gebhart/patrepeval huggingface dataset:
Novel Lobophorins Inhibit Oral Cancer Cell Growth and Induce Atf4- and Chop-Dependent Cell Death in Murine Fibroblasts (2015)

As part of the International Cooperative Biodiversity Groups (ICBG) Program, we were interested in identifying biologically active unfolded protein response (UPR) inducing compounds from marine microorganisms isolated from Costa Rican biota. With this aim in mind we have now generated more than 33,000 unique prefractionated natural product extracts from marine and terrestrial organisms that have been submitted to the Center of Chemical Genomics (CCG) at the University of Michigan for high throughput screening (HTS). An effective complementary cell-based assay to identify novel modulators of UPR signaling was used for screening extracts. Active fractions were iteratively subjected to reverse-phase HPLC chromatographic analysis, and together with lobophorin A, B, E, and F (1-4), three new lobophorin congeners, designated as CR1 (5), CR2 (6), and CR3 (7) were isolated. Herein, we report that secondary assays revealed that the new lobophorins induced UPR-associated gene expression, inhibited oral squamous cell carcinoma cell growth, and led to UPR-dependent cell death in murine embryonic fibroblast (MEF) cells.
Search for the Higgs Boson in theH→WW(*)→l+νl−ν¯Decay Channel inppCollisions ats=7  TeVwith the ATLAS Detector (2012)

A search for the Higgs boson has been performed in the H→WW(*)→ℓ(+)νℓ(-)ν[over ¯] channel (ℓ=e/μ) with an integrated luminosity of 2.05 fb(-1) of pp collisions at √s=7 TeV collected with the ATLAS detector at the Large Hadron Collider. No significant excess of events over the expected background is observed and limits on the Higgs boson production cross section are derived for a Higgs boson mass in the range 110 GeV<m(H)<300 GeV. The observations exclude the presence of a standard model Higgs boson with a mass 145<m(H)<206 GeV at 95% confidence level.
Lasso-Based Fast Residual Recovery For Modulo Sampling (2023)

In practice, Analog-to-Digital Converter (ADC) is used to perform sampling. A practical bottleneck of ADC is its lower dynamic range, leading to loss of information. To address this issue, researchers suggested folding operation on the signal using a modulo operator before passing it as an input to ADC. Though this process preserves the signal information, an unfolding algorithm is required to get the true samples from the folded samples. Noise robustness and computational time are two key parameters of an unfolding algorithm. In this paper, we propose a fast and robust algorithm for unfolding. Specifically, we first show that the first-order difference of the residual samples (the difference between the folded and true samples) is sparse by deriving an upper bound on its sparsity, and can be recovered from its partial Fourier measurements by formulating a sparse recovery problem. We demonstrate that the proposed algorithm is robust to noise and computationally efficient compared to the existing methods.
Asymmetric Catalysis Mediated by Synthetic Peptides (2007)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric Catalysis Mediated by Synthetic PeptidesElizabeth A. Colby Davie, Steven M. Mennen, Yingju Xu, and Scott J. MillerView Author Information Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Assumption College, 500 Salisbury Street, Worcester, Massachusetts 01609 Cite this: Chem. Rev. 2007, 107, 12, 5759–5812Publication Date (Web):December 12, 2007Publication History Received23 May 2007Published online12 December 2007Published inissue 1 December 2007https://pubs.acs.org/doi/10.1021/cr068377whttps://doi.org/10.1021/cr068377wresearch-articleACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views12642Altmetric-Citations584LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Aldol reactions,Catalysts,Monomers,Peptides and proteins,Stereoselectivity Get e-Alerts
Evaluating quality and comprehension of real-time sign language video on mobile phones (2011)

