gebhart/patrepeval huggingface dataset:
Comparative toxicoproteogenomics of mouse and rat liver identifies TCDD-resistance genes (2019)

The aryl hydrocarbon receptor (AHR) mediates many toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, the AHR alone does not explain the widely different outcomes among organisms. To identify the other factors involved, we evaluated three transgenic mouse lines, each expressing a different rat AHR isoform (rWT, DEL, and INS) providing widely different resistance to TCDD toxicity, as well as C57BL/6 and DBA/2 mice which exhibit a ~ tenfold divergence in TCDD sensitivity (exposures of 5-1000 μg/kg TCDD). We supplement these with whole-genome sequencing, together with transcriptomic and proteomic analyses of the corresponding rat models, Long–Evans (L–E) and Han/Wistar (H/W) rats (having a ~ 1000-fold difference in their TCDD sensitivities; 100 μg/kg TCDD), to identify genes associated with TCDD-response phenotypes. Overall, we identified up to 50% of genes with altered mRNA abundance following TCDD exposure are associated with a single AHR isoform (33.8%, 11.7%, 5.2% and 0.3% of 3076 genes altered unique to rWT, DEL, C57BL/6 and INS respectively following 1000 μg/kg TCDD). Hepatic Pxdc1 was significantly repressed in all three TCDD-sensitive animal models (C57BL/6 and rWT mice, and L–E rat) after TCDD exposure. Three genes, including Cxxc5, Sugp1 and Hgfac, demonstrated different AHRE-1 (full) motif occurrences within their promoter regions between rat strains, as well as different patterns of mRNA abundance. Several hepatic proteins showed parallel up- or downward alterations with their RNAs, with three genes (SNRK, IGTP and IMPA2) showing consistent, strain-dependent changes. These data show the value of integrating genomic, transcriptomic and proteomic evidence across multi-species models in toxicologic studies.
On Uncertainty in Wavelet-Based Signal Analysis (2005)

The evaluation of uncertainty is a task usually neglected by people performing wavelet-based measurements. In this paper, the wavelet analysis aimed at gauging the synthesis of transient disturbances is considered, and a general expression of the uncertainty affecting this synthesis is provided. Simulations have been performed to validate the above expression, which holds no matter which mother wavelet is used and the kind of disturbance. Results of experiments on actual signals are also reported and discussed.
Predicting purchase behaviors from social media (2013)

In the era of social commerce, users often connect from e-commerce websites to social networking venues such as Facebook and Twitter. However, there have been few efforts on understanding the correlations between users' social media profiles and their e-commerce behaviors. This paper presents a system for predicting a user's purchase behaviors on e-commerce websites from the user's social media profile. We specifically aim at understanding if the user's profile information in a social network (for example Facebook) can be leveraged to predict what categories of products the user will buy from (for example eBay Electronics). The paper provides an extensive analysis on how users' Facebook profile information correlates to purchases on eBay, and analyzes the performance of different feature sets and learning algorithms on the task of purchase behavior prediction.
Noninvasive estimation of FDG input function for quantification of cerebral metabolic rate of glucose: optimization and multicenter evaluation. (2000)

Noninvasive estimation of CMRGlc is made possible by careful measurement of the net injected dose and BSA.
IC‐P‐017: BLINDED VISUAL EVALUATION AND QUANTITATIVE SUVR THRESHOLD CLASSIFICATION OF [18F]FLUTEMETAMOL PET IMAGES IN JAPANESE SUBJECTS (2014)

