gebhart/patrepeval huggingface dataset:
Glucosylceramide Synthetase Inhibitors Sensitise B-CLL Cells to Cytotoxic Agents without Reversing P-gp Functional Activity. (2004)

Abstract Malignant B-cells from a high proportion of chronic lymphocytic leukaemia (B-CLL) patients over express the multidrug resistance (MDR) -1 gene encoded transmembrane efflux pump P-glycoprotein (P-gp). Inhibition of glucosylceramide synthesis has been shown to correlate with the expression and function of P-gp and sensitise cells to cytotoxic agents. We analysed the ability of glucosylceramide synthetase (GCS) inhibitors N-butyl-deoxygalactonojirimycin (OGB-1, 500μM) and N-nonyl-deoxygalactonojirimycin (OGB-2, 100μM) to sensitise B-CLL cells to conventional cytotoxic drugs 2-chlorodeoxyadenosine (CdA), chlorambucil (Chl) and fludarabine (FdR) using the in vitro cytotoxicity MTT assay. The effect on P-gp activity was also analysed using the calcein-AM accumulation assay and the results expressed as multidrug activity factor (MAF), where a MAF of &amp;gt;10 in the presence of a P-gp inhibitor denotes P-gp functional activity. GCS inhibitors were cultured with B-CLL cells for 24-48h before the assays were performed. The P-gp negative cell line CEM-CCRF had no MAF activity with an IC50 for vincristine (a known P-gp substrate) of &amp;lt;1ng/ml. The P-gp over expressing cell line CEM-VLB showed a MAF value of 96.4 with zosuquidar trihydrochloride (Z.3HCL), a specific inhibitor of P-gp, 15.7 with OGB-1 and 45.9 with OGB-2. The IC50 for vincristine was reduced from &amp;gt;10ug/ml to 55.5ng/ml in the presence of OGB-2. In peripheral blood mononuclear cells from 3 normal volunteers (all P-gp +ve), the mean MAF value for Z.3HCL was 23.86 and for OGB-2 was 16.2. In 9/13 B-CLL samples there was P-gp functional activity in the presence of Z.3HCL with a mean MAF value of 22.15 (range 11.27–37.3). P-gp was over expressed in10/13 B-CLL samples. However, when available samples from this cohort were assessed with OGB-1 (n=4) and OGB-2 (n=13) the MAF value was &amp;lt;10. Nevertheless, sensitisation of B-CLL cells was observed by a reduction in the IC50 in the presence of OGB-1 with CdA in 3/4 (to 40% in the presence of cytotoxic drug alone), Chl in 3/4 (39%), FdR in 2/4 (26%) and in the presence of OGB-2 with CdA in 8/13 (42%), Chl in 5/13 (40%) and FdR in 7/13 (34%). Although GCS inhibitors sensitize B-CLL cells to cytotoxic drugs in some B-CLL patients, they do not appear to have any effect on P-gp functional activity.
Dendritic Cell-Based Immunotherapy (2006)

Dendritic cells (DCs) play a crucial role in the induction of antigen-specific T-cell responses, and therefore their use for the active immunotherapy of malignancies has been studied with considerable interest. More than a decade has passed since the publication of the first clinical data of DC-based vaccines, and through this and subsequent studies, a number of important developmental insights have been gleaned. These include the ideal source and type of DCs, the discovery of novel antigens and methods of loading DCs, the role of DC maturation, and the most efficient route of immunization. The generation of immune responses against tumor antigens after DC immunization has been demonstrated, and favorable clinical responses have been reported in some patients; however, it is difficult to pool the results as a whole, and thus the body of data remains inconclusive, in part because of varying DC preparation and vaccination protocols, the use of different forms of antigens, and, most importantly, a lack of rigorous criteria for defining clinical responses. As such, the standardization of clinical and immunologic criteria utilized, as well as DC preparations employed, will allow for the comparison of results across multiple clinical studies and is required in order for future trials to measure the true value and role of this treatment modality. In addition, issues regarding the optimal dose and clinical setting for the application of DC vaccines remain to be resolved, and recent clinical studies have been designed to begin to address these questions.
Free fatty acid release from human breast cancer tissue inhibits cytotoxic T-lymphocyte-mediated killing (2005)

