gebhart/patrepeval huggingface dataset:
Detachment Lithography of Photosensitive Polymers: A Route to Fabricating Three‐Dimensional Structures (2009)

Abstract A technique to create arrays of micrometer‐sized patterns of photosensitive polymers on the surface of elastomeric stamps and to transfer these patterns to planar and nonplanar substrates is presented. The photosensitive polymers are initially patterned through detachment lithography (DL), which utilizes the difference in adhesion forces to induce the mechanical failure in the film along the edges of the protruded parts of the mold. A polydimethylsiloxane (PDMS) stamp with a kinetically and thermally adjustable adhesion and conformal contact can transfer the detached patterns to etched or curved substrates, as well as planar ones. These printed patterns remain photochemically active for further modification via photolithography, and/or can serve as resists for subsequent etching or deposition, such that photolithography can be used on highly nonconformal and nonplanar surfaces. Various 3D structures fabricated using the process have potential applications in MEMS (micro‐electromechanical systems) sensors/actuators, optical devices, and microfluidics.
Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression (2008)

This approach revealed C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5 genes to be important in chromosomal instability-related adenoma to carcinoma progression. These genes therefore may serve as highly specific biomarkers for colorectal cancer with potential clinical applications.
Zeroing in on the Pathogenic Form of α-Synuclein and Its Mechanism of Neurotoxicity in Parkinson's Disease (2003)

Parkinson's disease (PD) is linked to mutations in the protein alpha-synuclein, which can exist in vitro in several aggregation states, including a natively unfolded monomer, a beta-sheet rich oligomer, or protofibril, and a stable amyloid fibril. This work reviews the current literature that is relevant to two linked questions: which of these species is pathogenic, and what is the mechanism of neurotoxicity? The amyloid fibril, fibrillar aggregates, Lewy bodies, and the alpha-synuclein monomer, which is normally expressed at high levels, are all unlikely to be pathogenic, for reasons discussed here. We therefore favor a toxic protofibril scenario, and propose that the pathogenic species is transiently populated during the process of fibrillization. Toxicity may arise from pore-like protofibrils that cause membrane permeabilization. An approach to testing this hypothesis is discussed.
Characterization of prostatic epithelial cell lines derived from transgenic adenocarcinoma of the mouse prostate (TRAMP) model. (1997)

To develop a syngeneic transplantable system to study immunotherapeutic approaches for the treatment of prostate cancer, three cell lines were established from a heterogeneous 32 week tumor of the transgenic adenocarcinoma mouse prostate (TRAMP) model. TRAMP is a transgenic line of C57BL/6 mice harboring a construct comprised of the minimal -426/+28 rat probasin promoter driving prostate-specific epithelial expression of the SV40 large T antigen. TRAMP males develop histological prostatic intraepithelial neoplasia by 8-12 weeks of age that progress to adenocarcinoma with distant metastases by 24-30 weeks of age. The three cell lines (TRAMP-C1, TRAMP-C2, and TRAMP-C3) express cytokeratin, E-cadherin, and androgen receptor by immunohistochemical analysis and do not appear to have a mutated p53. Although TRAMP-C1 and TRAMP-C2 are tumorigenic when grafted into syngeneic C57BL/6 hosts, TRAMP-C3 grows readily in vitro but does not form tumors. The T antigen oncoprotein is not expressed by the cell lines in vitro or in vivo. The rationale for establishing multiple cell lines was to isolate cells representing various stages of cellular transformation and progression to androgen-independent metastatic disease that could be manipulated in vitro and, in combination with the TRAMP model, provide a system to investigate therapeutic interventions, such as immunotherapy prior to clinical trials.
Fabrication and performance of selectively oxidized vertical-cavity lasers (1995)

