gebhart/patrepeval huggingface dataset:
A High-Throughput Standard PCR-Based Genotyping Method for Determining Transgene Zygosity in Segregating Plant Populations (2017)

In crop research programs that implement transgene-based strategies for trait improvement it is necessary to distinguish between transgene homozygous and hemizygous individuals in segregating populations. Direct methods for determining transgene zygosity are technically challenging, expensive, and require specialized equipment. In this report, we describe a standard PCR-based protocol coupled with capillary electrophoresis that can identify transgene homozygous and hemizygous individuals in a segregating population without knowledge of transgene insertion site. PCR primers were designed to amplify conserved T-DNA segments of the 35S promoter, OCS terminator, and NPTII kanamycin resistance gene in the pHellsgate-8 RNAi construct for the <i>Gossypium hirsutum</i> phytochrome A1 gene. Using an optimized multiplexed reaction mixture and an amplification program of only 10 cycles we could discriminate between transgene homozygous and hemizygous cotton control DNA samples based on PCR product peak characteristics gathered by capillary electrophoresis. The protocol was refined by evaluating segregating transgenic progeny from nine BC<sub>1</sub>S<sub>1</sub> populations derived from crosses between the transgenic cotton parent 'E-1-7-6' and other cotton cultivars. OCS PCR product peak height and peak area, normalized by amplification of the native cotton gene GhUBC1, revealed clear bimodal distributions of OCS product characteristics for each BC<sub>1</sub>S<sub>1</sub> population indicating the presence of homozygous and hemizygous clusters which was further confirmed via K-means clustering. BC<sub>1</sub>S<sub>1</sub> plants identified as homozygous or hemizygous were self-fertilized to produce BC<sub>1</sub>S<sub>2</sub> progeny. For the homozygous class, 19/20 BC<sub>1</sub>S<sub>2</sub> families confirmed the homozygous BC<sub>1</sub>S<sub>1</sub> prediction while 21/21 BC<sub>1</sub>S<sub>2</sub> families confirmed the hemizygous prediction of the original parent. This relatively simple protocol provides a reliable, rapid, and high-throughput way of evaluating segregating transgenic populations using methods and equipment common to crop molecular breeding labs.
La<sub>6</sub>Ba<sub>3</sub>[Si<sub>17</sub>N<sub>29</sub>O<sub>2</sub>]Cl—An Oxonitridosilicate Chloride with Exceptional Structural Motifs (2015)

The oxonitridosilicate chloride La6Ba3[Si17N29O2]Cl was synthesized by a high-temperature reaction in a radiofrequency furnace starting from LaCl3, BaH2, and the ammonolysis product of Si2Cl6. Diffraction data of a micrometer-sized single crystal were obtained using microfocused synchrotron radiation at beamline ID11 of the ESRF. EDX measurements on the same crystal confirm the chemical composition. The crystal structure [space group P63/m (no. 176), a = 9.8117(14), c = 19.286(6) Å, Z = 2] contains an unprecedented interrupted three-dimensional network of vertex-sharing SiN4 and SiN3O tetrahedra. The SiN4 tetrahedra form dreier rings. Twenty of the latter condense in a way that the Si atoms form icosahedra. Each icosahedron is connected to others via six SiN4 tetrahedra that are part of dreier rings and via six Q(3)-type SiN3O tetrahedra. Rietveld refinements confirm that the final product contains only a small amount of impurities. Lattice energy (MAPLE) and bond-valence sum (BVS) calculations show that the structure is electrostatically well balanced. Infrared spectroscopy confirms the absence of N-H bonds.
Figure S4 from Modified RANO, Immunotherapy RANO, and Standard RANO Response to Convection-Enhanced Delivery of IL4R-Targeted Immunotoxin MDNA55 in Recurrent Glioblastoma (2023)

&lt;p&gt;Correlation between mRANO-defined PFS and OS excluding patients with PFS &gt; 120 days. (top) Correlation between radiographic PFS using the mRANO criteria applied to local measurements and OS for patients who died. (bottom) Correlation between radiographic PFS using the mRANO criteria applied to IRF-determined measurements and OS for patients who died. Open circles = patients who were censored (not used in correlation analysis, only for visualization purposes).&lt;/p&gt;
Multi-Task Learning for Extraction of Adverse Drug Reaction Mentions\n from Tweets (2018)

