gebhart/patrepeval huggingface dataset:
Reduced‐Linolenate Content Associations with Agronomic and Seed Traits of Soybean (1998)

Soybean [ Glycine max (L.) Merr.] lines with the fan1 (A5) fan1 (A5) fan2 fan2 genotype for reduced linolenate content produce an oil with improved oxidative stability. The improved oxidative stability reduces the formation of undesirable flavor compounds in the oil. The objective of this study was to determine if reduced linolenate influences agronomic or seed traits of soybean. The single‐cross populations AX11224, AX11227, and AX11240 were developed by crossing each of three high‐yielding parents with normal‐linolenate content of ≈77 g kg −1 to one of three reduced‐linolenate parents with ≈26 g kg −1 linolenate. From each of the populations, 27 F 3 ‐derived normal‐linolenate lines and 27 reduced‐linolenate lines were evaluated at three locations in Iowa during 1996. The mean seed yields of the reduced‐linolenate lines were not significantly different ( P > 0.05) from the normal‐linolenate lines for AX11224 and AX11227, but the mean yield of the reduced‐linolenate lines was significantly lower than the normal‐linolenate lines for AX11240. The means of the reduced‐linolenate lines were not significantly different from the normal‐linolenate lines for maturity, lodging, plant height, and protein content in the three populations. The mean oil, stearate, and linoleate contents of reduced‐linolenate lines were significantly greater ( P < 0.05) than normal‐linolenate lines in all populations. Differences between the means of the reduced‐ and normal‐linolenate lines for seed weight, palmitate content and oleate content were not consistent among the populations. The difference among crosses for the relationship of reduced linolenate with seed yield and other traits indicated that multiple reduced‐ and normal‐linolenate parents should be used in a cultivar development program.
Assembly and Immunological Processing of Polyelectrolyte Multilayers Composed of Antigens and Adjuvants (2016)

While biomaterials provide a platform to control the delivery of vaccines, the recently discovered intrinsic inflammatory characteristics of many polymeric carriers can also complicate rational design because the carrier itself can alter the response to other vaccine components. To address this challenge, we recently developed immune-polyelectrolyte multilayer (iPEMs) capsules electrostatically assembled entirely from peptide antigen and molecular adjuvants. Here, we use iPEMs built from SIINFEKL model antigen and polyIC, a stimulatory toll-like receptor agonist, to investigate the impact of pH on iPEM assembly, the processing and interactions of each iPEM component with primary immune cells, and the role of these interactions during antigen-specific T cell responses in coculture and mice. We discovered that iPEM assembly is pH dependent with respect to both the antigen and adjuvant component. Controlling the pH also allows tuning of the relative loading of SIINFEKL and polyIC in iPEM capsules. During in vitro studies with primary dendritic cells (DCs), iPEM capsules ensure that greater than 95% of cells containing at least one signal (i.e., antigen, adjuvant) also contained the other signal. This codelivery leads to DC maturation and SIINFEKL presentation via the MHC-I antigen presentation pathway, resulting in antigen-specific T cell proliferation and pro-inflammatory cytokine secretion. In mice, iPEM capsules potently expand antigen-specific T cells compared with equivalent admixed formulations. Of note, these enhancements become more pronounced with successive booster injections, suggesting that iPEMs functionally improve memory recall response. Together our results reveal some of the features that can be tuned to modulate the properties of iPEM capsules, and how these modular vaccine structures can be used to enhance interactions with immune cells in vitro and in mice.
Method To Generate Full-Bore Images Using Borehole Images and Multipoint Statistics (2011)

