gebhart/patrepeval huggingface dataset:
Degree of Pollen Dispersal by Insects from a Field Test of Genetically Engineered Cotton (1991)

This investigation was carried out to determine the movement of pollen from a field test site of genetically engineered cotton grown in 1989 at the Plant Science Research Farm of Mississippi State University. The objective was to evaluate the biosafety procedures used to reduce pollen movement. A field test of transgenic cotton measuring 136 by 30 m was bordered on all sides by 25 m of commercial cotton. All border rows were sampled from the lower, middle, and top fruiting positions of the plants. Seeds were analyzed for expression of the dominant selectable marker, neomycin phosphotransferase (npt II). Reliability of the assay was confirmed by polymerase chain reaction analysis. Results showed a consistent and significant reduction in pollen dissemination as distance from the test plot increased. Outcrossing went from 5 to <1% by 7 m away from the test plot. A low level of pollen dispersal of <1% continued to occur sporadically in the remaining border rows out to a distance of 25 m. No significant differences were noted for flower position on the plants, indicating there were no consistent seasonal effects on pollen dissemination. The border rows fulfilled their purpose of serving as a pollen sink to significantly reduce the amount of pollen dissemination from the test plot. At this location in Mississippi, the distance surrounding a transgenic cotton field test could be reduced and still provide reasonable pollen containment.
Multiple camera fusion for multi-object tracking (2002)

We propose a distributed, real-time computing platform for tracking multiple interacting persons in motion. To overcome occlusion and articulated motion we use a multi-view implementation, where 2-D semantic features are independently tracked in each view and then collectively integrated using a Bayesian belief network with a topology that varies as a function of scene content and feature confidence. The network fuses observations from multiple cameras by resolving independency relationships and confidence levels within the graph, thereby producing the most likely vector of 3-D state estimates given the available data. We demonstrate the efficacy of the proposed system using a multi-view sequence of several people in motion. Our experiments suggest that, when compared with data fusion based on averaging, the proposed technique yields a noticeable improvement in tracking accuracy.
Circular and annular sector planar components of arbitrary angle for n-way power dividers/combiners (1994)

Previously derived Green's function for circular and annular sectors restricted the sector angle to an integer submultiple of n/spl pi/. In this paper, using the single series Green's function approach, the Green's function is shown to hold for arbitrary sector angles. The removal of this restriction enables an effective sector angle to be introduced, which then can be used to account for the fringing fields. It is shown that the fringing fields at the straight edges of the sector are responsible for the unequal power division obtained experimentally, and thus by accounting for the fringing fields in the design, it is possible to eliminate the unequal power division. Experimental and theoretical results are in good agreement.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Flow-driven assembly of VWF fibres and webs in in vitro microvessels (2015)

Several systemic diseases, including thrombotic thrombocytopenic purpura, manifest much of their pathology through activation of endothelium and thrombotic occlusion of small blood vessels, often leading to multi-organ failure and death. Modelling these diseases is hampered by the complex three-dimensional architecture and flow patterns of the microvasculature. Here, we employ engineered microvessels of complex geometry to examine the pathological responses to endothelial activation. Our most striking finding is the capacity of endothelial-secreted von Willebrand factor (VWF) to assemble into thick bundles or complex meshes, depending on the vessel geometry and flow characteristics. Assembly is greatest in vessels of diameter ≤300 μm, with high shear stress or strong flow acceleration, and with sharp turns. VWF bundles and webs bind platelets, leukocytes and erythrocytes, obstructing blood flow and sometimes shearing passing erythrocytes. Our findings uncover the biophysical requirements for initiating microvascular thrombosis and suggest mechanisms for the onset and progression of microvascular diseases.
Facilitating software evolution research with kenyon (2005)

Software evolution research inherently has several resource-intensive logistical constraints. Archived project artifacts, such as those found in source code repositories and bug tracking systems, are the principal source of input data. Analysis-specific facts, such as commit metadata or the location of design patterns within the code, must be extracted for each change or configuration of interest. The results of this resource-intensive fact extraction phase must be stored efficiently, for later use by more experimental types of research tasks, such as algorithm or model refinement. In order to perform any type of software evolution research, each of these logistical issues must be addressed and an implementation to manage it created. In this paper, we introduce Kenyon, a system designed to facilitate software evolution research by providing a common set of solutions to these common logistical problems. We have used Kenyon for processing source code data from 12 systems of varying sizes and domains, archived in 3 different types of software configuration management systems. We present our experiences using Kenyon with these systems, and also describe Kenyon's usage by students in a graduate seminar class.
Structural basis for suppression of hypernegative DNA supercoiling by<i>E. coli</i>topoisomerase I (2015)

