gebhart/patrepeval huggingface dataset:
Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy (2003)

Decreased nitric oxide synthase (NOS) activity induces left ventricular hypertrophy (LVH), but the transcriptional pathways mediating this effect are unknown. We hypothesized that specific NOS isoform deletion (NOS3 or NOS1) would activate different transcriptional programs in LVH. We analyzed cardiac expression profiles (Affymetrix MG-U74A) from NOS-/- mice using robust multi-array average (RMA). Of 12,422 genes analyzed, 47 genes were differentially expressed in NOS3-/- and 67 in NOS1(-/-) hearts compared with wild type (WT). Only 16 showed similar changes in both NOS-/- strains, most notably decreased heat-shock proteins (HSP10, 40, 70, 86, 105). Hypertrophied NOS1-/- hearts had unique features, including decreased myocyte-enriched calcineurin interacting protein and paradoxical downregulation of fetal isoforms (alpha-skeletal actin and brain natriuretic peptide). Cluster analyses demonstrated that NOS1 deletion caused more pronounced changes in the myocardial transcriptome than did NOS3 deletion, despite similar cardiac phenotypes. These findings suggest that the transcriptional basis for LVH varies depending on the inciting biochemical stimulus. In addition, NOS isoforms appear to play distinct roles in modulating cardiac structure.
Real-Time Experiment of Snore Active Noise Control (2007)

This paper presents real-time experiment of active noise control (ANC) algorithms for reducing nonstationary, intermittent snore. Three snore ANC algorithms have been developed and tested to evaluate their performance. The ANC system uses both finite impulse response (FIR) and infinite impulse response (IIR) adaptive filters. Acoustic feedback was minimized by using both adaptive IIR filter and FIR filter with feedback neutralization. Real-time experiments were conducted using a digital signal processor development system and recorded snore samples. An average reduction of 15-20 dB can be achieved using multi-channel ANC systems.
A non-contact method for spatially localized sedimentation of particles from liquid suspensions using Marangoni forces (2011)

This paper presents the directed sedimentation of suspension particles in a thin layer of liquid (1 mm) onto a featureless glass substrate by Marangoni flows. A programmable 16 × 8 array of surface mount resistors suspended 0.1‐2 mm above the liquid provides dynamic millimeter-sized heat sources to locally heat the liquid surface to temperatures from approximately 28.5 to 36.5 ◦ C. The heaters in this array can be activated independently by a graphical user interface, creating surface tension gradients along the liquid surface. The resulting Marangoni flows direct spatially localized particle sedimentation on the substrate. The resultant sedimentation patterns and accumulation levels depend on factors such as the temperature gradient at the liquid surface, number of active heaters and type of liquid used. For example, when a single heater is activated, a liquid surface temperature elevation of 6.9 ◦ C results in a localized sedimentation of suspended weed pollen Kochia scoparia (� = 25 μm) in silicone oil DC-704 over a region of 2.9 mm 2 that is centered directly beneath the active heater. This sedimentation method is a contactless technique, which reduces the likelihood of sample contamination. (Some figures in this article are in colour only in the electronic version)
Prestack depth migration of primary and surface‐related multiple reflections (2005)

Surface‐related multiples may severely contaminate multicomponent seabed seismic recordings. Because conventional imaging techniques require input data that consist of primary reflections only, significant processing effort is commonly dedicated to attenuating multiples prior to migration. On the other hand, surface‐related multiples provide additional illuminations of the subsurface. We present a prestack depthmigration method that allows primary and multiple reflections to be imaged simultaneously. Depth imaging with primary and multiple reflections (DIPMR) involves decomposing the data into up‐ and downgoing wave constituents, followed by downward extrapolation. Artifacts generated by interference of up‐ and downgoing events not associated with the same subsurface reflection points (cross‐talk) are attenuated using a 2D deconvolution imaging condition. In contrast to existing methods, DIPMR does not require a priori information about the source signature or directivity, because the illuminating source wavefield is extracted directly from the data themselves via the up/down separation. Moreover, there is no need for elimination or identification of multiples prior to migration. By including surface‐related multiples in the imaging procedure, the effective source wavefield is stronger and the spatial aperture wider.
Proof-of-Principle Study in a Murine Lung Infection Model of Antipseudomonal Activity of Phage PEV20 in a Dry-Powder Formulation (2017)