Video and image quality are often objectively measured using peak signal-to-noise ratio (PSNR), but for sign language video, human comprehension is most important. Yet the relationship of human comprehension to PSNR has not been studied. In this survey, we determine how well PSNR matches human comprehension of sign language video. We use very low bitrates (10-60 kbps) and two low spatial resolutions (192×144 and 320×240 pixels) which may be typical of video transmission on mobile phones using 3G networks. In a national online video-based user survey of 103 respondents, we found that respondents preferred the 320×240 spatial resolution transmitted at 20 kbps and higher; this does not match what PSNR results would predict. However, when comparing perceived ease/difficulty of comprehension, we found that responses did correlate well with measured PSNR. This suggests that PSNR may not be suitable for representing subjective video quality, but can be reliable as a measure for comprehensibility of American Sign Language (ASL) video. These findings are applied to our experimental mobile phone application, MobileASL, which enables real-time sign language communication for Deaf users at low bandwidths over the U.S. 3G cellular network.
Receptor class desensitization of leukocyte chemoattractant receptors. (1991)

To better define their regulation, formylpeptide and C5a chemoattractant receptor cDNAs were transiently expressed with high efficiency (approximately 35-54%) in human kidney cells. As in neutrophils, both receptors were active in elevating intracellular calcium (ED50 approximately 0.5-1 nM). Agonist-specific desensitization for calcium elevation was observed for both chemoattractant receptors at doses of approximately 1 nM. Heterologous desensitization of formylpeptide, C5a, and alpha 1-adrenergic receptors required high doses of phorbol ester (100 nM phorbol 12-myristate 13-acetate). To further study the phenomenon of desensitization, formylpeptide and C5a receptor cDNAs were cotransfected resulting in approximately 80% of receptor-positive cells expressing both receptors. These cells also possessed endogenous alpha 1-adrenergic receptors. Interestingly, chemoattractant receptors were cross-desensitized by pretreatment with low doses of either C5a or formylmethionylleucylphenylalanine (10 nM) but not by the alpha 1-adrenergic agonist norepinephrine (up to 10 microM). Neither chemoattractant desensitized alpha 1-adrenergic receptors. This phenomenon was reproduced in human neutrophils. These data suggest a previously uncharacterized mechanism of receptor regulation, which is intermediate between homologous and heterologous desensitization. Class desensitization of chemoattractant receptors is less selective than homologous desensitization but is far more efficient and specific than heterologous desensitization. Receptor class desensitization may affect functional classes of receptors via modification of either the receptor or the shared guanine nucleotide-binding regulatory protein.
Role of CD4 T cell helper subsets in immune response and deviation of CD8 T cells in mice* (2017)

The ability of different CD4<sup>+</sup> T cell subsets to help CD8<sup>+</sup> T-cell response is not fully understood. Here, we found using the murine system that Th17 cells induced by IL-1β, unlike Th1, were not effective helpers for antiviral CD8 responses as measured by IFNγ-producing cells or protection against virus infection. However, they skewed CD8 responses to a Tc17 phenotype. Thus, the apparent lack of help was actually immune deviation. This skewing depended on both IL-21 and IL-23. To overcome this effect, we inhibited Th17 induction by blocking TGF-β. Anti-TGF-β allowed the IL-1β adjuvant to enhance CD8<sup>+</sup> T-cell responses without skewing the phenotype to Tc17, thereby providing an approach to harness the benefit of common IL-1-inducing adjuvants like alum without immune deviation.
Multi-dose Romidepsin Reactivates Replication Competent SIV in Post-antiretroviral Rhesus Macaque Controllers (2016)

