gebhart/patrepeval huggingface dataset:
Abstract 3353: ZNF414 as a functionally relevant transcription factor in pancreatic and breast cancer cells (2018)

Abstract Background: The Zinc Finger Protein 414 (ZNF414) is a member of the krüppel C2H2-type zinc-finger protein family. ZNF414 is a cargo protein for Karyopherin α7 (KPNA7), a nuclear importer expressed during embryogenesis, absent in most adult tissues but re-expressed in cancer cells. KPNA7 is involved in promoting proliferation and maintaining nuclear morphology in several breast and pancreatic cancer cell lines. Similar effects on cell growth have been evidenced for ZNF414 using in vitro knock-down experiments. Other than this, the function of ZNF414 remains uncharacterized but, as a zinc finger protein with nuclear localization, it is likely to act as a transcription factor. This study aimed at identifying target genes and DNA binding motifs of ZNF414 in pancreatic and breast cancer cells. Methods: We used next generation sequencing methods on Hs700T and MCF-7 cell lines. RNA-seq was used to identify genes regulated by ZNF414 and ChIP-exo and ATAC-seq analyses to uncover its genomic binding regions. Samples for RNA-seq were collected 12h and 24h after transfection with siRNAs targeting ZNF414. For ChIP-exo and ATAC-seq experiments, cells were transfected to transiently overexpress V5-tagged ZNF414. Results: RNA-seq data analyses revealed 33 and 296 differentially expressed genes (DEGs) in Hs700T cells at 12h and 24h time points, respectively. The corresponding amounts of DEGs in MCF-7 cell line were 177 and 556. There were 23 and 108 DEGs in common to both cell lines at 12h and 24h, respectively. Interestingly, gene ontology analyses revealed enrichment of many functional categories related to cellular proliferation in both cell lines, providing a molecular explanation for the observed ZNF414-elicited phenotype. ChIP-exo data was processed using MACE tool and then combined with the ATAC-seq open chromatin signal to identify the most reliable peaks. We looked at the genomic location of these peaks and observed clear enrichment in the promoter and 5'UTR regions, indicating that ZNF414 is a classical transcription factor. Using MEME for de novo motif discovery analyses, we identified several putative binding motifs common to both cell lines, some of which were also found in promoters of DEGs. Conclusion: This study uncovered the transcriptional regulation that underlies the role of ZNF414 as inducer of cellular proliferation in pancreatic and breast cancer cells. Citation Format: Alejandra Rodríguez Martínez, Elisa M. Vuorinen, Anastasia Shcherban, Nina K. Rajala, Matti Nykter, Anne Kallioniemi. ZNF414 as a functionally relevant transcription factor in pancreatic and breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3353.
Atomic Structure of the (310) Symmetrical TILT Grain Boundary in Strontium Titanate - A Comparison among Experimental Methods and Atomistic Simulations (1996)

Strontium Titanate is a prototypical perovskite oxide whose macroscopic electroceramic properties, like varistor and grain boundary barrier layer capacitor (GBBLC) behavior, are controlled by grain boundary (GB) phenomena. In this paper, we present a comparative analysis of the results of both experimental and theoretical investigations of the atomic structure of a (310) symmetrical tilt GB (a Σ=5 (310) [001] GB in the CSL notation) in SrTiO 3 . Bicrystals of SrTiO 3 were procured from Shinkosha Ltd., and electron backscatter kikuchi pattern analysis as well as transmission electron diffraction studies confirm that the GB conforms to the Σ =5 misorientation. The atomic structure of this GB has been investigated using high resolution transmission electron microscopy (HRTEM) and associated image simulations, as well as by atomistic simulations using static iterative energy minimization schemes (“lattice-statics”). 2
Hybrid quantum-classical algorithms for approximate graph coloring (2022)

