gebhart/patrepeval huggingface dataset:
Abstract A013: CDK2 and CDK4/6 inhibition in GIST: Mechanisms of response and resistance (2022)

Abstract Advanced GIST is characterized by genomic perturbations of key cell cycle regulators. Oncogenic activation of CDK4/6 results in RB1 inactivation and cell cycle progression. Given that single-agent CDK4/6 inhibitor (CDK4/6i) therapy failed to show clinical activity in advanced GIST, we evaluated strategies for maximizing response to therapeutic CDK4/6 inhibition. Targeted next-generation sequencing and multiplexed protein imaging were used to detect cell cycle regulator aberrations in GIST clinical samples (N=18), including 8 metastatic TKI-resistant GISTs. Multiple metastases were analyzed in 3 patients. The impact of CDK2i (CDK2 inhibitor-II), CDK4/6i (palbociclib or abemaciclib), and CDK2/4/6i (PF-06873600) was determined through cell proliferation and protein detection assays in vitro and in vivo. Mechanisms of acquired CDK2i and CDK4/6i resistance were characterized in GIST cell lines after long-term exposure. The results demonstrate recurrent genomic aberrations in cell cycle regulators causing co-activation of the CDK2 and CDK4/6 pathways. Identical aberrations of p16, RB1, and TP53 were present in all metastases from 3 patients. We show that therapeutic co-targeting of CDK2 and CDK4/6 is synergistic in GIST cell lines with intact RB1, through inhibition of RB1 hyperphosphorylation and cell proliferation (P&amp;lt;0.01). Intact RB1 predicted response to treatment, whereas RB1-deficient models were resistant. Moreover, we identify RB1 inactivation and a novel oncogenic cyclin D1 resulting from an intragenic rearrangement (CCND1::chr11.g:70025223) as mechanisms of acquired CDK inhibitor resistance in GIST. The CCND1 rearrangement deleted the cyclin D1 C-terminal Thr286 and Thr288 residues which mediate cyclin D1 proteasomal degradation, resulting in overexpression of an abnormal cyclin D1. CDK inhibitor resistance properties were corroborated by lentiviral transduction of the CCND1 fusion gene into fusion-negative GIST, leiomyosarcoma, and breast cancer cells. These studies establish the biologic rationale for CDK2 and CDK4/6 co-inhibition as therapeutic strategy in patients with advanced GIST, including patients with metastatic GIST progressing on TKIs. In addition, these findings expand the spectrum of potential CDK inhibitor resistance mechanisms with translational potential for improving cell cycle targeted therapies in other cancer types. Citation Format: Inga-Marie Schaefer, Matthew L. Hemming, Meijun Z. Lundberg, Matthew P. Serrata, Isabel Goldaracena, Ninning Liu, Peng Yin, Joao A. Paulo, Steven P. Gygi, Suzanne George, Jeffrey A. Morgan, Monica M. Bertagnolli, Ewa T. Sicinska, Adrian Mariño-Enríquez, Jason L. Hornick, Chandrajit P. Raut, George D. Demetri, Wen-Bin Ou, Sinem K. Saka, Jonathan A. Fletcher. CDK2 and CDK4/6 inhibition in GIST: Mechanisms of response and resistance [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A013.
Reconfigurable scan‐beam hollow patch reflectarray antenna loaded with tunable capacitor (2008)

Abstract In this article, the design concept of an active reconfigurable reflectarray antenna has been proposed and tested. The elementary radiators are hollow patch element loaded with varactor‐diode device in which the reflected phase can be varied. This phase alteration is based on the variation of the diode capacitance which can be achieved by varying the biasing voltage of the active varactor device. By activating these varactor devices, the phase of each antenna element in the array configuration can be adopted dynamically, and consequently, its radiation beam direction can be reconfigured. The advantage of the MEMS switches is the complexity of the integration and continuing beam scanning capability. The reflectarray incorporating active elements has been built and tested at 6.0 GHz. Narrow band multifrequency shared aperture is demonstrated theoretically and experimentally. The performance of the proposed active antenna is excellent, which pioneers the design of arbitrarily reconfigurable antennas. © 2008 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 367–374, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24050
Defluviimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat, and emended description of the genus Defluviimonas Foesel et al. 2011 (2013)

