gebhart/patrepeval huggingface dataset:
Interrogating Androgen Receptor Mediated Gene Expression and Tumor Progression by Molecular Imaging (2003)

Abstract : This final report summarizes our work on the effectiveness of a new adenovirus based optical imaging vector designed to detect MAP kinase levels in living subjects. The vector was injected into human tumors implanted into SCID mice. Animals were injected with D-luciferin and imaged in a Xenogen IVIS device. The vector was able to detect enhanced MAPK levels stimulated by Epidermal Growth Factor in prostate cancer tumors of xenograft animals. We interrogated two lines of androgen dependent (AD) and independent (Al) xenograft animal models (CWR22 and LAPC9) to determine MAPK levels. We found no significant difference between AD and Al cancer with respect to functional MAPK levels. However, CWR22 animals exhibit significantly higher MAPK levels than LAPC9 xenograft animals. The data suggest the possibility that gene expression based imaging may be able to detect augmented MAPK levels predictive of disease progression as well as the efficacy of cancer therapeutics.
Targeted therapy of gynecological tumors with cytotoxic peptide analogs (2006)

3082 A high percentage of gynecological tumors express receptors for luteinizing hormone releasing hormone (LHRH), bombesin and somatostatin. 2-Pyrrolinodoxorubicin, a highly potent derivative of doxorubicin, was coupled to peptide analogs of these hormones. These hybrid molecules can be used for the targeted therapy of gynecological cancers. Human breast (MX-1, MDA-MB-231, MDA-MB-435, MDA-MB-468, DU-4475, endometrial (HEC-1-A, RL-95-2, AN3CA) and ovarian cancer (ES-2, UCI-107, OV-1063) cell lines were tested for the presence of LHRH, bombesin and somatostatin recepetors. Anti-tumor activity and toxicity of targeted cytotoxic analogs of LHRH (AN-207), bombesin (AN-215) and somatostatin (AN-238) was evaluated in nude mouse models of these tumors and compared with the non-targeted cytoxic radical 2-pyrrolinodoxorubicin. Induction of MDR proteins MDR-1, MRP-1 and BCRP of targeted and non-targeted therapy were evaluated by real-time PCR. Growth of human MX-1, MDA-MB-231, MDA-MB-435, MDA-MB-468 and DU-4475 breast cancers were signifcantly inhibited by AN-215. Growth of ES-2, UCI-107 and OV-1063 ovarian cancers was significantly reduced by AN-215. UCI-107 tumors were also signifcantly inhibited by AN-238 or an equimolar mixture of AN-215 and AN-238. Significant tumor inhibition of HEC-1-A, RL-95-2 and AN3CA human endometrial cancers was achieved by targeted therapy with AN-207, AN-215 and AN-238. Tumor inhibition in these models ranged between 40-68%. The cytotoxic radical 2-pyrrolinodoxorubicin alone did not significantly affect tumor growth in any experiment. White blood cell count in nude mice was significantly affected by 2-pyrrolinodoxorubicin, but not by targeted therapy. Low or no induction of MDR-1, MRP-1 and BCRP occurred after targeted therapy with AN-215 and AN-238. Targeted therapy of breast, endometrial and ovarian cancer with cytotoxic peptide analogs AN-207, AN-215 and AN-238 is more effective and less toxic than non-targeted chemotherapy. AN-215 and AN-238 do not induce MDR proteins MDR-1, MRP and BCRP. Targeted therapy with cytotoxic peptide analogs should be a novel and effective treatment approach for gynecological cancers.
Supplementary Materials and Methods and Supplementary Figure Legends from <i>In Vitro</i> and <i>In Vivo</i> Activity of the Low-Immunogenic Antimesothelin Immunotoxin RG7787 in Pancreatic Cancer (2023)

&lt;p&gt;PDF - 261K, Supplementary methods related to the IHC protocol and supplementary figure legends.&lt;/p&gt;
Second‐order reflective‐type, absorptive notch filter with lumped elements (2014)

