gebhart/patrepeval huggingface dataset:
Abstract 4399: In vitro and in vivo evaluations of correlation between the activation status of signaling pathways and the efficacy of anticancer compounds in a panel of JFCR39 human cancer cell lines (2011)

Abstract The phosphoinositide 3-kinase (PI3K) pathway and the Ras/mitogen-activated protein kinase (MAPK) pathway are frequently activated in cancer. Activation of these pathways contribute to cell survival, cell cycle progression and cell growth in the tumor, and are expected to influence the efficacy of antitumor compounds including conventional antitumor drugs, PI3K pathway inhibitors and Ras/MAPK pathway inhibitors. However, it is not well understood whether the efficacies of anticancer compounds can be predicted based on these aberrations and on the activation status of signaling pathway members. To clarify this issue, we first examined the mutation, expression and phosphorylation status of PI3K and Ras/MAPK pathway members in a panel of 39 pharmacologically well-characterized human cancer cell lines (JFCR39). Second, we evaluated the in vitro efficacy of various anticancer compounds including PI3K and Ras/MAPK pathway inhibitors and conventional anticancer drugs, combining these data to construct an integrated database of pathway activation status and drug efficacies (JFCR39-DB). In silico analysis of JFCR39-DB enabled us to evaluate correlations between the status of pathway members and the drug efficacies in vitro. For example, KRAS/BRAF mutation prominently correlated with the efficacy of a MEK inhibitor and the inefficacy of PI3K inhibitors, respectively, while phosphorylation levels of Akt correlated with the efficacy of PI3K inhibitors. Some of these correlations were confirmed in human tumor xenografts in vivo, consistent with their ability to serve as predictive biomarkers. Our findings show that JFCR39-DB is a useful tool to identify predictive biomarkers and to study molecular pharmacology of the PI3K and Ras/MAPK pathways in cancer therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4399. doi:10.1158/1538-7445.AM2011-4399
STABLE WHITE LIGHT-EMITTING DIODE BASED ON POLYMER BILAYER STRUCTURE (2006)

White light-emitting diode was obtained based on polymer bilayer structure of poly(N-vinlycarbazole)(PVK) and green light-emitting copolymer(PFSeH) of 9'9-dioctylfluorene(DOF) and selenophene(SeH).The diode structure is ITO/PEDOT/PVK/PFSeH/Ba/Al.At the optimum layer thickness of PVK and PFSeH,respectively,the stable white light emission was realized.The maximum luminescence efficiency is 0.51 cd/A at a bias of 13 V,the corresponding brightness reaches 750 cd/m~2 and the Commission Internationale de I'Eclairage coordinates becomes around(0.32,0.32).In additional,white light emission spectrum of bilayer device remained invariable at the drive voltages such as 10 V to 18 V.The white light-emission of bilayer device was considered to be blue light-emitting of PVK layer,green light-emitting of PFSeH layer and red light-emitting of exciplexes in the interface between PFSeH layer and PVK layer.
Recent transposition of yabusame, a novel piggyBac-like transposable element in the genome of the silkworm, Bombyx mori (2010)

On the W chromosome of the silkworm, Bombyx mori , we found a novel piggyBac-like DNA transposon that potentially encodes an intact transposase (610 amino acid residues), which is flanked by 16-bp perfect inverted terminal repeats and a duplicated TTAA target site. Interestingly, we also identified another intact copy of this transposon on an autosome (chromosome 21), which showed 99.6% identity in the DNA sequence of the transposase (99.3% amino acid identity). These features raised the possibility that this novel piggyBac-like DNA transposon, designated as yabusame, may retain transposition activity. Here we report the identification and characterization of yabusame transposons from the silkworm. We cloned the full length of the yabusame transposon on the W chromosome (yabusame-W) and its autosomal copy (yabusame-1). Southern blot analysis showed that there are interstrain polymorphisms in yabusame elements for their insertion sites and copy number. We also found strong evidence for the recent transposition of yabusame elements in the silkworm genome. Although our in vitro excision assays suggested that the transposition activity of yabusame-1 and yabusame-W has been lost almost entirely, our data will lead to a greater understanding of the characteristics of piggyBac superfamily elements.
Early Endosomes Act as Local Exocytosis Hubs to Repair Endothelial Membrane Damage (2023)

