gebhart/patrepeval huggingface dataset:
Abstract LB-086: PARP-1 controls the DNA damage response by regulating E2F1 transcriptional activity (2017)

Abstract PARP-1 holds two major functions on chromatin, DNA damage repair and transcriptional regulation, both of which are relevant in the context of cancer. Notably, PARP-1 has been found to be a key modulator of androgen receptor (AR) function and AR-dependent phenotypes, which is a driving factor in prostate cancer (PCa) biology and therapeutic management. Recent studies indicate an unanticipated prevalence of DNA repair alterations in advanced PCa and showed that PARP-1 inhibitors (PARPi) can effectively manage of a subset of these tumors. Despite the functions of PARP-1 in DNA repair having been exploited as a therapeutic target for tumors with BRCA1/2 aberrations, factors beyond DNA repair alterations clearly play a role in the response to PARPi. Notably, in the TO-PARP trial, not all patients with DNA repair aberrations responded to PARPi; conversely, tumors lacking BRCA1/2 or other DNA repair alterations show objective response to PARPi in PCa and other tumor types. These clinical data suggest that the genetic (e.g. BRCA-ness) and pharmacologic interplay is complex in the context of PARPi. Given the preclinical and clinical data, pursuing a deeper understanding of the molecular underpinnings of PARPi action in PCa may yield significant benefit. Genome-wide transcriptional profiling in response to PARPi was performed and the PARP-1-regulated transcriptome was identified. Human tissue microarrays were utilized to quantify PARP-1 levels and activity as a function of PCa progression. Both the PARP-1-regulated transcriptome, as well as PARP-1 enzymatic activity, were found to be elevated as a function of PCa progression. Further interrogation of the PARP-1-regulated transcriptome revealed a major impact on E2F1-regulated genes, and chromatin immunoprecipitation analyses indicated that PARP-1 functions to regulate the chromatin architecture and E2F1 occupancy at E2F1 target gene loci. Most prominent among the E2F1-regulated genes responsive to PARPi were genes associated with DNA damage repair, with a particular enrichment for genes involved in homologous recombination (HR). In sum, these data indicate PARP-1 regulates the function of key oncogenic transcription factors (AR and E2F1) in PCa, and part of the effect of PARPi may be through down-regulation of DNA repair factors. Citation Format: Matthew J. Schiewer, Amy C. Mandigo, Nicolas Gordon, Fangjin Huang, Sanchaika Gaur, Shuang Zhao, Joseph Evans, Sumin Han, Theodore Parsons, Ruth Birbe, Peter McCue, Tapio Visakorpi, Ganesh Raj, Mark Rubin, Johann de Bono, Costas Lallas, Edouard Trabulsi, Leonard G. Gomella, Adam P. Dicker, Kevin Kelly, Beatrice Knudsen, Felix Feng, Karen E. Knudsen. PARP-1 controls the DNA damage response by regulating E2F1 transcriptional activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-086. doi:10.1158/1538-7445.AM2017-LB-086
Unmanned Aircraft Systems Detect and Avoid System: End-to-End Verification and Validation Simulation Study of Minimum Operational Performance Standards for Integrating Unmanned Aircraft into the National Airspace System (2017)

As Unmanned Aircraft Systems (UAS) make their way to mainstream aviation operations within the National Airspace System (NAS), research efforts are underway to develop a safe and effective environment for their integration into the NAS. Detect and Avoid (DAA) systems are required to account for the lack of eyes in the sky due to having no human on-board the aircraft. The technique, results, and lessons learned from a detailed End-to-End Verification and Validation (E2-V2) simulation study of a DAA system representative of RTCA SC-228's proposed Phase I DAA Minimum Operational Performance Standards (MOPS), based on specific test vectors and encounter cases, will be presented in this paper.
Fuzzy ants as a clustering concept (2004)

