gebhart/patrepeval huggingface dataset:
Oxygen uptake rates and liver‐specific functions of hepatocyte and 3T3 fibroblast co‐cultures (2006)

Bioartificial liver (BAL) devices have been developed to treat patients undergoing acute liver failure. One of the most important parameters to consider in designing these devices is the oxygen consumption rate of the seeded hepatocytes which are known to have oxygen consumption rates 10 times higher than most other cell types. Hepatocytes in various culture configurations have been tested in BAL devices including those formats that involve co-culture of hepatocytes with other cell types. In this study, we investigated, for the first time, oxygen uptake rates (OUR)s of hepatocytes co-cultured with 3T3-J2 fibroblasts at various hepatocyte to fibroblast seeding ratios. OURs were determined by measuring the rate of oxygen disappearance using a ruthenium-coated optical probe after closing and sealing the culture dish. Albumin and urea production rates were measured to assess hepatocyte function. Lower hepatocyte density co-cultures demonstrated significantly higher OURs (2 to 3.5-fold) and liver- specific functions (1.6-fold for albumin and 4.5-fold for urea production) on a per cell basis than those seeded at higher densities. Increases in OUR correlated well with increased liver-specific functions. OURs (V(m)) were modeled by fitting Michaelis-Menten kinetics and the model predictions closely correlated with the experimental data. This study provides useful information for predicting BAL design parameters that will avoid oxygen limitations, as well as maximize metabolic functions.
Ultra-fast aerial image simulation algorithm using wavelength scaling and fast Fourier transformation to speed up calculation by more than three orders of magnitude (2023)

An ultra-fast image simulation algorithm is proposed. The new algorithm uses full fast-Fourier-transform (FFT) to calculate the aerial image intensity. The wavelength, 193 nm, was scaled to a number of powers of 2, through scaling the mask with a scaling factor derived from the discrete Fourier transform (FT) format. The mask can then be transformed to the diffraction spectrum in terms of spatial frequency using the FFT algorithm. Similarly, this mask diffraction spectrum can be inverse transformed to the aerial-image by using the inverse-FFT algorithm. The image is finally scaled back to the original image amplitude of the original wavelength and squared to the image intensity. Comparing to the original FT, there is a 4000 × to 5000 × computation speed improvement with only about 3% intensity deviation. This algorithm provides an efficient engine for lithography optimization.
A self-amplifying mRNA COVID-19 vaccine drives potent and broad immune responses at low doses that protects non-human primates against SARS-CoV-2 (2021)

Abstract The coronavirus disease 2019 (COVID-19) pandemic continues to spread globally, highlighting the urgent need for safe and effective vaccines that could be rapidly mobilized to immunize large populations. We report the preclinical development of a self-amplifying mRNA (SAM) vaccine encoding a prefusion stabilized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein and demonstrate potent cellular and humoral immune responses at low doses in mice and rhesus macaques. The homologous prime-boost vaccination regimen of SAM at 3, 10 and 30 μg induced potent neutralizing antibody titers in rhesus macaques following two SAM vaccinations at all dose levels, with the 10 μg dose generating geometric mean titers (GMT) 48-fold greater than the GMT of a panel of SARS-CoV-2 convalescent human sera. Spike-specific T cell responses were observed at all dose levels. SAM vaccination provided protective efficacy against SARS-CoV-2 challenge as both a homologous prime-boost and as a single boost following ChAd prime, demonstrating reduction of viral replication in both the upper and lower airways. Protection was most effective with a SAM prime-boost vaccination regimen at 10 and 30 μg and with a ChAd/SAM heterologous prime-boost regimen. The SAM vaccine is currently being evaluated in clinical trials as both a homologous prime-boost regimen at low doses and as a boost following heterologous prime.
Stimulation and regulation of tumor cell motility in invasion and metastasis (1995)

In this review, the role of extracellular factors in the stimulation and regulation of tumor cell motility are discussed. Tumor cells respond in a motile fashion to a variety of external ligands including autocrine motility factors, growth factors, and components of the extracellular matrix. Since tumor cell motility is a necessary component of tumor invasion and metastasis, we speculate that these protein factors could play important regulatory roles in tumor motility at different stages of the metastatic cascade.
Enzymatic synthesis of a 6′-sulphated sialyl-Lewisx which is an inhibitor of L-selectin binding to peripheral addressin (1994)

