gebhart/patrepeval huggingface dataset:
The Open Reaction Database (2021)

Chemical reaction data in journal articles, patents, and even electronic laboratory notebooks are currently stored in various formats, often unstructured, which presents a significant barrier to downstream applications, including the training of machine-learning models. We present the Open Reaction Database (ORD), an open-access schema and infrastructure for structuring and sharing organic reaction data, including a centralized data repository. The ORD schema supports conventional and emerging technologies, from benchtop reactions to automated high-throughput experiments and flow chemistry. The data, schema, supporting code, and web-based user interfaces are all publicly available on GitHub. Our vision is that a consistent data representation and infrastructure to support data sharing will enable downstream applications that will greatly improve the state of the art with respect to computer-aided synthesis planning, reaction prediction, and other predictive chemistry tasks.
Task feasibility of V shape electrothermal actuators (2020)

Abstract This paper investigates the modeling, design, and task feasibility of V shape electrothermal actuators. In the first part, the force-deflection governing expressions are derived and the actuator performance is analyzed based on these expressions. The influence of the actuator dimensions and properties on its performance is clarified. In the second part, the task feasibility is further investigated. A performance measure is proposed for evaluating the capacity of the actuator to accomplish required tasks depending on the application. This measure is used for finding a feasible configuration and optimized design. A case study is finally presented, showing very good agreement between analytical model and finite element simulations, and demonstrating the robustness of the task feasibility measure.
Measurement of single top-quark production in association with a W boson in the single-lepton channel at $$\sqrt{s} = 8\,\text {TeV}$$ with the ATLAS detector (2021)

Abstract The production cross-section of a top quark in association with a W boson is measured using proton–proton collisions at $$\sqrt{s} = 8\,\text {TeV}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msqrt><mml:mi>s</mml:mi></mml:msqrt><mml:mo>=</mml:mo><mml:mn>8</mml:mn><mml:mspace/><mml:mtext>TeV</mml:mtext></mml:mrow></mml:math> . The dataset corresponds to an integrated luminosity of $$20.2\,\text {fb}^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>20.2</mml:mn><mml:mspace/><mml:msup><mml:mtext>fb</mml:mtext><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math> , and was collected in 2012 by the ATLAS detector at the Large Hadron Collider at CERN. The analysis is performed in the single-lepton channel. Events are selected by requiring one isolated lepton (electron or muon) and at least three jets. A neural network is trained to separate the tW signal from the dominant $$t{\bar{t}}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>t</mml:mi><mml:mover><mml:mrow><mml:mi>t</mml:mi></mml:mrow><mml:mrow><mml:mo>¯</mml:mo></mml:mrow></mml:mover></mml:mrow></mml:math> background. The cross-section is extracted from a binned profile maximum-likelihood fit to a two-dimensional discriminant built from the neural-network output and the invariant mass of the hadronically decaying W boson. The measured cross-section is $$\sigma _{tW} = 26 \pm 7\,\text {pb}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:mrow><mml:mi>tW</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mn>26</mml:mn><mml:mo>±</mml:mo><mml:mn>7</mml:mn><mml:mspace/><mml:mtext>pb</mml:mtext></mml:mrow></mml:math> , in good agreement with the Standard Model expectation.
Inhibition of HLA-DR Assembly, Transport, and Loading by Human Cytomegalovirus Glycoprotein US3: a Novel Mechanism for Evading Major Histocompatibility Complex Class II Antigen Presentation (2002)

