gebhart/patrepeval huggingface dataset:
Oxidative stress preconditioning of mouse perivascular myogenic progenitors selects a subpopulation of cells with a distinct survival advantage in vitro and in vivo (2018)

Cell engraftment, survival and integration during transplantation procedures represent the crux of cell-based therapies. Thus, there have been many studies focused on improving cell viability upon implantation. We used severe oxidative stress to select for a mouse mesoangioblast subpopulation in vitro and found that this subpopulation retained self-renewal and myogenic differentiation capacities while notably enhancing cell survival, proliferation and migration relative to unselected cells. Additionally, this subpopulation of cells presented different resistance and recovery properties upon oxidative stress treatment, demonstrating select advantages over parental mesoangioblasts in our experimental analysis. Specifically, the cells were resistant to oxidative environments, demonstrating survival, continuous self-renewal and improved migration capability. The primary outcome of the selected cells was determined in in vivo experiments in which immunocompromised dystrophic mice were injected intramuscularly in the tibialis anterior with selected or non-selected mesoangioblasts. Resistant mesoangioblasts exhibited markedly enhanced survival and integration into the host skeletal muscle, accounting for a more than 70% increase in engraftment compared with that of the unselected mesoangioblast cell population and leading to remarkable muscle recovery. Thus, the positive effects of sorting on mesoangioblast cell behaviour in vitro and in vivo suggest that a selection step involving oxidative stress preconditioning may provide a novel methodology to select for resistant cells for use in regenerative tissue applications to prevent high mortality rates upon transplantation.
TH‐A‐201C‐01: Quantitative Molecular Imaging Using PET/CT to Assess Response to Therapy (2010)

Recent publications have established quantitative measures of tracer uptake used in positron emission tomography (PET) imaging as a predictor of patient outcome including pathologic response disease‐free survival and overall survival in single institution imaging and therapy trials. There is increasing interest in using PET as a biomarker to evaluate response to therapy and possibly as an endpoint for cancer therapeutic response in multi‐center trials. However several sources of variance and inherent in quantifying PET tracer uptake should understood and determined in order to ascertain the significance of differences in serial measurements and aid estimation of expected variances during clinical trial design. In this presentation we will review the major sources of bias and variability from the patient imaging protocol data processing and image analysis. We will also briefly discuss artifacts from PET and PET/CT imaging. The presentation will conclude with a review of efforts to address complexities that arise from combining quantitative PET/CT data from multiple patients at multiple sites. Research partially supported by NIH grant U01‐CA148131 and NCI Contract 24XS036‐004 (RIDER).
Full-Range Three-Stage 16GSa/s Riemann Pump RF-Power DAC in GaN HEMT (2021)

In this study, we proposed a new encoding method to reduce power consumption and expanding the bit resolution of Riemann Pump (RP) digital-to-analog converters (DAC). In addition, a new circuit topology was demonstrated enabling high-side and low-side GaN transistors to operate independently such that the power consumption is significantly reduced by preventing unnecessary current flow. Moreover, our design realizes higher bit-level compared with the state-of-the-art complementary encoding method. We designed and fabricated a 3.9-bit RP using 0.15µm GaN process to validate its performance benefit. The simulation with practical device models confirms that our design can reduce power consumption and increase the bit-level with at least 16GSa/s sampling rate, which is the highest sampling rate reported so far in GaN technology to the best of our knowledge.
A Three-arm Randomized Clinical Trial Comparing Continuous Femoral Plus Single-injection Sciatic Peripheral Nerve Blocks versus Periarticular Injection with Ropivacaine or Liposomal Bupivacaine for Patients Undergoing Total Knee Arthroplasty (2017)

Ropivacaine-based periarticular injections provide pain control comparable on postoperative days 1 and 2 to a femoral catheter and single-injection sciatic nerve block. This study did not demonstrate an advantage of liposomal bupivacaine over ropivacaine in periarticular injections for total knee arthroplasty.
Enhanced Spontaneous Polarization in Ultrathin SnTe Films with Layered Antipolar Structure (2018)