Escherichia coli topoisomerase I has an essential function in preventing hypernegative supercoiling of DNA. A full length structure of E. coli topoisomerase I reported here shows how the C-terminal domains bind single-stranded DNA (ssDNA) to recognize the accumulation of negative supercoils in duplex DNA. These C-terminal domains of E. coli topoisomerase I are known to interact with RNA polymerase, and two flexible linkers within the C-terminal domains may assist in the movement of the ssDNA for the rapid removal of transcription driven negative supercoils. The structure has also unveiled for the first time how the 4-Cys zinc ribbon domain and zinc ribbon-like domain bind ssDNA with primarily π-stacking interactions. This novel structure, in combination with new biochemical data, provides important insights into the mechanism of genome regulation by type IA topoisomerases that is essential for life, as well as the structures of homologous type IA TOP3α and TOP3β from higher eukaryotes that also have multiple 4-Cys zinc ribbon domains required for their physiological functions.
Ene reactions of indane-1,2,3-trione (a super-enophile) and related vicinal tricarbonyl systems (1992)

Indane-1,2,3-trione 1 is conveniently prepared in quantitative yield by the azeotropic drying of ninhydrin 2 using chlorobenzene as solvent. The central CO group of the trione is extremely electrophilic and ene addition occurs at this site with a wide range of alkenes and with terminal alkynes in aprotic solvents at moderate temperatures (70–130 °C). The reactivity of trione 1 is somewhat attenuated by the solvent, and the ene additions are consistently faster in chloroform than in tetrahydrofuran. Stereoselectivity, when relevant, appears largely to be dictated by steric factors. Regiochemical control can be exercised if the ene contains two reaction sites. Isoprene and 2,4-dimethylpenta-1,3-diene, however, react by Diels–Alder rather than by ene addition; the adducts are the expected regioisomers 18 and 20, respectively. Attempts to catalyse the ene reactions with Lewis acids were unsuccessful. The analogous ene reactions of 4,4,5,5-tetramethyl-cyclo-pentane-1,2,3-trione 44, 4,4,6,6-tetramethylcyclohexane-1,2,3-trione 45, and 2,2-dimethyl-1,3-dioxane-4,5,6-trione (‘oxo-Meldrum's acid’)46 were also briefly investigated.
Oxidation of leukotrienes at the omega end: demonstration of a receptor for the 20-hydroxy derivative of leukotriene B4 on human neutrophils and implications for the analysis of leukotriene receptors. (1984)

Leukotriene B4 [LTB4; (5S,12R)-5,12-dihydroxy-6,14-cis-8,10-trans-icosatetraenoic acid] and its 20-hydroxy derivative [20-OH-LTB4; (5S,12R)-5,12,20-trihydroxy-6,14-cis-8,10-trans-icosatetraenoic acid] are principal metabolites produced when human neutrophils (hPMNs) are stimulated by the calcium ionophore A23187. These compounds were purified to homogeneity by Nucleosil C18 and silicic acid HPLC and identified by UV absorption and gas chromatographic/mass spectral analyses. 20-OH-LTB4 is considerably more polar than LTB4 and interacts weakly with the hydrophobic Nucleosil C18 resin, whereas LTB4 interacts strongly, reflecting the hydrophobic C13-C20 domain in LTB4. Specific binding of highly purified [3H]LTB4 and [3H]20-OH-LTB4 to hPMNs was assessed. Binding of [3H]20-OH-LTB4 could be largely displaced by an excess of nonlabeled LTB4 or 20-OH-LTB4 but not by 15-hydroxyicosatetraenoic acid (15-HETE), (5S,12S)-5,12-dihydroxy-6,10-trans-8,14-cis-icosatetraenoic acid [(5S,12S)-diHETE], or the 6-trans stereoisomer of LTB4 at 1 microM. In contrast, [3H]LTB4 displays a high level of nonspecific binding to human PMNs, which makes assessment of the Kd for LTB4 binding unobtainable. Binding measurements for [3H]LTB4 were performed in a buffer containing bovine serum albumin, and under these conditions significantly less nonspecific binding was observed. The apparent Kd for high-affinity binding sites on human PMNs at 0 degrees C was 31.3 X 10(-9) M for LTB4 and 14.3 X 10(-9) M for 20-OH-LTB4. In addition, we observed a saturable low-affinity receptor for 20-OH-LTB4 with a Kd of approximately 100 X 10(-9) M and 2 X 10(5) receptors per cell. The data from this study suggest that omega oxidation represents a major pathway for metabolism of LTB4 as well as other arachidonate metabolites. LTB4 and 20-OH-LTB4 express similar functional activities and share common binding properties to hPMNs but differ significantly in their physical properties. It is the unique physical characteristics of 20-OH-LTB4 that suggest that arachidonate metabolites oxidized at the omega position may be more important agents in inflammation than LTB4.
Multiparameter Structural Optimization of Single-Walled Carbon Nanotube Composites: Toward Record Strength, Stiffness, and Toughness (2009)

