gebhart/patrepeval huggingface dataset:
Multivariate analysis of energy dispersive X-ray diffraction data for the detection of illicit drugs in border control (2017)

A system using energy dispersive X-ray diffraction has been tested to detect the presence of illicit drugs concealed within parcels typical of those which are imported into the UK via postal and courier services. The system was used to record diffraction data from calibration samples of diamorphine (heroin) and common cutting agents and a partial least squares regression model was established between diamorphine concentration and diffraction spectra. Parcels containing various crystalline and amorphous materials, including diamorphine, were then scanned to obtain multiple localised diffraction spectra and to form a hyperspectral image. The calibration model was used for the prediction of diamorphine concentration throughout the volume of parcels and enabled the presence and location of diamorphine to be determined from the visual inspection of concentration maps. This research demonstrates for the first time the potential of an EDXRD system to generate continuous hyperspectral images of real parcels from volume scanning in security applications and introduces the opportunity to explore hyperspectral image analysis in chemical and material identification. However, more work must be done to make the system ready for implementation in border control operations by bringing down the procedure time to operational requirements and by proving the system’s portability.
Analysis of Clocked Schedules-High-Priority Tasks (1985)

Clocked schedules are used in a variety of real-time systems to perform tasks in accordance with their delay requirements. A comprehensive overview of various clocked schedules can be found in the accompanying paper by Fredericks et al. For one model of a clocked schedule we can see approximate and exact analysis of the relevant performance measures in the papers by Fredericks et al. and by Ackroyd in this issue of the Journal. These results can also be used to evaluate the long-term delays in the other models. For extremely time-critical (high-priority) tasks, the probability of tasks not getting served in the scheduled interval and the short-term delay distribution are important performance measures that are sensitive to the detail structure of the clocked schedule. In this paper, we show that these performance measures can be obtained in terms of steady-state distribution of an embedded Markov chain. This steady-state distribution is calculated, exactly or approximately, for a number of models, and the results are used to compare, numerically, various scheduling mechanisms.
What deliberately degrading search quality tells us about discount functions (2011)

Deliberate degradation of search results is a common tool in user experiments. We degrade high-quality search results by inserting non-relevant documents at different ranks. The effect of these manipulations, on a number of commonly-used metrics, is counter-intuitive: the discount functions implicit in P@k, MRR, NDCG, and others do not account for the true relationship between rank and value to the user. We propose an alternative, based on visibility data.
Photocatalytic Regioselective and Stereoselective [2 + 2] Cycloaddition of Styrene Derivatives Using a Heterogeneous Organic Photocatalyst (2017)

Photocatalytic [2 + 2] cycloaddition is a useful tool for the synthesis of cyclobutane derivatives, which contributes a large part to natural compound production. Usually, the [2 + 2] cycloadditions are catalyzed by transition-metal complexes. Here, we report the use of a pure organic photocatalyst based on a conjugated microporous polymer network for the [2 + 2] cycloaddition of styrene derivatives under the irradiation of visible light. Both unsymmetrical and homocycloaddition could be obtained with high conversion and selectivity. In addition, natural products, such as di-O-methylendiandrin A and endiandrin A are also synthesized with a high catalytic efficiency.
AID: An Automated Detector for Gender-Inclusivity Bugs in OSS Project Pages (2021)

The tools and infrastructure used in tech, including Open Source Software (OSS), can embed "inclusivity bugs"- features that disproportionately disadvantage particular groups of contributors. To see whether OSS developers have existing practices to ward off such bugs, we surveyed 266 OSS developers. Our results show that a majority (77%) of developers do not use any inclusivity practices, and 92% of respondents cited a lack of concrete resources to enable them to do so. To help fill this gap, this paper introduces AID, a tool that automates the GenderMag method to systematically find gender-inclusivity bugs in software. We then present the results of the tool's evaluation on 20 GitHub projects. The tool achieved precision of 0.69, recall of 0.92, an F-measure of 0.79 and even captured some inclusivity bugs that human GenderMag teams missed.
The Phospholipid Transfer Protein Gene Is a Liver X Receptor Target Expressed by Macrophages in Atherosclerotic Lesions (2003)

