gebhart/patrepeval huggingface dataset:
Visualization of Volatile Substances in Different Organelles with an Atmospheric-Pressure Mass Microscope (2009)

We have developed a mass microscope (mass spectrometry imager with spatial resolution higher than the naked eye) equipped with an atmospheric pressure ion-source chamber for laser desorption/ionization (AP-LDI) and a quadrupole ion trap time-of-flight (QIT-TOF) analyzer. The optical microscope combined with the mass spectrometer permitted us to precisely determine the relevant tissue region prior to performing imaging mass spectrometry (IMS). An ultraviolet laser tightly focused with a triplet lens was used to achieve high spatial resolution. An atmospheric pressure ion-source chamber enables us to analyze fresh samples with minimal loss of intrinsic water or volatile compounds. Mass-microscopic AP-LDI imaging of freshly cut ginger rhizome sections revealed that 6-gingerol ([M + K](+)at m/z 333.15, positive mode; [M - H](-) at m/z 293.17, negative mode) and the monoterpene ([M + K](+) at m/z 191.09), which are the compounds related to pungency and flavor, respectively, were localized in oil drop-containing organelles. AP-LDI-tandem MS/MS analyses were applied to compare authentic signals from freshly cut ginger directly with the standard reagent. Thus, our atmosphere-imaging mass spectrometer enabled us to monitor a quality of plants at the organelle level.
Role of PAX8 in the regulation of MET and RON receptor tyrosine kinases in non-small cell lung cancer (2014)

PAX8 provides signals for growth and motility of NSCLC cells and is necessary for MET and RON expression. Further investigations are necessary to investigate the therapeutic potential of PA8 in NSCLC.
MODL-17. SEGMENTATION OF PRE AND POST-TREATMENT GLIOMA TISSUE TYPES INCLUDING RESECTION CAVITIES (2022)

Abstract PURPOSE Measuring gliomas is a time-intensive process with significant inter-rater variability in post-surgical residual tumor and resection cavities. This likely contributes to the delayed assessment of progression and in-field recurrences from radiation. Automated segmentation of pre and post-treatment gliomas could reduce inter-rater variability and increase workflow efficiency for routine longitudinal radiographic assessment and treatment planning. We evaluated whether a 3D neural network is comparable to expert assessment of pre and post-treatment diffuse gliomas tissue types and resection cavities. METHODS A retrospective cohort of 647 MRIs of patients with diffuse gliomas (average 55.1 years, 45% female, 396 pre-treatment and 251 post-treatment, median 237 days post-surgery) from The Cancer Imaging Archive were stratified by operation status and tumor grade and randomly split into training (536) and testing (111) samples. T1, T1-post-contrast, T2, and FLAIR images were registered, skull-stripped, and interpolated to 1x1x1. Four classes — edema/infiltrative/post-treatment changes (ED), enhancing tissue (ET), necrotic core (NCR), and resection cavities (RC) — were manually segmented by an expert neuroradiologist. Using these segmentations and the four input image modalities, a nnU-Net, a state-of-the-art 3D U-Net convolutional neural network, was trained to predict segmentations of the four classes. RESULTS Segmentation performance in the test set for the ED, ET, and RC classes was at the level of inter-rater reliability with median Dice scores ranging from 0.85 to 1 and relative volume errors ranging from -0.05 to 0.02. There was a near-perfect correlation between manually segmented and predicted total lesion volumes (r2 values ranging from 0.95 to 0.98 among classes). CONCLUSIONS Accurate, automated volumetric quantification of diffuse glioma tissue volumes may improve response assessment in clinical trials and reduce provider burden and errors in measurement.
On Remote And Virtual Experiments In Elearning In Statistical Mechanics And Thermodynamics (2020)

The research of S. Jeschke is aimed at developing new concepts of service-oriented architectures for eLearning and eScience in particular in the fields of mathematics, natural sciences and engineering. She focuses on development and networking of interactive mathematical objects and remote/virtual experiments, on mechanisms for the creation, modification and storage of data in cooperative virtual knowledge spaces, and on the design of intelligent data analysis and validation schemes.
Mechanisms of cancer invasion and metastasis. (1985)