Adverse drug reactions (ADRs) are one of the leading causes of mortality in\nhealth care. Current ADR surveillance systems are often associated with a\nsubstantial time lag before such events are officially published. On the other\nhand, online social media such as Twitter contain information about ADR events\nin real-time, much before any official reporting. Current state-of-the-art in\nADR mention extraction uses Recurrent Neural Networks (RNN), which typically\nneed large labeled corpora. Towards this end, we propose a multi-task learning\nbased method which can utilize a similar auxiliary task (adverse drug event\ndetection) to enhance the performance of the main task, i.e., ADR extraction.\nFurthermore, in the absence of auxiliary task dataset, we propose a novel joint\nmulti-task learning method to automatically generate weak supervision dataset\nfor the auxiliary task when a large pool of unlabeled tweets is available.\nExperiments with 0.48M tweets show that the proposed approach outperforms the\nstate-of-the-art methods for the ADR mention extraction task by 7.2% in terms\nof F1 score.\n
Experimental dynamics of Akhmediev breathers in a dispersion varying optical fiber (2014)

We investigate experimentally the dynamics of Akhmediev breathers in an optical fiber with a longitudinally tailored dispersion that allows to nearly freeze the breather evolution near their point of maximal compression. Our results are in good agreement with numerical simulations.
Spectral shape analysis of ultraviolet luminescence in n-type ZnO:Ga (2005)

Thin films of laser molecular-beam epitaxy grown n-type Ga-doped ZnO were investigated with respect to their optical properties. Intense room-temperature photoluminescence (PL) in the near-band edge (NBE) region was observed. Moreover, its broadening of PL band was significantly larger than predicted by theoretical results modeled in terms of potential fluctuations caused by the random distribution of donor impurities. In addition, the line shape was rather asymmetrical. To explain these features of the NBE bands, a vibronic model was developed accounting for contributions from a series of phonon replicas.
Local Slot Attention for Vision and Language Navigation (2022)

Vision-and-language navigation (VLN), a frontier study aiming to pave the way for general-purpose robots, has been a hot topic in the computer vision and natural language processing community. The VLN task requires an agent to navigate to a goal location following natural language instructions in unfamiliar environments.
Uncertainty evaluation in measurement equipments for power systems (2016)

This paper presents the study of the propagation of the effects of uncertainties arising in two key elements of a measurement equipment for modern power systems. The first element is the LPIT (Low Power Instrument Transformer), which is the first element of the measurement chain that converts the primary quantities (voltage, current) into a low-value, low power voltage. The second element is the SAMU (Stand Alone Merging Unit), which collects all voltages from LPIT outputs and converts them into digital form, according to the 61850-9-2 protocol. The characteristics of the LPIT and SAMU will be described in the next IEC Standards 61869-6 and 61869-13, respectively. Both Standards are in the final stage of their preparation. In particular, in 61869-13 a Section is dedicated to the method (suitable and comprehensible by system operators) for evaluating the combined standard uncertainty of LPIT-SAMU. In this paper such a method will be presented along with its use and implementation in practical applications.
CD137 Signaling Regulates Acute Colitis via RALDH2-Expressing CD11b−CD103+ DCs (2020)

CD137, a potent costimulatory receptor for CD8<sup>+</sup> T cells, is expressed in various non-T cells, but little is known about its regulatory functions in these cells. In this study, we show that CD137 signaling, specifically in intestinal CD11b<sup>-</sup>CD103<sup>+</sup> dendritic cells (DCs), restricts acute colitis progression. Mechanistically, CD137 engagement activates TAK1 and subsequently stimulates the AMPK-PGC-1α axis to enhance expression of the Aldh1a2 gene encoding the retinoic acid (RA) metabolizing enzyme RALDH2. RA can act on CD11b<sup>+</sup>CD103<sup>-</sup> DCs and induce SOCS3 expression, which, in turn, suppresses p38MAPK activation and interleukin-23 (IL-23) production. Administration of RA in DC-specific CD137<sup>-/-</sup> mice represses IL-23-producing CD11b<sup>+</sup>CD103<sup>-</sup> DCs and T<sub>H</sub>17 cells, indicating that RA is a major inhibitory effector molecule against intestinal CD11b<sup>+</sup>CD103<sup>-</sup> DCs. Additionally, the therapeutic effect of the anti-CD137 antibody is abrogated in DC-specific CD137<sup>-/-</sup> mice. Taken together, our results define a mechanism of paracrine immunoregulation operating between adjacent DC subsets in the intestine.
Deep submicron CMOS transistors for low-noise front-end systems (2005)

