gebhart/patrepeval huggingface dataset:
Mutagenesis of aspartic acid-116 enhances the ribonucleolytic activity and angiogenic potency of angiogenin. (1988)

Site-specific mutagenesis of the blood vessel-inducing protein angiogenin has been used to further explore both its homology to pancreatic ribonuclease and the functional roles of particular residues. Replacement of Asp-116 in angiogenin by either asparagine (D116N), alanine (D116A), or histidine (D116H) markedly enhances both its ribonucleolytic activity and angiogenic potency. Activity toward tRNA is 8-, 15-, and 18-fold greater than native angiogenin for D116N-, D116A-, and D116H-angiogenin, respectively. The enzymatic specificity of angiogenin, however, has been maintained. Thus, cleavage of 18S and 28S rRNA by the most active His-116 mutant yields the same pattern of polynucleotide products as from angiogenin, whereas there are only minor alterations in activity with cytidylyl(3',5')adenosine and uridylyl(3',5')-adenosine. Extensive biological assays on the chicken embryo chorioallantoic membrane demonstrate that D116H-angiogenin is one to two orders of magnitude more potent in inducing neovascularization than native angiogenin, which correlates well with enhanced enzymatic action. These results support the proposition that the enzymatic and angiogenic activities on angiogenin are interrelated.
Anti-phosphotyrosine antibody PY20-4D5 Fab complexed with sulfate (2018)

Phosphotyrosine (pY) is one of the most highly studied posttranslational modifications that is responsible for tightly regulating many signaling pathways in eukaryotes. Pan-specific pY antibodies have emerged as powerful tools for understanding the role of these modifications. Nevertheless, structures have not been reported for pan-specific pY antibodies, greatly impeding the further development of tools for integrating this ubiquitous posttranslational modification using structure-guided designs. Here, we present the first crystal structures of two widely utilized pan-specific pY antibodies, PY20 and 4G10. The two antibodies, although developed independently from animal immunizations, have surprisingly similar modes of recognition of the phosphate group, implicating a generic binding structure among pan-specific pY antibodies. Sequence alignments revealed that many pY binding residues are predominant in the mouse V germline genes, which consequently led to the convergent antibodies. On the basis of the convergent structure, we designed a phage display library by lengthening the CDR-L3 loop with the aid of computational modeling. Panning with this library resulted in a series of 4G10 variants with 4 to 11-fold improvements in pY binding affinities. The crystal structure of one improved variant showed remarkable superposition to the computational model, where the lengthened CDR-L3 loop creates an additional hydrogen bond indirectly bound to the phosphate group via a water molecule. The engineered variants exhibited superior performance in Western blot and immunofluorescence.
The HOXB7 protein renders breast cancer cells resistant to tamoxifen through activation of the EGFR pathway (2011)

Multiple factors including long-term treatment with tamoxifen are involved in the development of selective estrogen receptor (ER) modulator resistance in ERα-positive breast cancer. Many underlying molecular events that confer resistance are known but a unifying theme is yet to be revealed. In this report, we provide evidence that HOXB7 overexpression renders MCF-7 cells resistant to tamoxifen via cross-talk between receptor tyrosine kinases and ERα signaling. HOXB7 is an ERα-responsive gene. Extended treatment of MCF-7 cells with tamoxifen resulted in progressively increasing levels of HOXB7 expression, along with EGFR and EGFR ligands. Up-regulation of EGFR occurs through direct binding of HOXB7 to the EGFR promoter, enhancing transcriptional activity. Finally, higher expression levels of HOXB7 in the tumor significantly correlated with poorer disease-free survival in ERα-positive patients with breast cancer on adjuvant tamoxifen monotherapy. These studies suggest that HOXB7 acts as a key regulator, orchestrating a major group of target molecules in the oncogenic hierarchy. Functional antagonism of HOXB7 could circumvent tamoxifen resistance.
Change Detection Techniques for Canopy Height Growth Measurements Using Airborne Laser Scanner Data (2006)