The main problem in cancer treatment is the prevention or destruction of disseminated metastases. The primary tumor can usually be eliminated by current therapeutic techniques. However, half of the patients with a newly diagnosed tumor will already have metastases. Therefore, understanding the mechanisms involved in the process of tumor invasion and metastases is a major challenge in cancer research. The identification of biochemical factors augmented in invasive tumor cells may lead to improved methods to predict whether an individual’s tumor has already metastasized, and may provide strategies for localization of clinically occult micrometastases.
On machine learning methods to estimate cannabidiolic acid content of Cannabis sativa L. from near-infrared hyperspectral imaging (2023)

This paper investigates the use of near-infrared hyperspectral imaging to estimate the cannabidiolic acid (CBDA) concentration of Cannabis sativa L. plant components such as buds and leaves. A total of 9 regression techniques were assessed with Gaussian Process Regression producing the best result. The least angle regression technique was the best performer of the interpretable models trialled. These models relate the measured pixel reflectance to cannabinoid content as determined by liquid chromatography-mass spectrometry. The regression models were applied to the complete hyperspectral image of the plant to produce CBDA estimation and distribution maps. The ultimate goal of this work is to develop a non-destructive method for Cannabis sativa L. assessment to improve both crop yield and the quality of the plant.
Coincident Aerosol and H2O Retrievals versus HSI Imager Field Campaign ReportH2O Retrievals versus HSI Imager Field Campaign Report (2016)

Two spectrally calibrated tarpaulins (tarps) were co-located at a fixed Global Positioning System (GPS) position on the gravel antenna field at the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Climate Research Facility’s Southern Great Plains (SGP) site. Their placement was timed to coincide with the overflight of a new hyperspectral imaging satellite. The intention was to provide an analysis of the data obtained, including the measured and retrieved spectral albedos for the calibration tarps. Subsequently, a full suite of retrieved values of H2O column, and the aerosol overburden, were to be compared to those determined by alternate SGP ground truth assets. To the extent possible, the down-looking cloud images would be assessed against the all-sky images. Because cloud contamination above a certain level precludes the inversion processing of the satellite data, coupled with infrequent targeting opportunities, clear-sky conditions were imposed. The SGP site was chosen not only as a target of opportunity for satellite validation, but as perhaps the best coincident field measurement site, as established by DOE’s ARM Facility. The satellite team had every expectation of using the information obtained from the SGP to improve the inversion products for all subsequent satellite images, including the cloud and radiative models and parameterizations and, thereby, the performance assessment for subsequent and historic image collections. Coordinating with the SGP onsite team, four visits, all in 2009, to the Central Facility occurred: • June 6-8 (successful exploratory visit to plan tarp placements, etc.) • July 18-24 (canceled because of forecast for heavy clouds) • Sep 9-12 (ground tarps placed, onset of clouds) • Nov 7-9 (visit ultimately canceled because of weather predictions). As noted, in each instance, any significant overcast prediction precluded image collection from the satellite. Given the long task-scheduling procedures (which were in place for each time period), coupled with other priorities and the satellite lifetime, no alternate SGP images could be obtained.
Goal Achievement Model for Low Back Pain (2013)

From the Department of Orthopaedics, Geisel School of Medicine at Dartmouth, Hanover, NH. Address correspondence and reprint requests to Rowland G. Hazard, MD, Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, One Medical Center Dr, Lebanon, NH 03756; E-mail: [email protected] Acknowledgment date: February 4, 2013. Revision date: March 25, 2013. Acceptance date: April 29, 2013. The manuscript submitted does not contain information about medical device(s)/drug(s). No funds were received in support of this work. No relevant financial activities outside the submitted work.
Acceleration of Photoinduced Electron Transfer in Porphyrin-Linked C70 (1999)

Abstract Porphyrin-linked C70 and porphyrin-linked C60 dyads have been designed and synthesized to evaluate the intrinsic properties of C70 in electron transfer. The photoinduced charge separation in the former is accelerated by a factor of about two compared with that in the latter. The result shows that C70 can be added to potential building blocks in artificial photosynthesis.
Intersubband absorption and photoluminescence in Si-doped self-organized InAs/Ga(Al)As quantum dots (1998)