Human cytomegalovirus (HCMV) establishes persistent lifelong infections and replicates slowly. To withstand robust immunity, HCMV utilizes numerous immune evasion strategies. The HCMV gene cassette encoding US2 to US11 encodes four homologous glycoproteins, US2, US3, US6, and US11, that inhibit the major histocompatibility complex class I (MHC-I) antigen presentation pathway, probably inhibiting recognition by CD8(+) T lymphocytes. US2 also inhibits the MHC-II antigen presentation pathway, causing degradation of human leukocyte antigen (HLA)-DR-alpha and -DM-alpha and preventing recognition by CD4(+) T cells. We investigated the effects of seven of the US2 to US11 glycoproteins on the MHC-II pathway. Each of the glycoproteins was expressed by using replication-defective adenovirus vectors. In addition to US2, US3 inhibited recognition of antigen by CD4(+) T cells by a novel mechanism. US3 bound to class II alpha/beta complexes in the endoplasmic reticulum (ER), reducing their association with Ii. Class II molecules moved normally from the ER to the Golgi apparatus in US3-expressing cells but were not sorted efficiently to the class II loading compartment. As a consequence, formation of peptide-loaded class II complexes was reduced. We concluded that US3 and US2 can collaborate to inhibit class II-mediated presentation of endogenous HCMV antigens to CD4(+) T cells, allowing virus-infected cells to resist recognition by CD4(+) T cells.
Shrinkage based features for slot tagging with conditional random fields (2014)

In this paper we propose a set of class-based features that are generated in an unsupservised fashion to improve slot tagging with Conditional Random Fields (CRFs). The feature generation is based on the idea behind shrinkage based language models, where shrinking the sum of parameter magnitudes in an exponential model tends to improve performance. We use these features with CRFs and show that they consistently improve the slot tagging performance against baselines on several natural language understanding tasks. Since the proposed features are generated in an unsupervised manner without significant computational overhead, the improvements in performance comes for free and we expect that the same features may result in gains in other tagging tasks.
Figure S2 from Elastography Can Map the Local Inverse Relationship between Shear Modulus and Drug Delivery within the Pancreatic Ductal Adenocarcinoma Microenvironment (2023)

&lt;p&gt;Montage of shear modulus elastograms obtained from (a) AsPC-1 and (b) BxPC-3 tumors. We acquired these images 2mm slice interval. The dotted lines denote the tumor in each scan plane. White stars indicated the scan plane along which the tumors were cut and stained for Masson's Trichrome (c, f), lectin (d, g) and Verteporfin uptake (e, h).&lt;/p&gt;
Fiber‐in‐Tube Design of Co9S8‐Carbon/Co9S8: Enabling Efficient Sodium Storage (2019)

The sodium-ion battery is a promising battery technology owing to its low price and high abundance of sodium. However, the sluggish kinetics of sodium ion makes it hard to achieve high-rate performance, therefore impairing the power density. In this work, a fiber-in-tube Co<sub>9</sub> S<sub>8</sub> -carbon(C)/Co<sub>9</sub> S<sub>8</sub> is designed with fast sodiation kinetics. The experimental and simulation analysis show that the dominating capacitance mechanism for the high Na-ion storage performance is due to abundant grain boundaries, three exposed layer interfaces, and carbon wiring in the design. As a result, the fiber-in-tube hybrid anode shows a high specific capacity of 616 mAh g<sup>-1</sup> after 150 cycles at 0.5 A g<sup>-1</sup> . At 1 A g<sup>-1</sup> , a capacity of ca. 451 mAh g<sup>-1</sup> can be achieved after 500 cycles. More importantly, a high energy density of 779 Wh kg<sup>-1</sup> and power density of 7793 W kg<sup>-1</sup> can be obtained simultaneously.
Distributed multiagent formation control with enhanced scalability (2007)

A one step ahead optimization based control of autonomous agents that modifies our earlier work, to enhance network scalability is proposed. As in our earlier work, each agent is modeled as a double integrator. The goal is to force the agents to converge to a formation specified by their desired relative positions, and moving with constant velocity. The earlier work had the property that in face of the arrival of a new agent the control laws of only the agents this new arrival attached it self to needed to be adjusted. However, this required that the largest possible network that may result be anticipated a priori, causing potentially sluggish responses when in a given epoch the network is much smaller than the largest anticipated size. In this paper we propose a new law that removes this difficulty.
Development of PC and transputer-based walking robots (1992)

Robotic walking is one of the key activities on the critical path to the integration of computers into a world designed for use by bipeds, the others being real-time image processing, scene analysis and depth ranging, and touch sensors for force feedback. The dynamic control of balance while walking, by stepwise refinement of controllers for successively decreasing numbers of legs is considered. With this aim the authors have constructed a 6, a 4, and most recently a 2 legged robot. The work done on PC and transputer-based hexapod and quadruped is described. >
A 180o Phase Shift Biasing Technique for Realizing High PSRR in Low Power Temperature Sensors (2022)