Bacteriophage therapy is a promising alternative treatment to antibiotics, as it has been documented to be efficacious against multidrug-resistant bacteria with minimal side effects. Several groups have demonstrated the efficacy of phage suspension <i>in vivo</i> to treat lung infections using intranasal delivery; however, phage dry-powder administration to the lungs has not yet been explored. Powder formulations provide potential advantages over a liquid formulation, including easy storage, transport, and administration. The purpose of this study was to assess the bactericidal activities of phage dry-powder formulations against multidrug-resistant (MDR) strain <i>Pseudomonas aeruginosa</i> FADDI-PA001 in a mouse lung infection model. Phage PEV20 spray dried with lactose and leucine produced an inhalable powder at a concentration of 2 × 10<sup>7</sup> PFU/mg. <i>P. aeruginosa</i> lung infection was established by intratracheal administration of the bacterial suspension to neutropenic mice. At 2 h after the bacterial challenge, the infected mice were treated with 2 mg of the phage powder using a dry-powder insufflator. At 24 h after the phage treatment, the bacterial load in the lungs was decreased by 5.3 log<sub>10</sub> (<i>P</i> < 0.0005) in the phage-treated group compared with that in the nontreated group. Additionally, the phage concentration in the lungs was increased by 1 log<sub>10</sub> at 24 h in the treated group. These results demonstrate the feasibility of a pulmonary delivery of phage PEV20 dry-powder formulation for the treatment of lung infection caused by antibiotic-resistant <i>P. aeruginosa</i>.
Interdisciplinary Design Research for End-User Software Engineering (2007)

How does EUSE research build on empirical studies of programmers, and what kinds of empirical research might provide foundations for future EUSE research? My own work on interdisciplinary design draws comparisons across academic and professional boundaries, applying the results to the design of new technologies, and the critical assessment of technology.
Gene Sequencing Identifies Perturbation in Nitric Oxide Signaling as a Nonlipid Molecular Subtype of Coronary Artery Disease (2022)

Beyond <i>LDLR</i>, we identified an additional nonlipid molecular subtype of CAD characterized by rare variants in the <i>NOS3</i> gene.
Macrophage-Targeted Photodynamic Therapy (2004)

Photodynamic therapy (PDT) uses light activatable molecules that after illumination produce reactive oxygen species and unwanted tissue destruction. PDT has dual selectivity due to control of light delivery and to some extent selective photosensitizer (PS) accumulation in tumors or other diseased tissue, additional targeted selectivity of PS for disease is necessary. The delivery of drugs to selected lesions can be enhanced by the preparation of targeted macromolecular conjugates that employ cell type specific targeting by ligand-receptor recognition. Macrophages and monocytes express a scavenger-receptor that is a high-capacity route for delivering molecules into endocytic compartments in a cell-type specific manner. We have shown that by attaching PS to scavenger-receptor ligands it is possible to get three logs of selective cell killing in macrophages while leaving non-macrophage cells unharmed. The capability to selectively kill macrophages has applications in treating cancer and in the detection and therapy of vulnerable atherosclerotic plaque and possibly for autoimmune disease and some infections.
Organic Carbon Sequestration in Soil Humic Substances As Affected by Application of Different Nitrogen Fertilizers in a Vegetable-Rotation Cropping System (2019)

Little is known on the effect of application of different nitrogen (N) fertilizers on soil organic carbon (SOC) sequestration in soil humic substances (HS). We investigated HS molecular characteristics in an Orthic Acrisol, southwestern China, under 2-year field fertilization of a urea (U), a polymer-coated urea (PCU) and a biochar-coated urea (BCU) using <sup>13</sup>C-CPMAS-NMR spectroscopy. Results showed that N fertilization promoted SOC sequestration into HS and favored alkyl-C and aromatic-C rather than O-alkyl-C and carbonyl-C for humic acids and humin in soil. Application of PCU and BCU may better enhance vegetable yield, SOC sequestration, and HS stability than the U application, which may benefit from longer time of N existence and higher total N in soil. Among the N treatments, BCU application mostly affected the compositions and stability of SOC in the HS for the OC input and prime effect of biochar for SOC transformation.
Dielectric Properties of Polymer Electrolyte Membranes Measured by Two-Port Transmission Line Technique (2010)