We report on far-infrared absorption in directly and modulation doped self-organized InAs quantum dots. Photoluminescence spectra demonstrate a blue shift in peak intensity for increasing doping in the quantum dots. Band to band transitions from InAs wetting layer, and InAs ground and excited states are observed from photovoltage spectroscopy. Far infrared absorption measurements using a Fourier transform infrared spectrometer show absorption in the range of 6–18 μm for InAs quantum dots using a waveguide (45°) geometry and under normal incidence.
A Guided Materials Screening Approach for Developing Quantitative Sol-gel Derived Protein Microarrays (2013)

Microarrays have found use in the development of high-throughput assays for new materials and discovery of small-molecule drug leads. Herein we describe a guided material screening approach to identify sol-gel based materials that are suitable for producing three-dimensional protein microarrays. The approach first identifies materials that can be printed as microarrays, narrows down the number of materials by identifying those that are compatible with a given enzyme assay, and then hones in on optimal materials based on retention of maximum enzyme activity. This approach is applied to develop microarrays suitable for two different enzyme assays, one using acetylcholinesterase and the other using a set of four key kinases involved in cancer. In each case, it was possible to produce microarrays that could be used for quantitative small-molecule screening assays and production of dose-dependent inhibitor response curves. Importantly, the ability to screen many materials produced information on the types of materials that best suited both microarray production and retention of enzyme activity. The materials data provide insight into basic material requirements necessary for tailoring optimal, high-density sol-gel derived microarrays.
Identification of intra‐ and intermolecular disulphide bonding in the plant mitochondrial proteome by diagonal gel electrophoresis (2007)

Redox active proteins in plant mitochondria were examined using 2-D oxidant/reductant diagonal-SDS-PAGE to separate and identify proteins with intermolecular or intramolecular disulphide bonds using diamide in the first dimension and DTT in the second dimension. Eighteen proteins spots were resolved either above or below the diagonal and these were in-gel digested and identified by MS/MS. This analysis revealed intermolecular disulphide bonds in alternative oxidase, O-acetylserine (thiol) lyase, citrate synthase and between subunits of the ATP synthase. Intramolecular disulphide bonds were observed in a range of mitochondrial dehydrogenases, elongation factor Tu, adenylate kinase and the phosphate translocator. Many of the soluble proteins found were known glutaredoxin/thioredoxin targets in other plants, but the membrane proteins were not found by these methods nor were the nature of the disulphides able to be investigated. The accessibility of thiols involved in disulphide bonds to modification by a lipid derived aldehyde gave an insight into the potential impact of Cys modification on redox-functions in mitochondria during lipid peroxidation. Comparison of the protein sequences of the identified proteins with homologs from other species has identified specific Cys residues that may be responsible for plant-specific redox modulations of mitochondrial proteins.
Custom Anatomical 3D Spacer for Temporomandibular Joint Resection and Reconstruction (2015)

