gebhart/patrepeval huggingface dataset:
The Ribonucleolytic Activity of Angiogenin (2002)

Angiogenin (ANG), a homologue of bovine pancreatic ribonuclease A (RNase A), promotes the growth of new blood vessels. The biological activity of ANG is dependent on its ribonucleolytic activity, which is far lower than that of RNase A. Here, the efficient heterologous production of human ANG in Escherichia coli was achieved by replacing two sequences of rare codons with codons favored by E. coli. Hypersensitive fluorogenic substrates were used to determine steady-state kinetic parameters for catalysis by ANG in continuous assays. The ANG pH-rate profile is a classic bell-shaped curve, with pK(1) = 5.0 and pK(2) = 7.0. The ribonucleolytic activity of ANG is highly sensitive to Na(+) concentration. A decrease in Na(+) concentration from 0.25 to 0.025 M causes a 170-fold increase in the value of k(cat)/K(M). Likewise, the binding of ANG to a tetranucleotide substrate analogue is dependent on [Na(+)]. ANG cleaves a dinucleotide version of the fluorogenic substrates with a k(cat)/K(M) value of 61 M(-1) s(-1). When the substrate is extended from two nucleotides to four or six nucleotides, values of k(cat)/K(M) increase by 5- and 12-fold, respectively. Together, these data provide a thorough picture of substrate binding and turnover by ANG.
Polarization-based material classification from specular reflection (1990)

A computationally simple yet powerful method for distinguishing metal and dielectric material surfaces from the polarization characteristics of specularly reflected light is introduced. The method is completely passive, requiring only the sensing of transmitted radiance of reflected light through a polarizing filter positioned in multiple orientations in front of a camera sensor. Precise positioning of lighting is not required. An advantage of using a polarization-based method for material classification is its immunity to color variations, which so commonly exist on uniform material samples. A simple polarization-reflectance model, called the Fresnel reflectance model, is developed. The fundamental assumptions are that the diffuse component of reflection is completely unpolarized and that the polarization state of the specular component of reflection is dictated by the Fresnel reflection coefficients. The material classification method presented results axiomatically from the Fresnel reflectance model, by estimating the polarization Fresnel ratio. No assumptions are required about the functional form of the diffuse and specular components of reflection. The method is demonstrated on some common objects consisting of metal and dielectric parts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Design, Implementation, and Utilization of a Common Data Model for Vehicle Health Management (2007)

Aircraft have multiple disparate data sources associated with maintaining vehicle health. Storing and retrieving data for correlation, trending, and analysis from these data sources is inefficient and expensive. To enable efficient data retrieval and storage, we have implemented an innovative software system based on a common data model that is independent of the data type or vehicle platform. We show that it is possible to integrate data from multiple aircraft platforms using a single data model to facilitate data interoperability and enable cross-platform application development.
Transcription initiation by human RNA polymerase II visualized at single-molecule resolution (2012)

Forty years of classical biochemical analysis have identified the molecular players involved in initiation of transcription by eukaryotic RNA polymerase II (Pol II) and largely assigned their functions. However, a dynamic picture of Pol II transcription initiation and an understanding of the mechanisms of its regulation have remained elusive due in part to inherent limitations of conventional ensemble biochemistry. Here we have begun to dissect promoter-specific transcription initiation directed by a reconstituted human Pol II system at single-molecule resolution using fluorescence video-microscopy. We detected several stochastic rounds of human Pol II transcription from individual DNA templates, observed attenuation of transcription by promoter mutations, observed enhancement of transcription by activator Sp1, and correlated the transcription signals with real-time interactions of holo-TFIID molecules at individual DNA templates. This integrated single-molecule methodology should be applicable to studying other complex biological processes.
DCC promoter hypermethylation in esophageal squamous cell carcinoma (2008)