Immune-mediated antitumor activities confront a variety of tumor-mediated defense mechanisms. Here, we describe a new mechanism involving FFA that may allow breast cancer to evade immune clearance. We determined the IC50 at which unbound free fatty acids (FFA(u)) inhibit murine cytotoxic T-lymphocyte (CTL)-mediated killing to assess the physiologic relevance of this phenomenon. We found that the IC50 for unbound oleate is 125 +/- 30 nM, approximately 200-fold greater than normal plasma levels. FFA inhibition, however, may play an important role in breast cancer because we found that large quantities of FFAs are released constitutively into the media surrounding samples of human breast cancer but not normal or benign tissue. FFA(u) concentration ([FFA(u)]) increased to at least 25 nM in 20 of 22 cancer tissue samples and exceeded 100 nM in 11 patients. Media from these samples inhibited CTL-mediated killing. Extrapolation from our in vitro conditions suggests that for tumor interstitial fluid, in vivo [FFA(u)] may be 300-fold greater than we observed in vitro. Although breast cancer release of FFA may suppress effector cell antitumor activity, strategies that reduce interstitial [FFA(u)] may significantly improve antitumor immune therapies.
Graphene-coated metal oxide spinel cathodes (2023)

Disclosed herein are graphene-coated lithium manganese oxide spinels cathodes for high-performance batteries Li-ion batteries and methods for making thereof. A single-layer graphene coating is shown to significantly reduce manganese loss in the cathodes while concurrently promoting the formation of a well-defined solid electrolyte interphase layer.
LASOIS: Enhancing the Spatial Orientation Capabilities of Astronauts on the Lunar Surface (2009)

CAPABILITIES OF ASTRONAUTS ON THE LUNAR SURFACE R. Li, S. He, B. Skopjlak, X. Meng, A. Yilmaz, J. Jiang, M.S. Banks, S. Kim, C. Oman Mapping and GIS Laboratory, CEEGS, The Ohio State University, 470 Hitchcock Hall, 2070 Neil Avenue, Columbus, OH 43210-1275, li.282@osu.edu, Photogrammetric Computer Vision Laboratory, CEEGS, The Ohio State University, Visual Space Perception Laboratory, University of California, Berkeley, Man Vehicle Laboratory, Massachusetts Institute of Technology.
DArT: A Component-Based DRAM Area, Power, and Timing Modeling Tool (2014)

DRAM renovation calls for a holistic architecture exploration to cope with bandwidth growth and latency reduction need. In this paper, we present DRAM area power timing (DArT), a DRAM area, power, and timing modeling tool, for array assembly and interface customization. Through proper design abstraction, our component-based modeling approach provides increased flexibility and higher accuracy, making DArT suitable for DRAM architecture exploration and performance estimation. We validate the accuracy of DArT with respect to the physical layout and circuit simulation of an industrial 68 nm commodity DRAM device as a reference. The experiment results show that the maximum deviations from the reference design, in terms of area, timing, and power, are 3.2%, 4.92%, and 1.73%, respectively. For an architectural projection by porting it to a 45 nm process, the maximum deviations are 3.4%, 3.42%, and 8.57%, respectively. The combination of modeling performance, flexibility, and accuracy of DArT allows us to easily explore new DRAM architectures in the future, including 3-D stacked DRAM.
An overview of NGSCB (2005)