This paper analyzes the potential of airborne laser scanner data for measuring individual tree height growth in a boreal forest using 82 sample trees of Scots pine. Point clouds (10 points/m 2 , beam size 40 cm) illuminating 50 percent of the treetops were acquired in September 1998 and May 2003 with the Toposys 83 kHz lidar system. The reference height and height growth of pines were measured with a tacheometer in the field. Three different types of features were extracted from the point clouds representing each tree; they were the difference between the highest z values, the difference between the DSMs of the tree crown, and the differences between the 85 th , 90 th and 95 th percentiles of the canopy height histograms corresponding to the crown. The best correspondence with the field measurements was achieved with an R 2 value of 0.68 and a RMSE of 43 cm. The results indicate that it is possible to measure the growth of an individual tree with multi-temporal laser surveys. We also demonstrated a new algorithm for tree-to-tree matching. It is needed in operational growth estimation based on individual trees, especially in dense spruce forests. The method is based on minimizing the distances between treetops in the Ndimensional data space. The experiments showed that the use of the location (derived from laser data) and height of the trees were together adequate to provide reliable tree-totree matching. In the future, a fourth dimension (the crown area) should also be included in the matching.
Energetics of the Local Environment of Structure-Directing Agents Influence Zeolite Synthesis (2021)

Organic structure-directing agents (SDAs) play a crucial role in the synthesis of zeolites like SSZ-13 (CHA structure), with novel frameworks and compositions. Zeolite crystallization is aided by the removal of the hydrophobic SDA organocations from an aqueous environment and their incorporation into an emerging silicate framework. This study combined several experimental approaches to understand the influence on nucleation to form SSZ-13 as the size of the SDA was changed. We studied crystallization rates, then modeled the SDA fit in the product to look at correlations for the rates, and then performed the measurement of SDA zeolite filling in the products. Then, we moved to determine the driving force for the transfer of this same series of organic SDAs, (C/N+ = 7–16) from water to chloroform, the latter a proxy for a much less hydrophilic zeolitic environment. Calorimetric measurements of dissolution enthalpy for each SDA in water and chloroform provided enthalpy data and the distribution coefficients for the transfer reaction were measured, both at room temperature. From these experiments, the corresponding transfer enthalpy, entropy, and free energy were calculated. The thermodynamic parameters of the transfer process depend on the C/N+ ratio, location, and environment of the charge in the SDA structure and are a good measure of the ability of the SDA to make the target zeolite, SSZ-13 (CHA). However, the use of a particular, hydrophilic SDA as a counter-example in this particular zeolite synthesis also produced rapid crystallization rates and demonstrated that the opportunity to initiate nucleation, by virtue of docking of the SDA coupled with best SDA-fit, may provide the optimum use of the SDA, providing a stronger factor than the solution transfer thermodynamics.
Quantum capacitance as a reagentless molecular sensing element (2017)

The application of nanoscale capacitance as a transduction of molecular recognition relevant to molecular diagnostics is demonstrated. The energy-related signal relates directly to the electron occupation of quantized states present in readily fabricated molecular junctions such as those presented by redox switchable self-assembled molecular monolayers, reduced graphene oxide or redox-active graphene composite films, assembled on standard metallic or micro-fabricated electrodes. Sensor design is thus based on the response of a confined and resolved electronic density of states to target binding and the associated change in interfacial chemical potential. Demonstrated herein with a number of clinically important markers, this represents a new potent and ultrasensitive molecular detection enabling energy transducer principle capable of quantifying, in a single step and reagentless manner, markers within biological fluid.
ORIGINAL ARTICLES—ALIMENTARY TRACT A Prospective Multivariate Analysis of Clinical Factors Associated With Pouchitis After Ileal Pouch-Anal Anastomosis (2007)

