gebhart/patrepeval huggingface dataset:
91 INTERACTION OF OXYGEN TENSION AND CYSTEAMINE SUPPLEMENTATION DURING IN VITRO CULTURE OF BOVINE EMBRYOS (2011)

Reactive oxygen species damage early mammalian embryos, so culture of bovine in vitro-produced (IVP) embryos at 5% O2 is clearly superior to 20% O2. The thiol compound cysteamine is an antioxidant and improves in vitro blastocyst production when added to in vitro maturation (IVM) medium. The purpose of this study was to investigate supplementation of IVP embryo culture medium with cysteamine at different oxygen tensions. Bovine ovaries from feedlot heifers were collected from a local abattoir and cumulus–oocyte complexes (COC) were aspirated from 3- to 8-mm follicles. COC were matured in maturation medium with 100µM cysteamine (Reprod. Fertil. Dev.18, 585) for 23 h in a humidified incubator at 38.5°C in 5% CO2 in air. COC at 23 h of maturation were co-incubated with sperm for 18 h. Cumulus cells were then removed and presumed zygotes were cultured in our chemically defined culture medium system (Reprod. Fertil. Dev.18, 585) in a 2 × 2 factorial arrangement: with or without 50 µM cysteamine × atmospheres of either 5% O2, 5% CO2, 90% N2, or 5% CO2 in air. There were no treatment differences (P &amp;gt; 0.01) in percentages of oocytes cleaving or reaching the 8-cell stage (Table 1). However, blastocyst production rates were lower (P &amp;lt; 0.01) in the group cultured without cysteamine at 20% O2 compared with all the other groups. Adding cysteamine for embryo culture at 20% O2 resulted in blastocyst rates similar to those cultured at 5% O2 with or without cysteamine. Cysteamine was not beneficial at 5% O2. Table 1. Cysteamine supplementation during in vitro culture of bovine embryos
Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation (2008)

The eukaryotic genome is packaged as chromatin with nucleosomes comprising its basic structural unit, but the detailed structure of chromatin and its dynamic remodeling in terms of individual nucleosome positions has not been completely defined experimentally for any genome.We used ultra-high-throughput sequencing to map the remodeling of individual nucleosomes throughout the yeast genome before and after a physiological perturbation that causes genome-wide transcriptional changes.Nearly 80% of the genome is covered by positioned nucleosomes occurring in a limited number of stereotypical patterns in relation to transcribed regions and transcription factor binding sites.Chromatin remodeling in response to physiological perturbation was typically associated with the eviction, appearance, or repositioning of one or two nucleosomes in the promoter, rather than broader region-wide changes.Dynamic nucleosome remodeling tends to increase the accessibility of binding sites for transcription factors that mediate transcriptional changes.However, specific nucleosomal rearrangements were also evident at promoters even when there was no apparent transcriptional change, indicating that there is no simple, globally applicable relationship between chromatin remodeling and transcriptional activity.Our study provides a detailed, highresolution, dynamic map of single-nucleosome remodeling across the yeast genome and its relation to global transcriptional changes.
Non-Invasive In-Home Sleep Stage Classification Using a Ballistocardiography Bed Sensor (2019)

Longitudinal monitoring of sleep related parameters can be used for early detection of diseases and also as an indication to physicians for effective adjustment of medication and dosage treatments for people at risk. The correlation between sleep disorders and health conditions such as Alzheimer's and Parkinson's diseases has already been reported in the literature. In this paper, we propose the use of a hydraulic bed sensor for sleep stage classification. Our main motivation of using the bed sensor is to provide a non-invasive, in-home monitoring system, which tracks the changes in health conditions of the subjects over time. Regular polysomnography data from a Sleep Lab have been used as the ground truth, with the focus on three sleep stages, namely, awake, rapid eye movement (REM) and non-REM sleep (NREM). A total of 74 features including heart rate variability (HRV) features, respiratory rate variability (RV) features, and linear frequency cepstral coefficients (LFCC) were extracted from the bed sensor data. Support Vector Machines (SVM) and K-Nearest Neighbors (KNN) classification methods were applied to these features. Our results show accuracy as good as 85% with 0.74 kappa, in the detection of these three sleep stages. These results show promise in the ability of the bed sensor to monitor and track sleep quality and sleep related disorders noninvasively.
Isolation and identification of a glutathione peroxidase homolog gene, gpxA, present in Neisseria meningitidis but absent in Neisseria gonorrhoeae (1995)

