gebhart/patrepeval huggingface dataset:
Immobilization of Gold Nanorods onto Acid-Terminated Self-Assembled Monolayers via Electrostatic Interactions (2004)

We report the immobilization of gold nanorods onto self-assembled monolayers (SAMs) of 16-mercaptohexadecanoic acid (16-MHA). The simple two step protocol involves formation of a SAM of 16-MHA molecules onto gold-coated glass slides and subsequent immersion of these slides into the gold nanorod solution. The nanorods, formed by a seed-mediated, surfactant-assisted synthesis protocol, are stabilized in solution due to surface modification by the surfactant cetyltrimethylammonium bromide (CTAB). Attractive electrostatic interactions between the carboxylic acid group on the SAM and the positively charged CTAB molecules are likely responsible for the nanorod immobilization. UV-vis spectroscopy has been used to follow the kinetics of the nanorod immobilization. The nature of interaction between the gold nanorods and the 16-MHA SAM has been probed by Fourier transform infrared spectroscopy (FTIR). The surface morphology of the immobilized rods is studied by scanning electron microscopy (SEM) and atomic force microscopy (AFM) measurements. SEM was also used to determine the density of the immobilized nanorods as a function of the pH of immobilization. Control over the surface coverage of the immobilized gold nanorods has been demonstrated by simple pH variation. Such well-dispersed immobilized gold nanorods with control over the surface coverage could be interesting substrates for applications such as surface-enhanced Raman spectroscopy (SERS).
Aberrant cleavage of TDP-43 enhances aggregation and cellular toxicity (2009)

Inclusions of TAR DNA-binding protein-43 (TDP-43), a nuclear protein that regulates transcription and RNA splicing, are the defining histopathological feature of frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-Us) and sporadic and familial forms of amyotrophic lateral sclerosis (ALS). In ALS and FTLD-U, aggregated, ubiquitinated, and N-terminally truncated TDP-43 can be isolated from brain tissue rich in neuronal and glial cytoplasmic inclusions. The loss of TDP-43 function resulting from inappropriate cleavage, translocation from the nucleus, or its sequestration into inclusions could play important roles in neurodegeneration. However, it is not known whether TDP-43 fragments directly mediate toxicity and, more specifically, whether their abnormal aggregation is a cause or consequence of pathogenesis. We report that the ectopic expression of a approximately 25-kDa TDP-43 fragment corresponding to the C-terminal truncation product of caspase-cleaved TDP-43 leads to the formation of toxic, insoluble, and ubiquitin- and phospho-positive cytoplasmic inclusions within cells. The 25-kDa C-terminal fragment is more prone to phosphorylation at S409/S410 than full-length TDP-43, but phosphorylation at these sites is not required for inclusion formation or toxicity. Although this fragment shows no biological activity, its exogenous expression neither inhibits the function nor causes the sequestration of full-length nuclear TDP-43, suggesting that the 25-kDa fragment can induce cell death through a toxic gain-of-function. Finally, by generating a conformation-dependent antibody that detects C-terminal fragments, we show that this toxic cleavage product is specific for pathologic inclusions in human TDP-43 proteinopathies.
(Invited) Sunlight-Driven Ionic Power Generation from Bipolar Ion-Exchange Membranes Functionalized with Photoacids (2016)

