gebhart/patrepeval huggingface dataset:
SU‐FF‐J‐18: Adaptive IMRT Using Cone‐Beam CT: A Case Study On Patients with Bulky Head and Neck Tumors (2006)

Purpose: The objective of this work is to demonstrate the feasibility and efficacy of acquiring on‐board Cone‐Beam CT (CBCT) volume images for adaptive radiotherapy (ART) and image‐guided‐radiotherapy (IGRT) for patients with bulky head and neck tumors treated with IMRT. Method and Materials: The quality of the CBCT volume images acquired on the treatment table was evaluated by measuring the spatial accuracy, contrast, resolution, and the curve for converting CT number to electron density. A patient planning CT volume images were acquired before treatment and at mid‐course. CBCT volume images were acquired weekly during treatment. To cover the IMRT fields, two CBCT acquisitions were combined into one volume image using in‐house software. PTV and organ contours were copied from the pretreatment CT volume to the CBCT volume and adjusted as necessary. The IMRT plan was applied to the CBCT volume and dose‐volume histograms were calculated for the adjusted PTV and spinal cord. The CBCT images were used for patient treatment verifications and dose calculations for ART. Results: Significant changes in the skin contours and PTV contours were seen on patients with bulky HNC after as few as five treatments. The dosimetric consequences were also significant. Adapting the IMRT plan to the changes in patient anatomy by re‐optimizing on the CBCT volume was found to be feasible. For patients whose Head and Neck cancer was not bulky, there were no significant changes in setup or anatomy. Conclusion: It is feasible to acquire weekly CBCT images on the treatment table for analyzing significant changes in anatomy and determine dosimetric consequences of those changes. The CBCT can be used to obtain the accumulative target dose and to modify treatment plans without performing additional planning CT. The CBCT is shown to be a very effective tool for ART for IMRT treatment.
Fully automated detection of diabetic macular edema and dry age-related macular degeneration from optical coherence tomography images (2014)

We present a novel fully automated algorithm for the detection of retinal diseases via optical coherence tomography (OCT) imaging. Our algorithm utilizes multiscale histograms of oriented gradient descriptors as feature vectors of a support vector machine based classifier. The spectral domain OCT data sets used for cross-validation consisted of volumetric scans acquired from 45 subjects: 15 normal subjects, 15 patients with dry age-related macular degeneration (AMD), and 15 patients with diabetic macular edema (DME). Our classifier correctly identified 100% of cases with AMD, 100% cases with DME, and 86.67% cases of normal subjects. This algorithm is a potentially impactful tool for the remote diagnosis of ophthalmic diseases.
Kinetics of Sorbitol Decomposition under Hydrothermal Condition (2016)

Sorbitol is widely used in food industries, and its decomposition behavior under hydrothermal condition is needed for its recovery from biomass and processing. In order to elucidate the decomposition behavior of sorbitol under hydrothermal conditions, hydrothermal decomposition of sorbitol was investigated in a flow reactor between 170 °C and 250 °C at 25 MPa. The decomposition was well expressed using a first-order reaction rate, and the rate constant followed the Arrhenius law. The pre-exponential factor and the activation energy were also determined. Compared with the decomposition of the sorbitol isomer mannitol, sorbitol was decomposed more rapidly, likely due to the variation in water molecule accessibility owing to different isomeric configurations. In addition, although activation energies were comparable for both mannitol and sorbitol (29.1 kJ mol−1 and 28.3 kJ mol−1, respectively), the pre-exponential factor of mannitol (6.19 s−1) was an order of magnitude lower than that of sorbitol (42.9 s−1).
X-ray holography for sequencing DNA (1990)