Amyloid imaging data are often quantified using a method where target region to cerebellar cortex tracer uptake ratios (SUVRcer) are computed. We investigated the agreement between blinded visual evaluations (BIE) and quantitative analysis of [18 F]f lutemetamol in a Japanese population. Healthy volunteers (HV; n=25, 15 elderly healthy volunteer ≥ 55 years (EHV), 10 young healthy volunteers <55 (YHV)) and patients with probable Alzheimer's Disease (pAD; n=20) and amnestic mild cognitive impairment (aMCI; n=20) each underwent a 30min dynamic PET scan, starting 90min post injection of 185MBq [18 F]flutemetamol. A 3D T 1 MRI was also obtained. Image data was processed to allow for application of a template set of regions of interest to a 30 min summation image to estimate a global cortical average SUVRcer. The optimal threshold was estimated as the midpoint between the mean of pAD and EHV cohorts in terms of standard deviation for the global SUVRcer. BIE were performed by 5 Japanese and 5 non-Japanese independent board-certified readers to obtain the majority outcomes of the ten readers. T he diagnostic capability of BIE and of global SUVRcer for differentiating AD from HV was evaluated, together with agreement between BIE and global SUVRcer. Optimal threshold for discriminating pAD from HV was 1.391 for the global cortical SUVRcer average. Sensitivity and specificity of discriminating pAD from HV in this cohort for BIE (majority outcome) were 90% and 100%, respectively, and for SUVR cer 90% and 100%. In the efficacy evaluation, the quantitative classification categorized 18 subjects as positive (18 pAD, 0 HV), all of these were classified as positive by BIE. 27 subjects were categorized as negative quantitatively (25 HV, 2 pAD) and also by BIE, resulting in a 100% agreement between BIE and quantification using this threshold. BIE categorized 10 of 20 aMCI subjects as positive, quantitative classification added three subjects to this category. Agreement between the visual and quantitative assessment of [18 F]flutemetamol images is high. While quantitative classification should not replace visual assessment, it may be useful as a tool for detecting early stages of amyloid accumulation.
Functional Protein Network Activation Mapping Reveals New Potential Molecular Drug Targets for Poor Prognosis Pediatric BCP-ALL (2010)

We conclude that functional protein pathway activation mapping revealed specific deranged signalling networks in BCP-ALL that could be potentially modulated to produce a better clinical outcome for patients resistant to standard-of-care therapies.
Low Body Weight in Females Is a Risk Factor for Increased Tenofovir Exposure and Drug-Related Adverse Events (2013)

Treatment with tenofovir sometimes leads to non-reversible kidney and/or bone diseases. Factors associated with these drug-related adverse events are poorly characterized. Our objective was to investigate such factors in patients treated long term with daily tenofovir. One-hundred Caucasian HIV-positive patients with basal creatinine clearance >80 mL/min treated with tenofovir for at least 6 months and with at least one assessment of tenofovir plasma trough concentrations were considered. Tenofovir-associated adverse events were defined as the appearance of pathological proteinuria, worsening of renal function or bone demineralization. By multivariate regression analysis, we found that serum creatinine (p = 0.003) and body weight (p = 0.002) were the factors independently associated with plasma tenofovir concentrations. In particular, women with body weight<50 kg had significantly higher plasma tenofovir concentrations than those weighting >50 Kg (160±93 vs.71±52 ng/mL, p<0.001). High tenofovir plasma trough concentrations and the age of the patients were independently associated with the development of drug-related kidney and bone toxicity. In this retrospective study we have shown that HIV-infected women with low body weight are at risk to be exposed to high tenofovir plasma trough concentrations, ultimately resulting in a significant hazard to develop long-term tenofovir complications.
Self-oscillating millimeter-wave generation using reciprocating optical modulator (2005)

A reciprocating optical modulator (ROM) effectively generates harmonic components of modulation signal. We propose a novel optoelectronic oscillator (OEO) consisting of the ROM. By single-mode self-oscillating operation of the OEO, millimeter-wave-band radio-on-fiber signal is generated.
1.8 mΩ·cm2vertical GaN-based trench metal–oxide–semiconductor field-effect transistors on a free-standing GaN substrate for 1.2-kV-class operation (2015)

In this paper, we report on 1.2-kV-class vertical GaN-based trench metal–oxide–semiconductor field-effect transistors (MOSFETs) on a free-standing GaN substrate with a low specific on-resistance. A redesigned epitaxial layer structure following our previous work with a regular hexagonal trench gate layout enables us to reduce the specific on-resistance to as low as 1.8 mΩ·cm2 while obtaining a sufficient blocking voltage for 1.2-kV-class operation. Normally-off operation with a threshold voltage of 3.5 V is also demonstrated. To the best of our knowledge, this is the first report on vertical GaN-based MOSFETs with a specific on-resistance of less than 2 mΩ·cm2.
Sensitive NMR method for detecting carbohydrate influx into competing chemocatalytic pathways (2020)

