gebhart/patrepeval huggingface dataset:
Telomere length and genetic variant associations with interstitial lung disease progression and survival (2019)

Leukocyte telomere length (LTL), <i>MUC5B</i> rs35705950 and <i>TOLLIP</i> rs5743890 have been associated with idiopathic pulmonary fibrosis (IPF).In this observational cohort study, we assessed the associations between these genomic markers and outcomes of survival and rate of disease progression in patients with interstitial pneumonia with autoimmune features (IPAF, n=250) and connective tissue disease-associated interstitial lung disease (CTD-ILD, n=248). IPF (n=499) was used as a comparator.The LTL of IPAF and CTD-ILD patients (mean age-adjusted log-transformed T/S of -0.05±0.29 and -0.04±0.25, respectively) is longer than that of IPF patients (-0.17±0.32). For IPAF patients, LTL <10th percentile is associated with faster lung function decline compared to LTL ≥10th percentile (-6.43% per year <i>versus</i> -0.86% per year; p<0.0001) and worse transplant-free survival (hazard ratio 2.97, 95% CI 1.70-5.20; p=0.00014). The <i>MUC5B</i> rs35705950 minor allele frequency (MAF) is greater for IPAF patients (23.2, 95% CI 18.8-28.2; p<0.0001) than controls and is associated with worse transplant-free IPAF survival (hazard ratio 1.92, 95% CI 1.18-3.13; p=0.0091). Rheumatoid arthritis (RA)-associated ILD (RA-ILD) has a shorter LTL than non-RA CTD-ILD (-0.14±0.27 <i>versus</i> -0.01±0.23; p=0.00055) and higher <i>MUC5B</i> MAF (34.6, 95% CI 24.4-46.3 <i>versus</i> 14.1, 95% CI 9.8-20.0; p=0.00025). Neither LTL nor <i>MUC5B</i> are associated with transplant-free CTD-ILD survival.LTL and <i>MUC5B</i> MAF have different associations with lung function progression and survival for IPAF and CTD-ILD.
Momentum and Thermal Boundary Layer Development on an Internally Cooled Turbine Vane (2010)

Recent advances in computing power have made conjugate heat transfer simulations of turbine components increasingly popular; however, limited experimental data exists with which to evaluate these simulations. The primary parameter used to evaluate simulations is often the external surface temperature distribution, or overall effectiveness. In this paper, the overlying momentum and thermal boundary layers at various streamwise positions around a conducting, internally cooled simulated turbine vane were measured under low (Tu = 0.5%) and high (Tu = 20%) freestream turbulence conditions. Furthermore, experimental results were compared to computational predictions. In regions were a favorable pressure gradient existed, the thermal boundary layer was found to be significantly thicker than the accompanying momentum boundary layer. Elevated freestream turbulence had the effect of thickening the thermal boundary layer much more effectively than the momentum boundary layer over the entire vane. This data is valuable in understanding the conjugate heat transfer effects on the vane as well as serving as a tool for computational code evaluation.
Iron Oxide Nanoparticle–labeled Rat Smooth Muscle Cells: Cardiac MR Imaging for Cell Graft Monitoring and Quantitation (2005)

Magnetic labeling of smooth muscle cells with anionic maghemite nanoparticles allows detection of cells with MR imaging after local transplantation in the heart.
Unusual Lesions of the Patella (1966)

A search of the files of the Mayo Clinic for tumors and tumor-like lesions of the patella yielded only seven cases. Except for one malignant lymphoma, which was part of a disseminated process, all the lesions were benign. They included one each of the following: benign osteoblastoma, ancurysmal bone cyst, hemangioma, chondroma, lesion of hyperparathyroidism, and an unclassified benign giant-cell variant. These benign conditions may be easily overlooked as a cause of pain in the knee but respond well to relatively simple surgical therapy.
A new inorganic EUV resist with high-etch resistance (2012)

