gebhart/patrepeval huggingface dataset:
Microsatellite instability at selected tetranucleotide repeats is associated with p53 mutations in non-small cell lung cancer. (2000)

Microsatellite alterations are useful clonal markers for the early detection of cancer. An increase in microsatellite instability has been observed at certain tetranucleotide repeat markers (AAAGn) in lung, head and neck, and bladder cancer. However, the genetic mechanism underlying these elevated microsatellite alterations at selected tetranucleotide repeat (EMAST) tumors is still unknown. The p53 gene plays an important role in maintaining genome integrity by repairing damaged DNA. Therefore, we tested 88 non-small cell lung cancers with a panel of 13 microsatellite markers previously shown to exhibit frequent instability and also performed p53 sequence analysis in these tumors. Thirty-one of these 88 cancers (35%) demonstrated a novel allele [EMAST(+)] in > or =1 of these 13 microsatellite markers. p53 mutations were detected in 50 of 88 (57%) cancers and were significantly (P = 0.001) more common in EMAST(+) tumors (25 of 31; 81%) than in EMAST(-) tumors (25 of 57; 44%). Among squamous cell cancers, p53 mutations were detected significantly (P = 0.04) more frequently in EMAST(+) tumors (17 of 19; 89%) than in EMAST(-) tumors (10 of 18; 55%). Similarly, among primary adenocarcinomas, p53 mutations were present in 67% of the EMAST(+) tumors and in 35% of EMAST(-) adenocarcinomas. None of the 31 EMAST(+) tumors demonstrated high frequency microsatellite instability when examined with a reference panel of five mono- and dinucleotide markers. Primary lung cancers with microsatellite alterations at selected tetranucleotide repeats have a high frequency of p53 mutations and do not display a phenotype consistent with defects in mismatch repair.
Mechanomyogram measurement by lead zirconate titanate-based acoustic sensor (2018)

In this research, we focused on the mechanomyogram (MMG) for evaluating muscle activity. MMG signals were measured using a lead zirconate titanate (PZT)-based acoustic sensor. In previous research on MMG measurement, low-frequency MMG signals ranging from 10 to 100 Hz were mainly measured. On the other hand, where, MMG signals higher than 100 Hz, which is considered to be related to the resonance of muscle fibers, were focused on. To measure high-frequency components of MMG signals, we used a PZT-based acoustic sensor and measured the MMG of the biceps brachii muscle of four subjects. As a result, it was confirmed that all the subjects showed frequency components of 10 Hz to 10 kHz in the MMG. In particular, we confirmed that as the force exerted by the muscles increases, MMG signals of 100 Hz to 10 kHz become larger.
Kinetic studies of reactions of hydrogen atoms with HCl, Cl2 and NOCl, and chlorine atoms with H2 and NOCl (1982)

Rate constants for the reaction pair [graphic omitted] have been measured from 295 to 425 K under pseudo-first-order conditions ([HCl]0/[H]0 and [H2]0/[Cl]0≫ 1) using the discharge-flow-resonance-fluorescence technique. The rate constants followed the Arrhenius expressions: kf=(2.01 ± 0.3)× 10–11 exp [–(1790 ± 140)/T], kr=(6.00 ± 0.5)× 10–11 exp [–(2470 ± 100)/T].The ratio of these rate constants agrees with the thermodynamic equilibrium constant, suggesting that the complicating wall effects and secondary H-atom reactions observed in previous discharge-flow studies of these reactions have been eliminated.Similar kinetic studies at room temperature of the reactions: [graphic omitted] gave the rate constants: k2=(1.70 ± 0.26)× 10–11 cm3 molecule–1 s–1, k3=(1.82 ± 0.27)× 10–11 cm3 molecule–1 s–1, k4=(7.2 ± 2.4)× 10–11 cm3 molecule–1 s–1. The values for k2 and k3 are in excellent agreement with those reported by previous discharge-flow–resonance-fluorescence studies. The value for k4 is approximately a factor of two larger than the only other direct determination.
Supplementary Figure S6 from Integrating RAS Status into Prognostic Signatures for Adenocarcinomas of the Lung (2023)