The plasma membrane of a cell is subject to stresses causing ruptures that must be repaired immediately to preserve membrane integrity and ensure cell survival. Yet, the spatio-temporal membrane dynamics at the wound site and the source of the membrane required for wound repair are poorly understood. Here, it is shown that early endosomes, previously only known to function in the uptake of extracellular material and its endocytic transport, are involved in plasma membrane repair in human endothelial cells. Using live-cell imaging and correlative light and electron microscopy, it is demonstrated that membrane injury triggers a previously unknown exocytosis of early endosomes that is induced by Ca<sup>2+</sup> entering through the wound. This exocytosis is restricted to the vicinity of the wound site and mediated by the endosomal soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) VAMP2, which is crucial for efficient membrane repair. Thus, the newly identified Ca<sup>2+</sup> -evoked and localized exocytosis of early endosomes supplies the membrane material required for rapid resealing of a damaged plasma membrane, thereby providing the first line of defense against damage in mechanically challenged endothelial cells.
Wavelength-Selective Sequential Polymer Network Formation Controlled with a Two-Color Responsive Initiation System (2017)

We report a wavelength-selective polymerization process controlled by visible/UV light, whereby a base is generated for anion-mediated thiol-Michael polymerization reaction upon exposure at one wavelength (400-500 nm), while radicals are subsequently generated for a second stage radical polymerization at a second, independent wavelength (365 nm). Dual wavelength, light controlled sequential polymerization not only provides a relatively soft intermediate polymer that facilitates optimum processing and modification under visible light exposure but also enables a highly cross-linked, rigid final material after the UV-induced second stage radical polymerization. A photobase generator, NPPOC-TMG, and a photo-radical initiator, Irgacure 2959, were selected as the appropriate initiator pair for sequential thiol-Michael polymerization and acrylate homopolymerization. FT-IR and rheological tests were utilized to monitor the dual cure photo-polymerization process, and mechanical performance of the polymer was characterized at each distinct stage by dynamic mechanical analysis (DMA). By demonstrating complete light control in another sequential polymerization system (thiol-Michael and thiol-ene hybrid polymerization), this initiator pair exhibits great potential to regulate many other coupled anion and radical hybrid polymerizations in both a sequential and controllable manner.
New Proton‐Sponge‐Like Macrocyclic Compound: Synergistic Hydrogen Bonds of Aminopyridine (2006)

Abstract N , N′ , N″ ‐Tris( p ‐tolyl)azacalix[3](2,6)pyridine ( 1 ) that shows a high proton affinity (p K BH+ = 23.1 in CD 3 CN) has been classified as a new type of proton‐sponge‐like compound. X‐ray crystallography reveals that 1 is ideal for accommodating a single proton in its cavity. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
Pharmacogenomics study of thiazide diuretics and QT interval in multi-ethnic populations: the cohorts for heart and aging research in genomic epidemiology (2018)

Thiazide diuretics, commonly used antihypertensives, may cause QT interval (QT) prolongation, a risk factor for highly fatal and difficult to predict ventricular arrhythmias. We examined whether common single-nucleotide polymorphisms (SNPs) modified the association between thiazide use and QT or its component parts (QRS interval, JT interval) by performing ancestry-specific, trans-ethnic and cross-phenotype genome-wide analyses of European (66%), African American (15%) and Hispanic (19%) populations (N=78 199), leveraging longitudinal data, incorporating corrected standard errors to account for underestimation of interaction estimate variances and evaluating evidence for pathway enrichment. Although no loci achieved genome-wide significance (P<5 × 10-8m), we found suggestive evidence (P<5 × 10-6) for SNPs modifying the thiazide-QT association at 22 loci, including ion transport loci (for example, NELL1, KCNQ3). The biologic plausibility of our suggestive results and simulations demonstrating modest power to detect interaction effects at genome-wide significant levels indicate that larger studies and innovative statistical methods are warranted in future efforts evaluating thiazide-SNP interactions.
Phosphine Oxides as Preligands in Ruthenium-Catalyzed Arylations via C−H Bond Functionalization Using Aryl Chlorides (2005)

The use of air-stable, electron-rich phosphine oxides as preligands allows for unprecedented general ruthenium-catalyzed arylation reactions of pyridines and imines through C−H-bond activation using aryl chlorides. The catalytic system derived from a sterically hindered adamantyl-substituted phosphine oxide proves highly efficient and tolerates a number of important functional groups.
AntimicrobialN-Halamine Polymers and Coatings: A Review of Their Synthesis, Characterization, and Applications (2013)