ABSTRACT In this article, a design methodology and equations necessary for a second‐order absorptive, reflective‐type, transmission zero notch filter are introduced, derived, and described in detail. Initially, a single (first order), absorptive, reflective‐type transmission zero notch filter is described. Based on this, improvements to the first‐order reflective‐type notch filter are discussed and a novel circuit that achieves a second‐order absorptive, reflective‐type, transmission zero notch response is proposed. The necessary conditions for the achievement of the second‐order absorptive, reflective‐type, transmission zero from the proposed circuit are derived. As an experimental verification, first‐ and second‐order absorptive, reflective‐type, transmission zero circuits are fabricated and their performance measured. It is shown that the first‐order notch circuit introduces a zero into the response of a main filter with a depth of over 12 dB in the frequency range 2.19–2.27 GHz, while the second‐order notch circuit introduces a transmission zero with a depth of over 20 dB GHz, in the same frequency range as its first‐order counterpart. © 2014 Wiley Periodicals, Inc. Microwave Opt Technol Lett 56:2542–2545, 2014
Fluorescent Ligand Enables Target Engagement Studies for the Intracellular Allosteric Binding Site of the Chemokine Receptor CXCR2 (2023)

Fluorescently labeled ligands are versatile molecular tools to study G protein-coupled receptors (GPCRs) and can be used for a range of different applications, including bioluminescence resonance energy transfer (BRET) assays and fluorescence microscopy. Herein, we report the structure-based development of a fluorescent ligand targeting the intracellular allosteric binding site (IABS) of the CXC chemokine receptor 2 (CXCR2), a class A GPCR that has been pursued as a drug target in oncology and inflammation. Starting from the co-crystallized intracellular CXCR2 antagonist 00767013 (1), a tetramethylrhodamine (TAMRA)-labeled CXCR2 ligand was designed, synthesized, and tested for its suitability as a fluorescent reporter to probe binding to the IABS of CXCR2. By means of these studies, we developed Mz438 (9) as a high affinity fluorescent CXCR2 ligand, enabling cell-free as well as cellular NanoBRET-based binding studies in a non-isotopic and high throughput manner. Further, we show that 9 can be used as a tool to visualize intracellular target engagement for CXCR2 via fluorescence microscopy. Thus, our small molecule-based fluorescent CXCR2 ligand 9 represents a promising tool for future studies of CXCR2 pharmacology.
Electrically detected magnetic resonance study of barium and nitric oxide treatments of 4H-SiC metal-oxide-semiconductor field-effect transistors (2019)

We report on the effects of barium interfacial layer (IL) deposition and nitric oxide (NO) anneals on interface/near-interface defects in 4H-SiC metal-oxide-semiconductor field-effect transistors utilizing electrically detected magnetic resonance (EDMR). The 4H-SiC/SiO2 interface has a large number of electrically active defects that reduce the effective channel mobility. Various passivation schemes have been utilized to decrease the interface defect density and thus increase mobility. Two passivation schemes of great interest are postoxidation annealing in nitric oxide (NO) and deposition of a barium interfacial layer (IL) before oxide growth. Our measurements compare the chemical nature of defects very near the 4H-SiC/SiO2 interface in devices utilizing both passivation schemes and nonpassivated devices. Both the NO anneal and the barium IL greatly reduce the interface region EDMR response, which corresponds to a large improvement in mobility. However, the EDMR response in devices subjected to the two passivation processes is somewhat different. We present results that suggest spin lattice relaxation times are longer in samples that received a barium IL than in samples with NO annealing; this result suggests a lower level of local strain within the vicinity of defects very near the 4H-SiC/SiO2 interface in barium treated samples over NO annealed samples.
Temporal Coupled mode theory for thermal emission from a single emitter (2013)

We propose a temporal coupled mode theory for thermal emission from a single emitter. We validate the coupled mode theory formalism by a direct numerical simulation of the emission properties of single emitters.
Cell-Wall Autohydrolysis in Isolated Endosperms of Lettuce (Lactuca sativa L.) (1994)

Cell walls prepared from the endosperm tissue of hydrated lettuce (Lactuca sativa L.) seeds undergo autohydrolysis. Release of carbohydrates is most rapid (0.4-0.6 [mu]g per endosperm) within the 1st h of incubation in buffer, but substantial autolysis is sustained for at least 10 h. Autolysis is temperature sensitive, and the optimum rate occurs at pH 5. The rate of autolysis increases markedly in the period just prior to radicle emergence. The cell-wall polysaccharide composition in micropylar and lateral endosperm regions differs significantly; the micropylar walls are rich in arabinose and glucose with substantially lower amounts of mannose. Although walls prepared from both micropylar and lateral regions undergo autolysis, micropylar walls release carbohydrates at a higher rate than lateral walls. Autolysis products elute as large polymers when subjected to size-exclusion chromatography, suggesting that endo-enzyme activity is responsible for release of fragments containing arabinose, galactose, mannose, and uronic acids. Arabinose, galactose, mannose, and glucose are also released as monomers. As a function of time, the ratio of polymers to monomers decreases, indicating that exo-enzyme activity is also present. Thermoinhibition or treatment with abscisic acid suppresses germination and reduces the rates of autolysis of walls isolated from the endosperm by about 25%. Treatments that alleviate thermoinhibition (kinetin and gibberellic acid) increase the rates of autolysis by 20 to 30% when compared to thermoinhibited controls.
Defect Energetics in Pseudo-Cubic Mixed Halide Lead Perovskites from First-Principles (2020)

