gebhart/patrepeval huggingface dataset:
Genetic variations of DNA bindings of FOXA1 and co-factors in breast cancer susceptibility (2021)

Identifying transcription factors (TFs) whose DNA bindings are altered by genetic variants that regulate susceptibility genes is imperative to understand transcriptional dysregulation in disease etiology. Here, we develop a statistical framework to analyze extensive ChIP-seq and GWAS data and identify 22 breast cancer risk-associated TFs. We find that, by analyzing genetic variations of TF-DNA bindings, the interaction of FOXA1 with co-factors such as ESR1 and E2F1, and the interaction of TFs with chromatin features (i.e., enhancers) play a key role in breast cancer susceptibility. Using genetic variants occupied by the 22 TFs, transcriptome-wide association analyses identify 52 previously unreported breast cancer susceptibility genes, including seven with evidence of essentiality from functional screens in breast relevant cell lines. We show that FOXA1 and co-factors form a core TF-transcriptional network regulating the susceptibility genes. Our findings provide additional insights into genetic variations of TF-DNA bindings (particularly for FOXA1) underlying breast cancer susceptibility.
A novel software tool for copolymer characterization by coupling of liquid chromatography with matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (2007)

The results of copolymer characterization by coupling of chromatography and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques and subsequent calculation of copolymer composition using a novel software tool 'MassChrom2D' are presented. For high-resolution mass analysis copolymer samples were fractionated by means of liquid adsorption chromatography (LAC). These fractions were investigated off-line by MALDI-TOF MS. Various mono-n-butyl ethers of polyethylene oxide-polypropylene oxide copolymers (PEO-co-PPO) were investigated. As well as the copolymer composition presented in two-dimensional plots, the applied approach can give additional hints on specific structure-dependent separation conditions in chromatography.
Neocartilage from human mesenchymal stem cells in alginate: Implied timing of transplantation (2005)

Previous reports have demonstrated the suitability of alginate microencapsulation for chondrogenesis of human mesenchymal stem cells (MSCs) in vitro. This study examined the MSCs-alginate constructs that were transplanted beneath the dorsal skin of nude mice for 8 weeks after a variety of in vitro culture periods. The in vitro culture had great effects on gross morphology and histological characteristics of transplants. The integrity of alginate of transplants increased as the in vitro culture period increased. Transplants were characterized by an opaque and yellowish color, fair burnish, a firm to elastic texture, but without any evidence of calcification spots. Histological findings agreed with the clinical determination of hyaline cartilage, characterized by isolated cells with basophilic ground substance positive in Safranin-O staining and collagen type II immunohistochemistry. Transplants with exposure to TGF-beta1 for more than 2 weeks before transplantation, lost burnish, were flexible in texture, and had an increased formation of calcification spots. Accordingly, 1-week exposure to TGF-beta1 in vitro before transplantation is appropriate for neocartilage formation of human MSCs in alginate. These findings suggested that regeneration using cell therapy or tissue engineering should assist in ascertaining the optimal timing of transplantation.
ADVANCED CEMENTS FOR GEOTHERMAL WELLS (2007)

