gebhart/patrepeval huggingface dataset:
Synthesis of Substituted 2-Pyridones via the Pummerer Cyclization−Deprotonation−Cycloaddition Cascade of Imidosulfoxides (1999)

1-Ethanesulfinylacetylpiperidin-2-one was prepared from delta-valerolactam in two steps by heating with ethylsulfenylacetyl chloride followed by sodium periodate oxidation. Slow addition of the imidosulfoxide to a refluxing mixture of toluene, acetic anhydride (10 equiv), and p-toluenesulfonic acid (1 mol %) resulted in the formation of an isomünchnone dipole which underwent bimolecular trapping in good yield. The stereochemical assignment of the cycloadduct was made on the basis of X-ray crystallography and is the consequence of an endo cycloaddition with respect to the dipole. The regiochemistry of the cycloaddition is consistent with a HOMO-dipole controlled process. Several related imidosulfoxides containing a tethered alkenyl group were prepared and subjected to the Pummerer reaction conditions. The resulting mesoionic dipoles formed by the cyclization-deprotonation sequence undergo ready dipolar cycloaddition across the pendant olefin to afford intramolecular cycloadducts in high yield. Exposure of these cycloadducts to acetic anhydride in the presence of a trace of p-toluenesulfonic acid results in ring opening to give 5-acetoxy-substituted 2-pyridones. The lone pair of electrons on the amide nitrogen assists in opening the oxy bridge to generate a transient N-acyliminium ion, which subsequently loses a proton. In certain cases, the amide electron pair with the oxy bridge is partially twisted from an antiperiplanar arrangement and a competive ring cleavage also occurs to give 5-thioethyl-substituted 2-pyridones.
Theranostic Mesoporous Silica Nanoparticles Loaded With a Curcumin-Naphthoquinone Conjugate for Potential Cancer Intervention (2021)

A novel theranostic molecule, derived from curcumin (Cur) and naphthoquinone (NQ), allowing for cancer targeting, detection and treatment was previously described and termed CurNQ. To allow for enhanced theranostic capabilities, advanced drug delivery techniques are required. To this end, mesoporous silica nanoparticles (MSN) were synthesized and CurNQ was loaded into its pores to form the novel nanosystem MSN_CurNQ. The formation of the nanosystem aimed to augment the drug delivery of CurNQ through the EPR effect and sustained release. Moreover, the loading of CurNQ into its pores, formed a fluorescent nanoparticle that can be tracked, detected and visualized. Herein, the synthesis of a novel nanosystem is described and its theranostic potential are explored <i>in vitro</i>. MSN with an average size of 108 d.nm, a zeta potential of -42 mV and a PDI of 0.150 were synthesized and were impregnated with CurNQ to form the novel nanosystem MSN_CurNQ. MSN_CurNQ was demonstrated to have pH-responsivity whereby after 96 h, at pH 7.4, 31.5% of CurNQ was released from the MSN compared to 57% release at pH 6.8, corresponding to an increase of 25.5% in release with a 0.6 pH drop. The innate fluorescence was then characterized through confocal and fluorescence microscopy. Microscopy images illustrated the distinct, high intensity innate fluorescence with a high background to target ratio, thus confirming detection capabilities and potentially extending MSN_CurNQ's application to molecular imaging purposes. Moreover, the chemotherapeutic potential of MSN_CurNQ was demonstrated as cell viability was reduced to below 50% in OVCAR-5, CACO-2, CHLA, and MCF-7 cell lines. Furthermore, MSN_CurNQ displayed tumor specific toxicity whereby the cell viability was reduced to a far greater extent in the cancer cell lines compared to a healthy fibroblast cell line (<i>p</i> = 0.000). Indeed, the novel MSN_CurNQ nanosystem has potential for applications in cancer targeting, detection and treatment.
A designed DNA binding motif that recognizes extended sites and spans two adjacent major grooves (2016)

We report the rational design of a DNA-binding peptide construct composed of the DNA-contacting regions of two transcription factors (GCN4 and GAGA) linked through an AT-hook DNA anchor. The resulting chimera, which represents a new, non-natural DNA binding motif, binds with high affinity and selectivity to a long composite sequence of 13 base pairs (TCAT-AATT-GAGAG).
The Fire-safe Cigarette (2000)