This paper presents a study of the noise behavior of submicron CMOS transistors, in view of applications to high density mixed-signal front-end systems for high granularity detectors. The goal of this work is extending the knowledge in this field, presently focused on 0.25 /spl mu/m processes, to the following generation of CMOS technologies (with 0.18 /spl mu/m minimum gate length). The white component of the noise voltage spectrum, which is most important for fast signal processing, and the 1/f noise contribution are experimentally characterized with noise measurements in a wide frequency range. A comparison with similar noise measurements on CMOS devices belonging to a 0.35 /spl mu/m process allows estimating the impact of gate length scaling on both white and 1/f noise components. The noise radiation tolerance is also a key parameter for many front-end systems, and it was evaluated by exposing the devices to high doses of ionizing radiation.
Reovirus Virotherapy Overrides Tumor Antigen Presentation Evasion and Promotes Protective Antitumor Immunity (2010)

Tumor-associated immunosuppressive strategies, such as lack of tumor antigen recognition and failure of lymphocyte activation and homing, resist the development of tumor-specific immunity and hamper the immune response-mediated elimination of cancerous cells. In this report, we show that reovirus virotherapy overrides such a tumor immune evasion and establishes clinically meaningful antitumor immunity capable of protecting against subsequent tumor challenge. Reovirus-mediated destruction of tumor cells facilitates the recognition of tumor antigens by promoting the display of otherwise inaccessible tumor-specific immunogenic peptides on the surface of dendritic cells (DC). Furthermore, on exposure to reovirus, DCs produce IL-1α, IL-1β, IL-6, IL-12p40/70, IL-17, CD30L, eotaxin, GM-CSF, KC, MCP-1, MCP-5, M-CSF, MIG, MIP-1α, RANTES, TNF-α, VCAM-1, VSGF, CXCL-16, AXL, and MCP-2; undergo maturation; and migrate into the tumor microenvironment along with CD8 T cells. These reovirus-activated DCs also acquire the capacity to prime tumor antigen-specific transgenic T cells in vitro and intrinsic antitumor T-cell response in vivo. Further, reovirus virotherapy augments the efficacy of DC- or T cell-based anticancer immunotherapies and synergistically enhances the survival in tumor-bearing mice. Most importantly, antitumor cellular immune responses initiated during reovirus oncotherapy protect the host against subsequent tumor challenge in a reovirus-independent but antigen-dependent manner. These reovirus oncotherapy-initiated antitumor immune responses represent an anticancer therapeutic entity that can maintain a long-term cancer-free health even after discontinuation of therapy.
Agonist-induced Internalization of the Platelet-activating Factor Receptor Is Dependent on Arrestins but Independent of G-protein Activation (2002)

As with most G-protein-coupled receptors, repeated agonist stimulation of the platelet-activating factor receptor (PAFR) results in its desensitization, sequestration, and internalization. In this report, we show that agonist-induced PAFR internalization is independent of G-protein activation but is dependent on arrestins and involves the interaction of arrestins with a limited region of the PAFR C terminus. In cotransfected COS-7 cells, both arrestin-2 and arrestin-3 could be coimmunoprecipitated with PAFR, and agonist stimulation of PAFR induced the translocation of both arrestin-2 and arrestin-3. Furthermore, coexpression of arrestin-2 with PAFR potentiated receptor internalization, whereas agonist-induced PAFR internalization was inhibited by a dominant negative mutant of arrestin-2. The coexpression of a minigene encoding the C-terminal segment of the receptor abolished PAF-induced arrestin translocation and inhibited PAFR internalization. Using C terminus deletion mutants, we determined that the association of arrestin-2 with the receptor was dependent on the region between threonine 305 and valine 330 because arrestin-2 could be immunoprecipitated with the mutant PAFRstop330 but not PAFRstop305. Consistently, stop330 could mediate agonist-induced arrestin-2 translocation, whereas stop305 could not. Two other deletion mutants with slightly longer regions of the C terminus, PAFRstop311 and PAFRstop317, also failed to induce arrestin-2 translocation. Finally, the PAFR mutant Y293A, containing a single substitution in the putative internalization motif DPXXY in the seventh transmembrane domain (which we had shown to be able to internalize but not to couple to G-proteins) could efficiently induce arrestin translocation. Taken together, our results indicate that ligand-induced PAFR internalization is dependent on arrestins, that PAFR can associate with both arrestin-2 and -3, and that their translocation involves interaction with the region of residues 318-330 in the PAFR C terminus but is independent of G-protein activation.
Disentangling Origins of Adhesive Bonding at Interfaces between Epoxy/Amine Adhesive and Aluminum (2023)