2D SnTe films with a thickness of as little as 2 atomic layers (ALs) have recently been shown to be ferroelectric with in-plane polarization. Remarkably, they exhibit transition temperatures (T<sub>c</sub> ) much higher than that of bulk SnTe. Here, combining molecular beam epitaxy, variable temperature scanning tunneling microscopy, and ab initio calculations, the underlying mechanism of the T<sub>c</sub> enhancement is unveiled, which relies on the formation of γ-SnTe, a van der Waals orthorhombic phase with antipolar inter-layer coupling in few-AL thick SnTe films. In this phase, 4n - 2 AL (n = 1, 2, 3…) thick films are found to possess finite in-plane polarization (space group Pmn2<sub>1</sub> ), while 4n AL thick films have zero total polarization (space group Pnma). Above 8 AL, the γ-SnTe phase becomes metastable, and can convert irreversibly to the bulk rock salt phase as the temperature is increased. This finding unambiguously bridges experiments on ultrathin SnTe films with predictions of robust ferroelectricity in GeS-type monochalcogenide monolayers. The observed high transition temperature, together with the strong spin-orbit coupling and van der Waals structure, underlines the potential of atomically thin γ-SnTe films for the development of novel spontaneous polarization-based devices.
A re-ranking algorithm for gene regulatory network predictions using graphlets and graph-invariant properties (2013)

A vast amount of algorithms have been proposed that try to deduce the topology of large gene regulatory networks from high throughput data.These algorithms typically produce a ranking of links between genes with associated confidence scores, after which a certain threshold is chosen to produce the inferred network.
Rapid changes in chromatin structure during dedifferentiation of primary hepatocyte s in vitro (2020)

Abstract Primary hepatocytes are widely used in the pharmaceutical industry to screen drug candidates for hepatotoxicity, but isolated hepatocytes quickly dedifferentiate and lose their mature metabolic function in culture. Attempts have been made to better recapitulate the in vivo liver environment in culture, but the full spectrum of signals required to maintain hepatocyte function in vitro remains elusive. Here we studied the dedifferentiation process in detail through RNA-sequencing of hepatocytes cultured over eight days. We identified three distinct phases of dedifferentiation. An early phase, where mature hepatocyte genes are rapidly downregulated in a matter of hours. A middle phase, where fetal genes are activated, leading to hepatocytes with a fetal phenotype. A late phase, where initially rare contaminating non-parenchymal cells over-grow the culture as the hepatocytes gradually die. Using genetically tagged hepatocytes, we demonstrate that the cells reactivating fetal marker alpha-fetoprotein arise from cells previously expressing the mature hepatocyte marker albumin, and not from albumin negative precursor cells, proving that hepatocytes undergo true dedifferentiation. To better understand the signaling events that result in the rapid down-regulation of mature hepatocyte genes, we examined changes in chromatin accessibility of hepatocytes during the first 24h of culture using ATAC-seq. We find that drastic and rapid changes in chromatin accessibility occurs immediately upon start of culture. Using binding motif analysis of the areas of open chromatin sharing similar temporal profiles, we identify several candidate transcription factors potentially involved in the dedifferentiation of primary hepatocytes in culture.
Simultaneous macromolecular proton fraction and proton density fat fraction quantification using chemical shift-encoding based spin-lock MRI (2023)

Chronic liver disease is a major healthcare problem worldwide. Liver fibrosis and fat fraction are two main features of chronic liver diseases. Recent work reported that macromolecular proton fraction (MPF) mapping has potential for diagnosis of liver fibrosis. In this work, we reported a novel technique to quantify MPF and fat fraction of the liver simultaneously in a brief breath hold.
Expression and regulation of monocyte chemoattractant protein‐1 by human eosinophils (1997)

Several recent studies have identified eosinophils as a cellular source of various cytokines, indicating that eosinophils play not only an effector role, but also a regulatory role within the allergic inflammatory cell network. In this study, we demonstrate that eosinophils can generate and secrete monocyte chemoattractant protein-1 (MCP-1), a prototype of C-C chemokines. Eosinophils generated immunoreactive MCP-1 in response to such diverse stimuli as C5a, formyl-methionyl-leucyl-phenylalanine (FMLP) and ionomycin, but MCP-1 production was not induced by interleukin (IL)-1 or tumor necrosis factor-alpha. C5a- and FMLP-induced eosinophil MCP-1 production was absolutely dependent on pretreatment with cytochalasin B. Eosinophils elaborated significantly more MCP-1 than neutrophils. Immunoreactive MCP-1 was detected at 6 h of incubation with C5a or FMLP. Expression of MCP-1 mRNA reached a maximum within the first 3 h after stimulation and then declined rapidly to a very low and stable level by 18 h. Pretreatment with IL-5 markedly amplified C5a-induced MCP-1 production, and the enhancement occurred at the pretranslational level. Eosinophil-active chemokines such as eotaxin failed to induce MCP-1 generation, even when eosinophils were primed by IL-5. Since MCP-1 exerts a potent histamine-releasing effect on human basophils, our results indicate that eosinophils may regulate basophil mediator release with possible consequent contribution to the pathogenesis of allergic inflammation via a paracrine mechanism.
Drosophila pro-apoptotic Bcl-2/Bax homologue reveals evolutionary conservation of cell death mechanisms. (2000)

