gebhart/patrepeval huggingface dataset:
Molecular Self-Assembly of Jointed Molecules on a Metallic Substrate: From Single Molecule to Monolayer (2006)

Because of its promising contribution to the bottom-up approach for nanofabrication of complex molecular architectures, self-organization is widely studied nowadays. Numerous studies have tackled supramolecular chirality or low-dimensional molecular nanostructures using in most cases small and rigid molecules adsorbed on metallic substrates. In this situation, self-assembled structures can be understood in relative simple terms considering molecule-molecule versus molecule-substrate interactions. In contrast, the case of large and three-dimensional molecules which can adopt different adsorption conformations is more complex. Here, we investigate the self-assembly of V-Landers molecules (C108H104) on Cu(100) by STM at room temperature under ultrahigh vacuum. This molecule is constituted of a central poly-aromatic board linked by sigma bonds to four 3,5-di-tert-butylphenyl legs.
Impact of Growth Kinetics on Morphology and Pore Structure of TiO2One-Pot Synthesis of Macroporous TiO2 Microspheres (2006)

Titanium dioxide was synthesized by the hydrolysis of titanium tetraisopropoxide (TTIP) in the presence of acetic acid, 2-propanol, and organic amines (octylamine, aniline, and isobutylamine). H2O was supplied by an esterification reaction between acetic acid and 2-propanol (denoted as H2Oe), and/or by intentionally adding it (denoted as H2Oa). It was found that the quantity of H2Oa plays a crucial role in the morphology and porous structure of the final TiO2 product. Without the addition of H2Oa, 1D and porous TiO2 was synthesized. With the addition of H2Oa, and when the H2Oa:TiO2 molar ratio was in the range of 1:1 to 60:1, macroporous TiO2 microspheres possessing a large surface area and high thermal stability were obtained. When the H2Oa:TiO2 molar ratio exceeded 60:1, porous TiO2 with an irregular shape was formed. The variation in the morphology and porous structure is attributed to the manipulation of the growth kinetics by the addition of water.
A novel trench routing for next-generation high-speed serial buses beyond 10Gbps applications (2016)

This work describes an innovative low-loss transmission line routing configuration, which enables improved channel margin in next-generation high-speed serial buses beyond 10Gbps applications. One such example is SuperSpeed Plus USB a.k.a. USB 3.1 Gen2. Ultimately, this novel routing when implemented in either substrate or printed circuit board (PCB) will extend platform length within the interconnect channel loss budget as stipulated by standard development body e.g. USB-IF specifications. This inventive routing provides huge benefit to original equipment manufacturer (OEM) in term of platform component removal (e.g. USB 3.1 re-timer that costs ~$1) for high-speed differential links >10Gbps data transfer rates. These cost-adding repeaters would be indispensable under conventional routing for instance microstrip, stripline and dual-stripline for high-speed applications. The PCB trench routing aims to mitigate the existing and future challenges of next-gen multi-Gbps signaling, of which one of the platform length limitations is PCB interconnect loss. In this work, signaling analysis in 10Gbps USB 3.1 and 32Gbps SerDes applications have shown feasibility of yielding significant eye margin improvements i.e. up-to 30% voltage margin improvements, which also translates into ample board design flexibility with extended platform routing length.
Low doses of αDCIR.Gagp24 expand a broad repertoire of HIV Gagp24-specific T cells. (2015)

&lt;p&gt;&lt;b&gt;A.&lt;/b&gt; Experimental procedure. ICS, intracellular staining. &lt;b&gt;B.&lt;/b&gt; PBMCs from an HIV-infected patient (patient A15) were cultured for 10 days in medium alone (top panel), or with 0.3 nM hIgG4.Gagp24 (middle panel), or 0.3 nM αDCIR.Gagp24 (lower panel) and then rechallenged for 6 h with or without (-C) 5 clusters (CL) of 15-mer overlapping peptides covering HIV Gagp24 in the presence of brefeldin A prior to intracellular IFNγ staining. The flow cytometry profiles are gated on the overall CD3&lt;sup&gt;+&lt;/sup&gt; T cell population. Data are representative of 4 different patients. &lt;b&gt;C.&lt;/b&gt; PBMCs from 4 HIV-infected patients (patient A1, A2. A12 and A15) were cultured for 10 days with 0.3 nM (filed symbols) or 30 pM (open symbols) of αDCIR.Gagp24 or hIgG4.Gagp24 and then restimulated for 48 hrs with 5 clusters (CL) of 15-mer overlapping peptides covering HIV Gagp24. The culture supernatants were then harvested and IFNγ produced by total T cells was analyzed by multiplex bead-based assay. Each patient is represented by a different symbol. Data are presented as mean of sum of HIV Gagp24 clusters. Differences between αDCIR.Gagp24 and hIgG4.Gagp24 were assessed by a matched paired t-test.&lt;/p&gt;
Improving fatty acid production in escherichia coli through the overexpression of malonyl coA‐Acyl carrier protein transacylase (2011)