Efficient coupling of mechanical properties of SWNTs with the matrix leading to the transfer of unique mechanical properties of SWNTs to the macroscopic composites is a tremendous challenge of today's materials science. The typical mechanical properties of known SWNT composites, such as strength, stiffness, and toughness, are assessed in an introductory survey where we focused on concrete numerical parameters characterizing mechanical properties. Obtaining ideal stress transfer will require fine optimization of nanotube-polymer interface. SWNT nanocomposites were made here by layer-by-layer (LBL) assembly with poly(vinyl alcohol) (PVA), and the first example of optimization in respect to key parameters determining the connectivity at the graphene-polymer interface, namely, degree of SWNT oxidation and cross-linking chemistry, was demonstrated. The resulting SWNT-PVA composites demonstrated tensile strength (σ(ult)) = 504.5 ± 67.3 MPa, stiffness (E) = 15.6 ± 3.8 GPa, and toughness (K) = 121.2 ± 19.2 J/g with maximum values recorded at σ(ult) = 600.1 MPa, E = 20.6 GPa, and K = 152.1 J/g. This represents the strongest and stiffest nonfibrous SWNT composites made to date outperforming other bulk composites by 2-10 times. Its high performance is attributed to both high nanotube content and efficient stress transfer. The resulting LBL composite is also one of the toughest in this category of materials and exceeding the toughness of Kevlar by 3-fold. Our observation suggests that the strengthening and toughening mechanism originates from the synergistic combination of high degree of SWNT exfoliation, efficient SWNT-PVA binding, crack surface roughening, and fairly efficient distribution of local stress over the SWNT network. The need for a multiscale approach in designing SWNT composites is advocated.
Pharmacokinetics of centhaquin citrate in a dog model (2016)

Abstract Objectives Centhaquin citrate is a novel agent that is being developed for use in the resuscitation of patients with haemorrhagic shock. While pharmacokinetics have been described in small animal models, the pharmacokinetic parameters of centhaquin citrate in large mammals have yet to be described. Methods Four healthy Beagle dogs (two males and two females) were given an intravenous bolus of 1.0 mg/kg centhaquin citrate. Plasma concentrations were measured at baseline and at ten time points within 24 h after administration. Multiple compartmental models were built and compared. The nonparametric adaptive grid function within the Pmetrics package for R was used for parameter estimation. Predicted concentrations were calculated using population mean and individual Bayesian posterior parameters. Key Findings Centhaquin citrate pharmacokinetic parameters were best described using a two-compartment model. Median (IQR) values for Ke, Vc, Vp, Kcp and Kpc were 4.9 (4.4–5.2) h−1, 328.4 (304.0–331.9) l, 1000.6 (912.3–1042.4) l, 10.6 (10.3–11.1) h−1 and 3.2 (2.9–3.7) h−1, respectively. Conclusions Pharmacokinetic parameters of centhaquin citrate in a large mammal have been described. A large volume of distribution and rapid elimination were observed, consistent with previous work in rats.
Metformin Regulates Glucose Transporter 4 (GLUT4) Translocation through AMP-activated Protein Kinase (AMPK)-mediated Cbl/CAP Signaling in 3T3-L1 Preadipocyte Cells (2012)