Reaction pathways are often tracked with stable isotopes in order to determine the provenance of products in the pathway and to deduce mechanistic information. NMR spectroscopy can provide direct insight into the specific labelling position of the stable isotope. We suggest a simple assay that allows rapid quantitative measurements of isotope distributions in biomass-derived products using commercially available carbohydrate substrates and routine instrumentation. In the assay, biomass-derived products in post reaction material are quantitatively reduced with NaBH<sub>4</sub> to install hydrogens at each carbon site in the product. In this manner, the detection of <sup>13</sup>C and <sup>12</sup>C sites becomes possible in multiplets of the sensitive 2D <sup>1</sup>H-<sup>1</sup>H TOCSY experiment. The approach detects the usage of competing upstream reactions from isotope patterns in chemically identical reaction products. Changing influx into Sn-Beta-catalysed carbohydrate conversion reactions in the absence and in the presence of K<sup>+</sup> was quantitatively assessed, showing how the presence of K<sup>+</sup> alters the intial reactions towards methyl lactate.
The microstructure and melt properties of CO–ethylene copolymers with remarkably low CO content (2014)

Unique structure–property relationships were revealed for non-alternating polyketones obtained with unprecedented efficiency by a new protocol for the palladium-catalysed copolymerisation of CO and ethylene.
Anomalously Large Threshold Voltage Fluctuation by Complex Random Telegraph Signal in Floating Gate Flash Memory (2006)

A threshold voltage fluctuation (DeltaV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) due to random telegraph signal (RTS) in a floating-gate (FG) flash memory was investigated. From statistical analysis of the DeltaV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> , we found an anomalously large DeltaV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> at high percentage region of the DeltaV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> distribution, which is caused by a complex RTS. Since the ratio of the complex RTS among the RTS is increased by charge injection to tunnel oxide, the dispersion of the DeltaV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> distribution increases after program/erase (P/E) cycle. Since the DeltaV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> due to the complex RTS is much larger than the simple RTS, the complex RTS become one of the reliability issues in larger capacity flash memory, especially after P/E cycle
A comparison of model-based and black-box methods for speed estimation in aircraft (2020)

The anti-skid control system in aircraft is confined to the landing-gear subsystem, and, for safety reasons, it must rely on local signals only. Therefore, it can use only two measurements: the wheel speed and the pilot braking pressure request. Therefore, the antiskid control logics are generally wheel deceleration-based, as the slip cannot be computed since the aircraft speed is not available. The vehicle speed estimation is commonly done in automotive systems, made possible also by the presence of additional sensors usually coming from an Inertial Measurement Unit (IMU). This work explores how the aircraft speed can be estimated using only the landing gear signals, and if the resulting estimate can be accurate enough to be used in closed-loop with a slip-based anti-skid controller. To do so, two estimation approaches are considered: a sliding-mode model-based one, and a black-box approach grounded on recurrent neural networks. Experimental results are shown, witnessing the potential of black-box approaches.
Evaluation of a high-resolution real-time capable 3D sonar camera for deep sea operation (2016)

In this work we present the evaluation results of our 3D sonar camera system. The system consists of a matrix antenna array with 1024 single transducer elements and our in house developed DiPhAS sonar beamformer - a 128 channel FPGA-based beamforming system with a 1:8 multiplexing device for each channel. The system is designed to be applicable to ROV and AUV systems for real-time volumetric imaging in a deep sea environment. Defocused excitation of the transducer array is used to achieve a sound field opening angle of up to 40° in lateral and elevational direction. The antenna's sound field can be adjusted electronically in order to increase either the imaged area or the image contrast in a specific area of interest. Different filter algorithms working on a raw data basis have been implemented in order to suppress image artifacts which occur during the reconstruction process. Measurements on different phantoms have been performed in order to prove the real-time imaging as well as spatial resolution capabilities of the camera system.
Complex Associations between Environmental Factors and Child Growth: Novel Mixed-Methods Approach (2019)

