gebhart/patrepeval huggingface dataset:
Regulation and Expression of Retinoblastoma Proteins p107 and p130 during 3T3-L1 Adipocyte Differentiation (1997)

During 3T3-L1 adipocyte differentiation, growth-arrested, postconfluent preadipocytes are required to reenter the cell cycle and proceed through a mitotic clonal expansion phase prior to terminal differentiation. The retinoblastoma proteins (pRB, p107, and p130) are thought to be critical in controlling cell cycle progression by binding to and regulating the activity of the E2F transcription factors. We show here that p130/p107 protein levels, p107 mRNA levels, and E2F DNA binding complexes are regulated during 3T3-L1 adipogenesis. The predominant E2F binding complex in day 0 preadipocytes was p130-E2F with no detectable free E2F or p107. On Day 1, during mitotic clonal expansion, there was a distinct switch to free E2F and p107-E2F complexes associated with increased p107 mRNA and protein along with decreased p130 protein levels. Following differentiation, the day 0 pattern is reestablished. The switch is not just a consequence of reentry into the cell cycle, in that p107 protein levels are both detectable and unchanged in dividing, serum-restricted, or serum restimulated preconfluent cells. Interestingly, hormonal stimulation of 3T3-C2 cells, a related nondifferentiating cell line, also induces a mitotic clonal expansion phase that is associated with the p130:p107 switch in a pattern very similar to 3T3-L1 cells, suggesting the block in differentiation observed in 3T3-C2 cells occurs after clonal expansion. Combined, these findings suggest that the regulatory mechanisms of the p130:p107 switch are not specific to differentiation but may play a key role in regulating the mitotic clonal expansion necessary for adipocyte differentiation in 3T3-L1 cells.
Abstract P320: Cooperative Signaling and Membrane Recruitment of the Dopamine-1 (D 1 R) and Angiotensin Type 2 (AT 2 R) Receptors in Human Renal Proximal Tubule Cells (RPTC) (2017)

The D 1 R and AT 2 R are interdependent natriuretic receptors that are critical for the regulation of renal sodium balance and are implicated in both hypertension and salt-sensitivity. D 1 R and AT 2 R stimulation with the D 1 R agonist fenoldopam (FEN) and Angiotensin III (AngIII), selectively increases cAMP and cGMP, respectively, leading to D 1 R and AT 2 R recruitment to the cell surface (measured by fluorescent extracellular receptor epitope specific antibodies). The interdependence of the D 1 R and AT 2 R recruitment was investigated following AT 2 R stimulation with AngIII (10 nmol/L 1 hour) which leads to D 1 R cell surface recruitment using a normally D 1 R/Gs coupled cell line (i22) (VEH 8209±863, AngIII 19485±3425 RFU, n=6, p&lt;0.05) but not in a D 1 R uncoupled from Gs cell line (i19). These data were verified by increasing intracellular sodium with monensin (100 μM, 1 hr) and measuring cell surface binding with a fluorescent labelled D 1 R agonist SKF83566 (10 nmol/L, 1 hr, i22 1.67±0.7 fold, n=5, p&lt;0.0001, i19, NS). The importance of dopamine in regulating these receptor actions was shown by stimulating the AT 2 R with AngIII and measuring D 1 R recruitment followed by blockade of amino acid decarboxylase using either carbidopa or benzeraside (100 μM each, 1 hour). Additionally, FEN stimulated D 1 R surface recruitment is blocked by the AT 2 R inhibitor PD123319 (1 μM, 1 hour) and the coupling defect is fully rescued by 8Br-cGMP (1 mmol/L, 1 hour), a cell permeable second messenger normally thought to signal specifically through the AT 2 R. We then show that FEN stimulation leads to increased production of AngIII only in the D 1 R/Gs coupled i22 cell line (5.82±0.43 fold, n=6, p&lt;0.05) but not in i19 the D 1 R/Gs uncoupled cell line and this production was blocked with an aminopeptidase A inhibitor, EC-33 (10 μmol/L, 1 hour). Addition of 8Br-cAMP (1mmol/L 1 hour) not only leads to an increase in AngIII production, but also cGMP production (4.33±0.36 fold, n=6, p&lt;0.05) that is blocked by PD123319 (potent, selective, non-peptide angiotensin AT 2 R antagonist, 1 μM, 1 hour). In summary we not only show that dopaminergic stimulation leads to increased AngIII production in a D 1 R coupled manner, but also that AngIII stimulation of AT 2 R leads to dopaminergic activation in a D 1 R coupled manner.
Measurements of energy distribution functions of xenon ions from laser-produced plasmas for lithography (2004)