The microbial biosynthesis of free fatty acid, which can be used as precursors for the production of fuels or chemicals from renewable carbon sources, has attracted significant attention in recent years. Free fatty acids can be produced by introducing an acyl-carrier protein (ACP) thioesterase (TE) gene into Escherichia coli. The first committed step of fatty acid biosynthesis is the conversion of acetyl-CoA to malonyl-CoA by an adenosine triphosphate (ATP)-dependent acetyl-CoA carboxylase followed by the conversion of malonyl-CoA to malonyl-ACP through the enzyme malonyl CoA-acyl carrier protein transacylase (MCT; FabD). The E. coli fabD gene encoding MCT has been cloned and studied. However, the effect of FabD overexpression in a fatty acid overproducing strain has not been examined. In this study, we examined the effect of FabD overexpression in a fatty acid overproducing strain carrying an acyl-ACP TE. Specifically, the effect of overexpressing a fabD gene from four different organisms on fatty acid production was compared. The strains carrying a fabD gene from E. coli, Streptomyces avermitilis MA-4680, or Streptomyces coelicolor A3(2) improved the free fatty acid production; these three strains produced more free fatty acids, about 11% more, than the control strain. The strain carrying a fabD gene from Clostridium acetobutylicum ATCC 824, however, produced similar quantities of free fatty acids as the control strain. In addition, the three FabD overexpressed strains also have higher fatty acid/glucose yields. The results suggested that FabD overexpression can be used to improve free fatty acid production by increasing the malonyl-ACP availability.
Classification, Morphology, Molecular Pathogenesis, and Outcome of Premalignant Lesions of the Pancreas (2017)

- Our understanding of the molecular alterations that lead from pancreatic precursor lesion to invasive carcinoma continues to evolve. These advances aid clinicians in their treatment decisions and researchers in their search for actionable, druggable targets.
Imaging Action Potentials with Calcium Indicators (2011)

INTRODUCTION The understanding of neuronal circuits has been greatly advanced by the ability to simultaneously image action-potential generation within large populations of neurons. This protocol describes bulk loading of brain slices with acetoxymethyl (AM) ester calcium indicators to monitor action-potential activity in functional neuronal circuits. The imaging of calcium influx into neurons provides an indirect but accurate measure of action-potential generation within individual neurons. The key advantage of the technique is that it allows the researcher to densely sample the activity of a large population of neurons with single-cell resolution.
Qualitative comparison of non-destructive methods for inspection of carbon fiber-reinforced polymer laminates (2020)

In the rapidly expanding composite industry, novel inspection methods have been developed in recent years. Particularly promising for air-coupled testing are cellular polypropylene transducers which offer better impedance matching to air than piezoelectric transducers. Furthermore, broadband transmitters (laser-induced ultrasound and thermoacoustic emitters) and receivers (optical microphones) have opened a completely new chapter for advanced contact-free ultrasound inspection. X-ray dark-field radiography offers a different approach to detect porosity and microcracks, employing small angle X-ray scattering. These innovative ultrasonic and radiographic alternatives were evaluated in comparison with well-established inspection techniques. We applied thirteen different non-destructive methods to inspect the same specimen (a carbon fiber-reinforced polymer laminate with induced impact damage): air-coupled ultrasound testing (using piezoelectric transducers, broadband optical microphones, cellular polypropylene transducers, and a thermoacoustic emitter), laser-induced ultrasound testing, ultrasonic immersion testing, phased array ultrasonic testing, optically excited lock-in thermography, and X-ray radiography (projectional absorption and dark-field, tomosynthesis, and micro-computed tomography). The inspection methods were qualitatively characterized by comparing the scan results. The conclusions are advantageous for a decision on the optimal method for certain testing constraints.
Syndrome-based error resilient scheme of distributed joint source-channel coding (2009)