Antioxidant enzymes are thought to be important for the survival of pathogenic Neisseria species. We isolated a glutathione peroxidase-related gene (gpxA) from Neisseria meningitidis FAM20. The N. meningitidis glutathione peroxidase homolog was 49 to 57% identical to seven other glutathione peroxidase family members over a 49-amino-acid region which is conserved among various species. The gpxA sequence was present in all 7 meningococcal strains tested but absent in 10 gonococcal strains and 6 nonpathogenic neisserial strains as determined by Southern hybridization. The homology of gpxA to mammalian glutathione peroxidases and the presence of this gene specifically in the meningococcus suggest that it is important in the cellular metabolism or defense processes particular to this pathogen.
Characterization of a 52K protein of murine cytomegalovirus and its immunological cross-reactivity with the DNA-binding protein ICP36 of human cytomegalovirus (1991)

We have developed a hybridoma, designated 25G11, which produced a monoclonal antibody (MAb) reactive with a 52K protein of murine cytomegalovirus (MCMV). This MAb, 25G11, was reactive with a protein band of 52K in MCMV-infected cell lysates and with a protein of 49K in human CMV (HCMV)-infected cell lysates as detected by immunoblot analysis. With purified MCMV virions, 25G11 gave a faintly immunoreactive band of 52K. However, no immunoreactive protein band was detected with purified HCMV virions, nor with purified HCMV or MCMV envelope preparations. By immunocytochemistry, 25G11 detected viral antigen primarily in the nucleus of HCMV- or MCMV-infected cells. The antibody 25G11 was used to screen a lambda gt11 library of HCMV DNA fragments. One of the isolated clones (lambda 32323B) was employed for gene mapping on the HCMV genome, which suggested that the immunoreactive HCMV protein was the DNA-binding protein (ICP36). Analysis of the recombinant fusion protein with antibody 25G11 and with an MAb (CH16) specific for an HCMV DNA-binding protein confirmed the identity of the cross-reacting protein as ICP36. Furthermore, we found that whereas the epitope recognized by 25G11 was conserved between HCMV and MCMV proteins, the epitope recognized by CH16 was unique to HCMV and thus represents a variable region in the protein.
Liver Tissue Engineering (2014)

We provide a description of the structure and function of the mammalian liver. This is followed by a discussion of medical conditions and current treatment modalities. We then provide specific examples of tissue engineering as it applies to fabricating the liver.
Mesh generation and fracture for deformable bodies (2004)

ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a disser-tation for the degree of Doctor of Philosophy.
Effect of vascular endothelial growth factor and its receptor KDR on the transendothelial migration and local trafficking of human T cells in vitro and in vivo (2010)

In these studies, we find that the vascular endothelial growth factor (VEGF) receptor KDR is expressed on subsets of mitogen-activated CD4(+) and CD8(+) T cells in vitro. We also found that KDR colocalizes with CD3 on mitogen-activated T cells in vitro and on infiltrates within rejecting human allografts in vivo. To evaluate whether VEGF and KDR mediate lymphocyte migration across endothelial cells (ECs), we used an in vitro live-time transmigration model and observed that both anti-VEGF and anti-KDR antibodies inhibit the transmigration of both CD4(+) and CD8(+) T cells across tumor necrosis factor α (TNFα)-activated, but not unactivated ECs. In addition, we found that interactions among CD4(+) or CD8(+) T cells and TNFα-activated ECs result in the induction of KDR on each T cell subset, and that KDR-expressing lymphocytes preferentially transmigrate across TNFα-activated ECs. Finally, using a humanized severe combined immunodeficient mouse model of lymphocyte trafficking, we found that KDR-expressing lymphocytes migrate into human skin in vivo, and that migration is reduced in mice treated with a blocking anti-VEGF antibody. These observations demonstrate that induced expression of KDR on subsets of T cells, and locally expressed VEGF, facilitate EC-dependent lymphocyte chemotaxis, and thus, the localization of T cells at sites of inflammation.
Human LineageSpecific Amplification, Selection, and Neuronal Expression of DUF1220 Domains (2006)

