gebhart/patrepeval huggingface dataset:
Fortification of Rice Noodles with Vitamin A: Quality, Sensory Evaluation, and Enhancement of Vitamin A Intakes (2020)

Vitamin A deficiency is common in many countries where rice is the staple food. Food fortification is an important strategy to address this problem. As rice noodle is the second principal form of rice products widely consumed in Asia, rice noodles could be a potential vehicle for fortification of vitamin A. In this study, rice noodles were prepared from 0, 300, 600, 1,050, and 1,500 μg of vitamin A per 100 g of rice flour. Samples were analyzed for quality, sensory evaluation, and enhancement of vitamin A intakes. Increasing level of vitamin A fortification did not influence quality and sensory properties of the rice noodles, except for the ash content, color, and appearance of the noodles. Rice noodle that was fortified with the highest level of vitamin A was found to be the darkest in color. However, this sample received scores higher than 6 (like slightly) for appearance. Furthermore, sample fortified with the highest level of vitamin A produced rice noodles with the highest level of vitamin A retention suggesting that noodles were good vehicle for vitamin A fortification. Fortification of rice flour with 1,500 μg of vitamin A produced rice noodles with 24.88% of the RDI for vitamin A per serving and provided an effective means of enhancing vitamin A intake.
The Role of the Microenvironment in Controlling the Fate of Bioprinted Stem Cells (2020)

The field of tissue engineering and regenerative medicine has made numerous advances in recent years in the arena of fabricating multifunctional, three-dimensional (3D) tissue constructs. This can be attributed to novel approaches in the bioprinting of stem cells. There are expansive options in bioprinting technology that have become more refined and specialized over the years, and stem cells address many limitations in cell source, expansion, and development of bioengineered tissue constructs. While bioprinted stem cells present an opportunity to replicate physiological microenvironments with precision, the future of this practice relies heavily on the optimization of the cellular microenvironment. To fabricate tissue constructs that are useful in replicating physiological conditions in laboratory settings, or in preparation for transplantation to a living host, the microenvironment must mimic conditions that allow bioprinted stem cells to proliferate, differentiate, and migrate. The advances of bioprinting stem cells and directing cell fate have the potential to provide feasible and translatable approach to creating complex tissues and organs. This review will examine the methods through which bioprinted stem cells are differentiated into desired cell lineages through biochemical, biological, and biomechanical techniques.
Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida (2011)

Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. To improve our understanding of the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second and third shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, and three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects have been studied both kinetically and structurally. The eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues (α-Asp164, β-Glu56, and β-His147) and one predicted third-shell residue (β-His71) have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues (α-Glu168) and the three residues not predicted (α-Arg170, α-Tyr171, and β-Tyr215) do not have any significant effects on the catalytic efficiency of the enzyme.
Using Non-Thermal Irreversible Electroporation to create an in Vivo Niche for Exogenous Cell Engraftment (2017)

The critical shortage of donor organs has spurred investigation of alternative approaches to either generate replacement organs or implant exogenous cells for treatment of end-stage organ failure. Non-thermal irreversible electroporation (NTIRE), which uses brief high electric field pulses to induce irreversible permeabilization of cell membranes, has emerged as a technique for tumor ablation. Here, we introduce a new application for NTIRE that employs in situ cell ablation to create a niche within a solid organ for engraftment of exogenous cells in vivo. We treated the livers of mice with NTIRE and subsequently implanted exogenous congenic hepatocytes within the zone of cell ablation. Donor hepatocytes engrafted and integrated with host liver parenchyma pre-treated with NTIRE. This new approach should have value for studying the effects of a native matrix scaffold on in vivo cell growth and may pioneer a new type of minimally-invasive regenerative surgery.
Ischemia/Reperfusion Injury and Oxidative Stress Impair Cardiac Desmin Proteostasis (2023)

Abstract Background Though acute mortality by myocardial infarction (MI) has declined in past decades, MI still represents one of the leading causes of heart failure (HF) development. We recently demonstrated the accumulation of toxic desmin aggregates in patients with HF of ischemic origin. Since desmin aggregates are toxic for the heart we aimed to test whether their formation can be induced by oxidative stress as a proxy for reperfusion injury, as well as addressing the effects of therapeutic strategies aimed at reducing desmin aggregation with cardiac oxidative stress. Methods and Results We demonstrate here that oxidative stress is able to induce desmin aggregation, acutely, in a cell-specific and dose-dependent fashion. We also show that elevation of O -linked β- N -acetylglucosamine ( O -GlcNAc) prior to or after oxidative stress reduces the formation of toxic desmin aggregates and its pro-aggregating desmin post-translational modifications (PTM). In addition, we show for the first time a role for the transmembrane protease serine 13 (TMPRSS13) with desmin cleavage in response to oxidative stress while desmin’s single cysteine plays a protective role from I/R injury, which is independent of gain or loss of desmin function. Conclusions The proliferation of desmin PTM-forms (i.e., proteoforms) and its aggregation hallmark acute and chronic cardiac stress and result in both loss of and gain of desmin function. We report here two novel mechanisms that could be targeted for therapy to preserve desmin homeostasis and cardiac function in the acute settings of oxidative stress and reperfusion injury.
Understanding the pathogenesis of occupational coal and silica dust-associated lung disease (2022)

