gebhart/patrepeval huggingface dataset:
Chronic Wounds, Biofilms and Use of Medicinal Larvae (2013)

Chronic wounds are a significant health problem in the United States, with annual associated costs exceeding $20 billion annually. Traditional wound care consists of surgical debridement, manual irrigation, moisture retentive dressings, and topical and/or systemic antimicrobial therapy. However, despite progress in the science of wound healing, the prevalence and incidence of chronic wounds and their complications are escalating. The presence &amp; complexity of bacterial biofilms in chronic wounds has recently been recognized as a key aspect of non-healing wounds. Bacterial biofilms are sessile colonies of polymicrobial organisms (bacteria, fungus, etc.) enclosed within a self-produced exopolymeric matrix that provides high levels of tolerance to host defenses, antibiotics and antiseptics. Thus, there is a need for alternative therapies to reduce biofilms in chronic wounds. In this report, we present initial findings from in vitro experiments which show that larval debridement therapy with disinfected blow fly larvae ( Phaenicia sericata ) reduced total CFUs (6-logs) of planktonic and mature biofilms of Pseudomonas aeruginosa or Staphylococcus aureus grown on dermal pig skin explants by 5-logs after 24 hours of exposure, and eliminated biofilms (no measurable CFUs) after 48 hours of exposure.
Theory and experiment on optical transverse intensity bistability in the transmission through a nonlinear thin (nematic liquid crystal) film (1984)

A theory is presented for the transverse intensity distribution bistability of a Gaussian optical beam after its passage through a nonlinear thin film. The equations governing the intensity distribution are cast in the form analogous to optical bistability in a longitudinal cavity (a Fabry-Perot interferometer), i.e., into two coupled transcendental equations from which multiple solutions are obtained. This formalism allows one to examine various physical approximations in obtaining the equations, and to improve on these approximations. It also lucidly illustrates the mechanisms of transverse intensity distribution bistability. The theoretical predictions are verified with quantitative experimental results on thin films of nematic liquid crystals.
Packaging Material Evaluation for 2.5D/3D TSV Application (2016)

Packaging material is one of the key components for through-silicon via (TSV) 2.5D/3D package giving a strong impact on the higher density integration and its reliability. In this paper, we report the assembly and reliability evaluation on film type underfill, photosensitive dielectric for redistribution layer as well as stress buffer, and molding compound. In the case of using our film type underfill, the chip is cracked by overflowed underfill during multi-die assembly in the conventional sequential method. By the collective staking method, the five-chip stacked package with TSV and 20 μm pitch bumps was demonstrated with excellent electrical yield. Also photosensitive dielectric realizes redistribution layers with 3 μm resolution and the raman shift in the 3D stack with photosensitive dielectric indicated lower stress than the one with silicon nitride as passivation layer. Finally we integrated our film type underfill, dielectric and molding compound in the stacked package, passing reliability tests such as thermal cycling and pressure cooker test.
Open-Access Biorepository for Idiopathic Pulmonary Fibrosis. The Way Forward (2014)

Although widespread use of animal modeling has transformed pulmonary research, the overarching goal of biomedical research is to enhance our understanding of human physiology and pathology. Thus, we believe that future gains in understanding human lung disease will be enhanced when studying patient-derived samples becomes an integral part of the investigational process. For idiopathic pulmonary fibrosis (IPF), investigators need quality human specimens, collected in a standardized fashion, along with carefully annotated, long-term clinical and outcomes data to address current knowledge gaps. Access to human lung tissues through commercial entities or the Lung Tissue Resource Consortium, an NHLBI-funded consortium, has demonstrated the feasibility of this approach. However, these samples are not always well annotated or collected uniformly and are limited in their breadth to address future IPF research needs. Therefore, we propose leveraging ongoing and future studies in IPF to establish a biorepository that will meet current and future needs of IPF investigations. Specifically, we propose that blood, cell, and lung samples, linked to robust longitudinal clinical phenotyping generated from future industry, federally sponsored, and investigator-initiated clinical studies be prospectively and uniformly collected and stored in a biorepository and linked registry. Here we outline standardized methodologies that would allow specimens and clinical data collected from different studies to be integrated and accessible to the IPF research community for investigations that will inform future basic and translational research in IPF. Such a biorepository needs the combined efforts of all stakeholders, to be driven by projected future scientific needs and to be available to all qualified researchers. We believe this infrastructure is crucial, is feasible, and would accelerate research in IPF.
Using Antigen–antibody Binding Kinetic Parameters to Understand Single-Molecule Array Immunoassay Performance (2016)