In this paper we discuss the potential for application of x-ray holographic imaging techniques to the sequencing of DNA. We formulate an approximate model for the scattering of partially coherent x-rays from an oriented DNA fiber and show the feasibility of reconstruction of heavy atom label positions from the x-ray scattering data. A series of simulations has been done to demonstrate the required reconstruction algorithms. An x-ray experiment is currently in progress to demonstrate the real feasibility of the technique. The potential of x-ray imaging techniques for the sequencing of DNA is attractive because of their inherently parallel nature. Hundreds or thousands of base pairs could be sequenced in a single set of x-ray images. The fundamental idea is to attach heavy atom labels to a selected base type on the DNA fragment to be sequenced. A large number (> 1012) of identical fragments can be constructed as an oriented fiber and illuminated with partially coherent x-rays. The heavy label positions can then be determined from the recorded pattern of scattered x-rays. If this operation is repeated for each of the four bases, the sequence can be reconstructed. The phase determination problem is solved by attaching to each DNA fragment a reference label in a known position. The scattered field then forms a Fourier transform hologram of the averaged DNA fragment. Because of the high photoelectric absorption of DNA relative to its coherent scattering cross-section, a single molecule would be damaged before an image could be formed. We solve this problem by distributing the damage over a large number of identical copies of the DNA fragment. In this paper we model a relatively simple experiment whose objective is to form a Fourier transform hologram of a labelled DNA fiber using 1 .54 A x-rays. We will first describe the hologram formation process and then the method for reconstructing the label positions.
Vibrationally Coherent Photochemistry in the Femtosecond Primary Event of Vision (1994)

Femtosecond pump-probe experiments reveal the impulsive production of photoproduct in the primary event in vision. The retinal chromophore of rhodopsin was excited with a 35-femtosecond pulse at 500 nanometers, and transient changes in absorption were measured with 10-femtosecond probe pulses. At probe wavelengths within the photo-product absorption band, oscillatory features with a period of 550 femtoseconds (60 wavenumbers) were observed whose phase and amplitude demonstrate that they are the result of nonstationary vibrational motion in the ground state of the photoproduct. The observation of coherent vibrational motion of the photoproduct supports the idea that the primary step in vision is a vibrationally coherent process and that the high quantum yield of the cis-->trans isomerization in rhodopsin is a consequence of the extreme speed of the excited-state torsional motion.
Environmental RNAi in herbivorous insects (2015)

Environmental RNAi (eRNAi) is a sequence-specific regulation of endogenous gene expression in a receptive organism by exogenous double-stranded RNA (dsRNA). Although demonstrated under artificial dietary conditions and via transgenic plant presentations in several herbivorous insects, the magnitude and consequence of exogenous dsRNA uptake and the role of eRNAi remains unknown under natural insect living conditions. Our analysis of coleopteran insects sensitive to eRNAi fed on wild-type plants revealed uptake of plant endogenous long dsRNAs, but not small RNAs. Subsequently, the dsRNAs were processed into 21 nt siRNAs by insects and accumulated in high quantities in insect cells. No accumulation of host plant-derived siRNAs was observed in lepidopteran larvae that are recalcitrant to eRNAi. Stability of ingested dsRNA in coleopteran larval gut followed by uptake and transport from the gut to distal tissues appeared to be enabling factors for eRNAi. Although a relatively large number of distinct coleopteran insect-processed plant-derived siRNAs had sequence complementarity to insect transcripts, the vast majority of the siRNAs were present in relatively low abundance, and RNA-seq analysis did not detect a significant effect of plant-derived siRNAs on insect transcriptome. In summary, we observed a broad genome-wide uptake of plant endogenous dsRNA and subsequent processing of ingested dsRNA into 21 nt siRNAs in eRNAi-sensitive insects under natural feeding conditions. In addition to dsRNA stability in gut lumen and uptake, dosage of siRNAs targeting a given insect transcript is likely an important factor in order to achieve measurable eRNAi-based regulation in eRNAi-competent insects that lack an apparent silencing amplification mechanism.
Interpreting Interactions between Ozone and Residual Petroleum Hydrocarbons in Soil (2016)

We evaluated how gas-phase O<sub>3</sub> interacts with residual petroleum hydrocarbons in soil. Total petroleum hydrocarbons (TPH) were 18 ± 0.6 g/kg soil, and TPH carbon constituted ∼40% of the dichloromethane-extractable carbon (DeOC) in the soil. At the benchmark dose of 3.4 kg O<sub>3</sub>/kg initial TPH, TPH carbon was reduced by nearly 6 gC/kg soil (40%), which was accompanied by an increase of about 4 gC/kg soil in dissolved organic carbon (DOC) and a 4-fold increase in 5-day biochemical oxygen demand (BOD<sub>5</sub>). Disrupting gas channeling in the soil improved mass transport of O<sub>3</sub> to TPH bound to soil and increased TPH removal. Ozonation resulted in two measurable alterations of the composition of the organic carbon. First, part of DeOC was converted to DOC (∼4.1 gC/kg soil), 75% of which was not extractable by dichloromethane. Second, the DeOC containing saturates, aromatics, resins, and asphaltenes (SARA), was partially oxidized, resulting in a decline in saturates and aromatics, but increases in resins and asphaltenes. Ozone attack on resins, asphaltenes, and soil organic matter led to the production of NO<sub>3</sub><sup>-</sup>, SO<sub>4</sub><sup>2-</sup>, and PO<sub>4</sub><sup>3-</sup>. The results illuminate the mechanisms by which ozone gas interacted with the weathered petroleum residuals in soil to generate soluble and biodegradable products.
Effect of size and curvature on the enzyme activity of bionanoconjugates (2017)