Workers in the mining and construction industries are at increased risk of respiratory and other diseases as a result of being exposed to harmful levels of airborne particulate matter (PM) for extended periods of time. While clear links have been established between PM exposure and the development of occupational lung disease, the mechanisms are still poorly understood. A greater understanding of how exposures to different levels and types of PM encountered in mining and construction workplaces affect pathophysiological processes in the airways and lungs and result in different forms of occupational lung disease is urgently required. Such information is needed to inform safe exposure limits and monitoring guidelines for different types of PM and development of biomarkers for earlier disease diagnosis. Suspended particles with a 50% cut-off aerodynamic diameter of 10 µm and 2.5 µm are considered biologically active owing to their ability to bypass the upper respiratory tract's defences and penetrate deep into the lung parenchyma, where they induce potentially irreversible damage, impair lung function and reduce the quality of life. Here we review the current understanding of occupational respiratory diseases, including coal worker pneumoconiosis and silicosis, and how PM exposure may affect pathophysiological responses in the airways and lungs. We also highlight the use of experimental models for better understanding these mechanisms of pathogenesis. We outline the urgency for revised dust control strategies, and the need for evidence-based identification of safe level exposures using clinical and experimental studies to better protect workers' health.
Effects of the rotating-wave and secular approximations on non-Markovianity (2013)

We study the effect of the rotating-wave approximation (RWA) and the secular approximation (SA) on the non-Markovian behavior in the spin-boson model at zero temperature. We find that both the RWA and SA lead to a dramatic reduction in the observed non-Markovianity. In general, non-Markovian dynamics is observed for the whole relaxation time of the system, whereas the RWA and SA lead to such dynamics only on the short time scale of the environmental correlation time. Thus, the RWA and SA are not necessarily justified in the studies of non-Markovianity, although they can estimate the state of the system precisely. Furthermore, we derive an accurate analytical expression for the non-Markovianity measure without the RWA or SA. This expression yields important insight into the physics of the problem.
Recurrence network analysis of wide band oscillations of local field potentials from the primary motor cortex reveals rich dynamics (2015)

Aggregate signals that reflect activities of a large number of neurons in the cerebral cortex, local field potentials (LFPs) have been observed to mediate gross functional activities of a relatively small volume of the brain tissues. There are several bands of the oscillations frequencies in LFPs that have been observed across multiple brain areas. The signature oscillation band of the LFPs in the primary motor cortex (MI) is over β range and it has been consistently observed both in human and non-human primates around the time of visual cues and movement onsets. However, its dynamical behavior has not been well characterized. Furthermore, dynamics of β oscillations has been documented based on the phase locking of β oscillations, but not in terms of the inherent dynamics of the oscillations themselves. Here, we used the complexity measure derived from cluster coefficients of a recurrence network and analyzed a pair of wide-band signals, one including β band of the LFPs and the other ranging the low γ band in MI recorded from a non-human primate. We show rather unique temporal profiles of the evoked responses using complexity of the dynamical behavior in both bands of the oscillation, either of which is not simply resembling either the power of the oscillation or the phase locking of β oscillations. Therefore, the current method can reveal a new type of dynamics of the underlying network complexity during the task simply based on event evoked potentials of wide-band oscillatory signals.
Mitogen and Stress-activated Protein Kinase 1 Negatively Regulates Hippocampal Neurogenesis (2020)