This paper provides insights into the performance of single-molecule array (Simoa) immunoassays by examining the effects of various capture and detector antibody-antigen binding kinetic parameters. Simoa is similar to other immunoassays in that the overall Simoa performance is heavily dependent on the choice of antibodies; however, little is known about how the different properties of the antibodies result in the wide variations in assay performance. Here, we focus on antibody-antigen binding kinetics and demonstrate how the association (k<sub>on</sub>) and dissociation (k<sub>off</sub>) rate constants of the capture and detection antibodies affect Simoa performance. We compared six different antibodies with over a four-log range of equilibrium dissociation constants (K<sub>D</sub>) and found that Simoa assay performance had an inverse relationship to the k<sub>off</sub> value of the detection antibody. The Simoa fluorescent signals were highest when the k<sub>off</sub> of the detection antibody was less than 10<sup>-5</sup> s<sup>-1</sup>. The capture antibody k<sub>off</sub> did not have as significant an effect, but a k<sub>off</sub> of less than 10<sup>-3</sup> s<sup>-1</sup> was preferred. We also found that the k<sub>on</sub> values of the capture and detection antibodies were not important factors for Simoa performance. Therefore, the assay optimization process could be accelerated by choosing detection antibodies with the slowest k<sub>off</sub> values.
Dynamic loss minimization using improved deadbeat-direct torque and flux control for interior permanent magnet synchronous machines (2012)

Direct torque control (DTC) has become a widely acceptable alternative to field oriented control (FOC). Deadbeat-direct torque and flux control (DB-DTFC) is a significant improvement over the classical DTC methods and provides the opportunities for fast torque control and dynamic loss minimization control. The existing high switching frequency DB-DTFC solution is based on approximate discrete time models. This paper presents a low switching frequency model so that even at low switching frequencies, proper DB-DTFC control can be achieved. The instantaneous dynamic loss model, which is a function of Volt-sec selection in each switching period, containing nonlinear effects such as minor hysteresis loops is theoretically derived and evaluated by both FEA simulation and experiments. With this calibrated dynamic loss model, deadbeat dynamic loss minimization control is implemented and integrated in DB-DTFC. Finally, the dynamic loss minimization control is evaluated experimentally and compared with the existing steady state loss minimization control.
Bioreactor model of neuromuscular junction with electrical stimulation for pharmacological potency testing (2017)

In vitro models of the neuromuscular junction (NMJ) are emerging as a valuable tool to study synaptogenesis, synaptic maintenance, and pathogenesis of neurodegenerative diseases. Many models have previously been developed using a variety of cell sources for skeletal muscle and motoneurons. These models can advanced by integrating beneficial features of the native developmental milieu of the NMJ. We created a functional in vitro model of NMJ by bioreactor cultivation of transdifferentiated myocytes and stem cell-derived motoneurons, in the presence of electrical stimulation. In conjunction with a coculture medium, electrical stimulation resulted in improved maturation and function of motoneurons and myocytes, as evidenced by mature cellular structures, increased expression of neuronal and muscular genes, clusterization of acetylcholine receptors (AChRs) in the vicinity of motoneurons, and the response to glutamate stimulation. To validate the model and demonstrate its utility for pharmacological testing, we documented the potency of drugs that affect key pathways during NMJ signal transduction: (i) acetylcholine (ACh) synthesis, (ii) ACh vesicular storage, (iii) ACh synaptic release, (iv) AChR activation, and (v) ACh inactivation in the synaptic cleft. The model properly responded to the drugs in a concentration-dependent manner. We thus propose that this in vitro model of NMJ could be used as a platform in pharmacological screening and controlled studies of neuromuscular diseases.
Creating Quantum Emitters in Hexagonal Boron Nitride Deterministically on Chip-Compatible Substrates (2021)

