gebhart/patrepeval huggingface dataset:
Mice with an N-Ethyl-N-Nitrosourea (ENU) Induced Tyr209Asn Mutation in Natriuretic Peptide Receptor 3 (NPR3) Provide a Model for Kyphosis Associated with Activation of the MAPK Signaling Pathway (2016)

Non-syndromic kyphosis is a common disorder that is associated with significant morbidity and has a strong genetic involvement; however, the causative genes remain to be identified, as such studies are hampered by genetic heterogeneity, small families and various modes of inheritance. To overcome these limitations, we investigated 12 week old progeny of mice treated with the chemical mutagen N-ethyl-N-nitrosourea (ENU) using phenotypic assessments including dysmorphology, radiography, and dual-energy X-ray absorptiometry. This identified a mouse with autosomal recessive kyphosis (KYLB). KYLB mice, when compared to unaffected littermates, had: thoraco-lumbar kyphosis, larger vertebrae, and increased body length and increased bone area. In addition, female KYLB mice had increases in bone mineral content and plasma alkaline phosphatase activity. Recombination mapping localized the Kylb locus to a 5.5Mb region on chromosome 15A1, which contained 51 genes, including the natriuretic peptide receptor 3 (Npr3) gene. DNA sequence analysis of Npr3 identified a missense mutation, Tyr209Asn, which introduced an N-linked glycosylation consensus sequence. Expression of wild-type NPR3 and the KYLB-associated Tyr209Asn NPR3 mutant in COS-7 cells demonstrated the mutant to be associated with abnormal N-linked glycosylation and retention in the endoplasmic reticulum that resulted in its absence from the plasma membrane. NPR3 is a decoy receptor for C-type natriuretic peptide (CNP), which also binds to NPR2 and stimulates mitogen-activated protein kinase (MAPK) signaling, thereby increasing the number and size of hypertrophic chondrocytes. Histomorphometric analysis of KYLB vertebrae and tibiae showed delayed endochondral ossification and expansion of the hypertrophic zones of the growth plates, and immunohistochemistry revealed increased p38 MAPK phosphorylation throughout the growth plates of KYLB vertebrae. Thus, we established a model of kyphosis due to a novel NPR3 mutation, in which loss of plasma membrane NPR3 expression results in increased MAPK pathway activation, causing elongation of the vertebrae and resulting in kyphosis.
Inside Cover: Stable, Non‐Destructive Immobilization of Native Nuclear Membranes to Micro‐Structured PDMS for Single‐Molecule Force Spectroscopy (ChemPhysChem 9‐10/2009) (2009)

Abstract The investigation of native nuclear pore complexes (NPCs) with single‐molecule force spectroscopy requires stable and non‐destructive attachment of the nuclear envelope. Modified, micro‐structured PDMS turns out to be perfectly suited for membrane preparation as it preserves structure and function of the entire NPC, as shown on p. 1553 by A. Ebner et al. magnified image
VIII.--THE LOGIC OF CAUSAL PROPOSITIONS (1951)

Journal Article VIII.—THE LOGIC OF CAUSAL PROPOSITIONS Get access ARTHUR W. BURKS ARTHUR W. BURKS University of Michigan Search for other works by this author on: Oxford Academic Google Scholar Mind, Volume LX, Issue 239, July 1951, Pages 363–382, https://doi.org/10.1093/mind/LX.239.363 Published: 01 July 1951
Evaluation and experimental demonstration of SDN-enabled flexi-grid optical domain controller based on NETCONF/YANG (2018)

