gebhart/patrepeval huggingface dataset:
Integrated cellular framework for modeling ecosystems: Theory and applications (2017)

We introduce an integrated framework for modeling and simulation of ecosystems based on cellular models. The framework integrates cellular modeling, web-based simulation, and geographic information systems (GISs) for data collection and visualization. In this framework, data extraction from GISs is automated; we use the Cell-DEVS formalism for modeling the ecosystem and the CD++ cellular modeling tool within the RISE (RESTful Interoperability Simulation Environment) middleware for web-based simulation. The simulation results are easily integrated with Google Earth data for visualization. We discuss the design, implementation, and benefits of the integrated approach for modeling and simulation in spatial analysis of ecosystem services. We show different case studies in the area of ecological systems, demonstrating how to apply the framework, its usability, and flexibility. We focus on the use of models available in remote servers, their integration with GIS data for inputs, and georeferenced visualization of the results. We show how the modeling methods based on DEVS and their modular interfaces make it easy to build such an architecture and we discuss its application to the field of environmental systems.
Irreversible and bivalent ligands for selected G-protein coupled receptors (2002)

\n\t\t\t\t\tDerivatives of pharmaceutical compounds that could potentially bind irreversibly to a hypertension controlling receptor were synthesised to provide tools for studying this receptor. Also compounds that simultaneously activate two cardiovascular receptors with opposing cellular mechanisms were synthesised. This resulted in a desired partial reduction in the activity of one receptor.\n\t\t\t\t
A phase I dose escalation trial of BI 2536, a novel Plk1 inhibitor, with standard dose pemetrexed in previously treated advanced or metastatic non-small cell lung cancer (NSCLC) (2008)

8115 Background: BI 2536 is a novel, highly selective, potent inhibitor of Polo-like kinase 1 (Plk1), a key regulator of mitotic progression. BI 2536 has demonstrated favorable tolerability and antitumor activity in Phase I trials. We investigated the MTD, safety and PK of BI 2536 in combination with standard dose pemetrexed in patients (pts) with previously treated advanced or metastatic NSCLC. Methods: Eligible pts included stage IIIB/IV NSCLC and ECOG PS 0–2, relapsing after 1st line platinum-based therapy. Pts were treated with 500 mg/m2 pemetrexed and escalating doses of BI 2536 given as a 1h i.v. infusion on Day 1 every three weeks. A standard Phase I 3+3 trial design was used. The primary objective was to determine the MTD of BI 2536 given with pemetrexed. Secondary endpoints were response rate (RECIST), overall safety and PK. AEs were evaluated using NCI-CTCAE v. 3.0. Pts not progressing after 6 cycles of combination therapy were eligible to continue BI 2536 monotherapy until tumor progression. Results: 33 pts were treated at doses from 100–325 mg BI 2536. The MTD was defined at 300 mg BI 2536 after the occurrence of dose limiting toxicities (Grade 3 rash and Grade 4 neutropenia) at 325 mg. The most common drug related AEs were mostly mild to moderate nausea (36%), rash (33%), anorexia (27%), stomatitis (24%) and pruritus (24%). Reversible Grade 3/4 neutropenia occurred in 18% of pts. Other drug related Grade 3 events were rash (n=2), acute renal failure (n=1) and confusion (n=1). There were 2 confirmed durable partial responses; 7 pts were treated for >4 courses. Up to 15 courses of BI 2536 therapy have been administered without cumulative toxicity. The MTD is being confirmed in expanded pt cohorts treated at doses of 200–300 mg. PK analysis showed similar BI 2536 exposure with/without pemetrexed. Pemetrexed exposure was not altered after co-administration of BI 2536. Conclusion: Preliminary results demonstrate that a combination of BI 2536 and pemetrexed has an acceptable safety profile in relapsed NSCLC without any PK interaction. Encouraging antitumor activity was observed. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Boehringer Ingelheim Pharma GmbH & Co. KG Boehringer Ingelheim, Eli Lilly Boehringer Ingelheim Pharma
Acceleration of Medical Imaging Algorithms Using Programmable Graphics Hardware (2008)

