gebhart/patrepeval huggingface dataset:
mTOR complex 2 (mTORC2) regulation of hepatic gene expression (2013)

mTORC2 has been connected to various disorders, including diabetes and cancer. It is required for insulin‐mediated suppression of hepatic glucose production. Our aim was to examine the role of mTORC2 in the regulation of liver metabolism. Control mice and RKO mice (liver‐specific knockout of Rictor, an mTORC2 constituent) were fasted overnight, fed for 3 hr, then sacrificed. Liver RNA (n = 4 per group) was analyzed using Affymetrix Genechip Mouse Gene 1.0 ST arrays. Gene Set Enrichment Analysis (GSEA) revealed upregulation of three categories of genes in the RKO mice: ribosomal proteins, TCA cycle/oxidative phosphorylation, and components of the 26S proteosome. GSEA results were consistent using both KEGG and Reactome datasets. Ingenuity Pathway Analysis (IPA) showed gene function categories relating to carbohydrate and lipid metabolism. In addition, three transcription factors were significantly altered in the RKO mice. FoxO1 was activated relative to the controls while CTNNB1 and NR1L3 were inactivated. Our results indicate that mTORC2 has broad effects on hepatic gene expression. mTORC2 is linked, in particular, to carbohydrate, lipid and mitochondrial energy metabolism. It also appears to regulate genes involved in ribosome and proteosome biogenesis. Supported by grants from NIH/NIA (DWL), the American Federation of Aging Research (DMS), Howard Hughes Medical Institute (DMS), and NIH/NICHD (PAG).
Supplementary Table 1 from A novel class of Ribosome Modulating Agents (RMAs) exploits cancer ribosome heterogeneity to selectively target the CMS2 subtype of colorectal cancer (2023)

&lt;p&gt;Table showing the top 20 MYC gene targets with the highest positive charge density&lt;/p&gt;
CC chemokine receptor-7 on dendritic cells is induced after interaction with apoptotic tumor cells: critical role in migration from the tumor site to draining lymph nodes. (2000)

Dendritic cells (DCs) are very potent antigen-presenting cells and play critical roles in regulating immune responses in cancer. The migrating of DCs from the tumor site to the lymphoid organs is believed to be one of the critical events. To examine this important DC function in tumor situations, bone marrow-derived DCs, cultured for 6 days with granulocyte macrophage colony-stimulating factor and interleukin 4, were inoculated at the tumor site. We have shown (Y. Nishioka et al., Cancer Res., 59: 40354041, 1999) that DCs can migrate from tumor site to the draining lymph nodes within 24 h (approximately 0.1% of administrated DCs). The DCs then form clusters with adjacent lymphoid cells, which produce IFN-gamma (1500-3200pg/10(6) cells/48 h) in response to tumor stimulation. The number of the DCs migrating into lymph nodes were greater when they were inoculated into the tumor rather than the skin. Coculture of DCs and apoptotic tumor cells resulted in decreased expression of CC chemokine receptor (CCR) 1 and increased CCR7 expression at mRNA level without alteration in other phenotypical markers on DCs. Chemotaxis assay showed that CCR7 ligands, macrophage inflammatory protein 3beta and secondary lymphoid-tissue chemokine significantly (P < 0.05) induced the migration of DCs when cocultured with apoptotic tumor cells. To directly examine the involvement of CCR7 expression in DC migration, we investigated the functions of DCs genetically modified to express high levels of CCR7. CCR7 transduction promotes DC migration in response to relevant ligands in vitro and in vivo. These results suggest that the CCR7 expression of DCs is enhanced with direct contact with apoptotic tumor cells and may have a critical role for DC migrating to regional lymph nodes. The means to promote DC delivery to tumor and to nodal sites represent novel targets for the biological therapy of cancer.
Compositional Dependence of Critical Point Transitions in Ge1−xSnx alloys (2005)

The compositional dependence of the E1, E1+Δ1, E0′, and E2 optical transition energies in Ge1−xSnx alloys has been measured in the 0 < x < 0.18 range. Deviations from linearity are clearly observed and characterized by a bowing parameter b. The value of this parameter is much larger in Ge1−xSnx alloys than in the isoelectronic Si1−xGex system.
Biomass and Carbon Stock Dynamics in Tropical Evergreen and Deciduous Forests of Uttara Kannada District, Western Ghats, India (2016)

