gebhart/patrepeval huggingface dataset:
Specialized Roles of the Conserved Subunit OST3/6 of the Oligosaccharyltransferase Complex in Innate Immunity and Tolerance to Abiotic Stresses (2013)

Asparagine-linked glycosylation of proteins is an essential cotranslational and posttranslational protein modification in plants. The central step in this process is the transfer of a preassembled oligosaccharide to nascent proteins in the endoplasmic reticulum by the oligosaccharyltransferase (OST) complex. Despite the importance of the catalyzed reaction, the composition and the function of individual OST subunits are still ill defined in plants. Here, we report the function of the highly conserved OST subunit OST3/6. We have identified a mutant in the OST3/6 gene that causes overall underglycosylation of proteins and affects the biogenesis of the receptor kinase EF-TU RECEPTOR involved in innate immunity and the endo-β-1,4-glucanase KORRIGAN1 required for cellulose biosynthesis. Notably, the ost3/6 mutation does not affect mutant variants of the receptor kinase BRASSINOSTEROID-INSENSITIVE1. OST3/6 deficiency results in activation of the unfolded protein response and causes hypersensitivity to salt/osmotic stress and to the glycosylation inhibitor tunicamycin. Consistent with its role in protein glycosylation, OST3/6 resides in the endoplasmic reticulum and interacts with other subunits of the OST complex. Together, our findings reveal the importance of Arabidopsis (Arabidopsis thaliana) OST3/6 for the efficient glycosylation of specific glycoproteins involved in different physiological processes and shed light on the composition and function of the plant OST complex.
The Origins of Genomic Duplications in Arabidopsis (2000)

Large segmental duplications cover much of the Arabidopsis thaliana genome. Little is known about their origins. We show that they are primarily due to at least four different large-scale duplication events that occurred 100 to 200 million years ago, a formative period in the diversification of the angiosperms. A better understanding of the complex structural history of angiosperm genomes is necessary to make full use of Arabidopsis as a genetic model for other plant species.
Supplementary Table 3 from Outlier Kinase Expression by RNA Sequencing as Targets for Precision Therapy (2023)

&lt;p&gt;XLSX file - 487K, Pancreatic sample kinome compendium by RNA-Seq.&lt;/p&gt;
Literature Fingerprinting: A New Method for Visual Literary Analysis (2007)

In computer-based literary analysis different types of features are used to characterize a text. Usually, only a single feature value or vector is calculated for the whole text. In this paper, we combine automatic literature analysis methods with an effective visualization technique to analyze the behavior of the feature values across the text. For an interactive visual analysis, we calculate a sequence of feature values per text and present them to the user as a characteristic fingerprint. The feature values may be calculated on different hierarchy levels, allowing the analysis to be done on different resolution levels. A case study shows several successful applications of our new method to known literature problems and demonstrates the advantage of our new visual literature fingerprinting.
Linearly polarized light emission from InGaN light emitting diode with subwavelength metallic nanograting (2009)

Surface emitting linearly polarized InGaN/GaN light emitting diode (LED) is demonstrated using a subwavelength metallic nanograting. The aluminum based grating with a period of 150 nm is fabricated on top of the p-contact layer in a conventional InGaN LED structure grown on (0001) oriented sapphire substrate. Polarization ratio can reach 7:1, the highest ever reported polarization ratio directly from a light emitting diode. The polarization characteristics are studied in details both experimentally and theoretically, suggesting an effective way to make polarized light emission devices.
Machine Learning-Guided Antibody Engineering That Leverages Domain Knowledge To Overcome The Small Data Problem (2023)