Neurogenesis in the subgranular zone (SGZ) of the adult hippocampus can be stimulated by a variety of means, including via exposure of experimental animals to an enriched environment that provides additional sensory, social, and motor stimulation. Tangible health and cognitive benefits accrue in enriched animals, including the amelioration of signs modelling psychiatric, neurological and neurodegenerative conditions that affect humans, which may in part be due to enhanced production of neurons. A key factor in the neuronal response to enrichment is the release of brain-derived neurotrophic factor (BDNF) and the activation of the Mitogen-Activated Protein Kinase (MAPK) cascade, which can lead to the stimulation of neurogenesis. Mitogen- and Stress-Activated protein Kinase 1 (MSK1) is a nuclear enzyme downstream of BDNF and MAPK that regulates transcription. MSK1 has previously been implicated in both basal and stimulated neurogenesis on the basis of studies with mice lacking MSK1 protein. In the present study, using mice in which only the kinase activity of MSK1 is lacking, we show that the rate of cellular proliferation in the SGZ (Ki-67 staining) is unaffected by the MSK1 kinase-dead (KD) mutation, and no different from controls levels after five weeks of enrichment. However, compared to wild-type mice, the number of doublecortin (DCX)-positive cells was greater in both standard-housed and enriched MSK1 KD mice. These observations suggest that, while MSK1 does not influence the basal rate of proliferation of neuronal precursors, MSK1 negatively regulates the number of cells destined to become neurons, potentially as a homeostatic control on the number of new neurons integrating into the dentate gyrus.
The Bioactivity of Cartilage Extracellular Matrix in Articular Cartilage Regeneration (2014)

Cartilage matrix is a promising material for cartilage regeneration given the evidence supporting its chondroinductive character. The "raw materials" of cartilage matrix can serve as building blocks and signals for tissue regeneration. These matrices can be created by chemical or physical processing: physical methods disrupt cellular membranes and nuclei but may not fully remove all cell components and DNA, whereas chemical methods combined with physical methods are effective in fully decellularizing such materials. It is important to delineate between the sources of the cartilage matrix, that is, derived from matrix in vitro or from native tissue, and then to further characterize the cartilage matrix based on the processing method, decellularization or devitalization. With these distinctions, four types of cartilage matrices exist: decellularized native cartilage (DCC), devitalized native cartilage (DVC), decellularized cell-derived matrix (DCCM), and devitalized cell-derived matrix (DVCM). One currently marketed cartilage matrix device is decellularized, although trends in patents suggest additional decellularized products may be available in the future. To identify the most relevant source and processing for cartilage matrix, testing needs to include targeting the desired application, optimizing delivery of the material, identify relevant FDA regulations, assess availability of materials, and immunogenic properties of the product.
Discrete Layer-by-Layer Magnetic Switching inFe/MgO(001)Superlattices (2016)

Like high-rise apartments for bits, stacked structures offer a means to increase the areal density of components on computer chips, despite the physical limits encountered at the nanoscale. The authors demonstrate a series of back-to-back Fe/MgO magnetic tunnel junctions with tunable interlayer coupling and discrete layer-by-layer switching, opening a path to three-dimensional magnetic storage and logic devices.
Field Trials of Chaotic Advection to Enhance Reagent Delivery (2019)

Abstract Chaotic advection is a novel approach that has the potential to enhance contact between an injected reagent and target contaminants, and thereby improve the effectiveness of in situ treatment technologies. One configuration that is capable of generating chaotic advection is termed the rotated potential mixing (RPM) flow. A conventional RPM flow system involves periodically reoriented dipole flow driven by transient switching of pressures at a series of radial wells. To determine whether chaotic advection can be engineered using such an RPM flow system, and to assess the consequent impact on the spatial distribution of a conservative tracer, a series of field‐scale experiments were conducted. These experiments involved the injection of a tracer in the center of a circular array of wells followed by either mixing using an engineered RPM flow system to invoke chaotic advection, or by natural processes (advection and diffusion) as the control. Pressure fluctuations from the mixing tests using the RPM flow system showed consistent peak amplitudes during injection and extraction at a frequency corresponding to the switching time, suggesting that the target hydraulic behavior was achieved with the time‐dependent flow field. The tracer breakthrough responses showed oscillatory behavior at all monitoring locations during the mixing tests which indicated that the desired RPM flow was generated. The presence of chaotic advection was supported by comparisons to observations from a previous laboratory experiment using RPM flow, and the Fourier spectrum of the temporal tracer data. Results from several quantitative metrics adopted to demonstrate field‐scale evidence of chaotic advection showed that mixing led to improved lateral tracer spreading and approximately uniform concentrations across the monitoring network. The multiple lines of evidence assembled in this proof‐of‐concept study conclusively demonstrated that chaotic advection can be engineered at the field scale. This investigation is a critical step in the development of chaotic advection as a viable and efficient approach to enhance reagent delivery.
High density optical interconnects for board and backplane applications using VCSELs and polymer waveguides (2002)