Two-dimensional hexagonal boron nitride (hBN) that hosts room-temperature single-photon emitters (SPEs) is promising for quantum information applications. An important step toward the practical application of hBN is the on-demand, position-controlled generation of SPEs. Strategies reported for deterministic creation of hBN SPEs either rely on substrate nanopatterning that is not compatible with integrated photonics or utilize radiation sources that might introduce unpredictable damage or contamination to hBN. Here, we report a radiation- and lithography-free route to deterministically activate hBN SPEs by nanoindentation with atomic force microscopy (AFM). The method applies to hBN flakes on flat silicon dioxide-silicon substrates that can be readily integrated into on-chip photonic devices. The achieved SPE yields are above 30% for multiple indent sizes, and a maximum yield of 36% is demonstrated for indents around 400 nm. Our results mark an important step toward the deterministic creation and integration of hBN SPEs with photonic and plasmonic devices.
Glycolytic and Non-glycolytic Functions of Mycobacterium tuberculosis Fructose-1,6-bisphosphate Aldolase, an Essential Enzyme Produced by Replicating and Non-replicating Bacilli (2011)

Background: New drugs active against persistent Mycobacterium tuberculosis are needed. Results: The fructose-1,6-bisphosphate aldolase (FBA-tb) is essential for growth of M. tuberculosis, is expressed by replicating and non-replicating bacilli, and displays plasminogen binding activity. Conclusion: FBA-tb is an essential TB enzyme that might also play a role in host/pathogen interactions. Significance: FBA-tb shows potential as a novel anti-TB therapeutic target.
Fermented Brown Rice Flour as Functional Food Ingredient (2014)

As fermentation could reduce the negative effects of bran on final cereal products, the utilization of whole-cereal flour is recommended, such as brown rice flour as a functional food ingredient. Therefore, this study aimed to investigate the effect of fermented brown rice flour on white rice flour, white rice batter and its steamed bread qualities. Brown rice batter was fermented using commercial baker's yeast (Eagle brand) according to the optimum conditions for moderate acidity (pH 5.5) to obtain fermented brown rice flour (FBRF). The FBRF was added to white rice flour at 0%, 10%, 20%, 30%, 40% and 50% levels to prepare steamed rice bread. Based on the sensory evaluation test, steamed rice bread containing 40% FBRF had the highest overall acceptability score. Thus, pasting properties of the composite rice flour, rheological properties of its batter, volume and texture properties of its steamed bread were determined. The results showed that peak viscosity of the rice flour containing 40% FBRF was significantly increased, whereas its breakdown, final viscosity and setback significantly decreased. Viscous, elastic and complex moduli of the batter having 40% FBRF were also significantly reduced. However, volume, specific volume, chewiness, resilience and cohesiveness of its steamed bread were significantly increased, while hardness and springiness significantly reduced in comparison to the control. These results established the effectiveness of yeast fermentation in reducing the detrimental effects of bran on the sensory properties of steamed white rice bread and encourage the usage of brown rice flour to enhance the quality of rice products.
Magnetic resonance imaging of ferumoxide-labeled mesenchymal stem cells in cartilage defects: in vitro and in vivo investigations. (2012)