Abstract The application of Machine Learning (ML) tools to engineer novel antibodies having predictable functional properties is gaining prominence. Herein, we present a platform that employs an ML-guided optimization of the complementarity-determining region (CDR) together with a CDR framework (FR) shuffling method to engineer affinity-enhanced and clinically developable monoclonal antibodies (mAbs) from a limited experimental screen space (order of 10^2 designs) using only two experimental iterations. Although high-complexity deep learning models like graph neural networks (GNNs) and large language models (LLMs) have shown success on protein folding with large dataset sizes, the small and biased nature of the publicly available antibody-antigen interaction datasets is not sufficient to capture the diversity of mutations virtually screened using these models in an affinity enhancement campaign. To address this key gap, we introduced inductive biases learned from extensive domain knowledge on protein-protein interactions through feature engineering and selected model hyper parameters to reduce overfitting of the limited interaction datasets. Notably we show that this platform performs better than GNNs and LLMs on an in-house validation dataset that is enriched in diverse CDR mutations that go beyond alanine-scanning. To illustrate the broad applicability of this platform, we successfully solved a challenging problem of redesigning two different anti-SARS-COV-2 mAbs to enhance affinity (up to 2 orders of magnitude) and neutralizing potency against the dynamically evolving SARS-COV-2 Omicron variants.
Phase Coherent Electronics:  A Molecular Switch Based on Quantum Interference (2002)

The phenomenon of quantum mechanical interference may be used to control the conductivity of ballistic molecular wires. Using a simple model we demonstrate plausible effects and discuss its potential uses for constructing coherence-based molecular electronics.
Abstract 692: The BET inhibitor INCB054329 is synergistic with JAK1 inhibition in models of multiple myeloma (2015)

Abstract Bromodomain and Extra Terminal (BET) protein inhibitors have emerged as a potentially effective therapeutic option for multiple tumor types, through their ability to regulate expression of genes necessary for proliferation and survival. For example, multiple myeloma (MM) cells have been shown to be highly sensitive to BET inhibition due in large part to the ability of BET proteins to control transcription of c-myc, an oncogene known to be dysregulated in MM. Likewise, some inflammatory response and cytokine signaling pathways associated with MM (eg. IL-6/JAK/STAT pathway) have also been shown to be reliant on BET proteins. Therefore, inhibition of both BET proteins and the JAK/STAT signaling pathway may be beneficial to MM patients. Here we assess the in vitro and in vivo effects of combining clinical compounds that target BET proteins and JAK in multiple myeloma cell lines. Studies were performed using the potent pan-BET inhibitor INCB054329 and selective JAK1 inhibitors. When tested in cell proliferation assays, the combination of BET and JAK1 inhibitors displayed strong synergistic effects in the IL-6 dependent INA-6 MM cell line in vitro. Western blots also revealed that several pharmacodynamic (PD) markers including c-MYC, PIM-2 and phospho-STAT3 were further repressed with the combination than with single agents alone. Likewise, the c-MYC and p-STAT3 PD markers could also be increasingly repressed in vivo by combined administration of BET and JAK1 inhibitors in the INA-6 mouse xenograft model. In vivo efficacy experiments in the INA-6 model resulted in enhanced, synergistic tumor growth inhibition in the BET/JAK inhibitor cohort as compared with the single drug cohorts. Interestingly, the cytokine independent MM1.S cell line was also sensitive to the BET/JAK inhibitor combination in vivo, while being far less sensitive to JAK1 inhibition as a monotherapy. In the MM1.S model, the c-MYC and p-STAT3 PD markers also behaved as seen in the INA-6 model. Our data indicate that the pharmacological inhibition of BET proteins and JAK1 yields strong combinatorial effects in MM cell lines both in vitro and in vivo. Therefore, dual inhibition of BET proteins and the JAK/STAT signaling pathway may offer a novel therapeutic approach and suggest a potential clinical utility for this drug combination in MM. Citation Format: Matthew C. Stubbs, Xuesong M. Liu, Xiaoming Wen, Jun Li, Valerie Dostalik, Sybil O'Connor, Eian Caulder, Margaret Favata, Mark Rupar, Yu Li, Beth Rumberger, Thomas Maduskuie, Richard Sparks, Nikoo Falahatpisheh, Padmaja Polam, Kris Vaddi, Timothy Burn, Andrew P. Combs, Wenqing Yao, Reid Huber, Gregory Hollis, Peggy Scherle, Phillip CC Liu. The BET inhibitor INCB054329 is synergistic with JAK1 inhibition in models of multiple myeloma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 692. doi:10.1158/1538-7445.AM2015-692
Preparation and characterization of green bio-composites based on modified spinifex resin and spinifex grass fibres (2013)