The collector mirror lifetime of a future extreme ultraviolet lithography light source system is an important development issue. Beside vacuum cleanliness and heat load, fast ions are especially critical in case of laser-produced plasmas causing quick degradation of the multilayer structure of near normal incidence collector mirrors. We are currently developing a light source system based on a laser-produced plasma for next generation lithography. The plasma target is a liquid xenon jet. Energy distributions of fast xenon ions from the laser-produced plasma have been measured by time-of-flight (TOF) experiments. Two low repetition rate Nd:YAG lasers at 1064 nm with pulse lengths of 8 ns and 150 ps have been used for plasma generation and mean ion energies of 3 keV and 7 keV have been measured, respectively. In addition, the effects of fast ions on Mo/Si multilayer mirrors have been studied using a Xe ion gun. Ion sputtering of the multilayer structure is the main damage mechanism but boundary layer mixing and increased surface roughness are also observed.
Large-Scale Single Guide RNA Library Construction and Use for CRISPR–Cas9-Based Genetic Screens (2016)

The ability to systematically disrupt genes serves as a powerful tool for understanding their function. The programmable CRISPR-Cas9 system enables efficient targeting of large numbers of genes through the use of single guide RNA (sgRNA) libraries. In cultured mammalian cells, collections of knockout mutants can be readily generated by means of transduction of Cas9-sgRNA lentiviral pools, screened for a phenotype of interest, and counted using high-throughput DNA sequencing. This technique represents the first general method for undertaking systematic loss-of-function genetic screens in mammalian cells. Here, we introduce the methodology and rationale for conducting CRISPR-based screens, focusing on distinguishing positive and negative selection strategies.
CMOS TECHNOLOGY FOR CCD VIDEO MEMORIES (1988)

A new double polysilicon gate technology for an 835 Kbit CCD video memory with a cell of 4x4 µm2 [1] is presented. The spacer technology for the LDD MOSFET's is integrated in the isolation of the double poly CCD structure. This makes the CCD fully compatible with standard CMOS processing and relaxes the anisotropic plasma etching of second poly electrodes. The charge transfer efficiency is high for a SCCD without fat zero (ε ≈ 2.10-4). Measurements and calculations on the charge transfer show no degradation for doping concentrations below 8.1015 cm-3. The leakage current density is measured on the 835 Kbit memory and agrees with earlier measurements on a 308 Kbit CCD video memory [2,6].
Identification of a marker chromosome in a rat ascitic tumor by flow cytometry using a modified method for preparing chromosome suspensions (1993)

Preparation of good chromosome suspensions is a crucial step in obtaining good flow karyotypes from different types of cells. Although several methods are in use, not all are suitable for all cell types. Primary cells from murine tissues are specially difficult to flow karyotype. We have modified the existing protocols for preparing chromosome suspensions from the Zajdela ascitic hepatoma (ZAH) cells of rat and have constructed their flow karyograms. Our karyograms show a distinct marker chromosome in these cells, which could not be resolved using other protocols. We have also used this method for preparing chromosomes from the bone marrow cells of the rat and have compared their flow karyograms with the ZAH karyotype. We expect that our protocol will be useful for studying other types of tumor and normal cells.
Proteoglycan-4 is correlated with longer survival in HCC patients and enhances sorafenib and regorafenib effectiveness via CD44 in vitro (2020)