Cigarettes are the most common ignition source for fatal house fires, which cause approximately 29% of the fire deaths in the United States. A common scenario is the delayed ignition of a sofa, chair, or mattress by a lit cigarette that is forgotten or dropped by a smoker whose alertness is impaired by alcohol or medication. Cigarettes are designed to continue burning when left unattended. If they are dropped on mattresses, upholstered furniture, or other combustible material while still burning, their propensity to start fires varies depending on the cigarette design and content. The term "fire-safe" has evolved to describe cigarettes designed to have a reduced propensity for igniting mattresses and upholstered furniture. Legislative interest in the development of fire-safe smoking materials has existed for more than 50 years. Studies that showed the technical and economic feasibility of commercial production of fire-safe cigarettes were completed more than 10 years ago. Despite this, commercial production of fire-safe smoking materials has not been undertaken. The current impasse relates to the lack of consensus on a uniform test method on which to base a standard for fire-safe cigarettes. Although the fire-safe cigarette is a potentially important burn prevention tool, commercial production of such cigarettes will not occur until a standard against which fire-starting performance can be measured has been mandated by law at the state or federal level. The burn care community can play a leadership role in such legislative efforts.
Porous‐Silicon/Polymer Nanocomposite Photonic Crystals Formed by Microdroplet Patterning (2005)

A simple method to construct composite microparticles consisting of porous-silicon one-dimensional photonic crystals infused with a polymer is described. The particles (see Figure) are generated by spray-coating a fine mist of polymer solution onto a photonic crystal layer and then removing the uncoated material by chemical dissolution. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2005/c1760_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Degradation of Si1−xGex epitaxial devices by proton irradiation (1996)

Irradiation damage in n+-Si/p+-Si1−xGex/n-Si epitaxial diodes and heterojunction bipolar transistors by protons is studied. The degradation of the performance increases with increasing proton fluence, whereas it decreases with increasing germanium content and proton energy. The damage coefficient for proton irradiation is nearly the same as for neutron irradiation and is about three orders of magnitude larger than that for electron irradiation. This difference is due to the different number of knock-on atoms and the nonionizing energy loss, which is correlated to the difference of mass and the possibility of nuclear collisions.
Excited-State Intramolecular Proton Transfer in Five-Membered Hydrogen-Bonding Systems:  2-Pyridyl Pyrazoles (2003)

The excited-state intramolecular proton transfer (ESIPT) reaction in five-membered N-H...N hydrogen-bonding systems has been explored through design and syntheses of a series of 5-(2-pyridyl) 1-H-pyrazoles 1a-d. The ESIPT mechanism was confirmed through spectroscopy, relaxation dynamics, and corresponding methylated analogues. The results demonstrate for the first time a unique system among ESIPT molecules, in which ESIPT incorporates an appreciably large energy barrier fine-tuned by the skeletal reorganization. This makes 1a-d systems ideal models for probing the reaction potential energy surface.
HIV versus the immune system: another apparent victory for the virus (2001)

The only realistic hope for curbing the expanding HIV pandemic is the development of an effective vaccine. Understanding the immune responses that might protect from infection is of utmost relevance to this effort. With the most recent global figures showing that over 36 million people are now living with HIV, and expectations for rapidly expanding epidemics in Asia and the former Soviet Union, the need to understand immune protection in HIV infection is paramount.
Partial Marginalization Soft MIMO Detection With Higher Order Constellations (2010)

A new method for multiple-input multiple-output (MIMO) detection with soft-output, the partial marginalization (PM) algorithm, was recently proposed. Advantages of the method are that it is straightforward to parallelize, and that it offers a fully predictable runtime. PM trades performance for computational complexity via a user-defined parameter. In the limit of high computational complexity, the algorithm becomes the MAP demodulator. The PM algorithm also works with soft-input, but until now it has been unclear how to apply it for other modulation formats than binary phase-shift keying (BPSK) per real dimension. In this correspondence, we explain how to extend PM with soft-input to general signaling constellations, while maintaining the low complexity advantage of the original algorithm.
Learning to Simulate Realistic LiDARs (2022)

Simulating realistic sensors is a challenging part in data generation for autonomous systems, often involving carefully handcrafted sensor design, scene properties, and physics modeling. To alleviate this, we introduce a pipeline for data-driven simulation of a realistic LiDAR sensor. We propose a model that learns a mapping between RGB images and corresponding LiDAR features such as raydrop or per-point intensities directly from real datasets. We show that our model can learn to encode realistic effects such as dropped points on transparent surfaces or high intensity returns on reflective materials. When applied to naively raycasted point clouds provided by off-the-shelf simulator software, our model enhances the data by predicting intensities and removing points based on the scene's appearance to match a real LiDAR sensor. We use our technique to learn models of two distinct LiDAR sensors and use them to improve simulated LiDAR data accordingly. Through a sample task of vehicle segmentation, we show that enhancing simulated point clouds with our technique improves downstream task performance.
Temperature‐dependency analysis and correction methods of in situ power‐loss estimation for crystalline silicon modules undergoing potential‐induced degradation stress testing (2015)

