gebhart/patrepeval huggingface dataset:
Luminescent mesoporous LaVO4:Eu3+ core-shell nanoparticles: synthesis, characterization, biocompatibility and their cytotoxicity (2011)

A general and facile method was used for preparation of water-soluble silica coated LaVO4:Eu3+ core-shell nanoparticles. In the present study, we have discussed and compared the cytotoxicity characteristics of the synthesized LaVO4:Eu3+ and silica coated LaVO4:Eu3+ core-shell nanoparticles. X-ray diffraction (XRD), field-emission transmission electron microscopy (FE-TEM), energy dispersive X-ray analysis (EDX), Fourier-transform infrared spectroscopy (FTIR), UV/Vis absorption spectroscopy and photoluminescence spectroscopic techniques were employed to characterize the structure and morphology of the prepared products. To obtain high aqueous solubility, luminescent LaVO4:Eu3+ nanoparticles were encapsulated with silica groups, giving the nanoparticles a negatively charged surface at physiological pH. The results of XRD confirm the formation of a well-crystallized LaVO4:Eu3+ phase with a tetragonal zircon structure. Optical absorption spectra show that the optical properties of silica-coated LaVO4:Eu3+ core-shell nanoparticles are related to their sizes and shapes. Further, in order to assess cytotoxicity, we investigated whether the LaVO4:Eu3+ nanoparticles could alter biological samples once they enter human H522 and peripheral blood mono nuclear cells (PBMCs). An MTT assay was performed to measure the mitochondrial activity that reflects the number of viable cells. Silica coated LaVO4:Eu3+ core-shell nanoparticles exhibited no significant effect on the viability of both types of cells up to 24 h after exposure. Strikingly, no dose effects were detected, even at highest concentrations.
CCDC 106509: Experimental Crystal Structure Determination (1999)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
A Hendecad Motif Is Preferred for Heterochiral Coiled-Coil Formation (2019)

The structural principles that govern interactions between l- and d-peptides are not well understood. Among natural proteins, coiled-coil assemblies formed between or among α-helices are the most regular feature of tertiary and quaternary structures. We recently reported the first high-resolution structures for heterochiral coiled-coil dimers, which represent a starting point for understanding associations of l- and d-polypeptides. These structures were an unexpected outcome from crystallization of a racemic peptide corresponding to the transmembrane domain of the influenza A M2 protein (M2-TM). The reported structures raised the possibility that heterochiral coiled-coil dimers prefer an 11-residue (hendecad) sequence repeat, in contrast to the 7-residue (heptad) sequence repeat that is dominant among natural coiled coils. To gain insight on sequence repeat preferences of heterochiral coiled-coils, we have examined three M2-TM variants containing substitutions intended to minimize steric clashes between side chains at the coiled-coil interface. In each of the three new crystal structures, we observed heterochiral coiled-coil associations that closely match a hendecad sequence motif, which strengthens the conclusion that this motif is intrinsic to the pairing of α-helices with opposite handedness. In each case, the presence of a hendecad motif was established by comparing the observed helical frequency to that of an ideal hendecad. This comparison revealed that decreasing the size of the amino acid side chain at positions that project toward the superhelical axis produces tighter packing, as determined by the size of the coiled-coil radius. These results provide a basis for future design of heterochiral coiled-coil pairings.
Challenges and Strategies for a Thorough Characterization of Antibody Acidic Charge Variants (2022)

Heterogeneity of therapeutic Monoclonal antibody (mAb) drugs are due to protein variants generated during the manufacturing process. These protein variants can be critical quality attributes (CQAs) depending on their potential impact on drug safety and/or efficacy. To identify CQAs and ensure the drug product qualities, a thorough characterization is required but challenging due to the complex structure of biotherapeutics. Past characterization studies for basic and acidic variants revealed that full characterizations were limited to the basic charge variants, while the quantitative measurements of acidic variants left gaps. Consequently, the characterization and quantitation of acidic variants are more challenging. A case study of a therapeutic mAb1 accounted for two-thirds of the enriched acidic variants in the initial characterization study. This led to additional investigations, closing the quantification gaps of mAb1 acidic variants. This work demonstrates that a well-designed study with the right choices of analytical methods can play a key role in characterization studies. Thus, the updated strategies for more complete antibody charge variant characterization are recommended.
Quantifying the nativeness of antibody sequences using long short-term memory networks (2019)