We present a swarm intelligence approach to data clustering. Data is clustered without initial knowledge of the number of clusters. Ant based clustering is used to initially create raw clusters and then these clusters are refined using the Fuzzy C Means algorithm. Initially the ants move the individual objects to form heaps. The centroids of these heaps are taken as the initial cluster centers and the Fuzzy C Means algorithm is used to refine these clusters. In the second stage the objects obtained from the Fuzzy C Means algorithm are hardened according to the maximum membership criteria to form new heaps. These new heaps are then sometimes moved and merged by the ants. The final clusters formed are refined by using the Fuzzy C Means algorithm. Results from three small data sets show that the partitions produced are competitive with those obtained from FCM.
Zinc ion-doped carbon dots with strong yellow photoluminescence (2016)

Carbon dots doped with zinc ions and displaying strong yellow photoluminescence and a QY of 51.2% were produced, as were various applications of these carbon dots.
Microscopic measurement of penetration depth in thin films by scanning Hall probe microscopy (1997)

We have used a low noise scanning Hall probe microscope to measure the penetration depth microscopically in a YBa2Cu3O7-delta thin film as a function of temperature. The instrument has high magnetic field (approximate to 2.9 x 10(-8) T HZ(-1/2) at 77 K) and spatial resolution ( approximate to 0.85 mu m). Magnetic field profiles of single vortices in the superconducting film have been successfully measured and the microscopic penetration depth of the superconductor has been extracted. We find surprisingly large variations in values of lambda for different vortices within the scanning field.
Rotation Plane Doubly Orthogonal Recurrent Neural Networks (2017)

Recurrent Neural Networks (RNNs) applied to long sequences suffer from the well known vanishing and exploding gradients problem. The recently proposed Unitary Evolution Recurrent Neural Network (uRNN) alleviates the exploding gradient problem and can learn very long dependencies, but its nonlinearities make it still affected by the vanishing gradient problem and so learning can break down for extremely long dependencies. We propose a new RNN transition architecture where the hidden state is updated multiplicatively by a time invariant orthogonal transformation followed by an input modulated orthogonal transformation. There are no additive interactions and so our architecture exactly preserves forward hid-den state activation norm and backwards gradient norm for all time steps, and is provably not affected by vanishing or exploding gradients. We propose using the rotation plane parameterization to represent the orthogonal matrices. We validate our model on a simplified memory copy task and see that our model can learn dependencies as long as 5,000 timesteps.
Degradation of halogenophosphazenes to a new phosphorane system (1968)

H. R. Allcock and R. L. Kugel, Chem. Commun. (London), 1968, 1606 DOI: 10.1039/C19680001606
Challenges and approaches to time-series forecasting in data center telemetry: A Survey (2021)

Time-series forecasting has been an important research domain for so many years. Its applications include ECG predictions, sales forecasting, weather conditions, even COVID-19 spread predictions. These applications have motivated many researchers to figure out an optimal forecasting approach, but the modeling approach also changes as the application domain changes. This work has focused on reviewing different forecasting approaches for telemetry data predictions collected at data centers. Forecasting of telemetry data is a critical feature of network and data center management products. However, there are multiple options of forecasting approaches that range from a simple linear statistical model to high capacity deep learning architectures. In this paper, we attempted to summarize and evaluate the performance of well known time series forecasting techniques. We hope that this evaluation provides a comprehensive summary to innovate in forecasting approaches for telemetry data.
Shima drinking water--a bacteriological analysis. (2001)

300 water samples, 60 from piped supply and 240 from 20 natural sources were analyzed bacteriologically for four important bacterial indicators every month over a period of one year. The MPN of total coliforms, Escherichia coli, Streptococcus faecalis were detected by multiple tube method and Clostridium perfringens was isolated using litmus milk medium. From piped water supply, only one sample was found unfit for human consumption. The plate count at 37 degrees C and 22 degrees C varied from 0.5 x 10(3) to 15 x 10(3) per ml. of water. From natural sources, MPN indices for coliforms, Esch. coli and S. faecalis varied from 3 to > 1800, 0 to > 1800 and 0 to 540 per 100 ml. of water respectively. About 1/3rd of samples showed presence of Cl. perfringens. The plate count varied from 1.0 x 10(3) to > 150 x 10(3) per ml. of water. Salmonella typhi was isolated in 1.25% samples by membrane filtration technique. The water from all the natural sources was unfit for human consumption whereas piped water supply was of good quality in general.
Using Response Surface Methodology for Optimizing Pigment Extraction from Acanthopanax senticosus Harms Fresh Fruit (2011)