This paper describes the technical approach and progresses of the POINT (Polymer Optical Interconnect Technology) program. This project is a collaborative effort among GE, Honeywell, AMP, AlliedSignal, Columbia University and University of California at San Diego (UCSD), sponsored by DARPA/ETO to develop affordable optoelectronic packaging and interconnect technologies for board and backplane applications. In this paper, we describe the recent development under this program in the following areas: (a) a high density optical interconnect for board and backplane applications using polymer waveguides (Polyguide) to demonstrate high I/O density (100 /spl mu/m channel spacing) and high speed (/spl sim/1 Gbps) interconnect with an interconnect distance to 280 mm, (b) a high density and high speed VCSEL array packaging technology that employs planar and batch fabrication processes scaleable to large volume, low-cost manufacturing, (c) passive alignment techniques for reducing the recurrent cost in an optoelectronic assembly, (d) low-loss optical polymers for board and backplane level interconnects, and (e) CAD tools for modeling multimode guided wave systems and assisting optoelectronic packaging mechanical design.
International workshop: islet transplantation without borders enabling islet transplantation in Greece with international collaboration and innovative technology (2013)

Recently, initiatives have been undertaken to establish an islet transplantation program in Athens, Greece. A major hurdle is the high cost associated with the establishment and maintenance of a clinical-grade islet manufacturing center. A collaboration was established with the University Hospitals of Geneva, Switzerland, to enable remote islet cell manufacturing with an established and validated fully operational team. However, remote islet manufacturing requires shipment of the pancreas from the procurement to the islet manufacturing site (in this case from anywhere in Greece to Geneva) and then shipment of the islets from the manufacturing site to the transplant site (from Geneva to Athens). To address challenges related to cold ischemia time of the pancreas and shipment time of islets, a collaboration was initiated with the University of Arizona, Tucson, USA. An international workshop was held in Athens, December 2011, to mark the start of this collaborative project. Experts in the field presented in three main sessions: (i) islet transplantation: state-of-the-art and the "network approach"; (ii) technical aspects of clinical islet transplantation and outcomes; and (iii) islet manufacturing - from the donated pancreas to the islet product. This manuscript presents a summary of the workshop.
Identification and Characterization of mGlu3 Ligands Using a High Throughput FLIPR Assay for Detection of Agonists, Antagonists, and Allosteric Modulators (2011)

When targeting G-protein coupled receptors (GPCRs) in early stage drug discovery, or for novel targets, the type of ligand most likely to produce the desired therapeutic effect may be unknown. Therefore, it can be desirable to identify potential lead compounds from multiple categories: agonists, antagonists, and allosteric modulators. In this study, we developed a triple addition calcium flux assay using FLIPR Tetra to identify multiple ligand classes for the metabotropic glutamate receptor 3 (mGlu3), using a cell line stably co-expressing the human G-protein-coupled mGlu3 receptor, a promiscuous G-protein (G(α16)), and rat Glast, a glutamate transporter. Compounds were added to the cells followed by stimulation with EC(10) and then EC(80) concentration of glutamate, the physiological agonist for mGlu receptors. This format produced a robust assay, facilitating the identification of agonists, positive allosteric modulators and antagonists/negative allosteric modulators. Follow up experiments were conducted to exclude false positives. Using this approach, we screened a library of approximately 800,000 compounds using FLIPR Tetra and identified viable leads for all three ligand classes. Further characterization revealed the selectivity of individual ligands.
Large-signal compression-current measurements inhigh-power microwave pin photodiodes (1999)

The authors present the first large-signal compression measurements for surface-illuminated pin microwave photodetectors. The maximum RF power delivered by the photodiodes was +12, +17 and +20 dBm for bandwidths of 25, 3 and 1 GHz, respectively.
Synthesis of an energy-optimal self-heating strategy for Li-ion batteries (2016)

The resistance of Lithium-ion cells increases at sub-zero temperatures reducing the cells' power availability. One way to improve the cells' performance in these adverse operation conditions is to proactively heat them. In this paper, we consider the scenario in which a cell is heated from both inside and outside; a current is drawn from the cell to power a convective heater; Joule heating warms the cell from inside. A problem formulation to derive the time-limited energy-optimal current policy is presented, analyzed and numerically solved. It is observed that the optimal current policy resembles a sequence of constant voltage, constant current and phases, mirroring conventional wisdom. Finally, the notion of productive warm-up-a warm-up procedure that ensures that the cell can perform work once warmed-up-is introduced; and an approximation of the optimal solution is used to identify the lowest state of charge at various operating conditions (portion of the state-space) from which productive warm-up is feasible.