gebhart/patrepeval huggingface dataset:
Final Report: DoE SBIR Phase 2 Low-Cost Small Diameter NMR Technologies for In-Situ Subsurface Characterization and Monitoring (2010)

In this Phase 2 SBIR program, Vista Clara successfully developed and field-tested small diameter NNR logging tools for subsurface characterization and monitoring. This effort involved the design and development surface electronics, a winch with 470ft cable, and three interchangeable downhole probes: a 3.5â diameter borehole NMR probe, a 1.67â diameter borehole NMR probe, and a 2.5â diameter NMR probe that can be deployed using a Geoprobe direct push machine. The 3.5â probe was tested extensively over a 6 week period including 4â to 8â boreholes in Washington, Idaho, Nebraska, Colorado, Kansas, Connecticut and Massachusetts. The field test campaign was highly successful. The 1.67â probe was assembled, tested and calibrated in the laboratory. The 2.5â Geoprobe probe is in final assembly and testing at the time of this report. The completed Phase 2 R&D program has resulted in the first NMR logging tool that can be deployed in boreholes of 4â diameter, the first NMR logging tool that can be deployed in boreholes on 2â diameter, and the first NMR logging tool that can be deployed by a direct push machine. These small diameter tools make NMR logging technically and economically feasible, for the first time. Previously available NMR logging tools were developed for oilfield applications and are prohibitively large and expensive for the majority of near surface groundwater characterization problems.
Well-to-wheel analysis and measurement of energy use and greenhouse gas and criteria emissions in a Plug-in Hybrid Vehicle: the EcoCAR 2 case study (2014)

This paper presents a detailed well-to-wheel analysis of energy use, greenhouse gas and criteria emissions for a prototype Parallel-Series Plug-in Hybrid Electric Vehicle (PHEV) developed as part of the EcoCAR 2 competition. The EcoCAR 2 team at the Ohio State University (OSU) has designed Parallel-Series Vehicle (PHEV) capable of 67 km all-electric range, which features a l8.9-kWh lithium-ion battery pack with range extending operation in both series and parallel modes made possible by a l.8-L ethanol (E85) engine and a 6-speed automated manual transmission. The vehicle also has two 8OkW peak electric machines, one on the front axle and one on the rear axle, that enable the vehicle to have an all-electric 4WD operating mode. The OSU vehicle is designed to reduce fuel consumption, with a utility factor-weighted fuel economy of 5.19 L/100km gasoline equivalent, while meeting the EPAs Tier II Bin 5 emissions standards. Over the course of the three year competition, the Ohio State team of approximately 40 students designed, built and tested their Parallel-Series PHEV. In addition to the mechanical and electrical fabrication work, the team also developed their own control code for the engine, transmission and supervisory controllers using Software-in-the-Loop (SIL) and Hardware-in-the-Loop (HIL) techniques. The EcoCAR 2 competition and the Ohio State teams participation in it were made possible through support from the U.S. Department of Energy, General Motors, The Ohio State University, and numerous competition and local sponsors. The analysis presented in this paper is based on road data collected before, during and after the EcoCAR2 competition. The OSU vehicle finished in first place in the competition, demonstrating a fully functional PHEV that achieved significant improvements in fuel economy, and in greenhouse gas and criteria emissions. This paper illustrates the application of analysis methods developed by Argonne National Laboratory to evaluate well-to-wheel energy and emissions performance, and compares these methods with the current procedures in use by the U.S. Environmental Protection Agency (EPA) and by the European Union (EU) to establish fuel economy and emissions labels for production vehicles.
Abstract B7: microRNA regulation of cell viability and drug sensitivity in lung cancer (2012)