Summary Borehole-image logs, which are produced by tools being lowered into a well, provide oriented electrical and acoustic maps of the rocks and fluids encountered in the borehole. Electrical borehole images in water-based (conducting) and oil-based (nonconducting) muds are generated from electrodes arranged in fixed patterns on pads that are pressed against the borehole wall. Depending on the borehole diameter, gaps nearly always occur between pads. Because of these gaps, it is common to have nonimaged parts of the borehole wall. Full-bore images are complete, 360° views of the borehole wall. They are generated by "filling in the gaps" between the pads in borehole-image logs. This method uses the Filtersim algorithm of multipoint statistics (MPS) to generate models, or realizations. Measured (incomplete) borehole images themselves are used as "training images." Recorded data are perfectly honored (i.e., the models are conditioned to the real data). Gaps are filled with patterns similar to those seen elsewhere in the log. Patterns in the gaps match the edges of the pads. The frequency distribution of continuously variable pixel colors in the gaps matches the distribution of pixel colors in the measured images. Full-bore images facilitate visualization and interpretation of borehole-image logs in any lithology, although case studies shown in this paper are developed in vuggy and fractured rocks. These images can be used to draw closed contours around electrically resistive or nonresistive patches in the borehole wall. Full-bore images can be used to repair logs with bad electrodes, low pad pressure, or poor acoustic reflections. Therefore, they can be used to enhance any commercially available electrical or acoustic borehole images.
Prediction of cytogenetic abnormalities with gene expression profiles (2012)

Cytogenetic abnormalities are important clinical parameters in various types of cancer, including multiple myeloma. We developed a model to predict cytogenetic abnormalities in patients with multiple myeloma using gene expression profiling and validated it by different cytogenetic techniques. The model has an accuracy rate up to 0.89. These results provide proof of concept for the hypothesis that gene expression profiling is a superior genomic method for clinical molecular diagnosis and/or prognosis.
Monolithically Integrated Solid-State Terahertz Transceivers (2011)

We monolithically integrated a Schottky diode and a THz quantum cascade laser to create a THz transceiver, capable of detecting incident THz radiation and/or characterizing the performance and dynamics of the QCL.
Improved Interband Cascade Lasers for λ = 3-5.6 μm (2012)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text C. L. Canedy, C. S. Kim, C. D. Merritt, W. W. Bewley, J. Abell, I. Vurgaftman, J. R. Meyer, and M. Kim, "Improved Interband Cascade Lasers for λ = 3-5.6 μm," in Conference on Lasers and Electro-Optics 2012, OSA Technical Digest (online) (Optical Society of America, 2012), paper CF1K.3. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Abstract 2936: <i>In situ</i> antitumor immunotherapy with pharmacological blockade of MFG-E8 and chemotherapy against solid and hematological tumors (2010)

Abstract The conventional anticancer strategies, such as chemotherapy and radiotherapy, induce the tumor cell death, which would theoretically become the source of tumor antigens to be recognized in situ by the immune system. However, most of the cytotoxic therapies rarely induce the immunological responses potent enough to cause obvious tumor destruction in the actual clinical settings. This discrepancy might be caused by the tumor evasion systems, which restrain the induction of host immune responses. Thus, the therapeutic efficacy of various anticancer agents could be improved if the novel strategies are found to reverse molecular machineries of tumor-mediated immune evasion. Milk-fat globule EGF-8 (MFG-E8) has been known to maintain tissue homeostasis in multiple aspects; regulating the phagocytosis of apoptotic cells, breast tissue morphogenesis, intestinal epithelium homeostasis and angiogenesis. Here we have shown that the therapeutic interference of MFG-E8 synergistically potentiates antitumor activities of various cytotoxic and target therapies, and radiotherapy, against various murine tumors. These antitumor activities relied on the induction of the potent and specific antitumor immune responses in situ. The MFG-E8 blockade triggered infiltration and activation of dendritic cells at the tumor sites, where apoptotic cells were made available with cytotoxic treatments, resulting in the potent antitumor effector T cell activation and inhibition of Foxp3+Treg cell function. Furthermore, the administration of anti-MFG-E8 antibodies switches the receptor for MFG-E8-mediated tumor cell ingestion from integrins αvβ3 to activating FcγRI/III receptors in dendritic cell recognition of tumor cells, augmenting dendritic cell-mediated cross-priming of tumor-specific T cells. These findings demonstrated that the blockade of MFG-E8, one of the key negative regulators to restrain immune responses against the dying cells, would be a novel strategy to improve durable antitumor responses by various anticancer therapeutic agents. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2936.
Use of Disulfide Cationic Lipids in Plasmid DNA Delivery (2003)