Metformin is a leading oral anti-diabetes mellitus medication and is known to stimulate GLUT4 translocation. However, the mechanism by which metformin acts is still largely unknown. Here, we showed that short time treatment with metformin rapidly increased phosphorylation of Cbl in an AMP-activated protein kinase (AMPK)-dependent fashion in 3T3-L1 preadipocytes. Metformin also increased phosphorylation of Src in an AMPK-dependent manner. Src inhibition blocked metformin-mediated Cbl phosphorylation, suggesting that metformin stimulates AMPK-Src-Cbl axis pathway. In addition, long term treatment with metformin stimulated the expression of Cbl-associated protein (CAP) mRNA and protein. Long term treatment with metformin stimulated phosphorylation of c-Jun N-terminal kinase (JNK) and its downstream molecule c-Jun, which is a critical molecule for CAP transcription. Knockdown of AMPK and JNK blocked metformin-induced expression of CAP, implying that metformin stimulates AMPK-JNK-CAP axis pathway. Moreover, AMPK knockdown attenuated metformin-induced Cbl/CAP multicomplex formation, which is critical for GLUT4 translocation. A colorimetric absorbance assay demonstrated that metformin-induced translocation of GLUT4 was suppressed in CAP or Cbl knockdown cells. Furthermore, the promoter activity of CAP was increased by metformin in an AMPK/JNK-dependent fashion. In summary, these results demonstrate that metformin modulates GLUT4 translocation by regulating Cbl and CAP signals via AMPK.
EVALUATION OF THE AVOBENZONE PHOTOSTABILITY IN SOLVENTS USED IN COSMETIC FORMULATIONS (2011)

The use of sunscreen products is very important nowadays. The photostability of UV filters incorporated in these products must be preserved during its storing and application processes in order to achieve the claims about photoprotection of the commercial products. The photostability of avobenzone, one of the most common UVA filters in commercial sunscreens, is assessed in solvents intended for cosmetic formulations. The study is carried out by following the spectral behavior of avobenzone solutions under irradiation and after storing them in the dark. Different photobehaviors of the avobenzona are found in the selected solvents, some of which can be explained in the same way than in analytical solvents; but for others, the structural and physical properties of the solvents must be taken into account. The most appropriate solvents for ensuring the photostability of avobenzona are mineral oil and isopropyl myristate.
The Homeobox Gene (1996)

The Pem gene encodes an atypical homeodomain protein, distantly related to Prd/Pax family members, that we demonstrate is regulated in a complex transcriptional and post-transcriptional manner. We show that the rat Pem genomic structure includes three 5'-untranslated (5'-UT) exons and four coding exons, three of which encode the homeodomain. Several alternatively spliced transcripts were identified, including one that skips an internal coding exon, enabling this mRNA to express a novel form of the Pem protein. Other alternatively spliced mRNAs were characterized that possess different 5'-UT regions, including a muscle-specific transcript. The different 5'-UT termini present in Pem transcripts conferred different levels of translatability in vitro. Two promoters containing multiple transcription initiation sites were identified: a distal promoter (Pd) in the first 5'-UT exon and a proximal promoter (Pp) located in the "intron" upstream of the first coding exon. The Pd was active in placenta, ovary, tumor cell lines, and to a lesser extent in skeletal muscle. In contrast, transcripts from the Pp were only detectable in testis and epididymis and were only expressed in epididymis in the presence of testosterone. To our knowledge no transcription factors have previously been identified that exhibit androgen-dependent expression in the epididymis.
Thermal protrusion of thermally assisted magnetic recording for binary gas mixture with temperature (2012)

Thermally assisted magnetic recording (TAMR) system is the most promising next generation magnetic recording technology. In the system, it is important to accurately predict thermal protrusion at near filed transducer (NFT). In this paper, we first constructed an iterative coupled-field analysis process and derived modified heat transfer equation with temperature using diffusion-based effective molecular diameter of gas mixture. Using the simulation process, the thermal protrusion of TAMR head was investigated for various temperature and helium fraction ratios. From the simulation results, the thermal protrusion occurred bigger in low temperature and low helium fraction ratio. And the thermal protrusion of TAMR head with laser diode (LD) was obtained from 3 nm to 1 nm.
Autonomous Vehicle-Intersection Coordination Method in a Connected Vehicle Environment (2017)

