targets may instead be modified by ubiquitin variants that are the products of wrongly annotated pseudogenes and induce different functional effects.
Heparin-binding epidermal-growth-factor-like growth factor gene expression is induced by scrape-wounding epithelial cell monolayers: involvement of mitogen-activated protein kinase cascades (2001)

Peptide growth factors can promote the cell migration and proliferation that is needed to repair epithelia after mechanical or chemical injury. We report here that scrape-wounding rat intestinal epithelial (RIE-1) cell monolayers caused a rapid increase in levels of heparin-binding epidermal-growth-factor-like growth factor (HB-EGF) mRNA, with a maximal response at approx. 1h. Hybridization in situ showed that transcript induction occurred primarily in cells at or near wound borders. The increase in HB-EGF mRNA was preceded by activation of the p42 mitogen-activated protein kinase (MAPK) in the wounded cell cultures. Moreover, the induction of HB-EGF mRNA was blocked by PD098059 and U0126, inhibitors that prevent the activation of p42/p44 MAPKs and extracellular signal-regulated protein kinase 5 (ERK5). Both p42 MAPK activation and HB-EGF mRNA induction were inhibited by genistein, indicating a requirement for an upstream tyrosine kinase activity. In contrast, neither response was affected by inhibition of phosphoinositide 3-kinase activity, down-regulation of protein kinase C, or disruption of the actin cytoskeleton with cytochalasin B. We conclude that scrape-wounding epithelial cell monolayers induces HB-EGF mRNA expression by a mechanism that most probably requires p42/p44 MAPK activation, although we cannot exclude a role for ERK5. Our results suggest a physiological role for locally synthesized HB-EGF in promoting epithelial repair after injury.
Effect of aluminium hydroxide and meningococcal serogroup C capsular polysaccharide on the immunogenicity and reactogenicity of a group B Neisseria meningitidis outer membrane vesicle vaccine. (1998)

Three different formulations of an outer membrane vesicle (OMV) vaccine against group B meningococcal disease have been prepared and tested for immunogenicity and reactogenicity in adult volunteers. The vaccines were prepared with or without aluminium hydroxide and serogroup C-polysaccharide (C-ps). Doses from 12.5 to 100 micrograms protein were given twice at a six weeks' interval. All three formulations were well tolerated and highly immunogenic, inducing bactericidal and opsonizing antibodies in humans. Adsorption of OMVs to aluminium hydroxide reduced the pyrogenicity in rabbits. The differences in immunogenicity between the formulations were relatively small, but after the second dose a stronger booster response was observed when the vaccines were adsorbed. Thus, a formulation with OMVs and C-ps represents a safe and highly immunogenic vaccine, even without aluminium hydroxide.
NF-κB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses (2006)

Activation of mammalian innate and acquired immune responses must be tightly regulated by elaborate mechanisms to control their onset and termination. MicroRNAs have been implicated as negative regulators controlling diverse biological processes at the level of posttranscriptional repression. Expression profiling of 200 microRNAs in human monocytes revealed that several of them (miR-146a/b, miR-132, and miR-155) are endotoxin-responsive genes. Analysis of miR-146a and miR-146b gene expression unveiled a pattern of induction in response to a variety of microbial components and proinflammatory cytokines. By means of promoter analysis, miR-146a was found to be a NF-kappaB-dependent gene. Importantly, miR-146a/b were predicted to base-pair with sequences in the 3' UTRs of the TNF receptor-associated factor 6 and IL-1 receptor-associated kinase 1 genes, and we found that these UTRs inhibit expression of a linked reporter gene. These genes encode two key adapter molecules downstream of Toll-like and cytokine receptors. Thus, we propose a role for miR-146 in control of Toll-like receptor and cytokine signaling through a negative feedback regulation loop involving down-regulation of IL-1 receptor-associated kinase 1 and TNF receptor-associated factor 6 protein levels.
The Cathepsin B Inhibitor z-FA.fmk Inhibits Cytokine Production in Macrophages Stimulated by Lipopolysaccharide (2001)

Cathepsin B has previously been shown to proteolytically activate the proinflammatory caspase-11 in vitro. Here we show that cathepsin B is not involved in activation of caspase-11 induced by lipopolysaccharide (LPS) and subsequent maturation of interleukin (IL)-1beta in macrophages. Nevertheless, we found that the cathepsin B inhibitor benzyloxycarbonyl-Phe-Ala-fluoromethylketone (z-FA.fmk) prevents LPS-induced production of IL-1alpha, IL-1beta, and tumor necrosis factor at the transcriptional level. The latter was not because of cathepsin B inhibition, but was mediated by inhibition of the transactivation potential of the nuclear factor kappaB (NF-kappaB). z-FA.fmk did not prevent LPS-induced activation of p38 mitogen-activated protein kinase, which was shown to be involved in NF-kappaB transactivation in response to LPS. These results suggest that the previously described therapeutic effect of z-FA.fmk in the treatment of rheumatoid arthritis might not only result from inhibition of cathepsin B but also implicates an important contribution from the inhibition of NF-kappaB-dependent gene expression.
Electrically resonant terahertz metamaterials: Theoretical and experimental investigations (2007)

We present a class of artificial materials that exhibit a tailored response to the electrical component of electromagnetic radiation. These electric metamaterials are investigated theoretically, computationally, and experimentally using terahertz time-domain spectroscopy. These structures display a resonant response including regions of negative permittivity ${ϵ}_{1}(\ensuremath{\omega})&lt;0$ ranging from $\ensuremath{\sim}500\phantom{\rule{0.3em}{0ex}}\mathrm{GHz}\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}1\phantom{\rule{0.3em}{0ex}}\mathrm{THz}$. Conventional electric media such as distributed wires are difficult to incorporate into metamaterials. In contrast, these localized structures will simplify the construction of future metamaterials, including those with negative index of refraction. As these structures generalize to three dimensions in a straightforward manner, they will significantly enhance the design and fabrication of functional terahertz devices.