The purpose of this study was to (1) compare three different techniques for ferumoxide labeling of mesenchymal stem cells (MSCs), (2) evaluate if ferumoxide labeling allows in vivo tracking of matrix-associated stem cell implants (MASIs) in an animal model, and (3) compare the magnetic resonance imaging (MRI) characteristics of ferumoxide-labeled viable and apoptotic MSCs. MSCs labeled with ferumoxide by simple incubation, protamine transfection, or Lipofectin transfection were evaluated with MRI and histopathology. Ferumoxide-labeled and unlabeled viable and apoptotic MSCs in osteochondral defects of rat knee joints were evaluated over 12 weeks with MRI. Signal to noise ratios (SNRs) of viable and apoptotic labeled MASIs were tested for significant differences using t-tests. A simple incubation labeling protocol demonstrated the best compromise between significant magnetic resonance signal effects and preserved cell viability and potential for immediate clinical translation. Labeled viable and apoptotic MASIs did not show significant differences in SNR. Labeled viable but not apoptotic MSCs demonstrated an increasing area of T2 signal loss over time, which correlated to stem cell proliferation at the transplantation site. Histopathology confirmed successful engraftment of viable MSCs. The engraftment of iron oxide-labeled MASIs by simple incubation can be monitored over several weeks with MRI. Viable and apoptotic MASIs can be distinguished via imaging signs of cell proliferation at the transplantation site.
Pancreatic Ductal Adenocarcinoma Subtyping Using the Biomarkers Hepatocyte Nuclear Factor-1A and Cytokeratin-81 Correlates with Outcome and Treatment Response (2017)

<b>Purpose:</b> Pancreatic ductal adenocarcinoma (PDAC) is associated with a dismal prognosis and poor therapeutic response to current chemotherapy regimens in unselected patient populations. Recently, it has been shown that PDAC may be stratified into functionally and therapeutically relevant molecular subgroups and that some of these subtypes can be recapitulated by IHC for KRT81 [quasi-mesenchymal (QM)/squamous/basal-like] and HNF1A (non-QM, overlap with exocrine/ADEX subtype).<b>Experimental Design:</b> We validated the different outcome of the HNF1A/KRT81 PDAC subtypes in two independent cohorts of surgically treated patients and examined the treatment response to chemotherapy in a third cohort of unresectable patients. The first two cohorts included 262 and 130 patients, respectively, and the third independent cohort comprised advanced-stage PDAC patients who were treated with either FOLFIRINOX (64 patients) or gemcitabine (61 patients).<b>Results:</b> In both cohorts with resected PDAC, the HNF1A-positive subtype showed the best, the KRT81-positive subtype the worst, and the double-negative subtype an intermediate survival (<i>P</i> < 0.013 and <i>P</i> < 0.009, respectively). In the chemotherapy cohort, the survival difference between the double-negative and the HNF1A-positive subtype was lost, whereas the dismal prognosis of KRT81-positive PDAC patients was retained (<i>P</i> < 0.021). Patients with a KRT81-positive subtype did not benefit from FOLFIRINOX therapy, whereas those with HNF1A-positive tumors responded better compared with gemcitabine-based treatment (<i>P</i> < 0.038).<b>Conclusions:</b> IHC stratification recapitulating molecular subtypes of PDAC using HNF1A and KRT81 is associated with significantly different outcomes and responses to chemotherapy. These results may pave the way toward future pretherapeutic biomarker-based stratification of PDAC patients. <i>Clin Cancer Res; 24(2); 351-9. ©2017 AACR</i>.
Confinement Heteroepitaxy: Realizing Atomically Thin, Half-van der Waals Materials (2019)

Three-dimensional epitaxial heterostructures are based on covalently-bonded interfaces, whereas those from 2-dimensional (2D) materials exhibit van der Waals interactions. Under the right conditions, however, material structures with mixed interfacial van der Waals and covalent bonding may be realized. Atomically thin layers formed at the epitaxial graphene (EG)/silicon carbide (SiC) interface indicate that EG/SiC interfaces provide this unique environment and enable synthesis of a rich palette of 2D materials not accessible with traditional techniques. Here, we demonstrate a method termed confinement heteroepitaxy (CHet), to realize air-stable, structurally unique, crystalline 2D-Ga, In, and Sn at the EG/SiC interface. The first intercalant layer is covalently-bonded to the SiC, and is accompanied by a vertical bonding gradient that ends with van der Waals interactions. Such structures break out of plane centrosymmetry, thereby introducing atomically thin, non-centrosymmetric 2D allotropes of 3D materials as a foundation for tunable superconductivity, topological states, and plasmonic properties.
Gas Flow in Nano-Channels:Thermal Transpiration Models (2007)