Two cases are presented using a two-stage approach and a custom antibiotic spacer placement. Temporomandibular reconstruction can be very demanding and accomplished with a variety of methods in preparation of a total joint and ramus reconstruction with total joint prostheses (TMJ Concepts, Ventura, CA). Three-dimensional reconstructions from diagnostic computed tomography were used to establish a virtually planned resection which included the entire condyle-ramus complex. From these data, digital designs were used to manufacture molds to facilitate intraoperative fabrication of precise custom anatomic spacers from rapidly setting antibiotic-impregnated polymethyl methacrylate. Molds were manufactured using vat polymerization (stereolithography) with a photopolymer in the first case and powder bed fusion (electron beam melting) with Ti6AL4V for the second. Surgical methodology and the use of molds for intraoperative spacer fabrication for each case are discussed.
Data from &lt;i&gt;In vivo&lt;/i&gt; Optical Molecular Imaging of Vascular Endothelial Growth Factor for Monitoring Cancer Treatment (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Vascular endothelial growth factor (VEGF) expression is a critical component in tumor growth and metastasis. Capabilities to monitor VEGF expression &lt;i&gt;in vivo&lt;/i&gt; can potentially serve as a useful tool for diagnosis, prognosis, treatment planning, monitoring, and research. Here, we present the first report of &lt;i&gt;in vivo&lt;/i&gt; hyperspectral molecular imaging strategy capable of monitoring treatment-induced changes in VEGF expression.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; VEGF was targeted with an anti-VEGF antibody conjugated with a fluorescent dye and was imaged &lt;i&gt;in vivo&lt;/i&gt; using a hyperspectral imaging system. The strategy was validated by quantitatively monitoring VEGF levels in three different tumors as well as following photodynamic treatment. Specificity of the molecular imaging strategy was tested using &lt;i&gt;in vivo&lt;/i&gt; competition experiments and mathematically using a quantitative pharmacokinetic model.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The molecular imaging strategy successfully imaged VEGF levels quantitatively in three different tumors and showed concordance with results from standard ELISA. Changes in tumoral VEGF concentration following photodynamic treatment and Avastin treatment were shown. Immunohistochemistry shows that (&lt;i&gt;a&lt;/i&gt;) the VEGF-specific contrast agent labels both proteoglycan-bound and unbound VEGF in the extracellular space and (&lt;i&gt;b&lt;/i&gt;) the bound VEGF is released from the extracellular matrix in response to photodynamic therapy. &lt;i&gt;In vivo&lt;/i&gt; competition experiments and quantitative pharmacokinetic model-based analysis confirmed the high specificity of the imaging strategy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; This first report of &lt;i&gt;in vivo&lt;/i&gt; quantitative optical molecular imaging-based monitoring of a secreted cytokine in tumors may have implications in providing tools for mechanistic investigations as well as for improved treatment design and merits further investigation.&lt;/p&gt;&lt;/div&gt;
Driving Affinity Selection by Centrifugal Force (2003)

We describe a new approach to affinity selection based on the application of centrifugal force to macromolecules in solution. The method relies on the well known macromolecular hydrodynamic principles of centrifugation. It can be automated and operated in a centralized fashion, or it can be decentralized and used by single researchers or networks of researchers with a minimal additional capital investment. In this method, a centrifugal driving force is used to establish a differential and selective concentration gradient between a therapeutic target and potential ligands in compound libraries. This concentration gradient, in turn, drives the binding of ligands. Once formed, the differential concentration gradient of target macromolecules and ligands is fractionated to capture the self-sorting binding events. Ligand binding is defined by the individual ligand binding constants, so tight binding ligands will essentially distribute identically with the protein target, and weaker binding ligands will not. The level of affinity needed to operationally define tight binding can be adjusted by selecting the initial concentration conditions or centrifugal force. A variety of rapid, commonly available, detection methods can be used to assess binding in the fractionated samples. The method can be broadly applied in drug discovery efforts to examine most types of cell–cell, protein–protein, and protein–small molecule interactions. We describe the application of this method to systems of small molecule interactions with several macromolecules of therapeutic interest.
ChemInform Abstract: SELECTIVE DEMETHYLATION IN THE OXIDATION OF ARYLALKYLMETHYLAMINES WITH METAL ACETATES (1975)

Abstract Bei der Reaktion der Aniline (I) mit den Metallacetaten (II) werden unter Desalkylierung die Acetylderivate (III) erhalten.
A specific non-bisphosphonate inhibitor of the bifunctional farnesyl/geranylgeranyl diphosphate synthase in malaria parasites (2017)

Summary Isoprenoid biosynthesis is essential for Plasmodium falciparum (malaria) parasites and contains multiple validated antimalarial drug targets, including a bifunctional farnesyl and geranylgeranyl diphosphate synthase (FPPS/GGPPS). We identified MMV019313 as an inhibitor of Pf FPPS/GGPPS. Though Pf FPPS/GGPPS is also inhibited by a class of bisphosphonate drugs, MMV019313 has significant advantages for antimalarial drug development. MMV019313 has superior physicochemical properties compared to charged bisphosphonates that have poor bioavailability and strong bone affinity. We also show that it is highly selective for Pf FPPS/GGPPS and showed no activity against human FPPS or GGPPS. Inhibition of Pf FPPS/GGPPS by MMV019313, but not bisphosphonates, was disrupted in an S228T variant, demonstrating that MMV019313 and bisphosphonates have distinct modes-of-inhibition against Pf FPPS/GGPPS. Altogether MMV019313 is the first specific, non-bisphosphonate inhibitor of Pf FPPS/GGPPS. Our findings uncover a new small molecule binding site in this important antimalarial drug target and provide a promising starting point for development of Plasmodium -specific FPPS/GGPPS inhibitors.
High-capacity free-space optical link in the midinfrared thermal atmospheric windows using unipolar quantum devices (2022)