Sorafenib and regorafenib administration is among the preferential approaches to treat hepatocellular carcinoma (HCC), but does not provide satisfactory benefits. Intensive crosstalk occurring between cancer cells and other multiple non-cancerous cell subsets present in the surrounding microenvironment is assumed to affect tumor progression. This interplay is mediated by a number of soluble and structural extracellular matrix (ECM) proteins enriching the stromal milieu. Here we assess the HCC tumor expression of the ECM protein proteoglycan 4 (PRG4) and its potential pharmacologic activity either alone, or in combination with sorafenib and regorafenib. PRG4 mRNA levels resulted strongly correlated with increased survival rate of HCC patients (p = 0.000) in a prospective study involving 78 HCC subjects. We next showed that transforming growth factor beta stimulates PRG4 expression and secretion by primary human HCC cancer-associated fibroblasts, non-invasive HCC cell lines, and ex vivo specimens. By functional tests we found that recombinant human PRG4 (rhPRG4) impairs HCC cell migration. More importantly, the treatment of HCC cells expressing CD44 (the main PRG4 receptor) with rhPRG4 dramatically enhances the growth-limiting capacity of sorafenib and regorafenib, whereas not significantly affecting cell proliferation per se. Conversely, rhPRG4 only poorly potentiates drug effectiveness on low CD44-expressing or stably CD44-silenced HCC cells. Overall, these data suggest that the physiologically-produced compound PRG4 may function as a novel tumor-suppressive agent by strengthening sorafenib and regorafenib effects in the treatment of HCC.
Quadrupole Time-Of-Flight (QTOF) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
In situ TEM investigation of the interfacial reaction between Ni and Al during rapid heating in a nanocalorimeter (2014)

Abstract not provided
ChemInform Abstract: Aplyronine A, a Potent Antitumor Substance of Marine Origin, Aplyronines B and C, and Artificial Analogues: Total Synthesis and Structure‐Cytotoxicity Relationships. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Detecting and reacting to unplanned-for world states (1997)

The degree to which a planner succeeds and meets response deadlines depends on the correctness and completeness of its models which describe events and actions that change the world state. It is often unrealistic to expect perfect models, so a planner must be able to detect and respond to states it had not planned to handle. In this paper, we characterize different classes of these &amp;quot;unhandled&amp;quot; states and describe planning algorithms to build tests for, and later respond to them. We have implemented these unhandled state detection and response algorithms in the Cooperative Intelligent Real-time Control Architecture (CIRCA), which combines an AI planner with a separate real-time system so that plans are built, scheduled, and then executed with real-time guarantees. Test results from flight simulation show the new algorithm enables a fully-automated aircraft to react appropriately to certain classes of unhandled states, averting failure and giving the aircraft a new chance to achieve its ...
Coupled Research in Ocean Acoustics and Signal Processing for the Next Generation of Underwater Acoustic Communication Systems (2014)

Abstract : Technical work this period focused on two areas. The first was continuation of work on developing a methodology within the framework of asymptotic random matrix theory (RMT) to explicitly model the time variability of acoustic channels and using this to predict underwater acoustic communications systems performance. Prior methods have accommodated time variability by assuming that the channel is time invariant over an appropriately short interval of time. By explicitly modeling the time variability within the RMT framework it is hoped that the resulting analysis will more accurately predict the trade-offs associated with the rate of channel fluctuations, the number and configuration of hydrophone array elements, the size of filters in subsequent equalizers, and the structure of the equalizer adaptation algorithms. The work has progressed with the development of a framework in which the channel variability represented by the Delay-Doppler spread function denoted by U(epsilon, nu).
Three additional inositol 1,4,5-trisphosphate receptors: molecular cloning and differential localization in brain and peripheral tissues. (1992)

Three inositol 1,4,5-trisphosphate receptor (IP3R) cDNAs, designated IP3R-II, -III, and -IV, were cloned from a mouse placenta cDNA library. All three display strong homology in membrane-spanning domains M7 and M8 to the originally cloned cerebellar IP3R-I, with divergences predominantly in cytoplasmic domains. Levels of mRNA for the three additional IP3Rs in general are substantially lower than for IP3R-I, though in the gastrointestinal tract the levels of IP3R-III may be comparable to IP3R-I. Cerebellar Purkinje cells express at least two and possibly three distinct IP3Rs, suggesting heterogeneity of IP3 action within a single cell.
Intestinal spirochete infections of chickens: a review of disease associations, epidemiology and control (2001)