Flexible spectrum assignment in Elastic Optical Networks (EON) has emerged as a potential solution for allowing dynamic and elastic management of available bandwidth resources. In this paper, we demonstrate and evaluate our developed flexi-grid optical domain controller based on NETCONF/YANG. Our proposed modular architecture, based on Finite State Machines (FSMs), allows the flexibility to deploy the controller either in a centralized or in a distributed state for on the fly encrypted device management connections. A testbed composed of two physical Sliceable Bandwidth Variable Transponders (SBVTs) and an emulated flexi-grid optical network was used for our software evaluation. Controller startup and synchronization time, as well as media channel setup time are evaluated to compare the two deployment options and assess network scaling effects. Results demonstrate that our software is scalable by maintaining a relatively constant startup time on the networks tested (i.e., 1 to 64 nodes) in both deployment options. Software scalability is also supported by the media channel setup time, which presents a modest log scale growth when increasing the number of nodes from one to 64.
Determining the Molecular Characteristics of How Ligands Interact with an ABC Transporter (2019)

ABC transporters have key roles in cellular response to chemotherapy and drug bioavailability. The engagement of drugs and other ligands with ABC transporters is the crucial first step in the transport cycle. For mammalian ABC transporters, conventional knowledge regards the high affinity ligand‐binding state as when ATP is not bound to the ABC transporter; however, in vivo , this circumstance would be rare as the ATP concentration in most cells is approximately 5 mM. Using ABCG2 and the important class of drugs (tyrosine kinase inhibitors) we performed a thermal shift assay using two models (intact cells and isolated membranes) to investigate how these ligands engage ABCG2. We discovered, unexpectedly, that drug binding to ABCG2 can be either ATP‐independent, or ATP‐dependent. These findings run counter to the prevailing concept that ligands engage ABC transporters with high affinity when ATP concentrations are low and are reduced when ATP concentrations are high. Further, for those ligands requiring ATP for binding, ATP‐binding (not hydrolysis) appears to be the sole determinant because an ABCG2 mutant incapable of hydrolyzing ATP appeared to have little effect on ligand binding. For the ATP‐independent ligand, the EC 50 of binding was minimally affected by ATP, while the affinity and maximum binding of the ATP‐dependent ligand was markedly enhanced by the presence of ATP. Using a non‐hydrolyzable ATP‐coupled bead as a probe for ATP binding, further studies showed that the binding to ABCG2 of this ATP mimetic was strongly influenced by the ligand, but only when the ligand's binding was impacted by ATP, thus suggesting communication occurs between the nucleotide binding domain and the ligand binding site. Previous studies have suggested ATP lowers the binding affinity for ligands. This contrasts with the current findings showing some ligands require ATP for ligand binding, while others do not. This has important mechanistic implications for interpreting not just ABC transporter function, studied in dynamic systems, but also for the development of ABCG2 inhibitors and understanding substrate interactions. Support or Funding Information This work was supported by NIH and by ALSAC. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
An HBT MMIC power amplifier with an integrated diode linearizer for low-voltage portable phone applications (1998)

This paper gives a detailed description of a novel linearization technique using a transistor base-collector junction diode. The novel linearization technique effectively improves the gain compression and phase distortion of the heterojunction bipolar transistor (HBT) with no additional dc consumption, leading to highly efficient linear amplification of the /spl pi//4 DQPSK modulation signals. An AlGaAs/GaAs HBT monolithic microwave integrated circuit (MMIC) linear power amplifier was fabricated using the novel linearization technique for the handsets used in the 1.9 GHz Japanese Personal Handy Phone System (PHS). The fabricated HBT MMIC power amplifier exhibits an output power of 21 dBm and a power-added efficiency as high as 37% at an operation voltage of 2.7 V. At this rated output power, the adjacent channel power rejection in /spl plusmn/600 kHz offset frequency bands is -55 dBc and the error vector magnitude is 4.3%. This measured linearity is well within the PHS standard.
A fine‐grained thread‐aware management policy for shared caches (2013)

