gebhart/patrepeval huggingface dataset:
SPDEF Inhibits Prostate Carcinogenesis by Disrupting a Positive Feedback Loop in Regulation of the Foxm1 Oncogene (2014)

SAM-pointed domain-containing ETS transcription factor (SPDEF) is expressed in normal prostate epithelium. While its expression changes during prostate carcinogenesis (PCa), the role of SPDEF in prostate cancer remains controversial due to the lack of genetic mouse models. In present study, we generated transgenic mice with the loss- or gain-of-function of SPDEF in prostate epithelium to demonstrate that SPDEF functions as tumor suppressor in prostate cancer. Loss of SPDEF increased cancer progression and tumor cell proliferation, whereas over-expression of SPDEF in prostate epithelium inhibited carcinogenesis and reduced tumor cell proliferation in vivo and in vitro. Transgenic over-expression of SPDEF inhibited mRNA and protein levels of Foxm1, a transcription factor critical for tumor cell proliferation, and reduced expression of Foxm1 target genes, including Cdc25b, Cyclin B1, Cyclin A2, Plk-1, AuroraB, CKS1 and Topo2alpha. Deletion of SPDEF in transgenic mice and cultures prostate tumor cells increased expression of Foxm1 and its target genes. Furthermore, an inverse correlation between SPDEF and Foxm1 levels was found in human prostate cancers. The two-gene signature of low SPDEF and high FoxM1 predicted poor survival in prostate cancer patients. Mechanistically, SPDEF bound to, and inhibited transcriptional activity of Foxm1 promoter by interfering with the ability of Foxm1 to activate its own promoter through auto-regulatory site located in the -745/-660 bp Foxm1 promoter region. Re-expression of Foxm1 restored cellular proliferation in the SPDEF-positive cancer cells and rescued progression of SPDEF-positive tumors in mouse prostates. Altogether, SPDEF inhibits prostate carcinogenesis by preventing Foxm1-regulated proliferation of prostate tumor cells. The present study identified novel crosstalk between SPDEF tumor suppressor and Foxm1 oncogene and demonstrated that this crosstalk is required for tumor cell proliferation during progression of prostate cancer in vivo.
Defined Nongrowth Media for Stage II Development of Competence in <i>Haemophilus influenzae</i> (1970)

The composition of a defined nongrowth medium used in stage II development of competence of Haemophilus influenzae affects the course of this development. The development of competence in two nongrowth media, M-IV and M-V, is rapid, logarithmic, and independent of the cell concentration. This last property indicates that there is probably no transfer of a competence factor from competent to noncompetent cells, in contrast to results reported for other organisms. Levels of competence reached in these completely defined media are such that 1 to 5% of the cells are transformed in the presence of an excess of marked deoxyribonucleic acid. The method of evaluating competence, which depends on the frequency of multiple independent transformations, has been reexamined. This and other methods are compared on samples taken from a culture during development of competence.
Heterogeneous Embedding For Subjective Artist Similarity. (2009)

[TODO] Add abstract here.
D-GAN: Deep Generative Adversarial Nets for Spatio-Temporal Prediction (2019)

Spatio-temporal (ST) data for urban applications, such as taxi demand, traffic flow, regional rainfall is inherently stochastic and unpredictable. Recently, deep learning based ST prediction models are proposed to learn the ST characteristics of data. However, it is still very challenging (1) to adequately learn the complex and non-linear ST relationships; (2) to model the high variations in the ST data volumes as it is inherently dynamic, changing over time (i.e., irregular) and highly influenced by many external factors, such as adverse weather, accidents, traffic control, PoI, etc.; and (3) as there can be many complicated external factors that can affect the accuracy and it is impossible to list them explicitly. To handle the aforementioned issues, in this paper, we propose a novel deep generative adversarial network based model (named, D-GAN) for more accurate ST prediction by implicitly learning ST feature representations in an unsupervised manner. D-GAN adopts a GAN-based structure and jointly learns generation and variational inference of data. More specifically, D-GAN consists of two major parts: (1) a deep ST feature learning network to model the ST correlations and semantic variations, and underlying factors of variations and irregularity in the data through the implicit distribution modelling; (2) a fusion module to incorporate external factors for reaching a better inference. To the best our knowledge, no prior work studies ST prediction problem via deep implicit generative model and in an unsupervised manner. Extensive experiments performed on two real-world datasets show that D-GAN achieves more accurate results than traditional as well as deep learning based ST prediction methods.
The Structure of Dimers from the Alkaline Hydrogenation of Lignin (1966)