Environmental risks associated with child growth are complex, and intervention effectiveness has been consistently poor. To improve effectiveness, proper intervention points inside the complex system must be identified. Integrating site-specific knowledge, machine learning, and statistical modeling offers a powerful approach to addressing this problem. In this study, a novel four-step method is employed to identify the key environmental factors to low child height-for-age in Guatemala. The four steps included (1) the development of a region-specific, ranked list of contributing factors to low child height-for-age via informal interviews and literature; (2) the application of a clustering method to a large regional data set; (3) the identification of the top six ranked variables shared between Step 1 and 2; and (4) the analysis of the clustered, regional data set in a multigroup path analysis incorporating the top six ranked variables, diarrheal prevalence, and child height-for-age. Results suggested that an increase in diarrheal prevalence was not consistently associated with a decrease in child height-for-age. Having soap for handwashing was significantly correlated with lower diarrhea and higher height-for-age. The effect was larger in the poorer population. Finally, disease in maize was significantly correlated with lower diarrhea. This method provided an approach to reducing, modeling, and ranking large numbers of environmental risk factors to child growth, identifying potential regional intervention points.
Image enhancement in two-photon laser scanning microscopy (2002)

Two-photon laser scanning microscopy (TPLSM) offers many advantages for exploring biological systems, allowing one to image living cells with less photo-bleaching and -toxicity than is possible with confocal laser scanning microscopy (CLSM). The authors investigated and compared the signal-to-noise ratio (SNR) and the resolution of TPLSM and CLSM on biological specimens. The S-D point spread functions (PSFs) of TPLSM at different excitation intensities demonstrate that resolution decreases with increased excitation intensity; for example, the lateral resolution is 12% worse and axial resolution is 30% worse at nearly 8-fold more intensity. The 3-D PSFs of CLSM, measured at different pinhole sizes, reveal that resolution improves at the smaller pinhole size, while it's optimal SNR lies at 35 /spl mu/m-pinhole. Image-deconvolution techniques improved the resolution of TPLSM from 400 nm to 240 nm in the lateral direction, and from 1080 nm to 540 nm in the axial direction. When combined with its ability to image at increased depth in living biological tissue, TPLSM offers a powerful tool for analyzing biological structures and mechanisms.
STUDY ON THE EARLY AGE VOLUME CHANGE OF BLAST-FURNACE SLAG CEMENT PASTE WITH HIGH TEMPERATURE HISTORY (2015)

高温履歴を有する高炉セメントペーストは、水和に伴う線膨張係数の経時変化によって温度ひずみが収縮側に推移し、温度ひび割れリスクが高まる可能性が指摘されている。本研究では自己乾燥に起因する線膨張係数の増大を抑制する手法として、複数の収縮低減剤を使用した実験的検討を行った。その結果、収縮低減剤の種類によっては線膨張係数の抑制に寄与しないものも見られたが、最高到達温度60℃の温度履歴を受ける場合には、収縮低減剤の種類によらず温度ひずみ、自己収縮ひずみが低減され、温度ひび割れのリスク低減にはいずれの収縮低減剤も有効であることが確認された。
Experimental and calculated vibrational spectra and structure of Ziegler‐Natta catalyst precursor: 50/1 comilled MgCl2‐TiCl4 (2004)