Abstract Introduction: Lung cancer is the leading cause of cancer-related deaths, with the majority of deaths due to failed therapy from tumor drug resistance. Third-generation chemotherapeutic agents represent the standard first-line treatment for advanced small cell (SCLC) and non-small cell (NSCLC) lung cancer patients. Response rates are poor (20–40%) with a median survival of 8–10 months. Methods: In an unbiased and comprehensive approach, we have combined a high-throughput screening platform with a library of chemically synthesized microRNA mimics and inhibitors. We have used this platform to identify mimics and inhibitors that reduce cell viability in general, and those that specifically sensitize cells to taxanes. Results: We have identified several miRNAs for which over-expression or inhibition has a dramatic and selective effect on cell viability or drug response. We have demonstrated that miR-337-3p mimic sensitizes NSCLC cells to taxanes. By combining in vitro and in silico approaches, we identified STAT3 and RAP1A as direct targets that mediate the effect of miR-337-3p by enhancing taxane-induced arrest in the G2 phase of the cell cycle. We have also identified an inhibitor of miR-139-5p as a potent and selective regulator of SCLC cell viability. Inhibiting miR-139-5p decreases SCLC cell viability by over 80%, but has a minimal cytotoxic effect on that of NSCLCs or immortalized human bronchial epithelial cells. We are currently investigating the targets of miR-139-5p that mediate its effect on SCLC cell viability. Conclusion: We have identified miR-337-3p as a regulator of taxane sensitivity in NSCLC, and miR-139-5p as a modulator of viability in SCLC. Increasing levels of miR-337-3p and inhibiting miR-139-5p may therefore provide novel therapeutic tools for the treatment of NSCLC and SCLC lung tumors, respectively. Citation Format: Liqin Du, Christopher DeSevo, Borkowski Robert, Baker Michael, Adi F. Gazdar, John D. Minna, Alexander Pertsemlidis. microRNA regulation of cell viability and drug sensitivity in lung cancer [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr B7.
IN SITU ANATOMICAL STUDY OF THE MALE URETHRAL SPHINCTERIC COMPLEX: RELEVANCE TO CONTINENCE PRESERVATION FOLLOWING MAJOR PELVIC SURGERY (1998)

The structural components and their relationships suggest mechanisms whereby the complex is suspended and stabilized within the deep pelvis, and achieves urethral closure. Our study furthers an understanding of the anatomical basis for male urinary continence and micturition, and is expected to have primary importance in the effort to preserve urinary function following major pelvic surgery.
The Dual Nature of Specific Immunological Activity of Tumor-derived gp96 Preparations (1999)

Mice immunized with optimal doses of autologous tumor-derived gp96 resist a challenge with the tumor that was the source of gp96. Immunization with quantities of gp96 5-10 times larger than the optimal dose does not elicit tumor immunity. This lack of effect is shown to be an active, antigen-specific effect, in that immunization with high doses of tumor-derived gp96, but not normal tissue-derived gp96, downregulates the antitumor immune response. Furthermore, immunization with fractionated doses of gp96 elicits the same kind and level of response as elicited by a single dose equivalent to the total of the fractionated doses. This is true of the tumor-protective doses as well as the high downregulatory doses of gp96. The downregulatory activity can be adoptively transferred by CD4(+) but not CD8(+) T lymphocytes from mice immunized with high doses of gp96. These observations indicate that immunization with gp96 induces a highly regulated immune response that, depending upon the conditions of immunization, results in tumor immunity or downregulation.
All My endeavors to Preserve Them: Protecting the Plates in Palmyra 22 September—December 1827 (1999)

Research Article| October 01 1999 All My endeavors to Preserve Them: Protecting the Plates in Palmyra 22 September—December 1827 Andrew H. Hedges; Andrew H. Hedges Search for other works by this author on: This Site Google ANDREW W. HEDGES ANDREW W. HEDGES Search for other works by this author on: This Site Google Journal of Book of Mormon Studies (1992-2007) (1999) 8 (2): 14–85. https://doi.org/10.2307/44747518 Cite Icon Cite Share Icon Share Facebook Twitter LinkedIn MailTo Permissions Search Site Citation Andrew H. Hedges, ANDREW W. HEDGES; All My endeavors to Preserve Them: Protecting the Plates in Palmyra 22 September—December 1827. Journal of Book of Mormon Studies (1992-2007) 1 October 1999; 8 (2): 14–85. doi: https://doi.org/10.2307/44747518 Download citation file: Zotero Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All Scholarly Publishing CollectiveUniversity of Illinois PressJournal of Book of Mormon Studies Search Advanced Search The text of this article is only available as a PDF. © Copyright 1999 Foundation for Ancient Research and Mormon Studies1999 Article PDF first page preview Close Modal You do not currently have access to this content.
Freeze-Fracture Imaging of Ordered Phases of Tobacco Mosaic Virus in Water (1986)