Gene therapy provides a paradigm of the treatment of human diseases. The ultimate goal of gene therapy is to cure both inherited and acquired disorders by removing the original causes, i.e., adding, blocking, correcting, or replacing genes. Although gene therapy trials have been initiated worldwide for more than two decades, little has been achieved in clinically curing diseases. One of the major hurdles for gene therapy is the lack of an efficient gene delivery system. An ideal gene delivery system should be specifically targeting, biodegradable, nontoxic, nonimmunogenic, and stable for storage. Cationic lipo-somes are the most extensively investigated nonviral vectors. It is generally believed that DNA-liposome complexes enter cells via endocytosis, although other pathways such as membrane fusion may exist (1,2). The barriers involved in the transfection process in vitro generally include the following aspects (3): 1. Formation of the liposome-DNA complexes. 2. Entry of complexes into cell. 3. Escape of DNA from the endosomes. 4. Dissociation of DNA from liposomes. 5. Entry of DNA into nucleus. 6. DNA transcription.
Reverse Transcription-Polymerase Chain Reaction Phenotyping of Metalloproteinases and Inhibitors Involved in Tumor Matrix Invasion (1993)

The matrix metalloproteinase enzymes have been implicated in tumor invasion and metastasis by a series of correlative immunohistochemical studies. In addition, direct evidence for the role of these enzymes in this pathologic process comes from studies using specific metalloproteinase inhibitors to block tumor invasion and metastasis formation, both in vitro and in vivo. Synthetic oligonucleotide primers for four metalloproteinases (MMP-1, MMP-2, MMP-9, MMP-10) and their tissue inhibitors (TIMP-1, TIMP-2) were selected, synthesized, and optimized in the reverse transcriptase-polymerase chain reaction (RT-PCR) to study the qualitative profile of these enzymes and inhibitors in cultured human tumor cells and tumor tissues. These primers are specific and generate unique amplification products for each appropriate enzyme and inhibitor. Slight enhancement in the amplification of cDNA products was achieved by adding dimethylsulfoxide to the reaction mixture, but commercial enhancement reagents were ineffective. Using this RT-PCR method, cDNA amplification was successful with RNA from as few as 20 cultured tumor cells. The RT-PCR analysis was done on three invasive human colon adenocarcinomas and their paired adjacent normal mucosa. The results show MMP-1 and MMP-2 products in all three tumors, and MMP-2 detected in one of the three normal mucosa samples; TIMP-2 expression was present in two of three patients and awaits quantitative assessment of RT-PCR products.
Volume Fresnel zone plates fabricated by femtosecond laser direct writing (2007)

In this letter, volume Fresnel zone plates fabricated inside fused silica using femtosecond laser direct writing are demonstrated. A volume zone plate consists of a number of layers of Fresnel zone plates designed to focus light together. Results indicate that volume Fresnel zone plates increase the overall diffraction efficiency significantly. Phase zone plates yield considerably higher diffraction efficiency due to a number of reasons including negligible light absorption, robustness against fabrication phase errors, and minimum interference between different zone plates in a volume.
Carbonic anhydrase inhibitors: Gd(iii) complexes of DOTA- and TETA-sulfonamide conjugates targeting the tumor associated carbonic anhydrase isozymes IX and XII (2010)

Gd(III)-sulfonamide complexes incorporating macrocyclic rings of the DOTA/TETA type have been prepared and assayed for the inhibition of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). The cytosolic isoform, CA I, was poorly inhibited, whereas cytosolic CA II and transmembrane, tumor-associated CA IX and XII were inhibited in the low nanomolar range by the Gd(III) complexes. Magnetic susceptibility and relaxivity measurements proved that the Gd(III) complexes have comparable parameters to those of clinically used MRI contrast agents like Dotarem, Prohance and Omniscan in aqueous solution. Some Gd(III) complexes were investigated for the inhibition of extracellular tumor acidification in two cell lines overexpressing CA IX, the colorectal HT-29 cell line and the cervical HeLa carcinoma cell line. In both tumor types, a slight but significant reduction of tumor acidosis was detected. Gd(III)-sulfonamide conjugates may thus be of interest for developing imaging techniques or novel treatment strategies for the management of hypoxic tumors overexpressing extracellular CA isozymes such as CA IX and XII.
Abstract 3515: Pathway convergent evolution underscores treatment response to MTOR inhibitors in kidney cancers. (2013)