Free-space optical communication is a very promising alternative to fiber communication systems, in terms of ease of deployment and costs. Midinfrared light has several features of utter relevance for free-space applications: low absorption when propagating in the atmosphere even under adverse conditions, robustness of the wavefront during long-distance propagation, and absence of regulations and restrictions for this range of wavelengths. A proof-of-concept of high-speed transmission taking advantage of intersubband devices has recently been demonstrated, but this effort was limited by the short-distance optical path (up to 1 m). In this work, we study the possibility of building a long-range link using unipolar quantum optoelectronics. Two different detectors are used: an uncooled quantum cascade detector and a nitrogen-cooled quantum well-infrared photodetector. We evaluate the maximum data rate of our link in a back-to-back configuration before adding a Herriott cell to increase the length of the light path up to 31 m. By using pulse shaping, pre- and post-processing, we reach a record bitrate of 30 Gbit s − 1 for both two-level (OOK) and four-level (PAM-4) modulation schemes for a 31-m propagation link and a bit error rate compatible with error-correction codes.
Resonance frequency analysis by galerkin's method for clamped‐free, stepped flexural mode quartz crystal resonators and its application to a quartz crystal tuning fork (1994)

Abstract This paper describes a stepped flexural mode quartz crystal resonator. The objective of this paper is to determine the resonant frequency, the motional series resistance R 1 , and the Q value of the stepped flexural mode tuning fork‐type quartz crystal resonator. The equation of motion is presented for a flexural mode resonator with nonuniform cross section with rotary inertia, and shear force is taken into consideration. Then, since the flexural mode quartz crystal resonator can be thought of as having two clamped‐free beams, the vibrational displacement computed from the boundary condition of clamped‐free ends and the condition of continuity of different cross sections are used to derive the frequency equation by Galerkin's method. In addition, the transcendental equation can be derived from the boundary conditions and the continuity condition. Further, from these relationships, the frequency constant ( f · l 1 ) and the resonant frequency are determined as functions of the width ratio W 21 (width w 2 /‐width w 1 ) and the length ratio L 21 (length l 2 /length l 1 ). As a result, it is shown that the frequency can be lowered without increasing the length of the resonator. These relationships are compared with the experimental results. It is shown that both agree very well. Hence, the present analysis results are effective for arbitrary frequency design. Finally, the typical values of the electrical equivalent circuit parameters are given. It is shown that, as L 21 is increased, the motional series resistance R 1 increases and the Q value decreases, although the characteristics are sufficient as a resonator. At the same time, the structure is resistant to vibration.
Non‐equilibrium Green function implementation of boundary conditions for full band simulations of substrate‐nanowire structures (2003)

Abstract The density of states of a nanowire exhibits peaks at energies in which the individual transverse modes begin to propagate. Under ideal conditions these modes are eigenstates solely determined by the cross sectional size and shape of the nanowire. However, for realistic nanowires, which are grown on semiconductor substrates, the density of states of the subsrate‐nanowire structure is dependent on the distance from the nanowire endpoints. Near the substrate, the density of states is is nonzero far below the energy corresponding to the first eigenstate of the ideal nanowire. This initial increase in the density of states occurs at energies near the conduction and valence band edges of the semiconductor substrate on which the nanowire is grown. Away from the substrate, the density of states begins to acquire ideal nanowire characteristics. In the present work this effect is captured by imposing boundary conditions, with properties of bulk material, at the nanowire base. The calculations utilize a first neighbor sp 3 s*d 5 orbital basis within the non‐equilibrium Green function formalism. (© 2003 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)