This thesis presents acceleration techniques for medical imaging algorithms. The rapid development of medical scanning devices produces huge amounts of raw data. On the one hand, high-resolution images can be computed from the raw data and, thus,
providing the physicians better basis for diagnosis. On the other hand, the amount of
raw data leads to longer processing times. About three years ago, graphics processing
units (GPUs) have become programmable and can be used for other tasks than graphics.
GPUs are very suitable for medical imaging algorithms – they are fast, relatively cheap,
the instruction set is powerful enough for many of algorithms, and with standard APIs
easy to program. In this work, medical imaging filtering, reconstruction, segmentation,
and registration algorithms are accelerated using GPUs. Averagely a 10-times speedup
is achieved compared to optimized SSE3 CPU implementations. Some implementations
run 100 times faster than their CPU counterparts. The results are already used
successfully in products by Siemens Medical Solutions.
FINESSE: An open, three-cohort, phase II trial testing oral administration of lucitanib in patients with FGFR1-amplified or nonamplified estrogen receptor-positive metastatic breast cancer. (2014)

TPS1134 Background: FGF aberrancy is observed in approximately 25% of breast cancer (BC) patients. Preclinical studies demonstrated that targeting FGFR could lead to antitumor effects. Lucitanib is a multikinase inhibitor targeting FGFR1-2, VEGFR1-3 and PDGFRA/B. In the phase I trial testing lucitanib continuous dosing, 6 objective responses were observed in 12 evaluable patients presenting with FGFR1 and/or FGF3-4-19 (11q) amplification. Based on this, a phase II trial has been initiated. Methods: This is a phase II trial testing the efficacy of lucitanib 15 mg daily in patients with ER+/HER2- metastatic BC who have received at least first line endocrine therapy in the metastatic setting. After informed consent, a biopsy of metastatic site is required to assess the presence of FGFR1- and/or 11q- amplification, which will be centrally evaluated using FISH. Testing could be also performed on archived metastatic biopsies. The primary objective is to evaluate the ORR of single agent lucitanib in metastatic BC patients with FGFR1-amplified, FGFR1-non-amplified with neither FGFR1- amplification nor 11q- amplification. Secondary objectives include clinical benefit rate, PFS, safety, pharmacokinetics and exploratory biomarker analyses. A Simon two-stage design will be used for each of the cohorts to test the null hypothesis that the ORR is 5% or less vs 20% using a one-sided test with 5% level of significance and 90% power. In each cohort separately, an initial 21 patients with measurable disease at baseline will be assessed at the end of stage 1. If at least 2 patients respond per the pre-specified criteria, this cohort will accrue additional 20 patients. The null hypothesis will be rejected if there are at least 5 responders among all 41 patients. The trial started in December 2013. It is planned to open in 9 countries and 30 centers. As of January 24, 5 patients have been screened, 1 of them in the FGFR1-amplified arm. Conclusion: FINESSE is a phase II trial testing lucitanib, a multikinase inhibitor, in three selected populations in order to define the efficacy of the drug and the predictive value of FGFR1 or 11q amplifications. Clinical trial information: 2013-000288-10.
A Colorimetric and Ratiometric Fluorescent Chemosensor with Three Emission Changes: Fluoride Ion Sensing by a Triarylborane– Porphyrin Conjugate (2003)

Störung des Energietransfer-Pfads und der π-Konjugation zwischen den Chromophoren in einem Triarylboran-Porphyrin-Konjugat nach Bindung eines Fluoridions an das Borzentrum sind vermutlich die Ursache für das Auftreten dreier Emissionsbanden (bei 356, 670 und 692 nm). Dieses System eignet sich zum Fluoridnachweis: Die Farbe ändert sich nach Bindung von Fluorid von Violett nach Grün (siehe Bild), die Fluoreszenz geht ins Bläuliche über. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2003/z50788_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.
Isomerization of Linear to Hyperbranched Polymers: Two Isomeric Lactones Converge via Metastable Isostructural Polyesters to a Highly Branched Analogue (2018)