SUMMARY Two of the main sources of inefficiency in current caches are the non‐uniform distribution of the memory accesses across the cache sets, which causes misses due to the mapping restrictions of non fully associative caches and the access patterns with little locality that degrade the performance of caches under the traditional least recently used. replacement policy. This paper proposes a technique to tackle in a coordinated way both kinds of problems in the context of chip multiprocessors, whose last level caches can be shared by threads with different patterns of locality. Our proposal, called thread‐aware mapping and replacement miss reduction (TAMR2) policy, tracks the behavior of each thread in each set in order to decide the appropriate combination of policies to deal with these problems. Despite its small overhead, TAMR2 achieved in our experiments average power consumption and memory latency reductions of 10% and 12%, respectively, resulting in an average throughput improvement of 5.6%, relative to a traditional cache design using four cores. TAMR2 also outperformed many recent related approaches in the field. Copyright © 2013 John Wiley &amp; Sons, Ltd.
Parameter Identification of a PV Source Dynamic Model with Piecewise-Linear Circuit-Based Approach (2012)

This paper deals with a method for the parameter identification of an improved dynamic model of a photovoltaic (PV) source, which encompasses a capacitor and an inductor. The method is based on piecewise-linear (PWL) circuit approximation and step load responses. Considering the PV I-V characteristic as a PWL function, if a transient occurs in a linear region, the PV source can be approximated according to Thvenin's theorem. The cases referred to either capacitive or inductive dominant time constant are explained. The identification of the circuit parameters by least squares regression (LSR) applied to experimental data is discussed and finally a case study is presented.
Clustering-based Unsupervised Generative Relation Extraction (2022)

Existing unsupervised relation extraction methods work by extracting sentence features and using these features as inputs to train a generative model. This model is then used to cluster similar relations. However, these methods do not consider correlations between sentences with the same entity pair during training, which can negatively impact model performance. To address this issue, we propose a Clustering-based Unsupervised generative Relation Extraction (CURE) framework that leverages an Encoder-Decoder architecture to train a relation extractor as the encoder. Given multiple sentences with the same entity pair as inputs, CURE is deployed by predicting the shortest path between entity pairs on the dependency graph of one of the sentences. After that, we extract the relation information using the encoder. Then, entity pairs that share the same relation are clustered based on their corresponding relation information. Each cluster is labeled based on the words in the shortest paths corresponding to the entity pairs in each cluster. Experimental results demonstrate the effectiveness of CURE compared to state-of-the-art models across all benchmark datasets.
Fabrication of ferromagnetic nanocluster rods by magnetic trapping (2004)

In a one-pot fabrication at room temperature, both an iron-neodymium-dysprosium-boron permanent magnet (Fe66Nd28Dy4B1) and cobalt (Co) metal have been directly converted into the corresponding ferromagnetic nanometer-scale cluster (nanocluster) rods using pulsed-laser ablation combined with magnetic-field trapping. The morphology of the produced nanomaterials was analyzed by electron microscopy and the composition by electron energy-loss spectroscopy, and it was found that one-dimensional structured soft magnets, up to ∼150 nm in length, consist of magnetic clusters a few nanometers in diameter. The mechanism and driving behind their growth process and their magnetic evolution have been proposed.
Abstract 4187: Expression of ion channels in a cervical cancer mouse model (2015)

Abstract Introduction. Because some ion channels have been suggested as early tumor markers and therapeutic targets, in the present study we examined the expression of ion channels in the cervical cancer transgenic mouse model K14E7 expressing the HPV16 E7 oncogene under the control of the human keratin 14 promoter. Methods. We used the K14E7 transgenic mouse; some groups were treated with 17β-estradiol. Continuous release pellets delivering 0.05 mg of 17β-estradiol were implanted into 4-6 weeks old female mice during 90 days to obtain low grade cervical dysplasia or during 180 days to produce cervical cancer. The cervix was removed at the end of the treatment. Protein and mRNA expression of 4 ion channels (Cav3.1, Cav3.2, Kv10.1, KCa1.1) were analyzed by qRT-PCR and immunohistochemistry, respectively. Results. We found increased expression of Cav3.1, Kv10.1 and KCa1.1 in mice with cervical dysplasia in comparison to control animals. This increase was even higher in animals with cervical cancer. In contrast, Cav3.2 expression decreased in animals with cervical dysplasia and increased in mice with cervical cancer. We also found overexpression of the KCa1.1 protein in the transformed zone of the cervical cancer group, but not in the control group. Conclusions. The channel expression profile here studied might serve as a cervical cancer marker. This work was partially supported by Conacyt grant 141126 to JC. Citation Format: ANA RAMIREZ, EUNICE VERA, PAUL LAMBERT, PATRICIO GARIGLIO, JAVIER CAMACHO. Expression of ion channels in a cervical cancer mouse model. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4187. doi:10.1158/1538-7445.AM2015-4187
Evaluation of a Prosthetic Swing-Phase Controller With Electrical Power Generation (2009)