We report the high yield fabrication and reproducible performance of selectively oxidized vertical-cavity surface emitting lasers. We show that linear oxidation rates of AlGaAs without an induction period allows reproducible fabrication of buried oxide current apertures within monolithic distributed Bragg reflectors. The oxide layers do not induce obvious crystalline defects, and continuous wave operation in excess of 650 h has been obtained. The high yield fabrication enables relatively high laser performance over a wide wavelength span. We observe submilliamp threshold currents over a wavelength range of up to 75 nm, and power conversion efficiencies at 1 mW output power of greater than 20% over a 50-nm wavelength range.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Enzymatic and Non-enzymatic Roles of Protein-disulfide Isomerase in Apolipoprotein B Secretion (1997)

1) the role of PDI in the MTP complex involves functions other than its known enzymatic activities; 2) one or both of the enzymatic activities of free PDI is/are important for the MTP-independent steps of apoB secretion; 3) oleate can affect apoB secretion at high physiological concentrations and compensate for the insufficiency of PDI activities.
Compression-based template matching (2002)

Textual image compression is a method of both lossy and lossless image compression that is particularly effective for images containing repeated sub-images, notably pages of text. This paper addresses the problem of pattern comparison by using an information or compression based approach. Following Mohiuddin et al. ( 1984), the authors use the amount of uncertainty or entropy between marks as the criterion for the matching process. The entropy model they use is the context-based compression model proposed by Langdon and Rissanen (1981) and further developed by Moffat (1991). There are two principal issues to investigate when studying template matching methods: their susceptibility to different kinds of noise, and how they respond to errors in the initial registration. Because of the computation-intensive nature of the comparison operation, many schemes have been devised to pre-filter or screen the marks in advance to determine those that will surely fail the match. They present a novel method of screening which uses a quad-tree decomposition and finds local centroids at each tree level.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Intravitreal Vancomycin (1987)

Some of the gram-positive isolates from exogenous bacterial endophthalmitis cases treated at our institution have been found to be resistant to either cefazolin sodium, gentamicin sulfate, or both. However, all of these isolates have been sensitive to vancomycin. These findings prompted us to reevaluate the retinal toxicity and clearance of intravitreal vancomycin in pigmented rabbits. Doses up to 2 mg were found to be nontoxic in phakic and aphakic-vitrectomized eyes. Clearance was determined in phakic and aphakic-vitrectomized rabbit eyes with or without intact lens capsules. The antibiotic was cleared most slowly in phakic eyes. Aphakic-vitrectomized eyes without an intact lens capsule cleared antibiotic most rapidly, while aphakic-vitrectomized eyes with intact capsules exhibited an intermediate clearance rate. In addition, the interaction between vancomycin and gentamicin on gram-positive endophthalmitis isolates was found to be additive or synergistic depending on the bacterial species. Based on these data, we recommend the combination of vancomycin and an aminoglycoside as the initial antibiotic therapy for exogenous bacterial endophthalmitis.
A data-driven approach to preprocessing Illumina 450K methylation array data (2013)

Careful selection of preprocessing steps can minimize variance and thus improve statistical power, especially for the detection of the small absolute DNA methylation changes likely associated with complex disease phenotypes. For the convenience of the research community we have created a user-friendly R software package called wateRmelon, downloadable from bioConductor, compatible with the existing methylumi, minfi and IMA packages, that allows others to utilize the same normalization methods and data quality tests on 450K data.
Human Physiology: The Basis of Medicine (1999)

What is physiology? The chemical constitution of the body Introducing cells The transport functions of the plasma membrane Principles of cell signaling Nerve cells and their connections Muscle Sensory systems The physiology of motor systems The autonomic nervous system Some aspects of higher nervous function The hormonal regulation of the body The properties of blood Defense against infection - inflammation and immunity The heart and circulation The respiratory system The kidney and the regulation of the internal environment The digestive system The nutritional needs of the body The physiology of the male and female productive systems Fertilization, pregnancy and lactation Fetal and neonatal physiology The control of growth Energy balance and the control of metabolic rate The physiology of exercise The regulation of body temperature The regulation of plasma glucose The regulation of body fluid volume Acid-base balance The physiology of high altitude and diving Clinical physiology.
Functional Magnetic Resonance Imaging of Human Brain Activation During Cue-Induced Cocaine Craving (1998)