A major challenge the computer industry is facing today is how to effectively protect end users against a plethora of email viruses and network intrusions. An obvious solution is to make the desktop operating system (OS) and applications flawless and bug-free. However, experience shows that this is an impractical goal. The reasons are threefold: the rich functionality users expect from mass market OSs makes these systems so large and complex that security bugs will exist even after rigorous testing and the use of advanced quality assurance methodology during the development process; similar problems apply to applications and device drivers; finally, configuration and maintenance are non-trivial, such that users often misconfigure the system. Security vulnerabilities exist largely due to software bugs, some of which are in the operating systems. Commercial OSs have rapidly grown in size in order to provide ever richer user experiences. Rigorous development and testing can uncover and eliminate a large percentage of these bugs. However, a small number will always remain. The problem is further compounded by the necessity to support an arbitrary number of devices in a consumer desktop OS. A bug in a device driver may be exploited to subvert the system. Again, although stringent testing standards are successful at reducing the number of driver bugs, security vulnerabilities cannot be completely eliminated in complex device drivers.
Squalenoylation of Chitosan: A Platform for Drug Delivery? (2015)

The present study describes the synthesis of chitosan-squalene (chitosan-SQ), a unique amphiphilic chitosan derivative, which enables the efficient formation of nanoparticles in acetate buffer by self-assembly. The influence of different parameters on the nanoparticle size such as percentage of substitution, pH of the acetate buffer, concentration in chitosan-SQ, and time of stirring was studied. It could be demonstrated that this new polymer was nontoxic to cells, biodegradable, and preserved the anti-infective properties of the initial chitosan.1 Moreover, chitosan-SQ showed good carrier properties by allowing the encapsulation of both hydrophilic and hydrophobic model drug compounds.
Preparation of (.eta.6-toluene)bis(trichlorosilyl)nickel(II) by oxidative addition of silicon-silicon and silicon-hydrogen bonds to nickel atoms and bis(1,5-cyclooctadiene)nickel(0). Extreme lability of the .pi.-toluene ligand (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of (.eta.6-toluene)bis(trichlorosilyl)nickel(II) by oxidative addition of silicon-silicon and silicon-hydrogen bonds to nickel atoms and bis(1,5-cyclooctadiene)nickel(0). Extreme lability of the .pi.-toluene ligandThomas J. Groshens and Kenneth J. KlabundeCite this: Organometallics 1982, 1, 3, 564–565Publication Date (Print):March 1, 1982Publication History Published online1 May 2002Published inissue 1 March 1982https://pubs.acs.org/doi/10.1021/om00063a031https://doi.org/10.1021/om00063a031research-articleACS PublicationsRequest reuse permissionsArticle Views161Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Acifluorfen Enhancement of Cryptochrome-Modulated Sporulation following an Inductive Light Pulse (1987)

Acifluorfen enhancement of blue-light mediated phototropism suggested that this diphenyl-ether herbicide augments the light reaction (TY Leong, WR Briggs 1983 Plant Physiol 70: 875-881). The separation of the possible direct interaction of acifluorfen with light reactions from interactions with dark pathways has been elucidated in this paper with Trichoderma harzianum. Acifluorfen at 30 micromolar, given for 5 hours in the growth medium, stimulated the conidiation of Trichoderma in response to blue light without apparently affecting growth. Enhanced conidiation could be elicited by dipping cultures into medium with acifluorfen both before as well as 0.5 hour after inductive blue light. This postphotoinduction stimulation indicates that acifluorfen does not directly augment the effect of light by interacting with cryptochrome(s) in Trichoderma. Instead, acifluorfen most probably interacted with the dark reactions following photoinduction.
Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts (2006)

These data support the notion that genome variability upon passage is a feature of B. mallei ATCC23344, and that within a host B. mallei generates a diverse population of clones that accumulate genome sequence variation at SSR and other loci.
Improving cluster utilization through intelligent processor sharing (2006)

A dedicated cluster is often not fully utilized even when all of its processors are allocated to jobs. This occurs any time that a running job does not use 100% of each of the processors allocated to it. We increase the throughput and efficiency of the cluster by scheduling background jobs to run concurrently with the jobs originally scheduled on the cluster. We do this while maintaining the quality of service provided to the primary jobs. Our results come from empirical measurements using production applications.
Modelling of Components of the Human Middle Ear and Simulation of Their Dynamic Behaviour (1999)