The paper presents a low-cost method (no extra LDO, Op-amp) to increase the PSRR of composite pair based temperature sensor. Composite pair is a commonly used circuit to generate a linear PTAT voltage for a wide temperature range. A 180° phase shift, voltage biasing technique is introduced at the gate of the NMOS transistor to obtain a supply independent bias current in composite pair. The proposed technique thus achieves a high supply noise rejection. The circuit as a whole does not require additional circuitry, therefore it saves power and area. A 6$\mu$W Temperature sensor with 1mV/°c slope is designed in TSMC 180nm technology and achieves PSRR of -80dB. Post-layout simulation results show that the temperature sensor achieves inaccuracy of ±0.1°C from −55°C to 125°C, PSRR of −80dB at 105Hz and -70dB at 200kHz at 1V power supply, and the line regulation of 0.016%/V in a supply voltage range of 1V to 2.5V. Monte-Carlo simulation result for the output PSRR shows −80.56dB as the mean-value with a maximum deviation of ±1.5dB.
Supplementary Figure 1 from Efficacy of Levo-1-Methyl Tryptophan and Dextro-1-Methyl Tryptophan in Reversing Indoleamine-2,3-Dioxygenase–Mediated Arrest of T-Cell Proliferation in Human Epithelial Ovarian Cancer (2023)

Supplementary Figure 1 from Efficacy of Levo-1-Methyl Tryptophan and Dextro-1-Methyl Tryptophan in Reversing Indoleamine-2,3-Dioxygenase–Mediated Arrest of T-Cell Proliferation in Human Epithelial Ovarian Cancer
Radical ipso-Substitution of a Carbon–Fluorine Bond Leading to Fluoro-7-azaindolines and Fluoro-7-azaindoles (2014)

Rare examples of a synthetically useful radical ipso-substitution of a carbon-fluorine bond are reported, leading to highly functionalized 5,6-difluoro-7-azaindolines. An unexpected hydrogen atom translocation and fragmentation with loss of molecular nitrogen and formation of a nitrile were observed in the case of an N-benzyl-tetrazole derivative.
Coding with Encoding Uncertainty (2013)

We study the channel coding problem when errors and uncertainty occur in the encoding process. For simplicity we assume the channel between the encoder and the decoder is perfect. Focusing on linear block codes, we model the encoding uncertainty as erasures on the edges in the factor graph of the encoder generator matrix. We first take a worst-case approach and find the maximum tolerable number of erasures for perfect error correction. Next, we take a probabilistic approach and derive a sufficient condition on the rate of a set of codes, such that decoding error probability vanishes as blocklength tends to infinity. In both scenarios, due to the inherent asymmetry of the problem, we derive the results from first principles, which indicates that robustness to encoding errors requires new properties of codes different from classical properties.
Connecting Markov random fields and active contour models: application to gland segmentation and classification (2017)