Western Ghats is one of the biodiversity ‘hotspots’ of the world and currently, there is limited evidence on the status and dynamics of tropical forests in the context of human disturbance and climate change. This study presents the findings of the study conducted under a citizen science programme. The biomass and carbon stocks in the evergreen and deciduous forests of the study area are comparable to the standing biomass of other tropical forests and range from 344-417 tC. There are no major differences between carbon stocks in less and more disturbed forests, which is of significance, given the large dependence of communities on the more disturbed forests. Periodic and long-term monitoring of forests is necessary in the context of potential increased human pressure and climate change to plan and manage forests for mitigation as well as adaptation in a synergistic manner.
Synaptotagmin Perturbs the Structure of Phospholipid Bilayers (2008)

Synaptotagmin I (syt), an integral protein of the synaptic vesicle membrane, is believed to act as a Ca2+ sensor for neuronal exocytosis. Syt's cytoplasmic domain consists largely of two C2 domains, C2A and C2B. In response to Ca2+ binding, the C2 domains interact with membranes, becoming partially embedded in the lipid bilayer. We have imaged syt C2AB in association with lipid bilayers under fluid, using AFM. As expected, binding of C2AB to bilayers required both an anionic phospholipid [phosphatidylserine (PS)] and Ca2+. C2AB associated with bilayers in the form of aggregates of varying stoichiometries, and aggregate size increased with an increase in PS content. Repeated scanning of bilayers revealed that as C2AB dissociated it left behind residual indentations in the bilayer. The mean depth of these identations was 1.81 nm, indicating that they did not span the bilayer. Individual C2 domains (C2A and C2B) also formed aggregates and produced bilayer indentations. Binding of C2AB to bilayers and the formation of indentations were significantly compromised by mutations that interfere with binding of Ca2+ to syt or reduce the positive charge on the surface of C2B. We propose that bilayer perturbation by syt might be significant with respect to its ability to promote membrane fusion.
Large-scale development – modularity, extensibility, and distribution (2014)

In this chapter, we study modularity, extensibility, and distribution. As part of modularity, we look at how types, functions, primitive, and composite operators can be organized into toolkits to facilitate the development of large-scale applications.
Synthesis of Four Novel Natural Product Inspired Scaffolds for Drug Discovery (2008)

Inspired by the novel spiro structures of a number of bioactive natural products such as the histrionicotoxins, a series of novel spiro scaffolds have been designed and robust syntheses developed. The scaffolds are ready-to-use building blocks and can be easily prepared on a 5-20 g scale. They contain two amino groups (one Boc-protected) and have been designed for ease of conversion to a lead generation library, using either amide formation or reductive amination procedures. The synthesis of the 1,9-diazaspiro[5.5]undecane and 3,7-diazaspiro[5.6]dodecane ring systems was achieved using RCM as the key step. A simple workup procedure is reported for the removal of highly colored ruthenium residues. The synthesis of the 1,8-diazaspiro[4.5]decane scaffold has been achieved using a bromine-mediated 5-endo cyclization of the corresponding 4-aminobutene intermediate under acidic conditions. This is the first example of this type of cyclization to be reported. A novel mechanism involving a bromine transfer reaction from an initially formed bromonium ion to a neighboring nitrogen atom is suggested as the reason for the failure of this type of reaction under "normal" bromination conditions. An unusual rearrangement of a 1-acyl-1,9-diazaspiro[5.5]undecane to the corresponding 9-acyl-1,9-diazaspiro[5.5]undecane is reported.
Semiclassical model for attosecond angular streaking: errata (2011)

Two different transport regimes of light are observed in reflection from the same disordered photonic crystal. A model based on the scaling theory of localization explains the behavior of the path length-resolved reflection at two different probing wavelengths. Our results demonstrate the continuous renormalization of the photon diffusion coefficient measured in reflection from random media.
Expression of MAC30 protein is related to survival and biological variables in primary and metastatic colorectal cancers (2007)