The liver X receptors (LXRs) are members of the nuclear receptor superfamily that are activated by oxysterols. In response to ligand binding, LXRs regulate a variety of genes involved in the catabolism, transport, and uptake of cholesterol and its metabolites. Here we demonstrate that LXRs also regulate plasma lipoprotein metabolism through control of the phospholipid transfer protein (PLTP) gene. LXR ligands induce the expression of PLTP in cultured HepG2 cells and mouse liver in vivo in a coordinate manner with known LXR target genes. Moreover, plasma phospholipid transfer activity is increased in mice treated with the synthetic LXR ligand GW3965. Unexpectedly, PLTP expression was also highly inducible by LXR in macrophages, a cell type not previously recognized to express this enzyme. The ability of synthetic and oxysterol ligands to regulate PLTP mRNA in macrophages and liver is lost in animals lacking both LXRalpha and LXRbeta, confirming the critical role of these receptors. We further demonstrate that the PLTP promoter contains a high-affinity LXR response element that is bound by LXR/RXR heterodimers in vitro and is activated by LXR/RXR in transient-transfection studies. Finally, immunohistochemistry studies reveal that PLTP is highly expressed by macrophages within human atherosclerotic lesions, suggesting a potential role for this enzyme in lipid-loaded macrophages. These studies outline a novel pathway whereby LXR and its ligands may modulate lipoprotein metabolism.
Chirale Induktion bei photochemischen Reaktionen, VIII. Diastereoselektive Photo‐Aldol‐Reaktion von chiralen α‐Ketoestern mit 2,3‐Dihydrooxazolen (1988)

Die photochemischen Reaktionen von 3-Acetyl-2,3-dihydro-2,2-dimethyloxazol (2) und 2,3-Dihydro-2,2-dimethyl-3-oxazolcarbonsäure-methylester (35) mit chiralen Phenylglyoxylsäure- und Brenztraubensäureestern im Sinne einer Paterno-Büchi-Reaktion werden beschrieben. Dabei bilden sich nach der Oxetanringöffnung erythro-Zucker- bzw. erythro-α-Aminozucker-Synthone. Die Diastereoselektivität liegt beim Phenylglyoxylsäure-[(–)-8-phenylmenthyl]ester über 95%. Die Konfiguration der Produkte zeigt einen re-Angriff von 2 bzw. 35 auf die prochirale 3(nη*)-angeregte Carbonylgruppe. Chiral Induction in Photochemical Reactions, VII. — Diasteroselective Photo-Aldol Reaction on Chiral α-keto esters with 2,3-Dihydrooxazoles Photochemical reactions of 2 as well as 35 with chiral phenyl-glyoxylic esters or chiral pyruvic esters, respectively, according to Paterno-Büchi are described. Solvolysis of the oxetanes yields erythro sugar or erythro α-amino sugar synthons, respectively. The diastereoselectivity is above 95% with phenylglyoxylic acid (–)-8-phenylmenthyl ester. The configurations of the products indicate the re-attack of 2 resp. 35 to the prochiral 3(nη*)-excited carbonyl group.
Abstract 3912: MM-310, a novel EphA2-targeted docetaxel nanoliposome (2016)