Antibodies often undergo substantial engineering en route to the generation of a therapeutic candidate with good developability properties. Characterization of antibody libraries has shown that retaining native-like sequence improves the overall quality of the library. Motivated by recent advances in deep learning, we developed a bi-directional long short-term memory (LSTM) network model to make use of the large amount of available antibody sequence information, and use this model to quantify the nativeness of antibody sequences. The model scores sequences for their similarity to naturally occurring antibodies, which can be used as a consideration during design and engineering of libraries. We demonstrate the performance of this approach by training a model on human antibody sequences and show that our method outperforms other approaches at distinguishing human antibodies from those of other species. We show the applicability of this method for the evaluation of synthesized antibody libraries and humanization of mouse antibodies.
Bridging Disciplines as a pathway to Finding New Solutions for Osteoarthritis a collaborative program presented at the 2019 Orthopaedic Research Society and the Osteoarthritis Research Society International (2020)

To advance new OA treatments that are safe and effective, OA should be considered as a "Whole Person" disease. This approach requires a concerted effort to bridge disciplines and include interactions across scales from the molecule to the whole body, including psychosocial aspects.
Changing the Approach to Anticoagulant Therapy in Older Patients with Multimorbidity Using a Precision Medicine Approach (2018)

The ageing of the world population has resulted in an increase in the number of older patients with multimorbid conditions receiving multiple therapies. This emerging clinical scenario poses new challenges, which are mostly related to the increased incidence of adverse effects. This translates into poor clinical care, reduced cost-effectiveness of drug therapies, and social isolation of multimorbid patients due to reduced autonomy. A strategy to address these emerging challenges could involve the personalization of therapies based on the clinical, molecular, and genetic characterization of multimorbid patients. Anticoagulation therapy is a feasible model to implement personalized medicine since it generally involves older multimorbid patients receiving multiple drugs. In this study, in patients with atrial fibrillation, the use of the new generation of anticoagulation therapy, i.e., direct oral anti-coagulants (DOACs), is based on a preliminary assessment of the molecular targets of DOACS and any possible drug⁻drug interactions. Then, the genetic polymorphism of enzymes metabolizing DOACs is studied. After DOAC prescription, its circulating levels are measured. Clinical data are being collected to assess whether this personalized approach improves the safety and efficacy profiles of anticoagulation therapy using DOACs, thereby reducing the costs of healthcare for ageing multimorbid patients.
Adaptive dynamic artificial poly-ligand targeting (ADAPT) of the plasma exosome proteome: A highly multiplexed non-invasive diagnostic discovery platform. (2016)

e23058 Background: Understanding individual biomarkers and multi-molecular complexes in their native states represents a major hurdle in the development of systems biology platforms and requires multiplexing capabilities many orders of magnitude greater than what is currently available. This knowledge is especially important in diseases like cancer, where perturbations in signaling pathways lead to the initiation and propagation of a vast range of molecularly heterogeneous phenotypes. Ideally, this information would be gathered non-invasively from peripheral compartments. We report ADAPT as an unbiased discovery method to identify native proteins and multi-molecular complexes in plasma. Methods: ssDNA libraries of 2x10^11 unique sequences were enriched towards association with exosomes of plasma pools from breast cancer patients (n=60) or from a control cohort of women without breast cancer (n=60). Two thousand ODNs were selected from the enriched library and used to profile 500 plasma samples: 206 breast cancer biopsy positive (BC+), 177 biopsy negative (BC-) and 117 self-declared healthy (H). Results: Random Forest Modeling (RFM) was used to build classifiers for BC+ vs. both BC- and H, BC+ vs. BC- and BC+ vs. H, with AUC values of 0.64, 0.64, and 0.73, respectively. Out-of-bag validation was used for this analysis. Notably, 10-fold cross-validation, repeated 20 times, resulted in ROC AUC values of 0.58 for BC+ vs. both controls, 0.59 for BC+ vs. BC-, 0.62 for BC+ vs. H. This difference between the out-of-bag and cross-validation result suggests that the study is underpowered to define an algorithm capable of handling the heterogeneity found in this set of breast cancer patients. Conclusions: The ADAPT platform uses ultra-high complexity libraries to improve the probability of identifying ODNs which recognize biomolecules in their native state. This unbiased approach quantifies differences between plasma from women with breast cancer and women without breast cancer, likely due to perturbations in molecular pathways. An ADAPT derived breast cancer test may find utility as a diagnostic tool in clinical practice.
VPS Tactile Display (2019)

