gebhart/patrepeval huggingface dataset:
New Results in Understanding Performance and Vulnerability in Complex Networks (2007)

New results can be obtained about performance and vulnerability of complex networks through the common intersection of the fields of graph theory, information theory, and optimization theory. Graph theory provides a basis of architecture and also constraint relationships for key flow variables. Information theory provides measures and metrics of flow performance. The optimization of complex networks is accomplished via genetic algorithms on the flow variables. By performing a minimum flow and maximum flow optimization, a sensitivity matrix of vulnerabilities of a network can be ascertained. Thus the most vulnerable set of nodes can be determined. This procedure is first applied to a logistics network. The generalization to communication's networks and other distributed complex systems is discussed.
Data from TAS6417, A Novel EGFR Inhibitor Targeting Exon 20 Insertion Mutations (2023)

&lt;div&gt;Abstract&lt;p&gt;Activating mutations in the &lt;i&gt;EGFR&lt;/i&gt; gene are important targets in cancer therapy because they are key drivers of non–small cell lung cancer (NSCLC). Although almost all common EGFR mutations, such as exon 19 deletions and the L858R point mutation in exon 21, are sensitive to EGFR-tyrosine kinase inhibitor (TKI) therapies, NSCLC driven by EGFR exon 20 insertion mutations is associated with poor clinical outcomes due to dose-limiting toxicity, demonstrating the need for a novel therapy. TAS6417 is a novel EGFR inhibitor that targets EGFR exon 20 insertion mutations while sparing wild-type (WT) EGFR. In cell viability assays using Ba/F3 cells engineered to express human EGFR, TAS6417 inhibited EGFR with various exon 20 insertion mutations more potently than it inhibited the WT. Western blot analysis revealed that TAS6417 inhibited EGFR phosphorylation and downstream molecules in NSCLC cell lines expressing EGFR exon 20 insertions, resulting in caspase activation. These characteristics led to marked tumor regression &lt;i&gt;in vivo&lt;/i&gt; in both a genetically engineered model and in a patient-derived xenograft model. Furthermore, TAS6417 provided a survival benefit with good tolerability in a lung orthotopic implantation mouse model. These findings support the clinical evaluation of TAS6417 as an efficacious drug candidate for patients with NSCLC harboring EGFR exon 20 insertion mutations. &lt;i&gt;Mol Cancer Ther; 17(8); 1648–58. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Design of a 1x4 CPW Microstrip Antenna Array on PET Substrate for Biomedical Applications (2019)

In this paper, a single layer Coplanar Waveguide-fed microstrip patch antenna array is presented for biomedical applications. The proposed antenna array is realized on a transparent and flexible Polyethylene Terephthalate substrate, has 1x4 radiating elements and measures only 280 x 192 mm2. The antenna array resonates at 2.68 GHz and has a peak-simulated gain of 10 dBi. A prototype is also fabricated, and the conductive patterns are drawn using cost-efficient adhesive copper foils instead of conventional copper or silver nanoparticle ink. The corresponding measured results agree well with the simulated results. The proposed low profile and cost-efficient transmit antenna array has the potential for wearable born-worn applications, including wireless powering of implantable medical devices.
Non-linear fluid-coupled computational model of the mitral valve. (2005)

The addition of blood flow and an experimentally driven microstructural description of mitral tissue represent a significant advance in computational studies of the mitral valve. This model will be the foundation for future computational studies on the effect of pathophysiological tissue alterations on mitral valve competence.
Interleukin 1 induces interleukin 1. I. Induction of circulating interleukin 1 in rabbits in vivo and in human mononuclear cells in vitro. (1987)