Abstract Taxanes are widely used to treat solid tumors either in the curative or palliative setting, in first or later lines of therapy. Analysis of docetaxel dose-response relationship strongly suggests that a higher dose would lead to high response, however will also lead to higher toxicity. This is likely related to the lack of organ and cellular specificity of docetaxel leading to high exposures in normal tissues and the relatively short circulation half-life which indirectly requires higher doses. With the goal of addressing the pharmacokinetic limitations of free docetaxel and the lack of cellular specificity, we developed a novel docetaxel-based nanoliposome (MM-310), targeted against Ephrin receptor A2 (EphA2) which is overexpressed in a wide range of tumors. MM-310 provides sustained release of docetaxel following accumulation in solid tumors. Preclinical models have demonstrated that MM-310 leverages tumor-specific accumulation through the enhanced permeability and retention effect, and cellular specificity through active targeting of EphA2 with specific scFv antibody fragments conjugated to the surface of the liposomes. Pharmacokinetic and biodistribution studies were performed in mice and rats to compare MM-310 to free docetaxel. Chronic tolerability studies were performed in rodent and non-rodent models with focus on overall animal health, as well as hematologic toxicities. Several cell-derived models of breast, lung and prostate xenografts were used to evaluate the differences betweenf MM-310 and free docetaxel. MM-310 had a significantly longer half-life than free docetaxel with prolonged exposure at the tumor site. In chronic tolerability studies, MM-310 was found to be 6-7 times better tolerated than free docetaxel with a maximum tolerated dose of at least 120 mpk, compared to 20 mpk for free docetaxel and no detectable hematological toxicity. At equitoxic dosing, MM-310 50 mpk showed greater activity than docetaxel 10 mpk in several breast, lung and prostate xenograft models. In conclusion, we developed a novel EphA2 targeted docetaxel nanoliposome with prolonged circulation time and slow and sustained drug release kinetics, to enable organ and cellular targeting. MM-310 was able to overcome hematologic toxicities observed upon treatment with free docetaxel in rodent and non-rodent models. MM-310 was also able to induce tumor regression or control tumor growth in several cell derived xenograft models, and was found to be more active than free docetaxel in most models. Citation Format: Dmitri B. Kirpotin, Suresh Tipparaju, Zhaohua Richard Huang, Walid S. Kamoun, Christine Pien, Tad Kornaga, Shinji Oyama, Ken Olivier, James D. Marks, Alexander Koshkaryev, Sarah S. Schihl, Gerald Fetterly, Birgit Schoeberl, Charles Noble, Mark Hayes, Daryl C. Drummond. MM-310, a novel EphA2-targeted docetaxel nanoliposome. [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 3912.
Treatment of Respiratory Syncytial Virus Infection: Past, Present and Future (2011)

Children with RSV infection < 5 y infants <35 weeks gestational period e.g. < 6months of age, with severe congenital heart and/or lung disease etc. e.g. immunocompromised or/with bronchiolitis, pneumonia e.g.
Fourier-space design of efficient photonic crystal cavity-Waveguide couplers (2006)

We design efficient photonic crystal (PC) cavity-waveguide couplers using the Fourier-space optimization. This system is a fundamental building block for integrated photonic circuits with direct applications in quantum information processing.
Cornell university's 2005 DARPA grand challenge entry (2006)

Abstract The 2005 DARPA Grand Challenge required teams to design and build autonomous off‐road vehicles capable of handling harsh terrain at high speeds while following a loosely defined path. This paper discusses the critical subsystems of Cornell University's entry, an autonomous Spider Light Strike Vehicle. An attitude and position estimator is presented with modifications for specific problems associated with high‐speed autonomous ground vehicles, including Global Positioning System signal loss and reacquisition. A novel terrain estimation algorithm is presented to combine attitude and position estimates with terrain sensors to generate a detailed elevation model. The elevation model is combined with a spline‐based path planner in a sensing/action feedback loop to generate smooth, human‐like paths that are consistent with vehicle dynamics. The performance of these subsystems is validated in a series of demonstrative experiments, along with an evaluation of the full system at the Grand Challenge. © 2006 Wiley Periodicals, Inc.
Echocardiographic findings of pulmonary atresia or critical pulmonary stenosis and intact ventricular septum in utero (1999)

Fetal hemodynamic information was useful for making decisions not only after birth, but also in utero, and may eventually result in improving the prognosis of babies with PA/CPS. Serial observation of the fetuses with PA/CPS may also suggest the possible pathogenesis of PA/CPS in utero.
Abstract PR15: Functional analysis of diverse oncogenic driver mutations using an isogenic cell line library identifies novel drug responses and alterations in metabolism (2015)

