gebhart/patrepeval huggingface dataset:
Abstract 3384: Cancer Core 125 Panel for quantitative expression and mutation profiling (2015)

Abstract Molecular profiling of heterogeneous circulating tumor cells (CTCs) and tumor biopsy samples at the single-cell level is critical for identifying different cancer cell subpopulations and understanding their value in predicting metastatic cancer progression and responses to treatment. Unfortunately, the isolation and comprehensive characterization of hundreds to thousands of individual cancer cells present formidable analytical and technical challenges. To this end, we developed a high-throughput (HT) HiCellex technology to obtain the genome-wide expression and mutation profiles of hundreds to thousands of epithelial cancer cells at the single cell level. Importantly, HiCellex allows selective molecular profiling of a complete set of viable cells at the single-cell level in the presence of contaminating leukocytes without physical separation of individual cells. The genetic profiling technology uses unique cell-specific molecular barcodes to label mRNAs in individual viable cancer cells by a spliceosome-mediated trans-splicing mechanism. Barcoded trans-splicing constructs, necessary for the labeling of the entire population of pre-mRNAs, are delivered and expressed in a pool of target cancer cells with lentiviral vectors. Digital expression data are generated by HT sequencing of barcoded amplified cDNAs and easily cluster to each cell in silico using cell-specific barcodes. This presentation will provide results of development and validation of genome-wide and multiplex RT-PCR profiling assay of the 500 most informative subtyping and metastatic signature genes (MGS) in model cancer cell lines, CTC and tumor samples. The developed HiCellex 500 MGS profiling assay is a cost-effective approach to effectively characterize, subtype and identify prognostic and diagnostic biomarkers in heterogeneous cancer cells at the single-cell level. Citation Format: Alex Chenchik, Mikhail Makhanov, Gregory Dolganov, Stefanie Jeffrey. Cancer Core 125 Panel for quantitative expression and mutation profiling. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3384. doi:10.1158/1538-7445.AM2015-3384
Characterization and discrimination of basal cell carcinoma and normal human skin tissues using resonance Raman spectroscopy (2017)

Resonance Raman spectroscopy is used for rapid detection of skin BCC cancer. The cross-validated classification accuracy is achieved to be as high as 98% using nonnegative matrix factorization along with support vector machine statistical method.
Pentarylene‐ and Hexarylenebis(dicarboximide)s: Near‐Infrared‐Absorbing Polyaromatic Dyes (2006)

Im Roten: Die Synthese und die optischen Eigenschaften homologer, im Nah-IR absorbierender Chromophore vom Leitertyp werden vorgestellt: von zwei Pentarylenbis(dicarboximiden) (grüne Spektren; siehe Bild) und einem Hexarylenbis(dicarboximid) (gelbes Spektrum). Wie die übrigen Spektren belegen, führt eine zunehmende Anellierung zu einer starken bathochromen Verschiebung des Absorptionsmaximums. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2006/z502998_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.
The ColR/S two-component system is a conserved determinant of host association across Pseudomonas species (2022)

Members of the bacterial genus Pseudomonas form mutualistic, commensal, and pathogenic associations with diverse hosts. The prevalence of host association across the genus suggests that symbiosis may be a conserved ancestral trait and that distinct symbiotic lifestyles may be more recently evolved. Here we show that the ColR/S two-component system, part of the Pseudomonas core genome, is functionally conserved between Pseudomonas aeruginosa and Pseudomonas fluorescens. Using plant rhizosphere colonization and virulence in a murine abscess model, we show that colR is required for commensalism with plants and virulence in animals. Comparative transcriptomics revealed that the ColR regulon has diverged between P. aeruginosa and P. fluorescens and deleting components of the ColR regulon revealed strain-specific, but not host-specific, requirements for ColR-dependent genes. Collectively, our results suggest that ColR/S allows Pseudomonas to sense and respond to a host, but that the ColR-regulon has diverged between Pseudomonas strains with distinct lifestyles. This suggests that conservation of two-component systems, coupled with life-style dependent diversification of the regulon, may play a role in host association and lifestyle transitions.
A servo system of AC motor based on voltage modulation fitting for FPGA and consideration of voltage saturation (2010)