In this paper, we consider the problem of distributed joint source and channel coding(DJSCC), which combines distributed source coding and channel coding into one single encoder. Unlike other parity-based DJSCC schemes,we here employ syndrome-based method which has been considered as optimal in compression but loss of error resilience, to achieve the same goal as parity-based method. The proposed syndrome-based scheme shows its efficiency of error resilient capability in the simulation results.
Bis[2-(N,N-dimethylamino)ethyl] Ether (2011)

[3033-62-3] C8H20N2O (MW 160.26)

InChI = 1S/C8H20N2O/c1-9(2)5-7-11-8-6-10(3)4/h5-8H2,1-4H3

InChIKey = GTEXIOINCJRBIO-UHFFFAOYSA-N





(ligand for transition metal complexes. Chelation with main group organometallics to moderate their activities. As a tertiary amine in organic synthesis)



Alternate Names: 2-(dimethylamino)ethyl ether; 2,2′-oxybis(N,N-dimethylethylamine).



Physical Data: bp 189 °C; colorless to yellow liquid.



Solubility: soluble in common organic solvents such as THF, DMF, methylene chloride, and acetonitrile.



Handling, Storage, and Precautions: moisture- sensitive. Handle and store under inert atmosphere. Refrigeration is recommended for storage. MSDS is available online from Sigma-Aldrich.



Form Supplied in: commercially available as a liquid.



Analysis of Reagent Purity: GC.



Preparative Methods: can be prepared utilizing dimethylaminoethyl chloride, dimethylaminoethanol, 50% NaOH, and Adogen 464 quaternary ammonium salt in THF at room temperature.1 The mixture was stirred for 6 h under reflux. After removing aqueous layer and being dried, the product was obtained via vacuum distillation.
Abstract 299: TAK1 signaling regulates p53 through a mechanism involving ribosomal stress (2020)

Abstract Triple-negative breast cancer (TNBC) is among the most aggressive forms of breast cancer with limited therapeutic options. TAK1 is implicated in aggressive behavior of TNBC, while means are not fully understood. Here, we report that pharmacological blockade of TAK1 signaling hampered ribosome biogenesis (RBG) by reducing expression of RBG regulators such as RRS1, while not changing expression of ribosomal core proteins. Importantly, TAK1 blockade upregulated expression of p53 target genes in cell lines carrying wild type (wt) TP53 but not in p53-mutant cells. By examining involvement of the ribosomal stress response, we found that p53 activation by blockade of TAK1 was prevented by depletion of ribosomal protein RPL11. Further, siRNA-mediated depletion of TAK1 or RELA resulted in activation of p53 signaling and this response was dependent on RPL11. Knockdown of RRS1 disrupted nucleolar organization and resulted in activation of p53. Genomic TCGA data showed that TNBCs express high levels of ribosome biogenesis regulators, and elevated RRS1 levels correlate with unfavorable prognosis. Cytotoxicity data showed that TNBC cell lines are more sensitive to TAK1 inhibitor compared to luminal and HER2+ cell lines. Together, the data indicate that TAK1 regulates p53 activation by controlling ribosome biogenesis factors, and the TAK1-ribosome axis is a potential therapeutic target in TNBC. Citation Format: Andrei V. Bakin, Justin Zonneville, Vincent Wong. TAK1 signaling regulates p53 through a mechanism involving ribosomal stress [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 299.
Regionalization in a Global Hydrologic Deep Learning Model: From Physical Descriptors to Random Vectors (2022)