Antimicrobial N-halamine polymers and coatings have been studied extensively over the past decade thanks to their numerous qualities such as effectiveness toward a broad spectrum of microorganisms, long-term stability, regenerability, safety to humans and environment and low cost. In this review, recent developments are described by emphasizing the synthesis of polymers and/or coatings having N-halamine moieties. Actually, three main approaches of preparation are given in detail: polymerization, generation by electrochemical route with proteins as monomers and grafting with precursor monomers. Identification and characterization of the formation of the N-halamine bonds (>N-X with X = Cl or Br or I) by physical techniques such as Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance spectroscopy (NMR), energy-dispersive X-ray spectroscopy (EDX), X-ray photoelectron spectroscopy (XPS), and by chemical reactions are described. In order to check the antimicrobial activity of the N-halamine compounds, bacterial tests are also described. Finally, some examples of application of these N-halamines in the water treatment, paints, healthcare equipment, and textile industries are presented and discussed.
Intravascular versus surface cooling for targeted temperature management after out-of-hospital cardiac arrest – an analysis of the TTM trial data (2016)

Endovascular cooling devices were more precise than SFC methods in patients cooled at 33 °C after out-of-hospital cardiac arrest. Main outcomes were similar with regard to the cooling methods.
Excentric labeling (1999)

The widespread use of information visualization is hampered by the lack of effective labeling techniques. An informal taxonomy of labeling methods is proposed. We then describe excentric labeling, a new dynamic technique to label a neighborhood of objects located around the cursor. This technique does not intrude into the existing interaction, it is not computationally intensive, and was easily applied to several visualization applications. A pilot study with eight subjects indicates a strong speed benefit over a zoom interface for tasks that involve the exploration of large numbers of objects. Observations and comments from users are presented.
Hardware architecture design for explicit model predictive control (2006)

Solutions to constrained linear and hybrid model predictive control (MPC) can be explicitly characterized in terms of piecewise linear (PWL) state feedback control. A PWL controller is pre-computed using parametric programming, and the exact explicit MPC implementation corresponds to the evaluation of a PWL function in the control unit. It has recently been shown that such evaluation can be boosted by binary search tree data structures. We report digital hardware architecture design results for this type of PWL control, and show that explicit MPC solutions can be implemented in a standard field programmable gate array (FPGA) or an application specific integrated circuit (ASIC) with about 20 kGates leading to computation times around one microsecond per evaluation for typical applications. This facilitates implementation of constrained MPC in small-scale industrial and consumer electronics applications that are characterized by fast sampling or low production cost, such as mechatronics, MEMS, rotating machinery, power electronics, and acoustics
Pre-exposure to gamma rays alleviates the harmful effect of salinity on cowpea plants (2012)

Soil salinity is one of the most severe factors limiting growth and physiological response in cowpea plants. In this study, the low concentrations of NaCl (25mM) increased plant growth, photosynthetic pigments content, total soluble protein content, nucleic acids contents (DNA and RNA), lipid peroxidation, non enzymatic antioxidants (anthocyanin, ascorbic acids and α-tocopherol), number of legumes per plant, number of seeds per legume, number of seeds per plants, legume length, fresh and dry weight of legumes and weight of 1000 seeds and total soluble proteins and carbohydrate contents in harvested seeds as compared to control. On the other hand, the high concentrations of NaCl (50, 100 and 200 mM) caused reduction in plant growth, photosynthetic pigments content, total soluble protein content, nucleic acids contents (DNA and RNA), all yield attributes and harvested seeds components but increased lipid peroxidation and non enzymatic antioxidants (anthocyanin, ascorbic acids and α-tocopherol). Electrophoretic studies of proteins showed three types of modifications are observed in the protein patterns of cowpea seeds, some protein bands were disappeared, other proteins were selectively increased and synthesis of new set of protein was induced. Some of these responses were observed under gamma rays and salinity treatments, while others were induced by either gamma rays or salinity. Seeds irradiation with gamma rays alleviates the adverse effect of salt stress compared to non irradiated seeds.
Suppression of protein synthesis in brain during hibernation involves inhibition of protein initiation and elongation (1998)

Protein synthesis (PS) has been considered essential to sustain mammalian life, yet was found to be virtually arrested for weeks in brain and other organs of the hibernating ground squirrel, Spermophilus tridecemlineatus. PS, in vivo, was below the limit of autoradiographic detection in brain sections and, in brain extracts, was determined to be 0.04% of the average rate from active squirrels. Further, it was reduced 3-fold in cell-free extracts from hibernating brain at 37 degreesC, eliminating hypothermia as the only cause for protein synthesis inhibition (active, 0.47 +/- 0.08 pmol/mg protein per min; hibernator, 0.16 +/- 0.05 pmol/mg protein per min, P < 0.001). PS suppression involved blocks of initiation and elongation, and its onset coincided with the early transition phase into hibernation. An increased monosome peak with moderate ribosomal disaggregation in polysome profiles and the greatly increased phosphorylation of eIF2alpha are both consistent with an initiation block in hibernators. The elongation block was demonstrated by a 3-fold increase in ribosomal mean transit times in cell-free extracts from hibernators (active, 2.4 +/- 0.7 min; hibernator, 7.1 +/- 1.4 min, P < 0.001). No abnormalities of ribosomal function or mRNA levels were detected. These findings implicate suppression of PS as a component of the regulated shutdown of cellular function that permits hibernating ground squirrels to tolerate "trickle" blood flow and reduced substrate and oxygen availability. Further study of the factors that control these phenomena may lead to identification of the molecular mechanisms that regulate this state.
Purification of peptidyl-tRNA on benzoylated DEAE-cellulose columns (1975)