Deleted in Colorectal Cancer (DCC) is a putative tumor suppressor gene, whose loss has been implicated in colorectal tumorigenesis. Decreased or loss of DCC expression has been demonstrated in a number of human cancers, including esophageal cancer. In this study, we analyzed esophageal squamous cell carcinoma (ESCC) cell lines and primary ESCCs as well as normal esophageal tissues for DCC methylation by bisulfite sequencing, methylation-specific PCR (MSP) and/or quantitative methylation-specific PCR (qMSP). When a qMSP cut-off value for positivity was set to 1.0, DCC methylation was detected in 10 of 12 ESCC cell lines tested, 74% of primary ESCCs (n = 70), 0% of corresponding normal esophageal tissues (n = 20) and 0% of normal esophagus from healthy individuals (n = 19). DCC expression was undetectable in the majority of ESCC cell lines, and treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine reactivated gene expression. DCC overexpression suppressed colony formation in ESCC cell lines, suggesting that DCC may function as a tumor suppressor gene in the esophagus. However, DCC methylation was not associated with any clinical or pathologic parameters measured. We have demonstrated that DCC methylation is a frequent and cancer-specific event in primary ESCCs, suggesting that DCC and associated pathways may represent a new diagnostical therapeutic target.
Human endogenous retrovirus HERV-K113 is capable of producing intact viral particles (2008)

Of all human endogenous retroviruses known today, HERV-K is the only one that has been shown to produce viral particles. While the first of the approximately 30 HERV-K sequences integrated into the human genome more than 40 million years ago, evidence is accumulating that HERV-K was active more recently, provirus HERV-K113 being the youngest sequence found. However, it is unclear which HERV-K sequences code for the viral particles that are produced by human germ-cell tumours or melanomas. Here, we show that the provirus HERV-K113, cloned into a baculovirus expression vector, is capable of producing intact particles of retroviral morphology, exhibiting the typical structure of those particles that were characterized in cell lines derived from human germ-cell tumours. Thus, the HERV-K113 sequence is a candidate for particle production in vivo and for an active human endogenous retrovirus of today.
Dealloying of Noble-Metal Alloy Nanoparticles (2014)

Dealloying is currently used to tailor the morphology and composition of nanoparticles and bulk solids for a variety of applications including catalysis, energy storage, sensing, actuation, supercapacitors, and radiation damage resistant materials. The known morphologies, which evolve on dealloying of nanoparticles, include core-shell, hollow core-shell, and porous nanoparticles. Here we present results examining the fixed voltage dealloying of AgAu alloy particles in the size range of 2-6 and 20-55 nm. High-angle annular dark-field scanning transmission electron microcopy, energy dispersive, and electron energy loss spectroscopy are used to characterize the size, morphology, and composition of the dealloyed nanoparticles. Our results demonstrate that above the potential corresponding to Ag(+)/Ag equilibrium only core-shell structures evolve in the 2-6 nm diameter particles. Dealloying of the 20-55 nm particles results and in the formation of porous structures analogous to the behavior observed for the corresponding bulk alloy. A statistical analysis that includes the composition and particle size distributions characterizing the larger particles demonstrates that the formation of porous nanoparticles occurs at a well-defined thermodynamic critical potential.
Batch and semicontinuous emulsion copolymerization of vinyl acetate–butyl acrylate. II. Morphological and mechanical properties of copolymer latex films (1983)

Abstract Vinyl acetate/(VAc)‐butyl acrylate/(BuA) copolymer latex films of various copolymer compositions were investigated for their morphological properties by electron microscopy techniques, and for their mechanical properties by dynamic mechanical spectroscopy (DMS), differential scanning calorimetry (DSC), and tensile strength measurements. Batch copolymer latex films showed domains of PBuA dispersed in PVAc matrix; the domain sizes were increased with increased BuA content. Semicontinuous latex films were homogeneous in composition. Glass transition temperatures T g determined from DMS and DSC indicated the presence of two, low and high, transition temperatures for batch latex films. The two temperatures approached the individual homopolymers, with increased PBuA content up to 51 mol %. Semicontinuous latex films showed only one single T g . Tensile properties of the batch copolymer films showed a higher ultimate tensile strength, higher Young's modulus, and lower percent elongation to break compared to semicontinuous latex films. These differences were found to reflect the effect of mode of monomer addition during the emulsion copolymerization process on the particle morphology, and confirmed earlier data on bulk, colloidal, and surface properties of the same copolymer latexes.
Tube−Tube and Tube−Surface Interactions in Straight Suspended Carbon Nanotube Structures (2006)