Genetic analysis of programmed cell death in Drosophila reveals many similarities with mammals. Heretofore, a missing link in the fly has been the absence of any Bcl-2/Bax family members, proteins that function in mammals as regulators of mitochondrial cytochrome c release. A Drosophila homologue of the human killer protein Bok (DBok) was identified. The predicted structure of DBok is similar to pore-forming Bcl-2/Bax family members. DBok induces apoptosis in insect and human cells, which is suppressible by anti-apoptotic human Bcl-2 family proteins. A caspase inhibitor suppressed DBok-induced apoptosis but did not prevent DBok-induced cell death. Moreover, DBok targets mitochondria and triggers cytochrome c release through a caspase-independent mechanism. These characteristics of DBok reveal evolutionary conservation of cell death mechanisms in flies and humans.
Chemogenetic activation of noradrenergic A5 neurons increases blood pressure and visceral sympathetic activity in adult rats (2022)

In mammals, the pontine noradrenergic system influences nearly every aspect of central nervous system function. A subpopulation of pontine noradrenergic neurons, called A5, are thought to be important in the cardiovascular response to physical stressors, yet their function is poorly defined. We hypothesized that activation of A5 neurons drives a sympathetically mediated increase in blood pressure (BP). To test this hypothesis, we conducted a comprehensive assessment of the cardiovascular effects of chemogenetic stimulation of A5 neurons in male and female adult rats using intersectional genetic and anatomical targeting approaches. Chemogenetic stimulation of A5 neurons in freely behaving rats elevated BP by 15 mmHg and increased cardiac baroreflex sensitivity with a negligible effect on resting HR. Importantly, A5 stimulation had no detectable effect on locomotor activity, metabolic rate, or respiration. Under anesthesia, stimulation of A5 neurons produced a marked elevation in visceral sympathetic nerve activity (SNA) and no change in skeletal muscle SNA, showing that A5 neurons preferentially stimulate visceral SNA. Interestingly, projection mapping indicates that A5 neurons target sympathetic preganglionic neurons throughout the spinal cord and parasympathetic preganglionic neurons throughout in the brainstem, as well as the nucleus of the solitary tract, and ventrolateral medulla. Moreover, in situ hybridization and immunohistochemistry indicate that a subpopulation of A5 neurons coreleases glutamate and monoamines. Collectively, this study suggests A5 neurons are a central modulator of autonomic function with a potentially important role in sympathetically driven redistribution of blood flow from the visceral circulation to critical organs and skeletal muscle.
Synthesis of Cyclic Hemiketals and Spiroketals from Dioxanorbornanes (2004)

[reaction: see text] A new method for the synthesis of substituted pyranone hemiketals from dioxanorbornanes via SmI(2) is described. Also reported is a synthesis of spiro[4.5]ketals from analogous intermediates via acid-promoted deprotection/ketalization.
High Temperature Creep Behavior and Effects of Stacking Fault Energy in Mg-Y and Mg-Y-Zn Dilute Solid Solution Alloys (2014)

Compressive creep behavior of hot-rolled (40%) Mg-Y binary and Mg-Y-Zn ternary dilute solid solution alloys are investigated in this study. Creep strength is substantially improved by the addition of zinc. Activation Energy for creep in Mg-Y and Mg-Y-Zn alloys are around 200 kJ/mol at the temperature range from 480 to 570 K. These values are higher than the activation energy for self-diffusion coefficient in magnesium (135 kJ/mol). Many stacking faults, which are planar type defects are observed on the basal planes of the magnesium matrix in Mg-Y-Zn ternary alloys. TEM observation has been revealed that the non-basal a -dislocation slip is significantly activated by these alloys. The rate controlling mechanism of Mg-Y and Mg-Y-Zn dilute alloys are considered to the cross-slip or prismatic-slip controlled dislocation creep with high activation energy for creep, more than 1.5 times higher than the activation energy for creep controlled dislocation climb.
Support Tools for Simulation-Based Optimal Design of Power Networks With Embedded Power Electronics (2008)