A sulphated form of sialyl-Lewisx, NeuAc alpha 2-3Gal beta 1-4(Fuc alpha 1-3)GlcNAc6OSO3 beta 1-3Gal, was synthesized enzymatically from a precursor disaccharide, GlcNAc6OSO3 beta 1-3Gal, using sequential steps involving beta 1,4-galactosyltransferase, alpha 2,3-trans-sialidase and recombinant alpha 1,3-fucosyltransferase, respectively. Successful enzymatic fucosylation at the 3 position of the GlcNAc6OSO3 residue demonstrated that fucosyltransferase are capable of generating, in situ, sulphated sialyl Lewisx structures containing sulphate at the 6 position of GlcNAc. The sulphated sialyl-Lewisx pentasaccharide produced by this procedure inhibited binding of a soluble form of L-selectin to 35SO4-labelled peripheral addressin with an IC50 of 0.8 mM, whereas sialyl-Lewisx tetrasaccharide was a weaker inhibitor, displaying an IC50 of 3.2 mM. Hemmerich and Rosen (Biochemistry, 33, 4820-4829, 1994) recently reported the presence of Gal beta 1-4GlcNAcO6SO3 structures on murine peripheral addressin Sgp50, in addition to sialyl Lewisx structures sulphated at the 6-O-galactose position. Based on our data, we suggest that sialyl Lewisx sulphated at the 6-O-GlcNAc position may also exist on receptors and function as a ligand for L-selectin.
ChemInform Abstract: The Electronic Structure of Some Mono‐ and Bisoxazolines. (2000)

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.
Stellar Variability in the VVV survey (2013)

The Vista Variables in the Vía Láctea (VVV) ESO Public Survey is an ongoing time-series, near-infrared (IR) survey of the Galactic bulge and an adjacent portion of the inner disk, covering 562 square degrees of the sky, using ESO's VISTA telescope. The survey has provided superb multi-color photometry in 5 broadband filters ($Z$, $Y$, $J$, $H$, and $K_s$), leading to the best map of the inner Milky Way ever obtained, particularly in the near-IR. The main variability part of the survey, which is focused on $K_s$-band observations, is currently underway, with bulge fields having been observed between 31 and 70 times, and disk fields between 17 and 36 times. When the survey is complete, bulge (disk) fields will have been observed up to a total of 100 (60) times, providing unprecedented depth and time coverage. Here we provide a first overview of stellar variability in the VVV data, including examples of the light curves that have been collected thus far, scientific applications, and our efforts towards the automated classification of VVV light curves.
Inactivation of the Pst System Reduces the Virulence of an Avian Pathogenic Escherichia coli O78 Strain (2005)

Escherichia coli O78 strains are frequently associated with extraintestinal diseases, such as airsacculitis and septicemia, in poultry, livestock, and humans. To understand the influence of the pst operon in the virulence of E. coli, we introduced mutations into the pst genes of the avian pathogenic E. coli (APEC) O78:K80 strain chi7122 by allelic exchange. The mutation of pst genes led to the constitutive expression of the Pho regulon. Furthermore, the virulence of APEC strain chi7122 in a chicken infection model was attenuated by inactivation of the Pst system. The pst mutant caused significantly fewer extraintestinal lesions in infected chickens, and bacterial numbers isolated from different tissues after infection were significantly lower for the mutant than for the wild-type strain. Moreover, resistance to the bactericidal effects of rabbit serum and acid shock was impaired in the pst mutant, in contrast to the wild-type strain. In addition, the MIC of polymyxin was twofold lower for the mutant than for the wild-type strain. Although the pst mutant demonstrated an increased susceptibility to rabbit serum, this strain was not killed by chicken serum, suggesting the presence of differences in host innate immune defenses and complement-mediated killing. In APEC O78 strain chi7122, a functional Pst system is required for full virulence and resistance to acid shock and polymyxin. Our results suggest that the mutation of pst genes induces a deregulation of phosphate sensing and changes in the cell surface composition that lead to decreased virulence, indicating the importance of the Pst system for the virulence of pathogenic E. coli strains from different hosts.
OWLKNEST: An Expert System to Provide Operator Workload Guidance (1989)

The Operator Workload Knowledge-based Expert System Tool (OWLKNEST) is a microcomputer-based tool that provides guidance in selecting the most appropriate technique to use for estimating Operator Workload (OWL) for developing Army systems. OWLKNEST is based on twenty years of workload research and on knowledge gained in the three-year Army Research Institute OWL Program. The design approach is presented along with a general description of targeted users and knowledge representation scheme. The criteria used to evaluate available OWL techniques for inclusion in the system are also presented. Sample system applications are presented which illustrate how OWLKNEST can be used for a variety of needs.
On Node Classification in Dynamic Content-based Networks (2011)