An investigation concerning the tautness of suspended carbon nanotubes (CNTs) grown using the chemical vapor deposition (CVD) method is presented. The suspended nanotubes were analyzed with both a transmission electron microscope (TEM) and a high-resolution scanning electron microscope (HR-SEM). The HR-SEM and TEM investigations revealed that the interaction between CNTs among themselves as well as with the surface on which they are grown is a primary cause for the tautness of suspended tubes. Specifically, the tube-tube and tube-surface dynamics cause adjoining tubes to create a "zipper-effect", thereby straightening and tightening them. Suspended CNTs cling to each other and to as much of the surface as possible and thus minimize their total energy, creating taut, suspended structures. This effect can be so strong so as to force wide tubes to buckle, with no other external force involved. The implications of this study include all forms of alignment processes of nanotubes using the CVD method. The results presented here provide the groundwork for the capability of fine-tuning the control of CNT network formation using substrate mechanical features.
A Finite Element Method Analysis of Heavy Duty Axle Bearing Loads (1991)

&lt;div class="htmlview paragraph"&gt;Pinion bearing loads of a heavy duty rear truck axle were determined by Finite Element Method Analysis (FEM). The results were compared with measured loads. This report describes the method used to measure bearing loads, the FEM model used, and the comparison of the results.&lt;/div&gt;
Diagnosis and characterization of presymptomatic patients with Wilson's disease and the use of molecular genetics to aid in the diagnosis. (1991)

Wilson's disease (WD) is an autosomal recessive disorder of copper accumulation leading to liver and/or brain damage. Although fatal if untreated, the condition can be treated effectively. Autosomal recessive inheritance indicates that siblings of affected patients are at 25% risk of having the disease. If they are diagnosed prior to becoming symptomatic, affected siblings can be kept free of symptoms by prophylactic therapy. In this paper we have examined the utility of copper-related variables, along with other clinical and molecular findings, in identifying those siblings of affected patients who should be further evaluated with a liver biopsy. Data are presented on a series of 13 presymptomatic patients in whom we have made the diagnosis of WD based on liver biopsy findings. Signs of liver disease were present in 12 out of 13 cases. The classic, noninvasive, screening approaches that we evaluated were not adequate to identify all cases of WD in this group of patients. These included positive Kayser-Fleischer (KF) rings, elevated liver serum alanine transferase, elevated urine copper, or elevated plasma nonceruloplasmin copper. We have introduced the use of molecular genetics for screening siblings of affected patients for WD. We show that a probe from the linked retinoblastoma (RB) gene can be very helpful in problem cases. However, at this time, the quantitative determination of liver copper concentration remains as the definitive diagnostic criterion.
Stable Expression of Human NMDA Receptors in Cultured Mammalian Cells (2003)

NMDA receptors are ligand-gated cation channels that are activated by glutamate and glycine. They are distributed throughout the mammalian CNS, and play an important role in normal development and plasticity of the CNS, and likely in such specialized functions as memory and learning. Prolonged activation of these channels has been implicated in several pathophysiological conditions, such as stroke and epilepsy. Therefore, NMDA receptors represent relevant molecular targets for therapeutic agents in the treatment of stroke, epilepsy, head trauma, and pain (, , ).
Maximum throughput in LA freeways occurs at 60 mph (2001)