This paper presents an overview of intestinal spirochete infections of chickens. It focuses particularly on studies in Australia, where recent surveys of 136 layer and broiler breeder flocks have revealed a high rate of infection (>40%) with intestinal spirochetes. Infection was not detected in broiler flocks. Approximately 50% of isolates from infected flocks were Brachyspira (Serpulina) intermedia or B. pilosicoli, with the other isolates being B. innocens, B. murdochii or the proposed species 'B. pulli'. No isolates of B. alvinipulli were found. Intestinal spirochetes were significantly associated with wet litter problems and/or reduced egg production. Experimental infection of point-of-lay birds with either B. intermedia or B. pilosicoli caused reduced egg production, and, with B. intermedia, a significant increase in fecal moisture content. Infection with B. innocens caused no significant changes. In-water treatment of a flock with a mixed spirochete infection using lincospectin resulted in a slimy diarrhea lasting for 2-3 weeks, followed by absence of spirochetes for 3 months. Birds treated with tiamulin remained healthy, and had a reduced level of infection with intestinal spirochetes (30%) for 3 months. Trials are under way to test the efficacy of antimicrobials in point-of-lay chickens experimentally infected with either B. intermedia or B. pilosicoli.
QMSum: A New Benchmark for Query-based Multi-domain Meeting Summarization (2021)

Ming Zhong, Da Yin, Tao Yu, Ahmad Zaidi, Mutethia Mutuma, Rahul Jha, Ahmed Hassan Awadallah, Asli Celikyilmaz, Yang Liu, Xipeng Qiu, Dragomir Radev. Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2021.
Gender differences in the handling of biologically‐active magnesium (Mg2+) and calcium (Ca2+) in short‐term (S‐T) dietary magnesium deficiency (MD); Implications for cardiovascular diseases (CVD) (2008)

There has been a steady decline in the dietary intake of Mg in the USA. Is there a gender difference in the handling of Mg2+? To test this hypothesis, we induced S‐T MD (10% normal intake)in young ,mature male and female Wistar rats and used ISEs to measure, precisely, serum levels of Mg2+, Ca2+, Ca2+/Mg2+ ratios and total Mg (tMg).The MD‐animals were allowed to drink triply‐distilled water containing one of five different levels of Mg ,while control animals received a normal Mg‐containing diet The data indicate that male and female rats, on normal Mg diets ,exhibit identical serum levels of Mg2+(0.64 +/− 0.02 vs.0.63 +/− 0.3 mM),Ca2+(1.47 +/− 0.08 vs 1.43 +/− 0.03 mM),and Ca2+/Mg2+ ratios (2.30 vs.2.17). The MD‐male and female rats exhibited different Mg2+(0.26+/−0.04 vs. 0.36+/−0.06 mM),tMg and Ca2+/Mg2+ ratios ( 6.19 vs 4.3) from one another and the controls ( p&lt; 0.01). Feeding water‐borne Mg failed to restore Mg2+ or tMg to normal serum levels in male animals ,but the higher water‐borne levels of Mg in females were able to restore serum Mg2+ and tMg to normal.We demonstrate ,for the first time, that ;1) mature male MD‐ rats do not have an ability to mobilize biologically‐active Mg2+ as do female mature MD‐ rats; 2) male rats exhibit high serum Ca2+/Mg2+ ratios in a S‐T MD state, which would result in increased risk for the development of CVD.
The 2.7-Å crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase (2006)