Abstract Aqueous solutions of Tobacco Mosaic Virus are ideal systems for visualizing "molecular" distributions in nematic and crystalline phases by freeze-fracture electron microscopy. Nematic phases of TMV in water are highly oriented with measured order parameters of 0.93. Twist deformations appear to be most common in the micrographs, confirming experimental and theoretical evidence that the twist elastic constant is smaller than either the splay or bend constants. Both edge and screw disclinations are observed in TMV nematics at molecular resolution, and their overall configurations correspond closely to those predicted by continuum theory. Disclination cores have been visualized for the first time. The edge disclination core is small, no more than a single virus length wide. The virus reorient abruptly by 90° at the core, but appear to remain in the plane of the disclination line. The screw disclination core is several virus lengths in diameter and much more disordered. The virus twist out of the plane perpendicular to the line and into the plane along the disclination line. The virus in colloidal crystal TMV solutions are more positionally ordered than the nematic samples. Although no distinct layers were visible along the virus axis in the freeze-fracture images, a sinusoidal density modulation was observed. With the experimental evidence at hand, it is possible to assign either a smectic-B liquid crystal or a true three-dimensional crystal structure to this phase. Perpendicular to the long axis of the virus, the particles appear hexagonally ordered. An average center-to-center distance of 50 nm, which agrees with that measured by X-ray diffraction, was measured from the micrographs. Freeze-fracture imaging of these anisotropic crystals is an alternative to the more common light microscopy of polymer latex colloid crystals.
Modulation frequency constraints on wow and flutter determination (2008)

Hitherto developed algorithms for wow and flutter characteristic determination were found useful in some real-life restoration procedures, however, there was no study of their capabili-ties in terms of the maximal parasite modulation frequency that can be determined with their application. This paper presents the study for three algorithms, i.e. the power-line hum tracker, high frequency bias tracker, and the center of gravity tracker. The short description of the algo-rithms is followed by the theoretical study on the maximal modulation frequency determined by the algorithms. Next, the experimental part is given, with simulations which confirm the findings from the theoretical part, and conclusions summarizing obtained results.
Solving the label resolution problem in supervised video content classification (2008)

Classifying video based on its content often requires learning a classifier from labeled samples. Sometimes the semantic labels available for a video refer to the class or category of the video as a whole; whereas the discriminative features that result in that categorization may only occur over a temporal subset of the video and may occur anywhere, leading to sub-optimal performance. We therefore need to simultaneously learn discriminative features and their temporal support while remaining independent of position within the video. We propose a solution to this label-resolution problem using a wavelet decomposition of frame-level feature time-series followed by learning discrimin ative extrema values over multiple time scales. We apply this approach to automatically detecting the presence of adult content in online videos with a resulting equal-error rate around 5%.
Fluorescence High-Throughput Screening for Inhibitors of TonB Action (2017)

