gebhart/patrepeval huggingface dataset:
Synthesis of exo‐3‐Amino‐7‐azabicyclo[2.2.1]heptanes as a Class of Malarial Aspartic Protease Inhibitors: Exploration of Two Binding Pockets (2009)

Abstract The increasing prevalence of drug‐resistant strains of malaria‐causing Plasmodium parasites necessitates the development of therapeutic agents that inhibit new biochemical targets. We herein describe the design, synthesis, and in vitro evaluation of a class of inhibitors that target the malarial aspartic proteases known as the plasmepsins. The title compounds feature a 7‐azanorbornane skeleton that bears an exo ‐amino function, which was designed to interact with the catalytic dyad of aspartic proteases while providing vectors for the attachment of binding elements that target the flap and S1/S3 binding pockets at the enzyme active site. Their synthesis takes advantage of a solvent‐free and highly diastereoselective conjugate addition of amines to bicyclic vinyl sulfones. Structural optimization based on a little‐known conformational preference of aryl sulfones produced the most potent inhibitors of this new class. In vitro assays demonstrate that the title compounds are capable of potent (IC 50 ≥ 10 n M ) inhibition of plasmepsins, while remaining relatively weak inhibitors of the closely related human enzymes cathepsins D and E. The ideal occupation of the flap pocket is crucial for both potency and selectivity over the human proteases. Differently functionalized compounds were synthesized to gain new insights into the molecular recognition properties of this cavity. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Exclusive dimuon production in ultraperipheral Pb+Pb collisions at sNN=5.02TeV with ATLAS (2021)

Exclusive dimuon production in ultraperipheral collisions (UPC), resulting from photon-photon interactions in the strong electromagnetic fields of colliding high-energy lead nuclei, PbPb( ) + -(Pb ( ) Pb ( ) ), is studied using L int = 0.48 nb -1 of s NN = 5.02 TeV lead-lead collision data at the LHC with the ATLAS detector. Dimuon pairs are measured in the fiducial region p T, > 4 GeV, | | < 2.4, invariant mass m > 10 GeV, and p T, < 2 GeV. The primary background from single-dissociative processes is extracted from the data using a template fitting technique. Differential cross sections are presented as a function of m , absolute pair rapidity (|y |), scattering angle in the dimuon rest frame (| cos | ), and the colliding photon energies.
Fabrication of Highly Metallic TiN Films by Pulsed Laser Deposition Method for Plasmonic Applications (2017)

We report the fabrication of titanium nitride (TiN) films with the “best” plasmonic behavior reported so far by the pulsed laser deposition method. Even though the deposition is done at room temperature (∼25 °C) and grown on an amorphous native oxide of a silicon wafer, the plasmonic property of the TiN is comparable to that of gold, which is a conventional plasmonic material in the visible to near-infrared region. Because of the highly plasmonic nature of the TiN, the near field around the TiN nanostructure can be as high as that of a gold nanostructure. A room-temperature process without a strict requirement on the substrate allows depositing a TiN film even on a flexible polymer film without degrading its property. Our results pave the way for using TiN as a truly practical plasmonic material, replacing the use of noble metals.
Pancreatic Tumor Sensitivity to Plasma L-Asparagine Starvation (2012)

Objectives In this study, our aim was to test whether asparagine synthetase (ASNS) deficiency in pancreatic malignant cells can lead to sensitivity to asparagine starvation. We also investigated, in tumor-bearing mice, the efficacy of L-asparaginase entrapped in red blood cells (RBCs), a safe formulation, to induce asparagine depletion. Methods First, ASNS expression was evaluated by immunohistochemistry in sporadic pancreatic ductal adenocarcinoma. Then, 4 pancreatic carcinoma cell lines were examined by Western blot, immunocytochemistry, and cytotoxicity assay to L-asparaginase and in asparagine-free or reduced-asparagine media. Finally, mice bearing the most in vitro sensitive cell line received RBC-entrapped L-asparaginase to investigate the anticancer efficacy of serum asparagine depletion in vivo. Results Approximately 52% of pancreatic adenocarcinomas expressed no or low ASNS. The highest in vitro cytotoxicity to L-asparaginase or to reduced asparagine medium was observed with SW1990 line when ASNS expression was the lowest. In vivo sensitivity was confirmed for this cell line. Conclusions Plasma asparagine depletion by RBC-entrapped L-asparaginase in selected patients having no low or no ASNS may be a promising therapeutic approach for pancreatic cancer.
CGRP induction in cystic fibrosis airways alters the submucosal gland progenitor cell niche in mice (2015)