Viruses that persist despite seemingly effective antiretroviral treatment (ART) and can reinitiate infection if treatment is stopped preclude definitive treatment of HIV-1 infected individuals, requiring lifelong ART. Among strategies proposed for targeting these viral reservoirs, the premise of the "shock and kill" strategy is to induce expression of latent proviruses [for example with histone deacetylase inhibitors (HDACis)] resulting in elimination of the affected cells through viral cytolysis or immune clearance mechanisms. Yet, ex vivo studies reported that HDACis have variable efficacy for reactivating latent proviruses, and hinder immune functions. We developed a nonhuman primate model of post-treatment control of SIV through early and prolonged administration of ART and performed in vivo reactivation experiments in controller RMs, evaluating the ability of the HDACi romidepsin (RMD) to reactivate SIV and the impact of RMD treatment on SIV-specific T cell responses. Ten RMs were IV-infected with a SIVsmmFTq transmitted-founder infectious molecular clone. Four RMs received conventional ART for >9 months, starting from 65 days post-infection. SIVsmmFTq plasma viremia was robustly controlled to <10 SIV RNA copies/mL with ART, without viral blips. At ART cessation, initial rebound viremia to ~106 copies/mL was followed by a decline to < 10 copies/mL, suggesting effective immune control. Three post-treatment controller RMs received three doses of RMD every 35-50 days, followed by in vivo experimental depletion of CD8+ cells using monoclonal antibody M-T807R1. RMD was well-tolerated and resulted in a rapid and massive surge in T cell activation, as well as significant virus rebounds (~104 copies/ml) peaking at 5-12 days post-treatment. CD8+ cell depletion resulted in a more robust viral rebound (107 copies/ml) that was controlled upon CD8+ T cell recovery. Our results show that RMD can reactivate SIV in vivo in the setting of post-ART viral control. Comparison of the patterns of virus rebound after RMD administration and CD8+ cell depletion suggested that RMD impact on T cells is only transient and does not irreversibly alter the ability of SIV-specific T cells to control the reactivated virus.
Characterization of HIFU ablation using DNA fragmentation labeling as apoptosis stain (2012)

The goal of this work was to compare modalities to precisely quantify the extent of thermally induced lesions: gross pathology vs. histopathology vs. devascularization. Liver areas of 14 rabbits were targeted with HIFU and RF ablations in an acute study. Contrast enhanced computorized tomography (CE-CT) scan images were acquired two hours after HIFU and RF treatment to obtain the devascularized volumes of the livers. The animals were then euthanized and deep frozen. The livers were sliced and each slice was photographed and stacked yielding a volume of gross pathology. The volume VGP of the HIFU lesions were derived. The area AGP of the lesions were computed on a particular slice. The lesions were segmented as hypo intense (devascularized) regions on CE-CT images and their volumes VC were computed. The ratios VC/VGP were computed for all the HIFU lesions on all the 14 subjects with a mean value of 1.2. Histology was performed on the livers using Hematoxyline Eosine Staining (HES) and DNA Fragmentation labeling (TUNEL® technology) which characterizes apoptosis. Apoptotic regions of area AT were segmented on the images stained by TUNEL®. No necrosis was identified on the HES data. While TUNEL® did not mark the cores of the RF lesions as apoptotic, the periphery of HIFU and RF lesions was always recognized with TUNEL® as apoptotic. The ratio AGP/AT was computed. The mean value was 0.95 and 0.25 for HIFU and RF lesions respectively. These findings show that the devascularized territory seen on CE-CT scan coincide with the coagulated territories seen with gross pathology. Those actually correspond to cells in apoptosis. It is confirmed that HES stain does not show necrosis 2 hours after thermal ablation. TUNEL® technology for DNA fragmentation labeling appears as a useful marker for thermally induced acute lesions in the liver.
Nanoalloy magnetic and optical properties, applications and structures: general discussion (2022)

Magnetic and optical properties of nanoalloys, part 1 Ewald Janssens opened discussion of the paper by Rolf Schäfer: From the deflection profiles of the superatomically behaving MSn12 clusters, you find using eqn (6) in the paper (https://doi.org/10.1039/d2fd00091a) a g-factor of 2.6–2.7
Abstract CT075: Tumor mutation status will predict metabolic response to metformin in lung cancer treated with stereotactic body radiation therapy (SBRT) (2016)