Based on one-factor-at-a-time experiments,response surface methodology was used to optimize the extraction of red pigments from the fresh fruits of Acanthopanax senticosus Harms wildly grown in Changbai Mountain.The optimal extraction conditions were found as follows: 36.83% ethanol as extraction solvent,23.78:1 material-to-liquid ratio,and 2.05 h extraction time.Under these conditions,the predicted and experimental absorbance values at 525 nm of extracts was 0.756 and 0.751,respectively.
Figurer l’espace/temps de Tours préindustriel: essai de chrono-chorématique urbaine. (2006)

Cette étude s’inscrit dans un ensemble de travaux qui portent sur l’élaboration d’une approche modélisatrice de la forme des villes et de leur dynamique. Dans le cas de Tours, il s’agit de passer des plans de topographie historique à un chrono-chorème représentant en une figure unique la trajectoire de l’espace urbain, tout en explicitant les différentes étapes de schématisation. Ce travail est conçu comme un outil de réflexion sur la dynamique urbaine de Tours et sa trajectoire dans la longue durée.
Rotor Wake Vortex Definition - Initial Evaluation of 3-C PIV Results of the HART-II Study (2002)

An initial evaluation is made of extensive three-component (3C) particle image velocimetry (PIV) measurements within the wake across a rotor disk plane. The model is a 40 percent scale BO-105 helicopter main rotor in forward flight simulation. This study is part of the HART II test program conducted in the German-Dutch Wind Tunnel (DNW). Included are wake vortex field measurements over the advancing and retreating sides of the rotor operating at a typical descent landing condition important for impulsive blade-vortex interaction (BVI) noise. Also included are advancing side results for rotor angle variations from climb to steep descent. Using detailed PIV vector maps of the vortex fields, methods of extracting key vortex parameters are examined and a new method was developed and evaluated. An objective processing method, involving a center-of-vorticity criterion and a vorticity 'disk' integration, was used to determine vortex core size, strength, core velocity distribution characteristics, and unsteadiness. These parameters are mapped over the rotor disk and offer unique physical insight for these parameters of importance for rotor noise and vibration prediction.
Image Mosaicing using Cylindrical Mapping (2014)

The objective of this paper is to provide extended field of view for aerial surveillance in MAV’s. Aerial surveillance on unmanned flying vehicles using a single monocular camera is a trade-off between the level of detail obtained at low altitudes and degree of coverage obtained by flying the vehicle at high altitudes. The effective footprint of the camera is smaller if the aerial vehicle flies at higher altitudes. On the other hand, the region can be quickly searched from a higher altitude. The demand for high detail and wider coverage can be satisfied using Image Mosaicing i.e. the stitching of selected frames of a video by estimating the camera motion between the frames and thereby registering successive frames of the video to arrive at the mosaic.
Technological Solutions for Energy Security and Sustainability (2008)

Abstract This paper addresses the question: how can we minimize the expected time between now and the time when we achieve three measures of sustainability and security together — independence from oil in cars and trucks, very deep reductions in greenhouse gas emissions and deep reductions in natural gas for electricity? Specific new technologies and metrics for progress are discussed, in context, linked to new information from IEEE, NSF, the State of the Future project and other sources.
Mixed-initiative nested classification by optimal thresholding (2011)

The purpose of this paper is to demonstrate that having two classifiers, a trichotomous classifier (true, false, or unknown) with workload-independent performance that turns over the data classified as unknown to a binary classifier (true or false) with workload-dependent performance, gives superior classification performance (lower probability of misclassification) compared to a single dichotomous classifier. We relate the classifier's performance to the inherent difficulty of the classification task at hand (classifiability), and compare the performance of different classifiers.
Cation-Disordered Li3VO4: Reversible Li Insertion/Deinsertion Mechanism for Quasi Li-Rich Layered Li1+x[V1/2Li1/2]O2 (x = 0–1) (2018)