A novel Gram-staining-negative, strictly aerobic bacterium, designated BS14(T), was isolated from a marine tidal flat of the South Sea in Korea. Colonies were opaque, white, smooth and circular on marine agar. Cells were moderately halophilic, non-motile rods showing catalase- and oxidase-positive reactions. Growth of strain BS14(T) was observed at 5-40 °C (optimum: 30 °C), pH 6.5-9.5 (optimum: 7.0-7.5) and 0-10 % (w/v) NaCl (optimum: 1-1.5 %). The G+C content of the genomic DNA was 61.6 mol%. Strain BS14(T) contained ubiquinone-10 (Q-10) as the sole respiratory quinone and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0 3-OH, C10 : 0 3-OH and C18 : 0 as the major fatty acids. The polar lipid pattern comprised phosphatidylethanolamine, diphosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and an unidentified polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BS14(T) formed a tight phylogenetic lineage with Defluviimonas denitrificans D9-3(T) with a bootstrap value of 100 %. The 16S rRNA gene sequence similarity between strain BS14(T) and D. denitrificans D9-3(T) was 97.4 % and their DNA-DNA relatedness was 19.1 ± 3.6 %. Based on the phenotypic and genotypic studies, strain BS14(T) represents a novel species of the genus Defluviimonas, for which the name Defluviimonas aestuarii sp. nov. is proposed. The type strain is BS14(T) (= KACC 16442(T) = JCM 18630(T)). An emended description of the genus Defluviimonas Foesel et al. 2011 is also proposed.
Improved room-temperature-selectivity between Nd and Fe in Nd recovery from Nd-Fe-B magnet (2015)

The sustainable society requires the recycling of rare metals. Rare earth Nd is one of rare metals, accompanying huge consumption especially in Nd-Fe-B magnets. Although the wet process using acid is in practical use in the in-plant recycle of sludge, higher selectivity between Nd and Fe at room temperature is desired. We have proposed a pretreatment of corrosion before the dissolution into HCl and the oxalic acid precipitation. The corrosion produces $γ$-FeOOH and a Nd hydroxide, which have high selectivity for HCl solution at room temperature. Nd can be recovered as Mn$_{2}$O$_{3}$-type Nd$_{2}$O$_{3}$. The estimated recovery-ratio of Nd reaches to 97\%.
Acyl-chain selectivity of the 85 kDa phospholipase A2 and of the release process in intact macrophages (1994)

The selectivity of the intracellular 85 kDa phospholipase A2 (PLA2-85) towards fatty acids closely related to arachidonic acid has been investigated, using purified PLA2-85 from J774 cells and mixed phospholipids, dually acyl-chain-labelled in the sn-2 position. In parallel experiments, we assessed the acyl-chain selectivity of the release process in intact, dually labelled, peritoneal mouse macrophages responding to either calcium ionophore or zymosan beads in the presence of indomethacin and BSA. The results obtained in the two systems were very similar, which supports previous evidence that PLA2-85 is responsible for stimulus-induced release of eicosanoid precursor in mouse macrophages. In the in vitro system, PLA2-85 was found to exhibit a moderate selectivity towards C20 acyl chains differing in double-bond structure, while the sensitivity to acyl-chain length was more pronounced. Together with previous data, these results demonstrate a striking preference for C20 over either C18 or C22 unsaturated acyl chains.
Plant Regeneration from Cotyledons of Cucumis melo `Topmark' (1991)

A procedure for the regeneration of muskmelon (Cucumis melo L.) cv . Topmark via shoot organogenesis from cotyledon explants is described. The best induction medium for a morphogenic response was MS salts and vitamins medium with BA at 1.0 mg·liter -1 . Further vegetative bud development was completed by transferring organogenic tissue to MS medium containing BA at 0.05 mg·liter -1 . The shoots were rooted in MS medium containing NAA at 0.01 mg·liter -1 . Morphologically normal plantlets were obtained. Chemical abbreviations used: 6-benzylaminopurine (BA); indoleacetic acid (IAA); naphthaleneacetic acid (NAA).
Organic–Inorganic Sn12 and Organic Sn6 Oxide–Hydroxide Clusters (2006)