Bipolar membranes are a class of polymeric ion-exchange materials that consist of a cation-exchange membrane that is in intimate contact with an anion-exchange membrane. They are unique among the ion-exchange membranes in that they that separate and maintain pH differences across the membrane even during passage of ionic current. Moreover, the physics of ion equilibration processes within these membranes resembles that which occurs during equilibration of semiconductor pn-junctions. In my presentation I will report on my research group’s recent results from measurements of the electrochemical behavior of bipolar membranes under conditions relevant to solar fuels devices. We identified a condition where the energy required to electrolyze water was seemingly less than 1.23 V, which we showed was due to transport of ions other than protons and hydroxide ions. This subtlety will be explained in great detail to clarify misunderstandings in the interpretation of current–voltage behavior of bipolar membranes. My research group has also recently successfully demonstrated ionic power generation through solar light harvesting in dye-sensitized ion-exchange membranes. Visible light illumination of photoacid-functionalized Nafion membranes drove endergonic excited-state proton transfer and a photovoltage and photocurrent resulted. Photoacid molecules convert the energy in light into a change in the chemical potential of protons via a weakening of protic functional groups on the photoacid, i.e. a drop in its p K a . Many photoacids absorb visible light poorly and so a secondary research thrust on this project is to develop new visible-light-absorbing photoacids. Toward this, we have developed the first Ir-based inorganic coordination compound photoacids and quantum dot photoacids. Visible-light excitation of these molecules resulted in clear observation of effective photoacid behavior. Calculation of the excited-state p K a and ongoing work to comprehend the analysis of photoacid behavior in complex systems will be covered. The applicability and practicality of bipolar membranes in solar fuels devices and as standalone ionic photoelectrochemical devices will also be discussed. As most of these materials, techniques, and analyses are new to the artificial photosynthesis community, we plan to carefully present the results of our studies and provide ample explanations. Collectively, this body of work represents several new directions in artificial photosynthesis research and development that are being pioneered by my research group.
A relational trace logic for simple hierarchical actor-based component systems (2012)

We present a logic for proving functional properties of concurrent component-based systems. A component is either a single actor or a group of dynamically created actors. The component hierarchy is based on the actor creation tree. The actors work concurrently and communicate asynchronously. Each actor is an instance of an actor class. An actor class determines the behavior of its instances. We assume that specifications of the behavior of the actor classes are available. The logic allows deriving properties of larger components from specifications of smaller components hierarchically.
Intrinsic Neurons of Fastigial Nucleus Mediate Neurogenic Neuroprotection against Excitotoxic and Ischemic Neuronal Injury in Rat (1999)

Electrical stimulation of the cerebellar fastigial nucleus (FN) elevates regional cerebral blood flow (rCBF) and arterial pressure (AP) and provides long-lasting protection against focal and global ischemic infarctions. We investigated which neuronal element in FN, perikarya or axons, mediates this central neurogenic neuroprotection and whether it also protects against excitotoxicity. In anesthetized rats, the FN was stimulated for 1 hr, and ibotenic acid (IBO) was microinjected unilaterally into the striatum. In unstimulated controls, the excitotoxic lesions averaged approximately 40 mm3. Stimulation of FN, but not dentate nucleus (DN), significantly reduced lesion volumes up to 80% when IBO was injected 15 min, 72 hr, or 10 d, but not 30 d, thereafter. In other rats, intrinsic neurons of FN or DN were destroyed by pretreatment with IBO. Five days later, the FN was stimulated, and 72 hr later, IBO was microinjected into the striatum. Lesions of FN, but not DN, abolished neuroprotection but not the elevations of rCBF and AP elicited from FN stimulation. Excitotoxic lesions of FN, but not DN, also abolished the 37% reduction in focal ischemic infarctions produced by middle cerebral artery occlusion. Excitation of intrinsic FN neurons provides long-lasting, substantial, and reversible protection of central neurons from excitotoxicity, as well as focal ischemia, whereas axons in the nucleus, probably collaterals of ramified brainstem neurons, mediate the elevations in rCBF, which do not contribute to neuroprotection. Long-lived protection against a range of injuries is an unrecognized function of FN neurons transmitted over pathways distinct from those regulating rCBF.
Tough dual nanocomposite hydrogels with inorganic hybrid crosslinking (2016)

A dual nanocomposite hydrogel with inorganic hybrid crosslinking was fabricated through a simultaneous sol-gel technique and free radical polymerization. Due to the multi-strengthening mechanism of the dual nanocomposite, the hydrogel was super tough and strong with a compressive stress of 32.00 MPa without rupture even at 100% strain, while it exhibited excellent fatigue resistant properties.
Opposing regulation of endolysosomal pathways by long-acting nanoformulated antiretroviral therapy and HIV-1 in human macrophages (2015)

