gebhart/patrepeval huggingface dataset:
Organic Redox-Initiated Polymerization Process for the Fabrication of Hydrogels for Colon-Specific Drug Delivery (2003)

Organic-redox initiated polymerization technique based on the co-initiators system comprising benzoyl peroxide and N-phenyldiethanolamine was used at ambient temperature to fabricate pH-responsive hydrogels. The effects of changes in the concentration of the co-initiators system, the ratio in which the co-initiators combined, the type of the polymerization solvent, the pH of the hydrating medium, the concentration of the cross-linking agent based on azo-bond and the pH-sensitive cross-linking agent on the properties of the hydrogels were investigated. Increasing the concentration of the co-initiators system, decreasing the concentration of the two types of cross-linking agents, and replacing DMSO by ethanol as the polymerization solvent resulted in hydrogels with increased equilibrium swelling ratio and increased molecular weight between cross-links at pH 7.4. Increasing the concentration of N-phenyldiethanolamine while keeping the concentration of benzoyl peroxide constant gave hydrogels with increased equilibrium swelling ratios. The equilibrium swelling ratios of the hydrogels at pH 2.0 were not affected by the factors investigated. The polymerization technique may be suitable for the design of drug delivery systems containing thermolabile bioactive agents like peptides and proteins.
Calcium-Induced Peptide Association to Form an Intact Protein Domain: 1 H NMR Structural Evidence (1990)

The 70-residue carboxyl-terminal domain of the muscle contractile protein troponin-C contains two helix-loop-helix calcium (Ca)-binding sites that are related to each other by approximate twofold rotational symmetry. Hydrophobic residues from the helices and a short three residue beta sheet at the interface of the two sites act to stabilize the protein domain in the presence of Ca. A synthetic 34-residue peptide representing one of these sites (site III) has been synthesized and studied by H-1 nuclear magnetic resonance (NMR) spectroscopy. In solution this peptide undergoes a Ca-induced conformational change to form the helix-loop-helix Ca-binding motif. Two-dimensional nuclear Overhauser effect spectra have provided evidence for the formation of a beta sheet and interactions between several hydrophobic residues from opposing helices as found in troponin-C. It is proposed that a symmetric two-site dimer similar in tertiary structure to the carboxyl-terminal domain of troponin-C forms from the assembly of two site III peptides in the Ca-bound form.
The structure of an active acoustic metamaterial with tunable effective density (2009)

A new class of one-dimensional active acoustic metamaterials (AAMMs) with programmable effective densities is presented. The proposed AAMM is capable of producing densities that are orders of magnitudes lower or higher than the ambient fluid. Such characteristics are achieved by using an array of fluid cavities separated by piezoelectric diaphragms that are controlled to generate constant densities over wide frequency bands. The piezodiaphragms are augmented with passive electrical components to broaden the operating frequency bandwidth and enable densities higher than the fluid medium to be generated. The use of these components is shown to be essential to maintain the closed-loop compliance of the piezodiaphragm away from the zone of elastic instabilities. The values of the passive components are selected on a rational basis in order to ensure a balance between the frequency bandwidth and control voltage. With this unique structure of the AAMM, physically realizable acoustic cloaks can be implemented and objects treated with these active metamaterials can become acoustically invisible.
Models and mechanisms for tangible user interfaces (1997)

Current human-computer interface design is dominated by the graphical user interface approach, where users interact with graphical abstractions of virtual interface devices through a few general-purpose input &amp;quot;peripherals.&amp;quot; The thesis develops models and mechanisms for &amp;quot;tangible user interfaces&amp;quot; -- user interfaces which use physical objects, instruments, surfaces, and spaces as physical interfaces to digital information. Prototype applications on three platforms -- the metaDESK, transBOARD, and ambientROOM -- are introduced as examples of this approach. These instances are used to generalize the &amp;quot;GUI widgetry,&amp;quot; &amp;quot;optical,&amp;quot; and &amp;quot;containers and conduits&amp;quot; interface metaphors. The thesis also develops engineering mechanisms called proxy-distributed or &amp;quot;proxdist&amp;quot; computation, which provide a layered approach for integrating physical objects with diverse sensing, display, communication, and computation capabilities into coherent interface implementations. The combined research provides a vehi...
Quantifying and Mitigating the Impact of Asymmetric Induced Hydraulic Fracturing from Horizontal Development Wellbores (2016)