At the request of the corresponding author, the JCI is retracting the paper "FOXO3 programs tumor-associated DCs to become tolerogenic in human and murine prostate cancer" based on findings of data falsification and fabrication regarding Figures
The raman contribution to the intensity dependent refractive index in optical fibers (2011)

We report on the Raman contribution to the intensity dependent refractive index in step-index fibers with germanium doped silica core. The f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> value is found to be 0.157 ± 0.07 for a field weighted germanium concentration between 5 and 25 mol %.
Quantification and Characterization of Autotransduction in Retroviral Vector Producer Cells (2007)

Gene therapy has evolved into a tempting strategy for the management of cancer and other life-threatening diseases. Various approaches employ retroviral vectors to deliver the therapeutic gene. The profound knowledge about retrovirus biology allows the generation of increasingly advanced vector systems as well as an accurate assessment and management of potential safety risks. This study focuses on the genetic stability of retrovirus producer cells as a basic safety requirement and its compromise by autotransduction. It has been shown previously that protection of retroviral packaging systems by superinfection interference is not guaranteed. The current study provides insight into the extent of autotransduction and the time point at which it occurs, and examines strategies to antagonize it. Therefore, a reconstituting vector system was used that obviates transgene expression in virus producer cells by physically separating transgene and promoter. Just on infection two functional expression cassettes are reconstituted, causing highly efficient transgene expression in transduced cells. Equipped with an enhanced green fluorescent protein-encoding gene, this vector allowed accurate quantification of autotransduced cells, which were then isolated by fluorescence-activated cell sorting and further characterized. Sequencing of recloned integrated vector copies demonstrated that high transgene expression levels were strictly associated with the presence of reverse-transcribed vector copies. Envelope protein expression levels, however, were found to be equal in autotransduced and noninfected virus producer cells. Finally, the occurrence of autotransduction could be assigned to an early time point after transfection and was successfully blocked by azidothymidine treatment, yielding a stable and homogeneous population of noninfected retrovirus producer cells.
Diagnosing Antibiotic Resistance Using Nucleic Acid Enzymes and Gold Nanoparticles (2021)

The rapid and accurate detection of antimicrobial resistance is critical to limiting the spread of infections and delivering effective treatments. Here, we developed a rapid, sensitive, and simple colorimetric nanodiagnostic platform to identify disease-causing pathogens and their associated antibiotic resistance genes within 2 h. The platform can detect bacteria from different biological samples (<i>i.e</i>., blood, wound swabs) with or without culturing. We validated the multicomponent nucleic acid enzyme-gold nanoparticle (MNAzyme-GNP) platform by screening patients with central line associated bloodstream infections and achieved a clinical sensitivity and specificity of 86% and 100%, respectively. We detected antibiotic resistance in methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) in patient swabs with 90% clinical sensitivity and 95% clinical specificity. Finally, we identified <i>mecA</i> resistance genes in uncultured nasal, groin, axilla, and wound swabs from patients with 90% clinical sensitivity and 95% clinical specificity. The simplicity and versatility for detecting bacteria and antibiotic resistance markers make our platform attractive for the broad screening of microbial pathogens.
Heat recovery of used petroleum, oil, and lubricants (POL) (2002)

US Air Force/DOD installations generate millions of gallons of used POL annually. The quantities and variety of used POL are a function of the mission of each individual installation. An operationally acceptable and environmentally clean method for disposing of used POL by burning in local heating plant boilers will save individual installations millions of dollars in transportation, fuel, and disposal costs.
FoCUS: Fourier-Based Coded Ultrasound (2017)

