gebhart/patrepeval huggingface dataset:
An implantable batteryless wireless impedance sensor for gastroesophageal reflux diagnosis (2010)

A new method for long term monitoring of gastroesophageal reflux is presented. The impedance of the reflux in the esophagus can be determined remotely without the need of a battery in the sensor implant. The implant includes an energy harvesting circuit, sensing electrodes, an antenna and an impedance to frequency converter. An external reader provides power to the implant and measures the impedance values simultaneously. A prototype with an overall size of 0.5cm×1cm×3.1cm was made with a printed circuit board and discrete components, and packaged in polydimethylsiloxane. In vivo experiments were conducted in pig cadavers. The results show good correlation between impedance and pH values of the solutions flushed into the esophagus, and good signal-to-noise ratios with the transducer inside the body. The batteryless wireless impedance sensor is able to detect every reflux episode, either acid or non-acid, which provides more accurate diagnosis for the gastroesophageal reflux disease.
Adenovirus vector infection of chronic lymphocytic leukemia B cells (1996)

Adenovirus vectors have several features that make them attractive for potential use in gene therapy, including a broad tissue tropism and an ability to infect quiescent or postmitotic cells. In light of this, we examined whether recombinant adenovirus vectors could transfer genes into neoplastic cells of patients with chronic lymphocytic leukemia (CLL), a leukemia of "resting" B cells. Using high-titer recombinant adenovirus vectors, we found we could transfer genes encoding beta-galactosidase or murine CD80 (B7-1) into the CLL B cells of all patients tested (n = 10). The efficiency of gene transduction into CLL B cells was approximately 100 to 1,000-fold lower than into HeLa cells at any given multiplicity of infection (MOI). At a MOI of 500, 10% to 70% of the CLL B cells from different patients were made to express the transgene, as assessed by multiparameter flow cytometric analysis. Sustained levels of expression with little loss in the percentage of infected cells were maintained for up to 9 days, at which point the analysis was stopped. We found that CLL B cells have markedly lower expression levels of integrins that facilitate internalization of adenovirus particles into target cells, perhaps accounting, in part, for the reduced efficiency of adenovirus-mediated gene transfer compared with that in HeLa cells. Although HeLa cells express high levels of alpha(v)beta5, and detectable amounts of alpha(v)beta3, we find CLL cells from all patients tested express only low amounts of alpha(v)beta3, and no detectable alpha(v)beta5. Activation of CLL cells via CD40 cross-linking enhances expression of alpha(v)beta3, and induces expression of alpha(v)beta5. This phenotypic change is associated with a fivefold increase in the efficiency of adenovirus-mediated gene transfer into such activated CLL B cells. This study demonstrates that adenovirus vectors can transduce genes into CLL B cells and that the efficiency of gene transduction is enhanced by activation via CD40 cross-linking. This is the first demonstration that high proportions of CLL B cells can be made to express a selected transgene, suggesting that such gene transfer methods may become useful for the study of the pathogenesis and/or treatment of this disease.
Examining the Lateral Displacement of HL60 Cells Rolling on Asymmetric P-Selectin Patterns (2010)

The lateral displacement of cells orthogonal to a flow stream by rolling on asymmetrical receptor patterns presents a new opportunity for the label-free separation and analysis of cells. Understanding the nature of cell rolling trajectories on such substrates is necessary to the engineering of substrates and the design of devices for cell separation and analysis. Here, we investigate the statistical nature of cell rolling and the effect of pattern geometry and flow shear stress on cell rolling trajectories using micrometer-scale patterns of biomolecular receptors with well-defined edges. Leukemic myeloid HL60 cells expressing the PSGL-1 ligand were allowed to flow across a field of patterned lines fabricated using microcontact printing and functionalized with the P-selectin receptor, leveraging both the specific adhesion of this ligand-receptor pair and the asymmetry of the receptor pattern inclination angle with respect to the fluid shear flow direction (α = 5, 10, 15, and 20°). The effects of the fluid shear stress magnitude (τ = 0.5, 1, 1.5, and 2.0 dyn/cm(2)), α, and P-selectin incubation concentration were quantified in terms of the rolling velocity and edge tracking length. Rolling cells tracked along the inclined edges of the patterned lines before detaching and reattaching on another line. The detachment of rolling cells after tracking along the edge was consistent with a Poisson process of history-independent interactions. Increasing the edge inclination angle decreased the edge tracking length in an exponential manner, contrary to the shear stress magnitude and P-selectin incubation concentration, which did not have a significant effect. On the basis of these experimental data, we constructed an empirical model that predicted the occurrence of the maximum lateral displacement at an edge angle of 7.5°. We also used these findings to construct a Monte Carlo simulation for the prediction of rolling trajectories of HL60 cells on P-selectin-patterned substrates with a specified edge inclination angle. The prediction of lateral displacement in the range of 200 μm within a 1 cm separation length supports the feasibility of label-free cell separation via asymmetric receptor patterns in microfluidic devices.
Regulation of mammalian pyruvate dehydrogenase α subunit gene expression by glucose in HepG2 cells (1998)