Extreme gene duplication is a major source of evolutionary novelty. A genome-wide survey of gene copy number variation among human and great ape lineages revealed that the most striking human lineage-specific amplification was due to an unknown gene, MGC8902, which is predicted to encode multiple copies of a protein domain of unknown function (DUF1220). Sequences encoding these domains are virtually all primate-specific, show signs of positive selection, and are increasingly amplified generally as a function of a species' evolutionary proximity to humans, where the greatest number of copies (212) is found. DUF1220 domains are highly expressed in brain regions associated with higher cognitive function, and in brain show neuron-specific expression preferentially in cell bodies and dendrites.
The Wild West of E-Cigarettes (2018)

The popularity of e-cigarettes is growing exponentially. Yet, the health risks associated with their use remain unclear, mainly due to the fact that they are not "one product", but a combination of ever-evolving designs, flavors, brands, and modes of use. Research needs to better understand how these variables affect toxicity.
Effect of Antitranspirant and Fertilization on Flowering, Fruiting, and Biomass Production in `Early Girl' Tomato Plants (1998)

Seedling plugs of `Early Girl' tomato plants ( Lycopersicon esculentum Mill.) were potted in peatmoss and perlite (60:40% by volume) medium, fertilized with 8, 16, 24, or 32 g NutriCote Total controlled-release fertilizer (type 100, 13N–5.67P–10.79K plus micronutrients) per pot (2.81 L), and treated with 0%, 2.5%, 5%, or 7.5% antitranspirant GLK-8924 solution, at the four true-leaf stage. Plants were tipped at the second inflorescence and laterals were removed upon emergence. Flowering of both clusters were advanced by higher fertilization rates and depressed by GLK-8924. Increasing rates of fertilization increased flower and fruit number of the lower cluster and fruit set of upper cluster. GLK-8924 had no effect on flower number, fruit number, and fruit set. Fertilization increased the biomass production of all plant parts while GLK-8924 reduced the biomass production of leaves and fruit only. Root and stem biomass was not influenced by GLK-8924. The effect of GLK-8924 on fruit dry weight was dependent on the position of the cluster and GLK-8924 concentration. Fertilization did not interact with GLK-8924 to influence flowering, fruiting, and biomass production.
A PHASE I TRIAL OF VACCINE THERAPY WITH TUMOR SPECIFIC MUTATED RAS PEPTIDES ADMINISTERED SUBCUTANEOUSLY IN CANCER PATIENTS (1995)

Khleif, S N; Abrams, S; Allegra, C; Chen, A; Chung, Y; Hamilton, J M; Kohler, D R; Schlom, J Author Information
Expletives in Universal Dependency Treebanks (2018)

Although treebanks annotated according to the guidelines of Universal Dependencies (UD) now exist for many languages, the goal of annotating the same phenomena in a crosslinguistically consistent fashion is not always met. In this paper, we investigate one phenomenon where we believe such consistency is lacking, namely expletive elements. Such elements occupy a position that is structurally associated with a core argument (or sometimes an oblique dependent), yet are non-referential and semantically void. Many UD treebanks identify at least some elements as expletive, but the range of phenomena differs between treebanks, even for closely related languages, and sometimes even for different treebanks for the same language. In this paper, we present criteria for identifying expletives that are applicable across languages and compatible with the goals of UD, give an overview of expletives as found in current UD treebanks, and present recommendations for the annotation of expletives so that more consistent annotation can be achieved in future releases.
Author Correction: Airway surface liquid acidification initiates host defense abnormalities in Cystic Fibrosis (2019)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Scalable metric for coverage evaluation in video-based wireless sensor networks (2009)

One of the most important aspects of wireless sensor networks applications is the network lifetime. A possibility of prolonging lifetime is to turn off some sensors, especially in dense deployed networks with high redundancy. However, to keep the application effectiveness a certain amount of coverage is needed. The coverage is usually quantized by various metrics. In this paper we propose a scalable metric to evaluate in a distributive manner the coverage in dense deployed video-based wireless sensor networks. It allows qualifying the coverage efficiency especially in case of surveillance applications. Metric definition is based on video-sensors field-of-view and it relays on network clustering infrastructure. Simulation results are presented to demonstrate this approach.
ChemInform Abstract: In vitro Studies of Phenol Coupling Enzymes Involved in Vancomycin Biosynthesis (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Influence of Layer Thickness on the Performance of Stacked Thick-Film Copper Air-Core Power Inductors (2012)

