gebhart/patrepeval huggingface dataset:
Mean-field Approximation for Stochastic Population Processes in Networks under Imperfect Information (2021)

This paper studies a general class of stochastic population processes in which agents interact with one another over a network. Agents update their behaviors in a random and decentralized manner based only on their current state and the states of their neighbors. It is well known that when the number of agents is large and the network is a complete graph (has all-to-all information access), the macroscopic behavior of the population converges to a differential equation called a {\it mean-field approximation}. When the network is not complete, it is unclear in general whether there exists a suitable mean-field approximation for the macroscopic behavior of the population. This paper provides general conditions on the network and policy dynamics for which a suitable mean-field approximation exists. First, we show that as long as the network is well-connected, the macroscopic behavior of the population concentrates around the {\it same} mean-field system as the complete-graph case. Next, we show that as long as the network is sufficiently dense, the macroscopic behavior of the population concentrates around a mean-field system that is, in general, {\it different} from the mean-field system obtained in the complete-graph case. Finally, we provide conditions under which the mean-field approximation is equivalent to the one obtained in the complete-graph case.
Saccharide-Protein Interactions (2007)

The sections in this article are 1 Introduction 2 Transferred NOE Studies 3 Residual Dipolar Coupling Studies 4 Acknowledgements 5 Biographical Sketches
Catalytic Asymmetric Dihydroxylation by Gold Colloids Functionalized with Self-Assembled Monolayers (1999)

This Letter demonstrates the design and synthesis of functional nanoparticles based on the assembly of terminally substituted alkanethiols on the surface of colloidal gold. The colloids were modified with alkanethiolates presenting methyl groups and dihydroquinidine ligands (in a ratio of 3:1) for the Sharpless asymmetric dihydroxylation of olefins. Dihydroxylation reactions were performed at room temperature in tert-butyl alcohol/water with functionalized colloid (0.1 equiv based on immobilized ligand) OsO4 (0.005 equiv) and K3Fe(CN)6 (3 equiv) as secondary oxidant. The dihydroxylation of trans-β-methylstyrene proceeded in 80% yield and gave diol with an enantiomeric excess of 90%. The dihydroxylation of trans-stilbene and methyl trans-cinnamate gave similar results and compare favorably with yields and selectivities obtained using polymer-supported alkaloid ligands. The colloids could be isolated from the reaction mixture by gel permeation chromatography and used again, but with a modest loss in efficiency. This report provides an early example of a functional monolayer protected colloid and, together with other examples to follow, will define the range of applications for which these nanoparticles will find use.
Human Peripheral Nerve-Derived Pluripotent Cells Can Be Stimulated by In Vitro Bone Morphogenetic Protein-2 (2021)

We have recently identified a population of cells within the peripheral nerves of adult rodent animals (mice and rats) that can respond to Bone Morphogenetic Protein-2 (BMP-2) exposure or physical injury to rapidly proliferate. More importantly, these cells exhibited embryonic differentiation potentials that could be induced into osteoblastic and endothelial cells in vitro. The current study examined human nerve specimens to compare and characterize the cells after BMP-2 stimulation. Fresh pieces of human nerve tissue were minced and treated with either BMP-2 (750 ng/mL) or a PBS vehicle for 12 h at 37 °C, before being digested in 0.2% collagenase and 0.05% trypsin-EDTA. Isolated cells were cultured in a restrictive stem cell medium. Significantly more cells were obtained from the nerve pieces with the BMP-2 treatment in comparison with the PBS vehicle controls. Cell colonies started to form at Day 3. Expressions of the four transcription factors, namely, Klf4, c-Myc, Sox2, and Oct4, were confirmed at both the transcriptional and translational levels. The cells can be maintained in the stem cell culture medium for at least 6 weeks without changing their morphology. When the cells were transferred to a fibroblast growth medium, dispersed spindle-shaped motile cells were noted and became fibroblast activated protein-α (FAP) positive with immunocytochemistry staining. The data suggest that human peripheral nerve tissue also contains a population of cells that can respond to BMP-2 and express Klf4, Sox2, cMyc, and Oct4-the four transcription factors driving cell pluripotency. These cells are able to differentiate into FAP-positive fibroblasts. In summary, in human peripheral nerves also reside a population of quiescent cells with pluripotency potential that may be the same cells as rodent nerve-derived adult stem (NEDAPS) cells. It is proposed that these cells are possibly at the core of a previously unknown natural mechanism for healing an injury.
Regulation of HIV-1 Gene Expression (1990)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Waiting for a pandemic (2008)