We report the effect of glucose on the expression of the gene encoding the pyruvate dehydrogenase (E1) alpha subunit (E1alpha) in human hepatoma (HepG2) cells. Total pyruvate dehydrogenase complex activity as well as the levels of protein and mRNA of the E1alpha subunit were significantly increased in HepG2 cells cultured in medium containing 16.7 mM glucose compared with 1.0 mM glucose for a period of 4 weeks. The level of E1alpha mRNA was elevated approx. 2-fold in HepG2 cells cultured for 24 h in medium containing 16.7 mM glucose compared with 1 mM glucose. This effect was specific to glucose and independent of insulin. Nuclear run-on assays and promoter analysis indicate that the glucose-induced increases in the levels of E1alpha mRNA in HepG2 cells are due to increased transcription of the human E1alpha (PDHA1) gene. Mutational analysis of the E1alpha promoter region has identified two regions, from -78 to -73 bp (CCCCTG) and from -8 to -3 bp (GCGGTG), that are responsible for the effect of glucose on promoter activity; the former exhibits a larger effect. These two sequences represent new variations of the carbohydrate-response element that has been identified in other genes. The stimulation of E1alpha promoter activity by glucose was abolished by okadaic acid at 100 nM but not at 5 nM, suggesting that glucose-mediated regulation of pyruvate dehydrogenase complex E1alpha gene transcription involves a phosphorylation/dephosphorylation mechanism, possibly involving protein phosphatase-1.
Broadband Acoustic Cloak for Ultrasound Waves (2011)

Invisibility devices based on coordinate transformation have opened up a new field of considerable interest. We present here the first practical realization of a low-loss and broadband acoustic cloak for underwater ultrasound. This metamaterial cloak is constructed with a network of acoustic circuit elements, namely, serial inductors and shunt capacitors. Our experiment clearly shows that the acoustic cloak can effectively bend the ultrasound waves around the hidden object, with reduced scattering and shadow. Because of the nonresonant nature of the building elements, this low-loss (∼6 dB/m) cylindrical cloak exhibits invisibility over a broad frequency range from 52 to 64 kHz. Furthermore, our experimental study indicates that this design approach should be scalable to different acoustic frequencies and offers the possibility for a variety of devices based on coordinate transformation.
Identification of transforming genes of subgroup A and C strains of Herpesvirus saimiri. (1991)

Herpesvirus saimiri is an oncogenic herpesvirus that induces rapidly progressing lymphomas in New World primates. Using retrovirus vectors for gene transfer, specific open reading frames of H. saimiri were tested for their ability to transform rodent cells in culture. One open reading frame, designated STP-C488 (for saimiri-transformation-associated protein of the subgroup C strain 488), phenotypically transformed Rat-1 cells, resulting in formation of foci, growth at reduced serum concentration, and growth to higher cell densities. Cells transformed by STP-C488 formed invasive tumors in nude mice. The STP-A11 reading frame of strain 11 (subgroup A) was much less potent in its transforming ability than STP-C488. These results demonstrate the oncogene nature of these two open reading frames and provide a means for studying their transforming functions independent of the rest of the H. saimiri genome.
Wideband transskull refocusing of ultrasound beams using dual-mode ultrasound arrays: Ex vivo results (2018)