Abstract Sufficient production and fracture mapping evidence across North America is now available to clearly demonstrate that pairs of delineation and development wells often underperform when there is substantial production time (months or years) between the completions of the two wells. The relative degree of impact on hydrocarbon extraction per acre varies from one play or formation to another, but the phenomena is generally attributed to asymmetric induced fracturing from the development (child) well into the previously partially drained and lower static pressure delineation (parent) well reservoir volume. This paper briefly discusses two solutions that have been employed to minimize the negative fiscal ramifications and improve recovery. Rigorous 3D unstructured grid reservoir modeling can assist in the quantification of the phenomena; however, options for mitigating the problem for cases where the impact is extreme are typically limited. Synthetic history matching and forward modeling were performed with a grid-based numerical simulator that mimicked a series of asymmetric oblique fractures interacting with a drained reservoir volume, comparing acceleration of reserve recovery and total recovered reserves with a similar case involving symmetric fracturing. Two scenarios for preventing extreme asymmetric fracturing are discussed. These included dramatic shortening of the time between completions, and performing pressure sink mitigation (PSM) via refracturing of the delineation wellbore. It is shown that the asymmetric fracturing into drained volumes can materially impact reserves and rate of recovery if the acreage position of a given project is substantial. It is demonstrated that the overall stimulated reservoir system permeability, the degree of permeability contrast between reservoir layers, and the degree of asymmetry are all factors that have an impact on the degree to which the long-term time between completions affects recovery of hydrocarbons over and above simple volumetric depletion. Integration of rigorous 3D reservoir modeling and far-field fracture mapping have established that the negative ramifications of extreme induced fracture asymmetry can be overcome with careful application of drilling and completion (D&amp;C) timing and offset drainage pressure management process.
A Better Model of Acute Pancreatitis for Evaluating Therapy (1992)

Existing models of acute pancreatitis have limitations to studying novel therapy. Whereas some produce mild self-limited pancreatitis, others result in sudden necrotizing injury. The authors developed an improved model providing homogeneous moderately severe injury by superimposing secretory hyperstimulation on minimal intraductal bile acid exposure. Sprague-Dawley rats (n = 231) received low-pressure intraductal glycodeoxycholic acid (GDOC) at very low (5 or 10 mmol/L) concentrations followed by intravenous cerulein. Cerulein or GDOC alone caused only very mild inflammation. However, GDOC combined with cerulein was uniformly associated with more edema (p less than 0.0005), acinar necrosis (p less than 0.01), inflammation (p less than 0.006), and hemorrhage (p less than 0.01). Pancreatic injury was further increased and death was potentiated by increasing volume and duration of intraductal low-dose GDOC infusion. There was significant morphologic progression between 6 and 24 hours. The authors conclude that (1) combining minimal intraductal bile acid exposure with intravenous hyperstimulation produces homogeneous pancreatitis of intermediate severity that can be modulated at will; (2) the injury is progressive over at least 24 hours with finite mortality rate; (3) the model provides superior opportunity to study innovative therapy.
Retinoids Assist the Cellular Folding of the Autosomal Dominant Retinitis Pigmentosa Opsin Mutant P23H (2004)