After a quiet period of nearly 30 years, influenza strains with hemagglutinin types that have not been seen in humans previously started to jump from birds to man, suggesting the risk of a new influenza pandemic. However, in contrast to the situation with all the other influenza pandemics occurring in the 20th century and before, in the 21st century we have sophisticated technologies for diagnosis, therapy and prevention. Modeling of the possible spread of a pandemic suggests that vaccination is by far the only way to eliminate the risk of a new pandemic. In this chapter we review the development of new vaccines against H5N1 viruses, showing that effective vaccines adjuvanted with oil-inwater emulsion are about to be licensed and will soon be available. The race against an influenza pandemic has begun; it is a battle against time that mankind cannot afford to lose.
Richard Lerner (1938–2021) (2022)

Fearless scientist and leader of Scripps Research.
Mycobacterium leprae Recombinant Antigen Induces High Expression of Multifunction T Lymphocytes and Is Promising as a Specific Vaccine for Leprosy (2018)

Leprosy is a chronic disease caused by <i>M. leprae</i> infection that can cause severe neurological complications and physical disabilities. A leprosy-specific vaccine would be an important component within control programs but is still lacking. Given that multifunctional CD4 T cells [i.e., those capable of simultaneously secreting combinations of interferon (IFN)-γ, interleukin (IL)-2, and tumor necrosis factor (TNF)] have now been implicated in the protective response to several infections, we tested the hypothesis if a recombinant <i>M. leprae</i> antigen-specific multifunctional T cells differed between leprosy patients and their healthy contacts. We used whole blood assays and peripheral blood mononuclear cells to characterize the antigen-specific T cell responses of 39 paucibacillary (PB) and 17 multibacillary (MB) leprosy patients and 31 healthy household contacts (HHC). Cells were incubated with either crude mycobacterial extracts (<i>M. leprae</i> cell sonicate-MLCS) and purified protein derivative (PPD) or recombinant ML2028 protein, the homolog of <i>M. tuberculosis</i> Ag85B. Multiplex assay revealed antigen-specific production of IFN-γ and IL-2 from cells of HHC and PB, confirming a Th1 bias within these individuals. Multiparameter flow cytometry then revealed that the population of multifunctional ML2028-specific T cells observed in HHC was larger than that observed in PB patients. Taken together, our data suggest that these multifunctional antigen-specific T cells provide a more effective response against <i>M. leprae</i> infection that prevents the development of leprosy. These data further our understanding of <i>M. leprae</i> infection/leprosy and are instructive for vaccine development.
The Essential Role of p53 in Hyperpigmentation of the Skin via Regulation of Paracrine Melanogenic Cytokine Receptor Signaling (2008)