MAC30 is highly expressed in several types of tumors including colorectal cancers, however, its clinicopathological and biological significance in colorectal cancers is currently not known. The aim of our study was to investigate MAC30 expression in distant normal mucosa, adjacent normal mucosa, primary tumors and metastases of colorectal cancer, and to determine the relationship between MAC30 expression and clinicopathological and biological variables. MAC30 expression was immunohistochemically examined in distant normal mucosa (n = 54), adjacent normal mucosa (n = 123), primary tumors (n = 217) and lymph node metastases (n = 56) from colorectal cancer patients. MAC30 cytoplasmic expression was increased from distant normal mucosa to primary tumor and to metastasis (p < 0.0001-0.04). Furthermore, 40% primary and 37% metastatic tumors showed stronger cytoplasmic expression of MAC30 at the tumor invasive margins compared to inner tumor areas. Strong cytoplasmic expression of MAC30 in the metastasis was related to a poor prognosis (p = 0.04). MAC30 cytoplasmic expression was positively related to expression of proliferating cell nuclear antigen (p = 0.04), p53 (p = 0.04), nucleoporin 88 (p = 0.001), legumain (p = 0.004) and particularly interesting new cysteine-histidine rich protein (p = 0.004). However, MAC30 expression in the nucleus and stroma did not have any clinicopathological and biological significance (p > 0.05). In conclusion, MAC30 protein may play a role in development of colorectal cancer, and can be considered as a prognostic factor.
Conquering the Low‐k Death Curve: Insulating Boron Carbide Dielectrics with Superior Mechanical Properties (2016)

To enable the continued scaling of integrated circuits, the semiconductor industry faces ongoing struggles to implement better low‐dielectric‐constant (low‐ k ) materials within the interconnect system. One of the biggest challenges to integrating new dielectrics is overcoming the low‐ k death curve—that is, the fatal falloff in mechanical properties associated with the low material densities required to achieve low k values. It is shown that amorphous hydrogenated boron carbide (a‐BC:H) films exhibit Young's modulus ( E ) values between two and ten times greater than those of state‐of‐the‐art Si‐based dielectric materials across a wide range of k values. In particular, optimized a‐BC:H films with moderate k values in the range of 3–4, in addition to possessing outstanding stiffness ( E ≈ 100–150 GPa), simultaneously exhibit excellent electrical properties (leakage current of &lt;10 –8 A cm –2 at 2 MV cm –1 and breakdown voltage of &gt;5 MV cm –1 ). Films in this range also demonstrate resistance to Cu diffusion to at least 600 °C, as well as chemical stability and etch properties suitable for low‐ k diffusion barrier/etch stop applications.
Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation* (2019)

Dendritic cells (DCs) are professional phagocytes that use innate sensing and phagocytosis to internalize and degrade self as well as foreign material, such as pathogenic bacteria, within phagosomes. These intracellular compartments are equipped to generate antigenic peptides that serve as source for antigen presentation to T cells initiating adaptive immune responses. The phagosomal proteome of DCs is only partially studied and is highly dynamic as it changes during phagosome maturation, when phagosomes sequentially interact with endosomes and lysosomes. In addition, the activation status of the phagocyte can modulate the phagosomal composition and is able to shape phagosomal functions.In this study, we determined spatiotemporal changes of the proteome of DC phagosomes during their maturation and compared resting and lipopolysaccharide (LPS)-stimulated bone marrow-derived DCs by label-free, quantitative mass spectrometry. Ovalbumin-coupled latex beads were used as phagocytosis model system and revealed that LPS-treated DCs show decreased recruitment of proteins involved in phagosome maturation, such as subunits of the vacuolar proton ATPase, cathepsin B, D, S, and RAB7. In contrast, those phagosomes were characterized by an increased recruitment of proteins involved in antigen cross-presentation, <i>e.g.</i> different subunits of MHC I molecules, the proteasome and tapasin, confirming the observed increase in cross-presentation efficacy in those cells. Further, several proteins were identified that were not previously associated with phagosomal functions. Hierarchical clustering of phagosomal proteins demonstrated that their acquisition to DC phagosomes is not only dependent on the duration of phagosome maturation but also on the activation state of DCs. Thus, our study provides a comprehensive overview of how DCs alter their phagosome composition in response to LPS, which has profound impact on the initiation of efficient immune responses.
Subglottic squamous cell carcinoma in Denmark 1971–2015 – a national population-based cohort study from DAHANCA, the Danish Head and Neck Cancer group (2019)