Abstract Streamflow prediction is a long‐standing hydrologic problem. Development of models for streamflow prediction often requires incorporation of catchment physical descriptors to characterize the associated complex hydrological processes. Across different scales of catchments, these physical descriptors also allow models to extrapolate hydrologic information from one catchment to others, a process referred to as “regionalization”. Recently, in gauged basin scenarios, deep learning models have been shown to achieve state of the art regionalization performance by building a global hydrologic model. These models predict streamflow given catchment physical descriptors and weather forcing data. However, these physical descriptors are by their nature uncertain, sometimes incomplete, or even unavailable in certain cases, which limits the applicability of this approach. In this paper, we show that by assigning a vector of random values as a surrogate for catchment physical descriptors, we can achieve robust regionalization performance under a gauged prediction scenario. Our results show that the deep learning model using our proposed random vector approach achieves a predictive performance comparable to that of the model using actual physical descriptors. The random vector approach yields robust performance under different data sparsity scenarios and deep learning model selections. Furthermore, based on the use of random vectors, high‐dimensional characterization improves regionalization performance in gauged basin scenario when physical descriptors are uncertain, or insufficient.
The Adaptor Protein p66Shc Inhibits mTOR-Dependent Anabolic Metabolism (2014)

Adaptor proteins link surface receptors to intracellular signaling pathways and potentially control the way cells respond to nutrient availability. Mice deficient in p66Shc, the most recently evolved isoform of the Shc1 adaptor proteins and a mediator of receptor tyrosine kinase signaling, display resistance to diabetes and obesity. Using quantitative mass spectrometry, we found that p66Shc inhibited glucose metabolism. Depletion of p66Shc enhanced glycolysis and increased the allocation of glucose-derived carbon into anabolic metabolism, characteristics of a metabolic shift called the Warburg effect. This change in metabolism was mediated by the mammalian target of rapamycin (mTOR) because inhibition of mTOR with rapamycin reversed the glycolytic phenotype caused by p66Shc deficiency. Thus, unlike the other isoforms of Shc1, p66Shc appears to antagonize insulin and mTOR signaling, which limits glucose uptake and metabolism. Our results identify a critical inhibitory role for p66Shc in anabolic metabolism.
A survey of types of text noise and techniques to handle noisy text (2009)

Often, in the real world noise is ubiquitous in text communications. Text produced by processing signals intended for human use are often noisy for automated computer processing. Automatic speech recognition, optical character recognition and machine translation all introduce processing noise. Also digital text produced in informal settings such as online chat, SMS, emails, message boards, newsgroups, blogs, wikis and web pages contain considerable noise. In this paper, we present a survey of the existing measures for noise in text. We also cover application areas that ingest this noisy text for various tasks like Information Retrieval and Information Extraction.
Development and Validation of a Photographic Scale for Assessment of Lip Fullness (2015)

The LFS is a reliable instrument for physician classification of lip fullness. A 1-point score difference can detect clinically meaningful differences in lip fullness.
Observation of Amplified Spontaneous Emission in GeSn Waveguides at Room Temperature (2018)

Room temperature amplified spontaneous emission at mid-IR has been observed from optically pumped GeSn waveguides on Si. For higher pump power, emission spectrum indicates the direct band to indirect band emission intensity ratio increases and the peak value increases nonlinearly due to the material gain.
Does My Model Work? Evaluation Abstractions of Cognitive Modelers (2010)

Are the abstractions that scientific modelers use to build their models in a modeling language the same abstractions they use to evaluate the correctness of their models? The extent to which such differences exist seems likely to correspond to additional effort of modelers in determining whether their models work as intended. In this paper, we therefore investigate the distinction between "programming abstractions" and "evaluation abstractions". As the basis of our investigation, we conducted a case study on cognitive modeling. We report modelers' evaluation abstractions, and the lengths they went to in evaluating their models. From these results, we derive design implications for several categories of persistent, first-class evaluation abstractions in future debugging tools for modelers.
Preferential flow paths in two alluvial soils with long-term additions of pig slurry in the Mediterranean zone of Chile (2015)