Biotic-abiotic hybrids comprised of globular proteins and functional nanostructures with complementary and synergistic properties are central to a number of bionanotechnological applications. A comprehensive understanding of the effect of physicochemical properties of abiotic nanostructures on the biological activity of the bionanoconjugates is critical in the design of these bio-nano hybrids. In this study, using size and curvature-controlled gold nanoparticles as a model abiotic system, we investigated the effect of hydrodynamic diameter and surface curvature on the activity of a model enzyme, horseradish peroxidase (HRP), adsorbed on the surface of the nanostructures. In contrast with the previous studies, we have employed a novel class of gold superstructures (gold nanoparticles on spheres) to deconvolute the effects of size and curvature on the catalytic activity of the bionanoconjugates. This study improves our understanding of the bio/nano interface and the design of bioinorganic hybrids with potential applications in biomimetic and bioenabled sensors, energy harvesting, optoelectronic components and devices, responsive and autonomous materials.
Modulation of cGAS-STING Pathway by Nicotinamide Riboside in Alzheimer's Disease (2021)

Numerous studies demonstrate a global decrease in nicotinamide adenine dinucleotide (NAD+) with aging. This decline is associated with the development of several of the hallmarks of aging such as reduced mitophagy and neuroinflammation, processes thought to play a significant role in the progression of Alzheimer's disease (AD). Augmentation of NAD+ by oral administration of a precursor, nicotinamide riboside (NR), reduces senescence of affected cells, attenuates DNA damage and neuroinflammation in the transgenic APP/PS1 murine model of AD. Inflammation mediated by microglial cells plays an important role in progression of AD and other neurodegenerative diseases. The cytoplasmic DNA sensor, cyclic GMP-AMP synthase (cGAS) and downstream stimulator of interferon genes (STING), generates an interferon signature characteristic of senescence and inflammaging in the brain of AD mice. Elevated cGAS-STING observed in the AD mouse brains and human AD fibroblasts was normalized by NR. This intervention also increased mitophagy with improved cognition and behavior in the APP/PS1 mice. These studies suggest that modulation of the cGAS-STING pathway may benefit AD patients and possibly other disorders characterized by compromised mitophagy and excessive neuroinflammation.
Towards unconditional tor-like anonymity (2015)

We design and evaluate a traffic anonymization protocol for wireless networks, aiming to protect against computationally powerful adversaries. Our protocol builds on recent key-generation techniques, that leverage intrinsic properties of the wireless together with standard coding techniques. We show how to exploit the security properties of such keys to design a Tor-like anonymity network, without making any assumptions about the computational capabilities of an adversary. Our analysis and evaluation on simulated ad-hoc wireless networks, shows that our protocol achieves a level of anonymity comparable to the level of the Tor network.
Novel polymer crosslinking chemistries for cable insulation (2014)

Peroxide crosslinked polyethylene is the major insulation material used in today's electric cables carrying voltages above 5 kV. Peroxide-mediated crosslinking presents cable manufacturing challenges in that there is a propensity for premature crosslinking (scorch) in the extruder. Additionally, peroxide-mediated crosslinking generates byproducts that need to be removed from the cable before final cable construction. Novel organic peroxides and crosslinking coagent technologies have been designed to address these challenges. A novel peroxide, isopropenyl dicumyl peroxide, was found to greatly improve the resistance to scorch. In addition, the novel peroxide reduced the need for degassing, since a significant amount of the crosslinking byproducts became grafted to the polyethylene during crosslinking. A novel coagent, 2-methoxy-4-allylphenyl allyl ether, provided significantly higher scorch retardance at a given level of crosslinking when compared to compositions without coagent. Polyethylene insulation compounds crosslinked using these new additives demonstrated excellent dissipation factor and dielectric constant values, indicating promise for demanding high voltage insulation applications.
Hydrocarbons identified in extracts from estuarine water accommodated no. 2 fuel oil by gas chromatography-mass spectrometry (1974)