The microwave dielectric properties of perfluorosulfonic acid membranes are characterized by a two-port transmission line technique. Two dielectric relaxation modes are observed in the microwave region (0.045-26 GHz) at 25{degree sign}C. The higher frequency process observed is identified as the cooperative relaxation of bulk-like water, whose amount was found to increase linearly with water content in the polymer. The lower-frequency process, characterized by longer relaxation times (20-70 picoseconds), is attributed to water molecules that are loosely bound to sulfonate groups. The loosely bound water amount was found to increase with hydration level at low water content, and levels-off at higher water contents. Flemion SH150, which has an equivalent weight of 909 g/equiv, displays higher dielectric strengths for both of these water modes compared to Nafion 117 (equivalent weight of 1100 g/equiv).
Dewatering and settling of activated sludges: The case for using cation analysis (1997)

Seven mixed liquor samples from full‐scale activated sludge systems were analyzed for their settling and dewatering properties, and the calcium, magnesium, sodium, and potassium concentrations were measured. The soluble cation concentrations were evaluated in terms of the monovalent to divalent cation ratio and the calcium to magnesium ratio. The monovalent to divalent ratio was positively correlated to activated sludge dewatering properties. In batch tests, the addition of calcium or magnesium to samples with a high monovalent to divalent cation ratio improved the dewatering rate of the suspensions by ≤30%. Conditioning and dewatering experiments were performed on thickened sludges from two of the industrial samples. Calcium was added to each sample, in one case, to lower the monovalent to divalent cation ratio and in the second case, to increase the calcium to magnesium ratio. In each case, addition of calcium to the sample reduced the optimum polymer dose for conditioning by 30% compared with control samples with no added calcium. Laboratory reactor studies were performed using mixed liquor and wastewater from three of the activated sludge plants. Two of the systems were deficient in magnesium, and one system was deficient in calcium. In each case, the deficient cation was added to the feed of the reactors, and settling and/or dewatering properties improved. Addition of cations to the feed of two full‐scale activated sludge systems improved the settling dramatically, and in one system, the thickened solids content was doubled. These results indicate that cation imbalances are a common cause of sludge settling and dewatering problems in industrial activated sludge plants, and these imbalances can be corrected by addition of the cation deemed to be deficient by analysis of the monovalent to divalent ratio or the calcium to magnesium ratio.
Eigenvalues of strictly regular Hall-plates (2023)

This work is about uniform, plane, singly connected, strictly regular Hall-plates with an arbitrary number of peripheral contacts exposed to a uniform magnetic field of arbitrary strength. The strictly regular symmetry is the highest possible degree of symmetry, and it is found in commercial Hall-plates for magnetic field sensors or circulators. It means that all contacts and contact spacings are equally large, if the Hall-plate is mapped conformally to the unit disk. The indefinite conductance matrices of such Hall-plates are circulant matrices, whose complex eigenvalues can be computed in closed form. It is shown how to express the conductance and resistance matrices of these Hall-plates, how to compute their equivalent resistor circuit, their Hall-output voltages or currents, their signal-to-thermal noise ratio, and their power as functions of the eigenvalues. It is also proven that the noise efficiency of strictly regular Hall-plates with many contacts can be up to 112% better than for conventional Hall-plates with four contacts, and it is explained why their optimal biasing uses patterns of supply voltages or currents, which vary sinusoidally along their boundary.
Generation of hyaline cartilaginous tissue from mouse adult dermal fibroblast culture by defined factors (2011)