Modern imaging systems typically use single-carrier short pulses for transducer excitation. Coded signals together with pulse compression are successfully used in radar and communication to increase the amount of transmitted energy. Previous research verified significant improvement in signal-to-noise ratio (SNR) and imaging depth for ultrasound imaging with coded signals. Since pulse compression needs to be applied at each transducer element, the implementation of coded excitation (CE) in array imaging is computationally complex. Applying pulse compression on the beamformer output reduces the computational load but degrades both the axial and lateral point spread function, compromising image quality. In this paper, we present an approach for efficient implementation of pulse compression by integrating it into frequency domain beamforming. This method leads to significant reduction in the amount of computations without affecting axial resolution. The lateral resolution is dictated by the factor of savings in computational load. We verify the performance of our method on a Verasonics imaging system and compare the resulting images to time-domain processing. The computational savings are evaluated for a minimal sampling rate of four times the central frequency. We show that from 4- to 33-fold reduction is achieved as a function of the resulting lateral resolution, with no degradation of axial resolution. For an imaging system operating at a higher sampling rate, e.g., 10 times the central frequency, the savings can be as high as 77-fold. The efficient implementation makes CE a feasible approach in array imaging with the potential to enhance SNR as well as improve imaging depth and frame rate.
One- and Two-Year Analysis of a Five-Year Prospective Multicenter Study Assessing Radiographic and Patient-Reported Outcomes Following Triplanar First Tarsometatarsal Arthrodesis With Early Weightbearing for Symptomatic Hallux Valgus (2022)

We report one- and 2-year results of a prospective, 5-year, multicenter study of radiographic, clinical, and patient-reported outcomes following triplanar first tarsometatarsal arthrodesis with early weightbearing. One-hundred and seventeen patients were included with a mean (95% confidence interval [CI]) follow-up time of 16.6 (15.5, 17.7) months. Mean (95% CI) time to weightbearing in a boot walker was 7.8 (6.6, 9.1) days, mean time to return to athletic shoes was 45.0 (43.5, 46.6) days, and mean time to return to unrestricted activity was 121.0 (114.5, 127.5) days. There was a significant improvement in radiographic measures with a mean corrective change of -18.0° (-19.6, -16.4) for hallux valgus angle, -8.3° (-8.9, -7.8) for intermetatarsal angle and -2.9 (-3.2, -2.7) for tibial sesamoid position at 12 months (n = 108). Additionally, there was a significant improvement in patient-reported outcomes (Visual Analog Scale, Manchester-Oxford Foot Questionnaire, and Patient-Reported Outcomes Measurement Information System) and changes were maintained at 12 and 24 months postoperatively. There was 1/117 (0.9%) reported recurrence of hallux valgus at 12 months. There were 16/117 (13.7%) subjects who experienced clinical complications of which 10/117 (8.5%) were related to hardware. Of the 7/117 (6.0%) who underwent reoperation, only 1/117 (0.9%) underwent surgery for a nonunion. The results of the interim report of this prospective, multicenter study demonstrate favorable clinical and radiographic improvement of the HV deformity, early return to weightbearing, low recurrence, and low rate of complications.
An Adapative Spread-Spectrum Data Hiding Technique For Digital Audio (2006)

In this paper we describe an application of spread spectrum techniques in audio data hiding for watermarking and steganography. The method is self-synchronizing, cover-dependent, and operates in the time domain. We use a special class of frequency-hop signal known as a Welch-Costas array. Welch-Costas arrays have the properties of range and Doppler resolution. This allows us to recover embedded data with a matched filter. We also demonstrate a special case of an adaptive method due to Su and Girod (2002).
Onboard Prediction of Propagation Loss in Shallow Water (1981)