These results suggest that functional MRI may be a useful tool to study the neurobiological basis of cue-induced craving.
Plasmon Resonances of Nanoshells of Spheroidal Shape (2007)

Plasmon resonances are computed for nanoshells of prolate and oblate spheroidal shape. Both longitudinal and transverse resonances are investigated as a function of aspect ratio and shell thickness. Formulas for the surface charge density on the outside and inside shell surfaces are derived.
Effector mechanism of adenosine in acute ischemic preconditioning of skeletal muscle against infarction (1997)

We used adenosine A1 receptor agonist N6-1(phenyl-2R-isopropyl)-adenosine (PIA), A1 receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine (DPCPX), and ATP-sensitive K+ (KATP) channel blockers sodium 5-hydroxydecanoate (5-HD) and glibenclamide (Glib), as probes to investigate the role and mechanism of adenosine in ischemic preconditioning (IPC) of noncontractile skeletal muscle against infarction, using the pig latissimus dorsi muscle flap model. Except for Glib, all drugs were delivered to each muscle flap by 10-min local intra-arterial infusion to avoid systemic effects. Muscle flaps that were subjected to 4 h of global ischemia and 48 h of reperfusion sustained 40 +/- 2% infarction. IPC with three cycles of 10 min ischemia and reperfusion, preischemic adenosine, or PIA treatment reduced (P < 0.05) muscle infarction to 24 +/- 2, 18 +/- 2, and 24 +/- 2%, respectively. The anti-infarction effect of IPC and adenosine was blocked by DPCPX, 5-HD, and Glib (P < 0.05). Preischemic adenosine treatment also maintained higher muscle contents of phosphocreatine, ATP, and energy charge potential and lower muscle contents of dephosphorylated metabolites and lactate during ischemia and a lower muscle myeloperoxidase (MPO) activity during reperfusion compared with the control (P < 0.05). Preischemic adenosine treatment did not increase muscle content of adenosine during ischemia or reperfusion. Furthermore, adenosine given at the onset of reperfusion was not effective in attenuating muscle MPO activity or infarction. Taken together, these observations indicate that adenosine, through A1 receptors, initiates the mechanism of IPC with postreceptor involvement of KATP channels in skeletal muscle. However, adenosine is unlikely to play a key role in the effector mechanism. Presently, the cause and role of energy sparing and neutrophil inhibitory effects associated with the anti-infarction effect of preischemic adenosine treatment are unknown.
Molecularly Tuned Size Selectivity in Thermal Processing of Gold Nanoparticles (2006)

This report demonstrates for the first time that the size selectivity of nanoparticles in the thermal processing solution of pre-synthesized nanoparticles can be achieved by molecularly tuning the chain length and concentration of alkanethiols.
Time synchronization in sensor networks: a survey (2004)

Time synchronization is an important issue in multihop ad hoc wireless networks such as sensor networks. Many applications of sensor networks need local clocks of sensor nodes to be synchronized, requiring various degrees of precision. Some intrinsic properties of sensor networks, such as limited resources of energy, storage, computation, and bandwidth, combined with potentially high density of nodes make traditional synchronization methods unsuitable for these networks. Hence, there has been an increasing research focus on designing synchronization algorithms specifically for sensor networks. This article reviews the time synchronization problem and the need for synchronization in sensor networks, then presents in detail the basic synchronization methods explicitly designed and proposed for sensor networks.
The role of ovarian hormones in initiating the induction of mammary cancer in rats by polynuclear hydrocarbons. (1962)