Interleukin 1 (IL-1) plays an important role in host defense mechanisms by increasing body temperature, inducing the synthesis of a variety of lymphokines and hepatic acute phase proteins and acting as a chemoattractant for lymphocytes. However, in some microenvironments such as injured tissue or joint spaces, elevated IL-1 levels may contribute to pathologic processes, for example, proliferation and fibrosis of tissue involved in pannus formation as well as degradation of matrix and abnormal tissue architecture. To investigate potential mechanisms that may lead to excessive production of IL-1, we have examined the ability of IL-1 to participate in an amplification event by inducing its own gene expression leading to synthesis of biologically active IL-1. When injected into rabbits, recombinant human IL-1-alpha induced biphasic fevers, and during the second temperature elevation 3 hr later, a circulating pyrogenic material was detected by passive transfer of plasma to other rabbits. Induction of the biphasic fever was not caused by endotoxin contamination of the recombinant IL-1. The 3-hr circulating pyrogen was heat-labile and was not residual injected IL-1-alpha. Chromatographic separation of this plasma and biologic assay suggested that it was new IL-1 of rabbit origin. We next incubated human blood mononuclear cells with recombinant IL-1-alpha and measured the intracellular and extracellular levels of IL-1 by bioassay using the D10.G4.1 murine T cell line. In order to control for the carryover of recombinant IL-1-alpha used to stimulate the mononuclear cells (MNC), we used neutralizing antibodies that were specific for IL-1-alpha or IL-1-beta. The results of these neutralizations showed that recombinant human IL-1-alpha induces the synthesis of IL-1-beta in human MNC in vitro. These results were verified with a radioimmunoassay specific for IL-1-beta. At concentrations of 100 ng/ml, IL-1-alpha induced prostaglandin E2 production in the MNC culture, and this was associated with decreased production of immunoreactive IL-1-beta. Adding indomethacin to the cultures prevented the decreased production of IL-1-beta induced by high concentrations of IL-1-alpha. Using nonadherent MNC, we observed an increase in IL-1-beta as well as IL-1-alpha mRNA after 4 hr of exposure to recombinant IL-1-alpha. These results demonstrate that IL-1-alpha induces biologically active and immunoreactive IL-1-beta from MNC in vitro and that the same concentrations of IL-1-alpha induce gene expression for both forms of IL-1.(ABSTRACT TRUNCATED AT 400 WORDS)
Case–control study of household contacts to examine immunological protection fromBordetella pertussistransmission — study protocol (2017)

The results of this study will be essential for understanding the immune response required for protection from infection with <i>B. pertussis</i> and will contribute to our understanding of the shortcomings of the current vaccine.
Highly stereoselective hydrogen transfer from alcohols to carbonyl compounds catalysed by aluminium porphyrins (1988)

Aluminium porphyrins, such as chloroaluminium porphyrin, catalyse a novel hydrogen transfer process in the reduction of aldehydes or ketones with alcohols, and the reactions eventually proceed with very high stereoselectivities.
Necessary Conditions on Realizable Two-Point Correlation Functions of Random Media (2006)

A fascinating inverse problem that has been receiving considerable attention is the construction of realizations of random two-phase heterogeneous media with a target two-point correlation function. However, not every hypothetical two-point correlation function corresponds to a realizable two-phase medium. Here we collect all of the known necessary conditions on the two-point correlation functions scattered throughout a diverse literature and derive a new but simple positivity condition. We apply the necessary conditions to test the realizability of certain classes of proposed correlation functions.
Probing Surface-Porphyrazine Reduction Potentials by Molecular Design (2006)

This manuscript reports electrochemical and angle-resolved X-ray photoelectron spectroscopy measurements of surface-bound porphyrazine monolayers in which the molecule-surface distance and molecular orientation of the porphyrazine are controlled through the design of the adsorbates. This system has allowed us to probe the importance of molecule-surface interaction in determining the shift in reduction potential upon binding to a gold surface. This quantity currently is in theoretical dispute, with one computation indicating that a porphyrazine/porphyrin exhibits an extremely large covalent binding energy ( approximately 10 eV) to a gold surface, whereas a more recent one finds the binding energy to be only a fraction of an electronvolt. Our study indicates that the shift in reduction potential upon surface binding is not a discontinuous function of the molecule-surface distance, as would be the case if covalent interaction of the porphyrazine core with the gold surface were controlling, but rather varies smoothly. This, therefore, rules out the possibility that the large potential shift seen for a porphyrazine whose macrocyclic core lies approximately 3.9 A above the gold surface, relative to one that lies approximately 8.9 A above the surface, DeltaDeltaE = 340 mV, is caused by direct covalent binding of the pi-system to the metal surface.
Characterization of double transgenic mice expressing hepatocye growth factor and transforming growth factor alpha. (1995)

Hepatocyte growth factor (HGF) and transforming growth factor alpha (TGF alpha) are potent mitogens for mature hepatocytes in primary culture (Nakamura, et al. 1984, Mead et al., 1989). However, these cytokines have completely different effects on tumor cell growth (Jhappan et al., 1990, Shiota et al, 1992). To clarify dual effects of these cytokines in liver, we developed double transgenic mice of HGF and TGF alpha using albumin promoter-HGF cDNA transgenic mice (AlbHGF) and metallothionein promoter-TGF alpha transgenic mice (MthTGF alpha). Double transgenic mice were examined on DNA synthesis, c-myc mRNA and occurrence of hepatocelular carcinoma (HCC). Higher labeling indices using BrDU were observed, in sequence, in AlbHGF mice, AlbHGF/MthTGF alpha, MthTGF alpha and wild type mice. Hepatic expression of c-myc mRNA in AlbHGF mice was elevated, compared to that in AlbHGF/MthTGF alpha or MthTGF alpha mice. After long-term observation, MthTGF alpha mice developed HCC in 6/10 (60%), whereas AlbHGF/MthTGF alpha mice developed HCC in 3/9 (33%). These data suggest that HGF is the potent mitogen, stimulating DNA synthesis and up-regulating c-myc mRNA. In addition, HGF may excert some inhibitory effect on occurrence of HCC by TGF alpha.
Mathematical Modeling Results in Improved Diagnosis of Gastric Emptying Abnormalities: ACG/AstraZeneca Fellow Award (2011)