Owing to the increasing popularity of lead-based hybrid perovskites for photovoltaic (PV) applications, it is crucial to understand their defect energetics and its influence on their optoelectronic properties. In this work, we simulate various point defects in pseudocubic structures of mixed iodide-bromide and bromide-chloride methylammonium lead perovskites with the general formula MAPbI3–yBry or MAPbBr3–yCly (where y is between 0 and 3), and use first-principles based density functional theory computations to study their relative formation energies and charge transition levels. We identify vacancy defects and Pb on MA antisite defect as the lowest energy native defects in each perovskite. We observe that while the low energy defects in all MAPbI3–yBry systems only create shallow transition levels, the Br or Cl vacancy defects in the Cl-containing pervoskites have low energy and form deep levels which become deeper for higher Cl content. We examine the structures and density of states of pure and defect-containing perovskite systems to obtain an understanding of the nature of defect levels. Further, we study extrinsic substitution by different elements at the Pb site in MAPbBr3, MAPbCl3, and the 50–50 mixed halide perovskite, MAPbBr1.5Cl1.5, and identify some transition metals that create lower energy defects than the dominant intrinsic defects and also create midgap charge transition levels.
Transnationality and Teacher Educator Identity Development: A Collaborative Autoethnographic Study (2019)

Transnational teacher educators, who cross national, social, and cultural boundaries to prepare teachers, play a vital role in nurturing teachers’ awareness and appreciation of learner diversity. However, transnational teacher educators tend to encounter tremendous challenges in developing their professional identities. To date, though many studies have investigated how teachers and teacher educators in general develop their professional identities, scant attention has been paid to that complex process of “transnational” teacher educators. To begin to close this research gap, this collaborative autoethnographic study examines how we develop our teacher educator identities through teaching a diversity course in the United States as transnational teacher educators from China and South Korea. The findings reveal that our transnational backgrounds (e.g., speaking English as a second language and holding particular cultural beliefs) initially challenged our identity development, but our continuous teaching and learning within a supportive institutional context turned the marginality of our transnational backgrounds into professional assets. The research findings can extend our understanding of teacher educators’ identity development. The study also suggests practical implications for teacher education programs to create an inclusive and supportive professional community in which all teacher educators may grow.
Tumorigenic activity of the 4,5- and 9,10-dihydrodiols of benzo[j]fluoranthene and their syn- and anti-diol epoxides in newborn mice. (1994)

Benzo[j]fluoranthene (B[j]F), trans-4,5-dihydro-4,5-dihydroxy-B[j]F, and trans-9,10-dihydro-9,10-dihydroxy-B[j]F were evaluated for tumorigenic activity in newborn CD1 mice. These dihydrodiols were assayed at doses of 1.10 and 0.275 mumol/mouse. B[j]F and the syn- and anti-diol epoxides derived from these dihydrodiols were evaluated at doses of 1.10, 0.275, and 0.110 mumol/mouse (80 mice/group). trans-4,5-Dihydro-4,5-dihydroxy-B[j]F was more potent than trans-9,10-dihydro-9,10-dihydroxy-B-[j]F in inducing pulmonary tumors in both female and male mice. Administration of 1.10 mumol of trans-4,5-dihydro-4,5-dihydroxy-B[j]F resulted in a 90-92% incidence of pulmonary tumors with an average of 3.6 and 4.2 tumors/mouse among female and male mice, respectively. A similar tumorigenic activity was observed for B[j]F in lung. trans-9,10-Dihydro-9,10-dihydroxy-B[j]F was significantly less tumorigenic (P < 0.05), producing a 44 and 64% incidence of pulmonary tumors at a dose of 1.10 mumol with an average of 0.8 and 1.0 tumor/mouse in female and male mice, respectively. A statistically significant (P < 0.001) incidence of hepatic tumors was also produced among male mice administered either B[j]F, trans-4,5-dihydro-4,5-dihydroxy-B[j]F, or trans-9,10-dihydro-9,10-dihydroxy-B[j]F at a dose of 1.10 mumol/mouse. In comparing the tumorigenicity of the diasteromeric diol epoxides derived from both trans-4,5-dihydro-4,5-dihydroxy-B[j]F and trans-9,10-dihydro-9,10-dihydroxy-B[j]F, the anti-diasteromers exhibited greater tumorigenic activity. The most tumorigenic diol epoxide was anti-4,5-dihydroxy-6,6a-epoxy-4,5,6,6a-tetrahydro-B[j]F. At a dose of 0.275 mumol, this diol epoxide induced a 96 and 100% incidence of pulmonary tumors in female and male mice, with an average of 8.6 and 5.0 tumors/mouse, respectively. anti-9,10-Dihydroxy-11,12-epoxy-9,10,11,12-tetrahydro-B[j]F at this dose produced a 56 and 95% incidence of pulmonary tumors in female and male mice with an average of 1.0 and 2.8 tumors/mouse, respectively. syn-4,5-Dihydroxy-6,6a-epoxy-4,5,6,6a-tetrahydro-B[j]F and syn-9,10-dihydroxy-11,12-epoxy-9,10,11,12-tetrahydro-B[j]F at a dose of 0.275 mumol did not induce a significant incidence (P > 0.05) of pulmonary tumors in female or male mice.(ABSTRACT TRUNCATED AT 400 WORDS)
Synergizing ontologies and graph databases for highly flexible materials-to-device workflow representations (2023)