Spatial variability of soil hydraulic properties helps to understand the complexity and dynamic patterns of solute distributions in soils. This study assessed the effects of slurry additions and soil physical properties on preferential flow and nitrate concentrations in two Mediterranean soils of central Chile under conventional agriculture management with long-term slurry additions. Two alluvial basins continuously cropped with maize (Zea mays) were selected, Pichidegua (Mollic Xerofluvent) and San Pedro (Fluventic Humixerept). Soils that had been amended with pig slurry were compared with unamended controls. Soil texture, bulk density, particle density, organic matter, porosity and hydraulic conductivity (Ks) were measured. Soil nitrate concentrations at different depths were determined every 2 weeks during the study, and a dye tracer test using Brilliant Blue FCF was conducted on each soil. Digital picture analysis was then performed to classify flow types in the soil profiles through the distribution of stained path width. Stained path width allowed classification of soil flow types. Preferential flow showed no evidence of being affected by pig slurry; the stained patterns were mainly explained by tillage and soil physical properties, such as texture and Ks. Matrix flow-types in the first horizon grading to macropore flow-types at depth characterised all profiles, except San Pedro amended soil, where homogeneous matrix flow dominated through the entire profile. Concentrations of nitrate showed temporal variation during the measurement season, mainly due to the mineralisation–immobilisation budget and leaching, both triggered by Mediterranean climate conditions. Physical properties helped to explain nitrate distribution in the studied soils.
Effect of cobalt supported on meso–macro porous hydrotalcite in Fischer–Tropsch synthesis (2016)

Hydrotalcite based cobalt catalysts were prepared by a slurry precipitation method, followed by a slurry impregnation method.
Deceptive Infusion of Data: A Novel Data Masking Paradigm for High-Valued Systems (2022)

This work addresses how analysts of a high-valued system (e.g., nuclear reactor, aircraft turbine designs) can extract findable, accessible, interoperable, and reusable scientific data for public dissemination to artificial intelligence and machine-learning (AI/ML) researchers in a manner that cannot be reverse-engineered, potentially compromising sensitive or proprietary information. State-of-the-art methods address this problem through data masking techniques, which allow access to a subset of the information while obfuscating private and potentially identifying information (e.g., personally identifying medical data). These methods are unsuitable for industrial engineering processes, where AI/ML tools need explicit access to all the data available to draw the best inference about the system to help optimize its performance and identify its vulnerabilities, etc. Our novel deceptive infusion of data paradigm provides a solution to this conundrum by developing a mathematical approach capable of concealing the identity of the system while providing full access to all the features employed by AI/ML tools to ensure their optimal performance.
Dynamic Head Space Analyses of Orange Juice Flavor Compounds and Their Absorption into Packaging Materials (2004)

ABSTRACT: A simple, rapid, sensitive, and reproducible dynamic headspace gas chromatography (DH‐GC) was developed to study the absorption of d‐limonene, α‐pinene, ethyl butyrate, and octanal into laminated polymeric packaging materials containing low‐density polyethylene, polyethylene terephthalate, polyvinylidene chloride, and ethyl‐ene‐vinyl alcohol copolymers. The linear regression lines showed that the flavor compound peak areas were directly proportional to the concentrations of the standard flavor compounds with R 2 ≥ 0.97. The coefficients of variation for the DH‐GC analyses were less than 4%. A test cell was designed to study orange juice flavor absorption into the packaging materials for 28 d at 25 °C. Ethyl butyrate or octanal absorption was not different among the 4 packaging materials ( P &gt; 0.05). Addition of a polyethylene terephthalate and a ethylene‐vinyl alcohol copolymer layer to the packaging materials reduced the d‐limonene and α‐pinene absorption by 20% and 50%, respectively.
Exposure assessment of mobile phone base station radiation in an outdoor environment using sequential surrogate modeling (2013)

Human exposure to background radiofrequency electromagnetic fields (RF-EMF) has been increasing with the introduction of new technologies. There is a definite need for the quantification of RF-EMF exposure but a robust exposure assessment is not yet possible, mainly due to the lack of a fast and efficient measurement procedure. In this article, a new procedure is proposed for accurately mapping the exposure to base station radiation in an outdoor environment based on surrogate modeling and sequential design, an entirely new approach in the domain of dosimetry for human RF exposure. We tested our procedure in an urban area of about 0.04 km(2) for Global System for Mobile Communications (GSM) technology at 900 MHz (GSM900) using a personal exposimeter. Fifty measurement locations were sufficient to obtain a coarse street exposure map, locating regions of high and low exposure; 70 measurement locations were sufficient to characterize the electric field distribution in the area and build an accurate predictive interpolation model. Hence, accurate GSM900 downlink outdoor exposure maps (for use in, e.g., governmental risk communication and epidemiological studies) are developed by combining the proven efficiency of sequential design with the speed of exposimeter measurements and their ease of handling.