Purpose: Gastric emptying scintigraphy (GES) of a solid phase meal is considered the gold standard for the diagnosis of gastric emptying disorders. Interpretation of GES is best performed when the lag time and gastric emptying rate are determined. These parameters may be difficult to assess when curve fitting of data is not performed, resulting in under and over diagnosis of gastric emptying disorders. Methods: A total of 291 GES scans performed in the NorthShore University HealthSystem from April 2009 to November 2010 were evaluated. Geometric means for anterior and posterior counts corrected for radioactive decay, recorded every 15 minutes to 120 minutes were utilized. Data was fitted to a two compartment model to determine the best fit for lag time and an exponential decay rate (following completion of lag times) were calculated using the Prism program (GraphPad Software, La Jolla, CA). This model generated the lag time and K (the slope of the emptying portion of the curve). The t1/2 (the time to empty 50% of the meal once the emptying process began) was calculated by 0.693/K. The T50% (the time to empty 50% of the initial counts) was calculated using the formula T50% = lag + t1/2. Previously published data were used to determine normal values for normal lag time (<21.9 minutes), t1/2 (52.2 minutes) and T50% (74.1 minutes). A gastric emptying disorder was diagnosed if one or more of these parameters were abnormal. The patients were divided into six groups based on the results of the biphasic model (group I: normal lag and K, group II: prolonged lag and normal K, group III: prolonged lag and prolonged K, group IV: normal lag and prolonged K, group V: no emptying and group VI: Pattern did not fit the model). Results: Using the model, there were 61 patients in group I (20.9%), 40 in group II (13.8%), 62 in group III (21.3%), 94 in group IV (32.3%), 9 in group V (3.1%) and 25 in group VI (8.6%). Using these criteria, 266/291 (91.4%) fit the model. Of these, the model predicted that 202/266 (75.9%) had gastric emptying abnormalities. Only 84/202 (41.6%) of these were described as abnormal in the radiology reports. In addition, 4/266 (1.5%) of patients in group I were read as delayed in the radiology reports. In total, using the model changed the diagnosis in 88/291 (30.2%) of patients. Conclusion: Fitting data collected during gastric emptying scintigraphy studies to a mathematical model that accounts for a lag followed by a decay is a more sensitive method to diagnose gastric emptying abnormalities.
The synthesis of combinational logic to generate probabilities (2009)

As CMOS devices are scaled down into the nanometer regime, concerns about reliability are mounting. Instead of viewing nano-scale characteristics as an impediment, technologies such as PCMOS exploit them as a source of randomness. The technology generates random numbers that are used in probabilistic algorithms. With the PCMOS approach, different voltage levels are used to generate different probability values. If many different probability values are required, this approach becomes prohibitively expensive.
Probing the D-1,4,5-IP3/D-1,3,4,5-IP4 functional interface. Synthesis and pharmacology of novel D-3-modified myo-inositol trisphosphate analogues (1994)

To explore the biological significance of the D-3 position phosphorylation of the second messenger D-myo-inositol 1,4,5-trisphosphate (IP3) in cellular signalling, three novel D-3-substituted analogues of IP3 have been synthesized; their binding and Ca2+-release profiles at the IP3-receptor have been studied and shown to correlate with the steric requirement of the D-3 substituent.
A wearable system for detecting eating activities with proximity sensors in the outer ear (2015)

This paper presents an approach for automatically detecting eating activities by measuring deformations in the ear canal walls due to mastication activity. These deformations are measured with three infrared proximity sensors encapsulated in an off-the-shelf earpiece. To evaluate our method, we conducted a user study in a lab setting where 20 participants were asked to perform eating and non-eating activities. A user dependent analysis demonstrated that eating could be detected with 95.3% accuracy. This result indicates that proximity sensing offers an alternative to acoustic and inertial sensing in eating detection while providing benefits in terms of privacy and robustness to noise.
Reformulating Inference Problems Through Selective Conditioning (2013)