In recent years, a large amount of information has become available online in the form of web documents, social networks, blogs, or other kinds of social entities. Such networks are large, heterogeneous, and often contain a huge number of links. This linkage structure encodes rich structural information about the underlying topical behavior of the network. Such networks are often dynamic and evolve rapidly over time. Much of the work in the literature has focussed either on the problem of classification with purely text behavior, or on the problem of classification with purely the linkage behavior of the underlying graph. Furthermore, the work in the literature is mostly designed for the problem of static networks. However, a given network may be quite diverse, and the use of either content or structure could be more or less effective in different parts of the network. In this paper, we examine the problem of node classification in dynamic information networks with both text content and links. Our techniques use a random walk approach in conjunction with the content of the network in order to facilitate an effective classification process. This results in an effective approach which is more robust to variations in content and linkage structure. Our approach is dynamic, and can be applied to networks which are updated incrementally. Our results suggest that an approach which is based on a combination of content and links is extremely robust and effective. We present experimental results illustrating the effectiveness and efficiency of our approach.
Verification of the Radio Wave Absorption Effect in the Millimeter Wave Band of SWCNTs and Conventional Carbon-Based Materials (2021)

Using a sample coated with three types of carbon-based paints, namely single-wall carbon nanotube (SWCNTs), carbon black, and graphite, the amount of radio wave absorption for each was measured. SWCNTs proved to have the superior radio wave absorption effect in the millimeter band. Considering the change in the amount of radio wave absorption depending on the coating amount, three different coating thicknesses were prepared for each test material. The measurement frequency was set to two frequency bands of 28 GHz and 75 GHz, and the measurement method was carried out based on Japanese Industrial Standard (JIS) R1679 “Radio wave absorption characteristic measurement method in the millimeter wave band of the radio wave absorber.” As for the amount of radio wave absorption in the 28 GHz band, a maximum amount of radio wave absorption of about 6 dB was obtained when 35 m of CNT spray paint was applied. It was confirmed that the carbon black paint came to about 60% that of the SWCNT, and the graphite paint did not obtain much radio wave absorption even when the coating thickness was changed. Furthermore, even in the 75 GHz band, the radio wave absorption was about 7 dB when 16 μm of CNT spray paint was applied, showing the maximum value. Within these experimental results, the CNT spray paint has a higher amount of radio wave absorption in the millimeter wave band than paints using general carbon materials. Its effectiveness could be confirmed even with a very thin coating thickness of 35 μm or less. It was also confirmed that even with the same paint, the radio wave absorption effect changes depending on the difference in coating thickness and the condition of the coated surface.
Extrusion Development of Graphite-Based Composite Fuel for Nuclear Thermal Propulsion (2015)

Graphite-based composite fuel forms for Nuclear Thermal Propulsion (NTP) technology are being developed at ORNL. This effort involves process development for extrusion and heat treatment of intermediate length fuel elements representative of historical NERVA fuel. Earlier efforts at ORNL involved identifying extrusion feedstock materials, extrusion equipment, and fabrication techniques based on historical work. This information was utilized to procure representative materials and establish an extrusion capability. Using the new equipment and applying information learned during earlier lab scale work, several extrusion studies were conducted. The focus of these studies included determining appropriate blending methods for the feedstock materials, range of binder fraction, extrusion die and layoff table requirements, and the development of an interconnected carbide network during heat treatment. The results from these studies are reported including microstructural analysis and characterization of a high temperature heat treated element. SEM images of specimens both before and after heat treatment were used to determine changes in microstructure. Large regions of coalesced particles after heat treatment indicate that the desired interconnected carbide network was achieved. Additional characterization included density, compressive strength, and coefficient of thermal expansion (CTE). Since it is important that fuel elements from this work be representative of the original elements, these results were compared to historical values. Physical properties data from the recently fabricated element show good agreement with some historical data.
MAPPIT as a High-Throughput Screening Assay for Modulators of Protein–Protein Interactions in HIV and HCV (2011)

The discovery of novel antivirals for HIV and HCV has been a focus of intensive research for many years. Where the inhibition of critical viral enzymes by small molecules has proven effective for many viruses, there is considerable merit in pursuing protein-protein interactions (PPIs) as targets for therapeutic intervention. The mammalian protein-protein interaction trap (MAPPIT) is a two-hybrid system used for the study of PPIs. The bait and prey proteins are linked to deficient cytokine receptor chimeras, where the bait and prey interaction and subsequent ligand stimulation restores JAK-STAT signaling, resulting in reporter gene expression controlled by a STAT3-responsive promoter. We report the use of MAPPIT as a high-throughput screening assay for the discovery of inhibitors or stimulators of the Vif-APOBEC3G interaction and the reverse transcriptase heterodimerization (RTp66-RTp51) for HIV and the NS4A-NS3 interaction for HCV.
Mechanism of Radiation Coupling to Plasma Wave Field Effect Transistor Sub-THz Detectors (2008)