Joining metals by adhesive bonding is essential in widespread fields such as mobility, dentistry, and electronics. Although adhesive technology has grown since the 1920s, the roles of interfacial phenomena in adhesive bonding are still elusive, which hampers the on-demand selection of surface treatment and adhesive types. In the present study, we clarified how chemical interactions and mechanical interlocking governed adhesive bonding by evaluating adhesion properties at the interfaces between epoxy/amine adhesive and two kinds of Al adherends: a flat aluminum hydroxide (Al<i><sub>x</sub></i>O<i><sub>y</sub></i>H<i><sub>z</sub></i>) and technical Al plate with roughness. Spectroscopic and microscopical data demonstrate that the protonation of the amino groups in an amine hardener converts Al(OH)<sub>3</sub> on the Al<i><sub>x</sub></i>O<i><sub>y</sub></i>H<i><sub>z</sub></i> surface to AlO(OH). The interfacial protonation results in an interfacial dipole layer with positive charges on the adhesive side, whose electrostatic interaction increases the interfacial fracture energy. The double cantilever beam tests for the flat Al<i><sub>x</sub></i>O<i><sub>y</sub></i>H<i><sub>z</sub></i> and technical Al substrates clarify that the mechanical interlocking originating from the surface roughness further increases the fracture energy. This study disentangles the roles of the chemical interactions and mechanical interlocking occurring at the epoxy adhesive/Al interface in the adhesion mechanism.
Abstract 2950: miR-34 prevents <i>in vivo</i> lung tumor initiation and progression in the therapeutically resistant Kras;p53 mouse model (2012)

Abstract Lung cancer represents the leading cause of cancers deaths in men and women worldwide, and current therapies fail to treat this disease in the overwhelming majority of cases. The RAS and p53 pathways are two of the most frequently genetically modified pathways in lung cancers. Alterations in both result in loss of responsiveness to current therapies leading to decreased overall patient survival. Because the microRNA, mir-34 is a downstream transcriptional target of p53, which is reduced in its expression in p53 null tumors, we hypothesized that targeting Kras;p53 tumors with miR-34 would represent a novel yet powerful therapeutic to suppress lung tumorigenesis. To this end we have made use of the therapeutically resistant KrasLSL-G12D/+;p53LSL-R172H/+ mouse model of lung cancer. In this work we characterized the tumor progression in these mice following transgene activation specifically in the lung through intratracheal administration of adenoviral particles expressing cre recombinase. We note that adenocarcinomas are evident as early as 10 weeks following cre-recombination with severe lung inflammation presenting at 22 weeks. Epithelial cells from these tumors were harvested and cultured in vitro where they remain propagating, currently at passage 45. All three lines generated support growth in soft agar assays and are invasive based on transwell migration assays. Because of the pro-apoptotic effects of miR-34, we transduced the cells with miR-34-expressing lentivirus. Transduced cells responded with reduced proliferation and decreased migration. Based on these promising results we began two series of in vivo experiments. We first assessed the contribution of miR-34 to prevent tumor formation in KrasLSL-G12D/+;p53LSL-R172H/+ mice. Animals that were treated with miR-34 at the same time as cre-induced recombination of transgenes show little to no evidence of tumorigenesis at 19 weeks, while control animals had multiple nodules that represented ∼8% of the total lung area. The second series of in vivo experiments evaluated the ability of miR-34 to act as a treatment in pre-formed tumors. While miR-34 was unable to reduce the preformed tumors in these animals it was able to prevent further tumor growth. These data support the use of miR-34 as a tumor preventive mechanism and suggest that miR-34 may be useful in sensitizing tumors to other conventional therapeutics. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2950. doi:1538-7445.AM2012-2950
Inhibition of pokeweed mitogen-induced B cell differentiation by compounds containing primary amine or hydrazine groups. (1985)