One of the challenges in the field of haptics is to provide meaningful and realistic sensations to users. While most real world tactile sensations are composed of multiple dimensions, most commercial product only include vibration as it is the most cost effective solution. To improve on this, we introduce VPS (Vibration, Pressure, Shear) display, a multi-dimensional tactile array that increases information transfer by combining Vibration, Pressure, and Shear similar to how RGB LED combines red, blue, and green to create new colors. We characterize the device performance and dynamics for each tactile dimension in terms of its force and displacement profiles, and evaluate information transfer of the VPS display through a stimulus identification task. Our results indicate that the information transfer through a single taxel increases from 0.56 bits to 2.15 bits when pressure and shear are added to vibrations with a slight decrease in identification accuracy. We also explored the pleasantness and continuity of VPS and the study results reveal that tactile strokes in shear mode alone are rated highest on perceived pleasantness and continuity.
Grating design for interlayer optical interconnection of in-plane waveguides (2016)

Corrections to Eqs. (25) and (32) in our recent publication [Appl. Opt.55, 2601-2610 (2016).APOPAI0003-693510.1364/AO.55.002601] are presented in this erratum.
Oxide Components for the Solid Oxide Fuel Cell (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
RF Front-End Architecture for 5G (2018)

With the development of millimeter wave communication technologies in 5G mobile communication systems, a large number of small cells will be deployed to form 5G high-capacity ultra-dense networks. Therefore the energy efficiency should be a main design target for 5G RF front-ends (RFFEs) in order to achieve a low network operation cost. In this work we investigated the effect of the Tx signal processing architecture on RFFE total DC power consumption and the quality of the transmitted signal in terms of ACLR and EVM. We show that for the most practical cases of power amplifiers for high-capacity ultra-dense small networks with low output power, the PAPR reduction (PAPR-R) does not improve the efficiency of the RFFE. Thus, PAPR-R can be successively excluded from the Tx signal processing chain in order to increase RFFE efficiency and simplify the hardware design. Thus, with the proposed architecture, the RFFE total DC power consumption can be reduced approximately twice. However, it is desirable to use the predistorter in order to maintain the required ACLR and EVM levels in the PA output signal. Finally, we make practical recommendations regarding RFFE architecture that depend on the PA operating class and FPGA DC power consumption.
New Isoxazolidine-Conjugates of Quinazolinones—Synthesis, Antiviral and Cytostatic Activity (2016)

A novel series of (3-diethoxyphosphoryl)isoxazolidines substituted at C5 with various quinazolinones have been synthesized by the 1,3-dipolar cycloaddition of N-methyl-C-(diethoxyphosphoryl)nitrone with N3-substitued 2-vinyl-3H-quinazolin-4-ones. All isoxazolidines were assessed for antiviral activity against a broad range of DNA and RNA viruses. Isoxazolidines trans-11f/cis-11f (90:10), trans-11h and trans-11i/cis-11i (97:3) showed weak activity (EC50 = 6.84, 15.29 and 9.44 μM) toward VZV (TK⁺ strain) which was only one order of magnitude lower than that of acyclovir used as a reference drug. Phosphonates trans-11b/cis-11b (90:10), trans-11c, trans-11e/cis-11e (90:10) and trans-11g appeared slightly active toward cytomegalovirus (EC50 = 27-45 μM). Compounds containing benzyl substituents at N3 in the quinazolinone skeleton exhibited slight antiproliferative activity towards the tested immortalized cells with IC50 in the 21-102 μM range.
Complex and revision problems in shoulder surgery (1997)