Using the conventional well cements consisting of the calcium silicate hydrates (CaO-SiO{sub 2}-H{sub 2}O system) and calcium aluminum silicate hydrates (CaO-Al{sub 2}O{sub 3}-SiO{sub 2}-H{sub 2}O system) for the integrity of geothermal wells, the serious concern confronting the cementing industries was their poor performance in mechanically supporting the metallic well casing pipes and in mitigating the pipe's corrosion in very harsh geothermal reservoirs. These difficulties are particularly acute in two geological regions: One is the deep hot downhole area ({approx} 1700 m depth at temperatures of {approx} 320 C) that contains hyper saline water with high concentrations of CO{sub 2} (> 40,000 ppm) in conjunction with {approx} 100 ppm H{sub 2}S at a mild acid of pH {approx} 5.0; the other is the upper well region between the well's surface and {approx} 1000 m depth at temperatures up to 200 C. The specific environment of the latter region is characterized by highly concentrated H{sub 2}SO{sub 4} (pH < 1.5) brine containing at least 5000 ppm CO{sub 2}. When these conventional cements are emplaced in these harsh environments, their major shortcoming is their susceptibility to reactions with hot CO{sub 2} and H{sub 2}SO4, thereby causing their deterioration brought about by CO{sub 2}-catalyzed carbonation and acid-initiated erosion. Such degradation not only reduced rapidly the strength of cements, lowering the mechanical support of casing pipes, but also increased the extent of permeability of the brine through the cement layer, promoting the rate of the pipe's corrosion. Severely carbonated and acid eroded cements often impaired the integrity of a well in less than one year; in the worst cases, casings have collapsed within three months, leading to the need for costly and time-consuming repairs or redrilling operations. These were the reasons why the geothermal well drilling and cementing industries were concerned about using conventional well cements, and further their deterioration was a major impediment in expediting the development of geothermal energy resources.
Long‐term androgen‐ablation causes increased resistance to PI3K/Akt pathway inhibition in prostate cancer cells (2003)

These results suggest that long-term androgen ablation therapy for prostate cancer reinforces the PI3K/Akt pathway and impedes its inhibition thus contributing to increased resistance of tumor cells to induction of apoptosis. With regard to treatment of therapy-refractory prostate cancer, these findings suggest effectiveness of a combination of cytotoxic treatment and inhibition of the PI3K-Akt survival pathway in tumor cells after failure of androgen-ablation therapy.
Inferring the shape of the real object from the object reconstructed by volume intersection (2002)

The volume intersection approach to the reconstruction of 3-D objects consists in intersecting the volumes obtained by back-projecting a number of silhouettes of an unknown object O. The problem of inferring, as far as possible, the shape of the unknown object O from the reconstructed object R is addressed. The points of the surface of R are divided into hard points, which belong to the surface of any possible object originating R, and soft points, which may or may not belong to O. Two cases are considered: in the first case R is the closest approximation of O which can be obtained with volume intersection techniques, i.e., its visual hull; in the second case, R is a generic reconstructed object. In both cases necessary and sufficient conditions are supplied for a point to be hard. Rules are given for computing the hard surfaces.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Influence of zirconium substitution on dielectric, ferroelectric and field-induced strain behaviors of lead-free 0.99[Bi1/2(Na0.82K0.18)1/2(Ti1−x Zr x )O3]-0.01LiSbO3 ceramics (2012)

The Crystal structure, dielectric, ferroelectric and field-induced strain behaviors of lead-free 0.99[Bi1/2(Na0.82K0.18)1/2(Ti1−x Zr x )O3]-0.01LiSbO3 (BNKTZ-LS) ceramics were investigated in the composition range x = 0 − 0.040. XRD patterns revealed the formation of a pure perovskite phase with no apparent structural phase transition. The temperature-dependent dielectric peaks of the BNKTZ-LS ceramics broadened and the ferroelectric polarizations decreased with increasing Zr concentration. Ferroelectric and bipolar field induced-strain curves indicated a disruption of ferroelectric order upon Zr addition into the BNKT-LS ceramics. This destabilization of the ferroelectric order was accompanied by an enhanced field-induced strain. A high field-induced strain (S = 0.30%) with a normalized strain (d*33 = S max /E max = 500 pm/V) was observed at an applied electric field of 6 kV/mm at x = 0.020.
An epidemic associated with echovirus type 18 (1972)

During the period October 1968 to March 1969 echovirus type 18 was isolated from 83 patients investigated at Fairfield Hospital for Communicable Diseases, Melbourne. The illnesses most commonly associated with these isolations were aseptic meningitis, and fever with rash.We believe that this is the first report of an epidemic due to echovirus type 18 and the first occasion on which this virus has been shown to produce disease in adults.
Multi-Path Search Algorithm for Block-Based Motion Estimation (2006)