Abstract Despite the established role of MTOR inhibitors (rapalogs) in treating advanced kidney cancer, therapeutic benefit varies and predictive biomarkers are lacking. Intratumor branching heterogeneity, a recently discovered hallmark of this disease, has raised concerns about the feasibility of developing genomic biomarkers for targeted agents in kidney cancer. We undertook an outlier approach to interrogate the genetic determinants underlying long-term therapeutic response (&gt;20 months) to rapalogs in 6 patients. An integrated ultra-deep targeted-exome (∼500x) and standard whole-exome (∼100x) sequencing was performed. Additionally, to address intratumor and intertumor heterogeneity, spatially separated tumor specimens from the same individuals were analyzed whenever possible. Multiregional sequencing unveiled surprising MTOR pathway convergent evolution, manifested by MTOR pathway activation by means of distinct genomic events in spatially separate sites of disease within the same individual. Amongst the core components of the MTORC1 pathway, complete functional loss of TSC1 and TSC2, and a hyperactive MTOR mutant were discovered in 4 of 6 long-term responders. Mutations in MTOR Clustered at FAT and kinase domains confer hyperactivity and yet remain sensitive to rapamycin. Here, we affirm intratumor heterogeneity, identify genomic determinants of drug response, and discover pathway convergent evolution in the majority of long-term responders. We propose a “river” model in which intratumor and intertumor clonal heterogeneity in cancer patients evolves like a branching river that converges at critical nodes. These convergent points provide unique opportunities for the treatment of genetically diverged yet functionally converged cancers in any given patient. Citation Format: Martin H. Voss, A Ari Hakimi, Can G. Pham, A Rose Brannon, Ying-Bei Chen, Luis F. Cunha, Oguz Akin, Han Liu, Shugaku Takeda, Sasinya N. Scott, Nicholas D. Socci, Agnes Viale, Nikolaus Schultz, Chris Sander, Victor E. Reuter, Paul Russo, Emily H. Cheng, Robert J. Motzer, Michael F. Berger, James J. Hsieh. Pathway convergent evolution underscores treatment response to MTOR inhibitors in kidney cancers. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3515. doi:10.1158/1538-7445.AM2013-3515
Development of pH-Responsive Fluorescent False Neurotransmitters (2010)

We introduce pH-responsive fluorescent false neurotransmitters (pH-responsive FFNs) as novel probes that act as vesicular monoamine transporter (VMAT) substrates and ratiometric fluorescent pH sensors. The development of these agents was achieved by systematic molecular design that integrated several structural elements, including the aminoethyl group (VMAT recognition), halogenated hydroxy-coumarin core (ratiometric optical pH sensing in the desired pH range), and N- or C-alkylation (modulation of lipophilicity). Of 14 compounds that were synthesized, the probe Mini202 was selected based on the highest uptake in VMAT2-transfected HEK cells and desirable optical properties. Using Mini202, we measured the pH of catecholamine secretory vesicles in PC-12 cells (pH approximately 5.9) via two-photon fluorescence microscopy. Incubation with methamphetamine led to an increase in vesicular pH (pH approximately 6.4), consistent with a proposed mechanism of action of this psychostimulant, and eventually to redistribution of vesicular content (including Mini202) from vesicles to cytoplasm. Mini202 is sufficiently bright, photostable, and suitable for two-photon microscopy. This probe will enable fundamental neuroscience and neuroendocrine research as well as drug screening efforts.
Initiator-Integrated 3D Printing Enables the Formation of Complex Metallic Architectures (2013)