Abstract This paper proposes a space voltage vector modulation (SVM) method for a speed servo system to obtain a quick current response. The proposed SVM method shortens the control lag time of the conventional SVM inverter. In addition, this proposed method is easily implemented in hardware using an FPGA (Field Programmable Gate Array) because the proposed SVM equations are transformed into expressions that hardly need multiplication. By using the proposed SVM method, the servo system realizes quick and stable current control with wide bandwidth. Moreover, by using PI controllers considering the voltage saturation and the torque limiter to the speed servo system, the servo system carries out stable speed control on voltage saturation. Both the proposed SVM method and the PI controllers considering voltage saturation are applied to the speed servo system of a vector controlled induction motor. The effectiveness of both the proposed SVM method and the PI controllers considering voltage saturation is verified by the experimental results. © 2010 Wiley Periodicals, Inc. Electr Eng Jpn, 173(1): 60–68, 2010; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/eej.20989
Functional Heterogeneity of Vaccine-Induced (2013)

Francesco M. MarincolaProvenzano, Mark E. Dudley, Steven A. Rosenberg and Vladia Monsurro, Dirk Nagorsen, Ena Wang, Mauriziohttp://www.jimmunol.org/content/168/11/5933J Immunol€2002; 168:5933-5942; ;Referenceshttp://www.jimmunol.org/content/168/11/5933.full#ref-list-1This article cites 49 articles, 27 of which you can access for free at: Subscriptionshttp://jimmunol.org/subscriptionsInformation about subscribing to The Journal of Immunology is online at: Permissionshttp://www.aai.org/ji/copyright.htmlSubmit copyright permission requests at: Email Alertshttp://jimmunol.org/cgi/alerts/etocReceive free email-alerts when new articles cite this article. Sign up at:
The SkipTrie (2013)

To date, all concurrent search structures that can support predecessor queries have had depth logarithmic in m, the number of elements. This paper introduces the SkipTrie, a new concurrent search structure supporting predecessor queries in amortized expected O(log log u + c) steps, insertions and deletions in O(c log log u), and using O(m) space, where u is the size of the key space and c is the contention during the recent past. The SkipTrie is a probabilistically-balanced version of a y-fast trie consisting of a very shallow skiplist from which randomly chosen elements are inserted into a hash-table based x-fast trie. By inserting keys into the x-fast-trie probabilistically, we eliminate the need for rebalancing, and can provide a lock-free linearizable implementation. To the best of our knowledge, our proof of the amortized expected performance of the SkipTrie is the first such proof for a tree-based data structure.
Optical Detection and Manipulation of Single Molecules in Room‐Temperature Solutions (1997)

Abstract With the tight focus of a gaussian laser beam, single molecules in solution at room temperature can be trapped and detected by observation of fluorescent photons. The focus defines an ultrasmall probe volume on the order of 1 femtoliter, and the electric field gradient associated with this focus enables an individual molecule to be trapped and manipulated.
Summation of dynamic transfer characteristics of left and right carotid sinus baroreflexes in rabbits (1999)

Although interactions among parallel negative-feedback baroreflex systems have been extensively investigated with respect to their steady-state responses, the dynamic interactions remain unknown. In anesthetized, vagotomized, and aortic-denervated rabbits, we perturbed isolated intracarotid sinus pressure (CSP) unilaterally or bilaterally around the physiological operating pressure according to binary white noise. The neural arc transfer function from CSP to cardiac sympathetic nerve activity (SNA) and the peripheral arc transfer function from SNA to aortic pressure were estimated. The gain values of the neural arc at 0.01 Hz estimated by the left (L) and right (R) CSP perturbations were 0.94 +/- 0.31 and 0.96 +/- 0.25, respectively. The gain value increased to 2.17 +/- 0.97 during the bilateral identical CSP perturbation and was not significantly different from L + R. The phase values of the neural arc did not differ among protocols. No significant differences were observed in the peripheral arc transfer functions among protocols. We conclude that summation of the dynamic transfer characteristics of the bilateral carotid sinus baroreflexes around the physiological operating pressure approximates simple addition.
Quinic Acid‐Conjugated Nanoparticles Enhance Drug Delivery to Solid Tumors via Interactions with Endothelial Selectins (2018)