We posit that modulation of endolysosomal pathways by antiretroviral nanoparticles provides a strategic path to combat HIV infection.
Detection of Adenoviruses (AdV) in Culture-Negative Environmental Samples by PCR during an AdV-Associated Respiratory Disease Outbreak (2000)

Since 1954, adenoviruses (AdV) have been recognized as an important cause of acute respiratory disease (ARD) among U.S. military recruits. Until recently, routine oral vaccination for AdV serotypes 4 and 7 eliminated epidemic AdV-associated ARD in this population. Now that the manufacturer has ceased production, vaccination has ended and AdV epidemics have reappeared. As part of a prospective epidemiological study during the high-risk ARD season, serial samples were obtained from ventilation system filters and tested for AdV by culture and PCR. An outbreak occurred during this surveillance. Of 59 air filters, 26 (44%) were AdV positive only by PCR. Sequence analysis confirmed the presence of AdV serotype 4, the implicated outbreak serotype. The number of AdV-related hospitalizations was directly correlated with the proportion of filters containing AdV; correlation coefficients were 0.86 (Pearson) and 0.90 (Spearman's rho). This is the first report describing a PCR method to detect airborne AdV during an ARD outbreak. It suggests that this technique can detect and quantify AdV-associated ARD exposure and may enable further definition of environmental effects on AdV-associated ARD spread.
Naturally occurring human antibodies against two distinct functional domains in the heavy chain of FXI/FXIa (1988)

We have isolated and probed the mechanism of action of two naturally occurring antibodies (Baltimore and Winston-Salem) against factor XI (FXI), that developed in patients congenitally deficient in FXI after replacement therapy. Purification on immobilized protein A and neutralization with monospecific antibodies against IgG heavy and light chain subtypes indicated that both antibodies were of restricted heterogeneity. Both Winston-Salem (IgG3 kappa) and Baltimore (IgG1 kappa) completely inhibited FXI coagulant activity at titers of 200 and 8 Bethesda units, respectively. Immunoaffinity columns prepared from each antibody were able to bind the heavy but not the light chain of reduced and alkylated activated FXI (FXIa). The activation of purified FXI by activated bovine factor XII (FXIIa), a reaction independent of high molecular weight kininogen (HK), was not inhibited by either antibody. The active site on the FXIa light chain was unaffected by either patient's IgG, as measured by its amidolytic activity. In contrast, one antibody (Baltimore) or its Fab' blocked the surface- mediated proteolytic activation of FXI by human FXIIa in a concentration-dependent fashion by preventing its binding to HK, but had no effect on the rate of activation of FIX by FXIa. In contrast, the other antibody (Winston-Salem) or its Fab' inhibited the activation of FIX by FXIa in a concentration-dependent fashion but did not inhibit binding of FXI to HK. We conclude that each of these two naturally occurring antibodies is directed against a specific, separate, and distinct epitope located in the heavy chain of FXIa, one near or at the domain essential for the activation of FIX by FXIa and the other close to the domain required for binding to HK.
Culture Medium Modulates Proinflammatory Conditions of Human Pancreatic Islets Before Transplantation (2006)

A portion of transplanted islets is lost during engraftment as a result of stressful events, involving hypoxia and production of proinflammatory molecules by islets. Two of these molecules (monocyte chemoattractant protein-1, CCL2/MCP-1 and tissue factor, TF) are directly correlated with reduced graft function. We evaluated which factors reduce islet proinflammatory conditions. In particular the effects of different culture media supplemented with proteins or antioxidant agents on CCL2/MCP-1 and TF human islet release were evaluated. We observed that human islets after culture in final wash culture medium (FW) significantly decreased CCL2/MCP-1 release and TF production compared with CMRL and M199. These effects were independent from the type of protein added to the media (human serum, human albumin, fetal calf serum). Glutathione in FW further decreased CCL2/MCP-1 in a dose-dependent manner. Culture conditions can modulate the proinflammatory state of islets, and could be used in clinical islet transplantation to reduce inflammation during engraftment.
Proteomic Analysis of Dendritic Cell-Derived Exosomes: A Secreted Subcellular Compartment Distinct from Apoptotic Vesicles (2001)