The clinically common mutant opsin P23H, associated with autosomal dominant retinitis pigmentosa, yields low levels of rhodopsin when retinal is added following induction of the protein in stably transfected HEK-293 cells. We previously showed that P23H rhodopsin levels could be increased by providing a 7-membered ring, locked analog of 11-cis-retinal during expression of P23H opsin in vivo. Here we demonstrate that the mutant opsin is effectively rescued by 9- or 11-cis-retinal, the native chromophore. When retinal was added during expression, P23H rhodopsin levels were 5-fold (9-cis) and 6-fold (11-cis) higher than when retinal was added after opsin was expressed and cells were harvested. Levels of P23H opsin were increased approximately 3.5-fold with both compounds, but wild-type protein levels were only slightly increased. Addition of retinal during induction promoted the Golgi-specific glycosylation of P23H opsin and transport of the protein to the cell surface. P23H rhodopsins containing 9- or 11-cis-retinal had blue-shifted absorption maxima and altered photo-bleaching properties compared with the corresponding wild-type proteins. Significantly, P23H rhodopsins were more thermally unstable than the wild-type proteins and more rapidly bleached by hydroxylamine in the dark. We suggest that P23H opsin is similarly unstable and that retinal binds and stabilizes the protein early in its biogenesis to promote its cellular folding and trafficking. The implications of this study for treating retinitis pigmentosa and other protein conformational disorders are discussed.
Transcriptional regulation of metabolic genes in the postprandial python heart: an extreme example of physiologic adaptation (2010)

In order to cope with the physiologic stresses of digesting large meals, the heart of the Burmese python undergoes significant hypertrophy in as little as 24 hours, returning to the fasted state a few days afterwards. This remarkable response has led us to investigate the molecular mechanisms utilized by python ventricular myocytes during the onset and regression of hypertrophy. We have initially focused on using quantitative PCR to examine changes in the transcripts of genes involved in metabolic processes and cardiac function between fasted and post‐fed states in the heart. We have demonstrated that genes involved in glycolysis and lipid import are downregulated during hypertrophy, while the expression of genes that control lipolytic processes are maintained in response to elevated serum lipid concentrations. Moreover, we have shown that the hypertrophic python heart favors the expression of genes that maintain a highly contractile state, and also exhibits a striking pattern of gene markers that would indicate both physiology and pathology in a mammalian system. These results implicate a novel mechanism of molecular regulation utilized by the python in order to facilitate the dynamic changes inherent to cardiac hypertrophy. This research was supported by a grant from Hiberna, Inc.
Biodegradable triboelectric nanogenerator as a life-time designed implantable power source (2016)

Transient electronics built with degradable organic and inorganic materials is an emerging area and has shown great potential for in vivo sensors and therapeutic devices. However, most of these devices require external power sources to function, which may limit their applications for in vivo cases. We report a biodegradable triboelectric nanogenerator (BD-TENG) for in vivo biomechanical energy harvesting, which can be degraded and resorbed in an animal body after completing its work cycle without any adverse long-term effects. Tunable electrical output capabilities and degradation features were achieved by fabricated BD-TENG using different materials. When applying BD-TENG to power two complementary micrograting electrodes, a DC-pulsed electrical field was generated, and the nerve cell growth was successfully orientated, showing its feasibility for neuron-repairing process. Our work demonstrates the potential of BD-TENG as a power source for transient medical devices.
Expression of the utrophin gene during myogenic differentiation (1999)

The process of myogenic differentiation is known to be accompanied by large increases ( approximately 10-fold) in the expression of genes encoding cytoskeletal and membrane proteins including dystrophin and the acetylcholine receptor (AChR) subunits, via the effects of transcription factors belonging to the MyoD family. Since in skeletal muscle (i) utrophin is a synaptic homolog to dystrophin, and (ii) the utrophin promoter contains an E-box, we examined, in the present study, expression of the utrophin gene during myogenic differentiation using the mouse C2 muscle cell line. We observed that in comparison to myoblasts, the levels of utrophin and its transcript were approximately 2-fold higher in differentiated myotubes. In order to address whether a greater rate of transcription contributed to the elevated levels of utrophin transcripts, we performed nuclear run-on assays. In these studies we determined that the rate of transcription of the utrophin gene was approximately 2-fold greater in myotubes as compared to myoblasts. Finally, we examined the stability of utrophin mRNAs in muscle cultures by two separate methods: following transcription blockade with actinomycin D and by pulse-chase experiments. Under these conditions, we determined that the half-life of utrophin mRNAs in myoblasts was approximately 20 h and that it remained largely unaffected during myogenic differentiation. Altogether, these results show that in comparison to other synaptic proteins and to dystrophin, expression of the utrophin gene is only moderately increased during myogenic differentiation.
Calcium Phosphate Phase Identification Using XPS and Time-of-Flight Cluster SIMS (1998)