Abstract : This report examines the state of the art in the prediction of propagation loss in shallow water as it pertains to onboard performance prediction. The following conclusions are drawn: (1) For simple cases, i.e., homogeneous liquid bottom, linear sound-speed gradient, no surface or bottom roughness, a simple algebraic model, for depth averaged propagation loss works as well as the more complex mode model. (The model is derived in the report.); (2) The uncertainty in bottom parameters, particularly sound velocity and attenuation makes it impossible to set meaningful bounds on propagation loss particularly for negative gradients or slow bottoms. (Useful predictions, however, can probably be made when a positive gradient is present.); (3) Details of the sound-speed profile can cause significant changes in propagation loss, therefore even if bottoms were well characterized, sophisticated computer models would be required to predict propagation loss; (4) Virtually all propagation loss curves can be described to within a fraction of a dB by the function PL = B + 15 log R + AR + CR-squared with the C coefficient usually zero. Thus, the output field can be described by two or, at most, three free parameters. Since there are no fewer than 24 input parameters it is thus easy to explain observed propagation loss and very difficult to predict it. Moreover, it is doubtful that propagation loss experiments can uniquely define bottom parameters; and (5) Certain aspects of the theory remain unverified and/or inadequately treated.
A Review on Recent Patents on Optical Coherence Tomography Applications in Ophthalmology (2012)

Optical coherence tomography (OCT) is a relatively new imaging modality that has been under investigation during the past two decades for a variety of ophthalmic applications. Because the eye is directly optically accessible, OCT enables visualization of the internal architecture of the eye which is hard to reach by other high resolution imaging methods. OCT hardware and software advances have facilitated the development of numerous OCT-based biomedical technologies. Consequently, there has been a worldwide surge in U.S issued patents on OCT ophthalmic applications. The focus of this review is to summarize the U.S issued patents on OCT ophthalmic applications.
Phenyltin-Substituted 9-Tungstogermanate and Comparison with Its Tungstosilicate Analogue (2008)

Reaction of (C 6H 5)SnCl 3 with Na 10[ A-alpha-GeW 9O 34] in water results in the monomeric, trisubstituted Keggin species [{(C 6H 5)Sn(OH)} 3( A-alpha-GeW 9O 34)] (4-) ( 1), constituting the first organotin derivative of a trilacunary Keggin tungstogermanate. Polyanion 1 could be obtained as two different cesium salts depending on the applied isolation strategy: Cs 3Na[{(C 6H 5)Sn(OH)} 3( A-alpha-GeW 9O 34)].9H 2O ( CsNa-1) and Cs 3[{(C 6H 5)Sn(OH)} 3( A-alpha-HGeW 9O 34)].8H 2O ( Cs-H1). The monomeric phenyltin-containing tungstosilicate [{(C 6H 5)Sn(OH)} 3( A-alpha-SiW 9O 34)] (4-) ( 2) and the dimeric, sandwich-type derivative [{(C 6H 5)Sn(OH)} 3( A-alpha-H 3SiW 9O 34) 2] (8-) ( 3) have also been isolated as the cesium salts Cs 3Na[{(C 6H 5)Sn(OH)} 3( A-alpha-SiW 9O 34)].9H 2O ( CsNa-2), Cs 4[{(C 6H 5)Sn(OH)} 3( A-alpha-SiW 9O 34)].13H 2O ( Cs-2), and Cs 8[{(C 6H 5)Sn(OH)} 3( A-alpha-H 3SiW 9O 34) 2].23H 2O ( Cs-3), respectively. We have investigated in detail the similarities and differences in the reactivity of (C 6H 5)Sn (3+) with [ A-alpha-GeW 9O 34] (10-) vs [ A-alpha-SiW 9O 34] (10-). All five compounds have been characterized in the solid state by means of elemental analysis, infrared spectroscopy, thermogravimetry, and single-crystal X-ray diffraction, representing the first structural analysis for polyanions 1- 3. A full solution characterization of 1 by multinuclear NMR spectroscopy ( (1)H, (13)C, (119)Sn, and (183)W) has also been performed. The monomeric polyanions 1 and 2 are closely associated in the solid state through (Sn)O-H...O t (O t: terminal oxygen atom) hydrogen bonds reinforced by weak C-H...O t contacts to form 2-dimensional ( CsNa-1 and CsNa-2) or 1-dimensional ( Cs-H1) arrangements, and also dimeric entities ( Cs-2) depending on the network of intermolecular interactions.
Discovery of GSK461364: A Polo‐Like Kinase 1 Inhibitor for the Treatment of Cancer (2009)