Many researchers are now working on composites systems where the fibers and polymers are either totally or predominantly based on renewable materials. The aim of this study is to develop renewable resource-based composites based on spinifex fibers and a polyurethane matrix prepared primarily from spinifex resin. Chemically cleaned and cryo-ground spinifex grass fibres have been used as a reinforcing phase in thermoplastic polyurethane prepared from spinifex resin biopolymer. The morphology, thermal and mechanical properties of the prepared composites were characterized using attenuated total reflection Fourier transform infrared spectroscopy, scanning electron microscopy, differential scanning calorimetry, thermogravimetric analysis and tensile tests. The results obtained by various characterization techniques indicate that interfacial interaction between the spinifex grass fillers and the polyurethane matrix occurs and that the ground spinifex cellulose fillers act as promising reinforcement for the relatively weak polyurethane matrix synthesized from renewable spinifex plant resin products.
Design of Neuraminidase-Targeted Imaging and Therapeutic Agents for the Diagnosis and Treatment of Influenza Virus Infections (2021)

The last step in influenza virus replication involves the assembly of viral components on the infected cell's plasma membrane followed by budding of intact virus from the host cell surface. Because viral neuraminidase and hemagglutinin are both inserted into the host cell's membrane during this process, influenza virus-infected cells are distinguished from uninfected cells by the presence of viral neuraminidase and hemagglutinin on their cell surfaces. In an effort to exploit this difference in cell surface markers for development of diagnostic and therapeutic agents, we have modified an influenza neuraminidase inhibitor, zanamivir, for targeting of attached imaging and therapeutic agents selectively to influenza viruses and virus-infected cells. We have designed here a zanamivir-conjugated rhodamine dye that allows visual monitoring of binding, internalization, and intracellular trafficking of the fluorescence-labeled neuraminidase in virus-infected cells. We also synthesize a zanamivir-<sup>99m</sup>Tc radioimaging conjugate that permits whole body imaging of the virus's biodistribution and abundance in infected mice. Finally, we create both a zanamivir-targeted cytotoxic drug (i.e., zanamivir-tubulysin B) and a viral neuraminidase-targeted CAR T cell and demonstrate that they are both able to kill viral neuraminidase-expressing cells without damaging healthy cells. Taken together, these data suggest that the influenza virus neuraminidase inhibitor, zanamivir, can be exploited to improve the diagnosis, imaging, and treatment of influenza virus infections.
Sharp-rejection highpass and dual-band bandpass planar filters with multi-transmission-zero-generation transversal cell (2015)

A method to produce multiple transmission zeros (TZs) is applied to design sharp-rejection planar highpass filters (HPFs) and dual-passband filters (BPFs). It consists of adding an external transversal cell to a basic filter to create TZs in its response without damaging its in-band amplitude and group-delay variation. Thus, contrary to other filter design techniques, in-band requisites and stopband TZ creation can be separately addressed in the entire filter synthesis process. Such technique could have great potential in other technologies, such as waveguide filters for satellite communications, in which low in-band group-delay variation and adjustable high selectivity are necessary. Measurements for a microstrip HPF and simulations for a stripline dual-band BPF are shown.
The BOLD sensitivity of rapid steady‐state sequences (2018)

The BOLD effect measured in steady-state sequences is most sensitive to microvessels and might therefore be closer to the underlying neuronal event compared to gradient echo sequences.
Efficacy and safety of autologous expanded tumor infiltrating lymphocytes (TILs) in multiple solid tumors. (2022)