Three-dimensional printing was used to fabricate various metallic structures by directly integrating a Br-containing vinyl-terminated initiator into the 3D resin followed by surface-initiated atomic-transfer radical polymerization (ATRP) and subsequent electroless plating. Cu- and Ni-coated complex structures, such as microlattices, hollow balls, and even Eiffel towers, were prepared. Moreover, the method is also capable of fabricating ultralight cellular metals with desired structures by simply etching the polymer template away. By combining the merits of 3D printing in structure design with those of ATRP in surface modification and polymer-assisted ELP of metals, this universal, robust, and cost-effective approach has largely extended the capability of 3D printing and will make 3D printing technology more practical in areas of electronics, acoustic absorption, thermal insulation, catalyst supports, and others.
Citrus tissue culture employing vegetative explants. (2001)

Citrus being a number one fruit of the world due to its high nutritional value, huge production of fruits and fruit products, the citrus industry may be considered a major fruit industry. Though citrus orchard area in India is comparable to USA, the produce is far less, while its export is nil. Biotechnology has played an outstanding role in boosting the citrus industry, e.g., in Spain, which is now the biggest exporter of citrus fruit with the application of micrografting. Amongst the fruit trees, perhaps the maximum tissue culture research has been done in citrus during the past four decades, however, the results of practical value are meagre. The shortfalls in citrus tissue culture research and some advancements made in this direction along with bright prospects are highlighted, restricting the review to vegetative explants only. Whilst utilization of nucellar embryogenesis is limited to rootstocks, the other aspects, like, regeneration and proliferation of shoot meristems measuring 200 microm in length--a global breakthrough--of two commercially important scion species, Citrus aurantifolia and C. sinensis and an important rootstock, C. limonia, improvement of micrografting technique, cloning of the same two scion species as well as some Indian rootstock species, employing nodal stem segments of mature trees, of immense practical value have been elaborated. A rare phenomenon of shift in the morphogenetic pattern of differentiation from shoot bud differentiation to embryoid formation occurred during the long-term culture of stem callus of C. grandis. Stem callus-regenerated plants of C. aurantifolia, C. sinensis and C. grandis showed variation in their ploidy levels and a somaclonal variant of C. sinensis, which produced seedless fruits was isolated. Tailoring of rooting in microshoots to a tap root-like system by changing the inorganic salt composition of the rooting medium, resulting in 100% transplant success, and germplasm preservation through normal growth culture of shoots of C grandis without loss of regeneration capacity during 31 years, observed so far, are some other significant results. Plants of C. aurantifolia and C. sinensis raised from shoot meristem and micrografting were grown in a nethouse and those from nodal stem segments in the field along with the in vitro-raised plants of rootstocks, namely, C. jambhiri, C. karna and C. limonia. All the plants showed normal healthy growth. Significantly enough, the meristem regenerated plants of C. aurantifolia attained the reproductive phase just in 1 year of transplantation to soil similar to those raised from nodal stem segments of mature trees, which also produced normal fruits in the subsequent year while growing under field conditions. Thus, a significant fundamental concept of a maturity factor, carried over through as small a shoot meristem as 200 microm in length to cloned plants has been demonstrated. The concept is of far-reaching significance in citrus industry besides production of pathogen-free orchards.
Efficient Solid-Phase Synthesis of 1,3,5-Trisubstituted 1,3,5-Triazine-2,4,6-triones (2002)

The solid-phase synthesis of 1,3-disubstituted and 1,3,5-trisubstituted 1,3,5-triazine-2,4,6-triones from MBHA and Wang resin is described. Reaction of resin-bound amino acids with isocyanates yield resin-bound ureas, which further react with chlorocarbonyl isocyanate in toluene at 65 degrees C to selectively afford the resin-bound 1,3-disubstituted 1,3,5-triazine-2,4,6-triones. Selective alkylation at the N-5 position of the resin-bound 1,3-disubstituted 1,3,5-triazine-2,4,6-triones was accomplished by treatment with alkyl halides in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU). The desired products were cleaved from their solid support and obtained in good yield and purity. The method can be employed in production of toltrazuril analogue libraries for identification of new anticoccidial agents.