Summary The current studies demonstrate the critical importance of ovarian hormones in the initiation and promotion of carcinogenesis of mammary glands in rats by polynuclear hydrocarbons. Removal of ovarian hormones from the rats immediately after the administration of the carcinogenic hydrocarbons either inhibited or profoundly reduced the incidence of mammary cancer. Excision of ovaries beyond 7 days after feeding of carcinogenic hydrocarbon, however, was unable to prevent or to reduce significantly the incidence of mammary cancer in these rats. Likewise, feeding of carcinogenic hydrocarbons to already castrated rats failed to induce any mammary cancer if the time between castration and feeding of carcinogen was prolonged. These experiments suggest that neoplastic transformation in the cells of the mammary glands in rats cannot take place in the absence of the participation of ovarian hormones, since subsequent supply of ovarian hormones from the functioning grafts failed to produce any mammary cancers. The experiments also indicate that there may be a quantitative balance between the carcinogenic polynuclear hydrocarbon and the hormones which govern the induction of mammary cancer in rats. In a small number of rats, a potent carcinogen was capable of inducing cancer in the mammary glands in which the metabolic activity was decreasing after the removal of ovarian hormones, whereas a “less potent” carcinogen failed to do so under the same circumstances. In these animals receiving a less potent carcinogen, mammary cancer could be induced if optimal ovarian hormones are present. Some of the rats receiving a toxic dose of DMBA (30 mg.) died of adrenal apoplexy. DMBA caused necrosis and hemorrhage mostly in the inner zones, especially the zona reticularis of the cortex, whereas zona glomerulosa and medulla were frequently spared. An incidental finding in the present experiment was the observation of chloroleukemia in two out of 100 rats receiving a single dose of 30 mg. DMBA.
Fluorous Reverse Phase Silia Gel. A New Tool for Preparative Separations in Synthetic Organic and Organofluorine Chemistry (2001)

Fluorous reverse phase silica gel, or silica gel with a fluorocarbon bonded phase, can be readily prepared by standard techniques, but shows unusual separation features. This silica gel separates primarily by fluorine content. Uses of fluorous reverse phase silica gel in both synthetic organic chemistry and organofluorine chemistry are introduced. Solid phase extraction can be used to separate fluorous or fluorous-tagged compounds from organic compounds. Fluorous chromatography can be used to purify mixtures of compounds with differing fluorine content as well as for "demixing" in the new technique of fluorous mixture synthesis.
Generating pancreatic β-cells from embryonic stem cells by manipulating signaling pathways (2010)

Type 1 diabetes results from an insufficiency of insulin production as a result of autoimmune destruction of the insulin-secreting pancreatic beta-cells. It can be treated by transplantation of islets of Langerhans from human donors, but widespread application of this therapy is restricted by the scarcity of donor tissue. Generation of functional beta-cells from embryonic stem (ES) cells in vitro could provide a source of an alternative graft material. Several ES cell differentiation protocols have reported the production of insulin-producing cells by mimicking the in vivo developmental stages of pancreatic organogenesis in which cells are transitioned through mesendoderm, definitive endoderm, foregut endoderm, pancreatic endoderm, and the endocrine precursor stage, until mature beta-cells are obtained. These studies provide proof of concept that recapitulating pancreatic development in vitro offers a useful strategy for generating beta-cells, but current differentiation protocols employ a bewildering variety of growth factors, mitogens, and pharmacological agents. In this review, we will attempt to clarify the functions of these agents in in vitro differentiation strategies by focusing on the intracellular signaling pathways through which they operate - phosphatidylinositol 3-kinase, transforming growth factor beta, Wnt/beta-catenin, Hedgehog, and Notch.
Vector mapping of myocardial activation. (1986)