Experimental problems occur in isolating lignin dimers from alkaline hydrogenation pulping of both softwoods and hardwoods. The structures of dimeric compounds isolated have the following carbon skeletons: diphenylmethane; 1,2-diphenylethane; 3,3′-diethylbiphenyl, and 1-phenyl-2-(3-ethyldiphenyl)-ethane. Mechanisms for their probable origin from lignin structural units are proposed. Nuclear magnetic resonance (NMR) spectra of a number of hydrogenated monomers and dimers can be used to prove structures of the products.
Multiple Primary Malignant Tumors in Patients With Head and Neck Cancer (1998)

Multiple primary tumors are a known phenomenon in head and neck cancer. They are partially responsible for the limited improvement in survival of head and neck cancer during the past 20 years. Only a few prospective data have been published about the incidence of metachronous tumors. The authors prospectively studied 127 patients with squamous cell carcinoma of the head and neck. The overall incidence of second primary tumors was 13.5% (simultaneously, 3%; synchronously, 5.5%; and metachronously, 8%). More than 90% of the recurrences of the first primary tumor occurred within the first 2 years following primary treatment, but the second primary tumors continued to occur gradually in the course of follow-up. Most of the second primary tumors were discovered because the patients developed symptoms (14/17). Survival after detection of the second primary tumor was poor. The development of a second primary tumor was of equivalent prognosis to a recurrence of the primary tumor. Future directives include the development of more adequate screening methods. Identification of potential early markers for the development of a squamous cell carcinoma at the level of the mucosa at risk and in serum could be of value for the early detection of individuals at risk.
A New Model for the Effect of Calcium Sulfate Scale Formation on Pool Boiling Heat Transfer (2004)

Abstract Scale deposition on the heat transfer surfaces from water containing dissolved salts considerably reduces fuel economy and performance of heat transfer equipment. This problem is more serious during nucleate boiling due to the mechanisms of bubble formation and detachment. Using a precision pool boiling test apparatus, the effects of heat flux and calcium sulfate concentration on heat transfer coefficient and formation and growth of deposits are investigated. The transient change in heat transfer is closely related to wick boiling, and the associated changes in bubble departure diameter and bubble site density. A physically sound prediction model was developed for the prediction of heat transfer coefficients as a function of time during deposition processes. Based on comparison with experimental data over a wide range of foulant concentrations and heat fluxes, the model is considered to be sufficiently accurate for practical application.
Atomic-Scale Morphology and Electronic Structure of Manganese Atomic Layers Underneath Epitaxial Graphene on SiC(0001) (2012)

We report the fabrication of a novel epitaxial graphene(EG)/Mn/SiC(0001) sandwiched structure through the intercalation of as-deposited Mn atoms on graphene surfaces, with the aid of scanning tunneling microscope, low energy electron diffraction, and X-ray photoelectron spectroscopy. We found that Mn can intercalate below both sp(3)-hybridized carbon-rich interface layer and monolayer graphene, along with the formation of various embedded Mn islands showing different surface morphologies. The unique trait of the sandwiched system is that the strong interaction between the carbon-rich interface layer and SiC(0001) can be decoupled to some degrees, and contemporaneous, an n-doping effect is observed by mapping the energy band of the system using angle-resolved photoemission spectroscopy. Moreover, what deserves our special attention is that the intercalated islands can only evolve below monolayer graphene when a bilayer coexists, accounting for an intriguing graphene thickness-dependent intercalation effect. In the long run, we believe that the construction of graphene/Mn/SiC(0001) systems offers ideal candidates for exploring some intriguing physical properties such as the magnetic property of two-dimensional transition metal systems.
Galvanomagnetic Properties of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>n</mml:mi></mml:math>-Type Cd<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">As</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math> (1961)