Detection of 100 GHz and 285 GHz electromagnetic radiation by GaAs/AlGaAs field effect transistors with the gate length of 150 nm was investigated at 300 K as a function of the angle between the direction of linear polarization of the radiation and the symmetry axis of the field effect transistors. The angular dependence of the detected signal was found to be A cos 2 (-0)+C. A response of the transistor chip (including bonding wires and the substrate) to the radiation was numerically simulated. Calculations confirmed experimentally observed dependences and allowed to investigate the role of bonding wires and contact pads in coupling of the radiation to the transistor channel.
Efficient Implementation of the Pairing on Mobilephones using BREW. (2007)

Pairing based cryptosystems can accomplish novel security applications such as ID-based cryptosystems, which have not been constructed efficiently without the pairing. The processing speed of the pairing based cryptosystems is relatively slow compared with the other conventional public key cryptosystems. However, several efficient algorithms for computing the pairing have been proposed, namely Duursma-Lee algorithm and its variant T pairing. In this paper, we present an efficient implementation of the pairing over some mobile phones. The processing speed of our implementation in ARM9 processors on BREW achieves under 100 milliseconds using the supersingular curve over F 3 97. It has become efficient enough to implement security applications, such as ID-based cryptosystems and broadcast encryption, using the pairing on BREW mobilephones.
Understanding the Importance of the Teres Minor for Shoulder Function: Functional Anatomy and Pathology (2018)

Although the teres minor is often overlooked in a normal shoulder, it becomes a key component in maintaining shoulder function when other rotator cuff tendons fail. The teres minor maintains a balanced glenohumeral joint and changes from an insignificant to the most significant external rotator in the presence of major rotator cuff pathology. The presence or absence of the teres minor provides prognostic information on the outcomes of reverse total shoulder arthroplasty and tendon transfers. Clinical tests include the Patte test, the Neer dropping sign, the external rotation lag sign, and the Hertel drop sign. Advanced imaging of the teres minor can be used for classification using the Walch system. Understanding the function and pathology surrounding the teres minor is paramount in comprehensive management of the patient with shoulder pathology. Appropriate clinical examination and imaging of the teres minor are important for preoperative stratification and postoperative expectations.
Probiotic and postbiotic activity in health and disease: comparison on a novel polarised ex-vivo organ culture model (2012)

Probiotics can have inflammatory activities in both healthy and IBD tissue. Valid preclinical data on proper model systems should therefore be obtained before specific probiotic strains enter the clinics, especially if administered during acute inflammatory responses. Postbiotics may be a safe alternative for the treatment of patients with IBD in the acute inflammatory phase.
Heteroclinic Cycles in Coupled Systems of Difference Equations (2003)

Cycling behavior, in which solution trajectories linger around steady-states and periodic solutions, is known to be a generic feature of coupled cell systems of differential equations. In this type of systems, cycling behavior can even occur independently of the internal dynamics of each cell. This conclusion has lead to the discovery of "cycling chaos", in which solution trajectories cycle around symmetrically related chaotic sets. In this work, we demonstrate that cycling behavior also occurs in coupled systems of difference equations. More specifically, we prove the existence of structurally stable cycles between fixed points, and use numerical simulations to illustrate that the resulting cycles can also persist independently of the internal dynamics of each cell. Consequently, we demonstrate that cycles involving periodic orbits as well as cycling chaos also occur in systems of difference equations.
Supplementary Figure 2 from Progesterone Receptor Signaling in the Microenvironment of Endometrial Cancer Influences Its Response to Hormonal Therapy (2023)

&lt;p&gt;PDF - 188K, Biologic behavior of PTENKO tumors during and after cessation of progesterone therapy.&lt;/p&gt;
Epigenetic Changes Induced by Green Tea Catechins a re Associated with Prostate Cancer (2017)

Prostate cancer is one of the most difficult cancers to treat especially when it becomes hormone resistant such as castrate resistant prostate cancer (CRPC) and subsequent metastatic CRPC. Apart from the genetic alterations in prostate cancer, epigenetic modifications also play an important role in the development and neoplastic progression of this disease. These include DNA methylation, histone modifications, and non-coding microRNAs. miRNAs are a novel class of small endogenous single-stranded non-coding RNAs of 19-25 nucleotides in length that typically silence gene expression. Considering the reversibility of epigenetic alterations in early carcinogenesis process, reversion (correction) of these modifications by green tea catechins could be a promising strategy for cancer chemoprevention and therapy. Recent evidence suggests that green tea catechins such as epigallocatechin gallate (EGCG) not only act as epigenetic modulators but can also modify miRNA expression and their target mRNAs, consistently contributing to the inhibition of prostate carcinogenesis. Various studies also indicate that several green tea polyphenols (GTPs) exert synergistic effects with other cancer chemotherapeutic agents. Therefore, the use of appropriate combinations of green tea catechins with the existing chemotherapeutics will lead to a reduction in side effects without decreasing the chemotherapeutic effects. This review will summarize the key results from recent studies detailing the effects of green tea catechins such as EGCG on epigenetic alterations and miRNA expression in prostate cancer.