Gram-negative bacteria acquire ferric siderophores through TonB-dependent outer membrane transporters (TBDT). By fluorescence spectroscopic hgh-throughput screening (FLHTS), we identified inhibitors of TonB-dependent ferric enterobactin (FeEnt) uptake through <i>Escherichia coli</i> FepA (EcoFepA). Among 165 inhibitors found in a primary screen of 17,441 compounds, we evaluated 20 in secondary tests: TonB-dependent ferric siderophore uptake and colicin killing and proton motive force-dependent lactose transport. Six of 20 primary hits inhibited TonB-dependent activity in all tests. Comparison of their effects on [<sup>59</sup>Fe]Ent and [<sup>14</sup>C]lactose accumulation suggested several as proton ionophores, but two chemicals, ebselen and ST0082990, are likely not proton ionophores and may inhibit TonB-ExbBD. The facility of FLHTS against <i>E. coli</i> led us to adapt it to <i>Acinetobacter baumannii</i> We identified its FepA ortholog (AbaFepA), deleted and cloned its structural gene, genetically engineered 8 Cys substitutions in its surface loops, labeled them with fluorescein, and made fluorescence spectroscopic observations of FeEnt uptake in <i>A. baumannii</i> Several Cys substitutions in AbaFepA (S279C, T562C, and S665C) were readily fluoresceinated and then suitable as sensors of FeEnt transport. As in <i>E. coli</i>, the test monitored TonB-dependent FeEnt uptake by AbaFepA. In microtiter format with <i>A. baumannii</i>, FLHTS produced Z' factors 0.6 to 0.8. These data validated the FLHTS strategy against even distantly related Gram-negative bacterial pathogens. Overall, it discovered agents that block TonB-dependent transport and showed the potential to find compounds that act against Gram-negative CRE (carbapenem-resistant <i>Enterobacteriaceae)</i>/ESKAPE (<i>Enterococcus faecium</i>, <i>Staphylococcus aureus</i>, <i>Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, <i>Pseudomonas aeruginosa</i>, and <i>Enterobacter</i> species) pathogens. Our results suggest that hundreds of such chemicals may exist in larger compound libraries.<b>IMPORTANCE</b> Antibiotic resistance in Gram-negative bacteria has spurred efforts to find novel compounds against new targets. The CRE/ESKAPE pathogens are resistant bacteria that include <i>Acinetobacter baumannii</i>, a common cause of ventilator-associated pneumonia and sepsis. We performed fluorescence high-throughput screening (FLHTS) against <i>Escherichia coli</i> to find inhibitors of TonB-dependent iron transport, tested them against <i>A. baumannii</i>, and then adapted the FLHTS technology to allow direct screening against <i>A. baumannii</i> This methodology is expandable to other drug-resistant Gram-negative pathogens. Compounds that block TonB action may interfere with iron acquisition from eukaryotic hosts and thereby constitute bacteriostatic antibiotics that prevent microbial colonization of human and animals. The FLHTS method may identify both species-specific and broad-spectrum agents against Gram-negative bacteria.
ChemInform Abstract: DYNAMISCHE (1)H‐NMR‐UNTERSUCHUNGEN DER IMINOPHOSPHORAN‐BENZOXAZAPHOSPHOLIN‐TAUTOMERIE (1981)

Abstract Für das Gleichgewicht der beiden Tautomeren A und B, das die nach bekannten Methoden zum Teil erstmalig dargestellten (Alkyl‐2‐hydroxyphenylimino)‐ phosphorane (IA) in Pyridin ausbilden, werden mittels 1 H‐NMR‐spektroskopischen Untersuchungen die Aktivierungsparameter bestimmt.
Electronic Structure Calculations and Experimental Studies on the Thermal Initiation of the Twin Polymerization Process (2017)

Presented here is a combined computational and experimental study on the thermal initiation process of the twin polymerization. Although thermally initiated twin polymerization offers a versatile scheme for obtaining hybrid organic/inorganic nanocomposite materials, the mechanism for its initiation is very different from the proton-initiated twin polymerization. In this study, the basic mechanism of the early steps of the polymerization process of 4 H,4 H'-2,2'-spirobi[benzo[d][1,3,2]dioxasiline] was investigated by using electronic structure calculations in conjunction with experimental differential scanning calorimetry studies. This way, the influences on the thermally initiated twin polymerization process could be analyzed in detail. The previous mechanistic hypotheses are systematically assessed herein to show that, based on the results, a new hypothesis for an initiation mechanism can be formulated that is in agreement with all experimental observations. These results suggest that, before the formation of the polymer networks, the thermal initiation starts with the formation of low-molecular-weight fragments that react to yield acidic groups. If a sufficient amount of these form, the reaction is ultimately funneled into a mechanism similar to that of proton-initiated twin polymerization.
Dandelion: cooperative content distribution with robust incentives (2007)