Abstract We propose a method for in situ characterization of the photovoltaic module power at standard test conditions, using superposition of the dark current–voltage ( I–V ) curve measured at the elevated stress temperature, during potential‐induced degradation (PID) testing. PID chamber studies were performed on several crystalline silicon module designs to determine the extent to which the temperature dependency of maximum power is affected by the degradation of the modules. The results using the superposition principle show a mismatch between the power degradation measured at stress temperature and the degradation measured at 25 °C, dependent on module design, stress temperature, and level of degradation. We investigate the correction of this mismatch using two maximum‐power temperature translation methods found in the literature. For the first method, which is based on the maximum‐power temperature coefficient, we find that the temperature coefficient changes as the module degrades by PID, thus limiting its applicability. The second method investigated is founded on the two‐diode model, which allows for fundamental analysis of the degradation, but does not lend itself to large‐scale data collection and analysis. Last, we propose and validate experimentally a simpler and more accurate maximum‐power temperature translation method, by taking advantage of the near‐linear relationship between the mismatch and power degradation. This method reduces test duration and cost, avoids stress transients while ramping to and from the stress temperature, eliminates flash testing except at the initial and final data points, and enables significantly faster and more detailed acquisition of statistical data for future application of various statistical reliability models. Copyright © 2015 John Wiley &amp; Sons, Ltd.
High-throughput tracking of single yeast cells in a microfluidic imaging matrix (2010)

Time-lapse live cell imaging is a powerful tool for studying signaling network dynamics and complexity and is uniquely suited to single cell studies of response dynamics, noise, and heritable differences. Although conventional imaging formats have the temporal and spatial resolution needed for such studies, they do not provide the simultaneous advantages of cell tracking, experimental throughput, and precise chemical control. This is particularly problematic for system-level studies using non-adherent model organisms such as yeast, where the motion of cells complicates tracking and where large-scale analysis under a variety of genetic and chemical perturbations is desired. We present here a high-throughput microfluidic imaging system capable of tracking single cells over multiple generations in 128 simultaneous experiments with programmable and precise chemical control. High-resolution imaging and robust cell tracking are achieved through immobilization of yeast cells using a combination of mechanical clamping and polymerization in an agarose gel. The channel and valve architecture of our device allows for the formation of a matrix of 128 integrated agarose gel pads, each allowing for an independent imaging experiment with fully programmable medium exchange via diffusion. We demonstrate our system in the combinatorial and quantitative analysis of the yeast pheromone signaling response across 8 genotypes and 16 conditions, and show that lineage-dependent effects contribute to observed variability at stimulation conditions near the critical threshold for cellular decision making.
Sitagliptin, a dipeptidyl peptidase‐4 inhibitor, improves recognition memory, oxidative stress and hippocampal neurogenesis and upregulates key genes involved in cognitive decline (2015)

These studies show that sitagliptin can reverse memory impairment in high-fat-fed mice and is also associated with improved insulin sensitivity, enhanced hippocampal neurogenesis and reduced oxidative stress. DPP-4 inhibitors may therefore exhibit dual benefits by improving metabolic control and reducing the decline in cognitive function.
Intercellular trafficking of the nuclear oncoprotein DEK (2013)

DEK is a biochemically distinct, conserved nonhistone protein that is vital to global heterochromatin integrity. In addition, DEK can be secreted and function as a chemotactic, proinflammatory factor. Here we show that exogenous DEK can penetrate cells, translocate to the nucleus, and there carry out its endogenous nuclear functions. Strikingly, adjacent cells can take up DEK secreted from synovial macrophages. DEK internalization is a heparan sulfate-dependent process, and cellular uptake of DEK into DEK knockdown cells corrects global heterochromatin depletion and DNA repair deficits, the phenotypic aberrations characteristic of these cells. These findings thus unify the extracellular and intracellular activities of DEK, and suggest that this paracrine loop involving DEK plays a role in chromatin biology.
Accelerating application-level security protocols (2004)

We present a minimal extension to the BSD socket layer that can improve the performance of application-level security protocols, such as SSH or SSL/TLS, by 10%, when hardware cryptographic accelerators are available in the system. Applications specify what cryptographic transforms must be applied to incoming and outgoing data frames, and such processing is applied by the operating system itself (exploiting hardware accelerators) when the application sends or receives data. Under this scheme, we can reduce the number of system calls and context switches by 50%, and the amount of data copying by 66%. We describe our prototype implementation for the openBSD system and quantify its performance implications. We conclude with a discussion of further possible performance improvements that our approach enables.
Microwave synthesis of [18F]FPEB in a semi-automated synthesis module (2010)