2536 Background: TIL therapy has been used extensively in metastatic melanoma patients for many years, now with ongoing efforts to commercialize treatment. The efficacy of TIL outside of melanoma is largely unknown thus we designed and implemented a trial using TIL manufactured at a single academic center for treatment refractory metastatic colorectal (CRC), pancreas (PDAC) and ovarian (OVA) cancers. Methods: Patients with CRC, PDAC and OVA refractory to standard therapies with ECOG PS 0-1 and normal organ function were eligible for TIL harvest. Ex vivo TIL expansion and manufacturing was conducted at the MD Anderson TIL lab under conditions that included IL2 and 41BB stimulation (using urelumab). All patients received a lymphodepletion regimen consisting of cyclophosphamide 60mg/kg days -7 and -6 and fludarabine 25mg/m2 days -5 through day -1, followed by infusion of pooled ex-vivo expanded TIL. Patients received up to 6 doses of high dose IL-2 (600,000 IU/kg) after TIL infusion. The primary endpoint was evaluation of the objective response rate (ORR) using RECIST 1.1 criteria with secondary endpoints including disease control rate, duration of response, PFS, OS and safety. Results: A total of 17 patients underwent TIL harvest and 16 were treated on protocol; including 8 CRC, 5 PDAC and 3 OVA. Median age was 57.5 (range 33-70) and 50% were females. Median number of lines of prior therapy was 2 (range 1-8). Median number of TIL infused was 76 X 10 9 (range 20.3 x 10 9 -150 x 10 9 ). Median doses of cyclophosphamide and fludarabine administered were 2 (range, 2-2) and 3 (range, 1-5), respectively. Median doses of IL-2 administered was 6 (range, 1-6). There were no responders. Best response included prolonged SD in a patient with PDAC lasting until 18 months. Grade 3 or higher toxicities attributable to therapy was seen in 14 subjects (87.5%; 95% CI: 61.7 – 98.4) with the majority of toxicities representing expected pancytopenia from lymphodepletion. Infusion product analysis showed the presence of effector memory cells with high expression of CD39 irrespective of tumor type. Early on-treatment biopsy of PDAC patient with prolonged SD showed presence of proliferating (KI67+) CD4+ and CD8+ TIL. Conclusions: Generation of TIL at a single academic center for CRC, PDAC and OVA is feasible and treatment is associated with no new safety signals. For these tumor types, further research is required to identify host factors associated with resistance to TIL therapy and optimize manufacturing processes to create more effective TIL cell therapy. Clinical trial information: NCT03610490.
"Erfahrung & Erlebnis" (2020)

Bodily play systems are becoming increasingly prevalent, with research aiming to understand the associated player experience. We argue that a more nuanced lexicon describing "bodily play experience" can be beneficial to drive the field forward. We provide game designers with two German words to communicate two different aspects of experience: "Erfahrung", referring to experience where one is actively engaged in and gains knowledge from; and "Erlebnis", referring to a tacit experience often translated as "lived experience". We use these words to articulate a suite of design strategies for bodily play experiences by referring to past design work. We conclude by discussing these two aspects of experience in conjunction with two previously established perspectives on the human body. We believe this more nuanced lexicon can provide a clearer understanding for designers about bodily play allowing them to guide players in gaining the many benefits from such experiences.
Pd-Catalysed Direct 5-Arylation of 1-Methylpyrazole with Aryl Bromides (2011)

International audience
Stereolithographic 3D printing of extrinsically self-healing composites (2019)

We demonstrate for the first time the direct stereolithographic 3D printing of an extrinsically self-healing composite, comprised of commercial photocurable resin modified with anisole and PMMA-filled microcapsules. The composites demonstrate solvent-welding based autonomous self-healing to afford 87% recovery of the initial critical toughness. This work illustrates the potential of stereolithographic printing to fabricate self-healing composites with user-defined structures, avoiding the need for extensive rheological optimization of printing inks, like in direct-write 3D printing. Importantly, this work also demonstrates the inclusion of microcapsules into 3D printing resins to incorporate additional functionality into printed composites, which could be adapted for applications beyond self-healing materials.
Acute ammonia toxicity is mediated by the NMDA type of glutamate receptors (1992)

Previous experiments in our laboratory suggested that ammonium toxicity could be mediated by the NMDA type of glutamate receptors. To assess this hypothesis we tested if MK-801, a specific antagonist of the NMDA receptor, is able to prevent ammonium toxicity. Mice and rats were injected i.p. with 12 and 7 mmol/kg of ammonium acetate, respectively. 73% of the mice and 70% of the rats died. However, when the animals were injected i.p. with 2 mg/kg of MK-801, 15 min before ammonium injection, only 5% of the mice and 15% of the rats died. The remarkable protection afforded by MK-801 indicates that ammonia toxicity is mediated by the NMDA receptor.
Direct Observation of Singlet Phenylnitrene and Measurement of Its Rate of Rearrangement (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDirect Observation of Singlet Phenylnitrene and Measurement of Its Rate of RearrangementNina P. Gritsan, Tetsuro Yuzawa, and Matthew S. PlatzView Author Information Newman and Wolfrom Laboratory of Chemistry The Ohio State University, 100 West 18th Avenue Columbus, Ohio 43210 Institute of Chemical Kinetics and Combustion 630090 Novosibirsk, Russia Cite this: J. Am. Chem. Soc. 1997, 119, 21, 5059–5060Publication Date (Web):May 28, 1997Publication History Received28 October 1996Published online28 May 1997Published inissue 1 May 1997https://doi.org/10.1021/ja963753nCopyright © 1997 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views529Altmetric-Citations79LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (140 KB) Get e-AlertsSUBJECTS:Absorption,Kinetic parameters,Light absorption,Phenyls,Rearrangement Get e-Alerts
A new approach to the discrete logarithm problem with auxiliary inputs (2016)