In the recent past, the first fully micromachined Knudsen pump was reported by our group followed by a preliminary system-level modeling that used analytical methods to predict the performance of a Knudsen pump. While this effort demonstrated the importance of analytical models for developing the understanding of the physics of the Knudsen pump, there was room for optimization of the modeling strategy.We are now benchmarking various analytical and semianalytical models against a very precise but computationally expensive molecule tracking technique known as direct simulation Monte Carlo (DSMC) technique. This details the applicability of various analytical and semi-analytical models to different flow conditions and highlights the potential of Sharipov’s model to serve as a computationally economical alternative to the DSMC technique for preliminary analysis of the thermal transpiration in microsystems. Characterization of Sharipov’s model against the DSMC technique, with the help of specially designed test cases, predicts that the Sharipov’s model is potentially the most representative model for DSMC in this context. Sharipov’s model is subsequently used to optimize the design parameters of the Knudsen pump. The analysis shows that a 200µm-long channel on a well-insulated glass substrate, with a channel height of 100nm and 10µm width, provides a mass-flow-rate of 1.5 x10
Demonstration of a Lossless Electron Beam Monochromator in an Ultrafast TEM Using Near-field THz Radiation (2022)

We realize a lossless electron beam monochromator in an ultrafast transmission electron microscope. The monochromator uses a single-cycle in-situ THz emitter, reducing the electron energy spread by a factor of 2.8 without losing electrons.
Synthesis of Cryptoacetalide (2010)

Cryptoacetalide and epi-crypto­acetalide were isolated from the root of Salvia ­miltiorrhiza, a common treatment for various diseases in Chinese medicine. They were isolated as an inseparable mixture of cryptoacetalide and epi-cryptoacetalide in a ratio of 3:1.
<title>Switchable Bragg grating devices for telecommunications applications</title> (2001)

Digilens is developing a new class of optical components based on the combination of Electrically Switchable Bragg Grating (ESBG) and waveguide technology. One or more optical waveguides are formed on a substrate which is used as one wall of a cell filled with an ESBG. The ESBG layer forms part of the waveguide cladding, such that the grating can interact with the evanescent field of the light energy traveling in the waveguide. This device architecture has been used to make Electrical Variable Optical Attenuators with more than 50 db of controllable range, flat attenuation over the optical communications C band, fast (<100 msecond) switching speed, and encouragingly low polarization dependent loss. Initial results on a variable wavelength-selective filter are also reported.
Multi-Agent Reinforcement Learning for Adaptive User Association in\n Dynamic mmWave Networks (2020)

Network densification and millimeter-wave technologies are key enablers to\nfulfill the capacity and data rate requirements of the fifth generation (5G) of\nmobile networks. In this context, designing low-complexity policies with local\nobservations, yet able to adapt the user association with respect to the global\nnetwork state and to the network dynamics is a challenge. In fact, the\nframeworks proposed in literature require continuous access to global network\ninformation and to recompute the association when the radio environment\nchanges. With the complexity associated to such an approach, these solutions\nare not well suited to dense 5G networks. In this paper, we address this issue\nby designing a scalable and flexible algorithm for user association based on\nmulti-agent reinforcement learning. In this approach, users act as independent\nagents that, based on their local observations only, learn to autonomously\ncoordinate their actions in order to optimize the network sum-rate. Since there\nis no direct information exchange among the agents, we also limit the signaling\noverhead. Simulation results show that the proposed algorithm is able to adapt\nto (fast) changes of radio environment, thus providing large sum-rate gain in\ncomparison to state-of-the-art solutions.\n
Entanglement swapping in a single-photon two-qubit logic circuit (2004)

Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. Fiorentino, T. Kim, and F. N. C. Wong, "Entanglement swapping in a single-photon two-qubit logic circuit," in Conference on Lasers and Electro-Optics/International Quantum Electronics Conference and Photonic Applications Systems Technologies, Technical Digest (CD) (Optica Publishing Group, 2004), paper IPDA11. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article