This paper presents a gradient-based nonlinear optimization wrapper for an electromagnetic transient simulation program to assist in the design of hardware and control parameters of flexible AC transmission system (FACTS) apparatus. A new second-order sensitivity analysis method is introduced that quantifies the sensitivity of the optimal solution to parameter uncertainties. Using this approach, the sensitivity of the harmonic elimination capability of a pulsewidth-modulated voltage-source converter to variations in switching angles is investigated. This paper also adapts the method of Pareto optimization to the simulation-based design of FACTS apparatus when multiple design objectives are to be satisfied. The developed Pareto optimization tool generates a Pareto frontier plot to visualize the design tradeoffs between the multiple objectives. The effectiveness of the tool is demonstrated through a design example that selects optimal values for the DC-bus capacitor and the control settings of a STATCOM.
International Expert Consensus on a Cell Therapy Communication Tool: DOSES (2019)

The DOSES tool for describing cell therapies can be utilized by researchers, clinicians, regulators, and industry professionals to improve standardization and transparency when describing cell therapies. The use of this tool may allow clinicians and patients to better understand the characteristics of current and future cell preparations.
Abstract WP100: Investigation of Secondary Thalamic Injury After Ischemic Stroke: A Time Course Study (2018)

Introduction: After a cortical stroke, secondary degeneration can occur in remotely connected regions such as thalamus. This progressive secondary thalamic injury leads to somatosensory dysfunctions and hinders recovery. The pathophysiology of primary ischemic injury has been well characterized; however, the mechanism underlying secondary thalamic injury is poorly understood. We conducted a time course study to identify the critical time window of thalamic injury development after stroke and to investigate the involved mediators. Methods: Cortical ischemic stroke was generated by permanent occlusion of left middle cerebral artery in male C57BL6J mice (12-15 weeks). Brain sections were collected on post-stroke days (PD) 1, 3, 7, 14 and 28. Fluoro Jade C and TUNEL staining were used to detect degenerative injury and apoptosis, respectively. Immunostaining were used to detect neuronal loss (NeuN &amp; MAP2) and inflammatory responses (CD68 &amp; GFAP). Results: In the somatosensory cortex, degenerative injury and apoptosis were detected as early as PD1. Reduced NeuN and MAP2 expression confirmed the cortical neuronal injury starting at PD1. Activated microglia (CD68) were initially detected around the infarct at PD1 and gradually showed in the infarct core at PD14. Activated astrocytes (GFAP) appeared sparsely around the infarct on PD3 and became densely packed and elongated at PD7. In the ipsilesional thalamus, degenerative injury and apoptosis were detected at PD7 and became aggravated on day 28, indicating a development of thalamic injury. Reduced NeuN and MAP2 expression in the thalamus began at PD14. Activated microglia were detected at PD1 and activated astrocytes were detected at PD3 in the ipsilesional thalamus. Clustered microglia/astrocytes started at PD7 and became more densely at PD14 and 28. Conclusion: Our data shows that thalamic degenerative injury begins on PD7 and continues to develop until at least PD28. Our data also shows robust inflammatory responses during thalamic injury development. Future study will identify the subtypes of activated microglia/astrocyte and the related molecular mediators. Our findings will enrich the understanding of thalamic injury and define specific cellular and molecular targets for stroke treatments.
Zeta-Fe2O3 – A new stable polymorph in iron(III) oxide family (2015)