This paper presents the fabrication and characterization of air-core power inductors that leverage vertically-stacked, thick copper spiral windings to deliver high inductance densities >; 100 nH/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and quality factors >; 10 on silicon substrates. The inductors are designed for on-chip or in-package integration with high-frequency power converter circuits to enable chip-scale power management in size-constrained applications. A process for realizing the inductors through multilevel, three-dimensional molding of electroplated copper structures has been enhanced with capabilities for four independent copper layers in thicknesses of up to 30 μm each. The impact of increasing the thickness of the stacked copper traces is specifically explored and compared to similar inductors with 10-μm-thick stacked windings. Impedance characterization revealed a drastic decrease in the series resistance in the thicker inductors as desired but also revealed undesired eddy current and magnetic coupling effects.
Genetic localization and regulation of the maltose phosphorylase gene, malP, in Lactococcus lactis The GenBank accession number for the sequence reported in this paper is AF327721. (2001)

Maltose phosphorylase (MP) from Lactococcus lactis was purified and the corresponding gene was cloned and expressed in Escherichia coli. The isoelectric point of the pure enzyme was determined to be 7.0. According to zymogram analysis and SDS-PAGE, the native MP was shown to be a monomeric enzyme with a molecular mass of 75 kDa. A polyclonal antiserum was produced to assess the regulation of the gene encoding MP in LC: lactis. According to immunoblot analysis, synthesis of the enzyme was markedly repressed by both glucose and lactose in the growth medium. When the lactococci were cultivated in the presence of other sugars, including maltose, trehalose or galactose, there was a pronounced expression of the MP gene. In addition, when the cells were grown in media without any added sugar, there was also pronounced expression of the enzyme, according to immunoblot analysis and specific activity data. These results indicated that no particular sugar specifically induces the gene encoding MP. However, an effect of glucose on MP expression was demonstrated by performing fermentations in the presence of both maltose and glucose. When glucose was added to maltose-grown lactococci in the mid-exponential growth phase, both the specific activity and amount of MP per millilitre of cell extract decreased rapidly. The genetic locus for the MP gene was found to be in the vicinity of the region encoding a possible regulator belonging to the LacI-GalR family of transcriptional regulators. Furthermore, this genetic location was separated from the previously characterized maltose-inducible and glucose-repressible beta-phosphoglucomutase (beta-PGM) gene. The different genetic loci for the genes encoding MP and beta-PGM explains the different gene regulation behaviour.
A low thermal conductivity compound for thermoelectric applications: β-Zn/sub 4/Sb/sub 3/ (2002)

The potential of the semiconducting compound /spl beta/-Zn/sub 4/Sb/sub 3/ for thermoelectric energy conversion was investigated. The thermoelectric properties were measured on hot-pressed samples characterized by X-ray and microprobe analysis. All samples had p-type conductivity and the thermoelectric properties of the samples were measured between room temperature and 400/spl deg/C. Exceptionally low thermal conductivity values were measured and the room temperature lattice thermal conductivity was estimated at 7 mW cm/sup -1/ K/sup -1/. High figures of merit were obtained between 200 and 400/spl deg/C and a maximum dimensionless thermoelectric figure of merit ZT of about 1.3 was obtained at a temperature of 400/spl deg/C. The stability of the compound was investigated by thermogravimetric studies and showed that the samples were stable under Ar atmosphere up to about 400/spl deg/C and up to 250/spl deg/C in dynamic vacuum. The high thermoelectric performance of /spl beta/-Zn/sub 4/Sb/sub 3/ in the 200 to 400/spl deg/C temperature range fills the gap established in the ZT spectrum of p-type state-of-the-art thermoelectric materials between Bi/sub 2/Te/sub 3/-based alloys and PbTe-based alloys. This material, relatively inexpensive, could be used in more efficient thermoelectric generators for waste heat recovery and automobile industry applications, for example.
Slum health: Diseases of neglected populations (2007)

Continued neglect of ever-expanding urban slum populations in the world could inevitably lead to greater expenditure and diversion of health care resources to the management of end-stage complications of diseases that are preventable. A new approach to health assessment and characterization of social-cluster determinants of health in urban slums is urgently needed.
Successful Model for Professional Development: (2015)