&lt;p&gt;Supplementary Figure S6. Prognostic signatures derived from all NSCLC patients consistently perform better in RASwt than in RASmt patients in current studies where the number of RASmt patients is smaller compared to the number of RASwt patients (A-C). When balancing the number of RASwt and RASmt patients it is clear that different signatures are prognostic in these patient groups (D-F). A,D, Distribution of logged HR in all, only RASwt and only RASmt patients (combined permutations of 5 - 100 genes). B,E, Percentages of random signatures vs. logged p-values in all, only RASwt and only RASmt patients (combined permutations of 5 - 100 genes). C,F, Log-odds of p-value Wald test in RASmt vs. p-value in RASwt patient groups as a function of gene-set size.&lt;/p&gt;
Traffic engineering with forward fault correction (2014)

Faults such as link failures and high switch configuration delays can cause heavy congestion and packet loss. Because it takes time to detect and react to faults, these conditions can last long---even tens of seconds. We propose forward fault correction (FFC), a proactive approach to handling faults. FFC spreads network traffic such that freedom from congestion is guaranteed under arbitrary combinations of up to k faults. We show how FFC can be practically realized by compactly encoding the constraints that arise from this large number of possible faults and solving them efficiently using sorting networks. Experiments with data from real networks show that, with negligible loss in overall network throughput, FFC can reduce data loss by a factor of 7--130 in well-provisioned networks, and reduce the loss of high-priority traffic to almost zero in well-utilized networks.
Gender differences in distress and depression following cardiac surgery (1997)

This study examined the effects of physical health and other psychosocial variables on psychological distress and depression following coronary artery bypass graft surgery (CABG), with a focus on gender differences. Information regarding psychological distress one year following surgery was obtained from a sample of 151 patients (112 males, 39 females), who also provided retrospective information about noncardiac chronic conditions, preoperative socioeconomic variables, postoperative social support, and immediately post-CABG depression. Medical and surgical data and postoperative cardiac conditions were retrieved from computerized medical records. Structural equation modeling with LISREL showed that distress one year following surgery was predicted by the number of noncardiac chronic illnesses, controlling for immediately post-CABG depression. Gender had only an indirect effect on distress; women reported more chronic medical conditions than did men. Analysis also revealed an interaction between gender and income: higher income men and lower income women were most likely to report depression immediately following surgery.
Graphene Cathode-Based ZnO Nanowire Hybrid Solar Cells (2012)

Growth of semiconducting nanostructures on graphene would open up opportunities for the development of flexible optoelectronic devices, but challenges remain in preserving the structural and electrical properties of graphene during this process. We demonstrate growth of highly uniform and well-aligned ZnO nanowire arrays on graphene by modifying the graphene surface with conductive polymer interlayers. On the basis of this structure, we then demonstrate graphene cathode-based hybrid solar cells using two different photoactive materials, PbS quantum dots and the conjugated polymer P3HT, with AM 1.5G power conversion efficiencies of 4.2% and 0.5%, respectively, approaching the performance of ITO-based devices with similar architectures. Our method preserves beneficial properties of graphene and demonstrates that it can serve as a viable replacement for ITO in various photovoltaic device configurations.
Monocrystalline Silicon Solar Cell Optimization and Modeling (2017)

The performance of a monocrystalline silicon solar cell is determined by a variety of optical and electronic physical mechanisms. Optimization of cell performance requires finding trade-offs for the competing physical mechanisms. This chapter uses three-dimensional (3D) optical analysis and electronic transport analysis to determine optimization space for a solar cell with textured surface and point rear contacts. It discusses the behavior of different light wavelengths with several types of silicon surface roughness and finds that the best optical performance is achieved by random texture. Typically, both the front and the rear surfaces of the silicon wafer are randomly textured, but will look at different cases, with flat, regularly textured, and randomly textured pyramids. The different optical reflectivity at the rear surface for silicon– aluminum interface and with passivated silicon– nitride interface determines the amount of light retention within silicon and thus the number of optically generated carriers that can be trapped and absorbed in the solar cell.
High-density lipoproteins suppress Aβ-induced PBMC adhesion to human endothelial cells in bioengineered vessels and in monoculture (2017)

Our results define a novel activity of HDL that suppresses Aβ-mediated monocyte adhesion to the cerebrovascular endothelium.
Establishing a Publicly Accessible Compound Repository to Stimulate Drug Discovery in Australia (2007)

The Eskitis Institute for Cell and Molecular Therapies at Griffith University in Brisbane, Australia is establishing a publicly accessible dedicated compound management repository. This facility, known as the Queensland Compound Library (QCL), will give Australian chemists the opportunity to screen their compounds against a wide range of biological targets, without loss of intellectual property (IP). Biologists who use of the facility, likewise, retain control of their IP. A key element of the QCL is the ability to store compounds format-free, allowing, therefore, the possibility to deliver samples in a wide range of formats as desired by the customers. The automation to support this process has been carefully chosen to ensure that it meets the rigorous demands of supporting a customer-focused facility. This presentation describes a unique approach to stimulating drug discovery that best suits Australian circumstances and the automation that is being used to accomplish this.
Data from Epidermal Growth Factor Receptors with Tyrosine Kinase Domain Mutations Exhibit Reduced Cbl Association, Poor Ubiquitylation, and Down-regulation but Are Efficiently Internalized (2023)