The x-ray crystal structure of a 194-kDa fragment from module 5 of the 6-deoxyerythronolide B synthase has been solved at 2.7 Angstrom resolution. Each subunit of the homodimeric protein contains a full-length ketosynthase (KS) and acyl transferase (AT) domain as well as three flanking "linkers." The linkers are structurally well defined and contribute extensively to intersubunit or interdomain interactions, frequently by means of multiple highly conserved residues. The crystal structure also reveals that the active site residue Cys-199 of the KS domain is separated from the active site residue Ser-642 of the AT domain by approximately 80 Angstrom. This distance is too large to be covered simply by alternative positioning of a statically anchored, fully extended phosphopantetheine arm of the acyl carrier protein domain from module 5. Thus, substantial domain reorganization appears necessary for the acyl carrier protein to interact successively with both the AT and the KS domains of this prototypical polyketide synthase module. The 2.7-Angstrom KS-AT structure is fully consistent with a recently reported lower resolution, 4.5-Angstrom model of fatty acid synthase structure, and emphasizes the close biochemical and structural similarity between polyketide synthase and fatty acid synthase enzymology.
Mechanical strength of single cellulose nanofibrils estimated from sonication-induced fragmentation (2013)

Mechanical strength of single cellulose nanofibrils estimated from sonication-induced fragmentation
Data from RNF6 Promotes Colorectal Cancer by Activating the Wnt/β-Catenin Pathway via Ubiquitination of TLE3 (2023)

&lt;div&gt;Abstract&lt;p&gt;Gene amplification is a hallmark of cancer and is frequently observed in colorectal cancer. Previous whole-genome sequencing of colorectal cancer clinical specimens identified amplification of Ring finger protein 6 (RNF6), a RING-domain E3 ubiquitin ligase. In this study, we showed that &lt;i&gt;RNF6&lt;/i&gt; is upregulated in 73.5% (147/200) of patients with colorectal cancer and was positively associated with &lt;i&gt;RNF6&lt;/i&gt; gene amplification. Furthermore, RNF6 expression and its gene amplification were independent prognostic factors for poor outcome of patients with colorectal cancer. RNF6 promoted cell growth, cell-cycle progression, and epithelial-to-mesenchymal transition in colorectal cancer cells; RNF6 also promoted colorectal tumor growth and lung metastasis in mouse models. Mechanistic investigations revealed that RNF6 bound and ubiquitylated transducin-like enhancer of split 3 (TLE3), a transcriptional repressor of the β-catenin/TCF4 complex. RNF6-mediated degradation of TLE3 significantly suppressed the association of TLE3 with TCF4/LEF, which in turn led to recruitment of β-catenin to TCF4/LEF, triggering Wnt/β-catenin activation. Restoration of TLE3 expression abolished the oncogenic effects of RNF6. Taken together, these results demonstrate that RNF6 plays a pivotal oncogenic role in colorectal tumorigenesis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Significance:&lt;/b&gt; RNF6-mediated ubiquitination and degradation of TLE3 activates the Wnt/β-catenin pathway in colorectal carcinogenesis. &lt;i&gt;Cancer Res; 78(8); 1958–71. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Measurement of the top quark pair production cross-section with ATLAS in the single lepton channel (2012)

A measurement of the production cross-section for top quark pairs (tt¯) in pp collisions at s=7TeV is presented using data recorded with the ATLAS detector at the Large Hadron Collider. Events are selected in the single lepton topology by requiring an electron or muon, large missing transverse momentum and at least three jets. With a data sample of 35 pb−1, two different multivariate methods, one of which uses b-quark jet identification while the other does not, use kinematic variables to obtain cross-section measurements of σtt¯=187±11(stat.)−17+18(syst.)±6(lumi.)pb and σtt¯=173±17(stat.)−16+18(syst.)±6(lumi.)pb respectively. The two measurements are in agreement with each other and with QCD calculations. The first measurement has a better a priori sensitivity and constitutes the main result of this Letter.
Transcription factor-based biosensor (2023)

The present invention provides for a system comprising a BmoR transcription factor, a .sigma..sup.54-RNA polymerase, and a pBMO promoter operatively linked to a reporter gene, wherein the pBMO promoter is capable of expression of the reporter gene with an activated form of the BmoR and the .sigma..sup.54-RNA polymerase.