The escalating adoption of high-throughput methods in applied materials science dramatically increases the amount of generated data, demandingthe deployment and use of sophisticated data-driven methods. To exploit the full potential of these accelerated approaches, the generated data needs to be managed, preserved, and shared. Its heterogeneity calls for highly flexible data models to represent data from fabrication workflows, measurements, and simulations. We propose employing a native graph database to store the data instead of relying on rigid relational data models. To develop a flexible and extendable data model, we have created an EMMO-based ontology, where EMMO stands for European Materials Modelling Ontology. The Python framework Django is used to allow for the intuitive integration into the virtual materials intelligence platform, VIMI. The Django framework relies on the Object-Graph-Mapper (OGM) neomodel to create a mapping between database classes and python objects. The model can store the whole bandwidth of data, from fabrication to simulation data. Implementing the database into a platform will encourage researchers to share data while profiting from rich and highly curated data to accelerate their research.
Terminal-Side Data Rate Prediction For High-Mobility Users (2021)

The possibility of predicting Quality of Service, and particularly data rates, in mobile networks will enable new applications for future automated and connected mobility, such as teleoperated driving. Since network data is difficult to acquire and usually of low granularity, robust prediction approaches are required that need to be trained with data sets and measurements generated by end devices. In this paper, we present uplink and downlink data sets, measured in extensive drive tests, that are made available for the evaluation of machine learning methods. Based on this data, we compare the data rate prediction performance in uplink and downlink for neural network, random forest and gradient boosting approaches. Our results show a significantly higher achievable accuracy in uplink than in downlink, and that, even with reduced feature sets, gradient boosting is particularly suited for the prediction task. Moreover, we investigate the use of quantile estimation methods for predicting bounds on the achievable data rate. We show that conformalized approaches, both based on neural networks and random forests, can predict quantiles with very high accuracy.
Supplementary data from Evolution of Cancer Stem-like Cells in Endocrine-Resistant Metastatic Breast Cancers Is Mediated by Stromal Microvesicles (2023)

&lt;p&gt;Supplementary Figures and Tables&lt;/p&gt;
Performance characteristics of newly developed whole-body multislice positron computed tomograph (1984)

The authors have constructed a whole-body multislice positron computed tomograph based on ''positology''. This machine has four continuously rotating detector rings with 192 BGO crystals (12 x 24 x 24mm), which are unequally arranged around each ring. Images of 7 slices at 16mm intervals can be obtained. The signals are transferred to the stationary part through photo-coupling system. The patient aperture is 54cm in diameter, and the field of view is 40cm in diameter and 12cm in depth, making it possible to take images of the whole heart at one scan. The sensitivity measured with 20cm diameter cylindrical phantom is 34.2 and 52.2 kcps/..mu..Ci/ml for in-plane and cross-plane respectively, including scattered coincidence. This high sensitivity enables the authors to make dynamic images of the heart following bolus injection of N-13 labeled ammonia, as well as wash-out dynamic images of the lungs following equilibration with N-13 labeled nitrogen gas. Spatial resolutions (FWHM) for in-plane measured with 1mm diameter Ga-68 line source in air is 7.6mm at the center of the field and 8.7mm at 20cm apart from the center. Axial resolution (FWHM) is 12mm at the center of the field. It can clearly delineate hot-spot images of Derenzo phantom of 3.0mmmore » in diameter. The authors' can also visualize fine structures in clinical studies such as papillary muscle of the heart. Thus the machine is extremely useful for all sorts of clinical studies using positron emitters.« less
Synthetic peptides caged on histidine residues with a bisbipyridyl ruthenium(ii) complex that can be photolyzed by visible light (2015)