Galvanomagnetic measurements on oriented, single crystals of $n$-type Cd${\mathrm{As}}_{2}$, a noncubic semiconductor, indicate the surfaces of constant energy to be ellipsoids of revolution, located along the symmetry axis of the crystal system. The ratio of electronic mobility is found to be $\frac{{\ensuremath{\mu}}_{\mathrm{II}}}{{\ensuremath{\mu}}_{\ensuremath{\perp}}}\ensuremath{\sim}4$, from Hall and resistivity data. Magnetoresistance measurements confirm this conduction-band model and indicate the scattering to be due primarily to acoustical lattice modes with some degree of impurity scattering.
DEVELOPMENT OF SOL-GEL-BASED BIOACTIVE PAPER SENSING PLATFORMS TOWARD NEUROTOXIN DETECTION (2009)

We report on a new solid-phase colorimetric bioassay format based on enzyme-catalyzed enlargement of gold nanoparticles (AuNP) that are coentrapped with the enzyme in a sol-gel based silica material. Biocatalysed hydrolysis of the enzyme substrate, acetylthiocholine (ATCh) leads to formation of thiocholine, which in turn reduces Au(III) onto the entrapped nanoparticles, producing particle growth and a concomitant increase in color intensity that can be correlated to the amount of substrate or inhibitor present in test solutions. The entrapped AuNP cannot leach from the silica material, leading to a solid-phase assay that has the potential to be integrated into a portable biosensing platform that can utilize visual detection of a color change as a simple readout. Toward this end, we cast an AChE-doped silica material onto a 40%MTMS/TMOS functionalized paper substrate to form the portable biosensor. Treatment with 40%MTMS/TMOS affords a more uniform paper surface allowing for more reproducible enzyme loading and better control over liquid penetration. Our results show that the assay is sufficiently sensitive to allow for detection of Paroxon to 1 μM. For automated sensor fabrication, we investigated piezoelectric inkjet printing of enzyme doped silica sols. A unique sandwich type fabr ication technique was devised whereby sol-gel materials (at stable pH) and the bio-materials were printed separately and in layers so that AChE was sandwiched between layers of silica to form the sensor. For these biosensors, a standard Ellman assay was used to monitor AChE activity with the cationic polymer, PVAm (polyvinylamine, 1.5 MDa), employed to trap and preserve the colored anionic product molecules (5-thio-2-nitrobenzoate) over a finite region. With this novel approach, a series of Paraoxon and Aflatoxin BI levels were assessed and it was determined that these compounds can be detected to 100 nM and 1 nM respectively, in ca. 5 min. The paper-based, colorimetric sensing platforms presented in this thesis are simple, cost-effective, portable, user-friendly, and need neither sophisticated instruments nor additional handling steps. Detection can be made by eye or by digital camera and image analysis software.
Large-Scale Generic Image Recognition and Image Representation (2011)

近年のインターネットの発達により大量の画像とそれ に付随するタグなどの付加的情報が容易に入手可能とな り,この大規模な情報を用いて一般画像認識を構築する 試みが盛んになってきている.本稿では大規模画像デー タセットを用いた一般画像認識の潮流を紹介する.また, 大規模画像認識を行うにはスケーラビリティを維持する ために線形識別機を用いることが多い.線形の識別機で あっても十分な識別能力を発揮するためには画像表現が 鍵となるため,近年の画像表現手法に関して解説を行う.
Biochemical Changes in the Rice Grain during Germination (1972)