Current nanoparticle (NP) drug carriers mostly depend on the enhanced permeability and retention (EPR) effect for selective drug delivery to solid tumors. However, in the absence of a persistent EPR effect, the peritumoral endothelium can function as an access barrier to tumors and negatively affect the effectiveness of NPs. In recognition of the peritumoral endothelium as a potential barrier in drug delivery to tumors, poly(lactic-co-glycolic acid) (PLGA) NPs are modified with a quinic acid (QA) derivative, synthetic mimic of selectin ligands. QA-decorated NPs (QA-NP) interact with human umbilical vein endothelial cells expressing E-/P-selectins and induce transient increase in endothelial permeability to translocate across the layer. QA-NP reach selectin-upregulated tumors, achieving greater tumor accumulation and paclitaxel (PTX) delivery than polyethylene glycol-decorated NPs (PEG-NP). PTX-loaded QA-NP show greater anticancer efficacy than Taxol or PTX-loaded PEG-NP at the equivalent PTX dose in different animal models and dosing regimens. Repeated dosing of PTX-loaded QA-NP for two weeks results in complete tumor remission in 40-60% of MDA-MB-231 tumor-bearing mice, while those receiving control treatments succumb to death. QA-NP can exploit the interaction with selectin-expressing peritumoral endothelium and deliver anticancer drugs to tumors to a greater extent than the level currently possible with the EPR effect.
Abstract 2316: GPC3-specific chimeric antigen receptor T cell in combination with Sorafenib as a novel therapeutic treatment for hepatocellular carcinoma (2016)

Abstract FDA-approved targeted therapy for advanced hepatocellular carcinoma (HCC) is limited with the only option of Sorafenib treatment with severe side effects. Immunotherapy based on adoptive transfer of tumor-specific T cells have demonstrated a promising clinical outcome for solid tumors. In our study, we developed T cells expressing the fourth generation of GPC3-specific chimeric antigen receptor (α-GPC3 CAR) that efficiently eliminated GPC3-positive HCC cells (Huh7 and HepG2) without killing GPC3-negative primary hepatocytes. This CAR was constructed using a lentiviral vector containing CD28, CD27 and 41BB costimulatory domains, a CD3ζ signaling domain fused to a FKBP-iCasp9 apoptosis inducing gene, and a GPC3-specific sequence derived from HN3, a single-domain VH human monoclonal antibody (gift from Mitchell Ho, NCI). After 16h of incubation at the E (α-GPC3 CAR T cells) : T (Huh7 or HepG2 cells) ratio of 1:1, α-GPC3 CAR T cells effectively lysed Huh7 (39%) and HepG2 (77%) but not primary hepatocytes (9%), while the control CAR T cells (α-CD30 CAR) could not initiate a specific lysis on those cells. At the E:T ration of 3:1, the specific killing increased to 78% (Huh7) and 99% (HepG2) while remaining low with primary hepatocytes (11%). Especially at the very low E:T ratio of 1:10, combination with Sorafenib priming (24h, IC10 concentration) prior to CAR T incubation boosted the specific lysis up to 25% (p = 0.0416). These results indicate that combination of GPC3-specificCAR T cells transfer and Sorafenib regimen could be a promising therapeutic option for the treatment of HCC, with the doses of both CAR T and Sorafenib reduced up to 10 times, hence lower side effects while preserving the efficacy of tumor-specific cytotoxicity. Citation Format: Thu Le Trinh, Qunfeng Wu, Lung-Ji Chang, Mitchell Ho, Chen Liu. GPC3-specific chimeric antigen receptor T cell in combination with Sorafenib as a novel therapeutic treatment for hepatocellular carcinoma. [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 2316.
Saints and CEOs: an historical experience of altruism, self‐interest and compromise (2003)

At a time when social and ethical responsibilities of companies and CEOs are being increasingly emphasised, this paper examines conduct of social business in a different age and culture to discern features of enduring relevance for ethical business practices today.The personal correspondence of three fourth‐century saints gives insights into their relationships and decision‐making.Community expectations were those of sharing rather than of outright giving, with ‘fusion of interest’ prevailing over concerns for ‘con?ict of interest’. Selected incidents show two entrepreneurial bishops, Basil and Gregory of Nyssa, struggling to balance tensions between ’liberality’ and ‘fairness’.They compromised, competed robustly for revenues and were vexed over limited budgets and resources for projects while their disapproving cousin, the academic Gregory of Nazianzus, criticised their worldliness. Their historical experiences suggest four pragmatic and possibly normative ways of blending altruism and self‐interest for the overall advancement of bene?cial change.
In vitro comparison of shock wave lithotripsy machines (2005)