Results are presented on a computerized gas chromatograph-mass spectrometer analysis of methylene chloride and n-heptane extracts of a No. 2 fuel oil accommodated estuarine water sample. The analytical method is briefly described, and the limitations on the identifications are categorized. Some attempt was made to determine major and trace constituents in the water accommodate. Altogether 66 hydrocarbon compounds were identified specifically, and 75 compounds were partially identified. Seven compounds could be recognized as major constituents of the water accommodated oil and ten were present only as traces. The aromatic compounds found were alkyl benzenes, naphthalene, tetralin, indane, biphenyl, fluorene, anthracene, and some of their alkyl substituted isomers in the range of carbon numbers C7 to C15. Four n-alkanes, C10 to C13, were found along with four other assorted hydrocarbons.
Utility of Resistance and Capacitance Response in Sensors Based on Monolayer-Capped Metal Nanoparticles (2011)

We investigate the utility of resistance and capacitance responses, as derived by impedance spectroscopy, in well-controlled and real-world applications of monolayer-capped metal nanoparticle (MCNP) sensors. Exposure of the MCNP films to well-controlled analytes showed stable sensing responses and low baseline drift of the pertinent capacitance signals, when compared with equivalent resistance signals. In contrast, exposure of the MCNP films to breath of chronic kidney disease patients under dialysis, as a representative example to real-world multicomponent mixtures, showed low baseline drift but relatively scattered signals when compared with the equivalent resistance response. We ascribe these discrepancies to the level and fluctuating concentration of water molecules in the real-world samples.
Electrophysiologic effects and outcomes of sympatholysis in patients with recurrent ventricular arrhythmia and structural heart disease (2019)

SGB increased cSNRT without changing heart rate. CSD was more beneficial for patients with mild-to-moderate heart failure and faster VA.
Segmental Dynamics and Ionic Conduction in Poly(vinyl methyl ether)-Lithium Perchlorate Complexes (2004)

Broadband dielectric spectroscopy was used to investigate the segmental dynamics and ionic conduction in LiClO4/PVME complexes with Li/O from 0.1/100 to 10/100, at temperatures from Tg to ∼Tg + 80 °C. Although no microphase separation is observed via DSC, dielectric experiments reveal two segmental relaxations and one localized ion motion process. The fastest process is attributed to relaxations of segments in ion-depleted domains and it slows down with increasing salt content, as does the ion motion. The segmental relaxation of PVME chains in ion-rich domains is even slower than the ion motion process, and about 104 times slower than the fast segmental process in the 0.5/100 complex. This process becomes faster with increasing LiClO4 content, despite the concurrent increase in the bulk Tg. Maximum molar conductivity is obtained in the 2/100 complex and the ionic conduction is about 10-9 S/cm at 30 °C. By using the dynamic bond percolation model, it was found that the ions move about 0.8 nm for the 0.5/10...
Genetic, developmental, and physical factors associated with attention deficit hyperactivity disorder in patients with velocardiofacial syndrome (2003)

Abstract Velocardiofacial syndrome (VCFS) is a relatively common developmental neuropsychiatric syndrome caused by a 22q11 microdeletion. There is an extensive variability in the phenotypic expression of this disease. The most common psychiatric disorder in VCFS is attention‐deficit/hyperactivity disorder (ADHD), affecting 35–55% of patients. This study investigated the association of familial, developmental, and physical factors with the occurrence of ADHD in 51 patients with nonfamilial VCFS. Twenty‐one patients (41.2%) were diagnosed with ADHD. There was a significantly greater prevalence of ADHD in the first‐degree relatives of the patients with ADHD than in those without (OR = 5.9, 95% CI = 1.6–22.1, P = 0.006). No differences were noted between the ADHD and non‐ADHD groups in mean Obstetric Complication Scale Score, gestational age, birth weight, age at first words, walking, and achieving bowel control. The two groups also had similar IQ scores (total, verbal, and performance) and had a similar average degree of severity of facial dysmorphism and cardiac and cleft anomalies. These findings indicate that ADHD in VCFS has a genetic contribution and the patients' VCFS‐related developmental factors and physical illnesses play a lesser role. © 2003 Wiley‐Liss, Inc.
ELLIPSOMETRIC STUDY OF OXYGEN ON A Ag(110) SURFACE AROUND THE PLASMA FREQUENCY OF SILVER (1983)