Dendritic cells constitutively secrete a population of small (50-90 nm diameter) Ag-presenting vesicles called exosomes. When sensitized with tumor antigenic peptides, dendritic cells produce exosomes, which stimulate anti-tumor immune responses and the rejection of established tumors in mice. Using a systematic proteomic approach, we establish the first extensive protein map of a particular exosome population; 21 new exosomal proteins were thus identified. Most proteins present in exosomes are related to endocytic compartments. New exosomal residents include cytosolic proteins most likely involved in exosome biogenesis and function, mainly cytoskeleton-related (cofilin, profilin I, and elongation factor 1alpha) and intracellular membrane transport and signaling factors (such as several annexins, rab 7 and 11, rap1B, and syntenin). Importantly, we also identified a novel category of exosomal proteins related to apoptosis: thioredoxin peroxidase II, Alix, 14-3-3, and galectin-3. These findings led us to analyze possible structural relationships between exosomes and microvesicles released by apoptotic cells. We show that although they both represent secreted populations of membrane vesicles relevant to immune responses, exosomes and apoptotic vesicles are biochemically and morphologically distinct. Therefore, in addition to cytokines, dendritic cells produce a specific population of membrane vesicles, exosomes, with unique molecular composition and strong immunostimulating properties.
LITHIUM CHLORIDE CATALYZED DECARBOXYLATION OF OXALACETIC ACID IN ETHANOL (1964)

The monovalent metal salt lithium chloride promotes the decarboxylation of oxalacetic acid in ethanol. The absorption peak which appears at 230 mμ during the reaction is interpreted to be the enol form of pyruvic acid. Hydrogen chloride has a similar effect on the decarboxylation.
Presence and phosphorylation of transcription factors in developing dendrites (1998)

In screening amplified poly(A) mRNA from hippocampal dendrites and growth cones in culture to determine candidates for local translation, we found that select transcription factor mRNAs were present. We hypothesized that synthesis of transcription factor proteins within dendrites would provide a direct signaling pathway between the distal dendrite and the nucleus resulting in modulation of gene expression important for neuronal differentiation. To evaluate this possibility, radiolabeled amplified antisense RNA was used to probe slot blots of transcription factor cDNAs as well as arrayed blots of zinc finger transcription factors. The mRNAs encoding the cAMP response element binding protein (CREB), zif 268, and one putative transcription factor were detected. We expanded upon these results showing that CREB protein is present in dendrites, that translation of CREB mRNA in isolated dendrites is feasible and that CREB protein found in dendrites can interact with the cis-acting cyclic AMP reponse element DNA sequence by using an in situ Southwestern assay. Further, CREB protein in dendrites is not transported to this site from the cell body because fluorescently tagged CREB microperfused into the soma did not diffuse into the dendrites. In addition, CREB protein microperfused into dendrites was rapidly transported to the nucleus, its likely site of bioactivity. Lastly, by using the isolated dendrite system we show that phosphorylation of Ser-133 on CREB protein can occur in isolated dendrites independent of the nucleus. These data provide a regulatory pathway in which transcription factors synthesized and posttranslationally modified in dendrites directly alter gene expression bypassing the integration of signal transduction pathways that converge on the nucleus.
Clinical Spectrum of Obesity and Mutations in the Melanocortin 4 Receptor Gene (2003)

Mutations in MC4R result in a distinct obesity syndrome that is inherited in a codominant manner. Mutations leading to complete loss of function are associated with a more severe phenotype. The correlation between the signaling properties of these mutant receptors and energy intake emphasizes the key role of this receptor in the control of eating behavior in humans.
Age-related changes in antibody-dependent cell-mediated cytotoxicity in mouse spleen. (1979)