The present study examined the effect of two drugs, which contain either an aromatic amine or hydrazine moiety and are known to induce lupus like syndromes in man (procainamide and hydralazine) and an aliphatic amine (dansylcadaverine), on pokeweed mitogen (PWM)-induced B cell production of immunoglobulin G (IgG). These compounds all inhibited IgG production and generation of IgG plaque forming cells, whereas derivatives of them, without free amine groups, had little or no effect. The compounds inhibited differentiation of B cells to plasma cells, rather than production and secretion of IgG. Mitogen free culture supernatants of peripheral blood mononuclear cells (PBM) activated by the oxidizing mitogen, neuraminidase and galactose oxidase (NAGO), prevented the inhibition of B cell maturation. Moreover, incubation of NAGO treated PBM with hydralazine prevented the production of soluble factors capable of promoting B cell maturation in the presence of hydralazine. We conclude from these studies that procainamide, hydralazine and dansylcadaverine inhibit PWM-induced B cell maturation to plasma cells by an indirect mechanism, via inhibition of production of lymphokines by helper cells. The primary amine or hydrazine group appears to be required for the inhibitory effect, since analogues of the inhibitory compounds, without primary amine groups, are non-inhibitory.
Chemical genomics reveals histone deacetylases are required for core regulatory transcription (2019)

Identity determining transcription factors (TFs), or core regulatory (CR) TFs, are governed by cell-type specific super enhancers (SEs). Drugs to selectively inhibit CR circuitry are of high interest for cancer treatment. In alveolar rhabdomyosarcoma, PAX3-FOXO1 activates SEs to induce the expression of other CR TFs, providing a model system for studying cancer cell addiction to CR transcription. Using chemical genetics, the systematic screening of chemical matter for a biological outcome, here we report on a screen for epigenetic chemical probes able to distinguish between SE-driven transcription and constitutive transcription. We find that chemical probes along the acetylation-axis, and not the methylation-axis, selectively disrupt CR transcription. Additionally, we find that histone deacetylases (HDACs) are essential for CR TF transcription. We further dissect the contribution of HDAC isoforms using selective inhibitors, including the newly developed selective HDAC3 inhibitor LW3. We show HDAC1/2/3 are the co-essential isoforms that when co-inhibited halt CR transcription, making CR TF sites hyper-accessible and disrupting chromatin looping.
Robust Centerline Extraction Framework Using Level Sets (2005)

In this paper, we present a novel framework for computing centerlines for both 2D and 3D shape analysis. The framework works as follows: an object centerline point is selected automatically as the point of global maximum Euclidean distance from the boundary, and is considered a point source (Ps) that transmits a wave front that evolves over time and traverses the object domain. The front propagates at each object point with a speed that is proportional to its Euclidean distance from the boundary. The motion of the front is governed by a nonlinear partial differential equation whose solution is computed efficiently using level set methods. Initially, the P/sub S/ transmits a moderate speed wave to explore the object domain and extract its topological information such as merging and extreme points. Then, it transmits a new front that is much faster at centerline points than non central ones. As a consequence, centerlines intersect the propagating fronts at those points of maximum positive curvature. Centerlines are computed by tracking them, starting from each topological point until the Ps is reached, by solving an ordinary differential equation using an efficient numerical scheme. The proposed method is computationally inexpensive, handles efficiently objects with complex topology, and computes centerlines that are centered, connected, one point thick, and less sensitive to boundary noise. In addition, the extracted paths form a tree graph without additional cost. We have extensively validated the robustness of the proposed method both quantitatively and qualitatively against several 2D and 3D shapes.
Current multidisciplinary management of brain metastases (2020)

Brain metastasis (BM), the most common adult brain tumor, develops in 20% to 40% of patients with late-stage cancer and traditionally are associated with a poor prognosis. The management of patients with BM has become increasingly complex because of new and emerging systemic therapies and advancements in radiation oncology and neurosurgery. Current therapies include stereotactic radiosurgery, whole-brain radiation therapy, surgical resection, laser-interstitial thermal therapy, systemic cytotoxic chemotherapy, targeted agents, and immune-checkpoint inhibitors. Determining the optimal treatment for a specific patient has become increasingly individualized, emphasizing the need for multidisciplinary discussions of patients with BM. Recognizing and addressing the sequelae of BMs and their treatment while maintaining quality of life and neurocognition is especially important because survival for patients with BMs has improved. The authors present current and emerging treatment options for patients with BM and suggest approaches for managing sequelae and disease recurrence.