Repair of cartilage injury with hyaline cartilage continues to be a challenging clinical problem. Because of the limited number of chondrocytes in vivo, coupled with in vitro de-differentiation of chondrocytes into fibrochondrocytes, which secrete type I collagen and have an altered matrix architecture and mechanical function, there is a need for a novel cell source that produces hyaline cartilage. The generation of induced pluripotent stem (iPS) cells has provided a tool for reprogramming dermal fibroblasts to an undifferentiated state by ectopic expression of reprogramming factors. Here, we show that retroviral expression of two reprogramming factors (c-Myc and Klf4) and one chondrogenic factor (SOX9) induces polygonal chondrogenic cells directly from adult dermal fibroblast cultures. Induced cells expressed marker genes for chondrocytes but not fibroblasts, i.e., the promoters of type I collagen genes were extensively methylated. Although some induced cell lines formed tumors when subcutaneously injected into nude mice, other induced cell lines generated stable homogenous hyaline cartilage–like tissue. Further, the doxycycline-inducible induction system demonstrated that induced cells are able to respond to chondrogenic medium by expressing endogenous Sox9 and maintain chondrogenic potential after substantial reduction of transgene expression. Thus, this approach could lead to the preparation of hyaline cartilage directly from skin, without generating iPS cells.
All-Printed Paper-Based Micro-supercapacitors Using Water-Based Additive-Free Oxidized Single-Walled Carbon Nanotube Pastes (2021)

Printing technologies that integrate wearable components onto flexible and stretchable substrates are crucial for the development of miniaturized wearable electronics. In this study, we developed all-printed paper-based flexible micro-supercapacitors based on water-based additive-free oxidized single-walled carbon nanotube pastes. The use of a modified Brodie’s method with mild oxidants and minimum usage of strong acids enabled the production of highly conductive and printable oxidized single-walled carbon nanotube pastes. Pseudo-plastic pastes were obtained because of the numerous hydrogen bonds between the oxidized single-walled carbon nanotubes. By photothermal treatment with intense pulsed light irradiation, a microporous structure was developed in the interdigitated energy storage electrodes to facilitate the infiltration of electrolytes. The paper-based flexible micro-supercapacitor exhibited a high energy density of 0.51 μW h cm–2 at a power density of 0.59 mW cm–2 and a superior capacity retention of 85% after 10,000 bending cycles with a bending radius of 3 mm. The all-printed flexible micro-supercapacitor array with a total capacitance of 0.1 mF charged to 4.0 V successfully powered a commercial digital clock for approximately 40 s. The micro-supercapacitor array operated properly under both tensile and compressive strains. These results demonstrate that the water-based additive-free oxidized single-walled carbon nanotube pastes are promising printable materials for the construction of flexible micro-supercapacitors.
Novel One‐Pot Vicinal Double C‐Acylation of Styrenes and Methacrylates by Electroreduction. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Mechanical Design And Theoretical Analysis Of A Four Fingered Prosthetic Hand Incorporating Embedded Sma Bundle Actuators (2007)

The psychological and physical trauma associated with the loss of a human limb can severely impact on the quality of life of an amputee rendering even the most basic of tasks very difficult. A prosthetic device can be of great benefit to the amputee in the performance of everyday human tasks. This paper outlines a proposed mechanical design of a 12 degree-of-freedom SMA actuated artificial hand. It is proposed that the SMA wires be embedded intrinsically within the hand structure which will allow for significant flexibility for use either as a prosthetic hand solution, or as part of a complete lower arm prosthetic solution. A modular approach is taken in the design facilitating ease of manufacture and assembly, and more importantly, also allows the end user to easily replace SMA wires in the event of failure. A biomimetric approach has been taken during the design process meaning that the artificial hand should replicate that of a human hand as far as is possible with due regard to functional requirements. The proposed design has been exposed to appropriate loading through the use of finite element analysis (FEA) to ensure that it is structurally sound. Theoretical analysis of the mechanical framework was also carried out to establish the limits of the angular displacement and velocity of the finger tip as well finger tip force generation. A combination of various polymers and Titanium, which are suitably lightweight, are proposed for the manufacture of the design.
Forensic engineering techniques for VLSI CAD tools (2000)