The reversible lithiation/delithiation mechanism of the cation-disordered Li3VO4 material was elucidated, including the understanding of structural and electrochemical signature changes during cycling. The initial exchange of two Li induces a progressive and irreversible migration of Li and V ions from tetrahedral to octahedral sites, confirmed by the combination of in situ/operando X-ray diffraction and X-ray absorption fine structure analyses. The resulting cation-disordered Li3VO4 can smoothly and reversibly accommodate two Li and shows a Li+ diffusion coefficient larger by 2 orders of magnitude than the one of pristine Li3VO4, leading to improved electrochemical performance. This cation-disordered Li3VO4 negative electrode offers new opportunities for designing high-energy and high-power supercapacitors. Furthermore, it opens new paths for preparing disordered compounds with the general hexagonal close-packing structure, including most polyanionic compounds, whose electrochemical performance can be easily improved by simple cation mixing.
Bone morphogenetic protein signaling in inflammation (2019)

By compiling findings from recent studies, this review will garner novel insight on the dynamic and complex role of BMP signaling in diseases of inflammation, highlighting the specific roles played by both individual ligands and endogenous antagonists. Ultimately, this summary will help inform the high therapeutic value of targeting this pathway for modulating diseases of inflammation.
Soluble IL-6 Receptor and IL-27 Subunit p28 Protein Complex Mediate the Antiviral Response through the Type III IFN Pathway (2016)

Previously, we demonstrated that the soluble IL-6R (sIL-6R) plays an important role in the host antiviral response through induction of type I IFN and sIL-6R-mediated antiviral action via the IL-27 subunit p28; however, the mechanism that underlies sIL-6R and p28 antiviral action and whether type III IFN is involved remain unknown. In this study, we constructed a sIL-6R and p28 fusion protein (sIL-6R/p28 FP) and demonstrated that the fusion protein has stronger antiviral activity than sIL-6R alone. Consequently, knockout of sIL-6R inhibited virus-triggered IFN-λ1 expression. In addition, sIL-6R/p28 FP associated with mitochondrial antiviral signaling protein and TNFR-associated factor 6, the retinoic acid-inducible gene I adapter complex, and the antiviral activity mediated by sIL-6R/p28 FP was dependent on mitochondrial antiviral signaling protein. Furthermore, significantly reduced binding of p50/p65 and IFN regulatory factor 3 to the IFN-λ1 promoter was observed in sIL-6R knockout cells compared with the control cells. Interestingly, a novel heterodimer of c-Fos and activating transcription factor 1 was identified as a crucial transcriptional activator of IFN-λ1 The sIL-6R/p28 FP upregulated IFN-λ1 expression by increasing the binding abilities of c-Fos and activating transcription factor 1 to the IFN-λ1 promoter via the p38 MAPK signaling pathway. In conclusion, these results demonstrate the important role of sIL-6R/p28 FP in mediating virus-induced type III IFN production.
Emerging technology in critical care: continuous intra-arterial blood gas monitoring (1996)

The blood-conserving technology of continuous intra-arterial blood gas monitoring has recently been introduced into the field of critical care. This type of monitoring is a real-time method for concomitantly assessing oxygenation, ventilation, and acid-base status in pediatric and adult populations through an indwelling (in vivo) sensor residing in a peripheral artery. This article examines the technology underpinning in vivo blood gas monitoring and reviews research documenting clinical performance, as well as benefits and clinical applications of three-analyte systems in critically ill patients. A majority of research has revealed clinically acceptable accuracy and reliability of in vivo blood gas sensors in critically ill adults subjected to a variety of adverse, but common, physiological conditions. Although most clinical research in critically ill adults has revealed good clinical performance of in vivo blood gas sensors, reports of aberrant blood gas values and sensor problems remain; no reports have been published to date evaluating continuous intra-arterial blood gas monitoring in children or infants. Many benefits of this technology have been postulated, and research examining its effect on patient and cost outcomes in critically ill populations is pending. Clinicians in critical care must keep abreast of this emerging technology, because it holds significant potential for improving the quality of care and outcomes of critically ill patients.
Compositional Structures of Boronized Tool Steels (1974)