We show how to apply the recursive quantum approximate optimization algorithm (RQAOA) to MAX-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>k</mml:mi></mml:math>-CUT, the problem of finding an approximate <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>k</mml:mi></mml:math>-vertex coloring of a graph. We compare this proposal to the best known classical and hybrid classical-quantum algorithms. First, we show that the standard (non-recursive) QAOA fails to solve this optimization problem for most regular bipartite graphs at any constant level <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>p</mml:mi></mml:math>: the approximation ratio achieved by QAOA is hardly better than assigning colors to vertices at random. Second, we construct an efficient classical simulation algorithm which simulates level-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mn>1</mml:mn></mml:math> QAOA and level-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mn>1</mml:mn></mml:math> RQAOA for arbitrary graphs. In particular, these hybrid algorithms give rise to efficient classical algorithms, and no benefit arising from the use of quantum mechanics is to be expected. Nevertheless, they provide a suitable testbed for assessing the potential benefit of hybrid algorithm: We use the simulation algorithm to perform large-scale simulation of level-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mn>1</mml:mn></mml:math> QAOA and RQAOA with up to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mn>300</mml:mn></mml:math> qutrits applied to ensembles of randomly generated <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mn>3</mml:mn></mml:math>-colorable constant-degree graphs. We find that level-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mn>1</mml:mn></mml:math> RQAOA is surprisingly competitive: for the ensembles considered, its approximation ratios are often higher than those achieved by the best known generic classical algorithm based on rounding an SDP relaxation. This suggests the intriguing possibility that higher-level RQAOA may be a potentially useful algorithm for NISQ devices.
Neue Katalysatorsysteme für die katalytische Oxidation von Methan zu Methanol (2002)

Palladiumkomplexe mit N-heterocyclischen Carbenen wie die hier gezeigten mit Biscarben-Chelatligand (R=tBu, Me; X=Br, I) erwiesen sich auch in stark sauren Medien als stabil und wurden für die katalytische Oxidation von Methan zu Methanol erprobt. Der bedeutende Einfluss der Halogenidliganden zeigt sich darin, dass der Iodkomplex im Unterschied zum Bromkomplex die Reaktion nicht katalysiert. Auch der sterische Anspruch des Substituenten R beeinflusst die Katalysatoraktivität. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2002/z18342_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Lithologic imaging using complex conductivity: Lessons learned from the Hanford 300 Area (2012)

ABSTRACT Field-scale lithologic applications of complex conductivity (σ*) imaging have been hindered by the challenges of (1) acquiring reliable induced polarization (IP) measurements and (2) obtaining reliable σ* images from the measurements. We performed a series of 2D time domain resistivity/IP surveys at the Hanford 300 Area (Richland, Washington) where the challenge was to image the spatial distribution of two lithologic units that control the exchange between groundwater and surface water of the Columbia River. Exploiting the equivalence between time domain and frequency domain measurements of polarization, a 2D σ* inversion (real conductivity σ′, imaginary conductivity σ′′, and phase angle ϕ) was used to image the spatial distribution of σ* across the site. Synthetic studies were carried out to investigate the effects of noise on the resolution of σ* images and to add confidence on the interpretation of possible paleochannels observed in the field data sets. The synthetic studies show that, with increasing representative noise levels, degradation of the resolution of lithologic structures in the parameters most controlled by the IP measurements (ϕ and σ′′) is significantly greater than degradation of resolution of σ′ images. However, the acquisition of IP measurements, and the analysis of changes in σ′ and σ′′ constrains the lithological interpretation of the geoelectrical data set due to the strong dependency of σ′′ on lithological properties. A threshold based on σ′′ measurements from cores at the site was used to estimate the elevation of the contact between the two key units, which is consistent with boreholes at the site. Variation in the elevation of this contact provides evidence of a depression in the Hanford-Ringold contact connecting the aquifer and the Columbia River; this depression likely represents a paleochannel regulating flow and transport at the site.
Photonic Crystals with a Twist (2023)

Twisted bilayer photonic crystal slabs have two degrees of freedom, twist angle and interlayer spacing, that permit the engineering of nanoscale devices that exhibit novel behavior and open the door to real-time reconfigurable devices.
Apathy correlates with prefrontal amyloid deposition in Alzheimer's disease (2013)

This study revealed that prefrontal Aβ deposition correlates with apathy.
ChemInform Abstract: Synthetic Evolutions in the Nucleophilic Addition to Alkynes (2011)

Abstract Review: 65 refs.
Repurposing Fragile X Drugs to Inhibit SARS-CoV-2 Viral Reproduction (2020)