Performance requirements for EUV resists will necessitate the development of entirely new resist platforms. As outlined in the ITRS, the new resists for EUVL must show high etch resistance (to enable pattern transfer using thinner films), improved LER and high sensitivity. A challenge in designing these new resists is the selection of molecular structures that will demonstrate superior characteristics in imaging and etch performance while maintaining minimal absorbance at EUV wavelengths. We have previously described the use of inorganic photoresists in 193 nm and e-beam lithography. These inorganic photoresists are made of HfO2 nanoparticles and have shown etch resistance that is 25 times higher than polymer resists. The high etch resistance of these materials allow the processing of very thin films (&lt; 40 nm) and will push the resolution limits below 20 nm without pattern collapse. Additionally, the small size of the nanoparticles (&lt; 5 nm) leads to low LER while the absorbance at EUV wavelengths is low. In this presentation we show that these inorganic resists can be applied to EUV lithography. We have successfully achieved high resolution patterning (&lt;30 nm) with very high sensitivity and low LER.
Nuclear receptors and metabolism: from feast to famine (2014)

The ability to adapt to cycles of feast and famine is critical for survival. Communication between multiple metabolic organs must be integrated to properly metabolise nutrients. By controlling networks of genes in major metabolic organs, nuclear hormone receptors (NHRs) play central roles in regulating metabolism in a tissue-specific manner. NHRs also establish daily rhythmicity by controlling the expression of core clock genes both centrally and peripherally. Recent findings show that many of the metabolic effects of NHRs are mediated through certain members of the fibroblast growth factor (FGF) family. This review focuses on the roles of NHRs in critical metabolic organs, including adipose tissue, liver and muscle, during the fed and fasted states, as well as their roles in circadian metabolism and downstream regulation of FGFs.
Ultrafast laser-scanning fluorescence microscopy with a compact inline implementation (Conference Presentation) (2019)

Frequency-division-multiplexed laser-scanning fluorescence microscopy is a powerful imaging method for biological tissues that enables an imaging speed of >10,000 frames/s. Despite its unprecedented high speed, its large-scale implementation that includes a bulky and unstable Mach-Zehnder interferometer has hampered its practical applications, especially in biomedical studies. Here we present a compact implementation of frequency-division-multiplexed microscopy to overcome this issue. The compactness is enabled by introducing an inline interferometer for generating an excitation beam array. In this setup, the laser beam is separated and recombined with small beam separation angles (<2°) by optical components such as acousto-optic deflectors or Wollaston prisms, thus implementing an interferometer with a relay lens system and drastically downsizing the setup. Compared with our previous setup with a Mach-Zehnder interferometer, the footprint of the optical setup for the excitation beam generation was downsized from ~20 cm x 70 cm to ~130 cm x 2.54 cm (defined by one-inch optical components used in the setup). Furthermore, our design concept allows for an ultra-compact implementation (~10 cm x 1 cm) by using custom optical components and omitting the relay lens systems. As a proof-of-concept demonstration, we obtained two-color (fluorescence and brightfield) images of Euglena gracilis cells (autofluorescent) and MCF-7 cells (fluorescence from nuclei stained by SYTO16) at a scanning speed of 0.84 m/s, which corresponds to a frame rate of 15,300 frames/s at a 55-μm field of view in the scanning direction. By virtue of the wide modulation bandwidth of the excitation beam (200 MHz), it is also possible to measure fluorescence lifetimes of target fluorophores, leading to potential applications for fluorescence lifetime imaging (FLIM).
Broadband Source Localization From an Eigenanalysis Perspective (2009)