141 Objectives To improve the synthesis of [18F]FPEB (3-[18FF]fluoro-5-(2-pyridinylethynyl)benzonitrile) by application of microwave acceleration in a modified semi-automated fluorination module. Methods A GE TRACERlab® FX-FN module was used with a microwave accelerator with detached resonance cavity. Aqueous [18F]fluoride (70-110 GBq) was collected on a QMA cartridge and eluted with Kryptofix-222 K2CO3 in CH3CN/H2O into a modified Pyrex® V-vial grafted onto a glass collar to allow it to mate with the module’s vessel head. The solution was dried with He(g) flow at 85-105°C followed by 1 mL CH3CN treatment and drying. The vessel was moved to the microwave cavity, precursor 3-nitro-5-(2-pyridinylethynyl)benzonitrile (3-5 mg) in 0.6 ± 0.1 mL DMSO was added, and the mixture was irradiated with a sequence of 3 x 30 sec at 80 watts and maximum temperature 120°C. Control reactions were carried out by thermal heating in the module for 15 min at 120°C. HPLC mobile phase was added and injected on an HPLC with semi-prep C18 column, eluting with EtOH/(10 mM NaH2PO4 pH 6.7), 50/50. The eluate was diluted, trapped on a C18 Sep-Pak® and eluted with 1 mL EtOH and 9 mL normal saline, then filtered through a 0.22 µm membrane filter. Specific activity and radiochemical purity were determined by analytical HPLC. Results The end-of-synthesis yield of [18F]FPEB was greater with microwave acceleration (10,320 MBq; n = 9) versus thermal heating (7,820 n = 8) and the specific activity was significantly greater (microwave 835 vs thermal 206 GBq/µmol). Radiochemical purity was >98% for both treatments. Overall time of synthesis was shorter by about 15 min for microwave acceleration for a total synthesis time from EOB to EOS of 215 min. Conclusions Microwave acceleration provided [18F]FPEB with higher specific activity and with higher efficiency than thermal heating. Research Support Supported in part by Vanderbilt Dept Radiology
Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition (2017)

Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. Here, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine-tryptophan cross-link, which is installed by the radical <i>S</i>-adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon-carbon cross-link in the streptide family of natural products.
<title>Optical scatter: an overview</title> (1991)

Optical scatter is a bothersome source of optical noise, limits resolution and reduces system throughput. However, it is also an extremely sensitive metrology tool. It is employed in a wide variety of applications in the optics industry (where direct scatter measurement is of concern) and is becoming a popular indirect measurement in other industries where its measurement in some form is an indicator of another component property - like roughness, contamination or position. This paper presents a brief review of the current state of this technology as it emerges from university and government laboratories into more general industry use. The bidirectional scatter distribution function (or BSDF) has become the common format for expressing scatter data and is now used almost universally. Measurements made at dozens of laboratories around the country cover the spectrum from the uv to the mid- IR. Data analysis of optical component scatter has progressed to the point where a variety of analysis tools are becoming available for discriminating between the various sources of scatter. Work has progressed on the analysis of rough surface scatter and the application of these techniques to some challenging problems outside the optical industry. Scatter metrology is acquiring standards and formal test procedures. The available scatter data base is rapidly expanding as the number and sophistication of measurement facilities increases. Scatter from contaminants is continuing to be a major area of work as scatterometers appear in vacuum chambers at various laboratories across the country. Another area of research driven by space applications is understanding the non-topographic sources of mid-IR scatter that are associated with Beryllium and other materials. The current flurry of work in this growing area of metrology can be expected to continue for several more years and to further expand to applications in other industries.
Characterization of High Alloy Steel Produced Via Electron Beam Melting (2003)

Electron Beam Melting (EBM) is a direct-to-metal freeform fabrication technique in which a 4 kW electron beam is used to melt metal powder in a layer-wise fashion. As this process is relatively new, there have not yet been any independently published studies of the high alloy steel microstructural properties. This paper describes the EBM process and presents results of microstructural analyses on H13 tool steel processed via EBM.
A General Class of Throughput Optimal Routing Policies in Multi-Hop Wireless Networks (2012)

This paper considers the problem of throughput optimal routing/scheduling in a multi-hop constrained queueing network with random connectivity whose special cases include opportunistic multi-hop wireless networks and input-queued switch fabrics. The main challenge in the design of throughput optimal routing policies is closely related to identifying appropriate and universal Lyapunov functions with negative expected drift. The few well-known throughput optimal policies in the literature are constructed using simple quadratic or exponential Lyapunov functions of the queue backlogs and as such they seek to balance the queue backlogs across network independent of the topology. By considering a class of continuous, differentiable, and piece-wise quadratic Lyapunov functions, this paper provides a large class of throughput optimal routing policies. The proposed class of Lyapunov functions allow for the routing policy to control the traffic along short paths for a large portion of state-space while ensuring a negative expected drift. This structure enables the design of a large class of routing policies. In particular, and in addition to recovering the throughput optimality of the well-known backpressure routing policy, an opportunistic routing policy with congestion diversity is proved to be throughput optimal.