Complex and revision problems in shoulder surgery , Complex and revision problems in shoulder surgery , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
A national survey on the prevalence and treatment outcome of active Cushing's disease in Belgium (2013)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Indoor field measurements with a configurable multi-antenna testbed (2005)

This paper reports the development of a configurable, non-real-time, 2/spl times/2 multi-antenna testbed operating at 5.25 GHz with a bandwidth of 25 MHz.. MIMO-OFDM modulation and demodulation are performed offline. The unit is fully calibrated and was used in extensive indoor wireless measurements at UCLA. The paper reports measurements for SISO, SIMO 1/spl times/2 and MIMO 2/spl times/2 setups in line of sight and nonline of sight channels. These measurements show that LOS channels are not necessarily detrimental for MIMO performance. Further experiments show that with -3 dBm of transmit power uncoded data rates of 140 Mbit/s are achievable.
Evaluation of optical reflectance techniques for imaging of alveolar structure (2012)

Three-dimensional (3-D) visualization of the fine structures within the lung parenchyma could advance our understanding of alveolar physiology and pathophysiology. Current knowledge has been primarily based on histology, but it is a destructive two-dimensional (2-D) technique that is limited by tissue processing artifacts. Micro-CT provides high-resolution three-dimensional (3-D) imaging within a limited sample size, but is not applicable to intact lungs from larger animals or humans. Optical reflectance techniques offer the promise to visualize alveolar regions of the large animal or human lung with sub-cellular resolution in three dimensions. Here, we present the capabilities of three optical reflectance techniques, namely optical frequency domain imaging, spectrally encoded confocal microscopy, and full field optical coherence microscopy, to visualize both gross architecture as well as cellular detail in fixed, phosphate buffered saline-immersed rat lung tissue. Images from all techniques were correlated to each other and then to corresponding histology. Spatial and temporal resolution, imaging depth, and suitability for in vivo probe development were compared to highlight the merits and limitations of each technology for studying respiratory physiology at the alveolar level.
Numerical Simulations of MitraClip Placement: Clinical Implications (2019)

Mitral regurgitation (MR) is the most common type of valvular heart disease in patients over the age of 75 in the US. Despite the prevalence of mitral regurgitation in the elderly population, however, almost half of patients identified with moderate-severe MR are turned down for traditional open heart surgery due to frailty and other existing co-morbidities. MitraClip (MC) is a recent percutaneous approach to treat mitral regurgitation by placement of MC in the center of the mitral valve to reduce MR. There are currently no computational simulations to elucidate the role of MC on both the fluid and solid mechanics of the mitral valve. Here, we use the Smoothed Particle Hydrodynamics (SPH) approach to study various positional placements of the MC in the mitral valve and its impact on reducing MR. SPH is a particle based (meshless) approach that handles flow through narrow regions quite efficiently. Fluid and surrounding anatomical structure interactions is handled via contact and hence can be used for studying fluid-structure interaction problems such as blood flow with surrounding tissues/structure. This method is available as part of the Abaqus/Explicit solver. Regurgitation was initiated by removing targeted chordae tendineae that are attached to specified leaflets of the mitral valve and, subsequently, MC implants are placed in various locations, starting from the region near where the chordae tendineae were removed and moving away from the location towards the center of the valve. The MC implant location closest to where the chordae tendineae were removed showed the least amount of residual MR post-clip implantation amongst all other locations of MC implant considered. These findings have important implications for strategic placement of the MC depending on the etiology of MR to optimize clinical outcome.
Mining Predicted Crystal Structure Landscapes with High Throughput Crystallization: Old Molecules, New Insights (2019)