Background & Aims: Although acute pouchitis (AP) after ileal pouch–anal anastomosis (IPAA) for UC is common and easily treated, chronic pouchitis (CP) remains a difficult management issue. The aim of this study was to identify important clinical risk factors associated with AP or CP. Methods: AP and CP were prospectively assessed, and demographic, disease, and treatment characteristics were tabulated. Univariate and multivariate analyses were performed to evaluate associations between AP or CP and potential risk factors. Results: Two hundred IPAA patients were followed for a median of 24 months (range, 3–117 months). Thirty-six patients (18%) developed AP, and 23 patients (12%) developed CP. On univariate analysis, the use of steroids before colectomy and smoking were associated with the development of AP. CP was associated with male gender, smoking, length of follow-up, extraintestinal manifestations, backwash ileitis, and elevated (45010 9 /L) platelet count. On multivariate analysis, the following risk factors were found to be independently associated with AP: use of steroids before colectomy (odds ratio [OR], 3.7; 95% confidence interval [CI], 1.5– 8.9; P .004) and smoking (OR, 2.3; 95% CI, 1.1–5.3; P .04). CP was directly associated with extraintestinal manifestations (OR, 3.5; 95% CI, 1.1–11.1; P .03), elevated platelet count (OR, 3.1; 95% CI, 1.1– 8.9; P .03), and increased length of follow-up (OR, 1.3; 95% CI, 1.1–1.6; P .002). Smoking reduced the incidence of CP (OR, 0.2; 95% CI, 0.05– 0.74; P .04). Conclusions: Clinical factors associated with AP included use of steroids before colectomy and smoking. Factors directly related to CP were extraintestinal manifestations, elevated platelet count, and length of follow-up after IPAA. Smoking appears to protect against the development of CP.
A new Methodology for Multi-Level Thermal Characterization of Complex Electronic Systems: From Die to Board Level (2013)

International audience
Ammonia synthesis for producing supercritical steam in the context of solar thermochemical energy storage (2016)

In ammonia-based solar thermochemical energy storage systems, the stored energy is released when the hydrogen (H2) and nitrogen (N2) react exothermically to synthesize ammonia (NH3), providing thermal energy to a power block for electricity generation. However, ammonia synthesis has not yet been shown to reach temperatures consistent with the highest performance modern power blocks. Two similar ammonia synthesis reactors with different lengths have been used to study the ammonia synthesis reaction at high temperature and pressure and to begin the process of model improvement and validation. With the longer reactor, supercritical steam with flow rate up to 0.09 g/s has been heated from less than 350°C to ∼650°C. This result shows the technical feasibility of using ammonia-based thermochemical energy storage in a CSP plant with a supercritical steam Rankine cycle power block.
Multi-capture Dynamic Calibration of Multi-camera Systems (2018)

Multi-camera systems have seen an emergence in various consumer devices enabling many applications e.g. bokeh (Apple IPhone), 3D measurement (Dell Venue 8) etc. An accurately calibrated multi-camera system is essential for proper functioning of these applications. Usually, a onetime factory calibration with technical targets is done to accurately calibrate such systems. Although accurate, factory calibration does not hold over the life time of the device as normal wear and tear, thermal effects, device usage etc. can cause calibration parameters to change. Thus, a dynamic or self-calibration based on multi-view image features is required to refine calibration parameters. One of the important factors governing the accuracy of dynamic calibration is the number and distribution of feature points in the captured scene. A dense feature distribution enables better sampling of the 3D scene, while avoiding degenerate situations (e.g. all features on one plane), thus sufficiently modeling the forward imaging process for calibration. But, single real life images with dense feature distribution are difficult or nearly impossible to capture e.g. texture-less indoor or occluded scenes. In this paper, we propose a new multi-capture paradigm for multi-camera dynamic calibration where multiple multiview images of different 3D scenes (thus varying feature point distribution) are jointly used to calibrate the multi-camera system. We present a new optimality criteria to select the best set of candidate images from a pool of multiview images, along with their order, to use for multi-capture dynamic calibration. We also propose a methodology to jointly model calibration parameters of multiple multi-view images. Finally, we show improved performance of multi-capture dynamic calibration over single-capture dynamic calibration in terms of lower epipolar rectification and 3D measurement error.
Dual-band Slot-Based MIMO Antenna Design with Independent Tuning (2020)