Reproducible time-of-flight cluster static secondary ion mass spectra (ToF-SSIMS) were obtained for various standard calcium phosphate (CP) powders, which allowed for phase identification. X-ray diffraction was not able to detect signals from microscopic amounts of CP (∼15 mmol m-2). The phases studied were α-tricalcium phosphate [α-Ca3(PO4)2], β-tricalcium phosphate [β-Ca3(PO4)2], amorphous calcium phosphate [Ca3(PO4)2·xH2O], octacalcium phosphate [Ca8H2(PO4)6·H2O], brushite (CaHPO4·2H2O), and hydroxyapatite [Ca10(PO4)6(OH)2]. The SIMS spectra were obtained via bombardment with (CsI)Cs+ projectiles. X-ray photoelectron spectroscopy (XPS) core levels of the P 2p, Ca 2p, and O 1s orbitals and the relative O 1s loss intensity were examined. The PO3-/PO2- ratios from ToF-SSIMS spectra in conjunction with XPS of the CP powders showed much promise in differentiating between these phases at microscopic CP coverages on the metal oxide surface.
Pulmonary and Activation-Regulated Chemokine Stimulates Collagen Production in Lung Fibroblasts (2003)

Levels of pulmonary and activation-regulated chemokine (PARC) mRNA and protein are increased in the lungs of patients with pulmonary fibrosis. The purpose of this study was to establish whether PARC could be directly involved in development of pulmonary fibrosis by stimulating collagen production in lung fibroblasts. Exposure to PARC increased production of collagen mRNA and protein by 3- to 4-fold in normal adult lung and dermal fibroblast cells. Collagen mRNA transiently increased after 3-6 h of activation with PARC, with an increase in collagen protein detected after 24 h of activation. At the same time, PARC had less pronounced effect on fibroblast proliferation, not exceeding 50% increase over control nonstimulated cells. PARC intracellular signaling led to activation of ERK1/2, but not p38, in fibroblasts; pharmacologic inhibition of ERK, but not p38, also blocked PARC's effect on collagen production. Inhibition experiments with pertussis toxin suggested that PARC receptor is G protein-coupled. Thus, PARC is a member of the CC chemokine family that acts directly as a profibrotic factor.
Granulocyte colony-stimulating factor improves function of neutrophils from patients with acute liver failure (2000)

G-CSF improves the neutrophil dysfunction of ALF.
Childhood maltreatment is associated with distinct genomic and epigenetic profiles in posttraumatic stress disorder (2013)

Childhood maltreatment is likely to influence fundamental biological processes and engrave long-lasting epigenetic marks, leading to adverse health outcomes in adulthood. We aimed to elucidate the impact of different early environment on disease-related genome-wide gene expression and DNA methylation in peripheral blood cells in patients with posttraumatic stress disorder (PTSD). Compared with the same trauma-exposed controls (n = 108), gene-expression profiles of PTSD patients with similar clinical symptoms and matched adult trauma exposure but different childhood adverse events (n = 32 and 29) were almost completely nonoverlapping (98%). These differences on the level of individual transcripts were paralleled by the enrichment of several distinct biological networks between the groups. Moreover, these gene-expression changes were accompanied and likely mediated by changes in DNA methylation in the same loci to a much larger proportion in the childhood abuse (69%) vs. the non-child abuse-only group (34%). This study is unique in providing genome-wide evidence of distinct biological modifications in PTSD in the presence or absence of exposure to childhood abuse. The findings that nonoverlapping biological pathways seem to be affected in the two PTSD groups and that changes in DNA methylation appear to have a much greater impact in the childhood-abuse group might reflect differences in the pathophysiology of PTSD, in dependence of exposure to childhood maltreatment. These results contribute to a better understanding of the extent of influence of differences in trauma exposure on pathophysiological processes in stress-related psychiatric disorders and may have implications for personalized medicine.
VEGF induces cardiovascular malformation and embryonic lethality. (1997)