We describe how we selectively reformulate portions of a belief network that pose difficulties for solution with a stochastic-simulation algorithm. With employ the selective conditioning approach to target specific nodes in a belief network for decomposition, based on the contribution the nodes make to the tractability of stochastic simulation. We review previous work on BNRAS algorithms- randomized approximation algorithms for probabilistic inference. We show how selective conditioning can be employed to reformulate a single BNRAS problem into multiple tractable BNRAS simulation problems. We discuss how we can use another simulation algorithm-logic sampling-to solve a component of the inference problem that provides a means for knitting the solutions of individual subproblems into a final result. Finally, we analyze tradeoffs among the computational subtasks associated with the selective conditioning approach to reformulation.
Early Detection of Lung Cancer in the NLST Dataset * (2023)

Lung Cancer is the leading cause of cancer mortality in the U.S. The effectiveness of standard treatments, including surgery, chemotherapy or radiotherapy, depends on several factors like type and stage of cancer, with the survival rate being much worse for later cancer stages. The National Lung Screening Trial (NLST) established that patients screened using low-dose Computed Tomography (CT) had a 15 to 20 percent lower risk of dying from lung cancer than patients screened using chest X-rays. While CT excelled at detecting small early stage malignant nodules, a large proportion of patients (> 25%) screened positive and only a small fraction (< 10%) of these positive screens actually had or developed cancer in the subsequent years. We developed a model to distinguish between high and low risk patients among the positive screens, predicting the likelihood of having or developing lung cancer at the current time point or in subsequent years non-invasively, based on current and previous CT imaging data. However, most of the nodules in NLST are very small, and nodule segmentations or even precise locations are unavailable. Our model comprises two stages: the first stage is a neural network model trained on the Lung Image Database Consortium (LIDC-IDRI) cohort which detects nodules and assigns them malignancy scores. The second part of our model is a boosted tree which outputs a cancer probability for a patient based on the nodule information (location and malignancy score) predicted by the first stage. Our model, built on a subset of the NLST cohort (<i>n</i> = 1138) shows excellent performance, achieving an area under the receiver operating characteristics curve (ROC AUC) of 0.85 when predicting based on CT images from all three time points available in the NLST dataset.
Plasmonic nanohole array biosensor for label-free and real-time analysis of live cell secretion (2017)

Cell secretion dynamics plays a central role in physiological and disease processes. Due to its various temporal profiles, it is essential to implement a precise detection scheme for continuous monitoring of secretion in real time. The current fluorescent and colorimetric approaches hinder such applications due to their multiple time-consuming steps, molecular labeling, and especially the 'snapshot' endpoint readouts. Here, we develop a nanoplasmonic biosensor for real-time monitoring of live cell cytokine secretion in a label-free configuration. Our nanoplasmonic biosensor is composed of gold nanohole arrays supporting extraordinary optical transmission (EOT), which enables sensitive and high-throughput analysis of biomolecules. The nanobiosensor is integrated with an adjustable microfluidic cell module for the analysis of live cells under well-controlled culture conditions. We achieved an outstanding sensitivity for the detection of vascular endothelial growth factor (VEGF) directly in complex cell media. Significantly, the secretion dynamics from live cancer cells were monitored and quantified for 10 hours while preserving good cell viability. This novel approach of probing cytokine secretion activity is compatible with conventional inverted microscopes found in a common biology laboratory. With its simple optical set-up and label-free detection configuration, we anticipate our nanoplasmonic biosensor to be a powerful tool as a lab-on-chip device to analyze cellular activities for fundamental cell research and biotechnologies.
Enantioselective Synthesis of Quaternary Carbon Stereogenic Centers through Copper‐Catalyzed Conjugate Additions of Aryl‐ and Alkylaluminum Reagents to Acyclic Trisubstituted Enones (2013)

Acyclische quartäre Zentren durch konjugierte Addition: Die ersten Beispiele katalytischer enantioselektiver konjugierter Additionen von Aryl- und Alkylgruppen zur Bildung acyclischer quartärer stereogener Zentren wurden entwickelt (siehe Schema). Die benötigten Organoaluminiumreagentien können entweder in situ aus leicht erhältlichen Organolithiumverbindungen hergestellt werden oder sind preiswert verfügbar. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. 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.
Three-Dimensional Finite-Element Time-Domain Beam Propagation Method and Its Application to 1-D Photonic Crystal-Coupled Resonator Optical Waveguide (2015)

A 3-D finite-element time-domain beam propagation method is described for the first time, to the best of our knowledge, for the analysis of transmission characteristics of any kind of photonic structures. In order to avoid nonphysical reflections from computational window edges, the perfectly matched layer boundary condition is introduced. Furthermore, the present method can treat wideband optical pulses owing to the use of Padé approximation. The validity of this method is verified by numerical simulations of a photonic crystal cavity and a microring resonator. In addition, in order to demonstrate the usefulness of the developed method, a taper waveguide for a highly efficient connection between a straight waveguide and a 1-D photonic crystal-coupled resonator optical waveguide is designed.