Organic meets inorganic: Hydrolysis of an aryl trialkynyl tin compound leads to an organic–inorganic tin oxide–hydroxide cluster, which consists of an inorganic tin oxide core surrounded by eight aryl tin fragments (see picture, left; Sn green, inorganic Sn blue, O red, C gray, H pink). Slightly modified reaction conditions produce a hexameric aryl tin oxide–hydroxide cage, which can be described as a double-twist Möbius band (see picture, right).
Effect of glucocorticoids on the passive transport of phosphate in different segments of the intestine in the rat. (1987)

We investigated the influence of glucocorticoids on phosphate absorption in the duodenum, mid-jejunum, ileum and colon. Phosphate transport, fluid absorption and sodium absorption were determined by the in vivo ligated loop technique. The administration of cortisone stimulated intestinal fluid absorption in each segment of the small intestine, but not in the colon. Cortisone enhanced net sodium absorption in proportion to the increase in fluid absorption. Phosphate was most effectively absorbed in the duodenum and jejunum. Net phosphate absorption in the ileum and colon was negligible. Administration of cortisone stimulated the passive transport of phosphate in each segment of the small intestine studied. The 32Pi absorption was increased 56, 54 and 97% in the duodenum, jejunum and ileum, respectively. There was no apparent stimulation of passive transport of phosphate by cortisone in the colon. Although the exact mechanism is unknown, increased luminal phosphate concentration gradient or enhanced sodium and water absorption after cortisone administration could account for the increase in phosphate transport in the small intestine. However, the effects of these factors vary from segment to segment.
An Algorithm of Large-Scale Approximate Multiple String Matching for Network Security (2006)

Payload checking has become the basic technique for network security applications, where the exact string matching technology is widely used. But as the game between attackers and defenders goes further into payload confusion, the approximate string matching technology is needed, especially large-scale approximate multiple string matching technology. In this paper, we propose one practical algorithm, LargePEX, for large scale approximate multiple string matching based on edit distance. The algorithm is basically extended from PEX, an algorithm of approximate single string matching, with the idea of filtering and verification. LargePEX is finely designed to fit for large-scale matching using fine grain steps analyses. Some experiments are presented to verify the efficiency of LargePEX. As the results show, for the set of 10k strings, the average network payload checking speed using this algorithm can achieve 25 MBps-40 MBps, enough for 100 Mbps Ethernet. With hardware upgrading, the algorithm is also practical for Gigabit Ethernet. So LargePEX provides a new way for defenders to develop more effective methods to protect valuable resources and prevent intrusions by payload checking.
Pseudouridine modifications influence binding of aminoglycosides to helix 69 of bacterial ribosomes (2017)

Development of antibiotics that target new regions of functionality is a possible way to overcome antibiotic resistance. In this study, the interactions of aminoglycoside antibiotics with helix 69 of the E. coli 23S rRNA in the context of complete 70S ribosomes or the isolated 50S subunit were investigated by using chemical probing and footprinting analysis. Helix 69 is a dynamic RNA motif that plays major roles in bacterial ribosome activity. Neomycin, paromomycin, and gentamicin interact with the stem region of helix 69 in complete 70S ribosomes, but have diminished binding to the isolated 50S subunit. Pseudouridine modifications in helix 69 were shown to impact the aminoglycoside interactions. These results suggest a requirement for a specific conformational state of helix 69 for efficient aminoglycoside binding, and imply that this motif may be a suitable target for mechanism-based therapeutics.
ChemInform Abstract: THERMISCHES VERHALTEN VON MESITYLALLENEN, AROMATISCHE (1,5S)‐SIGMATROPE H‐VERSCHIEBUNG (1970)