The COVID-19 pandemic is a global health crisis that requires the application of interdisciplinary research to address numerous knowledge gaps including molecular strategies to prevent viral reproduction in affected individuals. In response to the Frontiers Research Topic, "<i>Coronavirus disease (COVID-19): Pathophysiology, Epidemiology, Clinical Management, and Public Health Response</i>," this Hypothesis article proposes a novel therapeutic strategy to repurpose metabotropic glutamate 5 receptor (mGluR<sub>5</sub>) inhibitors to interfere with viral hijacking of the host protein synthesis machinery. We review pertinent background on SARS-CoV-2, fragile X syndrome (FXS) and metabotropic glutamate receptor 5 (mGluR<sub>5</sub>) and provide a mechanistic-based hypothesis and preliminary data to support testing mGluR<sub>5</sub> inhibitors in COVID-19 research.
A New Benchmark for Evaluation of Cross-Domain Few-Shot Learning. (2019)

Recent progress on few-shot learning largely relies on annotated data for meta-learning: base classes sampled from the same domain as the novel classes. However, in many applications, collecting data for meta-learning is infeasible or impossible. This leads to the cross-domain few-shot learning problem, where there is a large shift between base and novel class domains. While investigations of the cross-domain few-shot scenario exist, these works are limited to natural images that still contain a high degree of visual similarity. No work yet exists that examines few-shot learning across different imaging methods seen in real world scenarios, such as aerial and medical imaging. In this paper, we propose the Broader Study of Cross-Domain Few-Shot Learning (BSCD-FSL) benchmark, consisting of image data from a diverse assortment of image acquisition methods. This includes natural images, such as crop disease images, but additionally those that present with an increasing dissimilarity to natural images, such as satellite images, dermatology images, and radiology images. Extensive experiments on the proposed benchmark are performed to evaluate state-of-art meta-learning approaches, transfer learning approaches, and newer methods for cross-domain few-shot learning. The results demonstrate that state-of-art meta-learning methods are surprisingly outperformed by earlier meta-learning approaches, and all meta-learning methods underperform in relation to simple fine-tuning by 12.8% average accuracy. Performance gains previously observed with methods specialized for cross-domain few-shot learning vanish in this more challenging benchmark. Finally, accuracy of all methods tend to correlate with dataset similarity to natural images, verifying the value of the benchmark to better represent the diversity of data seen in practice and guiding future research.
Immune perturbations in HIV-1–infected individuals who make broadly neutralizing antibodies (2016)

Induction of broadly neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development. bnAbs occur in some HIV-1-infected individuals and frequently have characteristics of autoantibodies. We have studied cohorts of HIV-1-infected individuals who made bnAbs and compared them with those who did not do so, and determined immune traits associated with the ability to produce bnAbs. HIV-1-infected individuals with bnAbs had a higher frequency of blood autoantibodies, a lower frequency of regulatory CD4<sup>+</sup> T cells, a higher frequency of circulating memory T follicular helper CD4<sup>+</sup> cells, and a higher T regulatory cell level of programmed cell death-1 expression compared with HIV-1-infected individuals without bnAbs. Thus, induction of HIV-1 bnAbs may require vaccination regimens that transiently mimic immunologic perturbations in HIV-1-infected individuals.
Estimation of the baroreflex total loop gain by the power spectral analysis of continuous arterial pressure recordings (2019)