With the increased presence of microprocessor-based prostheses in the market place, the availability of a self-energizing system has practical applicability. At present, most commercially available systems require the user to routinely recharge on-board batteries, which reduces the utility of these prostheses. To address this limitation, we have proposed a unique system based on an electromechanical generator to not only continually recharge batteries that are on-board the prostheses, but to also serve as a real time swing-phase damper. A prototype system was developed and evaluated with three active individuals with above-knee amputations across four damping conditions and two gait speeds. Gait and power generation performance were assessed via selected temporal, kinematic and kinetic parameters. Gait parameters including cadence and knee angle symmetry were found to be acceptable when knee damping was adapted for each participant. Across the three subjects and two walking speeds, between 0.57 and 1.57 W of electrical power was produced. These results indicate that this technology may be utilized for prosthetic swing-phase control and ultimately may alleviate the need for manually charging of microprocessor-based prostheses.
The Efficiency and Time-Dependence of Luminescence in a High Electron Affinity Conjugated Polymer (1995)

Measurements of luminescence in conjugated polymers give insight into their photophysics and the operation of electroluminescent devices. The same excited state, the singlet exciton is believed to be responsible for both photoluminescence and electroluminescence. Excitons decay by a combination of radiative and non-radiative processes, and the relative rate of these processes determines the luminescence efficiency. An important feature of conjugated polymers is the possibility of chemical tailoring to realise desired properties. A recent innovation has been the development of high electron affinity polymers made by cyano substitution of members of the poly (arylene vinylene) family [1]. The increased electron affinity improves the performance of light-emitting-diodes by facilitating electron injection.
Terminal area operations for hybrid electric distributed propulsion (2014)

Purpose This paper aims to create a terminal area operations (TAO) analysis software that can accurately appreciate the nuances of hybrid electric distributed propulsion (HEDP), including unique failure modes and powered-lift effects.
Internalisation of the type I angiotensin II receptor (ATI) and angiotensin II function in the rat adrenal zona glomerulosa cell. (1994)

Little is known about the cellular localisation of the angiotensin II (AII) type 1 receptor (AT1) in the rat adrenal glomerulosa cell, but some studies have suggested that receptor internalisation and recycling may occur. Using a specific monoclonal antibody (6313/G2) to the first extracellular domain, we show here that most of the receptor is internalised in the unstimulated cell. When viable glomerulosa cells are incubated with 6313/G2, the receptor is transiently concentrated on the cell surface, and aldosterone output is stimulated. This stimulated output is enhanced by neither threshold nor maximal stimulatory concentrations of AII amide, although the antibody does not inhibit AII binding to the receptor. Conversely, the stimulatory actions of the antibody and those of ACTH are additive. The data suggest that recycling to the plasma membrane is constitutive, or regulated by unknown factors. Retention of the AT1 receptor in the membrane is alone enough to allow sufficient G protein interaction to generate maximal stimulatory events.
MPI collective communications on the blue gene/p supercomputer (2009)

The IBM Blue Gene/P (BG/P) system is a massively parallel supercomputer succeeding BG/L, and it is based on orders of magnitude in system size and significant power consumption efficiency. BG/P comes with many enhancements to the machine design and new architectural features at the hardware and software levels. In this work, we demonstrate techniques to leverage the architectural features of BG/P to deliver high performance MPI collective communication primitives.
IRS1 Regulation by Wnt/β-Catenin Signaling and Varied Contribution of IRS1 to the Neoplastic Phenotype (2009)