Abstract There is an urgent need in oncology to link molecular aberrations in tumors with altered cellular behaviors, such as metabolic derangements, and to identify novel therapeutics for cancer treatment. We have sought to identify synthetic-lethal genetic interactions that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated an unbiased and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model more complex cellular contexts. Applied to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene including resistance to PI3K/AKT pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic-lethal manner. These studies provide new drug and biomarker pairs for clinical investigation. We have also performed global metabolomics analysis in a subset of the isogenic cell lines demonstrating alterations in metabolic pathways that are shared across multiple oncogenes, as well as those that are distinct to specific oncogenic drivers. This scalable approach enables the prediction of drug responses from patient data and can be used to accelerate the development of new genotype-directed therapies. Citation Format: Maria M. Martins, Alicia Y. Zhou, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John D. Gordan, Rebecca S. Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul A. Clemons, Alykhan Shamji, Stuart Schreiber, Stuart Schreiber, Nevan J. Krogan, Kevan M. Shokat, Kevan M. Shokat, Frank McCormick, Daniel Nomura, Sourav Bandyopadhyay, Andrei Goga. Functional analysis of diverse oncogenic driver mutations using an isogenic cell line library identifies novel drug responses and alterations in metabolism. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr PR15.
ARMageddon: Last-Level Cache Attacks on Mobile Devices (2015)

In the last 10 years cache attacks on Intel CPUs have gained increasing attention among the scientific community. More specifically, powerful techniques to exploit the cache side channel have been developed. However, so far only a few investigations have been performed on modern smartphones and mobile devices in general. In this work, we describe Evict+Reload, the first access-based cross-core cache attack on modern ARM Cortex-A architectures as used in most of today’s mobile devices. Our attack approach overcomes several limitations of existing cache attacks on ARM-based devices, for instance, the requirement of a rooted device or specific permissions. Thereby, we broaden the scope of cache attacks in two dimensions. First, we show that all existing attacks on the x86 architecture can also be applied to mobile devices. Second, despite the general belief these attacks can also be launched on non-rooted devices and, thus, on millions of off-the-shelf devices. Similarly to the well-known Flush+Reload attack for the x86 architecture, Evict+Reload allows to launch generic cache attacks on mobile devices. Based on cache template attacks we identify information leaking through the last-level cache that can be exploited, for instance, to infer tap and swipe events, inter-keystroke timings as well as the length of words entered on the touchscreen, and even cryptographic primitives implemented in Java. Furthermore, we demonstrate the applicability of Prime+Probe attacks on ARM Cortex-A CPUs. The performed example attacks demonstrate the immense potential of our proposed attack techniques.
Biochemical and Structural Characterizations of Two Dictyostelium Cellobiohydrolases from the Amoebozoa Kingdom Reveal a High Level of Conservation between Distant Phylogenetic Trees of Life (2016)

GH7 CBHs are among the most important cellulolytic enzymes both in nature and for emerging industrial applications for cellulose breakdown. Understanding the diversity of these key industrial enzymes is critical to engineering them for higher levels of activity and greater stability. The present work demonstrates that two GH7 CBHs from social amoeba are surprisingly quite similar in structure and activity to the canonical GH7 CBH from the model biomass-degrading fungus T. reesei when tested under equivalent conditions (with added CBM-linker domains) on an industrially relevant substrate.
A Cloud Environment for Data-intensive Storage Services (2011)

The emergence of cloud environments has made feasible the delivery of Internet-scale services by addressing a number of challenges such as live migration, fault tolerance and quality of service. However, current approaches do not tackle key issues related to cloud storage, which are of increasing importance given the enormous amount of data being produced in today's rich digital environment (e.g. by smart phones, social networks, sensors, user generated content). In this paper we present the architecture of a scalable and flexible cloud environment addressing the challenge of providing data-intensive storage cloud services through raising the abstraction level of storage, enabling data mobility across providers, allowing computational and content-centric access to storage and deploying new data-oriented mechanisms for QoS and security guarantees. We also demonstrate the added value and effectiveness of the proposed architecture through two real-life application scenarios from the healthcare and media domains.
An Architectural Vision for a Data-Centric IoT: Rethinking Things, Trust and Clouds (2017)