&lt;div&gt;Abstract&lt;p&gt;Some non–small cell lung cancers (NSCLC) with epidermal growth factor receptor (EGFR) tyrosine kinase domain mutations require altered signaling through the EGFR for cell survival and are exquisitely sensitive to tyrosine kinase inhibitors. EGFR down-regulation was impaired in two NSCLCs with EGFR tyrosine kinase domain mutations. The mutant receptors were poorly ubiquitylated and exhibited decreased association with the ubiquitin ligase Cbl. Overexpression of Cbl increased the degradation of EGFR. Treatment with geldanamycin, an inhibitor of the chaperone heat shock protein 90, also increased both wild-type and mutant EGFR degradation without affecting internalization. The down-regulation of the mutant EGFRs was still impaired when they were stably expressed in normal human bronchial epithelial cells. Thus, the mutations that altered signaling also decreased the interaction of EGFRs with the mechanisms responsible for endosomal sorting. [Cancer Res 2007;67(16):7695–702]&lt;/p&gt;&lt;/div&gt;
CYP79F1 and CYP79F2 have distinct functions in the biosynthesis of aliphatic glucosinolates in Arabidopsis (2003)

Cytochromes P450 of the CYP79 family catalyze the conversion of amino acids to oximes in the biosynthesis of glucosinolates, a group of natural plant products known to be involved in plant defense and as a source of flavor compounds, cancer-preventing agents and bioherbicides. We report a detailed biochemical analysis of the substrate specificity and kinetics of CYP79F1 and CYP79F2, two cytochromes P450 involved in the biosynthesis of aliphatic glucosinolates in Arabidopsis thaliana. Using recombinant CYP79F1 and CYP79F2 expressed in Escherichia coli and Saccharomyces cerevisiae, respectively, we show that CYP79F1 metabolizes mono- to hexahomomethionine, resulting in both short- and long-chain aliphatic glucosinolates. In contrast, CYP79F2 exclusively metabolizes long-chain elongated penta- and hexahomomethionines. CYP79F1 and CYP79F2 are spatially and developmentally regulated, with different gene expression patterns. CYP79F2 is highly expressed in hypocotyl and roots, whereas CYP79F1 is strongly expressed in cotyledons, rosette leaves, stems, and siliques. A transposon-tagged CYP79F1 knockout mutant completely lacks short-chain aliphatic glucosinolates, but has an increased level of long-chain aliphatic glucosinolates, especially in leaves and seeds. The level of long-chain aliphatic glucosinolates in a transposon-tagged CYP79F2 knockout mutant is substantially reduced, whereas the level of short-chain aliphatic glucosinolates is not affected. Biochemical characterization of CYP79F1 and CYP79F2, and gene expression analysis, combined with glucosinolate profiling of knockout mutants demonstrate the functional role of these enzymes. This provides valuable insights into the metabolic network leading to the biosynthesis of aliphatic glucosinolates, and into metabolic engineering of altered aliphatic glucosinolate profiles to improve nutritional value and pest resistance.
Integrating Domain-Knowledge into Deep Learning (2019)

In this talk, I will first discuss deep learning models that can find semantically meaningful representations of words, learn to read documents and answer questions about their content. I will show how we can encode external linguistic knowledge as an explicit memory in recurrent neural networks, and use it to model co-reference relations in text. I will further introduce methods that can augment neural representation of text with structured data from Knowledge Bases for question answering, and show how we can use structured prior knowledge from Knowledge Graphs for image classification. Finally, I will introduce the notion of structured memory as being a crucial part of an intelligent agent's ability to plan and reason in partially observable environments. I will present a modular hierarchical reinforcement learning agent that can learn to store arbitrary information about the environment over long time lags, perform efficient exploration and long-term planning, while generalizing across domains and tasks.
Cooperative Dyads for Two-Photon Uncaging (2014)