Transcranial focused ultrasound (tFUS) is capable of providing subtherapeutic and therapeutic ablative treatments for a variety of brain disorders. A major challenge towards widespread use of tFUS-based therapies stems from the complexity of the skull that could result in severe loss of focusing gain. Using extensive hydrophone scan measurements in plain water as well as transskull, we have documented a range of tFUS beam distortions for a variety of target points and access angles. In this paper, we present quantitative measurements of tFUS distortions due to skull aberrations at different operating frequencies. In addition, refocusing results for a variety of target points at different frequencies within the transducer bandwidth are presented in terms of improvement in focusing gain. Dual-mode ultrasound array (DMUA) prototype (64 elements, concave with 40-mm radius of curvature) was used. Skull samples were extracted from animal subjects that have undergone tFUS treatments using the DMUA prototype were utilized. Experiments were performed at a set of 31 discrete frequencies in the range 2.0 MHz–5.0 MHz. A needle hydrophone was used to measure the pressure waveforms at the target locations. The element transmission efficiency varied as a function of frequency in a nonmonotonic manner with a range of 5–15 dB variation for the different target points. The array focusing gain also varied nonmonotonically suggesting the need for broadband refocusing.
An Activated Trifluoromethyl Group as a Novel Synthon for a Substituted Vinyl Function: Facile Synthesis of 2-(Substituted 1-Alkenyl)anilines (1994)

Abstract Treatment of 2-(trifluoromethyl)aniline with an alkyl Grignard reagent results in an efficient transformation of the trifluoromethyl substituent into a substituted vinyl group.
Cellular and molecular mechanisms of fibrosis (2007)

Fibrosis is defined by the overgrowth, hardening, and/or scarring of various tissues and is attributed to excess deposition of extracellular matrix components including collagen. Fibrosis is the end result of chronic inflammatory reactions induced by a variety of stimuli including persistent infections, autoimmune reactions, allergic responses, chemical insults, radiation, and tissue injury. Although current treatments for fibrotic diseases such as idiopathic pulmonary fibrosis, liver cirrhosis, systemic sclerosis, progressive kidney disease, and cardiovascular fibrosis typically target the inflammatory response, there is accumulating evidence that the mechanisms driving fibrogenesis are distinct from those regulating inflammation. In fact, some studies have suggested that ongoing inflammation is needed to reverse established and progressive fibrosis. The key cellular mediator of fibrosis is the myofibroblast, which when activated serves as the primary collagen-producing cell. Myofibroblasts are generated from a variety of sources including resident mesenchymal cells, epithelial and endothelial cells in processes termed epithelial/endothelial-mesenchymal (EMT/EndMT) transition, as well as from circulating fibroblast-like cells called fibrocytes that are derived from bone-marrow stem cells. Myofibroblasts are activated by a variety of mechanisms, including paracrine signals derived from lymphocytes and macrophages, autocrine factors secreted by myofibroblasts, and pathogen-associated molecular patterns (PAMPS) produced by pathogenic organisms that interact with pattern recognition receptors (i.e. TLRs) on fibroblasts. Cytokines (IL-13, IL-21, TGF-beta1), chemokines (MCP-1, MIP-1beta), angiogenic factors (VEGF), growth factors (PDGF), peroxisome proliferator-activated receptors (PPARs), acute phase proteins (SAP), caspases, and components of the renin-angiotensin-aldosterone system (ANG II) have been identified as important regulators of fibrosis and are being investigated as potential targets of antifibrotic drugs. This review explores our current understanding of the cellular and molecular mechanisms of fibrogenesis.
Photobleaching of Fluorescent Dyes under Conditions Used for Single-Molecule Detection:  Evidence of Two-Step Photolysis (1998)