In order to get a better insight into the function of the human middle ear it is necessary to simulate its dynamic behaviour by means of the finite-element method. Three-dimensional measurements of the surfaces of the tympanic membrane and of the auditory ossicles malleus, incus and stapes are carried out and geometrical models are created. On the basis of these data, finite-element models are constructed and the dynamic behaviour of the combinations tympanic membrane with malleus in its elastic suspensions and stapes with annular ligament is simulated. Natural frequencies and mode shapes are computed by modal analysis. These investigations showed that the ossicles can be treated as rigid bodies only in a restricted frequency range from 0 to 3.5 kHz.
The binding of metal ions to bovine factor IX. (1978)

The binding isotherms of Ca2+ and Mn2+ to bovine factor IX have been determined at pH 6.5 and pH 7.4, at 25 degrees C. At pH 7.4, at least 2 strong Ca2+ sites, with an average KDISS of 0.1 +/- 0.02 mM, are found. An additional 10 to 11 weaker Ca2+ binding sites, with an average KDISS of 1.3 +/- 0.2 mM are noted, at high levels of Ca2+. At pH 6.5, again at least 2 strong Ca2+ sites on factor IX are evident, with an average KDISS of 0.11 +/- 0.02 mM; but slightly fewer (7 to 8) weaker sites, with an average KDISS of 1.9 +/- 0.3 mM, are obtained. Qualitatively, the binding of Mn2+ to bovine factor IX appears similar to that of Ca2+. At pH 6.5, approximately 2 strong Mn2+ binding sites, with an average KDISS of 13 +/- 1.5 micrometer, and an additional 5 to 6 weak sites, with an average KDISS of 160 +/- 15 micrometer, are present. Manganese does not completely displace Ca2+; and Ca2+ does not completely displace Mn2+ from their respective binding sites. On the other hand, Tb3+ and Sm3+ readily displace Ca2+, at pH 6.5, from its sites on factor IX. The rate and extent of activation of bovine factor IX, by bovine factor XIa, is dependent on the Ca2+ concentration, up to concentrations of Ca2+ which saturate its effect on the system. Substitution of Sr2+ for Ca2+ leads to approximately 50% of the maximum rate of factor IXa formation, and final yield of factor IXa, in this activation system. Manganese does not substitute for Ca2+ in this activation, but does inhibit the stimulatory effect of Ca2+. Both Tb3+ and Sm3+ are effective inhibitors of Ca2+ in factor IX activation by factor XIa.
In Vitro Anti-Plasmodium falciparum Properties of the Full Set of Human Secreted Phospholipases A 2 (2015)

We have previously shown that secreted phospholipases A2 (sPLA2s) from animal venoms inhibit the in vitro development of Plasmodium falciparum, the agent of malaria. In addition, the inflammatory-type human group IIA (hGIIA) sPLA2 circulates at high levels in the serum of malaria patients. However, the role of the different human sPLA2s in host defense against P. falciparum has not been investigated. We show here that 4 out of 10 human sPLA2s, namely, hGX, hGIIF, hGIII, and hGV, exhibit potent in vitro anti-Plasmodium properties with half-maximal inhibitory concentrations (IC50s) of 2.9 ± 2.4, 10.7 ± 2.1, 16.5 ± 9.7, and 94.2 ± 41.9 nM, respectively. Other human sPLA2s, including hGIIA, are inactive. The inhibition is dependent on sPLA2 catalytic activity and primarily due to hydrolysis of plasma lipoproteins from the parasite culture. Accordingly, purified lipoproteins that have been prehydrolyzed by hGX, hGIIF, hGIII, and hGV are more toxic to P. falciparum than native lipoproteins. However, the total enzymatic activities of human sPLA2s on purified lipoproteins or plasma did not reflect their inhibitory activities on P. falciparum. For instance, hGIIF is 9-fold more toxic than hGV but releases a lower quantity of nonesterified fatty acids (NEFAs). Lipidomic analyses of released NEFAs from lipoproteins demonstrate that sPLA2s with anti-Plasmodium properties are those that release polyunsaturated fatty acids (PUFAs), with hGIIF being the most selective enzyme. NEFAs purified from lipoproteins hydrolyzed by hGIIF were more potent at inhibiting P. falciparum than those from hGV, and PUFA-enriched liposomes hydrolyzed by sPLA2s were highly toxic, demonstrating the critical role of PUFAs. The selectivity of sPLA2s toward low- and high-density (LDL and HDL, respectively) lipoproteins and their ability to directly attack parasitized erythrocytes further explain their anti-Plasmodium activity. Together, our findings indicate that 4 human sPLA2s are active against P. falciparum in vitro and pave the way to future investigations on their in vivo contribution in malaria pathophysiology.
A highly recurrent RPS27 5'UTR mutation in melanoma (2014)