Baroreflex dysfunction contributes to the pathogenesis of cardiovascular diseases. The baroreflex comprises a negative feedback loop to stabilize arterial pressure (AP); its pressure-stabilizing capacity is defined as the gain ( G) of the transfer function ( H) of the baroreflex total loop. However, no method exists to evaluate G in a clinical setting. A feedback system with H attenuates pressure disturbance (PD) to PD/(1 + H). We hypothesized that the baroreflex attenuates the power spectrum density (PSD) of AP in the baroreflex functioning frequency range. We created graded baroreflex dysfunction in rats using a modified sinoaortic denervation (SAD) method [SAD; control (no SAD): n = 9; partial SAD (SAD in the right carotid sinus): n = 6, and total SAD (SAD in the bilateral carotid sinuses): n = 6] and evaluated the PSD of 12-h telemetric AP recordings in the light phase. Using the ratio of PSD at 0.01-0.1 Hz (PSD slope), we normalized them with the PSD in rats with complete baroreflex failure and derived the baroreflex index (BRI), which directly reflects G. We compared BRI and G obtained from a baroreflex open-loop experiment (reference G). The PSD slope became steeper with progression of baroreflex dysfunction. BRI (control: 2.00 ± 0.31, partial SAD: 1.28 ± 0.30, and total SAD: 0.06 ± 0.10, P < 0.05) was linearly correlated with reference G ( R<sup>2</sup> = 0.91, P < 0.01). BRI accurately estimated G of the baroreflex and may serve as a novel tool for estimating the pressure-stabilizing capacity of the baroreflex in clinical settings. NEW & NOTEWORTHY This study proposed a novel method to estimate the gain of the baroreflex total loop, the so-called "baroreflex index" (BRI). BRI focuses on action potential variability in the frequency domain, considering baroreflex low-pass filter characteristics within 0.01-0.1 Hz. We demonstrated that BRI was linearly correlated with the reference gain of baroreflex in rats. Thus, BRI may contribute greatly to the development of a clinical tool for estimating baroreflex pressure-stabilizing capacity.
Effect of “Rosa Canina” Infusion and Magnesium on the Urinary Risk Factors of Calcium Oxalate Urolithiasis (1992)

The effects on the calcium oxalate urolithiasis urinary risk factors of "Rosa Canina", in herb infusion form, and magnesium chloride have been studied using female Wistar rats under balanced dietary conditions. No significant effects on the volume of liquids drunk or on creatinine, phosphate, and oxalate urinary concentrations and excretions were observed. The herb infusion did not cause any diuretic effect. Calciuria decreased and citraturia increased when taking the herb infusion, and vice versa when taking magnesium chloride. Magnesium chloride decreased the urinary pH value, but this effect was not observed when magnesium chloride was administered with herb infusion. In conclusion, the same beneficial effects of the studied infusion herb on calcium oxalate urolithiasis urinary risk factors can be clearly detected. An interesting fact is that it seems that some possible effects depend on dietary components, thus, i.e., an increase in the urinary pH was only detected when the intake of the herb infusion was studied in a magnesium chloride-supplemented diet.
Method for reducing peak phase current and decreasing staring time for an internal combustion engine having an induction machine (2023)

A method for reducing the starting time and reducing the peak phase currents for an internal combustion engine that is started using an induction machine starter/alternator. The starting time is reduced by pre-fluxing the induction machine and the peak phase currents are reduced by reducing the flux current command after a predetermined period of time has elapsed and concurrent to the application of the torque current command. The method of the present invention also provides a strategy for anticipating the start command for an internal combustion engine and determines a start strategy based on the start command and the operating state of the internal combustion engine.
Development of the pyrochemical DOS process for the recovery of actinides and its application for reprocessing of transmutation fuel targets (2015)

Pyrochemical technology using high-temperature molten salts and molten metal media presents a potential interest for an overall separation and transmutation strategy for long-lived radionuclides. Within the frame of the two French acts on radioactive waste management, a pyrochemical R&D program was launched at the CEA Marcoule in the late 90's. The developed so called DOS (Direct Oxide Solubilisation) process, based on a two- step liquid-liquid (molten salt/liquid metal) extraction, aims to demonstrate the feasibility of a group separation of actinides with sufficient decontamination from fission products.
The first step consists of a selective reductive extraction of actinides coming from direct dissolution of oxide fuel in the molten fluoride salt, into liquid aluminium metal. The second step is the actinides back-extraction, which consists of a liquid/liquid oxidative stripping of the An from aluminium matrix into molten chloride media. The DOS process has been successfully demonstrated for treatment of oxide type fuels within the last years: the core of the process has been already assessed and the studies have shown high selectivity and a quantitative recovery of actinides. 
Within the framework of the SACSESS European research program, the present work focuses on a potential application of the DOS process for the reprocessing of MgO based CERCER transmutation targets. The behaviour of Mg was investigated regarding the solubility of MgO in the fluoride salt and then regarding Mg reductive extraction in metallic Al. The impact of Mg on the efficiency of An reductive extraction was also studied using U3O8 simulating the behaviour of MA oxides. Eventually, the validity of the DOS process was demonstrated on a Pu0.5Am0.5O2-x-MgO FUTURIX CERCER pellet synthesized at the ATALANTE facility within the framework of Eurotrans program. Substantial amount of Nd2O3 was added during the demonstration experiment in order to simulate fission products behaviour. Quantitative recovery of purified Pu and Am was achieved in a single batch experiment.
Fabrication of Freestanding Pb(Zr,Ti)O Film Microstructures Using Ge Sacrificial Layer (2012)