The analysis of spectroscopic ellipsometric data for oxygen adsorption on silver by standard methods leads to implausible results, if the frequency range around the plasma frequency of silver (_ωp = 3.8 eV) is investigated. Usually the analysis yields two possible solutions for ε(ω) = εr(ω)+iεi(ω) of the adsorbate layer. Around ωp one derives for the adsorbate layer either a negative real part εr above ωp, which would mean that the oxygen layer is more metallic than silver, or an imaginary part εi, which is going negative around ωp. A model with a "soft" silver surface, which has proved useful also in other optical problems /1/, overcomes these difficulties. The gradual decay of the electron density at a free metal surface is approximately taken into account by a surface layer on the free metal. The parameters of this layer are fixed by other experiments. The layer is then replaced by the adsorbate layer. Such a model leads to an adsorbate dielectric function with positive real and imaginary part /2/. In order to evaluate the optical properties of the metal layer system around the plasma frequency, it is essential to include the plasma waves, i.e. spatial dispersion, in the treatment of metal optics.
CytochromeP-450 epoxygenases protect endothelial cells from apoptosis induced by tumor necrosis factor-α via MAPK and PI3K/Akt signaling pathways (2007)

Endothelial cells play a vital role in the maintenance of cardiovascular homeostasis. Epoxyeicosatrienoic acids (EETs), cytochrome P-450 (CYP) epoxygenase metabolites of arachidonic acid in endothelial cells, possess potent and diverse biological effects within the vasculature. We evaluated the effects of overexpression of CYP epoxygenases on tumor necrosis factor-alpha (TNF-alpha)-induced apoptosis in bovine aortic endothelial cells. CYP epoxygenase overexpression significantly increased endothelial cell viability and inhibited TNF-alpha induction of endothelial cell apoptosis as evaluated by morphological analysis of nuclear condensation, DNA laddering, and fluorescent-activated cell sorting (FACS) analysis. CYP epoxygenase overexpression also significantly inhibited caspase-3 activity and downregulation of Bcl-2 expression induced by TNF-alpha. The antiapoptotic effects of CYP epoxygenase overexpression were significantly attenuated by inhibition of the phosphatidylinositol 3-kinase (PI3K)/Akt and MAPK signaling pathways; however, inhibition of endothelial nitric oxide synthase activity had no effect. Furthermore, CYP epoxygenase overexpression significantly attenuated the extent of TNF-alpha-induced ERK1/2 dephosphorylation in a time-dependent manner and significantly increased PI3K expression and Akt phosphorylation in both the presence and absence of TNF-alpha. Collectively, these results suggest that CYP epoxygenase overexpression, which is known to increase EET biosynthesis, significantly protects endothelial cells from apoptosis induced by TNF-alpha. This effect is mediated, at least in part, through inhibition of ERK dephosphorylation and activation of PI3K/Akt signaling.
Identification of CDCP1 as a hypoxia-inducible factor 2α (HIF-2α) target gene that is associated with survival in clear cell renal cell carcinoma patients (2013)

CUB domain-containing protein 1 (CDCP1) is a transmembrane protein that is highly expressed in stem cells and frequently overexpressed and tyrosine-phosphorylated in cancer. CDCP1 promotes cancer cell metastasis. However, the mechanisms that regulate CDCP1 are not well-defined. Here we show that hypoxia induces CDCP1 expression and tyrosine phosphorylation in hypoxia-inducible factor (HIF)-2α-, but not HIF-1α-, dependent fashion. shRNA knockdown of CDCP1 impairs cancer cell migration under hypoxic conditions, whereas overexpression of HIF-2α promotes the growth of tumor xenografts in association with enhanced CDCP1 expression and tyrosine phosphorylation. Immunohistochemistry analysis of tissue microarray samples from tumors of patients with clear cell renal cell carcinoma shows that increased CDCP1 expression correlates with decreased overall survival. Together, these data support a critical role for CDCP1 as a unique HIF-2α target gene involved in the regulation of cancer metastasis, and suggest that CDCP1 is a biomarker and potential therapeutic target for metastatic cancers.