We report here the Zn(II)-catalyzed convergence of two metastable and isostructural polyesters to an isomeric polymer having a hyperbranched architecture. Ring-opening transesterification polymerization (ROTEP) of 4-carbomethoxyvalerolactone (<b>CMVL</b>) under Brønsted catalysis is known to give the linear polyester <b>PCMVL</b>. We show here that this can be isomerized to the equilibrated (and highly branched) polyester <b>EQ-PCMVL</b>. Analysis of the fragments obtained from eliminative degradation of <b>EQ-PCMVL</b> were critical in the formulation of its structure. The isomerization of <b>PCMVL</b> to <b>EQ-PCMVL</b> is a direct consequence of the presence of the second ester functional group in the <b>CMVL</b> ester-lactone, a rarely studied class of monomer. Zn(II)-catalysis of the ROTEP of the isomeric β-lactone, 2-(2-carbomethoxyethyl)propiolactone (<b><i>iso</i>CMVL</b>), as well as isomerization of the isostructural linear homopolymer derived from that isomeric monomer, led to the same <b>EQ-PCMVL</b>. These results suggest a new strategy for the introduction of branching into various polyesters.
Regulation of proximal tubule vacuolar H<sup>+</sup>-ATPase by PKA and AMP-activated protein kinase (2014)

The vacuolar H(+)-ATPase (V-ATPase) mediates ATP-driven H(+) transport across membranes. This pump is present at the apical membrane of kidney proximal tubule cells and intercalated cells. Defects in the V-ATPase and in proximal tubule function can cause renal tubular acidosis. We examined the role of protein kinase A (PKA) and AMP-activated protein kinase (AMPK) in the regulation of the V-ATPase in the proximal tubule as these two kinases coregulate the V-ATPase in the collecting duct. As the proximal tubule V-ATPases have different subunit compositions from other nephron segments, we postulated that V-ATPase regulation in the proximal tubule could differ from other kidney tubule segments. Immunofluorescence labeling of rat ex vivo kidney slices revealed that the V-ATPase was present in the proximal tubule both at the apical pole, colocalizing with the brush-border marker wheat germ agglutinin, and in the cytosol when slices were incubated in buffer alone. When slices were incubated with a cAMP analog and a phosphodiesterase inhibitor, the V-ATPase accumulated at the apical pole of S3 segment cells. These PKA activators also increased V-ATPase apical membrane expression as well as the rate of V-ATPase-dependent extracellular acidification in S3 cell monolayers relative to untreated cells. However, the AMPK activator AICAR decreased PKA-induced V-ATPase apical accumulation in proximal tubules of kidney slices and decreased V-ATPase activity in S3 cell monolayers. Our results suggest that in proximal tubule the V-ATPase subcellular localization and activity are acutely coregulated via PKA downstream of hormonal signals and via AMPK downstream of metabolic stress.
Performance Benchmark of Greenhouse Gas Emissions from Asphalt Pavement in the United States (2014)

Hot mix asphalt (HMA), used extensively in road construction, has the highest greenhouse gas (GHG) emission intensity among construction subsectors. In the absence of an authorized performance benchmark in the pavement industry, current prevailing practices of HMA form an institutional resistance to change, and emission mitigation efforts are unable to be quantified and rewarded. The objective of this paper is to develop a performance benchmark for sustainable asphalt production based on GHG emission performance. The baseline configuration is the use of conventional HMA. System boundary, functional unit, and calculation method are standardized to support the consistency of the benchmark. A sampling survey of hot mix facilities and placement projects has formed the data pool to conduct the statistics analysis. Results show that the performance benchmark is 115kgCO2e/MT HMA. It represents an emission level that 80% of existing HMA producers are unable to reach, which reasonably avoids the occurrence of free-riders. Under the carbon trading mechanism with an assumed price of $15/MT carbon, expected benefits from producing a foam stabilized base (FSB), a less carbon-intensive asphalt material, can be $0.7/MT asphalt using CCPR process and $4.2/MT asphalt using CIR process. With the aid of a predetermined performance benchmark, rapidly evolving carbon trading markets may increase the competitive advantages of "green" production in terms of investment offset through carbon trading.
Direct matter disassembly via electron beam control:\n Electron-beam-mediated catalytic etching of graphene by nanoparticles (2019)

We report electron-beam activated motion of a catalytic nanoparticle along a\ngraphene step edge and associated etching of the edge. This approach enables\nbeam-controlled etching of matter through activated electrocatalytic processes.\nThe applications of electron-beam control as a paradigm for molecular-scale\nrobotics are discussed.\n
Computational studies on organic reactivity in ionic liquids (2012)