Broadband source localization has several applications ranging from automatic video camera steering to target signal tracking and enhancement through beamforming. Consequently, there has been a considerable amount of effort to develop reliable methods for accurate localization over the last few decades. Essentially, the localization process consists in finding the candidate source location that maximizes the synchrony between the properly time-shifted microphone outputs. In addition to using well known cross-correlation-based criteria such as the steered response power (SRP), minimum variance (MV), and multichannel cross-correlation (MCCC), this synchrony can also be measured using the averaged magnitude difference function (AMDF) and the averaged magnitude sum function (AMSF) whose calculations involve low computational cost. In earlier related works, the latter techniques have been used for time delay estimation (TDE) of a target source observed by only one pair of microphones. Their generalization to the multiple microphone case and application to source localization have not been studied yet. In this paper, we consider both categories, i.e., cross-correlation and AMDF (with AMSF)-based approaches, using an arbitrary number of microphones, and analyze their performance. Specifically, we first provide a unifying study of the most popular cross-correlation-based techniques, such as the SRP, MV, and MCCC. In this paper, we use the eigenanalysis of the parameterized spatial correlation matrix (PSCM) to classify these methods and gain some insight into their performance. We demonstrate, for instance, that the MV and SRP consist in searching the major eigenvalue of the PSCM, while the MCCC, essentially, combines its minor eigenvalues when scanning for the source location. Inspired by this analysis, we show, in the second part of this work, the efficiency of the AMDF and AMSF in localizing an acoustic source using multiple microphones. Indeed, we propose two new parameterized matrices named as the parameterized averaged magnitude difference matrix (PAMDM) and the parameterized averaged magnitude sum matrix (PAMSM). The eigenanalysis of these matrices also reveals new criteria for acoustic source localization. Simulation results are provided to illustrate the effectiveness of all the investigated and proposed methods.
Rethinking surface reactions in nanoscale dry processes toward atomic precision and beyond: a physics and chemistry perspective (2019)

Abstract In this review, we discuss the progress of emerging dry processes with atomic precision. Researchers in the field of plasma processing and surface science have addressed the increasingly challenging demands of material selectivity by utilization of synergistic enhancement of etching or deposition. The discussion encompasses major challenges in the plasma science and technology community. The focus of the review is advances in atomic layer etching and area-selective deposition with activation or deactivation, especially in terms of materials scaling and variety. Control of high-aspect-ratio feature fabrication in semiconductor manufacturing and etched shapes of interior features at the nanoscale are needed. Issues related to profile distortion have received much attention. State-of-the-art techniques used in semiconductor manufacturing are reviewed and future challenges are outlined.
Comparison of the indicated work outputs, idle stabilities, and heat release characteristics of a direct-injection diesel engine operating cold at two compression ratios (2010)

A reduction in the compression ratio can adversely affect the cold-start and idling performance of diesel engines. The problems and potential solutions have been investigated. Studies have been carried out to compare the indicated performances and heat release characteristics of a direct-injection diesel engine during low-speed cold operation at compression ratios of 18.4:1 and 15.4:1. The test engine was a naturally aspirated single-cylinder design with a swept volume of 0.5l. Tests covered start temperatures between 10°C and 20°C. At around 300r/min, the indicated work output was higher at the lower compression ratio as a result of lower blow-by, and the cycle-by-cycle stabilities of the heat release and work output were similar at both compression ratios. The cycle-by-cycle stability deteriorated with increasing engine speed. At 1000r/min idling conditions, the stability was relatively poor and was worse for the low-compression-ratio case. At the high compression ratio, the cycle-by-cycle stability was improved by introducing multiple pilot injections and using metallic glow plugs operating at about 850°C. At the low compression ratio, improvements in stability could not be achieved without switching to glow plugs operating at about 1100°C.
Ex Vivo Gene Therapy to Produce Bone Using Different Cell Types (2000)

Gene therapy and tissue engineering promise to revolutionize orthopaedic surgery. This study comprehensively compares five different cell types in ex vivo gene therapy to produce bone. The cell types include a bone marrow stromal cell line, primary muscle derived cells, primary bone marrow stromal cells, primary articular chondrocytes, and primary fibroblasts. After transduction by an adenovirus encoding for bone morphogenetic protein-2, all of the cell types were capable of secreting bone morphogenetic protein-2. However, the bone marrow stromal cell line and muscle derived cells showed more responsiveness to recombinant human bone morphogenetic protein-2 than did the other cell types. In vivo injection of each of the cell populations transduced to secrete bone morphogenetic protein-2 resulted in bone formation. Radiographic and histologic analyses corroborated the in vitro data regarding bone morphogenetic protein-2 secretion and cellular osteocompetence. This study showed the feasibility of using primary bone marrow stromal cells, primary muscle derived cells, primary articular chondrocytes, primary fibroblasts, and an osteogenesis imperfecta stromal cell line in ex vivo gene therapy to produce bone. The study also showed the advantages and disadvantages inherent in using each cell type.
Control of organization and function of muscle and tendon by thrombospondin-4 (2014)