Long term survival and success of artificial tissue constructs depend greatly on vascularization. Endothelial cell (EC) differentiation and vasculature formation are dependent on spatio-temporal cues in the extracellular matrix that dynamically interact with cells, a process difficult to reproduce in artificial systems. Here we present a novel bifunctional peptide that mimics matrix-bound vascular endothelial growth factor (VEGF) and can be used to encode spatially controlled angiogenic signals in collagen scaffolds. The peptide is comprised of a collagen mimetic domain that was previously reported to bind to type I collagen by a unique hybridization mechanism, and a VEGF mimetic domain with pro-angiogenic activity. Circular dichroism and collagen binding studies confirm the triple helical structure and the collagen binding affinity of the collagen mimetic domain, and EC culture studies demonstrate the peptide's ability to induce endothelial cell morphogenesis and network formation as a matrix-bound factor in 2D and 3D collagen scaffolds. We also show spatial modification of collagen substrates with this peptide that allows localized EC activation and network formation. These results demonstrate that the peptide can be used to present spatially directed angiogenic cues in collagen scaffolds, which may be useful for engineering organized microvasculature.
IMS–MS and IMS–IMS Investigation of the Structure and Stability of Dimethylamine-Sulfuric Acid Nanoclusters (2015)

Recent studies of new particle formation events in the atmosphere suggest that nanoclusters (i.e, the species formed during the early stages of particle growth which are composed of 10(1)-10(3) molecules) may consist of amines and sulfuric acid. The physicochemical properties of sub-10 nm amine-sulfuric acid clusters are hence of interest. In this work, we measure the density, thermostability, and extent of water uptake of <8.5 nm effective diameter dimethylamine-sulfuric (DMAS) nanoclusters in the gas phase, produced via positive electrospray ionization. Specifically, we employ three systems to investigate DMAS properties: ion mobility spectrometry (IMS, with a parallel-plate differential mobility analyzer) is coupled with mass spectrometry to measure masses and collision cross sections for <100 kDa positively charged nanoclusters, two differential mobility analyzers in series (IMS-IMS) are used to examine thermostability, and finally a differential mobility analyzer coupled to an atmospheric pressure drift tube ion mobility spectrometer (also IMS-IMS) is used for water uptake measurements. IMS-MS measurements reveal that dry DMAS nanoclusters have densities of ∼1567 kg/m(3) near 300 K, independent of the ratio of dimethylamine to sulfuric acid originally present in the electrospray solution. IMS-IMS thermostability studies reveal that partial pressures of DMAS nanoclusters are dependent upon the electrospray solution concentration ratio, R = [H2SO4]/[(CH3)2NH]. Extrapolating measurements, we estimate that dry DMAS nanoclusters have surface vapor pressures of order 10(-4) Pa near 300 K, with the surface vapor pressure increasing with increasing values of R through most of the probed concentration range. This suggests that nanocluster surface vapor pressures are substantially enhanced by capillarity effects (the Kelvin effect). Meanwhile, IMS-IMS water uptake measurements show clearly that DMAS nanoclusters uptake water at relative humidities beyond 10% near 300 K, and that larger clusters uptake water to a larger extent. In total, our results suggest that dry DMAS nanoclusters (in the 5-8.5 nm size range in diameter) would not be stable under ambient conditions; however, DMAS nanoclusters would likely be hydrated in the ambient (in some cases above 20% water by mass), which could serve to reduce surface vapor pressures and stabilize them from dissociation.
Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours (2022)

In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortiumwere listed in the Supplementary Information; however, these members shouldhave been included in themainpaper.The originalArticle has been corrected to include the members and affiliations of the PCAWG Consortium in the main paper; the corrections have been made to the HTML version of the Article but not the PDF version. Additional minor corrections to affiliations have been made to the PDF and HTML versions of the original Article for consistency of information between the PCAWG list and themain paper.
Multinuclear NMR study of enzyme hydration in an organic solvent (1998)