Dysregulation of beta-catenin levels and localization and constitutive activation of beta-catenin/TCF (T cell factor)-regulated gene expression occur in many cancers, including the majority of colorectal carcinomas and a subset of ovarian endometrioid adenocarcinomas. Based on the results of microarray-based gene expression profiling we found the insulin receptor substrate 1 (IRS1) gene as one of the most highly up-regulated genes upon ectopic expression of a mutant, constitutively active form of beta-catenin in the rat kidney epithelial cell line RK3E. We demonstrate expression of IRS1 can be directly activated by beta-catenin, likely in part via beta-catenin/TCF binding to TCF consensus binding elements located in the first intron and downstream of the IRS1 transcriptional start site. Consistent with the proposal that beta-catenin is an important regulator of IRS1 expression in vivo, we observed that IRS1 is highly expressed in many cancers with constitutive stabilization of beta-catenin, such as colorectal carcinomas and ovarian endometrioid adenocarcinomas. Using a short hairpin RNA approach to abrogate IRS1 expression and function, we found that IRS1 function is required for efficient de novo neoplastic transformation by beta-catenin in RK3E cells. Our findings add to the growing body of data implicating IRS1 as a critical signaling component in cancer development and progression.
Epidemiological and Biological Determinants ofStaphylococcus aureusClinical Infection in New York State Maximum Security Prisons (2015)

Several inmate characteristics were strongly associated with SA infection in the prison setting. Although many of these factors were likely present prior to incarceration, they may help medical staff identify prisoners for targeted prevention strategies.
PET Image Denoising Using a Synergistic Multiresolution Analysis of Structural (MRI/CT) and Functional Datasets (2008)

The methodology is robust to errors in the coregistration parameters, practical to implement, and computationally fast.
Self Gravitating Incompressible Fluid in Two Dimensions (2015)

In this paper we develop two models for the steady states and evolution of two dimensional isothermal self gravitating and rotating incompressible gas which are based on the hydrodynamic equations for stratified fluid. The first model is for the steady states of the gas while the second addresses the time evolution of the gas subject to some constraints. These models reduce the initial five partial differential equations that govern this system to two for the steady state model and to three for the time dependent model. Analytical and numerical solutions of the model equations are used to study the structure of the resulting steady and time dependent states of the fluid with some possible astrophysical applications.
El elefante de plata: túnel de cavitación construido con una precisión de centésimas de milímetro (2006)

La experiencia y verificacion son los trabajos mas espectaculares de un proceso de desarrollo, sobre todo cuando los parametros de las pruebas son de grandes dimensiones. Un ejemplo clara es Elefante de Plata, entorno de prueba construido para evaluar la hidrodinamica de las helices de los barcos. La cavitacion es muy importante en el diseno de las helices de barcos. Este fenomeno se produce cuando las burbujas de vapor de agua formadas en zonas de baja presion penetran en zonas con presion mas alta, donde se destruyen. Este proceso puede provocar una erosion rapida de las superficies adyacentes. El Elefante de Plata salio de Polonia en enero de 20069 con destino a Vietnam, donde servira al sector de la construccion naval, que esta en pleno desarrollo. El comienzo de este viaje senalizo el final de uno de los proyectos de construccion mas grandes y retadores de la historia de ABB Zamech Marine de Polonia.
Surface plasmon-coupled emission on plasmonic Bragg gratings (2012)

Surface plasmon-coupled emission (SPCE) from emitters in a close proximity to a plasmonic Bragg grating is investigated. In this study, the directional fluorescence emission mediated by Bragg-scattered surface plasmons and surface plasmons diffraction cross-coupled through a thin metallic film is observed by using the reverse Kretschmann configuration. We show that controlling of dispersion relation of these surface plasmon modes by tuning the refractive index at upper and lower interfaces of a dense sub-wavelength metallic grating enables selective reducing or increasing the intensity of the light emitted to certain directions. These observations may provide important leads for design of advanced plasmonic structures in applications areas of plasmon-enhanced fluorescence spectroscopy and nanoscale optical sources.