The age-related variation in antibody-dependent cell-mediated cytotoxicity (ADCC) in spleen was examined in four different mouse strains (DBA/2, Balb/c, NZB and NZB/NZW). The ADCC effector activity against antibody-coated chicken red blood cells in untreated spleen from all four strains was roughly comparable. An initial rise in activity with increasing age until two to three months was followed by a sharp decline in effector activity. Treatment of the spleen cells with poly-l-lysine-coated carbonyl iron to remove phagocytes resulted in a decrease in ADCC activity in NZB, NZB/NZW and DBA/2 strains at all ages examined. The same general pattern of age-dependent decline was still seen in these depleted spleens. However, the same treatment essentially abolished ADCC in Balb/c spleen at all ages studied.
Chronic inflammatory responses to microgel‐based implant coatings (2010)

Inflammatory responses to implanted biomedical devices elicit a foreign body fibrotic reaction that limits device integration and performance in various biomedical applications. We examined chronic inflammatory responses to microgel conformal coatings consisting of thin films of poly(N-isopropylacrylamide) hydrogel microparticles cross-linked with poly(ethylene glycol) diacrylate deposited on poly(ethylene terephthalate) (PET). Unmodified and microgel-coated PET disks were implanted subcutaneously in rats for 4 weeks and explants were analyzed by histology and immunohistochemistry. Microgel coatings reduced chronic inflammation and resulted in a more mature/organized fibrous capsule. Microgel-coated samples exhibited 22% thinner fibrous capsules that contained 40% fewer cells compared to unmodified PET disks. Furthermore, microgel-coated samples contained significantly higher levels of macrophages (80%) than unmodified PET controls. These results demonstrate that microgel coatings reduce chronic inflammation to implanted biomaterials. (c) 2010 Wiley Periodicals, Inc. J Biomed Mater Res, 2010.
Propulsion mechanisms for Leidenfrost solids on ratchets (2013)

We propose a model for the propulsion of Leidenfrost solids on ratchets based on viscous drag due to the flow of evaporating vapor. The model assumes pressure-driven flow described by the Navier-Stokes equations and is mainly studied in lubrication approximation. A scaling expression is derived for the dependence of the propulsive force on geometric parameters of the ratchet surface and properties of the sublimating solid. We show that the model results as well as the scaling law compare favorably with experiments and are able to reproduce the experimentally observed scaling with the size of the solid.
The Combined Propranolol/TSST Paradigm – A New Method for Psychoneuroendocrinology (2013)

Upon perception of a stimulus as stressful, the human brain reacts with the activation of the hypothalamus-pituitary-adrenal (HPA) axis and the sympathetic nervous system (SNS), to mobilize energy resources to better cope with the stressor. Since the perception of the stressor is the initial stimulus, a synchronicity between the subjective perception of stress and the physiological stress reactivity should be expected. However, according to a recent meta-analysis, these associations are weak and inconsistent. The goal of the current study was to investigate the interaction between the SNS, HPA and subjective stress perceptions, by introducing an experimental manipulation of this interaction. For this purpose, we combined the SNS inhibitor propranolol with the Trier Social Stress Test, and measured endocrinological and psychological responses to the stressor. Thirty healthy male participants were recruited and randomly assigned to either a propranolol (PROP; n = 15) or placebo (PLC; n = 15) group. All subjects were administered 80 mg of propranolol 60 minutes prior to exposure to psychosocial stress. Salivary cortisol and alpha amylase (sAA), heart rate, blood pressure and subjective stress responses were assessed throughout the study. We observed significantly reduced sAA levels and heart rate increases in the PROP group in response to stress, with no effects of the drug on systolic or diastolic blood pressure changes. In line with previous studies, a significant increase in cortisol was seen in response to the stress exposure. Importantly, the cortisol increase was significantly higher in the PROP group. A typical increase in subjective stress could be seen in both groups, with no significant group differences emerging. Complementing previous work, this study further demonstrates a significant interaction between the HPA and the SNS during acute stress. The HPA activity was found to be elevated in the presence of a suppressed SNS in reactivity to the TSST.