&lt;a&gt;&lt;/a&gt;&lt;a&gt;Organic molecules tend to close pack to form dense structures when they are crystallized from organic solvents. Porous molecular crystals defy this rule: they typically crystallize with lattice solvent in the interconnected pores. However, the design and discovery of such structures is often challenging and time consuming, in part because it is difficult to predict solvent effects on crystallization. Here, we combine crystal structure prediction (CSP) with a high-throughput crystallization screening method to accelerate the discovery of stable hydrogen-bonded frameworks. We exemplify this strategy by finding new phases of two well-studied molecules in a computationally targeted way. Specifically, we find a new porous polymorph of trimesic acid, δ-&lt;b&gt;TMA&lt;/b&gt;, that has a guest free hexagonal pore structure, as well as three new solvent-stabilized diamondoid frameworks&lt;/a&gt; of adamantane-1,3,5,7-tetracarboxylic acid (&lt;b&gt;ADTA&lt;/b&gt;).
Radiation detectors based on 4H semi-insulating silicon carbide (2010)

In this work, radiation detectors were fabricated using 8 mm &times; 8 mm substrates, &#126; 390 &mu;m in thickness, diced from commercial (0001) 4H-SiC semi-insulating wafer (&gt; 10<sup>9</sup> Ohm-cm). Our characterization results, including x-ray diffraction (XRD), electron beam induced current (EBIC), chemical etching, cross-polarized imaging, thermally stimulated current (TSC) measurements, chemical etching and Raman spectroscopy, show the high quality of the semiinsulating SiC crystals, which are believed to meet the requirements of fabricating high performance radiation detectors. Current-voltage characteristics showed very low leakage current (&#126; 1.5 pA at -500 V) and the capability of detector's operation up to 200&#176;C.
Retinal optical coherence tomography image enhancement via deep learning (2018)

Optical coherence tomography (OCT) images of the retina are a powerful tool for diagnosing and monitoring eye disease. However, they are plagued by speckle noise, which reduces image quality and reliability of assessment. This paper introduces a novel speckle reduction method inspired by the recent successes of deep learning in medical imaging. We present two versions of the network to reflect the needs and preferences of different end-users. Specifically, we train a convolution neural network to denoise cross-sections from OCT volumes of healthy eyes using either (1) mean-squared error, or (2) a generative adversarial network (GAN) with Wasserstein distance and perceptual similarity. We then interrogate the success of both methods with extensive quantitative and qualitative metrics on cross-sections from both healthy and glaucomatous eyes. The results show that the former approach provides state-of-the-art improvement in quantitative metrics such as PSNR and SSIM, and aids layer segmentation. However, the latter approach, which puts more weight on visual perception, outperformed for qualitative comparisons based on accuracy, clarity, and personal preference. Overall, our results demonstrate the effectiveness and efficiency of a deep learning approach to denoising OCT images, while maintaining subtle details in the images.
Towards quantitative modeling of task confirmations in human-robot dialog (2011)

We present a technique for robust human-robot interaction taking into consideration uncertainty in input and task execution costs incurred by the robot. Specifically, this research aims to quantitatively model confirmation feedback, as required by a robot while communicating with a human operator to perform a particular task. Our goal is to model human-robot interaction from the perspective of risk minimization, taking into account errors in communication, "risk" involved in performing the required task, and task execution costs. Given an input modality with non-trivial uncertainty, we calculate the cost associated with performing the task specified by the user, and if deemed necessary, ask the user for confirmation. The estimated task cost and the uncertainty measure are given as input to a Decision Function, the output of which is then used to decide whether to execute the task, or request clarification from the user. We test our system through human-interface experiments, based on a framework custom-designed for our family of amphibious robots, and demonstrate the utility of the framework in the presence of large task costs and uncertainties. We also present qualitative results of our algorithm from field trials of our robots in both open-and closed-water environments.