Content distribution via the Internet is becoming increasingly popular. To be cost-effective, commercial content providers are considering the use of peer-to-peer (P2P) protocols such as BitTorrent to save on bandwidth costs and to handle peak demands. However, when an online content provider uses a P2P protocol, it faces a crucial issue: how to incentivize its clients to upload to their peers. This paper presents Dandelion, a system designed to address this issue in the case of paid content distribution. Unlike previous solutions, most notably BitTorrent, Dandelion provides robust (provably non-manipulable) incentives for clients to upload to others. In addition, unlike systems with tit-for-tat-based incentives, a client is motivated to upload to its peers even if the peers do not have content that interests the client. A client that honestly uploads to its peers is rewarded with credit, which can be redeemed for various types of rewards, such as discounts on paid content. In designing Dandelion, we trade scalability for the ability to provide robust incentives. The evaluation of our prototype system on PlanetLab demonstrates the viability of our approach. A Dandelion server that runs on commodity hardware with a moderate access link is capable of supporting up to a few thousand clients. These clients can download content at rates comparable to those of BitTorrent clients. 1
Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL®, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach (2021)

<i>Salmonella</i> infections (salmonellosis) pose serious health risks to humans, usually via food-chain contamination. This foodborne pathogen causes major food losses and human illnesses, with significant economic impacts. Overuse of antibiotics in the food industry has led to multidrug-resistant strains of bacteria, and governments are now restricting their use, leading the food industry to search for alternatives to secure food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics, as they are natural components of the ecosystem. However, when specifically used in the industry, they can also make their way into humans through our food chain or exposure, as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented to animal feeds. To our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in-vitro assay called RapidAIM to investigate the effect of a bacteriophage mixture, BAFASAL<sup>®</sup>, used in poultry farming on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex-vivo human gut microbiota composition and function were unaffected by BAFASAL<sup>®</sup> treatment, providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment.
Author response: Interplay between external inputs and recurrent dynamics during movement preparation and execution in a network model of motor cortex (2023)

A recurrent neural network model with parameters constrained by data explains mechanisms for how tuning properties of motor cortical neurons change during movement preparation and execution in a monkey performing a reaching task, and accurately reproduces neural dynamics from recordings.
Development of a Zinc-Mediated Approach to a 2,3-cis-Pyrrolidine Arginase Inhibitor (2020)

This manuscript outlines the development activities toward a robust synthesis of cis-2,3-pyrrolidine via tandem zinc-enolate cyclization/Negishi coupling that proceeds with high diastereoselectivity. The methodology facilitated a gram-scale delivery of the target API and eliminated the need for costly chiral resolutions and inefficient protecting group manipulations. A series of DFT experiments provided a transition-state model that agrees closely with the experimental observations and provides a more in-depth understanding of the observed selectivity.
Supplementary Tables 1-5, Supplementary Methods and Materials from Targeting Notch Signaling with a Notch2/Notch3 Antagonist (Tarextumab) Inhibits Tumor Growth and Decreases Tumor-Initiating Cell Frequency (2023)

&lt;p&gt;Table S1: OMP-59R5 binding data as assessed by surface plasmon resonance (Biacore); Table S2. Histopathology of human pancreatic tumors; Table S3. Effect of anti-Notch2/3 antibody OMP-59R5 in combination with gemcitabine on growth of pancreatic xenograft tumors and its association with Kras mutation status and molecular subtypes; Table S4. Gene Set Enrichment Analysis; Table S5. Effects of OMP-59R5 on Mouse Gene Expression in the Stroma of Xenograft Tumors.&lt;/p&gt;