Computational studies on organic reactions in ionic liquids (ILs) are analysed from different points of view. Important information about reaction mechanisms in ILs has been obtained from these studies although the theoretical approaches are still not able to give an exhaustive picture of the chemical processes occurring in ionic media. Challenges and perspectives of this investigation field are discussed and the fundamental role played by experimental results in the development of this intriguing sector is pointed out.
Chemoselective Coupling Preserves the Substrate Integrity of Surface-Immobilized Oligonucleotides for Emulsion PCR-Based Gene Library Construction (2016)

Combinatorial bead libraries figure prominently in next-generation sequencing and are also important tools for in vitro evolution. The most common methodology for generating such bead libraries, emulsion PCR (emPCR), enzymatically extends bead-immobilized oligonucleotide PCR primers in emulsion droplets containing a single progenitor library member. Primers are almost always immobilized on beads via noncovalent biotin-streptavidin binding. Here, we describe covalent bead functionalization with primers (∼10<sup>6</sup> primers/2.8-μm-diameter bead) via either azide-alkyne click chemistry or Michael addition. The primers are viable polymerase substrates (4-7% bead-immobilized enzymatic extension product yield from one thermal cycle). Carbodiimide-activated carboxylic acid beads only react with oligonucleotides under conditions that promote nonspecific interactions (low salt, low pH, no detergent), comparably immobilizing primers on beads, but yielding no detectable enzymatic extension product. Click-functionalized beads perform satisfactorily in emPCR of a site-saturation mutagenesis library, generating monoclonal templated beads (10<sup>4</sup>-10<sup>5</sup> copies/bead, 1.4-kb amplicons). This simpler, chemical approach to primer immobilization may spur more economical library preparation for high-throughput sequencing and enable more complex surface elaboration for in vitro evolution.
Photocurrent Enhancement in Hybrid Nanocrystal Quantum-Dot<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>p</mml:mi><mml:mtext mathvariant="normal">−</mml:mtext><mml:mi>i</mml:mi><mml:mtext mathvariant="normal">−</mml:mtext><mml:mi>n</mml:mi></mml:math>Photovoltaic Devices (2009)

We fabricate a hybrid nanocrystal quantum-dot patterned p-i-n structure that utilizes nonradiative energy transfer from highly absorbing colloidal nanocrystal quantum dots to a patterned semiconductor slab to demonstrate a sixfold increase of the photocurrent conversion efficiency compared to the bare p-i-n semiconductor device.
Design Exploration of Reliably Manufacturable Materials and Structures With Applications to a Microstereolithography System (2018)

One of the challenges in designing for additive manufacturing (AM) is accounting for the differences between as-designed and as-built geometries and material properties. From a designer’s perspective, these differences can lead to degradation of part performance, which is especially difficult to accommodate in small-lot or one-of-a-kind production. In this context, each part is unique, and therefore, extensive iteration is costly. Designers need a means of exploring the design space while simultaneously considering the reliability of additively manufacturing particular candidate designs. In this work, a design exploration approach, based on Bayesian network classifiers (BNC), is extended to incorporate manufacturability explicitly into the design exploration process. The example application is the design of negative stiffness (NS) metamaterials, in which small volume fractions of negative stiffness (NS) inclusions are embedded within a host material. The resulting metamaterial or composite exhibits macroscopic mechanical stiffness and loss properties that exceed those of the base matrix material. The inclusions are fabricated with microstereolithography with features on the scale of tens of microns, but variability is observed in material properties and dimensions from specimen to specimen. In this work, the manufacturing variability of critical features of a NS inclusion fabricated via microstereolithography are characterized experimentally and modelled mathematically. Specifically, the variation in the geometry of the NS inclusions and the Young’s modulus of the photopolymer are measured and modeled by both nonparametric and parametric joint probability distributions. Finally, the quantified manufacturing variability is incorporated into the BNC approach as a manufacturability classifier to identify candidate designs that achieve performance targets reliably, even when manufacturing variability is taken into account.
Deep manifold alignment for mid-grain sketch based image retrieval (2019)