A custom-made probe, consisting of four electrodes arranged so that two orthogonal bipolar electrograms could be recorded from a single site, was used to record epicardial activity during atrial and ventricular pacing in five normal and five anesthetized open-chest mongrel dogs with myocardial infarction. Unfiltered bipolar electrograms recorded with a 2 mm interelectrode distance averaged 36 +/- 15 mV in amplitude and 16 +/- 5 msec in duration in normal areas and 14 +/- 11 mV and 23 +/- 12 msec in infarcted areas (p less than .01 infarct vs normal). The bipolar electrograms were vector summed so that a vector loop could be generated at each site. The direction of epicardial impulse propagation as determined by multipoint isochronal activation mapping was compared with that indicated by maximum x,y deflection of the vector loop. At 203 sites (141 normal and 62 infarcted) there was a median error of only 13 degrees and an excellent correlation by linear regression (r2 = .95). In normal myocardium vector loops were straight (60%), open (21%), or hooked (19%). In infarcted myocardium, notched and irregular loops were occasionally seen. However, a clear maximum x,y deflection was still obtained from 98% of infarcted sites. During ventricular pacing in normal dogs, uniform epicardial conduction was observed for up to 4 cm longitudinal to fiber orientation but only 1 cm transverse to it. At selected sites longitudinal to fiber orientation conduction velocity was 0.618 m/sec, electrogram duration 12 msec, and vector amplitude 76 mV compared with 0.304 m/sec, 18 msec, and 38 mV during conduction transverse to fiber orientation (p less than .05 for all comparisons). Vector mapping of epicardial activation was performed during ventricular tachycardia induced by programmed stimulation in two of five 2-week-old canine myocardial infarcts. Aside from minor irregularities caused by impulse spread around areas of block, vector loops indicated when impulses were spreading away from the area of early epicardial activity and thus directed mapping to the region of earliest activation. We conclude that vector loops generated by summing orthogonal local bipolar electrograms accurately represent the direction of epicardial activation in both normal and infarcted myocardium. Such loops may prove useful in mapping tachycardias and in clarifying details about cardiac activation processes.
Packing and Thermal Stability of Polyoctadecylsiloxane Compared with Octadecylsilane Monolayers (2000)

FTIR, Raman spectroscopy, and thermogravimetric analysis (TGA) were used to compare the structure and thermal properties of polyoctadecylsiloxane (POS) and octadecyl trichlorosilane (OTS) monolayers. The octadecyl chains in POS had higher conformational and intermolecular order than the same chains of OTS adsorbed as self-assembled monolayers (SAMs) on 106 nm hydrated silica beads. The latter were identical to the structures observed for OTS SAMs on superhydrated fumed silica that had primary particle sizes an order of magnitude smaller than the 106 nm beads, indicating that curvature did not affect the chain packing. The chains on POS were also more thermally stable to conformational and intermolecular disorder than the OTS chains, and this was attributed to increased free volume in the latter case. The differences in structure were partially determined by steric restrictions that arise because the Si−O−Si bond distance is less than the van der Waals radii of the alkyl chains. In POS, the most likely structure is therefore one in which the octadecyl chains are pointing in the same direction from every other Si atom, permitting good lateral chain packing. In the OTS SAMs, the octadecyl chains must all point in the same direction, away from the silica surface. Therefore, linear chains would be excluded but small clusters of dimers or trimers could be accommodated. These restraints increase the nearest neighbor distance between alkyl chains on SAMs and do not permit them to be as closely packed as for POS. This in turn contributes to the increased irreversible disordering of the chains with temperature.
Cell Signalling - The Proteomics of It All (2001)

A challenge for biomedical scientists today is to arrive at an understanding of cellular behavior on a global scale. The advent of DNA microarrays has greatly facilitated discovery of gene expression profiles associated with different cellular states. The problem of understanding cellular signaling at the level of the interacting proteins is in some ways more challenging. Ashman et al. discuss the current methods available for studying protein interactions on a global scale, as well as directions for the future. Technical hurdles exist at many stages, from the isolation of protein complexes, to the determination of their composition, to the software and databases needed to analyze the results of large-scale, high-throughput datasets. Ashman et al. suggest that, with advances in technology and cooperation among academia and industry, a global protein interaction map that underlies cellular behavior will emerge as an essential resource for basic and applied research.