Abstract Durch Umlagerung der Dienole (I) werden die Mesitylallene (II) erhalten.Beim Erhitzen von (IIa) in der 100fachen Menge Decan auf 170° tritt in ei‐ner Reaktion 1. Ordnung eine glatte Umlagerung zu dem Naphthalin (III)ein.
Effect of water on the iron-catalyzed Fischer-Tropsch synthesis (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of water on the iron-catalyzed Fischer-Tropsch synthesisCharles N. Satterfield, Robert T. Hanlon, Shao E. Tung, Zuo Min Zou, and Georgia C. PapaefthymiouCite this: Ind. Eng. Chem. Prod. Res. Dev. 1986, 25, 3, 407–414Publication Date (Print):September 1, 1986Publication History Published online1 May 2002Published inissue 1 September 1986https://doi.org/10.1021/i300023a007RIGHTS & PERMISSIONSArticle Views478Altmetric-Citations57LEARN 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 InReddit PDF (911 KB) Get e-Alerts
Short Exposure to Sublethal Heat Shock Facilitates Dormancy Release in Grapevines (2011)

A wet heat shock (WHS) treatment in a water bath at 50°C for 1 hr is a powerful stimulus for grapevine budbreak. However, this treatment is not feasible as a horticultural practice in commercial vineyards. The development of an effective horticultural dormancy release practice favors a short, intense heat shock that combines convenient application and effective stimulation of budbreak. Thus, the influence of heat shock temperature and duration on dormancy release of grapevine buds was studied. Results suggested that in both WHS and dry heat shock (DHS) treatments, increased temperature can compensate for shortened shock duration. In addition, it appeared that buds better tolerate DHS than WHS. Based on these results, we analyzed the effect of short and intense heat shock on budbreak. A DHS of 10 to 30 sec at the sublethal temperature of 150°C served as a powerful stimulus of dormancy release. This short shock induced production of acetaldehyde and ethylene from the buds, as follows application of hydrogen cyanamide. This similarity suggests that analogous mechanisms are activated by the short, sublethal temperature pulse and the commercially used chemical stimulus. The efficiency of short and intense heat shock, which has not been previously documented, will aid the development of a feasible and practical treatment in commercial vineyards.
Influence of filler settling on the analysis of solder reliability of flip chip packaging (2008)

In the capillary-flow underfilling process many practical evidences suggest that the distribution of fillers is not uniform as is usually assumed. It is likely caused by filler sedimentation, variation of the flow pattern, and rheology of uncured underfill flow, etc. Such a nonuniform distribution of fillers requires that we modify the reliability estimates of flip chip packages that are based on an ideal, isotropic underfill. This paper reports an analytical study of the influence of filler settling on the flip chip solder reliability analysis. By taking 35% for the volume fraction of silica fillers, we have described the y-dependent filler settling by three settling scenarios and calculated the thermomechanical properties of the underfill by considering three types of temperature-dependent, linearly elastic epoxy resins for each settling profile. In total, nine underfill materials were individually introduced in a 2D finite element flip chip package model to comparatively study the thermal response of flip chip solder joints that are surrounded by the underfill. The FE results showed that the inelastic shear strains steadily accumulate in the flip chip solder joints. The inelastic shear strains increase significantly as filler settling is introduced. We also observed that as the extent of filler settling increases, the average inelastic shear strain energy density associated with the outermost solder joint increases.
Papillomavirus Trans-activator Protein E2 Activates Expression from the Promoter for the Ribonucleotide Reductase Large Subunit from Herpes Simplex Virus Type 2 (1990)

Activation of the herpes simplex virus type 2 (HSV-2) large subunit of the ribonucleotide reductase (ICP10) gene by papillomavirus DNA encoding the E2 or E7 proteins was studied directly by immunofluorescence or by chloramphenicol acetyltransferase (CAT) analysis with hybrid ICP10 or IE175 and 38K promoter constructions. Cotransfection with bovine papillomavirus type 1 or human papillomavirus type 16 (HPV-16) E2 DNA enhanced CAT expression from constructions in which CAT is regulated by the ICP10 but not by other HSV promoters. Expression was not enhanced by cotransfection with HPV-16 E7 DNA. Sequence analysis of the ICP10 promoter identified a consensus E2-binding motif. Activation was significantly reduced by site-directed mutagenesis of the consensus motif.
The Relationship between Internet Usage and the Marketing of Tourism in Libya (2009)