We tested the hypothesis that shock wave lithotripsy machines vary in the ability to fragment stones to small size. Calcium oxalate monohydrate, calcium phosphate, cystine and struvite calculi were fragmented in vitro with the Dornier HM3, Storz Modulith SLX, Siemens Lithostar C, Medstone STS-T, HealthTronics LithoTron 160, Dornier Doli S and Medispec Econolith lithotriptors. Stones were given 2000 shocks or the FDA limit. Post-lithotripsy fragment size was compared. Struvite calculi were completely fragmented by all devices. The mean incidence of calcium phosphate dihydrate, calcium oxalate monohydrate, and cystine stones rendered into fragments greater than 2 mm was 0% for the HM3, Modulith SLX and Lithostar C, 10% for the STS-T, 3% for the LithoTron 160, 29% for the Doli and 18% for the Econolith (p=0.04); 0% for the HM3, Modulith SLX, Lithostar C, STS-T and LithoTron 160, 4% for the Doli and 9% for the Econolith (p=0.15); 1% for the HM3, 0% for the Modulith SLX, 1% for the Lithostar C, 10% for the STS-T, 14% for the LithoTron 160, 3% for the Doli and 9% for the Econolith (p=0.44), respectively. Shock wave lithotriptors vary in fragmentation ability.
Mixing Preshared Keys in the Internet Key Exchange Protocol Version 2 (IKEv2) for Post-quantum Security (2020)

The possibility of quantum computers poses a serious challenge to
cryptographic algorithms deployed widely today. IKEv2 is one example
of a cryptosystem that could be broken; someone storing VPN
communications today could decrypt them at a later time when a quantum
computer is available. It is anticipated that IKEv2 will be extended
to support quantum-secure key exchange algorithms; however that is not
likely to happen in the near term. To address this problem before
then, this document describes an extension of IKEv2 to allow it to be
resistant to a quantum computer, by using preshared keys.
Surface-Initiated Passing-Through Polymerization on a Rubber Substrate: Supplying Monomer from Swollen Substrates (2022)

Passing-through polymerization is a technique for growing surface-initiated polymer brushes where monomers are supplied to the growing chains by diffusing through the initiator-functionalized surface. This inverts the monomer concentration gradient relative to conventional grafting-from mechanisms, allowing for the synthesis of thicker and more densely packed brushes. Here we use a combination of coarse-grained computer simulations and experimental techniques to demonstrate how this approach can be implemented, with swellable network-like substrates supplying monomers to the functionalized surface as they diffuse out of the swollen network. Compared to grafting-from polymer brushes, this method shows a higher contact angle and a greater brush mass. Additionally, we observed that the passing-through approach could lead to strain-induced crystallization in the brush layer or wrinkling of the brush surface, which we used to estimate the brush thickness. The developed method opens a path for large-scale synthesis of the brush-modified elastic substrates.
DPD CLUSTER REACTIONS IN LOW ENERGY NUCLEAR REACTIONS (LENRS) (2009)

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Detection of Avian Influenza Viruses and Differentiation of H5, H7, N1, and N2 Subtypes Using a Multiplex Microsphere Assay (2012)

In an outbreak of highly pathogenic H5 and H7 avian influenza, rapid analysis of a large number of clinical samples with the potential to rapidly identify the virus subtype is extremely important. Herein, we report on the development of a rapid multiplex microsphere assay for the simultaneous detection of all avian influenza viruses (AIV) as well as the differentiation of H5, H7, N1, and N2 subtypes. A reverse transcriptase-PCR (RT-PCR) reaction, followed by hybridization of the amplified product with specific oligonucleotide probe-coated microspheres, was conducted in a multiplex format. Following incubation with a reporter dye, the fluorescence intensity was measured using a suspension array system. The limit of detection of the probe-coupled microspheres ranged from 1 x 10(5) to 1 x 10(9) copies of RT-PCR amplified product and the sensitivity of the multiplex assay ranged from 1 x 10(2.5) to 1 x 10(3.2) 50% embryo infectious doses of virus. The diagnostic accuracy of the assay, compared to the standard real-time RT-PCR, was evaluated using 102 swab samples from chickens exposed to low pathogenic AIV, and 97.05% of samples gave identical results with both the assays. The calculated specificity of the assay was 97.43%. Although the assay still needs to be validated, it appears to be a suitable diagnostic tool for detection and differentiation of avian influenza virus H5, H7, N1, and N2 subtypes.
Composition, structure, and dielectric tunability of epitaxial SrTiO3 thin films grown by radio frequency magnetron sputtering (1999)