The o-nitrophenylsulfenyl group, and amino protecting group in the chemical synthesis of peptidyl-tRNA was used to attach newly synthesized peptidyl-tRNA to a benzoylated DEAE-cellulose column. This facilitated the isolation of a highly purified specific tRNA with a well defined peptide chain.
Effects of temporal variations in the acidity of rain on crop response to acidic deposition (Task Force Project) (1983)

The variation of rainfall pH from one event to another may have important biological consequences in several respects. A few rainfall events, or even only one, at low pH values may be more damaging than the same total hydrogen ion deposition spread out over a larger number of events with higher pH values. The variation of rainfall pH within events may also affect biological response. For example, during the early stages of an event, acid precipitation may be less effective in damaging vegetation since the water falling on the plant surfaces is continually being washed off by the subsequent rain. On the other hand, that rainwater which falls during the very last stages of an event remains on the vegetation until it evaporates. Since the concentration of contaminants remaining in solution on the leaves in these circumstances steadily increasing during evaporation, this particular rain may have a significantly greater effect. Of course, there is also a third hypothesis to the effect that it is primarily the total hydrogen ion deposition received by plant surfaces over a long period of time (conceivably, over an entire growing season) which is the most important parameter due to the cumulative stress imposed on themore » plant tissue over the entire period of exposure. The proposed experiments will determine which of these hypotheses best represents the response of a particular, economically-important crop species to the impact of more realistically programmed, acid rain simulant treatments. Design of the experiments is discussed.« less
Dynamics of mast cells in the nasal mucosa of patients with allergic rhinitis and non‐allergic controls: a biopsy study (1992)

Mast cell degranulation is thought to be an important component of the pathogenesis of allergic rhinitis. Quantitative studies on mast cells in nasal mucosa after allergen exposure have given widely divergent results, ranging from an overall decrease via redistribution to an overall increase. We investigated this problem by employing a combination of anti-IgE and toluidine blue staining of biopsy specimens. In allergic patients anti-IgE was found to identify all mast cells and toluidine blue to detect mast cells that were not (totally) degranulated. The study was composed of two parts done in different patient groups. In the first part of the study biopsies were performed in 23 patients with isolated grass-pollen allergy, once during natural provocation in the summer and once in the winter. Biopsies were also performed in 12 controls. Non-allergic controls were found to have the same number of mast cells in the lamina propria as asymptomatic allergic patients. The controls seldom have mast cells in the epithelium. The patients with isolated grass-pollen allergy showed an increase in the numbers of mast cells in the lamina propria during natural provocation and the same seemed to occur in the epithelium as well. During natural provocation almost all of the mast cells in the epithelium and half of those in the lamina propria were degranulated. In the second part of the study 17 patients with isolated grass-pollen allergy and four controls were challenged daily with allergen extract during a 2-week period in the winter. During this period biopsies were performed at eight different occasions, i.e. once before, six occasions during and once after the provocation period. The results of this part of the study showed that during provocation mast cells migrate to the surface of the nasal mucosa, where they become degranulated, and that the pool of mast cells in the lamina propria was apparently replenished by migration of mast cells from the vessels in the lamina propria. The total number of mast cells in the lamina propria remained approximately the same while the mast cells residing in an increasingly thick layer measured from the basal membrane into the lamina propria became degranulated. After 2 weeks, 82% of the mast cells in the lamina propria was degranulated and it was only in the deepest layers that some toluidine blue positive cells were found.(ABSTRACT TRUNCATED AT 400 WORDS)
Embedded Thin Film Sensors Based Multi-Mode Guided Wave Filter (2018)

Ultrasonic guided waves used in the diagnostic process exhibits multi-mode characteristics that make the damage detection process cumbersome. This paper presents the identification and selective filtering of multimodal Lamb wave in a composite laminate using embedded thin film sensors. A numerical approach based on finite element modeling is employed to estimate the response of embedded sensors. Using simple correlation of the sensor signal waveforms, the fundamental and higher order wave modes have been extracted from the mixed response. This technique is extendable to Rayleigh, Stoneley and Love waves.