The Internet of Things (IoT) is producing a tidal wave of data, much of it originating at the network edge, from applications with requirements unmet by the traditional back-end Cloud architecture. To address the disruption caused by the overabundance of data, this paper offers a holistic data-centric architectural vision for the data-centric IoT. It advocates that we rethink our approach to the design and definition of key elements: that we shift our focus from Things to Smart Objects; grow Trust organically; and evolve back-end Clouds toward Edge and Fog clouds, which leverage data-centric networks and enable optimal handling of upstream data flows. Along the way, we wax poetic about several blue-sky topics, assess the status of these elements in the context of related work, and identify known gaps in meeting this vision.
Isolation of Notoamide S and Enantiomeric 6-epi-Stephacidin A from the Fungus Aspergillus amoenus: Biogenetic Implications (2015)

Notoamide S has been hypothesized to be a key biosynthetic intermediate for characteristic metabolites stephacidin A, notoamide B, and versicolamide B in Aspergillus sp. but has not yet been isolated. The isolation of notoamide S and an enantiomeric mixture of 6-epi-stephacidin A enriched with the (-)-isomer from Aspergillus amoenus is reported. The presence of (+)-versicolamide B suggests that the fungus possesses only the oxidase, which converts (+)-6-epi-stephacidin A into (+)-Versicolamide B, but not for (-)-6-epi-Stephacidin A.
Optimizing block-thresholding segmentation for multilayer compression of compound images (2000)

Compound document images contain graphic or textual content along with pictures. They are a very common form of documents, found in magazines, brochures, Web sites, etc. We focus our attention on the mixed raster content (MRC) multilayer approach for compound image compression. We study block thresholding as a means to segment an image for MRC. An attempt is made to optimize the block threshold in a rate-distortion sense. Also, a fast algorithm is presented to approximate the optimized method. Extensive results are presented including rate-distortion curves, segmentation masks and reconstructed images, showing the performance of the proposed algorithm.
Controllable Electrical Properties of Metal-Doped In2O3 Nanowires for High-Performance Enhancement-Mode Transistors (2012)

In recent years, In(2)O(3) nanowires (NWs) have been widely explored in many technological areas due to their excellent electrical and optical properties; however, most of these devices are based on In(2)O(3) NW field-effect transistors (FETs) operating in the depletion mode, which induces relatively higher power consumption and fancier circuit integration design. Here, n-type enhancement-mode In(2)O(3) NW FETs are successfully fabricated by doping different metal elements (Mg, Al, and Ga) in the NW channels. Importantly, the resulting threshold voltage can be effectively modulated through varying the metal (Mg, Ga, and Al) content in the NWs. A series of scaling effects in the mobility, transconductance, threshold voltage, and source-drain current with respect to the device channel length are also observed. Specifically, a small gate delay time (0.01 ns) and high on-current density (0.9 mA/μm) are obtained at 300 nm channel length. Furthermore, Mg-doped In(2)O(3) NWs are then employed to fabricate NW parallel array FETs with a high saturation current (0.5 mA), on/off ratio (>10(9)), and field-effect mobility (110 cm(2)/V·s), while the subthreshold slope and threshold voltage do not show any significant changes. All of these results indicate the great potency for metal-doped In(2)O(3) NWs used in the low-power, high-performance thin-film transistors.
Automatically Deciding if a Document was Scanned or Photographed (2020)

Portable digital cameras are being used widely by students and professionals in different fields as a practical way to digitize documents. Tools such as PhotoDoc enable the batch processing of such documents, performing automatic border removal and perspective correction. A PhotoDoc processed document and a scanned one look very similar to the human eye if both are in true color. However, if one tries to automatically binarize a batch of documents digitized from portable cameras compared to scanners, they have different features. The knowledge of their source is fundamental for successful processing. This paper presents a classification strategy to distinguish between scanned and photographed documents. Over 16,000 documents were tested with a correct classification rate of over 99.96%.
Supplementary Figure 3 from An Epithelial–Mesenchymal Transition Gene Signature Predicts Resistance to EGFR and PI3K Inhibitors and Identifies Axl as a Therapeutic Target for Overcoming EGFR Inhibitor Resistance (2023)

&lt;p&gt;PDF file - 66K, CDH1 probes vary in their accuracy and dynamic range&lt;/p&gt;