Abstract At present, there are over 100 clinical trials examining the role of metformin in malignancy, either alone or in combination with chemotherapy. However, despite significant preclinical data, trials examining the role of metformin as a radiosensitizer are few. Moreover, the effects of endogenous tumor mutations on response to metformin are unknown, as some data suggests that certain mutations (eg. TP53, STK11) may confer sensitivity to this agent. Finally, the effects of metformin on FDG-uptake in solid tumors is far from clear, as this agent can actually lead to an increased uptake of FDG in normal bowel. Because of these questions, we have designed an imagining-guided trial of 70 patients, randomized 6:1 in favor of metformin treatment in patients with non-small cell lung cancer to be treated with stereotactic body radiotherapy (SBRT). Patients receive either placebo or metformin at a loading dose of 1,000 mg per day for one week followed by 1-2 weeks of metformin at 2,000 mg per day. Prior to study entry, an FDG-PET scan is performed which is then repeated after 2-3 weeks of metformin treatment. Metformin or placebo is maintained throughout SBRT and the standard daily cone-beam CTs are taken. Metformin or placebo stops at the end of SBRT followed by an additional FDG-PET scan 6 months after completion of therapy. All tumors with available tissue will be subjected to targeted sequencing. The primary outcome is FDG-PET response following initial metformin or placebo monotherapy as well as at 6 months. Secondary outcomes include the effect of common mutations (TP53, STK11, Kras) on metformin FDG-PET response. Currently, 14 patients have been registered for this trial. We anticipate that this study will provide a unique insight on how metformin affects FDG-PET response, if this response is affected by tumor mutation status, and provide preliminary data on the clinical efficacy of metformin in the setting of SBRT. Citation Format: Heath D. Skinner, Thomas Guerrero, Brian Hobbs, Laurence Court, Paige L. Nitsch, John Heymach. Tumor mutation status will predict metabolic response to metformin in lung cancer treated with stereotactic body radiation therapy (SBRT). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr CT075.
Seed based systematic discovery of specific transcription factor target genes (2009)

Reliable prediction of specific transcription factor target genes is a major challenge in functional genomics. Current sequence‐based methods yield many false predictions due to the short and degenerated DNA‐binding motifs. Here, we describe a new systematic genome‐wide approach, the seed‐distribution‐distance method that searches large scale genome wide expression data for genes that are similarly expressed as known targets. This method is used to identify genes that are likely targets and thereby sequence‐based methods can focus on a subset of genes, giving rise to fewer false positive predictions. We show by cross‐validation that this method is robust in recovering specific target genes. Further, this method identifies genes with typical functions and binding motifs of the seed. The method is illustrated by predicting novel targets of the transcription factor NFkB. Among the new targets is optineurin, which plays a key role in the pathogenesis of acquired blindness caused by adult‐onset primary open‐angle glaucoma. We show experimentally that optineurin as well as other predicted genes are targets of NFkB. We present a robust and reliable method to enhance the genome‐wide prediction of specific transcription factor target genes that exploits the vast expression information available in public databases today. A public web interface for customized searches will be available.
Intercalated Organic−Inorganic Perovskites Stabilized by Fluoroaryl−Aryl Interactions (2002)