The photostability of fluorescent dyes is of crucial importance for the statistical accuracy of single-molecule detection (SMD) and for the image quality of scanning confocal microscopy. Concurrent results for the photostability were obtained by two different experimental techniques. First, the photostabilities of several coumarin and rhodamine derivatives in aqueous solution were obtained by monitoring the steady-state fluorescence decay in a quartz cell. Furthermore, an epi-illuminated microscope, continuous wave (CW) excitation at 514.5 nm, and fluorescence correlation spectroscopy (FCS) with a newly developed theory were used to study the photobleaching characteristics of rhodamines under conditions used for SMD. Depending on the rhodamine structure, the probability of photobleaching, p(b), is in the order of 10(-)(6)-10(-)(7) for irradiances below 10(3) W/cm(2). However, a considerable increase of p(b) for irradiances above this level was observed which can only be described by photobleaching reactions from higher excited states (two-step photolysis). In view of these observations, the probability of photobleaching, p(b), as well as a closed expression of its dependence on the CW excitation irradiance considering a five-level molecular electronic state model with the possibility of photobleaching from higher excited electronic states, is derived. From this model, optimal conditions for SMD with respect to the number of emitted fluorescence photons and to the signal-to-background ratio are discussed, taking into account both saturation and photobleaching. The additional photobleaching due to two-step photolysis limits the applicable irradiance.
Comparison between Fenoprofen and Ibuprofen in the Treatment of Soft-Tissue Rheumatism (1983)

Fenoprofen calcium 600 mg, four times daily, and ibuprofen 400 mg, four times daily, were compared in a double-blind crossover study involving the treatment of soft-tissue rheumatism in fifty patients. After 7 days there was no significant difference between the efficacy of the two drugs with respect to 'pain at rest', 'pain on movement', 'tenderness' or 'sleep disturbance' but fenoprofen was significantly better when considering 'limitation of movement' and 'The physician's assessment of the severity of the condition'. Combining data from Weeks 1 and 2 of treatment, 14 days fenoprofen treatment brought about significant improvements in all of the above parameters. Ibuprofen did not significantly improve 'pain at rest' but did improve the other parameters.
The Importance of Imidazolium Substituents in the Use of Imidazolium-Based Room-Temperature Ionic Liquids as Solvents for Palladium-Catalyzed Telomerization of Butadiene with Methanol (2003)

Room-temperature ionic liquids are used as cosolvents in the palladium-catalyzed telomerization of butadiene with methanol. The basic catalyst is palladium(II) acetate with either triphenylphosphine or sodium diphenylphosphinobenzene-3-sulfonate (TPPMS), which was reacted with butadiene and methanol at 85 °C. It was found that the addition of several equivalents of 1,3-dialkylimidazolium salts per palladium leads to complete deactivation of the catalyst. It was suspected that the deactivation of the catalyst was due to the formation of highly stable palladium imidazolylidene complexes, but no direct evidence of this species was obtained. On the basis of this hypothesis, the use of pyridinium and 1,2,3-trialkylimidazolium salts was studied in an attempt to limit the formation of such species. It was found, particularly for the 1,2,3-trialkylimidazolium salts, that highly active and selective systems for the telomerization of butadiene with methanol were obtained. Furthermore, a biphasic catalytic system composed of palladium(II) acetate, TPPMS, heptane, and 1-butyl-2,3-dimethylimidazolium bis((trifluoromethyl)sulfonyl)imidate, [BMMI][TF2N], was used. In this case, after the telomerization reaction, the methoxyoctadiene products were recovered by simple decantation and the ionic liquid phase reintroduced to the reactor. In this way the catalyst was recycled four times (to total turnover number of 10 000) with little loss of activity.
Neuroprotectin D1: A docosahexaenoic acid-derived docosatriene protects human retinal pigment epithelial cells from oxidative stress (2004)