In response to the need for developing coordinated schemes of autonomous vehicles (AVs) at an intersection. This paper presents a novel coordination method for intersection management in a connected vehicle environment. The road network is divided into three logical sections, namely, buffer area, core area and free driving area. In addition, a buffer-assignment mechanism is developed to cooperatively assign a specific crossing span for an individual AV and guide each AV to adjust its entry time and corresponding speed in the core area. A set-projection algorithm and a three-segment linear speed profile are employed to control the trajectories of the AVs in the buffer area. Furthermore, the assignment failure handling process and the crossing rule for human-driven vehicles are advanced to enhance the practicability and reliability of the buffer-assignment mechanism. The performance of the proposed method is evaluated by simulating various traffic conditions on an actual urban network. The simulation experiments and sensitivity analyses demonstrate that the proposed method can significantly reduce 24.2%-77.1% of travel delays, decrease almost 99% of number of stops and improve the sustainability of the traffic system by saving 22.1%-52% of fuel consumption.
Luminescent Nanoparticles with Lanthanide-Containing Poly(ethylene glycol)–Poly(ε-caprolactone) Block Copolymers (2014)

Lanthanide-containing nanoparticles have attracted much attention due to their unique optical properties and potential in nanotechnological applications. An amphiphilic block copolymer of poly(ethylene glycol)-b-poly(ε-caprolactone) methyl ether (mPEG-PCL) was functionalized with a dipicolinic acid (dpa) moiety and coordinated to lanthanide ions to afford [Ln(dpa-PCL-PEG-OCH3)3](HNEt3)3 (Ln = Eu(3+), Tb(3+)). Micelle-like nanoparticles of dpa-PCL-PEG-OCH3 macroligand and metal-centered polymers were prepared by solvent displacement methods. Dynamic light scattering analysis (DLS) and cryogenic transmission electron microscopy images confirmed the presence of solid sphere (<47 nm in diameter) and vesicle (>47 nm in diameter) morphologies. The viability and stability of the lanthanide complexes in micelle-like nanoparticles was explored by DLS and luminescence spectroscopy, and found to be stable for several weeks.
Plasma Membrane-Cytoskeleton-Endoplasmic Reticulum Complexes in Neurons and Astrocytes (2004)

The possibility that certain integral plasma membrane (PM) proteins involved in Ca(2+) homeostasis form junctional units with adjacent endoplasmic reticulum (ER) in neurons and glia was explored using immunoprecipitation and immunocytochemistry. Rat brain membranes were solubilized with the mild, non-ionic detergent, IGEPAL CA-630. Na(+)/Ca(2+) exchanger type 1 (NCX1), a key PM Ca(2+) transporter, was immunoprecipitated from the detergent-soluble fraction. Several abundant PM proteins co-immunoprecipitated with NCX1, including the alpha2 and alpha3 isoforms of the Na(+) pump catalytic (alpha) subunit, and the alpha2 subunit of the dihydropyridine receptor. The adaptor protein, ankyrin 2 (Ank 2), and the cytoskeletal proteins, alpha-fodrin and beta-spectrin, also selectively co-immunoprecipitated with NCX1, as did the ER proteins, Ca(2+) pump type 2 (SERCA 2), and inositol-trisphosphate receptor type 1 (IP(3)R-1). In contrast, a number of other abundant PMs, adaptors, and cytoskeletal proteins did not co-immunoprecipitate with NCX1, including the Na(+) pump alpha1 isoform, PM Ca(2+) pump type 1 (PMCA1), beta-fodrin, and Ank 3. In reciprocal experiments, immunoprecipitation with antibodies to the Na(+) pump alpha2 and alpha3 isoforms, but not alpha1, co-immunoprecipitated NCX1; the antibodies to alpha1 did, however, co-immunoprecipitate PMCA1. Antibodies to Ank 2, alpha-fodrin, beta-spectrin and IP(3)R-1 all co-immunoprecipitated NCX1. Immunocytochemistry revealed partial co-localization of beta-spectrin with NCX1, Na(+) pump alpha3, and IP(3)R-1 in neurons and of alpha-fodrin with NCX1 and SERCA2 in astrocytes. The data support the idea that in neurons and glia PM microdomains containing NCX1 and Na(+) pumps with alpha2 or alpha3 subunits form Ca(2+) signaling complexes with underlying ER containing SERCA2 and IP(3)R-1. These PM and ER components appear to be linked through the cytoskeletal spectrin network, to which they are probably tethered by Ank 2.