We present an algorithm for visually searching image collections using free-hand sketched queries. Prior sketch based image retrieval (SBIR) algorithms adopt either a category-level or fine-grain (instance-level) definition of cross-domain similarity—returning images that match the sketched object class (category-level SBIR), or a specific instance of that object (fine-grain SBIR). In this paper we take the middle-ground; proposing an SBIR algorithm that returns images sharing both the object category and key visual characteristics of the sketched query without assuming photo-approximate sketches from the user. We describe a deeply learned cross-domain embedding in which ‘mid-grain’ sketch-image similarity may be measured, reporting on the efficacy of unsupervised and semi-supervised manifold alignment techniques to encourage better intra-category (mid-grain) discrimination within that embedding. We propose a new mid-grain sketch-image dataset (MidGrain65c) and demonstrate not only mid-grain discrimination, but also improved category-level discrimination using our approach.
Supplementary Table 3 from Genomic Profiling of MicroRNAs in Bladder Cancer: miR-129 Is Associated with Poor Outcome and Promotes Cell Death &lt;i&gt;In vitro&lt;/i&gt; (2023)

Supplementary Table 3 from Genomic Profiling of MicroRNAs in Bladder Cancer: miR-129 Is Associated with Poor Outcome and Promotes Cell Death &lt;i&gt;In vitro&lt;/i&gt;
Design and Test of a Solid State Charged Particle Detector for Cubesat (2002)

A solid state boron- ion implanted silicon Charged Particle Detector (CPD) was designed, built, and tested as one of the payloads for a Stanford University/Lockheed Martin Cubesat (10cm cube, 1 Kg) project intended for a low earth orbit. Design drivers to be discussed will include cost, size, mass and schedule. Two detectors were utilized with shielding to allow for two separate energy ranges to be detected. Stanford Research Institute facilities were used for testing. Design considerations will be discussed relating to tuning of the electronics for various low earth orbit altitudes, along with matching voltage requirements for the electronics with a low power, 3.7 Volt spacecraft bus (1 watt). Other payloads include a developmental sun sensor and Honeywell 3 axis solid state magnetometer. Overall cubesat development will also be discussed, including structure, communications, power, and processor. Testing techniques and current results will be shown for this ongoing project.
Towards a high-density photonic tensor core enabled by intensity-modulated microrings and photonic wire bonding (2023)

We propose a photonic processing unit for high-density analog computation using intensity-modulation-based microring modulators (IM-MRMs). The output signal at the fixed resonance wavelength is directly intensity modulated by changing the extinction ratio (ER) of the IM-MRM . Thanks to the intensity-modulated approach, the proposed photonic processing unit is less sensitive to the inter-channel crosstalk. Simulation results reveal that the proposed design offers a maximum of 17-fold increase in wavelength channel density compared to its wavelength-modulated counterpart. Therefore, a photonic tensor core of size 512 [Formula: see text] 512 can be realized by current foundry lines. A convolutional neural network (CNN) simulator with 6-bit precision is built for handwritten digit recognition task using the proposed modulator. Simulation results show an overall accuracy of 96.76%, when the wavelength channel spacing suffers a 3-dB power penalty. To experimentally validate the system, 1000 dot product operations are carried out with a 4-bit signed system on a co-packaged photonic chip, where optical and electrical I/Os are realized using photonic and electrical wire bonding techniques. Study of the measurement results show a mean squared error (MSE) of 3.09[Formula: see text]10[Formula: see text] for dot product calculations. The proposed IM-MRM, therefore, renders the crosstalk issue tractable and provides a solution for the development of large-scale optical information processing systems with multiple wavelengths.
Near-Field Investigation of Chevron Nozzle Mechanisms (2008)

A detailed investigation into the effect of chevron nozzles on the near-field acoustics of a separate flow exhaust system was conducted at the University of Cincinnati Anechoic Test Facility. Chevrons with varying numbers of lobes and levels of penetration were selected to provide insight into the effects of these geometric parameters on the acoustic near field. Tests were conducted at two different nozzle operating conditions and the chevrons were shown to produce substantial modifications to the near field over a wide range of frequencies. The chevrons were most effective at lower frequencies where the peak noise region was reduced by 5-7 dB and dramatically reduced in size. At higher frequencies, the chevrons provided strong noise suppression downstream of approximately seven equivalent nozzle diameters with increases closer to the nozzle lip. The nozzle penetration was shown to have the most significant impact on the acoustic near field with more subtle differences being seen with respect to the number of chevron lobes.