Thrombospondins (TSPs) are multifunctional proteins that are deposited in the extracellular matrix where they directly affect the function of vascular and other cell types. TSP-4, one of the 5 TSP family members, is expressed abundantly in tendon and muscle. We have examined the effect of TSP-4 deficiency on tendon collagen and skeletal muscle morphology and function. In Thbs4(-/-) mice, tendon collagen fibrils are significantly larger than in wild-type mice, and there is no compensatory over-expression of TSP-3 and TSP-5, the two TSPs most highly homologous to TSP-4, in the deficient mice. TSP-4 is expressed in skeletal muscle, and higher levels of TSP-4 protein are associated with the microvasculature of red skeletal muscle with high oxidative metabolism. Lack of TSP-4 in medial soleus, red skeletal muscle with predominant oxidative metabolism, is associated with decreased levels of several specific glycosaminoglycan modifications, decreased expression of a TGFβ receptor beta-glycan, decreased activity of lipoprotein lipase, which associates with vascular cell surfaces by binding to glycosaminoglycans, and decreased uptake of VLDL. The soleus muscle is smaller and hind- and fore-limb grip strength is reduced in Thbs4(-/-) mice compared to wild-type mice. These observations suggest that TSP-4 regulates the composition of the ECM at major sites of its deposition, tendon and muscle, and the absence of TSP-4 alters the organization, composition and physiological functions of these tissues.
Locomotor adaptations following repeated waist-pull perturbations (2015)

Falls are acknowledged as one of the most serious problems in the elderly. In order to develop effective interventions to reduce the fall risk, perturbation-based training programs are being adopted. The exposure to repeated unexpected perturbations can modify proactive strategies to control dynamical gait stability and decrease the risk of falling during unpreventable events encountered in everyday life. The aim of this study was to analyze to what extent healthy adult gait patterns would be affected by exposure to repeated unexpected force-controlled antero-posterior waist-pull perturbations. Results showed that repeated waist-pull perturbations produced short-term after effects able to modify stability in the direction of the applied perturbations. In particular, subjects increased their step length, the oscillation of the extrapolated center of mass along the antero-posterior and vertical direction, the antero-posterior Margin of Stability and the range of angular momentum in the sagittal plane. Future experiments will be conducted to verify if the present results can be confirmed with elderly subjects in order to finally improve their dynamical stability during unperturbed walking.
Involvement of glutamine synthetase 2 (GS2) amplification and overexpression in Amaranthus palmeri resistance to glufosinate (2022)

Amplification and overexpression of the target site glutamine synthetase, specifically the plastid-located isoform, confers resistance to glufosinate in Amaranthus palmeri. This mechanism is novel among glufosinate-resistant weeds. Amaranthus palmeri has recently evolved resistance to glufosinate herbicide. Several A. palmeri populations from Missouri and Mississippi, U.S.A. had survivors when sprayed with glufosinate-ammonium (GFA, 657 g ha<sup>-1</sup>). One population, MO#2 (fourfold resistant) and its progeny (sixfold resistant), were used to study the resistance mechanism, focusing on the herbicide target glutamine synthetase (GS). We identified four GS genes in A. palmeri; three were transcribed: one coding for the plastidic protein (GS2) and two coding for cytoplasmic isoforms (GS1.1 and GS1.2). These isoforms did not contain mutations associated with resistance. The 17 glufosinate survivors studied showed up to 21-fold increase in GS2 copies. GS2 was expressed up to 190-fold among glufosinate survivors. GS1.1 was overexpressed > twofold in only 3 of 17, and GS1.2 in 2 of 17 survivors. GS inhibition by GFA causes ammonia accumulation in susceptible plants. Ammonia level was analyzed in 12 F1 plants. GS2 expression was negatively correlated with ammonia level (r = - 0.712); therefore, plants with higher GS2 expression are less sensitive to GFA. The operating efficiency of photosystem II (ϕPSII) of Nicotiana benthamiana overexpressing GS2 was four times less inhibited by GFA compared to control plants. Therefore, increased copy and overexpression of GS2 confer resistance to GFA in A. palmeri (or other plants). We present novel understanding of the role of GS2 in resistance evolution to glufosinate.
A real-time system of distributed video coding (2010)