Abstract The vibrational Infrared and Raman Spectra of a MgCl 2 ‐TiCl 4 Ziegler‐Natta catalyst precursor with a 50/1 MgCl 2 /TiCl 4 ratio have been recorded. The Raman spectrum of this catalyst precursor, in the range 50‐500 cm −1 , shows clear scattering lines which can be assigned to the complex MgCl 2 ‐TiCl 4 , well separated from those of the initial species. Analogous, but less clear signals can be found in the infrared spectrum. Vibrational symmetry analysis and quantum chemical calculations of suitable models of MgCl 2 ‐TiCl 4 complex have been made for the interpretation of the experimentally recorded spectra. The observed spectroscopic signals can be explained in terms of the existence of only one type of MgCl 2 ‐TiCl 4 complex where the TiCl 4 molecules are complexed on the MgCl 2 along the (110) lateral cuts in a local C 2v symmetry with the Ti atoms in an octahedral coordination.
HEVC inter-frame skip enhancement at low bit rates (2014)

A method is introduced for HEVC to significantly reduce encoding time with minimal PSNR impact in low bit rate environment. Mobile devices are the main focus and a main beneficiary of this method since reduced encoding times lessens battery consumption. The proposed method shows encoding time decrease from 15.1% to 58.8% with and PSNR decrease of 0.05 to 0.12.
Successful Cryopreservation of Mouse Oocytes by Using Low Concentrations of Trehalose and Dimethylsulfoxide1 (2008)

Sugars such as trehalose, sucrose, and glucose are effectively used by a variety of animals (e.g., brine shrimp, tardigrades, some frogs, and insects), as well as by bacteria, yeasts, and plant seeds to survive freezing and extreme drying. The objective of this study was to examine the potential application of sugars to mammalian oocyte cryopreservation. To this end, we used trehalose, a nonreducing disaccharide, and mouse metaphase II oocytes as models. Our experiments show that extracellular trehalose alone affords some protection at high subzero temperatures (e.g., -15 degrees C), which diminishes with further cooling of the oocytes to -30 degrees C and below. When present both intracellularly and extracellularly, trehalose dramatically improves the cryosurvival with increasing extracellular concentrations to 0.5 M, even after cooling to -196 degrees C. Furthermore, the combination of intracellular and extracellular trehalose with small amounts of a conventional penetrating cryoprotectant (i.e., 0.5 M dimethylsulfoxide) provide high survival, fertilization, and embryonic development rates statistically similar to untreated controls. When transferred to foster mothers, cryopreserved oocytes give rise to healthy offspring showing the proof of principle. Our experiments with differential scanning calorimetry indicate that when cooled using the same cryopreservation protocol, the mixture of 0.5 M trehalose and cryopreservation medium undergoes glass transition at high subzero temperatures, which further substantiates the use of sugars as intracellular and extracellular cryoprotectants. Taken together, our results are in agreement with the survival schemes in nature and demonstrate the successful use of sugars in cryopreservation of mammalian oocytes.
A Model for Calculating Saliency from Both Input Image and Memory. (2002)

The Doppler method by permitting assessment of transvalvular blood flow velocity has provided a direct means to interrogate aortic regurgitant flow. Pulsed Doppler permits detection of disturbed diastolic flow by sampling proximal to the aortic valve in the outflow tract and is highly sensitive for diagnosis of aortic regurgitation (AR). For semi-quantitative assessment of the severity, left ventricular (LV) mapping can be performed and a ratio of the area of retrograde diastolic to antegrade systolic flow in the descending aorta can be used. According to the continuity principle, it should be possible to estimate regurgitant fraction by examination of forward flows from two different sites, one representative of forward output and one of total left ventricular output, but this method has not yet been sufficiently validated. Continuous wave (CW) Doppler is nearly as sensitive for detection of aortic regurgitation as pulsed wave (PW) Doppler. Signal strength of regurgitant jet provides an indirect clue to its severity: generally a strong signal indicates moderate to severe degree, a weak signal is associated with mild degrees of regurgitation. The spectral outline of regurgitant jet velocity is determined by instantaneous pressure difference between aortic root and the left ventricle during diastole and an indirect clue to severity of aortic regurgitation is provided by the slope of the curve. A steeper slope or shorter velocity half-time is associated with more severe degrees of regurgitation and vice versa. However, there is considerable scatter in this correlation for any given grade of severity of aortic regurgitation, providing a limited predictive value.(ABSTRACT TRUNCATED AT 250 WORDS)
Ring and Double Bond Equivalent (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.