Hyperpigmentation of the skin is characterized by increases in melanin synthesis and deposition. Although considered a significant psychosocial distress, little is known about the detailed mechanisms of hyperpigmentation. Recently, the tumor suppressor protein p53 has been demonstrated to promote ultraviolet B-induced skin pigmentation by stimulating the transcription of a melanogenic cytokine, POMC (pro-opiomelanocortin), in keratinocytes. Given that p53 can be activated by various kinds of diverse stresses, including sun exposure, inflammation, and aging, this finding led us to examine the involvement of p53 in cytokine receptor signaling, which might result in skin hyperpigmentation. Immunohistochemical and reverse transcription-PCR analyses revealed the increased expression and phosphorylation of p53 in the epidermis of hyperpigmented spots, accompanied by the higher expression of melanogenic cytokines, including stem cell factor, endothelin-1, and POMC. The involvement of p53 in hyperpigmentation was also indicated by the significantly higher expression of p53 transcriptional targets in the epidermis of hyperpigmented spots. Treatment of human keratinocytes and melanocytes with known p53 activators or inhibitors, including pifithrin-alpha (PFT), demonstrated significant increases or decreases, respectively, in the expression of melanogenic factors, including cytokines and their receptors. Additionally, PFT administration abolished stem cell factor-induced phosphorylation of mitogen-activated protein kinase in human melanocytes. Furthermore, when organ-cultured hyperpigmented spots, in vitro human skin substitutes, and mouse skin were treated with PFT or p53 small interfering RNA, the expression of melanogenic cytokines and their receptors was significantly decreased, as were levels of tyrosinase and melanogenesis. Taken together, these data reveal the essential role of p53 in hyperpigmentation of the skin via the regulation of paracrine-cytokine signaling, both in keratinocytes and in melanocytes.
Development of a new oral poliovirus vaccine for the eradication end game using codon deoptimization (2020)

Enormous progress has been made in global efforts to eradicate poliovirus, using live-attenuated Sabin oral poliovirus vaccine (OPV). However, as the incidence of disease due to wild poliovirus has declined, vaccine-derived poliovirus (VDPV) has emerged in areas of low-vaccine coverage. Coordinated global cessation of routine, type 2 Sabin OPV (OPV2) use has not resulted in fewer VDPV outbreaks, and continued OPV use in outbreak-response campaigns has seeded new emergences in low-coverage areas. The limitations of existing vaccines and current eradication challenges warranted development of more genetically stable OPV strains, most urgently for OPV2. Here, we report using codon deoptimization to further attenuate Sabin OPV2 by changing preferred codons across the capsid to non-preferred, synonymous codons. Additional modifications to the 5' untranslated region stabilized known virulence determinants. Testing of this codon-deoptimized new OPV2 candidate (nOPV2-CD) in cell and animal models demonstrated that nOPV2-CD is highly attenuated, grows sufficiently for vaccine manufacture, is antigenically indistinguishable from Sabin OPV2, induces neutralizing antibodies as effectively as Sabin OPV2, and unlike Sabin OPV2 is genetically stable and maintains an attenuation phenotype. In-human clinical trials of nOPV2-CD are ongoing, with potential for nOPV strains to serve as critical vaccine tools for achieving and maintaining polio eradication.
Mosaic copy number variation in schizophrenia (2020)

Recent reports suggest that somatic structural changes occur in the human genome, but how these genomic alterations might contribute to disease is unknown. Using samples collected as part of the International Schizophrenia Consortium (schizophrenia, n=3518; control, n=4238) recruited across multiple university research centers, we assessed single-nucleotide polymorphism genotyping arrays for evidence of chromosomal anomalies. Data from genotyping arrays on each individual were processed using Birdsuite and analyzed with PLINK. We validated potential chromosomal anomalies using custom nanostring probes and quantitative PCR. We estimate chromosomal alterations in the schizophrenia population to be 0.42%, which is not significantly different from controls (0.26%). We identified and validated a set of four extremely large (>10 Mb) chromosomal anomalies in subjects with schizophrenia, including a chromosome 8 trisomy and deletion of the q arm of chromosome 7. These data demonstrate that chromosomal anomalies are present at low frequency in blood cells of both control and schizophrenia subjects.
Reduction of  CO 2 on Fluorine‐Doped SnO2 Thin‐Film Electrodes (1992)

The reduction process of fluorine-doped SnO 2 (SnO 2 :F) electrode in the presence of CO 2 was investigated by x-ray diffraction, x-ray photoelectron spectroscopy (XPS), scanning electron microscope (SEM), colorimetry, and gas chromatography. It has been found that a SnO 2 :F with (200) preferred orientation undergoes the following five reduction stages: 1. Oxygen-defect formation and constant hydrogen evolution, 2. Acceleration of oxygen-defect formation and hydrogen evolution. At this stage, formyl -HCO- and methoxy -CH 3 O- are formed on the surface
Performance comparison of phase shifted PWM and sorting method for modular multilevel converters (2015)