A series of dyads that combine a photolabile protecting group (PPG) 4,5-dimethoxy-2-nitrobenzyl and different bis-donor or bis-acceptor dissymmetric chromophores acting as two-photon (2P) absorbers were synthesized. Even for low energy transfer efficiency from the 2PA subunit to the uncaging one, improvement of the 2P uncaging sensitivity in the NIR is achieved as compared to isolated PPG. Moreover enhancement of the 2PA response is achieved by tuning the electronic dissymmetry of the 2PA subunit and the arrangement of the complementary subunits in the dyads.
Complexity Scalable Hybrid End-to-End Distortion Estimation for Conversational Video Streaming (2007)

In conversational video streaming applications, periodic I-frame coding is not allowed due to strict low delay requirement. For this scenario, we propose a novel hybrid paradigm, which takes advantage of both accurate pixel-level estimation and efficient block-level estimation. Specifically, error propagated (EP) distortion from the last N coded frames are exactly calculated per pixel for high accuracy, while EP effect beyond the frame limit N are estimated per macroblock for low complexity. By varying the frame limit, flexible tradeoffs between complexity and performance can be achieved, rendering our scheme especially suitable for wireless video streaming, where stringent power resource is always a challenge. Simulation results justify the effectiveness of the proposed hybrid ED estimation scheme.
In Vivo Fluorescence Imaging of the Activity of CEA TCB, a Novel T-Cell Bispecific Antibody, Reveals Highly Specific Tumor Targeting and Fast Induction of T-Cell–Mediated Tumor Killing (2016)

Using optical imaging, we demonstrate specific tumor targeting and characterize the mode of CEA TCB-mediated target cell lysis in a mouse tumor model, which supports further clinical evaluation of CEA TCB. Clin Cancer Res; 22(17); 4417-27. ©2016 AACRSee related commentary by Teijeira et al., p. 4277.
Induction of a basement membrane glycoprotein in embryonic kidney: possible role of laminin in morphogenesis. (1980)

The glycoprotein laminin is found exclusively in the basement membranes of adult tissues, not in the mesenchymal stroma. We studied the appearance and distribution of laminin during the early formation of kidney tubules in mouse embryos and in an in vitro transfilter model system. In immunofluorescence using affinity-purified antibodies, the distribution of laminin showed a clear correlation, both spatially and temporally, to the early stages of tubule formation. In vivo, laminin was first detected in a punctate pattern in areas where the pretubular aggregates form; later, it became confined to the basement membranes of the tubules. In experiments in vitro, the nephrogenic mesenchyme was found to form tubules after 12-24 hr of transfilter contact with the inductor. The first laminin spots were found after 12 hr of culture, 24 hr before overt morphogenesis. As the mesenchymal cells began to aggregate and elongate (at 36 hr), laminin was detected in those cells destined to become epithelial, and at 48 hr it was not found in cells remaining in the stroma. In more mature tubules (at 72 hr), laminin was seen as a sharp band in the basement membranes. It is suggested that laminin is involved in the increased cell adhesiveness during the early aggregation of the nephrogenic mesenchyme.
Sites of Aggrecan Cleavage by Recombinant Human Aggrecanase-1 (ADAMTS-4) (2000)

Aggrecan, the major proteoglycan of cartilage that provides its mechanical properties of compressibility and elasticity, is one of the first matrix components to undergo measurable loss in arthritic diseases. Two major sites of proteolytic cleavage have been identified within the interglobular domain (IGD) of the aggrecan core protein, one between amino acids Asn(341)-Phe(342) which is cleaved by matrix metalloproteinases and the other between Glu(373)-Ala(374) that is attributed to aggrecanase. Although several potential aggrecanase-sensitive sites had been identified within the COOH terminus of aggrecan, demonstration that aggrecanase cleaved at these sites awaited isolation and purification of this protease. We have recently cloned human aggrecanase-1 (ADAMTS-4) (Tortorella, M. D., Burn, T. C., Pratta, M. A., Abbaszade, I., Hollis, J. M., Liu, R., Rosenfeld, S. A., Copeland, R. A., Decicco, C. P., Wynn, R., Rockwell, A., Yang, F., Duke, J. L., Solomon, K., George, H., Bruckner, R., Nagase, H., Itoh, Y., Ellis, D. M., Ross, H., Wiswall, B. H., Murphy, K., Hillman, M. C., Jr., Hollis, G. F., Newton, R. C., Magolda, R. L., Trzaskos, J. M., and Arner, E. C. (1999) Science 284, 1664-1666) and herein demonstrate that in addition to cleavage at the Glu(373)-Ala(374) bond, this protease cleaves at four sites within the chondroitin-sulfate rich region of the aggrecan core protein, between G2 and G3 globular domains. Importantly, we show that this cleavage occurs more efficiently than cleavage within the IGD at the Glu(373)-Ala(374) bond. Cleavage occurred preferentially at the KEEE(1667-1668)GLGS bond to produce both a 140-kDa COOH-terminal fragment and a 375-kDa fragment that retains an intact G1. Cleavage also occurred at the GELE(1480-1481)GRGT bond to produce a 55-kDa COOH-terminal fragment and a G1-containing fragment of 320 kDa. Cleavage of this 320-kDa fragment within the IGD at the Glu(373)-Ala(374) bond then occurred to release the 250-kDa BC-3-reactive fragment from the G1 domain. The 140-kDa GLGS-reactive fragment resulting from the preferential cleavage was further processed at two additional cleavage sites, at TAQE(1771)-(1772)AGEG and at VSQE(1871-1872)LGQR resulting in the formation of a 98-kDa fragment with an intact G3 domain and two small fragments of approximately 20 kDa. These data elucidate the sites and efficiency of cleavage during aggrecan degradation by aggrecanase and suggest potential tools for monitoring aggrecan cleavage in arthritis.
Hermit Points on a Box (2008)