Multinuclear NMR spectroscopy has been used to study water bound to subtilisin Carlsberg suspended in tetrahydrofuran (THF), with the water itself employed as a probe of the hydration layer's physicochemical and dynamic characteristics. The presence of the enzyme did not affect the intensity, chemical shift or linewidth of water (up to 8% v/v) added to THF, as measured by 17O- and 2H-NMR. This finding suggests that hydration of subtilisin can be described by a three-state model that includes tightly bound, loosely bound, and free water. Solid-state 2H-NMR spectra of enzyme-bound D2O support the existence of a non-exchanging population of tightly bound water. An important implication is that the loosely-bound water is the same as free water from an NMR viewpoint. This loosely bound water must also be the water responsible for the large increase in catalytic activity observed in previous hydration studies.
Toward a Role of Dendritic Cells in the Germinal Center Reaction: Triggering of B Cell Proliferation and Isotype Switching (1999)

We have reported previously that in vitro generated dendritic cells (DC) can directly regulate B cell responses. Recently, germinal center DC (GCDC) were identified within B cell follicles. Due to their particular localization, we have tested in the present study whether GCDC could contribute to key events characteristic of the GC reaction. Our present results demonstrate that 1) ex vivo GCDC induce a dramatic GC B cell expansion upon CD40 and IL-2 activation and drive plasma cell differentiation, 2) this property is shared by GCDC and blood DC, but not by Langerhans cells, 3) IL-12 production by GCDC is critical in GC B cell expansion and differentiation, and 4) importantly, GCDC also induce IL-10-independent isotype switching toward IgG1. These observations support the novel concept that GCDC directly contribute to the germinal center reaction.
Comprehensive DNA Methylation Analysis Indicates That Pancreatic Intraepithelial Neoplasia Lesions Are Acinar-Derived and Epigenetically Primed for Carcinogenesis (2023)

Analysis of DNA methylation landscapes provides insights into the cell-of-origin of PanIN lesions, clarifies the role of PanIN lesions as metaplastic precursors to human PDAC, and suggests potential targets for chemoprevention.
Acoustic mode-coupling loss caused by internal wave packets in shallow water (1990)

Previous work has shown that there is a strong interaction between acoustic waves and internal wave solitons in shallow water [Zhou et al., J. Acoust. Soc. Am. Suppl. 1 86, S8 (1989)]. The characteristics of internal waves in the coastal zone (deterministic, shoreward propagating packets with a well-defined wavelength and highly correlated with the local tides) are such that this interaction could possibly explain the anomalous, anisotropic frequency response of shallow-water sound propagation that is often observed in the summer. This anomalous propagation is a strong function of time and sometimes exhibits an abnormally large attenuation over some frequency range. By decomposing the acoustic field obtained using PE into normal modes, it is found that the additional “mode-coupling” loss caused by internal waves is a sensitive function of the signal frequency and the internal wave-packet parameters. The acoustic transmission loss is a “resonancelike” function of the number and wavelength of the solitons (with all other parameters held fixed). Hence, low-frequency acoustic measurements, including modal filtering, could be a powerful tool for remote monitoring of internal wave activity in the coastal zone in places such as the Massachussetts Bay, the New York Bight, and the Gulf of California and the Yellow Sea. [Work supported by ONR, IAAS, and GA Tech.]
Variable Geometry Chevrons for Jet Noise Reduction (2006)

Boeing is applying cutting edge smart material actuators to the next generation morphing technologies for aircraft. This effort has led to the Variable Geometry Chevrons (VGC), which utilize compact, light weight, and robust shape memory alloy (SMA) actuators. These actuators morph the shape of chevrons on a jet engine fan nozzle trailing edge in order to optimize acoustic and performance objectives at multiple flight conditions. We have completed a flight test of the VGC system on a Boeing 777-300ER with GE-115B engines. In this paper we describe the VGC design, development and performance during flight test. We demonstrated autonomous operation of the VGCs, which did not require a control system or aircraft power. The VGC concept demonstrated an exciting capability to optimize jet nozzle performance at multiple flight conditions. The VGC system provided a robust test vehicle to explore chevron configurations for community and shock-cell noise reduction. This capability was demonstrated with two examples of a parametric study which showed the influence of VGC configurations on community noise reduction and shock-cell generated cabin noise reduction during cruise.