Block-based motion estimation algorithms are widely adopted by video coding standards due to their simplicity and good distortion performance. Amongst these, pattern based search algorithms are very popular. The basic assumption made by these algorithms is that there exists a unimodal error surface within the search window. As seen in real world video sequences, this is far from reality and the algorithms often get stuck in local minimums yielding sub-optimal results. We propose a multi-path search (MPS) algorithm that utilizes more than one path to find the absolute minima. Wrong search paths are avoided early resulting in faster search. Better motion vectors are estimated increasing the video quality, consequently reducing the bitrate requirement. MPS algorithm offers flexibility and robustness with better speed and quality. Results show that a speedup of upto 34% is achieved with slight increase in PSNR as compared to its best competitor. When compared to full search, the proposed algorithm looses only 0.1%~2% in PSNR while saving 92%~95% computations.
A physiological approach to hepatic drug clearance (1975)

A physiological approach has been developed recognizing that hepatic blood flow, the activity of the overall elimination process (intrinsic clearance), drug binding in the blood, and the anatomical arrangement of the hepatic circulation are the major biological determinants of hepatic drug clearance. This approach permits quantitative prediction of both the unbound and total drug concentration/time relationships in the blood after intravenous and oral administration, and any changes that may occur as a result of alterations in the above biological parameters. These considerations have led to a classification of drug metabolism based on the hepatic extraction ratio. The proposed classification allows prediction and interpretation of the effects of individual variations in drug-metabolizing activity, route of administration, pharmacokinetic interactions, and disease states on hepatic drug elimination.
Speckle photography fringe analysis by the Walsh transform (1986)

Two-dimensional Walsh spectral analysis is presented as a new method of numerically processing the Young's fringes diffraction pattern from a double-exposure speckle photograph. The Walsh spectrum of the fringes is more complex than the Fourier spectrum but can be interpreted reliably by further cross correlation of the fringes with square waves. Compared with Fourier spectral analysis, the new technique gives results of almost identical accuracy but with substantially reduced computational effort. The ideas presented have relevance to the general problem of detecting and accurately determining the frequency components of a 2-D sinusoid in the presence of noise.
Adaptive Nonlinear Equalization for Digital Array Receivers (2019)

As low-cost fully digital array technology becomes more commercialized, techniques need to be developed to be able to deal with many of the inherent problems of these systems. This article focuses on mitigating the intermodulation distortion (IMD) caused by the low-input third-order intercept point (IIP3) of the low-noise amplifier (LNA) in a digital array element's channel. The performance of solid-state electronics also varies with the temperature of the device, thus changing the device's nonlinear characteristics. This article proposes an adaptive solution for nonlinear equalization (NLEQ) with the use of the least mean-square (LMS) algorithm. Data from a modern digital array channel are corrected using the proposed method; the channel nonlinearities are also characterized for further simulations. A simulation using these nonlinear coefficients shows that NLEQ can effectively mitigate the IMD of two strong interferers that had previously distorted the weak signal of interest. Finally, a nine-element fully digital array is simulated, showing the correlation of IMD with specific, predictable directions, and the decorrelation of these spurs after NLEQ is applied to each element of the array.
Study of hydrogen bonding in 1-ethyl-2-methyl-4-oxo-1,4-dihydro-pyridin-3-yloxyethanoic acid and 3-(1,2-diethyl-4-oxo-1,4-dihydropyridin-3-yloxy)propanoic acid by 1H NMR spectroscopy and X-ray crystallography (1993)

A series of 1,2-dialkyl-4-oxo-1,4-dihydropyridin-3-yloxyethanoic acids and 3-(1,2-dialkyl-4-oxo-1,4-dihydropyridin-3-yloxy)propanoic acids have been synthesized via the corresponding pyran-4-ones. Ring proton chemical shifts indicate hydrogen bonding between the side-chain carboxylic acid proton and the 4-oxo group of the heterocycle to be present only for the pyridinone species in DMSO solution. X-Ray crystallography demonstrates the hydrogen bonding in 1 -ethyl-2-methyl-4-oxo-1,4-dihydropyridin-3-yloxyethanoic acid to be very strong (O—O = 2.441 Å) and intramolecular, giving a unique 8-membered chelate ring. The analogous hydrogen bonding in 3-(1,2-diethyl-4-oxo-1,4-dihydropyridin-3-yloxy)propanoic acid is however strong (O—O = 2.541 Å) and inter-molecular, giving an infinite structure.
Pms2 Suppresses Large Expansions of the (GAA·TTC)n Sequence in Neuronal Tissues (2012)