Changes in the content of starch, protein, and RNA and in the activity of their hydrolases in the rice endosperm (Oryza sativa L., variety IR8) were determined during the first week of germination without added nutrient both in the dark and in the light. Changes were generally more rapid in the dark than in the light. Oxygen uptake and RNase activity started to increase and the root protruded on the second day, followed by the coleoptile on the third day, and the primary leaf on the fourth day. ATP level was at a maximum on the fourth day. The activity of amylases and R enzyme increased progressively, but that of phosphorylase tended to decrease during starch degradation. A new alpha amylase isozyme band appeared during germination. Glucose was the major product of starch degradation. Sucrose, maltose, maltotriose, raffinose, and fructose were also detected. Protease activity reached a maximum on the fifth or sixth day and closely paralleled the increase in soluble amino N and soluble protein.In embryoless seed halves with 0.12 muM gibberellin As, peak protease activity occurred in 2.5 days and peak alpha amylase activity on the fifth day of incubation. The production of alpha amylase, protease, and R enzyme was inhibited by 40 muM cycloheximide, but only alpha amylase and R enzyme were inhibited by 20 mug/ml actinomycin D.
A Seedling Screen for Phytophthora Root Rot of Pepper,<i>Capsicum annuum</i> (1991)

A new method to screen pepper seedlings that can help identify resistance and susceptibility of pepper cultivars to Phytophthora root rot, caused by Phytophthora capsici, is described. The technique was used to successfully screen peppers for PRR resistance at 14 days postemergence. Individual plants identified as resistant survived to maturity and, therefore, could be used directly in plant breeding schemes. Furthermore, the technique allows screening of large plant populations to segregate genetic material, permitting the plant breeder time- and space-efficient selection of resistant individuals
Influence of laser pulse characteristics on the hot electron contribution to the third-order nonlinear optical response of gold nanoparticles (2009)

The third-order nonlinear optical response of noble-metal nanoparticles embedded in a dielectric matrix depends on the particle intrinsic third-order susceptibility ${\ensuremath{\chi}}_{m}^{(3)}$. We propose a model which allows one to calculate the hot electron contribution ${\ensuremath{\chi}}_{\text{he}}^{(3)}$ to ${\ensuremath{\chi}}_{m}^{(3)}$ in the case of gold. This phenomenon stems from the modification of the conduction-electron distribution induced by an optical excitation, and is significant when picosecond or subpicosecond laser pulses are considered. We show, in the case of a weak perturbation, the importance of the athermal regime for pulse widths lower than about 1 ps. Applying this model to two different samples, we then highlight the strong influence of the linear optical properties of the material on the spectral dispersion of ${\ensuremath{\chi}}_{\text{he}}^{(3)}$. Finally, the variation in ${\ensuremath{\chi}}_{\text{he}}^{(3)}$ with intensity in the high excitation regime is discussed for picosecond pulses.
Dynamic simulation of electrorheological suspensions (1989)

A simulation method is developed to investigate structure formation in electrorheological suspensions. The suspension is treated as polarizable, spherical particles in a nonconducting medium, with the spheres subject to electric polarization forces due to an applied electric field and to hydrodynamic resistance due to their motion through the continuous phase. The fibrous structures obtained from these simulations are independent of electric field strength and continuous phase viscosity in agreement with experimental observation. We have also found that the details of the simulated structures are sensitive to the treatment of the short-range forces preventing particle overlap. When this force is represented by a form that accurately approximates a hard-sphere interaction, the simulated structures agree well with those obtained experimentally, both with respect to their appearance and the time scale for structure formation.
The influence of pressure on the infrared spectra of hydrogen-bonded solids. III. Compounds with N-H...X bonds (1976)

Infrared measurements have been made of the influence of pressures between 0 and 40 kbar on the stretching and bending frequencies of N-H groups in a range of crystalline compounds which have N-H. . .N, N-H. . .O, N-H. . .S or N-H. . .Cl hydrogen bonds. The frequencies have been found to change in accordance with rules that were derived and tested in Parts I and I1 for other kinds of hydrogen-bond systems.
HIPAA compliance for clinician texting. (2012)