Docosahexaenoic acid (DHA) is a lipid peroxidation target in oxidative injury to retinal pigment epithelium (RPE) and retina. Photoreceptor and synaptic membranes share the highest content of DHA of all cell membranes. This fatty acid is required for RPE functional integrity; however, it is not known whether specific mediators generated from DHA contribute to its biological significance. We used human ARPE-19 cells and demonstrated the synthesis of 10,17S-docosatriene [neuroprotectin D1 (NPD1)]. This synthesis was enhanced by the calcium ionophore A-23187, by IL-1beta, or by supplying DHA. Under these conditions, there is a time-dependent release of endogenous free DHA followed by NPD1 formation, suggesting that phospholipase A(2) releases the mediator's precursor. Added NPD1 potently counteracted H(2)O(2)/tumor necrosis factor alpha oxidative-stress-triggered apoptotic RPE DNA damage. NPD1 also up-regulated the antiapoptotic proteins Bcl-2 and Bcl-x(L) and decreased proapoptotic Bax and Bad expression. Moreover, NPD1 (50 nM) inhibited oxidative-stress-induced caspase-3 activation. NPD1 also inhibited IL-1beta-stimulated expression of cyclooxygenase 2 promoter transfected into ARPE-19 cells. Overall, NPD1 protected RPE cells from oxidative-stress-induced apoptosis, and we predict that it will similarly protect neurons. This lipid mediator therefore may indirectly contribute to photoreceptor cell survival as well. Because both RPE and photoreceptor cells die in retinal degenerations, our findings contribute to the understanding of retinal cell survival signaling and potentially to the development of new therapeutic strategies.
Mutations in the Glucose-6-Phosphatase Gene that Cause Glycogen Storage Disease Type 1a (1993)

Glycogen storage disease (GSD) type 1a is caused by the deficiency of D-glucose-6-phosphatase (G6Pase), the key enzyme in glucose homeostasis. Despite both a high incidence and morbidity, the molecular mechanisms underlying this deficiency have eluded characterization. In the present study, the molecular and biochemical characterization of the human G6Pase complementary DNA, its gene, and the expressed protein, which is indistinguishable from human microsomal G6Pase, are reported. Several mutations in the G6Pase gene of affected individuals that completely inactivate the enzyme have been identified. These results establish the molecular basis of this disease and open the way for future gene therapy.
The Basic Science of Gene Therapy (1993)

The development over the past decade of methods for delivering genes to mammalian cells has stimulated great interest in the possibility of treating human disease by gene-based therapies. However, despite substantial progress, a number of key technical issues need to be resolved before gene therapy can be safely and effectively applied in the clinic. Future technological developments, particularly in the areas of gene delivery and cell transplantation, will be critical for the successful practice of gene therapy.
Involvement of interleukin-15 and interleukin-21, two γ-chain-related cytokines, in celiac disease (2009)

Celiac disease (CD), an enteropathy caused by dietary gluten in genetically susceptible individuals, is histologically characterized by villous atrophy, crypt cell hyperplasia, and increased number of intra-epithelial lymphocytes. The nature of CD pathogenesis remains unclear, but recent evidence indicates that both innate and adaptive immune responses are necessary for the phenotypic expression and pathologic changes characteristic of CD. Extensive studies of molecules produced by immune cells in the gut of CD patients have led to identification of two cytokines, namely interleukin (IL)-15 and IL-21, which are thought to play a major role in orchestrating the mucosal inflammatory response in CD. Here we review the current knowledge of the expression and function of IL-15 and IL-21 in CD.
A Strategy for a Convergent Synthesis of N-Linked Glycopeptides on a Solid Support (1995)

Oligosaccharides and glycopeptides are of considerable importance in molecular biology and pharmacology. However, their synthesis is complicated by the large number of different linking sites between each saccharide unit, the need for stereochemical control, the chemical sensitivity of the glycopeptide bonds, and the need to harmonize diverse protecting groups. Here, an efficient solid-phase synthesis of three N-linked glycopeptides based on glycal assembly is presented. The peptide domain can be extended while the ensemble remains bound to the polymer. The glycopeptides synthesized here are among the largest N-linked glycopeptides ever accessed by either solution- or solid-phase synthesis.
MICON: A Knowledge Based Single Board Computer Designer (1984)

For some time there has been interest in automatically implementing designs described in a high level representation. This paper presents a workbench that allows a designer to describe a single board computer at the hardware requirements level and have a design produced automatically. The designs produced by the system, MICON, compare favorably to commercial designs. In comparison to manual techniques, the design time has been drastically reduced; a series of three commercial designs was reproduced in a few hours. MICON uses knowledge based engineering approaches in its implementation and is written in the OPS-5 production system language.