(2008). Hermit Points on a Box. The College Mathematics Journal: Vol. 39, No. 1, pp. 12-23.
The reaction of hydrogen sulfide with disulfides: formation of a stable trisulfide and implications for biological systems (2018)

This article is part of a themed section on Chemical Biology of Reactive Sulfur Species. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.4/issuetoc.
Phosphorylation of Serine‐256 is essential for downstream polyphosphorylation of AQP2 (2008)

Phosphorylation of AQP2 at S256 is essential for its membrane targeting. Recently, we determined that S261, S264 and S269 residues are also phosphorylated by AVP and have begun to examine their role in AQP2 trafficking. MDCK cells stably expressing constitutively non‐phosphorylated forms of AQP2 demonstrated that single mutations (S261A, S264A and S269A) had no significant effect on apical membrane targeting following either AVP or forskolin treatment. A mutation mimicking constitutively phosphorylated AQP2 at position S269 (S269D) resulted in predominantly apical membrane localization of AQP2 even in the absence of stimulation. Osmotically induced swelling assays determined that rates of swelling in S269D‐AQP2 mutants were increased relative to wt‐AQP2 or S269A‐AQP2. Time course studies determined that S256‐AQP2 phosphorylation occurs first, raising the possibility that downstream phosphorylation is dependent on S256 phosphorylation. MDCK cells stably transfected with S256A‐AQP2 showed an elimination of S264 or S269 phosphorylation, whereas WT‐AQP2 or S256D‐AQP2 transfected cells exbihited a high level of phosphorylation at these sites. Thus, these data are compatible with the view that S256 phosphorylation is required for downstream phosphorylation.
Ro 42-5892 is a potent orally active renin inhibitor in primates. (1991)

The goal of the present study was to characterize the new renin inhibitor Ro 42-5892 in vitro and in vivo. In vitro, Ro 42-5892 inhibited purified human renin and human plasma renin specifically with an IC50 of 0.7 nM and 0.8 nM, respectively. In vivo, Ro 42-5892 reduced mean arterial blood pressure in sodium-depleted marmosets and squirrel monkeys with as low a dose as 0.1 mg/kg orally. Higher doses reduced pressure by 30-35 mm Hg in both species. The duration of blood pressure decrease with 3 mg/kg orally was more than 24 hours. Maximal changes of plasma renin activity, immunoreactive angiotensin I, and immunoreactive angiotensin II were observed at 15 minutes. Renin was reduced by 74 +/- 31%, angiotensin I by 85 +/- 14%, angiotensin II by 89 +/- 17%, and immunoreactive active renin was increased by 70 +/- 39%. However, unlike pressure, these maximal effects were only transient with complete recovery of renin at 60 minutes under still reduced levels of angiotensin I (61 +/- 24%) and angiotensin II (71 +/- 38%) and increased concentrations of active renin (86 +/- 30%). The blood pressure lowering was due to specific renin inhibition as exemplified by the influence of the kidney, sodium status, species, or stereoselectivity. Moreover, the reduction of arterial blood pressure was similar to the action of the angiotensin converting enzyme inhibitor cilazapril and was not associated with reflex tachycardia in contrast to the pure vasodilator minoxidil. We conclude that Ro 42-5892 is a potent orally active renin inhibitor acting mainly by inhibition of renin in an extraplasmatic compartment.