The aim of the discrete logarithm problem with auxiliary inputs is to solve for ${\it\alpha}$ , given the elements $g,g^{{\it\alpha}},\ldots ,g^{{\it\alpha}^{d}}$ of a cyclic group $G=\langle g\rangle$ , of prime order $p$ . The best-known algorithm, proposed by Cheon in 2006, solves for ${\it\alpha}$ in the case where $d\mid (p\pm 1)$ , with a running time of $O(\sqrt{p/d}+d^{i})$ group exponentiations ( $i=1$ or $1/2$ depending on the sign). There have been several attempts to generalize this algorithm to the case of ${\rm\Phi}_{k}(p)$ where $k\geqslant 3$ . However, it has been shown by Kim, Cheon and Lee that a better complexity cannot be achieved than that of the usual square root algorithms. We propose a new algorithm for solving the DLPwAI. We show that this algorithm has a running time of $\widetilde{O}(\sqrt{p/{\it\tau}_{f}}+d)$ group exponentiations, where ${\it\tau}_{f}$ is the number of absolutely irreducible factors of $f(x)-f(y)$ . We note that this number is always smaller than $\widetilde{O}(p^{1/2})$ . In addition, we present an analysis of a non-uniform birthday problem.
Biosensors: Label‐Free Colorimetric Detection of Nucleic Acids Based on Target‐Induced Shielding Against the Peroxidase‐Mimicking Activity of Magnetic Nanoparticles (Small 11/2011) (2011)

The cover image illustrates how target polymerase chain reaction (PCR) products shield the peroxidase mimicking activity of magnetic nanoparticles (MNPs), leading to a significantly reduced colorimetric signal as compared to the intense colorimetric response by the normal peroxidase activity of MNPs. In the case where PCR products are not formed because a target DNA is absent, MNPs display their normal peroxidase activity generating the red color. On the other hand, peroxidase activity is significantly reduced in the presence of target DNA because the resulting PCR products greatly diminish the accessibility of the colorimetric substrate, o-phenylenediamine. In addition, DNA directly adsorbs onto the surface of MNPs, leading to significant inhibition of the substrate binding to the MNPs, which is required for the peroxidaselike reaction. As a result, the colorimetric substrate is not converted to a red product, retaining its original yellow color. For more information, please read the Communication “Label-Free Colorimetric Detection of Nucleic Acids Based on Target-Induced Shielding Against the Peroxidase-Mimicking Activity of Magnetic Nanoparticles” by H. G. Park and co-workers, beginning on page 1521.
Targeted Discovery of Cryptic Enediyne Natural Products via FRET-coupled High-Throughput Elicitor Screening (2023)

Enediyne antibiotics are a striking family of DNA-cleaving natural products with high degrees of cytotoxicity and structural complexity. Microbial genome sequences that have recently accumulated point to an untapped trove of ‘cryptic’ enediynes. Most of the cognate biosynthetic gene clusters (BGCs) are sparingly expressed under standard growth conditions, making it difficult to characterize their products. Herein, we report a fluorescence-based DNA cleavage assay coupled to high-throughput elicitor screening for the rapid, targeted discovery of cryptic enediyne metabolites. We applied the approach to Streptomyces clavuligerus, which harbors two such BGCs with unknown products, identified steroids as effective elicitors, and characterized ten cryptic enediyne-derived natural products, termed clavulynes A-J with unusual carbonate and terminal olefin functionalities. Our results contribute to the growing repertoire of enediynes and provide a blueprint for identifying additional ones in the future