We introduce a Markov random field (MRF)-driven region-based active contour model (MaRACel) for histological image segmentation. This Bayesian segmentation method combines a region-based active contour (RAC) with an MRF. State-of-the-art RAC models assume that every spatial location in the image is statistically independent, thereby ignoring valuable contextual information among spatial locations. To address this shortcoming, we incorporate an MRF prior into energy term of the RAC. This requires a formulation of the Markov prior consistent with the continuous variational framework characteristic of active contours; consequently, we introduce a continuous analog to the discrete Potts model. Based on the automated segmentation boundary of glands by MaRACel model, explicit shape descriptors are then employed to distinguish prostate glands belonging to Gleason patterns 3 (G3) and 4 (G4). To demonstrate the effectiveness of MaRACel, we compare its performance to the popular models proposed by Chan and Vese (CV) and Rousson and Deriche (RD) with respect to the following tasks: (1) the segmentation of prostatic acini (glands) and (2) the differentiation of G3 and G4 glands. On almost 600 prostate biopsy needle images, MaRACel was shown to have higher average dice coefficients, overlap ratios, sensitivities, specificities, and positive predictive values both in terms of segmentation accuracy and ability to discriminate between G3 and G4 glands compared to the CV and RD models.
Finite‐difference modeling of ground‐penetrating radar data in frequency‐dependent dielectric media (1996)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1996Finite‐difference modeling of ground‐penetrating radar data in frequency‐dependent dielectric mediaAuthors: Tim BergmannJohan O. A. RobertssonKlaus HolligerTim BergmannETH Zurich, Switzerland, Johan O. A. RobertssonETH Zurich, Switzerland, and Klaus HolligerETH Zurich, Switzerlandhttps://doi.org/10.1190/1.1826774 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1826774FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 1996ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1996 Pages: 2106 publication data© 1996 Copyright © 1996 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 10 Feb 2005 CITATION INFORMATION Tim Bergmann, Johan O. A. Robertsson, and Klaus Holliger, (1996), "Finite‐difference modeling of ground‐penetrating radar data in frequency‐dependent dielectric media," SEG Technical Program Expanded Abstracts : 801-804. https://doi.org/10.1190/1.1826774 Plain-Language Summary PDF DownloadLoading ...
Hindered lithium dialkylamide initiators for the living anionic polymerization of methacrylic esters (1994)

Abstract Lithium diisopropylamide is an efficient initiator for the anionic polymerization of methyl methacrylate in polar solvents at –78°C. Predictable molecular weights based on the initiator concentration were obtained, yields were quantitative, and molecular weight distributions were relatively narrow (&lt;1.30). The presence of an amino end group and confirmation of the initiation mechanism were confirmed by potentiometric titration using HClO 4 . Number‐average molecular weights determined by titration agreed well with values determined by SEC. Other lithium dialkylamides that contain larger alkyl groups such as lithium diisobutylamide were less efficient initiators. This was attributed to the more nucleophilic anion due to less steric hindrance near the nitrogen atom. Molecular weight distributions were significantly broadened (&gt;2.0), and molecular weight control was not achieved. However, polymer yields were quantitative. In all cases, PMMA stereochemistry was indicative of a solvent‐separated lithium counterion, and triad compositions were identical to organolithium initiated homopolymers, i.e., 78% syndiotactic, 20% heterotactic, and 2% isotactic. © 1994 John Wiley &amp; Sons, Inc.
Defining the Value of Injection Current and Effective Electrical Contact Area for EGaIn-Based Molecular Tunneling Junctions (2013)

Analysis of rates of tunneling across self-assembled monolayers (SAMs) of n-alkanethiolates SCn (with n = number of carbon atoms) incorporated in junctions having structure Ag(TS)-SAM//Ga2O3/EGaIn leads to a value for the injection tunnel current density J0 (i.e., the current flowing through an ideal junction with n = 0) of 10(3.6±0.3) A·cm(-2) (V = +0.5 V). This estimation of J0 does not involve an extrapolation in length, because it was possible to measure current densities across SAMs over the range of lengths n = 1-18. This value of J0 is estimated under the assumption that values of the geometrical contact area equal the values of the effective electrical contact area. Detailed experimental analysis, however, indicates that the roughness of the Ga2O3 layer, and that of the Ag(TS)-SAM, determine values of the effective electrical contact area that are ~10(-4) the corresponding values of the geometrical contact area. Conversion of the values of geometrical contact area into the corresponding values of effective electrical contact area results in J0(+0.5 V) = 10(7.6±0.8) A·cm(-2), which is compatible with values reported for junctions using top-electrodes of evaporated Au, and graphene, and also comparable with values of J0 estimated from tunneling through single molecules. For these EGaIn-based junctions, the value of the tunneling decay factor β (β = 0.75 ± 0.02 Å(-1); β = 0.92 ± 0.02 nC(-1)) falls within the consensus range across different types of junctions (β = 0.73-0.89 Å(-1); β = 0.9-1.1 nC(-1)). A comparison of the characteristics of conical Ga2O3/EGaIn tips with the characteristics of other top-electrodes suggests that the EGaIn-based electrodes provide a particularly attractive technology for physical-organic studies of charge transport across SAMs.
Cancer Detection Using an Artificial Secretable MicroRNA Found in Blood and Urine (2022)