A high quality freestanding Pb(Zr,Ti)O 3 (PZT) film with various micropatterns was fabricated using a Ge sacrificial layer in order to meet the need of micro-electromechanical system (MEMS) applications. A flat Pt film was released from a Si substrate by etching the Ge layer (∼1 µm) between the Pt film and the Si substrate. After that, PZT was deposited on the freestanding Pt film by low temperature rf-magnetron sputtering and then annealed. The obtained freestanding PZT film showed strong (100) orientation and good ferroelectric property. This might be due to the characteristics of the developed process, for example, the lattice parameter change of the Pt film, a small heat capacity in the annealing process of PZT, and an absence of clamping effect from the substrate.
Huntington's disease: from gene to potential therapy (2001)

Huntington's disease (HD) is a progressive, late-onset neurodegenerative illness with autosomal dominant inheritance that affects one in 10 000 individuals in Western Europe. The disease is caused by a polyglutamine repeat expansion located in the N-terminal region of the huntingtin protein. The mutation is likely to act by a gain of function, but the molecular mechanisms by which it leads to neuronal dysfunction and cell death are not yet known. The normal function of huntingtin in cell metabolism is also unclear. There is no therapy for HD. Research on HD should help elucidate the pathogenetic mechanism of this illness in order to develop successful treatments to prevent or slow down symptoms. This article presents new results in HD research focusing on in vivo and in vitro model systems, potential molecular mechanisms of HD, and the development of therapeutic strategies.
Methionine tumor starvation by erythrocyte‐encapsulated methionine gamma‐lyase activity controlled with per os vitamin B6 (2017)

Erymet is a new therapy resulting from the encapsulation of a methionine gamma-lyase (MGL; EC number 4.4.1.11) in red blood cells (RBC). The aim of this study was to evaluate erymet potential efficacy in methionine (Met)-dependent cancers. We produced a highly purified MGL using a cGMP process, determined the pharmacokinetics/pharmacodynamics (PK/PD) properties of erymet in mice, and assessed its efficacy on tumor growth prevention. Cytotoxicity of purified MGL was tested in six cancer cell lines. CD1 mice were injected with single erymet product supplemented or not with vitamin B6 vitamer pyridoxine (PN; a precursor of PLP cofactor). NMRI nude mice were xenografted in the flank with U-87 MG-luc2 glioblastoma cells for tumor growth study following five intravenous (IV) injections of erymet with daily PN oral administration. Endpoints included efficacy and event-free survival (EFS). Finally, a repeated dose toxicity study of erymet combined with PN cofactor was conducted in CD1 mice. Recombinant MGL was cytotoxic on 4/6 cell lines tested. MGL half-life was increased from <24 h to 9-12 days when encapsulated in RBC. Conversion of PN into PLP by RBC was demonstrated. Combined erymet + PN treatment led to a sustained Met depletion in plasma for several days with a 85% reduction of tumor volume after 45 days following cells implantation, and a significant EFS prolongation for treated mice. Repeated injections in mice exhibited a very good tolerability with only minor impact on clinical state (piloerection, lean aspect) and a slight decrease in hemoglobin and triglyceride concentrations. This study demonstrated that encapsulation of methioninase inside erythrocyte greatly enhanced pharmacokinetics properties of the enzyme and is efficacy against tumor growth. The perspective on these results is the clinical evaluation of the erymet product in patients with Met starvation-sensitive tumors.
Supplementary Tables 1-2 from Synthetic Triterpenoid Cyano Enone of Methyl Boswellate Activates Intrinsic, Extrinsic, and Endoplasmic Reticulum Stress Cell Death Pathways in Tumor Cell Lines (2023)

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