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macroglobulinemia SDF-1/CXCR4 and VLA-4 interaction regulates homing in Waldenstrom (2013)

doi:10.1182/blood-2007-12-129395Prepublished online April 30, 2008;2008 112: 150-158€€€€Farag, Robert Sackstein and Irene M. GhobrialMoreau, Nicholas Burwick, Abdel Kareem Azab, Aldo Roccaro, Feda Azab, Antonio Sacco, Mena Hai T. Ngo, Xavier Leleu, Jack Lee, Xiaoying Jia, Molly Melhem, Judith Runnels, Anne-Sophie€
Intra-cavity measurement concept of dispersion properties with a tunable fiber-integrated laser (2019)

The dispersion properties of fibers depict a key characteristic to model the propagation of ultra-short pulses in waveguides. In the following, a new method is presented to directly measure the dispersion properties of fibers and optical components in the time domain. The analysis is based on pulse shape variations along the tuning range of a theta cavity fiber laser (TCFL) depending on the adjusted repetition rate. The automated measurement procedure, evaluating pulse symmetry, achieves a temporal sensitivity below 5 ps surpassing the resolution of the acquisition electronics. Exemplarily, two samples of Nufern PM980-XP fiber are investigated with an Yb-doped tunable TCFL retrieving the mean dispersion parameter by comparative measurements. The obtained results are compared to a reference method based on spectral interferometry. With deviations in between either approach of and , respectively, the results agree well within the measurement errors of the TCFL, verifying the presented concept. Due to the pulse formation process extending over multiple round trips, this approach achieves an enhanced sensitivity compared to competing direct temporal methods. Together with an alignment free operation, the fiber-integrated TCFL depicts a simple and robust concept showing potential in specific measurement scenarios such as in quality management.
The 9 Lives of Bleichenbacher's CAT: New Cache ATtacks on TLS Implementations. (2018)

At CRYPTO'98, Bleichenbacher published his seminal paper which described a padding oracle attack against RSA implementations that follow the PKCS #1 v1.5 standard. Over the last twenty years researchers and implementors had spent a huge amount of effort in developing and deploying numerous mitigation techniques which were supposed to plug all the possible sources of Bleichenbacher-like leakages. However, as we show in this paper, most implementations are still vulnerable to several novel types of attack based on leakage from various microarchitectural side channels: Out of nine popular implementations of TLS that we tested, we were able to break the security of seven implementations with practical proof-of-concept attacks. We demonstrate the feasibility of using those Cache-like ATacks (CATs) to perform a downgrade attack against any TLS connection to a vulnerable server, using a BEAST-like Man in the Browser attack. The main difficulty we face is how to perform the thousands of oracle queries required before the browser's imposed timeout (which is 30 seconds for almost all browsers, with the exception of Firefox which can be tricked into extending this period). Due to its use of adaptive chosen ciphertext queries, the attack seems to be inherently sequential, but we describe a new way to parallelize Bleichenbacher-like padding attacks by exploiting any available number of TLS servers that share the same public key certificate. With this improvement, we can demonstrate the feasibility of a downgrade attack which could recover all the 2048 bits of the RSA plaintext (including the premaster secret value, which suffices to establish a secure connection) from five available TLS servers in under 30 seconds. This sequential-to-parallel transformation of such attacks can be of independent interest, speeding up and facilitating other side channel attacks on RSA implementations.
Incentive Spirometry (1996)

Hilling, Lana RCP, CRTT; Bakow, Eric RRT; Fink, James MS, RCP, RRT; Kelly, Chris BS, RRT; Southorn, Peter A. MD Author Information
Anthracyclines: Selected New Developments (2001)