Iron(III) oxide shows a polymorphism, characteristic of existence of phases with the same chemical composition but distinct crystal structures and, hence, physical properties. Four crystalline phases of iron(III) oxide have previously been identified: α-Fe2O3 (hematite), β-Fe2O3, γ-Fe2O3 (maghemite), and ε-Fe2O3. All four iron(III) oxide phases easily undergo various phase transformations in response to heating or pressure treatment, usually forming hexagonal α-Fe2O3, which is the most thermodynamically stable Fe2O3 polymorph under ambient conditions. Here, from synchrotron X-ray diffraction experiments, we report the formation of a new iron(III) oxide polymorph that we have termed ζ-Fe2O3 and which evolved during pressure treatment of cubic β-Fe2O3 (Ia3 space group) at pressures above 30 GPa. Importantly, ζ-Fe2O3 is maintained after pressure release and represents the first monoclinic Fe2O3 polymorph (I2/a space group) that is stable at atmospheric pressure and room temperature. ζ-Fe2O3 behaves as an antiferromagnet with a Néel transition temperature of ~69 K. The complex mechanism of pressure-induced transformation of β-Fe2O3, involving also the formation of Rh2O3-II-type Fe2O3 and post-perovskite-Fe2O3 structure, is suggested and discussed with respect to a bimodal size distribution of precursor nanoparticles.
An 8-channel Ku band transmit beamformer with low gain/phase imbalance between channels (2013)

An 8-channel Ku band (12.5 GHz-14.7 GHz) transmit beamformer has been proposed and fabricated in a 0.18um SiGe BiCMOS technology, which has small phase variation over gain states and low gain/phase imbalance between channels. A current-steering variable gain amplifier (VGA) is proposed with constant current consumption for all gain states to maintain the input impedance, which achieves a small RMS phase variation of ±0.07°/dB. In addition to parasitics prediction from electromagnetic simulations, the layout of the 8-channel transmit beamformer is symmetrically designed to reduce gain/phase imbalance between channels. The RMS gain imbalance for channels 2-7 is ±0.14 dB and the RMS phase imbalance is ±0.71°, which, to the best knowledge of the authors, is the lowest compared to recently reported beamformers.
Persistently Elevated Heart Rate Alters EEG Patterns and Locomotor Behavior in Mice (2021)

Descending autonomic signaling, traveling from central stations, contributes to regulating heart rate (HR) in response to environmental demands. However, whether and how cardiac rhythm influences central functions in a “bottom‐up modality” remains poorly understood. Here, we tested whether persistently elevated HR in mice affects the brain‐heart bidirectional communication, the electroencephalographic (EEG) patterns, and behavior. To this end, we used mice with cardiac‐selective overexpression of adenylyl cyclase type 8 (TGAC8 mice) that harbor continually heightened HR and autonomic surveillance escape. We implanted them with a double Holter system to obtain ECGs, EEGs, and evaluate changes in the ECG/EEG relationship via the Granger Causality statistical approach. Actigraphy, elevated plus maze, open field, Y‐maze, fear conditioning tests served to assess behavior. First, we confirmed that TGAC8s mice have continuously elevated HR, reduced HR variability (HRV), i.e., High (HF) /Low Frequency (LF) components of the ECG, and decreased alpha‐DFA. Moreover, as expected, TGAC8 mice isolated atria showed a substantially blunted response to sympathomimetic agents. When EEG rhythms are concerned, TGAC8 mice manifested a marked decrease in theta‐2 frequency (in the range of 6‐7 Hz), theta‐2 wave count, and amplitude. In terms of behavior, TGAC8 mice showed no basal difference in anxiety levels, mood, and memory compared to WT littermates. In contrast, their locomotor activity (i.e. time mobile, total distance traveled, average and maximum speed) was significantly increased, and these changes correlated with the blunting in theta‐2 activity. Of relevance, analysis of the informational flow between tachogram and EEG traces in theta‐2 range, via Granger analysis, revealed a substantial decrement in the extent of heart/brain bidirectional communication. For the first time, our study shows that persistently elevated cardiac chronotropic activity is penetrant enough to disrupt the brain/heart flow of information, influencing central physiological patterns that control complex activities, such as locomotion.
FREQUENCY TUNING AND PULSE GENERATION IN A FIBER LASER WITH AN INTRACAVITY SEMICONDUCTOR ACTIVE FILTER (1992)

Various laser structures based on doped fiber gain media and some form of an intracavity control element have recently been reported. Examples include a narrow linewidth laser based on an intracavity tunable fiber Fabry-Perot [1], actively mode-locked lasers based on intracavity LiNbO3 modulators (operating in AM [2] and FM modes [3]), or switchable diode lasers [4]. Passively mode- locked lasers based on either an intracavity multiple quantum well saturable absorber [5] or nonlinear fiber mirrors [6] have also been demonstrated.