Epitaxial (001) oriented SrTiO3 films have been deposited on LaAlO3(001) substrates by off-axis radio frequency magnetron sputtering in Ar:O2 gas mixtures at substrate temperatures ranging from 650 to 850 °C. For the deposition conditions used, stoichiometric targets yielded 20% Sr-deficient films, whereas Sr-enriched targets (Sr1.1Ti0.9O3.0) resulted in stoichiometric films. The Sr-deficient films had a mosaic structure and a larger lattice parameter in comparison to bulk SrTiO3. The stoichiometric films on the other hand had a much higher crystalline quality in the as-deposited condition. The mosaicity of the latter films was primarily limited by the crystalline quality of the LaAlO3 substrates. The lattice parameters of the stoichiometric films were also smaller than the Sr-deficient ones and closer to the bulk value. The dielectric properties of the stoichiometric films were superior to the Sr-deficient films. For films with a thickness of ∼300 nm, the typical dielectric constants as measured at ∼77 K and 1 MHz were determined to be 820 and 500, for the stoichiometric and Sr-deficient films, respectively. Also the capacitance change, as a direct current bias voltage was applied to an interdigital capacitor, was higher for the stoichiometric film, 27.3% as compared to 8.6% when applying a bias of 300 V at 77 K. We also demonstrate the effectiveness of thermal annealing in improving both crystalline quality and dielectric properties, especially for the Sr-deficient films.
Inertial cavitation and associated acoustic emission produced during electrohydraulic shock wave lithotripsy (1997)

The inertial cavitation and associated acoustic emission generated during electrohydraulic shock wave lithotripsy were studied using high-speed photography and acoustic pressure measurements. The dynamics of cavitation bubble clusters, induced in vitro by an experimental laboratory lithotripter, were recorded using a high-speed rotating drum camera at 20,000 frames/s. The acoustic emission, generated by the rapid initial expansion and subsequent violent collapse of the cavitation bubbles, was measured simultaneously using a 1-MHz focused hydrophone, The expansion duration of the cavitation bubble cluster was found to correlate closely with the time delay between the first two groups of pressure spikes in the acoustic emission signal. This correlation provides an essential physical basis to assess the inertial cavitation produced by a clinical Dornier HM-3 shock wave lithotripter, both in water and in renal parenchyma of a swine model. In the clinical output voltage range (16-24 kV), the expansion duration of the primary cavitation bubble cluster generated by the HM-3 lithotripter in water increases from 158 to 254 microseconds, whereas the corresponding values in renal parenchyma are much smaller and remain almost unchanged (from 71 to 72 microseconds). In contrast, subsequent oscillation of the bubble following its primary collapse is significantly prolonged (from 158-235 microseconds in water to 1364-1373 microseconds in renal parenchyma). These distinctive differences between lithotripsy-induced inertial cavitation in vitro and that in vivo are presumably due to the constraining effect of renal tissue on bubble expansion.
Using visual analytics to support decision making to solve the Kronos incident (VAST challenge 2014) (2014)

Gaining insights from different heterogeneous data sources is one of the biggest challenges in decision making support. The large volumes of data can only be combined by sophisticated automatic methods. However, unexpected patterns can only be identified with the help of human intuition. In this paper, we present our visual analytics work-flows and tools to process heterogeneous data such as social networks, text streams, and geo-temporal data. We apply these tools on the VAST Challenge data and present our findings and assumptions that we identified in our analysis.
Tables S1-S8 from The Evolutionary Origins of Recurrent Pancreatic Cancer (2023)

&lt;p&gt;Supplemental Tables&lt;/p&gt;