The incidence of melanoma continues to rise globally and is increasing at a rate greater than any other cancer. To systematically search for new genes involved in melanomagenesis, we collated exome sequencing data from independent melanoma cohort datasets, including those in the public domain. We identified recurrent mutations that may drive melanoma growth, survival or metastasis, and which may hold promise for the design of novel therapies to treat melanoma. These included a frequent recurrent (i.e. hotspot) mutation in the 5' untranslated region of RPS27 in ~10% of samples. We show that the mutation expands the 5'TOP element, a motif known to regulate the expression of most of the ribosomal protein family, to which RPS27 belongs, and thus might sensitize the mutated transcript to growth-mediated regulation. This finding highlights not only the important role of non-protein coding genetic aberrations in cancer development but also their potential as novel therapeutic targets.
Structural studies unravel the active conformation of apo RORγt nuclear receptor and a common inverse agonism of two diverse classes of RORγt inhibitors (2017)

The nuclear receptor retinoid acid receptor-related orphan receptor γt (RORγt) is a master regulator of the Th17/IL-17 pathway that plays crucial roles in the pathogenesis of autoimmunity. RORγt has recently emerged as a highly promising target for treatment of a number of autoimmune diseases. Through high-throughput screening, we previously identified several classes of inverse agonists for RORγt. Here, we report the crystal structures for the ligand-binding domain of RORγt in both apo and ligand-bound states. We show that apo RORγt adopts an active conformation capable of recruiting coactivator peptides and present a detailed analysis of the structural determinants that stabilize helix 12 (H12) of RORγt in the active state in the absence of a ligand. The structures of ligand-bound RORγt reveal that binding of the inverse agonists disrupts critical interactions that stabilize H12. This destabilizing effect is supported by <i>ab initio</i> calculations and experimentally by a normalized crystallographic B-factor analysis. Of note, the H12 destabilization in the active state shifts the conformational equilibrium of RORγt toward an inactive state, which underlies the molecular mechanism of action for the inverse agonists reported here. Our findings highlight that nuclear receptor structure and function are dictated by a dynamic conformational equilibrium and that subtle changes in ligand structures can shift this equilibrium in opposite directions, leading to a functional switch from agonists to inverse agonists.
Mouse Y-Specific Repeats Isolated by Whole Chromosome Representational Difference Analysis (1996)

Representational difference analysis (RDA) was used to generate Y-specific probes by enriching for and cloning the differences between the male (XY) and the female (XX) C57BL/6J mouse genomes. Characterization of 35 clones revealed 12 families related by sequence similarity. One clone from each family was chosen for detailed analysis by Southern blot hybridization, polymerase chain reaction (PCR) on normal and aberrant genomes (Sxr), and fluorescence in situ hybridization. From one difference product we have characterized 12 Y-specific probes for hybridization, created seven male-specific PCR assays, mapped all repeat families, and identified one repeat with a distinct XY homology. We report the first cloning of a Y-specific long interspersed repeat element (LINE) fragment. In total, RDA has identified six novel Y Chromosome repeat families and allowed us to extend the characterization of six known Y repeats. We conclude that this novel use of RDA for whole chromosome subtraction successfully enriches chromosome-specific sequences and is suitable for the rapid generation of new Y Chromosome-specific probes.