In this paper, a concentric annular slot based dual-band, low-profile frequency reconfigurable (FR) 2-element multiple-input-multiple-output (MIMO) antenna design is presented. FR is achieved using two varactor diodes per antenna element. The unique features of the proposed work is its independent and concurrent tuning of each band over a wide frequency range from 1.7~3.5 GHz. The proposed antenna is fabricated using RO-4350 substrate with dimensions 60×120×0.76 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . The proposed antenna is a low profile, compact planar structure with dual-bands of operation. The proposed antenna is suitable to be utilized in the current 4G wireless standards as well as for the upcoming 5G with sub 6-GHz bands of operation.
Bandwidth constraining and digital signal processing for high spectral efficiency optical fiber transmissions (2015)

We review bandwidth constraining and digital signal processing techniques for achieving high spectral efficiency optical fiber transmissions. We discuss advantages and disadvantages of three different combinations of adaptive equalization and sequence detection schemes, and show experimental demonstrations.
Split-superpositive GFP reassembly is a fast, efficient, and robust method for detecting protein–protein interactions <i>in vivo</i> (2012)

Split-GFP reassembly is an operationally simple in vivo technique used to identify and study interactions involving proteins and/or peptides. However, the instability of split-GFP fragments and their susceptibility to aggregation place limitations on the broader use of split-GFP reassembly. Supercharged proteins, including supercharged GFP, are variants with high theoretical negative or positive charge that are resistant to aggregation. We show that a split-superpositive GFP (split-spGFP) variant reassembles faster and more efficiently than previously reported split-sg100 GFP and split-folding-reporter GFP (split-frGFP) systems. In addition, interaction-dependent split-spGFP reassembly is efficient at physiological temperature. The increased efficiency and robustness of split-spGFP reassembly make this reporter system ideal for identifying and studying interactions involving proteins and/or peptides in vivo, and may be particularly useful for identifying or studying interactions involving proteins or peptides that are themselves susceptible to aggregation.
Energetic Ionic Liquids as TNT Replacements (2006)

The US munitions community is searching for advanced replacements for 2,4,6-trinitrotoluene (TNT) for use in melt castable explosives. The identification of such a replacement is constrained by many requirements such as: (1) The replacement must afford identical (preferably improved) performance over TNT; (2) The melting point of the replacement should fall into a temperature regime that is useful for cast operations; (3) The replacement must possess safety/sensitivity properties that are as good or better than TNT; (4) The replacement must have sufficient thermal stability to undergo casting at elevated temperature; and (5) Adequate compatibility must exist between the replacement and other compounds present in the explosive composition. The Air Force Research Laboratory (AFRL) has recently investigated the feasibility of replacing TNT with an ionic liquid (m.p.<100 deg C) for use in melt castable explosives. The approach focuses on synthesizing triazolium-based salts that have the appropriate physical and safety properties, thermal stability, and theoretical performance to potentially replace TNT. Individual salts selected from several families of energetic triazolium salts recently synthesized at AFRL possess high densities, relatively high heats of formation, and pass accepted thermal stability tests. The results and suitability of the explosive salts' physical properties, processing, hazards, compatibility, and ultimately their performance are presented.
The inhibitory activity of serum to prevent bacterial adhesion is mainly due to apo‐transferrin (2003)

A marked, up to 5-fold, reduction in bacterial adhesion to Tecoflex polyurethane (PU) surfaces was observed in the presence of bovine/human serum or plasma at 0.5% or higher concentrations in the medium. Further investigation of the phenomenon resulted in identification, isolation, and characterization of the serum component with the ability to significantly reduce bacterial adhesion. Upon fractionation of bovine serum by an anion exchange chromatography, protein pools were made and analyzed by immunoelectrophoresis and by polyacrylamide gel electrophoresis in the presence of SDS and were examined for their effect on the adhesion of Staphylococcus epidermidis to PU surfaces. The pool exhibiting a significant inhibitory effect was subjected to further biochemical tests, which resulted in the identification of transferrin (Tf) as its predominant protein. Bacterial adhesion studies in the presence of purified Tf revealed that holo-Tf (iron-containing form) had no influence on bacterial adhesion at any concentration. Only apo-Tf (iron-lacking form) exerted the inhibitory effect, in a dose responsive manner at concentrations of 10 microg/mL or higher. Bacteria remained viable when suspended at the low apo-Tf concentrations, sufficient to prevent bacterial adhesion.
Experimental Investigation of Forced Convection Enhancement by Acoustic Resonance Excitations in Turbulated Heat Exchangers (2019)