Expanded trinucleotide repeat sequences are the cause of several inherited neurodegenerative diseases. Disease pathogenesis is correlated with several features of somatic instability of these sequences, including further large expansions in postmitotic tissues. The presence of somatic expansions in postmitotic tissues is consistent with DNA repair being a major determinant of somatic instability. Indeed, proteins in the mismatch repair (MMR) pathway are required for instability of the expanded (CAG·CTG)(n) sequence, likely via recognition of intrastrand hairpins by MutSβ. It is not clear if or how MMR would affect instability of disease-causing expanded trinucleotide repeat sequences that adopt secondary structures other than hairpins, such as the triplex/R-loop forming (GAA·TTC)(n) sequence that causes Friedreich ataxia. We analyzed somatic instability in transgenic mice that carry an expanded (GAA·TTC)(n) sequence in the context of the human FXN locus and lack the individual MMR proteins Msh2, Msh6 or Pms2. The absence of Msh2 or Msh6 resulted in a dramatic reduction in somatic mutations, indicating that mammalian MMR promotes instability of the (GAA·TTC)(n) sequence via MutSα. The absence of Pms2 resulted in increased accumulation of large expansions in the nervous system (cerebellum, cerebrum, and dorsal root ganglia) but not in non-neuronal tissues (heart and kidney), without affecting the prevalence of contractions. Pms2 suppressed large expansions specifically in tissues showing MutSα-dependent somatic instability, suggesting that they may act on the same lesion or structure associated with the expanded (GAA·TTC)(n) sequence. We conclude that Pms2 specifically suppresses large expansions of a pathogenic trinucleotide repeat sequence in neuronal tissues, possibly acting independently of the canonical MMR pathway.
Certain Relationships between Chemical Composition and Properties of Petroleum Asphalts from Different Origin (2006)

Asphalts are classified according to three most commonly measured properties: ductility, penetration and the ring and ball softening point. The present study shows through many examples that these physical characteristics are not discriminating enough. It was revealed that the chemical composition sheds more light on the physical properties of the various grades of asphalt. There were significant differences between the chemical composition of asphalts having the same softening point and from the same origin. Increase in ductility has been accounted for by the high content of resins while lower penetration is due to high asphaltene content. The correlation of two asphalt indices with the composition shows that the Gaestel index (IC) proves to be a more adequate quality parameter than the asphaltene index (IA) for the characterization of asphalts. Both indices can be comparatively used to distinguish between asphalts of narrow softening point ranges.
Variation in free amino acid profile among some rice (Oryza sativa L.) cultivars (2010)

The free amino acid (FAA) concentration of rice is becoming an increasingly important grain quality factor because of its apparent influence on the organoleptic acceptability of cooked rice. To determine the variability of this character among rice cultivars the FAA profiles of 49 cultivars were determined using Pico-Tag method. Among these 13 cultivars were selected to determine variation in FAA accumulation pattern after 24-hour germination treatment. The results show significant variation in the concentrations of total as well as individual FAAs among cultivars. There were also significant differences between indica- and japonica-type cultivars in the concentrations of some FAAs. The ratio of the total concentration of aspartate-derived to glutamate-derived FAAs (A/G ratio) evaluated for the japonica group (0.68) was significantly lower than that for the indica group (1.07). This suggests that typically, japonica-type rice grains tend to accumulate more Glu-derived than Asp-derived FAAs. Other results show a decline in the A/G ratios of both groups in response to germination treatment, with the indica group exhibiting a more rapid response. These results appear to suggest key differences in the FAA accumulation patterns of japonica- and indica-type rice grains especially with respect to the contents of aspartate-derived and glutamate-derived amino acids.
Monitoring of Delamination Growth in CFRP Laminates using Chirped FBG Sensors (2007)