This paper presents a real-time system of distributed video coding (DVC). DVC is a current video compression paradigm. The decoding process of DVC is normally complex, which causes difficulty in real-time implementation. To address this problem, we propose a new configuration of DVC with three methods: simple rate control without the feedback channel, simple transmitting of dynamic range and simple bidirectional motion estimation to reduce complexity. Then we implement the system with parallelization techniques. We also develop the encoder for a low power processor. Experimental results show that the encoder on i.MX31 400 MHz could operates at about CIF 13 fps, and the decoder on Core 2 Quad 2.83 GHz operates at more than CIF 30 fps.
Inhibition of TNF-α Promoter Activity and Synthesis by A11-99-1, a New Cyclopentenone from the Ascomycete Mollisia melaleuca (2005)

In a search for inhibitors of the inducible tumor necrosis factor-a (TNF-a) promoter activity and synthesis, a new chlorinated cyclopentenone was isolated from fermentations of the ascomycete Mollisia melaleuca. The structure was determined by a combination of spectroscopic techniques The compound blocked the inducible human TNF-alpha promoter activity and synthesis with IC50-values of 2.5-5 microg/ml (8.1-16.1 microM). Studies on the mode of action of the compound revealed that the inhibition of TNF-a promoter activity is caused by an inhibition of the phosphorylation of the IkappaB protein which prevents the activation of the transcription factor NF-xB. No cytotoxic, antibacterial and antifungal activities could be observed up to 100 microg/ml (323 microM) of the compound.
A Low-power Liquid-fuelled Burner Using a Novel Atomization Concept (2019)

The design of and experimental results for a low-power heating oil burner, operating between 1.25 and 5.1 kW with exhaust gas emissions within the normative regulations for domestic usage, are presented. In contrast to common domestic heating oil burners, the atomization and combustion sections are spatially separated to allow the implementation of a novel atomization concept for low-power liquid-fuelled burners proposed in a previous study. The main working principle for spray generation is the secondary atomization of a droplet chain impinging on a pin downstream. Through pulse-width modulation (PWM) of the droplet generator, modulation of the spray flowrate over a wide range with constant spray quality was achieved. Phase-Doppler anemometry measurements under non-reacting conditions were performed to obtain the droplet size distribution of the spray. Three model liquids were used to determine the influence of liquid properties on the droplet size distribution. The Sauter mean diameter (SMD) values obtained for all liquids and operation parameters studied are in the range of 10% of the primary droplet diameter, which is 30 µm for the setup in this study.
Characterization of the AWARE 10 two-gigapixel wide-field-of-view visible imager (2014)

System requirements for many military electro-optic and IR camera systems reflect the need for both wide-field-of-view situational awareness as well as high-resolution imaging for target identification. In this work we present a new imaging system architecture designed to perform both functions simultaneously and the AWARE 10 camera as an example at visible wavelengths. We first describe the basic system architecture and user interface followed by a laboratory characterization of the system optical performance. We then describe a field experiment in which the camera was used to identify several maritime targets at varying range. The experimental results indicate that users of the system are able to correctly identify ~10 m targets at between 4 and 6 km with 70% accuracy.
10 Gbit/s-120 km standard fiber transmission employing a novel optical phase-encoded intensity modulation for signal spectrum compression (2002)

Recent reports have clarified that a duobinary three-level transmission and an optical duobinary modulation exhibit high chromatic dispersion tolerance at high bit rate, because spectrum bandwidth is much narrower than that of binary intensity modulation (IM). Compared with binary-IM, however, duobinary modulation requires higher amplification linearity for electrical devices, especially high-power modulator drivers, because the multilevel signal is more sensitive to intersymbol interference. This paper proposes the use of an optical phase-encoded intensity modulation as an equivalent scheme for optical duobinary modulation. Employing a separate binary modulation of intensity and phase of the carrier light, signal spectrum compression and resulting large chromatic dispersion tolerance have been observed at 10 Gbit/s.
T-Regulatory Cell Based Immunotherapy Using Yeast Display Constructed Antibodies for the Treatment of Cancer in Humans (2004)

s for the 19th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer, San Francisco, California, November 4-7, 2004: Antibody Therapy