Modular Multilevel Converters (MMC) are the solution of preference in HVDC applications due to modularity, scalability, low losses and low filtering requirement. Carrier-based (PWM) and carrier-less (nearest level control) modulation can be applied. By using advanced sorting methods focusing on keeping the capacitor voltage ripple under some limit, unnecessary switching events are eliminated leading to reduced switching losses. This paper presents a comparison between the steady-state performances in terms of output voltage THD and equivalent switching frequency of the Phase Shifted Carrier PWM and NLC plus sorting methods.
A Channel Probing Scheme for Wireless Networks (2000)

A channel probing scheme for wireless networks is presented. By transmittinga probing signal in a channel and measuring the signal-to-interferenceratio (SIR), a link can estimate the channel condition and predict therequired transmission power without fully powering up. The channel probingscheme can be used as part of a distributed channel allocation algorithm,and simulations have shown that it outperforms some other comparableschemes.
III-V-on-Silicon-Nitride Mode-Locked Laser with 2 pJ On-Chip Pulse Energy (2021)

We demonstrate a III-V-on-silicon-nitride electrically pumped mode-locked laser emitting at λ = 1.6 μm with an on-chip pulse energy of approximately 2 pJ, significantly higher than on III-V-on-Si and InP photonic integration platforms.
1‐Oxoniaadamantane (2008)

Abstract The missing member of the heteroadamantane series, 1‐oxoniaadamantane ( 4a ), was prepared by the ionization of suitable bicyclic precursors under strongly acidic conditions. The ion 4a was characterized by 1 H and 13 C NMR spectroscopy. The X‐ray crystal structure of ion 4a was also obtained with a CB 11 H 6 Cl 6 counter anion. DFT calculations were performed on 1‐elementaadamantane cations for comparison. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)
A conformational transition in the structure of a 2′-thiomethyl-modified DNA visualized at high resolution (2009)

Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.
The career of Maclyn McCarty (2005)

On January 2, 2005, the scientific community lost a valued colleague and friend. Maclyn McCarty, or "Mac," as he was better known, was perhaps most recognized for his part in the discovery of DNA as the carrier of genetic information. But McCarty's scientific career was long and fruitful, and his contributions to science were vast. This retrospective offers a look at some of Mac's other notable scientific achievements.
Accelerating the initial rate of hydrolysis of methyl parathion with laser excitation using monolayer protected 10 nm Au nanoparticles capped with a Cu(bpy) catalyst (2012)

Using a low power green laser, we have demonstrated a rate acceleration of ~2-fold for the hydrolysis of methyl parathion by irradiating the plasmon absorption band of Au nanoparticles capped with a Cu(bpy) catalyst.
Faculty Perspectives on Service-Learning in Engineering Education: Challenges and Opportunities (2020)

She is currently the associate chair for Undergraduate Education in CEAE and has served as the ABET assessment coordinator since 2008. She began incorporating service-learning (SL
Loss of Dopamine D2 Receptors Induces Atrophy in the Temporal and Parietal Cortices and the Caudal Thalamus of Ethanol‐Consuming Mice (2011)

The result suggests that (i) normal DRD2 expression has a protective role against alcohol-induced brain atrophy and (ii) in the absence of Drd2 expression, prolonged ethanol intake reproduces a distinct feature of human brain pathology in alcoholism, the atrophy of the temporal and parietal cortices.
Polar Forms of Benzo[a]pyrene May Be Ubiquitous in the Environment (1998)