Crystals of several new hybrid tin(II) iodide-based perovskites, involving 2,3,4,5,6- pentafluorophenethylammonium or phenethylammonium cation bilayers and intercalated aryl or perfluoroaryl molecules, were grown by slow evaporation of a methanol solution containing the hybrid perovskite and the intercalating species. The (C(6)F(5)C(2)H(4)NH(3))(2)SnI(4).(C(6)H(6)) structure was solved at -75 degrees C in a monoclinic C2/c subcell [a = 41.089(12) A, b = 6.134(2) A, c = 12.245(3) A, beta = 94.021(5) degrees, Z = 4] and consists of sheets of corner-sharing distorted SnI(6) octahedra separated by bilayers of pentafluorophenethylammonium cations. The intercalated benzene molecules form a single well-ordered layer interposed between adjacent fluoroaryl cation layers. The corresponding hybrid with an unfluorinated organic cation and fluorinated intercalating molecule, (C(6)H(5)C(2)H(4)NH(3))(2)SnI(4).(C(6)F(6)), is isostructural [a = 40.685(4) A, b = 6.0804(6) A, c = 12.163(1) A, beta = 93.136(2) degrees, Z = 4]. For each intercalated system, close C...C contacts (3.44-3.50 A) between the aromatic cation and the intercalated molecule are indicative of a significant face-to-face interaction, similar to that found in the complex C(6)H(6).C(6)F(6). Crystal growth runs with the organic cation and prospective intercalating molecule either both fluorinated or both unfluorinated did not yield stable intercalated compounds, demonstrating the significance of fluoroaryl-aryl interactions in the current intercalated structures. Thermal analysis of (C(6)F(5)C(2)H(4)NH(3))(2)SnI(4).(C(6)H(6)) and (C(6)H(5)C(2)H(4)NH(3))(2)SnI(4).(C(6)F(6)) crystals yields, in addition to the characteristic transitions of the parent perovskite, endothermic transitions [12.6(5) and 32.1(8) kJ/mol, respectively] with an onset at 145 degrees C and a weight loss corresponding to the complete loss of the intercalated molecule. The relatively high deintercalation temperature (well above the boiling point of benzene and hexafluorobenzene) demonstrates the usefulness of the hybrid perovskites in providing a stable framework for the examination of the fluoroaryl-aryl interaction, as well as the potential importance of this interaction in tailoring new hybrid perovskites. UV-vis absorption measurements on (C(6)H(5)C(2)H(4)NH(3))(2)SnI(4).(C(6)F(6)) thin films indicate a small reversible wavelength shift to higher energy for the tin(II) iodide framework exciton peak (with respect to that of the parent perovskite spectrum), from 608(2) nm [2.04 eV] to 595(2) nm [2.08 eV], and a corresponding shift in the band edge position. This spectral shift can most reasonably be attributed to subtle structural changes induced in the tin(II) iodide sheets by the intercalated hexafluorobenzene molecules.
Photovoltaic performance of Gallium-doped ZnO thin film/Si nanowires heterojunction diodes (2016)

In this work, photovoltaic performance of Ga-doped ZnO thin film/Si NWs heterojunction diodes was investigated. Highly dense and vertically well-aligned Si NW arrays were successfully synthesised on a p-type (1 0 0)-oriented Si wafer through cost-effective metal-assisted chemical etching technique. Ga-doped ZnO thin films were deposited onto Si NWs via radio frequency magnetron sputtering to construct three-dimensional heterostructures. Photovoltaic characteristics of the fabricated diodes were determined with current density (J)–voltage (V) measurements under simulated solar irradiation of AM 1.5 G. The optimal open-circuit voltage, short-circuit current density, fill factor and power conversion efficiency were found to be 0.37 V, 3.30 mA cm−2, 39.00 and 0.62%, respectively. Moreover, photovoltaic diodes exhibited relatively high external quantum efficiency over the broadband wavelengths between 350 and 1100 nm interval of the spectrum. The observed photovoltaic performance in this study clearly indicates that the investigated device structure composed of Ga-doped ZnO thin film/Si NWs heterojunctions could facilitate an alternative pathway for optoelectronic applications in future, and be a promising alternative candidate for high-performance low-cost new-generation photovoltaic diodes.
Rapid Molecular Testing for TB to Guide Respiratory Isolation in the U.S.: A Cost-Benefit Analysis (2013)

Background: Respiratory isolation of inpatients during evaluation for TB is a slow and costly process in low-burden settings. Xpert MTB/RIF (Xpert) is a novel molecular test for tuberculosis (TB) that is faster and more sensitive but substantially more expensive than smear microscopy. No previous studies have examined the costs of molecular testing as a replacement for smear microscopy in this setting.
Comparison of the Effects of Insulin and Insulin-like Agents on Different Aspects of Adipocyte Metabolism (1979)

The effect of insulin, spermine, cysteine, and diamide on glucose transport, glucose oxidation, and lipolysis were compared using isolated rat adipocytes. Each agent exerted insulin-like effects on glucose transport and glucose oxidation, whereas spermine and cysteine, but not diamide, inhibited lipolysis. Furthermore, the relative potencies of these agents on the various insulin responsive processes were markedly different. Thus, although these agents have much in common with insulin, the differences in relative potencies suggest that at least some of the insulin-like properties of these compounds may not be exerted through the same mechanisms as insulin.