Biomarkers can potentially help in the detection and prognosis of diseases such as cancer, its recurrence, predicting response to therapy, and monitoring of response during and/or after treatment. Endogenous tumor blood biomarkers suffer from low concentrations that are not distinguishable from background noise and, if identified, the localization of the biomarker production site is not known. The use of exogenously introduced or artificial biomarkers can eliminate these issues. In this study, we show that cancer cells can be made to produce an artificial secreted microRNA (Sec-miR) that can be detected in media from cells in culture, and from both blood and urine in living mice. In culture, we show that chaining a number of Sec-miR sequences in a plasmid and transfecting cells with the plasmids could increase Sec-miR secretion as the number of sequences increases. Tumor induction in mice with a stably transfected HeLa cell line shows the presence and significant increase in the Sec-miR with time and tumor growth in plasma (p < 0.001, R2 = 0.5542). The relative half-life of the Sec-miR was seen to be 1.2 h in the plasma of living mice and was seen to appear in urine within 12 h. The transgene for the Sec-miR within a minicircle was introduced via the tail-vein into subcutaneous tumor-bearing mice. As the tumor growth increased with time, further in vivo transfection of the Sec-miR minicircles showed an increase in Sec-miR in both plasma and urine (R2 = 0.4546). This study demonstrated that an exogenous Sec-miR biomarker would allow for early tumor detection using in vitro diagnostics techniques.
Continuous ex vivo glucose sensing in human physiological fluids using an enzymatic sensor in a vein replica (2023)

Managing blood glucose can affect important clinical outcomes during the intraoperative phase of surgery. However, currently available instruments for glucose monitoring during surgery are few and not optimized for the specific application. Here we report an attempt to exploit an enzymatic sensor in a vein replica that could continuously monitor glucose level in an authentic human bloodstream. First, detailed investigations of the superficial venous systems of volunteers were carried out using ocular and palpating examinations, as well as advanced ultrasound measurements. Second, a tubular glucose-sensitive biosensor mimicking a venous system was designed and tested. Almost ideal linear dependence of current output on glucose concentration in phosphate buffer saline was obtained in the range 2.2-22.0 mM, whereas the dependence in human plasma was less linear. Finally, the developed biosensor was investigated in whole blood under homeostatic conditions. A specific correlation was found between the current output and glucose concentration at the initial stage of the biodevice operation. However, with time, blood coagulation during measurements negatively affected the performance of the biodevice. When the experimental results were remodeled to predict the response without the influence of blood coagulation, the sensor output closely followed the blood glucose level.
Link adaptation in a multi-antenna system (2003)

We consider link adaptation for multi-antenna systems based on channel information also that at the transmitter. Using adaptive channel inversion (ACI), a step-wise trade-off between spatial multiplexing and diversity is realized. Due to pre- and post-processing, the channel is corrupted only by Gaussian noise in front of the detectors. By jointly optimizing the number of data streams and the common modulation, a nearly continuous adaptation of spectral efficiency is realized. Up to moderate powers, the channel capacity is approached in regular and singular MIMO channels, provided that scalar coding is applied.
Development of an All-Atom Force Field for Heterocycles. Properties of Liquid Pyrrole, Furan, Diazoles, and Oxazoles (1998)

The approach to the extension of the optimized potentials for liquid simulations all-atom (OPLS-AA) force field, which was tested for pyridine and the diazenes in the first paper of this series, has been extended to pyrrole, pyrazole, imidazole, furan, isoxazole, and oxazole. Standard OPLS Lennard-Jones parameters are used for the nonbonded interactions in conjunction with partial charges obtained from fitting to RHF/6-31G* electrostatic potential surfaces. The harmonic bond stretching and angle bending terms are adopted mostly from the AMBER force field, although the addition of two new atom types was required. The resultant force field was tested by computing the gas-phase structures of the heterocycles, heterocycle−water interaction energies, properties of the pure liquids, and the relative free energies of hydration for pyrrole and imidazole.