We report a light-sensitive histidine building block for Fmoc/tBu solid-phase peptide synthesis in which the imidazole side chain is coordinated to a ruthenium complex. We have applied this building block for the synthesis of caged-histidine peptides that can be readily deprotected by irradiation with visible light, and demonstrated the application of this approach for the photocontrol of the activity of Ni(II)-dependent peptide nucleases.
Anion Conducting Ionomers for Fuel Cells and Electrolyzers (2017)

The design of new anion exchange ionomers for use in electrochemical devices is a critical step in improvement of anionic fuel cells and electrolyzers.Although these materials share some targeted goals with anion exchange membranes (AEMs), there are several different property requirements.Since ionomers are used within electrode layers, they do not serve as a primary separator for fuel and air.Rather, they act as a transport facilitator in the electrode where a high degree of mass transport is required.In this study, a series of anionic ionomers is synthesized and tested in hybrid fuel cells and AEM electrolyzers.These ionomers are based on a series of materials which include block copolymer AEMs with alkyl tethers that have been modified to be used as anion conductors.The newly synthesized ionomers were tested in both fuel cell and electrolysis devices.In situ testing of these materials shows that lower molecular weight materials outperform their higher molecular weight counterparts.Additionally, the use of a block copolymer with the introduction of a hydrophobic spacer further increased device performance.
5-Methoxy-1-(3,4,5-trimethoxyphenyl)-1H-indole (2010)

The title compound, C(18)H(19)NO(4), was prepared as an indole derivative with possible anti-mitotic properties. The planes of the indole and trimethoxy-phenyl rings make a dihedral angle of 45.35 (5)° with one another. In the crystal, mol-ecules related by a twofold screw axis exhibit arene C-H⋯arene-π inter-actions which are 3.035 (1) Å in length.
Results of Automated Retinal Image Analysis for Detection of Diabetic Retinopathy from the Nakuru Study, Kenya (2015)

In this epidemiological sample, the IDP's grading was comparable to that of human graders'. It therefore might be feasible to consider inclusion into usual epidemiological grading.
Interstitial lung disease related surfactant protein-C mutations alter the transcriptome and progenitor cell function of alveolar epithelial cells in mice (2019)

Alveolar type 2 epithelial (AT2) cells are a key progenitor population critical to lung homeostasis whose dysfunction is implicated in pulmonary fibrosis (PF) pathogenesis. In a proof of concept study utilizing a murine model with inducible expression of a PF related missense mutation 218T&gt;C (= Ile-&gt;Thr at position 73 [I73T]) in the Surfactant Protein C [SP-C] gene we showed that proSP-C<sup>I73T</sup> was sufficient to cause early lung injury and late fibrotic remodeling. In this study, RNA-Seq profiling of SP-C<sup>I73T</sup> AT2 cells isolated prior to injury (day 3), at peak injury (day 14), and during fibrotic remodeling (day 42) revealed significant enrichment for gene ontology categories related to DNA replication/cell cycle, immune regulation, and matrix/cell-cell communication. Target validation confirmed upregulation of genes associated with cell proliferation, and identified altered signaling known to affect AT2 to AT1 transdifferentiation including Wnt, FGF, and Stat3. In vivo adult SP-C<sup>I73T</sup> mice showed AT2 hyperplasia while neonates displayed developmental alterations in alveolarization with reciprocal changes in the ratio of AT2 / AT1 cells. Ex vivo lung organoids containing SP-C<sup>I73T</sup> AT2 cells had increased colony formation but abnormal colony size consistent with a pro-proliferative/ impaired differentiation phenotype that was reversed by inhibition of canonical Wnt signaling. Our results reveal SP-C<sup>I73T</sup> causes a toxic gain of function in AT2 cells that includes robust expression profiles acquired from both intrinsic transcriptional changes and external queues capable of disrupting niche homeostasis to the detriment of repair programs.