Anthracycline antibiotics play an important role in cancer chemotherapy. The need for an improvement of their therapeutic index has stimulated an ongoing search for anthracycline analogues with improved properties. Analogue development was originally limited by a lack of information on the cellular drug target, nevertheless almost 20 years ago the mechanism of action of doxorubicin and daunorubicin was revealed and DNA topoisomerase II was recognised to be their main cellular target. Several anthracyclines interfere with topoisomerase II functions by stabilizing a reaction intermediate in which DNA strands are cut and covalently linked to tyrosine residues of the enzyme. Investigations on the sequence specificity of doxorubicin in vitro and in nuclear chromatin of living cell have led to a molecular model of drug receptor on the topoisomerase II-DNA complex. Anthracyclines are likely placed at the interface between the DNA cleavage site and the active site of the enzyme, forming a DNA-drug-enzyme ternary complex. Moreover, a quite detailed structure-function relationship has been established for anthracyclines. First, drug intercalation is necessary but not sufficient for topoisomerase II poisoning; second, the removal of the 4-methoxy and 3-amino substituents greatly increases the drug activity and third, the 3 substituent of the sugar moiety markedly influences the sequence selectivity of anthracycline-stimulated DNA cleavage. These relationships have been exploited during the last decade by several groups, including ours, in the search for new anthracycline drugs with lower side effects and higher activity against resistant cancer cells. This review will focus on areas of the anthracycline field including synthesis of new analogues, new strategies of synthesis and recent developments in the area of drug delivery. Keywords: anthracyclines, cancer, celluar drug target, topoisomerase II, methoxy, amino substituents, anthracycline cytotoxicity, men, oligosaccharidemodfied analogues, dna topisomerase, monosaccharide anthracyclines
Modélisation pour le dimensionnement d’une machine à commutation de flux à double excitation à bobinage global (2021)

International audience
Development of a Controller Area Network Based Handheld Data Acquisition System for Identity Preservation (2003)

The development of a diverse, modular and portable system to accurately measure andrecord field operations is required to effectively bring identity preservation of crops to all farms andfarmers. A demonstration system has been built based on a worldwide standard communicationsprotocol and was evaluated for its ability to efficiently measure a variety of field operations andmanagement practices. The CAN Bus 2.0B communication protocol was used to record GPSlocation data, ground speed and simulated spraying system data. This data was compiled andstored in a form that was compatible with multiple software programs for the purposes of economicand agronomic analysis. All data was recorded on a Compaq IPAQ using specially-written software. Results showed that tracking identity preservation characteristics was feasible with thissystem.
Recovery from control plane failures in the cr-ldp and o-uni signalling protocols (2004)

When the control and data planes are physically separate, it is important to maintain the established connections in the data plane even if the control plane fails. Channel status is maintained by a signalling protocol. A failure in the control plane having no recovery capability of the constraint-based routing label distribution protocol (CR-LDP) will cause the channel status information to be permanently lost. A recovery mechanism for channel status information is proposed in this paper. A downstream node stores a label information database (LID) of assignable (free) labels for each incoming link. A copy of the LID is redundantly stored in the upstream node as a label information mirror (LIM). Each LIM and the corresponding LID are kept synchronised to guarantee the recovery of channel status information. The proposed recovery mechanism is also shown to be applicable to CR-LDP based optical user network interface (O-UNI) signalling protocol.
Les Halles redevelopment: in Paris, a city center goes underground (1980)

A controversial multi-purpose underground project in the Les Halles district of Paris is the latest of many modernizations at an ancient market site in the center of the city. In an effort to avoid conventional urban-renewal tactics that would alter the surrounding area, the Conseil de Paris planned an underground city of commercial: leisure, and transport facilities, with the surface area restricted to pedestrian traffic and open space. The mechanisms for financing and managing the project are described and followed by a review of the construction techniques. The project is unique in tying together an existing urban environment with underground roads and pedestrian routes that are controlled by public statutes. The buildings have private ownership as in a conventional commercial district. (DCK)
Adaptive Digital Predistortion for Radar Applications using Convex Optimization (2020)

Much of the research to date in predistortion design and implementation has been focused on communication applications. While useful for radar applications, the approaches that work well for communications waveforms do not necessarily result in optimal utilization of computational resources. To this end, a special case of the memory polynomial model is explored. As time alignment of signals can pose a problem for predistortion parameter estimation, a method of calculating the ideal predistortion coefficients in the frequency-domain using convex optimization is explored.