The HIPAA privacy and security rules need not act as an obstacle to efficient communications, but keeping texting compliant requires planning and diligence.
Informedness vs. Computational Cost of Heuristics in Iterative Repair Scheduling. (1993)

The environmental bacterium <i>Legionella pneumophila</i> is an intracellular pathogen of various protozoan hosts and able to cause Legionnaires' disease, a severe pneumonia in humans. By encoding a wide selection of virulence factors, the infectious agent possesses several strategies to manipulate its host cells and evade immune detection. In the present study, we demonstrate that the <i>L. pneumophila</i> zinc metalloprotease ProA functions as a modulator of flagellin-mediated TLR5 stimulation and subsequent activation of the pro-inflammatory NF-κB pathway. We found ProA to be capable of directly degrading immunogenic FlaA monomers but not the polymeric form of bacterial flagella. These results indicate a role of the protease in antagonizing immune stimulation, which was further substantiated in HEK-Blue<sup>TM</sup> hTLR5 Detection assays. Addition of purified proteins, bacterial suspensions of <i>L. pneumophila</i> mutant strains as well as supernatants of human lung tissue explant infection to this reporter cell line demonstrated that ProA specifically decreases the TLR5 response via FlaA degradation. Conclusively, the zinc metalloprotease ProA serves as a powerful regulator of exogenous flagellin and presumably creates an important advantage for <i>L. pneumophila</i> proliferation in mammalian hosts by promoting immune evasion.
Plasma exudation in the airways: mechanisms and function (1991)

Inflammatory challenges of tracheobronchial and nasal mucosa produce prompt extravasation or exudation of plasma from the well developed microcirculation just beneath the epithelial base. Plasma exudation is not an exaggeration of the normal capilliary exchange of fluid and solutes but a specific inflammatory response of post-capilliary venules. The exuded plasma may not produce oedema. By a rapid, undirectional, unfiltered and yet non-injurious process, plasma exudates cross the mucosal lining to appear on the airway surface at the site of challenge. In vitro data suggests the possibility that a slightly increased hydrostatic pressure moves the acellular exudate through valve-like openings between epithelial cells. By the venular-mucosal exudation mechanism all the potent protein systems of circulating plasma will operate in respiratory defence on the surface of an intact mucosa. A further inference is that exudative indices obtained from the airway surface quantitatively reflect the intensity and time course of mucosal/submucosal inflammatory processes. Irrespective of which particular cellular mechanism happens to fuel the inflammation. Mucosal exudation of plasma characteristically occurs in health and disease also when there is no airway oedema, no epithelial disruption, and no increased absorbtion ability. However, exuded plasma and its derived peptide mediators potentially contribute to several pathophysical and pathophysiological characteristics of inflammatory airway diseases.
Damage to microsomal membrane by lipid peroxidation (1973)

Abstract Alterations of microsomal membrane integrity were examined during lipid peroxidation. Loss of membrane‐bound NADPH cytochrome c reductase activity and protein release into the aqueous phase were related to disruption of the lipophilic region of the membrane. Formation of fluorescent products in the lipid phase of the membrane occurred only in the presence of peroxidation products. Changes in the membrane lipid phase during peroxidation included a decrease in the reactive amino groups of the phospholipids and a decrease in detectable phosphatidyl ethanolamine. In an ultrafiltration continuous flow chamber, peroxidized microsomal membranes were hydrolyzed to a lesser degree by solubilized lysosomal cathepsins and to a greater degree by lysosomal nucleases than were nonperoxidized membranes.
A simplified method for testing the IBM pipeline partial-scan microprocessor (2003)

This paper describes a simple test generation method for a high-performance, pipelined partial-scan microprocessor using an automatic test generation tool which was optimized for combinational logic in generating manufacturing test data. Without this method the test generation tool would have had great difficulty in generating the test data needed to achieve the required high fault coverage. User-specified clocking sequences are also allowed for design flexibility. A description of this method is provided and the experimental results are discussed.