This chapter contains sections titled: Introduction Background Plk1 STRUCTURE-Activity Relationships Summary References
SI2-SSE: Collaborative Research: Integrated Tools for DNA Nanostructure Design and Simulation (2018)

One slide description of the collaborative project aimed at building a community of tools for structural DNA nanotechnology
Incremental structural modeling on sparse visual SLAM (2017)

This paper presents an incremental structural modeling approach that improves the precision and stability of existing batch based methods for sparse and noisy point clouds from visual SLAM. The main idea is to use the generating process of point clouds on SLAM effectively. First, a batch based method is applied to point clouds that are incrementally generated from SLAM. Then, the temporal history of reconstructed geometric primitives is statistically merged to suppress incorrect reconstruction. The evaluation shows that both precision and stability are improved compared to a batch based method and the proposed method is suitable for real-time structural modeling.
<title>Internet path inflation due to policy routing</title> (2001)

In our previous work, we used a simplified model of routing policy in the Internet to study the impact of policy routing on Internet path-lengths. This prior work suffered from two shortcomings--it was based on a single snapshot of the Internet topology, and our simplified policy model could generate AS paths that violate peering relationships. In this paper, we address these two shortcomings by re-examining our results with respect to a more recent snapshot of the Internet, and improving the policy model to avoid peering violation. We find that our prior observations regarding the path inflation due to routing policy appear to hold both across time and with respect to a more sophisticated model of routing policy.
Pathological Involvement of Astrocyte-Derived Lipocalin-2 in the Demyelinating Optic Neuritis (2015)

In this study, we demonstrated a significant induction of LCN2 expression in astrocytes of the optic nerve following EAON induction. Our results imply that astrocyte-derived LCN2 may have a pivotal role in the development of demyelinating optic neuritis, and LCN2 can be a therapeutic target to alleviate immune and inflammatory damage in the optic nerve.
Biomarkers for Prediction of Bovine Respiratory Disease Outcome (2009)

Fatal bovine respiratory disease (BRD) is frequently the result of a primary viral and a secondary bacterial respiratory infection. In cattle, BRD causes more than half of feedlot deaths and has a major impact on financial losses in the cattle industry in North America. It is, therefore, very important to understand the mechanism of this complex disease process as well to predict and identify BRD susceptible cattle to enhance treatment efficacy. We recently established the value of using combinatorial omics approaches to identify candidate biomarkers associated with stress responses, a factor that can increase the severity of BRD. The objective of the present investigation was to experimentally recreate fatal BRD and to use a combinatorial analysis of proteomic, metabonomic, and elemental profiles in serum samples to determine if multimethod analysis of these biomarkers could predict disease outcome. The proteomic studies revealed that changes in the serum proteome were significant on day 4 postviral infection when compared to preinfection (day 0) serum samples. Proteomic studies identified a group of acute phase proteins (haptoglobin and apolipoprotein AI), which could be linked to a primary viral respiratory infection, but there was no significant association observed with fatal BRD. In contrast, metabonomic and elemental analyses identified candidate biomarkers for viral infection (glucose, LDL, valine, phosphorous, and iron) and disease outcome (lactate, glucose, iron). While multivariate analysis of proteomic and metabolite profiles did not discriminate between animals that survived or died postsynergic viral-bacterial infection by analyzing preinfection (day 0) serum samples, analysis of serum elemental profiles prior to infection was, however, predictive of BRD outcome. Furthermore, discriminant analyses of all three methodologies used to profile serum (collected on day 4 postviral but prior to bacterial infection) revealed differential trends between animals that survived or died following synergic viral-bacterial infection. Thus, a combinatorial approach using proteomic, metabonomic, and elemental analyses of serum samples revealed that multimethod analysis could discriminate between the complex biological responses to secondary bacterial respiratory infection and predict disease outcome.