Diets have been shown to alter metabolism and gene expression. However, few data are available about changes in gene expression in liver after intake of different meat protein diets. This work aimed to explore the long-term effects of protein source on liver metabolic enzymes. Rats were fed protein diets for 90 days to study whether intake of chicken and pork protein diets promoted gene expression involved in hepatic metabolism. Liver proteome profiles were measured by iTRAQ labeling and LC-ESI-MS/MS. Chicken protein diet induced higher level of serum amino acids in rats than soy protein. Amino acid metabolizing enzymes were downregulated by pork and chicken protein diets compared with soy protein diet. Intake of meat protein diets downregulated enzymes involved in protein synthesis, disulfide bond formation, signal peptide addition, transport, localization, degradation and glycosylation modification, but upregulated enzymes involved in prolyl cis-trans isomerization for protein synthesis. Protein diets from different sources affected the amino acid supply, and further influenced ribosome assembly and protein synthesis through mTOR signaling pathway.
Rhythmic Serotonin N -Acetyltransferase mRNA Degradation Is Essential for the Maintenance of Its Circadian Oscillation (2005)

Serotonin N-acetyltransferase (arylalkylamine N-acetyltransferase [AANAT]) is the key enzyme in melatonin synthesis regulated by circadian rhythm. To date, our understanding of the oscillatory mechanism of melatonin has been limited to autoregulatory transcriptional and posttranslational regulations of AANAT mRNA. In this study, we identify three proteins from pineal glands that associate with cis-acting elements within species-specific AANAT 3' untranslated regions to mediate mRNA degradation. These proteins include heterogeneous nuclear ribonucleoprotein R (hnRNP R), hnRNP Q, and hnRNP L. Their RNA-destabilizing function was determined by RNA interference and overexpression approaches. Expression patterns of these factors in pineal glands display robust circadian rhythm. The enhanced levels detected after midnight correlate with an abrupt decline in AANAT mRNA level. A mathematical model for the AANAT mRNA profile and its experimental evidence with rat pinealocytes indicates that rhythmic AANAT mRNA degradation mediated by hnRNP R, hnRNP Q, and hnRNP L is a key process in the regulation of its circadian oscillation.
Additional file 3: Figure S1. of Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance (2017)

Comparative genome analysis of P. yonginensis DCY84T and P. polymyxa M1 using the Artemis software and ACT. (TIFF 16717 kb)
MINIMIZATION OF MICROABSORPTION EFFECTS IN COMPLEX MIXTURES (2003)

In using X-ray diffraction (XRD) and the Rietveld method there are many factors that affect the results and the interpretation of the data that are collected. One of these is microabsorption. Microabsorption has historically been ignored or accounted for using the Brindley correction. This correction has come under much debate in recent years. A recent Round Robin study on quantitative analysis included data that was less accurate overall when the correction was used. This study focuses on examining factors that will aid in minimizing microabsorption effects and assessing microabsorption effects under various conditions; including absorption characteristics of the sample, absorption characteristics of the internal standard and particle size of the internal standard. The data was examined using the Rietveld refinement method, and the results were then compared with and without the Brindley correction.
Wick Technique: Reference Method for Implanted Glucose Sensors (1989)

The control of function of experimentally implanted glucose sensors needs an independent reference method. Employing saline-impregnated cotton threads, an implanted wick-technique was adopted in dogs to obtain analytical specimen from the subcutaneous interstitial fluid compartment. By measuring the contents of potassium, calcium, and hemoglobin, the centrifuged wick fluid was validated to contain the interstitial concentrations of solutes after an equilibration time of approximately 15 min. Between 2 and 25 mmol/L, the steady state subcutaneous glucose concentration is nearly identical to circulating glycemia. Slow alterations, as during an oral glucose tolerance test, (OGTT) are well paralleled by the levels in the wick fluid. During alterations, however, a distinct delay is observed. The wick-based glucose levels are mirrored by the output of electrochemical sensors implanted at the same site. This method may be used in checking implanted sensors that can otherwise not be calibrated in situ.