The essential function of vascular endothelial growth factor (VEGF) in embryonic angiogenesis has clearly been documented in murine embryos with targeted deletions of either VEGF or its receptors. The effects of VEGF in the organogenetic phase of development have not been studied to date. Therefore, we applied 0.7 to 0.9 microgram of VEGF via methylcellulose carriers into the midbrain or onto the right forelimb of 4.5-day-old quail embryos. Another group of embryos was treated with 1 microgram of platelet-derived growth factor and controls were carried out using carriers without any growth factor. VEGF-induced cardiovascular malformations resulted in embryonic lethality. The venous area of the vasculature was dilated in almost all organs. The heart was most seriously affected and showed typical characteristics of insufficiency. VEGF strongly increased endocardial cell proliferation and obviously induced impairment of the growth rates of myocardium and endocardium. The myocardium of the ventricles was extremely thin, and septation defects were observed. As a result of the disturbed outflow, the atria were extremely dilated and thin-walled. The morphology of the hearts was reminiscent of that observed in congenital malformations such as Uhl's and Osler's syndromes. Our results show that expression of VEGF has to be tightly controlled during development.
Fits Like a Glove: Rapid and Reliable Hand Shape Personalization (2016)

We present a fast, practical method for personalizing a hand shape basis to an individual user's detailed hand shape using only a small set of depth images. To achieve this, we minimize an energy based on a sum of render-and-compare cost functions called the golden energy. However, this energy is only piecewise continuous, due to pixels crossing occlusion boundaries, and is therefore not obviously amenable to efficient gradient-based optimization. A key insight is that the energy is the combination of a smooth low-frequency function with a high-frequency, low-amplitude, piecewisecontinuous function. A central finite difference approximation with a suitable step size can therefore jump over the discontinuities to obtain a good approximation to the energy's low-frequency behavior, allowing efficient gradient-based optimization. Experimental results quantitatively demonstrate for the first time that detailed personalized models improve the accuracy of hand tracking and achieve competitive results in both tracking and model registration.
Use of Bone Morphogenetic Protein-2 in the Rabbit Ulnar Nonunion Model (1996)

The ability of the osteoinductive protein and recombinant human bone morphogenetic protein-2, combined with polylactic glycolic acid porous microspheres and autologous blood clot to heal a large segmental defect was tested in a rabbit diaphyseal defect model. Two centimeter nonuniting defects were surgically created in the bilateral ulnae of 50 male New Zealand white rabbits. Each defect was then implanted with a pastelike polylactic glycolic acid/blood clot combination that was mixed with 5 different concentrations of recombinant human bone morphogenetic protein-2. The forearms were radiographically assessed on a biweekly schedule for 8 weeks. At 8 weeks, all animals were sacrificed and forearms radiographed. Radiographs were then scored by 3 independent observers for bone formation and union rates. United limbs were tested in torsion for mechanical strength using a Burstein torsion tester. All nonunited limbs were analyzed histologically as were 2 united limbs from each dosage group. Radiographic evaluation revealed that there was a dose dependent response in healing of the ulnar defect with a higher bone formation rate in the 2 higher dose limbs than in the lower dose limbs. Union was achieved in 100% of the highest dose limbs, whereas only 50% of the lowest dose limbs achieved bony union. No defects implanted with carrier alone achieved union. Biomechanical studies revealed significantly stiffer bone than age matched controls. Histologic analysis demonstrated normal bone formation with abundant normal appearing osteoid. These dose response data further support the role of recombinant human bone morphogenetic protein-2 as a potent morphogen in bone regeneration.
Optical properties of CdSe nanocrystals in a polymer matrix (1999)

Cadmium selenide nanocrystals have been made in a transparent polymer matrix by synthesis at room temperature. Particle size is controlled by reaction time or reagent concentration. Larger nanocrystals (≳3 nm) show near-band-edge photoluminescence. Smaller ones have a broad emission extending across the visible region. Atmospheric moisture causes the emission intensity to decrease but subsequent exposure to light reverses this and gives a material which is no longer quenched by moisture. The broad emission and stability against atmospheric moisture leads to possible device applications of a “white” phosphor.