The proliferation of the Internet has affected the business model of almost all semiconductor and VLSI CAD companies that rely on intellectual property (IP) as their main source of revenues. The fact that IP has become more accessible and easily transferable, has influenced the emergence of copyright infringement as one of the most common obstructions to e-commerce of IP.
Evaluation of GATA-4 and GATA-5 methylation profiles in human pancreatic cancers indicate promoter methylation patterns distinct from other human tumor types (2007)

The GATA-4 and GATA-5 transcription factors are increasingly recognized as playing a role in carcinogenesis of human tumors derived of endodermal and mesodermal origin. The pancreas is derived from endodermal tissues suggesting GATA-4 and GATA-5 gene methylation may play a critical role in the biology of human pancreatic cancer as well. We investigated GATA-4 and -5 by methylation-specific PCR (MSP) in normal and neoplastic pancreatic tissues, including isogenic xenografts or cultured cell lines derived from the coexistent primary cancer and/or metastases in patients with pancreatic carcinoma. The relationship of promoter methylation was correlated with mRNA expression for each gene, and methylation patterns were correlated with known clinicopathologic features of patients. GATA-4 demonstrated a significantly lower methylation frequency than GATA-5 in low passage pancreatic cancer xenografts or cell lines (1/34 versus 21/34, p < 0.001). GATA-4 and -5 were also evaluated in microdissected samples of normal duct epithelium and cancer from pancreas cancer tissues which confirmed infrequent GATA-4 methylation in pancreatic cancers as well as in normal duct epithelium. GATA-4 was frequently overexpressed at the mRNA level with 27 of 30 (90%) pancreatic cancers showing >5.0-fold overexpression compared to normal duct epithelial cells. By contrast, high frequency methylation of GATA-5 was confirmed in pancreatic cancers tissues, but was rarely methylated in normal duct epithelium, indicating hypermethylation of this gene during pancreatic cancer development. GATA-5 mRNA expression did not correlate with its promoter hypermethylation, and treatment with the demethylating agent 5-aza-2'-deoxycytidine only partially restored mRNA expression suggesting additional regulatory mechanisms of GATA-5 expression. The presence of GATA-5 methylation showed a trend towards worse long-term survival (14.0 +/- 9.2 months versus 19.5 +/- 3.9 months, p = 0.06). While hypermethylation of GATA-5 seems to be a universal feature among human tumors, infrequent methylation of GATA-4, and its corresponding overexpression, appears unique to pancreatic cancer from other tumor types reported thus far.
Immune Thrombocytopenia (2010)

Abstract Immune thrombocytopenia (ITP) comprises a heterogeneous group of disorders characterized by autoimmune-mediated platelet destruction and impairment of thrombopoiesis. ITP may occur in the absence of an evident predisposing etiology (primary ITP) or secondary to a growing list of associated conditions (secondary ITP), and must be differentiated from other causes of thrombocytopenia. This review focuses on primary ITP in adults. The traditional goal of therapy in this population is to achieve a hemostatic platelet count of 30 × 109/L or above for most patients while minimizing treatment-related morbidity. This approach has been called into question by the recent advent of well-tolerated and effective agents for the management of ITP, including pulse-dose dexamethasone, rituximab, and the thrombopoietin receptor agonists. Recent studies suggest the potential for aggressive therapy at the time of diagnosis to alter the natural history of ITP and point to the importance of quality-of-life considerations in therapeutic decision making.
Introduction to the Special Section on Intelligent Visual Interfaces for Text Analysis (2012)

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Coherent fiber-optic sensor for vibration localization (2014)

A novel distributed fiber-optic vibration sensor is proposed and experimentally demonstrated. The sensor relies on a dual Mach-Zehnder ring interferometric architecture associated to a new coherent detection scheme, borrowed from high bit rate coherent optical communications, which performs a completely passive management of polarization and phase variables of the received optical signal. The proposed solution thus makes feasible the actual in-field applicability of the cost-effectiveness and high sensitivity featured by interferometric sensors. Sensor performance in terms of vibration localization accuracy has been experimentally verified.