The boronized surface of tool steels with high Si content was observed to have a complex structure comprising α-phase and granular phase zones in addition to the boronized layers of FeB and Fe2B. The formation mechanism of the structure was studied by X-ray diffraction analysis and EPMA. The results obtained were as follows.(1) Si was concentrated beneath the boronized layer through B impregnation, resulting in the transformation of the γ-phase into an α-phase.(2) Granular phases of M23(C, B)6 composition were observed in the α-phase and the matrix adjacent to it. B content was higher in the former, while C content was higher in the latter.(3) An α-phase was observed even in the boronized tool steel with low Si content. But, it was granular in shape and small in size.(4) Elements such as Ni and Co were concentrated towards the boronized layer, while Cr, Mo, V and Mn were diluted.
A Novel Synthesis of a Branched-chain Amino Sugar, Methyl 2-Amino-2,3-dideoxy-3-C-formyl-α-d-xylofuranoside-3′R,5-hemiacetal (1982)

Abstract Methyl 2-amino-2N,3O-(o-benzenedisulfonyl)-2-deoxy-α-d-glucopyranoside, which was prepared from methyl 2-amino-2-deoxy-α-d-glucopyranoside and o-benzenedisulfonyl dichloride, was treated with sodium methoxide to afford exclusively a branched-chain amino sugar, methyl 2,3-dideoxy-3-C-formyl-2-(o-sulfobenzenesulfonyl)amino-α-d-xylofuranoside-3′R,5-hemiacetal sodium salt (6). Some derivatives were synthesized from 6.
Using Raman spectroscopy and chemometrics to identify the growth phase of Lactobacillus casei Zhang during batch culture at the single-cell level (2017)

To conclude, Raman spectroscopy allows label-free, continuous monitoring of cell growth, which may facilitate more accurate estimates of the growth states of lactic acid bacterial populations during fermented batch culture in industry.
An Efficient Bayesian Optimization Approach for Analog Circuit Synthesis via Sparse Gaussian Process Modeling (2020)

Bayesian optimization with Gaussian Process (GP) models has been proposed for analog synthesis since it is efficient for the optimizations of expensive black-box functions. However, the computational cost for training and prediction of Gaussian process models are O(N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) and O(N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), respectively, where N is the number of data points. The overhead of the Gaussian process modeling would not be negligible as N is relatively large. Recently, a Bayesian optimization approach using neural network has been proposed to address this problem. It reduces the computational cost of training and prediction of Gaussian process models to O(N) and O(1), respectively. However, reducing the infinite-dimensional kernel to finite-dimensional kernel using neural network mapping would weaken the characterization ability of Gaussian process. In this paper, we propose a novel Bayesian optimization approach using Sparse Pseudo-input Gaussian Process (SPGP). The idea is to use M <; N so-called inducing points to build a sparse Gaussian process model to approximate the conventional exact Gaussian process model. Without the need to sacrifice the modeling ability of the surrogate model, it also reduces the computational cost of both training and prediction to O(N) and O(1), respectively. Several experiments were provided to demonstrate the efficiency of the proposed approach.
Improved Performance in Bulk Heterojunction Organic Solar Cells with a Sol‐Gel MgZnO Electron‐Collecting Layer (2014)

Enhanced power conversion efficiency is observed for inverted organic solar cells when a sol-gel deposited MgZnO is used in place of ZnO. The enhanced fill factor and open-circuit voltage suggest reduced recombination at the interface with bulk heterojunctions of poly(3-hexylthiophene) (P3HT) blended with either [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) or indene C60 bis-adduct (ICBA).