Abstract The present research deals with enhancing the thermal performance of turbulated heat exchangers through the application of sound pressure waves at acoustic resonance frequencies. Extending the findings of prior wind tunnel studies, where a standing wave greatly improved the forced convection in reattaching flows, this paper exploits such a phenomenon in a practical heat exchanger setting. The current experiments are conducted in representative turbulated plate and double-pipe heat exchanger geometries, mounted in a dedicated facility. After identifying the inherent acoustic resonance frequencies of the passageways, the impact of excitation is studied in various sound pressure levels, blockage ratios, as well as Strouhal and Reynolds numbers. The acoustic resonance excitation resulted in heat transfer enhancement of 20% and 10% in the plate and double-pipe designs, respectively, absence of additional pressure penalties. To the best knowledge of the authors, this is the first demonstration of acoustic forced convection enhancement in turbulated heat exchanger geometries. Such a technology can pave the way toward future designs that require low-pressure losses, minimal form factor, and/or process controllability.
Laser- and UV-LED-Induced Fluorescence Detection of Drinking Water and Water-Dissolved Organics (2008)

We have developed a deep-UV laser-induced fluorescence system for fluorescence detection of water-dissolved organic species. Deep-UV LEDs also were used as the excitation source. These systems have been employed for real-time monitoring of drinking water.
Real-time terahertz imaging over a standoff distance (&gt;25meters) (2006)

The authors demonstrate the use of a terahertz quantum cascade laser (QCL) for real-time imaging in transmission mode at a standoff distance of 25meters. Lasing frequency was selected for optimum transmission within an atmospheric window at ∼4.9THz. Coarse frequency selection was made by design of the QCL gain medium. Finer selection (to within 0.1THz) was made by judicious choice of laser cavity length to adjust facet losses and therefore lasing threshold bias, in order to overlap the peak frequency of the Stark-shifted gain spectrum with the atmospheric window. Images are shown using an uncooled 320×240 microbolometer camera.
Ceramic-Metal Brazing, From Fundamentals to Applications: A Review of Sandia National Laboratories Brazing Capabilities, Needs and Opportunities (2002)

The purpose of the report is to summarize discussions from a Ceramic/Metal Brazing: From Fundamentals to Applications Workshop that was held at Sandia National Laboratories in Albuquerque, NM on April 4, 2001. Brazing experts and users who bridge common areas of research, design, and manufacturing participated in the exercise. External perspectives on the general state of the science and technology for ceramics and metal brazing were given. Other discussions highlighted and critiqued Sandia's brazing research and engineering programs, including the latest advances in braze modeling and materials characterization. The workshop concluded with a facilitated dialogue that identified critical brazing research needs and opportunities.
Temperature stable crystal oscillator (1995)

A crystal oscillator is proposed which can exhibit a frequency versus temperature stability comparable to that of the best atomic frequency standards.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fiber mode converters: point-by-point fabrication of index gratings, visualization using thermoluminescence, and applications (1991)

Recently, we reported a technique for making a LP0l → LP11 fiber mode converter device.1 The technique differs from holographic techniques2,3 in that the periodic mode converter refractive index grating is written point-by-point in the, core of a two-mode photosensitive fiber with ultraviolet light, thereby allowing control of the pitch, length, and blaze of the perturbations. This paper provides further details on these fiber mode converters and reports the first direct observation of the index perturbations with thermoluminescence.
Composite Cell Sheets (2010)

These data collected in a clinically relevant nonhuman primate model show that developmentally restricted SSEA-1(+) cardiac progenitors appear to be safe and highlight the benefit of the epicardial delivery of a construct harboring cells with a cardiomyogenic differentiation potential and cells providing them the necessary trophic support.