Chirped fiber Bragg grating (FBG) sensors are applied to the monitoring of the propagation direction and the size of a delamination in CFRP cross-ply laminates, since it has been found previously that the reflection spectrum from chirped FBG sensors is expressed as a function of their positions along the grating. The reflection spectra are measured at various delamination lengths under a four-point bending test. Two chirped FBG sensors are embedded in two opposite directions in order to investigate the relationship between the deformation of the spectrum and the propagation direction of the delamination. The spectrum changes sensitively depending on both the size and the propagation direction of the delamination. For confirmation of the measured results, the spectra are simulated using FEA computed strain distributions of the chirped FBG sensors. In the simulation, a birefringence effect of the optical fiber on the spectrum is observed in the case of chirped FBG sensors. The relationship between the measured spectral change and the delamination growth is illustrated by the calculated spectra, the strain distributions, and the properties of the chirped FBG sensors. As a result, it is found that not only the delamination size, but also the propagation direction of the delamination can be evaluated by using chirped FBG sensors.
Single Flexible Hydrophobic Polyelectrolyte Molecules Adsorbed on Solid Substrate:  Transition between a Stretched Chain, Necklace-like Conformation and a Globule (2002)

Single flexible polyelectrolyte molecules of poly(2-vinylpyridine) undergo conformational transition from a stretched wormlike coil to a necklace-like globule, and to a compact globule depending on pH and ionic strength in aqueous solution in good agreement with recent theoretical reports. AFM investigations allow the visualization of details of the chain conformation on mica and the extraction of quantitative statistics of molecular dimensions.
Complex Protective Coatings for Graphite and Carbon-Carbon Composite Materials (2015)

The objective of this review is to present the results on the production techniques, process parameters and compositions of heat-resistant coatings for graphite and carbon-carbon composites. The data reported concern the resistance of such protective coatings in air at temperatures up to 2273 K and in the high-speed flows of oxidizing gas media taking place in the spacecraft equipment. Coatings of this type, generally, have a multilayer structure based on the refractory compounds such as carbides, borides, silicides of transition metals and oxides with a high melting temperature. An efficient heat-resistant coating for carbon-based materials should be composed of three layers from which each fulfills its own function. The paper presents a new complex method for formation of heat-resistant coatings on the carbon-based materials. The method combines the vacuum-activated diffusion saturation in the presence of a liquid-phase and self-propagating high-temperature synthesis (SHS) simultaneously.
P1J-4 High-Q FBARs Using Epitaxial AlN Films (2006)

FBARs (Film Bulk Acoustic Resonators) are attractive candidates for RF filtering in radar phased array modules providing that their insertion loss can be reduced to 1 dB or less. One of the factors that contributes to the increased insertion loss of FBAR filters at X-band is the difficulty in achieving high crystalline quality in thin (<0.5 mum) sputtered films. We describe an FBAR fabrication process using single crystal AlN films that are deposited epitaxially on SiC substrates. It is intended that this process would ultimately be compatible with GaN wide-band-gap integrated circuits that would provide the switches required for a switched filterbank and the LNAs. The single crystal FBARs showed the expected resonator behavior but with lower Q and lower piezoelectric coupling coefficient (k <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) than desired. Improvements to decrease film roughness, minimize electrode losses and improved fabrication process will result in the performance expected of single crystal films
On the fusion of prosody, voice spectrum and face features for multimodal person verification (2006)

Multimodal person recognition systems normally use shortterm spectral features as voice information.In this paper prosodic information is added to a system based on face and voice spectrum features.By using two fusion techniques, support vector machines and matcher weighting, different fusion strategies based on the fusion of monomodal scores in several steps are proposed.The performance of the system is clearly improved when the prosodic information is added and the best results are achieved when prosodic scores are previously fused and the resulting scores are fused again with spectral and facial scores.Speech and face scores have been obtained upon Switchboard-I and XM2VTS databases respectively.