Previously, we reported that polar polycyclic aromatic compounds (polar PAC) can be detected by first oxidizing them with KO2/O2 and then detecting the carboxylic acid products, after pentafluorobenzylation, by gas chromatography electron capture mass spectrometry (Allam et al. Anal. Chem. 1992, 65, 1723−1727). For example, we used the method in the cited study to detect a benzo[a]pyrene tetrahydrotetraol hydrolysis product derived from benzo[a]pyrene-exposed lymphocytes after isolation of the DNA. However, the method was limited in its sensitivity by the presence of an interfering, analyte-like peak in the final mass chromatograms. Now, the results of our current work strongly suggest that the contamination leading to the unwanted peak is ubiquitous in the urban environment. Results from the analysis of a standard reference sample of urban particulate matter (SRM 1649) yielded a level of 10 ng of contaminant in a 5-mg sample (2 μg/g). The concentration of this polar contaminant is comparable to the certified value for benzo[a]pyrene of 14.5 ng (2.9 μg/g). Furthermore, our mass spectral data show evidence for the presence of many other polar PAC in the sample. These observations add to the concern raised by related environmental health studies focused on the potential impact of airborne polar PAC on human health.
Reduction of spinning sidebands in proton NMR of human prostate tissue with slow high‐resolution magic angle spinning (2005)

High-resolution magic angle spinning (HRMAS) NMR spectroscopy has proven useful for analyzing intact tissue and permitting correlations to be made between tissue metabolites and disease pathologies. Extending these studies to slow-spinning methodologies helps protect tissue pathological structures from HRMAS centrifuging damage and may permit the study of larger objects. Spinning sidebands (SSBs), which are produced by slow spinning, must be suppressed to prevent the complication of metabolic spectral regions. In this study human prostate tissues, as well as gel samples of a metabolite mixture solution, were measured with continuous-wave (CW) water presaturation on a 14.1T spectrometer, with HRMAS spinning rates of 250, 300, 350, 600, and 700 Hz, and 3.0 kHz. Editing the spectra by means of a simple minimum function (Min(A, B, ..., N) for N spectra acquired at different but close spinning rates) produced SSB-free spectra. Statistically significant linear correlations were observed for metabolite concentrations quantified from the Min(A, B, ..., N)-edited spectra generated at low spinning rates, with concentrations measured from the 3 kHz spectra, and also with quantitative pathology. These results indicate the empirical utility of this scheme for analyzing intact tissue, which also may be used as an adjunct tool in pathology for diagnosing disease.
Optics and photonics education in central Florida (2003)

We will describe several education programs that serve the growing optics industry in the Central Florida region, including the School of Optics’ graduate programs and two-year and four-year programs in Photonics Technology taught by collaboration between the University of Central Florida and local community colleges.
Molecular Mechanisms of Neurological Alterations in Hepatic Encephalopathy (2010)

Frontiers Events is a rapidly growing calendar management system dedicated to the scheduling of academic events. This includes announcements and invitations, participant listings and search functionality, abstract handling and publication, related events and post-event exchanges. Whether an organizer or participant, make your event a Frontiers Event!
MODELING AND OPTIMIZATION OF OHMIC HEATING OF FOODS INSIDE A FLEXIBLE PACKAGE (2005)

ABSTRACT A pulsed ohmic heating system and flexible package for food reheating and sterilization were developed to minimize Equivalent System Mass during long‐duration space missions. A package made of flexible pouch materials was powered through a pair of metal foil electrodes extending out. Preliminary tests of the package within an ohmic heating enclosure show that International Space Shuttle menu items such as chicken noodle soup and black beans could be heated using pulsed ohmic heating technology. The electrical conductivities of selected samples ranged between 0.01 and 0.03 S/cm. A 2‐D thermal‐electric model was developed using commercial CFD software Fluent to optimize the design and layout of electrodes to ensure uniform heating of the material. A static system under the assumption of there being no fluid motion in a microgravity environment was implemented. A package configuration with V‐shaped electrodes with dimensionless width of 0.147 was validated to be most appropriate for uniform heating while minimizing the cold zone to 2% of total area. The effect of field overshoot near the electrode edge is expected to be crucial to determine the uniformity of heating.