Ann C. Smith, Gili Marbach-Ad, Ann M. Stevens, Sarah A. Balcom, John Buchner, Sandra L. Daniel, Jeffrey J. DeStefano, Najib M. El-Sayed, Kenneth Frauwirth, Vincent T. Lee, Kevin S. McIver, Stephen B. Melville, David M. Mosser, David L. Popham, Birgit E. Scharf, Florian D. Schubot, Richard W. Selyer Jr., Patricia Ann Shields, Wenxia Song, Daniel C. Stein, Richard C. Stewart, Katerina V. Thompson, Zhaomin Yang, Stephanie A. Yarwood, Successful Model for Professional Development:, Transforming Institutions, pp. 280-294
Supplementary Figure 2 from Alarmin IL-33 Acts as an Immunoadjuvant to Enhance Antigen-Specific Tumor Immunity (2023)

&lt;p&gt;PDF file - 58KB, IL-33 expands the frequency of the Ag-specific CD8+ T cells. P14 chimera mice (n=5) were vaccinated twice (on day 0 and day 41) containing GP33 with or without proIL-33. Displayed are representative fluorescent intensity plots of GP33/Ly5.1-specific CD8+ T cells responses in the blood of vaccinated mice at days 14, 21 and 31 after first vaccination and day 48 (day 7 after second immunization). Numbers indicate the percentage of Ag-specific CD8+ T Cells within the total CD8+ T cell populations. Experiments were performed independently at least two times and data are representative of the results.&lt;/p&gt;
Effect of isoliquiritigenin (ISL) on insulin‐like growth factor‐I receptor and ErbB3 signaling in prostate cancer cells (2006)

The insulin‐like growth factor (IGF) system has been implicated as a risk factor for the development of several human cancers. In addition, over‐expression of members of the ErbB receptor family is frequent event in several human cancers. The chalcone ISL has been recognized as a potent anti‐tumor promoting agent. We previously demonstrated that ISL decreased cell proliferation and induced apoptosis in prostate cancer cells. To examine the mechanisms underlying ISL regulation of prostate cancer cell growth, DU145 human prostate cancer cells and MAT‐LyLu (MLL) rat prostate cancer cells were cultured in serum‐free medium with various concentrations of ISL and/or IGF‐I or heregulin‐β (HRG). Exogenous IGF‐I or HRG alone increased viable cell numbers, whereas neither IGF‐I nor HRG counteracted growth inhibition induced by ISL. ISL decreased the protein and mRNA levels of IGF‐I receptor (IGF‐IR) and ErbB in does‐dependent manners. Immunoprecipitation/Western blot studies showed that ISL inhibited IGF‐I‐induced phosphorylation of IGF‐IR, recruitment of the p85 subunit of phosphoinositide 3‐kinase (PI3K) to IGF‐IR and phosphorylation of Akt in MLL and DU145 cells. In addition, ISL inhibited HRG‐induced phosphorylation of ErbB3, recruitment of p85 to ErbB3 and phosphorylation of Akt in DU145 cells. These results indicate that ISL inhibits proliferation of prostate cancer cells via its inhibition of IGF‐IR and ErbB3 signaling and the PI3K/Akt pathway.
Magnetic Double Resonance in Force Microscopy (2006)

Magnetic-resonance force microscopy is combined with cross-polarization and spin-decoupling NMR techniques to obtain double-resonance NMR signals of micrometer-scaled objects. The effective one-dimensional spatial resolution obtained in our experiments performed on a KPF6 single crystal sample is approximately 0.5 microm. The spectral linewidth of 900 Hz is sample limited. The described double-resonance techniques can introduce new chemical specificity to the magnetic-force sensor.
Effects of Applied Voltage on the Size of Phase-Separated Domains in DMPS-DOPC Lipid Binary Bilayers Supported on SiO&lt;sub&gt;2&lt;/sub&gt;/Si Substrates (2009)

Supported lipid bilayers (SLB) are expected to offer a potential as biological devices utilizing biological membranes and membrane proteins. In this work, we investigated the effect of an external DC field on the phase-separated structures of gel phase and liquid crystalline phase in the SLBs of the DMPS-DOPC binary systems. The electric field was vertically applied to the SLB using a three-electrode system. The voltage apply of −1.0 V at the backside of the SLB increased the gel-phase domain size, while the voltage apply of +1.0 V decreased the domain size. This electric field effect is strongly related with the existence of PS lipids that is a negatively-charged lipid. Previously it was reported that the size of brain-PS-rich domain depends on the Ca2+ concentration. This implies that it is possible to change the domain size due to the change of the Ca2+ concentration near the surface of the SLB by applying the electric field.